Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008893.1 Hibiscus syriacus cultivar Beakdansim tig00112159_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: 2797279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:993312 original size:6 final size:6
Alignment explanation
Indices: 993310--993369 Score: 65
Period size: 6 Copynumber: 10.3 Consensus size: 6
993300 TTAAAAATTA
*
993310 AAAAAT TAA-AT AAAAAT --AA-T AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
993354 AAAAATT AGAAAAT AA
1 AAAAA-T A-AAAAT AA
993370 TATATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 6 0.13
6 29 0.63
7 4 0.09
8 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:993334 original size:21 final size:21
Alignment explanation
Indices: 993301--993371 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 21
993291 TAAAAATATT
* *
993301 TAAAAATTA-AAAAAT-TAAA
1 TAAAAATAATAAAAATAAAAA
993320 TAAAAATAATAAAAATAAAAA
1 TAAAAATAATAAAAATAAAAA
993341 T--AAA-AATAAAAATAAAAA
1 TAAAAATAATAAAAATAAAAA
993359 TTAGAAAATAATA
1 -TA-AAAATAATA
993372 TATATATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
18 14 0.33
19 12 0.28
20 6 0.14
21 4 0.09
22 3 0.07
23 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.23
Consensus pattern (21 bp):
TAAAAATAATAAAAATAAAAA
Found at i:993353 original size:18 final size:20
Alignment explanation
Indices: 993327--993369 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
993317 AAATAAAAAT
993327 AATAAAAATAAAAA-TA-AA
1 AATAAAAATAAAAATTAGAA
993345 AATAAAAATAAAAATTAGAA
1 AATAAAAATAAAAATTAGAA
993365 AATAA
1 AATAA
993370 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 14 0.61
19 2 0.09
20 7 0.30
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (20 bp):
AATAAAAATAAAAATTAGAA
Found at i:993366 original size:27 final size:25
Alignment explanation
Indices: 993301--993369 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
993291 TAAAAATATT
*
993301 TAAAAATTAAAAAATTAAATAAAAA
1 TAAAAATTAAAAAATAAAATAAAAA
*
993326 TAATAAA-AATAAAAATAAAAATAAAAA
1 TAA-AAATTA-AAAAAT-AAAATAAAAA
*
993353 TAAAAATTAGAAAATAA
1 TAAAAATTAAAAAATAA
993370 TATATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
25 6 0.17
26 17 0.47
27 13 0.36
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.22
Consensus pattern (25 bp):
TAAAAATTAAAAAATAAAATAAAAA
Found at i:1003198 original size:15 final size:15
Alignment explanation
Indices: 1003174--1003205 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1003164 AGGCAGATCG
*
1003174 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
1003189 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
1003204 AA
1 AA
1003206 GAAAGATTTT
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:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:1017483 original size:41 final size:41
Alignment explanation
Indices: 1017421--1017585 Score: 231
Period size: 41 Copynumber: 4.0 Consensus size: 41
1017411 TGTTCAATCT
* **
1017421 GAGTGCAACAGCATACATTAGAGTGTTTGAAACTTACTTCC
1 GAGTGCAACAGCATACATTAGAGTATTCAAAACTTACTTCC
* * *
1017462 GAGTGCAAAAGCATTCGTTAGAGTATTCAAAACTTACTTCC
1 GAGTGCAACAGCATACATTAGAGTATTCAAAACTTACTTCC
* * *
1017503 GAGTACAACAGCATACGTTAAGAGTATTCGAAACTTACTTCC
1 GAGTGCAACAGCATACATT-AGAGTATTCAAAACTTACTTCC
*
1017545 GAGTGCAACAGCATCCATTAGAGTATTCAAAACTTACTTCC
1 GAGTGCAACAGCATACATTAGAGTATTCAAAACTTACTTCC
1017586 AGCATACATT
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 72 0.66
42 37 0.34
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (41 bp):
GAGTGCAACAGCATACATTAGAGTATTCAAAACTTACTTCC
Found at i:1017507 original size:21 final size:21
Alignment explanation
Indices: 1017482--1017548 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1017472 GCATTCGTTA
1017482 GAGTATTCAAAACTTACTTCC
1 GAGTATTCAAAACTTACTTCC
* * **
1017503 GAGTA--CAACAGCATACGTTAA
1 GAGTATTCAA-AACTTAC-TTCC
*
1017524 GAGTATTCGAAACTTACTTCC
1 GAGTATTCAAAACTTACTTCC
1017545 GAGT
1 GAGT
1017549 GCAACAGCAT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 18 0.55
22 5 0.15
23 2 0.06
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (21 bp):
GAGTATTCAAAACTTACTTCC
Found at i:1017566 original size:83 final size:82
Alignment explanation
Indices: 1017421--1017585 Score: 258
Period size: 83 Copynumber: 2.0 Consensus size: 82
1017411 TGTTCAATCT
* * * * *
1017421 GAGTGCAACAGCATACATTAGAGTGTTTGAAACTTACTTCCGAGTGCAAAAGCATTCGTTAGAGT
1 GAGTACAACAGCATACATTAGAGTATTCGAAACTTACTTCCGAGTGCAAAAGCATCCATTAGAGT
1017486 ATTCAAAACTTACTTCC
66 ATTCAAAACTTACTTCC
* *
1017503 GAGTACAACAGCATACGTTAAGAGTATTCGAAACTTACTTCCGAGTGCAACAGCATCCATTAGAG
1 GAGTACAACAGCATACATT-AGAGTATTCGAAACTTACTTCCGAGTGCAAAAGCATCCATTAGAG
1017568 TATTCAAAACTTACTTCC
65 TATTCAAAACTTACTTCC
1017586 AGCATACATT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
82 17 0.23
83 58 0.77
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (82 bp):
GAGTACAACAGCATACATTAGAGTATTCGAAACTTACTTCCGAGTGCAAAAGCATCCATTAGAGT
ATTCAAAACTTACTTCC
Found at i:1017596 original size:32 final size:32
Alignment explanation
Indices: 1017553--1017617 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1017543 CCGAGTGCAA
* * *
1017553 CAGCATCCATTAGAGTATTCAAAACTTACTTC
1 CAGCATACATTAAAGTACTCAAAACTTACTTC
* *
1017585 CAGCATACATTAAAGTACTCGAAACTTATTTC
1 CAGCATACATTAAAGTACTCAAAACTTACTTC
1017617 C
1 C
1017618 GAGCGCAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (32 bp):
CAGCATACATTAAAGTACTCAAAACTTACTTC
Found at i:1020778 original size:21 final size:20
Alignment explanation
Indices: 1020731--1020780 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1020721 TTAAAAAAGA
* *
1020731 AAAGAAAAATAAATATATAAT
1 AAAG-AAAATAAATAAAAAAT
1020752 ATAAGAAAATAAATGAAAAAAT
1 A-AAGAAAATAAAT-AAAAAAT
1020774 AAAGAAA
1 AAAGAAA
1020781 GACTTGTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (20 bp):
AAAGAAAATAAATAAAAAAT
Found at i:1021571 original size:9 final size:9
Alignment explanation
Indices: 1021544--1021612 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
1021534 CCCGCCCCGA
1021544 TTATATATAT
1 TTATATAT-T
*
1021554 ATATAATATT
1 TTAT-ATATT
1021564 TTATATATT
1 TTATATATT
*
1021573 TTATAT-TAA
1 TTATATAT-T
1021582 TTATATA-T
1 TTATATATT
*
1021590 ATA-ATATT
1 TTATATATT
1021598 TTATATATT
1 TTATATATT
1021607 TTATAT
1 TTATAT
1021613 TAATTATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
7 3 0.06
8 6 0.12
9 28 0.58
10 7 0.15
11 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATATATT
Found at i:1021592 original size:34 final size:34
Alignment explanation
Indices: 1021549--1021633 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
1021539 CCCGATTATA
1021549 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
1021583 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
1021617 TATATATAAAATATTTT
1 TATATATATAATATTTT
1021634 CGGGTTCGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:1023119 original size:24 final size:24
Alignment explanation
Indices: 1023060--1023120 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1023050 CGTTCATTAA
* *
1023060 AAATGATAAACAAACACAAATGAAC
1 AAAT-ATAAACGAACACAAAAGAAC
* *
1023085 AAATGTAAACGAACATAAAAGAAC
1 AAATATAAACGAACACAAAAGAAC
*
1023109 GAATATAAACGA
1 AAATATAAACGA
1023121 CCAAACATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.13
Consensus pattern (24 bp):
AAATATAAACGAACACAAAAGAAC
Found at i:1027237 original size:19 final size:19
Alignment explanation
Indices: 1027213--1027250 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1027203 TTTTTTTCAA
1027213 AATTTAATTTGAATTAATT
1 AATTTAATTTGAATTAATT
* *
1027232 AATTTATTTTGATTTAATT
1 AATTTAATTTGAATTAATT
1027251 TAAATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
AATTTAATTTGAATTAATT
Found at i:1027695 original size:2 final size:2
Alignment explanation
Indices: 1027690--1027740 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1027680 TTTTTGGAGT
1027690 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
1027732 TA TA TA TA T
1 TA TA TA TA T
1027741 GGTGGACTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1029017 original size:20 final size:21
Alignment explanation
Indices: 1028992--1029084 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1028982 TTTTCCCAAT
*
1028992 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1029012 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1029033 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1029053 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1029074 TCGCAATGCGA
1 TCGCAATGCGA
1029085 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1029098 original size:20 final size:20
Alignment explanation
Indices: 1029073--1029187 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
1029063 AATTGGGAAA
*
1029073 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1029093 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1029114 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1029134 TTCG-AACCGCGATACTGACT
1 ATCGCAA-CGCGATACTGACT
* *
1029154 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1029174 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1029188 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.77
