Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1958
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: 15846
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Found at i:1496 original size:64 final size:64
Alignment explanation
Indices: 1412--1588 Score: 249
Period size: 64 Copynumber: 2.8 Consensus size: 64
1402 ATATATATTT
*
1412 AAAGTTCTTGAGCTGTATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
*
1476 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACT-TACATATGTGGTTCGAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTA-TATACATATGTGGTTCAAATATAGGTTAC
*
1540 AAA-TTCTTTGAGCTGAATTTTAATGT-TGTAA--AT-TATACATATGTGGTTC
1 AAAGTTC-TTGAGCTGAA-TTTAATGTATG-AATTTTATATACATATGTGGTTC
1589 GAATGTTTGT
Statistics
Matches: 105, Mismatches: 3, Indels: 12
0.88 0.03 0.10
Matches are distributed among these distances:
61 1 0.01
62 14 0.13
63 4 0.04
64 75 0.71
65 11 0.10
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
Found at i:1814 original size:41 final size:41
Alignment explanation
Indices: 1707--1944 Score: 279
Period size: 41 Copynumber: 5.9 Consensus size: 41
1697 TATATGAGAT
* *
1707 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
*
1748 -TTCAGGC-TT-TGCCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
*
1786 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
1827 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * * * *
1868 ATTCCGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGA
1 TTTCAGGCTTTATGCCTAGCAGGC-TTGATGCCGGTG-AATTA
* * * *
1910 -ATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTG
1945 TTTTATATAG
Statistics
Matches: 174, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 29 0.17
39 8 0.05
40 10 0.06
41 120 0.69
42 7 0.04
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (41 bp):
TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
Found at i:2636 original size:14 final size:15
Alignment explanation
Indices: 2612--2646 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2602 TACTTTAATC
2612 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
2627 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
2642 ATGGT
1 ATGGT
2647 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:8421 original size:64 final size:64
Alignment explanation
Indices: 8337--8513 Score: 249
Period size: 64 Copynumber: 2.8 Consensus size: 64
8327 ATATATATTT
*
8337 AAAGTTCTTGAGCTGTATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
*
8401 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACT-TACATATGTGGTTCGAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTA-TATACATATGTGGTTCAAATATAGGTTAC
*
8465 AAA-TTCTTTGAGCTGAATTTTAATGT-TGTAA--AT-TATACATATGTGGTTC
1 AAAGTTC-TTGAGCTGAA-TTTAATGTATG-AATTTTATATACATATGTGGTTC
8514 GAATGTTTGT
Statistics
Matches: 105, Mismatches: 3, Indels: 12
0.88 0.03 0.10
Matches are distributed among these distances:
61 1 0.01
62 14 0.13
63 4 0.04
64 75 0.71
65 11 0.10
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
Found at i:8689 original size:41 final size:41
Alignment explanation
Indices: 8632--8872 Score: 367
Period size: 41 Copynumber: 5.9 Consensus size: 41
8622 TATATGAGAT
8632 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
8673 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
8714 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
*
8755 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
* * * * *
8796 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
* * * * *
8837 ATTCCGACTTTATGTCTAGCAGGCTTTG-TGCCGGTG
1 TTTCAGGCTTAATGCCTAGCAGGC-TTGATGCCGGTG
8873 AAATGAATCG
Statistics
Matches: 191, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
41 188 0.98
42 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.34
Consensus pattern (41 bp):
TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
Found at i:8887 original size:123 final size:123
Alignment explanation
Indices: 8634--8912 Score: 357
Period size: 123 Copynumber: 2.3 Consensus size: 123
8624 TATGAGATTT
* *
8634 TCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTT
1 TCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTATTTCAGACTTAATGCCTAGCAGGCTT
* * * * * *
8699 GATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTATT
66 GATGCCGGTGAATTAATTCAGACTTAATGCCTAGCAGGCTTGATGCCGGTGAATGATA
* * *
8757 TCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTATTTTAGACTTTATGTCTAGCAGGCTT
1 TCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTATTTCAGACTTAATGCCTAGCAGGCTT
* * *
8822 GATGCCGGTGAATTAATTCCGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGA-A
66 GATGCCGGTGAATTAATTCAGACTTAATGCCTAGCAGGC-TTGATGCCGGTG-AATGATA
* ** *
8880 TCGGGCTTTGTG-CTAGCAGGCTTTATGCCGGTG
1 TCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTG
8913 TTTTATATAG
Statistics
Matches: 136, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
122 20 0.15
123 110 0.81
124 6 0.04
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.33
Consensus pattern (123 bp):
TCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTATTTCAGACTTAATGCCTAGCAGGCTT
GATGCCGGTGAATTAATTCAGACTTAATGCCTAGCAGGCTTGATGCCGGTGAATGATA
Found at i:8903 original size:40 final size:41
Alignment explanation
Indices: 8647--8912 Score: 159
Period size: 41 Copynumber: 6.5 Consensus size: 41
8637 GGCTTAATGC
* * * * * * *
8647 CTAGCAGGC-TTGATGCCGGTGGATTATTTCAGGCTTAATGC
1 CTAGCAGGCTTTG-TGCCGGTGAATGAATTCCGACTTTATGT
* * * * * * *
8688 CTAGCAGGC-TTGATGCCGGTGGATTATTTCAGGCTTAATGC
1 CTAGCAGGCTTTG-TGCCGGTGAATGAATTCCGACTTTATGT
* * * * * * *
8729 CTAGCAGGC-TTGATGCCGGTGGATTATTTCAGGCTTAATGC
1 CTAGCAGGCTTTG-TGCCGGTGAATGAATTCCGACTTTATGT
* * **
8770 CTAGCAGGC-TTGATGCCGGTGAATTATTTTAGACTTTATGT
1 CTAGCAGGCTTTG-TGCCGGTGAATGAATTCCGACTTTATGT
*
8811 CTAGCAGGC-TTGATGCCGGTGAATTAATTCCGACTTTATGT
1 CTAGCAGGCTTTG-TGCCGGTGAATGAATTCCGACTTTATGT
* * *
8852 CTAGCAGGCTTTGTGCCGGTGAAATGAA-TCGGGCTTTGTG-
1 CTAGCAGGCTTTGTGCCGGTG-AATGAATTCCGACTTTATGT
*
8892 CTAGCAGGCTTTATGCCGGTG
1 CTAGCAGGCTTTGTGCCGGTG
8913 TTTTATATAG
Statistics
Matches: 210, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
40 20 0.10
41 182 0.87
42 8 0.04
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.33
Consensus pattern (41 bp):
CTAGCAGGCTTTGTGCCGGTGAATGAATTCCGACTTTATGT
Found at i:9602 original size:14 final size:15
Alignment explanation
Indices: 9578--9612 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
9568 TACTTTAATC
9578 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
9593 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
9608 ATGGT
1 ATGGT
9613 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:10886 original size:47 final size:46
Alignment explanation
Indices: 10817--10979 Score: 158
Period size: 46 Copynumber: 3.6 Consensus size: 46
10807 AATGCCGATT
* * *
10817 CCATGTCCCAGACATGGTCTTACATTGGCACATGCATCA-AGTCAATG
1 CCATGTCCCAGACATGGTCTTACACTGACACAT-C-TCATAGCCAATG
10864 CCATGTCCCAGACATGGTCTTACACTGACACATCTCATAGCCAATG
1 CCATGTCCCAGACATGGTCTTACACTGACACATCTCATAGCCAATG
* * * * **
10910 -CATGTCCCAAACAT-GTCTCACACTGGCTTACATCTCGA-GGCTGATG
1 CCATGTCCCAGACATGGTCTTACACTGAC--ACATCTC-ATAGCCAATG
10956 -CATGTCCCAGACAT-GTCTTACACT
1 CCATGTCCCAGACATGGTCTTACACT
10980 AGCTCTCATT
Statistics
Matches: 101, Mismatches: 11, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
44 11 0.11
45 16 0.16
46 42 0.42
47 32 0.32
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (46 bp):
CCATGTCCCAGACATGGTCTTACACTGACACATCTCATAGCCAATG
Found at i:11002 original size:46 final size:47
Alignment explanation
Indices: 10865--11076 Score: 172
Period size: 46 Copynumber: 4.6 Consensus size: 47
10855 AAGTCAATGC
* * *
10865 CATGTCCCAGACATGGTCTTACACT-G-ACACATCTC-ATAGCCAATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCAATAGCCGATG
* * * * *
10910 CATGTCCCAAACATGTCTCACACTGGCT-TACATCTCGA-GGCTGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCAATAGCCGATG
* *
10956 CATGTCCCAGACATGTCTTACACTAGCTCTCATTTCAAT-GCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAATAGCCGATG
*** * *
11002 CCACACCCCAGATATGGTCTTACACTGGCTCTCA--T-AATGTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCAA--TAGCCGATG
11050 CATGTCCCAGACATGTCTTACACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
11077 ACACAAATAA
Statistics
Matches: 134, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
44 9 0.07
45 16 0.12
46 62 0.46
47 23 0.17
48 24 0.18
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAATAGCCGATG
Done.