Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, 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: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 2 of 14
Found at i:508816 original size:113 final size:114
Alignment explanation
Indices: 508668--508896 Score: 388
Period size: 113 Copynumber: 2.0 Consensus size: 114
508658 AAAATACAAG
* * *
508668 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAGTATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAA
* * *
508733 TGTCATATATTTTATTTTTATTTATTTTTATAATATTTTATATTTTATT
66 TGTCATATATTTTATTTTCATTTATTATTATAATATTATATATTTTATT
508782 TTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAA
*
508846 TGTCATATATTTTATTTTCATTTATTATTATAATCTTATATATTTTATT
66 TGTCATATATTTTATTTTCATTTATTATTATAATATTATATATTTTATT
508895 TT
1 TT
508897 CATTTCTTTA
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
113 93 0.86
114 15 0.14
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (114 bp):
TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAA
TGTCATATATTTTATTTTCATTTATTATTATAATATTATATATTTTATT
Found at i:508819 original size:23 final size:22
Alignment explanation
Indices: 508751--508819 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
508741 ATTTTATTTT
508751 TATTTATTTTTATAATATTTTATA
1 TATTTA-TTTT-TAATATTTTATA
508775 T-TTTATTTTTAATATATTTATA
1 TATTTATTTTTAATAT-TTTATA
*
508797 T-TTATATTATTAAT-TTTTATA
1 TATT-TATTTTTAATATTTTATA
508818 TA
1 TA
508820 ATATCATATC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 13 0.32
22 14 0.34
23 13 0.32
24 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTATTTTTAATATTTTATA
Found at i:509020 original size:33 final size:33
Alignment explanation
Indices: 508971--509051 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
508961 AATGTTAATT
508971 TTTTATATT-T-TATTTTATTTTAA-TTTTTTA
1 TTTTATATTATATATTTTATTTTAAGTTTTTTA
509001 TTCTTATATTATATATTTTATTTTAATGTTTTTTA
1 TT-TTATATTATATATTTTATTTTAA-GTTTTTTA
509036 TTTTA-ATTATAATATT
1 TTTTATATTAT-ATATT
509052 ATAAAATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
30 2 0.04
31 7 0.16
32 1 0.02
33 18 0.40
34 8 0.18
35 9 0.20
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (33 bp):
TTTTATATTATATATTTTATTTTAAGTTTTTTA
Found at i:529777 original size:2 final size:2
Alignment explanation
Indices: 529772--529833 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
529762 ACTTCTTCAA
* * * *
529772 AT AT AT AC AT AC AT AT AT AT AT AT AT GT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
529814 TT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
529834 TTTCTCTCTG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:529795 original size:18 final size:18
Alignment explanation
Indices: 529772--529833 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
529762 ACTTCTTCAA
*
529772 ATATATACATACATATAT
1 ATATATATATACATATAT
*
529790 ATATATATGTACATATAT
1 ATATATATATACATATAT
* *
529808 ATATATTTATATATATAT
1 ATATATATATACATATAT
529826 ATATATAT
1 ATATATAT
529834 TTTCTCTCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATATATATACATATAT
Found at i:539717 original size:26 final size:26
Alignment explanation
Indices: 539688--539741 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
539678 TTTGTTCATG
539688 AACAACAACTATTTTTCAT-ATGAATA
1 AACAACAACTATTTTTCATAAT-AATA
539714 AACAACAACTATTTTTCATAATAATA
1 AACAACAACTATTTTTCATAATAATA
539740 AA
1 AA
539742 AAATAGTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (26 bp):
AACAACAACTATTTTTCATAATAATA
Found at i:541307 original size:25 final size:25
Alignment explanation
Indices: 541279--541329 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
541269 AAAAAGTTTC
*
541279 TCTTTATTTGCTTA-TCGTATATATA
1 TCTTTATTTCCTTATTC-TATATATA
*
541304 TCTTTGTTTCCTTATTCTATATATA
1 TCTTTATTTCCTTATTCTATATATA
541329 T
1 T
541330 TATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.59
Consensus pattern (25 bp):
TCTTTATTTCCTTATTCTATATATA
Found at i:542284 original size:14 final size:14
Alignment explanation
Indices: 542223--542328 Score: 59
Period size: 14 Copynumber: 7.3 Consensus size: 14
542213 AGAACCTTCC
542223 AAAACTTTGGAGGG
1 AAAACTTTGGAGGG
* *
542237 AAATCTTTTGGGGGGGG
1 AAAAC-TTT--GGAGGG
* * **
542254 AATACTTTGAATTG
1 AAAACTTTGGAGGG
542268 AAAACTTTGGAGGG
1 AAAACTTTGGAGGG
* *
542282 AAATCTTTTGGGGGG
1 AAAAC-TTTGGAGGG
* * ***
542297 AATACTTTGAATTA
1 AAAACTTTGGAGGG
542311 AAAACTTTGGAGGG
1 AAAACTTTGGAGGG
542325 AAAA
1 AAAA
542329 GTGGGTGGGG
Statistics
Matches: 62, Mismatches: 26, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
14 37 0.60
15 14 0.23
16 3 0.05
17 8 0.13
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.29
Consensus pattern (14 bp):
AAAACTTTGGAGGG
Found at i:542309 original size:43 final size:44
Alignment explanation
Indices: 542223--542327 Score: 185
Period size: 43 Copynumber: 2.4 Consensus size: 44
542213 AGAACCTTCC
*
542223 AAAACTTTGGAGGGAAATCTTTTGGGGGGGGAATACTTTGAATTG
1 AAAACTTTGGAGGGAAATCTTTT-GGGGGGGAATACTTTGAATTA
542268 AAAACTTTGGAGGGAAATCTTTT-GGGGGGAATACTTTGAATTA
1 AAAACTTTGGAGGGAAATCTTTTGGGGGGGAATACTTTGAATTA
542311 AAAACTTTGGAGGGAAA
1 AAAACTTTGGAGGGAAA
542328 AGTGGGTGGG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
43 36 0.61
45 23 0.39
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (44 bp):
AAAACTTTGGAGGGAAATCTTTTGGGGGGGAATACTTTGAATTA
Found at i:542396 original size:12 final size:12
Alignment explanation
Indices: 542379--542419 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
542369 TTGTGTAAAT
542379 CATCCATTTTTG
1 CATCCATTTTTG
542391 CATCCATTTTTG
1 CATCCATTTTTG
*
542403 CATCCATTCTTG
1 CATCCATTTTTG
542415 CATCC
1 CATCC
542420 TTTGTATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.17, C:0.32, G:0.07, T:0.44
Consensus pattern (12 bp):
CATCCATTTTTG
Found at i:542744 original size:18 final size:17
Alignment explanation
Indices: 542717--542762 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
542707 GCTATTTTTT
542717 ATAAAATAAA-TAAATAA
1 ATAAAATAAATTAAA-AA
542734 ATAATAATAAATTAAAAA
1 ATAA-AATAAATTAAAAA
542752 ATAAAAATAAA
1 AT-AAAATAAA
542763 AACACTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.15
18 16 0.62
19 6 0.23
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAAATAAATTAAAAA
Found at i:543126 original size:26 final size:25
Alignment explanation
Indices: 543070--543212 Score: 112
Period size: 25 Copynumber: 5.5 Consensus size: 25
543060 AAGTGCATAT
* *
543070 AAAAAAATTATTATTATATGTA-ATGTT
1 AAAAAAA--ATTATTACATGTATAT-TG
* *
543097 AAAAAAATTTATTTCATGCTATATTG
1 AAAAAAAATTATTACATG-TATATTG
*
543123 -AAAAAAATTATTACATGTCATGTTG
1 AAAAAAAATTATTACATGT-ATATTG
*
543148 AAAAAAAATTATTACATATTATATTG
1 AAAAAAAATTATTACAT-GTATATTG
* *
543174 AAACAAAAATTATTATATATCATATT-
1 AAA-AAAAATTATTACATGT-ATATTG
*
543200 CAAAAAAATTATT
1 AAAAAAAATTATT
543213 GTTACATGTT
Statistics
Matches: 97, Mismatches: 12, Indels: 16
0.78 0.10 0.13
Matches are distributed among these distances:
24 1 0.01
25 38 0.39
26 30 0.31
27 28 0.29
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (25 bp):
AAAAAAAATTATTACATGTATATTG
Found at i:543154 original size:53 final size:53
Alignment explanation
Indices: 543097--543212 Score: 139
Period size: 51 Copynumber: 2.2 Consensus size: 53
543087 ATGTAATGTT
