Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008290.1 Hibiscus syriacus cultivar Beakdansim tig00110954_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: 1890093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1479619 original size:20 final size:20
Alignment explanation
Indices: 1479584--1479651 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
1479574 AATCTGTAAA
* *
1479584 TCGCAACACATAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
* * *
1479604 TCACAACGCGATAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
*
1479624 TCGCAACACAAAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
1479644 TCGCAACG
1 TCGCAACG
1479652 TGGAATTTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.18
Consensus pattern (20 bp):
TCGCAACGCAAAAGTCAAAT
Found at i:1479678 original size:19 final size:20
Alignment explanation
Indices: 1479638--1479710 Score: 103
Period size: 19 Copynumber: 3.6 Consensus size: 20
1479628 AACACAAAAG
*
1479638 TCAAATTCGCAACGTGGAATT
1 TCAAATTCGCAAC-TAGAATT
1479659 TCAAATTCGCAACT-GAATT
1 TCAAATTCGCAACTAGAATT
*
1479678 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACTAGAATT
*
1479698 TCGAATTCGCAAC
1 TCAAATTCGCAAC
1479711 ACGAATTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 19 0.39
20 17 0.35
21 13 0.27
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (20 bp):
TCAAATTCGCAACTAGAATT
Found at i:1479727 original size:19 final size:19
Alignment explanation
Indices: 1479703--1479749 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1479693 GATTTTCGAA
*
1479703 TTCGCAACACGAATTTATT
1 TTCGCAACACGAATTTAGT
**
1479722 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAGT
1479740 TTCGCAACAC
1 TTCGCAACAC
1479750 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (19 bp):
TTCGCAACACGAATTTAGT
Found at i:1479729 original size:39 final size:40
Alignment explanation
Indices: 1479618--1479718 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
1479608 AACGCGATAG
* ** *
1479618 TCAAATTCGCAACACAAAAGTCAAATTCGCAACGTGGAATT
1 TCAAATTCGCAAC-CGAATTTCAAATTCGCAACGTAGAATT
* *
1479659 TCAAATTCGCAACTGAATTTCAAATTCGCAAC-TAGATTT
1 TCAAATTCGCAACCGAATTTCAAATTCGCAACGTAGAATT
*
1479698 TCGAATTCGCAACACGAATTT
1 TCAAATTCGCAAC-CGAATTT
1479719 ATTTTCGCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 17 0.33
40 21 0.41
41 13 0.25
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (40 bp):
TCAAATTCGCAACCGAATTTCAAATTCGCAACGTAGAATT
Found at i:1479851 original size:14 final size:15
Alignment explanation
Indices: 1479832--1479869 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1479822 TCTCCATCTC
1479832 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1479846 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1479862 TAATTTTT
1 TAATTTTT
1479870 CAATGATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1480483 original size:12 final size:12
Alignment explanation
Indices: 1480462--1480495 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1480452 ACCACATTTC
*
1480462 CAATACCAAACA
1 CAATATCAAACA
1480474 CAATATCAAACA
1 CAATATCAAACA
*
1480486 CAATCTCAAA
1 CAATATCAAA
1480496 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1480674 original size:24 final size:24
Alignment explanation
Indices: 1480616--1480662 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1480606 AGTCAGTATT
*
1480616 CAAAATTTGATCTTGGTCAATACC
1 CAAACTTTGATCTTGGTCAATACC
1480640 CAAACTTTGATCTTGGTCAATAC
1 CAAACTTTGATCTTGGTCAATAC
1480663 TCAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (24 bp):
CAAACTTTGATCTTGGTCAATACC
Found at i:1482955 original size:18 final size:18
Alignment explanation
Indices: 1482932--1482967 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1482922 AAGCAAAAGG
*
1482932 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1482950 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1482968 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1483300 original size:20 final size:20
Alignment explanation
Indices: 1483277--1483317 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1483267 AATTCACAAC
1483277 GCGAAATTGACTTTCGCGTT
1 GCGAAATTGACTTTCGCGTT
* *
1483297 GCGAATTTGACTTTCGTGTT
1 GCGAAATTGACTTTCGCGTT
1483317 G
1 G
1483318 ATAATTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (20 bp):
GCGAAATTGACTTTCGCGTT
Found at i:1483323 original size:20 final size:20
Alignment explanation
Indices: 1483283--1483325 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1483273 CAACGCGAAA
*
1483283 TTGACTTTCGCGTTGCGAAT
1 TTGACTTTCGCGTTGAGAAT
* *
1483303 TTGACTTTCGTGTTGATAAT
1 TTGACTTTCGCGTTGAGAAT
1483323 TTG
1 TTG
1483326 TACATTCAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.23, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCGTTGAGAAT
Found at i:1483518 original size:64 final size:65
Alignment explanation
Indices: 1483379--1483552 Score: 253
Period size: 65 Copynumber: 2.6 Consensus size: 65
1483369 AATTTAAAAC
*
1483379 AACAAATCAACTTTCACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTA
* *
1483444 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATC-AATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTA
1483508 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAA
1483553 AAGTGTACCC
Statistics
Matches: 100, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
64 16 0.16
65 58 0.58
68 4 0.04
69 22 0.22
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTA
Found at i:1484949 original size:21 final size:21
Alignment explanation
Indices: 1484925--1484980 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1484915 GATGACAGGG
*
1484925 GCCTCTTGAACGGTAGGAGAA
1 GCCTCTTGAACGATAGGAGAA
**
1484946 GCCTCTTGAACGATAGGAGGC
1 GCCTCTTGAACGATAGGAGAA
*
1484967 GCCTCTTAAACGAT
1 GCCTCTTGAACGAT
1484981 GATAGGTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (21 bp):
GCCTCTTGAACGATAGGAGAA
Found at i:1485383 original size:63 final size:63
Alignment explanation
Indices: 1485267--1485410 Score: 141
Period size: 63 Copynumber: 2.3 Consensus size: 63
1485257 TCTCGCGTAG
* * * * *
1485267 AGCAGCAACCTCATCACG-TAGCGCACCATTGTCATCGCGTAAAAAATCCACCTCACCACGTAA
1 AGCACCAACCTCATCACGCCA-TGCACCATTGTCATCACGTAAAAAATCCACCTCACCACGCAA
* ** **
1485330 AG-ACCAAACCTCATCACGCCATGCACCATTGTCTTCACGTAAAGTA-CCGACCTCATGACGCAA
1 AGCACC-AACCTCATCACGCCATGCACCATTGTCATCACGTAAAAAATCC-ACCTCACCACGCAA
*
1485393 AGCACCGACCTCATCACG
1 AGCACCAACCTCATCACG
1485411 TAACTCCCCT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
62 4 0.06
63 58 0.88
64 4 0.06
ACGTcount: A:0.32, C:0.36, G:0.15, T:0.17
Consensus pattern (63 bp):
AGCACCAACCTCATCACGCCATGCACCATTGTCATCACGTAAAAAATCCACCTCACCACGCAA
Found at i:1487771 original size:20 final size:20
Alignment explanation
Indices: 1487746--1487788 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1487736 TTTTGTGTTA
1487746 CGATTTACAAATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
*
1487766 CGATTTACAGATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
1487786 CGA
1 CGA
1487789 ATATGGAGTT
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:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTG
Found at i:1488909 original size:2 final size:2
Alignment explanation
Indices: 1488902--1488934 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1488892 AACAGTTTTA
1488902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1488935 CACACTGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1493501 original size:26 final size:26
Alignment explanation
Indices: 1493465--1493526 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
1493455 GCTTATCACT
1493465 GGTGACATACTCAAGTTCCTAATAGG
1 GGTGACATACTCAAGTTCCTAATAGG
1493491 GGTGACATACTCAAGTTCCTAATAGG
1 GGTGACATACTCAAGTTCCTAATAGG
* *
1493517 AGTAACATAC
1 GGTGACATAC
1493527 AAATGCATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (26 bp):
GGTGACATACTCAAGTTCCTAATAGG
Found at i:1497552 original size:6 final size:6
Alignment explanation
Indices: 1497541--1497576 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
1497531 CATTCATTCA
1497541 TTTATT TTTATT TTTATT TTTATT TTTATT TATTAT
1 TTTATT TTTATT TTTATT TTTATT TTTATT T-TTAT
1497577 AAATATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:1497583 original size:19 final size:19
Alignment explanation
Indices: 1497543--1497595 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
1497533 TTCATTCATT
***
1497543 TATTTTTATTT-TTATTTT
1 TATTTTTATTTATTATAAA
1497561 TATTTTTATTTATTATAAA
1 TATTTTTATTTATTATAAA
1497580 TA-TTTTATTATATTAT
1 TATTTTTATT-TATTAT
1497596 TATTATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTATTTATTATAAA
Found at i:1497602 original size:19 final size:18
Alignment explanation
Indices: 1497546--1497602 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
1497536 ATTCATTTAT
*
1497546 TTTTATTT-TTATTTTTA
1 TTTTATTTATTATTATTA
* *
1497563 TTTTTATTTATTATAAATA
1 -TTTTATTTATTATTATTA
1497582 TTTTATTATATTATTATTA
1 TTTTATT-TATTATTATTA
1497601 TT
1 TT
1497603 AAATAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATTTATTATTATTA
Found at i:1498666 original size:14 final size:14
Alignment explanation
Indices: 1498649--1498678 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1498639 TTCTTTAAAT
1498649 TTCAATAAGTTTAA
1 TTCAATAAGTTTAA
1498663 TTCAATAAGTTTAA
1 TTCAATAAGTTTAA
1498677 TT
1 TT
1498679 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TTCAATAAGTTTAA
Found at i:1498990 original size:2 final size:2
Alignment explanation
