Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 1 of 12
Found at i:2752 original size:2 final size:2
Alignment explanation
Indices: 2745--2771 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2735 NNNNNNNNNN
2745 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2772 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2776 original size:2 final size:2
Alignment explanation
Indices: 2771--2796 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2761 ATATATATAT
2771 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
2797 TAGCTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9279 original size:13 final size:13
Alignment explanation
Indices: 9263--9287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9253 AAAAAACCCT
9263 AAACCTCAAACCG
1 AAACCTCAAACCG
9276 AAACCTCAAACC
1 AAACCTCAAACC
9288 CCGACTCTCG
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:0.48, C:0.40, G:0.04, T:0.08
Consensus pattern (13 bp):
AAACCTCAAACCG
Found at i:9307 original size:6 final size:6
Alignment explanation
Indices: 9296--9339 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
9286 CCCCGACTCT
* *
9296 CGAACC CGAACC TGAACC TCGAACC CAAACC CGAACCC CGAACC
1 CGAACC CGAACC CGAACC -CGAACC CGAACC CGAA-CC CGAACC
9340 TGACTCCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 21 0.66
7 11 0.34
ACGTcount: A:0.34, C:0.48, G:0.14, T:0.05
Consensus pattern (6 bp):
CGAACC
Found at i:9318 original size:19 final size:19
Alignment explanation
Indices: 9294--9339 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
9284 AACCCCGACT
* *
9294 CTCGAACCCGAACCTGAAC
1 CTCGAACCCAAACCCGAAC
9313 CTCGAACCCAAACCCGAAC
1 CTCGAACCCAAACCCGAAC
*
9332 CCCGAACC
1 CTCGAACC
9340 TGACTCCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.48, G:0.13, T:0.07
Consensus pattern (19 bp):
CTCGAACCCAAACCCGAAC
Found at i:9335 original size:7 final size:7
Alignment explanation
Indices: 9296--9476 Score: 73
Period size: 7 Copynumber: 27.0 Consensus size: 7
9286 CCCCGACTCT
9296 CGAA-CC
1 CGAACCC
9302 CGAA-CC
1 CGAACCC
* *
9308 TGAACCT
1 CGAACCC
9315 CGAA-CC
1 CGAACCC
*
9321 C-AAACC
1 CGAACCC
9327 CGAACCC
1 CGAACCC
9334 CGAA-CC
1 CGAACCC
*
9340 TG-ACTCC
1 CGAAC-CC
9347 C-AACCCC
1 CGAA-CCC
9354 CG-ACCC
1 CGAACCC
9360 TCG-ACCC
1 -CGAACCC
*
9367 CGAGCCC
1 CGAACCC
*
9374 CGAACTCT
1 CGAAC-CC
9382 CGAACCC
1 CGAACCC
9389 C-AACCC
1 CGAACCC
*
9395 CCAACCC
1 CGAACCC
*
9402 CAAACCC
1 CGAACCC
*
9409 CGAACCT
1 CGAACCC
*
9416 CG-ACCA
1 CGAACCC
9422 CG-ACCC
1 CGAACCC
*
9428 TTGAACCC
1 -CGAACCC
*
9436 CGAA-GC
1 CGAACCC
*
9442 CGGACCC
1 CGAACCC
*
9449 CAAACCC
1 CGAACCC
* *
9456 CTAACCT
1 CGAACCC
*
9463 TGAACCC
1 CGAACCC
9470 CGAACCC
1 CGAACCC
9477 GACTCGAAAC
Statistics
Matches: 131, Mismatches: 29, Indels: 29
0.69 0.15 0.15
Matches are distributed among these distances:
5 3 0.02
6 40 0.31
7 77 0.59
8 11 0.08
ACGTcount: A:0.28, C:0.52, G:0.13, T:0.07
Consensus pattern (7 bp):
CGAACCC
Found at i:9339 original size:13 final size:13
Alignment explanation
Indices: 9296--9478 Score: 58
Period size: 13 Copynumber: 13.7 Consensus size: 13
9286 CCCCGACTCT
9296 CGAACCCGAA-CC
1 CGAACCCGAACCC
*
9308 TGAACCTCGAA-CC
1 CGAACC-CGAACCC
*
9321 CAAACCCGAACCC
1 CGAACCCGAACCC
*
9334 CGAACCTG-ACTCC
1 CGAACCCGAAC-CC
9347 C-AACCCCCG-ACCC
1 CGAA--CCCGAACCC
* *
9360 TCGACCCCGAGCCC
1 -CGAACCCGAACCC
9374 CGAACTCTCGAACCC
1 CGAAC-C-CGAACCC
*
9389 C-AACCCCCAACCC
1 CGAA-CCCGAACCC
* *
9402 CAAACCCCGAACCT
1 CGAA-CCCGAACCC
9416 CG-ACCACG-ACCC
1 CGAACC-CGAACCC
* *
9428 TTGAACCCCGAAGCC
1 -CGAA-CCCGAACCC
* * *
9443 GGACCCCAAACCC
1 CGAACCCGAACCC
* *
9456 CTAACCTTGAACCC
1 CGAACC-CGAACCC
9470 CGAACCCGA
1 CGAACCCGA
9479 CTCGAAACCC
Statistics
Matches: 125, Mismatches: 28, Indels: 35
0.66 0.15 0.19
Matches are distributed among these distances:
12 18 0.14
13 54 0.43
14 39 0.31
15 14 0.11
ACGTcount: A:0.28, C:0.51, G:0.13, T:0.07
Consensus pattern (13 bp):
CGAACCCGAACCC
Found at i:9383 original size:21 final size:20
Alignment explanation
Indices: 9325--9476 Score: 89
Period size: 20 Copynumber: 7.5 Consensus size: 20
9315 CGAACCCAAA
9325 CCCGAACCCCGAACCT-GAC
1 CCCGAACCCCGAACCTCGAC
*
9344 TCCC-AACCCCCGACCCTCGAC
1 -CCCGAA-CCCCGAACCTCGAC
*
9365 CCCGAGCCCCGAACTCTCGAAC
1 CCCGAACCCCGAAC-CTCG-AC
* * *
9387 CCC-AACCCCCAACCCCAAAC
1 CCCGAACCCCGAACCTC-GAC
* *
9407 CCCGAACCTCG-ACCACGAC
1 CCCGAACCCCGAACCTCGAC
* *
9426 CCTTGAACCCCGAAGCC-GGAC
1 CC-CGAACCCCGAA-CCTCGAC
* * *
9447 CCCAAACCCCTAACCTTGAAC
1 CCCGAACCCCGAACCTCG-AC
9468 CCCGAACCC
1 CCCGAACCC
9477 GACTCGAAAC
Statistics
Matches: 101, Mismatches: 19, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
19 8 0.08
20 49 0.49
21 37 0.37
22 7 0.07
ACGTcount: A:0.26, C:0.54, G:0.12, T:0.07
Consensus pattern (20 bp):
CCCGAACCCCGAACCTCGAC
Found at i:9495 original size:33 final size:34
Alignment explanation
Indices: 9426--9495 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
9416 CGACCACGAC
* **
9426 CCTTGAACCCCGAAGCCGGACCCCAAACCCCTAA
1 CCTTGAACCCCGAAGCCCGACCCCAAACCCAGAA
* *
9460 CCTTGAACCCCGAA-CCCGACTCGAAACCCAGAA
1 CCTTGAACCCCGAAGCCCGACCCCAAACCCAGAA
9493 CCT
1 CCT
9496 ACATTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.30, C:0.46, G:0.14, T:0.10
Consensus pattern (34 bp):
CCTTGAACCCCGAAGCCCGACCCCAAACCCAGAA
Found at i:9696 original size:21 final size:21
Alignment explanation
Indices: 9657--9733 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
9647 TTTCAAGGTC
*
9657 CTTTTTAAT-GA-TATTTAAA
1 CTTTTTAATAGATTTTTTAAA
*
9676 GTTTTTAATAGATTTTTTAAA
1 CTTTTTAATAGATTTTTTAAA
* * * *
9697 CATTTTGATAAATTTTTTATA
1 CTTTTTAATAGATTTTTTAAA
* *
9718 TTTTTTAAGA-ATTTTT
1 CTTTTTAATAGATTTTT
9734 AATTTTCTTA
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
19 8 0.18
20 8 0.18
21 29 0.64
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (21 bp):
CTTTTTAATAGATTTTTTAAA
Found at i:25116 original size:22 final size:22
Alignment explanation
Indices: 25088--25130 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
25078 TAAGAAATAA
*
25088 GAGAAATGTGTAGACATGTTAC
1 GAGAAATGTGCAGACATGTTAC
25110 GAGAAATGTGCAGACATGTTA
1 GAGAAATGTGCAGACATGTTA
25131 ATATCTGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (22 bp):
GAGAAATGTGCAGACATGTTAC
Found at i:26683 original size:16 final size:17
Alignment explanation
Indices: 26662--26705 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
26652 ACCGTTAACA
*
26662 TAAAATTT-ATATCTTT
1 TAAAATTTAATATATTT
26678 TAAAATTTAATATATTT
1 TAAAATTTAATATATTT
*
26695 AAAAATGTTAA
1 TAAAAT-TTAA
26706 ATTCTTATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.33
17 12 0.50
18 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TAAAATTTAATATATTT
Found at i:27527 original size:6 final size:6
Alignment explanation
Indices: 27516--27548 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
27506 CGAAGCCTGA
27516 CACGCC CACGCC CACGCC CACGCC CACGCC CAC
1 CACGCC CACGCC CACGCC CACGCC CACGCC CAC
27549 CATCACCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.67, G:0.15, T:0.00
Consensus pattern (6 bp):
CACGCC
Found at i:40346 original size:220 final size:219
Alignment explanation
Indices: 39918--40357 Score: 835
Period size: 220 Copynumber: 2.0 Consensus size: 219
39908 GTTAGGGGAA
39918 TTAAGCTATATCCTAATAGTAAAGTTAGACATTAATGAATAAGGAATGTTTTGTTATCATCAAAA
1 TTAAGCTATATCCTAATAGTAAAGTTAGACATTAATGAATAAGGAATGTTTTGTTATCATCAAAA
39983 ATATATGGACTCAACCGTATGTTCTCTTGATGGTGCCTTTAGAATTTTTTGCTGTTTCTTCTTAG
66 ATATATGGACTCAACCGTATGTTCTCTTGATGGTGCCTTTAGAATTTTTTGCTGTTTCTTCTTAG
*
40048 GTAAAGCATTGATACCGGTTTTTTTACCAGTATGTTAGGTTTTTTGGTGCCTTCGAGAATAACTC
131 GTAAAGCATTGATACCGGTTTCTTTACCAGTATGTTAGGTTTTTTGGTGCCTTCGAGAATAACTC
40113 TCTCTCTCTCTCTCTCTTGCATTC
196 TCTCTCTCTCTCTCTCTTGCATTC
40137 TTAAGCTATATCCTAATAGTAAAGTTAGACATTAATGAATAAGGAATGTTTTGTTATCATCAAAA
1 TTAAGCTATATCCTAATAGTAAAGTTAGACATTAATGAATAAGGAATGTTTTGTTATCATCAAAA
*
40202 ATATATGGACTCAACCGTATGTTCTCTTGATGGTGCTTTCTAGAATTTTTTGCTGTTTCTTCTTA