* * * * * *
543097 AAAAAAATTTATTTCATGCTATATTG-AA-AAAAATTATTACATGTCATGTTG
1 AAAAAAAATTATTACATACTATATTGAAACAAAAATTATTACATATCATATTC
* *
543148 AAAAAAAATTATTACATATTATATTGAAACAAAAATTATTATATATCATATTC
1 AAAAAAAATTATTACATACTATATTGAAACAAAAATTATTACATATCATATTC
543201 -AAAAAAATTATT
1 AAAAAAAATTATT
543213 GTTACATGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 22 0.40
52 14 0.25
53 19 0.35
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (53 bp):
AAAAAAAATTATTACATACTATATTGAAACAAAAATTATTACATATCATATTC
Found at i:543206 original size:25 final size:26
Alignment explanation
Indices: 543117--543212 Score: 124
Period size: 26 Copynumber: 3.7 Consensus size: 26
543107 ATTTCATGCT
*
543117 ATATTG-AAAAAAATTATTACATGTC
1 ATATTGAAAAAAAATTATTACATATC
* *
543142 ATGTTGAAAAAAAATTATTACATATT
1 ATATTGAAAAAAAATTATTACATATC
*
543168 ATATTGAAACAAAAATTATTATATATC
1 ATATTGAAA-AAAAATTATTACATATC
*
543195 ATATT-CAAAAAAATTATT
1 ATATTGAAAAAAAATTATT
543213 GTTACATGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
25 15 0.24
26 27 0.44
27 20 0.32
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (26 bp):
ATATTGAAAAAAAATTATTACATATC
Found at i:543237 original size:31 final size:28
Alignment explanation
Indices: 543214--543267 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
543204 AAAATTATTG
**
543214 TTACATGTTTTGTTAAAAGAAAAAATTA
1 TTACATGCCTTGTTAAAAGAAAAAATTA
*
543242 TTATATGCCTTGTTAAAAGAAAAAAT
1 TTACATGCCTTGTTAAAAGAAAAAAT
543268 CGTTATATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (28 bp):
TTACATGCCTTGTTAAAAGAAAAAATTA
Found at i:543261 original size:28 final size:28
Alignment explanation
Indices: 543223--543276 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
543213 GTTACATGTT
*
543223 TTGTTAAAAGAAAAAATTATTATATGCC
1 TTGTTAAAAGAAAAAATCATTATATGCC
*
543251 TTGTTAAAAGAAAAAATCGTTATATG
1 TTGTTAAAAGAAAAAATCATTATATG
543277 TTATATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (28 bp):
TTGTTAAAAGAAAAAATCATTATATGCC
Found at i:543739 original size:25 final size:24
Alignment explanation
Indices: 543686--543739 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
543676 CTCTATAGTT
*
543686 ATTTTTCACTTTCTTCTTCTTTCT
1 ATTTTTCACTTTCTTCTTCTTTCA
* *
543710 TTTTTTCCACTTTC-TCTTTGTTTCA
1 ATTTTT-CACTTTCTTC-TTCTTTCA
543735 ATTTT
1 ATTTT
543740 ACACCGAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.09, C:0.22, G:0.02, T:0.67
Consensus pattern (24 bp):
ATTTTTCACTTTCTTCTTCTTTCA
Found at i:551724 original size:63 final size:63
Alignment explanation
Indices: 551657--551816 Score: 176
Period size: 63 Copynumber: 2.5 Consensus size: 63
551647 CTTTTTTAAA
* ** * * * * *
551657 AAATTTTATAATTTCACTCTTTTAATAATTTTTAAATTTTTATGACTTATGTTTACTTTTTAG
1 AAATTTTATAATTTTACTCTTACAAAAATTTTAAAAATTTTATAACATATGTTTACTTTTTAG
* * * * *
551720 AAATTTTATAATTTTGCTCTTACAAAAATTTTAAAAATTTTCTAACATATTTTTATTTTTTTG
1 AAATTTTATAATTTTACTCTTACAAAAATTTTAAAAATTTTATAACATATGTTTACTTTTTAG
*
551783 AAATTTTATAATTTTACTCCTACAATAATATTTT
1 AAATTTTATAATTTTACTCTTACAA-AA-ATTTT
551817 GTTTAGTAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
63 73 0.91
64 2 0.03
65 5 0.06
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (63 bp):
AAATTTTATAATTTTACTCTTACAAAAATTTTAAAAATTTTATAACATATGTTTACTTTTTAG
Found at i:552116 original size:14 final size:16
Alignment explanation
Indices: 552099--552134 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
552089 TTTATTTACT
552099 TATTTT-AATTTT-AA
1 TATTTTAAATTTTAAA
552113 TATTTTAAATTTTAAA
1 TATTTTAAATTTTAAA
552129 TATTTT
1 TATTTT
552135 TTTTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 6 0.30
16 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTAAATTTTAAA
Found at i:552515 original size:18 final size:18
Alignment explanation
Indices: 552484--552521 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
552474 TTATCTAAAA
*
552484 ATTAAGATTATTATCATT
1 ATTAAGATTATTATAATT
552502 ATTAA-ATTATTTATAATT
1 ATTAAGATTA-TTATAATT
552520 AT
1 AT
552522 ACTAGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTAAGATTATTATAATT
Found at i:552668 original size:20 final size:20
Alignment explanation
Indices: 552640--552693 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
552630 TATTGTTACA
*
552640 TATTCAATTTTTAATATAAT
1 TATTTAATTTTTAATATAAT
* *
552660 TATTTAATTTATAAATATTAT
1 TATTTAATTT-TTAATATAAT
552681 T-TTTAACTTTTTA
1 TATTTAA-TTTTTA
552694 CTTTCTAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTAATTTTTAATATAAT
Found at i:554539 original size:2 final size:2
Alignment explanation
Indices: 554532--554560 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
554522 TGCATAAATT
554532 TA TA TA TA 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 T
554561 CAAGACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:555922 original size:29 final size:27
Alignment explanation
Indices: 555882--555942 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
555872 CCAATTTCAA
*
555882 AAAAAAATTATTCATAAAGTGTTAATT
1 AAAAAAATTATTCATAAAGTGGTAATT
* *
555909 AAAAAAATGATATTTATAAGGTGGTAATT
1 AAAAAAAT--TATTCATAAAGTGGTAATT
*
555938 GAAAA
1 AAAAA
555943 GAGAAAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.29
29 20 0.71
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (27 bp):
AAAAAAATTATTCATAAAGTGGTAATT
Found at i:562059 original size:2 final size:2
Alignment explanation
Indices: 562052--562076 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
562042 TAAATTGTTT
562052 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
562077 TTGAGTTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:567594 original size:15 final size:15
Alignment explanation
Indices: 567554--567594 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
567544 TTTTACAATA
*
567554 CAATGTGATTACAAG
1 CAATGTGATTGCAAG
*
567569 TAATGTGATTGCAAG
1 CAATGTGATTGCAAG
*
567584 CAATATGATTG
1 CAATGTGATTG
567595 TAGAGAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (15 bp):
CAATGTGATTGCAAG
Found at i:567864 original size:16 final size:18
Alignment explanation
Indices: 567843--567876 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
567833 TTATAATCTT
567843 ATATATTT-TAT-TTTTA
1 ATATATTTATATATTTTA
567859 ATATATTTATATATTTTA
1 ATATATTTATATATTTTA
567877 TTATTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATATTTATATATTTTA
Found at i:567869 original size:32 final size:31
Alignment explanation
Indices: 567795--567893 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 31
567785 TCATCTCTTA
* *
567795 AATATATTT-TAATGTCATATATTTA-TTTT
1 AATATATTTATAATCTTATATATTTATTTTT
* *
567824 CATTTATTATTATAATCTTATATATTTTATTTTT
1 AATATA-T-TTATAATCTTATATA-TTTATTTTT
* *
567858 AATATATTTATATATTTTAT-TATTAATTTTT
1 AATATATTTATA-ATCTTATATATTTATTTTT
567889 -ATATA
1 AATATA
567894 ATATCATCTC
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
29 4 0.07
30 6 0.11
31 10 0.18
32 17 0.30
33 11 0.20
34 8 0.14
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (31 bp):
AATATATTTATAATCTTATATATTTATTTTT
Found at i:567872 original size:24 final size:24
Alignment explanation
Indices: 567818--567893 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 24
567808 GTCATATATT
*
567818 TATTTTCATTTATTATTATAATCTTATA
1 TATTTT-ATTT-TTAATAT-AT-TTATA
567846 TATTTTATTTTTAATATATTTATA