Indices: 1498983--1499016 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1498973 ATAAAACCTA
1498983 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
1499017 TAAAGATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1501528 original size:63 final size:58
Alignment explanation
Indices: 1501449--1501601 Score: 155
Period size: 59 Copynumber: 2.5 Consensus size: 58
1501439 TTCAGTGTGT
* * * * *
1501449 ATCGATGCACAGGGAGTGCATCGATGCACCCATTAAAATGGAAACATCGAATGCGATTGGTGC
1 ATCGATGCATAAGGAGTGCATCGATGCACCC-CTAAAAT----ACATCGAATGAGATTGATGC
*
1501512 ATCGATGCATAAGGAGTGCATCGATGCATCCCCTAAAATACATCGAATGAGATTTATGC
1 ATCGATGCATAAGGAGTGCATCGATGCA-CCCCTAAAATACATCGAATGAGATTGATGC
* * *
1501571 ACCGATGCAT-AGATAGTGCATCAATGCACCC
1 ATCGATGCATAAG-GAGTGCATCGATGCACCC
1501602 GTCTAGGGAT
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
58 5 0.06
59 39 0.49
63 32 0.41
64 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (58 bp):
ATCGATGCATAAGGAGTGCATCGATGCACCCCTAAAATACATCGAATGAGATTGATGC
Found at i:1502377 original size:32 final size:31
Alignment explanation
Indices: 1502335--1502443 Score: 105
Period size: 31 Copynumber: 3.5 Consensus size: 31
1502325 AGAGTCGAGG
1502335 GTTTACCTATGTTCTACGGAATATATGGACA
1 GTTTACCTATGTTCTACGGAATATATGGACA
* * *
1502366 GTTTTACCTATG-TCTTTC-GAGATATATGAAAA
1 G-TTTACCTATGTTC-TACGGA-ATATATGGACA
* * * *
1502398 GTATACATATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAATATATGGACA
*
1502429 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
1502444 TTAGGACCTA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
31 34 0.57
32 26 0.43
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAATATATGGACA
Found at i:1502443 original size:31 final size:31
Alignment explanation
Indices: 1502335--1502462 Score: 98
Period size: 31 Copynumber: 4.1 Consensus size: 31
1502325 AGAGTCGAGG
* *
1502335 GTTTACCTATGTTCTACGGAATATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
*** * * *
1502366 GTTTTACCTATG-TCTTTCGAGATATATGAAAA
1 G-TTTACCTATGTTCTAAGGA-ACATATGGACA
* *
1502398 GTATACATATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* * *
1502429 GTTTACCTAGGTTCTTTAGG-ACCTATGGACA
1 GTTTACCTATGTTC-TAAGGAACATATGGACA
1502460 GTT
1 GTT
1502463 GCCGAGGTTC
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
31 46 0.61
32 29 0.39
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:1502510 original size:29 final size:30
Alignment explanation
Indices: 1502421--1502519 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
1502411 CTAAGGAACA
* * *
1502421 TATGGACAGTTTACCTAGGTTCTTTAGGACC
1 TATGGATAG-TTACCGAGGTTCTTTATGACC
* *
1502452 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGATAGTTACCGAGGTTCTTTATGACC
* *
1502482 TATGGATAGTTACCGTGG-TCTTTGTGACC
1 TATGGATAGTTACCGAGGTTCTTTATGACC
*
1502511 TCTGGATAG
1 TATGGATAG
1502520 GTCCTTCGGG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 18 0.30
30 33 0.55
31 9 0.15
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGTTCTTTATGACC
Found at i:1506175 original size:32 final size:31
Alignment explanation
Indices: 1506133--1506241 Score: 141
Period size: 31 Copynumber: 3.5 Consensus size: 31
1506123 AGATTCGAGG
1506133 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
1506164 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
1506196 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
1506227 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
1506242 TTAGGACCTA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
31 39 0.58
32 28 0.42
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:1506206 original size:31 final size:32
Alignment explanation
Indices: 1506133--1506260 Score: 131
Period size: 31 Copynumber: 4.1 Consensus size: 32
1506123 AGATTCGAGG
***
1506133 GTTTACCTATGTTCTACGGA-ACATATGGACA
1 GTTTACCTATGTTCTTTAGAGACATATGGACA
*
1506164 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTTTAGAGACATATGGACA
* *
1506196 GTATACCTATGTTC-TAAG-GAACATATGGACA
1 GTTTACCTATGTTCTTTAGAG-ACATATGGACA
* *
1506227 GTTTACCTAGGTTCTTTAG-GACCTATGGACA
1 GTTTACCTATGTTCTTTAGAGACATATGGACA
1506258 GTT
1 GTT
1506261 GCCGAGGTTC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.01
31 53 0.65
32 28 0.34
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (32 bp):
GTTTACCTATGTTCTTTAGAGACATATGGACA
Found at i:1506243 original size:63 final size:62
Alignment explanation
Indices: 1506136--1506259 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 62
1506126 TTCGAGGGTT
* * *
1506136 TACCTATGTTCTACGGAACATATGGACAGTTTTACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTAG-GACATATGGACAGTA
*
1506199 TACCTATGTTCTAAGGAACATATGGACAG-TTTACCTAGGTTCTTTAGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGG-TCTTTAGGACATATGGACAGT
1506260 TGCCGAGGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 22 0.39
63 34 0.61
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTAGGACATATGGACAGTA
Found at i:1506271 original size:30 final size:30
Alignment explanation
Indices: 1506188--1506291 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
1506178 TTTCGAGACA
* * * *
1506188 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
*
1506219 TATGGACAGTTTACCTAGGTTCTTTAGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
1506250 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
1506280 TCTGGATAGTTA
1 TATGGACAGTTA
1506292 TCGGGGTCTT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
30 27 0.44
31 30 0.48
32 5 0.08
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:1509468 original size:11 final size:12
Alignment explanation
Indices: 1509450--1509478 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1509440 CTCATTCATT
1509450 AGAAAAGGAAAA
1 AGAAAAGGAAAA
1509462 A-AAAAGGAAAA
1 AGAAAAGGAAAA
1509473 AGAAAA
1 AGAAAA
1509479 AAGAGGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AGAAAAGGAAAA
Found at i:1509477 original size:17 final size:17
Alignment explanation
Indices: 1509451--1509519 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
1509441 TCATTCATTA
*
1509451 GAAAAGGAAAAAAAAAG
1 GAAAAAGAAAAAAAAAG
* *
1509468 GAAAAAGAAAAAAGAGG
1 GAAAAAGAAAAAAAAAG
1509485 TGAAAAAGAAAAAAAGAA-
1 -GAAAAAGAAAAAAA-AAG
*
1509503 GAAAAAGAAGAAAAAAG
1 GAAAAAGAAAAAAAAAG
1509520 AAGAAAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.05
17 27 0.63
18 13 0.30
19 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.01
Consensus pattern (17 bp):
GAAAAAGAAAAAAAAAG
Found at i:1509479 original size:18 final size:17
Alignment explanation
Indices: 1509450--1509527 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
1509440 CTCATTCATT
*
1509450 AGAAAAGGAAAAAAAAA
1 AGAAAAAGAAAAAAAAA
* **
1509467 GGAAAAAGAAAAAAGAGG
1 AGAAAAAGAAAAAA-AAA
* *
1509485 TGAAAAAGAAAAAAAGA
1 AGAAAAAGAAAAAAAAA
1509502 AGAAAAAGAAGAAAAAAGA
1 AGAAAAAGAA-AAAAAA-A
1509521 AGAAAAA
1 AGAAAAA
1509528 TTGAATCAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
17 23 0.46
18 19 0.38
19 8 0.16
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (17 bp):
AGAAAAAGAAAAAAAAA
Found at i:1509491 original size:19 final size:17
Alignment explanation
Indices: 1509452--1509527 Score: 71
Period size: 19 Copynumber: 4.2 Consensus size: 17
1509442 CATTCATTAG
* * *
1509452 AAAAGGAAAAAAAAAGG
1 AAAAAGAAAAAAGAAGA
* *
1509469 AAAAAGAAAAAAGAGGTG
1 AAAAAGAAAAAAGAAG-A
1509487 AAAAAGAAAAAAAGAAGAA
1 AAAAAG-AAAAAAGAAG-A
1509506 AAAGAAGAAAAAAGAAGA
1 AAA-AAGAAAAAAGAAGA
1509524 AAAA
1 AAAA
1509528 TTGAATCAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
17 14 0.28
18 11 0.22
19 22 0.44
20 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (17 bp):
AAAAAGAAAAAAGAAGA
Found at i:1511305 original size:43 final size:43
Alignment explanation
Indices: 1511244--1511374 Score: 226
Period size: 43 Copynumber: 3.0 Consensus size: 43
1511234 GCCAAATCTA
**
1511244 CTCATCAATTGCTCAAACCGATCAATATTCAGTTCTTGCACAT
1 CTCATCAATTGCTCAAACCGATCACCATTCAGTTCTTGCACAT
*
1511287 CTCATCAATTGCTCAAACCAATCACCATTCAGTTCTTGCACAT
1 CTCATCAATTGCTCAAACCGATCACCATTCAGTTCTTGCACAT
*
1511330 CTCATCAATTGCTCTAACCGATCACCATTCAGTTCTTGCACAT
1 CTCATCAATTGCTCAAACCGATCACCATTCAGTTCTTGCACAT
1511373 CT
1 CT
1511375 GCTTTAAAAG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.32
Consensus pattern (43 bp):
CTCATCAATTGCTCAAACCGATCACCATTCAGTTCTTGCACAT
Found at i:1512947 original size:52 final size:52
Alignment explanation
Indices: 1512880--1513040 Score: 214
Period size: 52 Copynumber: 3.0 Consensus size: 52
1512870 TTCATTGATG
* * * *
1512880 AAACATCTGGACAGAAGCCATATGAACGGATGAATGTGTTGTCAAATGTTTT
1 AAACATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTT
* *
1512932 AAACATTTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTT
1 AAACATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTT
* *
1512984 ACGAAAACATCTGTGCAGAAGCCACAAGAAATGATGAATGTGTTGTCAAATGTTTT
1 ----AAACATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTT
1513040 A
1 A
1513041 CGAACCAGTA
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
52 48 0.50
56 48 0.50
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (52 bp):
AAACATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTT
Found at i:1513020 original size:56 final size:55
Alignment explanation
Indices: 1512880--1513044 Score: 221
Period size: 56 Copynumber: 3.0 Consensus size: 55
1512870 TTCATTGATG
* * *
1512880 AAACATCTGGACAGAAGCCATATGAACGGATGAATGTGTTGTCAAATGTTTT----
1 AAACATCTGG-CAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
* *
