Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 37 of 42
Found at i:8464517 original size:40 final size:40
Alignment explanation
Indices: 8464473--8464684 Score: 235
Period size: 40 Copynumber: 5.2 Consensus size: 40
8464463 CTTTTTAACG
* * * *
8464473 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
* * * *
8464513 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
* *
8464553 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTAAATCGCA
* * *
8464596 TTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
* *
8464636 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTAAATCGCA
8464679 TTGCGA
1 TTGCGA
8464685 ACTTGGAAGC
Statistics
Matches: 146, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
40 92 0.63
41 2 0.01
42 5 0.03
43 47 0.32
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
Found at i:8464620 original size:83 final size:83
Alignment explanation
Indices: 8464473--8464684 Score: 277
Period size: 83 Copynumber: 2.6 Consensus size: 83
8464463 CTTTTTAACG
* * * * * *
8464473 TTGCGATTTTCTAAATCGCGTTGCGA--TTC-TCTCAATCGCATTGCGATTCTATAAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
* * * *
8464535 GCGATTCTCTCAGTCGCA
66 GCGATTATATAAATCGCA
* * *
8464553 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
8464618 GCGATTATATAAATCGCA
66 GCGATTATATAAATCGCA
*
8464636 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
8464685 ACTTGGAAGC
Statistics
Matches: 114, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
80 22 0.19
82 3 0.03
83 89 0.78
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (83 bp):
TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
GCGATTATATAAATCGCA
Found at i:8464778 original size:19 final size:20
Alignment explanation
Indices: 8464738--8464788 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
8464728 TTCTTTTTAA
*
8464738 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
8464758 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
8464777 CGTTGCGATTTT
1 CGTTGCGATTTT
8464789 ATTGGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:8467044 original size:19 final size:19
Alignment explanation
Indices: 8467019--8467063 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
8467009 AATGATAAAG
*
8467019 AAAAAAAAGTAAATATAACC
1 AAAAAAACGTAAATATAA-C
*
8467039 AAAAAAACCGTTAATATAAC
1 AAAAAAA-CGTAAATATAAC
8467059 AAAAA
1 AAAAA
8467064 TAATACAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.69, C:0.11, G:0.04, T:0.16
Consensus pattern (19 bp):
AAAAAAACGTAAATATAAC
Found at i:8467045 original size:21 final size:20
Alignment explanation
Indices: 8467019--8467063 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
8467009 AATGATAAAG
8467019 AAAAAAAAGTAAATATAACCA
1 AAAAAAAAGTAAATATAA-CA
** *
8467040 AAAAAACCGTTAATATAACA
1 AAAAAAAAGTAAATATAACA
8467060 AAAA
1 AAAA
8467064 TAATACAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.69, C:0.11, G:0.04, T:0.16
Consensus pattern (20 bp):
AAAAAAAAGTAAATATAACA
Found at i:8471279 original size:25 final size:24
Alignment explanation
Indices: 8471213--8471281 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 24
8471203 AATCAAACTA
*
8471213 ACAATATTTAATATTTTAATGATT
1 ACAATATTTAATATTTTAATAATT
***
8471237 A-AA-ATTTAATAAAATAATAATAT
1 ACAATATTTAATATTTTAATAAT-T
8471260 ACAATATTTAATATTTTAATAA
1 ACAATATTTAATATTTTAATAA
8471282 CTAAAACTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 14 0.40
23 4 0.11
24 3 0.09
25 14 0.40
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (24 bp):
ACAATATTTAATATTTTAATAATT
Found at i:8471287 original size:47 final size:47
Alignment explanation
Indices: 8471213--8471309 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 47
8471203 AATCAAACTA
* * *
8471213 ACAATATTTAATATTTTAATGATTAAAATTTAATAAAATAATAATAT
1 ACAATATTTAATATTTTAATAACTAAAACTTAATAAAATAATAATAT
*
8471260 ACAATATTTAATATTTTAATAACTAAAACTTAGTAAAATAATAATAT
1 ACAATATTTAATATTTTAATAACTAAAACTTAATAAAATAATAATAT
8471307 ACA
1 ACA
8471310 TAATTAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (47 bp):
ACAATATTTAATATTTTAATAACTAAAACTTAATAAAATAATAATAT
Found at i:8471642 original size:31 final size:31
Alignment explanation
Indices: 8471584--8471693 Score: 116
Period size: 31 Copynumber: 3.5 Consensus size: 31
8471574 GATTTTAAAA
* *
8471584 AATAGAAGATATGATTAATTTTATTTTTACTT
1 AATA-AAGATATGATCACTTTTATTTTTACTT
* *
8471616 CATCAAAG-TATGATCAC-TTTAGTTTTTATTT
1 AAT-AAAGATATGATCACTTTTA-TTTTTACTT
* *
8471647 AATAAAGATATTATCACTTTTATTTTTAGTT
1 AATAAAGATATGATCACTTTTATTTTTACTT
*
8471678 AATTAAGATATGATCA
1 AATAAAGATATGATCA
8471694 TCACGAGTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
30 8 0.12
31 47 0.72
32 9 0.14
33 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.47
Consensus pattern (31 bp):
AATAAAGATATGATCACTTTTATTTTTACTT
Found at i:8471895 original size:22 final size:21
Alignment explanation
Indices: 8471870--8471932 Score: 51
Period size: 22 Copynumber: 2.9 Consensus size: 21
8471860 TATATTTAAA
8471870 TTAAGTTAATAATAAAATATAT
1 TTAAGTTAATAATAAAATAT-T
8471892 TTAA--TAAGTTAATATAAA-ATT
1 TTAAGTTAA--TAATA-AAATATT
*
8471913 TTAAGTTAATATATATAATA
1 TTAAGTTAATA-ATAAAATA
8471933 GGCTTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 14
0.69 0.02 0.29
Matches are distributed among these distances:
20 3 0.09
21 9 0.27
22 15 0.45
23 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
TTAAGTTAATAATAAAATATT
Found at i:8471899 original size:25 final size:27
Alignment explanation
Indices: 8471853--8471911 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
8471843 TAAAAATACA
8471853 AATAAAATATATTTAAATTAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
8471880 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
8471905 -ATAAAAT
1 AATAAAAT
8471912 TTTAAGTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 7 0.22
25 9 0.28
26 2 0.06
27 14 0.44
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (27 bp):
AATAAAATATATTTAAATTAAGTTAAT
Found at i:8503707 original size:21 final size:22
Alignment explanation
Indices: 8503674--8503718 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
8503664 ATTTAAATTT
* *
8503674 TTTTTATAACTATT-ATGAAAA
1 TTTTCATAACTATTAAAGAAAA
*
8503695 TTTTCATATCTATTAAAGAAAA
1 TTTTCATAACTATTAAAGAAAA
8503717 TT
1 TT
8503719 AAGTGTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTTCATAACTATTAAAGAAAA
Found at i:8505087 original size:17 final size:17
Alignment explanation
Indices: 8505067--8505110 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
8505057 TTATTGTATC
8505067 ATTTCTTTTATTACACT
1 ATTTCTTTTATTACACT
* * *
8505084 ATTTATCTTATTATACT
1 ATTTCTTTTATTACACT
*
8505101 ATATCTTTTA
1 ATTTCTTTTA
8505111 CTGTTCTGTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTCTTTTATTACACT
Found at i:8505628 original size:24 final size:26
Alignment explanation
Indices: 8505596--8505646 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
8505586 TAACGGATAT
* *
8505596 TCGATACTAA-TTT-ATTTTATCAAA
1 TCGAAACTAACTTTAATTCTATCAAA
8505620 TCGAAACTAACTTTAATTCTATCAAA
1 TCGAAACTAACTTTAATTCTATCAAA
8505646 T
1 T
8505647 TATTCTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 3 0.13
26 11 0.48
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (26 bp):
TCGAAACTAACTTTAATTCTATCAAA
Found at i:8509233 original size:2 final size:2
Alignment explanation
Indices: 8509226--8509260 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
8509216 AACTTTTATT
8509226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8509261 TTTTGGATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8515140 original size:63 final size:63
Alignment explanation
Indices: 8515067--8515196 Score: 251
Period size: 63 Copynumber: 2.1 Consensus size: 63
8515057 GTTACAAGGC
8515067 TGCTCACCTTTTGAACGGTTATTTTCGAGACAACCAATCTATGATCACTTACGCGTGTTTGGA
1 TGCTCACCTTTTGAACGGTTATTTTCGAGACAACCAATCTATGATCACTTACGCGTGTTTGGA
*
8515130 TGCTCACCTTTTGAACGGTTATTTTCGAGACAACCAATCTATGATCACTTACGCTTGTTTGGA
