Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1755
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: 33353
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Found at i:14112 original size:42 final size:42
Alignment explanation
Indices: 14057--14136 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
14047 TTCTTCTCTC
* *
14057 CTCCTCCTGTCATCCCTCC-ACTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTA-TCTCTACTATCTCTCCTGTCT
14099 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCT
14137 CCTATCATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.11, C:0.46, G:0.03, T:0.40
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
Found at i:14116 original size:12 final size:11
Alignment explanation
Indices: 14090--14148 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 11
14080 TCTATTATCT
*
14090 CTCCTGTCTCTC
1 CTCCTATCTC-C
14102 CTCCTATCATCC
1 CTCCTATC-TCC
14114 CTCCTATCT--
1 CTCCTATCTCC
*
14123 CTACTATCTCTC
1 CTCCTATCTC-C
14135 CTCCTATCATCC
1 CTCCTATC-TCC
14147 CT
1 CT
14149 ACTCTCTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
9 8 0.21
11 1 0.03
12 26 0.67
13 4 0.10
ACGTcount: A:0.12, C:0.47, G:0.02, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:14122 original size:33 final size:33
Alignment explanation
Indices: 14085--14166 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
14075 CACTCTCTAT
* * *
14085 TATCTCTCCTGTCTCTCCTCCTATCATCCCTCC
1 TATCTCTACTATCTCTCCTCCTATCATCCCTAC
14118 TATCTCTACTATCTCTCCTCCTATCATCCCTAC
1 TATCTCTACTATCTCTCCTCCTATCATCCCTAC
* * *
14151 TCTCTCTTCTTTCTCT
1 TATCTCTACTATCTCT
14167 TTGAGGGCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.11, C:0.44, G:0.01, T:0.44
Consensus pattern (33 bp):
TATCTCTACTATCTCTCCTCCTATCATCCCTAC
Found at i:15997 original size:251 final size:252
Alignment explanation
Indices: 15527--16034 Score: 876
Period size: 251 Copynumber: 2.0 Consensus size: 252
15517 AAGCAAGTCA
*
15527 CAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
1 CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
*
15592 TCCAAATATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
66 TCCAAATATATGCAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
*
15657 GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGACCTT
131 GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGACCTT
* * * *
15722 GAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCAT
196 GAAATCCTTCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
15779 CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
1 CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
* * *
15844 TCCAAATATATGCAATTGACCAGCTTGGGCTCTTCTAGCTCC-AATTGGGTTTACTTTCAAATAG
66 TCCAAATATATGCAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
* * *
15908 GGCAGCAACCGTCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTT
131 GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGACCTT
15973 GAAA-CCTTCCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
196 GAAATCCTT-CCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
16030 CAACC
1 CAACC
16035 CTTCCTTCTT
Statistics
Matches: 242, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
250 4 0.02
251 135 0.56
252 103 0.43
