Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 17 of 295
Found at i:5329659 original size:17 final size:17
Alignment explanation
Indices: 5329639--5329672 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5329629 TTTTATGATT
5329639 TTTTTGGTAATTTTTAA
1 TTTTTGGTAATTTTTAA
**
5329656 TTTTTTTTAATTTTTAA
1 TTTTTGGTAATTTTTAA
5329673 GTACTTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTTTGGTAATTTTTAA
Found at i:5329680 original size:28 final size:28
Alignment explanation
Indices: 5329618--5329682 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
5329608 CGCGTGCTTA
* **
5329618 TAATTTTTAATTTTTATGATTTTTTTGG
1 TAATTTTTAATTTTTATGAATTTTTAAG
* *
5329646 TAATTTTTAATTTTTTTTAATTTTTAAG
1 TAATTTTTAATTTTTATGAATTTTTAAG
*
5329674 TACTTTTTA
1 TAATTTTTA
5329683 TAGTTGTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.68
Consensus pattern (28 bp):
TAATTTTTAATTTTTATGAATTTTTAAG
Found at i:5348511 original size:90 final size:90
Alignment explanation
Indices: 5348338--5348516 Score: 306
Period size: 89 Copynumber: 2.0 Consensus size: 90
5348328 AGCCATTGAA
*
5348338 CAATTAGTCGTCACCCATCTTTGCTACTCCTGCTTCGACCATGATACCAATCATCAGTTATTTTT
1 CAATTAATCGTCACCCATCTTTGCTACTCCTGCTTCGACCATGATACCAATCATCAGTTATTTTT
5348403 TCGAAATAATAAAGTTTTTTCGTCC
66 TCGAAATAATAAAGTTTTTTCGTCC
* * * *
5348428 CAATTAATCGTCACCCGTCTTTGCTA-TCCTGCTTCGGCCATGATCCCAATCATCAGTTGTTTTT
1 CAATTAATCGTCACCCATCTTTGCTACTCCTGCTTCGACCATGATACCAATCATCAGTTATTTTT
5348492 TCGAAATAATAAAGTTTTTTCGTCC
66 TCGAAATAATAAAGTTTTTTCGTCC
5348517 AAGTGTTAGA
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 60 0.71
90 24 0.29
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (90 bp):
CAATTAATCGTCACCCATCTTTGCTACTCCTGCTTCGACCATGATACCAATCATCAGTTATTTTT
TCGAAATAATAAAGTTTTTTCGTCC
Found at i:5349479 original size:46 final size:46
Alignment explanation
Indices: 5349409--5349635 Score: 287
Period size: 46 Copynumber: 4.9 Consensus size: 46
5349399 TTTGACATGA
* * * * * *
5349409 TGCCATAGTGTCTTTAAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* * *
5349455 TGTCATGGTATCTTTCAACCATGGTCTTACTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
** *
5349501 TGTTATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* * *
5349547 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
5349593 TGCCATGGTATCTTTCAACCATGGTCTTACAT-ATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTCATATCA
5349636 GAGAGCACAC
Statistics
Matches: 161, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 4 0.02
46 157 0.98
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:5351739 original size:11 final size:11
Alignment explanation
Indices: 5351723--5351770 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
5351713 CTTTATATAC
5351723 TAATAAAATAA
1 TAATAAAATAA
*
5351734 TAATAAAATATC
1 TAATAAAATA-A
* *
5351746 TCATTAAAATAT
1 T-AATAAAATAA
5351758 TAATAAAATAA
1 TAATAAAATAA
5351769 TA
1 TA
5351771 TTTATCTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 20 0.67
12 2 0.07
13 8 0.27
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:5361232 original size:150 final size:150
Alignment explanation
Indices: 5360675--5361529 Score: 1236
Period size: 150 Copynumber: 5.7 Consensus size: 150
5360665 CACATTTTGT
* *
5360675 AATCATAAATTCCCAAGATTTTGAAATTCATGTTTTTCTATACATTTCAAATACATAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
* * * * *
5360740 TCAACCTTAACTAATTTGTC-TTTTCATAGCTCATAGTTAATATAACAAATAAAAAATCCAAATT
66 TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
* * *
5360804 CAGCTTTTCATAGCTTATAA
131 TAGCTTCTCATACCTTATAA
* *
5360824 AATCATAAATTCTTAAGATTTTGAAATAT-ATGTTTTTCTTAATGCATTTCAAATACATAATCAA
1 AATCATAAATTCCTAAGATTTTGAAAT-TCATGTTTTT-TT-ATACATTTCAAATACATAATCAA
* * *
5360888 AGTTCAACCTTAACTAATTTGGCCTTTTCATAGCTCAAAATTAATA-AACAAATCAAAAATCCAA
63 AGTTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAA
* * *
5360952 ATTCAGCTTTTCATAGCTTATAA
128 ATTTAGCTTCTCATACCTTATAA
* * * *
5360975 AATCATAAATTCCTAAGATTTTGAAATTCTTGTTTTCTTATGCATTTCAAATACATGATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
* *
5361040 TCAACCTTAACCAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAATATCCAAATT
66 TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
*
5361104 TAACTTCTCATACCTTATAA
131 TAGCTTCTCATACCTTATAA
* * *
5361124 AATCATAAATTTCTAAGATTTTGAAATTCATGTTTTTTTAATATATTTCAAATACATAGTCAAAG
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTT-ATACATTTCAAATACATAATCAAAG
*
5361189 TTCAACCTTAACTAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAATATCCAAAT
65 TTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAAT
*
5361253 TTAACTTCTCATACCTTATAA
130 TTAGCTTCTCATACCTTATAA
* * *
5361274 AATCATAAATTTCTAAGATTTTGAAATTCATGTTTTTTTAATATATTTCAAATACATAGTCAAAG
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTT-ATACATTTCAAATACATAATCAAAG
*
5361339 TTCAACCTTAACTAATTTGGTTTTTTCA-AGCTCAAAATCAATATAACAAATGAAAAATCCAAAT
65 TTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAAT
5361403 TTAGCTTCTCATACCTTATAA
130 TTAGCTTCTCATACCTTATAA
* * * * * * *
5361424 AATCCTAAATTCCTAATATTTTGACATTCATGTTTTCTTCTACAATTCAAATACAGAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
*
5361489 TCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCA
66 TCAACCTTAACT-AATTTGGCTTTTTCATAGCTCAAAATCA
5361530 TAAATTTCAA
Statistics
Matches: 654, Mismatches: 43, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
148 14 0.02
149 187 0.29
150 305 0.47
151 128 0.20
152 20 0.03
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.38
Consensus pattern (150 bp):
AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
TAGCTTCTCATACCTTATAA
Found at i:5365319 original size:26 final size:26
Alignment explanation
Indices: 5365271--5365320 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5365261 TTTTAAGCAT
*
5365271 GTAAAATTATAAAATTTTAAAAAGTA
1 GTAAAATTATAAAATTCTAAAAAGTA
*
5365297 GTAAAA-TATTAAAATTCTCAAAAG
1 GTAAAATTA-TAAAATTCTAAAAAG
5365321 AAACTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (26 bp):
GTAAAATTATAAAATTCTAAAAAGTA
Found at i:5370333 original size:49 final size:49
Alignment explanation
Indices: 5370262--5370364 Score: 199
Period size: 49 Copynumber: 2.1 Consensus size: 49
5370252 CCTCTATTAT
5370262 TAAA-TGGATCAATTTAGTCCCTATACTATTAAAAGAATTAAATAAGTC
1 TAAATTGGATCAATTTAGTCCCTATACTATTAAAAGAATTAAATAAGTC
5370310 TAAATTGGATCAATTTAGTCCCTATACTATTAAAAGAATTAAATAAGTC
1 TAAATTGGATCAATTTAGTCCCTATACTATTAAAAGAATTAAATAAGTC
5370359 TAAATT
1 TAAATT
5370365 AGCACAACAA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 4 0.07
49 50 0.93
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (49 bp):
TAAATTGGATCAATTTAGTCCCTATACTATTAAAAGAATTAAATAAGTC
Found at i:5381312 original size:15 final size:16
Alignment explanation
Indices: 5381292--5381321 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5381282 CTAACAAAAG
5381292 AACCCAAT-ACCCACA
1 AACCCAATAACCCACA
5381307 AACCCAATAACCCAC
1 AACCCAATAACCCAC
5381322 CTAAACACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.47, G:0.00, T:0.07
Consensus pattern (16 bp):
AACCCAATAACCCACA
Found at i:5382589 original size:19 final size:21
Alignment explanation
Indices: 5382565--5382606 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
5382555 TCCTGCTTTT
*
5382565 TATTTATTTA-ATAT-CTATA
1 TATTTATATATATATACTATA
5382584 TATTTATATATATATACTATA
1 TATTTATATATATATACTATA
5382605 TA
1 TA
5382607 ATATTTATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTATATATATATACTATA
Found at i:5382615 original size:20 final size:20
Alignment explanation
Indices: 5382569--5382629 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
5382559 GCTTTTTATT
*
5382569 TATTTA-ATAT-CTATATATT
1 TATTTATATATACTATATA-A
*
5382588 TATATATATATACTATATAA
1 TATTTATATATACTATATAA
** *
5382608 TATTTATACCTACAATATAA
1 TATTTATATATACTATATAA
5382628 TA
1 TA
5382630 CACGTGCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 5 0.15
20 22 0.65
21 7 0.21
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTTATATATACTATATAA
Found at i:5403726 original size:37 final size:37
Alignment explanation
Indices: 5403685--5403897 Score: 363
Period size: 37 Copynumber: 5.8 Consensus size: 37
5403675 TTTGAGTACT
5403685 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
5403722 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
5403759 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
* *
5403796 TCTGATCAAGAAACAAAGGGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
5403833 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
5403870 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
5403898 TAGCTTCAGC
Statistics
Matches: 169, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 169 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:5403969 original size:45 final size:46
Alignment explanation
Indices: 5403860--5403983 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
5403850 GTGATAAGTG
* *
5403860 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
