Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009066.1 Kokia drynarioides strain JFW-HI SEQ_123766, whole genome shotgun sequence
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: 86477
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:672 original size:16 final size:15
Alignment explanation
Indices: 648--689 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
638 ATTAAAACAA
648 TAAAAATATTATAATT
1 TAAAAATATTAT-ATT
* *
664 TAAATATA-TGTATT
1 TAAAAATATTATATT
678 TAAAAATATTAT
1 TAAAAATATTAT
690 TGATTAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 10 0.48
15 4 0.19
16 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TAAAAATATTATATT
Found at i:3080 original size:30 final size:30
Alignment explanation
Indices: 3045--3271 Score: 199
Period size: 30 Copynumber: 7.6 Consensus size: 30
3035 TTTGACCATC
*
3045 AAACTTTCCAAAAATTCCAATTTTACTCTT
1 AAACTTTCCAAAAATTCCAATTTTACCCTT
* *
3075 GAACTTTCTAAAAATT-CAAGTTTTACCCTT
1 AAACTTTCCAAAAATTCCAA-TTTTACCCTT
* * * *
3105 AAATTTTCCAAAAATTCAAATTTAAACCTT
1 AAACTTTCCAAAAATTCCAATTTTACCCTT
* * ** * *
3135 GAACTTT-TAAAAATTTGAATTTGATCCC-C
1 AAACTTTCCAAAAATTCCAATTTTA-CCCTT
* * * *
3164 AAACCTTCCAAAAATTCAAATTTAACCCCT
1 AAACTTTCCAAAAATTCCAATTTTACCCTT
* ** *
3194 AAACTTTCCAAATATTTGAATTTTACCCTC
1 AAACTTTCCAAAAATTCCAATTTTACCCTT
* *
3224 AAGCTTTCCAAAAATTCCAATTTGACCCTT
1 AAACTTTCCAAAAATTCCAATTTTACCCTT
3254 GAAACTTTCCAAAAATTC
1 -AAACTTTCCAAAAATTC
3272 AAATGTGACC
Statistics
Matches: 153, Mismatches: 38, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
29 24 0.16
30 111 0.73
31 18 0.12
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (30 bp):
AAACTTTCCAAAAATTCCAATTTTACCCTT
Found at i:3116 original size:60 final size:59
Alignment explanation
Indices: 3034--3273 Score: 241
Period size: 60 Copynumber: 4.0 Consensus size: 59
3024 TAAAATTATG
* * * * *
3034 TTTTGACCATCAAACTTTCCAAAAATTCCAATTTTACTCTTGAACTTTCTAAAAATTCAA
1 TTTT-ACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTGAACTTTCCAAAAATTCAA
* * * * *
3094 GTTTTACCCTTAAATTTTCCAAAAATTCAAATTTAAACCTTGAACTTT-TAAAAATTTGAA
1 -TTTTACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTGAACTTTCCAAAAA-TTCAA
* * * * * *
3154 TTTGATCCC-CAAACCTTCCAAAAATTCAAATTTAACCCCTAAACTTTCCAAATATTTGAA
1 TTTTA-CCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTGAACTTTCCAAA-AATTCAA
* * *
3214 TTTTACCCTCAAGCTTTCCAAAAATTCCAATTTGACCCTTGAAACTTTCCAAAAATTCAA
1 TTTTACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTG-AACTTTCCAAAAATTCAA
3274 ATGTGACCCG
Statistics
Matches: 147, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
59 45 0.31
60 86 0.59
61 16 0.11
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (59 bp):
TTTTACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTGAACTTTCCAAAAATTCAA
Found at i:3167 original size:119 final size:121
Alignment explanation
Indices: 3044--3270 Score: 280
Period size: 119 Copynumber: 1.9 Consensus size: 121
3034 TTTTGACCAT
* * * * * * * *
3044 CAAACTTTCCAAAAATTCCAATTTTACTCTTGAACTTTCTAAA-AATTCAAGTTTTACCCTTAAA
1 CAAACCTTCCAAAAATTCAAATTTAACCCCTAAACTTTCCAAATAATTCAA-TTTTACCCTCAAA
* *
3108 TTTTCCAAAAATTCAAATTTAAACCTTG-AACTTT-TAAAAATTTGAATTTGATCCC
65 CTTTCCAAAAATTCAAATTTAAACCTTGAAACTTTCCAAAAATTTGAATTTGATCCC
* * *
3163 CAAACCTTCCAAAAATTCAAATTTAACCCCTAAACTTTCCAAATATTTGAATTTTACCCTCAAGC
1 CAAACCTTCCAAAAATTCAAATTTAACCCCTAAACTTTCCAAATAATTCAATTTTACCCTCAAAC
* * *
3228 TTTCCAAAAATTCCAATTTGACCCTTGAAACTTTCCAAAAATT
66 TTTCCAAAAATTCAAATTTAAACCTTGAAACTTTCCAAAAATT
3271 CAAATGTGAC
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
119 71 0.80
120 11 0.12
121 7 0.08
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (121 bp):
CAAACCTTCCAAAAATTCAAATTTAACCCCTAAACTTTCCAAATAATTCAATTTTACCCTCAAAC
TTTCCAAAAATTCAAATTTAAACCTTGAAACTTTCCAAAAATTTGAATTTGATCCC
Found at i:13754 original size:3 final size:3
Alignment explanation
Indices: 13746--13781 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
13736 AATACAACAT
*
13746 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13782 CTTTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19165 original size:50 final size:50
Alignment explanation
Indices: 19090--19266 Score: 166
Period size: 50 Copynumber: 3.6 Consensus size: 50
19080 ATGACGATAG
