Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2128
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: 57304
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:2632 original size:259 final size:260
Alignment explanation
Indices: 2173--2686 Score: 1021
Period size: 259 Copynumber: 2.0 Consensus size: 260
2163 GTTTACCAAA
2173 TTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATACTCC
1 TTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATACTCC
2238 TCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATTGTT
66 TCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATTGTT
2303 CACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAACCC
131 CACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAACCC
2368 TTCATAACATACTCATAAAATAATCAAACAGATGATTTAAAGTGCC-TTTGCACTATGCTAGAAT
196 TTCATAACATACTCATAAAATAATCAAACAGATGATTTAAAGTGCCTTTTGCACTATGCTAGAAT
2432 TTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATACTCC
1 TTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATACTCC
2497 TCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATTGTT
66 TCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATTGTT
2562 CACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAACCC
131 CACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAACCC
2627 TTCATAACATACTCATAAAATAATCAAACAGATGATTTAAAGTGCCTTTTGCACTATGCT
196 TTCATAACATACTCATAAAATAATCAAACAGATGATTTAAAGTGCCTTTTGCACTATGCT
2687 TAAAATGCAA
Statistics
Matches: 254, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
259 241 0.95
260 13 0.05
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (260 bp):
TTTGTTGTGTTTGCTCACTATATAATTGATAACTACTTGAATTGTAATGTGGATTTACATACTCC
TCCGAAAGCAGGGAATCATCACCCCATGCAGACAAGACAAGATTTTTCTTTCCACTACGATTGTT
CACAGGACCGCTTTGCAGCAGAATGCTAGAATTCATTACTTGCACAAAAGAAACAAAGATAACCC
TTCATAACATACTCATAAAATAATCAAACAGATGATTTAAAGTGCCTTTTGCACTATGCTAGAAT
Found at i:5181 original size:17 final size:16
Alignment explanation
Indices: 5144--5180 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
5134 TAATAGCAAT
5144 AAAAATGTAAAGCTTA
1 AAAAATGTAAAGCTTA
5160 AAAAATGTAAAGCTTA
1 AAAAATGTAAAGCTTA
5176 AAAAA
1 AAAAA
5181 AGTGAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (16 bp):
AAAAATGTAAAGCTTA
Found at i:12460 original size:2 final size:2
Alignment explanation
Indices: 12453--12484 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12443 GGTTTCCATG
12453 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12485 CGCACAGTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12797 original size:28 final size:28
Alignment explanation
Indices: 12744--12797 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
12734 GTATTTTATT
* *
12744 AAATTAAAATTTTTAAATTTTTTAAAAA
1 AAATTAAAACTTTTAAATTTTATAAAAA
*
12772 AAATT-AAACTTTTGAATTTTAATAAA
1 AAATTAAAACTTTTAAATTTT-ATAAA
12798 TACTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
AAATTAAAACTTTTAAATTTTATAAAAA
Found at i:16773 original size:28 final size:28
Alignment explanation
Indices: 16714--16783 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 28
16704 CCACCCATTT
16714 ATTTGTCAAAAATGGTGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTGTG
16742 -TTTGTCAAAAATGGTGGTT-TCCTTTG-G
1 ATTTGTCAAAAATGGTGGTTAT--TTTGTG
*
16769 ATTTGTCAAATATGG
1 ATTTGTCAAAAATGG
16784 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATTTTGTG
Found at i:21342 original size:28 final size:28
Alignment explanation
Indices: 21283--21352 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 28
21273 CCACCTATTT
21283 ATTTGTCAAAAATGGTGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTGTG
21311 -TTTGTCAAAAATGGTGGTT-TCCTTTG-G
1 ATTTGTCAAAAATGGTGGTTAT--TTTGTG
*
21338 ATTTGTCAAATATGG