5403906 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
5403951 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
5403984 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:5411457 original size:37 final size:37
Alignment explanation
Indices: 5411416--5411627 Score: 363
Period size: 37 Copynumber: 5.8 Consensus size: 37
5411406 TTTGAGTACT
5411416 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
5411453 TCTGATCAAGAAACAAAGTGATAAGTGG-TACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
5411489 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
5411526 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
5411563 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
5411600 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
5411628 TAGCTTCAGC
Statistics
Matches: 170, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
36 36 0.21
37 134 0.79
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:5411699 original size:45 final size:46
Alignment explanation
Indices: 5411590--5411713 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
5411580 GTGATAAGTG
* *
5411590 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
5411636 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
5411681 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
5411714 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:5413030 original size:17 final size:17
Alignment explanation
Indices: 5413008--5413041 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5412998 CTTCTCTGTT
5413008 GCCATAATAGTTGAGAA
1 GCCATAATAGTTGAGAA
5413025 GCCATAATAGTTGAGAA
1 GCCATAATAGTTGAGAA
5413042 AAAAAGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
GCCATAATAGTTGAGAA
Found at i:5415449 original size:6 final size:6
Alignment explanation
Indices: 5415389--5415445 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
5415379 AGGGGTTACG
* * * *
5415389 GGTTCG GGTT-T GGGTCT GGTACT GGTTCA GGTTCT GGTTCT GGTTCT
1 GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT GGTTCT
*
5415436 GGTTAT GGTT
1 GGTTCT GGTT
5415446 ATGGGAGTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
5 3 0.07
6 39 0.93
ACGTcount: A:0.05, C:0.12, G:0.39, T:0.44
Consensus pattern (6 bp):
GGTTCT
Found at i:5415504 original size:3 final size:3
Alignment explanation
Indices: 5415496--5415549 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
5415486 AAGTGGAACC
**
5415496 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT TCT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
5415544 GGT GGT
1 GGT GGT
5415550 TCGACTGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.02, G:0.63, T:0.35
Consensus pattern (3 bp):
GGT
Found at i:5424629 original size:6 final size:6
Alignment explanation
Indices: 5424620--5424654 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5424610 TGTAAATGAT
*
5424620 GAAGAG GAAGAG GAAGAG GAAGAG GACGAG GAAGA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
5424655 TGAAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:5439889 original size:21 final size:20
Alignment explanation
Indices: 5439851--5439889 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5439841 TCAATCAGCA
*
5439851 AAATGGGATGAGGTAAAAAC
1 AAATGGGATGAGGAAAAAAC
*
5439871 AAATGAGGATGATGAAAAA
1 AAATG-GGATGAGGAAAAA
5439890 TGCATCAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.28, T:0.15
Consensus pattern (20 bp):
AAATGGGATGAGGAAAAAAC
Found at i:5443166 original size:59 final size:59
Alignment explanation
Indices: 5443101--5443217 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 59
5443091 TTTATTTTCT
5443101 AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATCTAAATTACTAATTGAGTA
1 AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATCTAAATTACTAATTGAGTA
*
5443160 AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATTTAAATTACTAATTGAGT
1 AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATCTAAATTACTAATTGAGT
5443218 TTTAACTCGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.38
Consensus pattern (59 bp):
AAATGAAAATTAAAACTATAATTTGTTAATTTTAAAAAATCTAAATTACTAATTGAGTA
Found at i:5443220 original size:28 final size:28
Alignment explanation
Indices: 5443130--5443222 Score: 73
Period size: 30 Copynumber: 3.2 Consensus size: 28
5443120 AATTTGTTAA
*
5443130 TTTTAAAAAATCTAAATTACTAATTGAG
1 TTTTAAAAAATTTAAATTACTAATTGAG
** * * *
5443158 -TAAAATGAAAATTAAAACTA-TAATTTGTTAA
1 TTTTAA--AAAATTTAAATTACTAA-TTG--AG
5443189 TTTTAAAAAATTTAAATTACTAATTGAG
1 TTTTAAAAAATTTAAATTACTAATTGAG
5443217 TTTTAA
1 TTTTAA
5443223 CTCGATTGGT
Statistics
Matches: 47, Mismatches: 11, Indels: 14
0.65 0.15 0.19
Matches are distributed among these distances:
27 3 0.06
28 10 0.21
29 13 0.28
30 14 0.30
31 4 0.09
32 3 0.06
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.41
Consensus pattern (28 bp):
TTTTAAAAAATTTAAATTACTAATTGAG
Found at i:5444288 original size:15 final size:16
Alignment explanation
Indices: 5444270--5444299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5444260 ATTTGAATAA
5444270 AAAAT-ATTTAAACCT
1 AAAATAATTTAAACCT
5444285 AAAATAATTTAAACC
1 AAAATAATTTAAACC
5444300 ACCTAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAATTTAAACCT
Found at i:5446327 original size:11 final size:10
Alignment explanation
Indices: 5446301--5446326 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5446291 TTATTTTACC
5446301 TTTTTTCTTT
1 TTTTTTCTTT
5446311 TTTTTTCTTT
1 TTTTTTCTTT
5446321 TTTTTT
1 TTTTTT
5446327 TGTCTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:5451960 original size:23 final size:23
Alignment explanation
Indices: 5451912--5451961 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5451902 TATTTATATC
* * *
5451912 ATATAAGAATTAAACATATAATA
1 ATATAAGAAATAAAAATATAAAA
5451935 ATATAA-AAATAAAAATATTAAAA
1 ATATAAGAAATAAAAATA-TAAAA
5451958 ATAT
1 ATAT
5451962 TTACTCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATATAAGAAATAAAAATATAAAA
Found at i:5452008 original size:15 final size:14
Alignment explanation
Indices: 5451970--5452015 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
5451960 ATTTACTCTT
5451970 AAATTT-AA-TAAA
1 AAATTTAAATTAAA
5451982 AACATATTAAATTATAA
1 AA-AT-TTAAATTA-AA
5451999 AAATTTAAATTAAA
1 AAATTTAAATTAAA
5452013 AAA
1 AAA
5452016 CATATATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 7 0.24
15 10 0.34
16 4 0.14
17 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTTAAATTAAA
Found at i:5454978 original size:17 final size:17
Alignment explanation
Indices: 5454952--5454992 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5454942 AAAACCAAAT
*
5454952 CAGTTTATTAGAAATAA
1 CAGTTCATTAGAAATAA
*
5454969 CAGTTCATTAGACATAA
1 CAGTTCATTAGAAATAA
*
5454986 CAATTCA
1 CAGTTCA
5454993 CACACACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (17 bp):
CAGTTCATTAGAAATAA
Found at i:5458337 original size:7 final size:7
Alignment explanation
Indices: 5458325--5458364 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
5458315 ATTACTCTCT
5458325 TTTTTTC
1 TTTTTTC
5458332 TTTTTTC
1 TTTTTTC
5458339 TTTTTTC
1 TTTTTTC
5458346 TTTTTTC
1 TTTTTTC
5458353 TTTTTTC
1 TTTTTTC
5458360 TTTTT
1 TTTTT
5458365 CATCATGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:5461844 original size:44 final size:45
Alignment explanation
Indices: 5461795--5461883 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
5461785 CATGAATTAT
* *
5461795 TCCTGTCTCCAATGCCATA-TATAATAAGGACTTACATGGCTCAA
1 TCCTGTCTCCAAAGCCATATTATAATAAGGACTTACATGACTCAA
* *
5461839 TCCTGTCTCCAAAGCCATATTTCTAATATGGACTTACATGACTCA
1 TCCTGTCTCCAAAGCCATA-TTATAATAAGGACTTACATGACTCA
5461884 TTTCTGTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 18 0.46
46 21 0.54
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (45 bp):
TCCTGTCTCCAAAGCCATATTATAATAAGGACTTACATGACTCAA
Found at i:5467206 original size:11 final size:11
Alignment explanation
Indices: 5467190--5467223 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
5467180 GGTGAGATTA
5467190 GATACTGTAGC
1 GATACTGTAGC
5467201 GATACTGTAGC
1 GATACTGTAGC
5467212 GATACTGTAGC
1 GATACTGTAGC
5467223 G
1 G
5467224 TGAGACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (11 bp):
GATACTGTAGC
Found at i:5471273 original size:8 final size:8
Alignment explanation
Indices: 5471262--5471288 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5471252 ATTTTACTAT
5471262 TTTTCAAA
1 TTTTCAAA
5471270 TTTTCAAA
1 TTTTCAAA
5471278 TTTTCAAA
1 TTTTCAAA
5471286 TTT
1 TTT
5471289 AGGTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTCAAA
Found at i:5473648 original size:174 final size:175
Alignment explanation
Indices: 5473341--5473680 Score: 477
Period size: 174 Copynumber: 1.9 Consensus size: 175
5473331 GAAGACGATT
* * * * * *
5473341 GAAAGATGTTAATGTTAACATCTTGTATTAGCATCTTTAGTTGTTTGTTTAGCTATATACAAGTC
1 GAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTATAGCTATATACAAATC
** * *
5473406 CGGATCGAAAACTTGTGTTATAAAGTCGTATATTAGTTGCTCGAAAACTCTGATGTAGTGAAAGG
