Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 104 of 202
Found at i:31719200 original size:25 final size:25
Alignment explanation
Indices: 31719152--31719204 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
31719142 GAATAATTTA
**
31719152 AAATAAATAATATAAATTTTAAAAT
1 AAATAAATAATATAAATTCAAAAAT
31719177 AAATAAATAA-ATAAATTGCAAAAAT
1 AAATAAATAATATAAATT-CAAAAAT
31719202 AAA
1 AAA
31719205 GTGAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (25 bp):
AAATAAATAATATAAATTCAAAAAT
Found at i:31719737 original size:25 final size:24
Alignment explanation
Indices: 31719690--31719758 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
31719680 CTGCTGAAAC
*
31719690 TTTTTTAGTTTGTGGGCTATTCGG
1 TTTTTTAATTTGTGGGCTATTCGG
* *
31719714 TTTTTTAATTTTTGGGCCTGTTCGG
1 TTTTTTAATTTGTGGG-CTATTCGG
*
31719739 TTAGATTTAATTT-TGGGCTA
1 TT--TTTTAATTTGTGGGCTA
31719759 GCATTTTGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 14 0.38
25 11 0.30
26 4 0.11
27 8 0.22
ACGTcount: A:0.13, C:0.09, G:0.25, T:0.54
Consensus pattern (24 bp):
TTTTTTAATTTGTGGGCTATTCGG
Found at i:31724522 original size:24 final size:23
Alignment explanation
Indices: 31724473--31724595 Score: 59
Period size: 24 Copynumber: 4.9 Consensus size: 23
31724463 GAAACAAAAT
* ** *
31724473 AATATATAGAACAATTTGGAGTA
1 AATATATAAAACAATTTAAAGCA
31724496 AATAGTATAAAACAATTTAAAGCA
1 AATA-TATAAAACAATTTAAAGCA
* *
31724520 AATAATATGTAAAACAAATTAAAATGAA
1 AAT-ATA--TAAAAC-AATTTAAA-GCA
* *
31724548 TAATAT-TCAAAGCAATTTAAAAGTA
1 -AATATAT-AAAACAATTT-AAAGCA
31724573 AATAACATATAAAACAATTTAAA
1 AAT---ATATAAAACAATTTAAA
31724596 ATAATATGTA
Statistics
Matches: 77, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
23 4 0.05
24 23 0.30
25 8 0.10
26 16 0.21
27 18 0.23
28 5 0.06
29 3 0.04
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.28
Consensus pattern (23 bp):
AATATATAAAACAATTTAAAGCA
Found at i:31724539 original size:27 final size:25
Alignment explanation
Indices: 31724469--31724666 Score: 101
Period size: 26 Copynumber: 7.8 Consensus size: 25
31724459 AAACGAAACA
* * **
31724469 AAATAATATATAGAACAATTTGGAG
1 AAATAATATGTAAAACAATTTAAAG
*
31724494 TAAATAGTA--TAAAACAATTTAAAG
1 -AAATAATATGTAAAACAATTTAAAG
*
31724518 CAAATAATATGTAAAACAAATTAAA-
1 -AAATAATATGTAAAACAATTTAAAG
*
31724543 ATGAATAATAT-TCAAAGCAATTTAAAAG
1 A--AATAATATGT-AAAACAATTT-AAAG
* *
31724571 TAAATAACATATAAAACAATTT--A-
1 -AAATAATATGTAAAACAATTTAAAG
* *
31724594 AAATAATATGTAAAA-AGTTTAAAAT
1 AAATAATATGTAAAACAATTT-AAAG
*
31724619 AAATAATATGTCAAAAGAAATCTTAAATG
1 AAATAATATGT-AAAA-CAAT-TTAAA-G
*
31724648 -AATAATATG-CAAACAATTT
1 AAATAATATGTAAAACAATTT
31724667 GATTTTTTTT
Statistics
Matches: 136, Mismatches: 18, Indels: 38
0.71 0.09 0.20
Matches are distributed among these distances:
21 4 0.03
22 13 0.10
24 24 0.18
25 15 0.11
26 43 0.32
27 19 0.14
28 15 0.11
29 3 0.02
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (25 bp):
AAATAATATGTAAAACAATTTAAAG
Found at i:31724587 original size:53 final size:52
Alignment explanation
Indices: 31724505--31724666 Score: 167
Period size: 53 Copynumber: 3.2 Consensus size: 52
31724495 AAATAGTATA
*
31724505 AAACAATTT-AAAGCAAATAATATGTAAAACAAATTAAAATGAATAATATTC
1 AAACAATTTAAAAGTAAATAATATGTAAAACAAATTAAAATGAATAATATTC
* * * *
31724556 AAAGCAATTTAAAAGTAAATAACATATAAAACAATTTAAAAT-AAT-AT-GT-
1 AAA-CAATTTAAAAGTAAATAATATGTAAAACAAATTAAAATGAATAATATTC
* * *
31724605 AAA-AAGTTTAAAA-TAAATAATATGTCAAAAGAAATCTTAAATGAATAATATGC
1 AAACAA-TTTAAAAGTAAATAATATGT-AAAACAAAT-TAAAATGAATAATATTC
31724658 AAACAATTT
1 AAACAATTT
31724667 GATTTTTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
47 12 0.13
48 14 0.16
49 8 0.09
50 4 0.04
51 7 0.08
52 9 0.10
53 33 0.37
54 2 0.02
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (52 bp):
AAACAATTTAAAAGTAAATAATATGTAAAACAAATTAAAATGAATAATATTC
Found at i:31724614 original size:21 final size:22
Alignment explanation
Indices: 31724572--31724620 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
31724562 ATTTAAAAGT
31724572 AAATAACATATAAAACAATTTA
1 AAATAACATATAAAACAATTTA
* * *
31724594 AAATAATATGTAAAA-AGTTTA
1 AAATAACATATAAAACAATTTA
31724615 AAATAA
1 AAATAA
31724621 ATAATATGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (22 bp):
AAATAACATATAAAACAATTTA
Found at i:31724652 original size:75 final size:77
Alignment explanation
Indices: 31724501--31724645 Score: 188
Period size: 75 Copynumber: 1.9 Consensus size: 77
31724491 GAGTAAATAG
* *
31724501 TATAAAACAATTTAAAGCAAATAATATGTAAAACAAATTAAAATGAATAATATTCAAAGCAATTT
1 TATAAAACAATTT-AA-CAAATAATATGTAAAACAAATTAAAATAAATAATATTCAAAGAAATTT
31724566 AAAAGTAAATAACA
64 AAAAGTAAATAACA
**
31724580 TATAAAACAATTT-A-AAATAATATGTAAAA-AGTTTAAAATAAATAATATGTCAAAAGAAATCT
1 TATAAAACAATTTAACAAATAATATGTAAAACAAATTAAAATAAATAATAT-TC-AAAGAAAT-T
31724642 TAAA
63 TAAA
31724646 TGAATAATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
74 16 0.27
75 17 0.29
76 7 0.12
77 6 0.10
79 13 0.22
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (77 bp):
TATAAAACAATTTAACAAATAATATGTAAAACAAATTAAAATAAATAATATTCAAAGAAATTTAA
AAGTAAATAACA
Found at i:31724810 original size:51 final size:46
Alignment explanation
Indices: 31724754--31724877 Score: 117
Period size: 51 Copynumber: 2.5 Consensus size: 46
31724744 TAAATAACAT
* *
31724754 ATATATATAAATTTAAAATGAATAATAGATTA-ACATAGTTTAAAATGCATA
1 ATATATATAAATTTAAAATAAATAATA-A-TAGA-ATAATTTAAAAT--A-A
* *
31724805 ATATATGAAAAAACTTAAAATAAATAATAATAGAATAATTTAAAATAA
1 ATATAT--ATAAATTTAAAATAAATAATAATAGAATAATTTAAAATAA
31724853 ATA-ATATAAAGTTTAAAATAAATAA
1 ATATATATAAA-TTTAAAATAAATAA
31724878 ATAAATAAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
45 4 0.06
46 13 0.21
47 2 0.03
48 4 0.06
49 1 0.02
51 19 0.30
52 2 0.03
53 18 0.29
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (46 bp):
ATATATATAAATTTAAAATAAATAATAATAGAATAATTTAAAATAA
Found at i:31724831 original size:26 final size:26
Alignment explanation
Indices: 31724793--31724860 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
31724783 TTAACATAGT
**
31724793 TTAAAATGCATAATATAT-GAAAAAAC
1 TTAAAATAAATAATATATAG-AAAAAC
* *
31724819 TTAAAATAAATAATA-ATAGAATAAT
1 TTAAAATAAATAATATATAGAAAAAC
31724844 TTAAAATAAATAATATA
1 TTAAAATAAATAATATA
31724861 AAGTTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 21 0.58
26 15 0.42
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAATATATAGAAAAAC
Found at i:31724850 original size:21 final size:20
Alignment explanation
Indices: 31724826--31724873 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
31724816 AACTTAAAAT
31724826 AAATAATAATAGAATAATTTA
1 AAATAATAATAGAA-AATTTA
* *
31724847 AAATAAATAATATAAAGTTTA
1 AAAT-AATAATAGAAAATTTA
31724868 AAATAA
1 AAATAA
31724874 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 13 0.54
22 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
AAATAATAATAGAAAATTTA
Found at i:31724874 original size:21 final size:21
Alignment explanation
Indices: 31724814--31724882 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 21
31724804 AATATATGAA
*
31724814 AAAACTTAAAATAAATAATAAT
1 AAAATTTAAAATAAATAAT-AT
31724836 AGAATAATTTAAAATAAATAATAT
1 --AA-AATTTAAAATAAATAATAT
*
31724860 AAAGTTTAAAATAAATAA-AT
1 AAAATTTAAAATAAATAATAT
31724880 AAA
1 AAA
31724883 TAAAGTGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.12
21 15 0.36
22 2 0.05
24 4 0.10
25 16 0.38
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (21 bp):
AAAATTTAAAATAAATAATAT
Found at i:31727754 original size:21 final size:21
Alignment explanation
Indices: 31727730--31727774 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31727720 AAAAAAAACT
** *
31727730 AAAAAAAGGTTGAAAAGGAAA
1 AAAAAAACATTGAAAAGCAAA
31727751 AAAAAAACATTGAAAAGCAAA
1 AAAAAAACATTGAAAAGCAAA
31727772 AAA
1 AAA
31727775 GCAATGGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.71, C:0.04, G:0.16, T:0.09
Consensus pattern (21 bp):
AAAAAAACATTGAAAAGCAAA
Found at i:31728695 original size:2 final size:2
Alignment explanation
Indices: 31728688--31728722 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31728678 ACTAATGCCT
*
31728688 TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31728723 GGTGAGGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31729788 original size:60 final size:59
Alignment explanation
Indices: 31729715--31729826 Score: 161
Period size: 60 Copynumber: 1.9 Consensus size: 59
31729705 AATTCCTTCT
* * *
31729715 TTATATTAAAACTTTACTCTAGAATAAATATATTATACGATTTAGTATAATTACCGTAAG
1 TTATATTAAAACTTTACTATAGAATAAATA-ATTAAACGATTTAATATAATTACCGTAAG
* * *
31729775 TTATATTAAAACTTTGCTATAGAATATATAATTAAATGATTTAATATAATTA
1 TTATATTAAAACTTTACTATAGAATAAATAATTAAACGATTTAATATAATTA
31729827 TTATAAGTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 19 0.41
60 27 0.59
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (59 bp):
TTATATTAAAACTTTACTATAGAATAAATAATTAAACGATTTAATATAATTACCGTAAG
Found at i:31730265 original size:6 final size:6
Alignment explanation
Indices: 31730254--31730279 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31730244 ATCCCCTCCT
31730254 CAATCC CAATCC CAATCC CAATCC CA
1 CAATCC CAATCC CAATCC CAATCC CA
31730280 TTTTACATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.00, T:0.15
Consensus pattern (6 bp):
CAATCC
Found at i:31739431 original size:3 final size:3
Alignment explanation
Indices: 31739423--31739447 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31739413 ATATTTACAT
31739423 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
31739448 ATTTTAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31741415 original size:24 final size:24
