Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 335 of 335
Found at i:97832542 original size:20 final size:18
Alignment explanation
Indices: 97832500--97832561 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
97832490 AACGATTAAT
97832500 ATATATATATAAAACATA
1 ATATATATATAAAACATA
* *
97832518 CTATATGATATAATAACTTA
1 ATATAT-ATATAA-AACATA
*
97832538 ATATATTTATAAAA-ATA
1 ATATATATATAAAACATA
97832555 ATA-ATAT
1 ATATATAT
97832562 GTTAAATAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 7 0.19
19 11 0.31
20 10 0.28
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATATATATAAAACATA
Found at i:97832693 original size:7 final size:7
Alignment explanation
Indices: 97832681--97832716 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
97832671 TTATATGTAC
97832681 TAATAAA
1 TAATAAA
97832688 TAATAAA
1 TAATAAA
97832695 TAATAAAA
1 TAAT-AAA
*
97832703 TAATATA
1 TAATAAA
97832710 TAATAAA
1 TAATAAA
97832717 ATGAAGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAATAAA
Found at i:97832705 original size:15 final size:15
Alignment explanation
Indices: 97832681--97832718 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
97832671 TTATATGTAC
97832681 TAAT-AAATAATAAA
1 TAATAAAATAATAAA
*
97832695 TAATAAAATAATATA
1 TAATAAAATAATAAA
97832710 TAATAAAAT
1 TAATAAAAT
97832719 GAAGATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATAAAATAATAAA
Found at i:97832747 original size:7 final size:7
Alignment explanation
Indices: 97832735--97832796 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
97832725 AATATAGGGA
97832735 ATAATAT
1 ATAATAT
97832742 ATAATA-
1 ATAATAT
97832748 A-AATAT
1 ATAATAT
97832754 ATAATAT
1 ATAATAT
97832761 ATAAT-T
1 ATAATAT
**
97832767 A-AAGCT
1 ATAATAT
97832773 ATAA-AT
1 ATAATAT
*
97832779 AAAATAT
1 ATAATAT
*
97832786 ATAAAAT
1 ATAATAT
97832793 ATAA
1 ATAA
97832797 ATAACATGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
5 6 0.13
6 10 0.22
7 29 0.64
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (7 bp):
ATAATAT
Found at i:97832775 original size:19 final size:19
Alignment explanation
Indices: 97832735--97832776 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
97832725 AATATAGGGA
*
97832735 ATAATATATAATAAAATAT
1 ATAATATATAATAAAAGAT
* *
97832754 ATAATATATAATTAAAGCT
1 ATAATATATAATAAAAGAT
97832773 ATAA
1 ATAA
97832777 ATAAAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAATATATAATAAAAGAT
Found at i:97832785 original size:23 final size:22
Alignment explanation
Indices: 97832734--97832812 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 22
97832724 TAATATAGGG
*
97832734 AATAATATATAA-TAAAATAT-
1 AATAAAATATAATTAAAATATA
* *
97832754 -ATAATATATAATTAAAGCTATA
1 AATAAAATATAATTAAA-ATATA
97832776 AATAAAATAT-A-TAAAATATA
1 AATAAAATATAATTAAAATATA
*
97832796 AATAACATGATAATTAA
1 AATAAAAT-ATAATTAA
97832813 TACGTAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
19 11 0.23
20 15 0.31
21 9 0.19
22 2 0.04
23 11 0.23
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (22 bp):
AATAAAATATAATTAAAATATA
Found at i:97832874 original size:19 final size:19
Alignment explanation
Indices: 97832852--97832889 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
97832842 TTTTACATGT
*
97832852 ATAAATAATATTTATAAAA
1 ATAAATAATATATATAAAA
97832871 ATAAATAATATATATAAAA
1 ATAAATAATATATATAAAA
97832890 TATTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAATAATATATATAAAA
Found at i:97832910 original size:26 final size:30
Alignment explanation
Indices: 97832858--97832918 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
97832848 ATGTATAAAT
97832858 AATATTTATAAAAATAAATAATATATATAA
