Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_062591
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 328819
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Found at i:47311 original size:24 final size:24
Alignment explanation
Indices: 47279--47326 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
47269 AATCAGTCTT
47279 CTTGTATGGTTCCTGCTTGTTGGA
1 CTTGTATGGTTCCTGCTTGTTGGA
47303 CTTGTATGGTTCCTGCTTGTTGGA
1 CTTGTATGGTTCCTGCTTGTTGGA
47327 TAAGGAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.17, G:0.29, T:0.46
Consensus pattern (24 bp):
CTTGTATGGTTCCTGCTTGTTGGA
Left flanking sequence: Indices 46779 -- 47278
AGATGCATCTCAATGACAAAAACATAATGGATGGTGGTCTTTCAATCATTTTAAGTGTAAGTGTA
TATAGGAAACTAGCATATCGCTATACCTAGCTATAGGGAGACTCACTTGTTATGAGATTTCCATA
ATCCATGTTAAGGTGCGGGGACAAAATACTGCAAGAGATGTACCTATAGGTACTCAGAATAGCTG
CAGGTATCTTTAGTTTCCGGGTGAGAGGCCTCCATGGTTTGTTCATCAGCTCAGTTGGTTCAACG
ACATCGTAGTCTTTTCCATTTCCTAAACCGAAACCTTGGACCATATAGCATTCCCATAGCCATAA
GTTCCCTTGGTTTCAAAGAGCCGTGATCCAAATCGCCAGTTTGACTCCTCATCAGGACCTACTTT
GTTGACTTCATGAGTGACAACCTCCTCTCCATTTTAGACATCCCATTAGGCAGAGGCAGGGGAAG
CGGAGGCAATGCACTCTCCATAGCCATTTCATCCAAATCAGTCTT
Right flanking sequence: Indices 47327 -- 47826
TAAGGAAGGTGGCTAGCGTTGCTAAAGGACATGCTACCACCCCCTGTTTTGACAGCATCAGTATA
ACAATCTCGACAAAGATTGAATCGAAATCGCTCAGGTCAGTGAGTCCTCACCTACTCCTTATCAC
ACCCACAAGGTAGAATGTCCTCCCCGCGTTGATCGCTCATCACCTTTGCATCACACCCAGGAATG
GCACATGATGACCCTTTGCCGCCATCTGAGGATGGTTGGCTTCGGATTCAATCACCTTGTCCATA
AGATGAGCTCGGGTAAGACTGTTGAATCCCCCAGTGAAGAGCGAATTGGACACATACTGCTCTTC
AACCTTCTGCGAAATGGATGGATCCATTGGCTGGTGTCGGAGGCCGTGTAGTTCATAAAGTCACC
ACTCCCAATTTCGCTATCGAGATCATCTCTGGAGTAGCTGATGTAGCGACCGGAGGAGGCGGCCG
AATGTGACTGTGGGAATTGGAGGCTTGCCGAGTGCATCGGGAATG
Found at i:56683 original size:31 final size:29
Alignment explanation
Indices: 56630--56705 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 29
56620 GTTGGAAAAA
* *
56630 AAGTCAAACTCCCTCTCCCTAAC-AGTCGAGT
1 AAGT-AAACTCCCT-TCCCTAACAAGT-AAGC
*
56661 AAGTGAAACTCCCTTACTCTAACAAGTAAGC
1 AAGT-AAACTCCCTT-CCCTAACAAGTAAGC
56692 AAGTAAACTCCCTT
1 AAGTAAACTCCCTT
56706 TGAATCTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 11 0.28
31 25 0.64
32 3 0.08
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.24
Consensus pattern (29 bp):
AAGTAAACTCCCTTCCCTAACAAGTAAGC
Left flanking sequence: Indices 56130 -- 56629
ACTTTAGGAGAGTCATATTTTCTGGTACGTCCATCTACTTATAAGCGGCCGGCTATGTTCTCTAA
ACTCATCTATTTCCTCTCGGCTCTCAGCGCAACGAGAAAGGATTCCCCAATAGCTGAGATTGGTA
CTAGAATTCGCGAATCTAGAGAGCACCAACGATGTTGACCGGGAGGGAAAGGAGCAATTAAAGCC
TTTCATCTCAATCAAATGACCGAAATGGAGACTCTATTCTTGTTGGCAAATGCAAATACGAATCC
