Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 23
Found at i:916764 original size:101 final size:101
Alignment explanation
Indices: 916589--916786 Score: 351
Period size: 101 Copynumber: 2.0 Consensus size: 101
916579 ACTCTTTTTT
*
916589 TTTAAGAAAACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAGGGAG
1 TTTAAGAAAACTTTAAGGGGAGTCAGCTAATCACACTACCATCCCACACTCTAAGTGAAAGGGAG
916654 CATACCTTCCACCCCCGAGCTAGTAAGGTAGATTTG
66 CATACCTTCCACCCCCGAGCTAGTAAGGTAGATTTG
* * *
916690 TTTAAGCATACTTTAAGGGGAGTCAGCTAATCACACTACCATCCCACACTCTAAGTGAATGGGAG
1 TTTAAGAAAACTTTAAGGGGAGTCAGCTAATCACACTACCATCCCACACTCTAAGTGAAAGGGAG
*
916755 CATACCTTCCACCCCCGAGCTAGTCAGGTAGA
66 CATACCTTCCACCCCCGAGCTAGTAAGGTAGA
916787 GTCATCCTGT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (101 bp):
TTTAAGAAAACTTTAAGGGGAGTCAGCTAATCACACTACCATCCCACACTCTAAGTGAAAGGGAG
CATACCTTCCACCCCCGAGCTAGTAAGGTAGATTTG
Found at i:919702 original size:18 final size:18
Alignment explanation
Indices: 919679--919720 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
919669 TTTCAATCTC
919679 AGGTTCAAAATGAGATAA
1 AGGTTCAAAATGAGATAA
919697 AGGTTCAAAATGAGATAA
1 AGGTTCAAAATGAGATAA
*
919715 TGGTTC
1 AGGTTC
919721 CTTGGCACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (18 bp):
AGGTTCAAAATGAGATAA
Found at i:922333 original size:16 final size:16
Alignment explanation
Indices: 922312--922353 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
922302 TTTTAAAAAT
922312 ATGTTTTAAATTGTTA
1 ATGTTTTAAATTGTTA
922328 ATGTTTTAAATTGTTA
1 ATGTTTTAAATTGTTA
922344 ATGTTTTAAA
1 ATGTTTTAAA
922354 AAGATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (16 bp):
ATGTTTTAAATTGTTA
Found at i:926440 original size:22 final size:22
Alignment explanation
Indices: 926413--926460 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
926403 TATTAGTAAA
926413 TTTTTATTAGGAGTTATCACAT
1 TTTTTATTAGGAGTTATCACAT
926435 TTTTTATTAGGAGTTATCACAT
1 TTTTTATTAGGAGTTATCACAT
926457 TTTT
1 TTTT
926461 GTTAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.54
Consensus pattern (22 bp):
TTTTTATTAGGAGTTATCACAT
Found at i:927593 original size:23 final size:22
Alignment explanation
Indices: 927566--927608 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
927556 ATATAATAAA
*
927566 TAATATTATTTATTATAAAAACT
1 TAATATTATTAATT-TAAAAACT
927589 TAATATTATTAATTTAAAAA
1 TAATATTATTAATTTAAAAA
927609 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTATTAATTTAAAAACT
Found at i:927677 original size:25 final size:25
Alignment explanation
Indices: 927635--927714 Score: 63
Period size: 28 Copynumber: 3.0 Consensus size: 25
927625 TTAATACTAT
*
927635 TTATTTCAAT-ATTATTATTAAAATA
1 TTATTTCTATAATT-TTATTAAAATA
927660 TTATTTCTATAATTTTATAAATAAAATA
1 TTATTTCTATAATTTTAT---TAAAATA
** *
927688 TTAACTCTAGTATATTCTATTAAAATA
1 TTATTTCTA-TA-ATTTTATTAAAATA
927715 AAAATATGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
25 13 0.29
26 3 0.07
27 7 0.16
28 14 0.31
29 2 0.04
30 6 0.13
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (25 bp):
TTATTTCTATAATTTTATTAAAATA
Found at i:927985 original size:23 final size:26
Alignment explanation
Indices: 927955--928011 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 26
927945 AATAGTATCA
927955 TATATTATTATAAT-AT-A-ATTGAG
1 TATATTATTATAATAATAATATTGAG
* *
927978 TATATTATTTTAATAATAATATTTAG
1 TATATTATTATAATAATAATATTGAG
928004 TATATTAT
1 TATATTAT
928012 ATTATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 13 0.45
24 2 0.07
25 1 0.03
26 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (26 bp):
TATATTATTATAATAATAATATTGAG
Found at i:928024 original size:26 final size:26
Alignment explanation
Indices: 927947--928026 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
927937 AAGAATATAA
*
927947 TAGTATCA-TATATTATTATAATATAATT
1 TAGTAT-ATTATATTATTA-AAAAT-ATT
* * * *
927975 GAGTATATTATTTTAATAATAATATT
1 TAGTATATTATATTATTAAAAATATT
928001 TAGTATATTATATTATTAAAAATATT
1 TAGTATATTATATTATTAAAAATATT
928027 AATAAATATA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
26 25 0.60
27 4 0.10
28 13 0.31
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (26 bp):
TAGTATATTATATTATTAAAAATATT
Found at i:930517 original size:19 final size:19
Alignment explanation
Indices: 930481--930530 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
930471 TGACTATAAC
*
930481 CGTTGACTCTGACATTGAT
1 CGTTGACTTTGACATTGAT
* *
930500 CGTTGACTTTGGCTTTGAT
1 CGTTGACTTTGACATTGAT
* *
930519 CATCGACTTTGA
1 CGTTGACTTTGA
930531 TCCAAAAAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (19 bp):
CGTTGACTTTGACATTGAT
Found at i:932324 original size:71 final size:70
Alignment explanation
Indices: 932194--932330 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 70
932184 AAGTTATGGT
* * **
932194 AGGTTCATCTTGTCAAACTGGTAATAACTTATATAGGTTCAAACGGATCGAACTAGTAATTCCTT
1 AGGTTCAGCTTGTCAAACTGATAATAACTTATATAGGTTCAAACCAATCGAACTAGTAATTCCTT
932259 ACGGG
66 ACGGG
** * ** *
932264 AGGTTCAGCTCTGTCAAACTGATAATTCCTTATATAGGTTCATACCAATCGAGTTGGTAATTCCT
1 AGGTTCAGCT-TGTCAAACTGATAATAACTTATATAGGTTCAAACCAATCGAACTAGTAATTCCT
932329 TA
65 TA
932331 TTGATCTAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
70 9 0.16
71 47 0.84
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (70 bp):
AGGTTCAGCTTGTCAAACTGATAATAACTTATATAGGTTCAAACCAATCGAACTAGTAATTCCTT
ACGGG
Found at i:937421 original size:38 final size:38
Alignment explanation
Indices: 937368--937691 Score: 385
Period size: 37 Copynumber: 8.5 Consensus size: 38
937358 ATTATTTAAA
937368 AAAACTA-ATATTATATATATTTTCGAAAAATGTTTTC
1 AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
* *
937405 AAAACTATACATTATATATATATTT-GAAAAATATTTTC
1 AAAACTATATATTATATATAT-TTTCGAAAAATGTTTTC
*
937443 AAAACTATATATTATATATATTTT-TAAAAATGTTTTC
1 AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
* * *
937480 CAAACTATATA-T-TATACATTTTCAAAAAAATGTTTTC
1 AAAACTATATATTATATATATTTTC-GAAAAATGTTTTC
* *
937517 AAAACTATATATTAAATATATATATTC-AAAAATGTTTTG
1 AAAACTATATATT--ATATATATTTTCGAAAAATGTTTTC
*
937556 AAAACTATATGTTATATATATTTTC-AAAAATGTTTTC
1 AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
* * *
937593 AAAACTATATATTATATATAATTTCAACAAAAT-TTCTC
1 AAAACTATATATTATATATATTTTCGA-AAAATGTTTTC
*
937631 AAAACTATATATTATATATATTTTCGAAAAAAATGCTTTC
1 AAAACTATATATTATATATATTTTCG--AAAAATGTTTTC
* *
937671 AACACTATATAATAATATATA
1 AAAACTATAT-ATTATATATA
937692 CATTATTTGT
Statistics
Matches: 249, Mismatches: 24, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
35 9 0.04
36 1 0.00
37 98 0.39
38 74 0.30
39 36 0.14
40 13 0.05
41 18 0.07
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (38 bp):
AAAACTATATATTATATATATTTTCGAAAAATGTTTTC
Found at i:937455 original size:76 final size:74
Alignment explanation
Indices: 937368--937691 Score: 375
Period size: 76 Copynumber: 4.3 Consensus size: 74
937358 ATTATTTAAA
*
937368 AAAACTA-ATATTATATATATTTTCGAAAAATGTTTTCAAAACTATACATTATATATATATTTGA
1 AAAACTATATATTATATATATTTTC-AAAAATGTTTTCAAAACTATATATTATATATAT-TTTGA
937432 AAAATATTTTC
64 AAAATATTTTC
* * * **
937443 AAAACTATATATTATATATATTTTTAAAAATGTTTTCCAAACTATATATTATACAT-TTTCAAAA
1 AAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTT-TGAA
*
937507 AAATGTTTTC
65 AAATATTTTC
* * * *
937517 AAAACTATATATTAAATATATATATTCAAAAATGTTTTGAAAACTATATGTTATATATATTTTCA
1 AAAACTATATATT--ATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTGA
*
937582 AAAATGTTTTC
64 AAAATATTTTC
* *
937593 AAAACTATATATTATATATAATTTCAACAAAAT-TTCTCAAAACTATATATTATATATATTTTCG
1 AAAACTATATATTATATATATTTTC-A-AAAATGTTTTCAAAACTATATATTATATATATTTT-G
*
937657 AAAAAAATGCTTTC
63 AAAAATAT--TTTC
* *
937671 AACACTATATAATAATATATA
1 AAAACTATAT-ATTATATATA
937692 CATTATTTGT
Statistics
Matches: 213, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
73 2 0.01
74 35 0.16
75 62 0.29
76 89 0.42
77 3 0.01
78 13 0.06
79 9 0.04
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (74 bp):
AAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTGAAA
AATATTTTC
Found at i:940468 original size:22 final size:22
Alignment explanation
Indices: 940443--940515 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
940433 CACATAGAAT
940443 GAAAGAAAATTAAATTCAAAAG
1 GAAAGAAAATTAAATTCAAAAG
* * * *
940465 GAAATG-AAATGAAGTACAAAAT
1 GAAA-GAAAATTAAATTCAAAAG
940487 GAAAGAAAATTAAATTCAAAAG
1 GAAAGAAAATTAAATTCAAAAG
*
940509 GTAAGAA
1 GAAAGAA
940516 GAAATGTTTG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.62, C:0.04, G:0.16, T:0.18
Consensus pattern (22 bp):
GAAAGAAAATTAAATTCAAAAG
Found at i:945134 original size:23 final size:23
Alignment explanation
Indices: 945097--945140 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
945087 ATGTGGGTCC
*
945097 TCTACAAAAACAAATCAAAATTA
1 TCTACAAAAACAAATAAAAATTA
945120 TCTACAAAATA-AAATAAAAAT
1 TCTACAAAA-ACAAATAAAAAT
945141 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.23
Consensus pattern (23 bp):
TCTACAAAAACAAATAAAAATTA
Found at i:945685 original size:15 final size:15
Alignment explanation
Indices: 945657--945694 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
945647 AAATCTACTT
945657 GATATCTC--GATTG
1 GATATCTCTGGATTG
945670 GATATCTCTGGATTG
1 GATATCTCTGGATTG
945685 GATATCTCTG
1 GATATCTCTG
945695 CTTGGCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.35
15 15 0.65
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (15 bp):
GATATCTCTGGATTG
