Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3766
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 44980
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6307 original size:1 final size:1
Alignment explanation
Indices: 6301--6330 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
6291 TTTGCTTCCT
6301 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6331 GGGACTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7952 original size:46 final size:46
Alignment explanation
Indices: 7880--8133 Score: 183
Period size: 46 Copynumber: 5.8 Consensus size: 46
7870 GAAGATCACA
* * * *
7880 TCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * *
7926 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG-ATA
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * * **
7971 T-A-ATCCTATCT-CCTGAAGTTACAGTGGAGCGGA-TTAA-AA-T
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
** * * * * * *
8011 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCA--
1 TCA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
* * * *
8053 TCAGGTCTTATTTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATT
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
*
8099 GCAGATCTTATC-CCCTGAGGTTACAGTGGAGCAGA
1 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGA
8134 TTGAAGCCAG
Statistics
Matches: 161, Mismatches: 35, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
41 34 0.21
42 20 0.12
43 17 0.11
44 21 0.13
45 24 0.15
46 45 0.28
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (46 bp):
TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATT
Found at i:8024 original size:43 final size:43
Alignment explanation
Indices: 7837--8134 Score: 155
Period size: 41 Copynumber: 6.9 Consensus size: 43
7827 TGGAGCGGAT
* * *
7837 TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATC--ACA
1 TAAA-GATCTTATCTC-CTGAAGTTACAGTGGAGCAGATCGAAAA
* * * * *
7880 T-CAGGTCTTATCTCCCTG-AGATTACAGTGGAACAGACCAAAGAA
1 TAAAGATCTTATCT-CCTGAAG-TTACAGTGGAGCAGATCGAA-AA
** * * *
7924 TTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGA
1 -TAAAGATCTTATCT-CCTGAAGTTACAGTGGAGCAGATCGAAAA
* * * *
7969 TATA-ATCCTATCTCCTGAAGTTACAGTGGAGCGGAT-TAAAA
1 TAAAGATCTTATCTCCTGAAGTTACAGTGGAGCAGATCGAAAA
* * *
8010 TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--CA
1 TAAA-GATCTTATCTC-CTGAAGTTACAGTGGAGCAGATCGAAAA
* * * * * *
8053 T-CAGGTCTTATTTCTCTGAGGTTACAGTGGAGTAGACCGAAGAA
1 TAAAGATCTTATCTC-CTGAAGTTACAGTGGAGCAGATCGAA-AA
** * *
8097 TTGCAGATCTTATCCCCTGAGGTTACAGTGGAGCAGAT
1 -TAAAGATCTTATCTCCTGAAGTTACAGTGGAGCAGAT
8135 TGAAGCCAGA
Statistics
Matches: 197, Mismatches: 41, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
40 2 0.01
41 62 0.31
42 23 0.12
43 21 0.11
44 23 0.12
45 23 0.12
46 42 0.21
47 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
TAAAGATCTTATCTCCTGAAGTTACAGTGGAGCAGATCGAAAA
Found at i:8031 original size:173 final size:169
Alignment explanation
Indices: 7779--8139 Score: 521
Period size: 173 Copynumber: 2.1 Consensus size: 169
7769 TCCTGCATTA
*
7779 ACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGA
1 ACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGA
7844 TCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAGTG
66 TCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAGTG
*
7909 GAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTT
131 GAACAGACCAAAGAATTGCAGATCTTATC-CCCTGAGGTT
*
7949 ACAGCGGAGCAGATCGAAGATA-TAATCCTATCTCC-TGA-AGTTACAGTGGAGCGGATTAAAAT
1 ACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCTTGAGA-TTACAATGGAGCGGA-T----T
* * * * *
8011 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATTTCTCTGAGGTT
60 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATT
** *
8076 ACAGTGGAGTAGACCGAAGAATTGCAGATCTTATCCCCTGAGGTT
125 ACAGTGGAACAGACCAAAGAATTGCAGATCTTATCCCCTGAGGTT
* *
8121 ACAGTGGAGCAGATTGAAG
1 ACAGCGGAGCAGATCGAAG
8140 CCAGAGGTCT
Statistics
Matches: 172, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
167 1 0.01
168 17 0.10
169 14 0.08
170 21 0.12
172 27 0.16
173 92 0.53
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (169 bp):
ACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGA
TCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAGTG
GAACAGACCAAAGAATTGCAGATCTTATCCCCTGAGGTT
Found at i:8122 original size:86 final size:87
Alignment explanation
Indices: 7842--8134 Score: 258
Period size: 86 Copynumber: 3.4 Consensus size: 87
7832 CGGATTAAAG
* * * * * *
7842 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATTTCTCTGAGGTTACAG
* *
7907 TGGAACAGACCAAAGAATTTCA
66 TGGAGCAGACCAAAGAATTACA
* ** * * * *
7929 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCG-A--AGATATAATCCTATCTCCTGAAGTT
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTAT--T-TCT-CTGAGGTT
* ** *
7991 ACAGTGGAGCGGA-TTAA-AA-TAAA
62 ACAGTGGAGCAGACCAAAGAATTACA
* *
8014 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATTTCTCTGAGGTTACA
1 -GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATTTCTCTGAGGTTACA
* * *
8079 GTGGAGTAGACCGAAGAATTGCA
65 GTGGAGCAGACCAAAGAATTACA
* *
8102 GATCTTATC-CCCTGAGGTTACAGTGGAGCAGAT
1 GATCTTATCTCCCTGAAGTTACAGTAGAGCAGAT
8135 TGAAGCCAGA
Statistics
Matches: 157, Mismatches: 38, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
84 6 0.04
85 20 0.13
86 59 0.38
87 47 0.30
88 19 0.12
89 6 0.04
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (87 bp):
GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATTTCTCTGAGGTTACAG
TGGAGCAGACCAAAGAATTACA
