Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007897.1 Hibiscus syriacus cultivar Beakdansim tig00110283_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: 862109
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:522782 original size:18 final size:19
Alignment explanation
Indices: 522755--522800 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
522745 AGAATTATTG
522755 AAAACTAAAAA-ATAA-AGGA
1 AAAAC-AAAAACATAATA-GA
522774 AAAACAAAAACATAATAGA
1 AAAACAAAAACATAATAGA
522793 AAAA-AAAA
1 AAAACAAAA
522801 TGAACCACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 9 0.36
19 15 0.60
20 1 0.04
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.09
Consensus pattern (19 bp):
AAAACAAAAACATAATAGA
Found at i:526947 original size:21 final size:22
Alignment explanation
Indices: 526909--526951 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
526899 TATGAGAAAT
526909 TGTTTCTAAAATATAAAAATGA
1 TGTTTCTAAAATATAAAAATGA
526931 TGTTTC-AAAAT-TGAAAAATGA
1 TGTTTCTAAAATAT-AAAAATGA
526952 AAACAAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.65
22 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (22 bp):
TGTTTCTAAAATATAAAAATGA
Found at i:530799 original size:23 final size:21
Alignment explanation
Indices: 530746--530827 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
530736 TTTGGTGCAA
530746 AGGGAATCGA-TCCCCCCATG
1 AGGGAATCGATTCCCCCCATG
* **
530766 AGGGAACCGATTCCCCCTTTG
1 AGGGAATCGATTCCCCCCATG
*
530787 AAGGGGAATCGATTCCCCCCA-C
1 -A-GGGAATCGATTCCCCCCATG
*
530809 AGGGGAATCGATACCCCCC
1 A-GGGAATCGATTCCCCCC
530828 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 9 0.18
21 26 0.51
22 1 0.02
23 15 0.29
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.16
Consensus pattern (21 bp):
AGGGAATCGATTCCCCCCATG
Found at i:537171 original size:31 final size:30
Alignment explanation
Indices: 537133--537210 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 30
537123 AAGACGGCCA
*
537133 TTGGGTAGGCTCCGAGGCCCCGAGATCTTTC
1 TTGGGTAGGC-CCGAGGCCCCGAGATCATTC
*
537164 TTGGGTAGGCCCTACGGCCCCGAGATCATTC
1 TTGGGTAGGCCCGA-GGCCCCGAGATCATTC
537195 TTGGGTAGGCGCCGAG
1 TTGGGTAGGC-CCGAG
537211 TAACTTTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 3 0.07
31 36 0.86
32 3 0.07
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.23
Consensus pattern (30 bp):
TTGGGTAGGCCCGAGGCCCCGAGATCATTC
Found at i:537780 original size:2 final size:2
Alignment explanation
Indices: 537773--537830 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
537763 TGTATTTTGT
537773 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
537815 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
537831 GTCTGAAATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:538120 original size:2 final size:2
Alignment explanation
Indices: 538115--538208 Score: 88
Period size: 2 Copynumber: 46.0 Consensus size: 2
538105 TATTTTTTAT
*
538115 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA GTT TGA -A GTCA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA -T-A TA
*
538156 TT TGA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
538198 TGA TA TA TA TA
1 T-A TA TA TA TA
538209 GTTTTTAAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 20
0.77 0.03 0.20
Matches are distributed among these distances:
1 4 0.05
2 70 0.89
3 4 0.05
4 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:538242 original size:65 final size:63
Alignment explanation
Indices: 538115--538244 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 63
538105 TATTTTTTAT
* * *
538115 TATATATATATATATATATATATTATATAGTTTGAAGTCATTTTGAATATATATATATATATA
1 TATATATATATATATATATATATTATATAGTTTAAAATCATTTTGAAAATATATATATATATA
538178 TATATATATATATATATATATGATATATATAGTTTTTAAAAT-ATTTTGAAAACT-TATATA-AT
1 TATATATATATATATATATAT-AT-TATATAG--TTTAAAATCATTTTGAAAA-TATATATATAT