1512932 AAACATTTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
1 AAACATCT-GGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
*
1512988 AAACATCTGTGCAGAAGCCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGA
1 AAACATCTG-GCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
1513044 A
1 A
1513045 CCAGTAATTA
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
52 45 0.45
53 2 0.02
55 1 0.01
56 52 0.52
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (55 bp):
AAACATCTGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
Found at i:1514260 original size:37 final size:36
Alignment explanation
Indices: 1514213--1514320 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 36
1514203 ACAAACTGGG
* *
1514213 TCTCGCTTGAGACAGTTTCACTCGAAACAACAATTTA
1 TCTCGCTTGAGACAGTTTCACTAGAAACAA-AATTCA
* ** ** * *
1514250 TCTCACTTGAGATTGTTTTTCTTA-AAACAAGATTCG
1 TCTCGCTTGAGACAGTTTCAC-TAGAAACAAAATTCA
1514286 TCTCGCTTGAGACAGTTTCACTAGAAACAGAAATT
1 TCTCGCTTGAGACAGTTTCACTAGAAACA-AAATT
1514321 TCCATCACTC
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
35 2 0.04
36 24 0.45
37 26 0.49
38 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (36 bp):
TCTCGCTTGAGACAGTTTCACTAGAAACAAAATTCA
Found at i:1514314 original size:36 final size:37
Alignment explanation
Indices: 1514212--1514314 Score: 102
Period size: 36 Copynumber: 2.8 Consensus size: 37
1514202 AACAAACTGG
* *
1514212 GTCTCGCTTGAGACAGTTTCACTCGAAACAACAATTT
1 GTCTCGCTTGAGACAGTTTCACTAGAAACAACAATTC
* * ** ** *
1514249 ATCTCACTTGAGATTGTTTTTCTTA-AAACAA-GATTC
1 GTCTCGCTTGAGACAGTTTCAC-TAGAAACAACAATTC
1514285 GTCTCGCTTGAGACAGTTTCACTAGAAACA
1 GTCTCGCTTGAGACAGTTTCACTAGAAACA
1514315 GAAATTTCCA
Statistics
Matches: 49, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
35 2 0.04
36 24 0.49
37 22 0.45
38 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (37 bp):
GTCTCGCTTGAGACAGTTTCACTAGAAACAACAATTC
Found at i:1514321 original size:73 final size:73
Alignment explanation
Indices: 1514171--1514314 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 73
1514161 TTCAAATAAT
* *
1514171 AATTTATCTCACATGAGATTGTTTTTCTTAAAACAAACTGGGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACATGAGATTGTTTTTCTTAAAACAAACTGCGTCTCGCTTGAGACAGTTTCACTA
1514236 GAAACAAC
66 GAAACAAC
* *
1514244 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGA-TTCGTCTCGCTTGAGACAGTTTCACT
1 AATTTATCTCACATGAGATTGTTTTTCTTAAAACAA-ACTGCGTCTCGCTTGAGACAGTTTCACT
1514308 AGAAACA
65 AGAAACA
1514315 GAAATTTCCA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
73 65 0.98
74 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (73 bp):
AATTTATCTCACATGAGATTGTTTTTCTTAAAACAAACTGCGTCTCGCTTGAGACAGTTTCACTA
GAAACAAC
Found at i:1514476 original size:30 final size:30
Alignment explanation
Indices: 1514440--1514507 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
1514430 TACTCTATCA
1514440 CAGAAGGAGATAGATTAACATCAACATTTC
1 CAGAAGGAGATAGATTAACATCAACATTTC
*
1514470 CAGAAGGAGATAGATTAGCATCAACATTTC
1 CAGAAGGAGATAGATTAACATCAACATTTC
1514500 CAG-AGGAG
1 CAGAAGGAG
1514508 TTCATAATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (30 bp):
CAGAAGGAGATAGATTAACATCAACATTTC
Found at i:1514693 original size:123 final size:122
Alignment explanation
Indices: 1514470--1514698 Score: 377
Period size: 123 Copynumber: 1.9 Consensus size: 122
1514460 TCAACATTTC
* *
1514470 CAGAAGGAGATAGATTAGCATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAG
1 CAGAAGGAGATAGATCAGCATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
1514535 AGGAAGAAGAAGTTCATAATGAGAAGAACTGGTTCAACCTTTTGCGTGATTCTATCA
66 AAGAAGAAGAAGTTCATAATGAGAAGAACTGGTTCAACCTTTTGCGTGATTCTATCA
* *
1514592 CAGAAGGAGATAGATCATCATCAACATTTCCAGATAGAGTTCATAATGAGAAGAATTCATCTGAA
1 CAGAAGGAGATAGATCAGCATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
1514657 GAAGAAGAATAAGTTCATAATGAGAATAACTTGTTCAACCTT
65 GAAGAAGAAGAAGTTCATAATGAGAAGAACTGGTTCAACCTT
1514699 AAATTGATTC
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
122 32 0.33
123 66 0.67
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (122 bp):
CAGAAGGAGATAGATCAGCATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGAAGAAGAAGTTCATAATGAGAAGAACTGGTTCAACCTTTTGCGTGATTCTATCA
Found at i:1515059 original size:3 final size:3
Alignment explanation
Indices: 1515038--1515131 Score: 97
Period size: 3 Copynumber: 32.0 Consensus size: 3
1515028 TTTCATCTAT
* * *
1515038 TTA TTT TTA TT- TATA TTA TTA TTA TTA TTA TTTA TTA TAA ATA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* *
1515084 TTA TAA ATA TT- TTA TTA TTA -TA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1515129 TTA
1 TTA
1515132 AATAATAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
2 7 0.09
3 64 0.85
4 4 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1515071 original size:25 final size:24
Alignment explanation
Indices: 1515038--1515131 Score: 101
Period size: 22 Copynumber: 4.1 Consensus size: 24
1515028 TTTCATCTAT
1515038 TTATT-TTTATTTATATTATTATTA
1 TTATTATTTA-TTATATTATTATTA
*
1515062 TTATTATTTATTATA--AATATTA
1 TTATTATTTATTATATTATTATTA
** *
1515084 TTA-TAAATATTTTATTATTA-TA
1 TTATTATTTATTATATTATTATTA
1515106 TTATTA-TTATTATATTATTATTA
1 TTATTATTTATTATATTATTATTA
1515129 TTA
1 TTA
1515132 AATAATAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
21 8 0.14
22 26 0.45
23 10 0.17
24 10 0.17
25 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATTATTTATTATATTATTATTA
Found at i:1515101 original size:17 final size:17
Alignment explanation
Indices: 1515038--1515131 Score: 79
Period size: 17 Copynumber: 5.5 Consensus size: 17
1515028 TTTCATCTAT
* *
1515038 TTATTTTTATTTATATTA
1 TTATTATTA-TTATAATA
*
1515056 TTATTATTATTAT-TTA
1 TTATTATTATTATAATA
1515072 TTATAAATATTATTATAA-A
1 TTAT---TATTATTATAATA
*
1515091 -TATT-TTATTATTATA
1 TTATTATTATTATAATA
*
1515106 TTATTATTATTATATTA
1 TTATTATTATTATAATA
1515123 TTATTATTA
1 TTATTATTA
1515132 AATAATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
14 8 0.12
15 2 0.03
16 11 0.17
17 22 0.34
18 11 0.17
19 10 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATTATTATAATA
Found at i:1516336 original size:13 final size:13
Alignment explanation
Indices: 1516309--1516346 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1516299 TTCTTTAAAT
1516309 TTCAATATGTTTAA
1 TTCAATAT-TTTAA
1516323 TTCAATATTTTAA
1 TTCAATATTTTAA
*
1516336 TT-ATTATTTTA
1 TTCAATATTTTA
1516347 TTATTATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.35
13 7 0.30
14 8 0.35
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (13 bp):
TTCAATATTTTAA
Found at i:1516351 original size:11 final size:12
Alignment explanation
Indices: 1516318--1516355 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1516308 TTTCAATATG
*
1516318 TTTAATTCAATAT
1 TTTAATT-ATTAT
1516331 TTTAATTATTAT
1 TTTAATTATTAT
1516343 TTT-ATTATTAT
1 TTTAATTATTAT
1516354 TT
1 TT
1516356 CATTTTAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.42
12 7 0.29
13 7 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTAATTATTAT
Found at i:1516504 original size:2 final size:2
Alignment explanation
Indices: 1516497--1516529 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1516487 ATATCATGCT
1516497 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1516530 AATTATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1518458 original size:182 final size:184
Alignment explanation
Indices: 1518150--1518515 Score: 718
Period size: 182 Copynumber: 2.0 Consensus size: 184
1518140 GATGACTAAA
1518150 GGAATTAATGTTGTTGTTAGAGGACACAAGTTTGAGTTTCAACGACTATAATAGAATGATTGAAT
1 GGAATTAATGTTGTTGTTAGAGGACACAAGTTTGAGTTTCAACGACTATAATAGAATGATTGAAT
1518215 ATTTATTATCAAATGATTGATAATATTTAGAACATATACTATTCGTAATAGCATTTACTTAATAA
66 ATTTATTATCAAATGATTGATAATATTTAGAACATATACTATTCGTAATAGCATTTACTTAATAA
1518280 AAAAATATTACAACCGCAACGTGGAAGTAACTGTCATCGTC-AAGTTCATTTTT
131 AAAAATATTACAACCGCAACGTGGAAGTAACTGTCATCGTCAAAGTTCATTTTT
1518333 GGAATTAATGTTGTTGTTAGAGGACAC-AGTTTGAGTTTCAACGACTATAATAGAATGATTGAAT
1 GGAATTAATGTTGTTGTTAGAGGACACAAGTTTGAGTTTCAACGACTATAATAGAATGATTGAAT
1518397 ATTTATTATCAAATGATTGATAATATTTAGAACATATACTATTCGTAATAGCATTTACTTAATAA
66 ATTTATTATCAAATGATTGATAATATTTAGAACATATACTATTCGTAATAGCATTTACTTAATAA
1518462 AAAAATATTACAACCGCAACGTGGAAGTAACTGTCATCGTCAAAGTTCATTTTT
131 AAAAATATTACAACCGCAACGTGGAAGTAACTGTCATCGTCAAAGTTCATTTTT
1518516 AACTAAGCCC
Statistics
Matches: 182, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
182 143 0.79
183 39 0.21
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (184 bp):
GGAATTAATGTTGTTGTTAGAGGACACAAGTTTGAGTTTCAACGACTATAATAGAATGATTGAAT
ATTTATTATCAAATGATTGATAATATTTAGAACATATACTATTCGTAATAGCATTTACTTAATAA
AAAAATATTACAACCGCAACGTGGAAGTAACTGTCATCGTCAAAGTTCATTTTT
Found at i:1519614 original size:60 final size:60
Alignment explanation
Indices: 1519521--1519641 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
1519511 TATTACAGAT
1519521 AACTTGCAGTTCAACACCATTGATTCTTCAATCCAACTTACAAACATACATAATAAATAC
1 AACTTGCAGTTCAACACCATTGATTCTTCAATCCAACTTACAAACATACATAATAAATAC
1519581 AACTTGCAGTTCAACACCATTGATTCTTCAATCCAACTTACAAACATACATAATAAATAC
1 AACTTGCAGTTCAACACCATTGATTCTTCAATCCAACTTACAAACATACATAATAAATAC
1519641 A
1 A
1519642 CCACATATTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.28
Consensus pattern (60 bp):
AACTTGCAGTTCAACACCATTGATTCTTCAATCCAACTTACAAACATACATAATAAATAC
Found at i:1523766 original size:51 final size:51
Alignment explanation
Indices: 1523685--1523785 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
1523675 TCAGGGGGAG
