Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold150
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: 1465027
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 98465 characters in sequence are not A, C, G, or T
File 9 of 9
Found at i:1427852 original size:20 final size:20
Alignment explanation
Indices: 1427827--1427892 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1427817 ATCGATACAT
1427827 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
1427847 TGTATCGAT---ACA---T-
1 TGTATCGATACAACACTTTA
1427860 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
1427880 TGTATCGATACAA
1 TGTATCGATACAA
1427893 ATCGTTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 22 0.56
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAACACTTTA
Found at i:1429042 original size:20 final size:20
Alignment explanation
Indices: 1429017--1429070 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1429007 GTTGGAAGCA
*
1429017 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
1429037 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
1429057 ATGTATCGATACAA
1 ATGTATCGATACAA
1429071 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1431644 original size:13 final size:13
Alignment explanation
Indices: 1431626--1431652 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1431616 ATAGTATCCC
1431626 ATGTATCGATACA
1 ATGTATCGATACA
1431639 ATGTATCGATACA
1 ATGTATCGATACA
1431652 A
1 A
1431653 GGAATGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1437837 original size:20 final size:20
Alignment explanation
Indices: 1437812--1437865 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1437802 GTTGGAAGCA
*
1437812 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
1437832 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
*
1437852 ATGTATTGATACAA
1 ATGTATCGATACAA
1437866 ATAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1440320 original size:19 final size:20
Alignment explanation
Indices: 1440298--1440336 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1440288 CTTAAAATTT
1440298 CATC-ATTTCTACATCAAAA
1 CATCTATTTCTACATCAAAA
* *
1440317 CATCTATTTTTTCATCAAAA
1 CATCTATTTCTACATCAAAA
1440337 TCTTCAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
CATCTATTTCTACATCAAAA
Found at i:1441693 original size:33 final size:33
Alignment explanation
Indices: 1441627--1441693 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
1441617 TGAAAGTTGA
* * *
1441627 TCACTTCACTTTCGCTGCACATGAATGAGCACT
1 TCACTTCACTCTCGCAGCACATGAATGAACACT
** *
1441660 TCACTTCACTCTCGCAGGGCATGGATGAACACT
1 TCACTTCACTCTCGCAGCACATGAATGAACACT
1441693 T
1 T
1441694 TAGTGCACTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (33 bp):
TCACTTCACTCTCGCAGCACATGAATGAACACT
Found at i:1442608 original size:20 final size:19
Alignment explanation
Indices: 1442585--1442657 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
1442575 CACATCCAGA
*
1442585 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
1442605 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
1442624 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
1442644 TGTATCGATACATG
1 TGTATCGATACATG
1442658 AAACTAGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1446105 original size:22 final size:22
Alignment explanation
Indices: 1446080--1446130 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1446070 CGTTGGCTGC
1446080 TGCTATTGCTACTGTTG-TTGG
1 TGCTATTGCTACTGTTGCTTGG
* * *
1446101 TTGCTGTGGCTGCTGTTGCTTGG
1 -TGCTATTGCTACTGTTGCTTGG
1446124 TGCTATT
1 TGCTATT
1446131 TTTGTTGCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.06, C:0.16, G:0.31, T:0.47
Consensus pattern (22 bp):
TGCTATTGCTACTGTTGCTTGG
Found at i:1446236 original size:42 final size:42
Alignment explanation
Indices: 1446177--1446283 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
1446167 CTGCCATTGG
1446177 TTGCTGCTGTTGGTGCTTGGTGTTGCAGCTACTGGTTGTTGA
1 TTGCTGCTGTTGGTGCTTGGTGTTGCAGCTACTGGTTGTTGA
* *
1446219 TTGCTGTTGTTGGTGCTTGGTGTTGCAGCTGCTGGTTGTTGA
1 TTGCTGCTGTTGGTGCTTGGTGTTGCAGCTACTGGTTGTTGA