66 ATATATGGACTCAACCGTATGTTCTCTTGATGGTGCCTT-TAGAATTTTTTGCTGTTTCTTCTTA
40267 GGTAAAGCATTGATACCGGTTTCTTTACCAGTATGTTAGGTTTTTTGGTGCCTTCGAGAATAACT
130 GGTAAAGCATTGATACCGGTTTCTTTACCAGTATGTTAGGTTTTTTGGTGCCTTCGAGAATAACT
* *
40332 CTGTTTCTCTCTCTCTCTTGCATTC
195 CTCTCTCTCTCTCTCTCTTGCATTC
40357 T
1 T
40358 CTCTTTCTTA
Statistics
Matches: 216, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
219 103 0.48
220 113 0.52
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (219 bp):
TTAAGCTATATCCTAATAGTAAAGTTAGACATTAATGAATAAGGAATGTTTTGTTATCATCAAAA
ATATATGGACTCAACCGTATGTTCTCTTGATGGTGCCTTTAGAATTTTTTGCTGTTTCTTCTTAG
GTAAAGCATTGATACCGGTTTCTTTACCAGTATGTTAGGTTTTTTGGTGCCTTCGAGAATAACTC
TCTCTCTCTCTCTCTCTTGCATTC
Found at i:51427 original size:29 final size:29
Alignment explanation
Indices: 51385--51443 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
51375 GCGACCGGCC
51385 TTGGACGGAATCTACCCAATTATATTCCG
1 TTGGACGGAATCTACCCAATTATATTCCG
51414 TTGGACGGAATCTACCCAATTATATTCCG
1 TTGGACGGAATCTACCCAATTATATTCCG
51443 T
1 T
51444 CCGGCAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (29 bp):
TTGGACGGAATCTACCCAATTATATTCCG
Found at i:59208 original size:2 final size:2
Alignment explanation
Indices: 59201--59241 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
59191 TTTTATTGGC
59201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59242 CACAAACATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59538 original size:13 final size:13
Alignment explanation
Indices: 59520--59545 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59510 GTAAATTTTT
59520 ACATAAATAAAAA
1 ACATAAATAAAAA
59533 ACATAAATAAAAA
1 ACATAAATAAAAA
59546 TAAAATAATC
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
ACATAAATAAAAA
Found at i:66487 original size:16 final size:16
Alignment explanation
Indices: 66468--66498 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
66458 TAGGTGGCTG
*
66468 AAAATGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
66484 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
66499 GGGATATCCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:68124 original size:7 final size:7
Alignment explanation
Indices: 68112--68152 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
68102 TCGACCATAG
68112 CTGTTGC
1 CTGTTGC
68119 CTGTTGC
1 CTGTTGC
68126 CTGTTGC
1 CTGTTGC
68133 CTGTTGC
1 CTGTTGC
68140 CTGTTGC
1 CTGTTGC
68147 CTGTTG
1 CTGTTG
68153 GTGTTGGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.00, C:0.27, G:0.29, T:0.44
Consensus pattern (7 bp):
CTGTTGC
Found at i:96213 original size:2 final size:2
Alignment explanation
Indices: 96206--96231 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
96196 AGGAAAGCTA
96206 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
96232 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:96236 original size:2 final size:2
Alignment explanation
Indices: 96231--96260 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
96221 TCTCTCTCTC
96231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
96261 ATTCTACTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:113799 original size:2 final size:2
Alignment explanation
Indices: 113794--113829 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
113784 AATTCATTAG
* *
113794 TA TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
113830 GCAGCTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:115599 original size:2 final size:2
Alignment explanation
Indices: 115592--115630 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
115582 ATGATTAATA
* * *
115592 AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115631 GATGATGCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:115609 original size:12 final size:12
Alignment explanation
Indices: 115592--115630 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
115582 ATGATTAATA
*
115592 ATATATATATAT
1 ATATATATCTAT
115604 ATATATATCTAT
1 ATATATATCTAT
*
115616 ATCTATATCTAT
1 ATATATATCTAT
115628 ATA
1 ATA
115631 GATGATGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATATATCTAT
Found at i:117527 original size:2 final size:2
Alignment explanation
Indices: 117522--117553 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
117512 GTGTGTTTAC
117522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117554 GTTAGAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118006 original size:6 final size:6
Alignment explanation
Indices: 117995--118020 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
117985 GAAATTCCCC
117995 CTTTCT CTTTCT CTTTCT CTTTCT CT
1 CTTTCT CTTTCT CTTTCT CTTTCT CT
118021 GTTTTAGGGT
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (6 bp):
CTTTCT
Found at i:128289 original size:43 final size:43
Alignment explanation
Indices: 128228--128373 Score: 274
Period size: 43 Copynumber: 3.4 Consensus size: 43
128218 AGAACCTTTC
*
128228 AAAACTTTAGAGGGAAATCTTTTGGGGGGAATACTTTGAATTG
1 AAAACTTTGGAGGGAAATCTTTTGGGGGGAATACTTTGAATTG
128271 AAAACTTTGGAGGGAAATCTTTTGGGGGGAATACTTTGAATTG
1 AAAACTTTGGAGGGAAATCTTTTGGGGGGAATACTTTGAATTG
*
128314 AAAACTTTGGAGGGAAATCTTTTGGGGGGAATACTTTGAATTA
1 AAAACTTTGGAGGGAAATCTTTTGGGGGGAATACTTTGAATTG
128357 AAAACTTTGGAGGGAAA
1 AAAACTTTGGAGGGAAA
128374 AGTGGGTGGG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.31
Consensus pattern (43 bp):
AAAACTTTGGAGGGAAATCTTTTGGGGGGAATACTTTGAATTG
Found at i:128349 original size:29 final size:28
Alignment explanation
Indices: 128231--128351 Score: 75
Period size: 29 Copynumber: 4.2 Consensus size: 28
128221 ACCTTTCAAA
* *
128231 ACTTTAGAGGGAAATCTTTTGGGGGGAAT
1 ACTTTGGAGGGAAATC-TTTGGAGGGAAT
* ** *
128260 ACTTTGAATTGAAAACTTTGGAGGGAA-
1 ACTTTGGAGGGAAATCTTTGGAGGGAAT
* * ** *
128287 ATCTTTTGG-GGGGAATACTTTGAATTGAAA
1 A-C-TTTGGAGGGAAAT-CTTTGGAGGGAAT
*
128317 ACTTTGGAGGGAAATCTTTTGGGGGGAAT
1 ACTTTGGAGGGAAATC-TTTGGAGGGAAT
128346 ACTTTG
1 ACTTTG
128352 AATTAAAAAC
Statistics
Matches: 66, Mismatches: 20, Indels: 12
0.67 0.20 0.12
Matches are distributed among these distances:
27 1 0.02
28 20 0.30
29 44 0.67
30 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (28 bp):
ACTTTGGAGGGAAATCTTTGGAGGGAAT
Found at i:128374 original size:14 final size:14
Alignment explanation
Indices: 128228--128374 Score: 87
Period size: 14 Copynumber: 10.3 Consensus size: 14
128218 AGAACCTTTC
*
128228 AAAACTTTAGAGGG
1 AAAACTTTGGAGGG
* *
128242 AAATCTTTTGGGGGG
1 AAAAC-TTTGGAGGG
* * **
128257 AATACTTTGAATTG
1 AAAACTTTGGAGGG
128271 AAAACTTTGGAGGG
1 AAAACTTTGGAGGG
* *
128285 AAATCTTTTGGGGGG
1 AAAAC-TTTGGAGGG
* * **
128300 AATACTTTGAATTG
1 AAAACTTTGGAGGG
128314 AAAACTTTGGAGGG
1 AAAACTTTGGAGGG
* *
128328 AAATCTTTTGGGGGG
1 AAAAC-TTTGGAGGG
* * ***
128343 AATACTTTGAATTA
1 AAAACTTTGGAGGG
128357 AAAACTTTGGAGGG
1 AAAACTTTGGAGGG
128371 AAAA
1 AAAA
128375 GTGGGTGGGG
Statistics
Matches: 91, Mismatches: 39, Indels: 6
0.67 0.29 0.04
Matches are distributed among these distances:
14 59 0.65
15 32 0.35
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.31
Consensus pattern (14 bp):
AAAACTTTGGAGGG
Found at i:129766 original size:19 final size:20
Alignment explanation
Indices: 129723--129772 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
129713 CTGTCAAATC
129723 AGATCAAAGATAAACAGTAA
1 AGATCAAAGATAAACAGTAA
129743 AGATCAAAGATAAACAGT-A
1 AGATCAAAGATAAACAGTAA
129762 AGATCAAAGAT
1 AGATCAAAGAT
129773 TTACAACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.58, C:0.10, G:0.16, T:0.16
Consensus pattern (20 bp):
AGATCAAAGATAAACAGTAA
Found at i:162153 original size:5 final size:5
Alignment explanation
Indices: 162145--162172 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
162135 TTCTTTTCAC
162145 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
162173 TTTGACCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:175939 original size:28 final size:28
Alignment explanation
Indices: 175871--175939 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
