Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007915.1 Hibiscus syriacus cultivar Beakdansim tig00110318_pilon, 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: 1667290
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1336096 original size:200 final size:200
Alignment explanation
Indices: 1335528--1336491 Score: 1742
Period size: 194 Copynumber: 4.9 Consensus size: 200
1335518 TATTTAAATT
*
1335528 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACTGGTA
1 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
1335593 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
66 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
*
1335658 GATCGACAC-TT-TATATATGGATCG-CACTTTATGGTTGCACCCTGTTTTCCATTCATTCAGGA
131 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
1335720 CC-AA
196 CCAAA
1335724 AA-ATCGACACAAACTAAAAATGTGTCGACACATT-TTTAGACATATTATCTCATAAAACCGGTA
1 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
*
1335787 CACTTGTACCGGTTAGATTG-AAAATTACCTAATA-TTTATACTTTTGGGTTTCGATG-TTTTGG
66 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
* **
1335849 GATCGACACTTTATATATATGGATCGATACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGA
131 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
1335914 CCAAA
196 CCAAA
*
1335919 AATATCGACACAAACTAAAAATGTGTCGACATATTATTTAGACATATTATCTCATAAAACCGGTA
1 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
1335984 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
66 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
1336049 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
131 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
1336114 CCAAA
196 CCAAA
*
1336119 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
1336184 CACTTGTACCGG-TAGATTGAAAAA-T---TAATACATTATACTTTTGGGTTTCGATG-TTTTGG
66 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
1336243 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
131 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
1336308 CCAAA
196 CCAAA
1336313 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
1 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
1336378 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
66 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
*
1336443 GATCGACACTTTATATATATGGATCGAAACTTTATGGTTGCACCCTGTT
131 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTT
1336492 GGCCATATTG
Statistics
Matches: 738, Mismatches: 15, Indels: 26
0.95 0.02 0.03
Matches are distributed among these distances:
191 15 0.02
192 23 0.03
193 27 0.04
194 236 0.32
195 76 0.10
196 34 0.05
197 49 0.07
198 15 0.02
199 61 0.08
200 202 0.27
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (200 bp):
AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
CCAAA
Found at i:1336319 original size:394 final size:393
Alignment explanation
Indices: 1335528--1336491 Score: 1751
Period size: 394 Copynumber: 2.5 Consensus size: 393
1335518 TATTTAAATT
*
1335528 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACTGGTA
1 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
1335593 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
66 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
1335658 GATCGACAC-TT-TATATATGGATCG-CACTTTATGGTTGCACCCTGTTTTCCATTCATTCAGGA
131 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCAGGA
1335720 CCAAAAATCGACACAAACTAAAAATGTGTCGACACATTTTTAGACATATTATCTCATAAAACCGG
196 CCAAAAATCGACACAAACTAAAAATGTGTCGACACATTTTTAGACATATTATCTCATAAAACCGG
*
1335785 TACACTTGTACCGGTTAGATTGAAAATTACCTAATATTTATACTTTTGGGTTTCGATGTTTTGGG
261 TACACTTGTACCGGTTAGATTGAAAA-TACCTAATAATTATACTTTTGGGTTTCGATGTTTTGGG
*
1335850 ATCGACACTTTATATATATGGATCGATACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGAC
325 ATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGAC
1335915 CAAA
390 CAAA
*
1335919 AATATCGACACAAACTAAAAATGTGTCGACATATTATTTAGACATATTATCTCATAAAACCGGTA
1 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
1335984 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
66 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
*
1336049 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
131 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCAGGA
*
1336114 CCAAAAATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTCTCTCATAAAAC
196 CC-AAAA-ATCGACACAAACTAAAAATGTGTCGACACATT-TTTAGACATATTATCTCATAAAAC
*
1336179 CGGTACACTTGTACCGG-TAGATTGAAAA-A-TTAATACATTATACTTTTGGGTTTCGATGTTTT
258 CGGTACACTTGTACCGGTTAGATTGAAAATACCTAATA-ATTATACTTTTGGGTTTCGATGTTTT
**
1336241 GGGATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
322 GGGATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTG
1336306 GACCAAA
387 GACCAAA
1336313 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
1 AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
1336378 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
66 CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
*
1336443 GATCGACACTTTATATATATGGATCGAAACTTTATGGTTGCACCCTGTT
131 GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTT
1336492 GGCCATATTG
Statistics
Matches: 555, Mismatches: 11, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
391 137 0.25
392 2 0.00
393 18 0.03
394 311 0.56
395 4 0.01
396 43 0.08
397 40 0.07
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (393 bp):
AATATCGACACAAACTAAAAATGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTA
CACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTTTGG
GATCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCAGGA
CCAAAAATCGACACAAACTAAAAATGTGTCGACACATTTTTAGACATATTATCTCATAAAACCGG
TACACTTGTACCGGTTAGATTGAAAATACCTAATAATTATACTTTTGGGTTTCGATGTTTTGGGA
TCGACACTTTATATATATGGATCGACACTTTATGGTTGCACCCTGTTGGCCATTCATTCTGGACC
AAA
Found at i:1336640 original size:19 final size:19
Alignment explanation
Indices: 1336608--1336655 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1336598 AATTATTCAC
1336608 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
1336626 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1336645 ATACAAAATTA
1 ATACAAAATTA
1336656 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1338550 original size:21 final size:20
Alignment explanation
Indices: 1338525--1338588 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
1338515 CCCCCTTATG
1338525 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGT-TATCTTCGACT
*
1338546 CTCTCAAGTTTTCTTCGACT
1 CTCTCAAGTTATCTTCGACT
* *
1338566 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAG-TTATCTTCGACT
1338587 CT
1 CT
1338589 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 17 0.44
21 22 0.56
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.42
Consensus pattern (20 bp):
CTCTCAAGTTATCTTCGACT
Found at i:1338562 original size:20 final size:20
Alignment explanation
Indices: 1338525--1338588 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1338515 CCCCCTTATG
*
1338525 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGT-TTTCTTCGACT
1338546 CTCTCAAGTTTTCTTCGACT
1 CTCTCAAGTTTTCTTCGACT
*
1338566 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTT-TCTTCGACT
1338587 CT
1 CT
1338589 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 20 0.50
21 20 0.50
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.42
Consensus pattern (20 bp):
CTCTCAAGTTTTCTTCGACT
Found at i:1340794 original size:17 final size:18
Alignment explanation
Indices: 1340772--1340814 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1340762 ATATATCCGG
1340772 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1340789 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1340809 TATCAT
1 TATCAT
1340815 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1340832 original size:20 final size:19
Alignment explanation
Indices: 1340777--1340823 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1340767 TCCGGTATCA
1340777 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1340796 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1340817 TTTTACC
1 TTTTACC
1340824 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1340980 original size:20 final size:20
Alignment explanation
Indices: 1340953--1340999 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1340943 ATCCGTAACG
1340953 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1340972 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1340993 TTTTACC
1 TTTTACC
1341000 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1341864 original size:39 final size:39
Alignment explanation
Indices: 1341810--1341896 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
1341800 TCAAGTTGTA
1341810 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
1341849 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1341888 GATTTTGAT
1 GATTTTGAT
1341897 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:1342177 original size:18 final size:18
Alignment explanation
Indices: 1342154--1342190 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1342144 CGAAATTTAT
1342154 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1342172 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1342190 A
1 A
1342191 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1342430 original size:14 final size:14
Alignment explanation
Indices: 1342411--1342443 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1342401 ATTGTTTAAT
1342411 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1342425 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1342439 TGATT
1 TGATT
1342444 CAATAGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1342514 original size:14 final size:14
Alignment explanation
Indices: 1342495--1342530 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1342485 ATTGTTTAAT
1342495 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1342509 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1342523 TGATTTGT
1 TGATTTGT
1342531 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1342654 original size:19 final size:19
Alignment explanation
Indices: 1342638--1342715 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
1342628 AAAAATGACT
1342638 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1342657 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