Alignment explanation
Indices: 31741388--31741463 Score: 100
Period size: 24 Copynumber: 3.1 Consensus size: 24
31741378 TGCTTTCTAA
31741388 TTAAGTGCTCTTCGGAGCTTCCCG
1 TTAAGTGCTCTTCGGAGCTTCCCG
*
31741412 TTAAGTGCTCTTCGGAGCTACCCG
1 TTAAGTGCTCTTCGGAGCTTCCCG
* *
31741436 ATATAG-GCTCTTTGTGAGCTTCCCG
1 TTA-AGTGCTCTTCG-GAGCTTCCCG
31741461 TTA
1 TTA
31741464 TTAAGTCCGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 32 0.71
25 13 0.29
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (24 bp):
TTAAGTGCTCTTCGGAGCTTCCCG
Found at i:31750286 original size:25 final size:25
Alignment explanation
Indices: 31750258--31750305 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
31750248 CACAGCTCAA
*
31750258 ATGAGCTTCTCGTTATTCAGCTCGC
1 ATGAGCTTCCCGTTATTCAGCTCGC
*
31750283 ATGAGCTTCCCGTTATTTAGCTC
1 ATGAGCTTCCCGTTATTCAGCTC
31750306 AGAAGAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.38
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATTCAGCTCGC
Found at i:31750313 original size:25 final size:25
Alignment explanation
Indices: 31750250--31750315 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
31750240 GGACTCACCA
*
31750250 CAGCTCA-AATGAGCTTCTCGTTATT
1 CAGCTCAGAA-GAGCTTCCCGTTATT
*
31750275 CAGCTC-GCATGAGCTTCCCGTTATT
1 CAGCTCAG-AAGAGCTTCCCGTTATT
*
31750300 TAGCTCAGAAGAGCTT
1 CAGCTCAGAAGAGCTT
31750316 ATTGTTTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 32 0.94
26 2 0.06
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (25 bp):
CAGCTCAGAAGAGCTTCCCGTTATT
Found at i:31752255 original size:504 final size:504
Alignment explanation
Indices: 31751307--31752269 Score: 1471
Period size: 504 Copynumber: 1.9 Consensus size: 504
31751297 TAAAGTTGCG
* ***
31751307 CAAGTCAGTATGCTCAACATGGCGTAGCACACGGGTGTGTGGCTTGGCCATGTGGCCCAAGTCAG
1 CAAGTCAGTATGCTCAACACGGCGTAGCACACGAACGTGTGGCTTGGCCATGTGGCCCAAGTCAG
* *
31751372 AGAGTTACACAGGCACAAACATGGGTTAGGACAAGACCGTGTGTCCCTATTTCGAATGCCCACAC
66 AGAGTTACACAGGCACAAACACGGGCTAGGACAAGACCGTGTGTCCCTATTTCGAATGCCCACAC
* * ** ** *
31751437 ATCCTGAGGCATGGGCGTGTCTCCTGACCGTGTGAGTCACACGGCCTGGCCACATGGTCGTGTGT
131 ATCCTGAGACACGGGCGTGTCTCCTGACCGTGTGAGTCACACGGCCTAACCACATGACCATGTGT
* * * * *
31751502 CCCCTACAGCTTTGAAAAATTTTAATGTTTTCTGAAAAAAATTTTGAGCACCCGAATTAGTCCTG
196 CCCCTACAGCTTTGAAAAATTTTAATGTTTTCTGAAAAAAAATTTAAGCACACGAATTAGCCCCG
* *
31751567 ACTTGTTTTAATGCGTATTTTGGGCTTCGAAGGCTCGCATAAGGGACAATATGTTTAATTTCAAT
261 ACTTGTTTTAATACGTATTTTGGGCCTCGAAGGCTCGCATAAGGGACAATATGTTTAATTTCAAT
* * *
31751632 TGGTTTCTGACATGAATGTTATATGATATGAAATGTCTATTTATTTGATCTGTAAATTATGGTAA
326 TGGTTTCTGACATAAATGTTATATGATATGAAATGTCTATTTATTTGATCTGTAAACTATAGTAA
* *
31751697 TGCTCTGTAACCCTGTTTCAACGATGGATACGGGTTAGGGGTGTTACTCCCTTCACACACACACA
391 TGCTCTGTAACCCTGTTTCAACGATGGATAAGGGTTAGGGGTGTTACACCCTTCACACACACACA
31751762 CACATATATATAACCCATTTCCTCATAGTGGAACTCAACAAGTGTCACT
456 CACATATATATAACCCATTTCCTCATAGTGGAACTCAACAAGTGTCACT
* * *
31751811 CAAGTCAGTATGCTCAACACGGCGTAGCACATGAACGTGTGGCTTGGCTGA-GTGGCCCAAGTTA
1 CAAGTCAGTATGCTCAACACGGCGTAGCACACGAACGTGTGGCTTGGC-CATGTGGCCCAAGTCA
* * *
31751875 GAGAGTTACACAGGCACAGACACGGGCTAGGACAAGGCTGTGTGTCCCTATTTCGAATGCCCACA
65 GAGAGTTACACAGGCACAAACACGGGCTAGGACAAGACCGTGTGTCCCTATTTCGAATGCCCACA
* * *
31751940 TGA-CTTGAGACACGGGCGTGTCTCCTGATCGTGTGAGTCACACGGCCTAACCACATGACCATGT
130 -CATCCTGAGACACGGGCGTGTCTCCTGACCGTGTGAGTCACACGGCCTAACCACATGACCATGT
** * *
31752004 GTCCCCTGTAGCTTTGAAAAATTTTAATGTTTTCTGAAAAAAAATTTAAGCACATGATTTAGCCC
194 GTCCCCTACAGCTTTGAAAAATTTTAATGTTTTCTGAAAAAAAATTTAAGCACACGAATTAGCCC
* *
31752069 CGACTTGTTTTAATACGTATTTTGGGCCTCGAAGGCTTGCATAAGGGACAATATGTTTGATTTCA
259 CGACTTGTTTTAATACGTATTTTGGGCCTCGAAGGCTCGCATAAGGGACAATATGTTTAATTTCA
* *
31752134 ATTGGTTTCTTACATAAATGTTATATGATATGAAATGTCTATTTATTTGATCTGTAAACTCTAGT
324 ATTGGTTTCTGACATAAATGTTATATGATATGAAATGTCTATTTATTTGATCTGTAAACTATAGT
*** **
31752199 AATGCTCTGTAATTTTGTTTCGGCGATGGATAAGGGTTAGGGGTGTTACACCCTTCACACACACA
389 AATGCTCTGTAACCCTGTTTCAACGATGGATAAGGGTTAGGGGTGTTACACCCTTCACACACACA
31752264 CACACA
454 CACACA
31752270 CACACACACA
Statistics
Matches: 410, Mismatches: 47, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
504 408 1.00
505 2 0.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (504 bp):
CAAGTCAGTATGCTCAACACGGCGTAGCACACGAACGTGTGGCTTGGCCATGTGGCCCAAGTCAG
AGAGTTACACAGGCACAAACACGGGCTAGGACAAGACCGTGTGTCCCTATTTCGAATGCCCACAC
ATCCTGAGACACGGGCGTGTCTCCTGACCGTGTGAGTCACACGGCCTAACCACATGACCATGTGT
CCCCTACAGCTTTGAAAAATTTTAATGTTTTCTGAAAAAAAATTTAAGCACACGAATTAGCCCCG
ACTTGTTTTAATACGTATTTTGGGCCTCGAAGGCTCGCATAAGGGACAATATGTTTAATTTCAAT
TGGTTTCTGACATAAATGTTATATGATATGAAATGTCTATTTATTTGATCTGTAAACTATAGTAA
TGCTCTGTAACCCTGTTTCAACGATGGATAAGGGTTAGGGGTGTTACACCCTTCACACACACACA
CACATATATATAACCCATTTCCTCATAGTGGAACTCAACAAGTGTCACT
Found at i:31752261 original size:2 final size:2
Alignment explanation
Indices: 31752254--31752281 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31752244 TTACACCCTT
31752254 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
31752282 TACATAACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:31759802 original size:21 final size:25
Alignment explanation
Indices: 31759777--31759822 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 25
31759767 TAAATGCATC
31759777 AATTT-ATT-TTTA-TATTG-GATA
1 AATTTAATTATTTATTATTGTGATA
31759798 AATTTAATTATTTATTATTGTGATA
1 AATTTAATTATTTATTATTGTGATA
31759823 TATAAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.24
22 3 0.14
23 4 0.19
24 5 0.24
25 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (25 bp):
AATTTAATTATTTATTATTGTGATA
Found at i:31763206 original size:17 final size:17
Alignment explanation
Indices: 31763181--31763224 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
31763171 TGAAATTTTT
31763181 ATATATAAAAAAGTAAA
1 ATATATAAAAAAGTAAA
* *
31763198 ATATTTAAAAATGTAAA
1 ATATATAAAAAAGTAAA
*
31763215 GAAATATAAA
1 -ATATATAAA
31763225 TTTCATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (17 bp):
ATATATAAAAAAGTAAA
Found at i:31763513 original size:20 final size:19
Alignment explanation
Indices: 31763434--31763515 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
31763424 TTTTGATGCA
*
31763434 TTTTATAAATTTTTATT-ATT
1 TTTTAT-AATTTTT-TTCAAT
** *
31763454 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTTCAAT
*
31763473 TTTTAT--TTTTTTTGCAGT
1 TTTTATAATTTTTTT-CAAT
31763491 TTTTATAATTTTTTTCTAAT
1 TTTTATAATTTTTTTC-AAT
31763511 TTTTA
1 TTTTA
31763516 ATAAATTTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
17 4 0.08
18 10 0.21
19 14 0.29
20 20 0.42
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTTTTTCAAT
Found at i:31763721 original size:86 final size:86
Alignment explanation
Indices: 31763611--31763816 Score: 271
Period size: 87 Copynumber: 2.4 Consensus size: 86
31763601 TAATAAGAGC
* * **
31763611 AAGGGCTTAATTGC-TATTTTG-AAAAATTTTGA-AGATCTTTTTGATGCATTTTGAAAGTTCAA
1 AAGGGCTTAATTACTTTTTTTGAAAAAAAATTGAGA-ATCTTTTTGATGCATTTTGAAAGTTCAA
*
31763673 GTACTTAATTGAGTGAAAAAAA
65 GTACTCAATTGAGTGAAAAAAA
* * *
31763695 CAGAGGCTTAATTACTTTTTTTGAAAAAAAATTGAGAATCTTTTTGATGTATTTTGAAAGTTTAA
1 AAG-GGCTTAATTACTTTTTTTGAAAAAAAATTGAGAATCTTTTTGATGCATTTTGAAAGTTCAA
*
31763760 GTTCTCAATTGAGTGAAAAAAA
65 GTACTCAATTGAGTGAAAAAAA
31763782 AAGGGCTTAATTA--TTTTTT-AAAAAAAATTGAGAAT
1 AAGGGCTTAATTACTTTTTTTGAAAAAAAATTGAGAAT
31763817 TTTCTACACC
Statistics
Matches: 108, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
83 16 0.15
84 8 0.07
85 10 0.09
86 16 0.15
87 57 0.53
88 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (86 bp):
AAGGGCTTAATTACTTTTTTTGAAAAAAAATTGAGAATCTTTTTGATGCATTTTGAAAGTTCAAG
TACTCAATTGAGTGAAAAAAA
Found at i:31764247 original size:5 final size:5
Alignment explanation
Indices: 31764237--31764262 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31764227 TGAGCATTCG
31764237 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
31764263 ATTTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:31764360 original size:5 final size:5
Alignment explanation
Indices: 31764352--31764382 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
31764342 GAGATGGAAT
31764352 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
31764383 ATATTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:31765347 original size:9 final size:9
Alignment explanation
Indices: 31765333--31765369 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31765323 TATAGTTTGA
31765333 TATTCGAAT
1 TATTCGAAT
31765342 TATTCGAAT
1 TATTCGAAT
*
31765351 TATTCGAGT
1 TATTCGAAT
31765360 TATTCGAAT
1 TATTCGAAT
31765369 T
1 T
31765370 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31765439 original size:9 final size:9
Alignment explanation
Indices: 31765422--31765452 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31765412 TCGAGTTGAT
31765422 TCGAATAAC
1 TCGAATAAC
*
31765431 TCGATTAAC
1 TCGAATAAC
31765440 TCGAATAAC
1 TCGAATAAC
31765449 TCGA
1 TCGA
31765453 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:31766150 original size:285 final size:285
Alignment explanation
Indices: 31765639--31766208 Score: 1086
Period size: 285 Copynumber: 2.0 Consensus size: 285
31765629 ATAAAAACAA
31765639 ACAACCCGAGACCCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
1 ACAACCCGAGACCCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
31765704 GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTCCCTCCACCTTCCGGCTT
66 GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTCCCTCCACCTTCCGGCTT
*
31765769 TCAGCCTCCAGTTCACCCGCCTTTAGCCGTCTGCTTCTCCGACGACCGTCCCTGCTGAAAAATGA