175861 ATTTAAAAAT
*
175871 TTTTAAATAATTTTTTATTATTTTATTA
1 TTTTAAATAAATTTTTATTATTTTATTA
* *
175899 TATTTAATTAAATTTTTA-TATTTTTTTA
1 T-TTTAAATAAATTTTTATTATTTTATTA
175927 TTTTAAATCAAAT
1 TTTTAAAT-AAAT
175940 AAATTTTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.17
28 15 0.43
29 14 0.40
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTTAAATAAATTTTTATTATTTTATTA
Found at i:185455 original size:5 final size:5
Alignment explanation
Indices: 185408--185461 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
185398 CATTAAGGTA
* *
185408 TTATT TTCTT TT-TT TT-TT TTATT TTA-T TTATTT TTATCA TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTA-TT TTAT-T TTATT TTATT
185457 TTATT
1 TTATT
185462 GAGTTTTGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 12 0.29
5 22 0.52
6 8 0.19
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:193439 original size:16 final size:16
Alignment explanation
Indices: 193418--193448 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
193408 CAGTTGCAAT
193418 ATCAAACAAACTTGAG
1 ATCAAACAAACTTGAG
*
193434 ATCAAAGAAACTTGA
1 ATCAAACAAACTTGA
193449 ACGTCATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.19
Consensus pattern (16 bp):
ATCAAACAAACTTGAG
Found at i:208020 original size:4 final size:4
Alignment explanation
Indices: 208011--208049 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
208001 CCAAAACTAG
208011 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
208050 TATGAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:211720 original size:12 final size:12
Alignment explanation
Indices: 211705--211750 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
211695 ATTCTCTCCT
211705 TTCTCTTCCTTC
1 TTCTCTTCCTTC
*
211717 TTCTCTTCTTTC
1 TTCTCTTCCTTC
211729 TTCTCTT-CTTCC
1 TTCTCTTCCTT-C
*
211741 TTCTTTTCCT
1 TTCTCTTCCT
211751 CATCCTTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 2 0.07
12 25 0.86
13 2 0.07
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTCTTCCTTC
Found at i:211758 original size:27 final size:26
Alignment explanation
Indices: 211701--211758 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
211691 CTTTATTCTC
* *
211701 TCCTT-TCTCTTCCTTCTTCTCTTCT
1 TCCTTCTCTCTTCCTTCTTCTCCTCA
* *
211726 TTCTTCTCTTCTTCCTTCTTTTCCTCA
1 TCCTTCTC-TCTTCCTTCTTCTCCTCA
211753 TCCTTC
1 TCCTTC
211759 ACTATGGACG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 4 0.15
26 2 0.08
27 20 0.77
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.59
Consensus pattern (26 bp):
TCCTTCTCTCTTCCTTCTTCTCCTCA
Found at i:213878 original size:27 final size:25
Alignment explanation
Indices: 213818--213884 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
213808 CTCTTGAGGC
* *
213818 TCTTCTTCCTTCTTTCCTTCCTTTT
1 TCTTCTTCCTTCTTTCCATCCTTCT
*
213843 TCTCGTCTTCCTTCTTTTCATCCTTGGCT
1 TCT--TCTTCCTTCTTTCCATCCTT--CT
*
213872 TCTTCTTTCTTCT
1 TCTTCTTCCTTCT
213885 CCTTACCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 3 0.09
27 27 0.79
29 4 0.12
ACGTcount: A:0.01, C:0.34, G:0.04, T:0.60
Consensus pattern (25 bp):
TCTTCTTCCTTCTTTCCATCCTTCT
Found at i:215451 original size:5 final size:5
Alignment explanation
Indices: 215421--215449 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
215411 AGATGGGCTG
215421 GAAAA GAAAA GAAAA GAAAA GAAAA -AAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
215450 AAGATGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:221327 original size:30 final size:30
Alignment explanation
Indices: 221293--221381 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
221283 CAAGGAGCCT
221293 GAGAAGAAACCTGAAAAGCCTAAA-AGACCC
1 GAGAAGAAACCTGAAAAGCCTAAAGA-ACCC
*
221323 GAGAAAAAACCTGAAAAGCCTAAAGAACCC
1 GAGAAGAAACCTGAAAAGCCTAAAGAACCC
* *
221353 GAGAAGAAACCTGAAAAACCCAAAGAACC
1 GAGAAGAAACCTGAAAAGCCTAAAGAACC
221382 TGCGAAGCCA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 53 0.98
31 1 0.02
ACGTcount: A:0.53, C:0.24, G:0.18, T:0.06
Consensus pattern (30 bp):
GAGAAGAAACCTGAAAAGCCTAAAGAACCC
Found at i:221410 original size:47 final size:48
Alignment explanation
Indices: 221330--221467 Score: 190
Period size: 47 Copynumber: 2.9 Consensus size: 48
221320 CCCGAGAAAA
* *
221330 AACCTGAAAAGCCTAAAGAACCCGAGAAGAAACCTGAAAAACCCAAAG
1 AACCTGAGAAGCCTAAAGAGCCCGAGAAGAAACCTGAAAAACCCAAAG
* * *
221378 AACCTGCGAAGCC-AAGGAGCCTGAGAAGAAACCTGAAAAA-CCAAAG
1 AACCTGAGAAGCCTAAAGAGCCCGAGAAGAAACCTGAAAAACCCAAAG
* * *
221424 AAGCTGAGAAGCCTAAAGAGCCCGAAAAGAAGCCTGAAAAACCC
1 AACCTGAGAAGCCTAAAGAGCCCGAGAAGAAACCTGAAAAACCC
221468 CCAGCCCCAG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
46 17 0.22
47 47 0.61
48 13 0.17
ACGTcount: A:0.48, C:0.25, G:0.21, T:0.07
Consensus pattern (48 bp):
AACCTGAGAAGCCTAAAGAGCCCGAGAAGAAACCTGAAAAACCCAAAG
Found at i:221477 original size:6 final size:6
Alignment explanation
Indices: 221466--221537 Score: 103
Period size: 6 Copynumber: 12.2 Consensus size: 6
221456 CCTGAAAAAC
221466 CCCCAG CCCCAG CCCCAG CCCCAG -CCCAG CCCCA- CGCCCAG CCCCAG
1 CCCCAG CCCCAG CCCCAG CCCCAG CCCCAG CCCCAG C-CCCAG CCCCAG
* *
221513 CTCCAG CCCCAG CCCCAG CGCCAG C
1 CCCCAG CCCCAG CCCCAG CCCCAG C
221538 ACCAAAGCCA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
5 6 0.10
6 53 0.88
7 1 0.02
ACGTcount: A:0.17, C:0.64, G:0.18, T:0.01
Consensus pattern (6 bp):
CCCCAG
Found at i:223225 original size:7 final size:7
Alignment explanation
Indices: 223215--223241 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
223205 GGCCTAAGCC
223215 TGGTGAA
1 TGGTGAA
223222 TGGTGAA
1 TGGTGAA
223229 TGGTGAA
1 TGGTGAA
223236 TGGTGA
1 TGGTGA
223242 TTGAAACAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.30
Consensus pattern (7 bp):
TGGTGAA
Found at i:225364 original size:18 final size:18
Alignment explanation
Indices: 225343--225407 Score: 121
Period size: 18 Copynumber: 3.6 Consensus size: 18
225333 CCTCCAACAA
225343 AACCAAAACCTGATCCAC
1 AACCAAAACCTGATCCAC
225361 AACCAAAACCTGATCCAC
1 AACCAAAACCTGATCCAC
225379 AACCAAAACCTGATCCAC
1 AACCAAAACCTGATCCAC
*
225397 AACCACAACCT
1 AACCAAAACCT
225408 CCACTGCTAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.45, C:0.40, G:0.05, T:0.11
Consensus pattern (18 bp):
AACCAAAACCTGATCCAC
Found at i:225549 original size:87 final size:87
Alignment explanation
Indices: 225398--225575 Score: 295
Period size: 87 Copynumber: 2.0 Consensus size: 87
225388 CTGATCCACA
* *
225398 ACCACAACCTCCACTGCTACCATGTTTTTGCATGCGATGTCATCGTGTCTGTGTTTGGGGACCTT
1 ACCAAAACCTCCACTGCTACCATGTTTTTGCATGCGATGTCATCGTGTCTGTGTCTGGGGACCTT
*
225463 GCTGCTGTGATGGACCACCCCC
66 GCTGCTGTGATGAACCACCCCC
*
225485 ACCAAAACCTCCACTGCTACCAT-TTTGTTGCATGCGATGTCATCGTTTCTGTGTCTGGGGACCT
1 ACCAAAACCTCCACTGCTACCATGTTT-TTGCATGCGATGTCATCGTGTCTGTGTCTGGGGACCT
*
225549 TGCTGCTGTGATGAACCATCCCC
65 TGCTGCTGTGATGAACCACCCCC
225572 ACCA
1 ACCA
225576 CCTCCACGCC
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
86 3 0.04
87 82 0.96
ACGTcount: A:0.18, C:0.31, G:0.21, T:0.30
Consensus pattern (87 bp):
ACCAAAACCTCCACTGCTACCATGTTTTTGCATGCGATGTCATCGTGTCTGTGTCTGGGGACCTT
GCTGCTGTGATGAACCACCCCC
Found at i:226272 original size:21 final size:21
Alignment explanation
Indices: 226248--226290 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
226238 AATTTACGTG
226248 AATAAT-TTTAGATTTTTTTAA
1 AATAATGTTTA-ATTTTTTTAA
*
226269 AATATTGTTTAATTTTTTTAA
1 AATAATGTTTAATTTTTTTAA
226290 A
1 A
226291 CACTTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (21 bp):
AATAATGTTTAATTTTTTTAA
Found at i:229551 original size:117 final size:117
Alignment explanation
Indices: 229404--229637 Score: 468
Period size: 117 Copynumber: 2.0 Consensus size: 117
229394 AATATGAAAG
229404 GAAAATGCTTTTAACGAGCATCAAATGCCAATGCTAAAAGGAGTTTGTCATACTTGATGAATGCT
1 GAAAATGCTTTTAACGAGCATCAAATGCCAATGCTAAAAGGAGTTTGTCATACTTGATGAATGCT
229469 GGCCATAAAGCCAAATATAAGTAGAAAGTTGACTTCCCACTCTGAATTTTAA
66 GGCCATAAAGCCAAATATAAGTAGAAAGTTGACTTCCCACTCTGAATTTTAA
229521 GAAAATGCTTTTAACGAGCATCAAATGCCAATGCTAAAAGGAGTTTGTCATACTTGATGAATGCT
