Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MT364442
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: 305144
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:37873 original size:18 final size:19
Alignment explanation
Indices: 37850--37888 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
37840 CTGGCCTATA
37850 ATATAAT-TAAAAAAAAAG
1 ATATAATATAAAAAAAAAG
*
37868 ATATAATATAAATAAAAAG
1 ATATAATATAAAAAAAAAG
37887 AT
1 AT
37889 TCGCTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
ATATAATATAAAAAAAAAG
Left flanking sequence: Indices 37350 -- 37849
CAACCTCTAGCAGATGGTTTGAAATTGATTCTAAAAGAACCTATTTCACCAAGTAGTGCTAATTT
CTCCCTTTTTAGAATGGCTCCAGTGACTACATTTATGTTAAGTCTGGTCGCTTGGGCCGTTGTAC
CTTTTGATTATGGTATGGTATTGTCAGATCCGAACATAGGGCTACTTTATTTGTTTGCCATATCT
TCGCTAGGTGTTTATGGAATTATTATAGCAGGTTGGTCTAGTAATTAGGGGGCGGCCGTTCGGTC
GCCTATGATACTAGGACCAATAGGTCCAAAATTGGTTTGTGCCGCAGGTGTTGAACGATATACTC
TACACAGGTGTGGGCTTACAGGGCTAGGGCTCATAAACCCTTTCTTTCATTCATCAATAGGGCCC
TGGTCGGTCACTTTTCTGGGCCGGGATCGATAAGTGGAAGTCATAAAAAAGAGATCTTTCTCTTC
GCACCTCAGATCAAGAGGAAGGGTTGCTTGTCAAGCTGGCCTATA
Right flanking sequence: Indices 37889 -- 38388
TCGCTGTTTTTTAACCGGCTTTTCTTCTTTGTCAACGCTACTAAGGACCTATAGGTTTGCCTACT
TGACTTATGAAAGATAATGAGAATGGGTTATTCAAACAAAAAGGAAAAGGCCCTACTTAGTTTCG
CAAGCCTTTGTCATTGTCAGTCAACTAAGTAGGGCCTGAGGCCCCCTTCGAATCCGTAAATCTGA
GGAGCATGCCGCAACAAAAGGATGGTCCCCTATGCATTTCATTTTTTCCGGAAGGGAAAAAAAAG
TACCCCCCATCATAGTGAACCTCTCCTTGTGATCGGGATGAGATAGATGCCTCCCGGCCGGGGGG
CGGATCGAATCGGAGTTTCCTTAGGTAGCCACCAACCTACAGTTATCCTTAAACTTCCGTGCTTG
GTGGAGAAGAAGCGAACAAAGGTACGCTCGCTTGCTGTCTTGTTCTCTGTCGCAAACTGGGATTG
CTCGCCAGCTAGGTCAGATTGGAGCAAGATTAAAAGAGAATATAT
Found at i:57694 original size:20 final size:21
Alignment explanation
Indices: 57669--57714 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
57659 GAATCTCTTG
* *
57669 AGAGAAG-AAGCGCCTTTCTA
1 AGAGAAGAAAACGCCTCTCTA
57689 AGAGAAGAAAACGCCTCTCTA
1 AGAGAAGAAAACGCCTCTCTA
57710 AGAGA
1 AGAGA
57715 GAGACTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (21 bp):
AGAGAAGAAAACGCCTCTCTA
Left flanking sequence: Indices 57169 -- 57668
GATCAAAGCCCGTCCTCCGGGAAAAGACAGCAAGAGATTGTGTAGAAAGGGGCTCGAAAGCTGAG
GAAAGAGATTCGGGATAAACAGGGCCGTTGCGCATCGCAAATGTACCTTCTAATGAATAAGTTAA
GGCAAGGGGATACAGAGCGTGTCTCAGTTGAGGGGGCCTCCGATCCTCTTAATCAAGGGCTTTTG
AAAGCGCCCCATCTACATCTATGTGCTTCCGCTCTCGTACAGTGACGGGGTAGAATTTTATCAAC
AAAATTTGATAACATAATAAGAAACCCTTGACTTATGAGTGTACCGATGCCGTCAGGAGGATCAA
CGAAAAGGTAAAGAAACTCCGCCCTGTCAGAGATGACACGATAGATCTTTTTTAGTACGAGATTG
CTCCCTTTGTTCCCAAGCAGAGCATTTTCGTGGCTTTTTAAACTTAAAGCAGCAAGCCCGATTGG
ATATGCAACATTCTCAAGAGTTATACACTGAATGGGAATCTCTTG