538240 ATA
61 ATA
538243 TA
1 TA
538245 GTTTTTAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
63 21 0.36
64 2 0.03
65 14 0.24
66 15 0.25
67 7 0.12
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (63 bp):
TATATATATATATATATATATATTATATAGTTTAAAATCATTTTGAAAATATATATATATATA
Found at i:538249 original size:36 final size:36
Alignment explanation
Indices: 538202--538537 Score: 405
Period size: 38 Copynumber: 9.2 Consensus size: 36
538192 TATATATGAT
*
538202 ATATATAGTTTTTAAAATATTTTGAAAACTTATATA
1 ATATATAGTTTTTAAAACATTTTGAAAACTTATATA
538238 ATATATAGTTTTTAAAACATTTTTGAAAA-TAAATATATA
1 ATATATAGTTTTTAAAACA-TTTTGAAAACT---TATATA
538277 ATATATAGTTTTTAAAACATTTTGAAAACTTATATA
1 ATATATAGTTTTTAAAACATTTTGAAAACTTATATA
538313 ATATATAGTTTTTTAAAACCATTTTGAAAACTTATATA
1 ATATATAG-TTTTTAAAA-CATTTTGAAAACTTATATA
538351 ATATATAGTTTTTTAAAAACATTTTGAAAACTTATATA
1 ATATATAG-TTTTT-AAAACATTTTGAAAACTTATATA
* * *
538389 ATATATAGTTTTGAAATCATTTTCAAAACTTATATA
1 ATATATAGTTTTTAAAACATTTTGAAAACTTATATA
* **
538425 ATATACAGTTTAAAAAAAGCATTTTGAAAA-TATATATA
1 ATATATAGTTT-TTAAAA-CATTTTGAAAACT-TATATA
* *
538463 ATATATGGTTTTTAAAATATTTTGAAAAC-TATATA
1 ATATATAGTTTTTAAAACATTTTGAAAACTTATATA
* * * **
538498 ATATATA-CTTTGAAAAC-TTTTTAAAAAATATAT-
1 ATATATAGTTTTTAAAACATTTTGAAAACTTATATA
538531 ATATATA
1 ATATATA
538538 CAATATATAG
Statistics
Matches: 267, Mismatches: 20, Indels: 29
0.84 0.06 0.09
Matches are distributed among these distances:
33 15 0.06
34 12 0.04
35 12 0.04
36 74 0.28
37 30 0.11
38 94 0.35
39 30 0.11
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (36 bp):
ATATATAGTTTTTAAAACATTTTGAAAACTTATATA
Found at i:538410 original size:74 final size:73
Alignment explanation
Indices: 538202--538537 Score: 402
Period size: 74 Copynumber: 4.6 Consensus size: 73
538192 TATATATGAT
*
538202 ATATATAGTTTTTAAAATATTTTGAAAACTTATATAATATATAGTTTTTAAAA-CATTTTTGAAA
1 ATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTTTAAAATCA-TTTTGAAA
538266 A-TAAATATATA
65 ACT---TATATA
*
538277 ATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTTTTAAAACCATTTTGAAA
1 ATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAG-TTTTTAAAATCATTTTGAAA
538342 ACTTATATA
65 ACTTATATA
* *
538351 ATATATAGTTTTTTAAAAACATTTTGAAAACTTATATAATATATAG-TTTTGAAATCATTTTCAA
1 ATATATAG-TTTTT-AAAACATTTTGAAAACTTATATAATATATAGTTTTTAAAATCATTTTGAA
538415 AACTTATATA
64 AACTTATATA
* ** *
538425 ATATACAGTTTAAAAAAAGCATTTTGAAAA-TATATATAATATATGGTTTTTAAAAT-ATTTTGA
1 ATATATAGTTT-TTAAAA-CATTTTGAAAACT-TATATAATATATAGTTTTTAAAATCATTTTGA
538488 AAAC-TATATA
63 AAACTTATATA
* * * **
538498 ATATATA-CTTTGAAAAC-TTTTTAAAAAATATAT-ATATATA
1 ATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATA
538538 CAATATATAG
Statistics
Matches: 234, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
68 6 0.03
69 13 0.06
70 1 0.00
71 4 0.02
72 2 0.01
73 20 0.09
74 80 0.34
75 56 0.24
76 49 0.21
77 3 0.01
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (73 bp):
ATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTTTAAAATCATTTTGAAAA
CTTATATA
Found at i:538537 original size:35 final size:36
Alignment explanation
Indices: 538451--538537 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 36
538441 AAGCATTTTG
** * *
538451 AAAATATATATAATATATGGTTTTTAAAATATTTTGA
1 AAAATATATAT-ATATATGACTTTGAAAATATTTTAA
*
538488 AAACTATATA-ATATAT-ACTTTGAAAACT-TTTTAA
1 AAAATATATATATATATGACTTTGAAAA-TATTTTAA
538522 AAAATATATATATATA
1 AAAATATATATATATA
538538 CAATATATAG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
34 21 0.50
35 12 0.29
37 9 0.21
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (36 bp):
AAAATATATATATATATGACTTTGAAAATATTTTAA
Found at i:539176 original size:19 final size:19
Alignment explanation
Indices: 539152--539200 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