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (252 bp):
CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
TCCAAATATATGCAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGACCTT
GAAATCCTTCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
Found at i:20347 original size:18 final size:19
Alignment explanation
Indices: 20305--20385 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 19
20295 TCCATCTTCT
*
20305 TCTCTCCTC-CTCCT-GTCA
1 TCTCTCCTCTCTCCTCCT-A
* *
20323 TCCCTCCTCTCT-CTGCTA
1 TCTCTCCTCTCTCCTCCTA
20341 TCTCTCCTATCTCTCCTCCTA
1 TCTCTCC--TCTCTCCTCCTA
* *
20362 TCTCTACTATCT-CTCCTA
1 TCTCTCCTCTCTCCTCCTA
20380 TCTCTC
1 TCTCTC
20386 TTTCTATCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
18 28 0.55
19 7 0.14
20 5 0.10
21 11 0.22
ACGTcount: A:0.09, C:0.47, G:0.02, T:0.42
Consensus pattern (19 bp):
TCTCTCCTCTCTCCTCCTA
Found at i:20350 original size:9 final size:9
Alignment explanation
Indices: 20326--20385 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
20316 CCTGTCATCC
*
20326 CTCCTCTCT
1 CTCCTATCT
*
20335 CTGCTATCT
1 CTCCTATCT
20344 CTCCTATCTCT
1 CTCCTA--TCT
20355 CCTCCTATCT
1 -CTCCTATCT
*
20365 CTACTATCT
1 CTCCTATCT
20374 CTCCTATCT
1 CTCCTATCT
20383 CTC
1 CTC
20386 TTTCTATCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 31 0.72
10 3 0.07
11 3 0.07
12 6 0.14
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.43
Consensus pattern (9 bp):
CTCCTATCT
Found at i:20364 original size:21 final size:21
Alignment explanation
Indices: 20329--20417 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
20319 GTCATCCCTC
* *
20329 CTCTCTCTGCTATCTCTCCTAT
1 CTCTC-CTCCTATCTCTTCTAT
*
20351 CTCTCCTCCTATCTCTACTAT
1 CTCTCCTCCTATCTCTTCTAT
* *
20372 CTCTCCT-ATCTCTCTTTCTAT
1 CTCTCCTCCTATCTC-TTCTAT
*
20393 CATC-CCTCCTATCTCTTCTTT
1 C-TCTCCTCCTATCTCTTCTAT
20414 CTCT
1 CTCT
20418 TTGAGGGCTA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
20 7 0.13
21 36 0.65
22 12 0.22
ACGTcount: A:0.10, C:0.42, G:0.01, T:0.47
Consensus pattern (21 bp):
CTCTCCTCCTATCTCTTCTAT
Found at i:20393 original size:30 final size:30
Alignment explanation
Indices: 20325--20385 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
20315 TCCTGTCATC
* *
20325 CCTCCTCTCTCTGCTATCTCTCCTATCTCT
1 CCTCCTATCTCTACTATCTCTCCTATCTCT
20355 CCTCCTATCTCTACTATCTCTCCTATCTCT
1 CCTCCTATCTCTACTATCTCTCCTATCTCT
20385 C
1 C
20386 TTTCTATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.10, C:0.46, G:0.02, T:0.43
Consensus pattern (30 bp):
CCTCCTATCTCTACTATCTCTCCTATCTCT
Found at i:26014 original size:9 final size:9
Alignment explanation
Indices: 26002--26062 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
25992 CTCTCTCTAT
26002 TATCTCTCC
1 TATCTCTCC
26011 TATCTCTCC
1 TATCTCTCC
* *
26020 T-CCTAT-C
1 TATCTCTCC
*
26027 -ATCCCTCC
1 TATCTCTCC
*
26035 TATCTCTAC
1 TATCTCTCC
26044 TATCTCTCC
1 TATCTCTCC
26053 TATCTCTCC
1 TATCTCTCC
26062 T
1 T
26063 CCTATCATCC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
9 34 0.83
ACGTcount: A:0.13, C:0.44, G:0.00, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:26022 original size:12 final size:12
Alignment explanation
Indices: 26007--26068 Score: 57
Period size: 12 Copynumber: 5.7 Consensus size: 12
25997 TCTATTATCT