66 CGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATGTAGTGAAAGG
* *
5473471 AAAAGAAATTTCTCCAGTGATCGATCATGCATCGTTTTAATCCGG
131 AAAAGAAATTTCTCCAGTGATCAATCATACATCGTTTTAATCCGG
5473516 GAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTT-ATTGTATAGCTATATACAAATC
1 GAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTATAGCTATATACAAATC
** * * * *
5473580 CGGATCGAAAACTCATGTTATAAAGTTTTATAGTAGTTGCTTGAAAACTCCGATTTATTTG-TAG
66 CGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATGTA-GTGAAAG
* *
5473644 GAAAAGAAATTTCTCCGGTGATCAATCTTACATCGTT
130 GAAAAGAAATTTCTCCAGTGATCAATCATACATCGTT
5473681 CTAAAGCAAG
Statistics
Matches: 144, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
174 103 0.72
175 41 0.28
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (175 bp):
GAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGATTGTATAGCTATATACAAATC
CGGATCGAAAACTCATGTTATAAAGTCGTATAGTAGTTGCTCGAAAACTCCGATGTAGTGAAAGG
AAAAGAAATTTCTCCAGTGATCAATCATACATCGTTTTAATCCGG
Found at i:5473884 original size:374 final size:372
Alignment explanation
Indices: 5473165--5473869 Score: 1008
Period size: 374 Copynumber: 1.9 Consensus size: 372
5473155 GGACCGGAAA
**
5473165 CTTGTATAAGCATCTTGTTAAAGATGCTAATATACAAATCCGGATCGAAAACTTGTGCTAGTAAG
1 CTTGTATAAGCATCTTGTTAAAGATGCTAATATACAAATCCGGATCGAAAACTCATGCTAGTAAG
* * * *
5473230 TCGTATATTTGTTGCTCGAAAACTCTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGAT
66 TCGTATAGTAGTTGCTCGAAAACTCCGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCAAT
* * * * *
5473295 CATACATCGTTGTAAAGCTAGTTTTCTTAATCCGGGGAAGACGATTGAAAGATGTTAATGTTAAC
131 CATACATCGTTCTAAAGCAAGTTTTCTTAATCCGGGGAAGACGATGGAAAGATGCTAATGGTAAC
* * * **
5473360 ATCTTGTATTAGCATCTTTAGTTGTTTGTTTAGCTATATACAAGTCCGGATCGAAAACTTGTGTT
196 ATCTTGTATAAGCATCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACTCATGTT
*
5473425 ATAAAGTCGTATATTAGTTGCTCGAAAACTCTGATGTAGTGAAAGGAAAAGAAATTTCTCCAGTG
261 ATAAAGTCGTATATTAGTTGCTCGAAAACTCCGATGTAGTGAAAGGAAAAGAAATTTCTCCAGTG
5473490 ATCGATCATGCATCGTTTTAATCCGGGAAAGATGCTAATGGTAACAT
326 ATCGATCATGCATCGTTTTAATCCGGGAAAGATGCTAATGGTAACAT
** *
5473537 CTTGTATAAGCATCTTTAGTTATTGTATAGCT-ATATACAAATCCGGATCGAAAACTCATGTTA-
1 CTTGTATAAGCATC-TT-GTTAAAG-AT-GCTAATATACAAATCCGGATCGAAAACTCATGCTAG
** * * *
5473600 TAAAGTTTTATAGTAGTTGCTTGAAAACTCCGATTTATTTG-TAGGAAAAGAAATTTCTCCGGTG
62 T-AAGTCGTATAGTAGTTGCTCGAAAACTCCGATTTA-GTGAAAGGAAAAGAAATTTCTCCGGTG
* *
5473664 ATCAATCTTACATCGTTCTAAAGCAAGTTTT-TTAATTCGGGGAAGACGATGGAAAGATGCTAAT
125 ATCAATCATACATCGTTCTAAAGCAAGTTTTCTTAATCCGGGGAAGACGATGGAAAGATGCTAAT
5473728 GGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACT
190 GGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACT
* * * * *
5473793 CATGTTATGAAGTTGTATATTAGTTGCTTGAAAACTCCGATTTATTTG-AAGGAAAAGAAATTTC
255 CATGTTATAAAGTCGTATATTAGTTGCTCGAAAACTCCGATGTA-GTGAAAGGAAAAGAAATTTC
5473857 T-CAGGTGATCGAT
319 TCCA-GTGATCGAT
5473870 ATCACGTCGT
Statistics
Matches: 293, Mismatches: 32, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
372 14 0.05
373 4 0.01
374 160 0.55
375 110 0.38
376 5 0.02
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (372 bp):
CTTGTATAAGCATCTTGTTAAAGATGCTAATATACAAATCCGGATCGAAAACTCATGCTAGTAAG
TCGTATAGTAGTTGCTCGAAAACTCCGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCAAT
CATACATCGTTCTAAAGCAAGTTTTCTTAATCCGGGGAAGACGATGGAAAGATGCTAATGGTAAC
ATCTTGTATAAGCATCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACTCATGTT
ATAAAGTCGTATATTAGTTGCTCGAAAACTCCGATGTAGTGAAAGGAAAAGAAATTTCTCCAGTG
ATCGATCATGCATCGTTTTAATCCGGGAAAGATGCTAATGGTAACAT
Found at i:5473907 original size:199 final size:200
Alignment explanation
Indices: 5473515--5473963 Score: 758
Period size: 200 Copynumber: 2.3 Consensus size: 200
5473505 TTTTAATCCG
*
5473515 GGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTT-ATTGTATAGCTATATACAAAT
1 GGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTATAGCTATATACAAAT
* *
5473579 CCGGATCGAAAACTCATGTTATAAAGTTTTATAGTAGTTGCTTGAAAACTCCGATTTATTTGTAG
66 CCGGATCGAAAACTCATGTTATAAAGTTGTATAGTAGTTGCTTGAAAACTCCGATTTATTTGAAG
* * *
5473644 GAAAAGAAATTTCTCCGGTGATCAATCTTACATCGTTCTAAAGCAAGTTTTTTAATTCGGGGAAG
131 GAAAAGAAATTTCTCAGGTGATCAATATCACATCGTTCTAAAGCAAGTTTTTTAATTCGGGGAAG
*
5473709 ACGAT
196 ACGAC
5473714 GGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTATAGCTATATACAAAT
1 GGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTATAGCTATATACAAAT
* *
5473779 CCGGATCGAAAACTCATGTTATGAAGTTGTATATTAGTTGCTTGAAAACTCCGATTTATTTGAAG
66 CCGGATCGAAAACTCATGTTATAAAGTTGTATAGTAGTTGCTTGAAAACTCCGATTTATTTGAAG
* * * *
5473844 GAAAAGAAATTTCTCAGGTGATCGATATCACGTCGTTTTAAAGCAAG-TTTTTAATTTGGGGAAG
131 GAAAAGAAATTTCTCAGGTGATCAATATCACATCGTTCTAAAGCAAGTTTTTTAATTCGGGGAAG
5473908 ACGAC
196 ACGAC
*
5473913 GGGAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTAT
1 GGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTAT
5473964 CGGTGTTGAA
Statistics
Matches: 235, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
199 113 0.48
200 122 0.52
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (200 bp):
GGAAAGATGCTAATGGTAACATCTTGTATAAGCATCTTTAGTTGTTTGTATAGCTATATACAAAT
CCGGATCGAAAACTCATGTTATAAAGTTGTATAGTAGTTGCTTGAAAACTCCGATTTATTTGAAG
GAAAAGAAATTTCTCAGGTGATCAATATCACATCGTTCTAAAGCAAGTTTTTTAATTCGGGGAAG
ACGAC
Found at i:5475954 original size:131 final size:131
Alignment explanation
Indices: 5475739--5475983 Score: 339
Period size: 131 Copynumber: 1.9 Consensus size: 131
5475729 TTTAAATTAC
* * * * **
5475739 TTAAATTATTTAAGTTGTAAAATTCAAGTATGATTCTAATTTGAAAAATTAATTATTAATTTAAA
1 TTAAATTATTCAAGTTATAAAACTCAAGTATGACTCTAATTAAAAAAATTAATTATTAATTTAAA
5475804 TTAATTAAAAAAAACTGAATAACTCCCTTCAATTAATTTGAAAGTTGAATTTTATCGATTTATTT
66 TTAATTAAAAAAAACTGAATAACTCCCTTCAATTAATTTGAAAGTTGAATTTTATCGATTTATTT
5475869 T
131 T
* *
5475870 TTAAATTATTCAAGTTATAAAACTGAAGTATTACTCTAATTAAAAAAATTAAATTATTAATTTAA
1 TTAAATTATTCAAGTTATAAAACTCAAGTATGACTCTAATTAAAAAAATT-AATTATTAATTTAA
* ** ** * *
5475935 GTTAATT-AAAAAAACTGAATTTCTCTTTTCGATTACTTTGAAAGTTGAA
65 ATTAATTAAAAAAAACTGAATAACTCCCTTCAATTAATTTGAAAGTTGAA
5475984 AATTTTAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
131 78 0.80
132 20 0.20
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (131 bp):
TTAAATTATTCAAGTTATAAAACTCAAGTATGACTCTAATTAAAAAAATTAATTATTAATTTAAA
TTAATTAAAAAAAACTGAATAACTCCCTTCAATTAATTTGAAAGTTGAATTTTATCGATTTATTT
T
Found at i:5481428 original size:18 final size:17
Alignment explanation
Indices: 5481405--5481462 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
5481395 TTGGAGTCAA
5481405 ATTTTTTGAACTTCCACT
1 ATTTTTTGAACTT-CACT
* * *
5481423 A-TTTTTGGA-GTCA-A
1 ATTTTTTGAACTTCACT
5481437 ATTTTTTGAACTTTCACT
1 ATTTTTTGAAC-TTCACT
5481455 ATTTTTTG
1 ATTTTTTG
5481463 TAAAAACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 1 0.03
15 9 0.30
16 1 0.03
17 10 0.33
18 9 0.30
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.53
Consensus pattern (17 bp):
ATTTTTTGAACTTCACT
Found at i:5481444 original size:15 final size:15
Alignment explanation
Indices: 5481393--5481444 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5481383 CAGCTGATAA
5481393 TTTTGGAGTCAAATT
1 TTTTGGAGTCAAATT
* * * *
5481408 TTTTGAACTTCCACTAT
1 TTTTGGA-GTCAAAT-T
5481425 TTTTGGAGTCAAATT
1 TTTTGGAGTCAAATT
5481440 TTTTG
1 TTTTG
5481445 AACTTTCACT
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 12 0.44
16 8 0.30
17 7 0.26
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (15 bp):
TTTTGGAGTCAAATT
Found at i:5481462 original size:33 final size:32
Alignment explanation
Indices: 5481393--5481460 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
5481383 CAGCTGATAA
5481393 TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
1 TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
*
5481425 TTTTGGAGTCAAATTTTTTGAACTTTCACTAT
1 TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
5481457 TTTT
1 TTTT
5481461 TGTAAAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (32 bp):
TTTTGGAGTCAAATTTTTTGAACTTCCACTAT
Found at i:5483155 original size:29 final size:29
Alignment explanation
Indices: 5483119--5483178 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
5483109 TCTTGTCTTG
5483119 TTCATAACATTTTTGTATTAAGATTGTAC
1 TTCATAACATTTTTGTATTAAGATTGTAC
*
5483148 TTCATAACATTTTTGTATTATGATTGTAC
1 TTCATAACATTTTTGTATTAAGATTGTAC
5483177 TT
1 TT
5483179 AATTATGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (29 bp):
TTCATAACATTTTTGTATTAAGATTGTAC
Found at i:5485697 original size:181 final size:180
Alignment explanation
Indices: 5485393--5485757 Score: 678
Period size: 181 Copynumber: 2.0 Consensus size: 180
5485383 ATCACAAACC
5485393 TCTCCTAAATCAAGGAGATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAAT
1 TCTCCTAAATCAAGGAGATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAAT
*
5485458 ATAATGAAATCAAAGGGTGACTCAGAGCTGACTAAGTGACGAAAACAGATTCTAAAGCACACCAA
66 ATAATGAAATCAAAGGGTGACTCAGAGCTGACTAAGTGACAAAAACAGATTCTAAAGCACACCAA
5485523 GAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTCAATTAGTAAGCCACCT
131 GAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTC-ATTAGTAAGCCACCT
*
5485574 TCTCCTAAATCAA-GACGATTGAAATAAGAAAGACACTAATTACTGATCTCCAGGCAGGCAGGAA
1 TCTCCTAAATCAAGGA-GATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAA
*
5485638 TATAATGAAATCAAAGGGTGACTCAGAGCTGACTAATTGACAAAAACAGATTCTAAAGCACACCA
65 TATAATGAAATCAAAGGGTGACTCAGAGCTGACTAAGTGACAAAAACAGATTCTAAAGCACACCA
5485703 AGAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTCATTAGTAAGCCACCT
130 AGAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTCATTAGTAAGCCACCT
5485754 TCTC
1 TCTC
5485758 TAAGGCATTC
Statistics
Matches: 180, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
180 21 0.12
181 159 0.88
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (180 bp):
TCTCCTAAATCAAGGAGATTGAAATAAGAAAGACACTAATTACCGATCTCCAGGCAGGCAGGAAT
ATAATGAAATCAAAGGGTGACTCAGAGCTGACTAAGTGACAAAAACAGATTCTAAAGCACACCAA
GAAAGGCTATTCTTCATTTTTGTGCTGTTCTTGTCATTAGTAAGCCACCT
Found at i:5488443 original size:8 final size:9
Alignment explanation
Indices: 5488423--5488452 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5488413 TATAAATTAT
5488423 AAAAATTCA
1 AAAAATTCA
5488432 AAAAATTCA
1 AAAAATTCA
*
5488441 AAAAATTTA
1 AAAAATTCA
5488450 AAA
1 AAA
5488453 TTACAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAATTCA
Found at i:5496850 original size:20 final size:21
Alignment explanation
Indices: 5496822--5496862 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5496812 TTGGACTAAA
5496822 AAATAA-TTTAAAAAATTATT
1 AAATAATTTTAAAAAATTATT
*
5496842 AAATTATTTTAAAAAATTATT
1 AAATAATTTTAAAAAATTATT
5496863 TAAGTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATAATTTTAAAAAATTATT
Found at i:5496854 original size:21 final size:22
Alignment explanation
Indices: 5496828--5496871 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
5496818 TAAAAAATAA
5496828 TTTAAAAAATTA-TTAAATTAT
1 TTTAAAAAATTATTTAAATTAT
*
5496849 TTTAAAAAATTATTTAAGTTAT
1 TTTAAAAAATTATTTAAATTAT
5496871 T
1 T
5496872 AGGCATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAAAAAATTATTTAAATTAT
Found at i:5508091 original size:23 final size:24
Alignment explanation
Indices: 5508029--5508091 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
5508019 TATGGACTAG
* *
5508029 ATATTATATATAAAATTTTAATAA
1 ATATTAAATATAAAAATTTAATAA
* * *
5508053 ATA-AAAATATATAAATTTATTAA
1 ATATTAAATATAAAAATTTAATAA
5508076 ATATTAAAT-TAAAAAT
1 ATATTAAATATAAAAAT
5508092 AATATAAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 24 0.77
24 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATTAAATATAAAAATTTAATAA
Found at i:5508748 original size:19 final size:19
Alignment explanation
Indices: 5508712--5508771 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
5508702 AGAAATAGTT
* *
5508712 TAATTGAATAATATACATTA
1 TAATT-AATATTACACATTA
*
5508732 TAATTAATATTACACATTG
1 TAATTAATATTACACATTA
*
5508751 TAATTAATATTACACAATA
1 TAATTAATATTACACATTA
5508770 TA
1 TA
5508772 TTATTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.86
20 5 0.14
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (19 bp):
TAATTAATATTACACATTA
Found at i:5512415 original size:15 final size:15
Alignment explanation
Indices: 5512395--5512424 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5512385 ATAGTTTAAT
5512395 TCAGTAACTAAATTA
1 TCAGTAACTAAATTA
5512410 TCAGTAACTAAATTA
1 TCAGTAACTAAATTA
5512425 ATTAATTTTT
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:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
TCAGTAACTAAATTA
Found at i:5513752 original size:15 final size:15
Alignment explanation
Indices: 5513732--5513766 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
5513722 ATAATATATT
5513732 ATATTAATAAAATAA
1 ATATTAATAAAATAA
5513747 ATATTAATAAAATAA
1 ATATTAATAAAATAA
5513762 ATATT
1 ATATT
5513767 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATTAATAAAATAA
Found at i:5513760 original size:20 final size:21
Alignment explanation
Indices: 5513719--5513762 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5513709 TTATTTGATA
*
5513719 AAAATAATATATTATATTAAT
1 AAAATAATATATTATATAAAT
5513740 AAAATAA-ATATTA-ATAAAAT
1 AAAATAATATATTATAT-AAAT
5513760 AAA
1 AAA
5513763 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATAATATATTATATAAAT
Found at i:5513814 original size:18 final size:18
Alignment explanation
Indices: 5513722--5513807 Score: 63
Period size: 17 Copynumber: 4.9 Consensus size: 18
5513712 TTTGATAAAA
5513722 ATAATATATTATATTAAT
1 ATAATATATTATATTAAT
*
5513740 A-AA-ATA-AATATTAAT
1 ATAATATATTATATTAAT
* * * *
5513755 AAAATAAATATTTTTTTAAA
1 ATAAT--ATATTATATTAAT
* *
5513775 AT-ATTTATTTTATTAAT
1 ATAATATATTATATTAAT
5513792 ATAATATATTATATTA
1 ATAATATATTATATTA
5513808 TATTAATTCA
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
15 9 0.18
16 5 0.10
17 14 0.27
18 12 0.24
19 5 0.10
20 6 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATATATTATATTAAT
Found at i:5530008 original size:24 final size:24
Alignment explanation
Indices: 5529980--5530030 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
5529970 GAATCTAAAT
5529980 CTTTCTTTTAAAAATACAACATGA
1 CTTTCTTTTAAAAATACAACATGA
*
5530004 CTTTCTTTTAAAAATACAACGTGA
1 CTTTCTTTTAAAAATACAACATGA
5530028 CTT
1 CTT
5530031 ACCATTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (24 bp):
CTTTCTTTTAAAAATACAACATGA
Found at i:5534405 original size:23 final size:23
Alignment explanation
Indices: 5534375--5534422 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5534365 TTGTCTTTTA
**
5534375 TGGTCAAATTGGATTGAGTTGGG
1 TGGTCAAATTGGACCGAGTTGGG
5534398 TGGTCAAATTGGACCGAGTTGGG
1 TGGTCAAATTGGACCGAGTTGGG
5534421 TG
1 TG
5534423 TGGGCAGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.40, T:0.31
Consensus pattern (23 bp):
TGGTCAAATTGGACCGAGTTGGG
Found at i:5537910 original size:13 final size:14
Alignment explanation
Indices: 5537894--5537935 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
5537884 TTTCAATTTT
5537894 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
5537907 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
5537922 ATTTTAAATAATAT
1 ATTTT-AATAATAT
5537936 TATTGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:5537920 original size:16 final size:16
Alignment explanation
Indices: 5537898--5537934 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
5537888 AATTTTATTT
5537898 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
5537915 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
5537930 TAATA
1 TAATA
5537935 TTATTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:5538006 original size:15 final size:15
Alignment explanation
Indices: 5537956--5538006 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 15
5537946 ATTCAATATT
5537956 AATAT-TTAATAATA
1 AATATATTAATAATA
*
5537970 AATATTTATTACAATTATA
1 AATA--TATT--AATAATA
5537989 AATATATTAATAATA
1 AATATATTAATAATA
5538004 AAT
1 AAT
5538007 GTTTTGTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 1 0.03
17 6 0.20
19 10 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:5538776 original size:90 final size:90
Alignment explanation
Indices: 5538623--5538796 Score: 330
Period size: 90 Copynumber: 1.9 Consensus size: 90
5538613 ATCTTGAATT
*
5538623 AGAGGCTTGAACTAGACAACTATTCTCACATTGGAGCTTGAATTTTTGTTTGTCCAAATTAATCA
1 AGAGGCTTGAACTAGACAACTATTCTCACATTAGAGCTTGAATTTTTGTTTGTCCAAATTAATCA
5538688 TTGAGCTTGATAATTGTTCCCACAC
66 TTGAGCTTGATAATTGTTCCCACAC
*
5538713 AGAGGCTTGAATTAGACAACTATTCTCACATTAGAGCTTGAATTTTTGTTTGTCCAAATTAATCA
1 AGAGGCTTGAACTAGACAACTATTCTCACATTAGAGCTTGAATTTTTGTTTGTCCAAATTAATCA
5538778 TTGAGCTTGATAATTGTTC
66 TTGAGCTTGATAATTGTTC
5538797 ATGCATTGGG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (90 bp):
AGAGGCTTGAACTAGACAACTATTCTCACATTAGAGCTTGAATTTTTGTTTGTCCAAATTAATCA
TTGAGCTTGATAATTGTTCCCACAC
Found at i:5543430 original size:18 final size:17
Alignment explanation
Indices: 5543407--5543441 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5543397 GGCTTGGTTG
5543407 CCTCAGGATCATCTATCT
1 CCTCAGGATCATC-ATCT
*
5543425 CCTCAGGCTCATCATCT
1 CCTCAGGATCATCATCT
5543442 AACCATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.37, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTCAGGATCATCATCT
Found at i:5545751 original size:31 final size:31
Alignment explanation
Indices: 5545713--5545834 Score: 165
Period size: 31 Copynumber: 3.9 Consensus size: 31
5545703 GAATAATTAT
*
5545713 TAAACTATTTGACAA-TTTTCATTTAAGTCAC
1 TAAACTATTTGA-AAGATTTCATTTAAGTCAC
* *
5545744 TAAACTATTTGAAAGATTTCATTGAATTCAC
1 TAAACTATTTGAAAGATTTCATTTAAGTCAC
* *
5545775 TAAATTATTTGAAATATTTCATTTAAGTCAC
1 TAAACTATTTGAAAGATTTCATTTAAGTCAC
* *
5545806 TGAACTATTTAAAAGATTTCATTTAAGTC
1 TAAACTATTTGAAAGATTTCATTTAAGTC
5545835 GCTATTAAGT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 2 0.03
31 77 0.97
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (31 bp):
TAAACTATTTGAAAGATTTCATTTAAGTCAC
Found at i:5546707 original size:58 final size:60