* * *
1523685 AGTTGCAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
1523736 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
1523786 CATTTCCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
Found at i:1530580 original size:37 final size:36
Alignment explanation
Indices: 1530511--1530582 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 36
1530501 CGAACCATGA
1530511 ACATTACATTAAGAAGAAGAAAAACAACAACCTTAAT
1 ACATTACATTAAG-AGAAGAAAAACAACAACCTTAAT
* *
1530548 ACATTACATTAAG-GAAGTAAATAGAACTAACCTTA
1 ACATTACATTAAGAGAAG-AAAAACAAC-AACCTTA
1530583 CACACACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 4 0.13
36 7 0.23
37 20 0.65
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.22
Consensus pattern (36 bp):
ACATTACATTAAGAGAAGAAAAACAACAACCTTAAT
Found at i:1531744 original size:142 final size:143
Alignment explanation
Indices: 1531233--1531811 Score: 809
Period size: 143 Copynumber: 4.0 Consensus size: 143
1531223 TTGTGAATTA
* *
1531233 AAAAGTTTATGCCATTGTGCATTATTTTGCCTATGAGAAATACACGTTTTTTCTTATATGAAGTG
1 AAAAGTTTCTGCCATGGTGCATTATTTTGCCTATGAGAAATACACG-TTTTTCTTATATGAAGTG
* * ** * *
1531298 ATATATCACCACTAAAAAGTTTTCTAAAATGAGTTGATAAATCACTGAAAAGTTGTTGAAGATTA
65 ATATATCACCACTAAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTACTGAAAATGA
**
1531363 TTAATTGAACACTG
130 TTAATTGGGCACTG
* * ** * * * *
1531377 AAAAGTTTCTGTCATGGTGCGTTATTTTGTTTATAAGAAATGCACGTTTTTCTGATATTAAGTGA
1 AAAAGTTTCTGCCATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTTCTTATATGAAGTGA
* *
1531442 TATATCACCACTGAAAAGTTTTCTTAAATGAGTTGATATATCACTGAAAAGTTACTGAAAATGAT
66 TATATCACCACTAAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTACTGAAAATGAT
*
1531507 TAATTGGGCACTA
131 TAATTGGGCACTG
*
1531520 AAAAGTTTTTGCCATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTTCTTATATGAAGTGA
1 AAAAGTTTCTGCCATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTTCTTATATGAAGTGA
* * *
1531585 TATATCATCACTAAAAAGTTTTCTGAAATGAGTTGATATATAACTGAAAAGTTACAGAAAATGAT
66 TATATCACCACTAAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTACTGAAAATGAT
* *
1531650 CAATTGGGCAAT-
131 TAATTGGGCACTG
* *
1531662 AAAAGTTTCTGCCATGGTGCATTATTTTGCCTATGAGAAATACATGTTTTTATTATATGAAGTGA
1 AAAAGTTTCTGCCATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTTCTTATATGAAGTGA
* * * ** * *
1531727 TTTATCACAACTGAAAAGTTTTCTGAAACAAGTTGATATATCACTGAAAAGTTGCTGAAGATGAT
66 TATATCACCACTAAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTACTGAAAATGAT
*
1531792 TAATTAGGCACTG
131 TAATTGGGCACTG
1531805 AAAAGTT
1 AAAAGTT
1531812 GAAGATGATT
Statistics
Matches: 382, Mismatches: 52, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
142 126 0.33
143 218 0.57
144 38 0.10
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (143 bp):
AAAAGTTTCTGCCATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTTCTTATATGAAGTGA
TATATCACCACTAAAAAGTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTACTGAAAATGAT
TAATTGGGCACTG
Found at i:1531773 original size:285 final size:287
Alignment explanation
Indices: 1531231--1531811 Score: 842
Period size: 285 Copynumber: 2.0 Consensus size: 287
1531221 CTTTGTGAAT
*
1531231 TAAAAAGTTTATGCCATTGTGCATTATTTTGCCTATGAGAAATACACGTTTTTTCTTATATGAAG
1 TAAAAAGTTTATGCCATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTTTCTTATATGAAG
* *** *
1531296 TGATATATCACCACTAAAAAGTTTTCTAAAATGAGTTGATAAATCACTGAAAAGTTGTTGAAGAT
66 TGATATATCACCACTAAAAAGTTTTCTAAAATGAGTTGATAAATAACTGAAAAGTTACAGAAAAT
* * * * * ** *
1531361 TATTAATTGAACACTGAAAAGTTTCTGTCATGGTGCGTTATTTTGTTTATAAGAAATGCACGTTT
131 GATCAATTGAACAATGAAAAGTTTCTGCCATGGTGCATTATTTTGCCTATAAGAAATACACGTTT
* * * * **
1531426 TTCTGATATTAAGTGATATATCACCACTGAAAAGTTTTCTTAAATGAGTTGATATATCACTGAAA
196 TTATGATATGAAGTGATATATCACAACTGAAAAGTTTTCTGAAACAAGTTGATATATCACTGAAA
*
1531491 AGTTACTGAAAATGATTAATTGGGCAC
261 AGTTACTGAAAATGATTAATTAGGCAC
*
1531518 TAAAAAGTTTTTGCCATGGTGCATTATTTTGCCTATGAGAAATACACG-TTTTTCTTATATGAAG
1 TAAAAAGTTTATGCCATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTTTCTTATATGAAG
* * *
1531582 TGATATATCATCACTAAAAAGTTTTCTGAAATGAGTTGATATATAACTGAAAAGTTACAGAAAAT
66 TGATATATCACCACTAAAAAGTTTTCTAAAATGAGTTGATAAATAACTGAAAAGTTACAGAAAAT
** * *
1531647 GATCAATTGGGCAAT-AAAAGTTTCTGCCATGGTGCATTATTTTGCCTATGAGAAATACATGTTT
131 GATCAATTGAACAATGAAAAGTTTCTGCCATGGTGCATTATTTTGCCTATAAGAAATACACGTTT
* *
1531711 TTATTATATGAAGTGATTTATCACAACTGAAAAGTTTTCTGAAACAAGTTGATATATCACTGAAA
196 TTATGATATGAAGTGATATATCACAACTGAAAAGTTTTCTGAAACAAGTTGATATATCACTGAAA
* *
1531776 AGTTGCTGAAGATGATTAATTAGGCAC
261 AGTTACTGAAAATGATTAATTAGGCAC
*
1531803 TGAAAAGTT
1 TAAAAAGTT
1531812 GAAGATGATT
Statistics
Matches: 260, Mismatches: 34, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
285 131 0.50
286 83 0.32
287 46 0.18
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (287 bp):
TAAAAAGTTTATGCCATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTTTCTTATATGAAG
TGATATATCACCACTAAAAAGTTTTCTAAAATGAGTTGATAAATAACTGAAAAGTTACAGAAAAT
GATCAATTGAACAATGAAAAGTTTCTGCCATGGTGCATTATTTTGCCTATAAGAAATACACGTTT
TTATGATATGAAGTGATATATCACAACTGAAAAGTTTTCTGAAACAAGTTGATATATCACTGAAA
AGTTACTGAAAATGATTAATTAGGCAC
Found at i:1531823 original size:29 final size:31
Alignment explanation
Indices: 1531768--1531831 Score: 105
Period size: 29 Copynumber: 2.1 Consensus size: 31
1531758 GTTGATATAT
1531768 CACTGAAAAGTTGCTGAAGATGATTAATTAGG
1 CACTGAAAAGTT-CTGAAGATGATTAATTAGG
1531800 CACTGAAAAG-T-TGAAGATGATTAATTAGG
1 CACTGAAAAGTTCTGAAGATGATTAATTAGG
1531829 CAC
1 CAC
1531832 ACTTAGATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 21 0.66
31 1 0.03
32 10 0.31
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (31 bp):
CACTGAAAAGTTCTGAAGATGATTAATTAGG
Found at i:1537421 original size:24 final size:25
Alignment explanation
Indices: 1537372--1537422 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
1537362 ATTCGACCCC
1537372 TAAATCTGAAAGACTTAGAATCCAA
1 TAAATCTGAAAGACTTAGAATCCAA
1537397 TAAATCT-AAATGACTT-GAATCCAA
1 TAAATCTGAAA-GACTTAGAATCCAA
1537421 TA
1 TA
1537423 GGGCAGCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (25 bp):
TAAATCTGAAAGACTTAGAATCCAA
Found at i:1548834 original size:17 final size:17
Alignment explanation
Indices: 1548773--1548835 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
1548763 AATGGTTAAC
*
1548773 GGTCAACGGTCGGGTCA
1 GGTCAACGGTCGGGTCG
1548790 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
**
1548807 GGTCGGTCGGTC-GGTCG
1 GGTC-AACGGTCGGGTCG
1548824 GGTCAGACGGTC
1 GGTCA-ACGGTC
1548836 AAACCGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
17 34 0.87
18 5 0.13
ACGTcount: A:0.11, C:0.24, G:0.46, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1552619 original size:16 final size:17
Alignment explanation
Indices: 1552594--1552635 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1552584 TCATATTGAA
*
1552594 CAAAATCAA-CACAAAG
1 CAAAAACAACCACAAAG
*
1552610 CAAAAACAACCACAAAT
1 CAAAAACAACCACAAAG
*
1552627 AAAAAACAA
1 CAAAAACAA
1552636 ATCAGAGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.69, C:0.24, G:0.02, T:0.05
Consensus pattern (17 bp):
CAAAAACAACCACAAAG
Found at i:1553060 original size:30 final size:30
Alignment explanation
Indices: 1553024--1553088 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1553014 CTATAATTGA
*
1553024 AAAAGCTGGAAATCACATATAAAGCAGTTG
1 AAAAGCTGGAAATCACATACAAAGCAGTTG
* *
1553054 AAAAGCTGGAAATCACATGCAGAGCAGTTG
1 AAAAGCTGGAAATCACATACAAAGCAGTTG
1553084 AAAAG
1 AAAAG
1553089 TTGAACAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.17
Consensus pattern (30 bp):
AAAAGCTGGAAATCACATACAAAGCAGTTG
Found at i:1554030 original size:20 final size:21
Alignment explanation
Indices: 1554005--1554100 Score: 110
Period size: 20 Copynumber: 4.7 Consensus size: 21
1553995 ATATGCCTTA
1554005 GGGTATCGGTACCACTTGA-G
1 GGGTATCGGTACCACTTGAGG
*
1554025 GGGTATCGGTACCACCTGAGG
1 GGGTATCGGTACCACTTGAGG
1554046 GGGTATCGGTACCA-TTGTATGG
1 GGGTATCGGTACCACTTG-A-GG
* *
1554068 GGGTATCGATACCTC-TG-GG
1 GGGTATCGGTACCACTTGAGG
*
1554087 GGGTATCGGCACCA
1 GGGTATCGGTACCA
1554101 TCCGAGCATT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
19 13 0.20
20 20 0.31
21 16 0.25
22 16 0.25
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
GGGTATCGGTACCACTTGAGG
Found at i:1554089 original size:41 final size:40
Alignment explanation
Indices: 1554005--1554101 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 40
1553995 ATATGCCTTA
*
1554005 GGGTATCGGTACCACTTGAGGGGTATCGGTACCACCTGAGG
1 GGGTATCGGTACCA-TTGAGGGGTATCGATACCACCTGAGG
*
1554046 GGGTATCGGTACCATTGTATGGGGGTATCGATACC-TCTG-GG
1 GGGTATCGGTACCATTG-A--GGGGTATCGATACCACCTGAGG
*
1554087 GGGTATCGGCACCAT
1 GGGTATCGGTACCAT
1554102 CCGAGCATTC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 3 0.06
41 31 0.62
42 3 0.06
43 13 0.26
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.25
Consensus pattern (40 bp):
GGGTATCGGTACCATTGAGGGGTATCGATACCACCTGAGG
Found at i:1555530 original size:23 final size:22
Alignment explanation
Indices: 1555498--1555580 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 22
1555488 CAGTACCATC
*
1555498 AGGGGCTATCGATACCCATTCAA
1 AGGGG-TATCGATACCTATTCAA
*
1555521 AGATGGTATCGATACCTATTGC--
1 AG-GGGTATCGATACCTATT-CAA
1555543 AGGGGTATCGATACCTATTCAA
1 AGGGGTATCGATACCTATTCAA
1555565 AGGGAGTATCGATACC
1 AGGG-GTATCGATACC
1555581 AGTCTTAGGG
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.02
21 16 0.31
22 6 0.12
23 26 0.50
24 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (22 bp):