1 TATTTTATTTTTAATATATTTATA
*
567870 TATTTTATTATTAAT-T-TTTATA
1 TATTTTATTTTTAATATATTTATA
567892 TA
1 TA
567894 ATATCATCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.17
23 1 0.02
24 19 0.41
25 2 0.04
26 6 0.13
27 4 0.09
28 6 0.13
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTTTATTTTTAATATATTTATA
Found at i:567969 original size:5 final size:5
Alignment explanation
Indices: 567959--568111 Score: 59
Period size: 5 Copynumber: 30.4 Consensus size: 5
567949 TAATCTTATA
* * * *
567959 TATTT TATTT T-TATT T-TTT TAATA TATTTT TATAT TA-TA TATTT TATTT
1 TATTT TATTT TAT-TT TATTT TATTT TA-TTT TATTT TATTT TATTT TATTT
* ** * * * *
568008 TAATT TATTT TA-CC TATAT TATATA AATTT TAATTT T-TTA TATTT TATTT
1 TATTT TATTT TATTT TATTT TAT-TT TATTT T-ATTT TATTT TATTT TATTT
* * *
568058 TATTTT TATTT TAGTTCT TATAT TA-TA TATTT TATTT TAATAT T-TTT
1 TA-TTT TATTT TA-TT-T TATTT TATTT TATTT TATTT T-ATTT TATTT
568105 TATTT TA
1 TATTT TA
568112 ATTATAACAG
Statistics
Matches: 107, Mismatches: 27, Indels: 28
0.66 0.17 0.17
Matches are distributed among these distances:
4 16 0.15
5 66 0.62
6 22 0.21
7 3 0.03
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (5 bp):
TATTT
Found at i:568027 original size:113 final size:113
Alignment explanation
Indices: 567746--568005 Score: 399
Period size: 113 Copynumber: 2.3 Consensus size: 113
567736 AAAATACAAG
*
567746 TTTAATATATTTAT-TTTTTTA-TA-TAATTTTTATATAATATCATCTCTTAAATATA-TTTTAA
1 TTTAATATATTTATATATTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
567807 TGTCATATATTTATTTTCATTTATTATTATAATCTTATATATTTTATT
66 TGTCATATATTTATTTTCATTTATTATTATAATCTTATATATTTTATT
567855 TTTAATATATTTATATATTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATATTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
567920 TGTCATATATTT-TGTTTCATTTATTATTATAATCTTATATATTTTATT
66 TGTCATATATTTAT-TTTCATTTATTATTATAATCTTATATATTTTATT
* *
567968 TTT-ATTTTTTTAATATATTTT-TATATTATATATTTTAT
1 TTTAATATATTT-ATATATTTTAT-TATTA-AT-TTTTAT
568006 TTTAATTTAT
Statistics
Matches: 139, Mismatches: 3, Indels: 12
0.90 0.02 0.08
Matches are distributed among these distances:
109 14 0.10
110 6 0.04
111 2 0.01
112 40 0.29
113 69 0.50
114 2 0.01
115 6 0.04
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (113 bp):
TTTAATATATTTATATATTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
TGTCATATATTTATTTTCATTTATTATTATAATCTTATATATTTTATT
Found at i:568052 original size:35 final size:32
Alignment explanation
Indices: 567989--568054 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 32
567979 AATATATTTT
567989 TATATTATATATTTTATTTTAATTTATTTTACC
1 TATATTATATATTTTATTTT-ATTTATTTTACC
568022 TATATTATATAAATTTTAATTTT-TTATATTTTA
1 TATATTATAT--ATTTT-ATTTTATT-TATTTTA
568055 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 10 0.34
34 2 0.07
35 12 0.41
36 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (32 bp):
TATATTATATATTTTATTTTATTTATTTTACC
Found at i:568111 original size:15 final size:15
Alignment explanation
Indices: 567975--568113 Score: 75
Period size: 15 Copynumber: 8.5 Consensus size: 15
567965 ATTTTTATTT
567975 TTTTAATATATTTTTA
1 TTTTAATATA-TTTTA
*
567991 TATT-ATATATTTTA
1 TTTTAATATATTTTA
*
568005 TTTTAATTTATTTTA
1 TTTTAATATATTTTA
*
568020 CCTATATTATATAAATTTTAA
1 --T-T-TTA-ATATATTTT-A
*
568041 TTTT-TTATATTTTA
1 TTTTAATATATTTTA
* *
568055 TTTTATTTTTATTTTA
1 TTTTA-ATATATTTTA
568071 GTTCTTATATTATATATTTTA
1 --T-TT-TA--ATATATTTTA
*
568092 TTTTAATATTTTTTA
1 TTTTAATATATTTTA
568107 TTTTAAT
1 TTTTAAT
568114 TATAACAGTA
Statistics
Matches: 98, Mismatches: 11, Indels: 29
0.71 0.08 0.21
Matches are distributed among these distances:
14 13 0.13
15 37 0.38
16 12 0.12
17 5 0.05
18 5 0.05
19 7 0.07
20 9 0.09
21 10 0.10
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (15 bp):
TTTTAATATATTTTA
Found at i:576340 original size:2 final size:2
Alignment explanation
Indices: 576333--576358 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
576323 TTGTTTCCAA
576333 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
576359 TTATCAGGCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:578377 original size:40 final size:40
Alignment explanation
Indices: 578317--578396 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
578307 ATAAATATCT
578317 TATTATATTTAATTATGAAGACTATAGAGTCCAACACCTC
1 TATTATATTTAATTATGAAGACTATAGAGTCCAACACCTC
*
578357 TATTGTATTTAATTATGAAGACTATAGAGTCCAACACCTC
1 TATTATATTTAATTATGAAGACTATAGAGTCCAACACCTC
578397 AAAATTGTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (40 bp):
TATTATATTTAATTATGAAGACTATAGAGTCCAACACCTC
Found at i:593482 original size:18 final size:18
Alignment explanation
Indices: 593459--593493 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
593449 TTTTTGTGCA
*
593459 TAATTTTGTAACATAAAC
1 TAATTTTGTAAAATAAAC
*
593477 TAATTTTTTAAAATAAA
1 TAATTTTGTAAAATAAA
593494 TATTACTAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
TAATTTTGTAAAATAAAC
Found at i:603875 original size:12 final size:12
Alignment explanation
Indices: 603838--603876 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
603828 AAGTGGCATT
*
603838 TATGTATATATG
1 TATGTATATATA
603850 TATGTATATATA
1 TATGTATATATA
* *
603862 TATATATATGTA
1 TATGTATATATA
603874 TAT
1 TAT
603877 TCATTTATTT
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:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (12 bp):
TATGTATATATA
Found at i:604633 original size:16 final size:16
Alignment explanation
Indices: 604612--604650 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
604602 ATTAATTTGA
604612 AATAAATTAAAAAAAT
1 AATAAATTAAAAAAAT
*
604628 AATAAATTAAAAAATT
1 AATAAATTAAAAAAAT
604644 AA-AAATT
1 AATAAATT
604651 TTCAGTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAATTAAAAAAAT
Found at i:604644 original size:8 final size:8
Alignment explanation
Indices: 604615--604648 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
604605 AATTTGAAAT
604615 AAATTAAA
1 AAATTAAA
* *
604623 AAAATAAT
1 AAATTAAA
604631 AAATTAAA
1 AAATTAAA
604639 AAATTAAA
1 AAATTAAA
604647 AA
1 AA
604649 TTTTCAGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATTAAA
Found at i:617540 original size:34 final size:34
Alignment explanation
Indices: 617502--617580 Score: 158
Period size: 34 Copynumber: 2.3 Consensus size: 34
617492 TTAATAAAAA
617502 AATTATTATATAATTATGTAAAATAAAATATTTT
1 AATTATTATATAATTATGTAAAATAAAATATTTT
617536 AATTATTATATAATTATGTAAAATAAAATATTTT
1 AATTATTATATAATTATGTAAAATAAAATATTTT
617570 AATTATTATAT
1 AATTATTATAT
617581 TAACAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (34 bp):
AATTATTATATAATTATGTAAAATAAAATATTTT
Found at i:618053 original size:18 final size:18
Alignment explanation
Indices: 618014--618069 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
618004 TGTTTTGTTG
*
618014 TTTTAATTTATATATT-TG
1 TTTTAATTTATAT-TTATT
618032 TTTTAATTTATATTTATT
1 TTTTAATTTATATTTATT
* *
618050 TTTTTATTTCTATTATATT
1 TTTTAATTTATATT-TATT
618069 T
1 T
618070 GCTCATATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.06
18 26 0.79
19 5 0.15
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTAATTTATATTTATT
Found at i:620010 original size:23 final size:24
Alignment explanation
Indices: 619974--620019 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