1 ATTTGTCAAAAATGG
21353 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATTTTGTG
Found at i:23332 original size:13 final size:15
Alignment explanation
Indices: 23299--23334 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
23289 TTAAAAAAAT
23299 TTAAAATATAATTAA
1 TTAAAATATAATTAA
23314 TT-AAATA-AATT-A
1 TTAAAATATAATTAA
23326 TTAAAATAT
1 TTAAAATAT
23335 GTTGTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.16
13 9 0.47
14 5 0.26
15 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAATATAATTAA
Found at i:24168 original size:2 final size:2
Alignment explanation
Indices: 24113--24157 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
24103 TGTGTGTGTT
24113 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
24155 TA T
1 TA T
24158 GTAAGTATAT
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:25301 original size:28 final size:29
Alignment explanation
Indices: 25229--25289 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
25219 CACATAACAA
* *
25229 AAAATAAAAACATTTTGATAAATTATTTT
1 AAAATAAAAATATTTTGATAAATTAATTT
25258 AAAATAAAAATATTTTGAT-AATTAATTT
1 AAAATAAAAATATTTTGATAAATTAATTT
25286 AAAA
1 AAAA
25290 AAATGCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATAAAAATATTTTGATAAATTAATTT
Found at i:25601 original size:45 final size:45
Alignment explanation
Indices: 25537--25626 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
25527 TTATATATAT
*
25537 ATATATATCTTTATGTTTGGATTAAATTTACTTTTCCTAGACTTA
1 ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
25582 ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
1 ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
25627 TGTGCTCCCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (45 bp):
ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
Found at i:29570 original size:42 final size:42
Alignment explanation
Indices: 29523--29603 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
29513 ATCAAGAATG
*
29523 GGTTCAGATTCTGGAGATTCAGGTTCGAACACATGGTCAATC
1 GGTTCAAATTCTGGAGATTCAGGTTCGAACACATGGTCAATC
*
29565 GGTTCAAATTCTGGAGATTCAGGTTCGGACACATGGTCA
1 GGTTCAAATTCTGGAGATTCAGGTTCGAACACATGGTCA
29604 GGTTTGGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (42 bp):
GGTTCAAATTCTGGAGATTCAGGTTCGAACACATGGTCAATC
Found at i:29589 original size:21 final size:21
Alignment explanation
Indices: 29523--29590 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
29513 ATCAAGAATG
*
29523 GGTTCAGATTCTGGAGATTCA
1 GGTTCAAATTCTGGAGATTCA
* ** ** *
29544 GGTTCGAACACATGGTCAATC-
1 GGTTCAAATTC-TGGAGATTCA
29565 GGTTCAAATTCTGGAGATTCA
1 GGTTCAAATTCTGGAGATTCA
29586 GGTTC
1 GGTTC
29591 GGACACATGG
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (21 bp):
GGTTCAAATTCTGGAGATTCA
Found at i:29606 original size:18 final size:18
Alignment explanation
Indices: 29583--29618 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29573 TTCTGGAGAT
29583 TCAGGTTCGGACACATGG
1 TCAGGTTCGGACACATGG
*
29601 TCAGGTTTGGACACATGG
1 TCAGGTTCGGACACATGG
29619 CTCGGACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (18 bp):
TCAGGTTCGGACACATGG
Found at i:31428 original size:62 final size:62
Alignment explanation
Indices: 31331--31452 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
31321 CCAACTATCA
* * *
31331 AACAAAATCAATCAGTAATGAAGGCTAACTGAATGAAATAATTTAGCGATAAAAGCTGATCT
1 AACAAAATCAATCAGCAATGAAGGCTAACTGAATGAAATAAATCAGCGATAAAAGCTGATCT
* *
31393 AACAAAATCAATCAGCACTGAAGGCTGACTGAATGAAATAAATCAGCGATAAAAGCTGAT
1 AACAAAATCAATCAGCAATGAAGGCTAACTGAATGAAATAAATCAGCGATAAAAGCTGAT
31453 TCAGAGAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (62 bp):
AACAAAATCAATCAGCAATGAAGGCTAACTGAATGAAATAAATCAGCGATAAAAGCTGATCT
