Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2496
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: 16383
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:192 original size:20 final size:20
Alignment explanation
Indices: 162--199 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
152 ATAAATTTTT
162 TATTTTTAATTA-TATATTA
1 TATTTTTAATTATTATATTA
181 TATTTTTAAATTATTATAT
1 TATTTTT-AATTATTATAT
200 ATAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTTAATTATTATATTA
Found at i:1525 original size:3 final size:3
Alignment explanation
Indices: 1517--1552 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1507 TGTCTTTTGA
1517 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1553 TAATACATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1728 original size:15 final size:15
Alignment explanation
Indices: 1692--1730 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1682 AATTTAAAAA
1692 ATAAATAAAAATAAG
1 ATAAATAAAAATAAG
*
1707 AGT-AATAAAAATAAT
1 A-TAAATAAAAATAAG
1722 ATAAATAAA
1 ATAAATAAA
1731 TAAGAGCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (15 bp):
ATAAATAAAAATAAG
Found at i:2084 original size:23 final size:22
Alignment explanation
Indices: 2029--2093 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
2019 ATATGATTAT
*
2029 ATAAAATGAATATAACATAAAA
1 ATAATATGAATATAACATAAAA
* *
2051 A-AAT-TAAAATATAATATGAAAA
1 ATAATAT-GAATATAACAT-AAAA
2073 ATAATATGAATATAACATAAA
1 ATAATATGAATATAACATAAA
2094 TACAGAAACG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 11 0.32
22 9 0.26
23 12 0.35
24 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (22 bp):
ATAATATGAATATAACATAAAA
Found at i:2150 original size:20 final size:20
Alignment explanation
Indices: 2127--2166 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2117 ATAAATAAAT
2127 TATAAATATATCAA-ATTTTA
1 TATAAATATAT-AATATTTTA
2147 TATAAATATATAATATTTTA
1 TATAAATATATAATATTTTA
2167 AATACAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TATAAATATATAATATTTTA
Found at i:2459 original size:15 final size:15
Alignment explanation
Indices: 2439--2467 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2429 TAAAATTTTT
2439 TAATTAATAAAATTA
1 TAATTAATAAAATTA
2454 TAATTAATAAAATT
1 TAATTAATAAAATT
2468 TATTTAAAAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATTAATAAAATTA
Found at i:3418 original size:23 final size:23
Alignment explanation
Indices: 3374--3428 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3364 TTAAATGTAC
*
3374 AAAA-AATAAAAATATGACATAA
1 AAAATAATAAAAATATAACATAA
* *
3396 AAAATAATTAAAATATAATATAA
1 AAAATAATAAAAATATAACATAA
3419 AAAATGAATA
1 AAAAT-AATA
3429 TGACATGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 20 0.74
24 3 0.11
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAATAATAAAAATATAACATAA
Found at i:3428 original size:13 final size:12
Alignment explanation
Indices: 3392--3429 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
3382 AAAATATGAC
3392 ATAAAAAATAAT
1 ATAAAAAATAAT
*
3404 -TAAAATATAAT
1 ATAAAAAATAAT
3415 ATAAAAAATGAAT
1 ATAAAAAAT-AAT
3428 AT
1 AT
3430 GACATGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 7 0.32
13 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:4023 original size:4 final size:4
Alignment explanation
Indices: 4014--4074 Score: 83
Period size: 4 Copynumber: 15.8 Consensus size: 4
4004 TTATTCTCCT
4014 TTTC TTTC TTTC TTTC TTTC TTT- TTTC TTT- TTT- TTCTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC TTTC TTTC
*
4060 TTTC TTTC TCTC TTT
1 TTTC TTTC TTTC TTT
4075 TCCCTCTTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 8 0.15
4 42 0.81
5 2 0.04
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:4419 original size:10 final size:10
Alignment explanation
Indices: 4404--4429 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4394 ATAAATTATT
4404 AATATATAAA
1 AATATATAAA
4414 AATATATAAA
1 AATATATAAA
4424 AATATA
1 AATATA
4430 ATATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATATATAAA
Found at i:4419 original size:36 final size:32
Alignment explanation
Indices: 4379--4455 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 32
4369 GAATACACGT
*
4379 ATATATAAAAATAAAATAAATTATTAATATATAAAA
1 ATATATAAAAATAAAAT--ATT-TTAA-ATACAAAA
*
4415 ATATATAAAAATATAATATTTTAAATACAAAA
1 ATATATAAAAATAAAATATTTTAAATACAAAA
*
4447 AAATATAAA
1 ATATATAAA
4456 TACCAATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 15 0.39
33 4 0.11
34 3 0.08
36 16 0.42
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (32 bp):
ATATATAAAAATAAAATATTTTAAATACAAAA
Found at i:4483 original size:4 final size:4
Alignment explanation
Indices: 4474--4524 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
4464 TATAAATTTT
* *
4474 TTTC TTTC TTTC CTT- TTT- TTTC -TCC TTTC TTTC -TTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
4518 TTTC TTT
1 TTTC TTT