Found at i:949714 original size:20 final size:20
Alignment explanation
Indices: 949689--949731 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
949679 TCTAACAGCC
*
949689 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
949709 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
949729 CAT
1 CAT
949732 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:978502 original size:20 final size:22
Alignment explanation
Indices: 978479--978526 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
978469 GAAAAATTGC
978479 AATAAAAAATAAA-ATAAAG-A
1 AATAAAAAATAAATATAAAGTA
*
978499 AATAAAAAATAAATATAATGTA
1 AATAAAAAATAAATATAAAGTA
978521 AATAAA
1 AATAAA
978527 TACCATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.52
21 5 0.20
22 7 0.28
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (22 bp):
AATAAAAAATAAATATAAAGTA
Found at i:978573 original size:20 final size:22
Alignment explanation
Indices: 978550--978589 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
978540 AAAATGTGTT
978550 CTAAAAATAT-TTTT-AAAAAA
1 CTAAAAATATGTTTTCAAAAAA
978570 CTAAAAATATGTTTTCAAAA
1 CTAAAAATATGTTTTCAAAA
978590 CTATATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (22 bp):
CTAAAAATATGTTTTCAAAAAA
Found at i:978652 original size:19 final size:19
Alignment explanation
Indices: 978628--978665 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
978618 AATGTTTTCA
978628 AAACTATATATTATATATT
1 AAACTATATATTATATATT
978647 AAACTATATATTATATATT
1 AAACTATATATTATATATT
978666 TTCAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
AAACTATATATTATATATT
Found at i:978676 original size:21 final size:21
Alignment explanation
Indices: 978622--978676 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 21
978612 GAAAAAAATG
978622 TTTTCAAAACTATATATTATATA
1 TTTTCAAAA--ATATATTATATA
*
978645 --TT-AAACTATATATTATATA
1 TTTTCAAA-AATATATTATATA
978664 TTTTCAAAAATAT
1 TTTTCAAAAATAT
978677 TTTCAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
19 12 0.46
20 3 0.12
21 8 0.31
22 3 0.12
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTCAAAAATATATTATATA
Found at i:978685 original size:54 final size:57
Alignment explanation
Indices: 978587--978699 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 57
978577 TATGTTTTCA
*
978587 AAACTATATATTATATATATTTTCGGAAAAAAATGTTTTCAAAACTATATATTATATATT
1 AAACTATATATTATATATATTTTC---AAAAAATATTTTCAAAACTATATATTATATATT
978647 AAACTATATA-T-TATATATTTTC-AAAAATATTTTCAAAACTATATATTATATAT
1 AAACTATATATTATATATATTTTCAAAAAATATTTTCAAAACTATATATTATATAT
978700 ATTTTATATA
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
54 30 0.58
58 11 0.21
59 1 0.02
60 10 0.19
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (57 bp):
AAACTATATATTATATATATTTTCAAAAAATATTTTCAAAACTATATATTATATATT
Found at i:978714 original size:44 final size:44
Alignment explanation
Indices: 978651--978734 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
978641 TATATTAAAC
*
978651 TATATATTATATATTTTCAAAAATATTTTCAAAACTATATATTA
1 TATATATTATATATATTCAAAAATATTTTCAAAACTATATATTA
* *
978695 TATATATTTTATATATTCAAAAATGTTTTCAAAACTATAT
1 TATATATTATATATATTCAAAAATATTTTCAAAACTATAT
978735 CAAACTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (44 bp):
TATATATTATATATATTCAAAAATATTTTCAAAACTATATATTA
Found at i:980193 original size:15 final size:17
Alignment explanation
Indices: 980163--980194 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
980153 ACAAGGATTG
980163 TGTGTGTAATTATACCC
1 TGTGTGTAATTATACCC
980180 TGTGTG-AATT-TACCC
1 TGTGTGTAATTATACCC
980195 AGGAGCCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (17 bp):
TGTGTGTAATTATACCC
Found at i:981502 original size:37 final size:37
Alignment explanation
Indices: 981452--981531 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
981442 TGATCTGATC
981452 TTGCTTCACTACTCTTTTTGTGAAGG-TTGAATTTGCA
1 TTGCTTCACTACTCTTTTTGTGAAGGCTTG-ATTTGCA
981489 TTGCTTCACTACTCTTTTTGTGAAGGCTTGATTTGCA
1 TTGCTTCACTACTCTTTTTGTGAAGGCTTGATTTGCA
981526 TTGCTT
1 TTGCTT
981532 GTTTCCACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 39 0.93
38 3 0.07
ACGTcount: A:0.16, C:0.17, G:0.19, T:0.47
Consensus pattern (37 bp):
TTGCTTCACTACTCTTTTTGTGAAGGCTTGATTTGCA
Found at i:995759 original size:25 final size:24
Alignment explanation
Indices: 995730--995791 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
995720 CTTGGCTTGC
995730 TTTTCTCTTTTTGAAATCTTT-TTCT
1 TTTTCTCTTTTTG-AAT-TTTCTTCT
995755 TTTTCTTCTTTTTTGAATTTTCTTCT
1 TTTTC-TC-TTTTTGAATTTTCTTCT
*
995781 TTTTGTCTTTT
1 TTTTCTCTTTT
995792 CTTTCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 4 0.12
25 10 0.30
26 13 0.39
27 6 0.18
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.73
Consensus pattern (24 bp):
TTTTCTCTTTTTGAATTTTCTTCT
Found at i:995780 original size:26 final size:28
Alignment explanation
Indices: 995732--995784 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
995722 TGGCTTGCTT
995732 TTCTCTTTTTGAAATCTTTTTCTTTTTC
1 TTCTCTTTTTGAAATCTTTTTCTTTTTC
995760 TTCT-TTTTTG-AAT-TTTCTTCTTTTT
1 TTCTCTTTTTGAAATCTTT-TTCTTTTT
995785 GTCTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 3 0.12
26 11 0.46
27 6 0.25
28 4 0.17
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (28 bp):
TTCTCTTTTTGAAATCTTTTTCTTTTTC
Found at i:995802 original size:17 final size:15
Alignment explanation
Indices: 995746--995803 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 15
995736 CTTTTTGAAA
*
995746 TCTTTTTCTTTTTCT
1 TCTTTTTGTTTTTCT
*
995761 TCTTTTTTGAATTTTCT
1 TC-TTTTTG-TTTTTCT
995778 TCTTTTTGTCTTTTCTT
1 TCTTTTTGT-TTTTC-T
995795 TCTTTTTGT
1 TCTTTTTGT
995804 ACTCCAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 2 0.06
16 16 0.44
17 18 0.50
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
TCTTTTTGTTTTTCT
Found at i:1000363 original size:25 final size:24
Alignment explanation
Indices: 1000334--1000395 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
1000324 CTTGGCTTGC
1000334 TTTTCTCTTTTTGAAATCTTT-TTCT
1 TTTTCTCTTTTTG-AAT-TTTCTTCT
1000359 TTTTCTTCTTTTTTGAATTTTCTTCT
1 TTTTC-TC-TTTTTGAATTTTCTTCT
*
1000385 TTTTGTCTTTT
1 TTTTCTCTTTT
1000396 CTTTCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 4 0.12
25 10 0.30
26 13 0.39
27 6 0.18
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.73
Consensus pattern (24 bp):
TTTTCTCTTTTTGAATTTTCTTCT
Found at i:1000384 original size:26 final size:28
Alignment explanation
Indices: 1000336--1000388 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
1000326 TGGCTTGCTT
1000336 TTCTCTTTTTGAAATCTTTTTCTTTTTC
1 TTCTCTTTTTGAAATCTTTTTCTTTTTC
1000364 TTCT-TTTTTG-AAT-TTTCTTCTTTTT
1 TTCTCTTTTTGAAATCTTT-TTCTTTTT
1000389 GTCTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 3 0.12
26 11 0.46
27 6 0.25
28 4 0.17
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (28 bp):
TTCTCTTTTTGAAATCTTTTTCTTTTTC
Found at i:1000406 original size:17 final size:15
Alignment explanation
Indices: 1000350--1000407 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 15
1000340 CTTTTTGAAA
*
1000350 TCTTTTTCTTTTTCT
1 TCTTTTTGTTTTTCT
*
1000365 TCTTTTTTGAATTTTCT
1 TC-TTTTTG-TTTTTCT
1000382 TCTTTTTGTCTTTTCTT
1 TCTTTTTGT-TTTTC-T
1000399 TCTTTTTGT
1 TCTTTTTGT
1000408 ACTCCAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 2 0.06
16 16 0.44
17 18 0.50
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
TCTTTTTGTTTTTCT
Found at i:1001846 original size:71 final size:71
Alignment explanation
Indices: 1001725--1001866 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
1001715 CATCTTGTAG
1001725 CTCAAATCTTCAGCTCAATCCAGCTATGAGCTCACGGCCTCAAAACAACTTTTCATCAATGATTC
1 CTCAAATCTTCAGCTCAATCCAGCTATGAGCTCACGGCCTCAAAACAACTTTTCATCAATGATTC
1001790 CTTATA
66 CTTATA
*
1001796 CTCAAATCTTCAGCTCAATCCAGCTATGAGCTCACGGCCTCAAAATAACTTTTCATCAATGATTC
1 CTCAAATCTTCAGCTCAATCCAGCTATGAGCTCACGGCCTCAAAACAACTTTTCATCAATGATTC
1001861 CTTATA
66 CTTATA
1001867 ATCTCCTAAG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.30
Consensus pattern (71 bp):
CTCAAATCTTCAGCTCAATCCAGCTATGAGCTCACGGCCTCAAAACAACTTTTCATCAATGATTC
CTTATA
Found at i:1004621 original size:3 final size:3
Alignment explanation
Indices: 1004613--1004653 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1004603 AACTATTAAA
1004613 AAT AAT AAT AAT AAT AAT AAT -AT AA- ATAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT A
1004654 TTTATTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 5 0.15
3 28 0.82
4 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1007417 original size:22 final size:22
Alignment explanation
Indices: 1007386--1007431 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1007376 AAAATAAAGT
*
1007386 AAAATAAAAT-ATTAATATATAA
1 AAAATAAAATAATT-ATAAATAA
*
1007408 AAAATCAAATAATTATAAATAA
1 AAAATAAAATAATTATAAATAA
1007430 AA
1 AA
1007432 CAACTATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATAAAATAATTATAAATAA
Found at i:1015821 original size:9 final size:9
Alignment explanation
Indices: 1015790--1015871 Score: 53
Period size: 9 Copynumber: 8.9 Consensus size: 9
1015780 ATAAATATGA
*
1015790 AAATAAAAA
1 AAATAAAAT
*
1015799 AAAGGAAAAT
1 AAA-TAAAAT
1015809 -AATAAAAT
1 AAATAAAAT
1015817 AAATAAAAT
1 AAATAAAAT
* *
1015826 AAAGATAA-
1 AAATAAAAT
1015834 AAATAACACA-
1 AAATAA-A-AT
1015844 AAATAAAAT
1 AAATAAAAT
*
1015853 TAATAAAACT
1 AAATAAAA-T
1015863 AAACTAAAA
1 AAA-TAAAA