1 TGCTCACCTTTTGAACGGTTATTTTCGAGACAACCAATCTATGATCACTTACGCGTGTTTGGA
8515193 TGCT
1 TGCT
8515197 TATGCTTTCC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (63 bp):
TGCTCACCTTTTGAACGGTTATTTTCGAGACAACCAATCTATGATCACTTACGCGTGTTTGGA
Found at i:8519688 original size:17 final size:18
Alignment explanation
Indices: 8519648--8519685 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
8519638 ACCGGTCACA
8519648 ACCCGA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
8519665 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
8519683 ACC
1 ACC
8519686 GACTCGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:8519709 original size:8 final size:7
Alignment explanation
Indices: 8519690--8519720 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
8519680 TTGACCGACT
8519690 CGTTGAC
1 CGTTGAC
8519697 CGTTGACC
1 CGTTGA-C
8519705 CGTTGAC
1 CGTTGAC
8519712 CGTTGAC
1 CGTTGAC
8519719 CG
1 CG
8519721 GAGTTGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CGTTGAC
Found at i:8519710 original size:15 final size:15
Alignment explanation
Indices: 8519674--8519719 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
8519664 GACCCGACCC
8519674 GACCCGTTGACC---
1 GACCCGTTGACCGTT
*
8519686 GACTCGTTGACCGTT
1 GACCCGTTGACCGTT
8519701 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
8519716 GACC
1 GACC
8519720 GGAGTTGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.38
15 18 0.62
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:8522205 original size:48 final size:48
Alignment explanation
Indices: 8522153--8522284 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 48
8522143 AATATTTTAC
*
8522153 CTGATTTTTGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTTGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * * *
8522201 CTGATATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTTGA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
8522249 CTG-TTACTT-AACCTGATTTCTGATATGATACTTGAC
1 CTGATT-TTTGAA-TTGATTTCTGATCTGATACTTGAC
8522285 CTGATTTATG
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
46 1 0.01
47 4 0.06
48 61 0.88
49 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (48 bp):
CTGATTTTTGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:8522291 original size:24 final size:24
Alignment explanation
Indices: 8522170--8522284 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
8522160 TTGATTTGAT
8522170 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
8522194 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
8522218 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* * *
8522242 TTCTGATCTGTTACTTAACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
8522265 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
8522285 CTGATTTATG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:8524447 original size:11 final size:11
Alignment explanation
Indices: 8524431--8524468 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8524421 GGTTTGACCG
8524431 GTTTTGGAACT
1 GTTTTGGAACT
* *
8524442 GTTTT-GACCG
1 GTTTTGGAACT
8524452 GTTTTGGAACT
1 GTTTTGGAACT
8524463 GTTTTG
1 GTTTTG
8524469 ACCGGTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.13, C:0.11, G:0.29, T:0.47
Consensus pattern (11 bp):
GTTTTGGAACT
Found at i:8524447 original size:21 final size:21
Alignment explanation
Indices: 8524423--8524476 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
8524413 AAGTGACCGG
8524423 TTTGACCGGTTTTGGAACTGT
1 TTTGACCGGTTTTGGAACTGT
8524444 TTTGACCGGTTTTGGAACTGT
1 TTTGACCGGTTTTGGAACTGT
8524465 TTTGACCGGTTT
1 TTTGACCGGTTT
8524477 GACCGGTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.44
Consensus pattern (21 bp):
TTTGACCGGTTTTGGAACTGT
Found at i:8524510 original size:13 final size:13
Alignment explanation
Indices: 8524510--8524567 Score: 71
Period size: 13 Copynumber: 4.3 Consensus size: 13
8524500 CCGTTGACCC
8524510 GACCCGACCCGTT
1 GACCCGACCCGTT
*
8524523 TACCCGACCCGTT
1 GACCCGACCCGTT
*
8524536 GACCCGACTCGTT
1 GACCCGACCCGTT
*
8524549 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
8524564 GACC
1 GACC
8524568 GTTGACCGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
13 27 0.71
15 11 0.29
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.21
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:8524511 original size:18 final size:18
Alignment explanation
Indices: 8524488--8524533 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
8524478 ACCGGTCACA
8524488 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
8524506 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
8524524 ACCCGACCCG
1 ACCCGACCCG
8524534 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:8524539 original size:8 final size:8
Alignment explanation
Indices: 8524528--8524574 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
8524518 CCGTTTACCC
8524528 GACCCGTT
1 GACCCGTT
8524536 GACCC---
1 GACCCGTT
*
8524541 GACTCGTT
1 GACCCGTT
8524549 GA-CCGTT
1 GACCCGTT
8524556 GACCCGTT
1 GACCCGTT
8524564 GA-CCGTT
1 GACCCGTT
8524571 GACC
1 GACC
8524575 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
5 4 0.12
7 13 0.41
8 15 0.47
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:8524557 original size:7 final size:7
Alignment explanation
Indices: 8524545--8524575 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
8524535 TGACCCGACT
8524545 CGTTGAC
1 CGTTGAC
8524552 CGTTGACC
1 CGTTGA-C
8524560 CGTTGAC
1 CGTTGAC
8524567 CGTTGAC
1 CGTTGAC
8524574 CG
1 CG
8524576 GAGTTGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CGTTGAC
Found at i:8524565 original size:15 final size:15
Alignment explanation
Indices: 8524528--8524574 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
8524518 CCGTTTACCC
*
8524528 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
*
8524541 GACTCGTTGACCGTT
1 GACCCGTTGACCGTT
8524556 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
8524571 GACC
1 GACC
8524575 GGAGTTGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.38
15 18 0.62
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:8527062 original size:48 final size:48
Alignment explanation
Indices: 8527010--8527141 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 48
8527000 AATATTTTAC
*
8527010 CTGATTTTTGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTTGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * * *
8527058 CTGATATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTTGA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
8527106 CTG-TTACTT-AACCTGATTTCTGATATGATACTTGAC
1 CTGATT-TTTGAA-TTGATTTCTGATCTGATACTTGAC
8527142 CTGATTTATG
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
46 1 0.01
47 4 0.06
48 61 0.88
49 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (48 bp):
CTGATTTTTGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:8527148 original size:24 final size:24
Alignment explanation
Indices: 8527027--8527141 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
8527017 TTGATTTGAT
8527027 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
8527051 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
8527075 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* * *
8527099 TTCTGATCTGTTACTTAACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
8527122 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
8527142 CTGATTTATG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:8529301 original size:11 final size:11
Alignment explanation
Indices: 8529285--8529322 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8529275 GGTTTGACCG
8529285 GTTTTGGAACT
1 GTTTTGGAACT
* *
8529296 GTTTT-GACCG
1 GTTTTGGAACT
8529306 GTTTTGGAACT
1 GTTTTGGAACT
8529317 GTTTTG
1 GTTTTG
8529323 ACCGGTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.13, C:0.11, G:0.29, T:0.47
Consensus pattern (11 bp):
GTTTTGGAACT
Found at i:8529301 original size:21 final size:21
Alignment explanation
Indices: 8529277--8529330 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