ACTGATTTCCATCCCCATGTTCTCTGAGCAATGACCTTTGTTTCCAACAGTAATGGAGATTTGTT
GCAAACTGTCTCCGAATCCCGTGCTTTTCAAGTAAGCACCAACTCCTGTGATGTGTATTCCCCTC
CAGAGTCTGTCCTCAAACATGGCTTTCTTTGCCTTGACTTTATAAGTTTCATTCTCCACTAAGCT
TCTGAACTCTATGAATTTTTGAAAGATTTCGGACCGTTGGAAAAA
Right flanking sequence: Indices 56706 -- 57205
TGAATCTTATCCATTGAAGAAGACAGACTTCAAGACTGAAACCCGCCCTTTATTATTATATTATT
AGTAAGATAGGTTTGGAACTCGGGCTATAGTTATACTATATGCCCGGGCTTTTCTCGCTTGTTGC
TTTCTTTCTTCGCATGCTTTCGCGCATTTTTTAAAAATTTTTCTTCTGGGGCCGAAGTCCTGAAA
GGCTTGGTTATGGCGGTCTATAAGATGTAGGCTTATCAAGCTGAGGGAATTGCATAGTCAAGAGG
AACTAAGTGCTGGTGATCGGAGCGTGGGGAACTCAGGCCGCTGGTAGTAGAGGCAATGCAATTGA
ACCAATTTCCTTACACTCGGAGAGACTTTACCTTTACTTAGAGAGGCAATACTACTATGCTCTTC
GGTGCTCGTAGGTTGACTTCCCTTATGCACCCAGCCGCTTCACTAATGTGAATAGGTTATACAGA
AGGGTGGGTTGGTTATATACTCTTATGCGCGTTCCTTCTTCGAAC
Found at i:59210 original size:39 final size:39
Alignment explanation
Indices: 59167--59245 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
59157 CGATTTTCTA
* *
59167 TTCACTCATGATCTGGCCTGGTCGACTCGATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
59206 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
59245 T
1 T
59246 GAAGGATGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (39 bp):
TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
Left flanking sequence: Indices 58667 -- 59166
GCCCACACCTGTGTAGAGTAGATCGTTCAACACCTGCGGCACAAACCGATTTTTGACCTATTGGT
CCTAGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACCAACCTGCTATAATAATTCC
ATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGAATCTGACAATACCA
TACCATAATCAAAAGGTACAACGGCCCGAGCAACCAGACTTAACATAAATGTAGTCACTGGAGCC
ATTCTAAAAAGGGAGAAATTAGCACTACTTGGTGAAATAGGTTCTTTTAGAATCAATTTCAAACC
ATCCGCTAGAGGTTGTAACAATCCGAACGCTCCCACTACATCAGGACCCTTTCGACGTTGCACAA
AAGCCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATT
CCAAGTATTTCGGCTGGAACAGCTATGTACGTTTTCGATTTTCTA
Right flanking sequence: Indices 59246 -- 59745
GAAGGATGGGACCTTTTCTCGAAAAACTCCGGATCGAGTTGAAGGTGGTGCAACATCGAATCTTG
TTACCTTACTTCGAATGGAATCTTAGCCCGCCTCACTTGCTTTCTGTACTGCATAAGGTTCTGAA
AGAAAGTAAAGGGATTTCCTTCTAACTAGTGGCTGAGAGTAAGCAAGCTACCTTCATTCAACAGA
TTTGTGGTTGAGTCAATAAGGGTCGGGAATCTTTGCTCTTCTCTTTTGCATTTCCGCTGCCTGCG
TTCTTCTTCGTGTCCGTACGTATCGCAAAGCTGGTCGACGCCAGCTGTAATGGTTCATTTCGGGA
GTTTGAACACCATCCCAAAAATACAACCCTGTCAAAGGTATTTAACCTTCCTTCCTTCTGAGTGG
AAATCCAATCCCGTTTTGTCTTTTTTGCATAAAAACCAAACTAATATAATATATATATATTTCTT
TTAAACCCGTTCTTCCGACCCCTCCAAAAATGACCTTCTCCAGTG
Found at i:84691 original size:15 final size:15
Alignment explanation
Indices: 84671--84703 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