1 GAAAATGCTTTTAACGAGCATCAAATGCCAATGCTAAAAGGAGTTTGTCATACTTGATGAATGCT
229586 GGCCATAAAGCCAAATATAAGTAGAAAGTTGACTTCCCACTCTGAATTTTAA
66 GGCCATAAAGCCAAATATAAGTAGAAAGTTGACTTCCCACTCTGAATTTTAA
229638 TTTTCGAAGA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (117 bp):
GAAAATGCTTTTAACGAGCATCAAATGCCAATGCTAAAAGGAGTTTGTCATACTTGATGAATGCT
GGCCATAAAGCCAAATATAAGTAGAAAGTTGACTTCCCACTCTGAATTTTAA
Found at i:231596 original size:14 final size:14
Alignment explanation
Indices: 231577--231617 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
231567 CTGAATATCT
231577 AGAGAGAACAGAGA
1 AGAGAGAACAGAGA
231591 AGAGAG--CAGAGA
1 AGAGAGAACAGAGA
231603 GAGAGAGAA-AGAGA
1 -AGAGAGAACAGAGA
231617 A
1 A
231618 TTCTGGTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 6 0.25
13 7 0.29
14 11 0.46
ACGTcount: A:0.56, C:0.05, G:0.39, T:0.00
Consensus pattern (14 bp):
AGAGAGAACAGAGA
Found at i:234803 original size:3 final size:3
Alignment explanation
Indices: 234775--234814 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
234765 CACACCAAGT
* * *
234775 ACA ACA GCA ACA AAA ACA AGA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
234815 AAGACTTGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.28, G:0.05, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:249173 original size:2 final size:2
Alignment explanation
Indices: 249166--249195 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
249156 ATCTATTGTA
249166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249196 TAAGAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250004 original size:2 final size:2
Alignment explanation
Indices: 249997--250033 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
249987 GTGCAGCAGC
* *
249997 TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
250034 TAATAGGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:258775 original size:39 final size:39
Alignment explanation
Indices: 258712--258790 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
258702 GCAGGTTCTG
* *
258712 TAGTAGGATTGACAGATGAAGGAGGATCACTCTTGTCCT
1 TAGTAGGATTGACAGATGAAGGAGGAACACTCTTGCCCT
** *
258751 TAGTAGGATTGACAGATGGGGGAGGAACCCTCTTGCCCT
1 TAGTAGGATTGACAGATGAAGGAGGAACACTCTTGCCCT
258790 T
1 T
258791 CTTACTGTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (39 bp):
TAGTAGGATTGACAGATGAAGGAGGAACACTCTTGCCCT
Found at i:267071 original size:2 final size:2
Alignment explanation
Indices: 267020--267052 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
267010 TCTAAAGTAG
267020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
267053 AAGAGAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:281581 original size:2 final size:2
Alignment explanation
Indices: 281574--281601 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
281564 TTATTGCAAC
281574 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
281602 TTTTCATCGT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:297334 original size:18 final size:18
Alignment explanation
Indices: 297311--297348 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
297301 TATCATTAAG
297311 TATCT-AATTTTAAAAATT
1 TATCTAAATTTT-AAAATT
297329 TATCTAAATTTTAAAATT
1 TATCTAAATTTTAAAATT
297347 TA
1 TA
297349 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TATCTAAATTTTAAAATT
Found at i:308041 original size:2 final size:2
Alignment explanation
Indices: 308036--308072 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
308026 GGTGAAAACA
308036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
308073 GTTTTGCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:320742 original size:2 final size:2
Alignment explanation
Indices: 320735--320796 Score: 79
Period size: 2 Copynumber: 30.0 Consensus size: 2
320725 GTAGCCAAGC
* * *
320735 CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT CGT GT AT ACT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT -CT CT
320779 CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
320797 TCTAAAAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.03, C:0.44, G:0.05, T:0.48
Consensus pattern (2 bp):
CT
Found at i:345225 original size:23 final size:22
Alignment explanation
Indices: 345182--345225 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
345172 AAAAACAAAT
* **
345182 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
345204 ATATTTTATATTAGAAGATAAT
1 ATATTTT-TATTAGAAGATAAT
345226 TGAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:345339 original size:45 final size:43
Alignment explanation
Indices: 345290--345381 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
345280 TCATTAAATT
* *
345290 TAATAATACTAAATAATATTATTTATTACATTTATTATA-TTCAAA
1 TAATAATACTAAACAATATT-TTT-TAACATTTATTATAGTT-AAA
* *
345335 TAATAATATTAAACAATATTTTTTAATATTTATTATAGTTAAA
1 TAATAATACTAAACAATATTTTTTAACATTTATTATAGTTAAA
345378 TAAT
1 TAAT
345382 GCTAATATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 19 0.45
44 5 0.12
45 18 0.43
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (43 bp):
TAATAATACTAAACAATATTTTTTAACATTTATTATAGTTAAA
Found at i:345568 original size:18 final size:18
Alignment explanation
Indices: 345545--345579 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
345535 TAAAATGATA
345545 TTTTTA-TCTAATCAATTT
1 TTTTTATTCTAA-CAATTT
345563 TTTTTATTCTAACAATT
1 TTTTTATTCTAACAATT
345580 CGAAATAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTATTCTAACAATTT
Found at i:345953 original size:23 final size:24
Alignment explanation
Indices: 345926--345972 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
345916 AGAGATACTC
345926 TTTATTAAAAG-TAAAGAAT-TTAT
1 TTTATTAAAAGATAAA-AATATTAT
345949 TTTATTAAAAGATAAAAATATTAT
1 TTTATTAAAAGATAAAAATATTAT
345973 AAGTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (24 bp):
TTTATTAAAAGATAAAAATATTAT
Found at i:346058 original size:22 final size:21
Alignment explanation
Indices: 345994--346061 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
345984 TCAAAATAAC
*
345994 TTTTACTATAATTAAATAATAT
1 TTTTA-TATAATTTAATAATAT
* * * *
346016 TTTCACAAAATATAA-ATATAT
1 TTTTATATAATTTAATA-ATAT
346037 TTTTATTATAATTTAATAATAT
1 TTTTA-TATAATTTAATAATAT
346059 TTT
1 TTT
346062 GTTGAGGAGA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 18 0.53
23 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTATATAATTTAATAATAT
Found at i:346199 original size:45 final size:45
Alignment explanation
Indices: 346142--346241 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
346132 CTTAAATCTA
* * * * *
346142 AATAATACTAAATATTATTCTTTATTACATTTATTATATTCAAAT
1 AATAATATTAAATAATATTCTTTATAACATTTATTATAGTAAAAT
*
346187 AATAATATTAAATAATATTCTTTATAATATTTATTATAGTAAAAT
1 AATAATATTAAATAATATTCTTTATAACATTTATTATAGTAAAAT
*
346232 AATATTATTA
1 AATAATATTA
346242 TATTAAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (45 bp):
AATAATATTAAATAATATTCTTTATAACATTTATTATAGTAAAAT
Found at i:348221 original size:6 final size:6
Alignment explanation
Indices: 348212--348241 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
348202 TAAAAAATAA
348212 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
348242 TGACATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:353695 original size:15 final size:15
Alignment explanation
Indices: 353675--353703 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
353665 ATTTTTTTTG
353675 GTATAATGTGAACTA
1 GTATAATGTGAACTA
353690 GTATAATGTGAACT
1 GTATAATGTGAACT
353704 TGATTTCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (15 bp):
GTATAATGTGAACTA
Found at i:364142 original size:27 final size:27
Alignment explanation
Indices: 364105--364166 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
364095 GAAGACGTTT
364105 GCAGCAGCAGTAGTTGTATCAGGTAGA
1 GCAGCAGCAGTAGTTGTATCAGGTAGA
364132 GCAGCAGCAGTAGTTGTATCAGGTAGA
1 GCAGCAGCAGTAGTTGTATCAGGTAGA
364159 GCAGCAGC
1 GCAGCAGC
364167 TTGCGAGAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.34, T:0.19