8529267 AAGTGACCGG
8529277 TTTGACCGGTTTTGGAACTGT
1 TTTGACCGGTTTTGGAACTGT
8529298 TTTGACCGGTTTTGGAACTGT
1 TTTGACCGGTTTTGGAACTGT
8529319 TTTGACCGGTTT
1 TTTGACCGGTTT
8529331 GACCGGTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.44
Consensus pattern (21 bp):
TTTGACCGGTTTTGGAACTGT
Found at i:8529364 original size:13 final size:13
Alignment explanation
Indices: 8529364--8529421 Score: 71
Period size: 13 Copynumber: 4.3 Consensus size: 13
8529354 CCGTTGACCC
8529364 GACCCGACCCGTT
1 GACCCGACCCGTT
*
8529377 TACCCGACCCGTT
1 GACCCGACCCGTT
*
8529390 GACCCGACTCGTT
1 GACCCGACCCGTT
*
8529403 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
8529418 GACC
1 GACC
8529422 GTTGACCGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
13 27 0.71
15 11 0.29
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.21
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:8529365 original size:18 final size:18
Alignment explanation
Indices: 8529342--8529387 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
8529332 ACCGGTCACA
8529342 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
8529360 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
8529378 ACCCGACCCG
1 ACCCGACCCG
8529388 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:8529393 original size:8 final size:8
Alignment explanation
Indices: 8529382--8529428 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
8529372 CCGTTTACCC
8529382 GACCCGTT
1 GACCCGTT
8529390 GACCC---
1 GACCCGTT
*
8529395 GACTCGTT
1 GACCCGTT
8529403 GA-CCGTT
1 GACCCGTT
8529410 GACCCGTT
1 GACCCGTT
8529418 GA-CCGTT
1 GACCCGTT
8529425 GACC
1 GACC
8529429 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
5 4 0.12
7 13 0.41
8 15 0.47
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:8529411 original size:7 final size:7
Alignment explanation
Indices: 8529399--8529429 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
8529389 TGACCCGACT
8529399 CGTTGAC
1 CGTTGAC
8529406 CGTTGACC
1 CGTTGA-C
8529414 CGTTGAC
1 CGTTGAC
8529421 CGTTGAC
1 CGTTGAC
8529428 CG
1 CG
8529430 GAGTTGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CGTTGAC
Found at i:8529419 original size:15 final size:15
Alignment explanation
Indices: 8529382--8529428 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
8529372 CCGTTTACCC
*
8529382 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
*
8529395 GACTCGTTGACCGTT
1 GACCCGTTGACCGTT
8529410 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
8529425 GACC
1 GACC
8529429 GGAGTTGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.38
15 18 0.62
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:8531914 original size:48 final size:48
Alignment explanation
Indices: 8531862--8531993 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 48
8531852 AATATTTTAC
*
8531862 CTGATTTTTGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTTGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * * *
8531910 CTGATATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTTGA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
8531958 CTG-TTACTT-AACCTGATTTCTGATATGATACTTGAC
1 CTGATT-TTTGAA-TTGATTTCTGATCTGATACTTGAC
8531994 CTGATTTATG
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
46 1 0.01
47 4 0.06
48 61 0.88
49 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (48 bp):
CTGATTTTTGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:8532000 original size:24 final size:24
Alignment explanation
Indices: 8531879--8531993 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
8531869 TTGATTTGAT
8531879 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
8531903 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
8531927 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* * *
8531951 TTCTGATCTGTTACTTAACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
8531974 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
8531994 CTGATTTATG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:8532214 original size:2 final size:2
Alignment explanation
Indices: 8532207--8532281 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
8532197 TGGATGGGGG
8532207 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
8532249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8532282 GTTTTTTTAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8533414 original size:2 final size:2
Alignment explanation
Indices: 8533407--8533433 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8533397 TGTTTCAGTC
8533407 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8533434 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8535931 original size:18 final size:18
Alignment explanation
Indices: 8535908--8535962 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
8535898 GATGATGATA
8535908 ATGAAGAATATTACGATG
1 ATGAAGAATATTACGATG
8535926 ATGAAGAATATTACGATG
1 ATGAAGAATATTACGATG
* *
8535944 ATGAAGAATGTTATGATG
1 ATGAAGAATATTACGATG
8535962 A
1 A
8535963 GAAAAATGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.29
Consensus pattern (18 bp):
ATGAAGAATATTACGATG
Found at i:8535946 original size:21 final size:21
Alignment explanation
Indices: 8535901--8535947 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 21
8535891 CAATGATGAT
*
8535901 GATGATAATGAAGAATATTAC
1 GATGATGATGAAGAATATTAC
8535922 ---GATGATGAAGAATATTAC
1 GATGATGATGAAGAATATTAC
8535940 GATGATGA
1 GATGATGA
8535948 AGAATGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 17 0.77
21 5 0.23
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.28
Consensus pattern (21 bp):
GATGATGATGAAGAATATTAC
Found at i:8540739 original size:14 final size:15
Alignment explanation
Indices: 8540703--8540740 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
8540693 CTAACTCCAA
8540703 TATTTATTAAAATTAT
1 TATTT-TTAAAATTAT
8540719 TATTTTTAAATATT-T
1 TATTTTTAAA-ATTAT
8540734 TATTTTT
1 TATTTTT
8540741 TTATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTTAAAATTAT
Found at i:8540940 original size:24 final size:25
Alignment explanation
Indices: 8540913--8540959 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
8540903 TGTATTATTT
8540913 TAAAATAAAA-AAATAAT-TAGTTGA
1 TAAAATAAAACAAA-AATATAGTTGA
8540937 TAAAATAAAACAAAAATATAGTT
1 TAAAATAAAACAAAAATATAGTT
8540960 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (25 bp):
TAAAATAAAACAAAAATATAGTTGA
Found at i:8544376 original size:23 final size:23
Alignment explanation
Indices: 8544350--8544433 Score: 150
Period size: 23 Copynumber: 3.7 Consensus size: 23
8544340 CTCGTATAAA
* *
8544350 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
8544373 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
8544396 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
8544419 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
8544434 TATAATAATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:8549444 original size:23 final size:23
Alignment explanation
Indices: 8549418--8549501 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
8549408 CTCGTATAAA
* *
8549418 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
8549441 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
8549464 TGCACCGTAGTGCCACGTAGATT
1 TGCACCGTAGTGCCACGTAGAAT
8549487 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
8549502 TATAATAATG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:8549840 original size:27 final size:27
Alignment explanation
Indices: 8549809--8549867 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
8549799 ATATCATGTT
*
8549809 ACATAAA-TCATA-CTTTCTCATATATTC
1 ACATAAACT-ATATCTTT-TCATATACTC
*
8549836 ACATATACTATATCTTTTCATATACTC
1 ACATAAACTATATCTTTTCATATACTC
8549863 ACATA
1 ACATA
8549868 GTTATATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (27 bp):
ACATAAACTATATCTTTTCATATACTC
Found at i:8563326 original size:19 final size:18
Alignment explanation