AGGGGTATCGATACCTATTCAA
Found at i:1564037 original size:18 final size:18
Alignment explanation
Indices: 1564016--1564050 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1564006 CAATTTTGAT
1564016 ATTTAATTTAATTTATTA
1 ATTTAATTTAATTTATTA
* *
1564034 ATTTATTTTTATTTATT
1 ATTTAATTTAATTTATT
1564051 TAGACAGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTAATTTAATTTATTA
Found at i:1569253 original size:29 final size:29
Alignment explanation
Indices: 1569201--1569258 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1569191 AACGAGTGCT
*
1569201 AAGGTTTTAATCTCCCTTTAATGACCTGA
1 AAGGTTTTAATCTCCCTTCAATGACCTGA
* * * *
1569230 AAGGTTTTAGTTTCCCTTCGATGAGCTGA
1 AAGGTTTTAATCTCCCTTCAATGACCTGA
1569259 GTCATCAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (29 bp):
AAGGTTTTAATCTCCCTTCAATGACCTGA
Found at i:1571666 original size:10 final size:10
Alignment explanation
Indices: 1571651--1571691 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
1571641 ATCTACAAAA
1571651 ATATTTTATT
1 ATATTTTATT
1571661 ATATTTTATT
1 ATATTTTATT
1571671 -TA-TTTATT
1 ATATTTTATT
1571679 ATTATTATTATT
1 A-TATT-TTATT
1571691 A
1 A
1571692 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 6 0.22
9 2 0.07
10 12 0.44
11 1 0.04
12 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATATTTTATT
Found at i:1571804 original size:33 final size:33
Alignment explanation
Indices: 1571758--1571844 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
1571748 TTCAAAAAAT
*
1571758 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACATATTTGAGTCCTATTGAAACACTA
*
1571791 AGACCAACATATTTGAGTCCTATTGAAACACTA
1 AAACCAACATATTTGAGTCCTATTGAAACACTA
1571824 AAACCGAAGCAT-TTTGAGTCC
1 AAACC-AA-CATATTTGAGTCC
1571845 AAGTAGGACT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
33 35 0.71
34 11 0.22
35 3 0.06
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (33 bp):
AAACCAACATATTTGAGTCCTATTGAAACACTA
Found at i:1573410 original size:18 final size:18
Alignment explanation
Indices: 1573383--1573422 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1573373 ATATCTGCAT
*
1573383 TAATGGACAAAGGGGTTA
1 TAATGCACAAAGGGGTTA
1573401 TAATGCACAAAGGGGTTA
1 TAATGCACAAAGGGGTTA
1573419 TAAT
1 TAAT
1573423 ACAAGAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (18 bp):
TAATGCACAAAGGGGTTA
Found at i:1576133 original size:100 final size:100
Alignment explanation
Indices: 1575859--1576190 Score: 544
Period size: 100 Copynumber: 3.3 Consensus size: 100
1575849 TTTTTTACAG
*
1575859 CTTTT-AGAGTCAAATTTCAACTTCACA-TGAAGGATATTGGACTCGAGACAACACAAGCTCAAC
1 CTTTTCAGAGTC-AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAAC
*
1575922 TTCACAGCGAAGGGGCAACTGCCTGTTAACAAACAA
65 TTCACAGCGAAGGGGCGACTGCCTGTTAACAAACAA
1575958 C-TTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACT
1 CTTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACT
* * *
1576022 TCACAGCGAAGGGGCGATTGCCTATTAACAAATAA
66 TCACAGCGAAGGGGCGACTGCCTGTTAACAAACAA
*
1576057 CTTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAATCTCAACT
1 CTTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACT
* * * *
1576122 TCACAGTGAAGGGGCGACTGGCTGTCAATAAACAA
66 TCACAGCGAAGGGGCGACTGCCTGTTAACAAACAA
1576157 CTTTTCAGAGTCAATTTCAACTTCACAGCGAAGG
1 CTTTTCAGAGTCAATTTCAACTTCACAGCGAAGG
1576191 GGCAACTGCC
Statistics
Matches: 217, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
98 18 0.08
99 75 0.35
100 124 0.57
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (100 bp):
CTTTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACT
TCACAGCGAAGGGGCGACTGCCTGTTAACAAACAA
Found at i:1576204 original size:57 final size:57
Alignment explanation
Indices: 1576111--1576219 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
1576101 CGAGACAACA
* * * *
1576111 CAATCTCAACTTCACAGTGAAGGGGCGACTGGCTGTCAATAAACAACTTTTCAGAGT
1 CAATCTCAACTTCACAGCGAAGGGGCAACTGCCTGTCAACAAACAACTTTTCAGAGT
*
1576168 CAATTTCAACTTCACAGCGAAGGGGCAACTGCCTGTCAACAAACAACTTTTC
1 CAATCTCAACTTCACAGCGAAGGGGCAACTGCCTGTCAACAAACAACTTTTC
1576220 GATTTCATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (57 bp):
CAATCTCAACTTCACAGCGAAGGGGCAACTGCCTGTCAACAAACAACTTTTCAGAGT
Found at i:1576381 original size:105 final size:107
Alignment explanation
Indices: 1576173--1576384 Score: 243
Period size: 105 Copynumber: 2.0 Consensus size: 107
1576163 AGAGTCAATT
* *
1576173 TCAACTTCACAGCGAAGGGGCAACTGCCTGTCAACAAACAACTTTTCGATTTCATTAAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAACTTTCCGATTTC---AAGAGTCAA
* * *
1576238 ATTCAACTTCACAACGAATGATATTGGACTCGAGACAACACATGC
63 ATTCAACTTCACAACGAAGGATATTGGACTCAAAACAACACATGC
* * * *
1576283 TCAACTTCACTGCG-AGGGGCGACTGACTGTCAATAAACAACTTTCC-AGTTTC-AGAGTCAATT
1 TCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAACTTTCCGA-TTTCAAGAGTCAAAT
* **
1576345 TTAACTTCACGGCGAAGGATATT-GACCTCAAAACAACACA
65 TCAACTTCACAACGAAGGATATTGGA-CTCAAAACAACACA
1576385 AATATTTGGA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
104 2 0.02
105 40 0.45
108 1 0.01
109 32 0.36
110 13 0.15
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (107 bp):
TCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAACTTTCCGATTTCAAGAGTCAAATT
CAACTTCACAACGAAGGATATTGGACTCAAAACAACACATGC
Found at i:1576651 original size:81 final size:81
Alignment explanation
Indices: 1576493--1576773 Score: 259
Period size: 81 Copynumber: 3.5 Consensus size: 81
1576483 ATCGTACCCA
* * * * * * ** * *
1576493 CCAAAG-CCTTCGAGTTTGACTACACTCAGCTCCAAGGCA-CATCATTTGCAGCATAGCTTAAGT
1 CCAAAGACCTTCGAGTTCGATTCCACTCAGCTCGAGGGCATCATCATTTACAGCATAAATCAAGG
1576556 CGAA-AAGGGCTATCTG
66 C-AAGAAGGGCTATCTG
* * *
1576572 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCA-CATCATTTACAGTATAAATCAAG
1 CCAAAGACCTTCGAGTTCGATTCCACTCAGC-TCGAGGGCATCATCATTTACAGCATAAATCAAG
*
1576636 G-ATAGAAGGGTTATCTG
65 GCA-AGAAGGGCTATCTG
* * * * *
1576653 TCAACAAA-ACCTTCGAGTTCGACTCCACTCAGCTCAAAGGCATCATCATTTGCAGCATAACTCA
1 -C--CAAAGACCTTCGAGTTCGATTCCACTCAGCTCGAGGGCATCATCATTTACAGCATAAATCA
*
1576717 AGGCAAGAAGGACTATCTG
63 AGGCAAGAAGGGCTATCTG
* * *
1576736 CCAAAGACTTTCGAGTTCAATTCCATTCAGCTCGAGGG
1 CCAAAGACCTTCGAGTTCGATTCCACTCAGCTCGAGGG
1576774 TGTATTTTAT
Statistics
Matches: 164, Mismatches: 28, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
79 7 0.04
80 26 0.16
81 62 0.38
82 9 0.05
83 55 0.34
84 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (81 bp):
CCAAAGACCTTCGAGTTCGATTCCACTCAGCTCGAGGGCATCATCATTTACAGCATAAATCAAGG
CAAGAAGGGCTATCTG
Found at i:1576700 original size:83 final size:78
Alignment explanation
Indices: 1576493--1576753 Score: 272
Period size: 83 Copynumber: 3.2 Consensus size: 78
1576483 ATCGTACCCA
* * * * *
1576493 CCAAAGCCTTCGAGTTTGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
1 CCAAAACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAG--G
1576558 AA-AAGGGCTATCTG
64 AAGAAGGGCTATCTG
* * * * * * *
1576572 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGTATAAATCAAGG
1 CCAAA-ACCTTCGAGTTCGACTACACTCAGC-TCAAAGGCACATCATTTGCAGCATAACTCAAGG
*
1576637 ATAGAAGGGTTATCTG
64 A-AGAAGGGCTATCTG
*
1576653 TCAACAAAACCTTCGAGTTCGACTCCACTCAGCTCAAAGGCATCATCATTTGCAGCATAACTCAA
1 -C--CAAAACCTTCGAGTTCGACTACACTCAGCTCAAAGGCA-CATCATTTGCAGCATAACTCAA
*
1576718 GGCAAGAAGGACTATCTG
62 GG-AAGAAGGGCTATCTG
*
1576736 CCAAAGACTTTCGAGTTC
1 CCAAA-ACCTTCGAGTTC
1576754 AATTCCATTC
Statistics
Matches: 149, Mismatches: 23, Indels: 18
0.78 0.12 0.09
Matches are distributed among these distances:
79 7 0.05
80 26 0.17
81 47 0.32
82 9 0.06
83 55 0.37
84 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (78 bp):
CCAAAACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGAA
GAAGGGCTATCTG
Found at i:1577080 original size:10 final size:10
Alignment explanation
Indices: 1577065--1577114 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
1577055 GTCTACAAAA
1577065 ATATTATATT
1 ATATTATATT
1577075 ATATTATATT
1 ATATTATATT
1577085 -TATT-TATT
1 ATATTATATT
1577093 -TATTATTATT
1 ATATTA-TATT
1577103 ATTATTAATATT
1 A-TATT-ATATT
1577115 TTTTATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 8 0.23
9 4 0.11
10 14 0.40
12 8 0.23
13 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATATTATATT
Found at i:1577094 original size:8 final size:9
Alignment explanation
Indices: 1577066--1577128 Score: 58
Period size: 8 Copynumber: 6.7 Consensus size: 9
1577056 TCTACAAAAA
1577066 TATTATATT
1 TATTATATT
1577075 ATATTATATT
1 -TATTATATT
1577085 TATT-TATT
1 TATTATATT
1577093 TATTATTATTAT
1 TATTA-TA-T-T
1577105 TATTAATATT
1 TATT-ATATT
*
1577115 TTTTAT-TT
1 TATTATATT
1577123 TATTAT
1 TATTAT
1577129 TTTTGCAGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
8 15 0.33
9 6 0.13
10 15 0.33
11 2 0.04
12 7 0.15
13 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TATTATATT
Found at i:1577100 original size:3 final size:3
Alignment explanation
Indices: 1577066--1577129 Score: 50
Period size: 3 Copynumber: 22.3 Consensus size: 3
1577056 TCTACAAAAA
*
1577066 TAT TA- TAT TA- TAT TA- TATT TATT TATT TAT TAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT
1577111 TAT T-T T-T TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
1577130 TTTGCAGGCC
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
2 12 0.23
3 31 0.58
4 10 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1577101 original size:30 final size:30
Alignment explanation
Indices: 1577066--1577129 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
1577056 TCTACAAAAA
1577066 TATTA-TATTA-TATT-ATATTTATTTA-TT