* *
1342671 ATCGCAATACGAAATTAAA
1 ATCGCAATGCGAAATGAAA
1342690 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1342709 ATCGCAA
1 ATCGCAA
1342716 CGAGAGAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 33 0.67
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1342781 original size:52 final size:52
Alignment explanation
Indices: 1342724--1342843 Score: 231
Period size: 52 Copynumber: 2.3 Consensus size: 52
1342714 AACGAGAGAA
1342724 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1342776 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1342828 TCCGCATTGCGATTTT
1 T-CGCATTGCGATTTT
1342844 CATGTTGGGA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 53 0.79
53 14 0.21
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1342818 original size:33 final size:33
Alignment explanation
Indices: 1342781--1342888 Score: 164
Period size: 33 Copynumber: 3.2 Consensus size: 33
1342771 TCATTTCGCA
*
1342781 TTGCGATTTTAATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1342814 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1342848 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1342881 TTGCGATT
1 TTGCGATT
1342889 GTATTTTCCG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
32 1 0.01
33 36 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1342874 original size:19 final size:19
Alignment explanation
Indices: 1342724--1342874 Score: 143
Period size: 19 Copynumber: 8.7 Consensus size: 19
1342714 AACGAGAGAA
*
1342724 TCGCATTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1342743 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1342759 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1342776 TCGCATTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1342795 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1342811 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1342828 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1342846 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1342862 TCGCATTGCGATT
1 TCGCATTGCGATT
1342875 CTCTCGTTGC
Statistics
Matches: 107, Mismatches: 9, Indels: 32
0.72 0.06 0.22
Matches are distributed among these distances:
14 23 0.21
16 16 0.15
17 11 0.10
18 3 0.03
19 42 0.39
20 12 0.11
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1345180 original size:12 final size:12
Alignment explanation
Indices: 1345163--1345187 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1345153 TCTTCGGGGA
1345163 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1345175 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1345187 C
1 C
1345188 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1345396 original size:24 final size:24
Alignment explanation
Indices: 1345362--1345408 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1345352 CTGAAACATC
*
1345362 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
*
1345386 ATCAAAGTCCGGGTATTGACCAA
1 ATCAAAATCCGGGTATTGACCAA
1345409 GACCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAT
Found at i:1345415 original size:24 final size:24
Alignment explanation
Indices: 1345364--1345415 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1345354 GAAACATCAT
* * *
1345364 CAAAATCCGTGTATTGACCAATAT
1 CAAAATCCGGGTATTGACCAAGAC
*
1345388 CAAAGTCCGGGTATTGACCAAGAC
1 CAAAATCCGGGTATTGACCAAGAC
1345412 CAAA
1 CAAA
1345416 TTTCGAATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (24 bp):
CAAAATCCGGGTATTGACCAAGAC
Found at i:1346371 original size:20 final size:20
Alignment explanation
Indices: 1346098--1346370 Score: 246
Period size: 20 Copynumber: 13.5 Consensus size: 20
1346088 AAATTTTAGT
1346098 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
* *
1346118 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTC
*
1346138 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTCTC
1346158 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
* *
1346178 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTC
* * *
1346198 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACAGATTCTC
*
1346218 GTTGCGATTTTAC-GTATTTTC
1 GTTGCGA-TTTACAG-ATTCTC
* * *
1346239 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACAGATTCTC
* *
1346259 GTTGCGATTTTTACGGATACTC
1 GTTGCGA--TTTACAGATTCTC
* * *
1346281 GTTGCGATAGTA-AGAATCGC
1 GTTGCGAT-TTACAGATTCTC
* *
1346301 GTTGCGATTTATATG-TTCGC
1 GTTGCGATTTACA-GATTCTC
* * *
1346321 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACAGATTCTC
* * *
1346341 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACAGATTCTC
1346361 GTTGCGATTT
1 GTTGCGATTT
1346371 TGGAAACTTA
Statistics
Matches: 218, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.01
20 178 0.82
21 19 0.09
22 19 0.09
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCTC
Found at i:1346982 original size:21 final size:22
Alignment explanation
Indices: 1346956--1347047 Score: 125
Period size: 22 Copynumber: 4.3 Consensus size: 22
1346946 CCAACACCCT
*
1346956 CAAGACGTC-GGAAATCCCAAA
1 CAAGACGCCGGGAAATCCCAAA
*
1346977 CAAGACGCC-AGAAATCCCAAA
1 CAAGACGCCGGGAAATCCCAAA
* *
1346998 CAAGACGCCGGGAGATCCCAAG
1 CAAGACGCCGGGAAATCCCAAA
*
1347020 CAAGACGCCGGGAGATCCCAAA
1 CAAGACGCCGGGAAATCCCAAA
1347042 CAAGAC
1 CAAGAC
1347048 CCAAAAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
21 28 0.44
22 36 0.56
ACGTcount: A:0.40, C:0.32, G:0.23, T:0.05
Consensus pattern (22 bp):
CAAGACGCCGGGAAATCCCAAA
Found at i:1347018 original size:43 final size:43
Alignment explanation
Indices: 1346956--1347047 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
1346946 CCAACACCCT
*
1346956 CAAGACGTCGGAAATCCCAAACAAGACGCC-AGAAATCCCAAA
1 CAAGACGCCGGAAATCCCAAACAAGACGCCGAGAAATCCCAAA
* * * *
1346998 CAAGACGCCGGGAGATCCCAAGCAAGACGCCGGGAGATCCCAAA
1 CAAGACGCC-GGAAATCCCAAACAAGACGCCGAGAAATCCCAAA
1347042 CAAGAC
1 CAAGAC
1347048 CCAAAAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 8 0.19
43 19 0.44
44 16 0.37
ACGTcount: A:0.40, C:0.32, G:0.23, T:0.05
Consensus pattern (43 bp):
CAAGACGCCGGAAATCCCAAACAAGACGCCGAGAAATCCCAAA
Found at i:1347500 original size:27 final size:27
Alignment explanation
Indices: 1347448--1347503 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1347438 CCGCCATCAC
*
1347448 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
* *
1347475 CACTTTGAACTTGAAAGTCTACAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
1347502 CA
1 CA
1347504 AGATCTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAGCAT
Found at i:1356977 original size:15 final size:16
Alignment explanation
Indices: 1356941--1356983 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1356931 AATTAACATC
1356941 ACATCTATTCATATTA
1 ACATCTATTCATATTA
* *
1356957 ATATCTTTTCA-ATTA
1 ACATCTATTCATATTA
*
1356972 ACATCTCTTCAT
1 ACATCTATTCAT
1356984 GAAATCATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.47
Consensus pattern (16 bp):
ACATCTATTCATATTA
Found at i:1359923 original size:18 final size:18
Alignment explanation
Indices: 1359900--1359942 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1359890 GAAATTTGTT
*
1359900 AAATAAACAAGGTAAAGA
1 AAATAAACAAGATAAAGA
*
1359918 AAATAAATAAGATAAAGA
1 AAATAAACAAGATAAAGA
*
1359936 GAATAAA
1 AAATAAA
1359943 ATAAAAGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (18 bp):
AAATAAACAAGATAAAGA
Found at i:1359974 original size:18 final size:18
Alignment explanation
Indices: 1359912--1359977 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
1359902 ATAAACAAGG
1359912 TAAAGAAAAT-AAATAAGA
1 TAAAGAAAATAAAATAA-A
*
1359930 TAAAGAGAATAAAATAAA
1 TAAAGAAAATAAAATAAA
1359948 -AGGAA-AAAATAAAATAAA
1 TA--AAGAAAATAAAATAAA
*
1359966 TAAATAAAATAA
1 TAAAGAAAATAA
1359978 GAAAAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 3 0.07
18 29 0.71
19 9 0.22
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (18 bp):
TAAAGAAAATAAAATAAA
Found at i:1360034 original size:2 final size:2
Alignment explanation
Indices: 1360027--1360063 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1360017 TGAAAAAGGA
1360027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1360064 CACATCAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1360222 original size:41 final size:39
Alignment explanation
Indices: 1360146--1360222 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
1360136 TCACTTCACC
* * *
1360146 GAAAGTGGGGGGCTTTAGTCAGAAATAAGATAAAAAGAG
1 GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
*
1360185 GAAAGTGGGAGAGACTTTAGTTAGAAATAAAACAAAAA
1 GAAAGTGGG-G-GACTTTAGTCAGAAATAAAACAAAAA
1360223 ATGGGTCCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 9 0.28
40 1 0.03
41 22 0.69
ACGTcount: A:0.48, C:0.05, G:0.29, T:0.18
Consensus pattern (39 bp):
GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
Found at i:1360334 original size:23 final size:22
Alignment explanation
Indices: 1360290--1360335 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1360280 ACAAGTTTTT
* **
1360290 AAAAATAATATAATAATGAATA
1 AAAAATAAAATAATAAAAAATA
1360312 AAAAATGAAAATAATAAAAAATA
1 AAAAAT-AAAATAATAAAAAATA
1360335 A
1 A
1360336 TATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAAATAAAATAATAAAAAATA
Found at i:1360340 original size:2 final size:2
Alignment explanation
Indices: 1360335--1360391 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1360325 ATAAAAAATA
1360335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1360377 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1360392 AAGTTATAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1360667 original size:17 final size:18
Alignment explanation
Indices: 1360634--1360669 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1360624 ATATATACGT
*
1360634 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1360652 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1360669 A
1 A
1360670 AATATCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1361083 original size:35 final size:35
Alignment explanation
Indices: 1361044--1361113 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1361034 CTAAAAAACC
1361044 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1361079 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1361114 ATTCTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:1361786 original size:106 final size:106