619964 GCTTACACTT
*
619974 CAAAAACTTAATCACATGTCAAGC
1 CAAAAACTTAATCAAATGTCAAGC
*
619998 CAAAATCTT-ATCAAATGTCAAG
1 CAAAAACTTAATCAAATGTCAAG
620020 ACAGGAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (24 bp):
CAAAAACTTAATCAAATGTCAAGC
Found at i:633270 original size:2 final size:2
Alignment explanation
Indices: 633265--633290 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
633255 CATATTATGC
633265 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
633291 CAAGGTTCAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:638266 original size:2 final size:2
Alignment explanation
Indices: 638259--638296 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
638249 ATTAGAAGGT
638259 TA TA TA TA 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 TA TA TA TA
638297 CTAGCATGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:643295 original size:3 final size:3
Alignment explanation
Indices: 643287--643314 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
643277 AATTTCTTTC
643287 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
643315 ATCGTACGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:649315 original size:30 final size:29
Alignment explanation
Indices: 649270--649329 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
649260 AACGGATATG
*
649270 GTATTTTTTTTTTTGAAACATT-TGAAATT
1 GTATTTTTTATTTTGAAAC-TTATGAAATT
649299 GTATTTATTTATTTTGAAACTTATGAAATT
1 GTATTT-TTTATTTTGAAACTTATGAAATT
649329 G
1 G
649330 AAATCGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (29 bp):
GTATTTTTTATTTTGAAACTTATGAAATT
Found at i:649378 original size:21 final size:21
Alignment explanation
Indices: 649354--649403 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
649344 GAAATATCGG
*
649354 AAATTTAATTGAAATTATTTA
1 AAATTTAATTGAAATTATCTA
* **
649375 AAATTTTATTTTAATTATCTA
1 AAATTTAATTGAAATTATCTA
*
649396 TAATTTAA
1 AAATTTAA
649404 CCAAAACCTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
AAATTTAATTGAAATTATCTA
Found at i:650707 original size:3 final size:3
Alignment explanation
Indices: 650699--650723 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
650689 TGGTTTTAAC
650699 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
650724 TCAATTAGAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:655452 original size:2 final size:2
Alignment explanation
Indices: 655445--655476 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
655435 ATATACATCC
655445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
655477 GTATTTCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:657430 original size:2 final size:2
Alignment explanation
Indices: 657423--657454 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
657413 GGGAGTGCAC
*
657423 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
657455 GGAGGGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:667313 original size:2 final size:2
Alignment explanation
Indices: 667306--667347 Score: 52
Period size: 2 Copynumber: 21.0 Consensus size: 2
667296 GGTTAATTAT
667306 TA TA TA TA TA TA TA TCA T- TCA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA TA TA TA TA TA TA TA
667348 GGCTCTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 2 0.06
2 31 0.86
3 3 0.08
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:672197 original size:29 final size:29
Alignment explanation
Indices: 672149--672204 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
672139 AATTGAACTT
672149 TTCAATTGAAAACCATTAGATATATAATAA
1 TTCAATTGAAAACCATTAGATA-ATAATAA
672179 TTCAATTG-AAACCATTAGATAATAAT
1 TTCAATTGAAAACCATTAGATAATAAT
672205 TAAAATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 5 0.19
29 13 0.50
30 8 0.31
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (29 bp):
TTCAATTGAAAACCATTAGATAATAATAA
Found at i:672200 original size:25 final size:26
Alignment explanation
Indices: 672149--672215 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 26
672139 AATTGAACTT
672149 TTCAATTGAAAACCATTAGATATATAATAA
1 TTCAATTG-AAACCATTAG--A-ATAATAA
672179 TTCAATTGAAACCATTAG-ATAATAA
1 TTCAATTGAAACCATTAGAATAATAA
*
672204 TTAAAATTGAAA
1 TT-CAATTGAAA
672216 ACTAAAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 9 0.26
26 8 0.23
29 10 0.29
30 8 0.23
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (26 bp):
TTCAATTGAAACCATTAGAATAATAA
Found at i:676151 original size:21 final size:20
Alignment explanation
Indices: 676109--676151 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
676099 CTTTAAAAAA
* **
676109 TTCTTTTTCTTTCTTCTTTT
1 TTCTTTTACTTTCTTCCCTT
676129 TTCTTTTAACTTTCTTCCCTT
1 TTCTTTT-ACTTTCTTCCCTT
676150 TT
1 TT
676152 ATCTCCTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTTTACTTTCTTCCCTT
Found at i:677468 original size:3 final size:3
Alignment explanation
Indices: 677462--677490 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
677452 AAAAATAGAA
677462 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
677491 GCAATTTTAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:679365 original size:30 final size:28
Alignment explanation
Indices: 679331--679405 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 28
679321 AACTATTAAT
*
679331 TATAAAAATTTATTTAATCTAAAATAAAAA
1 TATAAAAATTTATTTAA-ATAAAAT-AAAA
*
679361 TATAAAAACTTTA-TTAAATGAAATAAAA
1 TATAAAAA-TTTATTTAAATAAAATAAAA
679389 -ATAAAAATTTATTTAAA
1 TATAAAAATTTATTTAAA
679406 CTTTTTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.10
27 12 0.29
28 4 0.10
29 5 0.12
30 12 0.29
31 4 0.10
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (28 bp):
TATAAAAATTTATTTAAATAAAATAAAA
Found at i:680066 original size:23 final size:23
Alignment explanation
Indices: 680040--680083 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
680030 CTATGCTCTC
680040 GATTTCTCTCTTTT-GCACTTTCA
1 GATTTCTCT-TTTTAGCACTTTCA
680063 GATTTCTCTTTTTAGCACTTT
1 GATTTCTCTTTTTAGCACTTT
680084 GAAGATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.14, C:0.23, G:0.09, T:0.55
Consensus pattern (23 bp):
GATTTCTCTTTTTAGCACTTTCA
Found at i:680503 original size:27 final size:28
Alignment explanation
Indices: 680470--680522 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
680460 TGCATTAAAG
* *
680470 TGTAACAA-AATGTTTTTGAATATGATA
1 TGTAACAACAATATTTTTCAATATGATA
680497 TGTAACAACAATATTTTTCAATATGA
1 TGTAACAACAATATTTTTCAATATGA
680523 CGTGTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (28 bp):
TGTAACAACAATATTTTTCAATATGATA
Found at i:680542 original size:28 final size:27
Alignment explanation
Indices: 680469--680529 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
680459 ATGCATTAAA
* * *
680469 GTGTAACAAAATGTTTTTGAATATGAT
1 GTGTAACAAAATATTTTTCAATATGAC
*
680496 ATGTAACAACAATATTTTTCAATATGAC
1 GTGTAACAA-AATATTTTTCAATATGAC
680524 GTGTAA
1 GTGTAA
680530 TAATAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (27 bp):
GTGTAACAAAATATTTTTCAATATGAC
Found at i:680574 original size:31 final size:32
Alignment explanation
Indices: 680510--680592 Score: 114
Period size: 31 Copynumber: 2.6 Consensus size: 32
680500 AACAACAATA
* * * *
680510 TTTTTCAATATGACGTGTAATAATAATTTTTT
1 TTTTTTAACATGACGTGTAATAACAATTATTT
*
680542 TTTTTTAACATGGCGTGTAATAACAA-TATTT
1 TTTTTTAACATGACGTGTAATAACAATTATTT