84661 GAGCGAGTCA
*
84671 CTTTCAGTCTATCTC
1 CTTTCAGTCTATCAC
84686 CTTTCAGTCTATCAC
1 CTTTCAGTCTATCAC
84701 CTT
1 CTT
84704 CGGTCCCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.33, G:0.06, T:0.45
Consensus pattern (15 bp):
CTTTCAGTCTATCAC
Left flanking sequence: Indices 84171 -- 84670
GTAAGAGCTCCCGGCCTTTCAGTGAGGAAGCGAAGGCAATGTAATTGAGCAAGTCTTGATATTTG
CTTTGGAACGTTCAGTGCCTTATTGAAGGAACTAAAGTCCCGAACCACCTCACCTCCGAACCTGA
GCTCCCTTAGCTTTGTCAATTGTAGTCTATCTCCTTGAACTGAACTTGAAGTCCAAGCTTTCTTT
CAGAGCATCACTTTCTGAACTAGAAGTCCCTTATTGAACTGGAAGTGCCGATATTCCTAGCGATA
TTAGGTTCTTCCGGCTAAAAGTCTCTTAATCGAATGACCTGTCTTCATCTGATACAAAGTCTAAG
ACTAATTCCGATACCGGGACTCTTTCCTTTTTCGTTTCTGCAAGGGCTTTAGCGAACAGGAGGTA
AACCTTTCCTAATTCTGTGACAGTTCAGCTTTGAAATCTAAGGAATCAAACTGGGCCACGAAAGA
AAGGTGCTCGGTCCCTCTCCCTACCTTAGTAACTAGAGCGAGTCA
Right flanking sequence: Indices 84704 -- 85203
CGGTCCCTCTTCCGTTGGTCGAGCTCACCTTCTTTCAGAACCTCTTCCCTGAAATCTAATATGTA
ACGGTCCACTTTTACAAACTGATCAAGAAACTCCATTCGACACGGTCGCCTTTGGCTTTTCTTTT
GTAGCGGGAAGCCACTTTCCATTTGTTCAACCAATAAGGATGCTTTAAAGCAGTCGAACGCTTCT
ACTTTCAGTGCCTCAACTACGTTCGGTCTGGCCAATTGGTCCTTTTCGTTTTCCCGGGCGTAAAC
CGGATGGATCCCCTTTAGTAAATGCGGAATCGGAACCTTGCCTTTCAGATTCCAGGTCTTCTATC
TGCTGTCCAAGCGCAACAAAGCCTAATCCGTCAGCGGGAGAGGACTAAAATCATATTCCACAACA
CAAAATTTGTTCACTTGCAGTGCCTCTGTCAACAATAGAGAAGCACTACCCGCTCCGGCCCTTGA
CAAATCCCAACAAATTAGATGAGGCAATGAAATTGATTGACAAAG
Found at i:128230 original size:12 final size:12
Alignment explanation
Indices: 128213--128238 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
128203 GTAACCGGTG
128213 AAATAAAAAATA
1 AAATAAAAAATA
128225 AAATAAAAAATA
1 AAATAAAAAATA
128237 AA
1 AA
128239 GAAATTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAAAAATA
Left flanking sequence: Indices 127713 -- 128212
TAAATGATGTTAGGATCGGCCGGCTCGTTCTCGGAATCCTAAAATAAAACAGAGACAGAACGGAT
TGTTTCAGTGACATATCTAATCAGACTGAATAGGATTTGAAGAGCTGTCACGATCATTCACATCA
ATTTCAGCAGGCAGGAAGGGCGCGGAAGCTACCGTTTCTAGAATGCAAGCAAGGTAGCTTGCTTA
CTCTCCTAGTAGCGTACGTTGGCGGCAAGGAAGGAGGCATTGGAAAGACTAGACCATACTAAAGT
AAAGAGGCATTCGGGAAGCTACTAGTCGCTTCTGGCGAAGCTTATAGAAGGCCGACCGCTACATA
GAGAGATCCATATACTATACCAGTCATGAGCGATAGCGAAGCCTAGAGAGGCGGAAGCAGTCGCT
TCTAGGACGAAGCCGAGCCGATAGTCGGGCGAAGGAAGCGAGACCAAGCCGAGCCACTAGTGGAG
TGGCGAAGGAGGCCTACTATACGTATACTGGATTAGTAACCGGTG
Right flanking sequence: Indices 128239 -- 128738
GAAATTTCAGTGAACTATTGAACAGTGTGATTGATCAGACAAGTACCAAGGGCTTTCGGTAGACT
TCTTTCATTTCCGAATTAGCTTGCGAAAAGTCCTTGCATTAGTATGAGTTCGTTGACCGCGTAAG
GGCAATCCATCTTGATGACGAATTCCACGATAACAAGAAATCGAAATTAATCGTTCGATGTCTGC
TCGTTCTCCCCTCTTCAATTCCCAATGAACAACATGATCTTGACCTATCATTTGTTCAATTTGGT
