Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold85
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: 1350895
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.21
Warning! 487514 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:1312198 original size:31 final size:31
Alignment explanation
Indices: 1312160--1312263 Score: 199
Period size: 31 Copynumber: 3.4 Consensus size: 31
1312150 ATTGAGTATA
1312160 TATCGATACAATGACGTGTATCGATACAATG
1 TATCGATACAATGACGTGTATCGATACAATG
1312191 TATCGATACAATGACGTGTATCGATACAATG
1 TATCGATACAATGACGTGTATCGATACAATG
1312222 TATCGATACAATGACGTGTATCGATACAATG
1 TATCGATACAATGACGTGTATCGATACAATG
*
1312253 TATCAATACAA
1 TATCGATACAA
1312264 AGTAATATGT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (31 bp):
TATCGATACAATGACGTGTATCGATACAATG
Found at i:1313069 original size:21 final size:21
Alignment explanation
Indices: 1313039--1313087 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1313029 GTAAATTTTC
* *
1313039 AATAAATCTCCCTCTTAATAA
1 AATAATTCTCCCCCTTAATAA
**
1313060 AATAATTCTCCCCCTTGGTAA
1 AATAATTCTCCCCCTTAATAA
1313081 AATAATT
1 AATAATT
1313088 AAAGCTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (21 bp):
AATAATTCTCCCCCTTAATAA
Found at i:1319921 original size:19 final size:19
Alignment explanation
Indices: 1319881--1319935 Score: 92
Period size: 19 Copynumber: 2.8 Consensus size: 19
1319871 TGCCAGTTTC
1319881 ATGTATCGATACAATAGAGT
1 ATGTATCGATACAAT-GAGT
*
1319901 ATGTATTGATACAATGAGT
1 ATGTATCGATACAATGAGT
1319920 ATGTATCGATACAATG
1 ATGTATCGATACAATG
1319936 TATCGATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGAGT
Found at i:1319938 original size:13 final size:13
Alignment explanation
Indices: 1319920--1319948 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1319910 TACAATGAGT
1319920 ATGTATCGATACA
1 ATGTATCGATACA
1319933 ATGTATCGATACA
1 ATGTATCGATACA
1319946 ATG
1 ATG
1319949 ATACAAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1322971 original size:2 final size:2
Alignment explanation
Indices: 1322964--1323008 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1322954 TGACTTTTAT
1322964 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1323006 TA T
1 TA T
1323009 TTCATGGTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1326656 original size:186 final size:184
Alignment explanation
Indices: 1326323--1326675 Score: 471
Period size: 186 Copynumber: 1.9 Consensus size: 184
1326313 TCTAATTCTT
* * * * ** *
1326323 AATTTAATGAATTTAGAATTAAAAGTGAATATGATAAATTATTCAAATACGGGATGAATTGGGAT
1 AATTCAATGAACTTAGAATTAAAAGTAAATATGACAAATTATTCAAATACGGGATGAATTAAGAC
*
1326388 ATAACATGAAAAAATAAATTAAAAATAATATGACATAAAAAATAATATAAACATGACTTAAATAC
66 ATAACATAAAAAAATAAATTAAAAATAATATGACATAAAAAATAATATAAACATGACTTAAATAC
*
1326453 ATGAATGTGGTAAAATCTACATAAAACATATTATTATCATGACAAACTTATATA
131 ATGAATATGGTAAAATCTACATAAAACATATTATTATCATGACAAACTTATATA
**
1326507 AATTCAATGAACTTAGAATTAAATTTAAATATGACAAATTATTCAAACTA-GGAGATGAATTAAG
1 AATTCAATGAACTTAGAATTAAAAGTAAATATGACAAATTATTCAAA-TACGG-GATGAATTAAG
* *
1326571 ACATAACATTAAAAAAAT-AATT-AAAATACGATATGATATAAAAAATAATATAAACTTGACTTA
64 ACATAACA-TAAAAAAATAAATTAAAAATA--ATATGACATAAAAAATAATATAAACATGACTTA
** * *
1326634 AATATTTGAATAT-GTCAAAATCTATATAAAATATATTATTAT
126 AATACATGAATATGGT-AAAATCTACATAAAACATATTATTAT
1326676 GTTAAAAAAT
Statistics
Matches: 146, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
184 49 0.34
185 24 0.16
186 73 0.50
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (184 bp):
AATTCAATGAACTTAGAATTAAAAGTAAATATGACAAATTATTCAAATACGGGATGAATTAAGAC
ATAACATAAAAAAATAAATTAAAAATAATATGACATAAAAAATAATATAAACATGACTTAAATAC
ATGAATATGGTAAAATCTACATAAAACATATTATTATCATGACAAACTTATATA
Found at i:1331101 original size:32 final size:32
Alignment explanation
Indices: 1331060--1331154 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
1331050 TTCAACGATT
*
1331060 TGTATCGATACACAAATGTTGTATCAATACAA
1 TGTATCGATACACAAATGTTGTATCGATACAA
*
1331092 TGTATCGATACACAAATTTTGTATCGATACAA
1 TGTATCGATACACAAATGTTGTATCGATACAA
*
1331124 TGTATCGATACATAAATGTTGTATCGATACA
1 TGTATCGATACACAAATGTTGTATCGATACA
1331155 TAAGTGTTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACACAAATGTTGTATCGATACAA
Found at i:1331129 original size:13 final size:13
Alignment explanation