Indices: 8563304--8563347 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
8563294 TTAACCGGTT
*
8563304 TTGACCGGTCTGAACCTGG
1 TTGACCGATCTGAA-CTGG
8563323 TTGACCGATCTGAACTGG
1 TTGACCGATCTGAACTGG
8563341 TTCGACC
1 TT-GACC
8563348 CGGCCCGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (18 bp):
TTGACCGATCTGAACTGG
Found at i:8563390 original size:18 final size:17
Alignment explanation
Indices: 8563344--8563400 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
8563334 GAACTGGTTC
8563344 GACCCGGCCCGACCCGTT
1 GACCCGGCCCGA-CCGTT
*
8563362 GACTCGGCCCGACCAGTT
1 GACCCGGCCCGACC-GTT
* *
8563380 GACCCGACCCGATCGTT
1 GACCCGGCCCGACCGTT
8563397 GACC
1 GACC
8563401 GTTGACAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.26
18 25 0.74
ACGTcount: A:0.16, C:0.44, G:0.26, T:0.14
Consensus pattern (17 bp):
GACCCGGCCCGACCGTT
Found at i:8563470 original size:29 final size:29
Alignment explanation
Indices: 8563413--8563554 Score: 83
Period size: 29 Copynumber: 4.8 Consensus size: 29
8563403 TGACAAGTGT
* * *
8563413 TATTCTGGGAATTAATTTG-ATTTTGGTGC
1 TATTCTTGGAATTAATTTGAAATAT-GTGC
8563442 TATTCTTGGAATTAATTTGAAATATGTGC
1 TATTCTTGGAATTAATTTGAAATATGTGC
** * * *
8563471 TATT-TTGGTAATTTTTTTCGGAAAAAAAAGTGA
1 TATTCTTGG-AATTAATTT--G--AAATATGTGC
* * * *
8563504 TATTCTAGGAATTAATTCGCAATTTGTGC
1 TATTCTTGGAATTAATTTGAAATATGTGC
*
8563533 TATT-TTGGTAATTAATTCGAAA
1 TATTCTTGG-AATTAATTTGAAA
8563555 AGAGTGATAT
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
28 7 0.08
29 54 0.63
30 3 0.03
31 2 0.02
33 17 0.20
34 3 0.03
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.44
Consensus pattern (29 bp):
TATTCTTGGAATTAATTTGAAATATGTGC
Found at i:8563566 original size:91 final size:91
Alignment explanation
Indices: 8563407--8563579 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 91
8563397 GACCGTTGAC
* * * * * * *
8563407 AAGTGTTATTCTGGGAATTAATTTGATTTTGGTGCTATTCTTGGAATTAATTTGAAATATGTGCT
1 AAGTGATATTCTAGGAATTAATTCGAATTTGGTGCTATTCTTGGAATTAATTCGAAATAAGTGAT
*
8563472 ATTTTGGTAATTTTTTTCGGAAAAAA
66 ATTTTGGTAATTATTTTCGGAAAAAA
8563498 AAGTGATATTCTAGGAATTAATTCGCAATTT-GTGCTATT-TTGGTAATTAATTCGAAA-AGAGT
1 AAGTGATATTCTAGGAATTAATTCG-AATTTGGTGCTATTCTTGG-AATTAATTCGAAATA-AGT
8563560 GATATTTTGGTAATTATTTT
63 GATATTTTGGTAATTATTTT
8563580 AAAAAGGGTG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
90 5 0.07
91 62 0.87
92 4 0.06
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (91 bp):
AAGTGATATTCTAGGAATTAATTCGAATTTGGTGCTATTCTTGGAATTAATTCGAAATAAGTGAT
ATTTTGGTAATTATTTTCGGAAAAAA
Found at i:8563584 original size:29 final size:29
Alignment explanation
Indices: 8563533--8563595 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
8563523 CAATTTGTGC
*
8563533 TATTTTGGTAATTAATTCGAAAAGAGTGA
1 TATTTTGGTAATTAATTCAAAAAGAGTGA
* * * *
8563562 TATTTTGGTAATTATTTTAAAAAGGGTGT
1 TATTTTGGTAATTAATTCAAAAAGAGTGA
8563591 TATTT
1 TATTT
8563596 CTGTAAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (29 bp):
TATTTTGGTAATTAATTCAAAAAGAGTGA
Found at i:8564348 original size:24 final size:24
Alignment explanation
Indices: 8564305--8564350 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
8564295 TTATCTGATT
*
8564305 TTTGACCTGGATTCTGATATGAGA
1 TTTGACCTGAATTCTGATATGAGA
* *
8564329 TTTGACCTGAATTTTTATATGA
1 TTTGACCTGAATTCTGATATGA
8564351 TACTTGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGACCTGAATTCTGATATGAGA
Found at i:8564357 original size:24 final size:24
Alignment explanation
Indices: 8564306--8564357 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
8564296 TATCTGATTT
* *
8564306 TTGACCTGGATTCTGATATGAGAT
1 TTGACCTGAATTCTGATATGAGAC
* * *
8564330 TTGACCTGAATTTTTATATGATAC
1 TTGACCTGAATTCTGATATGAGAC
8564354 TTGA
1 TTGA
8564358 TATGGACTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (24 bp):
TTGACCTGAATTCTGATATGAGAC
Found at i:8566155 original size:18 final size:19
Alignment explanation
Indices: 8566134--8566175 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
8566124 ATTGTAATTT
8566134 TTTACGA-TAATTTTTTAA
1 TTTACGATTAATTTTTTAA
* * *
8566152 TTTATGATTAGTTTTTTAT
1 TTTACGATTAATTTTTTAA
8566171 TTTAC
1 TTTAC
8566176 AACGATTTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTACGATTAATTTTTTAA
Found at i:8569963 original size:4 final size:4
Alignment explanation
Indices: 8569954--8569978 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
8569944 GTTACAATAT
8569954 ATAG ATAG ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG A
8569979 ATAATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:8581654 original size:2 final size:2
Alignment explanation
Indices: 8581647--8581706 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
8581637 CATTTATAAT
8581647 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
8581689 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
8581707 AACTTCATTT
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:8586356 original size:18 final size:18
Alignment explanation
Indices: 8586314--8586381 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
8586304 ATTCTAAATG
*
8586314 TTTACAGTTATCATAT-A
1 TTTACAGTTATCAGATAA
*
8586331 TTTTCAGTTATCAGATAA
1 TTTACAGTTATCAGATAA
* * *
8586349 TTTCCAGTTATAAGATAT
1 TTTACAGTTATCAGATAA
*
8586367 TTTACAATTATCAGA
1 TTTACAGTTATCAGA
8586382 CGTAGATTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 14 0.33
18 28 0.67
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (18 bp):
TTTACAGTTATCAGATAA
Found at i:8589416 original size:16 final size:17
Alignment explanation
Indices: 8589394--8589442 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
8589384 TAATTTAATA
8589394 AAATATTAATAAATT-T
1 AAATATTAATAAATTAT
* *
8589410 AAGTATTCA-AAATTAT
1 AAATATTAATAAATTAT
8589426 AAATA-TAATAAAATTAT
1 AAATATTAAT-AAATTAT
8589443 TTCTAAATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 7 0.27
16 12 0.46
17 7 0.27
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATATTAATAAATTAT
Found at i:8589895 original size:18 final size:20
Alignment explanation
Indices: 8589856--8589895 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
8589846 TGAATTAGTT
*
8589856 TTTATATATTCTTTTACATA
1 TTTATATATTCTTATACATA
8589876 TTTAT-TATTCTTAT-CATA
1 TTTATATATTCTTATACATA
8589894 TT
1 TT
8589896 CATTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 8 0.42
20 5 0.26
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATATATTCTTATACATA
Found at i:8593892 original size:29 final size:29
Alignment explanation
Indices: 8593854--8593930 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
8593844 TTCTATATTG
* *
8593854 ATCCCCAAACTTTTAAATGTTCTAATTTT
1 ATCCCTAAACTTTTGAATGTTCTAATTTT
* *
8593883 ATCTCTAAACTTTTGAATATTCTAATTTT
1 ATCCCTAAACTTTTGAATGTTCTAATTTT
8593912 ATCCCTAAACTTTTGAATG
1 ATCCCTAAACTTTTGAATG
8593931 ATTTTGGAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.45
Consensus pattern (29 bp):
ATCCCTAAACTTTTGAATGTTCTAATTTT
Found at i:8593980 original size:29 final size:29
Alignment explanation
Indices: 8593947--8594037 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
8593937 GAGGAAATTG
8593947 TTAGAATAATCAAAAGTTTAAGGATCAAT
1 TTAGAATAATCAAAAGTTTAAGGATCAAT
* * **
8593976 TTAGAATGAGAGTC-ATAGTTT-GGGATGGAT
1 TTAGAAT-A-A-TCAAAAGTTTAAGGATCAAT
*
8594006 TT-GAAATATTCAAAAGTTTAAGGATCAAT
1 TTAG-AATAATCAAAAGTTTAAGGATCAAT
8594035 TTA
1 TTA
8594038 AAATGAAAGC
Statistics
Matches: 46, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
27 2 0.04
28 6 0.13
29 17 0.37
30 12 0.26
31 7 0.15
32 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
TTAGAATAATCAAAAGTTTAAGGATCAAT
Found at i:8606582 original size:74 final size:74
Alignment explanation
Indices: 8606472--8606663 Score: 287
Period size: 74 Copynumber: 2.6 Consensus size: 74
8606462 TTTTTTTTTT
* * *
8606472 TGAAATAAAGATCAATCGAAATAATCATGGTAGAGTAGGTTAAGTAGTTGTTGTCCCCATAAATG
1 TGAAATAAAGATCAATCAAAATAATCAAGGTTGAGTAGGTTAAGTAGTTGTTGTCCCCATAAATG
*
8606537 ATGAAAATC-
66 AT-AAAAACA
* *
8606546 TGAAATAAAGATCAATCAAAACAATCAAGGTTGAGTAGGTTAAGTAGTTGTTGTCCCCATAACTG