21 16 0.21
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1029099 original size:41 final size:41
Alignment explanation
Indices: 1028992--1029084 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1028982 TTTTCCCAAT
1028992 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1029033 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1029074 TCGCAATGCGA
1 TCGCAATGCGA
1029085 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1029115 original size:41 final size:41
Alignment explanation
Indices: 1029070--1029207 Score: 127
Period size: 41 Copynumber: 3.4 Consensus size: 41
1029060 GCGAATTGGG
* * *
1029070 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* * * *
1029111 AAAATCGCAACGAGATACTTACTTTCG-AACCGCGATACT-G
1 AAAATCGCAACGCGATACTGACTTTCGCAA-CGCGATAATAA
*** * *
1029151 ACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* *
1029192 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1029208 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
40 31 0.41
41 44 0.59
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
Found at i:1029684 original size:20 final size:20
Alignment explanation
Indices: 1029661--1029703 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1029651 GATAGTCGAA
1029661 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
1029681 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
1029701 TTC
1 TTC
1029704 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:1031044 original size:18 final size:18
Alignment explanation
Indices: 1031023--1031067 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1031013 TCCACTTCGG
*
1031023 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1031041 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1031059 GAGCCATCA
1 GAGCCATCA
1031068 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1031591 original size:19 final size:20
Alignment explanation
Indices: 1031537--1031603 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1031527 TAGTTTACTT
* *
1031537 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1031557 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1031577 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1031596 TCGCAACG
1 TCGCAACG
1031604 ATAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1031611 original size:14 final size:14
Alignment explanation
Indices: 1031592--1031649 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1031582 ATGCGAAATG
1031592 AAAATCGCAACGAT
1 AAAATCGCAACGAT
1031606 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
* * *
1031624 GAAATCGCAATGAC
1 AAAATCGCAACGAT
1031638 AAAATCGCAACG
1 AAAATCGCAACG
1031650 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 21 0.60
16 3 0.09
18 11 0.31
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:1031642 original size:32 final size:33
Alignment explanation
Indices: 1031576--1031668 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 33
1031566 GGAAATGGCT
* *
1031576 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1031609 ATCGCAATGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
* *
1031641 ATCGCAACGCGAAATGAAAATCGTAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
1031669 CGATTTGTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.53
33 26 0.47
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:1031721 original size:32 final size:33
Alignment explanation
Indices: 1031682--1031756 Score: 125
Period size: 32 Copynumber: 2.3 Consensus size: 33
1031672 TTTGTGTTTT
*
1031682 GCATTGCGATTTTGTCGTTGTGA-TTTCATTTC
1 GCATTGCGATTTTGTCGTTGCGATTTTCATTTC
*
1031714 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTC
1 GCATTGCGATTTTGTCGTTGCGATTTTCATTTC
1031747 GCATTGCGAT
1 GCATTGCGAT
1031757 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 21 0.54
33 18 0.46
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.47
Consensus pattern (33 bp):
GCATTGCGATTTTGTCGTTGCGATTTTCATTTC
Found at i:1031734 original size:14 final size:14
Alignment explanation
Indices: 1031685--1031740 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
1031675 GTGTTTTGCA
1031685 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
* *
1031699 TTGTGATTTCATTTCGCG
1 TTGCGATTT--TGT--CG
1031717 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
1031731 TTGCGATTTT
1 TTGCGATTTT
1031741 CATTTCGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.59
16 4 0.12
18 10 0.29
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:1031755 original size:19 final size:19
Alignment explanation
Indices: 1031729--1031795 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1031719 GCGATTTTGT
**
1031729 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
1031748 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1031768 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
1031787 CGTTGCGAT
1 CGTTGCGAT
1031796 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1031775 original size:20 final size:19
Alignment explanation
Indices: 1031741--1031795 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1031731 TTGCGATTTT
*
1031741 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1031760 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1031780 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1031796 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1034404 original size:24 final size:24
Alignment explanation
Indices: 1034353--1034406 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1034343 GTATTTGAAA
* * * *
1034353 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATATTGGTCAATACACAGAC
*
1034377 TTTGATATTGGTCAATACACAGAT
1 TTTGATATTGGTCAATACACAGAC
1034401 TTTGAT
1 TTTGAT
1034407 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:1036927 original size:33 final size:33
Alignment explanation
Indices: 1036885--1037011 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1036875 GGAAATTACT
*
1036885 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1036918 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1036950 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1036984 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1037012 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1036992 original size:66 final size:66
Alignment explanation
Indices: 1036886--1037018 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1036876 GAAATTACTA
* *
1036886 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1036951 T
66 T
* *
1036952 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1037017 T
66 T
1037018 T
1 T
1037019 AATTTCACGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1037014 original size:19 final size:19
Alignment explanation
Indices: 1036885--1037015 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
1036875 GGAAATTACT
*
1036885 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1036904 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1036918 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1036937 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1036951 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1036970 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
1036984 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1037003 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1037016 TTTAATTTCA
Statistics
Matches: 81, Mismatches: 16, Indels: 30
0.64 0.13 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 5 0.06
18 3 0.04
19 38 0.47
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1037033 original size:19 final size:20
Alignment explanation
Indices: 1037011--1037053 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1037001 AAATCGCAAC
1037011 GCGAATTT-AATTTCACGTT
1 GCGAATTTCAATTTCACGTT
* * *
1037030 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCACGTT
1037050 GCGA
1 GCGA
1037054 TTCTCTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCACGTT
Found at i:1037213 original size:14 final size:14
Alignment explanation
Indices: 1037194--1037230 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1037184 CATCAATTAA
1037194 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1037208 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1037222 ACAAATCAA
1 ACAAATCAA
1037231 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1038654 original size:21 final size:21
Alignment explanation
Indices: 1038588--1038654 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1038578 GTGAATCGGG
*
1038588 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1038608 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1038630 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1038651 CTCT
1 CTCT
1038655 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1040743 original size:20 final size:21
Alignment explanation
Indices: 1040713--1040772 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
1040703 CTTTTGGTTG
1040713 AAATGAAAATCGCAACGAGAT
1 AAATGAAAATCGCAACGAGAT
* *
1040734 -AATGAGAATCGCAACGCG-T
1 AAATGAAAATCGCAACGAGAT
**
1040753 AAATGACTATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