131 TCAGCCTCCAATTCACCCGCCTTTAGCCGTCTGCTTCTCCGACGACCGTCCCTGCTGAAAAATGA
* *
31765834 GAAAGTCAGAAAGACAGGTTTGGTGGTAAAGGACAAATGAGAATTGAAAATAGTTAACGATAATA
196 GAAAGTCAGAAAGACAGGTTTGGTGGTAAAGGACAAATGAGAATTGAAAAGAGTTAACAATAATA
31765899 ATTTTTTAGGTTTTCGTACTTTATG
261 ATTTTTTAGGTTTTCGTACTTTATG
*
31765924 ACAACCCGAGACTCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
1 ACAACCCGAGACCCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
31765989 GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTCCCTCCACCTTCCGGCTT
66 GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTCCCTCCACCTTCCGGCTT
*
31766054 TCAGCCTCCAATTCACCCGCCTTTAGCCGTCTGCTTCTTCGACGACCGTCCCTGCTGAAAAATGA
131 TCAGCCTCCAATTCACCCGCCTTTAGCCGTCTGCTTCTCCGACGACCGTCCCTGCTGAAAAATGA
*
31766119 GAAAGTCAGAAAGACAGGTTTGGTTGTAAAGGACAAATGAGAATTGAAAAGAGTTAACAATAATA
196 GAAAGTCAGAAAGACAGGTTTGGTGGTAAAGGACAAATGAGAATTGAAAAGAGTTAACAATAATA
31766184 ATTTTTTAGGTTTTCGTACTTTATG
261 ATTTTTTAGGTTTTCGTACTTTATG
31766209 TTGGGTATGG
Statistics
Matches: 279, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
285 279 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (285 bp):
ACAACCCGAGACCCACCCCCTCCCGGGCAACCACCACTCTCGTCACTCGTCCATCCGGCCTCTCT
GACTCTCTGACTCTCTCAACCTCTCTTCACTCTTTAGTCTCCAATCTCCCTCCACCTTCCGGCTT
TCAGCCTCCAATTCACCCGCCTTTAGCCGTCTGCTTCTCCGACGACCGTCCCTGCTGAAAAATGA
GAAAGTCAGAAAGACAGGTTTGGTGGTAAAGGACAAATGAGAATTGAAAAGAGTTAACAATAATA
ATTTTTTAGGTTTTCGTACTTTATG
Found at i:31770714 original size:30 final size:30
Alignment explanation
Indices: 31770659--31770795 Score: 91
Period size: 30 Copynumber: 4.6 Consensus size: 30
31770649 ACAAACTCAT
* * * * *
31770659 GAAGCAGCTCCTCAGGAGGTATCCCATCAT
1 GAAGTAGCTCATCAAGAAGTATCCCATCAA
*
31770689 GAAGTAGCTCATCAAGAAG-ATTCCCATCAC
1 GAAGTAGCTCATCAAGAAGTA-TCCCATCAA
* * * *
31770719 GATGTTGCTCATCGAGAAGTATCCGATCAA
1 GAAGTAGCTCATCAAGAAGTATCCCATCAA
* * * *
31770749 GAAGTAG-ACAGTCAAGAAATAACCCATCAG
1 GAAGTAGCTCA-TCAAGAAGTATCCCATCAA
*
31770779 GAAGAAGCCTC-TCAAGA
1 GAAGTAG-CTCATCAAGA
31770796 GGTACCTTCT
Statistics
Matches: 82, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
29 3 0.04
30 77 0.94
31 1 0.01
32 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (30 bp):
GAAGTAGCTCATCAAGAAGTATCCCATCAA
Found at i:31772601 original size:17 final size:17
Alignment explanation
Indices: 31772579--31772613 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31772569 TCAAATGATT
**
31772579 ATTAAAAATTAAAAAGA
1 ATTAAAAAGAAAAAAGA
31772596 ATTAAAAAGAAAAAAGA
1 ATTAAAAAGAAAAAAGA
31772613 A
1 A
31772614 AAAAAATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
ATTAAAAAGAAAAAAGA
Found at i:31773261 original size:18 final size:17
Alignment explanation
Indices: 31773219--31773261 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
31773209 TTTTTAAGTT
*
31773219 TGTAATATTTTATATTA
1 TGTAATTTTTTATATTA
* *
31773236 TATTATTTTTATATATTA
1 TGTAATTTTT-TATATTA
31773254 TGTAATTT
1 TGTAATTT
31773262 ATAATATATA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TGTAATTTTTTATATTA
Found at i:31781249 original size:23 final size:23
Alignment explanation
Indices: 31781219--31781285 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
31781209 CCTTTTTGAA
31781219 CCATTTCCATTTCGTACCAAATT
1 CCATTTCCATTTCGTACCAAATT
31781242 CCATTTCCATTTCGTACCAAATT
1 CCATTTCCATTTCGTACCAAATT
* *
31781265 ACATTACCATTTCGTACCAAA
1 CCATTTCCATTTCGTACCAAA
31781286 CCCAAACCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.36
Consensus pattern (23 bp):
CCATTTCCATTTCGTACCAAATT
Found at i:31783812 original size:19 final size:21
Alignment explanation
Indices: 31783783--31783826 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
31783773 CAAATGAGAG
31783783 AAAAAGAAAAGAAAA-ATGAA
1 AAAAAGAAAAGAAAACATGAA
*
31783803 AAAAAG-AAAGAAAACTTGAA
1 AAAAAGAAAAGAAAACATGAA
31783823 AAAA
1 AAAA
31783827 GAGAGTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (21 bp):
AAAAAGAAAAGAAAACATGAA
Found at i:31788045 original size:23 final size:23
Alignment explanation
Indices: 31788015--31788081 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
31788005 CCTTTTTGAA
31788015 CCATTTCCATTTCGTACCAAATT
1 CCATTTCCATTTCGTACCAAATT
*
31788038 CCATTTCCATTTCATACCAAATT
1 CCATTTCCATTTCGTACCAAATT
* *
31788061 ACATTACCATTTCGTACCAAA
1 CCATTTCCATTTCGTACCAAA
31788082 CCCAAACCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.31, C:0.30, G:0.03, T:0.36
Consensus pattern (23 bp):
CCATTTCCATTTCGTACCAAATT
Found at i:31794923 original size:15 final size:16
Alignment explanation
Indices: 31794894--31794923 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31794884 TAAACATGCT
31794894 TTAACACATTATCAAA
1 TTAACACATTATCAAA
31794910 TTAACACA-TATCAA
1 TTAACACATTATCAA
31794924 CGGGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:31804767 original size:302 final size:302
Alignment explanation
Indices: 31804221--31804826 Score: 1016
Period size: 302 Copynumber: 2.0 Consensus size: 302
31804211 TAGGGGACCG
* * *
31804221 AGACAGATCGATGGAATCCCTTCCCATTGTGCATGTCTTTAATTTTGAGAAAGAAGAGAACTCAA
1 AGACAGATCGATGGAATCCCCTCCCATTGTGCATGTCTCTAATTTTGAGAAAAAAGAGAACTCAA
31804286 GAGATGTTGAGGAGTGCATGCGAAGGATTGATAGCCTAATCGAGGATGACGCAATTACTGCTCAA
66 GAGATGTTGAGGAGTGCATGCGAAGGATTGATAGCCTAATCGAGGATGACGCAATTACTGCTCAA
* *
31804351 GAGGCGTCCGCTGTTGAAGAAGAAGATGCCTGTGTTGAAATTGTGAACGAGAAGGCCGAGGAAGA
131 GAGGCGTCCGCTGTTGAAGAAGAAGACGCCTGTGTTGAAATTGTGAACGAAAAGGCCGAGGAAGA
* *
31804416 AAATACTGAGACAATAGCTATTGAGAAAGAATCGGTTGAGAACATTGTAAATGCATCCAAGTTTG
196 AAATACTGAGACAATAGCTATTGAGAAAGAATCGGCTGAGAACATTGTAAATGCATCCAAGTCTG
*
31804481 CGGATGCAAATAATGATAATCT-GGAGTGAGATGGAGCTAGAC
261 CGGATGCAAATAATGATAATCTAGG-GCGAGATGGAGCTAGAC
* *
31804523 AGACAGATCGGTGGAATCCCCTCCCATTGTGCATGTCTCTGATTTTGAGAAAAAAGAGAACTCAA
1 AGACAGATCGATGGAATCCCCTCCCATTGTGCATGTCTCTAATTTTGAGAAAAAAGAGAACTCAA
* *
31804588 GGGATGTTGAGGAGTGCATGCGAAGGATTGATAGCCTAATCGAGGATGACGCAATTGCTGCTCAA
66 GAGATGTTGAGGAGTGCATGCGAAGGATTGATAGCCTAATCGAGGATGACGCAATTACTGCTCAA
* **
31804653 GAGGTGTCCGCTGTTGAAGAAGAAGACGCCTGTGTTGAAATTGTGAACGAAAAGGTTGAGGAAGA
131 GAGGCGTCCGCTGTTGAAGAAGAAGACGCCTGTGTTGAAATTGTGAACGAAAAGGCCGAGGAAGA
* * *
31804718 AAATACTGTGACAATAGCTATTGAGAAAGAATCTGCTGAGAACATTGTAAATGCATCCAGGTCTG
196 AAATACTGAGACAATAGCTATTGAGAAAGAATCGGCTGAGAACATTGTAAATGCATCCAAGTCTG
* *
31804783 TGGATGCAAATAATGATAATTTAGGGCGAGATGGAGCTAGAC
261 CGGATGCAAATAATGATAATCTAGGGCGAGATGGAGCTAGAC
31804825 AG
1 AG
31804827 GCGGAAGCTG
Statistics
Matches: 283, Mismatches: 20, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
302 281 0.99
303 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (302 bp):
AGACAGATCGATGGAATCCCCTCCCATTGTGCATGTCTCTAATTTTGAGAAAAAAGAGAACTCAA
GAGATGTTGAGGAGTGCATGCGAAGGATTGATAGCCTAATCGAGGATGACGCAATTACTGCTCAA
GAGGCGTCCGCTGTTGAAGAAGAAGACGCCTGTGTTGAAATTGTGAACGAAAAGGCCGAGGAAGA
AAATACTGAGACAATAGCTATTGAGAAAGAATCGGCTGAGAACATTGTAAATGCATCCAAGTCTG
CGGATGCAAATAATGATAATCTAGGGCGAGATGGAGCTAGAC
Found at i:31822611 original size:47 final size:47
Alignment explanation
Indices: 31822557--31822667 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 47
31822547 ACCAGTAATA
* * *
31822557 CAGATAAACTACCACTTAATAATATTGTGGACAAGCCACCACTTTTG
1 CAGATAAACTACCACATAAAAATATCGTGGACAAGCCACCACTTTTG
* * * *
31822604 CATATAAACTGCCACATAAAAATATCGTTGACAAGCCACCATTTTTG
1 CAGATAAACTACCACATAAAAATATCGTGGACAAGCCACCACTTTTG
*
31822651 TAGATAAAC-AGCCACAT
1 CAGATAAACTA-CCACAT
31822668 CTTCCACCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (47 bp):
CAGATAAACTACCACATAAAAATATCGTGGACAAGCCACCACTTTTG
Found at i:31827683 original size:11 final size:11
Alignment explanation
Indices: 31827667--31827701 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
31827657 CATTGAAGGT
31827667 GGTATGGCTTA
1 GGTATGGCTTA
31827678 GGTATGGCTTA
1 GGTATGGCTTA
31827689 GGTATGGCTTA
1 GGTATGGCTTA
31827700 GG
1 GG
31827702 GTGTTTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.40, T:0.34
Consensus pattern (11 bp):
GGTATGGCTTA
Found at i:31829199 original size:9 final size:9
Alignment explanation
Indices: 31829187--31829223 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
31829177 TATTTTTTTA
31829187 TTTTTTCAC
1 TTTTTTCAC
31829196 TTTTTTCAC
1 TTTTTTCAC
31829205 TTTTTGATCAC
1 TTTTT--TCAC
31829216 TTTTTTCA
1 TTTTTTCA
31829224 TGAGAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 17 0.65
11 9 0.35
ACGTcount: A:0.14, C:0.19, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTTTCAC
Found at i:31840288 original size:10 final size:10
Alignment explanation
Indices: 31840273--31840314 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
31840263 TTTGCAAGTT
31840273 TTGAGCTAAA
1 TTGAGCTAAA
* *
31840283 TTGAGCTGAT
1 TTGAGCTAAA
*
31840293 TTGAGCT-CA
1 TTGAGCTAAA
31840302 TTGAGCTAAA
1 TTGAGCTAAA
31840312 TTG
1 TTG
31840315 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:31842505 original size:27 final size:27
Alignment explanation
Indices: 31842446--31842651 Score: 234
Period size: 27 Copynumber: 7.6 Consensus size: 27
31842436 CATCTCTTAG
* * * *
31842446 GGGTATATCAGTCATTTTACCCTATAA
1 GGGTATTTCGGTCATTTTACCCTTTGA
* ** *
31842473 AGGTATTTTAGTTATTTTACCCTTTG-
1 GGGTATTTCGGTCATTTTACCCTTTGA
* **
31842499 GGCGTATTTCGGTCATCTTACCCTACGA
1 GG-GTATTTCGGTCATTTTACCCTTTGA
*
31842527 GGGCATTTCGGTCATTTTACCCTTTGA
1 GGGTATTTCGGTCATTTTACCCTTTGA
* *
31842554 GGGTATTTTGATCATTTTACCCTTTGA
1 GGGTATTTCGGTCATTTTACCCTTTGA
*
31842581 GGGTATTTCGGTCATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTTGA
* * *
31842608 GGATATTTTGGTCATTTTACCCTTCGA
1 GGGTATTTCGGTCATTTTACCCTTTGA
31842635 GGGTATTTCGGTCATTT
