Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold376
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: 30976
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:1224 original size:27 final size:27
Alignment explanation
Indices: 1037--1380 Score: 358
Period size: 27 Copynumber: 13.1 Consensus size: 27
1027 AAAGTACTCC
1037 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
1064 C-AGTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
1090 CGATTTACAGAATTA-CG-TTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1115 C-AGTTTACAGAA-TACTGTTTT-CCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
1140 CGATTTATAGAATTACCG--TTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* ** * *
1165 TGATTTGTAAAATTATCG-TTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1191 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
1218 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
1245 CGATTTACAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
1271 CGATTTGA-A-AATTACCGTTTTACCCT
1 CGATTT-ACAGAATTACCGTTTTACCCT
* * *
1297 CGATTTACAAAATTACTGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
1324 C-AGTTTACAAAATTA-TTTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
1350 CGATTTATAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
1377 CGAT
1 CGAT
1381 GTGAAATTAC
Statistics
Matches: 269, Mismatches: 30, Indels: 36
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.02
25 67 0.25
26 87 0.32
27 109 0.41
28 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:1282 original size:105 final size:105
Alignment explanation
Indices: 1037--1390 Score: 451
Period size: 105 Copynumber: 3.4 Consensus size: 105
1027 AAAGTACTCC
*
1037 CGATTTACAGAATTACCGTTTTACCCTC-AGTTAT-AGAATTACTGTTTTACCCTCGATTTACAG
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TT-TGAAAATTAC-GTTTTACCCTCGATTTACAG
*
1100 AATTA-CGTTTACCCTCAGTTTACAGAA-TACTGTTTT-CCCT
63 AATTACCGTTTACCCTCAGTTTACAGAATTACTATTTTACCCT
* *
1140 CGATTTATAGAATTACCG--TTACCCTTGATTTGTAAAATTATCG-TTTACCCTCGATTTACAGA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTG-AAAATTA-CGTTTTACCCTCGATTTACAGA
*
1202 ATTACCATTTTACCCTCAGTTTACAGAATTACTATTTTACCCT
64 ATTACC-GTTTACCCTCAGTTTACAGAATTACTATTTTACCCT
*
1245 CGATTTACAGAATTACCGTTTTACCC-CGATTTGAAAATTACCGTTTTACCCTCGATTTACAAAA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTGAAAATTA-CGTTTTACCCTCGATTTACAGAA
* * *
1309 TTACTGGTTTACCCTCAGTTTACAAAATTA-TTTTTTACCCT
65 TTAC-CGTTTACCCTCAGTTTACAGAATTACTATTTTACCCT
* * *
1350 CGATTTATAGAATTATCGTTTTACCCTCGATGTG-AAATTAC
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTGAAAATTAC
1391 TGAAATACCC
Statistics
Matches: 222, Mismatches: 16, Indels: 25
0.84 0.06 0.10
Matches are distributed among these distances:
100 1 0.00
101 32 0.14
102 9 0.04
103 38 0.17
104 9 0.04
105 70 0.32
106 57 0.26
107 6 0.03
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (105 bp):
CGATTTACAGAATTACCGTTTTACCCTCGATTTGAAAATTACGTTTTACCCTCGATTTACAGAAT
TACCGTTTACCCTCAGTTTACAGAATTACTATTTTACCCT
Found at i:1479 original size:27 final size:27
Alignment explanation
Indices: 1385--1574 Score: 212
Period size: 26 Copynumber: 7.3 Consensus size: 27
1375 CTCGATGTGA
*
1385 AATTACTGAAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
1411 AATT--CTAAATATCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
1436 AATTA-CGAAATACCCCTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
1462 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
1489 AATTATCGAAATA-CCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
1515 AAATACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
1542 AATTACCGAGATA-CCCTTTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
1568 AATTACC
1 AATTACC
1575 ATTTGCCCCT
Statistics
Matches: 140, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
24 5 0.04
25 16 0.11
26 66 0.47
27 53 0.38
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:1488 original size:53 final size:53
Alignment explanation
Indices: 1385--1575 Score: 226
Period size: 53 Copynumber: 3.6 Consensus size: 53
1375 CTCGATGTGA
* * * *
1385 AATTACTGAAATACCCTGTAGGGTAGAATT--CTAAATATCCCTATAGGGTAG
1 AATTACCGAAATACCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* * *
1436 AATTA-CGAAATACCCCTATAGGATAGAATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATA-CCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* * *
1489 AATTATCGAAATACCTTGTAGGGTAGAAATACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* * * *
1542 AATTACCGAGATACCCTTTGGGGTAAAATTACCA
1 AATTACCGAAATACCCTGTAGGGTAGAATTACCA
1576 TTTGCCCCTA
Statistics
Matches: 118, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
50 6 0.05
51 20 0.17
53 85 0.72
54 7 0.06
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (53 bp):
AATTACCGAAATACCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
Found at i:1816 original size:26 final size:26
Alignment explanation
Indices: 1768--1849 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
1758 CGGAGGAAGC
*
1768 GTTCT-GTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
1794 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
1820 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
1847 GTT
1 GTT
1850 GATCGATCGA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.30
27 35 0.70
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:1965 original size:22 final size:22
Alignment explanation
Indices: 1933--1992 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1923 CCCGTTATTA
*
1933 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