Alignment explanation
Indices: 1361600--1362365 Score: 914
Period size: 106 Copynumber: 7.4 Consensus size: 106
1361590 TGTATTGTTC
* * * * *
1361600 CGAGTCCAATAT-CTTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTGTTTGTTGA
1 CGAGTCCAATATCCTT-CGAT-GTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGA
* * * * * * *
1361663 CAGCCAACCGCCCCTTCGCTATGAAGTTGAGCTTGTGATGTCT
64 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
1361706 TGAGTCTAATATCATTCGATGTGAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
1361771 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCT-TCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT-TGTCT
*
1361812 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG-----G--A-----AAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
*
1361865 ACCAGCCGTTCCTTCGTTGTGAAGTTGAACTTGTG--GTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
1361904 CAAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAATTAGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
* *
1361969 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTCTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * ** ** * *
1362010 CGAGTCCAATGAGT-C--CAATAT--CCTTCGCTATTGGCTCTGAAATTGGGAGATTATTTGTTG
1 CGAGTCCAAT-A-TCCTTCGATGTGAAGTT-GAAATTGACTCTGAAATTGGGAAATTATTTGTTG
* *
1362070 ACAACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
63 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
1362114 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
*
1362179 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
1362220 CGAGTCCAACATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAGATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
*
1362285 ACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
1362326 TGAGTCCAATATCCATT--ACTGTGAAGTTGAAATTGACTCT
1 CGAGTCCAATATCC-TTCGA-TGTGAAGTTGAAATTGACTCT
1362366 AGCTAAAATC
Statistics
Matches: 568, Mismatches: 64, Indels: 56
0.83 0.09 0.08
Matches are distributed among these distances:
92 36 0.06
94 50 0.09
97 1 0.00
99 2 0.00
101 1 0.00
102 1 0.00
103 4 0.01
104 126 0.22
105 8 0.01
106 328 0.58
107 10 0.02
108 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1362351 original size:212 final size:209
Alignment explanation
Indices: 1361628--1362365 Score: 873
Period size: 198 Copynumber: 3.6 Consensus size: 209
1361618 TCGTGAAGTT
* * * * * * * * * *
1361628 GAAATTGGCTCTGGAACTGGAAAATTGTTTGTTGACAGCCAACCGCCCCTTCGCTATGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAGATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGA
* * * * * *
1361693 GCTTGTGATGTCTTGAGTCTAATATCATTCGATGTGAAGTTGAAATTGACCCTGAAATTGGGAAA
66 ACTTGTGTTGTCTTGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGACTCTGAAATTAGGAAA
* * *
1361758 TTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCTTCTCGAGTCCAAT-
130 TTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTCTCGTCCCGAGTCCAATC
*
1361822 A-TCC--T-TCGCTGT-
195 AGTCCAATAT-ACT-TC
* * *
1361834 G-AA---G-T-TGAAATTGGAAAATTATTTGTTGACAACCAGCCGTTCCTTCGTTGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAGATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGA
** *
1361893 ACTTGTG--GTCTCAAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAATTAGGAAA
66 ACTTGTGTTGTCTTGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGACTCTGAAATTAGGAAA
* *
1361956 TTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTCTCGTCTCGAGTCCAATG
130 TTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTCTCGTCCCGAGTCCAATC
*
1362021 AGTCCAATATCCTTC
195 AGTCCAATATACTTC
** * *
1362036 GCTATTGGCTCTGAAATTGGGAGATTATTTGTTGACAACCAGTCATCCCTTCGTTGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAGATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGA
*
1362101 ACTTGTGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAA
66 ACTTGTGTTGTCTTGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGACTCTGAAATTAGGAAA
* *
1362166 TTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAA-C
130 TTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTCTCGTCCCGAGTCCAATC
* * *
1362230 A-TCCTTCGATGTGAAGTT-
195 AGT-C--CAATAT--ACTTC
* *
1362248 GAAATTGGCTCTGAAATTGGGAGATTGTTTGTTGACAACTAGCCGTCCCTTCGTTGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAGATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGA
1362313 ACTTGTGTTGTCTTGAGTCCAATATCCATTAC-TGTGAAGTTGAAATTGACTCT
66 ACTTGTGTTGTCTTGAGTCCAATATCC-TT-CGTGTGAAGTTGAAATTGACTCT
1362366 AGCTAAAATC
Statistics
Matches: 468, Mismatches: 43, Indels: 36
0.86 0.08 0.07
Matches are distributed among these distances:
198 113 0.24
199 1 0.00
200 54 0.12
201 2 0.00
202 5 0.01
203 2 0.00
205 2 0.00
206 2 0.00
207 1 0.00
208 57 0.12
209 2 0.00
210 111 0.24
211 4 0.01
212 107 0.23
213 4 0.01
214 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (209 bp):
GAAATTGGCTCTGAAATTGGGAGATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGA
ACTTGTGTTGTCTTGAGTCCAATATCCTTCGTGTGAAGTTGAAATTGACTCTGAAATTAGGAAAT
TATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTCTCGTCCCGAGTCCAATCA
GTCCAATATACTTC
Found at i:1363119 original size:51 final size:51
Alignment explanation
Indices: 1363037--1363135 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 51
1363027 CTTTTTTCTC
* ** * *
1363037 TTTTTCATTTTTTTCAATTTAGGGCGTCCTTTCGGGTTTTCACCCTAAACA
1 TTTTTCATTTTTTTCAACTTAGAACGCCCTTTCAGGTTTTCACCCTAAACA
* * * *
1363088 TTTTTCCTTTTTTTCAACTTAGAATGCCCTTTCATGTTTTCATCCTAA
1 TTTTTCATTTTTTTCAACTTAGAACGCCCTTTCAGGTTTTCACCCTAA
1363136 GAGAAGTATT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.18, C:0.22, G:0.10, T:0.49
Consensus pattern (51 bp):
TTTTTCATTTTTTTCAACTTAGAACGCCCTTTCAGGTTTTCACCCTAAACA
Found at i:1373499 original size:38 final size:35
Alignment explanation
Indices: 1373456--1373530 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 35
1373446 TATATATATA
*
1373456 TATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATACAACAAA-TATT--TAAAATATAA-AAGC
1373494 TATATATATACAACAAATATTTAAAATATAAAAGC
1 TATATATATACAACAAATATTTAAAATATAAAAGC
1373529 TA
1 TA
1373531 CCCTCTCACT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
35 13 0.37
36 2 0.06
37 4 0.11
38 16 0.46
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (35 bp):
TATATATATACAACAAATATTTAAAATATAAAAGC
Found at i:1373815 original size:2 final size:2
Alignment explanation
Indices: 1373808--1373851 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1373798 ATATTTAAGA
*
1373808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1373849 AT A
1 AT A
1373852 AATAAACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1374004 original size:35 final size:36
Alignment explanation
Indices: 1373930--1374004 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
1373920 ATAATAGACT
* *
1373930 TATA-AGTAAAATATTAAAGAAATATATATATATAA
1 TATATAGTAAAAAATTAAAGAAATATATATATAAAA
*
1373965 -ATATAGTAAAAAATTAAATGAAA-ATA-ATTTAAAA
1 TATATAGTAAAAAATTAAA-GAAATATATATATAAAA
1373999 TATATA
1 TATATA
1374005 TATATATACG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
34 9 0.26
35 21 0.62
36 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (36 bp):
TATATAGTAAAAAATTAAAGAAATATATATATAAAA
Found at i:1374049 original size:17 final size:18
Alignment explanation
Indices: 1374016--1374051 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1374006 ATATATACGT
*
1374016 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1374034 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1374051 A
1 A
1374052 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1374325 original size:35 final size:35
Alignment explanation
Indices: 1374286--1374357 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
1374276 CTAAAAAATC
* * *
1374286 CTATTTTAAATTAGTATTTGAGTCTTAATTCAATT
1 CTATTTTAAACTAATATTTGAGTCCTAATTCAATT
*
1374321 CTATTTTAAACTAATATTTGAGTCCTAATTTAATT
1 CTATTTTAAACTAATATTTGAGTCCTAATTCAATT
1374356 CT
1 CT
1374358 TCTTTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (35 bp):
CTATTTTAAACTAATATTTGAGTCCTAATTCAATT
Found at i:1376159 original size:21 final size:21
Alignment explanation
Indices: 1376133--1376174 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1376123 TTTTTTACAT
1376133 TATATAGTATA-ATATATAATA
1 TATATA-TATATATATATAATA
1376154 TATATATATATATATATAATA
1 TATATATATATATATATAATA
1376175 ATTTCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATATATATATATATATAATA
Found at i:1376191 original size:2 final size:2
Alignment explanation
Indices: 1376133--1376171 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
1376123 TTTTTTACAT
1376133 TA TA TA GTA TA -A TA TA TA -A 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 TA
1376172 ATAATTTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1376291 original size:36 final size:35
Alignment explanation
Indices: 1376211--1376420 Score: 122
Period size: 38 Copynumber: 5.7 Consensus size: 35
1376201 GATATGGTAT
*
1376211 AATTTTTGAAAACATACAATATATAGTTTTTAAAAAAC
1 AATTTTTGAAAACATA-TA-ATATAG-TTTTAAAAAAC
* **
1376249 AGTTTTTGAAAACATATAATATAGTTTTCGAAAAC
1 AATTTTTGAAAACATATAATATAGTTTTAAAAAAC
* *
1376284 ATATTTTTG-AAA-ATATAATATAGTTTTTCAAAAGC
1 A-ATTTTTGAAAACATATAATATAG-TTTTAAAAAAC
* * *
1376319 GA-TTTTGAAAATATATATAATATAATTCTT-AAAAAC
1 AATTTTTG-AAA-ACATATAATATAGTT-TTAAAAAAC
* * *
1376355 ATATTATTTTGAATATATATATACATATAGTTTAAAAAAAG
1 A-A-T-TTTTGAA-A-ACATATA-ATATAGTTTTAAAAAAC
**
1376396 GGTTTTTGAAAACGTATATAATATA
1 AATTTTTGAAAAC--ATATAATATA
1376421 TATAACCTTT
Statistics
Matches: 139, Mismatches: 17, Indels: 33
0.74 0.09 0.17
Matches are distributed among these distances:
33 5 0.04
34 12 0.09
35 24 0.17
36 21 0.15
37 20 0.14
38 27 0.19
39 3 0.02
40 15 0.11
41 12 0.09
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (35 bp):
AATTTTTGAAAACATATAATATAGTTTTAAAAAAC
Found at i:1376324 original size:34 final size:32
Alignment explanation
Indices: 1376231--1376337 Score: 103
Period size: 35 Copynumber: 3.2 Consensus size: 32
1376221 AACATACAAT
*
1376231 ATATAGTTTTTAAAAAACAGTTTTTGAAAACATATA
1 ATATAGTTTTT-CAAAACA-TTTTTG-AAA-ATATA
1376267 ATATAG-TTTTCGAAAACATATTTTTGAAAATATA
1 ATATAGTTTTTC-AAAAC--ATTTTTGAAAATATA
1376301 ATATAGTTTTTCAAAAGCGA-TTTTGAAAATAT-