1 TGAAATAAAGATCAATCAAAATAATCAAGGTTGAGTAGGTTAAGTAGTTGTTGTCCCCATAAATG
8606611 ATAAAAACA
66 ATAAAAACA
* *
8606620 TGAAATAAAGATCAATAAAAAATAATCAAGGTTGGGTAGGTTAA
1 TGAAATAAAGATCAAT-CAAAATAATCAAGGTTGAGTAGGTTAA
8606664 TTATTTTATC
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
73 5 0.05
74 78 0.73
75 24 0.22
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (74 bp):
TGAAATAAAGATCAATCAAAATAATCAAGGTTGAGTAGGTTAAGTAGTTGTTGTCCCCATAAATG
ATAAAAACA
Found at i:8607933 original size:58 final size:59
Alignment explanation
Indices: 8607822--8607933 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 59
8607812 TTTTATACCA
* *
8607822 ATTTAGAATGAAAGTCATAGTCTAGGGATGAAATTGAAATATTCAAAAGTTTAATAATTG
1 ATTTAGAAT-AAAGTCATAATCTAGGGATGAAATTGAAATATTCAAAAATTTAATAATTG
* *
8607882 ATTTAGAAT-AAGTCATAATTTAGGGATGAAATTGAAA-ATTTTAAAAATTTAA
1 ATTTAGAATAAAGTCATAATCTAGGGATGAAATTGAAATA-TTCAAAAATTTAA
8607934 GGAATAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
57 1 0.02
58 37 0.79
60 9 0.19
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.35
Consensus pattern (59 bp):
ATTTAGAATAAAGTCATAATCTAGGGATGAAATTGAAATATTCAAAAATTTAATAATTG
Found at i:8613488 original size:2 final size:2
Alignment explanation
Indices: 8613481--8613507 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8613471 ATATTTAAGA
8613481 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8613508 CTAACATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8614277 original size:149 final size:149
Alignment explanation
Indices: 8614007--8614301 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
8613997 AACTTGTGAA
8614007 TGGCTCGAACGAGTGCAAAGTGACTCAACATAGCTTTTACATCAGTGACCAGCTTAATCGTAGTG
1 TGGCTCGAACGAGTGCAAAGTGACTCAACATAGCTTTTACATCAGTGACCAGCTTAATCGTAGTG
*
8614072 GCAGAGTAAGATTGGACTTTCAGCATTTCTATGCCAAGGTTTCACATATGTTGGAGATTCACAAA
66 GCAGAGTAAGATTGGACTTTCAGCAATTCTATGCCAAGGTTTCACATATGTTGGAGATTCACAAA
8614137 CAAAACCCACAATTCGTAG
131 CAAAACCCACAATTCGTAG
*
8614156 TGGCTCGAACGAGTGCAAAGTGACTCAGCATAGCTTTTACATCAGTGACCAGCTTAATCGTAGTG
1 TGGCTCGAACGAGTGCAAAGTGACTCAACATAGCTTTTACATCAGTGACCAGCTTAATCGTAGTG
*
8614221 GCAGAGTCAGATTGGACTTTCAGCAATTCTATGCCAAGGTTTCACATATGTTGGAGATTCACAAA
66 GCAGAGTAAGATTGGACTTTCAGCAATTCTATGCCAAGGTTTCACATATGTTGGAGATTCACAAA
8614286 CAAAACCCACAATTCG
131 CAAAACCCACAATTCG
8614302 ACTTGAAGAA
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 143 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (149 bp):
TGGCTCGAACGAGTGCAAAGTGACTCAACATAGCTTTTACATCAGTGACCAGCTTAATCGTAGTG
GCAGAGTAAGATTGGACTTTCAGCAATTCTATGCCAAGGTTTCACATATGTTGGAGATTCACAAA
CAAAACCCACAATTCGTAG
Found at i:8616221 original size:21 final size:23
Alignment explanation
Indices: 8616179--8616222 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
8616169 AATTTTAATC
8616179 AAAATACTAATTATTAAATATTT
1 AAAATACTAATTATTAAATATTT
*
8616202 AAAATA-TATTTATT-AATATTT
1 AAAATACTAATTATTAAATATTT
8616223 CTAATAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATACTAATTATTAAATATTT
Found at i:8616291 original size:29 final size:29
Alignment explanation
Indices: 8616218--8616297 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
8616208 TATTTATTAA
* *
8616218 TATTTCTAATAATGT-AATATTATATTTT
1 TATTTATAATAATATAAATATTATATTTT
*
8616246 TAATATTAAAATAATATAAGATATTATATTTT
1 T-AT-TTATAATAATATAA-ATATTATATTTT
8616278 TATTT-TAATAATATACAATA
1 TATTTATAATAATATA-AATA
8616298 AATTATTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 1 0.02
29 14 0.33
30 12 0.28
31 3 0.07
32 13 0.30
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (29 bp):
TATTTATAATAATATAAATATTATATTTT
Found at i:8616395 original size:27 final size:27
Alignment explanation
Indices: 8616296--8616396 Score: 76
Period size: 27 Copynumber: 3.5 Consensus size: 27
8616286 TAATATACAA
*
8616296 TAAATTATTAATAAAATTTATATTATTTAT
1 TAAA-TATTAATAATA-TTAT-TTATTTAT
* * *
8616326 TAATTTCATTCAAATAATATTATTAAATTAT
1 TAA-AT-ATT--AATAATATTATTTATTTAT
** *
8616357 TAACGATGAATAATATTATTTATTTAT
1 TAAATATTAATAATATTATTTATTTAT
8616384 TAAATATTAATAA
1 TAAATATTAATAA
8616397 AATAATCTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
27 27 0.49
29 2 0.04
30 4 0.07
31 12 0.22
32 4 0.07
33 6 0.11
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.49
Consensus pattern (27 bp):
TAAATATTAATAATATTATTTATTTAT
Found at i:8616440 original size:23 final size:24
Alignment explanation
Indices: 8616408--8616460 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
8616398 ATAATCTTAT
* *
8616408 AATATTTTAA-TAATGATGTTGAA
1 AATATATTAATTAATGATGTTCAA
* *
8616431 AATATATTAATTAATTATTTTCAA
1 AATATATTAATTAATGATGTTCAA
8616455 AATATA
1 AATATA
8616461 ATATGATACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (24 bp):
AATATATTAATTAATGATGTTCAA
Found at i:8619281 original size:15 final size:15
Alignment explanation
Indices: 8619257--8619301 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
8619247 TAAAAGTATT
8619257 TTAAAT-TTAAAATA
1 TTAAATATTAAAATA
8619271 TTAAATATTAAAA-A
1 TTAAATATTAAAATA
*
8619285 GTTAAATATAAAAATA
1 -TTAAATATTAAAATA
8619301 T
1 T
8619302 CATTAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.26
15 19 0.70
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TTAAATATTAAAATA
Found at i:8619298 original size:14 final size:13
Alignment explanation
Indices: 8619257--8619299 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
8619247 TAAAAGTATT
*
8619257 TTAAATTTAAAATA
1 TTAAATATAAAA-A
8619271 TTAAATATTAAAAA
1 TTAAATA-TAAAAA
8619285 GTTAAATATAAAAA
1 -TTAAATATAAAAA
8619299 T
1 T
8619300 ATCATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 13 0.50
15 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
TTAAATATAAAAA
Found at i:8619328 original size:16 final size:16
Alignment explanation
Indices: 8619307--8619341 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
8619297 AATATCATTA
8619307 ATTATTAGTA-TTATTT
1 ATTATTA-TATTTATTT
8619323 ATTATTATATTTATTT
1 ATTATTATATTTATTT
8619339 ATT
1 ATT
8619342 TATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
ATTATTATATTTATTT
Found at i:8620256 original size:13 final size:14
Alignment explanation
Indices: 8620240--8620269 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
8620230 GATTTATTAA
8620240 ATAAAATTATA-AT
1 ATAAAATTATATAT
8620253 ATAAAATTATATAT
1 ATAAAATTATATAT
8620267 ATA
1 ATA
8620270 TATATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAAATTATATAT
Found at i:8632638 original size:20 final size:19
Alignment explanation
Indices: 8632591--8632629 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
8632581 ATGACCAACA
*
8632591 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
8632610 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
8632629 A
1 A
8632630 GTATCGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:8632718 original size:21 final size:21
Alignment explanation
Indices: 8632678--8632718 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8632668 GACTATTGCA
*
8632678 TTGCGATTTTTCAAATTCGCG
1 TTGCGATTTTTCAAAATCGCG
8632699 TTGCGATTTTGT-AAAATCGC
1 TTGCGATTTT-TCAAAATCGC
8632719 AATGCGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTTCAAAATCGCG
Found at i:8632737 original size:20 final size:20
Alignment explanation
Indices: 8632712--8632785 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
8632702 CGATTTTGTA
*
8632712 AAATCGCAATGCGAATATGT
1 AAATCGCAACGCGAATATGT
* *
8632732 AAATCGCAACGCGATTCTG-
1 AAATCGCAACGCGAATATGT
* *
8632751 ACTATCGCAATGCGAATATGT
1 A-AATCGCAACGCGAATATGT
8632772 AAATCGCAACGCGA
1 AAATCGCAACGCGA
8632786 TTCTGACTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:8632759 original size:40 final size:40
Alignment explanation
Indices: 8632714--8632805 Score: 175
Period size: 40 Copynumber: 2.3 Consensus size: 40
8632704 ATTTTGTAAA
8632714 ATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACT
1 ATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACT
8632754 ATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACT
1 ATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACT
*
8632794 ATCGCAACGCGA
1 ATCGCAATGCGA
8632806 TAATACAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (40 bp):
ATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACT
Found at i:8632797 original size:20 final size:20
Alignment explanation
Indices: 8632734--8632806 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
8632724 GAATATGTAA
8632734 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * * *
8632754 ATCGCAATGCGAATATGTA-A
1 ATCGCAACGCGATTCTG-ACT
8632774 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
8632794 ATCGCAACGCGAT
1 ATCGCAACGCGAT
8632807 AATACAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:8632829 original size:122 final size:121
Alignment explanation
Indices: 8632590--8632830 Score: 263
Period size: 122 Copynumber: 2.0 Consensus size: 121
8632580 AATGACCAAC
* * * * *
8632590 AAAATCGCAATGCGATCTCTAAATCGCAACGCGATCTCTAGTATCGCAAATCAGTTTCTAGATTC
1 AAAATCGCAATGCGATATCTAAATCGCAACGCGATCTCTACTATCGCAAATCAATATCTAGAATC
* * ** ** * * **
8632655 GCAACGCGATTTTGACTATTGCATTGCGATTTTTCAAATTCGCGTTGCGATTTTGT
66 GCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAATGCGATTTTGT
* *
8632711 AAAATCGCAATGCGAATATGTAAATCGCAACGCGAT-TCTGACTATCGC-AATGCGAATATGTA-
1 AAAATCGCAATGCG-ATATCTAAATCGCAACGCGATCTCT-ACTATCGCAAAT-C-AATATCTAG
*
8632773 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAATGTGATTTT
62 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAATGCGATTTT
8632831 CAAAGCGCCA
Statistics
Matches: 98, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
121 20 0.20
122 73 0.74
123 5 0.05
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (121 bp):
AAAATCGCAATGCGATATCTAAATCGCAACGCGATCTCTACTATCGCAAATCAATATCTAGAATC
GCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAATGCGATTTTGT
Found at i:8632997 original size:22 final size:22
Alignment explanation
Indices: 8632972--8633022 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
8632962 CTACGGCGAC
8632972 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
8632994 ATCCATCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
8633016 ATCCGTC
1 ATCCGTC
8633023 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:8633460 original size:19 final size:20
Alignment explanation
Indices: 8633423--8633460 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
8633413 GTTGCAATAG
*
8633423 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGCGTTGCGATTT
*
8633443 TCATTTT-GCGTTGTGATT
1 TCATTTTCGCGTTGCGATT
8633461 ATCTCATTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.11, C:0.13, G:0.21, T:0.55
Consensus pattern (20 bp):
TCATTTTCGCGTTGCGATTT
Found at i:8635402 original size:20 final size:20
Alignment explanation
Indices: 8635377--8635445 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
8635367 CGAAACTTAA
8635377 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
8635397 ATCGCAACTCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
8635417 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
8635437 ATCGCAACG
1 ATCGCAACG
8635446 GGATAATCGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:8635585 original size:20 final size:20
Alignment explanation
Indices: 8635560--8635608 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
8635550 GCAATTATCC
8635560 CGTTGCGATAGTCAAATT-CG
1 CGTTGCGATAGTC-AATTCCG
*
8635580 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
8635600 CGTTGCGAT
1 CGTTGCGAT
8635609 TTAAGTTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:8635617 original size:20 final size:21
Alignment explanation
Indices: 8635594--8635637 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
8635584 GCGATAGTCA
8635594 TTTCCGCGTTGCGA-TTTAAG
1 TTTCCGCGTTGCGATTTTAAG
*
8635614 TTT-CGTGTTGCGATTTTAAG
1 TTTCCGCGTTGCGATTTTAAG
8635634 TTTC
1 TTTC
8635638 AGAAACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.48
Consensus pattern (21 bp):
TTTCCGCGTTGCGATTTTAAG
Found at i:8636209 original size:21 final size:20
Alignment explanation
Indices: 8636146--8636234 Score: 65
Period size: 21 Copynumber: 4.2 Consensus size: 20
8636136 CCTATCGTTC
8636146 AAGAGGCCCCTATCATTCC-TT-
1 AAGAGGCCCCT-TCA--CCATTA
* *
8636167 AAGAGTCCCCTTCCACCGTTA
1 AAGAGGCCCCTT-CACCATTA
*
8636188 AAGAGGCCCCTGTCATCATTA
1 AAGAGGCCCCT-TCACCATTA
* *
8636209 AAGAGGTCCCTCTCACCATTC
1 AAGAGGCCCCT-TCACCATTA
8636230 AAGAG
1 AAGAG
8636235 CCTGATTCGT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.04
20 3 0.05
21 50 0.89
22 1 0.02
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.24
Consensus pattern (20 bp):
AAGAGGCCCCTTCACCATTA
Found at i:8636234 original size:42 final size:42
Alignment explanation
Indices: 8636143--8636234 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
8636133 TCTCCTATCG
* *
8636143 TTCAAGAGGCCCCTATCATTCCTTAAGAGTCCCCTTCCACCG
1 TTCAAGAGGCCCCTATCATTCATTAAGAGTCCCCTTCCACCA
* *
8636185 TTAAAGAGGCCCCTGTCA-TCATTAAAGAGGT-CCC-TCTCACCA
1 TTCAAGAGGCCCCTATCATTCATT-AAGA-GTCCCCTTC-CACCA
8636227 TTCAAGAG
1 TTCAAGAG
8636235 CCTGATTCGT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
41 6 0.14
42 34 0.81
43 2 0.05
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATTCATTAAGAGTCCCCTTCCACCA
Found at i:8637639 original size:14 final size:15
Alignment explanation
Indices: 8637605--8637644 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
8637595 TTGCTTGTTT
*
8637605 AATTTATTTGTAAAA
1 AATTGATTTGTAAAA
8637620 AATTGATTTGT-AAA
1 AATTGATTTGTAAAA
*
8637634 AGTTGATTTGT
1 AATTGATTTGT
8637645 TTAATAGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (15 bp):
AATTGATTTGTAAAA
Found at i:8637791 original size:20 final size:20
Alignment explanation
Indices: 8637766--8637819 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
8637756 AGGTACACTT
*
8637766 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
**
8637786 TCGCAATACGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
8637806 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
8637820 TCAATTCGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:8637835 original size:19 final size:20
Alignment explanation
Indices: 8637813--8637855 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
8637803 AAATCGCAAC
*
8637813 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
8637832 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
8637852 GCGA
1 GCGA
8637856 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:8637891 original size:54 final size:54
Alignment explanation
Indices: 8637828--8637964 Score: 177
Period size: 54 Copynumber: 2.5 Consensus size: 54
8637818 AGTCAATTCG
* * * *
8637828 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT-CGTTATGATAGTTAAATACC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGCGTTATGATAGTCAAATACC
* * * *
8637882 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGTGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTATGATAGTCAAATACC
*
8637936 CGTTGTGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT
8637965 AGTCAAATTC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 72 0.99
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTATGATAGTCAAATACC
Found at i:8637945 original size:74 final size:74
Alignment explanation
Indices: 8637862--8638046 Score: 253
Period size: 74 Copynumber: 2.5 Consensus size: 74
8637852 GCGATTTTCT
* * * * * ** *
8637862 CGTTATGATAGTTAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGTGATAG
1 CGTTGTGATAGTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTACGATAA
*
8637927 TCATATTCG
66 TCAAATTCG
*
8637936 CGTTGTGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTACGATAA
1 CGTTGTGATAGTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTACGATAA
8638001 TCAAATTCG
66 TCAAATTCG
* * *
8638010 TGTTGCGATAGTCAAATTCACGTTGCGATATTCAAAT
1 CGTTGTGATAGTCAAATTCACGTTGCGATAGTCAAAT
8638047 GAATGTGTAA