CGATCTGATACTTAGTTAACTCTTTTATCTTTATGTTCCCACTGATACCTAATCGATAACGAACC
TGAATGGCTTTTTTAGGTCCAATTCCATCAATTTTTGTTGAGGCAATTCTTACTTGTTCATCGGC
AACTGATCTAGCTCCTGAAATATATGACATTCTTGATCCTTCCTTTTACTAGTCTTCTCGGCTGG
AATCAAAAATGGGGTGTCTCCTCTCTGATGATCTTTTCTATAGGT
Found at i:183735 original size:17 final size:17
Alignment explanation
Indices: 183709--183741 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
183699 TTCCTATCTC
183709 TAAAGGGGC-TTACCCA
1 TAAAGGGGCTTTACCCA
183725 TAAAGGGGGCTTTACCC
1 TAAA-GGGGCTTTACCC
183742 TGACACAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (17 bp):
TAAAGGGGCTTTACCCA
Left flanking sequence: Indices 183209 -- 183708
TTTCTTGCGGATGTCCTAATCAGTTTCTCTGAGGCTCTCAAGCTGAGATAAAGTGTTTGGATGAT
TTTTGCATGGTTTCAGGGCGCTTTGAGAAATCGAATATCTTATGTTCTCCTAATATCGATAGGCA
AGTTGCTTATTTCTGTGTGCTCTAGGCTTGACAAGCTAAACAGAAAAACTTTTTTTGGAGGAAGA
TCCATCTTGCTAATTAGGATTTGGTGTGTAGACCAAAAGGTATGGGCGCCGGAGTTTCCTCTCGT
TGAGATTTTGGCAATCTCGTGCGGGTTGAAACAAGCATTAGATATGGGCCTTTCTTCTCTGATGC
TGGAGTCAGACGCGACGCTCAGGCGGTTGTCTTTGCATTGAATGAAGAGGAGAGAAGCGCGCAAA
CAGTGTCGGACGTTACTTAGGCAATGCCGACCGGCACTTCAACCGCAGCAAATTCTTTTTTAAAT
TCTCAATGTTGCCTCAATAAAGCAGCTAGGCCGTTTTCCTATCTC
Right flanking sequence: Indices 183742 -- 184241
TGACACAAGTAGTCTCCGCGGCTATACTATATCAAATAGCCTATAGCGCTACTGTACTTGTTTTT
TTTTGTCTGGTTCTTTGCTAGCCAGACACCTGTCAACCAACCATCCTGCAACTATAAGTTCTTTC
GCAAGCCAAGCCAATATCCCTTGATCCGCCCGAGGAGAATCCGAGTGAAAGCAGCAACCAGCGGC
GTGTGTCAGCAAACAACTCTAAGCTGAACTGATTACAGATAGGTAGTGCATTCTCTGAGGTGAGT
GAAGTGCCCTACTTCTATCTTACGGGTAGTGGTAGTGTAGCTGGGCTATTGATCCTGGTGAAGGA
GCCCTATCAATCAAGTAAAGGCGGGTGATAGAATAGCAAGCAGGGTAACTTACGCAAGCAAAGGA
AAAGACCCTTCCGACGACGCAGCAGCCAACCACCTATTCGAGCCTGCAAAAATCTATGTGAACAA
CTAGGGGCCCGCGATTACTAAGGATCGATTGCTAAGAGCACTTTT
Found at i:236172 original size:25 final size:23
Alignment explanation
Indices: 236124--236170 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
236114 ATATTCGAAA
236124 AAATATATTCTCTTTTATACTAT
1 AAATATATTCTCTTTTATACTAT
236147 AAATATATTCTCTTTTATACTAT
1 AAATATATTCTCTTTTATACTAT
236170 A
1 A
236171 TAGTATATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATATTCTCTTTTATACTAT
Left flanking sequence: Indices 235624 -- 236123
GTCGGATAAACAGAATGTCCGAGTAAGGCCGTGAGATGGGAGACTTCGAGAGGATCACCAGTCCT
CTGCCACTATTTCCTTACGATTCTGTTAGTGAGTTCCGTCCCGCAAGAAGCCACCATAGGGGCTT
TAATGCGACTCCTATGACTACTCAATCGATTAGCGGTAAGAGTTTTTCTCCGGAAGGATAAAGTG
CCCTAGAATATCCTGGAGTACTTGTCCTCATGGACCCATTAGCAGTGGGAAATCCATGGGCGTCG
TACTGCATTTAACCCACTTGAATCGGGAAGAATATACTGTACGTTTCTCCGACGGCCGAGATGAA
GTATATGCCTAATAGCATTTCTATCTATCAATTTATGGTCAAAACCCCCTGAGAGGTAAACTTTC
AGAACACGACATTCTTACCCGTAAGGAATTGAACCATAAAAGGCTTCTCCGGCGGTAAGATTTTA