1 GGGTATTTCGGTCATTT
31842652 CCCCACGAAT
Statistics
Matches: 150, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 147 0.98
28 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCCTTTGA
Found at i:31843403 original size:10 final size:10
Alignment explanation
Indices: 31843357--31843395 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
31843347 GACAAAGAGG
31843357 GAAAAAGAG-A
1 GAAAAA-AGCA
31843367 GAAAAAAGCA
1 GAAAAAAGCA
31843377 GAAAAAAGCA
1 GAAAAAAGCA
31843387 GAAAAAAGC
1 GAAAAAAGC
31843396 GAACAAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 2 0.07
10 26 0.93
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (10 bp):
GAAAAAAGCA
Found at i:31849513 original size:28 final size:28
Alignment explanation
Indices: 31849481--31849555 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
31849471 AGTAATAGTC
* *
31849481 TGGGCCTGAGCCCTAA-GCAGTATCAGTG
1 TGGGCCTGAGCCC-AATACAGTAGCAGTG
* *
31849509 TGGGCCTTAGCCCAATACGGTAGCAGTG
1 TGGGCCTGAGCCCAATACAGTAGCAGTG
* *
31849537 TGGGCCTTAGCTCAATACA
1 TGGGCCTGAGCCCAATACA
31849556 ATAACAGTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 2 0.05
28 38 0.95
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (28 bp):
TGGGCCTGAGCCCAATACAGTAGCAGTG
Found at i:31849563 original size:28 final size:28
Alignment explanation
Indices: 31849504--31849563 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
31849494 TAAGCAGTAT
** *
31849504 CAGTGTGGGCCTTAGCCCAATACGGTAG
1 CAGTGTGGGCCTTAGCCCAATACAATAA
*
31849532 CAGTGTGGGCCTTAGCTCAATACAATAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
31849560 CAGT
1 CAGT
31849564 ACAGTGCAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAATAA
Found at i:31849930 original size:27 final size:27
Alignment explanation
Indices: 31849912--31850081 Score: 236
Period size: 27 Copynumber: 6.3 Consensus size: 27
31849902 GGGTATATTG
31849912 GTCATTTTACCCTTCAAGGGTATTTCA
1 GTCATTTTACCCTTCAAGGGTATTTCA
* *
31849939 GTCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTTCA
* *
31849966 GTCAATTCACCCTTCGAA-GGTATTTCA
1 GTCATTTTACCCTTC-AAGGGTATTTCA
*
31849993 GTCATTTTATCCTT-AGAGGGTATTTCA
1 GTCATTTTACCCTTCA-AGGGTATTTCA
*
31850020 GTTATTTTACCCTTCAAGGGTATTTCA
1 GTCATTTTACCCTTCAAGGGTATTTCA
*
31850047 GTCATTTTATCCTTCAAGGGTATTTCA
1 GTCATTTTACCCTTCAAGGGTATTTCA
*
31850074 ATCATTTT
1 GTCATTTT
31850082 CCTATGAATC
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 121 0.97
28 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTTCAAGGGTATTTCA
Found at i:31853108 original size:32 final size:32
Alignment explanation
Indices: 31853072--31853135 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
31853062 AAATATGAGT
*
31853072 TAACTAAGAAATTGTATGGTATAGTGAGTATA
1 TAACTAAGAAATTGTATGGTATAGGGAGTATA
31853104 TAACTAAGAAATTGTATGGTATAGGGAGTATA
1 TAACTAAGAAATTGTATGGTATAGGGAGTATA
31853136 AGATTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (32 bp):
TAACTAAGAAATTGTATGGTATAGGGAGTATA
Found at i:31854586 original size:13 final size:13
Alignment explanation
Indices: 31854568--31854593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31854558 GGATATCAAG
31854568 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
31854581 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
31854594 GCTAGTTTTG
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:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:31857934 original size:25 final size:25
Alignment explanation
Indices: 31857903--31857969 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
31857893 AGCTTAGATC
31857903 AGTATGCTTACACGAGCTAAAAATT
1 AGTATGCTTACACGAGCTAAAAATT
* *
31857928 AGTATGCTTATACGAGCTATAAATT
1 AGTATGCTTACACGAGCTAAAAATT
* * *
31857953 GGTATGCTCACAGGAGC
1 AGTATGCTTACACGAGC
31857970 GGTGGGTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (25 bp):
AGTATGCTTACACGAGCTAAAAATT
Found at i:31861001 original size:50 final size:50
Alignment explanation
Indices: 31860885--31861123 Score: 250
Period size: 50 Copynumber: 4.7 Consensus size: 50
31860875 CATGCCAAAA
* *
31860885 CCATGTCCCAGACATGGTCTTACATGGGATG-TTTCATGTAC--TGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATAT-CGGTGCCAATG
* * * *
31860934 CCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATG
* *
31860984 CCATGTCCCAGACATGGTCTTACATGGGAGCTCTCGTCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATG
** * *
31861034 CCATGTCATAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAGTG
1 CCATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT-A--TC--GG-TGCCAATG
* * *
31861090 TCATGTCCCATACATGGTCTTACATGGGATCTCT
1 CCATGTCCCAGACATGGTCTTACATGGGAGCTCT
31861124 TTACCCAAAT
Statistics
Matches: 159, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
48 2 0.01
49 33 0.21
50 84 0.53
53 2 0.01
55 2 0.01
56 36 0.23
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAATG
Found at i:31863802 original size:13 final size:13
Alignment explanation
Indices: 31863786--31863828 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
31863776 ATACAACCAA
31863786 TTCATATAGCCAT
1 TTCATATAGCCAT
* *
31863799 TTCATATAACAAT
1 TTCATATAGCCAT
*
31863812 TTCATATGGCCAT
1 TTCATATAGCCAT
31863825 TTCA
1 TTCA
31863829 AAGTGTTAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (13 bp):
TTCATATAGCCAT
Found at i:31877644 original size:30 final size:30
Alignment explanation
Indices: 31877608--31877690 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
31877598 GTGTGCTAAA
* *
31877608 CGATGGTCGAAACCATCCCTTTTCCTTAAT
1 CGATGGTCAAAACCATCCCTTTTCATTAAT
*
31877638 CGATGGTCAAAACCATCCTTTTTCATTAAT
1 CGATGGTCAAAACCATCCCTTTTCATTAAT
*
31877668 CGATGATCAAAACCATCCCTTTT
1 CGATGGTCAAAACCATCCCTTTT
31877691 TATAGATGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.34
Consensus pattern (30 bp):
CGATGGTCAAAACCATCCCTTTTCATTAAT
Found at i:31888162 original size:36 final size:36
Alignment explanation
Indices: 31888092--31888162 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
31888082 GGAGCACATT
* *
31888092 AGTCAGAGTAGATCTGAAAAGCTACTGAATTGAATC
1 AGTCAGAATAGATCTGAAAAGCTACTGAACTGAATC
**
31888128 AGTCAGAATAGATCT-AAAAGGCTGTTGAACTGAAT
1 AGTCAGAATAGATCTGAAAA-GCTACTGAACTGAAT
31888163 AGAGTTTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (36 bp):
AGTCAGAATAGATCTGAAAAGCTACTGAACTGAATC
Found at i:31890111 original size:33 final size:33
Alignment explanation
Indices: 31890000--31890111 Score: 84
Period size: 33 Copynumber: 3.3 Consensus size: 33
31889990 CATAGCTTCG
** *
31890000 CCATGGTCTTACATAAACATTGCCATTGTCCAA
1 CCATGGTCTTATGTAAACATTGCCATAGTCCAA
* * ** *
31890033 CCATGGTCTTGTGTCTAAAAAATCACCATAG-CC-T
1 CCATGGTCTTATG--T-AAACATTGCCATAGTCCAA
*
31890067 CGCTATGGTCTTATGTAAACATTGCCATGGTCCAA
1 C-C-ATGGTCTTATGTAAACATTGCCATAGTCCAA
31890102 CCATGGTCTT
1 CCATGGTCTT
31890112 GTACATCTTT
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
33 28 0.48
34 5 0.09
35 5 0.09
36 20 0.34
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (33 bp):
CCATGGTCTTATGTAAACATTGCCATAGTCCAA
Found at i:31890112 original size:69 final size:69
Alignment explanation
Indices: 31889951--31890113 Score: 238
Period size: 69 Copynumber: 2.4 Consensus size: 69
31889941 ATATATACAC
** * *
31889951 TGCCATGGTCCAACCATGGTCTTACGTCTGAAAAACTACCATAGCTTCGCCATGGTCTTACATAA
1 TGCCATGGTCCAACCATGGTCTTGTGTCTAAAAAACTACCATAGCCTCGCCATGGTCTTACATAA
31890016 ACAT
66 ACAT
* * **
31890020 TGCCATTGTCCAACCATGGTCTTGTGTCTAAAAAA-TCACCATAGCCTCGCTATGGTCTTATGTA
1 TGCCATGGTCCAACCATGGTCTTGTGTCTAAAAAACT-ACCATAGCCTCGCCATGGTCTTACATA
31890084 AACAT
65 AACAT
31890089 TGCCATGGTCCAACCATGGTCTTGT
1 TGCCATGGTCCAACCATGGTCTTGT
31890114 ACATCTTTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
68 1 0.01
69 83 0.99
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (69 bp):
TGCCATGGTCCAACCATGGTCTTGTGTCTAAAAAACTACCATAGCCTCGCCATGGTCTTACATAA
ACAT
Found at i:31907658 original size:17 final size:16
Alignment explanation
Indices: 31907627--31907660 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
31907617 AAATATTATG
31907627 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
31907643 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
31907660 A
1 A
31907661 CGCCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:31915679 original size:6 final size:6
Alignment explanation
Indices: 31915668--31915737 Score: 63
Period size: 6 Copynumber: 11.8 Consensus size: 6
31915658 AATAAATAAA
* *
31915668 TTTTAT TTTTAT GTTTAT TTTTA- TTTTA- TTTTAT TTTTAA TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * * *
31915714 TATATCT TTTTAA GTTTAT TTTTA
1 T-TTTAT TTTTAT TTTTAT TTTTA
31915738 ATTAAATTTT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
5 10 0.20
6 36 0.72
7 4 0.08
ACGTcount: A:0.21, C:0.01, G:0.03, T:0.74
Consensus pattern (6 bp):
TTTTAT
Found at i:31915731 original size:25 final size:25
Alignment explanation
Indices: 31915703--31915750 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31915693 TTATTTTATT
*
31915703 TTTAATTTT-ATTATATCTTTTTAAG
1 TTTAATTTTAATTAAAT-TTTTTAAG
*
31915728 TTTATTTTTAATTAAATTTTTTA
1 TTTAATTTTAATTAAATTTTTTA
31915751 GATAAGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTAATTTTAATTAAATTTTTTAAG
Found at i:31918800 original size:41 final size:41
Alignment explanation
Indices: 31918727--31918847 Score: 156
Period size: 41 Copynumber: 3.0 Consensus size: 41
31918717 AAGTGTTTTT
*
31918727 AGGGGTACTGAAGTAAAAAC-GGGGCACATATGTGCAATTC
1 AGGGGTACCGAAGTAAAAACAGGGGCACATATGTGCAATTC
* * *
31918767 AGGGGTACCGAACTATAAACAGGGGCACGTATGTGCAATTC
1 AGGGGTACCGAAGTAAAAACAGGGGCACATATGTGCAATTC
* * *
