Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1396
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: 71863
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:346 original size:40 final size:40
Alignment explanation
Indices: 203--383 Score: 205
Period size: 39 Copynumber: 4.7 Consensus size: 40
193 TTGAATGATG
* * * *
203 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
243 TCCGGACTAAG---AGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
280 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
319 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
360 -CCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
384 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
37 21 0.17
38 7 0.06
39 46 0.38
40 45 0.37
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:390 original size:79 final size:78
Alignment explanation
Indices: 255--416 Score: 202
Period size: 79 Copynumber: 2.1 Consensus size: 78
245 CGGACTAAGA
* **
255 GAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTA-CTAAA
1 GAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TAGCTAAA
*
319 TCCGGGTTAAGTCCC
65 TCC-GGTTAAATCCC
* * * *
334 GAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCGAAGGCATTTGAACGAGTAGCTATA
1 GAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAGCCCGAAGGCATTTGAACGAGTAGCTAAA
*
398 TCCGGTTAAATTCC
65 TCCGGTTAAATCCC
412 GAAGG
1 GAAGG
417 TACGTGATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 18 0.25
79 54 0.75
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (78 bp):
GAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTAGCTAAAT
CCGGTTAAATCCC
Found at i:413 original size:39 final size:40
Alignment explanation
Indices: 255--416 Score: 156
Period size: 39 Copynumber: 4.1 Consensus size: 40
245 CGGACTAAGA
* * **
255 GAAGGCATTTGTGCGAGATACTA-ATTCCGGGCT-AAGCCC
1 GAAGGCATTTGTGCGAGTTACTATA-TCCGGGTTAAATTCC
* * *
294 GAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCC
1 GAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAATTCC
* *
334 GAAGGCATTTGTGCGAGTTACTATAACCGGGCT--ATGTCC
1 GAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAAT-TCC
**
373 GAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCC
1 GAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAATTCC
412 GAAGG
1 GAAGG
417 TACGTGATTT
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
38 6 0.06
39 61 0.59
40 37 0.36
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (40 bp):
GAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAATTCC
Found at i:5459 original size:3 final size:3
Alignment explanation
Indices: 5451--5478 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5441 ACTACTGCTC
5451 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5479 ATCTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27272 original size:5 final size:5
Alignment explanation
Indices: 27262--27300 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
27252 ATATAATGCT
27262 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
27301 ATTAATAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:28146 original size:16 final size:17
Alignment explanation
Indices: 28108--28146 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28098 AAAAAATTAT
*
28108 AAATAAAATATTCAAAA
1 AAATAAAACATTCAAAA
*
28125 ATATAAAACATT-AAAA
1 AAATAAAACATTCAAAA
28141 AAATAA
1 AAATAA
28147 TCAATCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAACATTCAAAA
Found at i:28361 original size:4 final size:4
Alignment explanation
Indices: 28352--28393 Score: 75
Period size: 4 Copynumber: 10.2 Consensus size: 4
28342 TGTAAAACAA
28352 CATT CATT CATT CATT CATT CATT CATT CATT CATCT CATT C
1 CATT CATT CATT CATT CATT CATT CATT CATT CAT-T CATT C
28394 CTTGTTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.48
Consensus pattern (4 bp):
CATT
Found at i:29925 original size:27 final size:27
Alignment explanation
Indices: 29875--29927 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
29865 TGTCCACTTC
* *
29875 TCCTAAATTGGTACTTAAGGTTTTTTA
1 TCCTAAATTGGTACTGAAGCTTTTTTA
29902 TCCTAAATTGGTACTCGAA-CTTTTTT
1 TCCTAAATTGGTACT-GAAGCTTTTTT
29928 TCCGTCAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (27 bp):
TCCTAAATTGGTACTGAAGCTTTTTTA
Found at i:30543 original size:22 final size:23
Alignment explanation
Indices: 30499--30566 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
30489 CTAATACATT
30499 ATAATA-TATATATATTATGTATT-C
1 ATAATAGT-TATATATTA--TATTAC
30523 ATAATAGTTATATATTATATTAC
1 ATAATAGTTATATATTATATTAC
* *
30546 TTAATAG-TATATATTCTATTA
1 ATAATAGTTATATATTATATTA
30567 TTCTATTGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
22 17 0.43
23 7 0.17
24 15 0.38
25 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (23 bp):
ATAATAGTTATATATTATATTAC
Found at i:30904 original size:11 final size:11
Alignment explanation
Indices: 30890--30915 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30880 AGAATTATCA
30890 TTTATTTATAT
1 TTTATTTATAT
30901 TTTATTTATAT
1 TTTATTTATAT
30912 TTTA
1 TTTA
30916 AGTAATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATTTATAT
Found at i:31082 original size:16 final size:16
Alignment explanation
Indices: 31058--31102 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
31048 TGGGCTCGAG
**
31058 CTTTCTTGGGCTTGAAT
1 CTTT-TTGGGCTCCAAT
31075 CTTTTTGGGCTCCAAT
1 CTTTTTGGGCTCCAAT
*
31091 TTTTTTGGGCTC
1 CTTTTTGGGCTC
31103 AAAATTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.09, C:0.20, G:0.22, T:0.49