* * *
19090 AATGATAAATC-CTATACCCCTAAAGCTGTAGAGGAACGGATTGAAGCCGC
1 AATGACAAATCTC-ATACACCTAAAGCTGTAGAGGAACAGATTGAAGCCGC
* ***
19140 AATGACAAATCTCATACACCTAAAGCTGTAAAGGGGTAGATTGAAGCCGC
1 AATGACAAATCTCATACACCTAAAGCTGTAGAGGAACAGATTGAAGCCGC
* * *
19190 AATGGCAAATCTCATTCACCTAAAGCTGTTGAGAGGAA-A-ATTGAAGCTGC
1 AATGACAAATCTCATACACCTAAAGCTG-T-AGAGGAACAGATTGAAGCCGC
* * *
19240 AA-GAGC-AATCTTATACTCCTGAAGCTG
1 AATGA-CAAATCTCATACACCTAAAGCTG
19267 AAAAAGGGTA
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
49 18 0.17
50 80 0.76
51 3 0.03
52 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (50 bp):
AATGACAAATCTCATACACCTAAAGCTGTAGAGGAACAGATTGAAGCCGC
Found at i:19300 original size:99 final size:99
Alignment explanation
Indices: 19108--19300 Score: 221
Period size: 99 Copynumber: 1.9 Consensus size: 99
19098 ATCCTATACC
* * *
19108 CCTAAAGCTGTAGAGGAACGGATTGAAGCCGCAATGACAAATCTCATACACCTAAAGCTGTAAAG
1 CCTAAAGCTGTAGAGGAAC-AATTGAAGCCGCAATGACAAATCTCATACACCTAAAGCTGAAAAA
* * *
19173 GGGTAGATTGAAGCCGCAATGGCAAATCTCATTCA
65 GGGTAAATTGAAGCCACAATAGCAAATCTCATTCA
* * * *
19208 CCTAAAGCTGTTGAGAGGAA-AATTGAAGCTGCAA-GAGC-AATCTTATACTCCTGAAGCTGAAA
1 CCTAAAGCTG-T-AGAGGAACAATTGAAGCCGCAATGA-CAAATCTCATACACCTAAAGCTGAAA
* *
19270 AAGGGTAAATTGAATCTACAATAGCAAATCT
63 AAGGGTAAATTGAAGCCACAATAGCAAATCT
19301 TATACCCTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
99 47 0.60
100 23 0.29
101 1 0.01
102 7 0.09
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (99 bp):
CCTAAAGCTGTAGAGGAACAATTGAAGCCGCAATGACAAATCTCATACACCTAAAGCTGAAAAAG
GGTAAATTGAAGCCACAATAGCAAATCTCATTCA
Found at i:19313 original size:99 final size:98
Alignment explanation
Indices: 19096--19313 Score: 217
Period size: 99 Copynumber: 2.2 Consensus size: 98
19086 ATAGAATGAT
* *
19096 AAATCCTATACCCCTAAAGCTGTAGAGGAACGGATTGAAGCCGCAATGACAAATCTCATACACCT
1 AAATCTTATA-CCCTAAAGCTGTAGAGGAAC-AATTGAAGCCGCAATGACAAATCTCATACACCT
* * * * *
19161 AAAGCTGTAAAGGGGTAGATTGAAGCCGCAATGGC
64 AAAGCTGAAAAAGGGTAAATTGAAGCCACAATAGC
* * * * *
19196 AAATCTCATTCACCTAAAGCTGTTGAGAGGAA-AATTGAAGCTGCAA-GAGC-AATCTTATACTC
1 AAATCTTATAC-CCTAAAGCTG-T-AGAGGAACAATTGAAGCCGCAATGA-CAAATCTCATACAC
* * *
19258 CTGAAGCTGAAAAAGGGTAAATTGAATCTACAATAGC
62 CTAAAGCTGAAAAAGGGTAAATTGAAGCCACAATAGC
19295 AAATCTTATACCCTTAAAG
1 AAATCTTATACCC-TAAAG
19314 TTATGGAGGG
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
98 2 0.02
99 56 0.58
100 30 0.31
101 1 0.01
102 7 0.07
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (98 bp):
AAATCTTATACCCTAAAGCTGTAGAGGAACAATTGAAGCCGCAATGACAAATCTCATACACCTAA
AGCTGAAAAAGGGTAAATTGAAGCCACAATAGC
Found at i:19478 original size:39 final size:39
Alignment explanation
Indices: 19434--19726 Score: 223
Period size: 39 Copynumber: 7.4 Consensus size: 39
19424 AGAAGTCACT
*
19434 ATCCAATCTCTTACCCTGACCATGAGGCAGATTGAAGAA
1 ATCCAATCTTTTACCCTGACCATGAGGCAGATTGAAGAA
* * ** * *
19473 ATCCAATCTTTTACCATAATTA-GAGGGCATATTGAAGACC
1 ATCCAATCTTTTACCCTGACCATGA-GGCAGATTGAAGA-A
* * * *
19513 ATCCAATCTTTTACCCCGACCATGGGGCAGATTAAAGCA
1 ATCCAATCTTTTACCCTGACCATGAGGCAGATTGAAGAA
** * ** * * *
19552 ATCCAATCTTTTATGCTAAGTA-AAGGGAAGATTGAAGACC
1 ATCCAATCTTTTACCCTGACCATGA-GGCAGATTGAAGA-A
* * * * *
19592 ATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCA
1 ATCCAATCTTTTACCCTGACCATGAGGCAGATTGAAGAA
* * *
19631 ATCCAATCTTTTACCCTAATCA-GATGGCAGATTGAAGACC
1 ATCCAATCTTTTACCCTGACCATGA-GGCAGATTGAAGA-A
* * * * *
19671 ATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCA
1 ATCCAATCTTTTACCCTGACCATGAGGCAGATTGAAGAA
19710 ATCCAATCTTTTACCCT
1 ATCCAATCTTTTACCCT
19727 TAAAGCTATA
Statistics
Matches: 184, Mismatches: 61, Indels: 18
0.70 0.23 0.07
Matches are distributed among these distances:
38 3 0.02
39 98 0.53
40 81 0.44
41 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (39 bp):
ATCCAATCTTTTACCCTGACCATGAGGCAGATTGAAGAA
Found at i:19709 original size:158 final size:158
Alignment explanation
Indices: 19434--19722 Score: 479
Period size: 158 Copynumber: 1.8 Consensus size: 158
19424 AGAAGTCACT
* *
19434 ATCCAATCTCTTACCCTGACCATGAGGCAGATTGAAGAAATCCAATCTTTTACCATAATTAGAGG
1 ATCCAATCTCTTACCCCGACCATGAGGCAGATTGAAGAAATCCAATCTTTTACCATAATCAGAGG
* *
19499 GCATATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTT
