Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 206 of 206
Found at i:62674622 original size:10 final size:10
Alignment explanation
Indices: 62674609--62674652 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
62674599 AGTTTAATTA
62674609 TAATTAAACT
1 TAATTAAACT
62674619 TAATT-AA-T
1 TAATTAAACT
62674627 TAACTTAAACT
1 TAA-TTAAACT
62674638 TAATTAAACCT
1 TAATTAAA-CT
62674649 TAAT
1 TAAT
62674653 AACCAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 12 0.40
11 10 0.33
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (10 bp):
TAATTAAACT
Found at i:62674636 original size:19 final size:20
Alignment explanation
Indices: 62674602--62674644 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
62674592 TATAGTTAGT
62674602 TTAATTATAATTAAACTTAA
1 TTAATTATAATTAAACTTAA
*
62674622 TTAATTA-ACTTAAACTTAA
1 TTAATTATAATTAAACTTAA
62674641 TTAA
1 TTAA
62674645 ACCTTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTATAATTAAACTTAA
Found at i:62677376 original size:21 final size:21
Alignment explanation
Indices: 62677350--62677390 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
62677340 ATTACATTTT
*
62677350 CAAGTTTTCAATTTCAATTAA
1 CAAGTTTCCAATTTCAATTAA
62677371 CAAGTTTCCAATTTCAATTA
1 CAAGTTTCCAATTTCAATTA
62677391 TAGTGTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (21 bp):
CAAGTTTCCAATTTCAATTAA
Found at i:62687223 original size:27 final size:27
Alignment explanation
Indices: 62687193--62687279 Score: 67
Period size: 27 Copynumber: 3.4 Consensus size: 27
62687183 AGCTTAAAGT
*
62687193 TTATTTTTCTGCATTTACTTCTTGTTC
1 TTATTGTTCTGCATTTACTTCTTGTTC
** ***
62687220 TTATTGTTCT---TAAAGCTTAAAG-T-
1 TTATTGTTCTGCATTTA-CTTCTTGTTC
*
62687243 TTATTTTTCTGCATTTACTTCTTGTTC
1 TTATTGTTCTGCATTTACTTCTTGTTC
62687270 TTATTGTTCT
1 TTATTGTTCT
62687280 TAGTGTTAGT
Statistics
Matches: 41, Mismatches: 13, Indels: 12
0.62 0.20 0.18
Matches are distributed among these distances:
23 9 0.22
24 3 0.07
25 8 0.20
26 3 0.07
27 18 0.44
ACGTcount: A:0.16, C:0.15, G:0.09, T:0.60
Consensus pattern (27 bp):
TTATTGTTCTGCATTTACTTCTTGTTC
Found at i:62687244 original size:50 final size:50
Alignment explanation
Indices: 62687183--62687281 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
62687173 ATTCTACCTT
62687183 AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTCTTATTGTTCTTAA
1 AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTCTTATTGTTCTTAA
62687233 AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTCTTATTGTTCTTA
1 AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTCTTATTGTTCTTA
62687282 GTGTTAGTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (50 bp):
AGCTTAAAGTTTATTTTTCTGCATTTACTTCTTGTTCTTATTGTTCTTAA
Found at i:62693675 original size:87 final size:87
Alignment explanation
Indices: 62693567--62693730 Score: 267
Period size: 87 Copynumber: 1.9 Consensus size: 87
62693557 AGTTTTAAAC
* *
62693567 AACAACCTCCTCAAGGACTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAACAGCAGAGT
1 AACAACCACCTCAAGGACTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAACAACAGAGT
*
62693632 TTTCGCGGTGTTATGACAGAAA
66 TTCCGCGGTGTTATGACAGAAA
*
62693654 AACAACCACCTCAACGG-CTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAGCAACAGAG
1 AACAACCACCTCAA-GGACTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAACAACAGAG
*
62693718 TTTCCGTGGTGTT
65 TTTCCGCGGTGTT
62693731 TCAAGTGAGA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
87 69 0.97
88 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (87 bp):
AACAACCACCTCAAGGACTCCTGGAGAAGCAACAAAGTTTTAAACAATCTGAAAAACAACAGAGT
TTCCGCGGTGTTATGACAGAAA
Found at i:62707772 original size:40 final size:40
Alignment explanation
Indices: 62707725--62707803 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
62707715 ATAATTATGT
* * *
62707725 ATAATTATGTCTGTTTTATTGATATTATTATTTAGAAAAG
1 ATAATTATATCTCTTTTATTGATATTATTATTCAGAAAAG
*
62707765 ATAATTATATTTCTTTTATTGATATTATTATTCAGAAAA
1 ATAATTATATCTCTTTTATTGATATTATTATTCAGAAAA
62707804 TGTATATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATAATTATATCTCTTTTATTGATATTATTATTCAGAAAAG