1 AATATTTATAAAAATAAATAATATATATAA
*
97832888 AATATTTAAAAAAATAAAT--TATATATAA
1 AATATTTATAAAAATAAATAATATATATAA
97832916 AAT
1 AAT
97832919 GTATGTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 12 0.40
30 18 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AATATTTATAAAAATAAATAATATATATAA
Found at i:97832917 original size:17 final size:17
Alignment explanation
Indices: 97832864--97832935 Score: 57
Period size: 17 Copynumber: 4.5 Consensus size: 17
97832854 AAATAATATT
*
97832864 TATAAAAATAAATAATA
1 TATAAAAATAAATTATA
97832881 TATATAAAAT--ATT-TA
1 TATA-AAAATAAATTATA
97832896 -A-AAAAATAAATTATA
1 TATAAAAATAAATTATA
**
97832911 TAT-AAAATGTATGTATA
1 TATAAAAATAAAT-TATA
97832928 TATAAAAA
1 TATAAAAA
97832936 GATTAAGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
12 5 0.11
13 1 0.02
14 4 0.09
15 4 0.09
16 10 0.23
17 11 0.25
18 9 0.20
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TATAAAAATAAATTATA
Found at i:97834578 original size:45 final size:45
Alignment explanation
Indices: 97834529--97834808 Score: 193
Period size: 45 Copynumber: 6.2 Consensus size: 45
97834519 CGAATGTCAG
*
97834529 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * *
97834574 ATCTG-TCATCTTCGATCTGCT--TCGATGTAA-ACACACGAATGTCAG
1 ATCTGCT-ATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAA
* * *
97834619 ATCTGCTATCTTCGATCTACTCTCCGTCTAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * * * * *
97834664 AACTG-TCATCTTCAATCTACT--TCGATGTAA-ACACACGAATGTCAG
1 ATCTGCT-ATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAA
*
97834709 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * *
97834754 ATCTG-TCATCTTCAATTTGTTCCCTGTC-AAGACAGAGATGCCAA
1 ATCTGCT-ATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
*
97834798 ATTTGCTATCT
1 ATCTGCTATCT
97834809 ACATTGTCCC
Statistics
Matches: 180, Mismatches: 37, Indels: 37
0.71 0.15 0.15
Matches are distributed among these distances:
43 12 0.07
44 35 0.19
45 109 0.61
46 12 0.07
47 12 0.07
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:97834769 original size:90 final size:90
Alignment explanation
Indices: 97834365--97834766 Score: 594
Period size: 90 Copynumber: 4.5 Consensus size: 90
97834355 AATATTCTTA
** * * *
97834365 ATCTGCTCCTTGTCAAATACAGAGACGCCAAATCTGTCATCTTTGATCTGCTTCGATG-CAA-AC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
* *
97834428 ACGAATGTCAGAT-TCGTTATCTTTG
66 ACGAATGTCAGATCT-GCTATCTTCG
* * * * * *
97834453 ATCTTCTCCCTGCCTAATACAGAGACGCCAAACCTGTCATTTTCGATCTGCTTCAATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
*
97834518 ACGAATGTCAGATCTGCTATCTTTG
66 ACGAATGTCAGATCTGCTATCTTCG
*
97834543 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
97834608 ACGAATGTCAGATCTGCTATCTTCG
66 ACGAATGTCAGATCTGCTATCTTCG
* * * * *
97834633 ATCTACTCTCCGTCTAATACAGAGACGCCAAAACTGTCATCTTCAATCTACTTCGATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
97834698 ACGAATGTCAGATCTGCTATCTTCG
66 ACGAATGTCAGATCTGCTATCTTCG
97834723 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTC
97834767 AATTTGTTCC
Statistics
Matches: 284, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
88 50 0.18
89 2 0.01
90 231 0.81
91 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (90 bp):
ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
ACGAATGTCAGATCTGCTATCTTCG
Found at i:97835690 original size:13 final size:13
Alignment explanation
Indices: 97835674--97835698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
97835664 CCATTTTTAT
97835674 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
97835687 TTTTTTCTTTTT
1 TTTTTTCTTTTT
97835699 TAGAAGTCTC