TATTCGAATACATATATTATGTATACGTTTTATATATATTCGAAA
Right flanking sequence: Indices 236171 -- 236670
TAGTATATCACCGGAATGCAATATATTACGCTTTGTCAACCGGAAGAAAGTGACTCGGGGCGTTG
TCAACTTCGTTTCTGCGAGGAATGATAATGCATAAAACCCAATCTTCGATTCCCTTATGACACCC
CATTACGTTTTCAAGGGCTTTAAACGGGCTTCTTTTGAGTTCCATTCTACTCGTGTAGACTTAAT
ATGCTATTAATTTCATAGCGGGTTGCAACAAGCACCGATCTTTAGGGCGGCTTTCTATGAATAAT
TCCTCTGACTCGAACCTCCACGCTTTTTAGCACGAGATTTTGAGTCTCGCGTGTCTACCATTTCA
CCACCAAGGCATCTTGAAAGGGAATAGTATTCCATGAATATGATATCTATCCAGTGCGATGTATG
GAATATATGACAAGGGTCGAGTGTTAGGGTATTTCTATTGATCAGTCATGTCAGAATGGACAATC
AAACCGATTTCTCGATTCAATAGAAGCCAAAAGAGGTGAGGTGAA
Found at i:263702 original size:16 final size:16
Alignment explanation
Indices: 263681--263711 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
263671 ACGATCTCCT
263681 CTTTCTTATAGTTATG
1 CTTTCTTATAGTTATG
263697 CTTTCTTATAGTTAT
1 CTTTCTTATAGTTAT
263712 AGATAGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.58
Consensus pattern (16 bp):
CTTTCTTATAGTTATG
Left flanking sequence: Indices 263181 -- 263680
TTATTTCTTTCACCGTTCCAAACATGCCGTACTGATGGTACGTAAATGTAATTCGTTGTTCAAAC
AACTATTGCCCTGTAAGGCTTGTTGAAAAACCCGTTGTCGAACTGCTCTTTGTTGTTCAAAATGA
ATGGTTTAATTTTTGTAATTTTCTAACTGTTCCATTAATCAAATTTAATTTTTCTCGCTCTATTT
CAGAGTATCCAGTCATTCGAAACTGATTCGCTTCTATTTCGACTTTCCGTAAGCGGGCCCGGGCT
TTTTCTAACTGGTTTAGGGCCCCCTCGCGTAATTCTTCTGAATTTTGAATAGTCTTCAAGATCCT
CTGTTTTCGATTATCTAATAAATCACTTAACACCCCCCTTCCAAAAAAAATCAACACACCAAGCA
CTACGCTTAGATTTATTAGATTGGTTGCAAAAATATCAGTATTAAACCCGGCGGATGGCCAATAA
CCCAAGGAAAGGAAAGAATCGGTTACATTTTTCATACGATCTCCT
Right flanking sequence: Indices 263712 -- 264211
AGATAGACTATTTATATTCTTTTATTATGAATTTCCCTATTTCTAAATAGAAAATACTAAATTGA
GTCAAAAAATATATTGATTTAGAAATGGGTTTTAATGGATTTTTTTCAATTGGAAATTTCCAATA
AGCCTGATACTTATTCGATTCGAATTAGGTACCAGGTCTTATACGGGTCAGTTGCGAAATACCTC
GTTTGTTACAATACAATTGCAATACTTCCTAAAAAAAGTTCGTCCATTGGACTAAGAAGGTAAAG
GAAAAAATGAGTTGTATCCTCATCCTCAAACCGGCGATTTCCGTGGGTTGTTGTTCCTAAGTAAT
TTAATTGTAGAAGTTAAATATTAAAAGAATTTGAAAAAAAGCGGAAATAAACAAAAATATGTGTT
TTTAGGATTAAACAAAAGGATTCGCAAATAAAAGAGCTAATGCTACAACCAGCCCATAAATTGTT
AAAGCTTCCATGAAAGCTAGACTAAGCAATAAAGTACCCCGTATT
Found at i:275588 original size:28 final size:28
Alignment explanation
Indices: 275552--275607 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
275542 GCTTTTGGTT
*
275552 TTTCATGTTGTCAAAGAGTTGAACAATG
1 TTTCATGTTGTCAAAGAGCTGAACAATG
*
275580 TTTCGTGTTGTCAAAGAGCTGAACAATG
1 TTTCATGTTGTCAAAGAGCTGAACAATG
275608 AAAATAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.34
Consensus pattern (28 bp):
TTTCATGTTGTCAAAGAGCTGAACAATG