1446261 TTGCTGCTG-T--TGCTTGGTGTTGC
1 TTGCTGCTGTTGGTGCTTGGTGTTGC
1446284 TACTTGCTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
39 13 0.21
41 1 0.02
42 48 0.77
ACGTcount: A:0.05, C:0.14, G:0.36, T:0.45
Consensus pattern (42 bp):
TTGCTGCTGTTGGTGCTTGGTGTTGCAGCTACTGGTTGTTGA
Found at i:1446395 original size:23 final size:22
Alignment explanation
Indices: 1446369--1446413 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1446359 TCAGTTGTTG
*
1446369 TTTTCGTTTCCTTGCTTTCTCTT
1 TTTTCATTTCCTT-CTTTCTCTT
*
1446392 TTTTTATTTCCTTCTTTCTCTT
1 TTTTCATTTCCTTCTTTCTCTT
1446414 CCTTTGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.02, C:0.24, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTCATTTCCTTCTTTCTCTT
Found at i:1446465 original size:27 final size:27
Alignment explanation
Indices: 1446432--1446527 Score: 165
Period size: 27 Copynumber: 3.6 Consensus size: 27
1446422 CTATTATCTG
*
1446432 TTTCTTTCATTTGCTACAGCTATTCCA
1 TTTCTTTCATTTGCTACAGCTATTTCA
*
1446459 TTTCTTTCATTTGCTGCAGCTATTTCA
1 TTTCTTTCATTTGCTACAGCTATTTCA
*
1446486 TTTCTTTCATTTGCTATAGCTATTTCA
1 TTTCTTTCATTTGCTACAGCTATTTCA
1446513 TTTCTTTCATTTGCT
1 TTTCTTTCATTTGCT
1446528 GATGTTGGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.16, C:0.22, G:0.08, T:0.54
Consensus pattern (27 bp):
TTTCTTTCATTTGCTACAGCTATTTCA
Found at i:1448294 original size:42 final size:42
Alignment explanation
Indices: 1447483--1448474 Score: 500
Period size: 42 Copynumber: 23.6 Consensus size: 42
1447473 AAGCAAAGAA
* * ** *
1447483 TAAAGAAGTCTCTCGGGTCAAAG-TCGATGGGCAGATGAAGGG
1 TAAAGAAGTCTCTAGGGTCAAAGCT-GATAGGCAGACAAAAGG
* * * *
1447525 TGAAGAAGTCTCCTA-GGTTAAAGCTGA-CGAGTAGAC-AAAGG
1 TAAAGAAGTCT-CTAGGGTCAAAGCTGATAG-GCAGACAAAAGG
* * * * * *
1447566 ATAAAAAAGTCTTTTGGGTTAAAGCCGATAGGCAGAC-AAAGAA
1 -TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAG-G
* * * * ** *
1447609 TATAGAACTCTCTCGGGTCAAAGTTGACGGGTAGAC-AAAGG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * * * ** *
1447650 ATTTATAGAAGTCTCTTGGTTCAAGGCCAACT-GGCAGACAAGAGG
1 ---TAAAGAAGTCTCTAGGGTCAAAGCTGA-TAGGCAGACAAAAGG
* ** * * ** * *
1447695 TAAAGAAGTTTCCCGGATCAAAGCCGACGGGTAGACAAAGGG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * ** * * ** *
1447737 TAAATAAATCTCCCGAGTCAAAGTTGACGGGTAGACAAAAGG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * ** * *
1447779 CAAAGAAGTCTTCCA-AATCTAAGCT-A-ACGAGCAGACAAAGGG
1 TAAAGAAGTC-TCTAGGGTCAAAGCTGATA-G-GCAGACAAAAGG
* * ** ** *
1447821 CAAAGAAGTCTCCAAAGTCAAAGCCAACAGGCAGACAAAAGG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * *
1447863 TAAAAAAATCTCTAGGGTCAAAGCCGATAGGCAGACAAAAGG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * *
1447905 TAAA-AATGTCTCTCGGGTTAAAGCT-A-ACGAGCAGATAAAAGG
1 TAAAGAA-GTCTCTAGGGTCAAAGCTGATA-G-GCAGACAAAAGG
* * *
1447947 -AAAGTAAGTCTCCAAGGTCAAAGCTGATAGGCAGACAAAAAG
1 TAAAG-AAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * * *
1447989 TAAAGAAGTCTCTCGGGTCAAAGTTGATAGGTAGA-GAAAGG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * * * *
1448030 ATATAA-AAGTCTCCAAGATCAAAGCCGATAGGCAAACAAAAGG
1 -TA-AAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * * ** *
1448073 TAAA-AATATCTCTCA-AGTCTAAGCCAATGGGCAGAC-AAAGG
1 TAAAGAA-GTCTCT-AGGGTCAAAGCTGATAGGCAGACAAAAGG
* * * * * * ** *
1448114 TAAAGAAATCTCCAAGGTTAAACCCGGCAGGTAGACAAAAGG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * ** * *
1448156 TAAAAAAGTCT-TCAAGGTCAAAGCCAACAGGTAGACAAAAGG
1 TAAAGAAGTCTCT-AGGGTCAAAGCTGATAGGCAGACAAAAGG
* * * * * *
1448198 TAAAGAAGTATCTCGAGTCAAAG-TCGACAAGCAGACAAAAGA
1 TAAAGAAGTCTCTAGGGTCAAAGCT-GATAGGCAGACAAAAGG
1448240 TAAAGAAGTCTCTAGGGTCCAAA-CTGATAGGCAGACAAAAGG
1 TAAAGAAGTCTCTAGGGT-CAAAGCTGATAGGCAGACAAAAGG
* * *
1448282 TAAAGAAGTCTCTTGGGTCAAAGTTGATGGGCAGACAAAAGG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * * * *
1448324 TAAAGAAATCTTTAGGGTCAAAGCTGATGGGCAGATAATAGG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* * *
1448366 TAAAGAAGTCTCCTA-GGTGAAAGCTGATAGGTAGAAAAAAAGG
1 TAAAGAAGTCT-CTAGGGTCAAAGCTGATAGGCAG-ACAAAAGG
* * * *
1448409 TAAAGAAGTCTCCAAGGTCAAAGCCGATAGGCAGACAAAAAG