66 GCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTT
19564 ATGCTAAGTAAAGGGAAGATTGAAGACC
131 ATGCTAAGTAAAGGGAAGATTGAAGACC
* * * * *
19592 ATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATCAGATG
1 ATCCAATCTCTTACCCCGACCATGAGGCAGATTGAAGAAATCCAATCTTTTACCATAATCAGAGG
* *
19657 GCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTT
66 GCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTT
19722 A
131 A
19723 CCCTTAAAGC
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
158 120 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (158 bp):
ATCCAATCTCTTACCCCGACCATGAGGCAGATTGAAGAAATCCAATCTTTTACCATAATCAGAGG
GCAGATTGAAGACCATCCAATCTCTTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTT
ATGCTAAGTAAAGGGAAGATTGAAGACC
Found at i:19725 original size:79 final size:78
Alignment explanation
Indices: 19434--19726 Score: 433
Period size: 79 Copynumber: 3.7 Consensus size: 78
19424 AGAAGTCACT
* * * *
19434 ATCCAATCTCTTACCCTGACCATGAGGCAGATTGAAGAAATCCAATCTTTTACCATAATTAGAGG
1 ATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAA-TAGAGG
*
19499 GCATATTGAAGACC
65 GCAGATTGAAGACC
* * ** *
19513 ATCCAATCTTTTACCCCGACCATGGGGCAGATTAAAGCAATCCAATCTTTTATGCTAAGTAAAGG
1 ATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAA-TAGAGG
*
19578 GAAGATTGAAGACC
65 GCAGATTGAAGACC
* *
19592 ATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATCAGATG
1 ATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAAT-AGAGG
19657 GCAGATTGAAGACC
65 GCAGATTGAAGACC
*
19671 ATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCT
1 ATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCT
19727 TAAAGCTATA
Statistics
Matches: 193, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
78 1 0.01
79 192 0.99
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (78 bp):
ATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATAGAGGG
CAGATTGAAGACC
Found at i:21238 original size:27 final size:28
Alignment explanation
Indices: 21203--21256 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
21193 AAGGAAAAGC
21203 TTTGATTTTGAGAGA-AAAAGAAATGGG
1 TTTGATTTTGAGAGAGAAAAGAAATGGG
* * *
21230 TTTGCTTTTTAGATAGAAAAGAAATGG
1 TTTGATTTTGAGAGAGAAAAGAAATGG
21257 AGAAAATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (28 bp):
TTTGATTTTGAGAGAGAAAAGAAATGGG
Found at i:23239 original size:2 final size:2
Alignment explanation
Indices: 23232--23256 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23222 TCACACCGCA
23232 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
23257 AAGAATTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24177 original size:40 final size:40
Alignment explanation
Indices: 24133--24324 Score: 253
Period size: 40 Copynumber: 4.8 Consensus size: 40
24123 ATAACCTTAC
24133 AGTGTTTACAGTGTCACTGCTAGTTCAATTGTAATATTGT
1 AGTGTTTACAGTGTCACTGCTAGTTCAATTGTAATATTGT
***
24173 AGTGTTTACAGTGTCACTGCTAGTTCAATTGTAATATCAC
1 AGTGTTTACAGTGTCACTGCTAGTTCAATTGTAATATTGT
* * * *
24213 AGTGTTTACAATGTCATTGCCAGTTCAATAGT-ATATTGT
1 AGTGTTTACAGTGTCACTGCTAGTTCAATTGTAATATTGT
* * *
24252 AGTGTTTTCAGTGTCACTGCTAGTTCAGTAGT-ATATTGT
1 AGTGTTTACAGTGTCACTGCTAGTTCAATTGTAATATTGT
* * *
24291 AGTGTTTACAGTGTCACTACCAATTCAATTGTAA
1 AGTGTTTACAGTGTCACTGCTAGTTCAATTGTAA
24325 CATTAGATAT
Statistics
Matches: 130, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 64 0.49
40 66 0.51
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (40 bp):
AGTGTTTACAGTGTCACTGCTAGTTCAATTGTAATATTGT
Found at i:24276 original size:79 final size:80
Alignment explanation
Indices: 24131--24324 Score: 248
Period size: 79 Copynumber: 2.5 Consensus size: 80
24121 TGATAACCTT
* * *
24131 ACAGTGTTTACAGTGTCACTGCTAGTTCAATTGTAATATTGTAGTGTTTACAGTGTCACTGCTAG
1 ACAGTGTTTACAATGTCACTGCCAGTTCAATAGTAATATTGTAGTGTTTACAGTGTCACTGCTAG
24196 TTCAATTGTAATATC
66 TTCAATTGTAATATC
* *
24211 ACAGTGTTTACAATGTCATTGCCAGTTCAATAGT-ATATTGTAGTGTTTTCAGTGTCACTGCTAG
1 ACAGTGTTTACAATGTCACTGCCAGTTCAATAGTAATATTGTAGTGTTTACAGTGTCACTGCTAG
* * *
24275 TTCAGTAGT-ATATT
66 TTCAATTGTAATATC
** * * * *
24289 GTAGTGTTTACAGTGTCACTACCAATTCAATTGTAA
1 ACAGTGTTTACAATGTCACTGCCAGTTCAATAGTAA
24325 CATTAGATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
78 31 0.32
79 37 0.38
80 30 0.31
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (80 bp):