1015872 AATAAAAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
8 10 0.18
9 28 0.49
10 14 0.25
11 5 0.09
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1015878 original size:5 final size:5
Alignment explanation
Indices: 1015789--1015871 Score: 50
Period size: 5 Copynumber: 16.8 Consensus size: 5
1015779 CATAAATATG
*
1015789 AAAAT AAAA- AAAAGG AAAAT --AAT AAAAT -AAAT AAAAT AAAGAT AAAAAT
1 AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT -AAAAT
* * * *
1015838 AACAC AAAAT AAAAT -TAAT AAAACT AAACT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAA
1015872 AATAAAAATA
Statistics
Matches: 60, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
3 3 0.05
4 11 0.18
5 31 0.52
6 12 0.20
7 3 0.05
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1016409 original size:7 final size:7
Alignment explanation
Indices: 1016399--1016453 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
1016389 CAAAAAATAA
1016399 AATAAAT
1 AATAAAT
1016406 AATAAAT
1 AATAAAT
1016413 AA-AAAT
1 AATAAAT
1016419 AAAATAAAT
1 --AATAAAT
1016428 AATAAAT
1 AATAAAT
1016435 AATAAA-
1 AATAAAT
*
1016441 AACATAAT
1 AATA-AAT
1016449 AATAA
1 AATAA
1016454 TAGGGCTAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
6 7 0.17
7 25 0.61
8 5 0.12
9 4 0.10
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:1016414 original size:11 final size:11
Alignment explanation
Indices: 1016398--1016453 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
1016388 GCAAAAAATA
1016398 AAATAAATAAT
1 AAATAAATAAT
1016409 AAATAAA-AAT
1 AAATAAATAAT
1016419 AAAATAAATAAT
1 -AAATAAATAAT
1016431 AAAT-AATAA-
1 AAATAAATAAT
*
1016440 AAACATAATAAT
1 AAATA-AATAAT
1016452 AA
1 AA
1016454 TAGGGCTAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 3 0.08
10 8 0.21
11 23 0.59
12 5 0.13
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:1016419 original size:22 final size:22
Alignment explanation
Indices: 1016391--1016453 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
1016381 AAGTAAAGCA
1016391 AAAAATAAAATAAATAATAAAT
1 AAAAATAAAATAAATAATAAAT
1016413 AAAAATAAAATAAATAATAAAT
1 AAAAATAAAATAAATAATAAAT
*
1016435 AATAAA-AACAT-AATAATAA
1 AA-AAATAAAATAAATAATAA
1016454 TAGGGCTAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 8 0.21
22 28 0.72
23 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAAATAAAATAAATAATAAAT
Found at i:1017533 original size:24 final size:25
Alignment explanation
Indices: 1017489--1017554 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
1017479 TCTGTAAACA
* *
1017489 AATAAAATAAATAATATATATATAATT
1 AATATAATATATAA-ATAT-TATAATT
1017516 AATATAATATATAAATATTATAATT
1 AATATAATATATAAATATTATAATT
* *
1017541 -ATGTAAGATATAAA
1 AATATAATATATAAA
1017555 AATGGGACGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.34
25 7 0.20
26 4 0.11
27 12 0.34
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
AATATAATATATAAATATTATAATT
Found at i:1018439 original size:85 final size:85
Alignment explanation
Indices: 1018293--1019299 Score: 1148
Period size: 85 Copynumber: 11.8 Consensus size: 85
1018283 ATGTGTCATC
* * ** * * *
1018293 GAGCTGAATGGAATCGAACTCGATA-GTTTTTGTTGACAGATAGCTTTTCTTGACTTAAGTTATG
1 GAGCTGAATGGAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* *
1018357 CTGTAAATTTGACATGCCCTT
65 CTGTAAATTTGATATGCCTTT
* * * * *
1018378 AAGCTGAATGGAATCGAACTCGAAAGTATTTGTTGACAGATAACCCTTCTCACATTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
1018443 TGTAAATTTGATATGTCCTTT
66 TGTAAATTTGATATG-CCTTT
* * * * *
1018464 -AGTTGAA-GGTAATCGAAATCGAAGGTCTTTGTTTATAGATAACCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGG-AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
1018527 CTGTAAATTTGATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
* * *
1018548 GAGCTGAATGGAATCGAACTCGAATGTCTTTATTGACAGACAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
1018613 TATAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCTTT
* * * * * *
1018633 GAGCTGAATGTAATCGAACTCGAAGGTCTTCGTTGAGAGATAGCCCTTCTCTCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
1018698 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * * * * * *
1018718 GAGCTGAATGGAATTGAAATCAAAGGACTTTATTAACAAATAACCCTTCTCACCTTGAGTTATGT
1 GAGCTGAATGGAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
1018783 TATAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCTTT
* * * * * *
1018803 GAGTTGAATGTAATC-AATCTCGAAGGTCTTGGTTGATAGATAGCCCTTCTCGCCTTGGGTTATG
1 GAGCTGAATGGAATCGAA-CTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
*
1018867 TTGTAAATTTGATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
* * * * *
1018888 TAGCTGAATAGAATC-AATCTCGAAGGTCTTTATTGATAGATAACCCTTTTCGCCTTGAGTTATG
1 GAGCTGAATGGAATCGAA-CTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* *
1018952 TTGTAAATTTAATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
* * * *
1018973 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGA-CCTTCTCGCCTTGAGCTACG
1 GAGCTGAATGGAATCGAACTCGAAGGTCTTTGTTGACAGATA-ACCCTTCTCGCCTTGAGTTATG
*
1019037 CTGT-AATTCTAATATGCCTTT
65 CTGTAAATT-TGATATGCCTTT
** * * * * *
1019058 GAGCTGAATTTAATCGAACTCAAAGGTTTTTGATGACAGATAACCCTTCTTGGCTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
1019123 TGTAAATTTTATATGCCTTT
66 TGTAAATTTGATATGCCTTT
** ** *
1019143 GAGCTGAATATAATCGAACTC-AATGGTCTTTACTGACAGATAACCCTTATCGCCTTGAGTTATG
1 GAGCTGAATGGAATCGAACTCGAA-GGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
*
1019207 CTGTAAATTTGATATGACTTT
65 CTGTAAATTTGATATGCCTTT
* * * * * * *
1019228 GAGCTGAATGAAATTGAACTCGAAGGTATTTGATGACAGATAGCCTTTCTCGTCTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
1019293 TGCAAAT
66 TGTAAAT
1019300 AGTTAAGTGA
Statistics
Matches: 785, Mismatches: 124, Indels: 26
0.84 0.13 0.03
Matches are distributed among these distances:
84 17 0.02
85 753 0.96
86 15 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
TGTAAATTTGATATGCCTTT
Found at i:1020712 original size:99 final size:99
Alignment explanation
Indices: 1020540--1020736 Score: 285
Period size: 99 Copynumber: 2.0 Consensus size: 99
1020530 GGACAACTCA
** *
1020540 ATATTATTGTCACCTTTATAAGGCTAACTGAATCTTATTCATAAAGTTAGGACGTTTAACCAATT
1 ATATTATAATCACCTTTATAAGGCTAACTGAATCTTATCCATAAAGTTAGGACGTTTAACCAATT
*
1020605 GCTTTAGAGGGATAGCTCAAGCTTTATTGTATAG
66 GCTTTAGAGGGACAGCTCAAGCTTTATTGTATAG
*
1020639 ATATTATAATCACCTTTATCAA-GCTAGCTGAATCTTATCCATAAAGCTGT-GG-CGTTTAACCA
1 ATATTATAATCACCTTTAT-AAGGCTAACTGAATCTTATCCATAAAG-T-TAGGACGTTTAACCA
1020701 ATTG-TTCTAGAGGGACAGCTCAAGCTTTATTGTATA
63 ATTGCTT-TAGAGGGACAGCTCAAGCTTTATTGTATA
1020737 TATAATATTA
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
98 2 0.02
99 81 0.91
100 5 0.06
101 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (99 bp):
ATATTATAATCACCTTTATAAGGCTAACTGAATCTTATCCATAAAGTTAGGACGTTTAACCAATT
GCTTTAGAGGGACAGCTCAAGCTTTATTGTATAG
Found at i:1024441 original size:6 final size:6
Alignment explanation
Indices: 1024408--1024504 Score: 52
Period size: 6 Copynumber: 14.8 Consensus size: 6
1024398 CATAAATATG
* * * *
1024408 AAAATA AAAAGGA AAAATAA TAAAATA AAGATA AAAATA AAAAT- AAGACA
1 AAAATA AAAA-TA AAAAT-A -AAAATA AAAATA AAAATA AAAATA AAAATA
* *
1024458 AAAATAA AATTAATA AAACTAA ACTAAACA AAAATA AAAATA AAAAT
1 AAAAT-A AA--AATA AAAAT-A A--AAATA AAAATA AAAATA AAAAT
1024505 TATGGAAGTA
Statistics
Matches: 69, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
5 3 0.04
6 39 0.57
7 12 0.17
8 10 0.14
9 5 0.07
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1024446 original size:12 final size:12
Alignment explanation
Indices: 1024408--1024504 Score: 52
Period size: 15 Copynumber: 7.4 Consensus size: 12
1024398 CATAAATATG
*
1024408 AAAATAAAAAGGA
1 AAAATAAAAA-TA
1024421 AAAATAATAAAATA
1 AAAAT-A-AAAATA
*
1024435 AAGATAAAAATA
1 AAAATAAAAATA
* *
1024447 AAAAT-AAGACA
1 AAAATAAAAATA
1024458 AAAATAAAATTAATA
1 AAAAT-AAA--AATA
* *
1024473 AAACTAAACTAAACA
1 AAAAT-AA--AAATA
1024488 AAAATAAAAATA
1 AAAATAAAAATA
1024500 AAAAT
1 AAAAT
1024505 TATGGAAGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
11 9 0.14
12 19 0.29
13 8 0.12
14 8 0.12
15 20 0.31
17 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:1024448 original size:17 final size:18
Alignment explanation
Indices: 1024426--1024467 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1024416 AAGGAAAAAT
*
1024426 AATAAAATA-AAGATAAA
1 AATAAAATATAAGACAAA
1024443 AATAAAA-ATAAGACAAA
1 AATAAAATATAAGACAAA
1024460 AATAAAAT
1 AATAAAAT
1024468 TAATAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (18 bp):
AATAAAATATAAGACAAA
Found at i:1025017 original size:3 final size:3
Alignment explanation
Indices: 1025009--1025057 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
1024999 TAAAGCAAAA
*
1025009 AAT AAT AAT AAT AAT AA- AAT AA- AAA AAT AA- AAT AAAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT
1025053 AAT AA
1 AAT AA
1025058 AAACATAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
2 6 0.15
3 28 0.70
4 6 0.15
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:1025022 original size:25 final size:24
Alignment explanation
Indices: 1024994--1025060 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
1024984 GTACAAATGT
*
1024994 ATAAGTAAAGCAAAAAATAATAAT-A
1 ATAA-TAAAGAAAAAAATAA-AATAA
*
1025019 ATAATAAAATAAAAAAATAAAATAA
1 ATAAT-AAAGAAAAAAATAAAATAA
*
1025044 ATAATAAATAATAAAAA
1 ATAATAAAGAA-AAAAA