1 TATTATTATTATTATTAATATTT-TTTATTT
1577093 TATTATTATTATTATTAATATTTTTTATTT
1 TATTATTATTATTATTAATATTTTTTATTT
1577123 TATTATT
1 TATTATT
1577130 TTTGCAGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
27 5 0.15
28 5 0.15
29 8 0.24
30 15 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (30 bp):
TATTATTATTATTATTAATATTTTTTATTT
Found at i:1577222 original size:33 final size:33
Alignment explanation
Indices: 1577177--1577262 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
1577167 TTCCGAAAAT
** *
1577177 AAACCAAAGTATTTGAGTTTTATTGAAACACTA
1 AAACCAAAGTATTTGAGTCATATTAAAACACTA
*
1577210 AAACCAACGTATTTGAGTCATATTAAAACACTA
1 AAACCAAAGTATTTGAGTCATATTAAAACACTA
* *
1577243 AAACCGAAGAATTTTGAGTC
1 AAACCAAAGTA-TTTGAGTC
1577263 CAAGTAGGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 37 0.82
34 8 0.18
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (33 bp):
AAACCAAAGTATTTGAGTCATATTAAAACACTA
Found at i:1577621 original size:30 final size:29
Alignment explanation
Indices: 1577587--1577662 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
1577577 TTTCTCATAA
*
1577587 TTTTAATATTTTTCATTTCTTTTTACATTG
1 TTTTAATATTTTT-ATTTATTTTTACATTG
* * *
1577617 TTTTATATATATTTATTTATTTTTTCATTT
1 TTTTA-ATATTTTTATTTATTTTTACATTG
*
1577647 TTATTAATATTATTAT
1 TT-TTAATATTTTTAT
1577663 ATTAATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
30 28 0.74
31 10 0.26
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.68
Consensus pattern (29 bp):
TTTTAATATTTTTATTTATTTTTACATTG
Found at i:1584283 original size:3 final size:3
Alignment explanation
Indices: 1584275--1584303 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1584265 TACTGTGCAA
1584275 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1584304 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1585284 original size:11 final size:11
Alignment explanation
Indices: 1585241--1585278 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
1585231 AAAATGGTTT
1585241 AATATGATGAA
1 AATATGATGAA
*
1585252 AATAAGATGAA
1 AATATGATGAA
1585263 AATATGATGAA
1 AATATGATGAA
1585274 AATAT
1 AATAT
1585279 TTTGAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (11 bp):
AATATGATGAA
Found at i:1585375 original size:54 final size:54
Alignment explanation
Indices: 1585312--1585421 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
1585302 GTGACATGGC
* *
1585312 AACTGCTTTAGTTTTCTTATCCAAGTTAAATTCTTATTAACTATGTTATCTTCT
1 AACTGCTTTAGTTTTCTTATCCAAGTTAAATTCTTATTAACCATGTTAACTTCT
1585366 AACTGCTTTAGTTTTCTTATCCAAGTTAAATTCTTATTAACCATGTTAACTTCT
1 AACTGCTTTAGTTTTCTTATCCAAGTTAAATTCTTATTAACCATGTTAACTTCT
1585420 AA
1 AA
1585422 AAGAATAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (54 bp):
AACTGCTTTAGTTTTCTTATCCAAGTTAAATTCTTATTAACCATGTTAACTTCT
Found at i:1586792 original size:2 final size:2
Alignment explanation
Indices: 1586785--1586809 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1586775 AAACTTTCTA
1586785 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 A
1586810 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1592763 original size:30 final size:30
Alignment explanation
Indices: 1592727--1592784 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1592717 TACAACAGCT
1592727 AACTAA-TCAGCTAACTAATAAACTAACTTG
1 AACTAATTCAGCTAACTAAT-AACTAACTTG
* *
1592757 AACTAATTGAGCTAACTGATAACTAACT
1 AACTAATTCAGCTAACTAATAACTAACT
1592785 AATTACAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.28
Consensus pattern (30 bp):
AACTAATTCAGCTAACTAATAACTAACTTG
Found at i:1592822 original size:13 final size:13
Alignment explanation
Indices: 1592804--1592828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1592794 CAACAATGTA
1592804 AGCTGATATATCG
1 AGCTGATATATCG
1592817 AGCTGATATATC
1 AGCTGATATATC
1592829 CTGATAACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
AGCTGATATATCG
Found at i:1594354 original size:23 final size:23
Alignment explanation
Indices: 1594328--1594385 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1594318 GACACGTTTA
1594328 TCTCTGTCTTTTTGGCATACTTT
1 TCTCTGTCTTTTTGGCATACTTT
* *
1594351 TCTCTGTCTTTGTGGCATGCTTT
1 TCTCTGTCTTTTTGGCATACTTT
*
1594374 TCTCTGCCTTTT
1 TCTCTGTCTTTT
1594386 GGTAGCTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.05, C:0.24, G:0.16, T:0.55
Consensus pattern (23 bp):
TCTCTGTCTTTTTGGCATACTTT
Found at i:1597462 original size:35 final size:35
Alignment explanation
Indices: 1597415--1597528 Score: 147
Period size: 35 Copynumber: 3.3 Consensus size: 35
1597405 AAAATAGTCC
* * *
1597415 TCAATTTCATTCTAAACCCCAATTTCTAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
* * *
1597450 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
* * *
1597485 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
1597520 TCAATTTAA
1 TCAATTTAA
1597529 GGTTTAGAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
Found at i:1597590 original size:35 final size:35
Alignment explanation
Indices: 1597522--1597596 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
1597512 AAAATACTTC
* * *
1597522 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
1597557 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
1597592 AATTT
1 AATTT
1597597 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:1600344 original size:20 final size:21
Alignment explanation
Indices: 1600319--1600364 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1600309 CTGACGTGAT
*
1600319 ATTTTTCAATTATT-TTTAAA
1 ATTTTTAAATTATTATTTAAA
*
1600339 ATTTTTAAATTATTATTTATA
1 ATTTTTAAATTATTATTTAAA
1600360 ATTTT
1 ATTTT
1600365 ATTTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTTAAATTATTATTTAAA
Found at i:1600357 original size:12 final size:11
Alignment explanation
Indices: 1600318--1600379 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
1600308 GCTGACGTGA
*
1600318 TATTTTTCAAT
1 TATTTTTAAAT
1600329 TATTTTTAAA-
1 TATTTTTAAAT
1600339 -ATTTTTAAAT
1 TATTTTTAAAT
1600349 TATTATTTATAAT
1 TATT-TTTA-AAT
1600362 T-TTATTT-AAT
1 TATT-TTTAAAT
*
1600372 TAATTTTA
1 TATTTTTA
1600380 TTTAAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
10 7 0.16
11 13 0.30
12 10 0.23
13 4 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTTTAAAT
Found at i:1600375 original size:14 final size:13
Alignment explanation
Indices: 1600346--1600384 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
1600336 AAAATTTTTA
1600346 AATTATTATTT-AT
1 AATT-TTATTTAAT
1600359 AATTTTATTTAATT
1 AATTTTATTTAA-T
1600373 AATTTTATTTAA
1 AATTTTATTTAA
1600385 AAATAGACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 5 0.21
14 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATTTTATTTAAT
Found at i:1601339 original size:81 final size:81
Alignment explanation
Indices: 1601204--1601365 Score: 297
Period size: 81 Copynumber: 2.0 Consensus size: 81
1601194 GCGGGTACTA
*
1601204 AAATGAAACAAAAATTAAACATTAGGTATGATTTTGTAAAAATGAAAAGTTCAAATACTAAAACG
1 AAATGAAACAAAAACTAAACATTAGGTATGATTTTGTAAAAATGAAAAGTTCAAATACTAAAACG
1601269 TACAAAAAGTGAAACT
66 TACAAAAAGTGAAACT
1601285 AAATGAAACAAAAACTAAACATTAGGTATGATTTTGTAAAAATGAAAAGTTCAAATACTAAAACG
1 AAATGAAACAAAAACTAAACATTAGGTATGATTTTGTAAAAATGAAAAGTTCAAATACTAAAACG
* *
1601350 TACAACAATTGAAACT
66 TACAAAAAGTGAAACT
1601366 TTAAGAACTA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.25
Consensus pattern (81 bp):
AAATGAAACAAAAACTAAACATTAGGTATGATTTTGTAAAAATGAAAAGTTCAAATACTAAAACG
TACAAAAAGTGAAACT
Found at i:1601794 original size:174 final size:173
Alignment explanation
Indices: 1601485--1602004 Score: 833
Period size: 174 Copynumber: 3.0 Consensus size: 173
1601475 ATTGGTCAAT
* * * *
1601485 TGTTCATCATAATTCTCTCATTTTCTCTTATATCATGAGTTTTAGACTCACTAGTATCACTTTCA
1 TGTTCATCTTAATTCTCTCATATTCTCTTATATCATGAGTTTTAGACTCACTAGCATCACCTTCA
* *
1601550 GAGACAGTGCACGTTATAGGTGGGAGGAGCAAGGCAATTGTCCCTCCCAACTTTGATGGTTTAAT
66 GAGACAATGCACGTTATAGGTGGGAGGGGCAAGGCAATTGTCCCTCCCAACTTTGATGGTTTAAT
* * *
1601615 TATATTTTAGGTCATTAATAATTTTAAATCATTACAAATATGA
131 TATATTTTAGGTCATTAATAGTTTTAAACCATTACAAATAAGA
*
1601658 TGTTCATCTTAATTCTCTCATATTCTCTTATATCATGAATTTTAGACTCACTAGCATCACCTTCA
1 TGTTCATCTTAATTCTCTCATATTCTCTTATATCATGAGTTTTAGACTCACTAGCATCACCTTCA
* *
1601723 GAGACATATGCACGTTCTAGGTGGGAGGGGCAAGGCAATTGTCCCTCCCAACTTTAATGGTTTAA
66 GAGACA-ATGCACGTTATAGGTGGGAGGGGCAAGGCAATTGTCCCTCCCAACTTTGATGGTTTAA
*
1601788 TTATATTTTAGGTCATTAATAGTTTTAAACCATTACAAATAAGT
130 TTATATTTTAGGTCATTAATAGTTTTAAACCATTACAAATAAGA
* * * *
1601832 TATTCATCTTAATTCTCTCATATTATCCTATATCATGAGTTTTAGACTCACTAGCATCGCCTTCA
1 TGTTCATCTTAATTCTCTCATATTCTCTTATATCATGAGTTTTAGACTCACTAGCATCACCTTCA
* * * *
1601897 TAGACAGATGCACGTTATAGGTGAGAGGGGCAAGGCAATTGTCCTTTCCAACTTTGATGGTTTAA
66 GAGACA-ATGCACGTTATAGGTGGGAGGGGCAAGGCAATTGTCCCTCCCAACTTTGATGGTTTAA
1601962 TTATATTTTAGGTCATTAATAGTTTTAAACCATTACAAATAAG
130 TTATATTTTAGGTCATTAATAGTTTTAAACCATTACAAATAAG
1602005 CCATCATATC
Statistics
Matches: 321, Mismatches: 25, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
173 66 0.21
174 255 0.79
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (173 bp):
TGTTCATCTTAATTCTCTCATATTCTCTTATATCATGAGTTTTAGACTCACTAGCATCACCTTCA
GAGACAATGCACGTTATAGGTGGGAGGGGCAAGGCAATTGTCCCTCCCAACTTTGATGGTTTAAT
TATATTTTAGGTCATTAATAGTTTTAAACCATTACAAATAAGA
Found at i:1604138 original size:167 final size:166
Alignment explanation
Indices: 1603949--1604278 Score: 579
Period size: 167 Copynumber: 2.0 Consensus size: 166
1603939 TTGTTTAAGG
* * *
1603949 CCTATCTTGATTTTTTTTATTAATATGGATTAGGTACAATGTAATATTTGTTTAAAGATAATTTA