ACAGTGTTTACAATGTCACTGCCAGTTCAATAGTAATATTGTAGTGTTTACAGTGTCACTGCTAG
TTCAATTGTAATATC
Found at i:27478 original size:13 final size:14
Alignment explanation
Indices: 27455--27483 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
27445 TTCCCATTTT
27455 TTCATTTTTTAGCA
1 TTCATTTTTTAGCA
27469 TTCA-TTTTTAGCA
1 TTCATTTTTTAGCA
27482 TT
1 TT
27484 TTTAACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (14 bp):
TTCATTTTTTAGCA
Found at i:27505 original size:20 final size:21
Alignment explanation
Indices: 27480--27518 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27470 TCATTTTTAG
*
27480 CATTTT-TAACTTAGTGATTA
1 CATTTTCTAACTCAGTGATTA
27500 CATTTTCTAACTCAGTGAT
1 CATTTTCTAACTCAGTGAT
27519 GCTTGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (21 bp):
CATTTTCTAACTCAGTGATTA
Found at i:29938 original size:28 final size:28
Alignment explanation
Indices: 29879--29938 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
29869 TATATAGACC
* *
29879 GATTATTTAACTAGTAGACGAAGTATAA
1 GATTATTTAACTAATAAACGAAGTATAA
29907 GATTATTTAACTACATAAAC-AA-TATAA
1 GATTATTTAACTA-ATAAACGAAGTATAA
29934 TGATT
1 -GATT
29939 TTTCTTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.18
28 19 0.68
29 4 0.14
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (28 bp):
GATTATTTAACTAATAAACGAAGTATAA
Found at i:31669 original size:40 final size:40
Alignment explanation
Indices: 31612--31768 Score: 183
Period size: 40 Copynumber: 4.0 Consensus size: 40
31602 AGTGATAAAC
* *
31612 TTGCAGTGTTTACAGTGTCACTATCGGTTC-GATTGTAATA
1 TTGCAGTGTTTACAGTGTCACTACCAGTTCAG-TTGTAATA
* *
31652 TTGCAGTGTTTATAGTGTCACTACCAGTTCAGCTGTAATA
1 TTGCAGTGTTTACAGTGTCACTACCAGTTCAGTTGTAATA
* * * * *
31692 TCGCAGTGTTTACAATGTCACTGCCAATTCAGTAGT-ATA
1 TTGCAGTGTTTACAGTGTCACTACCAGTTCAGTTGTAATA
* * *
31731 TTGCAGTGTTTACAGTGTCACTGCCAATTTAGTTGTAA
1 TTGCAGTGTTTACAGTGTCACTACCAGTTCAGTTGTAA
31769 CATATTTTAA
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 35 0.35
40 64 0.64
41 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCAGTGTTTACAGTGTCACTACCAGTTCAGTTGTAATA
Found at i:37094 original size:24 final size:22
Alignment explanation
Indices: 36997--37095 Score: 119
Period size: 22 Copynumber: 4.4 Consensus size: 22
36987 CGTTTCGTGC
36997 CCTCTGTTCAGCACTGTGTGTG
1 CCTCTGTTCAGCACTGTGTGTG
37019 CCTCTGTTCAGCACTGTGTGTG
1 CCTCTGTTCAGCACTGTGTGTG
* * *
37041 CTTCTGTTTAGCACTTTGTGTG
1 CCTCTGTTCAGCACTGTGTGTG
*
37063 CCTACTGTTGCCAGCACT-TATGTG
1 CCT-CTGTT--CAGCACTGTGTGTG
37087 CCCTCTGTT
1 -CCTCTGTT
37096 AAGTACTTCG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
22 43 0.64
23 5 0.07
24 10 0.15
25 9 0.13
ACGTcount: A:0.10, C:0.27, G:0.23, T:0.39
Consensus pattern (22 bp):
CCTCTGTTCAGCACTGTGTGTG
Found at i:40926 original size:26 final size:26
Alignment explanation
Indices: 40897--40987 Score: 112
Period size: 26 Copynumber: 3.5 Consensus size: 26
40887 ATAAAAGCGT
* *
40897 ACTCTATCTGGGCTTATGAGAGCTAA
1 ACTCTATTTGGGCTTATAAGAGCTAA
*
40923 ACTCTATTTGGGCTCATAAGAGCTAA
1 ACTCTATTTGGGCTTATAAGAGCTAA
* *
40949 ACTCTGTTTGGGCTT-TTAGAGCTAA
1 ACTCTATTTGGGCTTATAAGAGCTAA
* *
40974 AATCTGTTTGGGCT
1 ACTCTATTTGGGCT
40988 CGTATGAGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
25 22 0.38
26 36 0.62
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (26 bp):
ACTCTATTTGGGCTTATAAGAGCTAA
Found at i:41001 original size:25 final size:25
Alignment explanation
Indices: 40905--41000 Score: 111
Period size: 26 Copynumber: 3.7 Consensus size: 25
40895 GTACTCTATC
* *
40905 TGGGCTTATGAGAGCTAAACTCTATT
1 TGGGCTCAT-AGAGCTAAACTCTGTT
40931 TGGGCTCATAAGAGCTAAACTCTGTT
1 TGGGCTCAT-AGAGCTAAACTCTGTT
** *
40957 TGGGCTTTTAGAGCTAAAATCTGTT
1 TGGGCTCATAGAGCTAAACTCTGTT
*
40982 TGGGCTCGTATGAGCTAAA
1 TGGGCTCATA-GAGCTAAA
41001 TTTCTAGAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
25 23 0.38
26 38 0.62
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (25 bp):
TGGGCTCATAGAGCTAAACTCTGTT
Found at i:42317 original size:24 final size:24
Alignment explanation
Indices: 42283--42450 Score: 129
Period size: 24 Copynumber: 7.0 Consensus size: 24
42273 TTTTTACTTC
* *
42283 AGTAGCTGGCGAGCATAAACGCAT
1 AGTAGCTGGCGAGCATAAACGTAA
* * * * *
42307 ATTAGCTGGCGAGCGTAAATGCAT
1 AGTAGCTGGCGAGCATAAACGTAA
* * * *
42331 ATTAGCTAGAGAGCGTAAACGTAA