1 ATATAGTTTTTCAAAA-C-ATTTTTGAAAATATA
1376333 ATATA
1 ATATA
1376338 ATATAATTCT
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
32 5 0.08
33 12 0.19
34 16 0.25
35 18 0.28
36 12 0.19
37 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (32 bp):
ATATAGTTTTTCAAAACATTTTTGAAAATATA
Found at i:1376463 original size:21 final size:22
Alignment explanation
Indices: 1376428--1376472 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1376418 ATATATAACC
*
1376428 TTTGAAAATAAATTATATTGTT
1 TTTGAAAATAAATTATATAGTT
*
1376450 TTTG-AAATATATTATATAGTT
1 TTTGAAAATAAATTATATAGTT
1376471 TT
1 TT
1376473 AATACATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TTTGAAAATAAATTATATAGTT
Found at i:1376547 original size:18 final size:17
Alignment explanation
Indices: 1376522--1376555 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1376512 ATTTTACCTT
*
1376522 ATTTATTTATTTATTTA
1 ATTTATTTAATTATTTA
1376539 ATTTAATTTAATTATTT
1 ATTT-ATTTAATTATTT
1376556 TCAGGTCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTATTTAATTATTTA
Found at i:1380851 original size:24 final size:24
Alignment explanation
Indices: 1380824--1380892 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
1380814 TCAAGGAGAC
1380824 TCATCTGCTGCAAAAGCACAAACT
1 TCATCTGCTGCAAAAGCACAAACT
*
1380848 TCATCTGCTGCAAAAGCACAAGCT
1 TCATCTGCTGCAAAAGCACAAACT
*
1380872 TCATC-GGTCGCAAAAGCACAA
1 TCATCTGCT-GCAAAAGCACAA
1380893 GCTTTTGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 2 0.05
24 40 0.95
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.19
Consensus pattern (24 bp):
TCATCTGCTGCAAAAGCACAAACT
Found at i:1388500 original size:12 final size:11
Alignment explanation
Indices: 1388480--1388519 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
1388470 TTTTTTACAT
1388480 TATATAATATA
1 TATATAATATA
1388491 TATGATAATATA
1 TAT-ATAATATA
1388503 TATATAATA-A
1 TATATAATATA
1388513 TA-ATAAT
1 TATATAAT
1388520 TTCAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.18
10 3 0.11
11 9 0.32
12 11 0.39
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
TATATAATATA
Found at i:1388628 original size:38 final size:37
Alignment explanation
Indices: 1388556--1388793 Score: 203
Period size: 38 Copynumber: 6.1 Consensus size: 37
1388546 GAAGATATAG
*
1388556 TATAGTTTTTGAAAAACATGTTTTTTGAAAACATACAATA
1 TATAGTTTTT-AAAAA-ATGGTTTTTGAAAACATA-AATA
*
1388596 TATAGTTTTTAAAAAATGGTTTTTGAAAACATATATAA
1 TATAGTTTTTAAAAAATGGTTTTTGAAAACATAAAT-A
* * * *
1388634 TATAGTTTTCGAAAACAT-ATTTTTGAAAACATATA-A
1 TATAGTTTT-TAAAAAATGGTTTTTGAAAACATAAATA
*
1388670 TATAGTTTTTAAAAAATGG-TTTTGAAAACATATATAA
1 TATAGTTTTTAAAAAATGGTTTTTGAAAACATAAAT-A
**
1388707 TATAGTTTTTTAAAAACATATTATTTTGAAAACATATATATA
1 TATAG-TTTTTAAAAA-ATGGT-TTTTGAAAACATA-A-ATA
* ** *
1388749 TAGAGTTTTTTAAAAAGCGGTTTTTAAAAACGTATATAATA
1 TATAG-TTTTTAAAAAATGGTTTTTGAAAAC--ATA-AATA
1388790 TATA
1 TATA
1388794 TAACCTTTGA
Statistics
Matches: 167, Mismatches: 18, Indels: 25
0.80 0.09 0.12
Matches are distributed among these distances:
35 21 0.13
36 10 0.06
37 8 0.05
38 53 0.32
39 13 0.08
40 19 0.11
41 20 0.12
42 21 0.13
43 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (37 bp):
TATAGTTTTTAAAAAATGGTTTTTGAAAACATAAATA
Found at i:1388666 original size:76 final size:75
Alignment explanation
Indices: 1388550--1388791 Score: 299
Period size: 74 Copynumber: 3.1 Consensus size: 75
1388540 GTTTTTGAAG
* *
1388550 ATATAGTATAGTTTTTGAAAAACATGTTTTTTGAAAACATACAATATATAGTTTTTAAAAAATGG
1 ATATAATATAGTTTTTG-AAAACAT-ATTTTTGAAAACATA-AATATATAGTTTTTAAAAAATGG
1388615 TTTTTGAAAACAT
63 TTTTTGAAAACAT
* *
1388628 ATATAATATAGTTTTCGAAAACATATTTTTGAAAACATATA-ATATAGTTTTTAAAAAATGG-TT
1 ATATAATATAGTTTTTGAAAACATATTTTTGAAAACATAAATATATAGTTTTTAAAAAATGGTTT
1388691 TTGAAAACAT
66 TTGAAAACAT
* * *
1388701 ATATAATATAGTTTTTTAAAAACATATTATTTTGAAAACATATATATATAGAGTTTTTTAAAAAG
1 ATATAATATAG-TTTTTGAAAACATA-T-TTTTGAAAACATA-A-ATATATAG-TTTTTAAAAAA
* * *
1388766 CGGTTTTTAAAAACGT
60 TGGTTTTTGAAAACAT
1388782 ATATAATATA
1 ATATAATATA
1388792 TATAACCTTT
Statistics
Matches: 144, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
73 23 0.16
74 32 0.22
75 2 0.01
76 27 0.19
77 7 0.05
78 16 0.11
79 5 0.03
80 12 0.08
81 20 0.14
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (75 bp):
ATATAATATAGTTTTTGAAAACATATTTTTGAAAACATAAATATATAGTTTTTAAAAAATGGTTT
TTGAAAACAT
Found at i:1388791 original size:41 final size:38
Alignment explanation
Indices: 1388550--1388791 Score: 215
Period size: 37 Copynumber: 6.3 Consensus size: 38
1388540 GTTTTTGAAG
* * *
1388550 ATATAGTATAGTTTTTGAAAAACATGTTTTTTGAAAACAT
1 ATATAATATAGTTTTTTAAAAAC--GGTTTTTGAAAACAT
* * *
1388590 ACA-ATATATAGTTTTTAAAAAATGGTTTTTGAAAACAT
1 ATATA-ATATAGTTTTTTAAAAACGGTTTTTGAAAACAT
** **
1388628 ATATAATATAG-TTTTCGAAAACATATTTTTGAAAAC--
1 ATATAATATAGTTTTTTAAAAAC-GGTTTTTGAAAACAT
* *
1388664 ATATAATATAGTTTTTAAAAAATGG-TTTTGAAAACAT
1 ATATAATATAGTTTTTTAAAAACGGTTTTTGAAAACAT
**
1388701 ATATAATATAGTTTTTTAAAAACATATTATTTTGAAAACAT
1 ATATAATATAGTTTTTTAAAAAC--GGT-TTTTGAAAACAT
* * *
1388742 ATATATATAGAGTTTTTTAAAAAGCGGTTTTTAAAAACGT
1 ATATA-ATATAGTTTTTTAAAAA-CGGTTTTTGAAAACAT
1388782 ATATAATATA
1 ATATAATATA
1388792 TATAACCTTT
Statistics
Matches: 164, Mismatches: 26, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
35 10 0.06
36 11 0.07
37 37 0.23
38 33 0.20
39 6 0.04
40 32 0.20
41 18 0.11
42 16 0.10
43 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (38 bp):
ATATAATATAGTTTTTTAAAAACGGTTTTTGAAAACAT
Found at i:1388863 original size:6 final size:5
Alignment explanation
Indices: 1388836--1388891 Score: 67
Period size: 5 Copynumber: 10.2 Consensus size: 5
1388826 TTAATACATA
1388836 TATTT TATTT TCCATTTT TATCTT TATCTT TATTT TATTT TATTT TATTT
1 TATTT TATTT T--A-TTT TAT-TT TAT-TT TATTT TATTT TATTT TATTT
1388886 TATTT T
1 TATTT T
1388892 CATGTCCAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
5 30 0.64
6 12 0.26
7 1 0.02
8 4 0.09
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:1391926 original size:22 final size:21
Alignment explanation
Indices: 1391899--1391950 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1391889 CGCAACGCGA
*
1391899 TTCTGACTATAGCATTGCGATT
1 TTCTGAAT-TAGCATTGCGATT
* *
1391921 TTCTGAATTCGCGTTGCGATT
1 TTCTGAATTAGCATTGCGATT
*
1391942 TTCCGAATT
1 TTCTGAATT
1391951 CACAATGCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (21 bp):
TTCTGAATTAGCATTGCGATT
Found at i:1391959 original size:21 final size:21
Alignment explanation
Indices: 1391914--1391962 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1391904 ACTATAGCAT
* * **
1391914 TGCGATTTTCTGAATTCGCGT
1 TGCGATTTTCCGAATTCACAA
1391935 TGCGATTTTCCGAATTCACAA
1 TGCGATTTTCCGAATTCACAA
1391956 TGCGATT
1 TGCGATT
1391963 ATGTATCGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (21 bp):
TGCGATTTTCCGAATTCACAA
Found at i:1391991 original size:20 final size:20
Alignment explanation
Indices: 1391957--1392034 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
1391947 AATTCACAAT
*
1391957 GCGATTATG--TATCGCAAT
1 GCGATTATGACTATCGCAAC
1391975 GCGATTATGACTATCGCAAC
1 GCGATTATGACTATCGCAAC
*
1391995 GCGATTCTGACTATCGCAAC
1 GCGATTATGACTATCGCAAC
* *
1392015 GAGATTCTGACTATCGCAAC
1 GCGATTATGACTATCGCAAC
1392035 ACTGAATTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
18 9 0.16
20 46 0.84
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (20 bp):
GCGATTATGACTATCGCAAC
Found at i:1392882 original size:24 final size:24
Alignment explanation
Indices: 1392855--1392908 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1392845 GTATTCGAAA
1392855 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1392879 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1392903 TTTGAT
1 TTTGAT
1392909 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1395390 original size:20 final size:20
Alignment explanation
Indices: 1395365--1395575 Score: 194
Period size: 20 Copynumber: 11.2 Consensus size: 20
1395355 TTACACATTC
*
1395365 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1395385 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1395405 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1395425 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
1395444 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1395459 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
1395479 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
* *
1395499 ATTTGACTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
** *
1395519 ATTCAACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1395539 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
1395553 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1395573 ATT
1 ATT
1395576 GAATTTCTCG
Statistics
Matches: 159, Mismatches: 20, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
14 19 0.12
15 3 0.02
16 1 0.01
18 1 0.01
19 3 0.02
20 132 0.83
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1395494 original size:74 final size:74
Alignment explanation
Indices: 1395373--1395514 Score: 239
Period size: 74 Copynumber: 1.9 Consensus size: 74
1395363 TCATTTGAAT
*
1395373 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
1395438 AACTCAAAA
66 AACTCAAAA
* * * *
1395447 ATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
1395512 AAC
66 AAC
1395515 GGGTATTCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
AACTCAAAA
Found at i:1395530 original size:94 final size:94
Alignment explanation
Indices: 1395365--1395575 Score: 280
Period size: 94 Copynumber: 2.2 Consensus size: 94
1395355 TTACACATTC
* **
1395365 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTCA
* *
1395430 ATTATCGCAACTCA-AAAATCGCAACGCGA
66 ACTATCGCAAC-CAGAAAATCGCAAAGCGA
* * * * * *
1395459 ATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGGGTATTCA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTCA
* *
1395524 ACTATCGCAACGAGAAAATCGCAAAGCGT
66 ACTATCGCAACCAGAAAATCGCAAAGCGA
*
1395553 ATTAGACTATCGCAACGCGAATT
1 ATTTGACTATCGCAACGCGAATT
1395576 GAATTTCTCG
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
93 1 0.01
94 100 0.99
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (94 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTCA
ACTATCGCAACCAGAAAATCGCAAAGCGA