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:97839921 original size:46 final size:46
Alignment explanation
Indices: 97839871--97840042 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
97839861 TGAGCATCCA
97839871 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * * * *
97839917 AACTCGTTGGGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG
* *
97839964 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* *
97840010 AGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
97840043 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 57 0.55
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:97840024 original size:93 final size:93
Alignment explanation
Indices: 97839864--97840035 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
97839854 GGATGGTTGA
* * *
97839864 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGGGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
97839929 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
97839957 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
97840022 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
97840036 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:97844286 original size:41 final size:41
Alignment explanation
Indices: 97844210--97844501 Score: 338
Period size: 41 Copynumber: 7.1 Consensus size: 41
97844200 GCAAAAATTG
* * * ** *
97844210 TAAAACACAGAGCAATAGAGGCG-TTTTATTAAAAACGCCAC
1 TAAAAGACGGAGCAATAGCGGCGCTTTTGGT-AAAACGCCGC
* * * *
97844251 TAAAA-ACAGAGCAATAGTGGCGTTTTTTGTTAAAACGCCGC
1 TAAAAGACGGAGCAATAGCGGCG-CTTTTGGTAAAACGCCGC
**
97844292 TAAAA-ATAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* * * * *
97844332 AAAAAGTCGGAGCATTAGCGGCGCTTTTTGTAAAACGCTGC
1 TAAAAGACGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* *
97844373 TAAAAGTCGGAGCAATAGCGGCGCTTTTGGTAAAACGCCAC
1 TAAAAGACGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* *
97844414 TAAAAGTCGGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* *
97844455 TAAAAGTCGGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
97844496 TAAAAG
1 TAAAAG
97844502 TCATATAACC
Statistics
Matches: 227, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
40 36 0.16
41 185 0.81
42 6 0.03
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (41 bp):
TAAAAGACGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
Found at i:97844360 original size:82 final size:82
Alignment explanation
Indices: 97844219--97844503 Score: 387
Period size: 82 Copynumber: 3.5 Consensus size: 82
97844209 GTAAAACACA
* ** * * * * * *
97844219 GAGCAATAGAGGCG-TTTTATTAAAAACGCCACTAAAA-ACAGAGCAATAGTGGCGTTTTTTGTT
1 GAGCAATAGCGGCGCTTTTGGT-AAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGCTTTTTG-T
* *
97844282 AAAACGCCGCTAAAAAT-A
64 AAAACGCCGCTAAAAGTCG
*
97844300 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCAAAAAGTCGGAGCATTAGCGGCGCTTTTTGTAA
1 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGCTTTTTGTAA
*
97844365 AACGCTGCTAAAAGTCG
66 AACGCCGCTAAAAGTCG
* *
97844382 GAGCAATAGCGGCGCTTTTGGTAAAACGCCACTAAAAGTCGGAGCATTAGCGGCGCTTTTGGTAA
1 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGCTTTTTGTAA
97844447 AACGCCGCTAAAAGTCG
66 AACGCCGCTAAAAGTCG
*
97844464 GAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
1 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
97844504 ATATAACCCC
Statistics
Matches: 182, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
81 42 0.23
82 140 0.77
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (82 bp):
GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGCTTTTTGTAA
AACGCCGCTAAAAGTCG
Found at i:97844447 original size:123 final size:123
Alignment explanation
