Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2443
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: 54163
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:2085 original size:32 final size:32
Alignment explanation
Indices: 2047--2130 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
2037 ATCTTTTACA
*
2047 AAGGCTAAGATAGAACCTCTACATTATCTTTC
1 AAGGCTAAGATAGAACCTCTACACTATCTTTC
*
2079 AAGGCTAAGATAGAACCTCTACACTATCTTTT
1 AAGGCTAAGATAGAACCTCTACACTATCTTTC
2111 AAGGCTAAGATAGAACCTCT
1 AAGGCTAAGATAGAACCTCT
2131 CAATCACTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (32 bp):
AAGGCTAAGATAGAACCTCTACACTATCTTTC
Found at i:2612 original size:13 final size:13
Alignment explanation
Indices: 2594--2622 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2584 GATACTATTC
2594 ACAATGTATCGAT
1 ACAATGTATCGAT
2607 ACAATGTATCGAT
1 ACAATGTATCGAT
2620 ACA
1 ACA
2623 TGAATAGTGA
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:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:5222 original size:23 final size:24
Alignment explanation
Indices: 5177--5223 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
5167 CAAAGAATTG
*
5177 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
5201 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
5224 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:6539 original size:21 final size:21
Alignment explanation
Indices: 6513--6570 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
6503 TACATGTTGC
6513 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
6534 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
6555 AATGTATCGATACATG
1 AATGTATCGATACATG
6571 TCATTGGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:6637 original size:13 final size:13
Alignment explanation
Indices: 6619--6644 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6609 TACACCAAGT
6619 ATGTATCGATACA
1 ATGTATCGATACA
6632 ATGTATCGATACA
1 ATGTATCGATACA
6645 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:10731 original size:15 final size:15
Alignment explanation
Indices: 10711--10741 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10701 TAAAAATGTC
*
10711 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
10726 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
10741 C
1 C
10742 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:12840 original size:13 final size:13
Alignment explanation
Indices: 12822--12847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12812 ACATTTTTCT
12822 TTGTATCGATACA
1 TTGTATCGATACA
12835 TTGTATCGATACA
1 TTGTATCGATACA
12848 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:13011 original size:20 final size:20
Alignment explanation
Indices: 12968--13013 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
12958 AAATCTTTTA
12968 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
12989 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
13009 CAAAA
1 CAAAA
13014 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:15419 original size:13 final size:13
Alignment explanation
Indices: 15401--15426 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15391 TACACCAAGT
15401 ATGTATCGATACA
1 ATGTATCGATACA
15414 ATGTATCGATACA
1 ATGTATCGATACA
15427 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:20649 original size:38 final size:38
Alignment explanation
Indices: 20607--20702 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
20597 TATTAAACTG
* * *
20607 TGTCACTAGTTAAGAATAGTGATTTTCGTTTCTAACCA
1 TGTCACTAGTTTAGAATAGTGATTTTCATTTATAACCA
* *
20645 TGTCACTAATTTAGAATAGTGATTTTCATTTATAACTA
1 TGTCACTAGTTTAGAATAGTGATTTTCATTTATAACCA
*
20683 TGTCATTAGTTTAGAATAGT
1 TGTCACTAGTTTAGAATAGT
20703 AGTTTTTATC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (38 bp):
TGTCACTAGTTTAGAATAGTGATTTTCATTTATAACCA
Found at i:21581 original size:20 final size:21
Alignment explanation
Indices: 21556--21600 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
21546 GTTTAGATGG
21556 AAAACAA-GCATTGGTTGGAT
1 AAAACAATGCATTGGTTGGAT
*
21576 AAAACAATGCATTTGTTGGAT
1 AAAACAATGCATTGGTTGGAT
21597 AAAA
1 AAAA
21601 AGATACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (21 bp):
AAAACAATGCATTGGTTGGAT
Found at i:22338 original size:23 final size:23
Alignment explanation
Indices: 22274--22330 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
22264 ATAACATTTA
* *
22274 AAAATAATTAATTACATTAAAACT
1 AAAATAATAAAAT-CATTAAAACT
*
22298 ATAATAATAAAATCATTAAAAC-
1 AAAATAATAAAATCATTAAAACT
22320 AAAATAATAAA
1 AAAATAATAAA
22331 CCTTATTAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 10 0.34
23 9 0.31
24 10 0.34
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAATAATAAAATCATTAAAACT
Found at i:22882 original size:13 final size:13
Alignment explanation
Indices: 22864--22889 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22854 TACACCAAGT
22864 ATGTATCGATACA
1 ATGTATCGATACA
22877 ATGTATCGATACA
1 ATGTATCGATACA
22890 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:22887 original size:32 final size:33
Alignment explanation
Indices: 22846--22909 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
22836 TAGCCAAACT
* **
22846 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
22878 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
22910 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:26975 original size:15 final size:15
Alignment explanation