1040773 GAATCGCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAT
Found at i:1040795 original size:33 final size:33
Alignment explanation
Indices: 1040737--1040835 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1040727 ACGAGATAAT
*
1040737 GAGAATCGCAACGCGTAAATGACTATCGCAACGA
1 GAGAATCGCAACGCG-AAATGACTATCGCAACCA
*
1040771 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1040804 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1040836 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 44 0.75
34 15 0.25
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1040829 original size:19 final size:19
Alignment explanation
Indices: 1040712--1040896 Score: 158
Period size: 19 Copynumber: 10.1 Consensus size: 19
1040702 TCTTTTGGTT
*
1040712 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1040731 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1040751 GTAAATGACTATCGCAA--C
1 G-AAATGAAAATCGCAACGC
*
1040769 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1040785 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1040803 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1040818 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1040838 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1040857 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1040876 GAAAT-AAAATTCGCAATGC
1 GAAATGAAAA-TCGCAACGC
1040895 GA
1 GA
1040897 TTTTTGTTTC
Statistics
Matches: 137, Mismatches: 15, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
18 9 0.07
19 57 0.42
20 46 0.34
21 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1040850 original size:39 final size:38
Alignment explanation
Indices: 1040807--1040896 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
1040797 GCGACCAGAC
1040807 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
1040846 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
* *
1040884 ATTCGCAATGCGA
1 AATCGCAACGCGA
1040897 TTTTTGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:1040907 original size:19 final size:19
Alignment explanation
Indices: 1040885--1040927 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1040875 CGAAATAAAA
*
1040885 TTCGCAATGCGATTTTTGT
1 TTCGCAATGCGATTTTTAT
** *
1040904 TTCGCGTTGCGTTTTTTAT
1 TTCGCAATGCGATTTTTAT
1040923 TTCGC
1 TTCGC
1040928 GTTGCGATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (19 bp):
TTCGCAATGCGATTTTTAT
Found at i:1040928 original size:19 final size:19
Alignment explanation
Indices: 1040892--1040972 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
1040882 AAATTCGCAA
*
1040892 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1040911 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1040930 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
1040944 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1040964 TGCGATTTT
1 TGCGATTTT
1040973 CATTCTCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 22 0.45
20 11 0.22
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1041513 original size:20 final size:20
Alignment explanation
Indices: 1041488--1041540 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1041478 GCGCTATGTA
1041488 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1041508 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1041528 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1041541 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1041574 original size:20 final size:20
Alignment explanation
Indices: 1041549--1041602 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1041539 GATTTTGTAT
1041549 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1041569 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1041589 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1041603 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1041587 original size:61 final size:61
Alignment explanation
Indices: 1041489--1041605 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1041479 CGCTATGTAA
* * * * *
1041489 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1041550 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1041606 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1041621 original size:61 final size:61
Alignment explanation
Indices: 1041489--1041623 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1041479 CGCTATGTAA
* * * * * ** *
1041489 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1041550 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1041612 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1041624 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1041713 original size:21 final size:21
Alignment explanation
Indices: 1041673--1041713 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1041663 ATTGTATACC
**
1041673 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1041694 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1041714 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1043816 original size:26 final size:26
Alignment explanation
Indices: 1043786--1043870 Score: 152
Period size: 26 Copynumber: 3.3 Consensus size: 26
1043776 TGATTCCTCT
* *
1043786 TGCAGCTGCTCACGAGACCTCATACA
1 TGCAGTTGCTCACGAGACCTCATGCA
1043812 TGCAGTTGCTCACGAGACCTCATGCA
1 TGCAGTTGCTCACGAGACCTCATGCA
1043838 TGCAGTTGCTCACGAGACCTCATGCA
1 TGCAGTTGCTCACGAGACCTCATGCA
1043864 TGCAGTT
1 TGCAGTT
1043871 ATAATAGCTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.24
Consensus pattern (26 bp):
TGCAGTTGCTCACGAGACCTCATGCA
Found at i:1044188 original size:5 final size:5
Alignment explanation
Indices: 1044175--1044218 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
1044165 TTTGGCGAGA
*
1044175 GAAAG GAAAA GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
1044219 AGAAGAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:1044189 original size:10 final size:10
Alignment explanation
Indices: 1044174--1044228 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
1044164 ATTTGGCGAG
1044174 AGAAAGGAAA
1 AGAAAGGAAA
1044184 AGAAAGGAAA
1 AGAAAGGAAA
*
1044194 GGAAAGGAAA
1 AGAAAGGAAA
*
1044204 GGAAAGGAAA
1 AGAAAGGAAA
* *
1044214 GGAAAAGAAGA
1 AGAAAGGAA-A
1044225 AGAA
1 AGAA
1044229 GAAAGGGAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
10 37 0.90
11 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (10 bp):
AGAAAGGAAA
Found at i:1044193 original size:15 final size:15
Alignment explanation
Indices: 1044174--1044222 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1044164 ATTTGGCGAG
*
1044174 AGAAAGGAAAAGAAA
1 AGAAAGGAAAGGAAA
*
1044189 GGAAAGGAAAGGAAA
1 AGAAAGGAAAGGAAA
*
1044204 GGAAAGGAAAGGAAA
1 AGAAAGGAAAGGAAA
1044219 AGAA
1 AGAA
1044223 GAAGAAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AGAAAGGAAAGGAAA
Found at i:1044375 original size:21 final size:21
Alignment explanation
Indices: 1044350--1044393 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1044340 AATTTAGTTA
1044350 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1044371 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1044392 AT
1 AT
1044394 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1044403 original size:28 final size:28
Alignment explanation
Indices: 1044370--1044423 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1044360 TAGTATAAAT
1044370 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATTA
1044398 TATTAGTTTGTTAGTTTAAGTTATAT
1 TATTAGTTTGTTAGTTTAAGTTATAT
1044424 ATTAGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (28 bp):
TATTAGTTTGTTAGTTTAAGTTATATTA
Found at i:1044972 original size:15 final size:15
Alignment explanation
Indices: 1044954--1044991 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1044944 TTTATTTTAT
1044954 ATTAGATTATATAA-A
1 ATTA-ATTATATAACA
*
1044969 ATTAATTTTATAACA
1 ATTAATTATATAACA
1044984 ATTAATTA
1 ATTAATTA
1044992 ACAAATTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
ATTAATTATATAACA
Found at i:1047634 original size:18 final size:19
Alignment explanation
Indices: 1047611--1047646 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1047601 AACACTTGTT
1047611 TGATTTG-TAATCATGATA
1 TGATTTGATAATCATGATA
1047629 TGATTTGATAATCATGAT
1 TGATTTGATAATCATGAT
1047647 TTAATAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (19 bp):
TGATTTGATAATCATGATA
Found at i:1047739 original size:49 final size:49
Alignment explanation
Indices: 1047686--1047899 Score: 374
Period size: 49 Copynumber: 4.3 Consensus size: 49
1047676 AATAATTATT
1047686 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1047735 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* *
1047784 TATTAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* * *
1047833 TATTAATAATTAATAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1047882 TAGTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
1047900 TATTAGTAAT
Statistics
Matches: 158, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
49 151 0.96
50 7 0.04
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:1047767 original size:21 final size:21
Alignment explanation