680573 TTTTTTAACATGACGTGTAA
1 TTTTTTAACATGACGTGTAA
680593 CAACTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
31 23 0.51
32 22 0.49
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTTTTAACATGACGTGTAATAACAATTATTT
Found at i:680600 original size:27 final size:27
Alignment explanation
Indices: 680539--680727 Score: 117
Period size: 26 Copynumber: 7.0 Consensus size: 27
680529 ATAATAATTT
* *
680539 TTTTTTTTTAACATGGCGTGTAATAACAATA
1 TTTTTTTTTAACATGACGTG---TAACAA-C
680570 TTTTTTTTTAACATGACGTGTAACAAC
1 TTTTTTTTTAACATGACGTGTAACAAC
*
680597 -TTTTTTTTAACTATGACTTGTAAC-A-
1 TTTTTTTTTAAC-ATGACGTGTAACAAC
* * * *
680622 TGTTTTTGT-ATATAACGTGTAACAAC
1 TTTTTTTTTAACATGACGTGTAACAAC
*
680648 --TTTTTTTAACCATGACTTGTAAC-A-
1 TTTTTTTTTAA-CATGACGTGTAACAAC
* * *
680672 TGTTTTTGT-ATATGACGTGTAACAAC
1 TTTTTTTTTAACATGACGTGTAACAAC
* *
680698 AGTATTTTTTTTAACATGGCATGTAACAAC
1 --T-TTTTTTTTAACATGACGTGTAACAAC
680728 CTAATCATGA
Statistics
Matches: 124, Mismatches: 20, Indels: 29
0.72 0.12 0.17
Matches are distributed among these distances:
24 27 0.22
25 6 0.05
26 34 0.27
27 11 0.09
28 7 0.06
29 6 0.05
30 14 0.11
31 19 0.15
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (27 bp):
TTTTTTTTTAACATGACGTGTAACAAC
Found at i:680642 original size:24 final size:24
Alignment explanation
Indices: 680582--680695 Score: 95
Period size: 24 Copynumber: 4.5 Consensus size: 24
680572 TTTTTTTAAC
*
680582 ATGACGTGTAACAACT-TTTTTTTAACT
1 ATGACGTGTAAC-A-TGTTTTTGT-A-T
*
680609 ATGACTTGTAACATGTTTTTGTAT
1 ATGACGTGTAACATGTTTTTGTAT
* ** * *
680633 ATAACGTGTAACAACTTTTTTTAACC
1 ATGACGTGTAACATGTTTTTGT-A-T
*
680659 ATGACTTGTAACATGTTTTTGTAT
1 ATGACGTGTAACATGTTTTTGTAT
680683 ATGACGTGTAACA
1 ATGACGTGTAACA
680696 ACAGTATTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
24 30 0.43
25 4 0.06
26 24 0.35
27 11 0.16
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (24 bp):
ATGACGTGTAACATGTTTTTGTAT
Found at i:680657 original size:50 final size:51
Alignment explanation
Indices: 680585--680697 Score: 201
Period size: 50 Copynumber: 2.2 Consensus size: 51
680575 TTTTAACATG
*
680585 ACGTGTAACAACTTTTTTTTAACTATGACTTGTAACATGTTTTTGTATATA
1 ACGTGTAACAACTTTTTTTTAACCATGACTTGTAACATGTTTTTGTATATA
*
680636 ACGTGTAACAAC-TTTTTTTAACCATGACTTGTAACATGTTTTTGTATATG
1 ACGTGTAACAACTTTTTTTTAACCATGACTTGTAACATGTTTTTGTATATA
680686 ACGTGTAACAAC
1 ACGTGTAACAAC
680698 AGTATTTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
50 48 0.80
51 12 0.20
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (51 bp):
ACGTGTAACAACTTTTTTTTAACCATGACTTGTAACATGTTTTTGTATATA
Found at i:680840 original size:45 final size:45
Alignment explanation
Indices: 680711--680924 Score: 202
Period size: 45 Copynumber: 4.8 Consensus size: 45
680701 ATTTTTTTTA
*
680711 ACATGGCATGTAACAACCTAATCATGACGTGTAACATG--TTTGT
1 ACATGGCGTGTAACAACCTAATCATGACGTGTAACATGTTTTTGT
* * * *
680754 ACATAGCGTGTAACAACTTAACCATGAC--GTATCATGCGTTTTTGT
1 ACATGGCGTGTAACAACCTAATCATGACGTGTAACAT--GTTTTTGT
* * * *
680799 ATATGGCGTGTAATAACCTAATCATAACGTGTAACATGTTTTTGC
1 ACATGGCGTGTAACAACCTAATCATGACGTGTAACATGTTTTTGT
* * * * *
680844 ACATGACGTGTAACACCCTAATCATGATGTGTCACACGTTTTTGT
1 ACATGGCGTGTAACAACCTAATCATGACGTGTAACATGTTTTTGT
*** * * *
680889 ACATTATGTGTAATAACCTAACCACGACGTGTAACA
1 ACATGGCGTGTAACAACCTAATCATGACGTGTAACA
680925 ACCTAACCAC
Statistics
Matches: 135, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
41 6 0.04
43 25 0.19
45 98 0.73
47 6 0.04
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (45 bp):
ACATGGCGTGTAACAACCTAATCATGACGTGTAACATGTTTTTGT
Found at i:680900 original size:90 final size:88
Alignment explanation
Indices: 680719--680924 Score: 234
Period size: 90 Copynumber: 2.3 Consensus size: 88
680709 TAACATGGCA
* * *
680719 TGTAACAACCTAATCATGACGTGTAACATGTTTGTACATAGCGTGTAACAACTTAACCATGACGT
1 TGTAATAACCTAATCATGACGTGTAACATGTTTGCACATAGCGTGTAACAACCTAACCATGACGT
** * *
680784 ATCATGCGTTTTTGTATATGGCG
66 ATCACACGTTTTTGTACATGACG
* * *
680807 TGTAATAACCTAATCATAACGTGTAACATGTTTTTGCACAT-GACGTGTAACACCCTAATCATGA
1 TGTAATAACCTAATCATGACGTGTAACATG--TTTGCACATAG-CGTGTAACAACCTAACCATGA
* * * *
680871 TGTGTCACACGTTTTTGTACATTATG
63 CGTATCACACGTTTTTGTACATGACG
* *
680897 TGTAATAACCTAACCACGACGTGTAACA
1 TGTAATAACCTAATCATGACGTGTAACA
680925 ACCTAACCAC
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
88 28 0.29
89 1 0.01
90 69 0.70
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (88 bp):
TGTAATAACCTAATCATGACGTGTAACATGTTTGCACATAGCGTGTAACAACCTAACCATGACGT
ATCACACGTTTTTGTACATGACG
Found at i:680922 original size:21 final size:21
Alignment explanation
Indices: 680896--680941 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
680886 TGTACATTAT
*
680896 GTGTAATAACCTAACCACGAC
1 GTGTAACAACCTAACCACGAC
*
680917 GTGTAACAACCTAACCACGAT
1 GTGTAACAACCTAACCACGAC
680938 GTGT
1 GTGT
680942 CACATATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (21 bp):
GTGTAACAACCTAACCACGAC
Found at i:698273 original size:15 final size:15
Alignment explanation
Indices: 698245--698290 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
698235 TCTCTTTAGA
698245 TATATATATTTATAAT
1 TATA-ATATTTATAAT
698261 TAATAAT-TTTATAAAT
1 T-ATAATATTTAT-AAT
698277 TATAATATTTATAA
1 TATAATATTTATAA
698291 CCTTAACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 12 0.44
16 12 0.44
17 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATAATATTTATAAT
Found at i:698287 original size:16 final size:16
Alignment explanation
Indices: 698245--698290 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
698235 TCTCTTTAGA
698245 TATATATATTTAT-AAT
1 TATA-ATATTTATAAAT
698261 TAATAAT-TTTATAAAT
1 T-ATAATATTTATAAAT
698277 TATAATATTTATAA
1 TATAATATTTATAA
698291 CCTTAACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.37
16 14 0.52
17 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATAATATTTATAAAT
Found at i:698543 original size:2 final size:2
Alignment explanation
Indices: 698536--698565 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
698526 CTCTTTTTAA
698536 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
698566 AGTTTACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:701834 original size:2 final size:2
Alignment explanation
Indices: 701827--701856 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
701817 AAAGCTATTT
701827 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
701857 AAAGTATGGA
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:708887 original size:6 final size:6
Alignment explanation
Indices: 708878--708905 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
708868 ATTGGCATTA
708878 GCAGTG GCAGTG GCAGTG GCAGTG GCAG
1 GCAGTG GCAGTG GCAGTG GCAGTG GCAG
708906 ATGAAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.50, T:0.14
Consensus pattern (6 bp):
GCAGTG
Found at i:713809 original size:1 final size:1
Alignment explanation
Indices: 713803--713827 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
713793 TTCTTCTTTC
713803 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
713828 CTAAGGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:730183 original size:2 final size:2
Alignment explanation
Indices: 730172--730209 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
730162 AGGCAAATAC
* *