Left flanking sequence: Indices 275052 -- 275551
CCTCTAGCGCGTAGCTACCTATAGAATAGTGCCAGCTCGCATCTTTACCAAGCTCCGTTATCTAT
AGCCTTATAAGGAAGGGAAGTCTTTTTAGGCAACAGAAGTGGAACTGTTTCATTATATAAGCTAT
ATAGACCTCAACACTATTCTTTAGTTACTACCAAAGCAGCTATACGGCTAGTTTAAGTCTATAAA
GAAAAAGGCTAGTTATGTCATCTACCCTCGCTTTACCAAATGTTTACCAAATCAAGCAGGCAAAG
CCAGTTAGATAAGCTATATAAACATCAGTGCAGCCCCTACAGTATCGTCACCGCAGTAGAGTTTA
ACCACCAAGTTCGGGATGGATTGGTGTGGTTCCTCTACGCCTAGGACACCAGAATATCGAACCAT
GAGCGAACAAAGGCATGAGAGAAAAGCATATTGGCTAGTGATTGTGAGGCCAAAATTCTTGGAAC
ACCAAAGGCCTCCGCCCTCCGGATGGAAGGGCAGAGCTTTTGGTT
Right flanking sequence: Indices 275608 -- 276107
AAAATAGATGGCGAGTGCCTGATCAATTGATCGGGTCATGTAGGAACAAGGTTCAAGTCTACCGG
TCTGTTAGGATGCCTCAGCTGCATACATCACTGCACTTCCACTTGACACCTATCGTAATGATAAA
CGGCTCGTCTCGCCGTGACCTTCTCTTGAATTCTCAAAACTTCTGTCGCTCCACCCCCGCAGGGG
CAGAAAACCCATCGCCGTCTTGGCTGTGCTACCGGAGGCTCTGGGGAAGTCGGAATAGGAGAGCA
CTCATCTTGGGGTGGGCTTACTACTTAGATGCTTTCAGCAGTTATCCGCTCCGCACTTGGCTACC
CAGCGTTTACCGTGGGCACGATAACTGGTACACCAGAGGTGCGTCCTTCCCGGTCCTCTCGTACT
AGGGAAAGGTCCTCTCAATGCTCTAACGCCCACACCGGATATGGACCGAACTGTCTCACGACGTT
CTGAACCCAGCTCACGTACCGCTTTAATGGGCGAACAGCCCAACC
Found at i:305055 original size:13 final size:13
Alignment explanation
Indices: 305037--305062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
305027 AACAGGCAAT
305037 GCATTCTATCAAA
1 GCATTCTATCAAA
305050 GCATTCTATCAAA
1 GCATTCTATCAAA
305063 ACATAGCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
GCATTCTATCAAA
Left flanking sequence: Indices 304537 -- 305036
GTCGCTAGCCAATCAAGCAAATAGGCGCGGGTGTCTTATACATTTCCTTATGACTATCTTATAGC
CTGCCATATACAGGATTGCTGTAACTGGTGCAGGGGCGGGGCAACTACTCTTTCTAAAGGAGGGG
AATGCAAGGGATGGATCTTTGTATCGGATGCTACTGGTAGCTAAGCATTTGGATCTGCTACTCGG
ATTGCAAGTGGTGAAAAAAACTGGTGGTTCTTCAACTGAATCACAAATAGAAATTGGGAGAACTA
CTACTGATGAGTCAACTGGGTCAAGTACTGCAACTTTTCTTAGGCGCTGAGCTATGCATGGACGC
CTATCGAGCCGCCGTTGGCGCCTGATTATGATCCCCTCCACGATATATATAGATATATATAATAG
ATCTTTGCCTTTGCATAGTATACGGGTCGGGAGGTAAAACCTTTCTAAAAAAACCAAAAAGACTA
GAGCACATCTTTCGTGAGAGAGGGATGCTAAGAACAACAGGCAAT
Right flanking sequence: Indices 305063 -- 305562
ACATAGCCATTTCTCGTAACATAAACAGGAACGCCTCCTCGAAACAACAGGGATGCTGTCTAGGA
CTGGTTCAATAGGTGCTCTGGCTGGGTCAACTACTGAGCTGAATCAACAACTTATATTAGCTTAG
ATGCAGCAGTATCCGCATTTCCACTGGGTCAATTGGATCTGATTCAATCCGCCTTTGACGCTGAT
CCACTGGATGCTGCGGAAACTCCCTTTGCGACTTTTCGACTAAAATGGGTGAAGCTTCTGCCTTC
CTCGCTTCCACTCTACCCGCCTCTGACTCGGCCTTTTCTGTTGAAACGAATGCTGTAGAGATGGT
GGTGCCTTTGCCTTTGCTTGCTCTGCCCCTGTTTCTGGTGGGCTGCTGCTTCCACTGATTAATCG
GGTCTTCAACCACTGCTTCCGCAGCCCCCATGTTAACTCTAGCGGGCTCTAGATCAATAGAATAA
ACTGCAACTGGGGGACTGATACTGATGCTTTTGGTTCCGAGCGCT