1 AGTAGCTGGCGAGCATAAACGTAA
* * * *
42355 AGTAGTTGACAAACATAAACGTAA
1 AGTAGCTGGCGAGCATAAACGTAA
* *
42379 AGTGGCTGACGAGCATAAACGTAA
1 AGTAGCTGGCGAGCATAAACGTAA
* *
42403 AGTGGCTGGCGAGCATAAACGTAT
1 AGTAGCTGGCGAGCATAAACGTAA
* * * *
42427 AGTGGCTGACAAGCATAAATGTAA
1 AGTAGCTGGCGAGCATAAACGTAA
42451 CTGAAACTTG
Statistics
Matches: 118, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 118 1.00
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (24 bp):
AGTAGCTGGCGAGCATAAACGTAA
Found at i:44996 original size:7 final size:7
Alignment explanation
Indices: 44986--45041 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
44976 ACCGTTGACC
44986 GACCGTT
1 GACCGTT
44993 GACCGTT
1 GACCGTT
45000 GACCGTT
1 GACCGTT
*
45007 TACCGTT
1 GACCGTT
* *
45014 TACTGTT
1 GACCGTT
**
45021 GAATGTT
1 GACCGTT
45028 GACCGTT
1 GACCGTT
45035 GACCGTT
1 GACCGTT
45042 AATTTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (7 bp):
GACCGTT
Found at i:45013 original size:21 final size:20
Alignment explanation
Indices: 44976--45041 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
44966 ACCAAGTCAA
44976 ACCGTTGACCG--ACCGTTG
1 ACCGTTGACCGTTACCGTTG
*
44994 ACCGTTGACCGTTTACCGTTT
1 ACCGTTGACCG-TTACCGTTG
* **
45015 ACTGTTGAATGTTGACCGTTG
1 ACCGTTGACCGTT-ACCGTTG
45036 ACCGTT
1 ACCGTT
45042 AATTTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 11 0.29
20 2 0.05
21 25 0.66
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (20 bp):
ACCGTTGACCGTTACCGTTG
Found at i:50047 original size:7 final size:7
Alignment explanation
Indices: 50038--50189 Score: 121
Period size: 7 Copynumber: 21.9 Consensus size: 7
50028 TTCATCAACT
*
50038 GTTGACT
1 GTTGACC
*
50045 GTTTACC
1 GTTGACC
50052 GTTGACC
1 GTTGACC
*
50059 GTTGAAC
1 GTTGACC
*
50066 ATTGA-C
1 GTTGACC
50072 GTTGACC
1 GTTGACC
* *
50079 ATTGATC
1 GTTGACC
50086 GTTGACC
1 GTTGACC
50093 GTTGACC
1 GTTGACC
*
50100 AATTGACC
1 -GTTGACC
*
50108 ATTGACC
1 GTTGACC
*
50115 GATGA-C
1 GTTGACC
50121 GTTGACC
1 GTTGACC
*
50128 ATTGACC
1 GTTGACC
* *
50135 ATTGATC
1 GTTGACC
*
50142 GTTGACT
1 GTTGACC
50149 GTTGACC
1 GTTGACC
50156 GTTGACC
1 GTTGACC
50163 GATTGA-C
1 G-TTGACC
* *
50170 TTTTACC
1 GTTGACC
50177 GTTGACC
1 GTTGACC
*
50184 GCTGAC
1 GTTGAC
50190 TTTGGCCATT
Statistics
Matches: 115, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
6 13 0.11
7 92 0.80
8 10 0.09
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (7 bp):
GTTGACC
Found at i:50113 original size:56 final size:56
Alignment explanation
Indices: 50049--50169 Score: 158
Period size: 56 Copynumber: 2.2 Consensus size: 56
50039 TTGACTGTTT
* *
50049 ACCG-TTGACCGTTGAACATTGA-CGTTGACCATTGATCGTTGACCGTTGACCAATTG
1 ACCGATTGACCGATG-ACATTGACCATTGACCATTGATCGTTGACCGTTGACC-ATTG
* * *
50105 ACC-ATTGACCGATGACGTTGACCATTGACCATTGATCGTTGACTGTTGACCGTTG
1 ACCGATTGACCGATGACATTGACCATTGACCATTGATCGTTGACCGTTGACCATTG
50160 ACCGATTGAC
1 ACCGATTGAC
50170 TTTTACCGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
55 12 0.21
56 45 0.79
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (56 bp):
ACCGATTGACCGATGACATTGACCATTGACCATTGATCGTTGACCGTTGACCATTG
Found at i:55180 original size:18 final size:18
Alignment explanation
Indices: 55134--55183 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
55124 AATCCCAGCA
**
55134 CAATTCCCATCACCACCT
1 CAATTCCCATTGCCACCT
*
55152 CAATTCACATTGCCACCT
1 CAATTCCCATTGCCACCT
55170 CAATTCCCATTGCC
1 CAATTCCCATTGCC
55184 TTACGGGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.26, C:0.44, G:0.04, T:0.26
Consensus pattern (18 bp):
CAATTCCCATTGCCACCT
Found at i:55494 original size:62 final size:60
Alignment explanation
Indices: 55374--55545 Score: 209
Period size: 62 Copynumber: 2.8 Consensus size: 60
55364 GCATTGATTT
* * *
55374 ATTTCGAATATTTTTGTAAACATTATTTTTTATAATGTTTCATTTAATAAAATAGAAGTTC
1 ATTT-GAATATTTTTGTACACATTATTTTTAATATTGTTTCATTTAATAAAATAGAAGTTC
* * *
55435 ATTTGAATATTTTTGTACACATTAGTTTTATCATATTGTATCATTTAATGAAATAGAAGTTC
1 ATTTGAATATTTTTGTACACATTA-TTTT-TAATATTGTTTCATTTAATAAAATAGAAGTTC
* * **
55497 TTTTAAATATTTTTCAACACATTATTTTTGGAATATTGTTTCATTTAAT
1 ATTTGAATATTTTTGTACACATTATTTTT--AATATTGTTTCATTTAAT
55546 TGAGAACCAA
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
60 20 0.21
61 12 0.12
62 64 0.67