Found at i:62711479 original size:16 final size:16
Alignment explanation
Indices: 62711458--62711496 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
62711448 ATGAAATAGC
62711458 ATAAAT-AAACAATTAA
1 ATAAATCAAA-AATTAA
62711474 ATAAATCAAAAATTAA
1 ATAAATCAAAAATTAA
62711490 ATTAAAT
1 A-TAAAT
62711497 TGAGAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAATCAAAAATTAA
Found at i:62712536 original size:11 final size:11
Alignment explanation
Indices: 62712514--62712553 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
62712504 AAAAAAATGG
*
62712514 TAAATTGAAAA
1 TAAAGTGAAAA
*
62712525 TAAAGTGTAAA
1 TAAAGTGAAAA
*
62712536 TTAAGTGAAAA
1 TAAAGTGAAAA
62712547 TAAAGTG
1 TAAAGTG
62712554 GTCATCTTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (11 bp):
TAAAGTGAAAA
Found at i:62718280 original size:24 final size:24
Alignment explanation
Indices: 62718233--62718280 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
62718223 TTTTGAGCAA
* * *
62718233 TTTAATTTTTTTCTTTTATGTTCT
1 TTTAACTTTTTTATTTTATATTCT
*
62718257 TTTAACTTTTTTATTTTCTATTCT
1 TTTAACTTTTTTATTTTATATTCT
62718281 CTTCTGTTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTAACTTTTTTATTTTATATTCT
Found at i:62725578 original size:31 final size:31
Alignment explanation
Indices: 62725543--62725608 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
62725533 CTTAACAACC
* *
62725543 TAATGACTT-AAATAAAAACTTTTGAATAGTT
1 TAATGA-TTAAAATAAAAACTCTCGAATAGTT
*
62725574 TAATGATTAAAATGAAAACTCTCGAATAGTT
1 TAATGATTAAAATAAAAACTCTCGAATAGTT
62725605 TAAT
1 TAAT
62725609 CACTATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (31 bp):
TAATGATTAAAATAAAAACTCTCGAATAGTT
Found at i:62726207 original size:19 final size:19
Alignment explanation
Indices: 62726183--62726220 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
62726173 TTATATCAAG
62726183 GCACCAAGTTTGAGCCTAT
1 GCACCAAGTTTGAGCCTAT
62726202 GCACCAAGTTTGAGCCTAT
1 GCACCAAGTTTGAGCCTAT
62726221 AAAAACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
GCACCAAGTTTGAGCCTAT
Found at i:62726513 original size:34 final size:34
Alignment explanation
Indices: 62726466--62726541 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
62726456 AGGGAGATTT
62726466 TTAGCTTGCTAATAGGAGTAGGAAGCTAAGTTTG
1 TTAGCTTGCTAATAGGAGTAGGAAGCTAAGTTTG
* * *
62726500 TTAGCTTGGTAATAGGAGTAGGAAGTTGAGTTTG
1 TTAGCTTGCTAATAGGAGTAGGAAGCTAAGTTTG
62726534 TTAGCTTG
1 TTAGCTTG
62726542 AGTCATGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.26, C:0.07, G:0.32, T:0.36
Consensus pattern (34 bp):
TTAGCTTGCTAATAGGAGTAGGAAGCTAAGTTTG
Found at i:62731621 original size:32 final size:33
Alignment explanation
Indices: 62731585--62731648 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
62731575 TCAATACTTG
* *
62731585 ATTTCATTTTTCAATTCACATTTCAT-TTCATC
1 ATTTCATATTTCAATTCACATATCATGTTCATC
* *
62731617 ATTTCATATTTCATTTCTCATATCATGTTCAT
1 ATTTCATATTTCAATTCACATATCATGTTCAT
62731649 TTCTCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.25, C:0.20, G:0.02, T:0.53
Consensus pattern (33 bp):
ATTTCATATTTCAATTCACATATCATGTTCATC
Found at i:62731649 original size:18 final size:19
Alignment explanation
Indices: 62731606--62731655 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
62731596 CAATTCACAT
* *
62731606 TTCATTTCATCATTTCATAT
1 TTCATTTC-TCATATCATAG
62731626 TTCATTTCTCATATCAT-G
1 TTCATTTCTCATATCATAG
62731644 TTCATTTCTCAT
1 TTCATTTCTCAT
62731656 TTTTGCCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.43
19 8 0.29
20 8 0.29
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.54
Consensus pattern (19 bp):
TTCATTTCTCATATCATAG
Found at i:62738428 original size:6 final size:6
Alignment explanation
Indices: 62738417--62738443 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
62738407 CAGCCAAAAC
62738417 ATCCAG ATCCAG ATCCAG ATCCAG ATC
1 ATCCAG ATCCAG ATCCAG ATCCAG ATC
62738444 ATCATCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.19
Consensus pattern (6 bp):
ATCCAG
Found at i:62740193 original size:16 final size:16