1025061 CATAATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 10 0.27
25 27 0.73
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (24 bp):
ATAATAAAGAAAAAAATAAAATAA
Found at i:1025052 original size:24 final size:25
Alignment explanation
Indices: 1025005--1025067 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 25
1024995 TAAGTAAAGC
1025005 AAAAAATAATAATAATAATAAAATA
1 AAAAAATAATAATAATAATAAAATA
1025030 AAAAAATAA-AATAAATAATAAATAATA
1 AAAAAATAATAAT-AATAAT-AA-AATA
*
1025057 AAAACATAATA
1 AAAAAATAATA
1025068 TTAGTAGGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 3 0.09
25 15 0.45
26 2 0.06
27 12 0.36
28 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (25 bp):
AAAAAATAATAATAATAATAAAATA
Found at i:1025067 original size:25 final size:25
Alignment explanation
Indices: 1025005--1025067 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
1024995 TAAGTAAAGC
1025005 AAAAAATA-ATAAT-AATAATAAAAT
1 AAAAAA-ACATAATAAATAATAAAAT
* *
1025029 AAAAAAATAAAATAAATAAT-AAAT
1 AAAAAAACATAATAAATAATAAAAT
1025053 AATAAAAACATAATA
1 AA-AAAAACATAATA
1025068 TTAGTAGGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 1 0.03
24 16 0.48
25 16 0.48
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (25 bp):
AAAAAAACATAATAAATAATAAAAT
Found at i:1026053 original size:16 final size:16
Alignment explanation
Indices: 1026009--1026065 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
1025999 TCTATAAACA
* * *
1026009 AATAAAATAAATAATA
1 AATATAATATATAATT
*
1026025 AATACATATATATAATT
1 AATATA-ATATATAATT
*
1026042 AATATAATATATAAAT
1 AATATAATATATAATT
*
1026058 ATTATAAT
1 AATATAAT
1026066 TATGTAAGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 21 0.62
17 13 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATAATATATAATT
Found at i:1026059 original size:24 final size:23
Alignment explanation
Indices: 1026032--1026085 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1026022 ATAAATACAT
*
1026032 ATATATAATTAATATAATATATAA
1 ATATATAATT-ATATAAGATATAA
*
1026056 ATATTATAATTATGTAAGATATAA
1 ATA-TATAATTATATAAGATATAA
*
1026080 AAATAT
1 ATATAT
1026086 GACGAAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 3 0.12
24 16 0.62
25 7 0.27
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
ATATATAATTATATAAGATATAA
Found at i:1027490 original size:13 final size:14
Alignment explanation
Indices: 1027463--1027492 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1027453 TATTTCTAAC
1027463 ACTACTAACCTCTT
1 ACTACTAACCTCTT
1027477 ACTACTAA-CTCTT
1 ACTACTAACCTCTT
1027490 ACT
1 ACT
1027493 TTATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (14 bp):
ACTACTAACCTCTT
Found at i:1027768 original size:17 final size:17
Alignment explanation
Indices: 1027746--1027783 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1027736 TTAAATTGAG
1027746 TTTCA-TATTCTGTTTAT
1 TTTCATTATTCT-TTTAT
1027763 TTTCATTTATTCTTTTAT
1 TTTCA-TTATTCTTTTAT
1027781 TTT
1 TTT
1027784 ATTTATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 8 0.42
19 6 0.32
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTCATTATTCTTTTAT
Found at i:1027787 original size:17 final size:19
Alignment explanation
Indices: 1027751--1027789 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1027741 TTGAGTTTCA
1027751 TATTCTGTTTATTTTCATT
1 TATTCTGTTTATTTTCATT
1027770 TATTCT-TTTATTTT-ATT
1 TATTCTGTTTATTTTCATT
1027787 TAT
1 TAT
1027790 GAATTTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 6 0.30
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (19 bp):
TATTCTGTTTATTTTCATT
Found at i:1028422 original size:16 final size:15
Alignment explanation
Indices: 1028400--1028435 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1028390 CTATTTTGTC
1028400 TTTAAAAATTATTTT
1 TTTAAAAATTATTTT
1028415 TATT-AAAATTATTTT
1 T-TTAAAAATTATTTT
1028430 TTTAAA
1 TTTAAA
1028436 GAGATTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.11
15 15 0.79
16 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAAAATTATTTT
Found at i:1028434 original size:14 final size:15
Alignment explanation
Indices: 1028404--1028435 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1028394 TTTGTCTTTA
1028404 AAAATTATTTTTATT
1 AAAATTATTTTTATT
1028419 AAAATTATTTTT-TT
1 AAAATTATTTTTATT
1028433 AAA
1 AAA
1028436 GAGATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAAATTATTTTTATT
Found at i:1035950 original size:13 final size:13
Alignment explanation
Indices: 1035934--1035960 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1035924 AATGATATTG
1035934 TCAAATGAATTTT
1 TCAAATGAATTTT
1035947 TCAAATGAATTTT
1 TCAAATGAATTTT
1035960 T
1 T
1035961 AAAGAAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TCAAATGAATTTT
Found at i:1036279 original size:7 final size:7
Alignment explanation
Indices: 1036269--1036345 Score: 118
Period size: 7 Copynumber: 10.6 Consensus size: 7
1036259 AATTAAATTC
1036269 AAAATGA
1 AAAATGA
1036276 AAAATGA
1 AAAATGA
1036283 AAAATGA
1 AAAATGA
1036290 AAAATGA
1 AAAATGA
1036297 AAAATGA
1 AAAATGA
1036304 AAAATGA
1 AAAATGA
1036311 AAAATGAAA
1 AAAATG--A
1036320 AAAATGA
1 AAAATGA
1036327 AAAATGA
1 AAAATGA
*
1036334 AAGAAAGA
1 AA-AATGA
1036342 AAAA
1 AAAA
1036346 AAGGAAAAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
7 53 0.80
8 6 0.09
9 7 0.11
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (7 bp):
AAAATGA
Found at i:1036324 original size:9 final size:9
Alignment explanation
Indices: 1036310--1036355 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
1036300 ATGAAAAATG
1036310 AAAAATGAA
1 AAAAATGAA
1036319 AAAAATG--
1 AAAAATGAA
1036326 AAAAATGAA
1 AAAAATGAA
*
1036335 AGAAA-GAA
1 AAAAATGAA
*
1036343 AAAAAGGAA
1 AAAAATGAA
1036352 AAAA
1 AAAA
1036356 TGTTAAATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 7 0.22
8 7 0.22
9 18 0.56
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (9 bp):
AAAAATGAA
Found at i:1037546 original size:12 final size:12
Alignment explanation
Indices: 1037529--1037554 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1037519 GAGAGTGAGA
1037529 GTAGAAAATAGG
1 GTAGAAAATAGG
1037541 GTAGAAAATAGG
1 GTAGAAAATAGG
1037553 GT
1 GT
1037555 CCGTCACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (12 bp):
GTAGAAAATAGG
Found at i:1038744 original size:10 final size:10
Alignment explanation
Indices: 1038729--1038803 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1038719 GGGTCTCCAA
1038729 CGTTTATGTT
1 CGTTTATGTT
1038739 CGTTTATGTT
1 CGTTTATGTT
1038749 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
1038760 ATGTTCGTGTT
1 -CGTTTATGTT
1038771 CGTTTATGTT
1 CGTTTATGTT
1038781 CG----TGTT
1 CGTTTATGTT
1038787 CGTTTATGTT
1 CGTTTATGTT
1038797 CGTTTAT
1 CGTTTAT
1038804 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1038760 original size:16 final size:16
Alignment explanation
Indices: 1038735--1038799 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1038725 CCAACGTTTA
1038735 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1038751 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
1038767 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1038783 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1038799 T
1 T
1038800 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1038890 original size:16 final size:16
Alignment explanation
Indices: 1038869--1038901 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1038859 AAAAAAATTT
1038869 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1038885 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1038901 T
1 T
1038902 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1039763 original size:13 final size:14
Alignment explanation
Indices: 1039736--1039765 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1039726 TATTTCTAAC
1039736 ACTACTAACCTCTT
1 ACTACTAACCTCTT
1039750 ACTACTAA-CTCTT
1 ACTACTAACCTCTT
1039763 ACT
1 ACT
1039766 TTATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (14 bp):
ACTACTAACCTCTT
Found at i:1041392 original size:23 final size:23
Alignment explanation
Indices: 1041366--1041462 Score: 74
Period size: 23 Copynumber: 4.2 Consensus size: 23
1041356 ATAGTATCCA
1041366 GAGTACACAAATGTACTAAACAT
1 GAGTACACAAATGTACTAAACAT
*
1041389 GAGTAC-CAAATGGTACT-AATAT
1 GAGTACACAAAT-GTACTAAACAT
* *
1041411 GGGAGTGCACAAA-GTACTAAACAG
1 --GAGTACACAAATGTACTAAACAT
* * * *
1041435 GAGTGCTCAAATGCACTAATACAA
1 GAGTACACAAATGTACTAA-ACAT
1041459 GAGT
1 GAGT
1041463 GCTCAAAGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
22 19 0.32
23 22 0.37
24 15 0.25
25 4 0.07
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (23 bp):
GAGTACACAAATGTACTAAACAT
Found at i:1041429 original size:46 final size:47
Alignment explanation
Indices: 1041366--1041455 Score: 121
Period size: 46 Copynumber: 1.9 Consensus size: 47
1041356 ATAGTATCCA
* *
1041366 GAGTACACAAATGTACTAAACATGAGTAC-CAAATGGTACTAATATGG
1 GAGTACACAAATGTACTAAACAGGAGTACTCAAAT-GCACTAATATGG
* *
1041413 GAGTGCACAAA-GTACTAAACAGGAGTGCTCAAATGCACTAATA
1 GAGTACACAAATGTACTAAACAGGAGTACTCAAATGCACTAATA
1041456 CAAGAGTGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 23 0.61
47 15 0.39
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (47 bp):
GAGTACACAAATGTACTAAACAGGAGTACTCAAATGCACTAATATGG
Found at i:1041463 original size:46 final size:46
Alignment explanation
Indices: 1041365--1041476 Score: 118