Consensus pattern (16 bp):
CTTTTTGGGCTCCAAT
Found at i:32672 original size:18 final size:17
Alignment explanation
Indices: 32641--32675 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
32631 AAGTATACTA
32641 TTTTGGTATTTTTTAAT
1 TTTTGGTATTTTTTAAT
*
32658 TTTTTGTATTATTTTAAT
1 TTTTGGTATT-TTTTAAT
32676 AAAAAACCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (17 bp):
TTTTGGTATTTTTTAAT
Found at i:32750 original size:17 final size:17
Alignment explanation
Indices: 32728--32760 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32718 AATAAAAAGC
32728 TATAAAATTTTTAATAT
1 TATAAAATTTTTAATAT
*
32745 TATAAACTTTTTAATA
1 TATAAAATTTTTAATA
32761 AAAACTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAAATTTTTAATAT
Found at i:33199 original size:11 final size:11
Alignment explanation
Indices: 33180--33249 Score: 77
Period size: 11 Copynumber: 6.4 Consensus size: 11
33170 TATCGAAACC
*
33180 ATAACAACAAA
1 ATAATAACAAA
* *
33191 ATAAAAACAAT
1 ATAATAACAAA
*
33202 ATAATAATAAA
1 ATAATAACAAA
33213 ATAATAACAAA
1 ATAATAACAAA
* **
33224 ACAATAATGAA
1 ATAATAACAAA
33235 ATAATAACAAA
1 ATAATAACAAA
33246 ATAA
1 ATAA
33250 CAACGAAACA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 47 1.00
ACGTcount: A:0.71, C:0.09, G:0.01, T:0.19
Consensus pattern (11 bp):
ATAATAACAAA
Found at i:33404 original size:14 final size:14
Alignment explanation
Indices: 33381--33413 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
33371 AACTAATTAA
33381 CTTTTCGAGTATAC
1 CTTTTCGAGTATAC
*
33395 CTTTTTGAGTATAC
1 CTTTTCGAGTATAC
33409 CTTTT
1 CTTTT
33414 GGATCTGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (14 bp):
CTTTTCGAGTATAC
Found at i:33717 original size:35 final size:31
Alignment explanation
Indices: 33637--33705 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
33627 TTCCTTCGCA
* *
33637 CAAACAGCATGACAGAAACTAACAAAGCAAG
1 CAAACAGCACGACAGAAACCAACAAAGCAAG
33668 CAAACAGCACGACAGAAACCAACAAAGCAAG
1 CAAACAGCACGACAGAAACCAACAAAGCAAG
33699 CAAACAG
1 CAAACAG
33706 GCAACTGGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.55, C:0.26, G:0.16, T:0.03
Consensus pattern (31 bp):
CAAACAGCACGACAGAAACCAACAAAGCAAG
Found at i:47055 original size:61 final size:58
Alignment explanation
Indices: 46983--47115 Score: 178
Period size: 61 Copynumber: 2.2 Consensus size: 58
46973 TCCAAAAATA
* * *
46983 ATATTATTTTAATAGTTTTAATATTAAATTAAAT-TAAATATTTATCTTGTATATAAGTATT
1 ATATTAATTTAATAGATTTAATATAAAATTAAATCT-AATATTTATCTTG-ATA-AA-TATT
* *
47044 CTATTAATTTAATAGATTTAATATAAAATTTAATCTAATATTTATCTTGATAAATATT
1 ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTGATAAATATT
47102 ATATTAATTTAATA
1 ATATTAATTTAATA
47116 TTAAAGTGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
58 17 0.26
59 2 0.03
60 3 0.05
61 42 0.65
62 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (58 bp):
ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTGATAAATATT
Found at i:47553 original size:25 final size:26
Alignment explanation
Indices: 47512--47563 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
47502 AAAAAATTAA
* *
47512 CTTTGGTTTTCTTAAA-CTTATTTTC
1 CTTTGGTTTTCTCAAACCTGATTTTC
47537 CTTTGTGTTTT-TCAAACCTGATTTTC
1 CTTTG-GTTTTCTCAAACCTGATTTTC
47563 C
1 C
47564 AATAGCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.15, C:0.19, G:0.10, T:0.56
Consensus pattern (26 bp):
CTTTGGTTTTCTCAAACCTGATTTTC
Found at i:60689 original size:22 final size:22
Alignment explanation
Indices: 60664--60707 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
60654 ATTACATTCA
*
60664 AATT-ATTAATATATTGAATTTT
1 AATTAATT-ATATAATGAATTTT
*
60686 AATTAATTTTATAATGAATTTT
1 AATTAATTATATAATGAATTTT
60708 CATAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTAATTATATAATGAATTTT
Found at i:60715 original size:22 final size:22
Alignment explanation
Indices: 60673--60717 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
60663 AAATTATTAA
* *
60673 TATATTGAATTTTAATTAATTT
1 TATAATGAATTTTAATAAATTT
*
60695 TATAATGAATTTTCATAAATTT
1 TATAATGAATTTTAATAAATTT
60717 T
1 T
60718 GATTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TATAATGAATTTTAATAAATTT
Found at i:64638 original size:39 final size:40
Alignment explanation
Indices: 64561--64667 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
64551 TAGCTCCTCG
* * *
64561 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
64601 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
**
64640 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
64668 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:64745 original size:38 final size:39
Alignment explanation
Indices: 64607--64785 Score: 188
Period size: 40 Copynumber: 4.5 Consensus size: 39
64597 CTCATTCAAT
* * * *
64607 GCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACGAAT
1 GCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCAC-AAA
64647 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
1 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
64686 GGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
1 -GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
** *
64726 -CCTTC-GGATCTTAGTCCGG-ATATAGTCA-CTTAGCACAAA
1 GCCTTCGGGA-CTTAACCCGGAAT-TAGT-ATC-TCGCACAAA
*
64765 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
64786 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 8, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
37 5 0.04
38 18 0.15
39 14 0.11
40 82 0.67
41 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
Done.