Indices: 1047743--1047868 Score: 72
Period size: 21 Copynumber: 5.3 Consensus size: 21
1047733 GATAGTAATG
*
1047743 ATTAGTAATAATGAAATTATT
1 ATTAATAATAATGAAATTATT
* *
1047764 ATTAATATTTAATGATTTGATATTAATA
1 ATTAATA-ATAATGA----A-ATT-ATT
*
1047792 ATTAGTAATAATGAAATTATT
1 ATTAATAATAATGAAATTATT
* *
1047813 ATTAATATTTAATGATTTGATATTAATA
1 ATTAATA-ATAATGA----A-ATT-ATT
1047841 ATTAATAATAATGAAATTATT
1 ATTAATAATAATGAAATTATT
1047862 ATTAATA
1 ATTAATA
1047869 TTTAATGATT
Statistics
Matches: 80, Mismatches: 11, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
21 23 0.29
22 18 0.22
23 2 0.03
26 2 0.03
27 18 0.22
28 17 0.21
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (21 bp):
ATTAATAATAATGAAATTATT
Found at i:1048147 original size:35 final size:35
Alignment explanation
Indices: 1048107--1048351 Score: 239
Period size: 35 Copynumber: 7.5 Consensus size: 35
1048097 AACCATAAAA
*
1048107 ATGATTTAATAATGATTTTAAT-ATTTAATGATTTG
1 ATGATTTAGTAATGA-TTTAATGATTTAATGATTTG
*
1048142 ATGATTTAGTAATGATTTTAAT-ATTTAATGATTTT
1 ATGATTTAGTAATGA-TTTAATGATTTAATGATTTG
1048177 ATGA-TT--T-A-G---TAATGATTTAATGATTTG
1 ATGATTTAGTAATGATTTAATGATTTAATGATTTG
*
1048204 ATGATTTAGTAATGATTTTAATG-TTTAATGATTTA
1 ATGATTTAGTAATGA-TTTAATGATTTAATGATTTG
1048239 ATGATTTAGTAATGATTTTAAT-ATTTAATGATTTG
1 ATGATTTAGTAATGA-TTTAATGATTTAATGATTTG
1048274 ATGATTTAGTAATGA-TT--TGA--TAAT-A----
1 ATGATTTAGTAATGATTTAATGATTTAATGATTTG
* *
1048299 ATGATTTAATAATGTTTTCAAT-ATTTAATGATTTG
1 ATGATTTAGTAATGATTT-AATGATTTAATGATTTG
1048334 ATGATTTAGTAATGATTT
1 ATGATTTAGTAATGATTT
1048352 GATAAAAACT
Statistics
Matches: 178, Mismatches: 9, Indels: 46
0.76 0.04 0.20
Matches are distributed among these distances:
25 13 0.07
26 6 0.03
27 16 0.09
28 3 0.02
29 2 0.01
30 10 0.06
31 4 0.02
32 3 0.02
33 2 0.01
34 2 0.01
35 112 0.63
36 5 0.03
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (35 bp):
ATGATTTAGTAATGATTTAATGATTTAATGATTTG
Found at i:1048232 original size:7 final size:8
Alignment explanation
Indices: 1048116--1048281 Score: 124
Period size: 8 Copynumber: 19.2 Consensus size: 8
1048106 AATGATTTAA
1048116 TAATGATTT
1 TAATGA-TT
1048125 TAAT-ATT
1 TAATGATT
1048132 TAATGATT
1 TAATGATT
*
1048140 TGATGATTT
1 TAATGA-TT
1048149 AGTAATGATTT
1 --TAATGA-TT
1048160 TAAT-ATT
1 TAATGATT
1048167 TAATGATT
1 TAATGATT
*
1048175 TTATGATTT
1 TAATGA-TT
1048184 AGTAATGATT
1 --TAATGATT
1048194 TAATGATT
1 TAATGATT
*
1048202 TGATGATTT
1 TAATGA-TT
1048211 AGTAATGATTT
1 --TAATGA-TT
1048222 TAATG-TT
1 TAATGATT
1048229 TAATGATT
1 TAATGATT
1048237 TAATGATTT
1 TAATGA-TT
1048246 AGTAATGATTT
1 --TAATGA-TT
1048257 TAAT-ATT
1 TAATGATT
1048264 TAATGATT
1 TAATGATT
*
1048272 TGATGATT
1 TAATGATT
1048280 TA
1 TA
1048282 GTAATGATTT
Statistics
Matches: 133, Mismatches: 8, Indels: 33
0.76 0.05 0.19
Matches are distributed among these distances:
7 25 0.19
8 51 0.38
9 25 0.19
10 2 0.02
11 30 0.23
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (8 bp):
TAATGATT
Found at i:1048278 original size:97 final size:95
Alignment explanation
Indices: 1048101--1048471 Score: 451
Period size: 97 Copynumber: 3.8 Consensus size: 95
1048091 TCAATTAACC
*
1048101 ATAAAAATGATTTAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTTAATAT
1 ATAATAATGATTTAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTTAATAT
*
1048166 TTAATGATTTTATGATTTAGTAATGATTTA
66 TTAATGATTTGATGATTTAGTAATGATTTA
* * * * *
1048196 ATGATTTGATGATTTAGTAATGATTTTAATGTTTAATGATTTAATGATTTAGTAATGATTTTAAT
1 AT-A-ATAATGATTTAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTTAAT
*
1048261 ATTTAATGATTTGATGATTTAGTAATGATTTG
64 ATTTAATGATTTGATGATTTAGTAATGATTTA
1048293 ATAATAATGATTTAATAATG-TTTTCAATATTTAATGATTTGATGATTTAGTAATGATTTGATAA
1 ATAATAATGATTTAATAATGATTTT-AATATTTAATGATTTGATGATTTAGTAATGATTT--TAA
* ** * * * *
1048357 AAACT-ATTATAATAATGATTTAGTAATAATCATT-
63 TATTTAATGAT-TTGATGATTTAGTAATGAT--TTA
1048391 ATAATAATGATTTAATAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTGAT
1 ATAATAATGA-TT--TAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTT--T
*
1048456 GATATATTAATGATTT
61 AATAT-TTAATGATTT
1048472 AATAATTATT
Statistics
Matches: 236, Mismatches: 26, Indels: 21
0.83 0.09 0.07
Matches are distributed among these distances:
94 4 0.02
95 48 0.20
96 6 0.03
97 107 0.45
98 10 0.04
99 4 0.02
101 47 0.20
102 6 0.03
103 4 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (95 bp):
ATAATAATGATTTAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTTAATAT
TTAATGATTTGATGATTTAGTAATGATTTA
Found at i:1048288 original size:19 final size:19
Alignment explanation
Indices: 1048132--1048354 Score: 116
Period size: 19 Copynumber: 11.6 Consensus size: 19
1048122 TTTTAATATT
1048132 TAATGATTTGATGATTTAG
1 TAATGATTTGATGATTTAG
*
1048151 TAATGATTT--TAATATT--
1 TAATGATTTGATGAT-TTAG
*
1048167 TAATGATTTTATGATTTAG
1 TAATGATTTGATGATTTAG
*
1048186 TAATGATTTAATGATTT-G
1 TAATGATTTGATGATTTAG
1048204 --ATGATTTAGTAATGATTTTAATG
1 TAATGATTT-G--ATGA-TTT-A-G
*
1048227 TTTAATGATTTAATGATTTAG
1 --TAATGATTTGATGATTTAG
*
1048248 TAATGATTT--TAATATT--
1 TAATGATTTGATGAT-TTAG
1048264 TAATGATTTGATGATTTAG
1 TAATGATTTGATGATTTAG
*
1048283 TAATGATTTGATAATAATGATTTAA
1 TAATGATTTG------ATGATTTAG
* *
1048308 TAATGTTTTCA--ATATT--
1 TAATGATTTGATGAT-TTAG
1048324 TAATGATTTGATGATTTAG
1 TAATGATTTGATGATTTAG
1048343 TAATGATTTGAT
1 TAATGATTTGAT
1048355 AAAAACTATT
Statistics
Matches: 160, Mismatches: 12, Indels: 64
0.68 0.05 0.27
Matches are distributed among these distances:
16 34 0.21
17 14 0.09
18 15 0.09
19 61 0.38
20 3 0.02
21 1 0.01
22 1 0.01
23 4 0.03
24 4 0.03
25 16 0.10
27 7 0.04
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (19 bp):
TAATGATTTGATGATTTAG
Found at i:1048322 original size:60 final size:60
Alignment explanation
Indices: 1048177--1048377 Score: 225
Period size: 60 Copynumber: 3.3 Consensus size: 60
1048167 TAATGATTTT
* * * *
1048177 ATGATTTAGTAATGA-TTTAATGATTTGATGATTTAGTAATGATTT--TAATG-TTTAATGATTT
1 ATGATTTAATAATGATTTTAAT-ATTTAATGATTT-G--ATGATTTAGTAATGATTTGAT-A-AT
1048238 A
60 A
*
1048239 ATGATTTAGTAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATA
1 ATGATTTAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATA
*
1048299 ATGATTTAATAATG-TTTTCAATATTTAATGATTTGATGATTTAGTAATGATTTGATAAAA
1 ATGATTTAATAATGATTTT-AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATA
1048359 ACT-ATTATAATAATGATTT
1 A-TGATT-TAATAATGATTT
1048378 AGTAATAATC
Statistics
Matches: 126, Mismatches: 5, Indels: 16
0.86 0.03 0.11
Matches are distributed among these distances:
59 11 0.09
60 59 0.47
61 16 0.13
62 34 0.27
63 6 0.05
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (60 bp):
ATGATTTAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATA
Found at i:1048385 original size:14 final size:13
Alignment explanation
Indices: 1048363--1048422 Score: 79
Period size: 14 Copynumber: 4.6 Consensus size: 13
1048353 ATAAAAACTA
1048363 TTATAATAATGAT
1 TTATAATAATGAT
*
1048376 TTAGTAATAATCA-
1 TTA-TAATAATGAT
1048389 TTATAATAATGAT
1 TTATAATAATGAT
1048402 TTAATAATAATGAT
1 TT-ATAATAATGAT
1048416 TT-TAATA
1 TTATAATA
1048423 TTTAATGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 13 0.31
13 8 0.19
14 21 0.50
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (13 bp):
TTATAATAATGAT
Found at i:1048406 original size:23 final size:25
Alignment explanation
Indices: 1048343--1048422 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 25
1048333 GATGATTTAG
*
1048343 TAATGATTTGATAA-AAACTATTATAA
1 TAATGATTT-ATAATAATC-ATTATAA
1048369 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
1048395 TAATGATTTAATAATAATGATTTTAA
1 TAATGATTT-ATAATAATCATTATAA
1048421 TA
1 TA
1048423 TTTAATGATT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 1 0.02
26 43 0.90
27 4 0.08
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (25 bp):
TAATGATTTATAATAATCATTATAA
Found at i:1048430 original size:16 final size:15
Alignment explanation
Indices: 1048365--1048433 Score: 67
Period size: 14 Copynumber: 4.9 Consensus size: 15
1048355 AAAAACTATT
1048365 ATAATAATGA-TTTA
1 ATAATAATGATTTTA
* *
1048379 GTAATAATCA--TT-
1 ATAATAATGATTTTA
1048391 ATAATAATGA-TTTA
1 ATAATAATGATTTTA
1048405 ATAATAATGATTTTA
1 ATAATAATGATTTTA
*
1048420 ATATTTAATGATTT
1 ATA-ATAATGATTT
1048434 GATGATTTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
12 8 0.17
13 4 0.09
14 18 0.39
15 7 0.15
16 9 0.20
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (15 bp):
ATAATAATGATTTTA
Found at i:1048441 original size:16 final size:17
Alignment explanation
Indices: 1048408--1048471 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 17
1048398 TGATTTAATA
*
1048408 ATAATGATTTTAAT-ATT
1 ATAATGA-TTTGATGATT
1048425 -TAATGATTTGATGATTT
1 ATAATGATTTGATGA-TT
1048442 AGTAATGATTTGATGATAT
1 A-TAATGATTTGATGAT-T
1048461 ATTAATGATTT
1 A-TAATGATTT
1048472 AATAATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 5 0.12
16 7 0.17
17 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (17 bp):
ATAATGATTTGATGATT
Found at i:1048447 original size:19 final size:19
Alignment explanation
Indices: 1048425--1048471 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1048415 TTTTAATATT