Found at i:1395749 original size:29 final size:28
Alignment explanation
Indices: 1395715--1395769 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
1395705 ATAAGAATTA
*
1395715 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAAT-TTAAACAAATCAACT
**
1395744 TTTACAAATCAATTTTTACAAATCAA
1 TTTACAAATCAATTTAAACAAATCAA
1395770 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (28 bp):
TTTACAAATCAATTTAAACAAATCAACT
Found at i:1395770 original size:14 final size:14
Alignment explanation
Indices: 1395710--1395771 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
1395700 CACAAATAAG
*
1395710 AATTATTTACACATC
1 AATT-TTTACAAATC
**
1395725 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
1395740 AACTTTTACAAATC
1 AATTTTTACAAATC
1395754 AATTTTTACAAATC
1 AATTTTTACAAATC
1395768 AATT
1 AATT
1395772 AAACAAGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:1397225 original size:21 final size:21
Alignment explanation
Indices: 1397170--1397276 Score: 90
Period size: 21 Copynumber: 5.1 Consensus size: 21
1397160 TCTAGAATGT
* *
1397170 TGGGAGGGACCTCTTCAACGA
1 TGGGAGGGGCCTCTTGAACGA
** *
1397191 TGACAGTGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
* **
1397212 TGGGAGGGGACTCTTGAGGGA
1 TGGGAGGGGCCTCTTGAACGA
**
1397233 TGATAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
**
1397254 TAGGG-GATGCCTCTTGAACGA
1 T-GGGAGGGGCCTCTTGAACGA
1397275 TG
1 TG
1397277 ACAGGTGAGT
Statistics
Matches: 65, Mismatches: 20, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTGAACGA
Found at i:1397268 original size:42 final size:42
Alignment explanation
Indices: 1397189--1397281 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1397179 CCTCTTCAAC
* *
1397189 GATGACAGTGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * * **
1397231 GATGATAGGGGCCTCTTGAACGATAGGG-GATGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
1397273 GATGACAGG
1 GATGACAGG
1397282 TGAGTCGGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1397797 original size:18 final size:18
Alignment explanation
Indices: 1397767--1397833 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 18
1397757 GAAACTTAAA
*
1397767 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
*
1397785 ATTGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
1397805 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
*
1397825 AACGCAACG
1 ATCGCAACG
1397834 AGAGAATCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 11 0.27
20 30 0.73
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:1397803 original size:20 final size:20
Alignment explanation
Indices: 1397778--1397833 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1397768 TCGCAACACG
*
1397778 AATGACTATTGCAACGCGAA
1 AATGACTATCGCAACGCGAA
1397798 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
** *
1397818 TTTGACTAACGCAACG
1 AATGACTATCGCAACG
1397834 AGAGAATCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:1397903 original size:20 final size:20
Alignment explanation
Indices: 1397878--1397923 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1397868 GATTCTTTCA
1397878 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
**
1397898 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCG
1397918 TTGCGA
1 TTGCGA
1397924 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:1398093 original size:18 final size:18
Alignment explanation
Indices: 1398070--1398119 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1398060 TTTACTAAGC
*
1398070 AATCTAATTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
1398088 AATCTAAGTAAAATGGTT
1 AATCTAAGTGAAATGGTT
1398106 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
1398120 TACGAGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:1399873 original size:20 final size:20
Alignment explanation
Indices: 1399850--1399917 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1399840 TCTGAAACTT
1399850 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
1399870 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
1399890 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
1399909 AAAATCGCA
1 AAAATCGCA
1399918 TTGCGATTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 7 0.17
20 33 0.82
ACGTcount: A:0.50, C:0.22, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1400511 original size:20 final size:20
Alignment explanation
Indices: 1400482--1400534 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1400472 CGCTTTGAAA
1400482 ATCGCATTGCGATAGTCAGC
1 ATCGCATTGCGATAGTCAGC
* *
1400502 ATCGCGTTGCGATAGTCA-T
1 ATCGCATTGCGATAGTCAGC
1400521 ATTCGCATTGCGAT
1 A-TCGCATTGCGAT
1400535 TTACATATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGC
Found at i:1400574 original size:21 final size:21
Alignment explanation
Indices: 1400550--1400595 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1400540 TATTCGCATT
*
1400550 GCGAATTCGGAGAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
1400571 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
1400592 GCGA
1 GCGA
1400596 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:1402443 original size:170 final size:175
Alignment explanation
Indices: 1402260--1402616 Score: 539
Period size: 170 Copynumber: 2.1 Consensus size: 175
1402250 ATAAAAATTA
* * *
1402260 AATATTTTTTAATT-CAAAAAACAGTTT-CTAATTAATTTAAATAATATCTAATTATAAAATATA
1 AATA-TTTTTAATTAAAAAAAACA-TTTAC-AATTAATTTAAATAATATATAATTATAAAATAAA
*
1402323 AATTTTATATAAATTTTTTAATTAA-T-A-ATTGATTTAGGTTTAAAAGTTATTGGATCTTAAAT
63 AAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAAT
* *
1402385 TATTAATTGGATTTTAAAAGGTTTGGGCTGAGC-C-TATATTATATAT
128 TATTAATTAGATTTTAAAAGATTTGGGCTGAGCTCATATATTATATAT
*
1402431 AATATTTTTAATTAAAAAAAACATTTACAATTAATTTAAATTATATATAATTATAAAATAAAAAA
1 AATATTTTTAATTAAAAAAAACATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAA
1402496 TTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTAT
66 TTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTAT
* * *
1402561 TAATTAGATTTTAAATGATTTGGGTTGAGCTCATATGTTATATAT
131 TAATTAGATTTTAAAAGATTTGGGCTGAGCTCATATATTATATAT
*
1402606 AATATATTTAA
1 AATATTTTTAA
1402617 AATTTAAAAT
Statistics
Matches: 168, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
170 67 0.40
171 14 0.08
172 1 0.01
173 64 0.38
174 1 0.01
175 21 0.12
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (175 bp):
AATATTTTTAATTAAAAAAAACATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAA
TTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTAT
TAATTAGATTTTAAAAGATTTGGGCTGAGCTCATATATTATATAT
Found at i:1408517 original size:16 final size:16
Alignment explanation
Indices: 1408478--1408518 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1408468 TTTGCTTTTG
*
1408478 CCATCCCACCCCAACC
1 CCATCCCCCCCCAACC
**
1408494 CCCCCCCCCCCCAACC
1 CCATCCCCCCCCAACC
1408510 CCATCCCCC
1 CCATCCCCC
1408519 AAATTGGTAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.78, G:0.00, T:0.05
Consensus pattern (16 bp):
CCATCCCCCCCCAACC
Found at i:1409009 original size:3 final size:3
Alignment explanation
Indices: 1409003--1409078 Score: 77
Period size: 3 Copynumber: 25.0 Consensus size: 3
1408993 AATATAATAT
*
1409003 TTA TTA TTA TTCA -TA TTA TTA -AA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1409047 TTA TTA TGT- TTA TTTA TTTG TTA TTA TTA TTA
1 TTA TTA T-TA TTA -TTA -TTA TTA TTA TTA TTA
1409079 ATACAAGTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.05
3 52 0.83
4 8 0.13
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1410548 original size:29 final size:28
Alignment explanation
Indices: 1410515--1410587 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
1410505 CTTTTACTTA
*
1410515 TTTTTTTTACTATTTAATCCTTTAAGAT-
1 TTTTTTTTACTATTTAATCCCTTAA-ATG
* *
1410543 TCTTTTTTACTGTTTTAATCCCTTAAATG
1 TTTTTTTTACT-ATTTAATCCCTTAAATG
1410572 TTTGTTTTTACTATTT
1 TTT-TTTTTACTATTT
1410588 TAGACCTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 12 0.32
29 17 0.46
30 8 0.22
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.62
Consensus pattern (28 bp):
TTTTTTTTACTATTTAATCCCTTAAATG
Found at i:1410608 original size:30 final size:30
Alignment explanation
Indices: 1410518--1410678 Score: 125
Period size: 30 Copynumber: 5.4 Consensus size: 30
1410508 TTACTTATTT
*
1410518 TTTTTACTA-TTTA-ATCCTTTAAGATTCT-
1 TTTTTACTATTTTAGA-CCTTTAAGTTTCTG
* * *
1410546 TTTTTACTGTTTTA-ATCCCTTAAATGTT-TG
1 TTTTTACTATTTTAGA-CCTTTAAGT-TTCTG
*
1410576 TTTTTACTATTTTAGACCTTTAAGTTTATG
1 TTTTTACTATTTTAGACCTTTAAGTTTCTG
* * *
1410606 TTTATGCTATTTTAGCCCTTTAAGTTTCTG
1 TTTTTACTATTTTAGACCTTTAAGTTTCTG
** ** * *
1410636 TTTTTGTTATTTTAGTGCTTTAAATTCCTG
1 TTTTTACTATTTTAGACCTTTAAGTTTCTG
*
1410666 TTTGTACTATTTT
1 TTTTTACTATTTT
1410679 GGTCCTTTGG
Statistics
Matches: 108, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
28 8 0.07
29 15 0.14
30 84 0.78
31 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (30 bp):
TTTTTACTATTTTAGACCTTTAAGTTTCTG
Found at i:1412555 original size:29 final size:29
Alignment explanation
Indices: 1412522--1412579 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1412512 ATGTCTTACA
*
1412522 TGTACTAAATAATTTCTTTTCTTTTGTTT
1 TGTACTAAATAATTTCTTTTCTATTGTTT
* *
1412551 TGTACTAATTTATTTCTTTTCTATTGTTT
1 TGTACTAAATAATTTCTTTTCTATTGTTT
1412580 GTATCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.10, G:0.07, T:0.64
Consensus pattern (29 bp):
TGTACTAAATAATTTCTTTTCTATTGTTT
Found at i:1417399 original size:23 final size:22
Alignment explanation
Indices: 1417359--1417436 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
1417349 GAGATATTTT
*
1417359 ATACCCCTATG-ATGGGTATCA
1 ATACCCCTATGAAAGGGTATCA
* * *
1417380 ATACCTCTTATGAACGGGTATCG
1 ATACC-CCTATGAAAGGGTATCA
1417403 ATACCCCTATGAAAGGGTATCA
1 ATACCCCTATGAAAGGGTATCA
1417425 ATACCCC-ATGAA
1 ATACCCCTATGAA
1417437 GGCTCAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.20
22 26 0.53
23 13 0.27
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (22 bp):
ATACCCCTATGAAAGGGTATCA
Found at i:1418175 original size:36 final size:35
Alignment explanation
Indices: 1418116--1418209 Score: 118
Period size: 37 Copynumber: 2.6 Consensus size: 35
1418106 CAAAACAAAG
* * **
1418116 AGAAAAGAAGCAAGGAAAAAAACAAAGAG-CGAAA
1 AGAAAAAAAGCAAAGAAAAAAACAAAGAGAAAAAA