Consensus pattern (27 bp):
GCAGCAGCAGTAGTTGTATCAGGTAGA
Found at i:379262 original size:47 final size:47
Alignment explanation
Indices: 379138--379254 Score: 155
Period size: 47 Copynumber: 2.5 Consensus size: 47
379128 AGCTGTATAC
* * *
379138 AAATTTGCTGTCCAACCAGGAAAGAGAAAGAATGTAAATCTATACAT
1 AAATTTGCTGTCCAACCAGGAAAGAGAAAGAATGCAAAGCTACACAT
* * *
379185 AAATTTGCTGTCCAGCCAGGAAAGAGAAAGAATGCCAAGCTACATAT
1 AAATTTGCTGTCCAACCAGGAAAGAGAAAGAATGCAAAGCTACACAT
*
379232 AAATTTCCTG-CCTAACCAGGAAA
1 AAATTTGCTGTCC-AACCAGGAAA
379255 TTGAAAGAGC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 2 0.03
47 59 0.97
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (47 bp):
AAATTTGCTGTCCAACCAGGAAAGAGAAAGAATGCAAAGCTACACAT
Found at i:380687 original size:16 final size:17
Alignment explanation
Indices: 380649--380687 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
380639 CATAATGGTT
380649 TTTTTTATAAAATTATA
1 TTTTTTATAAAATTATA
* *
380666 TCTTTTA-ATAATTATA
1 TTTTTTATAAAATTATA
380682 TTTTTT
1 TTTTTT
380688 CGATATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTTATAAAATTATA
Found at i:399000 original size:2 final size:2
Alignment explanation
Indices: 398907--398988 Score: 96
Period size: 2 Copynumber: 41.5 Consensus size: 2
398897 AAGAAACGTT
* * *
398907 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TGC GC TC TG TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC
* *
398950 TC TC TC TC TC TC TC T- TC CC T- TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
398989 ACGGCTCTCT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
1 2 0.03
2 64 0.96
3 1 0.01
ACGTcount: A:0.00, C:0.45, G:0.04, T:0.51
Consensus pattern (2 bp):
TC
Found at i:414529 original size:243 final size:243
Alignment explanation
Indices: 414179--414665 Score: 728
Period size: 243 Copynumber: 2.0 Consensus size: 243
414169 TTGTATAGCA
414179 AGAAATATAAAACACAATAATTTTAAATTTAAATTCGTTTAATTTCGTACTTTTTGTTATTATAT
1 AGAAATATAAAACACAATAATTTTAAATTTAAATTCGTTTAATTTCGTACTTTTTGTTATTATAT
*
414244 TAACAAATTATGTCCAAAATTAGTAAATCAATGCATGTTAATTAGCAAGTTGATTTTTAGACTCG
66 TAACAAATTATGTCCAAAATTAGTAAATCAATGCATGTTAATTAGCAAGTTGACTTTTAGACTCG
* * * * * **
414309 TATTAATT-AGTTTTATATATTTTTTATACTTTTCGAATTATACATTTTTGTTGAAACTCAATTT
131 TATTAATTAACTTTTATATATTTTTCATACTTTACAAATCATACATTTACGTTGAAACTCAATTT
* *
414373 ATTTTTTTTAAGAGTAAAATATTTTTACTTCTTAAAGTTTTGATCGAAATT
196 A--TTTTTTAAAAGTAAAATATTTTTACTTCTTAAA-TTTTGATAGAAATT
* * *
414424 AGAAATATGAAATACGATAATTTTAAATTTAAATTCGTTTAATTTCGTA-TTTTT-TTATTATAT
1 AGAAATATAAAACACAATAATTTTAAATTTAAATTCGTTTAATTTCGTACTTTTTGTTATTATAT
* * *
414487 TAATAAATTATGTCCAAAATTAGTAAATCAATGCATGTTAATTAGTAGGTTGACTTTTAGACTCG
66 TAACAAATTATGTCCAAAATTAGTAAATCAATGCATGTTAATTAGCAAGTTGACTTTTAGACTCG
* * * *
414552 TATTAATTAACTTTTTTATCTTTTTCATACTTTACAAATCATACATTTACGTTGAAATTTAATTT
131 TATTAATTAACTTTTATATATTTTTCATACTTTACAAATCATACATTTACGTTGAAACTCAATTT
* *
414617 ATTTTTTAAAAGTAAAATATTTTTATTTTTTAAATTTTGATAGAAATT
196 ATTTTTTAAAAGTAAAATATTTTTACTTCTTAAATTTTGATAGAAATT
414665 A
1 A
414666 TATAAAAATT
Statistics
Matches: 219, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
241 14 0.06
242 30 0.14
243 78 0.36
244 51 0.23
245 46 0.21
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (243 bp):
AGAAATATAAAACACAATAATTTTAAATTTAAATTCGTTTAATTTCGTACTTTTTGTTATTATAT
TAACAAATTATGTCCAAAATTAGTAAATCAATGCATGTTAATTAGCAAGTTGACTTTTAGACTCG
TATTAATTAACTTTTATATATTTTTCATACTTTACAAATCATACATTTACGTTGAAACTCAATTT
ATTTTTTAAAAGTAAAATATTTTTACTTCTTAAATTTTGATAGAAATT
Found at i:414977 original size:23 final size:22
Alignment explanation
Indices: 414927--414978 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
414917 TCCAAGCTCT
414927 TTATTTTTAAAAAATATAATAA
1 TTATTTTTAAAAAATATAATAA
* *
414949 TAATTTTTAAATTAATTATAA-AA
1 TTATTTTTAAA--AAATATAATAA
414972 TTATTTT
1 TTATTTT
414979 AATTTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 10 0.40
23 8 0.32
24 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTTTTAAAAAATATAATAA
Found at i:454659 original size:15 final size:15
Alignment explanation
Indices: 454622--454651 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
454612 AAGCCAAAAC
*
454622 AACAACAACAGCAAT
1 AACAACAACAACAAT
454637 AACAACAACAACAAT
1 AACAACAACAACAAT
454652 TCCAACAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.27, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAACAACAACAAT
Found at i:476180 original size:22 final size:21
Alignment explanation
Indices: 476130--476182 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
476120 TATTCACATA
476130 AAATATAAAATAAAAATATTAT
1 AAATAT-AAATAAAAATATTAT
*
476152 AATTATAAATAAATAATA-TATT
1 AAATATAAATAAA-AATATTA-T
476174 AAATATAAA
1 AAATATAAA
476183 CTTATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATATAAATAAAAATATTAT
Found at i:484064 original size:18 final size:18
Alignment explanation
Indices: 484043--484077 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
484033 ATAATGGATA
484043 CATTTAATCCCATGGACG
1 CATTTAATCCCATGGACG
*
484061 CATTTAATCTCATGGAC
1 CATTTAATCCCATGGAC
484078 CGTCACATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (18 bp):
CATTTAATCCCATGGACG
Found at i:500993 original size:4 final size:4
Alignment explanation
Indices: 500984--501008 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
500974 TTGAACAATA
500984 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
501009 GCGTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:514927 original size:33 final size:32
Alignment explanation
Indices: 514878--514946 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 32
514868 ATATTTATTT
* *
514878 TATT-TAAATCTCTTGTTAATTATTCTAATTG
1 TATTATAAATCTATTGTTAACTATTCTAATTG
* *
514909 TATTATAATATCTATTGTTAACTGTTTTAATTG
1 TATTATAA-ATCTATTGTTAACTATTCTAATTG
514942 TATTA
1 TATTA
514947 CATTCTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 4 0.12
32 3 0.09
33 25 0.78
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (32 bp):
TATTATAAATCTATTGTTAACTATTCTAATTG
Found at i:515531 original size:22 final size:22
Alignment explanation
Indices: 515506--515547 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
515496 AAAACGGAAG
515506 GTCTTGGACTCTTTATAAGTAA
1 GTCTTGGACTCTTTATAAGTAA
515528 GTCTTGGACTCTTTATAAGT
1 GTCTTGGACTCTTTATAAGT
515548 GGGTGTGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (22 bp):
GTCTTGGACTCTTTATAAGTAA
Found at i:517822 original size:5 final size:5
Alignment explanation
Indices: 517801--517836 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
517791 ACACATCCCA
* *
517801 TTTTC TTTTC CTTTC TTCTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
517837 CGCAAACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:518166 original size:3 final size:3
Alignment explanation
Indices: 518153--518193 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
518143 CAGCTCCGCT
*
518153 TCC TTC TCC TCC TCC TCC TCC TCC TCC TCC TTCC -CC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC -TCC TCC TCC TC
518194 TTTCTCCTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:518168 original size:12 final size:12
Alignment explanation
Indices: 518161--518206 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
518151 CTTCCTTCTC
*
518161 CTCCTCCTCCTC
1 CTCCTCCTCCTT
518173 CTCCTCCTCCTT
1 CTCCTCCTCCTT
* *
518185 CCCCTCCTCTTT
1 CTCCTCCTCCTT
*
518197 CTCCTTCTCC
1 CTCCTCCTCC
518207 ACCTGCGATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (12 bp):
CTCCTCCTCCTT
Found at i:524915 original size:14 final size:14
Alignment explanation
Indices: 524876--524917 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
524866 CAAATTTGAT
524876 ATTTTTTT-TA-TA
1 ATTTTTTTATATTA
*
524888 ATTTTTATATTATTA
1 ATTTTTTTA-TATTA
524903 ATTTTTTTATATTA
1 ATTTTTTTATATTA
524917 A
1 A
524918 CATTACTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
14 8 0.32
15 10 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTTTATATTA
Found at i:527809 original size:7 final size:7
Alignment explanation
Indices: 527797--527821 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
527787 CTACAAGAGT
527797 TGGGGCA
1 TGGGGCA
527804 TGGGGCA
1 TGGGGCA
527811 TGGGGCA
1 TGGGGCA
527818 TGGG
1 TGGG
527822 CTCATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.60, T:0.16
Consensus pattern (7 bp):
TGGGGCA
Found at i:537698 original size:27 final size:27
Alignment explanation
Indices: 537668--537736 Score: 108
Period size: 24 Copynumber: 2.7 Consensus size: 27
537658 CATCTCGAGG
537668 CACCATCACCACCATCATTCATTCATT
1 CACCATCACCACCATCATTCATTCATT
537695 CACCAT---CACCATCATTCATTCATT
1 CACCATCACCACCATCATTCATTCATT
*
537719 CACCATCACCATCATCAT
1 CACCATCACCACCATCAT
537737 CATGATGACA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
24 24 0.63
27 14 0.37
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.29
Consensus pattern (27 bp):
CACCATCACCACCATCATTCATTCATT
Found at i:537709 original size:24 final size:24
Alignment explanation
Indices: 537677--537733 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
537667 GCACCATCAC
537677 CACCATCATTCATTCATTCACCAT
1 CACCATCATTCATTCATTCACCAT
537701 CACCATCATTCATTCATTCACCAT
1 CACCATCATTCATTCATTCACCAT
537725 CACCATCAT
1 CACCATCAT
537734 CATCATGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.30, C:0.39, G:0.00, T:0.32
Consensus pattern (24 bp):
CACCATCATTCATTCATTCACCAT
Found at i:545845 original size:85 final size:86
Alignment explanation
Indices: 545700--545872 Score: 285
Period size: 85 Copynumber: 2.0 Consensus size: 86
545690 ACTAGTAAGG
* ** *
545700 TATTTTCATTAATAATCTGCCCAAGACAGTAAGGGTACAGAAAGCTGTTCCTACTGCAACCAGAT
1 TATTTTCATTAAGAATCTGCCCAAGACAGTAAGGGTACAGAAAGCTGTTCCTACAACAACCAGAG
*
545765 TATAACTGGTTTGTGCA-ACA
66 TATAACTGGTGTGTGCATACA
*
545785 TATTTTCATTAAGAATCTGCCCAAGACAGTAAGGGTACAGAAAGCTGTTCCTGCAACAACCAGAG
1 TATTTTCATTAAGAATCTGCCCAAGACAGTAAGGGTACAGAAAGCTGTTCCTACAACAACCAGAG
545850 TATAACTGGTGTGTGCATACA
66 TATAACTGGTGTGTGCATACA
545871 TA
1 TA
545873 ATAGCAGCGA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 76 0.94
86 5 0.06
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (86 bp):
TATTTTCATTAAGAATCTGCCCAAGACAGTAAGGGTACAGAAAGCTGTTCCTACAACAACCAGAG
TATAACTGGTGTGTGCATACA
Found at i:556981 original size:2 final size:2
Alignment explanation
Indices: 556968--556997 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
556958 ACATTGTTAA
*
556968 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
556998 GCATTAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:560516 original size:3 final size:3
Alignment explanation
Indices: 560510--560550 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
560500 ATGATGATGA
*
560510 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGC TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
560551 ATCCATTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.02, G:0.63, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:573177 original size:12 final size:12
Alignment explanation
Indices: 573162--573188 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
573152 AAGGATAAAG
573162 AGAAAGAGAAGA
1 AGAAAGAGAAGA
573174 AGAAAGAGAAGA
1 AGAAAGAGAAGA
573186 AGA
1 AGA
573189 GTCAGAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
AGAAAGAGAAGA
Found at i:581643 original size:34 final size:33
Alignment explanation
Indices: 581600--581702 Score: 84
Period size: 33 Copynumber: 3.1 Consensus size: 33
581590 ATTTAATTAT
581600 GTATATTTAAATTTGGATGTAAATTAGATAAGA
1 GTATATTTAAATTTGGATGTAAATTAGATAAGA
* * * * *
581633 GTATAATTT-AATTTGAACTCTTAAATTTGATTA-T
1 GTAT-ATTTAAATTTGGA-T-GTAAATTAGATAAGA
* * **
581667 GTATACTTAGATTTGGATGTAAATTATTTAAGA
1 GTATATTTAAATTTGGATGTAAATTAGATAAGA
581700 GTA
1 GTA
581703 CAATTTGATT
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
32 8 0.16
33 18 0.35
34 15 0.29
35 10 0.20
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.44
Consensus pattern (33 bp):
GTATATTTAAATTTGGATGTAAATTAGATAAGA
Found at i:581666 original size:67 final size:68
Alignment explanation
Indices: 581586--581897 Score: 353
Period size: 67 Copynumber: 4.6 Consensus size: 68
581576 TACAGGATTA
* * * *
581586 TTAAATTTAATTATGTATATTTAAATTTGGATGTAAATTAGATAAGAGTATAATTTAATTTGAA-
1 TTAAATTTGATTATGTATATTTAGATTTGGATATAAATTAGATAAGAGTATAATTTGATTTGAAT
581650 CTC
66 CTC
* * ** *
581653 TTAAATTTGATTATGTATACTTAGATTTGGATGTAAATTATTTAAGAGTACAATTTGATTT-AAT
1 TTAAATTTGATTATGTATATTTAGATTTGGATATAAATTAGATAAGAGTATAATTTGATTTGAAT
581717 CTC
66 CTC
*** * * *
581720 TTAAATTTGATTAAAAATATTTAAATTTGAATATAAATTAGATAAAAGTATAATTTGATTTGAAT
1 TTAAATTTGATTATGTATATTTAGATTTGGATATAAATTAGATAAGAGTATAATTTGATTTGAAT
*
581785 -TT
66 CTC
* * * *
581787 TTAAATTTGATTAAGTATCTATAGATTTGGAT-TAAATTAGATAGGAGTATAATTTGATTTGAAT
1 TTAAATTTGATTATGTATATTTAGATTTGGATATAAATTAGATAAGAGTATAATTTGATTTGAA-
*
581851 TCTAAAA
65 TCT---C
* *
581858 TTAAATTTGATGATGTATATTTAGATTTGTATATAAATTA
1 TTAAATTTGATTATGTATATTTAGATTTGGATATAAATTA
581898 AATTAAAATA
Statistics
Matches: 204, Mismatches: 33, Indels: 11
0.82 0.13 0.04
Matches are distributed among these distances:
66 31 0.15
67 135 0.66
68 4 0.02
71 27 0.13
72 7 0.03
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (68 bp):
TTAAATTTGATTATGTATATTTAGATTTGGATATAAATTAGATAAGAGTATAATTTGATTTGAAT
CTC
Found at i:581757 original size:20 final size:20
Alignment explanation
Indices: 581720--581757 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
581710 ATTTAATCTC
*
581720 TTAAATTTGATTAAAAATAT
1 TTAAATTTGAATAAAAATAT
*
581740 TTAAATTTGAATATAAAT
1 TTAAATTTGAATAAAAAT
581758 TAGATAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAAATTTGAATAAAAATAT
Found at i:582030 original size:40 final size:42
Alignment explanation
Indices: 581971--582053 Score: 125
Period size: 40 Copynumber: 2.0 Consensus size: 42
581961 GTTTCATTCC
*
581971 GCTCGACGCTTTGAAACAAACACCAG-G-GAAGAGAGGCTGA
1 GCTCGACGCTTTGAAACAAACACAAGAGAGAAGAGAGGCTGA
* *
582011 GCTCGACGCTTTGACACAAACACAAGAGAGAAGAGATGCTGA
1 GCTCGACGCTTTGAAACAAACACAAGAGAGAAGAGAGGCTGA
582053 G
1 G
582054 AAAGTCACGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 24 0.63
41 1 0.03
42 13 0.34
ACGTcount: A:0.36, C:0.22, G:0.29, T:0.13
Consensus pattern (42 bp):
GCTCGACGCTTTGAAACAAACACAAGAGAGAAGAGAGGCTGA
Found at i:583890 original size:21 final size:21
Alignment explanation
Indices: 583866--583908 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
583856 ATTTTACCCC
583866 CTTT-TTTTTGTTAGTTTTATT
1 CTTTATTTTTGTTA-TTTTATT
*
583887 CTTTATTTTTTTTATTTTATT
1 CTTTATTTTTGTTATTTTATT
583908 C
1 C
583909 ATGTGAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.77
Consensus pattern (21 bp):
CTTTATTTTTGTTATTTTATT
Found at i:587873 original size:2 final size:2
Alignment explanation
Indices: 587866--587890 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
587856 AGAGAATTTC
587866 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
587891 CAAACTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:595378 original size:5 final size:5
Alignment explanation
Indices: 595368--595396 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
595358 GGAAGGGTAT
595368 AAAGA AAAGA AAAGA AAAGA AAAGA AAAG
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAG
595397 CAAGAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:596600 original size:3 final size:3
Alignment explanation
Indices: 596586--596626 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
596576 TCATGACTTC
* * *
596586 TCA TCC TCA TCA TCA ACA TCA TCA TCA TCA TCA TCC TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
596627 CTCCGAATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:602972 original size:26 final size:29
Alignment explanation
Indices: 602934--602990 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
602924 ACATATCCTT
*
602934 AATCATATCA-TT-TTTGTTAGTAA-AAA
1 AATCATATAATTTATTTGTTAGTAATAAA
*