539142 CCGAAGAAAC
539152 CACCGGAAAAGTGAGAGGT
1 CACCGGAAAAGTGAGAGGT
539171 CACCGGAAAAGTGAGAGGT
1 CACCGGAAAAGTGAGAGGT
* *
539190 CGCCGAAAAAG
1 CACCGGAAAAG
539201 GTAAAACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.35, T:0.08
Consensus pattern (19 bp):
CACCGGAAAAGTGAGAGGT
Found at i:539789 original size:27 final size:27
Alignment explanation
Indices: 539764--539822 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
539754 ATCTCTTTTC
539764 TTTT-TTTAAAT-TTTTTTAAATATTT
1 TTTTATTTAAATATTTTTTAAATATTT
** *
539789 TTTTATTTAGCTATTTTTTAAATTTCTT
1 TTTTATTTAAATATTTTTTAAATAT-TT
539817 TTTTAT
1 TTTTAT
539823 CTAGTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.14
26 5 0.18
27 11 0.39
28 8 0.29
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTATTTAAATATTTTTTAAATATTT
Found at i:539833 original size:28 final size:28
Alignment explanation
Indices: 539774--539848 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
539764 TTTTTTTAAA
* *
539774 TTTTTTTAAATAT-TTTTTTATTTAGCT
1 TTTTTTTAAATTTCTTTTTTATCTAGCT
*
539801 ATTTTTTAAATTTCTTTTTTATCTAG-T
1 TTTTTTTAAATTTCTTTTTTATCTAGCT
*
539828 TTTTTTCATCAATTTCTTTTT
1 TTTTTT--TAAATTTCTTTTT
539849 CCTCTTCTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 17 0.43
28 11 0.28
29 12 0.30
ACGTcount: A:0.20, C:0.08, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTTTAAATTTCTTTTTTATCTAGCT
Found at i:539914 original size:7 final size:7
Alignment explanation
Indices: 539893--539942 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
539883 ATTTATTTTA
*
539893 TTAATAT
1 TTAATTT
539900 TT-ATTT
1 TTAATTT
539906 TTAATTT
1 TTAATTT
539913 TTAATTT
1 TTAATTT
539920 TTAATTT
1 TTAATTT
539927 TTAATTT
1 TTAATTT
539934 TT-ATTT
1 TTAATTT
539940 TTA
1 TTA
539943 CACTTTGATT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 11 0.28
7 29 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTAATTT
Found at i:540095 original size:6 final size:6
Alignment explanation
Indices: 540084--540110 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
540074 AACCGAATGT
540084 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
540111 TCGTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:540350 original size:3 final size:3
Alignment explanation
Indices: 540342--540388 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
540332 ACGGTTGCGA
540342 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
540389 CTTCTACGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:540657 original size:5 final size:5
Alignment explanation
Indices: 540647--540672 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
540637 CATAATTGGT
540647 TGAAA TGAAA TGAAA TGAAA TGAAA T
1 TGAAA TGAAA TGAAA TGAAA TGAAA T
540673 TTTATCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (5 bp):
TGAAA
Found at i:540884 original size:2 final size:2
Alignment explanation
Indices: 540877--540914 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
540867 TCCAAAATGA
540877 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
540915 TAAAATGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:540948 original size:6 final size:6
Alignment explanation
Indices: 540937--540961 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
540927 AATTGAAGAA
540937 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
540962 TGTATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:546401 original size:3 final size:3
Alignment explanation
Indices: 546393--546419 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
546383 AAAATTTCTC
546393 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
546420 TTACCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:547233 original size:67 final size:67
Alignment explanation
Indices: 547125--547267 Score: 286
Period size: 67 Copynumber: 2.1 Consensus size: 67