Found at i:310507 original size:18 final size:18
Alignment explanation
Indices: 310486--310522 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
310476 GTCACGGCCG
310486 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
310504 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
310522 A
1 A
310523 CAAGAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATCGTCACTATCATCA
Left flanking sequence: Indices 309986 -- 310485
TACTAATCGATAGGGCCTCATCGGTAAGTGCTACAAGATCTCGTACATTGGAACCCATGGTTATG
GACCCGAATCCATTAGTATAGAACATTTTCTTTTCCAAGTGAAATCCCCTAGTATATGAAAGAGT
GAAAAAGTGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCATGTATTTAATTTAT
TCGGAGCTATTAGAGCGGGATCCACTTTTTGGGGAATATGAGTCGAAGCAATAACAAGAATATTT
CTAGTGGAACATCTTTCACAATCCCTGGAGAGATAGTTCACTAATAAACCGAGGGATAAGTAATT
CGACTCATTCACATCCAGATCATGAATGTTTGGAATCCATATTATGCAAGGAGACATTGCTTTTG
CTAATTCGAATTGAAGGGTGATATAAAATAGGTCTATTTCCGGCATCATATCCATAGTTAGCGCA
TTCATCATAGTTAGAAGCTCCAGCTCCGTATCAAGGTCACGGCCG
Right flanking sequence: Indices 310523 -- 311022
CAAGAAAACCCTTGGGCTTGTTATCCAGGAACTTGTTCAGAAATACTGTAATGAAAGGAACATAG
GAGTTTGTCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTATCACTAAAAT
ACCCCTAGAGAGGGATAGGGCTAAACGGAGCGAAAAGGGTTTTCCATGAGATGGGAAATGAAAAC
TATTAGCCCCACAGGAGGTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGAATATCCGCCTT
TCTGCTAAACAGGATGTATTGAACTCATAATTCATTAGATACTTTTTATGAATGTCAACTAAGTA
TCGTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCAGAGTCATTCTTTGATAAATGAT
CACTATGAGTCAGACTCAATAGAATTTGATCAATCCTTTTTTCTGTCGTTAAGGTGGAGAACTGA
ACCAAGAATTCTCTTTCTTTATCACCAATCGAATCACTGTTCGAG
Found at i:321974 original size:18 final size:18
Alignment explanation
Indices: 321934--321976 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
321924 ACCGCCCTGC
321934 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
321953 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
321970 CATAGTC
1 CATAGTC
321977 AACAAGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 321434 -- 321933
GAAAGCTTTTTTTTCAAGTGTCAGTAGCGGAACGTTCTGTCAATCGGGGAAGGTTTTTGGTGACA
ACACCTGGAGATATCAGAAGTGAGAATGCTGACATGAGTAACGAAAAATCCTGTGAAAAACACGA
TCGCCTGCCAGTGGAAGGCTTTCTGCGTTCAGTCAATCTACGCAGAGTGAATCGGTCCCTAAGGA
ACCCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACC
ATGCCTGTCTGTTGGAGCGAATTGAATGATCGGGCCGAGGGCAGCCCCCTCTTCCCCTCACTCTC
CTTTCCCTAATATGAACCTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGTCGCCCTAC
GCGACTGGCGCTTCAAAAGACGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCCTTTACTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 321977 -- 322476
AACAAGGTTTAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:328541 original size:26 final size:23