Alignment explanation
Indices: 62740163--62740206 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
62740153 AAAAAATAGA
*
62740163 TTTAAATATTTTGTGGT
1 TTTAAATA-TTTGTGAT
62740180 TTTAAATATTTGTGAT
1 TTTAAATATTTGTGAT
*
62740196 TATAAAT-TTTG
1 TTTAAATATTTG
62740207 AACAAAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 8 0.32
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (16 bp):
TTTAAATATTTGTGAT
Found at i:62741956 original size:22 final size:22
Alignment explanation
Indices: 62741911--62741956 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
62741901 TTATTCTGAT
*
62741911 TTTTATTTTTATTTTCTTTTTC
1 TTTTATTTTTATTTTCTTTCTC
*
62741933 TTTTGTTTTTATTTAT-TTTCTC
1 TTTTATTTTTATTT-TCTTTCTC
62741955 TT
1 TT
62741957 CCTCCCTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTATTTTTATTTTCTTTCTC
Found at i:62742807 original size:31 final size:32
Alignment explanation
Indices: 62742768--62742856 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
62742758 TATTCCAGAC
*
62742768 AGGGATATCCTATTCGAGGGATATCCCG-GTT
1 AGGGATATCCTATTCGAGGGATATCCCGTCTT
* * * *
62742799 GGGGATATCCT-TTTGAAGGATACCCCGTCTT
1 AGGGATATCCTATTCGAGGGATATCCCGTCTT
* * *
62742830 AGGTATATCCCATTCCAGGGATATCCC
1 AGGGATATCCTATTCGAGGGATATCCC
62742857 CTCGTTTTTA
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 13 0.30
31 20 0.45
32 11 0.25
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (32 bp):
AGGGATATCCTATTCGAGGGATATCCCGTCTT
Found at i:62755079 original size:21 final size:21
Alignment explanation
Indices: 62755055--62755095 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
62755045 AGAATTTCCC
62755055 TGTCCGGGTCAG-TTGTTTTAG
1 TGTCCGGGTCAGATT-TTTTAG
*
62755076 TGTCCGGTTCAGATTTTTTA
1 TGTCCGGGTCAGATTTTTTA
62755096 TGCTTCTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.46
Consensus pattern (21 bp):
TGTCCGGGTCAGATTTTTTAG
Found at i:62756617 original size:12 final size:12
Alignment explanation
Indices: 62756602--62756631 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
62756592 TTTCTTTGCC
62756602 TTTGTCTTTGTT
1 TTTGTCTTTGTT
*
62756614 TTTGTTTTTGTT
1 TTTGTCTTTGTT
62756626 TTTGTC
1 TTTGTC
62756632 CTTCGCCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.17, T:0.77
Consensus pattern (12 bp):
TTTGTCTTTGTT
Found at i:62764241 original size:19 final size:20
Alignment explanation
Indices: 62764217--62764255 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
62764207 CAATTGTTTT
62764217 AAAA-TTAA-ATAAGTTTAAA
1 AAAATTTAATATAA-TTTAAA
62764236 AAAATTTAATATAATTTAAA
1 AAAATTTAATATAATTTAAA
62764256 TTTTTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAATTTAATATAATTTAAA
Found at i:62769419 original size:7 final size:7
Alignment explanation
Indices: 62769180--62769416 Score: 215
Period size: 7 Copynumber: 33.3 Consensus size: 7
62769170 GTTTTGGGGT
*
62769180 TTAGGGT
1 TTAGGGC
*
62769187 TTAGGGT
1 TTAGGGC
*
62769194 TTAGGGT
1 TTAGGGC
*
62769201 TTAGGGT
1 TTAGGGC
*
62769208 TTTGGG-
1 TTAGGGC
*
62769214 TTAGGGG
1 TTAGGGC
*
62769221 TTTGGGC
1 TTAGGGC
*
62769228 TTAGGGG
1 TTAGGGC
* *
62769235 TTTGGGG
1 TTAGGGC
*
62769242 TTTGGGC
1 TTAGGGC
*
62769249 TTAGGGG
1 TTAGGGC
* *
62769256 TTTGGGG
1 TTAGGGC
* *
62769263 TTTGGGG
1 TTAGGGC
62769270 TTAGGGC
1 TTAGGGC
62769277 TTTAGGGC
1 -TTAGGGC
62769285 TTTAGGGC
1 -TTAGGGC
62769293 TTAGGGC
1 TTAGGGC
62769300 TTAGGGC
1 TTAGGGC
62769307 TTAGGGC
1 TTAGGGC
62769314 TTTAGGGC
1 -TTAGGGC
62769322 TTTAGGGC
1 -TTAGGGC
62769330 TTTAGGGC
1 -TTAGGGC
62769338 TTAGGGC
1 TTAGGGC
62769345 TTAGGGC
1 TTAGGGC
62769352 TTAGGGC
1 TTAGGGC
62769359 TTAGGGC
1 TTAGGGC
*
62769366 TTGGGGC
1 TTAGGGC
*
62769373 TTGGGGC
1 TTAGGGC
*
62769380 TTGGGGC
1 TTAGGGC
*
62769387 TTGGGGC
1 TTAGGGC
*
62769394 TTGGGGC
1 TTAGGGC
*
62769401 TTGGGGC
1 TTAGGGC
*
62769408 TTGGGGC
1 TTAGGGC
62769415 TT
1 TT
62769417 GGGTTTTAGG
Statistics
Matches: 213, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
6 5 0.02
7 170 0.80
8 38 0.18
ACGTcount: A:0.08, C:0.09, G:0.47, T:0.35
Consensus pattern (7 bp):
TTAGGGC
Done.