Indices: 1331079--1331135 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1331069 ACACAAATGT
*
1331079 TGTATCAATACAA
1 TGTATCGATACAA
1331092 TGTATCGATACACAAA
1 TGTATCGAT--AC-AA
1331108 TTTTGTATCGATACAA
1 ---TGTATCGATACAA
1331124 TGTATCGATACA
1 TGTATCGATACA
1331136 TAAATGTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
15 2 0.05
16 4 0.11
17 2 0.05
19 9 0.24
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1331174 original size:19 final size:19
Alignment explanation
Indices: 1331059--1331175 Score: 105
Period size: 19 Copynumber: 6.8 Consensus size: 19
1331049 ATTCAACGAT
*
1331059 TTGTATCGATACACAAATG
1 TTGTATCGATACATAAATG
*
1331078 TTGTATCAATAC---AA--
1 TTGTATCGATACATAAATG
* *
1331092 -TGTATCGATACACAAATT
1 TTGTATCGATACATAAATG
1331110 TTGTATCGATAC---AA--
1 TTGTATCGATACATAAATG
1331124 -TGTATCGATACATAAATG
1 TTGTATCGATACATAAATG
*
1331142 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAATG
1331161 TTGTATCGATACATA
1 TTGTATCGATACATA
1331176 CGAAGCTACT
Statistics
Matches: 83, Mismatches: 3, Indels: 24
0.75 0.03 0.22
Matches are distributed among these distances:
13 21 0.25
16 8 0.10
19 54 0.65
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAATG
Found at i:1334702 original size:13 final size:13
Alignment explanation
Indices: 1334680--1334737 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
1334670 TGCAGTAGCT
*
1334680 TTGTAGCGATACA
1 TTGTATCGATACA
1334693 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
1334709 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1334725 TTGTATCGATACA
1 TTGTATCGATACA
1334738 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1334718 original size:19 final size:19
Alignment explanation
Indices: 1334694--1334756 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1334684 AGCGATACAT
1334694 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1334713 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1334726 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1334745 TGTATCGATACA
1 TGTATCGATACA
1334757 TTTACTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.55
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1334727 original size:32 final size:32
Alignment explanation
Indices: 1334681--1334758 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
1334671 GCAGTAGCTT
*
1334681 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1334713 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1334745 TGTATCGATACATT
1 TGTATCGATACATT
1334759 TACTGTTTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:1335830 original size:21 final size:22
Alignment explanation
Indices: 1335790--1335834 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1335780 AAATTATTTT
1335790 TATATAAATTTAATTATAAAAA
1 TATATAAATTTAATTATAAAAA
1335812 TATATAAATTTAA-TATAAAAA
1 TATATAAATTTAATTATAAAAA
1335833 TA
1 TA
1335835 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TATATAAATTTAATTATAAAAA
Found at i:1336842 original size:37 final size:38
Alignment explanation
Indices: 1336795--1336867 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
1336785 GAAAATTTTT
*
1336795 GTTTGTTTGACA-TTTTTGAAATTAACAAAAAAAATTA
1 GTTTGGTTGACATTTTTTGAAATTAACAAAAAAAATTA
* *
1336832 GTTTGGTTGACATTTTTTGAAATTTACCAAAAAAAT
1 GTTTGGTTGACATTTTTTGAAATTAACAAAAAAAAT
1336868 CTATTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 11 0.34
38 21 0.66
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (38 bp):
GTTTGGTTGACATTTTTTGAAATTAACAAAAAAAATTA
Found at i:1336904 original size:19 final size:19
Alignment explanation
Indices: 1336882--1336925 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1336872 TTTTTATGTC
* *
1336882 AAATATTAGTTTTGTTAAT
1 AAATAATAGTTTTATTAAT
1336901 AAATAATAGTTTTATTAAT
1 AAATAATAGTTTTATTAAT
*
1336920 TAATAA
1 AAATAA
1336926 CTAAAGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (19 bp):
AAATAATAGTTTTATTAAT
Found at i:1337629 original size:29 final size:30
Alignment explanation
Indices: 1337596--1337679 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 30
1337586 TTATACACTT
* *
1337596 AAATAAGTTTTTAATATTTAATTTAAACTC
1 AAATAAATTTTTAATTTTTAATTTAAACTC
* **
1337626 -AATAATTTTTTAATTTTTAATTTGTACTC
1 AAATAAATTTTTAATTTTTAATTTAAACTC
*
1337655 AAATAAAATTTTAATTTTTAATTTA