1418150 AGAAAAAAAGCAAAGAAAATGAAACAAAGAGAAAAAA
1 AGAAAAAAAGCAAAGAAAA--AAACAAAGAGAAAAAA
1418187 AGAAAAAAAGCAAAGAAAGAAAA
1 AGAAAAAAAGCAAAGAAA-AAAA
1418210 AACAAAGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
34 17 0.33
36 13 0.25
37 21 0.40
38 1 0.02
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.01
Consensus pattern (35 bp):
AGAAAAAAAGCAAAGAAAAAAACAAAGAGAAAAAA
Found at i:1418179 original size:14 final size:13
Alignment explanation
Indices: 1418148--1418233 Score: 65
Period size: 13 Copynumber: 6.7 Consensus size: 13
1418138 CAAAGAGCGA
1418148 AAAGAAAAAAAGC
1 AAAGAAAAAAAGC
1418161 AAAGAAAATGAAA-C
1 AAAGAAAA--AAAGC
*
1418175 AAAG-AGAAAA--
1 AAAGAAAAAAAGC
1418185 AAAGAAAAAAAGC
1 AAAGAAAAAAAGC
*
1418198 AAAGAAAGAAAAAAC
1 AAAG-AA-AAAAAGC
* *
1418213 AAAG-AAAATAGT
1 AAAGAAAAAAAGC
1418225 AAAGAAAAA
1 AAAGAAAAA
1418234 GGATACAAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.07
11 8 0.14
12 8 0.14
13 19 0.32
14 7 0.12
15 13 0.22
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAAAGC
Found at i:1418192 original size:8 final size:8
Alignment explanation
Indices: 1418147--1418211 Score: 67
Period size: 8 Copynumber: 7.4 Consensus size: 8
1418137 ACAAAGAGCG
1418147 AAAAGAAA
1 AAAAGAAA
1418155 AAAAGCAAA
1 AAAAG-AAA
1418164 GAAAATGAAA
1 -AAAA-GAAA
1418174 CAAAGAGAAA
1 -AAA-AGAAA
1418184 AAAAGAAA
1 AAAAGAAA
1418192 AAAAGCAAA
1 AAAAG-AAA
*
1418201 GAAAGAAA
1 AAAAGAAA
1418209 AAA
1 AAA
1418212 CAAAGAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
8 20 0.41
9 13 0.27
10 14 0.29
11 2 0.04
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAGAAA
Found at i:1418209 original size:23 final size:23
Alignment explanation
Indices: 1418161--1418219 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 23
1418151 GAAAAAAAGC
1418161 AAAGAAAATGAAACAAAGAGAAAA
1 AAAGAAAA-GAAACAAAGAGAAAA
1418185 AAAGAAAA-AAAGCAAAGA-AAGAA
1 AAAGAAAAGAAA-CAAAGAGAA-AA
1418208 AAA-ACAAAGAAA
1 AAAGA-AAAGAAA
1418220 ATAGTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 6 0.19
23 14 0.45
24 11 0.35
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (23 bp):
AAAGAAAAGAAACAAAGAGAAAA
Found at i:1418215 original size:15 final size:17
Alignment explanation
Indices: 1418148--1418219 Score: 78
Period size: 17 Copynumber: 4.2 Consensus size: 17
1418138 CAAAGAGCGA
1418148 AAAGAAAAAAAGCAAAG
1 AAAGAAAAAAAGCAAAG
*
1418165 AAAATGAAACAAAGAG-AAAA
1 -AAA-GAAA-AAA-AGCAAAG
1418185 AAAGAAAAAAAGCAAAG
1 AAAGAAAAAAAGCAAAG
1418202 AAAG-AAAAAA-CAAAG
1 AAAGAAAAAAAGCAAAG
1418217 AAA
1 AAA
1418220 ATAGTAAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
15 8 0.17
16 8 0.17
17 10 0.21
18 7 0.15
19 7 0.15
20 6 0.12
21 2 0.04
ACGTcount: A:0.78, C:0.06, G:0.15, T:0.01
Consensus pattern (17 bp):
AAAGAAAAAAAGCAAAG
Found at i:1418219 original size:36 final size:38
Alignment explanation
Indices: 1418132--1418220 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 38
1418122 GAAGCAAGGA
**
1418132 AAAAAACAAAGAGCGAAAAGAAAAAAAGCAAAGAAAATG
1 AAAAAACAAAGA-AAAAAAGAAAAAAAGCAAAGAAAATG
* *
1418171 AAACAA-AGAGAAAAAAAGAAAAAAAGCAAAG-AAA-G
1 AAAAAACAAAGAAAAAAAGAAAAAAAGCAAAGAAAATG
1418206 AAAAAACAAAGAAAA
1 AAAAAACAAAGAAAA
1418221 TAGTAAAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
35 6 0.14
36 10 0.23
37 18 0.42
38 4 0.09
39 5 0.12
ACGTcount: A:0.76, C:0.07, G:0.16, T:0.01
Consensus pattern (38 bp):
AAAAAACAAAGAAAAAAAGAAAAAAAGCAAAGAAAATG
Found at i:1418228 original size:27 final size:26
Alignment explanation
Indices: 1418148--1418231 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 26
1418138 CAAAGAGCGA
*
1418148 AAAGAAAAAAAGCAAAGAAAAT-GAAAC
1 AAAG-AAAAAA-CAAAGAAAATAGAAAG
* *
1418175 AAAGAGAAAA-AAAGAAAAAAAGCAAAG
1 AAAGAAAAAACAAAG-AAAATAG-AAAG
1418202 AAAGAAAAAACAAAGAAAATAGTAAAG
1 AAAGAAAAAACAAAGAAAATAG-AAAG
1418229 AAA
1 AAA
1418232 AAGGATACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
24 4 0.09
25 4 0.09
26 6 0.13
27 29 0.62
28 4 0.09
ACGTcount: A:0.76, C:0.05, G:0.15, T:0.04
Consensus pattern (26 bp):
AAAGAAAAAACAAAGAAAATAGAAAG
Found at i:1419891 original size:2 final size:2
Alignment explanation
Indices: 1419884--1419943 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1419874 TAAATATTGG
1419884 TA TA 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 TA TA
1419926 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1419944 AATGATTATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1420587 original size:20 final size:19
Alignment explanation
Indices: 1420537--1420592 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1420527 AAACCATAAT
1420537 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
1420556 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
1420576 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
1420593 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:1420777 original size:22 final size:21
Alignment explanation
Indices: 1420750--1420791 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1420740 AATGTATGTA
*
1420750 TAATATAATAAATACTAAATAG
1 TAATATAAT-AATAATAAATAG
1420772 TAATATAATAATAATAAATA
1 TAATATAATAATAATAAATA
1420792 AATGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
TAATATAATAATAATAAATAG
Found at i:1420855 original size:25 final size:25
Alignment explanation
Indices: 1420798--1420858 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 25
1420788 AATAAATGAA
1420798 AAATAAATATACATAGAATATAACT
1 AAATAAATATACATAGAATATAACT
* *
1420823 AAAAAAATAGTAATCATAGAAATATAAAT
1 AAATAAATA-T-A-CATAG-AATATAACT
1420852 AAATAAA
1 AAATAAA
1420859 GTAAGAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 8 0.28
26 1 0.03
27 1 0.03
28 5 0.17
29 14 0.48
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (25 bp):
AAATAAATATACATAGAATATAACT
Found at i:1422410 original size:106 final size:106
Alignment explanation
Indices: 1422229--1423799 Score: 2420
Period size: 106 Copynumber: 14.9 Consensus size: 106
1422219 AGCTTGTTTC
* * **
1422229 GAGTCCAATATCCTCCG-TGTGAAGTT-AAATTGGCTCTGGAATCAGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
1422292 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1422333 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
1422398 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCATTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1422439 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGG-AA--GTTTGTTGA-AA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1422500 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1422541 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
1422606 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1422647 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1422712 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1422753 GAGTCCAATATCTTTCGCTGTAAAGTTGAAATTGGCTCCGAAATTGGGAAATTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
1422818 CCTGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1422859 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1422924 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1422965 AAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1423030 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1423071 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
1423136 CCAGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1423177 GAGTCCAATA-CACTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 GAGTCCAATATC-CTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * *
1423241 ACCAGCGGTCCCATCATCGTTAAGTTGAACTTGCGTTGTATG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1423283 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1423348 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1423389 GAGTACAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
1423454 CCGGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1423495 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1423560 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTAC-G
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT-CTG
* * *
1423601 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
1423666 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1423707 GAGTCCAATATCCTTCGCCGTGAAATTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1423772 CCAGCCGTCCCTTCGTTGTGAAGTTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAA
1423800 ATCCACTCTC
Statistics
Matches: 1343, Mismatches: 114, Indels: 18
0.91 0.08 0.01
Matches are distributed among these distances:
102 85 0.06
103 11 0.01
104 15 0.01
105 22 0.02
106 1208 0.90
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1425196 original size:8 final size:8
Alignment explanation
Indices: 1425183--1425236 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
1425173 TTTTTGTCCC
1425183 TTTTTCTT
1 TTTTTCTT
1425191 TTTTTCTT
1 TTTTTCTT
*
1425199 TTTCTTTTT
1 TTT-TTCTT
1425208 TTTCTTCTT
1 TTT-TTCTT
*
1425217 TTTTGCTT
1 TTTTTCTT
*
1425225 CTTTTCTT
1 TTTTTCTT
1425233 TTTT
1 TTTT
1425237 GTTTTTGCCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
8 24 0.62
9 15 0.38
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1425201 original size:14 final size:14
Alignment explanation
Indices: 1425182--1425236 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 14
1425172 TTTTTTGTCC
1425182 CTTTTTCTTTTTTT
1 CTTTTTCTTTTTTT
1425196 CTTTTTC-TTTTTT
1 CTTTTTCTTTTTTT
* *
1425209 -TTCTTCTTTTTTG
1 CTTTTTCTTTTTTT
1425222 CTTCTTTTCTTTTTT
1 C-T-TTTTCTTTTTT
1425237 GTTTTTGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 5 0.15
13 11 0.32
14 7 0.21
15 1 0.03
16 10 0.29
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (14 bp):
CTTTTTCTTTTTTT
Found at i:1425206 original size:12 final size:12
Alignment explanation
Indices: 1425183--1425234 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 12
1425173 TTTTTGTCCC
1425183 TTTTTCTT-TTT
1 TTTTTCTTCTTT
1425194 TTCTTT-TTCTTT
1 TT-TTTCTTCTTT
1425206 TTTTTCTTC-TT
1 TTTTTCTTCTTT
*
1425217 TTTTGCTTCTTT
1 TTTTTCTTCTTT
1425229 TCTTTT
1 T-TTTT
1425235 TTGTTTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 17 0.50
12 14 0.41
13 3 0.09
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:1425226 original size:23 final size:23
Alignment explanation