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 98 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (74 bp):
CGTTGTGATAGTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTACGATAA
TCAAATTCG
Found at i:8637981 original size:20 final size:20
Alignment explanation
Indices: 8637868--8638046 Score: 148
Period size: 20 Copynumber: 9.6 Consensus size: 20
8637858 TTCTCGTTAT
* * *
8637868 GATAGTTAAATACCCGTTGC
1 GATAGTCAAATTCGCGTTGC
8637888 GATAGTCAAATTCGCGTTGC
1 GATAGTCAAATTCGCGTTGC
* *
8637908 GAT--T----TTTGCGTTGT
1 GATAGTCAAATTCGCGTTGC
* *
8637922 GATAGTCATATTCGCGTTGT
1 GATAGTCAAATTCGCGTTGC
8637942 GATAGTCAAATTCGCGTTGC
1 GATAGTCAAATTCGCGTTGC
8637962 GATAGTCAAATTCGCGTTGC
1 GATAGTCAAATTCGCGTTGC
* * *
8637982 GAT--T----TTTGAGTTAC
1 GATAGTCAAATTCGCGTTGC
* *
8637996 GATAATCAAATTCGTGTTGC
1 GATAGTCAAATTCGCGTTGC
*
8638016 GATAGTCAAATTCACGTTGC
1 GATAGTCAAATTCGCGTTGC
*
8638036 GATATTCAAAT
1 GATAGTCAAAT
8638047 GAATGTGTAA
Statistics
Matches: 129, Mismatches: 18, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
14 21 0.16
16 2 0.02
18 2 0.02
20 104 0.81
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (20 bp):
GATAGTCAAATTCGCGTTGC
Found at i:8638269 original size:140 final size:140
Alignment explanation
Indices: 8638017--8638299 Score: 494
Period size: 140 Copynumber: 2.0 Consensus size: 140
8638007 TCGTGTTGCG
*
8638017 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
8638082 TAGCAATCTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATCTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
8638147 AATACACATA
131 AATACACATA
** *
8638157 ATAGTCAAATTCGTATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCACATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
* * * *
8638222 TAGTAATGTTTAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAATTTTACACATAA
66 TAGCAATCTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
8638287 AATACACATA
131 AATACACATA
8638297 ATA
1 ATA
8638300 CAACGTTTGC
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCACATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
TAGCAATCTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:8638380 original size:18 final size:18
Alignment explanation
Indices: 8638357--8638391 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
8638347 AAGCCGGTTG
8638357 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
8638375 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
8638392 GCCTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:8640685 original size:24 final size:24
Alignment explanation
Indices: 8640651--8640704 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
8640641 ATGAAACATC
8640651 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
8640675 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
8640699 ATCAAA
1 ATCAAA
8640705 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:8641585 original size:21 final size:21
Alignment explanation
Indices: 8641561--8641614 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
8641551 ATTTAAATAT
* *
8641561 TCGCATTGCGATTTTATAAAA
1 TCGCAATGCGATTTTAGAAAA
* * *
8641582 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATTTTAGAAAA
8641603 TCGCAATGCGAT
1 TCGCAATGCGAT
8641615 AATCAAAATC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (21 bp):
TCGCAATGCGATTTTAGAAAA
Found at i:8641643 original size:20 final size:21
Alignment explanation
Indices: 8641620--8641673 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
8641610 GCGATAATCA
8641620 AAATCGCGTTGCGAAT-CTGG
1 AAATCGCGTTGCGAATACTGG
* **
8641640 AAATTGATTTGCG-ATACTGG
1 AAATCGCGTTGCGAATACTGG
*
8641660 AGATCGCGTTGCGA
1 AAATCGCGTTGCGA
8641674 TTTAGAGATC
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
AAATCGCGTTGCGAATACTGG
Found at i:8641674 original size:20 final size:19
Alignment explanation
Indices: 8641648--8641693 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
8641638 GGAAATTGAT
* *
8641648 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
8641668 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
8641687 TTGCGAT
1 TTGCGAT
8641694 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:8641683 original size:19 final size:19
Alignment explanation
Indices: 8641659--8641695 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8641649 TGCGATACTG
*
8641659 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
8641678 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
8641696 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:8648211 original size:14 final size:14
Alignment explanation
Indices: 8648194--8648221 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8648184 ACCACAAAAG
8648194 TTCATTAATTCAAA
1 TTCATTAATTCAAA
8648208 TTCATTAATTCAAA
1 TTCATTAATTCAAA
8648222 CACATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
TTCATTAATTCAAA
Found at i:8648793 original size:16 final size:16
Alignment explanation
Indices: 8648774--8648825 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
8648764 TTGATTAAAG
8648774 GAATAAAAGATTATTA
1 GAATAAAAGATTATTA
*
8648790 GAATAAAAGATTATTG
1 GAATAAAAGATTATTA
8648806 GAATAAAAGATTATTA
1 GAATAAAAGATTATTA
8648822 GAAT
1 GAAT
8648826 GTATATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (16 bp):
GAATAAAAGATTATTA
Found at i:8651552 original size:14 final size:14
Alignment explanation
Indices: 8651516--8651552 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
8651506 TTTTGGTTTA
*
8651516 AGTGTTATATAATC
1 AGTGTTATGTAATC
8651530 AGTGTTATGTAATC
1 AGTGTTATGTAATC
8651544 AGTGTTATG
1 AGTGTTATG
8651553 CTGTAACAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (14 bp):
AGTGTTATGTAATC
Found at i:8659771 original size:15 final size:16
Alignment explanation
Indices: 8659751--8659818 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 16
8659741 CCGAGTATAT
8659751 ATATATTTAA-ATTAA
1 ATATATTTAATATTAA
* *
8659766 ATATA-TAAATATTAT
1 ATATATTTAATATTAA
8659781 ATATTAATTTAA-ATTAA
1 ATA-T-ATTTAATATTAA
* *
8659798 ATTTA-TTAATATTAT
1 ATATATTTAATATTAA
8659813 ATATAT
1 ATATAT
8659819 AAATAATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
14 7 0.17
15 21 0.52
16 2 0.05
17 7 0.17
18 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATATTTAATATTAA
Found at i:8659782 original size:32 final size:32
Alignment explanation
Indices: 8659746--8659819 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
8659736 TCGGACCGAG
8659746 TATATATATATTTAAATTAAATATATAAATAT
1 TATATATATATTTAAATTAAATATATAAATAT
* *
8659778 TATATAT-TAATTTAAATTAAATTTATTAATAT
1 TATATATAT-ATTTAAATTAAATATATAAATAT
8659810 TATATATATA
1 TATATATATA
8659820 AATAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 1 0.03
32 36 0.95
33 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATATATATTTAAATTAAATATATAAATAT
Found at i:8660825 original size:34 final size:34
Alignment explanation
Indices: 8660787--8660858 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
8660777 AAAATCAATG
* * *
8660787 AAATAGAATTATATATACGTTTCAGATAAATGCA
1 AAATAGAATTAAAAATACATTTCAGATAAATGCA
8660821 AAATAGAATTAAAAATACATTTCAGATAAATGCA
1 AAATAGAATTAAAAATACATTTCAGATAAATGCA
8660855 AAAT
1 AAAT
8660859 GAACTTTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (34 bp):
AAATAGAATTAAAAATACATTTCAGATAAATGCA
Found at i:8665540 original size:3 final size:3
Alignment explanation
Indices: 8665534--8665627 Score: 136
Period size: 3 Copynumber: 31.7 Consensus size: 3
8665524 TTTTTATCCA
* ** *
8665534 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
8665582 TAT TA- TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
8665628 AATATATTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
2 2 0.03
3 78 0.98
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:8665678 original size:20 final size:20
Alignment explanation
Indices: 8665653--8665705 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
8665643 AATAATTACA
8665653 GGCCCAATTACAATTGGACC
1 GGCCCAATTACAATTGGACC
8665673 GGCCCAATTACAATTGGACC
1 GGCCCAATTACAATTGGACC
*