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.50
Consensus pattern (60 bp):
ATTTGAATATTTTTGTACACATTATTTTTAATATTGTTTCATTTAATAAAATAGAAGTTC
Found at i:56545 original size:15 final size:15
Alignment explanation
Indices: 56521--56553 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
56511 GCTAAATGAT
56521 AAATAAATATATA-A
1 AAATAAATATATATA
56535 AAATAAAATATATATA
1 AAAT-AAATATATATA
56551 AAA
1 AAA
56554 AAGGGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 9 0.53
16 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAATATATATA
Found at i:57709 original size:11 final size:9
Alignment explanation
Indices: 57684--57722 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 9
57674 TACTTCTTTC
57684 AAAAATAAA
1 AAAAATAAA
57693 AAAAATAGAA
1 AAAAATA-AA
57703 AATAAATAGAA
1 AA-AAATA-AA
57714 AAAAATAAA
1 AAAAATAAA
57723 TATAAATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.32
10 9 0.32
11 10 0.36
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (9 bp):
AAAAATAAA
Found at i:57727 original size:20 final size:20
Alignment explanation
Indices: 57686--57729 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
57676 CTTCTTTCAA
57686 AAATAAAAAAAATAGAAAAT
1 AAATAAAAAAAATAGAAAAT
*
57706 AAATAGAAAAAAATA-AATAT
1 AAATA-AAAAAAATAGAAAAT
57726 AAAT
1 AAAT
57730 GTATATGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (20 bp):
AAATAAAAAAAATAGAAAAT
Found at i:58584 original size:24 final size:24
Alignment explanation
Indices: 58557--58634 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
58547 GATAAAAACC
*
58557 ATAAACATAGGCCCTAATTTGTAA
1 ATAAACATAGGCCCTAATTTGCAA
*
58581 ATAAACTTAGGCCCTAATTTGCAA
1 ATAAACATAGGCCCTAATTTGCAA
* *
58605 ATAAGCCTAGGCCCTAATTTGCAA
1 ATAAACATAGGCCCTAATTTGCAA
58629 ATAAAC
1 ATAAAC
58635 CACTAAGATG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.27
Consensus pattern (24 bp):
ATAAACATAGGCCCTAATTTGCAA
Found at i:59550 original size:12 final size:12
Alignment explanation
Indices: 59535--59577 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
59525 TATAATTTTG
59535 TTTTAATAAATA
1 TTTTAATAAATA
* *
59547 TTTTTACAGAATA
1 TTTTAATA-AATA
*
59560 TTTTAATAACTA
1 TTTTAATAAATA
59572 TTTTAA
1 TTTTAA
59578 AGTAGGATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (12 bp):
TTTTAATAAATA
Found at i:60123 original size:18 final size:19
Alignment explanation
Indices: 60107--60142 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
60097 TATTGGTATT
60107 AAATAAATTATTAGTATAA
1 AAATAAATTATTAGTATAA
*
60126 AAATAATTTA-TAGTATA
1 AAATAAATTATTAGTATA
60143 CATTGTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
AAATAAATTATTAGTATAA
Found at i:61758 original size:13 final size:13
Alignment explanation
Indices: 61742--61766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61732 AATTTTGTCA
61742 TTTTATTTATTTG
1 TTTTATTTATTTG
61755 TTTTATTTATTT
1 TTTTATTTATTT
61767 AACCTCTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTG
Found at i:61841 original size:11 final size:11
Alignment explanation
Indices: 61825--61864 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
61815 GCTCACCACA
61825 TTATTGCTATT
1 TTATTGCTATT
61836 TTATTGCTATTT
1 TTATTGCTA-TT
*
61848 TTTTTGTCTATT
1 TTATTG-CTATT
61860 TTATT
1 TTATT
61865 AAGTTGTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.36
12 13 0.52
13 3 0.12
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (11 bp):
TTATTGCTATT
Found at i:62798 original size:53 final size:52
Alignment explanation
Indices: 62728--62837 Score: 184
Period size: 53 Copynumber: 2.1 Consensus size: 52
62718 ACTTGGTTTA
* *
62728 AATTTAATTTGTGATCCTTTCTTGCATTTTGTATTCGTGTTTGGTTTAAATT
1 AATTTAACTTGCGATCCTTTCTTGCATTTTGTATTCGTGTTTGGTTTAAATT
*
62780 ATATTTAACTTGCGATCCTTTCTTGTATTTTGTATTCGTGTTTGGTTTAAATT
1 A-ATTTAACTTGCGATCCTTTCTTGCATTTTGTATTCGTGTTTGGTTTAAATT
62833 AATTT
1 AATTT
62838 TTTTATTAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 5 0.09
53 49 0.91
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.55
Consensus pattern (52 bp):
AATTTAACTTGCGATCCTTTCTTGCATTTTGTATTCGTGTTTGGTTTAAATT
Found at i:67651 original size:29 final size:28
Alignment explanation
Indices: 67581--67653 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
67571 CAAATACAAT
*