Indices: 1425183--1425242 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
1425173 TTTTTGTCCC
**
1425183 TTTTTCTTTTTTTCTTTTTCTTT
1 TTTTTCTTTTTTTCTGCTTCTTT
1425206 TTTTTCTTCTTTTT-TGCTTCTTT
1 TTTTTCTT-TTTTTCTGCTTCTTT
1425229 TCTTTT-TTGTTTTT
1 T-TTTTCTT-TTTTT
1425243 GCCCTTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 23 0.72
24 9 0.28
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (23 bp):
TTTTTCTTTTTTTCTGCTTCTTT
Found at i:1426910 original size:15 final size:15
Alignment explanation
Indices: 1426890--1426921 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1426880 GATCAGCCAT
*
1426890 TTGGATTCTCAGGAG
1 TTGGATTCTCAGAAG
1426905 TTGGATTCTCAGAAG
1 TTGGATTCTCAGAAG
1426920 TT
1 TT
1426922 ATCTTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (15 bp):
TTGGATTCTCAGAAG
Found at i:1429704 original size:12 final size:11
Alignment explanation
Indices: 1429687--1429798 Score: 63
Period size: 11 Copynumber: 10.0 Consensus size: 11
1429677 ATATATGAAA
1429687 ATAAATAATAGT
1 ATAAATAATA-T
1429699 ATAAATAA-AT
1 ATAAATAATAT
*
1429709 AATAAAAAATAT
1 -ATAAATAATAT
*
1429721 ATAAAAAATAT
1 ATAAATAATAT
* *
1429732 AAAAAT-GTAT
1 ATAAATAATAT
*
1429742 ATATAATAAAAT
1 ATA-AATAATAT
*
1429754 ACTAAATAGTA-
1 A-TAAATAATAT
*
1429765 AT-AATAATAA
1 ATAAATAATAT
1429775 ATAAA-AATAAT
1 ATAAATAAT-AT
1429786 ATACATATAATAT
1 ATA-A-ATAATAT
1429799 TAACTAAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
9 6 0.08
10 12 0.15
11 33 0.42
12 19 0.24
13 5 0.06
14 3 0.04
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (11 bp):
ATAAATAATAT
Found at i:1429719 original size:23 final size:23
Alignment explanation
Indices: 1429686--1429814 Score: 76
Period size: 22 Copynumber: 5.6 Consensus size: 23
1429676 AATATATGAA
*
1429686 AATAAATAATAGTATAAATAAAT
1 AATAAAAAATAGTATAAATAAAT
1429709 AATAAAAAATA-TATAAA-AAAT
1 AATAAAAAATAGTATAAATAAAT
* *
1429730 -AT-AAAAAT-GTATATATAATAA
1 AATAAAAAATAGTATAAATAA-AT
**
1429751 AATACTAAATAGTA-ATAAT-AAT
1 AATAAAAAATAGTATA-AATAAAT
*
1429773 AA-ATAAAAATAATATACATATAATATT
1 AATA-AAAAATAGTATA-A-ATAA-A-T
1429800 AACTAAAAAATAGTA
1 AA-TAAAAAATAGTA
1429815 ATCATAGAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
19 11 0.14
20 4 0.05
21 6 0.08
22 18 0.23
23 18 0.23
24 7 0.09
25 1 0.01
26 1 0.01
27 3 0.04
28 9 0.11
29 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.29
Consensus pattern (23 bp):
AATAAAAAATAGTATAAATAAAT
Found at i:1429726 original size:10 final size:10
Alignment explanation
Indices: 1429674--1429742 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
1429664 CAAAGAAACT
*
1429674 AAAATATATG
1 AAAATATATA
*
1429684 AAAATAAATA
1 AAAATATATA
* *
1429694 ATAGTATA-A
1 AAAATATATA
1429703 ATAAATA-ATAA
1 A-AAATATAT-A
1429714 AAAATATATA
1 AAAATATATA
1429724 AAAA-ATATA
1 AAAATATATA
*
1429733 AAAATGTATA
1 AAAATATATA
1429743 TATAATAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
9 12 0.26
10 30 0.65
11 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (10 bp):
AAAATATATA
Found at i:1429759 original size:25 final size:23
Alignment explanation
Indices: 1429725--1429775 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
1429715 AAATATATAA
1429725 AAAATATAAAAATGTATATATAAT
1 AAAATATAAAAA-GTATATATAAT
*
1429749 AAAATACTAAATAGTA-ATAATAAT
1 AAAATA-TAAAAAGTATAT-ATAAT
1429773 AAA
1 AAA
1429776 TAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.08
24 17 0.71
25 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (23 bp):
AAAATATAAAAAGTATATATAAT
Found at i:1430001 original size:21 final size:21
Alignment explanation
Indices: 1429969--1430016 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1429959 ACGCAAAGAA
*
1429969 AAATGAAAAAAAAAGTATAA-T
1 AAAT-AAAAAAAAAATATAATT
1429990 AAATAAATAAAAAAATATAATT
1 AAATAAA-AAAAAAATATAATT
1430012 AAATA
1 AAATA
1430017 TATACAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 15 0.62
22 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (21 bp):
AAATAAAAAAAAAATATAATT
Found at i:1430762 original size:21 final size:21
Alignment explanation
Indices: 1430710--1430772 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1430700 AGTCGAGGGT
1430710 TCTACGAGGTCCTTCGGGACA
1 TCTACGAGGTCCTTCGGGACA
* * *
1430731 TATATGTGGTCCTTCGGGACA
1 TCTACGAGGTCCTTCGGGACA
* *
1430752 TCTACGAGGTCTTTTGGGACA
1 TCTACGAGGTCCTTCGGGACA
1430773 ATTTTATATG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (21 bp):
TCTACGAGGTCCTTCGGGACA
Found at i:1431082 original size:9 final size:9
Alignment explanation
Indices: 1430988--1431085 Score: 51
Period size: 9 Copynumber: 10.8 Consensus size: 9
1430978 AAAAAGAGAT
1430988 TAATGATAA
1 TAATGATAA
*
1430997 TAATGTTATA
1 TAATGATA-A
1431007 TATATGATATGA
1 TA-ATGATA--A
1431019 TAATGATAA
1 TAATGATAA
*
1431028 TGATG-T--
1 TAATGATAA
* *
1431034 TAGTAATAA
1 TAATGATAA
* *
1431043 TAAGGATCA
1 TAATGATAA
1431052 TAATGA-ACA
1 TAATGATA-A
* *
1431061 TAATGAGAT
1 TAATGATAA
1431070 TAATGATAA
1 TAATGATAA
1431079 TAATGAT
1 TAATGAT
1431086 TAGATATGTG
Statistics
Matches: 65, Mismatches: 16, Indels: 16
0.67 0.16 0.16
Matches are distributed among these distances:
6 2 0.03
7 1 0.02
8 1 0.02
9 43 0.66
10 4 0.06
11 11 0.17
12 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.36
Consensus pattern (9 bp):
TAATGATAA
Found at i:1432710 original size:63 final size:63
Alignment explanation
Indices: 1432595--1432748 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 63
1432585 TATTAGTATC
*
1432595 CTTTGAGT-TGTTTCTCTTGAAACAAATTTTGCCTTTCAAGACAGTTTCTTTT-GAAAAAAAAT
1 CTTTGAGTATGTTTCTCTTGAAACAAATTTTG-CTTTCAAGACAATTTCTTTTAGAAAAAAAAT
* *
1432657 CTTTGAGTATGTTTCTCTGGAAACAAAGTTTTG-TTTCTTGAGACAATTT-TTTTGAGAAAAAAA
1 CTTTGAGTATGTTTCTCTTGAAACAAA-TTTTGCTTTC--AAGACAATTTCTTTT-AGAAAAAAA
1432720 AT
62 AT
*
1432722 CTTTGAGTATGTTTCCCTTGAAACAAA
1 CTTTGAGTATGTTTCTCTTGAAACAAA
1432749 ACAAACATCT
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
62 12 0.15
63 21 0.26
64 13 0.16
65 35 0.43
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (63 bp):
CTTTGAGTATGTTTCTCTTGAAACAAATTTTGCTTTCAAGACAATTTCTTTTAGAAAAAAAAT
Found at i:1432772 original size:35 final size:33
Alignment explanation
Indices: 1432713--1432780 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 33
1432703 TTTTTTTGAG
1432713 AAAAAAAATCTTTGAGTATGTTTCCCTTGAAAC
1 AAAAAAAATCTTTGAGTATGTTTCCCTTGAAAC
*
1432746 AAAACAAACATCTTTGAGT-CGTTTTCCCTTGAAAC
1 AAAA-AAA-ATCTTTGAGTATG-TTTCCCTTGAAAC
1432781 GAATTTGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 4 0.13
34 4 0.13
35 23 0.74
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (33 bp):
AAAAAAAATCTTTGAGTATGTTTCCCTTGAAAC
Found at i:1433241 original size:131 final size:131
Alignment explanation
Indices: 1432852--1433244 Score: 461
Period size: 131 Copynumber: 3.0 Consensus size: 131
1432842 AACCATTATC
* * *
1432852 CCTAAATATGGCATGACGTCCTCATCGCGTAGGGACTGTGTCATCCCCCGACCAGACCTTCTCAT
1 CCTAAAGATGGCATGACGTCCTCATAGCGTAGGAACTGTGTCATCCCCCGACCAGACCTTCTCAT
* * * ** * **
1432917 CATGTAGGAGTCGTGTCA-CCCTTGATAACCAGCCGTCCTCATCGTGTAGGAACCGTGTTATTGC
66 CACGTAGGAGTCATGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAAATGTGTTA-T--
*
1432981 CCTT
128 CATT
* * *
1432985 CCTAAAGATGGCATGCCGTCCTCATCA-CGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCA
1 CCTAAAGATGGCATGACGTCCTCAT-AGCGTAGGAACTGTGTCATCCCCCGACCAGACCTTCTCA
* ** * *
1433049 TCACGTAGGAGTCATGTCACCCCTAGACAACCTTTCGTCCTTATCACGTAGG-AATCGTGTTATC
65 TCACGTAGGAGTCATGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAAAT-GTGTTATC
1433113 ATT
129 ATT
* * * *
1433116 TCTAAAGATGGCATGTCGTCCTCATAGTGTAGGAACTATGTCATCCCCCGACCAGACCTTCTCAT
1 CCTAAAGATGGCATGACGTCCTCATAGCGTAGGAACTGTGTCATCCCCCGACCAGACCTTCTCAT
* * *
1433181 CACGTAGGAG-CTATGTCACCCCTAGATAATCAATCGTCCTCATCGCATAGGAAATATGTTATCA
66 CACGTAGGAGTC-ATGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAAATGTGTTATCA
1433245 CCCCTCATAA
Statistics
Matches: 221, Mismatches: 33, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
130 2 0.01
131 110 0.50
132 3 0.01
133 76 0.34
134 30 0.14
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (131 bp):
CCTAAAGATGGCATGACGTCCTCATAGCGTAGGAACTGTGTCATCCCCCGACCAGACCTTCTCAT
CACGTAGGAGTCATGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAAATGTGTTATCAT
T
Found at i:1433334 original size:265 final size:264
Alignment explanation
Indices: 1432853--1433341 Score: 606
Period size: 265 Copynumber: 1.8 Consensus size: 264
1432843 ACCATTATCC
* * * *
1432853 CTAAATATGGCATGACGTCCTCATCGCGTAGGGACTGTGTCATCCCCCGACCAGACCTTCTCATC
1 CTAAAGATGGCATGACGTCCTCATAGCGTAGGAACTATGTCATCCCCCGACCAGACCTTCTCATC
* * * * ** * * **
1432918 ATGTAGGAGTCGTGTCACCCTTGATAACCAGCCGTCCTCATCGTGTAGGAACCGTGTTATTGCCC
66 ACGTAGGAGTCATGTCACCCTAGATAACCAACCGTCCTCATCGCATAGGAAACATGTTATCACCC
* * * * * * *
1432983 TTCCTAAAGATGGCATGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTC
131 CTCATAAAGATGGCATGACGTCCTCATCACGTAGGAACCATGTCATCCACAGACCAGAACTCCTC
*
1433048 ATCACGTAGGAGTCATGTCACCCCTAGACAACCTTTCGTCCTTATCACGTAGGAATCGTGTTATC
196 ATCACATAGGAGTCATGTCACCCCTAGACAACCTTTCGTCCTTATCACGTAGGAATCGTGTTATC
1433113 ATTT
261 ATTT
* *
1433117 CTAAAGATGGCATGTCGTCCTCATAGTGTAGGAACTATGTCATCCCCCGACCAGACCTTCTCATC
1 CTAAAGATGGCATGACGTCCTCATAGCGTAGGAACTATGTCATCCCCCGACCAGACCTTCTCATC
* * *
1433182 ACGTAGGAG-CTATGTCACCCCTAGATAATCAATCGTCCTCATCGCATAGGAAATATGTTATCAC
66 ACGTAGGAGTC-ATGTCA-CCCTAGATAACCAACCGTCCTCATCGCATAGGAAACATGTTATCAC
* * * * *
1433246 CCCTCATAAAGATGGCCA-GAAC-TCTTCCTCATGTATGAGCCATGTCATCCACAGACCAGAACT
129 CCCTCATAAAGATGG-CATG-ACGTCCTCATCACGTAGGAACCATGTCATCCACAGACCAGAACT
* * *
1433309 CCTCATCATATAGGAGTCGTGTCACCCTTAGAC
192 CCTCATCACATAGGAGTCATGTCACCCCTAGAC
1433342 GACCAGAACT
Statistics
Matches: 186, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
263 1 0.01
264 72 0.39
265 110 0.59
266 3 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (264 bp):
CTAAAGATGGCATGACGTCCTCATAGCGTAGGAACTATGTCATCCCCCGACCAGACCTTCTCATC
ACGTAGGAGTCATGTCACCCTAGATAACCAACCGTCCTCATCGCATAGGAAACATGTTATCACCC
CTCATAAAGATGGCATGACGTCCTCATCACGTAGGAACCATGTCATCCACAGACCAGAACTCCTC
ATCACATAGGAGTCATGTCACCCCTAGACAACCTTTCGTCCTTATCACGTAGGAATCGTGTTATC
ATTT
Found at i:1433374 original size:43 final size:40
Alignment explanation
Indices: 1433261--1433374 Score: 104