Indices: 97844241--97844503 Score: 386
Period size: 123 Copynumber: 2.1 Consensus size: 123
97844231 CGTTTTATTA
* * * * * * *
97844241 AAAACGCCACTAAAA-ACAGAGCAATAGTGGCGTTTTTTGTTAAAACGCCGCTAAAAATAGAGCA
1 AAAACGCCGCTAAAAGTCGGAGCAATAGCGGCGTCTTTTGGTAAAACGCCACTAAAAATAGAGCA
*
97844305 ATAGCGGCGCTTTTGGTAAAACGCCGCAAAAAGTCGGAGCATTAGCGGCGCTTTTTGT
66 ATAGCGGCGCTTTTGGTAAAACGCCGCAAAAAGTCGGAGCATTAGCGGCGCTTTTGGT
* * *
97844363 AAAACGCTGCTAAAAGTCGGAGCAATAGCGGCG-CTTTTGGTAAAACGCCACTAAAAGTCGGAGC
1 AAAACGCCGCTAAAAGTCGGAGCAATAGCGGCGTCTTTTGGTAAAACGCCACTAAAAAT-AGAGC
* *
97844427 ATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGCTTTTGGT
65 AATAGCGGCGCTTTTGGTAAAACGCCGCAAAAAGTCGGAGCATTAGCGGCGCTTTTGGT
97844486 AAAACGCCGCTAAAAGTC
1 AAAACGCCGCTAAAAGTC
97844504 ATATAACCCC
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
122 34 0.27
123 91 0.73
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (123 bp):
AAAACGCCGCTAAAAGTCGGAGCAATAGCGGCGTCTTTTGGTAAAACGCCACTAAAAATAGAGCA
ATAGCGGCGCTTTTGGTAAAACGCCGCAAAAAGTCGGAGCATTAGCGGCGCTTTTGGT
Found at i:97844502 original size:41 final size:41
Alignment explanation
Indices: 97844275--97844503 Score: 370
Period size: 41 Copynumber: 5.6 Consensus size: 41
97844265 TAGTGGCGTT
* * * *
97844275 TTTTGTTAAAACGCCGCTAAAAAT-AGAGCAATAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGC
*
97844315 TTTTGGTAAAACGCCGCAAAAAGTCGGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGC
* * *
97844356 TTTTTGTAAAACGCTGCTAAAAGTCGGAGCAATAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGC
*
97844397 TTTTGGTAAAACGCCACTAAAAGTCGGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGC
97844438 TTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGC
97844479 TTTTGGTAAAACGCCGCTAAAAGTC
1 TTTTGGTAAAACGCCGCTAAAAGTC
97844504 ATATAACCCC
Statistics
Matches: 174, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 21 0.12
41 153 0.88
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (41 bp):
TTTTGGTAAAACGCCGCTAAAAGTCGGAGCATTAGCGGCGC
Found at i:97845533 original size:20 final size:19
Alignment explanation
Indices: 97845505--97845544 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
97845495 AAAGAAAAAG
* *
97845505 AATAGAAAAAATATGTTAAA
1 AATAAAAAAAAAAT-TTAAA
97845525 AATAAAAAAAAAATTTAAA
1 AATAAAAAAAAAATTTAAA
97845544 A
1 A
97845545 TTAAGCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AATAAAAAAAAAATTTAAA
Found at i:97863930 original size:67 final size:63
Alignment explanation
Indices: 97863818--97863940 Score: 165
Period size: 67 Copynumber: 1.9 Consensus size: 63
97863808 TACTTTAACA
** *
97863818 ATTTATGCAAATATAATATAGAAAATGATAAATAACGACATAAATTACATAATATACATTATC
1 ATTTATGCAAATATAATATAGAAAACAATAAATAACAACATAAATTACATAATATACATTATC
* *
97863881 ATTTCATGCAGATATAATCATAGAAAACAATGAATATAACAATATAAATTACATAATATA
1 ATTT-ATGCAAATATAAT-ATAGAAAACAAT-AA-ATAACAACATAAATTACATAATATA
97863941 TATACAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 4 0.08
64 12 0.24
65 10 0.20
66 2 0.04
67 23 0.45
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.31
Consensus pattern (63 bp):
ATTTATGCAAATATAATATAGAAAACAATAAATAACAACATAAATTACATAATATACATTATC
Found at i:97863967 original size:71 final size:64
Alignment explanation
Indices: 97863818--97863968 Score: 162
Period size: 71 Copynumber: 2.3 Consensus size: 64
97863808 TACTTTAACA
** * *
97863818 ATTT-ATGCAAATATAATATAGAAAATGATAAATAACGACATAAATTACATAATATACATTATC
1 ATTTCATGCAAATATAATATAGAAAACAATAAATAACAACATAAATTACATAATATACATAATC
* *
97863881 ATTTCATGCAGATATAATCATAGAAAACAATGAATATAACAATATAAATTACATAATATATATAC
1 ATTTCATGCAAATATAAT-ATAGAAAACAAT-AA-ATAACAACATAAATTAC---ATA-ATATAC
97863946 AATAAT-
59 -ATAATC