Indices: 26955--26985 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
26945 TAAAAATGTC
*
26955 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
26970 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
26985 C
1 C
26986 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:29072 original size:13 final size:13
Alignment explanation
Indices: 29054--29092 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
29044 ACATTTTTCT
29054 TTGTATCGATACA
1 TTGTATCGATACA
*
29067 TTGTATCAATACA
1 TTGTATCGATACA
*
29080 CTGTATCGATACA
1 TTGTATCGATACA
29093 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:29256 original size:20 final size:19
Alignment explanation
Indices: 29215--29257 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
29205 ATCTTTTACA
29215 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
29235 AAATCACTTAGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
29255 AAA
1 AAA
29258 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:31654 original size:13 final size:13
Alignment explanation
Indices: 31636--31661 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31626 TACACCAAGT
31636 ATGTATCGATACA
1 ATGTATCGATACA
31649 ATGTATCGATACA
1 ATGTATCGATACA
31662 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:31659 original size:32 final size:33
Alignment explanation
Indices: 31618--31681 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
31608 TAGCCAAACT
* **
31618 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
31650 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
31682 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:40507 original size:9 final size:9
Alignment explanation
Indices: 40493--40538 Score: 67
Period size: 9 Copynumber: 5.1 Consensus size: 9
40483 AAGGTTCAAC
40493 AAAAAAAAG
1 AAAAAAAAG
40502 AAAAAAAAG
1 AAAAAAAAG
40511 AAAAAAAA-
1 AAAAAAAAG
40519 AGAAAAAAAG
1 A-AAAAAAAG
*
40529 AAAGAAAAG
1 AAAAAAAAG
40538 A
1 A
40539 GAGAAGAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
8 1 0.03
9 32 0.94
10 1 0.03
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:40508 original size:10 final size:10
Alignment explanation
Indices: 40493--40527 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
40483 AAGGTTCAAC
40493 AAAAAAAAG-
1 AAAAAAAAGA
40502 AAAAAAAAGA
1 AAAAAAAAGA
40512 AAAAAAAAGA
1 AAAAAAAAGA
40522 AAAAAA
1 AAAAAA
40528 GAAAGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:40543 original size:9 final size:9
Alignment explanation
Indices: 40497--40543 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
40487 TTCAACAAAA
*
40497 AAAAGAAAA
1 AAAAGAAAG
*
40506 AAAAGAAAAA
1 AAAAG-AAAG
40516 AAAAGAAA-
1 AAAAGAAAG
40524 AAAAGAAAG
1 AAAAGAAAG
*
40533 AAAAGAGAG
1 AAAAGAAAG
40542 AA
1 AA
40544 GAAATGGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
8 8 0.23
9 18 0.51
10 9 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:42375 original size:97 final size:97
Alignment explanation
Indices: 42241--42436 Score: 311
Period size: 97 Copynumber: 2.0 Consensus size: 97
42231 AAAATTCTTT
* ** * * * *
42241 TTATCGGGGATACTCTGACCCTATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCA
1 TTATCGAGGATACTCCAACCCCATTCCTCCAAAGGGATAATCCAACCCCGCTTTTAAACACATCA
*
42306 AAGTTTAAATCTTATTCTCACTTAAATTGTCA
66 AAGTTTAAATCTTATTCTCACTCAAATTGTCA
*
42338 TTATCGAGGATACTCCAACCCCATTCCTCCAAAGGGATAATCCAACCCCGCTTTTCAACACATCA
1 TTATCGAGGATACTCCAACCCCATTCCTCCAAAGGGATAATCCAACCCCGCTTTTAAACACATCA
42403 AAGTTTAAATCTTATTCTCACTCAAATTGTCA
66 AAGTTTAAATCTTATTCTCACTCAAATTGTCA
42435 TT
1 TT
42437 CTCACTCAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (97 bp):
TTATCGAGGATACTCCAACCCCATTCCTCCAAAGGGATAATCCAACCCCGCTTTTAAACACATCA
AAGTTTAAATCTTATTCTCACTCAAATTGTCA
Found at i:42439 original size:18 final size:18
Alignment explanation
Indices: 42416--42453 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
42406 TTTAAATCTT
42416 ATTCTCACTCAAATTGTC
1 ATTCTCACTCAAATTGTC
42434 ATTCTCACTCAAATTGTC
1 ATTCTCACTCAAATTGTC
42452 AT
1 AT
42454 CATCGGGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.39
Consensus pattern (18 bp):
ATTCTCACTCAAATTGTC
Found at i:47429 original size:22 final size:22
Alignment explanation
Indices: 47399--47471 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
47389 ATTACTGTTG
47399 ATCACTGTTCATGTATCAATAC
1 ATCACTGTTCATGTATCAATAC
* * * *
47421 ATCATTGTTCA--TAACTATTC
1 ATCACTGTTCATGTATCAATAC
*
47441 ATCACTATTCATGTATCAATAC
1 ATCACTGTTCATGTATCAATAC
*
47463 ATCATTGTT
1 ATCACTGTT
47472 TATCATTGTT
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
20 15 0.39
22 23 0.61
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.41
Consensus pattern (22 bp):
ATCACTGTTCATGTATCAATAC
Found at i:48751 original size:15 final size:15
Alignment explanation
Indices: 48731--48759 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48721 GCTTGCTACT
48731 ACACATGAGGGGACC
1 ACACATGAGGGGACC
48746 ACACATGAGGGGAC
1 ACACATGAGGGGAC
48760 AAACCAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.24, G:0.34, T:0.07
Consensus pattern (15 bp):
ACACATGAGGGGACC
Found at i:53053 original size:13 final size:13
Alignment explanation
Indices: 53035--53072 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
53025 ACATAAGTGT
53035 TGTATCGATACAA
1 TGTATCGATACAA
*
53048 TGTATCGATATAA
1 TGTATCGATACAA
53061 TGTATCGATACA
1 TGTATCGATACA
53073 TAAGTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Done.