602960 AATCATATAATTTATTTTTTAGTAATAAA
1 AATCATATAATTTATTTGTTAGTAATAAA
602989 AA
1 AA
602991 AGTAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.35
27 2 0.08
28 10 0.38
29 5 0.19
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (29 bp):
AATCATATAATTTATTTGTTAGTAATAAA
Found at i:624726 original size:14 final size:14
Alignment explanation
Indices: 624707--624736 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
624697 AGAGAGATTC
*
624707 GAAGCTTGAAGCCT
1 GAAGCTAGAAGCCT
624721 GAAGCTAGAAGCCT
1 GAAGCTAGAAGCCT
624735 GA
1 GA
624737 GAGTAGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (14 bp):
GAAGCTAGAAGCCT
Found at i:660494 original size:115 final size:113
Alignment explanation
Indices: 660218--660516 Score: 354
Period size: 115 Copynumber: 2.6 Consensus size: 113
660208 TACTTAAATG
* * * * * *
660218 TTAATAATATTTAAATTTTATGTATGTATGTACGTCTAGGTATGTA-GTGTATTCAT-TTTTGTA
1 TTAATAATATATAAATTTTATGTATGTATGTATGTGTAGGTATGTACGTGTATGCATAATATGTA
* * * ** * *
660281 TATCAACACCATCAAATATCAAATTAGTGGTACGAAAATCTTTAGATA
66 TAGCAACACCATCAAACATCAAATCAGTAATACGAAAATATTTAGAAA
* * *
660329 TTAA-AA-ATATAAATTTTATGTCTGTATGTATGTGTAGGTATGTACTTGTATGCATACCTATGT
1 TTAATAATATATAAATTTTATGTATGTATGTATGTGTAGGTATGTACGTGTATGCATA-ATATGT
* *
660392 ATCAGCAATACCATCAAACATCAAATCAGTAATACGAAAATATTTATAAA
65 AT-AGCAACACCATCAAACATCAAATCAGTAATACGAAAATATTTAGAAA
* *
660442 TTAATAATATATAAATTTTATGTTTGCATGTATGTGTAGGTATGTACGTGTATGCATATATATGT
1 TTAATAATATATAAATTTTATGTATGTATGTATGTGTAGGTATGTACGTGTATGCATA-ATATGT
660507 ATTAGCAACA
65 A-TAGCAACA
660517 TCAAGATACG
Statistics
Matches: 158, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
109 34 0.22
110 10 0.06
111 4 0.03
112 6 0.04
113 42 0.27
114 2 0.01
115 59 0.37
116 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (113 bp):
TTAATAATATATAAATTTTATGTATGTATGTATGTGTAGGTATGTACGTGTATGCATAATATGTA
TAGCAACACCATCAAACATCAAATCAGTAATACGAAAATATTTAGAAA
Found at i:687823 original size:202 final size:202
Alignment explanation
Indices: 687470--687873 Score: 682
Period size: 202 Copynumber: 2.0 Consensus size: 202
687460 AATTTTTGGA
*
687470 TTGAAATGTTATCATTCGAATTACCTTCAGAAATTAACGTACGTGAACAATTAGAACGCAGCTGT
1 TTGAAATGTTATCATTCGAATTACCTTCAGAAATTAACATACGTGAACAATTAGAACGCAGCTGT
* * * * *
687535 TCTAGCAACAAAAGGGAATCAAATTCCATGAGGAACAATTTGACGAAATCAGGGATATACGTTTT
66 TCTAACAACAAAAGAGAATCAAATTACATGAGGAACAATTTGACGAAATCAAGAATATACGTTTT
* *
687600 GTATAAAGAGACTTCTGTTCTTGTTGGTAAGTGTCAAAACTTTGCAACAATGTCAAAGAGACGCA
131 GTATAAAGAGACTTCTGTTCTTGTTGGTAAGTGTCAAAACTTTACAACAATGGCAAAGAGACGCA
687665 ATCAATC
196 ATCAATC
* *
687672 TTGAAATGTTGTCATTCGAATTACCTTCAGAAATTAACATACGTTAACAATTAGAACGCAGCTGT
1 TTGAAATGTTATCATTCGAATTACCTTCAGAAATTAACATACGTGAACAATTAGAACGCAGCTGT
* *
687737 TCTAACAACAAAAGAGAATCAAATTACATGAGGAACGATTTGATGAAATCAAGAATATACGTTTT
66 TCTAACAACAAAAGAGAATCAAATTACATGAGGAACAATTTGACGAAATCAAGAATATACGTTTT
* *
687802 GTATAAAGAGACTTTTGTTCTTGTTGGTAAGTGTCAAATCTTTACAACAATGGCAAAGAGACGCA
131 GTATAAAGAGACTTCTGTTCTTGTTGGTAAGTGTCAAAACTTTACAACAATGGCAAAGAGACGCA
687867 ATCAATC
196 ATCAATC
687874 GCACCAAGAC
Statistics
Matches: 188, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
202 188 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (202 bp):
TTGAAATGTTATCATTCGAATTACCTTCAGAAATTAACATACGTGAACAATTAGAACGCAGCTGT
TCTAACAACAAAAGAGAATCAAATTACATGAGGAACAATTTGACGAAATCAAGAATATACGTTTT
GTATAAAGAGACTTCTGTTCTTGTTGGTAAGTGTCAAAACTTTACAACAATGGCAAAGAGACGCA
ATCAATC
Found at i:706936 original size:52 final size:52
Alignment explanation
Indices: 706875--706974 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 52
706865 GATTAATATC
* **
706875 AAAATTGAAAA-TCCAAACCTACCTAATTAATCATAAAATTATTAATAATGTT
1 AAAATTGAAAACT-CAAACCCAAATAATTAATCATAAAATTATTAATAATGTT
* * *
706927 AAAATTGAAAACTCGAACCCAAATTATTAATCATAAGATTATTAATAA
1 AAAATTGAAAACTCAAACCCAAATAATTAATCATAAAATTATTAATAA
706975 ACGGTTACGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 40 0.98
53 1 0.02
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (52 bp):
AAAATTGAAAACTCAAACCCAAATAATTAATCATAAAATTATTAATAATGTT
Found at i:707559 original size:21 final size:21
Alignment explanation
Indices: 707514--707562 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
707504 TTTTTTTCAC
*
707514 AATAAA-ATATATAAAACGAT
1 AATAAATATATATAAAACAAT
*
707534 TATAAATATATATAAAA-AAT
1 AATAAATATATATAAAACAAT
707554 AAATAAATA
1 -AATAAATA
707563 ATCTCAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AATAAATATATATAAAACAAT
Found at i:724799 original size:25 final size:25
Alignment explanation
Indices: 724743--724792 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
724733 TTGGAACAAA
724743 AAATTTTCATATGATTTTACTTAAC
1 AAATTTTCATATGATTTTACTTAAC
*
724768 AAATTTTCATATGATTTTAGTTAAC
1 AAATTTTCATATGATTTTACTTAAC
724793 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (25 bp):
AAATTTTCATATGATTTTACTTAAC
Found at i:727368 original size:20 final size:22
Alignment explanation
Indices: 727340--727389 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
727330 CTACTACTGT
*
727340 ACGAAAAAAAAACTGA-TGTTGC
1 ACGAAAAAAACAC-GAGTGTTGC
727362 ACGAAAAAAACACGAGTGTTGC
1 ACGAAAAAAACACGAGTGTTGC
727384 ACGAAA
1 ACGAAA
727390 TATGAGCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.50, C:0.16, G:0.20, T:0.14
Consensus pattern (22 bp):
ACGAAAAAAACACGAGTGTTGC
Found at i:743018 original size:19 final size:18
Alignment explanation
Indices: 742996--743039 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
742986 TTATTGATAT
*
742996 TAAATTTTATTATATTTGA
1 TAAATTTTATAATATTT-A
*
743015 TAAATATTATAATATTTA
1 TAAATTTTATAATATTTA
743033 T-AATTTT
1 TAAATTTT
743040 TTGTTGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 5 0.23
18 2 0.09
19 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TAAATTTTATAATATTTA
Found at i:761000 original size:15 final size:15
Alignment explanation
Indices: 760980--761009 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
760970 ACAGAAAGAC
760980 AGTAAATAAAAAAAA
1 AGTAAATAAAAAAAA
760995 AGTAAATAAAAAAAA
1 AGTAAATAAAAAAAA
761010 TGTGTACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AGTAAATAAAAAAAA
Found at i:762550 original size:39 final size:39
Alignment explanation
Indices: 762493--762585 Score: 161
Period size: 39 Copynumber: 2.4 Consensus size: 39
762483 TGCCATTTCC
762493 ACCACCATGTCCTCCGCCTAAGCCTTTCTCATTGTTGGA
1 ACCACCATGTCCTCCGCCTAAGCCTTTCTCATTGTTGGA
*
762532 ACCACCATGTCCTTCGCCTAAGCCTTTCTCATTGTTGGA
1 ACCACCATGTCCTCCGCCTAAGCCTTTCTCATTGTTGGA
762571 ACCACCAAT-TCCTCC
1 ACCACC-ATGTCCTCC
762586 TCCAAACCCC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
39 49 0.96
40 2 0.04
ACGTcount: A:0.19, C:0.38, G:0.13, T:0.30
Consensus pattern (39 bp):
ACCACCATGTCCTCCGCCTAAGCCTTTCTCATTGTTGGA
Found at i:789237 original size:264 final size:264
Alignment explanation
Indices: 788767--789282 Score: 852
Period size: 264 Copynumber: 2.0 Consensus size: 264
788757 ACTCTTTGGG
*
788767 CCTAAACCACGTGGCCTTCAAAAGCTTAAACTTAAGTTACTTGTAGTAATAGACTTGGATTATTA
1 CCTAAACCACGTGGCCTTCAAAAGCTTAAACTCAAGTTACTTGTAGTAATAGACTTGGATTATTA
* *
788832 TATAGATCTTCACAATCACATTCACATCAGATATGGGATGTTGGGTCAGAAGTGGGATGTTAGGT
66 TATAGATCTTAACAATCACATTCACATCAGATATGAGATGTTGGGTCAGAAGTGGGATGTTAGGT
* *
788897 ATCACAATCTTACCCACTCAAATCCTTGATATCCTCATCAAGACCACACATCACATCCACATATC
131 ATCACAATCTCACCCACTCAAATCCTTGATATCATCATCAAGACCACACATCACATCCACATATC
*
788962 CAAGATCACAGGTCCAGGATCTCATCAGTGAAGGCCCAACCATTTGTAACGACCCAAGTCTAACC
196 CAAGATCACAGGTCCAGGATCTCACCAGTGAAGGCCCAACCATTTGTAACGACCCAAGTCTAACC
789027 AAGA
261 AAGA
* * * * * *
789031 CCTAAACTAGGTGGCCTTCAAAAGCTTAAGCTCAAGTTACTTGTAGTAGTAGACTTTGATTGTTA
1 CCTAAACCACGTGGCCTTCAAAAGCTTAAACTCAAGTTACTTGTAGTAATAGACTTGGATTATTA
* * *
789096 TATAGATTTTAACAATCACATTCACATCAGATGTGAGATGTTGGGTCAGATGTGGGATGTTAGGT
66 TATAGATCTTAACAATCACATTCACATCAGATATGAGATGTTGGGTCAGAAGTGGGATGTTAGGT
* * *
789161 ATCACAATCTCACCTACTCAAATCCTTGATATCATCATCAAGACCACACATCGCATTCACATATC