1 CCTATCTTGATTTTTTTTATTAATATGGATTAGATACAATATAATATTTGTTTAAAGATAACTTA
* *
1604014 TAATCACATGACATTAAACGTTCGTATCCCTAACATTCTTTGTATTCGAACTTAAGACCTCAAAG
66 TAATCACATGACATTAAACGTTCATACCCCTAACATTCTTTGTATTCGAACTTAAGACCTCAAAG
* *
1604079 AATGACAACAATTCATTTGCTACTAAAATTATCGCC
131 AATGACAACAATTCATTTGCCACTAAAAATATCGCC
1604115 CCTATCTTGATATTTTTTTATTAATATGGATTAGATACAATATAATATTTGTTTAAAGATAACTT
1 CCTATCTTGAT-TTTTTTTATTAATATGGATTAGATACAATATAATATTTGTTTAAAGATAACTT
*
1604180 ATAATCACTTGACATTAAACGTTCATACCCCTAACATTCTTTGTATTCGAACTTAAGACCTCAAA
65 ATAATCACATGACATTAAACGTTCATACCCCTAACATTCTTTGTATTCGAACTTAAGACCTCAAA
1604245 GAATGACAACAATTCATTTGCCACTAAAAATATC
130 GAATGACAACAATTCATTTGCCACTAAAAATATC
1604279 CGGGGCGATC
Statistics
Matches: 155, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
166 11 0.07
167 144 0.93
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (166 bp):
CCTATCTTGATTTTTTTTATTAATATGGATTAGATACAATATAATATTTGTTTAAAGATAACTTA
TAATCACATGACATTAAACGTTCATACCCCTAACATTCTTTGTATTCGAACTTAAGACCTCAAAG
AATGACAACAATTCATTTGCCACTAAAAATATCGCC
Found at i:1605973 original size:30 final size:31
Alignment explanation
Indices: 1605913--1605973 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1605903 TGAAAGTCAA
*
1605913 GGTTGGCACCGAATGGTGCTTAATTTCAATG
1 GGTTGGCACCGAATGGTGCATAATTTCAATG
1605944 GGTTGGCACCGAATGGTGCATAA-TTCAATG
1 GGTTGGCACCGAATGGTGCATAATTTCAATG
1605974 AATTGGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (31 bp):
GGTTGGCACCGAATGGTGCATAATTTCAATG
Found at i:1607765 original size:22 final size:22
Alignment explanation
Indices: 1607740--1607790 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1607730 AAAGGAAAGT
1607740 TGTCGGATCTAAAGAATGTAGA
1 TGTCGGATCTAAAGAATGTAGA
1607762 TGTCGGATCTAAAGAATGTAGA
1 TGTCGGATCTAAAGAATGTAGA
1607784 TGTCGGA
1 TGTCGGA
1607791 CTATGTGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (22 bp):
TGTCGGATCTAAAGAATGTAGA
Found at i:1613016 original size:3 final size:3
Alignment explanation
Indices: 1613008--1613066 Score: 52
Period size: 3 Copynumber: 19.3 Consensus size: 3
1612998 TTTTACTTTA
*
1613008 ATT ATT ATT -TT ATT ATT ATT -TAT AAT ATCT ATT A-T ATCT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT AT-T ATT AT-T
1613054 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
1613067 AATAAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
2 5 0.11
3 33 0.70
4 9 0.19
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1614151 original size:2 final size:2
Alignment explanation
Indices: 1614144--1614175 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1614134 TTATCTGTGC
1614144 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
1614176 TTAGGGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1614825 original size:20 final size:21
Alignment explanation
Indices: 1614785--1614832 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
1614775 ATATTTTTAA
1614785 ATAAATAAATATCTTAATTTT
1 ATAAATAAATATCTTAATTTT
*
1614806 -TAAATAAATAT-TGTACTTTT
1 ATAAATAAATATCT-TAATTTT
1614826 ATAAATA
1 ATAAATA
1614833 TTATTTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 17 0.71
21 6 0.25
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAAATAAATATCTTAATTTT
Found at i:1614946 original size:2 final size:2
Alignment explanation
Indices: 1614939--1614990 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
1614929 CTTATTTAAA
1614939 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
1614981 AT -T A- AT AT AT
1 AT AT AT AT AT AT
1614991 TTCTTAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1616258 original size:22 final size:20
Alignment explanation
Indices: 1616203--1616245 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1616193 TACATCTACA
1616203 CTCTTCAAAGATGATAGATT
1 CTCTTCAAAGATGATAGATT
1616223 CTCTTCAAAGATGATAGATT
1 CTCTTCAAAGATGATAGATT
1616243 CTC
1 CTC
1616246 ATTTTAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (20 bp):
CTCTTCAAAGATGATAGATT
Found at i:1616995 original size:46 final size:45
Alignment explanation
Indices: 1616939--1617582 Score: 1011
Period size: 45 Copynumber: 14.2 Consensus size: 45
1616929 GAGCTTTTTG
* *
1616939 GTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTTAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
* * * *
1616984 GTTTTCAAAAACCTCCGGGTCATTTGTAAGCCCTTTAGTGCATGCT
1 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
*
1617030 GTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
* * *
1617075 GTTCTCAAAAACTTTCAGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1617121 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
*
1617166 GTTTTCAAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
**
1617212 GTTTTCAAAACCTTCGAATCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1617257 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
*
1617303 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTTCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
* *
1617348 GTTCTTAAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTT-TTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1617394 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
*
1617439 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTACATGAT
1 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
*
1617485 GTTTTC-AAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
* * ** * *
1617529 GTTCTCAAAACCTCCGGGTCATCCATAAGACCTTCAGTGCAGGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1617574 GTTTTCAAA
1 GTTTTCAAA
1617583 TGAGATTTTA
Statistics
Matches: 553, Mismatches: 39, Indels: 14
0.91 0.06 0.02
Matches are distributed among these distances:
44 41 0.07
45 257 0.46
46 255 0.46
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (45 bp):
GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
Found at i:1617096 original size:91 final size:91
Alignment explanation
Indices: 1616939--1617582 Score: 1051
Period size: 91 Copynumber: 7.1 Consensus size: 91
1616929 GAGCTTTTTG
* * *
1616939 GTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAAACCTCCGGGT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
1617004 CATTTGTAAGCCCTTTAGTGCATGCT
66 CATCTGTAAGCCCTTCAGTGCATGAT
* * * *
1617030 GTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGTTCTCAAAAACTTTCAGGT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1617095 CATCTGTAAGCCCTTCAGTGCATGAT
66 CATCTGTAAGCCCTTCAGTGCATGAT
*
1617121 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGGT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1617186 CATCTGTAAGCCCTTCAGTGCATGAT
66 CATCTGTAAGCCCTTCAGTGCATGAT
**
1617212 GTTTTCAAAACCTTCGAATCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1617277 CATCTGTAAGCCCTTCAGTGCATGAT
66 CATCTGTAAGCCCTTCAGTGCATGAT
* *
1617303 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTTCATGATGTTCTT-AAAAACCTTTGGG
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTT-TTCAAAAACCTTCGGG
1617367 TCATCTGTAAGCCCTTCAGTGCATGAT
65 TCATCTGTAAGCCCTTCAGTGCATGAT
1617394 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
1617459 CATCTGTAAGCCCTTCAGTACATGAT
66 CATCTGTAAGCCCTTCAGTGCATGAT
* * *
1617485 GTTTTC-AAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTCTC-AAAACCTCCGGGT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
** * *
1617548 CATCCATAAGACCTTCAGTGCAGGAT
66 CATCTGTAAGCCCTTCAGTGCATGAT
1617574 GTTTTCAAA
1 GTTTTCAAA
1617583 TGAGATTTTA
Statistics
Matches: 519, Mismatches: 31, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
89 39 0.08
90 46 0.09
91 432 0.83
92 2 0.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (91 bp):
GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
CATCTGTAAGCCCTTCAGTGCATGAT
Found at i:1617856 original size:3 final size:3
Alignment explanation
Indices: 1617835--1617897 Score: 56
Period size: 3 Copynumber: 20.3 Consensus size: 3
1617825 TTTTACTTTA
* * * *
1617835 ATT ATT TTT ATT TTT ATT ATT ATT ATT AAT AAT ATCT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
1617880 ATAT ATAT ATT ATT ATT A
1 AT-T AT-T ATT ATT ATT A
1617898 AATAAAGAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.76
4 10 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1617860 original size:15 final size:15
Alignment explanation
Indices: 1617817--1617861 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1617807 TAAATACTAA
*
1617817 TTTT-TTATTTTTAC
1 TTTTATTATTTTTAT
*
1617831 TTTAATTATTTTTAT
1 TTTTATTATTTTTAT
*
1617846 TTTTATTATTATTAT
1 TTTTATTATTTTTAT
1617861 T
1 T
1617862 AATAATATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTATTTTTAT
Found at i:1618786 original size:29 final size:27
Alignment explanation
Indices: 1618705--1618816 Score: 158
Period size: 25 Copynumber: 4.2 Consensus size: 27
1618695 GCAGATCCTT
* *
1618705 TTAGAGAGAAGTGAGAGGGTTATCTCG
1 TTAGAGAGAAGGGAGAGGGTTCTCTCG
*
1618732 TTAGAGAG-AGGAAGAGGGTTCTCTCG
1 TTAGAGAGAAGGGAGAGGGTTCTCTCG
1618758 TTAGAGAGAGAAGGGAGAGGGTTCTCTCG
1 TT--AGAGAGAAGGGAGAGGGTTCTCTCG
1618787 TTAGAGAGAA--GAGAGGGTTCTCTCG
1 TTAGAGAGAAGGGAGAGGGTTCTCTCG
1618812 TTAGA
1 TTAGA
1618817 AAGAGAACCC
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
25 20 0.26
26 17 0.22
27 16 0.21
28 6 0.08
29 19 0.24
ACGTcount: A:0.29, C:0.10, G:0.38, T:0.24
Consensus pattern (27 bp):
TTAGAGAGAAGGGAGAGGGTTCTCTCG
Found at i:1618821 original size:29 final size:28
Alignment explanation
Indices: 1618707--1618823 Score: 154
Period size: 26 Copynumber: 4.3 Consensus size: 28
1618697 AGATCCTTTT
*
1618707 AGAGAGAAGTGAGAGGGTTATCTCGTTAG