Alignment explanation
Indices: 5546639--5546770 Score: 157
Period size: 58 Copynumber: 2.3 Consensus size: 60
5546629 GTTAATGTTA
* * *
5546639 ATATAATTTAAAATTTTAATTTATTATTATAATTT-TT-TTAAAAATATTTTTCT-TATTT
1 ATATATTTTAAAATTTTAATATATTATTATAATTTCTTGTCAAAAATATTTTT-TATATTT
* * * *
5546697 ATATATTTT--AATTTTTATATATTATTATTATTTCTTGTCAACAATATTTTTTATTTTT
1 ATATATTTTAAAATTTTAATATATTATTATAATTTCTTGTCAAAAATATTTTTTATATTT
5546755 ATATATTTTAAAATTT
1 ATATATTTTAAAATTT
5546771 ATTTTTTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
56 21 0.34
57 3 0.05
58 33 0.53
60 5 0.08
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (60 bp):
ATATATTTTAAAATTTTAATATATTATTATAATTTCTTGTCAAAAATATTTTTTATATTT
Found at i:5547718 original size:19 final size:17
Alignment explanation
Indices: 5547653--5547737 Score: 59
Period size: 19 Copynumber: 4.8 Consensus size: 17
5547643 TAAAATATTT
*
5547653 ATAAAGTTATTAAAATTA
1 ATAAA-TTAATAAAATTA
5547671 AT-AATTAATAAAACTT-
1 ATAAATTAATAAAA-TTA
*
5547687 ATAAATATTATAAAATATA
1 ATAAAT-TAATAAAAT-TA
*
5547706 ATAAATCTAATAAATTTCA
1 ATAAAT-TAATAAAATT-A
*
5547725 ATAAGTT-ATAAAA
1 ATAAATTAATAAAA
5547738 AATTTATAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
16 10 0.19
17 13 0.24
18 12 0.22
19 19 0.35
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (17 bp):
ATAAATTAATAAAATTA
Found at i:5548037 original size:23 final size:23
Alignment explanation
Indices: 5548007--5548057 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
5547997 TACTATTTTA
5548007 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
5548030 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
5548053 TATTT
1 TATTT
5548058 GAAATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (23 bp):
TATTTAAGCTTTATTCACCAAAG
Found at i:5548764 original size:42 final size:42
Alignment explanation
Indices: 5548701--5548815 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
5548691 CTTCGTTTTC
** * *
5548701 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCAGATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGAT-A
* *
5548744 T-GATGCCATAGGCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
5548785 TCGATGCCATAGCCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
5548816 GAATCACATA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.03
42 62 0.95
43 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
Found at i:5548915 original size:31 final size:31
Alignment explanation
Indices: 5548880--5549028 Score: 219
Period size: 31 Copynumber: 4.8 Consensus size: 31
5548870 CTTGTCACTT
*
5548880 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCAAAGCTACCACTTTTCACTGATCAG
* *
5548911 GTAGCCAGAGCTACCATTTTTCACTGATCAG
1 GTAGCCAAAGCTACCACTTTTCACTGATCAG
***
5548942 GTAGCTGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCAAAGCTACCACTTTTCACTGATCAG
5548973 GTAG-CAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCA-AAGCTACCACTTTTCACTGATCAG
*
5549004 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCAAAGCTACCACTTTTCACT
5549029 TGTTATTGTC
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
31 105 0.99
32 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCAAAGCTACCACTTTTCACTGATCAG
Found at i:5549079 original size:50 final size:51
Alignment explanation
Indices: 5549004--5549132 Score: 190
Period size: 50 Copynumber: 2.6 Consensus size: 51
5548994 CACTGATCAG
* * *
5549004 GTAGCCGAAGCTACCACTTTTCACTTGTTA-TTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTTATTTGTCATTGATCAAATAAGT
* * *
5549054 GTAGCCGAAGCTATTACTTATCACTT-TCATTTGTCCTTGATCAAATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTTATTTGTCATTGATCAAATAAGT
5549104 GTAGCCGAAGCTATCACTTATCACTTGTT
1 GTAGCCGAAGCTATCACTTATCACTTGTT
5549133 GCTATGGTCA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 2 0.03
50 66 0.96
51 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTTATTTGTCATTGATCAAATAAGT
Found at i:5554666 original size:27 final size:25
Alignment explanation
Indices: 5554600--5554753 Score: 116
Period size: 27 Copynumber: 6.0 Consensus size: 25
5554590 TTTTGAACAG
* * * *
5554600 TTTTATTATTATATATTTTAAGTTT
1 TTTTAATATTATTTATTTTAAATTA
* *
5554625 TTTTCATATGGTATTTGTTTTAAATTA
1 TTTTAATAT--TATTTATTTTAAATTA
* *
5554652 TTTTACCATATTATTTATTTTAATTTG
1 TTTTA--ATATTATTTATTTTAAATTA
*
5554679 TTTT-GTATTA-TTATTTTAAATTA
1 TTTTAATATTATTTATTTTAAATTA
* *
5554702 TTTTATATATTATTTACTTTAAATTGC
1 TTTTA-ATATTATTTATTTTAAATT-A
*
5554729 TTTATAA-ATTATTTATTTCAAATTA
1 TTT-TAATATTATTTATTTTAAATTA
5554754 AATTATACTT
Statistics
Matches: 101, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
23 15 0.15
24 5 0.05
25 12 0.12
26 26 0.26
27 37 0.37
28 2 0.02
29 4 0.04
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTTAATATTATTTATTTTAAATTA
Found at i:5554724 original size:26 final size:25
Alignment explanation
Indices: 5554643--5554753 Score: 102
Period size: 26 Copynumber: 4.4 Consensus size: 25
5554633 TGGTATTTGT
*
5554643 TTTAAATTATTTTACCATATTATTTA
1 TTTAAATTATTTTA-TATATTATTTA
* *
5554669 TTTTAATT-TGTTT-TGTATTA-TTA
1 TTTAAATTAT-TTTATATATTATTTA
5554692 TTTTAAATTATTTTATATATTATTTA
1 -TTTAAATTATTTTATATATTATTTA
** *
5554718 CTTTAAATTGCTTTATAAATTATTTA
1 -TTTAAATTATTTTATATATTATTTA
5554744 TTTCAAATTA
1 TTT-AAATTA
5554754 AATTATACTT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
23 3 0.04
24 15 0.22
25 11 0.16
26 40 0.58
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (25 bp):
TTTAAATTATTTTATATATTATTTA
Found at i:5557096 original size:16 final size:18
Alignment explanation
Indices: 5557075--5557112 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5557065 TTTTAGACAT
*
5557075 TATATAA-AA-AAGAACA
1 TATATAATAATAACAACA
5557091 TATATAATAATAACAACA
1 TATATAATAATAACAACA
5557109 TATA
1 TATA
5557113 ATAAGATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 10 0.53
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.26
Consensus pattern (18 bp):
TATATAATAATAACAACA
Found at i:5558386 original size:3 final size:3
Alignment explanation
Indices: 5558378--5558402 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5558368 GAGAAGCAAA
5558378 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
5558403 GCTTTAGTAT
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:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5560424 original size:13 final size:13
Alignment explanation
Indices: 5560408--5560432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5560398 TGCCGTAAAA
5560408 AAGTACTTTTGAG
1 AAGTACTTTTGAG
5560421 AAGTACTTTTGA
1 AAGTACTTTTGA
5560433 AAATTTGAGT
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:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
AAGTACTTTTGAG
Found at i:5566148 original size:23 final size:23
Alignment explanation
Indices: 5566092--5566142 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5566082 ATTTTATTAG
**
5566092 ATAATAATTTTAAATATTAAGTT
1 ATAATAATAATAAATATTAAGTT
* *
5566115 ATTATAATAATAAATATTATGTT
1 ATAATAATAATAAATATTAAGTT
5566138 ATAAT
1 ATAAT
5566143 TTTAATTAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
ATAATAATAATAAATATTAAGTT
Found at i:5566726 original size:17 final size:17
Alignment explanation
Indices: 5566696--5566729 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5566686 GCACATGCCT
5566696 CTAAAATAATAACAAAA
1 CTAAAATAATAACAAAA
5566713 CTAACAATAA-AACAAAA
1 CTAA-AATAATAACAAAA
5566730 TTTATACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (17 bp):
CTAAAATAATAACAAAA
Found at i:5568058 original size:22 final size:22
Alignment explanation
Indices: 5568033--5568085 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
5568023 ATTATAAGGA
5568033 TTATAATAAGTATAAATTTTAC
1 TTATAATAAGTATAAATTTTAC
5568055 TTATAATAAGTATAAATTTTAC
1 TTATAATAAGTATAAATTTTAC
5568077 TTATAATAA
1 TTATAATAA
5568086 ATTTTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
TTATAATAAGTATAAATTTTAC
Found at i:5568825 original size:15 final size:15
Alignment explanation
Indices: 5568805--5568834 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5568795 TATTTTATTT
*
5568805 ATATTAGGATAATTA
1 ATATTAAGATAATTA
5568820 ATATTAAGATAATTA
1 ATATTAAGATAATTA
5568835 TTAGGATTAT
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:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:5568862 original size:27 final size:26
Alignment explanation
Indices: 5568801--5568863 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
5568791 ACTTTATTTT
5568801 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * * *
5568828 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
5568856 ATTTTATT
1 ATTTTATT
5568864 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:5569792 original size:12 final size:12
Alignment explanation
Indices: 5569775--5569807 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5569765 CTACTTCCCC
*
5569775 TTTACTATTATT
1 TTTACTATTAAT
5569787 TTTACTATTAAT
1 TTTACTATTAAT
5569799 TTTACTATT
1 TTTACTATT
5569808 TTACAGGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTACTATTAAT
Found at i:5571386 original size:38 final size:38
Alignment explanation
Indices: 5571344--5571424 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
5571334 AACAACTTTA
5571344 CACTACAACCAAGAGTTACATTATTCACGCCTATGTAT
1 CACTACAACCAAGAGTTACATTATTCACGCCTATGTAT
*
5571382 CACTACAACCAAGAGTTACATTATTCATGCCTATGTAT
1 CACTACAACCAAGAGTTACATTATTCACGCCTATGTAT
5571420 CACTA
1 CACTA
5571425 ATTTCACAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.30
Consensus pattern (38 bp):
CACTACAACCAAGAGTTACATTATTCACGCCTATGTAT
Found at i:5572715 original size:21 final size:21
Alignment explanation
Indices: 5572689--5572731 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5572679 TTCACGAAAA
5572689 AAATTGTTATATCAAATAAAC
1 AAATTGTTATATCAAATAAAC
5572710 AAATTGTTATATCAAATAAAC
1 AAATTGTTATATCAAATAAAC
5572731 A
1 A
5572732 TTTTAATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (21 bp):
AAATTGTTATATCAAATAAAC
Found at i:5574916 original size:24 final size:23
Alignment explanation
Indices: 5574859--5574917 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
5574849 CAATGACTGT
* * *
5574859 ACTCTTTTAATTTTTAAAATTTA
1 ACTCTTCTACTTTTTAAAATTCA
*
5574882 A-TCTCTGTACTTTTTAAATATTCA
1 ACTCT-TCTACTTTTTAAA-ATTCA
5574906 ACTCTTCTACTT
1 ACTCTTCTACTT
5574918 ATTTGATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 3 0.10
23 12 0.41
24 11 0.38
25 3 0.10
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.53
Consensus pattern (23 bp):
ACTCTTCTACTTTTTAAAATTCA
Found at i:5577460 original size:11 final size:11
Alignment explanation
Indices: 5577444--5577468 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5577434 ATTTTGGAGC
5577444 AAAATGAGCAA
1 AAAATGAGCAA
5577455 AAAATGAGCAA
1 AAAATGAGCAA
5577466 AAA
1 AAA
5577469 TTGGAGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAATGAGCAA
Found at i:5585414 original size:52 final size:52
Alignment explanation
Indices: 5585258--5585417 Score: 205
Period size: 52 Copynumber: 3.1 Consensus size: 52
5585248 CGGACCACAT
* * *
5585258 ATCATACCGATGCCATATCCCGGATATGGTCTTATACGGAATCACATAATCAC
1 ATCATACCGATGCCATAGCCCGGCTATGGTCTTATACGGAATCACGT-ATCAC
* * * *
5585311 ATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGGGAT-ACGAATCAC
1 ATCATACCGATGCCATAGCCCGGCTATGGTCTTATAC-GGAATCACGTATCAC
** *
5585363 ATGGTACCGATGCCATAGCCCGGCTATGGTCTTATACGGAATCATGTATCAC
1 ATCATACCGATGCCATAGCCCGGCTATGGTCTTATACGGAATCACGTATCAC
5585415 ATC
1 ATC
5585418 TTTTCCGTCA
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
51 4 0.04
52 47 0.52
53 35 0.39
54 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (52 bp):
ATCATACCGATGCCATAGCCCGGCTATGGTCTTATACGGAATCACGTATCAC
Found at i:5587439 original size:36 final size:35
Alignment explanation
Indices: 5587397--5587483 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 35
5587387 CACTGTTGTT
** *
5587397 TTGTTATCATTTTGCTATTATATTGCTATTATTTTG
1 TTGTTAT-ATTTTGCTATTATATAACTATTATTTTA
* * *
5587433 TTGTTATTATTTGGATATTGTATAACTATTATTTTA
1 TTGTTA-TATTTTGCTATTATATAACTATTATTTTA
5587469 TTGTTA-ATTTTGCTA
1 TTGTTATATTTTGCTA
5587484 CTATTTTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
34 7 0.17
36 34 0.81
37 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (35 bp):
TTGTTATATTTTGCTATTATATAACTATTATTTTA
Found at i:5593889 original size:16 final size:16
Alignment explanation
Indices: 5593868--5593922 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
5593858 GTTTGGTTTA
5593868 CTGTAATGGAATA-AGG
1 CTGTAATGGAATAGA-G
5593884 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
5593900 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
5593916 CTGTAAT
1 CTGTAAT
5593923 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 35 0.97
17 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:5593990 original size:44 final size:46
Alignment explanation
Indices: 5593904--5593996 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
5593894 ATAGAGTTGT
5593904 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATAG
1 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATAG
* *
5593950 AATGGAATAGAGCTGTAAT-AG-AATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGAATAG
5593994 AAT
1 AAT
5593997 AGATGTTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATAG
Found at i:5594164 original size:15 final size:15
Alignment explanation
Indices: 5594130--5594177 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
5594120 TCATATTTTA
* *
5594130 ATATAATTATTATTAT
1 ATATAATT-TAATAAT
5594146 ATATAATTTAATAAT
1 ATATAATTTAATAAT
5594161 ATATAATTTAATAAT
1 ATATAATTTAATAAT
5594176 AT
1 AT
5594178 TTTTAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 22 0.73
16 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATAATTTAATAAT
Found at i:5594182 original size:12 final size:14
Alignment explanation
Indices: 5594144--5594185 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
5594134 AATTATTATT
5594144 ATATATAATTTAATA
1 ATATAT-ATTTAATA
5594159 ATATATAATTTAATA
1 ATATAT-ATTTAATA
5594174 ATAT-T-TTTAATA
1 ATATATATTTAATA
5594186 TAATTATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.26
14 1 0.04
15 19 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATATTTAATA
Found at i:5594184 original size:17 final size:17
Alignment explanation
Indices: 5594112--5594199 Score: 56
Period size: 17 Copynumber: 5.1 Consensus size: 17
5594102 TAATAATAAA
*
5594112 TAATTTAATCATA-TTT
1 TAATTTAATAATATTTT
* *
5594128 TAATATAATTATTATTATAT
1 TAATTTAA-TAATATT-T-T
*
5594148 ATAATTTAATAATA--TA
1 -TAATTTAATAATATTTT
5594164 TAATTTAATAATATTTT
1 TAATTTAATAATATTTT
* * *
5594181 TAATATAATTATGTTTT
1 TAATTTAATAATATTTT
5594198 TA
1 TA
5594200 TTTTTGTAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
15 13 0.24
16 7 0.13
17 21 0.38
18 1 0.02
19 1 0.02
20 5 0.09
21 7 0.13
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
TAATTTAATAATATTTT
Found at i:5595923 original size:33 final size:34
Alignment explanation
Indices: 5595885--5595949 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
5595875 GAACAAAATA
*
5595885 TAATATTATTAAT-TAATAGTA-AATATTCAATTT
1 TAATATTAAT-ATGTAATAGTATAATATTCAATTT
*
5595918 TAATATTAATATGTAATATTATAATATTCAAT
1 TAATATTAATATGTAATAGTATAATATTCAAT
5595950 ATTATTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 2 0.07
33 16 0.57
34 10 0.36
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (34 bp):
TAATATTAATATGTAATAGTATAATATTCAATTT
Found at i:5596181 original size:23 final size:23
Alignment explanation
Indices: 5596155--5596222 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
5596145 ATAATCTATC
**
5596155 TATATTATAATTTATAAATATTT
1 TATATTATAAAATATAAATATTT
*
5596178 TATAGTATAAAATATAAATATTT
1 TATATTATAAAATATAAATATTT
* *
5596201 TA-ATTACATAAATATAAGTATT
1 TATATTATA-AAATATAAATATT
5596223 GATTTAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.11
23 34 0.89
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (23 bp):
TATATTATAAAATATAAATATTT
Found at i:5596448 original size:12 final size:12
Alignment explanation
Indices: 5596431--5596463 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
5596421 TAGTAAGAAA
5596431 AAGGAATTATTG
1 AAGGAATTATTG
5596443 AAGGAATTATTG
1 AAGGAATTATTG
5596455 AAGGAATTA
1 AAGGAATTA
5596464 GGTAAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (12 bp):
AAGGAATTATTG
Found at i:5601257 original size:42 final size:42
Alignment explanation
Indices: 5601208--5601354 Score: 170
Period size: 42 Copynumber: 3.3 Consensus size: 42
5601198 CATAGTTCAA
5601208 CTATGGTCTTACACATCTTCACATAAT-GATGCCATAGCCCAG
1 CTATGGTCTTACACATCTTCACAT-ATCGATGCCATAGCCCAG
* * *
5601250 CTATGGTCTTACTCATATTCATATATCGATGCCATAGCCCAG
1 CTATGGTCTTACACATCTTCACATATCGATGCCATAGCCCAG
*
5601292 CTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAACCCAG
1 CTATGGTCTTACAC---AT--C-T-TCACATATCGATGCCATAGCCCAG
*
5601341 CTATGGTCGTACAC
1 CTATGGTCTTACAC
5601355 GAATCACATA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.02
42 49 0.55
45 2 0.02
48 1 0.01
49 35 0.39
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (42 bp):
CTATGGTCTTACACATCTTCACATATCGATGCCATAGCCCAG
Found at i:5601340 original size:49 final size:48
Alignment explanation
Indices: 5601274--5601444 Score: 179
Period size: 47 Copynumber: 3.6 Consensus size: 48
5601264 ATATTCATAT
* *
5601274 ATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACA
1 ATCGATGCCATATCCCAGATATGGTCTTACACGTAATCACATATCACA
* * * *
5601322 TATCGATGCCATAACCCAGCTATGGTCGTACACG-AATCACATATCTCA
1 -ATCGATGCCATATCCCAGATATGGTCTTACACGTAATCACATATCACA
* * * * *
5601370 CT-GATGCCATATCCCATATATGGTCTTATACAGT-AGCATATATCAC-
1 ATCGATGCCATATCCCAGATATGGTCTTACAC-GTAATCACATATCACA
* *
5601416 ACCGATGCCATATCCCAAATATGGTCTTA
1 ATCGATGCCATATCCCAGATATGGTCTTA
5601445 TACGGAAATC
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 24 0.23
47 36 0.35
48 13 0.12
49 31 0.30
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (48 bp):
ATCGATGCCATATCCCAGATATGGTCTTACACGTAATCACATATCACA
Found at i:5601501 original size:31 final size:31