131 ATCACAATCTCACCCACTCAAATCCTTGATATCATCATCAAGACCACACATCACATCCACATATC
* *
789226 CAAGATCACAGGTCCAGGATCTCACCAGTGAAGGCCCAGCCATTTGTAAGGACCCAA
196 CAAGATCACAGGTCCAGGATCTCACCAGTGAAGGCCCAACCATTTGTAACGACCCAA
789283 ATNNNNNNNN
Statistics
Matches: 232, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
264 232 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (264 bp):
CCTAAACCACGTGGCCTTCAAAAGCTTAAACTCAAGTTACTTGTAGTAATAGACTTGGATTATTA
TATAGATCTTAACAATCACATTCACATCAGATATGAGATGTTGGGTCAGAAGTGGGATGTTAGGT
ATCACAATCTCACCCACTCAAATCCTTGATATCATCATCAAGACCACACATCACATCCACATATC
CAAGATCACAGGTCCAGGATCTCACCAGTGAAGGCCCAACCATTTGTAACGACCCAAGTCTAACC
AAGA
Found at i:789560 original size:113 final size:113
Alignment explanation
Indices: 789362--789582 Score: 379
Period size: 113 Copynumber: 2.0 Consensus size: 113
789352 ACCACACATC
*
789362 ACATCCACATGTCCAATATCACAAGTCCAAGATCTCACCAGTGAAGGCCCAACCATTTGTAACGA
1 ACATCCACATGTCCAAGATCACAAGTCCAAGATCTCACCAGTGAAGGCCCAACCATTTGTAACGA
*
789427 CCCAAGTCCAACCACTGATCCACAAGTTATTAATAGCAGTAGACTATT
66 CCCAAGTCCAACCACTGATCCACAAGTTACTAATAGCAGTAGACTATT
* * *
789475 ACATCCACATGTCCAAGATCACAAGTCCAAGATCTCACTAGTGAAGGCCTAGCCATTTGTAACGA
1 ACATCCACATGTCCAAGATCACAAGTCCAAGATCTCACCAGTGAAGGCCCAACCATTTGTAACGA
* *
789540 CCCAAGTCCAACCACTGATCCACAAGTTACTAGTAGTAGTAGA
66 CCCAAGTCCAACCACTGATCCACAAGTTACTAATAGCAGTAGA
789583 TTTGGATTGT
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 101 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.22
Consensus pattern (113 bp):
ACATCCACATGTCCAAGATCACAAGTCCAAGATCTCACCAGTGAAGGCCCAACCATTTGTAACGA
CCCAAGTCCAACCACTGATCCACAAGTTACTAATAGCAGTAGACTATT
Found at i:813368 original size:24 final size:23
Alignment explanation
Indices: 813319--813377 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
813309 AGATGAAACT
*
813319 ATAAAATTTT-TAAAAAATAAAA
1 ATAAAATTTTAAAAAAAATAAAA
**
813341 ATAAAATTTTAAAACAAAATAAGG
1 ATAAAATTTTAAAA-AAAATAAAA
*
813365 ATAAAATTATAAA
1 ATAAAATTTTAAA
813378 CTATGGAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 10 0.32
23 2 0.06
24 19 0.61
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (23 bp):
ATAAAATTTTAAAAAAAATAAAA
Found at i:821751 original size:63 final size:63
Alignment explanation
Indices: 821648--821892 Score: 341
Period size: 63 Copynumber: 3.9 Consensus size: 63
821638 CTGTCACGGA
* * *
821648 TAGATCCATGGAGCTATCCAAACCAGTCCCCACTCTTGAAAATGGCTGGATAGCAAAGTATGG
1 TAGATCCATGGAGCTACCCAAACCAGTCCCCACTCTTGAAAATGGCTGGATAACAAAATATGG
* * * *
821711 TAGTTCCATGGAGCTGCCTAAACCAGTCCCCACTCTTGAAAATGGCTGTG-TAACAAACTATGG
1 TAGATCCATGGAGCTACCCAAACCAGTCCCCACTCTTGAAAATGGCTG-GATAACAAAATATGG
** *
821774 TAGATCCCCGGAGCTACCCAAACCAGTCCCCACTCTTGAAAAGGGCTGGATAACAAAATATGG
1 TAGATCCATGGAGCTACCCAAACCAGTCCCCACTCTTGAAAATGGCTGGATAACAAAATATGG
* * *
821837 TAGCTCCATGGAACAACCCCAAA-CAGTCCCCACTCTTGAAAATGGCTGGATAACAA
1 TAGATCCATGGAGCTA-CCCAAACCAGTCCCCACTCTTGAAAATGGCTGGATAACAA
821893 TTTTGCCAGG
Statistics
Matches: 160, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
62 1 0.01
63 152 0.95
64 7 0.04
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (63 bp):
TAGATCCATGGAGCTACCCAAACCAGTCCCCACTCTTGAAAATGGCTGGATAACAAAATATGG
Found at i:823126 original size:2 final size:2
Alignment explanation
Indices: 823121--823147 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
823111 AAAATGGGAA
823121 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
823148 TATCCTCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:851198 original size:6 final size:6
Alignment explanation
Indices: 851189--851226 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
851179 CTCAAAATCA
851189 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AA
1 AACAAG AACAAG AACAAG AACAAG AACAAG AACAAG AA
851227 TACTGAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AACAAG
Found at i:862972 original size:22 final size:21
Alignment explanation
Indices: 862937--862986 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
862927 TTTTAATTCC
* * *
862937 TTTTAGAAATATAATAATAATT
1 TTTTA-AAATATAAAAAAAATA
862959 TTTTAAAATAATAAAAAAAATA
1 TTTTAAAAT-ATAAAAAAAATA
862981 TTTTAA
1 TTTTAA
862987 TCTTTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTTAAAATATAAAAAAAATA
Found at i:874613 original size:18 final size:18
Alignment explanation
Indices: 874592--874633 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
874582 ATCTACATCT
*
874592 TCCTCCTCATCTTCCTCA
1 TCCTCCACATCTTCCTCA
*
874610 TCCTCCACTTCTTCCTCA
1 TCCTCCACATCTTCCTCA
*
874628 GCCTCC
1 TCCTCC
874634 CACTCCACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.52, G:0.02, T:0.36
Consensus pattern (18 bp):
TCCTCCACATCTTCCTCA
Found at i:876811 original size:209 final size:208
Alignment explanation
Indices: 876446--877007 Score: 903
Period size: 209 Copynumber: 2.7 Consensus size: 208
876436 TTCCATTCAG
* * *
876446 ATAAATAACAAATTAAGCATAAGACACGTGTTTATCATTTCTACTTATCTTGTTGTAATAATTCA
1 ATAAATAACAAATTAAGCATAAGATACATGTTTATCATTTTTACTTATCTTGTTGTAATAATTCA
*
876511 TAATATAATAATTGAATTACACATGATAGAGAGTAAGACCACAATAATTCATTAAGAGAGCATTG
66 TAATGTAATAATTGAATTACACATGATAGAGAGTAAGACCACAATAATTCATTAAGAGAGCATTG
** * *
876576 ATGTCTTATCACTTAACTGTTTAATGAAATGTTATTAGTAAATGATCCATAGTTTGACATGAAAG
131 ATGTCTTATCACTTAACTAATTAATGAAATGTTATTAGTAAATGATCCACAATTTGACATGAAAG
876641 GTGATTAAAGGGC
196 GTGATTAAAGGGC
* * *
876654 ATAAGTAACAAATTAAGCACAAGATACATGTTTATCATTTTTTACTGATCTTGTTGTAATAATTC
1 ATAAATAACAAATTAAGCATAAGATACATGTTTATCA-TTTTTACTTATCTTGTTGTAATAATTC
*
876719 ATAATGTAATTATTGAATTACACATGATAGAGAGTAAGACCACAATAATTCATTAAGAGAGCATT
65 ATAATGTAATAATTGAATTACACATGATAGAGAGTAAGACCACAATAATTCATTAAGAGAGCATT
* * *
876784 GATGTCTTGTCACTTAACTAATTAATGAAATGTTATTAGTAAATGATCCACAATTTTACATGAAG
130 GATGTCTTATCACTTAACTAATTAATGAAATGTTATTAGTAAATGATCCACAATTTGACATGAAA
876849 GGTGATTAAAGGGC
195 GGTGATTAAAGGGC
* * *
876863 ATAAAAAACAAATTAAGTATAAGATACATGTTTATCATTTTTGCTTATCTTGTTGTAATAATTCA
1 ATAAATAACAAATTAAGCATAAGATACATGTTTATCATTTTTACTTATCTTGTTGTAATAATTCA
*
876928 TAATGTAATAATTGAATTACACAAGATAGAGAGAATAAG--CACAATAATTCATTAAGAGAGCAT
66 TAATGTAATAATTGAATTACACATGATAGAGAG--TAAGACCACAATAATTCATTAAGAGAGCAT
*
876991 TGATGTCTTATTACTTA
129 TGATGTCTTATCACTTA
877008 TTATCAGTAA
Statistics
Matches: 326, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
208 129 0.40
209 193 0.59
210 4 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (208 bp):
ATAAATAACAAATTAAGCATAAGATACATGTTTATCATTTTTACTTATCTTGTTGTAATAATTCA
TAATGTAATAATTGAATTACACATGATAGAGAGTAAGACCACAATAATTCATTAAGAGAGCATTG
ATGTCTTATCACTTAACTAATTAATGAAATGTTATTAGTAAATGATCCACAATTTGACATGAAAG
GTGATTAAAGGGC
Found at i:884220 original size:2 final size:2
Alignment explanation
Indices: 884176--884201 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
884166 NNNNNCTCTT
884176 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
884202 GCACGCACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:904746 original size:2 final size:2
Alignment explanation
Indices: 904739--904766 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
904729 GGAAATAACC
904739 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
904767 CTTTGGAAAC
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:905852 original size:25 final size:25
Alignment explanation
Indices: 905824--905871 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
905814 AATATTCAAC
*
905824 ACCCCAAAAAAGAAAATTAAAAAAA
1 ACCCCAAAAAAGAAAATGAAAAAAA
*
905849 ACCCCAAAAACGAAAATGAAAAA
1 ACCCCAAAAAAGAAAATGAAAAA
905872 GAAAAAAATC
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:0.69, C:0.19, G:0.06, T:0.06
Consensus pattern (25 bp):
ACCCCAAAAAAGAAAATGAAAAAAA
Found at i:909407 original size:13 final size:13
Alignment explanation
Indices: 909389--909417 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
909379 ATAATATATC
909389 AATTAATAAATTA
1 AATTAATAAATTA
909402 AATTAATAAATTA
1 AATTAATAAATTA
909415 AAT
1 AAT
909418 ACTCGAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTAATAAATTA
Done.