1 AGAGAGAAG-GAGAGGGTTCTCTCGTTAG
*
1618736 AGAGAG--GAAGAGGGTTCTCTCGTTAG
1 AGAGAGAAGGAGAGGGTTCTCTCGTTAG
1618762 AGAGAGAAGGGAGAGGGTTCTCTCGTT--
1 AGAGAGAA-GGAGAGGGTTCTCTCGTTAG
1618789 AGAGAGAA-GAGAGGGTTCTCTCGTTAG
1 AGAGAGAAGGAGAGGGTTCTCTCGTTAG
*
1618816 AAAGAGAA
1 AGAGAGAA
1618824 CCCAAAGAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
25 17 0.22
26 23 0.29
27 16 0.20
29 23 0.29
ACGTcount: A:0.32, C:0.09, G:0.38, T:0.21
Consensus pattern (28 bp):
AGAGAGAAGGAGAGGGTTCTCTCGTTAG
Found at i:1619709 original size:21 final size:21
Alignment explanation
Indices: 1619685--1619731 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1619675 ATATTTTTAA
1619685 ATAAATAAATATCT-TACATTT
1 ATAAATAAATAT-TGTACATTT
*
1619706 ATAAATAAATATTGTACTTTT
1 ATAAATAAATATTGTACATTT
1619727 ATAAA
1 ATAAA
1619732 ATTATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAAATAAATATTGTACATTT
Found at i:1621239 original size:2 final size:2
Alignment explanation
Indices: 1621232--1621257 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1621222 TAAAAGAGTG
1621232 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
1621258 ACAATGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1621295 original size:24 final size:25
Alignment explanation
Indices: 1621265--1621320 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 25
1621255 ATAACAATGT
1621265 AAAGAAATAAAAAAAATT-AAATTA
1 AAAGAAATAAAAAAAATTAAAATTA
*
1621289 AAAGAAATAAAAAATATTAAAATTA
1 AAAGAAATAAAAAAAATTAAAATTA
1621314 AAAGAAA
1 AAAGAAA
1621321 AGAAAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (25 bp):
AAAGAAATAAAAAAAATTAAAATTA
Found at i:1628485 original size:12 final size:12
Alignment explanation
Indices: 1628468--1628494 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1628458 TTAATTGTGA
1628468 AAATTAAAAATT
1 AAATTAAAAATT
1628480 AAATTAAAAATT
1 AAATTAAAAATT
1628492 AAA
1 AAA
1628495 AGTTCGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAAAAATT
Found at i:1629739 original size:3 final size:3
Alignment explanation
Indices: 1629731--1629772 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1629721 AAATAGAATA
1629731 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1629773 TATATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1629756 original size:20 final size:19
Alignment explanation
Indices: 1629727--1629770 Score: 79
Period size: 20 Copynumber: 2.3 Consensus size: 19
1629717 AAAGAAATAG
1629727 AATAAATAATAATAATAAT
1 AATAAATAATAATAATAAT
1629746 AATATAATAATAATAATAAT
1 AATA-AATAATAATAATAAT
1629766 AATAA
1 AATAA
1629771 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAATAATAATAATAAT
Found at i:1629777 original size:2 final size:2
Alignment explanation
Indices: 1629770--1629810 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1629760 AATAATAATA
*
1629770 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1629811 TTTCAAAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1629824 original size:21 final size:21
Alignment explanation
Indices: 1629800--1629839 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1629790 AAATATATAT
*
1629800 ATATATTATATTTTCAAAATC
1 ATATAATATATTTTCAAAATC
*
1629821 ATATAATATGTTTTCAAAA
1 ATATAATATATTTTCAAAA
1629840 AAAAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (21 bp):
ATATAATATATTTTCAAAATC
Found at i:1629841 original size:23 final size:23
Alignment explanation
Indices: 1629796--1629984 Score: 115
Period size: 23 Copynumber: 8.0 Consensus size: 23
1629786 ATATAAATAT
*
1629796 ATATATATATTATATTTTC--AAA
1 ATATATATA-TATGTTTTCAAAAA
1629818 ATCATATA-ATATGTTTTCAAAAAA
1 AT-ATATATATATGTTTTC-AAAAA
* *
1629842 AAATATTACATATGTTTTTCAAAAA
1 ATATA-TATATATG-TTTTCAAAAA
1629867 CTATATATATTATATGTTTTC-AAAA
1 --ATATATA-TATATGTTTTCAAAAA
* * *
1629892 CTATATAATAATATGTTTTTAGAAA
1 ATATAT-AT-ATATGTTTTCAAAAA
*
1629917 CTATACTATATAT-TTTT-AAAAA
1 ATATA-TATATATGTTTTCAAAAA
**
1629939 ACTATATATTATATGTTTT-TTAAA
1 A-TATATA-TATATGTTTTCAAAAA
*
1629963 CTATATA-ATATGTTTTCAAAAA
1 ATATATATATATGTTTTCAAAAA
1629985 CAAGTTTAAA
Statistics
Matches: 135, Mismatches: 14, Indels: 36
0.73 0.08 0.19
Matches are distributed among these distances:
21 17 0.13
22 12 0.09
23 33 0.24
24 27 0.20
25 24 0.18
26 13 0.10
27 9 0.07
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (23 bp):
ATATATATATATGTTTTCAAAAA
Found at i:1629843 original size:25 final size:24
Alignment explanation
Indices: 1629815--1630114 Score: 90
Period size: 22 Copynumber: 12.4 Consensus size: 24
1629805 TTATATTTTC
1629815 AAAATCATATAATATGTTTTCAAAA
1 AAAAT-ATATAATATGTTTTCAAAA
1629840 AAAA-ATATTACATATGTTTTTCAAAA
1 AAAATATA-TA-ATATG-TTTTCAAAA
* *
1629866 ACTATATATATTATATGTTTTC-AAA
1 A--AAATATATAATATGTTTTCAAAA
** * *
1629891 ACTATATAATAATATGTTTTTAGAA
1 AAAATAT-ATAATATGTTTTCAAAA
**
1629916 ACTATACTAT-ATAT-TTTT-AAAA
1 AAAATA-TATAATATGTTTTCAAAA
* * **
1629938 AACTATATATTATATGTTTT---TT
1 AA-AATATATAATATGTTTTCAAAA
*
1629960 AAACTATATAATATGTTTTCAAAAA
1 AAAATATATAATATGTTTTC-AAAA
* * *
1629985 CAAGTTTAAAACTATACTATATATTTCAAAA
1 -AA----AATA-TATAATATGT-TTTCAAAA
* **
1630016 AAATATATATTATATGTTTT--TTA
1 AAA-ATATATAATATGTTTTCAAAA
*
1630039 AAACTATATAATATGTTTTC--AA
1 AAAATATATAATATGTTTTCAAAA
* **
1630061 AAACTATACCATATGTTTT---AA
1 AAAATATATAATATGTTTTCAAAA
* * *
1630082 AAACTATATTATATATTTTCAAAA
1 AAAATATATAATATGTTTTCAAAA
*
1630106 ATAATATAT
1 AAAATATAT
1630115 TATTTTTTGA
Statistics
Matches: 212, Mismatches: 35, Indels: 57
0.70 0.12 0.19
Matches are distributed among these distances:
21 32 0.15
22 41 0.19
23 24 0.11
24 30 0.14
25 26 0.12
26 26 0.12
27 7 0.03
28 3 0.01
29 3 0.01
30 4 0.02
31 12 0.06
32 4 0.02
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAATATATAATATGTTTTCAAAA
Found at i:1629844 original size:26 final size:26
Alignment explanation
Indices: 1629814--1629910 Score: 94
Period size: 26 Copynumber: 3.8 Consensus size: 26
1629804 ATTATATTTT
1629814 CAAAATCATATAATATGTTTTCAAAAA
1 CAAAAT-ATATAATATGTTTTCAAAAA
1629841 -AAAATAT-TACATATGTTTTTCAAAAA
1 CAAAATATATA-ATATG-TTTTCAAAAA
* * *
1629867 CTATATATATTATATGTTTTC-AAAA
1 CAAAATATATAATATGTTTTCAAAAA
* *
1629892 CTATATA-ATAATATGTTTT
1 CAAAATATATAATATGTTTT
1629911 TAGAAACTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
24 13 0.21
25 18 0.29
26 20 0.32
27 10 0.16
28 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (26 bp):
CAAAATATATAATATGTTTTCAAAAA
Found at i:1629882 original size:52 final size:51
Alignment explanation
Indices: 1629821--1629928 Score: 137
Period size: 52 Copynumber: 2.1 Consensus size: 51
1629811 TTTCAAAATC
*
1629821 ATATAATATGTTTTCAAAAAAAAATATTACATATGTTTTTCAAAAACTATA-T
1 ATATAATATGTTTTCAAAAAAAAATAATA-ATATGTTTTT-AAAAACTATACT
* ** * *
1629873 ATATTATATGTTTTCAAAACTATATAATAATATGTTTTTAGAAACTATACT
1 ATATAATATGTTTTCAAAAAAAAATAATAATATGTTTTTAAAAACTATACT
1629924 ATATA
1 ATATA
1629929 TTTTTAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 9 0.19
51 15 0.31
52 24 0.50
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (51 bp):
ATATAATATGTTTTCAAAAAAAAATAATAATATGTTTTTAAAAACTATACT
Found at i:1629967 original size:46 final size:47
Alignment explanation
Indices: 1629821--1629985 Score: 144
Period size: 48 Copynumber: 3.4 Consensus size: 47
1629811 TTTCAAAATC
* * *
1629821 ATATAATATGTTTTCAAAAAA--AAATATTACATATGTTTTTCAAAAACTAT
1 ATATAATATGTTTT-AAAAAACTATATAATA-ATATGTTTTT-AGAAAC--T
*
1629871 ATATATTATATGTTTT-CAAAACTATATAATAATATGTTTTTAGAAACT
1 ATATA--ATATGTTTTAAAAAACTATATAATAATATGTTTTTAGAAACT
* *
1629919 ATACTATATAT-TTTTAAAAAACTATAT-ATTATATGTTTTT-TAAACT
1 ATA-TA-ATATGTTTTAAAAAACTATATAATAATATGTTTTTAGAAACT
*
1629965 ATATAATATGTTTTCAAAAAC
1 ATATAATATGTTTTAAAAAAC
1629986 AAGTTTAAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
44 4 0.04
45 12 0.12
46 8 0.08
47 16 0.16
48 19 0.19
49 2 0.02
50 14 0.14
51 10 0.10
52 15 0.15
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (47 bp):
ATATAATATGTTTTAAAAAACTATATAATAATATGTTTTTAGAAACT
Found at i:1630006 original size:79 final size:80
Alignment explanation
Indices: 1629909--1630064 Score: 271
Period size: 79 Copynumber: 2.0 Consensus size: 80
1629899 ATAATATGTT
* *
1629909 TTTAGAAACTATACTATATATTTTTAAAAAACTATATATTATATGTTTTTT-AAACTATATAATA
1 TTTAGAAACTATACTATATA-TTTCAAAAAAATATATATTATATGTTTTTTAAAACTATATAATA
1629973 TGTTTTCAAAAACAAG
65 TGTTTTCAAAAACAAG
1629989 TTTA-AAACTATACTATATATTTCAAAAAAATATATATTATATGTTTTTTAAAACTATATAATAT
1 TTTAGAAACTATACTATATATTTCAAAAAAATATATATTATATGTTTTTTAAAACTATATAATAT
1630053 GTTTTCAAAAAC
66 GTTTTCAAAAAC
1630065 TATACCATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
78 28 0.38
79 41 0.56
80 4 0.05
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (80 bp):
TTTAGAAACTATACTATATATTTCAAAAAAATATATATTATATGTTTTTTAAAACTATATAATAT
GTTTTCAAAAACAAG
Found at i:1630046 original size:22 final size:22
Alignment explanation
Indices: 1630021--1630135 Score: 103
Period size: 22 Copynumber: 5.2 Consensus size: 22
1630011 CAAAAAAATA
*
1630021 TATATTATATGTTTTTTAAAAC
1 TATATTATATGTTTTTAAAAAC
* *
1630043 TATATAATATGTTTTCAAAAAC
1 TATATTATATGTTTTTAAAAAC
**
1630065 TATACCATATG-TTTTAAAAAC
1 TATATTATATGTTTTTAAAAAC
* *
1630086 TATATTATATATTTTCAAAAA-
1 TATATTATATGTTTTTAAAAAC
1630107 TA-ATATATTAT-TTTTTGACAAAAC
1 TATAT-TA-TATGTTTTT-A-AAAAC
1630131 TATAT
1 TATAT
1630136 ATTAAATATT
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.03
21 25 0.33
22 40 0.53
23 4 0.05
24 2 0.03
25 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (22 bp):
TATATTATATGTTTTTAAAAAC
Done.