8665693 GGCCCAGTTACAA
1 GGCCCAATTACAA
8665706 ACCAACCAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (20 bp):
GGCCCAATTACAATTGGACC
Found at i:8667081 original size:20 final size:21
Alignment explanation
Indices: 8667041--8667084 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
8667031 GTGATATTTT
**
8667041 TATTTTTATTATATTGTTAAA
1 TATTTTTATTATATTCATAAA
8667062 TATTTTTA-TATATTCATAAA
1 TATTTTTATTATATTCATAAA
8667082 TAT
1 TAT
8667085 ACATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTTTTATTATATTCATAAA
Found at i:8667829 original size:18 final size:18
Alignment explanation
Indices: 8667782--8667830 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
8667772 CTTTTCATTC
8667782 TTTTTA-TTTATTTATTA
1 TTTTTATTTTATTTATTA
**
8667799 TTTTTATAATATTTA-TA
1 TTTTTATTTTATTTATTA
8667816 TGTTTTATTTTATTT
1 T-TTTTATTTTATTT
8667831 GCAAGCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTATTTATTA
Found at i:8678520 original size:7 final size:7
Alignment explanation
Indices: 8678460--8678527 Score: 54
Period size: 7 Copynumber: 9.9 Consensus size: 7
8678450 ATGCTTGAAG
8678460 AGAAAAA
1 AGAAAAA
8678467 A-AAAAA
1 AGAAAAA
8678473 A-AAAAA
1 AGAAAAA
8678479 A-AAAAA
1 AGAAAAA
8678485 TAG-AAAA
1 -AGAAAAA
*
8678492 TGAAAAA
1 AGAAAAA
*
8678499 GAAAAAAA
1 -AGAAAAA
*
8678507 AAAAAAA
1 AGAAAAA
8678514 AGGAAAAA
1 A-GAAAAA
8678522 AGAAAA
1 AGAAAA
8678528 GGGGGTCAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
6 18 0.35
7 23 0.44
8 11 0.21
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (7 bp):
AGAAAAA
Found at i:8678520 original size:8 final size:8
Alignment explanation
Indices: 8678460--8678527 Score: 59
Period size: 8 Copynumber: 8.8 Consensus size: 8
8678450 ATGCTTGAAG
8678460 AGAAAAAA
1 AGAAAAAA
*
8678468 AAAAAAAA
1 AGAAAAAA
*
8678476 AAAAAAAA
1 AGAAAAAA
* *
8678484 ATAGAAAA
1 AGAAAAAA
*
8678492 TG--AAAA
1 AGAAAAAA
8678498 AGAAAAAA
1 AGAAAAAA
*
8678506 AAAAAAAA
1 AGAAAAAA
*
8678514 AGGAAAAA
1 AGAAAAAA
8678522 AGAAAA
1 AGAAAA
8678528 GGGGGTCAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
6 5 0.10
8 43 0.90
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (8 bp):
AGAAAAAA
Found at i:8678522 original size:1 final size:1
Alignment explanation
Indices: 8678462--8678514 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
8678452 GCTTGAAGAG
* * ** *
8678462 AAAAAAAAAAAAAAAAAAAAAAATAGAAAATGAAAAAGAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8678515 GGAAAAAAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.04
Consensus pattern (1 bp):
A
Found at i:8680160 original size:82 final size:82
Alignment explanation
Indices: 8679653--8680158 Score: 856
Period size: 82 Copynumber: 6.2 Consensus size: 82
8679643 AAACATTAAA
* * *
8679653 TGGAAGATGAATTTACCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGACTTGGTTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
* *
8679718 AGAACCAAACATT-AA-A
66 AGAA-CAATCATTGAATT
*
8679734 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
8679799 AGAACCAATCATTGAATT
66 AGAA-CAATCATTGAATT
8679817 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
*
8679882 AGAACAGTCATTGAATT
66 AGAACAATCATTGAATT
8679899 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
*
8679964 AGAACAGTCATTGAATT
66 AGAACAATCATTGAATT
8679981 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
8680046 AGAACAATCATTGAATT
66 AGAACAATCATTGAATT
* * * *
8680063 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGA
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG-
8680127 CAGAACAATCATTGAATT
65 CAGAACAATCATTGAATT
8680145 TGGAAGATGAATTT
1 TGGAAGATGAATTT
8680159 GCTCATAGTA
Statistics
Matches: 410, Mismatches: 12, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
81 78 0.19
82 264 0.64
83 68 0.17
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (82 bp):
TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
AGAACAATCATTGAATT
Found at i:8680987 original size:113 final size:113
Alignment explanation
Indices: 8680804--8681432 Score: 1037
Period size: 113 Copynumber: 5.6 Consensus size: 113
8680794 TATTTTTTGA
* *
8680804 AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* *
8680869 TTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCC
66 TTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAACTTTTCC
8680917 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* *
8680982 TTGTTCAACCTTTTACCTGAATCCATCATTTGATGGAACAGCTTTTCC
66 TTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAACTTTTCC
* *
8681030 AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* *
8681095 TTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCC
66 TTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAACTTTTCC
8681143 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* * * * *
8681208 TTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCC
66 TTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAACTTTTCC
8681256 AG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 AGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* * * * *
8681320 TTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCC
65 TTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAACTTTTCC
*
8681369 AG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAA
1 AGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
8681433 CTCATCAAGA
Statistics
Matches: 495, Mismatches: 20, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
112 1 0.00
113 494 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
TTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAACTTTTCC
Found at i:8681690 original size:3 final size:3
Alignment explanation
Indices: 8681684--8681769 Score: 127
Period size: 3 Copynumber: 28.7 Consensus size: 3
8681674 TTTTTATCCA
* ** *
8681684 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
8681732 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
8681770 AATATATTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:8681777 original size:12 final size:11
Alignment explanation
Indices: 8681690--8681778 Score: 54
Period size: 12 Copynumber: 7.5 Consensus size: 11
8681680 TCCATATTAT
8681690 TATTATTAATA
1 TATTATTAATA
*
8681701 TTATTATT-ATCCT
1 -TATTATTAAT--A
*
8681714 TATTATTATTAA
1 TATTATTAAT-A
*
8681726 TATTATTATTA
1 TATTATTAATA
*
8681737 TCATTATTATTA
1 T-ATTATTAATA
*
8681749 TTATTATTATTA
1 -TATTATTAATA
8681761 TTATTATTAAATA
1 -TATTATT-AATA
8681774 TATTA
1 TATTA
8681779 AAAATAATAA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
11 4 0.06
12 57 0.86
13 5 0.08
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATTAATA
Found at i:8683208 original size:20 final size:21
Alignment explanation
Indices: 8683168--8683211 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
8683158 GTGATATTTT
**
8683168 TATTTTTATTATATTGTTAAA
1 TATTTTTATTATATTCATAAA
8683189 TATTTTTA-TATATTCATAAA
1 TATTTTTATTATATTCATAAA
8683209 TAT
1 TAT
8683212 ACATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTTTTATTATATTCATAAA
Found at i:8691608 original size:29 final size:29
Alignment explanation
Indices: 8691566--8691623 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
8691556 TGAGTTAACA
8691566 TACACATTAAACTAATAAATTGTTTTTGT
1 TACACATTAAACTAATAAATTGTTTTTGT
*
8691595 TACATATTAAACTAATAAATTGTTTTTGT
1 TACACATTAAACTAATAAATTGTTTTTGT
8691624 AAGCAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (29 bp):
TACACATTAAACTAATAAATTGTTTTTGT
Found at i:8691635 original size:28 final size:29
Alignment explanation
Indices: 8691574--8691638 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
8691564 CATACACATT
* *
8691574 AAACTAATAAATTGTTTTTGTTACATATT
1 AAACTAATAAATTGTTTTTGTAACATATC
8691603 AAACTAATAAATTGTTTTTGTAAGCA-A-C
1 AAACTAATAAATTGTTTTTGTAA-CATATC
8691631 AAACTAAT
1 AAACTAAT
8691639 TCAATAGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 8 0.24
29 23 0.70
30 2 0.06
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (29 bp):
AAACTAATAAATTGTTTTTGTAACATATC
Done.