97863952 ATTTCATGCAAATATAA
1 ATTTCATGCAAATATAA
97863969 CTTAAAATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
63 4 0.06
64 12 0.17
65 10 0.14
66 2 0.03
67 15 0.21
70 3 0.04
71 22 0.31
72 4 0.06
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (64 bp):
ATTTCATGCAAATATAATATAGAAAACAATAAATAACAACATAAATTACATAATATACATAATC
Found at i:97864293 original size:19 final size:18
Alignment explanation
Indices: 97864246--97864306 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
97864236 TGATATATAT
97864246 ATATATATATAAAACATA
1 ATATATATATAAAACATA
* * *
97864264 CTATATGTATAATAACTTA
1 ATATATATATAA-AACATA
*
97864283 ATATATTTATAAAA-ATA
1 ATATATATATAAAACATA
97864300 ATA-ATAT
1 ATATATAT
97864307 GTTACATAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
16 3 0.09
17 5 0.14
18 12 0.34
19 15 0.43
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATATATATAAAACATA
Found at i:97864439 original size:7 final size:7
Alignment explanation
Indices: 97864427--97864480 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
97864417 TTATATGTAT
97864427 TAATAAA
1 TAATAAA
97864434 TAATAAA
1 TAATAAA
*
97864441 TAAAAAA
1 TAATAAA
*
97864448 TAATATA
1 TAATAAA
97864455 TAAT-AA
1 TAATAAA
*
97864461 -AATATA
1 TAATAAA
*
97864467 TAATATA
1 TAATAAA
97864474 TAATAAA
1 TAATAAA
97864481 AGCTATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 3 0.08
6 2 0.05
7 34 0.87
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAATAAA
Found at i:97864466 original size:12 final size:12
Alignment explanation
Indices: 97864449--97864501 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
97864439 AATAAAAAAT
97864449 AATATATAATAA
1 AATATATAATAA
97864461 AATATATAAT-A
1 AATATATAATAA
*
97864472 TATA-ATAA-AA
1 AATATATAATAA
**
97864482 GCTATA-AATAA
1 AATATATAATAA
97864493 AATATATAA
1 AATATATAA
97864502 AATATAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
10 9 0.28
11 11 0.34
12 12 0.38
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (12 bp):
AATATATAATAA
Found at i:97864478 original size:14 final size:14
Alignment explanation
Indices: 97864427--97864552 Score: 59
Period size: 14 Copynumber: 9.4 Consensus size: 14
97864417 TTATATGTAT
* *
97864427 TAATAAATAATAAA
1 TAATATATAATATA
* *
97864441 TAAAAAATAATATA
1 TAATATATAATATA
97864455 TAATA-A-AATATA
1 TAATATATAATATA
97864467 TAATATATAATA-A
1 TAATATATAATATA
**
97864480 -AAGCTATAA-ATA
1 TAATATATAATATA
* *
97864492 AAATATATAAAATA
1 TAATATATAATATA
* * *
97864506 TAAATAACATGATAAA
1 T-AAT-ATATAATATA
*
97864522 TAATACATAA-ATA
1 TAATATATAATATA
* *
97864535 -AAAATATTATATA
1 TAATATATAATATA
97864548 TAATA
1 TAATA
97864553 ATTTTACATG
Statistics
Matches: 85, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
11 1 0.01
12 25 0.29
13 15 0.18
14 31 0.36
15 6 0.07
16 7 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
TAATATATAATATA
Found at i:97864647 original size:19 final size:19
Alignment explanation
Indices: 97864440--97864649 Score: 82
Period size: 19 Copynumber: 11.3 Consensus size: 19
97864430 TAAATAATAA
*
97864440 ATAAAAAATA-ATATATA-
1 ATAAAATATATATATATAT
97864457 ATAAAATATATA-ATATAT
1 ATAAAATATATATATATAT
* *
97864475 AATAAAAGCTATAAATAAAATAT
1 -ATAAAA--TATATAT-ATATAT
* *
97864498 ATAAAATATAAATA-ACAT
1 ATAAAATATATATATATAT
* *
97864516 GAT-AAATA-ATACATAAAT
1 -ATAAAATATATATATATAT
97864534 A-AAAATAT-TATATATA-
1 ATAAAATATATATATATAT
* * * * *
97864550 AT-AATTTTACATGTATAA
1 ATAAAATATATATATATAT
* * * * *
97864568 ATAATATTTATAAAAATAA
1 ATAAAATATATATATATAT
* *
97864587 ATAATATATATA-AAATAT
1 ATAAAATATATATATATAT
* * * *
97864605 TTAAAATAAATAAATTACAT
1 ATAAAATATATATA-TATAT
97864625 ATAAAATATATATATATAT