Found at i:8152 original size:130 final size:127
Alignment explanation
Indices: 7926--8177 Score: 285
Period size: 130 Copynumber: 2.0 Consensus size: 127
7916 CCAAAGAATT
* *
7926 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCTGAAGTT
1 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCCCCTGAAGTT
* * *
7991 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA
66 ACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGATA-TTACAGTAGAGTAGATCGCA
* * * * * *
8053 TCAGGTCTTATTTCTCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTGCAGATCTTATCCCCTGA
1 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATA-T--A-ATCCTATCCCCTGA
* ** * *
8117 GGTTACAGTGGAGCAGATTGAAGCCAGAGG-TCTTATCTCCCTGATATTACAGTGGAGTAGA
62 AGTTACAGTGGAGCAGATT-AAAACAAAGGATCTTATCTCCCTGATATTACAGTAGAGTAGA
8178 CTTAAACCTA
Statistics
Matches: 103, Mismatches: 16, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
126 1 0.01
127 38 0.37
129 1 0.01
130 56 0.54
131 7 0.07
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (127 bp):
TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCCCCTGAAGTT
ACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGATATTACAGTAGAGTAGATCGCA
Found at i:9533 original size:3 final size:3
Alignment explanation
Indices: 9472--9524 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
9462 TTTGTTAACT
* *
9472 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
9517 TTA GTA TT
1 TTA TTA TT
9525 GGTATTATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:9603 original size:20 final size:20
Alignment explanation
Indices: 9556--9604 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
9546 ACATCTCTAT
*
9556 TCATATATACTTATGTATTT
1 TCATATATACTTATGTATTA
9576 TCAAATATATATCTTAT-TATTA
1 TC--ATATATA-CTTATGTATTA
9598 TCATATA
1 TCATATA
9605 AGTGCTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 7 0.28
22 13 0.52
23 5 0.20
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (20 bp):
TCATATATACTTATGTATTA
Found at i:9726 original size:34 final size:34
Alignment explanation
Indices: 9651--9728 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 34
9641 AATTTGTTTA
* *
9651 ATATATATACGTATACTCATATTTCTTTTTATAT
1 ATATATATACATATACTCATATTTATTTTTATAT
* *
9685 ATCTATATACATATACAT-ATTTTTATTTTTATAAGT
1 ATATATATACATATAC-TCATATTTATTTTTAT-A-T
9721 ATATATAT
1 ATATATAT
9729 TTATATGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 26 0.72
35 2 0.06
36 8 0.22
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (34 bp):
ATATATATACATATACTCATATTTATTTTTATAT
Found at i:12442 original size:16 final size:16
Alignment explanation
Indices: 12421--12451 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12411 AATGAAGGAT
12421 TTCATAAACATAAATA
1 TTCATAAACATAAATA
*
12437 TTCATACACATAAAT
1 TTCATAAACATAAAT
12452 TCCTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (16 bp):
TTCATAAACATAAATA
Found at i:14579 original size:21 final size:22
Alignment explanation
Indices: 14541--14581 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
14531 GGTTCAAAGC
*
14541 AAATAAATTATTAAAAAATCAA
1 AAATAAATAATTAAAAAATCAA
*
14563 AAATAAA-AATTATAAAATC
1 AAATAAATAATTAAAAAATC
14582 TGTCCACTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATAATTAAAAAATCAA
Found at i:16789 original size:3 final size:3
Alignment explanation
Indices: 16781--16815 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
16771 TGGGATCATC
16781 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16816 ATAGGCAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:24433 original size:15 final size:14
Alignment explanation
Indices: 24413--24442 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
24403 TAGAACATGT
24413 TATATATAGTAGATA
1 TATATATAGT-GATA
24428 TATATATAGTGATA
1 TATATATAGTGATA
24442 T
1 T
24443 CTAAATCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TATATATAGTGATA
Found at i:24528 original size:26 final size:26
Alignment explanation
Indices: 24499--24553 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
24489 GTAATACCCC
24499 TACCCGTATTCATTGCCGGAATAGGG
1 TACCCGTATTCATTGCCGGAATAGGG
*
24525 TACCCGTATTTATTGCCGGAATAGGG
1 TACCCGTATTCATTGCCGGAATAGGG
24551 TAC
1 TAC
24554 GAGGCATTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (26 bp):
TACCCGTATTCATTGCCGGAATAGGG
Found at i:33470 original size:44 final size:44
Alignment explanation
Indices: 33422--33783 Score: 562
Period size: 44 Copynumber: 8.2 Consensus size: 44
33412 CTCAGGAACA
* * * *
33422 CCAAATTTGCTATCTGCGATTTGCTCTCCGCCAATACATAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
*
33466 CCAAATCTGCTATCTTTGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
33510 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAAAAACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
33554 CCAAATCTACTATCTTCGATCTGCTCTCTGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
33598 CCAAATCTGCTATCTTCGATCTGCTCTTCGCCACTACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
33642 CCAAATCTGCTACCTTCGATCTGCTCTCTGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
*
33686 CCGAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * * *
33730 CCAAATCTGTTATCTTTGATCTGCTCTCCACCAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
33774 CCAAATCTGC
1 CCAAATCTGC
33784 AAGATTTACC
Statistics
Matches: 289, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 289 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (44 bp):
CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
Done.