67581 TAATAACACAATAAAAATATAATTATAG
1 TAATAACACAATAAAAACATAATTATAG
* * * *
67609 TATTAAATAAAATAACAACATAATTATAG
1 TAAT-AACACAATAAAAACATAATTATAG
67638 TAATAACGACAATAAA
1 TAATAAC-ACAATAAA
67654 TATTAATTAA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (28 bp):
TAATAACACAATAAAAACATAATTATAG
Found at i:68862 original size:51 final size:52
Alignment explanation
Indices: 68705--68901 Score: 179
Period size: 51 Copynumber: 3.8 Consensus size: 52
68695 TTCTTTTTTA
*
68705 TTTTTT-TAGGGTGTAAGATTCGCCGTTGTGGCTTCAATCTGTTCCCTCTTT
1 TTTTTTATAGGGTGTAAGATTCGCCGTTGCGGCTTCAATCTGTTCCCTCTTT
** * * ** * * *
68756 GGTTTTA-A-GGTGTTAGATCCATCGTCGTGGCTTCAGTCT-TTCCCTCTTT
1 TTTTTTATAGGGTGTAAGATTCGCCGTTGCGGCTTCAATCTGTTCCCTCTTT
* * *
68805 GGTTTTTTATTGGGTCTAAGATTCGCCGTTGCGGCTTCAATTTGTTCCCT-TTT
1 --TTTTTTATAGGGTGTAAGATTCGCCGTTGCGGCTTCAATCTGTTCCCTCTTT
* * * * *
68858 TTTTTCAAAAGGTGTAAGATTCGCCATTGCAGCTTCAATCTGTT
1 TTTTTTATAGGGTGTAAGATTCGCCGTTGCGGCTTCAATCTGTT
68902 TCCTATTTGG
Statistics
Matches: 112, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
49 10 0.09
50 25 0.22
51 46 0.41
53 25 0.22
54 6 0.05
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.44
Consensus pattern (52 bp):
TTTTTTATAGGGTGTAAGATTCGCCGTTGCGGCTTCAATCTGTTCCCTCTTT
Found at i:68980 original size:49 final size:48
Alignment explanation
Indices: 68907--69265 Score: 211
Period size: 49 Copynumber: 7.3 Consensus size: 48
68897 CTGTTTCCTA
* * * *
68907 TTTGGTTTTAAGGTGTTAGATCCATCATCATGGCTTTAATCTATCCCTC
1 TTTGGTTTTAGGGTGTTAGGTCCATCAT-ATGGCTTCAACCTATCCCTC
* * *
68956 TTTGGTTTTAGGGTATTAGGTCCATCGTCATGGCTTCAACCTATCCTTC
1 TTTGGTTTTAGGGTGTTAGGTCCATCAT-ATGGCTTCAACCTATCCCTC
*** * * * * ** * *
69005 TTCCATTTTAAGGTGTAAGATCCGTCAT-TGCGACTTCAATTTTTTCCTC
1 TTTGGTTTTAGGGTGTTAGGTCCATCATATG-G-CTTCAACCTATCCCTC
* * * * *
69054 TTCGATTTTAGGGTGTTAGGTTCGTCGT-TGCAGCTTCAACCTATCCCTC
1 TTTGGTTTTAGGGTGTTAGGTCCATCATATG--GCTTCAACCTATCCCTC
** * * * * * * *
69103 TTCAGTTTTAAGGTGTAAGGTCTATCGTTACGGCTTTAACCTTTCCCTC
1 TTTGGTTTTAGGGTGTTAGGTCCATC-ATATGGCTTCAACCTATCCCTC
* * * * * *
69152 TTTGGTTTTAGGGTGTTAGATTCACCATTGTGGCTTTAATCTATCCCTC
1 TTTGGTTTTAGGGTGTTAGGTCCATCA-TATGGCTTCAACCTATCCCTC
* * * * *
69201 TTTGATTTTAGGATGTTAGGTCCATCGTTACGACTTCAACCTATCCCTC
1 TTTGGTTTTAGGGTGTTAGGTCCATC-ATATGGCTTCAACCTATCCCTC
*
69250 -TTGAGTTTTAAGGTGT
1 TTTG-GTTTTAGGGTGT
69266 AAGATTTGTC
Statistics
Matches: 232, Mismatches: 70, Indels: 16
0.73 0.22 0.05
Matches are distributed among these distances:
47 2 0.01
48 4 0.02
49 223 0.96
50 2 0.01
51 1 0.00
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (48 bp):
TTTGGTTTTAGGGTGTTAGGTCCATCATATGGCTTCAACCTATCCCTC
Found at i:69099 original size:147 final size:147
Alignment explanation
Indices: 68947--69268 Score: 333
Period size: 147 Copynumber: 2.2 Consensus size: 147
68937 TGGCTTTAAT
* * * *
68947 CTATCCCTCTTTGGTTTTAGGGTATTAGGTCCATCGTCATGGCTTCAACCTATCCTTCTTCCATT
1 CTATCCCTCTTTGGTTTTAAGGTATAAGGTCCATCGTCACGGCTTCAACCTATCCCTCTTCCATT
** * * * * *
69012 TTAAGGTGTAAGATCCGTCATTGCGACTTCAATTTTTTCCTCTTCGATTTTAGGGTGTTAGGTTC
66 TTAAGGTGTAAGATCCACCATTGCGACTTCAATCTATCCCTCTTCGATTTTAGGATGTTAGGTCC
* *
69077 GTCGTTGC-AGCTTCAAC
131 ATCGTTACGA-CTTCAAC
** * * * * * ***
69094 CTATCCCTCTTCAGTTTTAAGGTGTAAGGTCTATCGTTACGGCTTTAACCTTTCCCTCTTTGGTT
1 CTATCCCTCTTTGGTTTTAAGGTATAAGGTCCATCGTCACGGCTTCAACCTATCCCTCTTCCATT
* * * * * * *
69159 TTAGGGTGTTAGATTCACCATTGTGGCTTTAATCTATCCCTCTTTGATTTTAGGATGTTAGGTCC
66 TTAAGGTGTAAGATCCACCATTGCGACTTCAATCTATCCCTCTTCGATTTTAGGATGTTAGGTCC
69224 ATCGTTACGACTTCAAC
131 ATCGTTACGACTTCAAC
*
69241 CTATCCCTC-TTGAGTTTTAAGGTGTAAG
1 CTATCCCTCTTTG-GTTTTAAGGTATAAG
69269 ATTTGTCGTT
Statistics
Matches: 141, Mismatches: 32, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
146 1 0.01
147 139 0.99
148 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (147 bp):
CTATCCCTCTTTGGTTTTAAGGTATAAGGTCCATCGTCACGGCTTCAACCTATCCCTCTTCCATT
TTAAGGTGTAAGATCCACCATTGCGACTTCAATCTATCCCTCTTCGATTTTAGGATGTTAGGTCC
ATCGTTACGACTTCAAC
Found at i:69196 original size:98 final size:98
Alignment explanation
Indices: 68911--69271 Score: 298
Period size: 98 Copynumber: 3.7 Consensus size: 98
68901 TTCCTATTTG
* * * * * * * *
68911 GTTTTAAGGTGTTAGATCCATCATCATGGCTTTAATCTATCCCTCTTTGGTTTTAGGGTATTAGG