Right flanking sequence: Indices 57715 -- 58214
GAGACTTTTTCTTCTCGACAGGGAAAAGGGGAAAGCCCCATAACATTCTTTTTTGTTGGTTGTTT
AAAAAGTTCTGATCAATGTAGTGATGTCCATAATCAATCCTATTTGTTAATGAATCGAATCCTAT
CAAATATTTCTATTTATCCTTTGAATTACTCATATATATTCTATGAATTTCATTTCGCATCGGAA
ACTATTCTAGGAGAAGTTCGAATCCGTTCCGTTCGGATATTGATTGGTCTTGGTTTGACATGGTT
TACGCGTTACTGGTTCCCGGAAGAGTTAATATCTCCATTAGCTAAACCCTTTCTTACCCTGCCTT
TGGACTCGTATTTTGTTCGTACACAATCAACGGAGGCCTTCCCGACATATGTTGCAACGTCTCCA
ATAGCATGCTCTTACTTCATCTTTCCCTTAATAAGTCATCAAATTTGGTGCTTTTTGATCCCCAG
TTGCTATGGGGAACAAAGGACGAAATACAATCGATTCCTCCATTT
Found at i:97552 original size:21 final size:21
Alignment explanation
Indices: 97526--97568 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
97516 CGGAGCTGCT
97526 ACTACTAGC-GGAAGAAAAGGA
1 ACTACTA-CTGGAAGAAAAGGA
*
97547 ACTACTACTGGAAGGAAAGGA
1 ACTACTACTGGAAGAAAAGGA
97568 A
1 A
97569 AAGGACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.47, C:0.14, G:0.28, T:0.12
Consensus pattern (21 bp):
ACTACTACTGGAAGAAAAGGA
Left flanking sequence: Indices 97026 -- 97525
CGAACCTGAATGGCTTTTTTGGGTCCAATTCCATCCATTTTGGTTGAGGCAATTCTTACTTGTTC
ATCGGCAACTGATCTAGCTCCTGAAATATATAACATTCTTTATCCTTCCTTTTACTAGTCTTCTC
GGCTGGAATCATAAATGGGTTGTCTCCTCTCTGATGATCTTTTCTATAGGTAGAACTACTGTGAG
CGGTCTAAACTTCACTTTTTCTTACTTTTCACGACCTTCTTTAATAAAAATTGAAAGAACTCGCT
TTCCTTTCCTTTCTCTTGGATTTCGGACAAGAGCCCGGCAGGGAGCTCCCAATTTGTTCCCTCCT
TCGGAATGATCTCATGGAGAACAGCACCCCACGTGCGATAGTGCACTTGTTGGGGCAATAAATCT
TTTGACTGAGCAGCAAGCTCCTGTATTAAACTTTTGAAGTAGCCATCATATAGGGTCCGCTTACT
TTGAAGAGCTTTTTTATCATCTTCCTTTGGAAGATCGGAGCTGCT
Right flanking sequence: Indices 97569 -- 98068
AAGGACTTTCTTTTTCGAATAGAGGAGGAGTCCTCCATGTCCATAATATATATGGCAATATAGAA
AGTCAAGAGGAAAAGGCATGACCAGAAGAATTGTGTGAAATAAGTGAATTTATCCAGTTGAGGCA
TGATTGATTGATGAAAAATGATTCCCTCCAGACAGAAAGAGAAAGAGAGTCCTTCCTGTAGGAGT
AGTGAATAAATATAGAGAGTTTTGCTTGGTTGTTAACCAAGGGAAAAAAGAAAAAGAAAACCACT
ACCGTAATGCCTTGAAGGGCCGTTAAAGCGAAGCATCCCTCTCTTAGCATCTTACCCGGTTCGCC
CTTTACAAAAGACTAGTCCGGGGGGCTCCTCACCCATCCAAACTTCTTCGAAAACCCCTTTCCCA
TGTTGCCTGTCAACGAGAATTGGTACTTTTGGGTCATCAACAGAGGCCCCGCCCACCCCACCTTT
TACATTCTTGATCTATTTTGACCCAAGTTTCATTTTTTTCTAGGT
Found at i:140601 original size:18 final size:19
Alignment explanation
Indices: 140566--140604 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
140556 AAAACAGCGA
140566 ATCTTTTTATTTATATTAT
1 ATCTTTTTATTTATATTAT
*
140585 ATCTTTTTTTTTA-ATTAT
1 ATCTTTTTATTTATATTAT
140603 AT
1 AT
140605 TATAGGCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (19 bp):
ATCTTTTTATTTATATTAT
Left flanking sequence: Indices 140066 -- 140565
ATATATTCTCTTTTAATCTTGCTCCAATCTGACCTAGCTGGCGAGCAATCCCAGTTTGCGACAGA