4525 TTCACCAACG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 10 0.25
4 30 0.75
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:4512 original size:11 final size:11
Alignment explanation
Indices: 4475--4524 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
4465 ATAAATTTTT
4475 TTCTTTCTTTCC
1 TTCTTTCTTT-C
4487 TT-TTT-TTTC
1 TTCTTTCTTTC
*
4496 TCCTTTCTTTC
1 TTCTTTCTTTC
4507 TTCTTTCTTTC
1 TTCTTTCTTTC
4518 TTTCTTT
1 -TTCTTT
4525 TTCACCAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 6 0.18
11 17 0.52
12 8 0.24
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTCTTTC
Found at i:5160 original size:15 final size:14
Alignment explanation
Indices: 5133--5166 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
5123 CACTTATCAT
*
5133 AAAAAGAAGAAAAG
1 AAAAAGAAAAAAAG
5147 AAAAGAGAAAAAAAG
1 AAAA-AGAAAAAAAG
5162 AAAAA
1 AAAAA
5167 AATCTATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:6331 original size:2 final size:2
Alignment explanation
Indices: 6324--6356 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6314 TTGAGTCTTT
6324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6357 CCATTTCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6798 original size:21 final size:22
Alignment explanation
Indices: 6774--6821 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
6764 AATAGTTAGG
6774 TTTTAAATTTTAAATTATGATT
1 TTTTAAATTTTAAATTATGATT
* *
6796 TTTTTATTTTTAAATTATGATT
1 TTTTAAATTTTAAATTATGATT
6818 TTTT
1 TTTT
6822 TATACCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTAAATTTTAAATTATGATT
Found at i:6806 original size:22 final size:22
Alignment explanation
Indices: 6781--6824 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
6771 AGGTTTTAAA
6781 TTTTAAATTATGATTTTTTTAT
1 TTTTAAATTATGATTTTTTTAT
6803 TTTTAAATTATGATTTTTTTAT
1 TTTTAAATTATGATTTTTTTAT
6825 ACCAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTAAATTATGATTTTTTTAT
Found at i:6834 original size:2 final size:2
Alignment explanation
Indices: 6829--6871 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
6819 TTTTATACCA
6829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
6872 GCATAGCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8137 original size:19 final size:18
Alignment explanation
Indices: 8115--8159 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
8105 ATCATGCCAT
*
8115 GTCATCATCAATAAACAAC
1 GTCATCAAC-ATAAACAAC
* *
8134 GTCATCAACATTAGCAAC
1 GTCATCAACATAAACAAC
8152 GTCATCAA
1 GTCATCAA
8160 ACACGTCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.22
Consensus pattern (18 bp):
GTCATCAACATAAACAAC
Found at i:12409 original size:19 final size:17
Alignment explanation
Indices: 12385--12482 Score: 77
Period size: 19 Copynumber: 5.8 Consensus size: 17
12375 TAGCTTAAAT
12385 TGTATCGATACAAAACGTA
1 TGTATCGATAC-AAAC-TA
12404 TGTATCGATAC--A-T-
1 TGTATCGATACAAACTA
12417 TGTATCGATACAACACTTA
1 TGTATCGATACAA-AC-TA
12436 TGTATCGATAC--A-T-
1 TGTATCGATACAAACTA
12449 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC--TA
12469 TGTATCGATACAAA
1 TGTATCGATACAAA
12483 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (17 bp):
TGTATCGATACAAACTA
Found at i:12422 original size:13 final size:13
Alignment explanation
Indices: 12404--12460 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
12394 ACAAAACGTA
12404 TGTATCGATACAT
1 TGTATCGATACAT
12417 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
12435 ATGTATCGATACAT
1 -TGTATCGATACAT
12449 TGTATCGATACA
1 TGTATCGATACA
12461 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12424 original size:32 final size:32
Alignment explanation
Indices: 12383--12480 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
12373 AGTAGCTTAA
* *
12383 ATTGTATCGATACAAAACGTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
12415 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
12447 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
12480 A
1 A
12481 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 48 0.76
33 15 0.24
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:15858 original size:15 final size:16
Alignment explanation
Indices: 15832--15861 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15822 AATTGCTTTG
15832 TAAATAATGTGATTTA
1 TAAATAATGTGATTTA
15848 TAAAT-ATGTGATTT
1 TAAATAATGTGATTT
15862 TTGCTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (16 bp):
TAAATAATGTGATTTA
Found at i:16053 original size:37 final size:37
Alignment explanation
Indices: 15998--16083 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
15988 AAACTGGTTT
* **
15998 CGACCTGTGCCACTAGTAAAAATAGTGCTTTTTGTTC
1 CGACCTGTGCCACCAGTAAAAATAGTAATTTTTGTTC
* *
16035 CGACCTGTGCCACCAGTAAGAATAGTAATTTTTGTTT
1 CGACCTGTGCCACCAGTAAAAATAGTAATTTTTGTTC
*
16072 CGAACTGTGCCA
1 CGACCTGTGCCA
16084 TTGAAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (37 bp):
CGACCTGTGCCACCAGTAAAAATAGTAATTTTTGTTC
Done.