*
1048425 TAATGATTTGATGATTTAG
1 TAATGATTTGATGATATAG
*
1048444 TAATGATTTGATGATATAT
1 TAATGATTTGATGATATAG
1048463 TAATGATTT
1 TAATGATTT
1048472 AATAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (19 bp):
TAATGATTTGATGATATAG
Found at i:1048645 original size:17 final size:17
Alignment explanation
Indices: 1048606--1048646 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1048596 ATGATTTAGC
1048606 AATTATTATTAATAATG
1 AATTATTATTAATAATG
* * *
1048623 ATTTATTATTAATATTT
1 AATTATTATTAATAATG
1048640 AATTATT
1 AATTATT
1048647 TGATGCTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTATTATTAATAATG
Found at i:1049885 original size:14 final size:14
Alignment explanation
Indices: 1049866--1049894 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1049856 TTTTAATCAA
1049866 AATAAATATTTTAT
1 AATAAATATTTTAT
1049880 AATAAATATTTTAT
1 AATAAATATTTTAT
1049894 A
1 A
1049895 TTTAAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAAATATTTTAT
Found at i:1050948 original size:16 final size:16
Alignment explanation
Indices: 1050915--1050961 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1050905 CAAAAAAATT
1050915 TAATATAAT-AACTAA
1 TAATATAATAAACTAA
*
1050930 TAATATAATAAACTTA
1 TAATATAATAAACTAA
* *
1050946 TAAAATAACAAACTAA
1 TAATATAATAAACTAA
1050962 ACTTTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:1051036 original size:30 final size:30
Alignment explanation
Indices: 1051001--1051088 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
1050991 TTCCCTTAAA
1051001 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
*
1051031 CAACTAATAAATTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
1051061 AAACTAATAAACAATTTTTTAATTATAA
1 CAACTAATAAACTATTCTTTAA-TATAA
1051089 TTTACTACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:1051624 original size:14 final size:14
Alignment explanation
Indices: 1051605--1051637 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1051595 GGGAGCAGGC
*
1051605 GAGCATGCAGTGGG
1 GAGCATGCAGCGGG
1051619 GAGCATGCAGCGGG
1 GAGCATGCAGCGGG
1051633 GAGCA
1 GAGCA
1051638 GGCGCAGGAA
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:0.24, C:0.18, G:0.48, T:0.09
Consensus pattern (14 bp):
GAGCATGCAGCGGG
Found at i:1051746 original size:23 final size:23
Alignment explanation
Indices: 1051720--1051764 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1051710 ACCCTTGCTC
*
1051720 GCTCGCTCGGATGCCCTCGCATA
1 GCTCGCTCAGATGCCCTCGCATA
1051743 GCTCGCTCAGATGCCCTCGCAT
1 GCTCGCTCAGATGCCCTCGCAT
1051765 TCCCTCGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.40, G:0.24, T:0.22
Consensus pattern (23 bp):
GCTCGCTCAGATGCCCTCGCATA
Found at i:1051792 original size:33 final size:33
Alignment explanation
Indices: 1051733--1051797 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1051723 CGCTCGGATG
*
1051733 CCCTCGCATAGCTCGCTCAGATGCCCTCGCATT
1 CCCTCGCATAGCTCGCTCAGACGCCCTCGCATT
** *
1051766 CCCTCGCATAGCTCGCTTGGCCGCCCTCGCAT
1 CCCTCGCATAGCTCGCTCAGACGCCCTCGCAT
1051798 AACTCACTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.12, C:0.45, G:0.20, T:0.23
Consensus pattern (33 bp):
CCCTCGCATAGCTCGCTCAGACGCCCTCGCATT
Found at i:1051828 original size:33 final size:33
Alignment explanation
Indices: 1051791--1051855 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
1051781 CTTGGCCGCC
* *
1051791 CTCGCATAACTCACTCGAATGGCCTCGGATGCT
1 CTCGCATAACTCACTCGAATGCCCTCAGATGCT
* * *
1051824 CTCGCATAGCTCAGTCGGATGCCCTCAGATGC
1 CTCGCATAACTCACTCGAATGCCCTCAGATGC
1051856 CCAACGTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (33 bp):
CTCGCATAACTCACTCGAATGCCCTCAGATGCT
Found at i:1051848 original size:56 final size:56
Alignment explanation
Indices: 1051720--1051849 Score: 147
Period size: 56 Copynumber: 2.3 Consensus size: 56
1051710 ACCCTTGCTC
* * *
1051720 GCTCGCTCGGATGCCCTCGCATAGCTCGCTCAGATGCCCTCGCATTCCCTCGCATA
1 GCTCGCTCGGATGCCCTCGCATAACTCACTCAGATGCCCTCGCATGCCCTCGCATA
* ** * * *
1051776 GCTCGCTTGGCCGCCCTCGCATAACTCACTC-GAATGGCCTCGGATGCTCTCGCATA
1 GCTCGCTCGGATGCCCTCGCATAACTCACTCAG-ATGCCCTCGCATGCCCTCGCATA
1051832 GCTCAG-TCGGATGCCCTC
1 GCTC-GCTCGGATGCCCTC
1051850 AGATGCCCAA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
55 1 0.02
56 58 0.97
57 1 0.02
ACGTcount: A:0.15, C:0.39, G:0.23, T:0.23
Consensus pattern (56 bp):
GCTCGCTCGGATGCCCTCGCATAACTCACTCAGATGCCCTCGCATGCCCTCGCATA
Found at i:1053707 original size:14 final size:14
Alignment explanation
Indices: 1053688--1053743 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
1053678 ATCGAGATGC
1053688 TAAGTTAAATATGA
1 TAAGTTAAATATGA
*
1053702 TAAGTTAAAATATAA
1 TAAGTT-AAATATGA
* *
1053717 TTAATTTAAAGATGA
1 -TAAGTTAAATATGA
1053732 TAAGTTAAATAT
1 TAAGTTAAATAT
1053744 AATTGAGAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 16 0.47
15 13 0.38
16 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.38
Consensus pattern (14 bp):
TAAGTTAAATATGA
Found at i:1053714 original size:15 final size:15
Alignment explanation
Indices: 1053688--1053740 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1053678 ATCGAGATGC
1053688 TAAGTT-AAATATGA
1 TAAGTTAAAATATGA
*
1053702 TAAGTTAAAATATAA
1 TAAGTTAAAATATGA
* *
1053717 TTAA-TTTAAAGATGA
1 -TAAGTTAAAATATGA
1053732 TAAGTTAAA
1 TAAGTTAAA
1053741 TATAATTGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.29
15 19 0.61
16 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (15 bp):
TAAGTTAAAATATGA
Found at i:1068539 original size:4 final size:4
Alignment explanation
Indices: 1068532--1068558 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1068522 AACACTTTTG
1068532 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1068559 TTTGGTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1077751 original size:17 final size:17
Alignment explanation
Indices: 1077731--1077778 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1077721 TTTAATCATT
*
1077731 AAAAATAAATAAAAAAC
1 AAAAATAAATAAAAAAA
**
1077748 AAAAATAGTTAAAAAAA
1 AAAAATAAATAAAAAAA
1077765 AATAAGATAAATAA
1 AA-AA-ATAAATAA
1077779 TTAGGCCAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 16 0.67
18 2 0.08
19 6 0.25
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAAATAAATAAAAAAA
Found at i:1079318 original size:2 final size:2
Alignment explanation
Indices: 1079311--1079367 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1079301 ATAATGATTC
1079311 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
*
1079353 AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT A
1079368 AAGGGGAGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1079688 original size:20 final size:22
Alignment explanation
Indices: 1079650--1079693 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1079640 TAACTTTTTC
*
1079650 TTTTCTATTTCTTTATTAA-TT
1 TTTTCTATTTCATTATTAACTT
*
1079671 TTTTCTCTTTCATT-TTAACTT
1 TTTTCTATTTCATTATTAACTT
1079692 TT
1 TT
1079694 ACTTTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCTATTTCATTATTAACTT
Found at i:1083031 original size:24 final size:24
Alignment explanation
Indices: 1083004--1083053 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1082994 GTGTGGTTGA
* *
1083004 TTTAATGGT-TGTTTGAATTTTATT
1 TTTAATGGTATATTT-AAGTTTATT
1083028 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAAGTTTATT
1083052 TT
1 TT
1083054 GTTCTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (24 bp):
TTTAATGGTATATTTAAGTTTATT
Found at i:1089879 original size:20 final size:22
Alignment explanation
Indices: 1089841--1089884 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1089831 TAACTTTTTC
*
1089841 TTTTCTCTTTCTTTATTAA-TT
1 TTTTCTCTTTCATTATTAACTT
1089862 TTTTCTCTTTCATT-TTAACTT
1 TTTTCTCTTTCATTATTAACTT
1089883 TT
1 TT
1089885 ACTTTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCTCTTTCATTATTAACTT
Found at i:1089917 original size:46 final size:46
Alignment explanation
Indices: 1089828--1089917 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
1089818 CCTCTTAAAT
* * * *
1089828 TTTTAACTTTTTCTTTTCTCTTTCTTTATTAATTTTTTCTCTTTCA
1 TTTTAACTTTTACTTTTCTCTTTCTTCATTAATCTTCTCTCTTTCA
*
1089874 TTTTAACTTTTACTTTTCTCTTTCCTTCATTCATCTTCT-TCTTT
1 TTTTAACTTTTACTTTTCTCTTT-CTTCATTAATCTTCTCTCTTT
1089918 GTTATTCTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
46 27 0.71
47 11 0.29
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (46 bp):
TTTTAACTTTTACTTTTCTCTTTCTTCATTAATCTTCTCTCTTTCA
Found at i:1090673 original size:142 final size:142
Alignment explanation
Indices: 1090417--1090695 Score: 558
Period size: 142 Copynumber: 2.0 Consensus size: 142
1090407 GTCTTGGAGG
1090417 ACCTTTGTTTTGAAAACACTGAGTGGAATGGACGTCAAACGAGTCGATACTCGGTCAACCGAGAA
1 ACCTTTGTTTTGAAAACACTGAGTGGAATGGACGTCAAACGAGTCGATACTCGGTCAACCGAGAA
1090482 TGTCTTCAGCCGCGCGCCAAGTTATGGAATCACTTCCTTAAGCATAAACTCATGCCGACTTCTCA
66 TGTCTTCAGCCGCGCGCCAAGTTATGGAATCACTTCCTTAAGCATAAACTCATGCCGACTTCTCA
1090547 CAACACGGTATC
131 CAACACGGTATC
1090559 ACCTTTGTTTTGAAAACACTGAGTGGAATGGACGTCAAACGAGTCGATACTCGGTCAACCGAGAA
1 ACCTTTGTTTTGAAAACACTGAGTGGAATGGACGTCAAACGAGTCGATACTCGGTCAACCGAGAA