GAACAAGACAGCAAGCGAGCGTACCTTTGTTCGCTTCTTCTCCACCAAGCACGGAAGTTTAAGGA
TAACTGTAGGTTGGTGGCTACCTAAGGAAACTCCGATTCGATCCGCCCCCCGGCCGGGAGGCATC
TATCTCATCCCGATCACAAGGAGAGGTTCACTATGATGGGGGGTACTTTTTTTTCCCTTCCGGAA
AAAATGAAATGCATAGGGGACCATCCTTTTGTTGCGGCATGCTCCTCAGATTTACGGATTCGAAG
GGGGCCTCAGGCCCTACTTAGTTGACTGACAATGACAAAGGCTTGCGAAACTAAGTAGGGCCTTT
TCCTTTTTGTTTGAATAACCCATTCTCATTATCTTTCATAAGTCAAGTAGGCAAACCTATAGGTC
CTTAGTAGCGTTGACAAAGAAGAAAAGCCGGTTAAAAAACAGCGA
Right flanking sequence: Indices 140605 -- 141104
TATAGGCCAGCTTGACAAGCAACCCTTCCTCTTGATCTGAGGTGCGAAGAGAAAGATCTCTTTTT
TATGACTTCCACTTATCGATCCCGGCCCAGAAAAGTGACCGACCAGGGCCCTATTGATGAATGAA
AGAAAGGGTTTATGAGCCCTAGCCCTGTAAGCCCACACCTGTGTAGAGTATATCGTTCAACACCT
GCGGCACAAACCAATTTTGGACCTATTGGTCCTAGTATCATAGGCGACCGAACGGCCGCCCCCTA
ATTACTAGACCAACCTGCTATAATAATTCCATAAACACCTAGCGAAGATATGGCAAACAAATAAA
GTAGCCCTATGTTCGGATCTGACAATACCATACCATAATCAAAAGGTACAACGGCCCAAGCGACC
AGACTTAACATAAATGTAGTCACTGGAGCCATTCTAAAAAGGGAGAAATTAGCACTACTTGGTGA
AATAGGTTCTTTTAGAATCAATTTCAAACCATCTGCTAGAGGTTG
Found at i:239390 original size:18 final size:18
Alignment explanation
Indices: 239341--239391 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
239331 CCCTTTCTTC
239341 GGGGTTGTCGTCTTCAGA
1 GGGGTTGTCGTCTTCAGA
* ** *
239359 GGTGTCATCCTCTTCAGA
1 GGGGTTGTCGTCTTCAGA
239377 GGGGTTGTCGTCTTC
1 GGGGTTGTCGTCTTC
239392 CGGAGAACCA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.10, C:0.22, G:0.33, T:0.35
Consensus pattern (18 bp):
GGGGTTGTCGTCTTCAGA
Left flanking sequence: Indices 238841 -- 239340
AAGGAGCTAGCCAGGTTGTCAAGGGATGTAACTTCGCTAAGACGCCAAAAGGAGAGTAACGAATC
TTAGAATATAGCTATGCTATACCTTTTGAAGTTGGGGTTCACCATACGTGACCGGCGAGTCCCAT
CGCTGCATTCTTTGACCGTCAAGGGTCGAGCAACCGCTACATTTTTTGAACGGCCACAGCCTACA
TAAACTCTTTCTCCCTCTTTTCAAGGAAGTGAGTCTCAGACCTAATGTAGTTCTCGGTCCTTTTT
ATACAGTTCCTGGCAGGTGCTTTTGTGGCTCTTCACTCCAGCCCTGAAGTATTCTGTGAGCCCCA
TTTGTTTAACATGGGGCCTCCCCCTCCCTCCGGACCGACAAGATCCCAGACCTAACGAGAGATCT
CTCTCTCCCTCTCTTTTTGGGCATAGCTTACTGCTTTGTTTTAGTTTCCATTTTCTTTTATACTT
ATTTTGCTTTTTTTTTATGGCTTTCTGAAGACGTACCCTTTCTTC
Right flanking sequence: Indices 239392 -- 239891
CGGAGAACCAGACTGGGCGGGCCCTGGCTCGCGTGAAGTCGAGGCACCGTTCCAATCAATCCGTT
TCCTTTTATGTCCTTTCCTTATATATATATAAAACTTTTGGAAAGAAAAAAAAAGAAAAAGAAGA
TGAAAAAAAGACCCAAGAAAACTAAAAAAGAATCTTTTGTAGTTTTATTAGAAAAATTTAGATGG
AAATTCAAATAATGTAAGCATCGCTCTTTTTCCTTAAATTAAATAAAAGCTAAAGCACTTTCTTT
TAAGAATTCATCTGGTTCCATCTTTCTTTCGTTAGTTAAGCCACCTTTTTCTAAAAAGGATTTTA
GTAATTCTGATTTTACACTATTTGGAATAACTCTCTCATATTGAGAAATTTTGTCTAGTGGCATT
CGATCACAGAATCCATTGACAGCTGCATAAATGACTAGAATTTGTTTTTCAATTGGAAGTGGTGC
ATATTGTGGTTGTTTCGGTACTTCTGTCAGCCTTGCACCTCTATT
Done.