Alignment explanation
Indices: 5601466--5601668 Score: 287
Period size: 31 Copynumber: 6.8 Consensus size: 31
5601456 CTTGTCACTT
*
5601466 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
5601497 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
5601528 GTAACCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5601559 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
5601590 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5601621 GTAGCAGAAGCTACCAC--TT--CTGATCA-
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
5601647 GTAGCCG-AGCTA-C-CTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
5601669 TGTCATTTGT
Statistics
Matches: 157, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
23 1 0.01
24 1 0.01
25 7 0.04
26 6 0.04
27 9 0.06
29 2 0.01
31 131 0.83
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:5601735 original size:50 final size:51
Alignment explanation
Indices: 5601647--5601772 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
5601637 CTTCTGATCA
* *
5601647 GTAGCCG-AGCTA-C-CTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
*
5601695 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCTTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
5601745 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
5601773 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
48 7 0.10
49 5 0.07
50 49 0.69
51 10 0.14
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
Found at i:5607815 original size:27 final size:27
Alignment explanation
Indices: 5607757--5607815 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
5607747 TTGCCCATAT
* *
5607757 TATT-TTTTTAATTTTTTAAATACTGA
1 TATTATTTTTAATTTTATAAATACTAA
**
5607783 TATTATTTTTAATTTTATATTTACTAA
1 TATTATTTTTAATTTTATAAATACTAA
*
5607810 TTTTAT
1 TATTAT
5607816 ATATTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTATTTTTAATTTTATAAATACTAA
Found at i:5610399 original size:2 final size:2
Alignment explanation
Indices: 5610394--5610422 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5610384 ACACACATAA
5610394 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 A
5610423 AGTTGTTTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5614311 original size:8 final size:8
Alignment explanation
Indices: 5614293--5614330 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
5614283 TTTAAGAAAT
5614293 TAATAATTA
1 TAATAA-TA
5614302 TAATAATA
1 TAATAATA
*
5614310 TAATAGT-
1 TAATAATA
5614317 TAATAATA
1 TAATAATA
5614325 TAATAA
1 TAATAA
5614331 AAGAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 14 0.54
9 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
TAATAATA
Found at i:5614338 original size:24 final size:24
Alignment explanation
Indices: 5614292--5614338 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5614282 ATTTAAGAAA
* *
5614292 TTAATAATTATAATAATATAATAG
1 TTAATAATTATAATAAAAAAATAG
5614316 TTAATAA-TATAATAAAAGAAATA
1 TTAATAATTATAATAAAA-AAATA
5614339 ATAAAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
TTAATAATTATAATAAAAAAATAG
Found at i:5614369 original size:15 final size:15
Alignment explanation
Indices: 5614349--5614425 Score: 50
Period size: 15 Copynumber: 4.9 Consensus size: 15
5614339 ATAAAAGAAT
5614349 AAAGAAAAAGGAAAG
1 AAAGAAAAAGGAAAG
* * *
5614364 AAAGAAGGACGAAACAG
1 AAAGAA-AAAGGAA-AG
**
5614381 AACAGGGAAA-GAAAG
1 AA-AGAAAAAGGAAAG
5614396 AAAGAAAAAGGGAAAG
1 AAAGAAAAA-GGAAAG
5614412 AAA-AATAAAGGAAA
1 AAAGAA-AAAGGAAA
5614426 AATAGGGTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
14 5 0.11
15 17 0.37
16 17 0.37
17 5 0.11
18 2 0.04
ACGTcount: A:0.68, C:0.04, G:0.27, T:0.01
Consensus pattern (15 bp):
AAAGAAAAAGGAAAG
Found at i:5616212 original size:14 final size:15
Alignment explanation
Indices: 5616181--5616215 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
5616171 TTTAATTTTC
5616181 AAATTTTCAAAAAAA
1 AAATTTTCAAAAAAA
5616196 AAATTTT-AAAAATAA
1 AAATTTTCAAAAA-AA
5616211 AAATT
1 AAATT
5616216 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATTTTCAAAAAAA
Found at i:5616274 original size:30 final size:30
Alignment explanation
Indices: 5616211--5616312 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
5616201 TTAAAAATAA
* * *
5616211 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCTTAAACTTTCT-TT
5616241 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCTTAAACTTTCTTT
* * *
5616271 AAATTTCACTTAGACCCTTAAACTTTCATT
1 AAATTTCATTTTGACCCTTAAACTTTCTTT
5616301 AAATTTCATTTT
1 AAATTTCATTTT
5616313 AATCCTAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 62 0.98
31 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (30 bp):
AAATTTCATTTTGACCCTTAAACTTTCTTT
Found at i:5616721 original size:3 final size:3
Alignment explanation
Indices: 5616700--5616771 Score: 53
Period size: 3 Copynumber: 24.0 Consensus size: 3
5616690 GCTAGACTTT
* *
5616700 GAA GAA AAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
*
5616747 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
5616772 ATAATAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 8 0.14
3 36 0.63
4 13 0.23
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5616722 original size:10 final size:10
Alignment explanation
Indices: 5616707--5616731 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5616697 TTTGAAGAAA
5616707 AAGAAGGAAG
1 AAGAAGGAAG
5616717 AAGAAGGAAG
1 AAGAAGGAAG
5616727 AAGAA
1 AAGAA
5616732 AAGAGGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (10 bp):
AAGAAGGAAG
Found at i:5616738 original size:14 final size:13
Alignment explanation
Indices: 5616700--5616772 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
5616690 GCTAGACTTT
5616700 GAAGAAAAA-GAA
1 GAAGAAAAAGGAA
*
5616712 GGAAGAAGAAGGAA
1 -GAAGAAAAAGGAA
5616726 GAAGAAAAGAGGAA
1 GAAGAAAA-AGGAA
*
5616740 GAAGAAAGAAAGAAA
1 GAAG-AA-AAAGGAA
*
5616755 AAAGAAAAA-GAA
1 GAAGAAAAAGGAA
5616767 -AAGAAA
1 GAAGAAA
5616773 TAATAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
11 6 0.12
12 2 0.04
13 18 0.35
14 14 0.27
15 9 0.18
16 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAGGAA
Found at i:5617070 original size:22 final size:21
Alignment explanation
Indices: 5617036--5617091 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
5617026 GGCCCAGCAG
5617036 AGAA-AAAAAAGAAA-AGAAAA
1 AGAAGAAAAAAGAAAGA-AAAA
*
5617056 AGAAGAAAAAGAGAAGGAAAAA
1 AGAAGAAAAA-AGAAAGAAAAA
5617078 AGAAGGAAAAAAGA
1 AGAA-GAAAAAAGA
5617092 GGTTCAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 4 0.13
21 5 0.16
22 15 0.48
23 7 0.23
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAGAAAGAAAAA
Found at i:5617081 original size:11 final size:11
Alignment explanation
Indices: 5617052--5617091 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
5617042 AAAAGAAAAG
5617052 AAAAAGAA-GA
1 AAAAAGAAGGA
5617062 AAAAGAGAAGGA
1 AAAA-AGAAGGA
5617074 AAAAAGAAGGA
1 AAAAAGAAGGA
5617085 AAAAAGA
1 AAAAAGA
5617092 GGTTCAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 4 0.14
11 18 0.64
12 6 0.21
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGGA
Found at i:5617257 original size:16 final size:17
Alignment explanation
Indices: 5617231--5617268 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5617221 TTATATTTAT
5617231 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
5617248 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
5617264 ATTTT
1 ATTTT
5617269 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:5617482 original size:16 final size:16
Alignment explanation
Indices: 5617431--5617484 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
5617421 CGTGCTTTTA
5617431 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
5617447 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
5617465 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
5617481 AAAA
1 AAAA
5617485 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:5617614 original size:73 final size:74
Alignment explanation
Indices: 5617477--5617650 Score: 192
Period size: 73 Copynumber: 2.4 Consensus size: 74
5617467 AATTCTAGTG
* * *** * * **
5617477 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTGTTTTATAAATTTCCGTATTTTCAAAAA
1 TTTCAAAAATTTTCATGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTA-TTAAAAAAA
5617542 ATCAT-GT-C
65 ATCATCGTAC
*
5617550 TTTCAAAAATTTTCATGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
1 TTTCAAAAATTTTCATGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTATTAAAAAAAA
* *
5617615 TCTTCGTAT
66 TCATCGTAC
*
5617624 TTTCAAAAAATTTTCGTG-TTTCAAAAA
1 TTTC-AAAAATTTTCATGTTTTCAAAAA
5617651 TCTTCGTGTT
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
72 11 0.13
73 49 0.58
74 13 0.15
75 12 0.14
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (74 bp):
TTTCAAAAATTTTCATGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTATTAAAAAAAA
TCATCGTAC
Found at i:5617791 original size:18 final size:17
Alignment explanation
Indices: 5617420--5617935 Score: 232
Period size: 17 Copynumber: 29.8 Consensus size: 17