1 AAATAAATTTTTAATTTTTAATTTA
1337680 TACTTAAAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
29 25 0.54
30 21 0.46
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (30 bp):
AAATAAATTTTTAATTTTTAATTTAAACTC
Found at i:1337667 original size:30 final size:29
Alignment explanation
Indices: 1337604--1337683 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 29
1337594 TTAAATAAGT
* * **
1337604 TTTTAATATTTAATTTAAACTCAATAATT
1 TTTTAATTTTTAATTTATACTCAATAAAA
*
1337633 TTTTAATTTTTAATTTGTACTCAAATAAAA
1 TTTTAATTTTTAATTTATACTC-AATAAAA
1337663 TTTTAATTTTTAATTTATACT
1 TTTTAATTTTTAATTTATACT
1337684 TAAAGAAACC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 19 0.43
30 25 0.57
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (29 bp):
TTTTAATTTTTAATTTATACTCAATAAAA
Found at i:1337699 original size:30 final size:30
Alignment explanation
Indices: 1337635--1337699 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
1337625 CAATAATTTT
* * **
1337635 TTAATTTTTAATTTGTACTCAAATAAAATT
1 TTAATTTTTAATTTATACTCAAAGAAAACC
* *
1337665 TTAATTTTTAATTTATACTTAAAGAAACCC
1 TTAATTTTTAATTTATACTCAAAGAAAACC
1337695 TTAAT
1 TTAAT
1337700 ATAAATCAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (30 bp):
TTAATTTTTAATTTATACTCAAAGAAAACC
Found at i:1339091 original size:2 final size:2
Alignment explanation
Indices: 1339084--1339115 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1339074 CTATTTTCAC
1339084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1339116 GATGGCTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1339367 original size:2 final size:2
Alignment explanation
Indices: 1339316--1339356 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1339306 CTGCGTATGC
* *
1339316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1339357 CATGCATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1342666 original size:54 final size:54
Alignment explanation
Indices: 1342584--1342689 Score: 203
Period size: 54 Copynumber: 2.0 Consensus size: 54
1342574 ACAATTTGAT
1342584 TGAATACCCAACAAATGTTACTTGAAGTTAAGGGGAATATGTAATATAAGTACG
1 TGAATACCCAACAAATGTTACTTGAAGTTAAGGGGAATATGTAATATAAGTACG
*
1342638 TGAATACCCAACAAATGTTACTTGAAGTTAAGGTGAATATGTAATATAAGTA
1 TGAATACCCAACAAATGTTACTTGAAGTTAAGGGGAATATGTAATATAAGTA
1342690 TGAGTCGACT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (54 bp):
TGAATACCCAACAAATGTTACTTGAAGTTAAGGGGAATATGTAATATAAGTACG
Found at i:1345797 original size:23 final size:22
Alignment explanation
Indices: 1345762--1345814 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
1345752 TTTTAATTAA
1345762 AATA-AAAATTTTATTTAAAT-TT
1 AATATAAAATTTTA--TAAATATT
1345784 AATTATAAAA-TTTATAAATATT
1 AA-TATAAAATTTTATAAATATT
1345806 AATATAAAA
1 AATATAAAA
1345815 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
21 12 0.43
22 6 0.21
23 6 0.21
24 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATAAAATTTTATAAATATT
Found at i:1346010 original size:2 final size:2
Alignment explanation
Indices: 1346003--1346035 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1345993 ATTGTGTTTC
*
1346003 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1346036 ATGTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1347717 original size:23 final size:23
Alignment explanation
Indices: 1347680--1347736 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1347670 TAGCCTTTGA
1347680 TCATGCA-TTTTTTTATTATGTT
1 TCATGCATTTTTTTTATTATGTT
1347702 TCATGCATTTTTTTTATTATGTT
1 TCATGCATTTTTTTTATTATGTT
1347725 TCATGCATTTTT
1 TCATGCATTTTT
1347737 AACATGTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 7 0.21
23 27 0.79
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (23 bp):
TCATGCATTTTTTTTATTATGTT
Found at i:1347743 original size:20 final size:21
Alignment explanation
Indices: 1347680--1347743 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 21
1347670 TAGCCTTTGA
**
1347680 TCATGCATTTTTTTATTATGTT
1 TCATGCA-TTTTTTAACATGTT
**
1347702 TCATGCATTTTTTTTATTATGTT
1 TCATGCA--TTTTTTAACATGTT
1347725 TCATGCA-TTTTTAACATGT
1 TCATGCATTTTTTAACATGT
1347744 CCAGCATCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.26
22 7 0.18
23 22 0.56
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.59
Consensus pattern (21 bp):
TCATGCATTTTTTAACATGTT
Done.