Period size: 46 Copynumber: 2.4 Consensus size: 46
1041355 TATAGTATCC
* * * **
1041365 AGAGTACACAAATGTACTAAACATGAGTACCAAATGGTACTAATATG
1 AGAGTGCACAAA-GTACTAAACAGGAGTACCAAATGGCACTAATACA
* *
1041412 GGAGTGCACAAAGTACTAAACAGGAGTGCTCAAAT-GCACTAATACA
1 AGAGTGCACAAAGTACTAAACAGGAGTAC-CAAATGGCACTAATACA
* *
1041458 AGAGTGCTCAAAGCACTAA
1 AGAGTGCACAAAGTACTAA
1041477 TATAAGATCG
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
46 39 0.72
47 15 0.28
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (46 bp):
AGAGTGCACAAAGTACTAAACAGGAGTACCAAATGGCACTAATACA
Found at i:1041473 original size:23 final size:23
Alignment explanation
Indices: 1041413--1041483 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
1041403 ACTAATATGG
* * *
1041413 GAGTGCACAAAGTACTAA-ACAG
1 GAGTGCTCAAAGCACTAATACAA
1041435 GAGTGCTCAAATGCACTAATACAA
1 GAGTGCTCAAA-GCACTAATACAA
*
1041459 GAGTGCTCAAAGCACTAATATAA
1 GAGTGCTCAAAGCACTAATACAA
1041482 GA
1 GA
1041484 TCGATCTATG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 10 0.23
23 19 0.44
24 14 0.33
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (23 bp):
GAGTGCTCAAAGCACTAATACAA
Found at i:1044960 original size:43 final size:43
Alignment explanation
Indices: 1044899--1044980 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
1044889 CATCGGGAAA
1044899 TTCCGTTAAGAAGGCATGTATTTGTTTAGGAGGCTAATAGAAG
1 TTCCGTTAAGAAGGCATGTATTTGTTTAGGAGGCTAATAGAAG
1044942 TTCCGTTAAGAAGGCATGTATTTGTTTAGGAGGCTAATA
1 TTCCGTTAAGAAGGCATGTATTTGTTTAGGAGGCTAATA
1044981 TTTGGGAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (43 bp):
TTCCGTTAAGAAGGCATGTATTTGTTTAGGAGGCTAATAGAAG
Found at i:1048371 original size:55 final size:55
Alignment explanation
Indices: 1048310--1048555 Score: 352
Period size: 55 Copynumber: 4.5 Consensus size: 55
1048300 TTCCTAGGTT
* * *
1048310 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTTCGTGGGG
* *
1048365 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTTGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTTCGTGGGG
* * * * * *
1048420 TTTCACACATAGTTCCAATACAGAAATT--CATAGTCAGTATGAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTTCGTGGGG
* *
1048473 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTTCGTGGGG
*
1048528 TTGCACACATATTGCCAATACGGAAATT
1 TTGCACACATAGTGCCAATACGGAAATT
1048556 GCAACATATA
Statistics
Matches: 166, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 44 0.27
55 122 0.73
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (55 bp):
TTGCACACATAGTGCCAATACGGAAATTCACAAACTCATTATGAATTTCGTGGGG
Found at i:1048483 original size:108 final size:108
Alignment explanation
Indices: 1048349--1048555 Score: 353
Period size: 108 Copynumber: 1.9 Consensus size: 108
1048339 ACAAACTCAT
* *
1048349 TATGAATTACGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTT
1 TATGAATTACGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTC
*
1048414 GTGGGGTTTCACACATAGTT-CCAATACAGAAATTCATAGTCAG
66 GTGGGGTTGCACACATA-TTGCCAATACAGAAATTCATAGTCAG
*
1048457 TATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTC
1 TATGAATTACGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTC
*
1048522 GTGGGGTTGCACACATATTGCCAATACGGAAATT
66 GTGGGGTTGCACACATATTGCCAATACAGAAATT
1048556 GCAACATATA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
107 2 0.02
108 91 0.98
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (108 bp):
TATGAATTACGTGGGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTC
GTGGGGTTGCACACATATTGCCAATACAGAAATTCATAGTCAG
Found at i:1058572 original size:23 final size:23
Alignment explanation
Indices: 1058546--1058597 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1058536 ATGCGTATAT
* * * *
1058546 ATTCTACGCGGTTCTTCGGGATA
1 ATTCTACACGGTCCTTCAGGACA
1058569 ATTCTACACGGTCCTTCAGGACA
1 ATTCTACACGGTCCTTCAGGACA
1058592 ATTCTA
1 ATTCTA
1058598 TGTGACACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (23 bp):
ATTCTACACGGTCCTTCAGGACA
Found at i:1058742 original size:18 final size:19
Alignment explanation
Indices: 1058705--1058742 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1058695 GTTGGGCTAT
* *
1058705 TTAAACAAGTTAATATAAA
1 TTAAACAAGTGAATAAAAA
1058724 TTAAAC-AGTGAATAAAAA
1 TTAAACAAGTGAATAAAAA
1058742 T
1 T
1058743 ATATGTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (19 bp):
TTAAACAAGTGAATAAAAA
Found at i:1064137 original size:36 final size:36
Alignment explanation
Indices: 1064097--1064165 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1064087 CTTTAAAAAA
*
1064097 CTTTTCTTCATTTGAATTTTCCTCAAAACGTTCAAG
1 CTTTTATTCATTTGAATTTTCCTCAAAACGTTCAAG
*
1064133 CTTTTATTCATTTGAATTTTCCTCCAAACGTTC
1 CTTTTATTCATTTGAATTTTCCTCAAAACGTTC
1064166 TCCTACAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.46
Consensus pattern (36 bp):
CTTTTATTCATTTGAATTTTCCTCAAAACGTTCAAG
Found at i:1064179 original size:36 final size:36
Alignment explanation
Indices: 1064103--1064180 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 36
1064093 AAAACTTTTC
* ***
1064103 TTCATTTGAATTTTCCTCAAAACGTTCAAGCTTTTA
1 TTCATTTGAATTTTCCTCAAAACGTTCAACCTACAA
* *
1064139 TTCATTTGAATTTTCCTCCAAACGTTC-TCCTACAA
1 TTCATTTGAATTTTCCTCAAAACGTTCAACCTACAA
1064174 TTTCATT
1 -TTCATT
1064181 GTCTTTAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 3 0.09
36 32 0.91
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (36 bp):
TTCATTTGAATTTTCCTCAAAACGTTCAACCTACAA
Found at i:1065490 original size:24 final size:24
Alignment explanation
Indices: 1065463--1065521 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
1065453 AATAAAGATT
*
1065463 ATAAGAAATGGTATTAGTAATGGA
1 ATAAGAAATGGTATTACTAATGGA
1065487 ATAAGAAATGGTATTACTAATGGA
1 ATAAGAAATGGTATTACTAATGGA
1065511 ATAAGAAATGG
1 ATAAGAAATGG
1065522 ATAAATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.47, C:0.02, G:0.24, T:0.27
Consensus pattern (24 bp):
ATAAGAAATGGTATTACTAATGGA
Found at i:1065496 original size:12 final size:12
Alignment explanation
Indices: 1065463--1065522 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
1065453 AATAAAGATT
*
1065463 ATAAGAAATGGT
1 ATAAGAAATGGA
* *
1065475 ATTAGTAATGGA
1 ATAAGAAATGGA
*
1065487 ATAAGAAATGGT
1 ATAAGAAATGGA
* **
1065499 ATTACTAATGGA
1 ATAAGAAATGGA
1065511 ATAAGAAATGGA
1 ATAAGAAATGGA
1065523 TAAATAAATA
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.27
Consensus pattern (12 bp):
ATAAGAAATGGA
Found at i:1081961 original size:24 final size:24
Alignment explanation
Indices: 1081933--1081984 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1081923 GAGGGAAACA
* *
1081933 AAAGATGAAGATGA-AAAGTGAGT
1 AAAGAGGAAGATGATAAAGAGAGT
*
1081956 GAAAGAGGAAGGTGATAAAGAGAGT
1 -AAAGAGGAAGATGATAAAGAGAGT
1081981 AAAG
1 AAAG
1081985 TGGCAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.52, C:0.00, G:0.35, T:0.13
Consensus pattern (24 bp):
AAAGAGGAAGATGATAAAGAGAGT
Found at i:1085632 original size:14 final size:14
Alignment explanation
Indices: 1085602--1085637 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1085592 AAAGTCAACA
1085602 AGTTGACT-TAATG
1 AGTTGACTCTAATG
*
1085615 AGTTGACTCTACTG
1 AGTTGACTCTAATG
1085629 AGTTGACTC
1 AGTTGACTC
1085638 AGTGACTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (14 bp):
AGTTGACTCTAATG
Found at i:1091416 original size:34 final size:34
Alignment explanation
Indices: 1091366--1091430 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1091356 CTTTGGCATC
* *
1091366 CTTTCATGCCAGTAATGCACCCATATGCATTATT
1 CTTTCATGCCAATAATGCACCCATAAGCATTATT
*
1091400 CTTTTATGCCAATAATGCACCCATAAGCATT
1 CTTTCATGCCAATAATGCACCCATAAGCATT
1091431 TTAGCTATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (34 bp):
CTTTCATGCCAATAATGCACCCATAAGCATTATT
Found at i:1091473 original size:109 final size:109
Alignment explanation
Indices: 1091339--1091549 Score: 296
Period size: 109 Copynumber: 1.9 Consensus size: 109
1091329 TTAATAAAGC
* * * * *
1091339 ACCCATATACATTTCAACTTTGGCATCCTTTCATGCCAGTAATGCACCCATATGCATTATTCTTT
1 ACCCATATACATTTCAACTATGGCATCATTTCATGACAATAATGCACCCATATGCATTATTCTAT
1091404 TATGCCAATAATGCACCCATAAGCATTTTAGCTATGGTATCCTT
66 TATGCCAATAATGCACCCATAAGCATTTTAGCTATGGTATCCTT
* ** *
1091448 ACCCATATGCATTTCTGCTATGGCATCATTTCATGATAATAATGCACCCATATGCATTATTCTAT
1 ACCCATATACATTTCAACTATGGCATCATTTCATGACAATAATGCACCCATATGCATTATTCTAT
* * ** *
1091513 TATGTCGATAATGCACTTATATGCATTTTAGCTATGG
66 TATGCCAATAATGCACCCATAAGCATTTTAGCTATGG
1091550 CATTTTTTCA
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
109 88 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (109 bp):
ACCCATATACATTTCAACTATGGCATCATTTCATGACAATAATGCACCCATATGCATTATTCTAT
TATGCCAATAATGCACCCATAAGCATTTTAGCTATGGTATCCTT
Found at i:1096509 original size:22 final size:22
Alignment explanation
Indices: 1096460--1096522 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
1096450 TCTAATTTTG
*
1096460 GTATCGATACC--AGTAGTG-A
1 GTATCGATACCATAGTAGGGTA
*
1096479 GAATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
* *
1096501 GTATCGATACCATGGTAAGGTA
1 GTATCGATACCATAGTAGGGTA
1096523 TCGACACTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 10 0.28
21 6 0.17
22 20 0.56
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.25
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:1096584 original size:94 final size:95
Alignment explanation
Indices: 1096401--1096589 Score: 227
Period size: 94 Copynumber: 2.0 Consensus size: 95
1096391 ATACCAATGA
* * *