1 TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
* *
1448451 TAAAAAAGTCTCTTGGGTCAAAGC
1 TAAAGAAGTCTCTAGGGTCAAAGC
1448475 CAATTGGCAG
Statistics
Matches: 734, Mismatches: 172, Indels: 88
0.74 0.17 0.09
Matches are distributed among these distances:
40 2 0.00
41 57 0.08
42 577 0.79
43 66 0.09
44 28 0.04
45 4 0.01
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (42 bp):
TAAAGAAGTCTCTAGGGTCAAAGCTGATAGGCAGACAAAAGG
Found at i:1449968 original size:13 final size:12
Alignment explanation
Indices: 1449951--1449975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1449941 TTTTTTTTTG
1449951 CTTTTTTTTAAA
1 CTTTTTTTTAAA
1449963 CTTTTTTTTAAA
1 CTTTTTTTTAAA
1449975 C
1 C
1449976 ATAATACTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (12 bp):
CTTTTTTTTAAA
Found at i:1453274 original size:22 final size:21
Alignment explanation
Indices: 1453249--1453310 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 21
1453239 AATTTTGAAT
*
1453249 TTCAATAATTTGTATCGATACA
1 TTCAATAA-ATGTATCGATACA
*
1453271 TTCAGTAAATGTATCGATACA
1 TTCAATAAATGTATCGATACA
1453292 -T-AAGT-AATGTATCGATACA
1 TTCAA-TAAATGTATCGATACA
1453311 GTGTATTGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.42
20 2 0.06
21 12 0.33
22 7 0.19
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (21 bp):
TTCAATAAATGTATCGATACA
Found at i:1453302 original size:19 final size:21
Alignment explanation
Indices: 1453259--1453310 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1453249 TTCAATAATT
*
1453259 TGTATCGATACATTCAGTAAA
1 TGTATCGATACATTAAGTAAA
1453280 TGTATCGATACA-TAAGT-AA
1 TGTATCGATACATTAAGTAAA
1453299 TGTATCGATACA
1 TGTATCGATACA
1453311 GTGTATTGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
21 12 0.40
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATTAAGTAAA
Found at i:1455894 original size:52 final size:53
Alignment explanation
Indices: 1455742--1455979 Score: 238
Period size: 51 Copynumber: 4.6 Consensus size: 53
1455732 TTAAGTTTCT
* * *
1455742 CAATTTTTCAAAATCGGGGGTACTCCAACCCCGG-TTTTA-TTCCTAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGATTTTATTTCCAAAAACAC
* * ** * * ***
1455793 TAATTTTCCACAATTAGGGATACTCTAACTCC-GATTTTATTT-TTGAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGATTTTATTTCCAAAAACAC
* *
1455844 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTTATTTTC-AAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGATTTTATTTCCAAAAACAC
* * *
1455896 CAA-TTTTCTATAATCGGGGATACTCCAA-CTCTGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCCAACCCCGGATTTTATTTCCAAAAACAC
* * *
1455948 TAATTTCTCATAATCGGGGATACTCCAACCCC
1 CAATTTTTCACAATCGGGGATACTCCAACCCC
1455980 ATTATTTTCA
Statistics
Matches: 152, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
50 1 0.01
51 79 0.52
52 66 0.43
53 6 0.04
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (53 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGGATTTTATTTCCAAAAACAC
Found at i:1455932 original size:103 final size:103
Alignment explanation
Indices: 1455742--1455979 Score: 300
Period size: 103 Copynumber: 2.3 Consensus size: 103
1455732 TTAAGTTTCT
* *
1455742 CAATTTTTCAAAATCGGGGGTACTCCAACCCCGGTTTTATTCCTAAAACACTAATTTTCCACAAT
1 CAATTTTTCAAAATCGGGGATACTCCAACCCCGGTTTTATTCCTAAAACACCAATTTTCCACAAT
* * ***
1455807 TAGGGATACTCTAACTCCGATTTTATTT-TTGAAACAC
66 CAGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
* * * *
1455844 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTTATT-TTCAAAACACCAATTTTCTATA
1 CAATTTTTCAAAATCGGGGATACTCCAACCCCGG-TTTTATTCCT-AAAACACCAATTTTCCACA
* *
1455908 ATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACAC
64 ATCAGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
* * *
1455948 TAATTTCTCATAATCGGGGATACTCCAACCCC
1 CAATTTTTCAAAATCGGGGATACTCCAACCCC
1455980 ATTATTTTCA
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
102 33 0.28
103 49 0.42
104 35 0.30
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (103 bp):
CAATTTTTCAAAATCGGGGATACTCCAACCCCGGTTTTATTCCTAAAACACCAATTTTCCACAAT
CAGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
Done.