1090624 TGTCTTCAGCCGCGCGCCAAGTTATGGAATCACTTCCTTAAGCATAAACTCATGCCGACTTCTCA
66 TGTCTTCAGCCGCGCGCCAAGTTATGGAATCACTTCCTTAAGCATAAACTCATGCCGACTTCTCA
1090689 CAACACG
131 CAACACG
1090696 ACGGTATCAC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 137 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (142 bp):
ACCTTTGTTTTGAAAACACTGAGTGGAATGGACGTCAAACGAGTCGATACTCGGTCAACCGAGAA
TGTCTTCAGCCGCGCGCCAAGTTATGGAATCACTTCCTTAAGCATAAACTCATGCCGACTTCTCA
CAACACGGTATC
Found at i:1093228 original size:24 final size:24
Alignment explanation
Indices: 1093201--1093250 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1093191 GTGTGGTTGA
* *
1093201 TTTAATGGT-TGTTTGAATTTTATT
1 TTTAATGGTATATTT-AAATTTATT
1093225 TTTAATGGTATATTTAAATTTATT
1 TTTAATGGTATATTTAAATTTATT
1093249 TT
1 TT
1093251 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (24 bp):
TTTAATGGTATATTTAAATTTATT
Found at i:1103204 original size:24 final size:24
Alignment explanation
Indices: 1103177--1103226 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1103167 TGGTGGTTGA
*
1103177 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1103201 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1103225 TT
1 TT
1103227 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1111297 original size:23 final size:24
Alignment explanation
Indices: 1111243--1111294 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1111233 TAAGTTACTG
*
1111243 TTTTTATTGAATAAAAATATTATT
1 TTTTTATTGAATAAAAATAATATT
1111267 TTTTTATTGAATAAAAATAATATT
1 TTTTTATTGAATAAAAATAATATT
1111291 TTTT
1 TTTT
1111295 ATTATATCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTTATTGAATAAAAATAATATT
Found at i:1122167 original size:81 final size:81
Alignment explanation
Indices: 1122032--1122200 Score: 329
Period size: 81 Copynumber: 2.1 Consensus size: 81
1122022 ACCGGATGGA
1122032 TCGTGTTATCGTCTGATCTCAATGTCAATAACTGGTTACTTTGACCACGTACACATTTCCTCATG
1 TCGTGTTATCGTCTGATCTCAATGTCAATAACTGGTTACTTTGACCACGTACACATTTCCTCATG
1122097 ATTATCTTGTTCCCAT
66 ATTATCTTGTTCCCAT
1122113 TCGTGTTATCGTCTGATCTCAATGTCAATAACTGGTTACTTTGACCACGTACACATTTCCTCATG
1 TCGTGTTATCGTCTGATCTCAATGTCAATAACTGGTTACTTTGACCACGTACACATTTCCTCATG
1122178 ATTATCTTGTTCCCAT
66 ATTATCTTGTTCCCAT
*
1122194 TGGTGTT
1 TCGTGTT
1122201 GTTATAGTTG
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 87 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (81 bp):
TCGTGTTATCGTCTGATCTCAATGTCAATAACTGGTTACTTTGACCACGTACACATTTCCTCATG
ATTATCTTGTTCCCAT
Found at i:1124231 original size:33 final size:34
Alignment explanation
Indices: 1124172--1124261 Score: 155
Period size: 33 Copynumber: 2.7 Consensus size: 34
1124162 CCCATGTGCA
* *
1124172 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGACCACCAACCAAAGATGAATTTTCCAAT
1124206 AAGTTGACCACCAACC-AAGATGAATTTTCCAAT
1 AAGTTGACCACCAACCAAAGATGAATTTTCCAAT
1124239 AAGTTGACCACCAACCAAAGATG
1 AAGTTGACCACCAACCAAAGATG
1124262 TCAACTTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 33 0.62
34 20 0.38
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.22
Consensus pattern (34 bp):
AAGTTGACCACCAACCAAAGATGAATTTTCCAAT
Found at i:1138354 original size:39 final size:34
Alignment explanation
Indices: 1138276--1138354 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 34
1138266 TAATATCTAT
*
1138276 ATTTAATTTTTTATTTTTTAAAAATTGTACTTAAT
1 ATTT-ATTTTTTATTTTTTAAAAATTGTACTTAAA
*
1138311 ATTTATTTTTTATTTCATTTTAAAAATTCGTAGTTAAAA
1 ATTTATTTTTTA-TT--TTTTAAAAATT-GTACTT-AAA
1138350 ATTTA
1 ATTTA
1138355 ATGGATGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 8 0.22
35 6 0.16
37 11 0.30
38 5 0.14
39 7 0.19
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (34 bp):
ATTTATTTTTTATTTTTTAAAAATTGTACTTAAA
Found at i:1140105 original size:62 final size:62
Alignment explanation
Indices: 1140002--1140135 Score: 207
Period size: 62 Copynumber: 2.2 Consensus size: 62
1139992 GCATTGCATT
* * *
1140002 TCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTTCATTTCGT-GTTGCAATAGTTGGAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC-TCGTTGCAATAGTTGAAAA
* *
1140064 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATTTCTCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCTCGTTGCAATAGTTGAAAA
1140126 TCGCGTTGCG
1 TCGCGTTGCG
1140136 CTTTTCCATT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 1 0.02
62 65 0.98
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (62 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCTCGTTGCAATAGTTGAAAA
Found at i:1140112 original size:41 final size:41
Alignment explanation
Indices: 1140064--1140198 Score: 225
Period size: 41 Copynumber: 3.3 Consensus size: 41
1140054 TAGTTGGAAA
1140064 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
*
1140105 TCTCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
* * * *
1140146 TCGCGTTGTGGTAGTTGAAAATCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
1140187 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1140199 TTTTCATTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATT
Found at i:1140146 original size:103 final size:102
Alignment explanation
Indices: 1139998--1140218 Score: 289
Period size: 103 Copynumber: 2.2 Consensus size: 102
1139988 ATTCGCATTG
* * * *
1139998 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTTCATTTCGTGTTGCAATAGTTGGAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTTGAAA
*
1140063 ATCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTC
66 ATCGCGTTGCGAT-GTTGAAAATCGCGTTGCGATTTTC
* * ***
1140101 CATTTCTCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGTGGTAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTTGAAA
* ** ** *
1140166 ATCGCGTTGCGATTTTTCATTTCGCGTTGCGATTTTT
66 ATCGCGTTGCGATGTTGAAAATCGCGTTGCGATTTTC
1140203 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1140219 TGCGATTTTC
Statistics
Matches: 101, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
102 32 0.32
103 69 0.68
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (102 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTTGAAA
ATCGCGTTGCGATGTTGAAAATCGCGTTGCGATTTTC
Found at i:1140151 original size:20 final size:20
Alignment explanation
Indices: 1140085--1140219 Score: 99
Period size: 20 Copynumber: 6.7 Consensus size: 20
1140075 TAGTTGAAAA
*
1140085 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
1140105 TCTCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
1140126 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * * ** **
1140146 TCGCGTTGTGGTAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
1140167 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
*
1140187 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
1140207 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1140220 GCGATTTTCC
Statistics
Matches: 85, Mismatches: 28, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
20 59 0.69
21 26 0.31
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1140282 original size:19 final size:19
Alignment explanation
Indices: 1140218--1140283 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
1140208 CGCGTTGCGA
* *
1140218 TTGCGATTTTCCAAATTCG
1 TTGCGATTTTCTAAATTTG
** *
1140237 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATTTTCTA-AATT-T-G
1140259 TTGCGATTTTCTAAATTTG
1 TTGCGATTTTCTAAATTTG
1140278 TTGCGA
1 TTGCGA
1140284 AAATTCGTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 17 0.47
20 4 0.11
21 3 0.08
22 12 0.33
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (19 bp):
TTGCGATTTTCTAAATTTG
Found at i:1141053 original size:41 final size:41
Alignment explanation
Indices: 1141006--1141150 Score: 130
Period size: 42 Copynumber: 3.3 Consensus size: 41
1140996 GCAACGAATT
*
1141006 TGGAAAATCACAACAATAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCACAAC-ACAACTGTAGACTATCGCAACGCGAAA
* * * * * *
1141048 TGAAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAATGGA
1 TGGAAAATCACAACACAACTGT-AGACTATCGCAACGCG-AA---A
*
1141093 TTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 --TGGAAAATCACAAC-ACAACTGTAGACTATCGCAACGCGAAA
1141137 TGGAAAATCACAAC
1 TGGAAAATCACAAC
1141151 GCGATTTTCA
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
41 17 0.21
42 28 0.35
44 1 0.01
45 1 0.01
47 16 0.20
48 18 0.22
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (41 bp):
TGGAAAATCACAACACAACTGTAGACTATCGCAACGCGAAA
Found at i:1141116 original size:89 final size:89
Alignment explanation
Indices: 1141003--1141172 Score: 295
Period size: 89 Copynumber: 1.9 Consensus size: 89
1140993 TTCGCAACGA
* *
1141003 ATTTGGAAAATCACAACAATAACTGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGCGATT
1 ATTTGGAAAATCACAACAACAACTGTAGACTATCGCAACGCGAAATGAAAAATCACAACGCGATT
1141068 TTCAACTATCGCAACGCGAAATGG
66 TTCAACTATCGCAACGCGAAATGG
* * *
1141092 ATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCACAACGCGATT
1 ATTTGGAAAATCACAACAACAACTGTAGACTATCGCAACGCGAAATGAAAAATCACAACGCGATT
1141157 TTCAACTATCGCAACG
66 TTCAACTATCGCAACG
1141173 TGAATTTGCG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 76 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (89 bp):