1 GTTTTAAGGTGTAAGATCCATCATTACGACTTCAACCTATCCCTCTTTGGTTTTAGGGTGTTAGA
* ** *
68976 TCCATCGTCATGGCTTCAACCTATCCTTCTTCCA
66 TTCATCGTTGTGGCTTCAACCTATCCCTCTT-CA
* * ** * * * * *
69010 -TTTTAAGGTGTAAGATCCGTCATTGCGACTTCAATTTTTTCCTCTTCGATTTTAGGGTGTTAGG
1 GTTTTAAGGTGTAAGATCCATCATTACGACTTCAACCTATCCCTCTTTGGTTTTAGGGTGTTAGA
* **
69074 TTCGTCGTTGCAGCTTCAACCTATCCCTCTTCA
66 TTCATCGTTGTGGCTTCAACCTATCCCTCTTCA
* * * * * *
69107 GTTTTAAGGTGTAAGGTCTATCGTTACGGCTTTAACCTTTCCCTCTTTGGTTTTAGGGTGTTAGA
1 GTTTTAAGGTGTAAGATCCATCATTACGACTTCAACCTATCCCTCTTTGGTTTTAGGGTGTTAGA
* * * * *
69172 TTCACCATTGTGGCTTTAATCTATCCCTCTT-T
66 TTCATCGTTGTGGCTTCAACCTATCCCTCTTCA
* * * * *
69204 GATTTT-AGGATGTTAGGTCCATCGTTACGACTTCAACCTATCCCTC-TTGAGTTTTAAGGTGTA
1 G-TTTTAAGG-TGTAAGATCCATCATTACGACTTCAACCTATCCCTCTTTG-GTTTTAGGGTGTT
69267 AGATT
63 AGATT
69272 TGTCGTTGCA
Statistics
Matches: 210, Mismatches: 48, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
97 9 0.04
98 201 0.96
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (98 bp):
GTTTTAAGGTGTAAGATCCATCATTACGACTTCAACCTATCCCTCTTTGGTTTTAGGGTGTTAGA
TTCATCGTTGTGGCTTCAACCTATCCCTCTTCA
Found at i:69291 original size:98 final size:99
Alignment explanation
Indices: 68868--69300 Score: 283
Period size: 98 Copynumber: 4.4 Consensus size: 99
68858 TTTTTCAAAA
* * * * * * * * *
68868 GGTGTAAGATTCGCCATTGCAGCTTCAATCTGTTTCCTATTT-GGTTTTAAGGTGTTAGATCCAT
1 GGTGTTAGATTCGTCGTTGCAGCTTCAATCT-ATCCCTCTTTCAGTTTTAAGGTGTAAGGTCCAT
* * * * * *
68932 CATCATGGCTTTAATCTATCCCTCTTTG-GTTTTAG
65 CGTTACGACTTCAACCTATCCCTC-TTGAGTTTTAG
* * * * * * * * *
68967 GGTATTAGGTCCATCG-T-CATGGCTTCAACCTATCCTTCTTCCA-TTTTAAGGTGTAAGATCCG
1 GGTGTTAGATTCGTCGTTGCA--GCTTCAATCTATCCCTCTTTCAGTTTTAAGGTGTAAGGTCCA
* * ** * *
69029 TCATTGCGACTTCAATTTTTTCCTCTTCGA-TTTTAG
64 TCGTTACGACTTCAACCTATCCCTCTT-GAGTTTTAG
* * *
69065 GGTGTTAGGTTCGTCGTTGCAGCTTCAACCTATCCCTC-TTCAGTTTTAAGGTGTAAGGTCTATC
1 GGTGTTAGATTCGTCGTTGCAGCTTCAATCTATCCCTCTTTCAGTTTTAAGGTGTAAGGTCCATC
* * *
69129 GTTACGGCTTTAACCTTTCCCTCTTTG-GTTTTAG
66 GTTACGACTTCAACCTATCCCTC-TTGAGTTTTAG
** * ** * * *
69163 GGTGTTAGATTCACCATTGTGGCTTTAATCTATCCCTCTTTGA-TTTT-AGGATGTTAGGTCCAT
1 GGTGTTAGATTCGTCGTTGCAGCTTCAATCTATCCCTCTTTCAGTTTTAAGG-TGTAAGGTCCAT
*
69226 CGTTACGACTTCAACCTATCCCTCTTGAGTTTTAA
65 CGTTACGACTTCAACCTATCCCTCTTGAGTTTTAG
* * * * *
69261 GGTGTAAGATTTGTCGTTGCAACTTGAATCTTTCCCTCTT
1 GGTGTTAGATTCGTCGTTGCAGCTTCAATCTATCCCTCTT
69301 CGAAAAAGTT
Statistics
Matches: 257, Mismatches: 64, Indels: 27
0.74 0.18 0.08
Matches are distributed among these distances:
97 13 0.05
98 218 0.85
99 24 0.09
100 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.41
Consensus pattern (99 bp):
GGTGTTAGATTCGTCGTTGCAGCTTCAATCTATCCCTCTTTCAGTTTTAAGGTGTAAGGTCCATC
GTTACGACTTCAACCTATCCCTCTTGAGTTTTAG
Found at i:71558 original size:23 final size:23
Alignment explanation
Indices: 71530--71604 Score: 111
Period size: 23 Copynumber: 3.3 Consensus size: 23
71520 TGCTGGACAA
71530 CAGTAAGCACACACAGTGCTGAT
1 CAGTAAGCACACACAGTGCTGAT
71553 CAGTAAG--CACACAGTGC-GAAT
1 CAGTAAGCACACACAGTGCTG-AT
*
71574 CAGTAAGCACACACAGTGCTGAA
1 CAGTAAGCACACACAGTGCTGAT
71597 CAGTAAGC
1 CAGTAAGC
71605 GTGCTAGTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
20 1 0.02
21 19 0.40
23 26 0.55
24 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCTGAT
Found at i:73532 original size:13 final size:14
Alignment explanation
Indices: 73512--73546 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
73502 ATTGTTATGC
*
73512 ATTATAAATAATAT
1 ATTATAAATAACAT
73526 A-TATAAATAACAT
1 ATTATAAATAACAT
73539 ATTATAAA
1 ATTATAAA
73547 AAATTATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTATAAATAACAT
Found at i:75974 original size:51 final size:51
Alignment explanation
Indices: 75908--76008 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
75898 TAAATATCGG
*
75908 GCCTTGAGCCGGTGACATTTAG-CAGGTTTCGAGCC-GATGATTAAATAGCAT
1 GCCTTGAGCCGGTGACATTT-GTCAGGCTTCGAGCCAG-TGATTAAATAGCAT
75959 GCCTTGAGCCGGTGACATTTGTCAGGCTTCGAGCCAGTGATTAAATAGCA
1 GCCTTGAGCCGGTGACATTTGTCAGGCTTCGAGCCAGTGATTAAATAGCA
76009 GGCTGATGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
50 1 0.02
51 45 0.96
52 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (51 bp):
GCCTTGAGCCGGTGACATTTGTCAGGCTTCGAGCCAGTGATTAAATAGCAT
Done.