Found at i:31437 original size:31 final size:30
Alignment explanation
Indices: 31348--31439 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
31338 TCAATCAGTA
* * *
31348 ATGAAGGCTAACTGAATGAAATAATTTAGC
1 ATGAAGGCTGACTGAATGAAATAAATCAGC
* * ** *
31378 GATAAAAGCTGATCT-AACAAAATCAATCAGC
1 -ATGAAGGCTGA-CTGAATGAAATAAATCAGC
31409 ACTGAAGGCTGACTGAATGAAATAAATCAGC
1 A-TGAAGGCTGACTGAATGAAATAAATCAGC
31440 GATAAAAGCT
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
30 3 0.07
31 40 0.89
32 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (30 bp):
ATGAAGGCTGACTGAATGAAATAAATCAGC
Found at i:31451 original size:31 final size:31
Alignment explanation
Indices: 31358--31451 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
31348 ATGAAGGCTA
* *
31358 ACTGAATGAAATAATTTAGCGATAAAAGCTG
1 ACTGAATGAAATAAATCAGCGATAAAAGCTG
** * * *
31389 ATCT-AACAAAATCAATCAGC-ACTGAAGGCTG
1 A-CTGAATGAAATAAATCAGCGA-TAAAAGCTG
31420 ACTGAATGAAATAAATCAGCGATAAAAGCTG
1 ACTGAATGAAATAAATCAGCGATAAAAGCTG
31451 A
1 A
31452 TTCAGAGAGA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
30 3 0.06
31 41 0.87
32 3 0.06
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (31 bp):
ACTGAATGAAATAAATCAGCGATAAAAGCTG
Found at i:31506 original size:26 final size:25
Alignment explanation
Indices: 31461--31521 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
31451 ATTCAGAGAG
*
31461 AAAAGGAATCCCAAAATTTTTTTTTC
1 AAAA-GAATTCCAAAATTTTTTTTTC
31487 AAAAGAATTCCAAAATTTTTTTTTC
1 AAAAGAATTCCAAAATTTTTTTTTC
*
31512 AGAAGAATTC
1 AAAAGAATTC
31522 GAACCTATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 29 0.88
26 4 0.12
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (25 bp):
AAAAGAATTCCAAAATTTTTTTTTC
Found at i:44077 original size:58 final size:59
Alignment explanation
Indices: 43978--44095 Score: 184
Period size: 58 Copynumber: 2.0 Consensus size: 59
43968 TTCCCCGGTT
* *
43978 ACAGGATCTGTTTATGCCCCCGCCAATACAGAAACAAGTAATTTCCAATTCTAAGACATA
1 ACAGGATCTGTTTATG-CCCCGCAAATACAGAAACAAGTAATTTCCAATTCCAAGACATA
* *
44038 ACAGGATCTGTTTATG-CCTGCAAATACAGAAACAAGTAATTTCTAATTCCAAGACATA
1 ACAGGATCTGTTTATGCCCCGCAAATACAGAAACAAGTAATTTCCAATTCCAAGACATA
44096 GCATGACATT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 38 0.70
60 16 0.30
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (59 bp):
ACAGGATCTGTTTATGCCCCGCAAATACAGAAACAAGTAATTTCCAATTCCAAGACATA
Found at i:49361 original size:13 final size:15
Alignment explanation
Indices: 49342--49383 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
49332 TATATTTTAA
49342 AAAAAATAAA-AT-T
1 AAAAAATAAATATGT
*
49355 AATAAATAAATATGT
1 AAAAAATAAATATGT
49370 AAAAAATAATATAT
1 AAAAAATAA-ATAT
49384 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 2 0.08
15 9 0.38
16 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAAAATAAATATGT
Found at i:56017 original size:13 final size:13
Alignment explanation
Indices: 55975--56023 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
55965 CAGTGAAAAA
*
55975 ATATTTTAATTTTT
1 ATATTTT-ATATTT
*
55989 ATATTATTAAATTT
1 ATATT-TTATATTT
56003 ATATTTTATATTT
1 ATATTTTATATTT
56016 ATATTTTA
1 ATATTTTA
56024 AAATATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 15 0.48
14 14 0.45
15 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATATTTTATATTT
Found at i:56042 original size:16 final size:18
Alignment explanation
Indices: 56023--56061 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
56013 TTTATATTTT
56023 AAAATA-TAATAA-ATAA
1 AAAATATTAATAACATAA
*
56039 AAAATATTAATAACTTAA
1 AAAATATTAATAACATAA
56057 AAAAT
1 AAAAT
56062 TTATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 6 0.30
18 8 0.40
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATTAATAACATAA
Done.