31918808 AAGGGT-CTCAAAGTACAAACAGGGGCACATATGTGCAATT
1 AGGGGTAC-CGAAGTAAAAACAGGGGCACATATGTGCAATT
31918848 TAACGCTACT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 18 0.26
41 52 0.74
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (41 bp):
AGGGGTACCGAAGTAAAAACAGGGGCACATATGTGCAATTC
Found at i:31931427 original size:16 final size:16
Alignment explanation
Indices: 31931406--31931460 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
31931396 GTTTGGTTCA
*
31931406 CTGTAATGGAATAGAG
1 CTGTAATAGAATAGAG
31931422 CTGTAATTA-AATAGAG
1 CTGTAA-TAGAATAGAG
* *
31931438 CAGTAATAGAATAAAG
1 CTGTAATAGAATAGAG
*
31931454 TTGTAAT
1 CTGTAAT
31931461 CAGTAATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (16 bp):
CTGTAATAGAATAGAG
Found at i:31935643 original size:23 final size:23
Alignment explanation
Indices: 31935579--31935989 Score: 281
Period size: 23 Copynumber: 18.0 Consensus size: 23
31935569 TTTGCAGCAC
* *
31935579 TTAAACACTTCAATTGACATCAT
1 TTAAACACTTCAATTTACAACAT
* * * *
31935602 TTGAGCACCTT-AATTTACAATAA
1 TTAAACA-CTTCAATTTACAACAT
*
31935625 TTAAACACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAACAT
* * *
31935648 TTAAACACCTCAACTTACATCACT
1 TTAAACACTTCAATTTACAACA-T
*
31935672 TT-AACA-TCTCAATTAACAACAT
1 TTAAACACT-TCAATTTACAACAT
* * *
31935694 TTATACACCTGAA-TTACAACAT
1 TTAAACACTTCAATTTACAACAT
* *
31935716 TTAAATACTTCAATTTGCAACACT
1 TTAAACACTTCAATTTACAACA-T
*
31935740 TT-AACACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAACAT
*
31935762 TTAAACACTTCAATTTGCAACACT
1 TTAAACACTTCAATTTACAACA-T
31935786 TT-AACACTTCAATTTACAACAT
1 TTAAACACTTCAATTTACAACAT
** *
31935808 TTAAACACTTCAATTTGTAGCACT
1 TTAAACACTTCAATTTACAACA-T
* *
31935832 TT-AACA-TCTCTATTAACAACAT
1 TTAAACACT-TCAATTTACAACAT
* *
31935854 TTATACACTTCAA-TTACAGCA-
1 TTAAACACTTCAATTTACAACAT
* * * ** *
31935875 ATAAA-AATCTCAATTTCCAGGAA
1 TTAAACACT-TCAATTTACAACAT
* * **
31935898 CTAAACAATTCAATTTGTAGTAC-T
1 TTAAACACTTCAA-TT-TACAACAT
* *
31935922 TAAAACACTTTAATTTACAACAT
1 TTAAACACTTCAATTTACAACAT
* *
31935945 TTAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAACA-T
31935969 TT-AACACTTCAATTTACAACA
1 TTAAACACTTCAATTTACAACA
31935990 AACATGTTGG
Statistics
Matches: 296, Mismatches: 69, Indels: 46
0.72 0.17 0.11
Matches are distributed among these distances:
20 2 0.01
21 7 0.02
22 49 0.17
23 204 0.69
24 33 0.11
25 1 0.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
TTAAACACTTCAATTTACAACAT
Found at i:31935834 original size:160 final size:157
Alignment explanation
Indices: 31935568--31935986 Score: 450
Period size: 160 Copynumber: 2.6 Consensus size: 157
31935558 ATTATATATT
* * * * * * *
31935568 ATTTGCAGCACTTAAACACTTCAATTGACATCATTTGAGCACCTTAATTTACAATAATTAAACAC
1 ATTTGCAACACTTAAACACTTCAATTTACAGCATTTAAACA-CTTAATTTACAA-CATTTAACAC
* * *
31935633 TTCAATTTACAGCATTTAAACACCTCAACTTACATCACTTTAACATCTCAATTAACAACATTTAT
64 TTCAATTTACAGCATTTAAACACTTCAATTTACAGCACTTTAACATCTCAATTAACAACATTTAT
* **
31935698 ACACCTGAATTACAAC-ATTTAAATACTTCA
129 ACACCTCAATTACAACAATAAAAAT-C-TCA
* *
31935728 ATTTGCAACACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAACACTTTAACAC
1 ATTTGCAACACTTAAACACTTCAATTTACAGCATTTAAACACTT-AATTTACAACA-TTTAACAC
* ** *
31935793 TTCAATTTACAACATTTAAACACTTCAATTTGTAGCACTTTAACATCTCTATTAACAACATTTAT
64 TTCAATTTACAGCATTTAAACACTTCAATTTACAGCACTTTAACATCTCAATTAACAACATTTAT
* *
31935858 ACACTTCAATTACAGCAATAAAAATCTCA
129 ACACCTCAATTACAACAATAAAAATCTCA
* * ** * *
31935887 ATTTCCAGGA-AC-TAAACAATTCAATTTGTAGTACTTAAAACACTTTAATTTACAACATTTAAA
1 ATTTGCA--ACACTTAAACACTTCAATTTACAGCA-TTTAAACAC-TTAATTTACAACATTT-AA
*
31935950 CACTTCAATTTGCAGCACTTT-AACACTTCAATTTACA
61 CACTTCAATTTACAGCA-TTTAAACACTTCAATTTACA
31935987 ACAAACATGT
Statistics
Matches: 217, Mismatches: 33, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
159 32 0.15
160 173 0.80
161 12 0.06
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (157 bp):
ATTTGCAACACTTAAACACTTCAATTTACAGCATTTAAACACTTAATTTACAACATTTAACACTT
CAATTTACAGCATTTAAACACTTCAATTTACAGCACTTTAACATCTCAATTAACAACATTTATAC
ACCTCAATTACAACAATAAAAATCTCA
Found at i:31940571 original size:21 final size:21
Alignment explanation
Indices: 31940522--31940561 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31940512 TGACACGTCT
*
31940522 GGAAAGAAAAATACATAATAC
1 GGAAAAAAAAATACATAATAC
31940543 GGAAAAAAAAATACATAAT
1 GGAAAAAAAAATACATAAT
31940562 CTTAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.12, T:0.15
Consensus pattern (21 bp):
GGAAAAAAAAATACATAATAC
Found at i:31941424 original size:23 final size:25
Alignment explanation
Indices: 31941371--31941436 Score: 100
Period size: 23 Copynumber: 2.7 Consensus size: 25
31941361 TTTTAAAAGT
*
31941371 TAGACTACATTTAATATTGATTCATG
1 TAGACTACATTTAATATTGA-TAATG
31941397 TAGACTACATTTAATATT-A-AATG
1 TAGACTACATTTAATATTGATAATG
31941420 TAGACTACATTTAATAT
1 TAGACTACATTTAATAT
31941437 AGTACATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 20 0.51
25 1 0.03
26 18 0.46
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (25 bp):
TAGACTACATTTAATATTGATAATG
Found at i:31943825 original size:20 final size:20
Alignment explanation
Indices: 31943802--31943841 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31943792 TTATTTTTAC
31943802 ATATACTAATAAATTTATAT
1 ATATACTAATAAATTTATAT
*
31943822 ATATATTAATAAATTTATAT
1 ATATACTAATAAATTTATAT
31943842 TTTAAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATACTAATAAATTTATAT
Found at i:31944892 original size:18 final size:18
Alignment explanation
Indices: 31944866--31944923 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
31944856 ACTCCCCGTA
* *
31944866 TTTACTTTCCCTCAAACT
1 TTTATTTTCCCACAAACT
* *
31944884 TTTATTTT-CCAAAAATT
1 TTTATTTTCCCACAAACT
*
31944901 TTTATTTTCCCCCTAAACT
1 TTTATTTTCCCAC-AAACT
31944920 TTTA
1 TTTA
31944924 CTTCTCACCC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 14 0.45
18 9 0.29
19 8 0.26
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATTTTCCCACAAACT
Found at i:31947512 original size:28 final size:28
Alignment explanation
Indices: 31947480--31947535 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
31947470 TAAAATATTT
31947480 TTAATGCTATAATTATACTTATACCTAC
1 TTAATGCTATAATTATACTTATACCTAC
31947508 TTAATGCTATAATTATACTTATACCTAC
1 TTAATGCTATAATTATACTTATACCTAC
31947536 AATAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.43
Consensus pattern (28 bp):
TTAATGCTATAATTATACTTATACCTAC
Found at i:31947657 original size:12 final size:14
Alignment explanation
Indices: 31947639--31947675 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
31947629 GGATGAATAG
31947639 ATATATTATAT-AT
1 ATATATTATATGAT
31947652 -TATATTATATGAT
1 ATATATTATATGAT
31947665 ATAATATTATA
1 AT-ATATTATA
31947676 GAATATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.48
13 2 0.10
14 1 0.05
15 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
ATATATTATATGAT
Found at i:31947671 original size:15 final size:15
Alignment explanation
Indices: 31947641--31947685 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
31947631 ATGAATAGAT
31947641 ATATTATAT-AT-T-
1 ATATTATATGATATA
31947653 ATATTATATGATATA
1 ATATTATATGATATA
31947668 ATATTATA-GAATATA
1 ATATTATATG-ATATA
31947683 ATA
1 ATA
31947686 GAAGCAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.31
13 2 0.07
14 2 0.07
15 16 0.55
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
ATATTATATGATATA
Found at i:31954686 original size:30 final size:31
Alignment explanation
Indices: 31954652--31954714 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
31954642 TAAACCTCTT
*
31954652 CACTTTCCTCCCAAAACTTTTACT-CCCTCC
1 CACTTTCCCCCCAAAACTTTTACTCCCCTCC
* *
31954682 CACTTTCCCCCCATAACTTTTGCTCCCCTCC
1 CACTTTCCCCCCAAAACTTTTACTCCCCTCC
31954713 CA
1 CA
31954715 TCCCACCCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.17, C:0.49, G:0.02, T:0.32
Consensus pattern (31 bp):
CACTTTCCCCCCAAAACTTTTACTCCCCTCC
Found at i:31955269 original size:19 final size:19
Alignment explanation
Indices: 31955245--31955282 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31955235 AAAGTTAATA
31955245 ACAAATTTGATTACAGTGG
1 ACAAATTTGATTACAGTGG
*
31955264 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACAGTGG
31955283 GTGATATTGA
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:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ACAAATTTGATTACAGTGG
Found at i:31962512 original size:80 final size:80
Alignment explanation
Indices: 31962375--31962534 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 80
31962365 AACCACATGA
31962375 ATACATTCATGGAAAAAACCTAACCTTTTAACGATTTTGCAAATTAGTCCCTAGGCTAGCTAGAT
1 ATACATTCATGGAAAAAACCTAACCTTTTAACGATTTTGCAAATTAGTCCCTAGGCTAGCTAGAT
31962440 TAAGCTACAACGACT
66 TAAGCTACAACGACT
* * * *
31962455 ATACATTCATGGGAAAAACCTAACCTTTTAATGGTTTTGCAAATTAGTCCCTGGGCTAGCTAGAT
1 ATACATTCATGGAAAAAACCTAACCTTTTAACGATTTTGCAAATTAGTCCCTAGGCTAGCTAGAT
31962520 TAAGCTACAACGACT
66 TAAGCTACAACGACT
31962535 CCAAAAACAT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (80 bp):
ATACATTCATGGAAAAAACCTAACCTTTTAACGATTTTGCAAATTAGTCCCTAGGCTAGCTAGAT
TAAGCTACAACGACT
Found at i:31963326 original size:24 final size:24
Alignment explanation
Indices: 31963298--31963363 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
31963288 AAGGCAACAT
*
31963298 AGAATATGCCACAAAGGTATTTAC
1 AGAATACGCCACAAAGGTATTTAC
* ** *
31963322 AGAATACACCACAAAGGCGTTTAT
1 AGAATACGCCACAAAGGTATTTAC
*
31963346 AGAATACGCTACAAAGGT
1 AGAATACGCCACAAAGGT
31963364 GTCATAGAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (24 bp):
AGAATACGCCACAAAGGTATTTAC