1 ATAAAATATATATATATAT
97864644 ATAAAA
1 ATAAAA
97864650 GGATTAAAAT
Statistics
Matches: 146, Mismatches: 30, Indels: 32
0.70 0.14 0.15
Matches are distributed among these distances:
16 5 0.03
17 35 0.24
18 28 0.19
19 41 0.28
20 21 0.14
21 5 0.03
22 6 0.04
23 5 0.03
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (19 bp):
ATAAAATATATATATATAT
Found at i:97864657 original size:48 final size:46
Alignment explanation
Indices: 97864564--97864659 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 46
97864554 TTTTACATGT
* *
97864564 ATAAATAATATTTATAAAAATAAATAATATATATAAAATATTTAAA
1 ATAAATAATATTCATAAAAATAAATAATATATATAAAAGATTTAAA
*
97864610 ATAAATAA-ATTACATATAAAATATATATATATATATAAAAGGA-TTAAA
1 ATAAATAATATT-CATA-AAAATAAATA-ATATATATAAAA-GATTTAAA
97864658 AT
1 AT
97864660 TGAATTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
45 3 0.07
46 11 0.26
47 9 0.21
48 19 0.44
49 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (46 bp):
ATAAATAATATTCATAAAAATAAATAATATATATAAAAGATTTAAA
Found at i:97866462 original size:26 final size:26
Alignment explanation
Indices: 97866433--97866482 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
97866423 AATAAAAGAA
97866433 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
* *
97866459 AACATTTAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
97866483 AGCATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:97869974 original size:26 final size:26
Alignment explanation
Indices: 97869945--97869995 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
97869935 AATAAAAGAA
97869945 AACATTCAATATTTCTA-TTTAATTAT
1 AACATTCAATATTTC-AGTTTAATTAT
97869971 AACATTCAATATTTCAGTTTAATTA
1 AACATTCAATATTTCAGTTTAATTA
97869996 GCATTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAT
Found at i:97873487 original size:40 final size:40
Alignment explanation
Indices: 97873366--97873513 Score: 133
Period size: 40 Copynumber: 3.7 Consensus size: 40
97873356 AATGATGTCC
* *
97873366 GGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGCT-ACCAAATCCG
* * *
97873406 GACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAATCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGCTACCAAATCCG
* **
97873446 GGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCA-AATCCG
* * *
97873486 GGCTATGTCCCGAAGGCTTTTGAGCGAG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAG
97873514 TCGCTATATC
Statistics
Matches: 89, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
39 1 0.01
40 77 0.87
41 11 0.12
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCAAATCCG
Found at i:97875285 original size:26 final size:26
Alignment explanation
Indices: 97875256--97875306 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
97875246 AATAAAAGAA
97875256 AACATTCAATATTTCTA-TTTAATTAT
1 AACATTCAATATTTC-AGTTTAATTAT
97875282 AACATTCAATATTTCAGTTTAATTA
1 AACATTCAATATTTCAGTTTAATTA
97875307 GCATTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAT
Found at i:97878759 original size:40 final size:40
Alignment explanation
Indices: 97878676--97878828 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 40
97878666 TCGAATGATG
* *
97878676 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAA
* **
97878716 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAA
* **
97878756 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCT-ATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACCA-AA
* * *
97878797 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
97878829 CGCTATATCC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 81 0.86
41 11 0.12
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAA
Done.