1096401 GGTAGTATCGATACCATGATAAGGGGTATTAATACCAAGAAACATCAAATCTAATTTTGGTATCG
1 GGTAGTATCGATACCATGATAA-GGGTATCAACACCAAGAAACATCAAACCTAATTTTGGTATCG
* *
1096466 ATACCAGTAGTGAGAATCGATACCATAGTAG
65 ATACCAGAAGGGAGAATCGATACCATAGTAG
* * * * *
1096497 GGTAGTATCGATACCATGGTAA-GGTATCGACACTAAGAAACATCGAACCTATTTTTGGTATCGA
1 GGTAGTATCGATACCATGATAAGGGTATCAACACCAAGAAACATCAAACCTAATTTTGGTATCGA
* * * * *
1096561 TACCTGAAGGGGGTATTGGTACCATAGTA
66 TACCAGAAGGGAGAATCGATACCATAGTA
1096590 TAGAAGTATT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
94 57 0.73
96 21 0.27
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (95 bp):
GGTAGTATCGATACCATGATAAGGGTATCAACACCAAGAAACATCAAACCTAATTTTGGTATCGA
TACCAGAAGGGAGAATCGATACCATAGTAG
Found at i:1096827 original size:68 final size:68
Alignment explanation
Indices: 1096710--1096855 Score: 186
Period size: 68 Copynumber: 2.1 Consensus size: 68
1096700 GTATAATTGC
* ** * **
1096710 TAGATGAAAGGCTAAGTGACTTTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTACGCC
1 TAGATGAAAGGCTAAGTGACTTTGAGGCCTAACTACGCAATTGACAGAAAGGTACCAATTACGCC
1096775 AGT
66 AGT
* ** *
1096778 TAGATGAAAGGCTAAGTG-CATTTGAGGCCTAACTACGTAATTGGTAGAAAGGTACCAATTATGC
1 TAGATGAAAGGCTAAGTGAC-TTTGAGGCCTAACTACGCAATTGACAGAAAGGTACCAATTACGC
1096842 CAGT
65 CAGT
1096846 TAGATGAAAG
1 TAGATGAAAG
1096856 CTTTAATACT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
67 1 0.01
68 66 0.99
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (68 bp):
TAGATGAAAGGCTAAGTGACTTTGAGGCCTAACTACGCAATTGACAGAAAGGTACCAATTACGCC
AGT
Found at i:1096942 original size:81 final size:81
Alignment explanation
Indices: 1096816--1097119 Score: 412
Period size: 81 Copynumber: 3.8 Consensus size: 81
1096806 CTAACTACGT
* * **
1096816 AATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAAAGCTTTAATACTGTTGAGTAAAATAAT
1 AATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGATTTAATACCATTGAGTAAAATAAT
* *
1096881 AATAGCCTAACTGTAC
66 AATGGCCTAACTGTGC
* * * * *
1096897 AATTGGTAGAAAAGTATCAATTATGCCAGTTAAATGAATGGTTTAATACCATTGAGT-AAATGAA
1 AATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGATTTAATACCATTGAGTAAAAT-AA
*
1096961 TAATGGCCTAACTATGC
65 TAATGGCCTAACTGTGC
* **
1096978 AATTGGTAGAAAGGTACCAATTATGCCAATTAGATGAACGATTTAATACCATTGAGTAAAGGAAT
1 AATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGATTTAATACCATTGAGTAAAATAAT
1097043 AATGGCCTAACTGTGC
66 AATGGCCTAACTGTGC
* * * **
1097059 AATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACGATTAAACACTGTTGAGTAAAA
1 AATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGATTTAATACCATTGAGTAAAA
1097120 ATGAAAGGTT
Statistics
Matches: 195, Mismatches: 26, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
80 4 0.02
81 189 0.97
82 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (81 bp):
AATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGATTTAATACCATTGAGTAAAATAAT
AATGGCCTAACTGTGC
Found at i:1101347 original size:95 final size:95
Alignment explanation
Indices: 1101248--1101431 Score: 228
Period size: 95 Copynumber: 1.9 Consensus size: 95
1101238 GAGGAAGTAG
* ** *
1101248 TATCGATACCATGATAAGGGGTATCGATACCATG-AAAATTGAATCTAATTTTGGTATCGATAC-
1 TATCGATACCATGATAA-GGGTATCGATACCAAGCAAAATCAAACCTAATTTTGGTATCGATACT
* *
1101311 CGGTAGGGAGTATCGGTACCATAGTAGGGTAA
65 C-GAAGGGAGAATCGGTACCATAGTAGGGTAA
* * * *
1101343 TATCGATATCATGGTAAGGGTATCGATACCAAGCAACATCAAACCTATTTTTGGTATCGATACTC
1 TATCGATACCATGATAAGGGTATCGATACCAAGCAAAATCAAACCTAATTTTGGTATCGATACTC
* *
1101408 GAAGGGGGAATTGGTACCATAGTA
66 GAAGGGAGAATCGGTACCATAGTA
1101432 TAGATGTATC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
94 15 0.20
95 59 0.79
96 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (95 bp):
TATCGATACCATGATAAGGGTATCGATACCAAGCAAAATCAAACCTAATTTTGGTATCGATACTC
GAAGGGAGAATCGGTACCATAGTAGGGTAA
Found at i:1101898 original size:58 final size:58
Alignment explanation
Indices: 1101778--1101913 Score: 193
Period size: 59 Copynumber: 2.3 Consensus size: 58
1101768 ATTACCAAAT
* * ** *
1101778 GGCACTAAGTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTT
1 GGCACTATGTGTGCAAAATATTAAGAAATTCATACTAAGTGTATGAATTTCCATATTG
*
1101836 GGCACTTTGTGTGCTAAAATATTAAGAAATTCATACTAAGTGTATGAATTTCCATA-TG
1 GGCACTATGTGTGC-AAAATATTAAGAAATTCATACTAAGTGTATGAATTTCCATATTG
*
1101894 GGCACTATGTGTGCGAAATA
1 GGCACTATGTGTGCAAAATA
1101914 AGAAATTAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
57 5 0.07
58 26 0.38
59 38 0.55
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.35
Consensus pattern (58 bp):
GGCACTATGTGTGCAAAATATTAAGAAATTCATACTAAGTGTATGAATTTCCATATTG
Found at i:1102244 original size:68 final size:68
Alignment explanation
Indices: 1102158--1102481 Score: 441
Period size: 68 Copynumber: 4.8 Consensus size: 68
1102148 AAAGATTAAT
* * * *
1102158 AGGCCTAACTGTGCATTTGACAGAAAGGTGTTATTTATGCCATTTAGATGAAAGGCTAACTGCCT
1 AGGCCTAACTGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1102223 TTG
66 TTG
* * * *
1102226 AGGCCTAATTGTGCATTTGACAAAAAGGTGTTATTTATGCCAGTTAAATTAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1102291 TTG
66 TTG
* * *
1102294 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTCT
1 AGGCCTAACTGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1102359 TTG
66 TTG
* *
1102362 AGGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTTCCT
1 AGGCCTAACTGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1102427 TTG
66 TTG
* * * ** * ** * *
1102430 AGGGCTAACTATGCAATTGGTAGAAAGGTACCAATTATGCCAATTAGATGAA
1 AGGCCTAACTGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAA
1102482 CGGTTTAATA
Statistics
Matches: 229, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 229 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:1102533 original size:81 final size:81
Alignment explanation
Indices: 1102434--1102739 Score: 367
Period size: 81 Copynumber: 3.9 Consensus size: 81
1102424 CCTTTGAGGG
* *
1102434 CTAACTATGCAATTGGTAGAAAGGTACCAATTATGCCAATTAGATGAACGGTTTAATACAGTTAA
1 CTAACTATGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTTAA
*
1102499 GTAAAAGAATAATAGC
66 GTAAAAGAATAATGGC
* * **
1102515 CTAACTGTGCAATTGGTAGAAAAGTGTCAATTATGCCAGTTAGAT-----G---AATACCGTTAA
1 CTAACTATGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTTAA
*
1102572 GTAAAGGAATAATGGC
66 GTAAAAGAATAATGGC
* * * *
1102588 CTAACTATGCAATTGGTATAAAGGTACCAATTATACTAGTTAGATGAACGGTTTAATACCGTTGA
1 CTAACTATGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTTAA
*
1102653 GTAAAGGAATAATGGC
66 GTAAAAGAATAATGGC
* * ** * * * *
1102669 CTAACTGTGCAATTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAACACTGTTGA
1 CTAACTATGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTTAA
1102734 GTAAAA
66 GTAAAA
1102740 ACGAAAGGTT
Statistics
Matches: 190, Mismatches: 27, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
73 62 0.33
76 1 0.01
78 1 0.01
81 126 0.66
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (81 bp):
CTAACTATGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTTAA
GTAAAAGAATAATGGC
Found at i:1102575 original size:73 final size:73
Alignment explanation
Indices: 1102488--1102716 Score: 278
Period size: 73 Copynumber: 3.0 Consensus size: 73
1102478 TGAACGGTTT
* * *
1102488 AATACAGTTAAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAAGTGTCAATTATGCCA
1 AATACCGTTAAGTAAAGGAATAATGGCCTAACTGTGCAATTGGTAGAAAAGTGTCAATTATGCCA
1102553 GTTAGATG
66 GTTAGATG
* * * ** * *
1102561 AATACCGTTAAGTAAAGGAATAATGGCCTAACTATGCAATTGGTATAAAGGTACCAATTATACTA
1 AATACCGTTAAGTAAAGGAATAATGGCCTAACTGTGCAATTGGTAGAAAAGTGTCAATTATGCCA
1102626 GTTAGATGAACGG
66 GTTAGAT-----G
* *
1102639 TTTAATACCGTTGAGTAAAGGAATAATGGCCTAACTGTGCAATTGGTAGAAATGTGTCAATTATG
1 ---AATACCGTTAAGTAAAGGAATAATGGCCTAACTGTGCAATTGGTAGAAAAGTGTCAATTATG
1102704 CCAGTTAGATG
63 CCAGTTAGATG
1102715 AA
1 AA
1102717 CGGTTAAACA
Statistics
Matches: 130, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
73 64 0.49
76 1 0.01
78 1 0.01
81 64 0.49
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (73 bp):
AATACCGTTAAGTAAAGGAATAATGGCCTAACTGTGCAATTGGTAGAAAAGTGTCAATTATGCCA
GTTAGATG
Found at i:1102639 original size:154 final size:154
Alignment explanation
Indices: 1102434--1102716 Score: 485
Period size: 154 Copynumber: 1.8 Consensus size: 154
1102424 CCTTTGAGGG
*
1102434 CTAACTATGCAATTGGTAGAAAGGTACCAATTATGCCAATTAGATGAACGGTTTAATACAGTTAA
1 CTAACTATGCAATTGGTAGAAAGGTACCAATTATACCAATTAGATGAACGGTTTAATACAGTTAA
1102499 GTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAAGTGTCAATTATGCCAGTTAGATGAAT
66 GTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAAGTGTCAATTATGCCAGTTAGATGAAT
1102564 ACCGTTAAGTAAAGGAATAATGGC
131 ACCGTTAAGTAAAGGAATAATGGC
* * * * *
1102588 CTAACTATGCAATTGGTATAAAGGTACCAATTATACTAGTTAGATGAACGGTTTAATACCGTTGA
1 CTAACTATGCAATTGGTAGAAAGGTACCAATTATACCAATTAGATGAACGGTTTAATACAGTTAA
* * *
1102653 GTAAAGGAATAATGGCCTAACTGTGCAATTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAA
66 GTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAAGTGTCAATTATGCCAGTTAGATGAA
1102717 CGGTTAAACA
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 120 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (154 bp):
CTAACTATGCAATTGGTAGAAAGGTACCAATTATACCAATTAGATGAACGGTTTAATACAGTTAA
GTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAAGTGTCAATTATGCCAGTTAGATGAAT
ACCGTTAAGTAAAGGAATAATGGC
Found at i:1112180 original size:79 final size:79
Alignment explanation