Period size: 40 Copynumber: 2.8 Consensus size: 40
1433251 ATAAAGATGG
* ** *
1433261 CCAGAACTCTTCCTCATGTATGAGCCATGTCATCCACAGA
1 CCAGAACTCTTCATCATGTATGAGCTGTGTCACCCACAGA
* * * *
1433301 CCAGAACTCCTCATCATATAGGAG-TCGTGTCACCCTTAGACGA
1 CCAGAACTCTTCATCATGTATGAGCT-GTGTCACCC--ACA-GA
*
1433344 CCAGAACTCTTCATCACGTATGAGCTGTGTC
1 CCAGAACTCTTCATCATGTATGAGCTGTGTC
1433375 GCCCCCAAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
40 27 0.47
42 2 0.04
43 27 0.47
44 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (40 bp):
CCAGAACTCTTCATCATGTATGAGCTGTGTCACCCACAGA
Found at i:1433543 original size:3 final size:3
Alignment explanation
Indices: 1433530--1433615 Score: 97
Period size: 3 Copynumber: 28.7 Consensus size: 3
1433520 CTACAAAAAA
* * *
1433530 TAT TA- TAT TAT TATT TAC TAT TAT TAA TAT TAT TA- AAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1433574 TAT TAT TAT TAT TAT GT-T TAT TAAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT T-AT TAT TAT TAT TAT TAT TA
1433616 ATACAAGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.06
3 60 0.85
4 7 0.10
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1433845 original size:39 final size:39
Alignment explanation
Indices: 1433796--1433872 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
1433786 CAAAGGTCCA
*
1433796 GATCGTCCCGAACCTAGGGTTTCACCCTAATGGATAATT
1 GATCGCCCCGAACCTAGGGTTTCACCCTAATGGATAATT
1433835 GATCGCCCCGAACCTAGGGTTTCACCCTAATGGATAAT
1 GATCGCCCCGAACCTAGGGTTTCACCCTAATGGATAAT
1433873 AGCTAGCCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
GATCGCCCCGAACCTAGGGTTTCACCCTAATGGATAATT
Found at i:1434836 original size:30 final size:29
Alignment explanation
Indices: 1434802--1435015 Score: 135
Period size: 30 Copynumber: 7.2 Consensus size: 29
1434792 TAATAATTAT
*
1434802 TATTTTAGTCCTTTTAGTTATTGTTTTTAC
1 TATTTTAGTCCTTTAAGTT-TTGTTTTTAC
* *
1434832 TA-TTTAATCCTTTAAGATTTG-TTTTAC
1 TATTTTAGTCCTTTAAGTTTTGTTTTTAC
* * * * *
1434859 TATTTTAATCCGTTAAATGTATGTTTTTAT
1 TATTTTAGTCCTTTAAGT-TTTGTTTTTAC
* * * * **
1434889 TACTTTGGACCTTTAAGTTTATGTTTATGT
1 TATTTTAGTCCTTTAAGTTT-TGTTTTTAC
* **
1434919 TATTTTAGCCCTTTAAGTTTTTTGTTTTTGT
1 TATTTTAGTCCTTTAAG--TTTTGTTTTTAC
* * * *
1434950 TATTTTAGTCTTTTAAATTCCTGTTTATAC
1 TATTTTAGTCCTTTAAGTT-TTGTTTTTAC
* * *
1434980 TATTTTAGTCCTTTGATTTTATGTTTTTTC
1 TATTTTAGTCCTTTAAGTTT-TGTTTTTAC
1435010 TATTTT
1 TATTTT
1435016 GGTTCTTGAA
Statistics
Matches: 142, Mismatches: 34, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
27 8 0.06
28 15 0.11
29 19 0.13
30 75 0.53
31 22 0.15
32 3 0.02
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (29 bp):
TATTTTAGTCCTTTAAGTTTTGTTTTTAC
Found at i:1434842 original size:29 final size:28
Alignment explanation
Indices: 1434802--1434874 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
1434792 TAATAATTAT
* * *
1434802 TATTTTAGTCCTTTTAGTTATTGTTTTTAC
1 TATTTTAATCCTTTAAGAT-TTG-TTTTAC
1434832 TA-TTTAATCCTTTAAGATTTGTTTTAC
1 TATTTTAATCCTTTAAGATTTGTTTTAC
*
1434859 TATTTTAATCCGTTAA
1 TATTTTAATCCTTTAA
1434875 ATGTATGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 8 0.21
28 15 0.39
29 13 0.34
30 2 0.05
ACGTcount: A:0.23, C:0.11, G:0.08, T:0.58
Consensus pattern (28 bp):
TATTTTAATCCTTTAAGATTTGTTTTAC
Found at i:1434854 original size:28 final size:29
Alignment explanation
Indices: 1434822--1434887 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
1434812 CTTTTAGTTA
*
1434822 TTGTTTTTACTA-TTTAATCCTTTAAGAT-
1 TTGTTTTTACTATTTTAATCCGTTAA-ATG
1434850 TTG-TTTTACTATTTTAATCCGTTAAATG
1 TTGTTTTTACTATTTTAATCCGTTAAATG
1434878 TATGTTTTTA
1 T-TGTTTTTA
1434888 TTACTTTGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.30
28 16 0.48
29 2 0.06
30 5 0.15
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (29 bp):
TTGTTTTTACTATTTTAATCCGTTAAATG
Found at i:1434965 original size:61 final size:60
Alignment explanation
Indices: 1434900--1435015 Score: 135
Period size: 61 Copynumber: 1.9 Consensus size: 60
1434890 ACTTTGGACC
* * ** *
1434900 TTTAAGTTTATGTTTATGTTATTTTAGCCCTTTAAGTTTTTTGTTTTTGT-TATTTTAGTCT
1 TTTAAATTCATGTTTATACTATTTTAGCCCTTTAA-TTTTATGTTTTT-TCTATTTTAGTCT
* * *
1434961 TTTAAATTCCTGTTTATACTATTTTAGTCCTTTGATTTTATGTTTTTTCTATTTT
1 TTTAAATTCATGTTTATACTATTTTAGCCCTTTAATTTTATGTTTTTTCTATTTT
1435016 GGTTCTTGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.02
60 17 0.37
61 28 0.61
ACGTcount: A:0.17, C:0.09, G:0.10, T:0.64
Consensus pattern (60 bp):
TTTAAATTCATGTTTATACTATTTTAGCCCTTTAATTTTATGTTTTTTCTATTTTAGTCT
Found at i:1435932 original size:2 final size:2
Alignment explanation
Indices: 1435925--1436008 Score: 115
Period size: 2 Copynumber: 44.5 Consensus size: 2
1435915 GTTTTATTAT
1435925 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1435965 TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA TT TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1436004 TA TA T
1 TA TA T
1436009 TTTTTATTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
1 5 0.07
2 68 0.93
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1435967 original size:36 final size:36
Alignment explanation
Indices: 1435927--1436008 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
1435917 TTTATTATTA
1435927 TATATATATATATATATATATATATTATATATATAT
1 TATATATATATATATATATATATATTATATATATAT
* *
1435963 TATATATATATATATATATATATATTATTTATTTAT
1 TATATATATATATATATATATATATTATATATATAT
1435999 TATAT-TATAT
1 TATATATATAT
1436009 TTTTTATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 5 0.11
36 39 0.89
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
TATATATATATATATATATATATATTATATATATAT
Found at i:1436014 original size:21 final size:21
Alignment explanation
Indices: 1435949--1436057 Score: 85
Period size: 22 Copynumber: 4.9 Consensus size: 21
1435939 TATATATATA
* *
1435949 TATTATATATATATTATATATATA
1 TATTATAT-TATATT-T-TTTATT
*
1435973 TATATATATATATATTATTTATT
1 TAT-TATAT-TATATTTTTTATT
1435996 TATTATATTATATTTTTTATT
1 TATTATATTATATTTTTTATT
*
1436017 TTTTATTATTAT-TTTATTTATT
1 TATTA-TATTATATTT-TTTATT
* *
1436039 TGTTTTATTTATATTTTTT
1 TATTATA-TTATATTTTTT
1436058 TTATTTTTCT
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
21 21 0.29
22 27 0.37
23 10 0.14
24 3 0.04
25 12 0.16
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (21 bp):
TATTATATTATATTTTTTATT
Found at i:1436015 original size:9 final size:9
Alignment explanation
Indices: 1436003--1436093 Score: 55
Period size: 10 Copynumber: 9.9 Consensus size: 9
1435993 ATTTATTATA
1436003 TTATA-TTT
1 TTATATTTT
1436011 TT-TATTTT
1 TTATATTTT
1436019 TTATTATTATT
1 TTA-TATT-TT
*
1436030 TTAT-TTAT
1 TTATATTTT
*
1436038 TTGT-TTTAT
1 TTATATTT-T
1436047 TTATATTTT
1 TTATATTTT
*
1436056 TTTTATTTT
1 TTATATTTT
*
1436065 TCTTTATTTT
1 T-TATATTTT
*
1436075 TCTTTATTTTT
1 T-TATA-TTTT
1436086 TTATATTT
1 TTATATTT
1436094 ATTTTACTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
7 2 0.03
8 13 0.19
9 19 0.28
10 25 0.36
11 10 0.14
ACGTcount: A:0.18, C:0.02, G:0.01, T:0.79
Consensus pattern (9 bp):
TTATATTTT
Found at i:1436015 original size:25 final size:25
Alignment explanation
Indices: 1435917--1436097 Score: 81
Period size: 24 Copynumber: 7.3 Consensus size: 25
1435907 TGTTATCAGT
* *
1435917 TTTA-TTATTATATATATATATATATA
1 TTTATTTATTATAT-TATAT-TTTTTA
* * * *
1435943 TATATATATTATA-TATATATTATA
1 TTTATTTATTATATTATATTTTTTA
* * * *
1435967 TATATATA-TATA-TATATATATTA
1 TTTATTTATTATATTATATTTTTTA
1435990 TTTATTTATTATATTATATTTTTTA
1 TTTATTTATTATATTATATTTTTTA
* *
1436015 TTT-TTTATTATTATTTTATTTATTTGT
1 TTTATTTATTA-TATTATATTT-TTT-A
* * * *
1436042 TTTATTTA-TATTTTTTTTATTTTTC
1 TTTATTTATTATATTATAT-TTTTTA
* *
1436067 TTTATTT-TTCT-TTATTTTTTTATA
1 TTTATTTATTATATTATATTTTT-TA
1436091 TTTATTT
1 TTTATTT
1436098 TACTGACTAT
Statistics
Matches: 127, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
23 23 0.18
24 36 0.28
25 35 0.28
26 15 0.12
27 14 0.11
28 4 0.03
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.69
Consensus pattern (25 bp):
TTTATTTATTATATTATATTTTTTA
Found at i:1436021 original size:24 final size:23
Alignment explanation
Indices: 1435973--1436098 Score: 95
Period size: 22 Copynumber: 5.6 Consensus size: 23
1435963 TATATATATA
* *
1435973 TATATATATATATATTATTTATTTAT
1 TATAT-TATATTTTTTATTT-TTT-T
*
1435999 TATATTATATTTTTTATTTTTTA
1 TATATTATATTTTTTATTTTTTT
*
1436022 T-TATTAT-TTTATTTATTTGTTT
1 TATATTATATTT-TTTATTTTTTT
*
1436044 TAT-TTATATTTTTT-TTATTTT
1 TATATTATATTTTTTATTTTTTT
* *
1436065 TCT-TTATTTTTCTTTA-TTTTTT
1 TATATTATATTT-TTTATTTTTTT
1436087 TATATT-TATTTT
1 TATATTATATTTT
1436099 ACTGACTATT
Statistics
Matches: 82, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
21 18 0.22
22 37 0.45
23 7 0.09
24 3 0.04
25 12 0.15
26 5 0.06
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.75
Consensus pattern (23 bp):
TATATTATATTTTTTATTTTTTT
Found at i:1436035 original size:43 final size:43
Alignment explanation
Indices: 1435987--1436098 Score: 115
Period size: 43 Copynumber: 2.6 Consensus size: 43
1435977 TATATATATA
1435987 TTATTTATTTATTATATTATA--TTTTTTATTTTT-TATTATTATT
1 TTATTTATTTATTATATTATATTTTTTTTATTTTTCT-TTA-T-TT
* *
1436030 TTATTTATTTGTTTTATTTATATTTTTTTTATTTTTCTTTATTT
1 TTATTTATTTATTATA-TTATATTTTTTTTATTTTTCTTTATTT
* *
1436074 TTCTTTATTTTTTTATATT-TATTTT
1 TTATTTA-TTTATTATATTATATTTT
1436099 ACTGACTATT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
43 20 0.34
44 15 0.25
45 8 0.14
46 15 0.25
47 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.78
Consensus pattern (43 bp):
TTATTTATTTATTATATTATATTTTTTTTATTTTTCTTTATTT
Found at i:1436089 original size:39 final size:39
Alignment explanation
Indices: 1435985--1436099 Score: 112
Period size: 39 Copynumber: 3.0 Consensus size: 39
1435975 TATATATATA
*
1435985 TATTA-TTTATTTATTATATTATATTT-T-TTATTTTTTAT
1 TATTATTTTATTTATT-TATTTTATTTATATT-TTTTTTAT
*
1436023 TATTATTTTATTTATTTGTTTTATTTATATTTTTTTTAT
1 TATTATTTTATTTATTTATTTTATTTATATTTTTTTTAT
* * * * *
1436062 TTTTCTTTATTTTTCTTTATTTT-TTTATATTTATTTTA
1 TATTATTT-TATTTATTTATTTTATTTATATTTTTTTTA
1436100 CTGACTATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
38 13 0.20
39 39 0.60
40 13 0.20
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.77
Consensus pattern (39 bp):
TATTATTTTATTTATTTATTTTATTTATATTTTTTTTAT
Done.