730172 AT AT -T AT AT AT AT AT AT AT AT AT AT TT GT 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 A
730210 CACTTTACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:734970 original size:2 final size:2
Alignment explanation
Indices: 734957--735002 Score: 65
Period size: 2 Copynumber: 22.0 Consensus size: 2
734947 ACTATAATAA
*
734957 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT
735001 AT
1 AT
735003 CATCTCATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 36 0.90
3 4 0.10
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:742075 original size:21 final size:22
Alignment explanation
Indices: 742040--742080 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
742030 CATCCGAATC
742040 CTCTCCATAAACCAATTTTGCA
1 CTCTCCATAAACCAATTTTGCA
*
742062 CTCTCC-TCAACCAATTTTG
1 CTCTCCATAAACCAATTTTG
742081 AGCCAAGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.34, G:0.05, T:0.34
Consensus pattern (22 bp):
CTCTCCATAAACCAATTTTGCA
Found at i:743696 original size:4 final size:4
Alignment explanation
Indices: 743687--743714 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
743677 TTCTTTGCAC
743687 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
743715 TAGACAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:746418 original size:82 final size:83
Alignment explanation
Indices: 746269--746430 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 83
746259 TTTCGAGTCT
* * * * * *
746269 TATGCTTGTTTGCAAAAGACTCTCATGGCATAAACGTTGGTGGGGGAAACACAAGCTGTACAGTT
1 TATGCTTGTTTGCAAAAGAC-CTCATGACAGAAACGTTGGTGGGGGAAACAAAAACCGCACAGTT
746334 TCCCAAAG-GGCCTGCGTCC
65 TCCC-AAGCGGCCTGCGTCC
* *
746353 TATGCTTGTTTGCAAAAGA-CTCATGACAGAAAGGTTGGTGGGGGAAACAAAAACCGCACATTTT
1 TATGCTTGTTTGCAAAAGACCTCATGACAGAAACGTTGGTGGGGGAAACAAAAACCGCACAGTTT
746417 CCCAAGCGGCCTGC
66 CCCAAGCGGCCTGC
746431 TACTCAATAG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
81 3 0.04
82 47 0.68
84 19 0.28
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (83 bp):
TATGCTTGTTTGCAAAAGACCTCATGACAGAAACGTTGGTGGGGGAAACAAAAACCGCACAGTTT
CCCAAGCGGCCTGCGTCC
Found at i:756591 original size:16 final size:15
Alignment explanation
Indices: 756570--756609 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 15
756560 CCCTGAATCC
756570 TAAATAAAAATAATAA
1 TAAATAAAAATAA-AA
756586 TAAATAATAAATAAAA
1 TAAATAA-AAATAAAA
756602 TAAATAAA
1 TAAATAAA
756610 TCTCTTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.04
16 16 0.70
17 6 0.26
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAATAAAAATAAAA
Found at i:757358 original size:32 final size:32
Alignment explanation
Indices: 757279--757344 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
757269 GCAAAGAGGC
* * *
757279 TTTCTCAAATGAATGCCATTTTAATGTCTCCT
1 TTTCTCAAATGACTGACGTTTTAATGTCTCCT
757311 TTTCTCAAATGACTGACGTTTTAATGTCTCCT
1 TTTCTCAAATGACTGACGTTTTAATGTCTCCT
757343 TT
1 TT
757345 CTTATATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (32 bp):
TTTCTCAAATGACTGACGTTTTAATGTCTCCT
Found at i:758613 original size:2 final size:2
Alignment explanation
Indices: 758606--758635 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
758596 AGCTCAAGGG
*
758606 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
758636 GAAGAAATTG
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:759999 original size:74 final size:75
Alignment explanation
Indices: 759906--760054 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
759896 TTAGAGTTAA
759906 AATAATTTTTTTTTCAACATGACGTGTAACAATA-TTTTTTTAACACCGTACACTTGAATATGAA
1 AATAATTTTTTTTTCAACATGACGTGTAACAATATTTTTTTTAACACCGTACACTTGAATATGAA
*
759970 AATATTTCAT
66 AAGATTTCAT
759980 AATAATTTTTTTTTCAACATGACGTGTAACAATATTTTTTTTAACACCGTACACTTGAATATGAA
1 AATAATTTTTTTTTCAACATGACGTGTAACAATATTTTTTTTAACACCGTACACTTGAATATGAA
760045 AAGATTTCAT
66 AAGATTTCAT
760055 TAAAGATAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 34 0.47
75 39 0.53
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (75 bp):
AATAATTTTTTTTTCAACATGACGTGTAACAATATTTTTTTTAACACCGTACACTTGAATATGAA
AAGATTTCAT
Found at i:776104 original size:42 final size:40
Alignment explanation
Indices: 776057--776134 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
776047 GTCAAAATAA
776057 TTAATAAAATTACATATTCTCTTAT-TTTTTTCAATTCTGTGC
1 TTAAT-AAATT-CATATT-TCTTATCTTTTTTCAATTCTGTGC
* *
776099 TTAATAAATTTATATTTTTTATCTTTTTTCAATTCT
1 TTAATAAATTCATATTTCTTATCTTTTTTCAATTCT
776135 CATAATGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 5 0.15
40 18 0.55
41 5 0.15
42 5 0.15
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.58
Consensus pattern (40 bp):
TTAATAAATTCATATTTCTTATCTTTTTTCAATTCTGTGC
Found at i:776256 original size:34 final size:33
Alignment explanation
Indices: 776213--776282 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
776203 CAACTAATGA
776213 TAATTTTTTTAATTTCA-ATAAAAAGAGCCTCATT
1 TAATTTTTTT--TTTCACATAAAAAGAGCCTCATT
* * *
776247 TAATTTTTTTTTTTACTTAATAAGAGCCTCATT
1 TAATTTTTTTTTTCACATAAAAAGAGCCTCATT
776280 TAA
1 TAA
776283 ATACTTAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 4 0.12
33 18 0.56
34 10 0.31
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (33 bp):
TAATTTTTTTTTTCACATAAAAAGAGCCTCATT
Found at i:786746 original size:15 final size:15
Alignment explanation
Indices: 786726--786789 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
786716 TTCTCTTTAG
786726 GTTTATATATTATAA
1 GTTTATATATTATAA
* *
786741 GTTTATATA-AACAAA
1 GTTTATATATTA-TAA
786756 GTTATATATATTATAA
1 GTT-TATATATTATAA
* *
786772 -TTAATAATTTTATAA
1 GTTTAT-ATATTATAA
786787 GTT
1 GTT
786790 AAATTTTGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 3 0.08
15 24 0.63
16 10 0.26
17 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (15 bp):
GTTTATATATTATAA
Found at i:786891 original size:28 final size:28
Alignment explanation
Indices: 786830--786893 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
786820 GTAAATATGT
786830 TTATATTTAAAGTATATATATATACTAA
1 TTATATTTAAAGTATATATATATACTAA
** * *
786858 AAATATTT-TAGTATATATATAATAGTAA
1 TTATATTTAAAGTATATATAT-ATACTAA
786886 TTATATTT
1 TTATATTT
786894 CTTATAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (28 bp):
TTATATTTAAAGTATATATATATACTAA
Found at i:789119 original size:19 final size:20
Alignment explanation
Indices: 789079--789123 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
789069 ATTTTACAAA
*
789079 AAAATGTACTTTTAATTTTT
1 AAAATGTACTTTTAATTATT
789099 AAAAT-TACTTTT-ATCTATT
1 AAAATGTACTTTTAAT-TATT
789118 AAAATG
1 AAAATG
789124 CAAGTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.09
19 15 0.68
20 5 0.23
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (20 bp):
AAAATGTACTTTTAATTATT
Found at i:789191 original size:24 final size:25
Alignment explanation
Indices: 789143--789192 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
789133 TATCAAAATT
* *
789143 ACCTAAAAAACATTAAATATATAAA
1 ACCTAAAAAACATAAAAAATATAAA
*
789168 ACCTAAATAA-ATAAAAAATATAAA
1 ACCTAAAAAACATAAAAAATATAAA
789192 A
1 A
789193 ATTTGTGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (25 bp):
ACCTAAAAAACATAAAAAATATAAA
Found at i:789326 original size:23 final size:23
Alignment explanation
Indices: 789291--789345 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
789281 TCTTAATGAT