Indices: 1112091--1112386 Score: 441
Period size: 79 Copynumber: 3.7 Consensus size: 79
1112081 TAATGCACCT
* *
1112091 ATATGCATTTCAAATTTGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATG
1 ATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATG
1112156 TCAAAAATAGACCC
66 TCAAAAATAGACCC
* * * *
1112170 ATATGTATTTCAGCTATCGCATCCTTTCATGTCAATAATGCACCCATATGCATTATTCTTTTATG
1 ATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATG
1112235 TCAAAAATAGACCC
66 TCAAAAATAGACCC
* * * * *
1112249 ATATGTATTTCAGCTATTGCATCCTTTCATGCCAATAATGCACCTATATGTATTATTCTTTTATG
1 ATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATG
* * *
1112314 TCGATAAT-GCACTC
66 TCAAAAATAG-ACCC
*
1112328 ATATGCATTTCAACTATGGCATCCTTTCATGACAATAATGCACCCATATGCATTATTCT
1 ATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCT
1112387 ATTAATTTTT
Statistics
Matches: 197, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
78 1 0.01
79 196 0.99
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (79 bp):
ATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATG
TCAAAAATAGACCC
Found at i:1112217 original size:45 final size:43
Alignment explanation
Indices: 1112148--1112377 Score: 158
Period size: 45 Copynumber: 5.6 Consensus size: 43
1112138 ATGCATTATT
* *
1112148 CTTTTATGTCAAAAATAG-ACCCATATGTATTTCAGCTATCGCATC
1 CTTTCATGTCAATAAT-GCACCCATATGTATTTCA-CTAT-GCATC
*
1112193 CTTTCATGTCAATAATGCACCCATATGCA-TT-A-T-T-C-T-
1 CTTTCATGTCAATAATGCACCCATATGTATTTCACTATGCATC
*
1112229 -TTT-ATGTCAAAAATAG-ACCCATATGTATTTCAGCTATTGCATC
1 CTTTCATGTCAATAAT-GCACCCATATGTATTTCA-CTA-TGCATC
* *
1112272 CTTTCATGCCAATAATGCACCTATATGTA-TT-A-T-T-C-T-
1 CTTTCATGTCAATAATGCACCCATATGTATTTCACTATGCATC
* * *
1112308 -TTT-ATGTCGATAATGCACTCATATGCATTTCAACTATGGCATC
1 CTTTCATGTCAATAATGCACCCATATGTATTTC-ACTAT-GCATC
*
1112351 CTTTCATGACAATAATGCACCCATATG
1 CTTTCATGTCAATAATGCACCCATATG
1112378 CATTATTCTA
Statistics
Matches: 144, Mismatches: 16, Indels: 50
0.69 0.08 0.24
Matches are distributed among these distances:
34 39 0.27
35 11 0.08
36 1 0.01
37 3 0.02
38 4 0.03
39 2 0.01
40 2 0.01
41 4 0.03
42 2 0.01
43 2 0.01
44 12 0.08
45 62 0.43
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (43 bp):
CTTTCATGTCAATAATGCACCCATATGTATTTCACTATGCATC
Found at i:1112925 original size:17 final size:19
Alignment explanation
Indices: 1112883--1112961 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 19
1112873 AGATTCGATG
1112883 TTACC-TGGTATCGATACCC
1 TTACCATGGTATCGATA-CC
1112902 TTACCATGGTATCGATACTACC
1 TTACCATGGTATCG--A-TACC
* * *
1112924 ATACTATGGTACCGATACC
1 TTACCATGGTATCGATACC
*
1112943 TTCCCATGGTATCGATACC
1 TTACCATGGTATCGATACC
1112962 ATTTTACATT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 24 0.49
20 9 0.18
22 14 0.29
23 2 0.04
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.30
Consensus pattern (19 bp):
TTACCATGGTATCGATACC
Found at i:1114366 original size:23 final size:23
Alignment explanation
Indices: 1114313--1114369 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1114303 TATGAAGGAC
1114313 CGCGTAGAATTGTCCCAAAGAAT
1 CGCGTAGAATTGTCCCAAAGAAT
***
1114336 CATATAGAATTGTCCCAAATG-AT
1 CGCGTAGAATTGTCCCAAA-GAAT
1114359 CGCGTAGAATT
1 CGCGTAGAATT
1114370 CTCGACTCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (23 bp):
CGCGTAGAATTGTCCCAAAGAAT
Found at i:1114508 original size:57 final size:57
Alignment explanation
Indices: 1114441--1114550 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
1114431 CATATAAATG
** *
1114441 TTCACATAGCATTATTCAAATTGTCATTTATTCACATAGAACATATATGCATAATAT
1 TTCACATAGCATTATTCAAATTAACATTTATTCACATAGAACATATACGCATAATAT
* *
1114498 TTCACATAGCATTATTCAAATTAACGTTTATTCACATATAACATATACGCATA
1 TTCACATAGCATTATTCAAATTAACATTTATTCACATAGAACATATACGCATA
1114551 GCAATGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.37
Consensus pattern (57 bp):
TTCACATAGCATTATTCAAATTAACATTTATTCACATAGAACATATACGCATAATAT
Found at i:1114534 original size:30 final size:29
Alignment explanation
Indices: 1114441--1114535 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 29
1114431 CATATAAATG
**
1114441 TTCACATAGCATTATTCAAATTGTCATTTA
1 TTCACATAGCATTATTCAAATTAAC-TTTA
* *
1114471 TTCACATAGAACATATATGC--A-TAA-TAT-
1 TTCACATAG--CAT-TATTCAAATTAACTTTA
1114498 TTCACATAGCATTATTCAAATTAACGTTTA
1 TTCACATAGCATTATTCAAATTAAC-TTTA
1114528 TTCACATA
1 TTCACATA
1114536 TAACATATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
24 4 0.08
25 3 0.06
26 1 0.02
27 12 0.24
28 2 0.04
29 2 0.04
30 18 0.36
31 1 0.02
32 3 0.06
33 4 0.08
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (29 bp):
TTCACATAGCATTATTCAAATTAACTTTA
Found at i:1119939 original size:82 final size:83
Alignment explanation
Indices: 1119784--1119941 Score: 182
Period size: 82 Copynumber: 1.9 Consensus size: 83
1119774 TTCAATAGCA
* * * *
1119784 TTTTGATACAAATGTCATAATAGGGTTTGTTTATAGTGGAGATTTTCTAATAACGTCGTGATAGA
1 TTTTGATACAAATGTCATAATAGGGTTTGTTTATAGTGGAGATTTTCCAAAAACGTCATGATAAA
1119849 GTAATACTTTAGTTGTGT
66 GTAATACTTTAGTTGTGT
* *
1119867 TTTTG-TACAAATGTCATAATAGGGTTCT-TTCT-TAGTGGCA-TTTTTCCAAAAGATGTCATGA
1 TTTTGATACAAATGTCATAATAGGGTT-TGTT-TATAGTGG-AGATTTTCCAAAA-ACGTCATGA
*
1119928 TAAAG-AGTACTTTA
62 TAAAGTAATACTTTA
1119942 TGGGGCGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
82 45 0.70
83 19 0.30
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (83 bp):
TTTTGATACAAATGTCATAATAGGGTTTGTTTATAGTGGAGATTTTCCAAAAACGTCATGATAAA
GTAATACTTTAGTTGTGT
Found at i:1124708 original size:30 final size:29
Alignment explanation
Indices: 1124667--1124738 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 29
1124657 TGGGTCAACT
*
1124667 TGTTAACTTTGACCGAGTCAACCCGTTGA
1 TGTTGACTTTGACCGAGTCAACCCGTTGA
*
1124696 CTGTTGACTTTGACCGAGTCAACCTGTTGA
1 -TGTTGACTTTGACCGAGTCAACCCGTTGA
1124726 TCGTTGACTTTGA
1 T-GTTGACTTTGA
1124739 GCAAAAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (29 bp):
TGTTGACTTTGACCGAGTCAACCCGTTGA
Found at i:1126808 original size:24 final size:24
Alignment explanation
Indices: 1126755--1126839 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
1126745 TCCCATTTGA
* * * *
1126755 ATTCTATTATCATACCTGACATGG
1 ATTCTGTTATGATATCTGACCTGG
*
1126779 ATTCTGTTATGATATCTGACCTTG
1 ATTCTGTTATGATATCTGACCTGG
* * *
1126803 ATTCTGCTCTGATATCTGACCTGA
1 ATTCTGTTATGATATCTGACCTGG
* *
1126827 ATTATGTTTTGAT
1 ATTCTGTTATGAT
1126840 TTTTTATATA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (24 bp):
ATTCTGTTATGATATCTGACCTGG
Found at i:1136555 original size:15 final size:14
Alignment explanation
Indices: 1136535--1136569 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1136525 GTAGCAGCGT
*
1136535 AAAAAAAAGTTAAGA
1 AAAAAAAAG-AAAGA
1136550 AAAAAAAAGAAAGA
1 AAAAAAAAGAAAGA
1136564 AAAAAA
1 AAAAAA
1136570 TGTGTAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (14 bp):
AAAAAAAAGAAAGA
Found at i:1139918 original size:12 final size:12
Alignment explanation
Indices: 1139903--1139951 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
1139893 CTGAAGCAAA
*
1139903 AGAAGCAGTGAG
1 AGAAGCAGAGAG
1139915 AGAAGC--AGAG
1 AGAAGCAGAGAG
1139925 AG-AGCAGAGAG
1 AGAAGCAGAGAG
*
1139936 AGAAGTAGAGAG
1 AGAAGCAGAGAG
1139948 AGAA
1 AGAA
1139952 ACAACATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 3 0.09
10 5 0.16
11 6 0.19
12 18 0.56
ACGTcount: A:0.49, C:0.06, G:0.41, T:0.04
Consensus pattern (12 bp):
AGAAGCAGAGAG
Found at i:1139919 original size:21 final size:21
Alignment explanation
Indices: 1139895--1139949 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1139885 AGCCGAAGCT
*
1139895 GAAGCAAA-AGAAGCAGTGAGA
1 GAAGCAAAGAG-AGCAGAGAGA
*
1139916 GAAGCAGAGAGAGCAGAGAGA
1 GAAGCAAAGAGAGCAGAGAGA
* *
1139937 GAAGTAGAGAGAG
1 GAAGCAAAGAGAG
1139950 AAACAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.49, C:0.07, G:0.40, T:0.04
Consensus pattern (21 bp):
GAAGCAAAGAGAGCAGAGAGA
Found at i:1141876 original size:16 final size:16
Alignment explanation
Indices: 1141822--1141885 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
1141812 AGAATTGAAA
*
1141822 TTAACCTGAACCGAATT
1 TTAACCCGAACCGAA-T
* * *
1141839 TTAACCCGATCTGAAA
1 TTAACCCGAACCGAAT
**
1141855 GCAACCCGAACCGAAT
1 TTAACCCGAACCGAAT
*
1141871 TTAACCCGATCCGAA
1 TTAACCCGAACCGAA
1141886 AGCAATCTGG
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.20
Consensus pattern (16 bp):
TTAACCCGAACCGAAT
Found at i:1141879 original size:32 final size:33
Alignment explanation
Indices: 1141824--1141890 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
1141814 AATTGAAATT
* *
1141824 AACCTGAACCGAATTTTAACCCGATCTGAAAGC
1 AACCCGAACCGAATTTTAACCCGATCCGAAAGC
1141857 AACCCGAACCGAA-TTTAACCCGATCCGAAAGC
1 AACCCGAACCGAATTTTAACCCGATCCGAAAGC
1141889 AA
1 AA
1141891 TCTGGACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.39, C:0.30, G:0.15, T:0.16
Consensus pattern (33 bp):
AACCCGAACCGAATTTTAACCCGATCCGAAAGC
Found at i:1141993 original size:18 final size:19
Alignment explanation
Indices: 1141954--1142009 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
1141944 GAATAAATTA
*
1141954 ATTTAT-ATAAAATTGATA-
1 ATTTATAATAAAA-TAATAG
* *
1141972 ATTTATTA-AAAATATTAG
1 ATTTATAATAAAATAATAG
1141990 ATTTATAATAAAATAATAG
1 ATTTATAATAAAATAATAG
1142009 A
1 A
1142010 AAGTTTAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 3 0.10
18 17 0.55
19 11 0.35
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTTATAATAAAATAATAG
Found at i:1142256 original size:25 final size:24
Alignment explanation
Indices: 1142228--1142275 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1142218 TGTATTATTT
* *
1142228 TTTAAAATTTAATAAAAATATTAAA
1 TTTAAAATTGAA-AAAAAAATTAAA
*
1142253 TTTATAATTGAAAAAAAAATTAA
1 TTTAAAATTGAAAAAAAAATTAA
1142276 TAAAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TTTAAAATTGAAAAAAAAATTAAA
Found at i:1149735 original size:19 final size:18
Alignment explanation
Indices: 1149690--1149753 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
1149680 ATTGTACCTG
1149690 AAAA-ATAAATAATAATAA
1 AAAATATAAATAAT-ATAA
* *
1149708 CAAATAT-AAT-ATA-CA
1 AAAATATAAATAATATAA
1149723 AAAATATAAATAAATATAA
1 AAAATATAAAT-AATATAA
*
1149742 ATAATATAAATA
1 AAAATATAAATA
1149754 TAATATATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
15 7 0.19
16 4 0.11
17 2 0.06
18 10 0.28
19 13 0.36
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATATAAATAATATAA
Found at i:1149748 original size:34 final size:34
Alignment explanation
Indices: 1149690--1149755 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1149680 ATTGTACCTG
1149690 AAAAATAAATAATAATAACAAATAT-AATATACA
1 AAAAATAAATAATAATAACAAATATAAATATACA
1149723 AAAATATAAATAA-ATATAA-ATAATATAAATATA
1 AAAA-ATAAATAATA-ATAACA-AATATAAATATA
1149756 ATATATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 6 0.21
34 17 0.59
35 6 0.21
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (34 bp):
AAAAATAAATAATAATAACAAATATAAATATACA
Found at i:1149790 original size:15 final size:15
Alignment explanation
Indices: 1149698--1149817 Score: 51
Period size: 15 Copynumber: 8.2 Consensus size: 15
1149688 TGAAAAATAA
*
1149698 ATAATA-ATAACAAAT
1 ATAATATATAAC-TAT
* **
1149713 ATAATATACAAAAAT
1 ATAATATATAACTAT
1149728 ATAA-ATA-AA-TAT
1 ATAATATATAACTAT
1149740 A-AATAATATAA--AT
1 ATAAT-ATATAACTAT
*
1149753 ATAATATATAA-TGT
1 ATAATATATAACTAT
*
1149767 AATGAAATATATTACTAT
1 -AT--AATATATAACTAT
* *
1149785 ATAATATGTAAGTAT
1 ATAATATATAACTAT
1149800 ATAATAATATAA-TAT
1 ATAAT-ATATAACTAT
1149815 ATA
1 ATA
1149818 TTACATTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
11 2 0.02
12 3 0.04
13 14 0.17
14 9 0.11
15 36 0.43
16 8 0.10
17 10 0.12
18 2 0.02
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (15 bp):
ATAATATATAACTAT
Found at i:1149905 original size:40 final size:37
Alignment explanation
Indices: 1149852--1150033 Score: 172
Period size: 37 Copynumber: 4.9 Consensus size: 37
1149842 AATATATATG
*
1149852 TTTTTTAAAACTATATATTATATACGTTCTTTAGAACAT-T
1 TTTTTTAAAACTATATATTATAT--GTT-TTCA-AACATGT
1149892 TTTTTTAAAACTATATATTATATGTTTTCAAACATGT
1 TTTTTTAAAACTATATATTATATGTTTTCAAACATGT
* * * *
1149929 GTTTTCAAAACTATATAATATATGTTTTTAAA-ATGT
1 TTTTTTAAAACTATATATTATATGTTTTCAAACATGT
* * * * * * *
1149965 ATTTTCAAAACCATATATCATATGCTTTCAAAAACG-
1 TTTTTTAAAACTATATATTATATGTTTTCAAACATGT
* *
1150001 TTTTCTAAAAGTTATATATTATATGTTTTCAAA
1 TTTTTTAAAA-CTATATATTATATGTTTTCAAA
1150034 AAATTGTATT
Statistics
Matches: 120, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
36 42 0.35
37 52 0.43
38 3 0.03
40 23 0.19
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (37 bp):
TTTTTTAAAACTATATATTATATGTTTTCAAACATGT
Found at i:1155519 original size:20 final size:21
Alignment explanation
Indices: 1155468--1155521 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1155458 ATAAATAGTA
1155468 ATAAATATAATATACAGAAAT
1 ATAAATATAATATACAGAAAT
1155489 ATAAATA-AATATA-A-ATAAT
1 ATAAATATAATATACAGA-AAT
*
1155508 ATTAATATAATATA
1 ATAAATATAATATA
1155522 TAATGTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 10 0.33
20 12 0.40
21 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAATATAATATACAGAAAT
Found at i:1155538 original size:15 final size:16
Alignment explanation
Indices: 1155452--1155539 Score: 53
Period size: 15 Copynumber: 5.8 Consensus size: 16
1155442 GGACCTGAAA
*
1155452 AAATAAATA-AATAGT
1 AAATATATATAATAGT
*
1155467 -AATAAATATAATA-T
1 AAATATATATAATAGT
* * *
1155481 ACAGAAATATAA-A-T
1 AAATATATATAATAGT
* *
1155495 AAATATAAATAATATT
1 AAATATATATAATAGT
1155511 AATATAATATATAAT-GT
1 AA-AT-ATATATAATAGT
1155528 AAATATATATAA
1 AAATATATATAA
1155540 CTTTTCAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.32
15 22 0.37
16 5 0.08
17 5 0.08
18 8 0.14
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATATATATAATAGT
Found at i:1156717 original size:135 final size:132
Alignment explanation
Indices: 1156547--1156935 Score: 370
Period size: 137 Copynumber: 2.9 Consensus size: 132
1156537 AATAAATTAG
* * * ** *
1156547 AAATTCTTTTAATTTACGGACTAAAAGGGACATTAATCTAAATTTAGGCTCTAATCATTAGTCCT
1 AAATTC-TTTAATTTAAGGACTAAAAGTGAAATTAATCTAAATGAAGGCTCTAAT-ATTAATCCT
* * *
1156612 AATCAAAATAAGCAAATTATTGGTTCGAATAATCAAAATGGAACCTCGGGCAAAACGAGGACCAA
64 AATCAAATTAAGCAAATTATTGGTTCGAGTAATCAAAATGGAACCTCGGGCAAAACAAGGACCAA
1156677 ATAAA
129 AT-AA
* * * * *
1156682 AAATTCTTCTAAATTAAAGGACT-AAAGTGAAATTAAACCTAATATGAAGGCTCTTATACTAAAA
1 AAATTCTT-T-AATTTAAGGACTAAAAGTGAAATT-AATCTAA-ATGAAGGCTCTAATA-TTAAT
* * * * ** * * * * *
1156746 CTTAAT-AATTTTTAGCCAATTATTGAATCGAGTAAT-TAATTCGAAATCTCGGGCTAAAGCAAG
61 CCTAATCAA-ATTAAGCAAATTATTGGTTCGAGTAATCAAAAT-GGAACCTCGGGC-AAAACAAG
1156809 GACCAAATAA
123 GACCAAATAA
** * *
1156819 AAATTCAAATAATTTAAGGACTAAAAGTGAAATTAATCTATATGAAGCCTCTAATTATTAATCCT
1 AAATTC-TTTAATTTAAGGACTAAAAGTGAAATTAATCTAAATGAAGGCTCTAA-TATTAATCCT
*
1156884 AATCAAATTAAGCAAATTATTGGTTCGAGTAATCAAAATGGAACCTCAGGCA
64 AATCAAATTAAGCAAATTATTGGTTCGAGTAATCAAAATGGAACCTCGGGCA
1156936 TAAAAACGAG
Statistics
Matches: 196, Mismatches: 45, Indels: 27
0.73 0.17 0.10
Matches are distributed among these distances:
134 3 0.02
135 66 0.34
136 45 0.23
137 68 0.35
138 14 0.07
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (132 bp):
AAATTCTTTAATTTAAGGACTAAAAGTGAAATTAATCTAAATGAAGGCTCTAATATTAATCCTAA
TCAAATTAAGCAAATTATTGGTTCGAGTAATCAAAATGGAACCTCGGGCAAAACAAGGACCAAAT
AA
Found at i:1157232 original size:14 final size:14
Alignment explanation
Indices: 1157216--1157300 Score: 71
Period size: 16 Copynumber: 5.6 Consensus size: 14
1157206 TAACTACTGG
*
1157216 AAATTAAAATACAG
1 AAATTAAAATACAA
*
1157230 AAATTAAAATACAGG
1 AAATTAAAATACA-A
* *
1157245 AAATTGAAGTACTAA
1 AAATTAAAATAC-AA
1157260 AAATTTAAAATGACAA
1 AAA-TTAAAAT-ACAA
*
1157276 AAATGTAAAATGATAA
1 AAAT-TAAAAT-ACAA
1157292 AAATTAAAA
1 AAATTAAAA
1157301 GTAGGTTCGT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
14 13 0.22
15 20 0.33
16 25 0.42
17 2 0.03
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.24
Consensus pattern (14 bp):
AAATTAAAATACAA
Found at i:1157249 original size:15 final size:15
Alignment explanation
Indices: 1157214--1157249 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
1157204 TGTAACTACT
1157214 GGAAATTAAAATACA
1 GGAAATTAAAATACA
1157229 -GAAATTAAAATACA
1 GGAAATTAAAATACA
1157243 GGAAATT
1 GGAAATT
1157250 GAAGTACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (15 bp):
GGAAATTAAAATACA
Found at i:1158314 original size:19 final size:19
Alignment explanation
Indices: 1158290--1158326 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1158280 TCTTGACTGG
*
1158290 CTCAAATCATTATTTCTGA
1 CTCAAATAATTATTTCTGA
*
1158309 CTCAAATAATTCTTTCTG
1 CTCAAATAATTATTTCTG
1158327 CATGCATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (19 bp):
CTCAAATAATTATTTCTGA
Found at i:1176379 original size:24 final size:24
Alignment explanation
Indices: 1176347--1176395 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1176337 TCATCCTCAA
1176347 AACATATAAGTACATAATAAATGC
1 AACATATAAGTACATAATAAATGC
1176371 AACATATAAGTACATAATAAATGC
1 AACATATAAGTACATAATAAATGC
1176395 A
1 A
1176396 CTCACCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.24
Consensus pattern (24 bp):
AACATATAAGTACATAATAAATGC
Found at i:1178311 original size:54 final size:54
Alignment explanation
Indices: 1178229--1178338 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
1178219 AACCATGTAG
1178229 GTCGAGTAAATCAATGATGTTTTGATTTAGACCGACTACAAATATGTTCATTGT
1 GTCGAGTAAATCAATGATGTTTTGATTTAGACCGACTACAAATATGTTCATTGT
1178283 GTCGAGTAAATCAATGATGTTTTGATTTAGACCGACTACAAATATGTTCATTGT
1 GTCGAGTAAATCAATGATGTTTTGATTTAGACCGACTACAAATATGTTCATTGT
1178337 GT
1 GT
1178339 GTTTGTCTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (54 bp):
GTCGAGTAAATCAATGATGTTTTGATTTAGACCGACTACAAATATGTTCATTGT
Found at i:1178329 original size:27 final size:27
Alignment explanation
Indices: 1178245--1178330 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
1178235 TAAATCAATG
1178245 ATGTTTTGATTTAGACCGACTACAAAT
1 ATGTTTTGATTTAGACCGACTACAAAT
* * * *
1178272 ATG--TTCATTGT-G-TCGAGTAAATCAAT
1 ATGTTTTGATT-TAGACCGACTACA--AAT
1178298 GATGTTTTGATTTAGACCGACTACAAAT
1 -ATGTTTTGATTTAGACCGACTACAAAT
1178326 ATGTT
1 ATGTT
1178331 CATTGTGTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
24 6 0.14
25 6 0.14
26 4 0.09
27 11 0.26
28 4 0.09
29 6 0.14
30 6 0.14
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (27 bp):
ATGTTTTGATTTAGACCGACTACAAAT
Found at i:1181269 original size:19 final size:19
Alignment explanation
Indices: 1181232--1181268 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1181222 CTTATTTATC
*
1181232 CTTTTCCTCTCTTTCTTTT
1 CTTTTCCTCTATTTCTTTT
1181251 CTTTTCCTCTATTT-TTTT
1 CTTTTCCTCTATTTCTTTT
1181269 TTTGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTCCTCTATTTCTTTT
Done.