Found at i:31967464 original size:49 final size:46
Alignment explanation
Indices: 31967392--31967498 Score: 123
Period size: 49 Copynumber: 2.3 Consensus size: 46
31967382 ATATTTTTAG
* *
31967392 TAATAA-TT-ATATA-T-TATAATATTATTTTATGTAATAGTAATG
1 TAATAATTTAATATATTATATAATATTATTTTATGTAATACTAATA
*
31967434 TAATACATTATAATATATTATATATATATTATTTTATGTATTACTAATA
1 TAATA-ATT-TAATATATTATATA-ATATTATTTTATGTAATACTAATA
*
31967483 TACTAATTTAATATAT
1 TAATAATTTAATATAT
31967499 CGTTTTAAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
42 5 0.09
43 1 0.02
44 1 0.02
45 1 0.02
46 5 0.09
47 9 0.17
48 7 0.13
49 25 0.46
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (46 bp):
TAATAATTTAATATATTATATAATATTATTTTATGTAATACTAATA
Found at i:31967492 original size:23 final size:23
Alignment explanation
Indices: 31967449--31967492 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
31967439 CATTATAATA
* *
31967449 TATTATATATATATTATTTTATG
1 TATTATATATATACTAATTTATG
31967472 TATTACTA-ATATACTAATTTA
1 TATTA-TATATATACTAATTTA
31967493 ATATATCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (23 bp):
TATTATATATATACTAATTTATG
Found at i:31967610 original size:25 final size:23
Alignment explanation
Indices: 31967572--31967617 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
31967562 TATTATCATT
*
31967572 AAAATTAAATTTTATAGATTTTA
1 AAAATTAAATTTTATAAATTTTA
31967595 AAAATTATTAATTTTATAAATTT
1 AAAATTA--AATTTTATAAATTT
31967618 ATTATACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
25 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AAAATTAAATTTTATAAATTTTA
Found at i:31972532 original size:12 final size:12
Alignment explanation
Indices: 31972515--31972539 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31972505 TGCTTTTGTG
31972515 AGTTCAAATTAT
1 AGTTCAAATTAT
31972527 AGTTCAAATTAT
1 AGTTCAAATTAT
31972539 A
1 A
31972540 TATTTTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
AGTTCAAATTAT
Found at i:31979841 original size:100 final size:100
Alignment explanation
Indices: 31979616--31979923 Score: 427
Period size: 102 Copynumber: 3.0 Consensus size: 100
31979606 CCATGTTGCA
*
31979616 AGCATCCATATATTTTCAGAATTTGTTGCATGCATAACATACTCATTCATTGTGATTACGCACAA
1 AGCATCCATATATTTTCAGAATTTGTTGCATGCATAACATACTCATTCACTGTGATTA--CACAA
*
31979681 CCATAGAAAATTACACAGAATTCATAGCAAACATTTG
64 CCATAGAAAATTACACAAAATTCATAGCAAACATTTG
* * * * *
31979718 ATCATCCATATATATTCAGAATTTGTTGCATGCATAGCATACTCATTCACTGTGATTACATAGCC
1 AGCATCCATATATTTTCAGAATTTGTTGCATGCATAACATACTCATTCACTGTGATTACACAACC
* *
31979783 ATAGAAAATTATACAAAATTCATAGCAGACATTTG
66 ATAGAAAATTACACAAAATTCATAGCAAACATTTG
* * *
31979818 AGCATCCATATATTTTCACAATTTGTTGCATGCATAATATACTCATTCACCGTGATTACACACAA
1 AGCATCCATATATTTTCAGAATTTGTTGCATGCATAACATACTCATTCACTGTGATT--ACACAA
* * * * *
31979883 CCGTAGAAAATTACATAGAGTTCATAGCAAACATTCG
64 CCATAGAAAATTACACAAAATTCATAGCAAACATTTG
31979920 AGCA
1 AGCA
31979924 CAACAACACA
Statistics
Matches: 180, Mismatches: 24, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
100 88 0.49
102 92 0.51
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (100 bp):
AGCATCCATATATTTTCAGAATTTGTTGCATGCATAACATACTCATTCACTGTGATTACACAACC
ATAGAAAATTACACAAAATTCATAGCAAACATTTG
Found at i:31985970 original size:27 final size:27
Alignment explanation
Indices: 31985936--31986091 Score: 168
Period size: 27 Copynumber: 5.8 Consensus size: 27
31985926 AAATGGTCGT
31985936 AATACCCCCGAAGGGTAAAATTACCGA
1 AATACCCCCGAAGGGTAAAATTACCGA
* * * * *
31985963 AATGCCCCTGAAGGATAAAATTATCAA
1 AATACCCCCGAAGGGTAAAATTACCGA
* * * *
31985990 AATGCCCTCGAAAGGTAAAATTACTGA
1 AATACCCCCGAAGGGTAAAATTACCGA
*
31986017 AATACCCCCGAAGGGTAAAATTATCGA
1 AATACCCCCGAAGGGTAAAATTACCGA
*** * *
31986044 AATACCATTGAAAGGTAAAATTATCGA
1 AATACCCCCGAAGGGTAAAATTACCGA
*
31986071 AATACCCCCGATGGGTAAAAT
1 AATACCCCCGAAGGGTAAAAT
31986092 GGCCGTAATG
Statistics
Matches: 103, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 103 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (27 bp):
AATACCCCCGAAGGGTAAAATTACCGA
Found at i:31986012 original size:54 final size:54
Alignment explanation
Indices: 31985944--31986091 Score: 188
Period size: 54 Copynumber: 2.7 Consensus size: 54
31985934 GTAATACCCC
* * * * *
31985944 CGAAGGGTAAAATTACCGAAATGCCCCTGAAGGATAAAATTATCAAAATGCCCT
1 CGAAAGGTAAAATTACCGAAATACCCCCGAAGGATAAAATTATCAAAATACCAT
* * *
31985998 CGAAAGGTAAAATTACTGAAATACCCCCGAAGGGTAAAATTATCGAAATACCAT
1 CGAAAGGTAAAATTACCGAAATACCCCCGAAGGATAAAATTATCAAAATACCAT
* * * *
31986052 TGAAAGGTAAAATTATCGAAATACCCCCGATGGGTAAAAT
1 CGAAAGGTAAAATTACCGAAATACCCCCGAAGGATAAAAT
31986092 GGCCGTAATG
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (54 bp):
CGAAAGGTAAAATTACCGAAATACCCCCGAAGGATAAAATTATCAAAATACCAT
Found at i:31986063 original size:81 final size:81
Alignment explanation
Indices: 31985936--31986091 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
31985926 AAATGGTCGT
* * * *
31985936 AATACCCCCGAAGGGTAAAATTACCGAAATGCCCCTGAAGGATAAAATTATCAAAATGCCCTCGA
1 AATACCCCCGAAGGGTAAAATTACCGAAATACCACTGAAGGATAAAATTATCAAAATACCCCCGA
31986001 AAGGTAAAATTACTGA
66 AAGGTAAAATTACTGA
* * *
31986017 AATACCCCCGAAGGGTAAAATTATCGAAATACCATTGAAAGG-TAAAATTATCGAAATACCCCCG
1 AATACCCCCGAAGGGTAAAATTACCGAAATACCACTG-AAGGATAAAATTATCAAAATACCCCCG
**
31986081 ATGGGTAAAAT
65 AAAGGTAAAAT
31986092 GGCCGTAATG
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
81 61 0.94
82 4 0.06
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (81 bp):
AATACCCCCGAAGGGTAAAATTACCGAAATACCACTGAAGGATAAAATTATCAAAATACCCCCGA
AAGGTAAAATTACTGA
Found at i:31987308 original size:20 final size:20
Alignment explanation
Indices: 31987267--31987308 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
31987257 TCGACCCACC
* *
31987267 TTTTGCTTCATTGTCCTTGT
1 TTTTGCTTAATTGTCCTCGT
31987287 TTTTGCTTGAATTG-CCTCGT
1 TTTTGCTT-AATTGTCCTCGT
31987307 TT
1 TT
31987309 CTTTCTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.07, C:0.19, G:0.17, T:0.57
Consensus pattern (20 bp):
TTTTGCTTAATTGTCCTCGT
Found at i:31989614 original size:54 final size:53
Alignment explanation
Indices: 31989547--31989672 Score: 137
Period size: 55 Copynumber: 2.3 Consensus size: 53
31989537 TCCAAGCCCG
* *
31989547 TGTGTCCACCCGTGTGAGTATTCAAA-ATAGGCCACACGGTCGTGTCGTAAGCCA
1 TGTG-CCAACCGTGTGA-TATTCAAAGATAGGCCACACAGTCGTGTCGTAAGCCA
* * * * *
31989601 TGTGCCAGACCGTGTGTATATTCAAAGTTGGGTCACACAGTCGTGTCGTAGGCCG
1 TGTGCCA-ACCGTGTG-ATATTCAAAGATAGGCCACACAGTCGTGTCGTAAGCCA
31989656 TGTGCCAACCTGTGTGA
1 TGTGCCAACC-GTGTGA
31989673 CAAACTGGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
53 3 0.05
54 23 0.38
55 35 0.57
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (53 bp):
TGTGCCAACCGTGTGATATTCAAAGATAGGCCACACAGTCGTGTCGTAAGCCA
Found at i:31991313 original size:27 final size:27
Alignment explanation
Indices: 31991263--31991343 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
31991253 CTCGCTAGTG
* *
31991263 AGGA-TTCACTAGTGTTTTCAGCGAACT
1 AGGAGTTCACCAGTGTTTT-GGCGAACT
*
31991290 AGGAGTTCCCCAGTGTTTTGGCGAACT
1 AGGAGTTCACCAGTGTTTTGGCGAACT
* * *
31991317 GGGAGTTCACCAGTGTTCTGGTGAACT
1 AGGAGTTCACCAGTGTTTTGGCGAACT
31991344 GGTTCCCATC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 34 0.74
28 12 0.26
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (27 bp):
AGGAGTTCACCAGTGTTTTGGCGAACT
Found at i:31998938 original size:22 final size:23
Alignment explanation
Indices: 31998913--31998955 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
31998903 GTTTTGATTC
31998913 TCCAAACCCATCTTTT-TTGTCG
1 TCCAAACCCATCTTTTATTGTCG
*
31998935 TCCAAACCCCTCTTTTATTGT
1 TCCAAACCCATCTTTTATTGT
31998956 TTTGATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.19, C:0.33, G:0.07, T:0.42
Consensus pattern (23 bp):
TCCAAACCCATCTTTTATTGTCG
Found at i:32003533 original size:16 final size:17
Alignment explanation
Indices: 32003506--32003541 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
32003496 AGAGAGTTGA
32003506 GAGAGAGGATGAAAGAT
1 GAGAGAGGATGAAAGAT
*
32003523 GAGAG-GGATGAAGGAT
1 GAGAGAGGATGAAAGAT
32003539 GAG
1 GAG
32003542 GGATGATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.47, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAAAGAT
Found at i:32006384 original size:19 final size:18
Alignment explanation
Indices: 32006335--32006385 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
32006325 CTACAAGATA
*
32006335 AATATTAAATTAA-ATTT
1 AATATTAAATTAATACTT
32006352 AATATTAAGA-TAATCACTT
1 AATATTAA-ATTAAT-ACTT
32006371 AATATTAAATTAATA
1 AATATTAAATTAATA
32006386 AAATACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 11 0.38
18 3 0.10
19 15 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
AATATTAAATTAATACTT
Found at i:32006878 original size:19 final size:19
Alignment explanation
Indices: 32006845--32006884 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
32006835 AAAGTATCAT
*
32006845 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
32006864 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
32006883 AT
1 AT
32006885 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:32013454 original size:3 final size:3
Alignment explanation
Indices: 32013446--32013472 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
32013436 AACAGCAAAC
32013446 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
32013473 CCACTGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:32020827 original size:18 final size:20
Alignment explanation
Indices: 32020787--32020837 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
32020777 TTAATTTCAA
*