5617410 TCAATAATCC
*
5617420 TCGTGCTTTTAAAAATTC
1 TCGTG-TTTTAAAAATTT
* * *
5617438 TCATGTTTCAAAAATCT
1 TCGTGTTTTAAAAATTT
* *
5617455 TCGTGTTTTCAAAATTC
1 TCGTGTTTTAAAAATTT
* *
5617472 TAGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTT
*
5617489 TCTTGTTTTCAGAAAAAATTT
1 TCGTGTTTT----AAAAATTT
*
5617510 TCGTGTTTTATAAATTT
1 TCGTGTTTTAAAAATTT
* * *
5617527 CCGTATTTTCAAAAA--A
1 TCGTGTTTT-AAAAATTT
*
5617543 TCATGTCTTTCAAAAATTT
1 TCGTGT-TTT-AAAAATTT
* **
5617562 TCATGTTTTCAAAAAAAATGA
1 TCGTGTTTT----AAAAATTT
* *
5617583 CCGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTT
* ** *
5617600 CCGTGTTAAAAAAAATCT
1 TCGTGTT-TTAAAAATTT
*
5617618 TCGTATTTTCAAAAAATTT
1 TCGTGTTTT--AAAAATTT
* *
5617637 TCGTGTTTCAAAAATCT
1 TCGTGTTTTAAAAATTT
*
5617654 TCGTGTTTTCAAAA-TT
1 TCGTGTTTTAAAAATTT
* *
5617670 TCGGTGTTTCAAAGATTT
1 TC-GTGTTTTAAAAATTT
*
5617688 TCGTGTTTTCAAAAA-CT
1 TCGTGTTTT-AAAAATTT
* ***
5617705 CCGGTGATTTTAAAAAAAA
1 TC-GTG-TTTTAAAAATTT
*
5617724 TCAT-TTTCTAAAAATTT
1 TCGTGTTT-TAAAAATTT
* *
5617741 CCGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTT
*
5617758 CCGTGTTTTAAAAATTT
1 TCGTGTTTTAAAAATTT
*
5617775 TCGTGTTTTTAAAAATTC
1 TCGTG-TTTTAAAAATTT
*
5617793 TCGTATTTT--AAATTT
1 TCGTGTTTTAAAAATTT
*** **
5617808 T--T-TAAGAAAAAAAT
1 TCGTGTTTTAAAAATTT
* * *
5617822 T-GTGTTTCAAAAAAATG
1 TCGTGTTT-TAAAAATTT
* *
5617839 TCTTGTTTTAAAAATTC
1 TCGTGTTTTAAAAATTT
* *
5617856 TCGTGTTTCAAAAA-TG
1 TCGTGTTTTAAAAATTT
5617872 TCGTGTTTTAAAAATTT
1 TCGTGTTTTAAAAATTT
*
5617889 TCGTGTTTCT-GAAATTT
1 TCGTGTTT-TAAAAATTT
* *
5617906 CCGTG-TTTAAAAATTC
1 TCGTGTTTTAAAAATTT
5617922 TCGTGTTTTAAAAA
1 TCGTGTTTTAAAAA
5617936 AAAAACTTTC
Statistics
Matches: 371, Mismatches: 94, Indels: 67
0.70 0.18 0.13
Matches are distributed among these distances:
12 1 0.00
13 1 0.00
14 5 0.01
15 8 0.02
16 35 0.09
17 204 0.55
18 64 0.17
19 25 0.07
21 28 0.08
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (17 bp):
TCGTGTTTTAAAAATTT
Found at i:5617851 original size:16 final size:16
Alignment explanation
Indices: 5617832--5617886 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
5617822 TGTGTTTCAA
5617832 AAAAATGTCTTGTTTT
1 AAAAATGTCTTGTTTT
*
5617848 AAAAAT-TCTCGTGTTTC
1 AAAAATGTCT--TGTTTT
*
5617865 AAAAATGTCGTGTTTT
1 AAAAATGTCTTGTTTT
5617881 AAAAAT
1 AAAAAT
5617887 TTTCGTGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.09
16 17 0.52
17 11 0.33
18 2 0.06
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (16 bp):
AAAAATGTCTTGTTTT
Found at i:5617869 original size:33 final size:32
Alignment explanation
Indices: 5617823--5617935 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 32
5617813 GAAAAAAATT
5617823 GTGTTTCAAAAAAATGTCTTGTTTTAAAAATTCTC
1 GTGTTTC--AAAAATGTC-TGTTTTAAAAATTCTC
*
5617858 GTGTTTCAAAAATGTCGTGTTTTAAAAATTTTC
1 GTGTTTCAAAAATGTC-TGTTTTAAAAATTCTC
** * *
5617891 GTGTTTCTGAAATTTCCGTGTTTAAAAATTCTC
1 GTGTTTCAAAAATGTCTGT-TTTAAAAATTCTC
*
5617924 GTGTTTTAAAAA
1 GTGTTTCAAAAA
5617936 AAAAACTTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 58 0.87
35 7 0.10
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (32 bp):
GTGTTTCAAAAATGTCTGTTTTAAAAATTCTC
Found at i:5617976 original size:21 final size:21
Alignment explanation
Indices: 5617914--5617968 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
5617904 TTCCGTGTTT
5617914 AAAAATTCTCGTGTTTTAAAAA
1 AAAAATT-TCGTGTTTTAAAAA
*
5617936 AAAAACTTTCAT-TTTTAAAAA
1 AAAAA-TTTCGTGTTTTAAAAA
5617957 AAAAATTTCGTG
1 AAAAATTTCGTG
5617969 CTTCAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 5 0.17
21 14 0.48
22 8 0.28
23 2 0.07
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.36
Consensus pattern (21 bp):
AAAAATTTCGTGTTTTAAAAA
Found at i:5642878 original size:16 final size:16
Alignment explanation
Indices: 5642840--5642978 Score: 71
Period size: 17 Copynumber: 8.8 Consensus size: 16
5642830 AGAAAACAAA
*
5642840 TTTGTAAACA-GAAAAT
1 TTTG-AAACACGAAATT
*
5642856 TTAGAAACACGAAATT
1 TTTGAAACACGAAATT
5642872 TTTG-AA-A-G-AA-T
1 TTTGAAACACGAAATT
*
5642883 TTT-AAA-ACGACATTTT
1 TTTGAAACACGA-A-ATT
*
5642899 TTCTGAAACACGGGAATT
1 TT-TGAAACAC-GAAATT
* *
5642917 TTTAAAACAGGGAAATT
1 TTTGAAACA-CGAAATT
*
5642934 TTAGAAACACGAAAATT
1 TTTGAAACACG-AAATT
*
5642951 TTT-AAACACGACATTT
1 TTTGAAACACGA-AATT
5642967 TTTGAAACACGA
1 TTTGAAACACGA
5642979 TTTAAAAAAC
Statistics
Matches: 94, Mismatches: 14, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
11 7 0.07
12 3 0.03
13 1 0.01
14 2 0.02
15 8 0.09
16 28 0.30
17 34 0.36
18 7 0.07
19 3 0.03
20 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (16 bp):
TTTGAAACACGAAATT
Found at i:5642922 original size:34 final size:32
Alignment explanation
Indices: 5642882--5642978 Score: 97
Period size: 34 Copynumber: 2.9 Consensus size: 32
5642872 TTTGAAAGAA
**
5642882 TTTTAAAACGACATTTTTTCTGAAACACGGGAAT
1 TTTTAAAACGACA-TTTTT-TGAAACACGAAAAT
* *
5642916 TTTTAAAACAGGGA-AATTTTAGAAACACGAAAAT
1 TTTTAAAAC---GACATTTTTTGAAACACGAAAAT
5642950 TTTTAAACACGACATTTTTTGAAACACGA
1 TTTTAAA-ACGACATTTTTTGAAACACGA
5642979 TTTAAAAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
32 2 0.04
33 14 0.27
34 27 0.52
35 6 0.12
36 1 0.02
37 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (32 bp):
TTTTAAAACGACATTTTTTGAAACACGAAAAT
Found at i:5642924 original size:17 final size:17
Alignment explanation
Indices: 5642904--5642960 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
5642894 ATTTTTTCTG
5642904 AAACACGGGAATTTTTA
1 AAACACGGGAATTTTTA
*
5642921 AAACA-GGGAAATTTTA
1 AAACACGGGAATTTTTA
**
5642937 GAAACACGAAAATTTTT-
1 -AAACACGGGAATTTTTA
5642954 AAACACG
1 AAACACG
5642961 ACATTTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 17 0.50
17 10 0.29
18 7 0.21
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (17 bp):
AAACACGGGAATTTTTA
Found at i:5643106 original size:17 final size:16
Alignment explanation
Indices: 5643066--5643114 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
5643056 ATGGAGTTTT
*
5643066 TGAAACACGAGATTTG
1 TGAAACACGAAATTTG
5643082 TGAAACACGAAATTTG
1 TGAAACACGAAATTTG
5643098 TGAAAACACGTAAATTT
1 TG-AAACACG-AAATTT
5643115 TTTTTTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 17 0.57
17 7 0.23
18 6 0.20
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (16 bp):
TGAAACACGAAATTTG
Found at i:5643493 original size:7 final size:7
Alignment explanation
Indices: 5643481--5643556 Score: 63
Period size: 7 Copynumber: 11.4 Consensus size: 7
5643471 GACTCGAGCC
5643481 TTCTTTT
1 TTCTTTT
5643488 TTC-TTT
1 TTCTTTT
5643494 TTC--TT
1 TTCTTTT
*
5643499 TTCCTTT
1 TTCTTTT
*
5643506 TCCTTTT
1 TTCTTTT
5643513 TT-TTTCT
1 TTCTTT-T
*
5643520 TT-TCTT
1 TTCTTTT
5643526 TTCTTTT
1 TTCTTTT
*
5643533 TTCTGTT
1 TTCTTTT
*
5643540 TTCTGTT
1 TTCTTTT
5643547 TTCTTTT
1 TTCTTTT
5643554 TTC
1 TTC
5643557 CTTCTTTCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
5 5 0.09
6 12 0.21
7 41 0.71
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (7 bp):
TTCTTTT
Found at i:5643496 original size:6 final size:6
Alignment explanation
Indices: 5643485--5643554 Score: 67
Period size: 6 Copynumber: 11.8 Consensus size: 6
5643475 CGAGCCTTCT
* *
5643485 TTTTTC TTTTTC -TTTTC CTTTTC CTTTT- TTTTTC -TTTTC -TTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
5643529 TTTTTTC TGTTTTC TGTTTTC TTTTT
1 -TTTTTC T-TTTTC T-TTTTC TTTTT
5643555 TCCTTCTTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
5 19 0.33
6 21 0.36
7 18 0.31
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:5643500 original size:5 final size:5
Alignment explanation
Indices: 5643486--5643532 Score: 58
Period size: 5 Copynumber: 8.8 Consensus size: 5
5643476 GAGCCTTCTT
*
5643486 TTTTC TTTTTC TTTTCC TTTTCC TTTTT TTTTC TTTTC TTTTC TTTT
1 TTTTC -TTTTC TTTT-C TTTT-C TTTTC TTTTC TTTTC TTTTC TTTT
5643533 TTCTGTTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 22 0.58
6 16 0.42
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:5643541 original size:27 final size:28
Alignment explanation
Indices: 5643484--5643541 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
5643474 TCGAGCCTTC
*
5643484 TTTTTTCTTTTTCTTTTCCTTTTCCTTT
1 TTTTTTCTTTTTCTTTTCCTTTTCCTGT
* *
5643512 TTTTTTC-TTTTCTTTTCTTTTTTCTGT
1 TTTTTTCTTTTTCTTTTCCTTTTCCTGT
5643539 TTT
1 TTT
5643542 CTGTTTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (28 bp):
TTTTTTCTTTTTCTTTTCCTTTTCCTGT
Found at i:5643554 original size:27 final size:26
Alignment explanation
Indices: 5643480--5643554 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 26
5643470 CGACTCGAGC
*
5643480 CTTCTTTTTTCTTTTTCTTTTCCTTTT
1 CTTC-TTTTTCTTTTTCTTTTTCTTTT
*
5643507 CCTT-TTTTTTTCTTTTC-TTTTCTTTT
1 -CTTCTTTTTCT-TTTTCTTTTTCTTTT
5643533 -TTCTGTTTTCTGTTTTCTTTTT
1 CTTCT-TTTTCT-TTTTCTTTTT
5643555 TCCTTCTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 2 0.05
25 1 0.03
26 24 0.62
27 9 0.23
28 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.79
Consensus pattern (26 bp):
CTTCTTTTTCTTTTTCTTTTTCTTTT
Done.