ATTTGGAAAATCACAACAACAACTGTAGACTATCGCAACGCGAAATGAAAAATCACAACGCGATT
TTCAACTATCGCAACGCGAAATGG
Found at i:1141126 original size:48 final size:48
Alignment explanation
Indices: 1141003--1141140 Score: 157
Period size: 48 Copynumber: 3.0 Consensus size: 48
1140993 TTCGCAACGA
* * *
1141003 ATTTGGAAAATCACAACAATAACTGTAGACTATCGCAACGCGAAAT-G
1 ATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGG
* * *
1141050 A-----AAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAATGG
1 ATTTGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAATGG
1141092 ATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGG
1 ATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGG
1141140 A
1 A
1141141 AAATCACAAC
Statistics
Matches: 73, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
41 21 0.29
42 13 0.18
47 14 0.19
48 25 0.34
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.20
Consensus pattern (48 bp):
ATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGG
Found at i:1145020 original size:31 final size:31
Alignment explanation
Indices: 1144982--1145073 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
1144972 TTATTTTCTT
1144982 TAATTTGACTCTTAAATTTTAAATAAAATAC
1 TAATTTGACTCTTAAATTTTAAATAAAATAC
* * * *
1145013 TAATTTGACAT-TTAAGTGTTAGATAAAATAT
1 TAATTTGAC-TCTTAAATTTTAAATAAAATAC
* * *
1145044 TAAGTTGACTCTTACACTTTAAATAAAATA
1 TAATTTGACTCTTAAATTTTAAATAAAATA
1145074 TCAATTTAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.02
31 47 0.96
32 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (31 bp):
TAATTTGACTCTTAAATTTTAAATAAAATAC
Found at i:1150229 original size:30 final size:30
Alignment explanation
Indices: 1150153--1150231 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
1150143 TGAAATACCT
*
1150153 TTTTGATCCCTTAACTTTTGAAAATTAATC
1 TTTTGATCCTTTAACTTTTGAAAATTAATC
* *
1150183 TTTTGGT-CTCTAAACTTTTGAAAATT-ATCC
1 TTTTGATCCT-TTAACTTTTGAAAATTAAT-C
1150213 TTTTGATCCTTTAACTTTT
1 TTTTGATCCTTTAACTTTT
1150232 CAAACTTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
29 3 0.07
30 36 0.88
31 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.51
Consensus pattern (30 bp):
TTTTGATCCTTTAACTTTTGAAAATTAATC
Found at i:1154228 original size:17 final size:17
Alignment explanation
Indices: 1154206--1154238 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1154196 TTCTTAAACT
1154206 ATTTTTTTAATAATTTG
1 ATTTTTTTAATAATTTG
*
1154223 ATTTTTTTAGTAATTT
1 ATTTTTTTAATAATTT
1154239 TATATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
ATTTTTTTAATAATTTG
Found at i:1154850 original size:14 final size:13
Alignment explanation
Indices: 1154812--1154863 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 13
1154802 TGAATTTATA
1154812 TAATAAA-TATTT
1 TAATAAATTATTT
*
1154824 TAATAATTATATTT
1 TAATAAAT-TATTT
1154838 TAATATAATTA-TT
1 TAATA-AATTATTT
1154851 TAATAAA-TATTT
1 TAATAAATTATTT
1154863 T
1 T
1154864 TCATCTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 2 0.06
12 11 0.32
13 7 0.21
14 12 0.35
15 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATAAATTATTT
Found at i:1159400 original size:173 final size:173
Alignment explanation
Indices: 1159085--1159432 Score: 655
Period size: 173 Copynumber: 2.0 Consensus size: 173
1159075 CTTTTCTCGA
1159085 TATATTTAAATAAACCAACATTTCTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAATTTT
1 TATATTTAAATAAACCAACATTTCTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAATTTT
1159150 TGGTTTCACTTTCGGGATACCTTTTATTTTAAAATCATTAAAAGCGGACCTCAAATCAGTTATGA
66 TGGTTTCACTTTCGGGATACCTTTTATTTTAAAATCATTAAAAGCGGACCTCAAATCAGTTATGA
1159215 CTGGCCCACTTAAAACAATTTTAAATTAAAAATATATTACCCT
131 CTGGCCCACTTAAAACAATTTTAAATTAAAAATATATTACCCT
*
1159258 TATATTTAAAT-AACGAACATTTCTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAATTTT
1 TATATTTAAATAAACCAACATTTCTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAA-TTT
1159322 TTGGTTTCACTTTCGGGATACACTTTTATTTTAAAATCATTAAAAGCGGACCTCAAATCAGTTAT
65 TTGGTTTCACTTTCGGGATAC-CTTTTATTTTAAAATCATTAAAAGCGGACCTCAAATCAGTTAT
1159387 GACT-GCCCACTTAAAACAATTTTAAATTAAAAATATATTACCCT
129 GACTGGCCCACTTAAAACAATTTTAAATTAAAAATATATTACCCT
1159431 TA
1 TA
1159433 ATCCAATTAT
Statistics
Matches: 172, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
172 48 0.28
173 77 0.45
174 47 0.27
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (173 bp):
TATATTTAAATAAACCAACATTTCTTTTTCTCTCGTTCCCAAATTTTAGGTGACGAATCAATTTT
TGGTTTCACTTTCGGGATACCTTTTATTTTAAAATCATTAAAAGCGGACCTCAAATCAGTTATGA
CTGGCCCACTTAAAACAATTTTAAATTAAAAATATATTACCCT
Found at i:1161450 original size:55 final size:54
Alignment explanation
Indices: 1161390--1161722 Score: 291
Period size: 55 Copynumber: 6.0 Consensus size: 54
1161380 AGACTTGAAA
* * * * *
1161390 AATCTTCGAATGACGGGTTTGCTCCCTATCCCTTCAGGGAGTATAAGACTCGACC
1 AATCTTC-AATAACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
**
1161445 AATCTTCAGCA-AACATGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
1 AATCTTCA--ATAACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
* * * *
1161500 AATCTTCAACAAGCGTGTCTGCTCCCTATTCATTTAGGGAGTATAAGACTCAATC
1 AATCTTCAATAA-CGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
* *
1161555 AATCTTCAATAAACGGGT-TCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAAC
1 AATCTTCAAT-AACGGGTCT-GCTCCCTATTCATTCAGGGAGTATAAG-ACTCGATC
* * * * *
1161610 AATCTTCAACAAACGAGTCTGCTCCCTATTCTTCTACCAGAGAGTAT-AGAACTCGAAC
1 AATCTTCAA-TAACGGGTCTGCTCCCTATTCAT-T--CAGGGAGTATAAG-ACTCGATC
* * * *
1161668 AATCTTCACCA-AACGAGTCCGCTCCCTATTC-TACCAGAGAGTATAAGACTCGATC
1 AATCTTCA--ATAACGGGTCTGCTCCCTATTCAT-TCAGGGAGTATAAGACTCGATC
1161723 TTCATAAAAT
Statistics
Matches: 239, Mismatches: 24, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
53 1 0.00
54 6 0.03
55 176 0.74
56 7 0.03
57 1 0.00
58 47 0.20
60 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (54 bp):
AATCTTCAATAACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
Found at i:1163157 original size:55 final size:58
Alignment explanation
Indices: 1163055--1163186 Score: 154
Period size: 55 Copynumber: 2.4 Consensus size: 58
1163045 TTTATTTCTC
* * *
1163055 TTTTT-TCATTTTTCTCTT-TTTGTTTTTCTCTTACATTTTTCTTATA-TTTTCCA-T
1 TTTTTCTCATTTTTTTCTTCTTTGTTCTTCTCTTACATTTTTATTATATTTTTCCATT
*
1163109 TTTTTCTCATTTTTTTCTTCTTT-TTCTTCT-TCT-CATTTTTATTAATATTTTTTCATT
1 TTTTTCTCATTTTTTTCTTCTTTGTTCTTCTCT-TACATTTTTATT-ATATTTTTCCATT
1163166 TTTTTCTC-TTTTTTTCTTCTT
1 TTTTTCTCATTTTTTTCTTCTT
1163187 CAAGCGAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
54 15 0.22
55 22 0.32
56 22 0.32
57 9 0.13
ACGTcount: A:0.10, C:0.17, G:0.01, T:0.73
Consensus pattern (58 bp):
TTTTTCTCATTTTTTTCTTCTTTGTTCTTCTCTTACATTTTTATTATATTTTTCCATT
Found at i:1163170 original size:9 final size:9
Alignment explanation
Indices: 1163088--1163181 Score: 59
Period size: 9 Copynumber: 10.1 Consensus size: 9
1163078 TTTTCTCTTA
1163088 CATTTTTCTT
1 CATTTTT-TT
* *
1163098 -ATATTTTC
1 CATTTTTTT
1163106 CATTTTTTCT
1 CATTTTTT-T
1163116 CATTTTTTT
1 CATTTTTTT
1163125 C-TTCTTTTT
1 CATT-TTTTT
* *
1163134 C-TTCTTCT
1 CATTTTTTT
1163142 CATTTTTATT
1 CATTTTT-TT
*
1163152 AATATTTTTT
1 CAT-TTTTTT
1163162 CATTTTTTT
1 CATTTTTTT
*
1163171 CTCTTTTTTT
1 C-ATTTTTTT
1163181 C
1 C
1163182 TTCTTCAAGC
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
8 7 0.11
9 32 0.48
10 23 0.35
11 4 0.06
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (9 bp):
CATTTTTTT
Found at i:1176141 original size:13 final size:13
Alignment explanation
Indices: 1176123--1176149 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1176113 TTTATTTGTA
1176123 TTTTGATTTTTTT
1 TTTTGATTTTTTT
1176136 TTTTGATTTTTTT
1 TTTTGATTTTTTT
1176149 T
1 T
1176150 AATTCGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (13 bp):
TTTTGATTTTTTT
Found at i:1176746 original size:45 final size:47
Alignment explanation
Indices: 1176694--1176782 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
1176684 TCGAATAAAT
1176694 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
*
1176739 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1176783 TAACAAAGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:1186449 original size:8 final size:8
Alignment explanation
Indices: 1186438--1186553 Score: 87
Period size: 8 Copynumber: 13.9 Consensus size: 8
1186428 AAATAAAAGA
1186438 GAAAAAAT
1 GAAAAAAT
1186446 GAAAAAAT
1 GAAAAAAT
*
1186454 GAGAAAAAA
1 GA-AAAAAT
1186463 GAAAAATGAT
1 GAAAAA--AT
*
1186473 GGAAAAAAC
1 -GAAAAAAT
1186482 GAAAAGAA-
1 GAAAA-AAT
* *
1186490 AAAAAAAA
1 GAAAAAAT
1186498 GAAAAAAT
1 GAAAAAAT
1186506 GGAAAAGGGAA-
1 -GAAAA---AAT
1186517 GAAAAAAT
1 GAAAAAAT
1186525 G-AAAAAT
1 GAAAAAAT
1186532 GAAAAAAT
1 GAAAAAAT
1186540 G-AAAAAT
1 GAAAAAAT
1186547 GAAAAAA
1 GAAAAAA
1186554 AAAAGAGAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 26
0.74 0.05 0.21
Matches are distributed among these distances:
7 18 0.20
8 42 0.47
9 15 0.17
10 6 0.07
11 6 0.07
12 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:1187940 original size:51 final size:51
Alignment explanation
Indices: 1187879--1188242 Score: 365
Period size: 51 Copynumber: 6.9 Consensus size: 51