32020787 TTTTTTAATATTATTTAATT
1 TTTTTTAATATTATGTAATT
*
32020807 TTTTTTCAT-TTATGTAATT
1 TTTTTTAATATTATGTAATT
**
32020826 TTAATTAATATT
1 TTTTTTAATATT
32020838 TATTTATGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTTAATATTATGTAATT
Found at i:32021795 original size:7 final size:7
Alignment explanation
Indices: 32021783--32021829 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
32021773 TAGTTGTTTC
32021783 GTATTTA
1 GTATTTA
32021790 GTATTTA
1 GTATTTA
32021797 GTATTTA
1 GTATTTA
32021804 GTATTTA
1 GTATTTA
32021811 GTATTTA
1 GTATTTA
32021818 GTATTTA
1 GTATTTA
32021825 GTATT
1 GTATT
32021830 ATGTATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:32022890 original size:59 final size:61
Alignment explanation
Indices: 32022798--32022926 Score: 192
Period size: 59 Copynumber: 2.1 Consensus size: 61
32022788 TGTATTGATT
* * *
32022798 TTTTTAATATATTTGTACAAATTGTTTTTATATTGTT-T-C-ATTTAATAAAATAGAAGTTG
1 TTTTTAATATATTTGTACAAATTATTTCTATATT-TTGTCCAATTTAATAAAATAGAAGTTC
32022857 TTTTTAATATATTTGTACAAATTATTTCTATATTTTGTCCAATTTAATAAAATAGAAGTTC
1 TTTTTAATATATTTGTACAAATTATTTCTATATTTTGTCCAATTTAATAAAATAGAAGTTC
*
32022918 TTTTGAATA
1 TTTTTAATA
32022927 AGGCAATAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
58 2 0.03
59 33 0.52
60 1 0.02
61 27 0.43
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (61 bp):
TTTTTAATATATTTGTACAAATTATTTCTATATTTTGTCCAATTTAATAAAATAGAAGTTC
Found at i:32025071 original size:3 final size:3
Alignment explanation
Indices: 32025063--32025091 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
32025053 GAATCGCGGA
32025063 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
32025092 ATCCGAACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:32026040 original size:25 final size:25
Alignment explanation
Indices: 32025981--32026043 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
32025971 TAACTTCTAC
32025981 CTTCTCAACTTCTTCAATTTATAAT
1 CTTCTCAACTTCTTCAATTTATAAT
* * * * *
32026006 CTCCTTAACTTTTTCAATTTTTATT
1 CTTCTCAACTTCTTCAATTTATAAT
*
32026031 CTTCTGAACTTCT
1 CTTCTCAACTTCT
32026044 CTAATTTCTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.52
Consensus pattern (25 bp):
CTTCTCAACTTCTTCAATTTATAAT
Found at i:32026508 original size:123 final size:124
Alignment explanation
Indices: 32026120--32026775 Score: 656
Period size: 126 Copynumber: 5.4 Consensus size: 124
32026110 AAGCAGGATG
* * * * *
32026120 TACTGTAGAAAAAGAGTGTCTAGGTGAGAGCTTTTTTCAATACTTTTGCTGACAGTGCATCC-GA
1 TACTGTAGAAAAAGAGCGTCCAAGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCTG-
* * ** *
32026184 CTTGAAGTGTTTTTGACTGTATCTTTTCAGAACCATCTTCTCAAAATTATTTTTTTAGAAAC
65 CTTGAAGCGTTTTTTACCCTAT-TTTTCAGAACCATCTTCTCAAAATTA-TTTTTCAGAAAC
* * * * * *
32026246 TACTGTAGAAAAAGAGTGTCTAGGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGT
1 TACTGTAGAAAAAGAGCGTCCAAGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCTGC
* * * * *
32026311 TTGAAGTGTTTTTGACCCTATCTTTTTAGAATCATCTTCTCAAAATTATTTTTTAGAAAC
66 TTGAAGCGTTTTTTACCCTAT-TTTTCAGAACCATCTTCTCAAAATTATTTTTCAGAAAC
* * *
32026371 TACTATA-AATAAGAGCGTCCAAGTGGGAGCTTTTTT-AGTACTTTTGCTGACAATGCATCCTGC
1 TACTGTAGAAAAAGAGCGTCCAAGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCTGC
*
32026434 TTGAAGCGTTTTTTACACTATTTTTCAGAACCATCTTCTCAAAATTATTTTTCAGAAAC
66 TTGAAGCGTTTTTTACCCTATTTTTCAGAACCATCTTCTCAAAATTATTTTTCAGAAAC
* * * * * *
32026493 TACTGTAGAAAAAGAGTGTCTAGGTGGGAGCTTTTTTTAGTACTTTTGTTGACAGTGCATCCTAC
1 TACTGTAGAAAAAGAGCGTCCAAGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCTGC
* * *
32026558 TTGAAACATTTTTTACCCTATTTTTTCAGAACCA-----TC--------TTTTCAAAAAC
66 TTGAAGCGTTTTTTACCCTA-TTTTTCAGAACCATCTTCTCAAAATTATTTTTCAGAAAC
* * * * * *
32026605 TACAGTAGAAAAATAGCGTTC-AGCTAGGAGCTTTTTTCAGTACTTTTGGTGATAGTGCA---T-
1 TACTGTAGAAAAAGAGCGTCCAAG-TGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCTG
*
32026665 -TTGAAGCCTTTTTTACCCTATTTTATCAGAACCATCTTCTCAAAATTAGTTTTTCAGAAAC
65 CTTGAAGCGTTTTTTACCCTATTTT-TCAGAACCATCTTCTCAAAATTA-TTTTTCAGAAAC
* * * * *
32026726 TAGTGTAGAAAAATAGCATTC-AGCTGGGAACTTTTTTCAGTACTTTTGCT
1 TACTGTAGAAAAAGAGCGTCCAAG-TGGGAGCTTTTTTCAGTACTTTTGCT
32026776 AACTGAACCA
Statistics
Matches: 455, Mismatches: 55, Indels: 45
0.82 0.10 0.08
Matches are distributed among these distances:
106 4 0.01
107 27 0.06
109 1 0.00
111 1 0.00
112 59 0.13
120 2 0.00
121 54 0.12
122 41 0.09
123 67 0.15
124 65 0.14
125 31 0.07
126 102 0.22
127 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (124 bp):
TACTGTAGAAAAAGAGCGTCCAAGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCTGC
TTGAAGCGTTTTTTACCCTATTTTTCAGAACCATCTTCTCAAAATTATTTTTCAGAAAC
Found at i:32026635 original size:112 final size:107
Alignment explanation
Indices: 32026482--32026709 Score: 278
Period size: 112 Copynumber: 2.1 Consensus size: 107
32026472 TCAAAATTAT
* * * * * * *
32026482 TTTTCAGAAACTACTGTAGAAAAAGAGTGTCTAGGTGGGAGCTTTTTTTAGTACTTTTGTTGACA
1 TTTTCAAAAACTACAGTAGAAAAAGAGCGTCTAGCTAGGAGCTTTTTTCAGTACTTTTGGTGACA
*
32026547 GTGCATCCTACTTGAAACATTTTTTACCCTATTTTTTCAGAACCATC
66 GTGCA---T--TTGAAACATTTTTTACCCTATTTTATCAGAACCATC
* *
32026594 TTTTCAAAAACTACAGTAGAAAAATAGCGT-TCAGCTAGGAGCTTTTTTCAGTACTTTTGGTGAT
1 TTTTCAAAAACTACAGTAGAAAAAGAGCGTCT-AGCTAGGAGCTTTTTTCAGTACTTTTGGTGAC
* *
32026658 AGTGCATTTGAAGCCTTTTTTACCCTATTTTATCAGAACCATC
65 AGTGCATTTGAAACATTTTTTACCCTATTTTATCAGAACCATC
*
32026701 TTCTCAAAA
1 TTTTCAAAA
32026710 TTAGTTTTTC
Statistics
Matches: 102, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
107 41 0.40
109 1 0.01
111 1 0.01
112 59 0.58
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (107 bp):
TTTTCAAAAACTACAGTAGAAAAAGAGCGTCTAGCTAGGAGCTTTTTTCAGTACTTTTGGTGACA
GTGCATTTGAAACATTTTTTACCCTATTTTATCAGAACCATC
Found at i:32026889 original size:27 final size:27
Alignment explanation
Indices: 32026859--32026999 Score: 129
Period size: 27 Copynumber: 4.9 Consensus size: 27
32026849 ACAAAAACCT
* *
32026859 AAAACCCTAAACACAAATTTATTTTTA
1 AAAACCCTAAACCCTAATTTATTTTTA
32026886 AAAATCCCTAAACCCTAATTTATTTTTTA
1 AAAA-CCCTAAACCCTAATTTA-TTTTTA
***
32026915 AAAATAATAAACCCTAATTTAATTTATTTTTTA
1 AAAACCCTAAACCC-----TAATTTA-TTTTTA
* *
32026948 AAAACCATAAACCCTAATTTATTTTTT
1 AAAACCCTAAACCCTAATTTATTTTTA
* *
32026975 AAATCCCTAAACCTTAATTTATTTT
1 AAAACCCTAAACCCTAATTTATTTT
32027000 CTCCAAAACT
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
27 31 0.32
28 29 0.30
29 10 0.10
33 26 0.27
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAACCCTAAACCCTAATTTATTTTTA
Found at i:32026896 original size:28 final size:29
Alignment explanation
Indices: 32026859--32026999 Score: 98
Period size: 28 Copynumber: 4.9 Consensus size: 29
32026849 ACAAAAACCT
32026859 AAAA-CCCTAAACACAAATTTA-TTTTTA
1 AAAATCCCTAAACACAAATTTATTTTTTA
* *
32026886 AAAATCCCTAAACCCTAATTTATTTTTTA
1 AAAATCCCTAAACACAAATTTATTTTTTA
** *
32026915 AAAAT-AATAAACCCTAATTTAATTTATTTTTTA
1 AAAATCCCTAAACAC--A---AATTTATTTTTTA
* * *
32026948 AAAA-CCATAAACCCTAATTTATTTTTT-
1 AAAATCCCTAAACACAAATTTATTTTTTA
*
32026975 -AAATCCCTAAAC-CTTAATTTATTTT
1 AAAATCCCTAAACAC-AAATTTATTTT
32027000 CTCCAAAACT
Statistics
Matches: 96, Mismatches: 8, Indels: 20
0.77 0.06 0.16
Matches are distributed among these distances:
26 4 0.04
27 22 0.23
28 34 0.35
29 11 0.11
33 25 0.26
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATCCCTAAACACAAATTTATTTTTTA
Found at i:32026943 original size:33 final size:33
Alignment explanation
Indices: 32026901--32026968 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
32026891 CCCTAAACCC
*
32026901 TAATTTATTTTTTAAAAATAATAAACCCTAATT
1 TAATTTATTTTTTAAAAACAATAAACCCTAATT
*
32026934 TAATTTATTTTTTAAAAACCATAAACCCTAATT
1 TAATTTATTTTTTAAAAACAATAAACCCTAATT
32026967 TA
1 TA
32026969 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (33 bp):
TAATTTATTTTTTAAAAACAATAAACCCTAATT
Found at i:32030101 original size:93 final size:94
Alignment explanation
Indices: 32029946--32030120 Score: 298
Period size: 93 Copynumber: 1.9 Consensus size: 94
32029936 AGATAAAAAG
*
32029946 AGGATTTGATATATTTCTTATCAGATAAGAAAATAGAATTTAATTATTATTTAAAAGAGTTTTAG
1 AGGATTTGATATATTTCTTATCAAATAAGAAAATAGAATTTAATTATTATTTAAAAGAGTTTTAG
*
32030011 ATAAATAATAATTAAAATTCAAAATCAAA
66 ATAAATAATAAATAAAATTCAAAATCAAA
* * *
32030040 AGGATTTGATATATTTCTTATCAAATAAG-GAATAGAATTTAGTTGTTATTTAAAAGAGTTTTAG
1 AGGATTTGATATATTTCTTATCAAATAAGAAAATAGAATTTAATTATTATTTAAAAGAGTTTTAG
32030104 ATAAATAATAAATAAAA
66 ATAAATAATAAATAAAA
32030121 CATAATTTAA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 48 0.63
94 28 0.37
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.38
Consensus pattern (94 bp):
AGGATTTGATATATTTCTTATCAAATAAGAAAATAGAATTTAATTATTATTTAAAAGAGTTTTAG
ATAAATAATAAATAAAATTCAAAATCAAA
Found at i:32030129 original size:49 final size:48
Alignment explanation
Indices: 32030073--32030199 Score: 157
Period size: 49 Copynumber: 2.6 Consensus size: 48
32030063 AATAAGGAAT
* * *
32030073 AGAATTTAGTTGTTATTTAAAAGAGTTTTAGATAAATA-ATAAATAAAAC
1 AGAATTTAATTATTATTTAAAAGAGTTTTAAATAAA-AGATAAAT-AAAC
* * * *
32030122 ATAATTTAATTATTATTTGAAAGAGTTTTAAATAAAAGATAACTAAAT
1 AGAATTTAATTATTATTTAAAAGAGTTTTAAATAAAAGATAAATAAAC
32030170 AGAATTTAAATTATTATTTAAAAGAGTTTT
1 AGAATTT-AATTATTATTTAAAAGAGTTTT
32030200 TAAAATTCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
48 10 0.15
49 57 0.85
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (48 bp):
AGAATTTAATTATTATTTAAAAGAGTTTTAAATAAAAGATAAATAAAC
Found at i:32045624 original size:18 final size:18
Alignment explanation
Indices: 32045590--32045625 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32045580 GATGTGTACA