789291 TTCTTA-A-ACCAAT-CAAAAGAC
1 TTCTTATACACCAATGC-AAAGAC
789312 TTCTTATACACCAATGCAAAGAC
1 TTCTTATACACCAATGCAAAGAC
* *
789335 TCCTTGTACAC
1 TTCTTATACAC
789346 TCTCTCTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 1 0.03
23 21 0.72
24 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.27
Consensus pattern (23 bp):
TTCTTATACACCAATGCAAAGAC
Found at i:792287 original size:13 final size:13
Alignment explanation
Indices: 792269--792295 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
792259 GGAATTTGAC
792269 TTTAGATAATAAA
1 TTTAGATAATAAA
792282 TTTAGATAATAAA
1 TTTAGATAATAAA
792295 T
1 T
792296 CAATAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTAGATAATAAA
Found at i:798452 original size:2 final size:2
Alignment explanation
Indices: 798445--798487 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
798435 CGCTTGTATG
* * *
798445 TA TA TA TA TA TA TA TG TA TA TA TA TA GA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
798487 T
1 T
798488 TCAGTACCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
TA
Found at i:798462 original size:16 final size:16
Alignment explanation
Indices: 798441--798487 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
798431 AACACGCTTG
798441 TATGTATATATATATA
1 TATGTATATATATATA
*
798457 TATGTATATATATAGA
1 TATGTATATATATATA
798473 TATGTATATATATAT
1 TATGTATATATATAT
798488 TCAGTACCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (16 bp):
TATGTATATATATATA
Found at i:817993 original size:2 final size:2
Alignment explanation
Indices: 817986--818010 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
817976 TCCTTTTGTC
817986 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
818011 CGTTATCTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:821578 original size:29 final size:27
Alignment explanation
Indices: 821544--821624 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 27
821534 AAAAAATTTA
*
821544 AATAAATCTTTATATTTTTATTATGTTC
1 AATAAAT-TTTATATTTTTATTAAGTTC
*
821572 AATTAAATTTTTATATTTTTATTTTAAGTTG
1 AA-TAAA-TTTTATATTTTTA--TTAAGTTC
821603 AATAAATTTTAATATTTTTATT
1 AATAAATTTT-ATATTTTTATT
821625 TTAAGTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
28 4 0.09
29 20 0.43
30 14 0.30
31 8 0.17
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (27 bp):
AATAAATTTTATATTTTTATTAAGTTC
Found at i:821611 original size:30 final size:30
Alignment explanation
Indices: 821541--821637 Score: 126
Period size: 30 Copynumber: 3.3 Consensus size: 30
821531 TTTAAAAAAT
* *
821541 TTAAATAAATCTTTATATTTTTA--TTATG
1 TTAAATAAATTTTTATATTTTTATTTTAAG
*
821569 TTCAATTAAATTTTTATATTTTTATTTTAAG
1 TT-AAATAAATTTTTATATTTTTATTTTAAG
* *
821600 TTGAATAAATTTTAATATTTTTATTTTAAG
1 TTAAATAAATTTTTATATTTTTATTTTAAG
821630 TTAAATAA
1 TTAAATAA
821638 GCTCTTATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 2 0.03
29 19 0.32
30 32 0.54
31 6 0.10
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (30 bp):
TTAAATAAATTTTTATATTTTTATTTTAAG
Found at i:821965 original size:22 final size:23
Alignment explanation
Indices: 821931--821973 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
821921 TTTAAAATAA
821931 TAATATAAAAATTTAATTAAATG
1 TAATATAAAAATTTAATTAAATG
*
821954 TAATA-AAAAATTTATTTAAA
1 TAATATAAAAATTTAATTAAA
821974 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATATAAAAATTTAATTAAATG
Found at i:828333 original size:2 final size:2
Alignment explanation
Indices: 828326--828366 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
828316 TGTTACCGTT
828326 TA TA TA TA TA TA TA TA TA TA 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 TA TA T
828367 TAAAAAAAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:829024 original size:27 final size:28
Alignment explanation
Indices: 828962--829018 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
828952 TGTCTATTGA
828962 TTTAATTTTCAACAGATACAACCTTTCC
1 TTTAATTTTCAACAGATACAACCTTTCC
828990 TTTAATTTTCAACAG-TCACAA-CTTTCC
1 TTTAATTTTCAACAGAT-ACAACCTTTCC
829017 TT
1 TT
829019 CTATTTCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.42
Consensus pattern (28 bp):
TTTAATTTTCAACAGATACAACCTTTCC
Found at i:833738 original size:2 final size:2
Alignment explanation
Indices: 833725--833757 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
833715 TGAGAAGTTA
*
833725 AT AT AA 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
833758 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:833762 original size:2 final size:2
Alignment explanation
Indices: 833757--833786 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
833747 ATATATATAT
833757 AG AG 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 AG AG
833787 TTAGAAGTAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:834209 original size:28 final size:29
Alignment explanation
Indices: 834157--834211 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
834147 TAATGTCATA
* **
834157 TATTTTATTTTTATTTCTTGTTATAATCT
1 TATTTTATTTTCATTTCTTAATATAATCT
834186 TATTTT-TTTTCATTTCTTAATATAAT
1 TATTTTATTTTCATTTCTTAATATAAT
834212 TTTTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (29 bp):
TATTTTATTTTCATTTCTTAATATAATCT
Found at i:834216 original size:25 final size:24
Alignment explanation
Indices: 834154--834216 Score: 56
Period size: 28 Copynumber: 2.5 Consensus size: 24
834144 TTTTAATGTC
* *
834154 ATAT-ATTTTATTTTTATTTCTTG
1 ATATAATTTTTTTTTTATTTCTTA
*
834177 TTATAATCTTATTTTTTTTCATTTCTTA
1 ATATAA--TT-TTTTTTTT-ATTTCTTA
834205 ATATAATTTTTT
1 ATATAATTTTTT
834217 ATATTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
23 3 0.10
24 1 0.03
25 4 0.13
26 4 0.13
27 7 0.23
28 12 0.39
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (24 bp):
ATATAATTTTTTTTTTATTTCTTA
Found at i:834794 original size:16 final size:15
Alignment explanation
Indices: 834773--834802 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
834763 TTATCCTCAA
834773 CTTCTTCTTTCTTTTT
1 CTTCTTC-TTCTTTTT
834789 CTTCTTCTTCTTTT
1 CTTCTTCTTCTTTT
834803 ACCTTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTCTTCTTCTTTTT
Found at i:835243 original size:33 final size:32
Alignment explanation
Indices: 835180--835261 Score: 114
Period size: 33 Copynumber: 2.6 Consensus size: 32
835170 AAAATAAAAA
* *
835180 TAATTAATAT-TTATAAATTAATTAAATTAAC
1 TAATTAATTTATTATAAAATAATTAAATTAAC
835211 TAATTAATTTATTATAAAATAATTTAAATTAAC
1 TAATTAATTTATTATAAAATAA-TTAAATTAAC
*
835244 TAATTTATTTATT-TAAAA
1 TAATTAATTTATTATAAAA
835262 CTTAACTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 9 0.20
32 15 0.33
33 22 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TAATTAATTTATTATAAAATAATTAAATTAAC
Found at i:835269 original size:24 final size:22
Alignment explanation
Indices: 835232--835276 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
835222 TTATAAAATA
835232 ATTTAAATTAACTAATTTATTT
1 ATTTAAATTAACTAATTTATTT
835254 ATTTAAAACTTAACTAATTTATT
1 ATTT-AAA-TTAACTAATTTATT
835277 AAAAATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.19
23 3 0.14
24 14 0.67
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAAATTAACTAATTTATTT
Found at i:838544 original size:11 final size:11
Alignment explanation
Indices: 838528--838562 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
838518 AAATTATAGA