26007 CTCCTATCTCTC
1 CTCCTATCTCTC
26019 CTCCTATCATC-C
1 CTCCTATC-TCTC
26031 CTCCTA--TCT-
1 CTCCTATCTCTC
*
26040 CTACTA--TCT-
1 CTCCTATCTCTC
26049 CTCCTATCTCTC
1 CTCCTATCTCTC
26061 CTCCTATC
1 CTCCTATC
26069 ATCCATCCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
9 15 0.35
11 3 0.07
12 23 0.53
13 2 0.05
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:26026 original size:42 final size:42
Alignment explanation
Indices: 25974--26092 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
25964 TTCTTCTCTC
*
25974 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
*
26016 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
* * *
26058 CTCCTCCTATCATCCATCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
26093 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.12, C:0.45, G:0.00, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
Found at i:28483 original size:859 final size:857
Alignment explanation
Indices: 26812--28521 Score: 2973
Period size: 859 Copynumber: 2.0 Consensus size: 857
26802 TTGTATTCTT
26812 TTTTTTTTTTGTATTCTTGAAAAAAAAAATAACAGCAACAAGATCAAATGAGTTCAAGATTCAAA
1 TTTTTTTTTTGTATTCTTG-AAAAAAAAATAACAGCAACAAGATCAAATGAGTTCAAGATTCAAA
*
26877 ACTAACAGAAATAGTAGGATGAACAGTAAACACGAACCTGATAGTGATAATGAATTTAATCCAAC
65 ACTAACAGAAACAGTAGGATGAACAGTAAACACGAACCTGATAGTGATAATGAATTTAATCCAAC
*
26942 TCCAAACCAAAGCTCTAATACCAATTGATGACAACCATTAACCAAGGTTGCCTAAATAATGATCT
130 TCCAAACCAAAGCTCTAATACCAATTGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCT
* * *
27007 TGAGATGGATTTCTAATAATAAACAGAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAA
195 TGAGATGGATTTCTAACAATAAACAGAATTATTAATGCAAGAACAAAAATTGAAAGAAGCAGAAA
27072 AAAATAACAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCA
260 AAAATAACAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCA
27137 AAAGGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAG
325 AAAGGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAG
27202 AACCTAAGAATCACTCTCACACAAAATGTGTTTAATCTGCAAATATCAATGTCTGCCCCCTCCAA
390 AACCTAAGAATCACTCTCACACAAAATGTGTTTAATCTGCAAATATCAATGTCTGCCCCCTCCAA
27267 ATATGTTTACAAGAGCTTATATATGCCCTCATAAGCCATAGTTAACACAAGCCCTAAGGGGCTTA
455 ATATGTTTACAAGAGCTTATATATGCCCTCATAAGCCATAGTTAACACAAGCCCTAAGGGGCTTA
27332 TTATGCTAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGATTTTTTATGCTAAATAAAGCC
520 TTATGCTAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGATTTTTTATGCTAAATAAAGCC
*
27397 CAAAGCAAGTCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATACAATCCATTG
585 CAAAGCAAGCCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATACAATCCATTG
* *
27462 GAGCCCATATCTTCCAAATATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCT
650 GAGCCCATATCTTCCAAATATATACAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCT
*
27527 ACTTTCAAATAGGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTCGCCTTTGCCCTCG
715 ACTTTCAAATAGGCCAGCAACCATCTTCTCTAAGTCTTCCTTTATCCTCTTCGCCTTTGCCCTCG
* *
27592 TTATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTCT-TTGTCTTCAATGGGCCTTCCTTGGTT
780 TCATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGT-TGTTGTCTTCAATGGACCTTCCTTGGTT
*
27656 TTCATCATTTTGTA
844 CTCATCATTTTGTA