**
32045590 TACAACTAGAGGGTTTTG
1 TACAACTAGAGAATTTTG
32045608 TACAACTAGAGAATTTTG
1 TACAACTAGAGAATTTTG
32045626 GTAAAGTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (18 bp):
TACAACTAGAGAATTTTG
Found at i:32046924 original size:7 final size:7
Alignment explanation
Indices: 32046874--32046908 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
32046864 AGAAAATCAC
32046874 AAAAAAT
1 AAAAAAT
*
32046881 AAAGAAT
1 AAAAAAT
*
32046888 AAAGAAT
1 AAAAAAT
32046895 AAAAAAT
1 AAAAAAT
32046902 AAAAAAT
1 AAAAAAT
32046909 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:32046936 original size:18 final size:18
Alignment explanation
Indices: 32046892--32046937 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
32046882 AAGAATAAAG
*
32046892 AATAAAAAATAAAAAATT
1 AATAAAAAATAAAAAATA
*
32046910 AATTAAAAAT-AAAAATA
1 AATAAAAAATAAAAAATA
32046927 AATAACAAAAT
1 AATAA-AAAAT
32046938 TGCAACAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (18 bp):
AATAAAAAATAAAAAATA
Found at i:32065511 original size:12 final size:12
Alignment explanation
Indices: 32065489--32065528 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
32065479 ATCAAAGATT
32065489 AGAATAGTAAAGA
1 AGAA-AGTAAAGA
32065502 AGAAAGTAAAGA
1 AGAAAGTAAAGA
**
32065514 AGAAAACAAAGA
1 AGAAAGTAAAGA
32065526 AGA
1 AGA
32065529 TAGATGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.68, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
AGAAAGTAAAGA
Found at i:32065542 original size:9 final size:9
Alignment explanation
Indices: 32065530--32065555 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
32065520 CAAAGAAGAT
32065530 AGATGGAAA
1 AGATGGAAA
32065539 AGATGGAAA
1 AGATGGAAA
32065548 AGATGGAA
1 AGATGGAA
32065556 CATGACATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.12
Consensus pattern (9 bp):
AGATGGAAA
Found at i:32069791 original size:68 final size:68
Alignment explanation
Indices: 32069682--32069817 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
32069672 TCGATTATCT
*
32069682 ATAAAACATGGGAAATGAGACTATGTAAGGATAAAATGCTTAGTAAGTTCTTATAACATAAAACA
1 ATAAAACATGGGAAATGAGACTATGTAAGCATAAAATGCTTAGTAAGTTCTTATAACATAAAACA
32069747 CAA
66 CAA
32069750 ATAAAACATGGGAAATGAGACTATGTAAGCATAAAATGCTTAGTAAGTTCTTATAACATAAAACA
1 ATAAAACATGGGAAATGAGACTATGTAAGCATAAAATGCTTAGTAAGTTCTTATAACATAAAACA
32069815 CAA
66 CAA
32069818 CTTACCATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (68 bp):
ATAAAACATGGGAAATGAGACTATGTAAGCATAAAATGCTTAGTAAGTTCTTATAACATAAAACA
CAA
Found at i:32070226 original size:26 final size:26
Alignment explanation
Indices: 32070188--32070256 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
32070178 CTTACATCGT
* *
32070188 TGCTCACACGAGCTGTGAAATG-GATC
1 TGCTCACATGAGCTGTGAAATGTG-CC
*
32070214 TGCTCACATGAGCTGTAAAATGTGCC
1 TGCTCACATGAGCTGTGAAATGTGCC
*
32070240 TGCTCACATGAGGTGTG
1 TGCTCACATGAGCTGTG
32070257 GGTCGGGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 36 0.97
27 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (26 bp):
TGCTCACATGAGCTGTGAAATGTGCC
Found at i:32078152 original size:18 final size:18
Alignment explanation
Indices: 32078129--32078164 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
32078119 TTTAAATGTC
32078129 ATTAATTT-TAGAAAAGGG
1 ATTAATTTGTA-AAAAGGG
32078147 ATTAATTTGTAAAAAGGG
1 ATTAATTTGTAAAAAGGG
32078165 TCAAATTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (18 bp):
ATTAATTTGTAAAAAGGG
Found at i:32085256 original size:25 final size:24
Alignment explanation
Indices: 32085194--32085266 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
32085184 TTATCAATTC
* *
32085194 TCAACTTGTGAGAGCTTACCAATT
1 TCAACTCGTGAGAGCTTACCGATT
* *
32085218 TGAGCTCGTGAGAGCTTACCGATT
1 TCAACTCGTGAGAGCTTACCGATT
* *
32085242 TACAACTCGTGAGAGCATATCGATT
1 T-CAACTCGTGAGAGCTTACCGATT
32085267 CATAGCTCCT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 21 0.52
25 19 0.47
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (24 bp):
TCAACTCGTGAGAGCTTACCGATT
Found at i:32086090 original size:34 final size:34
Alignment explanation
Indices: 32086047--32086116 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
32086037 TTATTCACTT
32086047 GTGAGTTGTTGGATATGGTTTCATGAACTTTACA
1 GTGAGTTGTTGGATATGGTTTCATGAACTTTACA
32086081 GTGAGTTGTTGGATATGGTTTCATGAACTTTACA
1 GTGAGTTGTTGGATATGGTTTCATGAACTTTACA
32086115 GT
1 GT
32086117 ATTGTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (34 bp):
GTGAGTTGTTGGATATGGTTTCATGAACTTTACA
Found at i:32094875 original size:68 final size:68
Alignment explanation
Indices: 32094766--32094918 Score: 270
Period size: 68 Copynumber: 2.2 Consensus size: 68
32094756 CTTGGCTCGA
*
32094766 CTATGGTCTTACACATTATGATCCCATGTTTACTATCCTGGCAGACTTTATATGTTGCCATAGCC
1 CTATGGTCTTACACATTATGATCCCATGTTTACTATCCTGGCAGACTTCATATGTTGCCATAGCC
*
32094831 CAG
66 AAG
* *
32094834 CTATGATCTTACACATTATGATCCTATGTTTACTATCCTGGCAGACTTCATATGTTGCCATAGCC
1 CTATGGTCTTACACATTATGATCCCATGTTTACTATCCTGGCAGACTTCATATGTTGCCATAGCC
32094899 AAG
66 AAG
32094902 CTATGGTCTTACACATT
1 CTATGGTCTTACACATT
32094919 TTGGTGCCAT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 80 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (68 bp):
CTATGGTCTTACACATTATGATCCCATGTTTACTATCCTGGCAGACTTCATATGTTGCCATAGCC
AAG
Found at i:32095778 original size:42 final size:42
Alignment explanation
Indices: 32095732--32095812 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
32095722 TGTGCTCACC
* * *
32095732 CGTGTAACTCACTGAGTTGCCCCACATGCCTGTGTGCCAAGT
1 CGTGTAACTCACTGAGTTGACACACATGCCCGTGTGCCAAGT
**
32095774 CGTGTAACTCTTTGAGTTGACACACATGCCCGTGTGCCA
1 CGTGTAACTCACTGAGTTGACACACATGCCCGTGTGCCA
32095813 GGCAATGTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (42 bp):
CGTGTAACTCACTGAGTTGACACACATGCCCGTGTGCCAAGT
Found at i:32096805 original size:40 final size:40
Alignment explanation
Indices: 32096504--32096793 Score: 404
Period size: 40 Copynumber: 7.3 Consensus size: 40
32096494 ATACTATTTG
* * * * *
32096504 ATTCAGGGTTACCAAAGTGCAAA-TGGGGCAAGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
*
32096543 ATTCAGGGGTACCGAAGTACAAATAGGGGCACGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
* * *
32096583 ATTCAGGGGTACCTAAGTACAAACAGGGGAACGTATATGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
* * *
32096623 ATTTAAGGGTACCGAAGTACAAACAGGGGCACATATGCT-C
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATG-TGC
32096663 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
* * *
32096703 ATTTAGGGGTACCAAAGTACAAACAGGGGCACTTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
* *
32096743 ATTCAGGGGTACCGAAGTATAAATAGGGGCACGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
32096783 ATTCAGGGGTA
1 ATTCAGGGGTA
32096794 ATTATCTATA
Statistics
Matches: 222, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 21 0.09
40 200 0.90
41 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (40 bp):
ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
Found at i:32098823 original size:17 final size:17
Alignment explanation
Indices: 32098798--32098831 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32098788 ATAATATATA
32098798 AAAAATTTAAAGTAAAT
1 AAAAATTTAAAGTAAAT
* *
32098815 AAAAGTTTAAATTAAAT
1 AAAAATTTAAAGTAAAT
32098832 GATTTATAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
AAAAATTTAAAGTAAAT
Found at i:32098900 original size:25 final size:25
Alignment explanation
Indices: 32098872--32098939 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
32098862 AAAAATTTTC
*
32098872 AAATAAACAAAATAAAAAAAACTTA
1 AAATAAATAAAATAAAAAAAACTTA
* *
32098897 AAATAAATAACAAT-AAAATAATTTA
1 AAATAAATAA-AATAAAAAAAACTTA
*
32098922 AAATAAATAATATAAAAA
1 AAATAAATAAAATAAAAA
32098940 TAACATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.05
25 32 0.86
26 3 0.08
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (25 bp):
AAATAAATAAAATAAAAAAAACTTA
Found at i:32098915 original size:15 final size:16
Alignment explanation
Indices: 32098895--32098955 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 16
32098885 AAAAAAAACT
32098895 TAAAATAA-ATAACAA
1 TAAAATAATATAACAA
*
32098910 TAAAATAATTTAA-AA
1 TAAAATAATATAACAA
*
32098925 T-AAATAATATAAAAA
1 TAAAATAATATAACAA
* *
32098940 TAACAT-ATAAAACAA
1 TAAAATAATATAACAA
32098955 T
1 T
32098956 TTTTTAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.26
15 22 0.58
16 6 0.16
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATAATATAACAA
Found at i:32098931 original size:14 final size:14
Alignment explanation
Indices: 32098897--32098938 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
32098887 AAAAAACTTA
32098897 AAATAA-ATAACAAT
1 AAATAATATAA-AAT
*
32098911 AAAATAATTTAAAAT
1 -AAATAATATAAAAT
32098926 AAATAATATAAAA
1 AAATAATATAAAA
32098939 ATAACATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.50
15 9 0.38
16 3 0.12
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAATATAAAAT
Found at i:32099084 original size:26 final size:26
Alignment explanation
Indices: 32098988--32099086 Score: 112
Period size: 26 Copynumber: 3.8 Consensus size: 26
32098978 ATTTGAAAGT
* * *
32098988 TATATATAATAGTTTACAATAAATAA
1 TATATATAAAAATTTAAAATAAATAA
*
32099014 TATATAAAAGAAATTT-AAATAAATAA
1 TATATATAA-AAATTTAAAATAAATAA
* *
32099040 TATGTA-AAACAACTTAAAATAAATAA
1 TATATATAAA-AATTTAAAATAAATAA
32099066 TATATATAAAAATTTAAAATA
1 TATATATAAAAATTTAAAATA
32099087 GAGGATGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
24 1 0.02
25 6 0.10
26 47 0.77
27 7 0.11
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (26 bp):
TATATATAAAAATTTAAAATAAATAA
Done.