838528 TAATATTTTTT
1 TAATATTTTTT
838539 TAATATTTATTT
1 TAATATTT-TTT
838551 TAAT-TTTTTT
1 TAATATTTTTT
838561 TA
1 TA
838563 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 11 0.48
12 7 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TAATATTTTTT
Found at i:844527 original size:2 final size:2
Alignment explanation
Indices: 844514--844543 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
844504 GTTAATAGTG
*
844514 TA TA TA TC 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
844544 AAAGAAAATT
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:862759 original size:18 final size:18
Alignment explanation
Indices: 862736--862772 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
862726 ACAGTTACGG
862736 ATTTTACAACCAAACTAA
1 ATTTTACAACCAAACTAA
*
862754 ATTTTACATCCAAACTAA
1 ATTTTACAACCAAACTAA
862772 A
1 A
862773 GCAAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (18 bp):
ATTTTACAACCAAACTAA
Found at i:866359 original size:2 final size:2
Alignment explanation
Indices: 866342--866378 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
866332 TAATATTTTA
866342 AT AT AT ACT -T AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
866379 GTTTGTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 29 0.91
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:874544 original size:18 final size:18
Alignment explanation
Indices: 874521--874556 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
874511 TAAGATTTAA
*
874521 ATTAAAAAAATATTATTT
1 ATTAAAAAAATAATATTT
*
874539 ATTAAAATAATAATATTT
1 ATTAAAAAAATAATATTT
874557 TTGGGTCGGG
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAAAAAAATAATATTT
Found at i:876839 original size:17 final size:16
Alignment explanation
Indices: 876819--876851 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
876809 TGAGAGCACT
876819 AATAAAAATACAAAAAA
1 AATAAAAATA-AAAAAA
876836 AATAAAAATAAAAAAA
1 AATAAAAATAAAAAAA
876852 TCAGAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (16 bp):
AATAAAAATAAAAAAA
Found at i:879965 original size:12 final size:11
Alignment explanation
Indices: 879938--879963 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
879928 CAACCAATTT
879938 AAAAGCAAAAA
1 AAAAGCAAAAA
879949 AAAAGCAAAAA
1 AAAAGCAAAAA
879960 AAAA
1 AAAA
879964 AGTCAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAGCAAAAA
Found at i:896319 original size:33 final size:33
Alignment explanation
Indices: 896276--896352 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 33
896266 AATTAATAAC
* * ** *
896276 TTGATTCTCTTCATCATTATTTTTATGATCATT
1 TTGAATCTCTTCATCATGATTTCAATGATAATT
896309 TTGAATCTC-T--TCATGATTTCAATGATAATT
1 TTGAATCTCTTCATCATGATTTCAATGATAATT
896339 TTGAATCTCTTCAT
1 TTGAATCTCTTCAT
896353 TAACTTCTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
30 25 0.69
31 1 0.03
32 1 0.03
33 9 0.25
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.52
Consensus pattern (33 bp):
TTGAATCTCTTCATCATGATTTCAATGATAATT
Found at i:910278 original size:21 final size:22
Alignment explanation
Indices: 910249--910289 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
910239 GAGGCACTTC
* *
910249 TACGTCAGACGGAGGCGACAGA
1 TACGTCAGACGCAGGAGACAGA
910271 TACG-CAGACGCAGGAGACA
1 TACGTCAGACGCAGGAGACA
910290 CCTCAGCCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.34, C:0.24, G:0.34, T:0.07
Consensus pattern (22 bp):
TACGTCAGACGCAGGAGACAGA
Found at i:918304 original size:18 final size:18
Alignment explanation
Indices: 918281--918319 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
918271 TGCTCAATAC
918281 TTTATTA-TATTTACTATA
1 TTTATTATTATTTA-TATA
*
918299 TTTATTATTTTTTATATA
1 TTTATTATTATTTATATA
918317 TTT
1 TTT
918320 TAAACCTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTATTATTTATATA
Found at i:926461 original size:56 final size:56
Alignment explanation
Indices: 926367--926498 Score: 140
Period size: 56 Copynumber: 2.3 Consensus size: 56
926357 ACTTGAATGT
* * * * * * *
926367 TTGTTATCTTTGCACTTTGTGTGTGATATCCTGTAATTTGTTTATATATTACGTGG-
1 TTGTT-TCTTTTCACTTTCTGTATGATATCCTATAATTTGATAATATATTACATGGA
* * *
926423 TTAGTTTCTTTTCACTTTCTGTATGATGTCCTATAATTTGATAATTTGTTACATGGA
1 TT-GTTTCTTTTCACTTTCTGTATGATATCCTATAATTTGATAATATATTACATGGA
*
926480 TTTTTTCTTTTCACTTTCT
1 TTGTTTCTTTTCACTTTCT
926499 ATGGATTTTG
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
56 58 0.92
57 5 0.08
ACGTcount: A:0.18, C:0.13, G:0.14, T:0.55
Consensus pattern (56 bp):
TTGTTTCTTTTCACTTTCTGTATGATATCCTATAATTTGATAATATATTACATGGA
Found at i:937449 original size:17 final size:18
Alignment explanation
Indices: 937399--937471 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 18
937389 TCTTTGTATT
* * *
937399 AACATAACTGTTTAAACA
1 AACATAATTATTTAAAAA
*
937417 AATATAATTATTTAAAAA
1 AACATAATTATTTAAAAA
*
937435 AACATAATT-TTTAAACA
1 AACATAATTATTTAAAAA
* *
937452 ATCATAATTGTTTAAAAA
1 AACATAATTATTTAAAAA
937470 AA
1 AA
937472 ATTCTTTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 15 0.33
18 30 0.67
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (18 bp):
AACATAATTATTTAAAAA
Found at i:937450 original size:35 final size:36
Alignment explanation
Indices: 937399--937471 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 36
937389 TCTTTGTATT
937399 AACATAACTGTTTAAACAAAT-ATAATTATTTAAAAA
1 AACATAACTGTTTAAAC-AATCATAATTATTTAAAAA
* *
937435 AACATAA-TTTTTAAACAATCATAATTGTTTAAAAA
1 AACATAACTGTTTAAACAATCATAATTATTTAAAAA
937470 AA
1 AA
937472 ATTCTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 3 0.09
35 24 0.71
36 7 0.21
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (36 bp):
AACATAACTGTTTAAACAATCATAATTATTTAAAAA
Found at i:937589 original size:18 final size:18
Alignment explanation
Indices: 937544--937591 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
937534 ATTTCTTAAT
937544 ATAGATATAACTATTTGA
1 ATAGATATAACTATTTGA
* *
937562 ATAAATATAATTATTTGA
1 ATAGATATAACTATTTGA
*
937580 ATAGACATAACT
1 ATAGATATAACT
937592 TTTAAACAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (18 bp):
ATAGATATAACTATTTGA
Found at i:937636 original size:3 final size:3
Alignment explanation
Indices: 937628--937653 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
937618 ATTTTTTATC
937628 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
937654 TTCATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:939977 original size:23 final size:22
Alignment explanation
Indices: 939936--939978 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
939926 TTTTAATTTT
*
939936 ATAAAATATTCATTAATAAAAG
1 ATAAAATATTAATTAATAAAAG
939958 ATAAAATAATTAATTAATAAA
1 ATAAAAT-ATTAATTAATAAA
939979 TTATGCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAAAATATTAATTAATAAAAG
Found at i:941720 original size:24 final size:24
Alignment explanation
Indices: 941685--941755 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 24
941675 ATATAAGTAA
* *
941685 TAAAAAGA-TAATTAATAATTTAT
1 TAAAAATATTAATTAATTATTTAT
*
941708 TAAAAATATTAATAAATTA-TTAT
1 TAAAAATATTAATTAATTATTTAT
*
941731 T-TAAATATTTAATATAATTATTTAT
1 TAAAAATA-TTAAT-TAATTATTTAT
941756 AGTTATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 5 0.13
23 17 0.44
24 13 0.33
25 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
TAAAAATATTAATTAATTATTTAT
Done.