** * *
27670 TTTTTTTTTTGTATTCTTG-AAAAAATCTAACAGCAACAAGATCCAATGAGTTCAAGATTCAGAA
1 TTTTTTTTTTGTATTCTTGAAAAAAAAATAACAGCAACAAGATCAAATGAGTTCAAGATTCAAAA
* *
27734 CTAACAGCAACAGTATGATGAACAGTAAACACGAACCTGATAGTGATAATGAATTTAATCCAACT
66 CTAACAGAAACAGTAGGATGAACAGTAAACACGAACCTGATAGTGATAATGAATTTAATCCAACT
* *
27799 CCAAACCAAAGCTCTGATACCAATTGATGACAACCATGATCCAAGGTTGCCTAAATAATGATCTT
131 CCAAACCAAAGCTCTAATACCAATTGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTT
27864 GAGATGGATTTCTAACAATAAACAGAATTATTAATGCAAGAACAAAAATTGAAAGAAGCAG-AAA
196 GAGATGGATTTCTAACAATAAACAGAATTATTAATGCAAGAACAAAAATTGAAAGAAGCAGAAAA
27928 AAATAACAAAACTGGAATAGATTAGAGATGAA-GATGGCGCCACAATCACAAGATTGATAAGCCA
261 AAATAACAAAA-TGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCA
*
27992 AAAGGAATGATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAAATTGGCTCACTCAA
325 AAAGGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAG-AAAAATTGGCTCACTCAA
28057 GAACCTAAGAATCACACTCTCACACAAAATGTGTTTAAT-TCGCAAATATCAATGTCTGCCCCCT
389 GAACCTAAGAAT--CACTCTCACACAAAATGTGTTTAATCT-GCAAATATCAATGTCTGCCCCC-
* * * *
28121 TCTAAATCTGTTTACAAGAGTTTATATATGCCTTCATAAGCCATAGTTAACACAAGCCCTAAGGG
450 TCCAAATATGTTTACAAGAGCTTATATATGCCCTCATAAGCCATAGTTAACACAAGCCCTAAGGG
* *
28186 GCTTATTGTGCTAACAAGCCCAACTCTTAGTTAAACCCAAATAACAAGATTTTTTATGCTAAATA
515 GCTTATTATGCTAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGATTTTTTATGCTAAATA
* * * *
28251 AAGCCCAAAGTAGGCCACAACCAGCAGGCCCTTTATTACAAAATAACCCAATTCCTAATTCAATC
580 AAGCCCAAAGCAAGCCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATACAATC
*
28316 CATTGGAGCCCATATCTTCCAAATATATACAATTGACCAGCTTGGGCTCTTCTAACTCCAAATTG
645 CATTGGAGCCCATATCTTCCAAATATATACAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTG
* *
28381 GGTCTACTTTCAAATAGGGCAGCAACCATCTTCTCTAAGTCTTCCTTTATCCTCTTTGCCTTTGC
710 GGTCTACTTTCAAATAGGCCAGCAACCATCTTCTCTAAGTCTTCCTTTATCCTCTTCGCCTTTGC
* *
28446 CCTCGTCATTGGTCCTTGAAA-CCTTCCCAATGCCTTCAGGTTGTTGTCTTCAGTGGACCTTCCT
775 CCTCGTCATTGGTCCTTGAAATCCTT-CCAACGCCTTCAGGTTGTTGTCTTCAATGGACCTTCCT
28510 TGGTTCTCATCA
839 TGGTTCTCATCA
28522 GTAGTAGAAT
Statistics
Matches: 808, Mismatches: 36, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
855 91 0.11
856 273 0.34
857 1 0.00
858 71 0.09
859 372 0.46
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (857 bp):
TTTTTTTTTTGTATTCTTGAAAAAAAAATAACAGCAACAAGATCAAATGAGTTCAAGATTCAAAA
CTAACAGAAACAGTAGGATGAACAGTAAACACGAACCTGATAGTGATAATGAATTTAATCCAACT
CCAAACCAAAGCTCTAATACCAATTGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTT
GAGATGGATTTCTAACAATAAACAGAATTATTAATGCAAGAACAAAAATTGAAAGAAGCAGAAAA
AAATAACAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAA
AAGGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGA
ACCTAAGAATCACTCTCACACAAAATGTGTTTAATCTGCAAATATCAATGTCTGCCCCCTCCAAA
TATGTTTACAAGAGCTTATATATGCCCTCATAAGCCATAGTTAACACAAGCCCTAAGGGGCTTAT
TATGCTAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGATTTTTTATGCTAAATAAAGCCC
AAAGCAAGCCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATACAATCCATTGG
AGCCCATATCTTCCAAATATATACAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTA
CTTTCAAATAGGCCAGCAACCATCTTCTCTAAGTCTTCCTTTATCCTCTTCGCCTTTGCCCTCGT
CATTGGTCCTTGAAATCCTTCCAACGCCTTCAGGTTGTTGTCTTCAATGGACCTTCCTTGGTTCT
CATCATTTTGTA
Done.