1187869 AAATTCGTTT
*
1187879 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1187930 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1187981 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * ** *
1188032 GTTGAAGATTGAGTCATATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* * **
1188084 GTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTT-
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACAAGTTC
* * * * **
1188138 TTATGAAGATTTTCCGAGTTCTATACTTTCTGAAAGAATAGGGAGCGGACCTGTTTC
1 GT-TGAAGA--TT--GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* * *
1188195 -ATGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
1188243 TCGTTTTATT
Statistics
Matches: 277, Mismatches: 24, Indels: 20
0.86 0.07 0.06
Matches are distributed among these distances:
51 142 0.51
52 10 0.04
54 5 0.02
55 82 0.30
56 36 0.13
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:1188005 original size:102 final size:105
Alignment explanation
Indices: 1187875--1188349 Score: 384
Period size: 111 Copynumber: 4.5 Consensus size: 105
1187865 AAGCAAATTC
1187875 GTTT-GTTGAAGA-TT-GAGTCCTATACTCTCTGAAGGAATAAGGAGCGGACAAGTTCGTTGAAG
1 GTTTCGTTGAAGATTTCGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGACAAGTTCGTTGAAG
*
1187937 ATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
66 ATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAA
* *
1187977 G-TTCGTTGAAGA-TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAG
1 GTTTCGTTGAAGATTTCGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGACAAGTTCGTTGAAG
* * * **
1188039 ATTGAGTCATATACTCTCTGAAGGAATAGAGAGCGAACCC
66 ATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAA
* * * * ** *
1188079 GTTTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTT-TTAT
1 GTTTCGTTGAAGA-T-TTCGAGTCCTATACTCTCTGAA-GGAATAAGGAGCGGACAAGTTCGT-T
* * * * **
1188142 GAAGATTTTCCGAGTTCTATACTTTCTGAAAGAATAGGGAGCGGACCT
62 GAAGA--TT--GAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAA
* * ** **
1188190 GTTTC-ATGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAAT-AGAGAGCGGACTCGTTTTATT
1 GTTTCGTTGAAGA--TTTCGAGTCCTATACTCTCTGAAGGAATAAG-GAGCGGACAAG-TTCGTT
* *
1188253 GAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACA
62 GAAGATTG----AGTCCTATACTCTCTGAATGAATAGAGAGCGGACA-A
* *
1188302 -TTT--TATGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GTTTCGT-TGAAGA-T-TTCGAGTCCTATACTCT-CTGAAGGAATAAGGAGC
1188350 AGGCTCGTCA
Statistics
Matches: 307, Mismatches: 40, Indels: 43
0.79 0.10 0.11
Matches are distributed among these distances:
101 2 0.01
102 92 0.30
103 10 0.03
106 3 0.01
107 40 0.13
108 1 0.00
109 7 0.02
110 42 0.14
111 108 0.35
112 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (105 bp):
GTTTCGTTGAAGATTTCGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGACAAGTTCGTTGAAG
ATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAA
Found at i:1188258 original size:166 final size:161
Alignment explanation
Indices: 1187881--1188349 Score: 498
Period size: 166 Copynumber: 2.9 Consensus size: 161
1187871 ATTCGTTTGT
* * *
1187881 TGAAGATTGAGTCCTATACTCTCTGAAGGAATA-AGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 TGAAGATTGAGTTCTATACTCTCTGAAGGAATAGA-GAGCGGACACGTTTTGTTGAAGATTGTTC
* * * *
1187940 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT-TGAAGA--TT-GAGTCCTATA
65 GAGTTCTATACTCTCTGAATGAATAGGGAGCGGACACGTT-TTATGAAGATTTTCGAGTTCTATA
* * *
1188001 CTCTCTGAATGAATAGGGAGCGGACAAGTTCGT
129 CTTTCTGAAAGAATAGGGAGCGGACAAGTTCGA
* *
1188034 TGAAGATTGAG-TCATATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
1 TGAAGATTGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTGTTGAAGATTGTTC
* * * *
1188098 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTTTCCGAGTTCTATA
65 GAGTTCTATACTCTCTGAATGAATAGGGAGCGGACACGTTTTATGAAGATTTT-CGAGTTCTATA
**
1188163 CTTTCTGAAAGAATAGGGAGCGGACCTGTTTC-A
129 CTTTCTGAAAGAATAGGGAGCGGACAAG-TTCGA
* *
1188196 TGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTG
1 TGAAGA---TT-GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTGTTGAAGATTG
* * * *
1188261 TTCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTCGAG-TC
62 TTCGAGTTC-TATACTCTCTGAATGAATAGGGAGCGGACACGTTTTATGAAGATT-TTCGAGTTC
* *
1188324 TTATACTTCCTGAAGGAATAGGGAGC
125 -TATACTTTCTGAAAGAATAGGGAGC
1188350 AGGCTCGTCA
Statistics
Matches: 264, Mismatches: 31, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
152 1 0.00
153 38 0.14
154 11 0.04
157 3 0.01
158 40 0.15
160 2 0.01
162 39 0.15
163 3 0.01
165 6 0.02
166 117 0.44
167 4 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (161 bp):
TGAAGATTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTGTTGAAGATTGTTCG
AGTTCTATACTCTCTGAATGAATAGGGAGCGGACACGTTTTATGAAGATTTTCGAGTTCTATACT
TTCTGAAAGAATAGGGAGCGGACAAGTTCGA
Found at i:1188351 original size:55 final size:55
Alignment explanation
Indices: 1187889--1188349 Score: 363
Period size: 55 Copynumber: 8.6 Consensus size: 55
1187879 GTTGAAGATT
* ** *
1187889 GAGTCCTATACTCTCTGAAGGAATA-AGGAGCGGACAAGTTCGT-TGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGA-GAGCGGACCCGTT-TTATGAAGATTGTTC
* * * ** *
1187940 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT-TGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TTATGAAGATTGTTC
* * * ** *
1187991 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT-TGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TTATGAAGATTGTTC
* *
1188042 GAG-TCATATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTGTTGAAGATTGTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-ATGAAGATTGTTC
* *
1188098 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTTTTATGAAGATT-TTCC
1 GAGTTCTATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTTTATGAAGATTGTT-C
* * * * * *
1188153 GAGTTCTATACTTTCTGAAAGAATAGGGAGCGGACCTGTTTCATGAAGATTTTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
*
1188208 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGTTC
* * * * *
1188264 AAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
*
1188319 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGAGAGC
1188350 AGGCTCGTCA
Statistics
Matches: 361, Mismatches: 33, Indels: 28
0.86 0.08 0.07
Matches are distributed among these distances:
50 2 0.01
51 131 0.36
52 6 0.02
54 4 0.01
55 133 0.37
56 81 0.22
57 4 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
Found at i:1198719 original size:43 final size:43
Alignment explanation
Indices: 1198652--1198738 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1198642 CTGCATTTGC
* *
1198652 ATAACATATAATTAACATCGCATAAAGGGTACAACTGTTATAT
1 ATAACATATAATTAAAATCACATAAAGGGTACAACTGTTATAT
*
1198695 ATAACATATAATTAAAATCACATAAAGTGTACAACTGTTATAT
1 ATAACATATAATTAAAATCACATAAAGGGTACAACTGTTATAT
1198738 A
1 A
1198739 ATGAGAAGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (43 bp):
ATAACATATAATTAAAATCACATAAAGGGTACAACTGTTATAT
Found at i:1201704 original size:49 final size:49
Alignment explanation
Indices: 1201632--1201729 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
1201622 ATCCCACAAG
1201632 TAAACTGGTTGGGAAGCAATAATATGTGTCAGAGGCACAGACTTTGCAA
1 TAAACTGGTTGGGAAGCAATAATATGTGTCAGAGGCACAGACTTTGCAA
1201681 TAAACTGGTTGGGAAGCAATAATATGTGTCAGAGGCACAGACTTTGCAA
1 TAAACTGGTTGGGAAGCAATAATATGTGTCAGAGGCACAGACTTTGCAA
1201730 GGATGAACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (49 bp):
TAAACTGGTTGGGAAGCAATAATATGTGTCAGAGGCACAGACTTTGCAA
Found at i:1213789 original size:12 final size:12
Alignment explanation
Indices: 1213772--1213808 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1213762 GTCCTTTCGT
1213772 TCTTACCACATG
1 TCTTACCACATG
1213784 TCTTACCACATG
1 TCTTACCACATG
1213796 TCTTACCACATG
1 TCTTACCACATG
1213808 T
1 T
1213809 TGGTTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.35
Consensus pattern (12 bp):
TCTTACCACATG
Found at i:1220359 original size:20 final size:20
Alignment explanation
Indices: 1220296--1220389 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
1220286 AAATAACCAA
**
1220296 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGATTTC
* * *
1220316 CAATTTTGCAACAC-AGTTTC
1 CAAATTCGCAACGCGA-TTTC
*
1220336 CAAATTCGCAACGCGATTTT
1 CAAATTCGCAACGCGATTTC
** * *
1220356 CAAATTTACAACGTGATTTT
1 CAAATTCGCAACGCGATTTC
*
1220376 CAAATTCACAACGC
1 CAAATTCGCAACGC
1220390 TAATTACCGA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
19 1 0.02
20 56 0.97
21 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:1225821 original size:18 final size:17
Alignment explanation
Indices: 1225782--1225824 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1225772 ATTTTATGGA
1225782 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1225798 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1225816 TATTATTAT
1 TATTATTAT
1225825 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1227498 original size:5 final size:5
Alignment explanation
Indices: 1227488--1227516 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1227478 TTCATCTTTC
1227488 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1227517 CATCACTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Done.