Alignment explanation
Indices: 328493--328545 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
328483 AGGAATGGGT
328493 GAACGGGAAACCTGTTGTTAGGA
1 GAACGGGAAACCTGTTGTTAGGA
328516 GAACGGGAAACCTGTTGTTAGGA
1 GAACGGGAAACCTGTTGTTAGGA
*
328539 GGACGGG
1 GAACGGG
328546 GCCTGTTGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.40, T:0.19
Consensus pattern (23 bp):
GAACGGGAAACCTGTTGTTAGGA
Left flanking sequence: Indices 327993 -- 328492
CCGTCCTTTCATCACTTAAAGGTAACACCGGAAGGATGTTATTTAAAACCAATAACAACGTAAAA
AACACGTGGTTTTGCATGGGTCAAATTGATCAAAAAAGGAACGCTCTCACTAAGTAAAACGGCTT
TTCTAGGTTTTGTAGCTAGGGCTAGATGGATTTCGTGTCAAAAGAAAAACGAGTGAAAAGACCGG
TTTTAGACTTTTTTCCAAAAAGCATGCCACTTCACTTCTTATTCACTTCCTCACTTTGTTTACTT
CGTAACCTTTGGTATTGCGTCTCATCCAGGTGATTAATATCACGTCATAGCATTTCTTCCCGAAA
GAAAAGAATCATATGACTTACCTAGGCGGTTGTACCACTTGAAAGGTGACATTGAAGAAGCTGAA
TCGAAACTTATACGATATTGTAGAGAACCACTCTGAGTCTTTATTCCCCTAGTCTTCTTCGCATC
CTTACTTACCTCCTTATACTACTGTAAGCATATGAAGGAATGGGT
Right flanking sequence: Indices 328546 -- 328819
GCCTGTTGCCAAGGAGAACGGATAACATGGAAAGACAAGGAATACAAGGAAAGACAAGGAAAGCG
TGGGAGTTGCCGGGGTAACCTCCCTCTCCGGTCGAGTAACCTTCTACCTCTCCTTGTTGCCGAGG
AATTCGGAAAGTCGACTTTGTTCGATAGTTCCCATCTCTCGATCACCCCACAAGAGAAGCCACTC
GAACGAATAGCTCCCCGTGGAATTCCTCAAAGCTATAATATAAATGGAATTCTCCCTTGACTCGA
TCTTTAAAAAAATT
Found at i:328602 original size:10 final size:10
Alignment explanation
Indices: 328574--328608 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
328564 CGGATAACAT
328574 GGAAAGACAA
1 GGAAAGACAA
*
328584 GG-AATACAA
1 GGAAAGACAA
328593 GGAAAGACAA
1 GGAAAGACAA
328603 GGAAAG
1 GGAAAG
328609 CGTGGGAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.57, C:0.09, G:0.31, T:0.03
Consensus pattern (10 bp):
GGAAAGACAA
Left flanking sequence: Indices 328074 -- 328573
TGGGTCAAATTGATCAAAAAAGGAACGCTCTCACTAAGTAAAACGGCTTTTCTAGGTTTTGTAGC
TAGGGCTAGATGGATTTCGTGTCAAAAGAAAAACGAGTGAAAAGACCGGTTTTAGACTTTTTTCC
AAAAAGCATGCCACTTCACTTCTTATTCACTTCCTCACTTTGTTTACTTCGTAACCTTTGGTATT
GCGTCTCATCCAGGTGATTAATATCACGTCATAGCATTTCTTCCCGAAAGAAAAGAATCATATGA
CTTACCTAGGCGGTTGTACCACTTGAAAGGTGACATTGAAGAAGCTGAATCGAAACTTATACGAT
ATTGTAGAGAACCACTCTGAGTCTTTATTCCCCTAGTCTTCTTCGCATCCTTACTTACCTCCTTA
TACTACTGTAAGCATATGAAGGAATGGGTGAACGGGAAACCTGTTGTTAGGAGAACGGGAAACCT
GTTGTTAGGAGGACGGGGCCTGTTGCCAAGGAGAACGGATAACAT
Right flanking sequence: Indices 328609 -- 328819
CGTGGGAGTTGCCGGGGTAACCTCCCTCTCCGGTCGAGTAACCTTCTACCTCTCCTTGTTGCCGA
GGAATTCGGAAAGTCGACTTTGTTCGATAGTTCCCATCTCTCGATCACCCCACAAGAGAAGCCAC
TCGAACGAATAGCTCCCCGTGGAATTCCTCAAAGCTATAATATAAATGGAATTCTCCCTTGACTC
GATCTTTAAAAAAATT
Done.