1955 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
1977 ATGGCTTCGTGCCAAC
1 ATGGCTTTGTGCCAAC
1993 GTATTTACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:2181 original size:27 final size:27
Alignment explanation
Indices: 2151--2224 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
2141 TAGGTGGGTT
* *
2151 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGACTC
*
2178 TGCCACAATGTCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGACTC
* * *
2205 TGTCACGACATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
2225 CAGCCATGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
26 5 0.13
27 33 0.85
28 1 0.03
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.35
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGACTC
Found at i:2347 original size:6 final size:6
Alignment explanation
Indices: 2338--2522 Score: 134
Period size: 6 Copynumber: 30.8 Consensus size: 6
2328 TTGCATTCAC
* * *
2338 ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTTTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
2387 -TTACTA ATACTG ATTCTG ATTCTG ATTCT- ATTATTG ATTCTG GTTCTG
1 ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * * * *
2435 ATTCTG -TCACCTA ATTTTG ATTCTG ATTCTG ATTCT- -TACTA ATAT-TG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT-TCTG
2482 ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
2523 CATTTTGGTT
Statistics
Matches: 140, Mismatches: 23, Indels: 32
0.72 0.12 0.16
Matches are distributed among these distances:
4 3 0.02
5 10 0.07
6 115 0.82
7 10 0.07
8 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:9944 original size:30 final size:30
Alignment explanation
Indices: 9908--9968 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
9898 TCCTTAACTC
9908 AAACTTTGGAAAATTTACAATTTTACCCCT
1 AAACTTTGGAAAATTTACAATTTTACCCCT
* * * * *
9938 AAACTTTTGCATATTTACACTTTTTCCCCT
1 AAACTTTGGAAAATTTACAATTTTACCCCT
9968 A
1 A
9969 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTGGAAAATTTACAATTTTACCCCT
Found at i:18498 original size:40 final size:40
Alignment explanation
Indices: 18414--18597 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
18404 TTGAATGCTG
* * * *
18414 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
18453 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
18494 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
18534 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
*
18574 TCCGGGTTAAGTCCTGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
18598 GAATGAGTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 110 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:18551 original size:80 final size:81
Alignment explanation
Indices: 18414--18594 Score: 212
Period size: 80 Copynumber: 2.3 Consensus size: 81
18404 TTGAATGCTG
* * *
18414 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
18478 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
18494 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
18555 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
*
18574 TCCGGGTTAAGTCCTGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
18595 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
79 4 0.05
80 75 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:18618 original size:39 final size:39
Alignment explanation
Indices: 18494--18644 Score: 126
Period size: 40 Copynumber: 3.8 Consensus size: 39
18484 AGTTATTAAT
* ** * *
18494 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACT-AAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
** *
18534 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* * *
18574 TCCGGGTTAAGTCCTGAAGGCATTGAATGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
18614 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
18645 GAGCTATATC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 29 0.31
40 64 0.69
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:26416 original size:40 final size:40
Alignment explanation
Indices: 26370--26500 Score: 192
Period size: 40 Copynumber: 3.3 Consensus size: 40
26360 GGACTAAGAT
*
26370 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
26410 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* *
26450 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATT-AATTCCGGGTTAAGTC
26490 CCGAAGGCATT
1 CCGAAGGCATT
26501 GAATGAGTTA
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 80 0.99
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
Found at i:26521 original size:39 final size:38
Alignment explanation
Indices: 26398--26547 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
26388 GTTATTAATT
* ** * *
26398 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
26438 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
26477 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
26517 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
26548 GAGCTATATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:26555 original size:40 final size:39
Alignment explanation
Indices: 26438--26560 Score: 97
Period size: 40 Copynumber: 3.1 Consensus size: 39
26428 GATACTAATT
* ** ** *
26438 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
1 CCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACTATAA
* * *
26477 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
* *
26517 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA
26557 CCGG
1 CCGG
26561 TTAAATTCCG
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 25 0.36
40 44 0.64
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
Done.