547115 GTGGTTTGCC
547125 ATCATTCCCTTTTGGCGGTAATAACTTGTTATCAATCGTTGTACTTTTTGTTTAAAACGGTGAGA
1 ATCATTCCCTTTTGGCGGTAATAACTTGTTATCAATCGTTGTACTTTTTGTTTAAAACGGTGAGA
547190 AT
66 AT
547192 ATCATTCCCTTTTGGCGGTAATAACTTGTTATCAATCGTTGTACTTTTTGTTTAAAACGGTGAGA
1 ATCATTCCCTTTTGGCGGTAATAACTTGTTATCAATCGTTGTACTTTTTGTTTAAAACGGTGAGA
547257 AT
66 AT
547259 ATCATTCCC
1 ATCATTCCC
547268 CAAATTCTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 76 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (67 bp):
ATCATTCCCTTTTGGCGGTAATAACTTGTTATCAATCGTTGTACTTTTTGTTTAAAACGGTGAGA
AT
Found at i:547685 original size:13 final size:13
Alignment explanation
Indices: 547669--547693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
547659 GAGTATTTAT
547669 TGTATATTTGTTA
1 TGTATATTTGTTA
547682 TGTATATTTGTT
1 TGTATATTTGTT
547694 TGATTCAAGT
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:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (13 bp):
TGTATATTTGTTA
Found at i:554034 original size:29 final size:29
Alignment explanation
Indices: 553977--554038 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
553967 GATGAAAAAG
* *
553977 GCGGGAGTGGTGGCTGTGAGCCTAGTACA
1 GCGGGAGTGGTGGCTGTGAGCCGAATACA
*
554006 GCGGGAGTGGTGGCTGTGAGCGGAATACA
1 GCGGGAGTGGTGGCTGTGAGCCGAATACA
554035 GCGG
1 GCGG
554039 AAATGAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.48, T:0.18
Consensus pattern (29 bp):
GCGGGAGTGGTGGCTGTGAGCCGAATACA
Found at i:556588 original size:35 final size:35
Alignment explanation
Indices: 556543--556617 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
556533 TTCATATTCA
556543 AAATTCCAAAACACTTCAATTACATTCTAAATCCC
1 AAATTCCAAAACACTTCAATTACATTCTAAATCCC
* * * *
556578 AAATTTCAAAATACTTTAATTACATTCTAAATCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAATCCC
556613 AAATT
1 AAATT
556618 AAAGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAATCCC
Found at i:556688 original size:35 final size:34
Alignment explanation
Indices: 556612--556689 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
556602 TTCTAAATCC
*
556612 TAAATTAAAGTATTTTAGAATTTACAGTTTAAAA
1 TAAATTGAAGTATTTTAGAATTTACAGTTTAAAA
* * ** *
556646 TATAATTGAATTATTTTGGAATTTGGAGTTTATAA
1 TA-AATTGAAGTATTTTAGAATTTACAGTTTAAAA
556681 TGAAATTGA
1 T-AAATTGA
556690 GGACTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
34 2 0.06
35 33 0.92
36 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (34 bp):
TAAATTGAAGTATTTTAGAATTTACAGTTTAAAA
Found at i:560590 original size:19 final size:19
Alignment explanation
Indices: 560552--560596 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
560542 ATTGAAGTTC
*
560552 TACTTTTCTTTCATCTTTT
1 TACTTTTCTTTCATCATTT
560571 TACTTTTCTTTCAAT-ATTT
1 TACTTTTCTTTC-ATCATTT
560590 TA-TTTTC
1 TACTTTTC
560597 ATAATGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 17 0.71
20 2 0.08
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.67
Consensus pattern (19 bp):
TACTTTTCTTTCATCATTT
Found at i:563500 original size:27 final size:30
Alignment explanation
Indices: 563455--563520 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 30
563445 AGAGAAAAGA
*
563455 ATAATAAAAAATATTAATATA-ATA-ATAT
1 ATAATAAAAAATATAAATATATATATATAT
563483 -TAATAAAAAA-ATGAAATATATATATATAT
1 ATAATAAAAAATAT-AAATATATATATATAT
563512 ATATATAAA
1 ATA-ATAAA
563521 TGTAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 2 0.06
27 16 0.50
28 3 0.09
29 4 0.12
30 2 0.06
31 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
ATAATAAAAAATATAAATATATATATATAT
Found at i:563598 original size:19 final size:19
Alignment explanation
Indices: 563524--563613 Score: 58
Period size: 19 Copynumber: 4.7 Consensus size: 19
563514 ATATAAATGT
*
563524 AAAAA-AAATAAAAAATAT
1 AAAAATAAATAAAAAATAA
* * * * *
563542 TAAAATTAGTAGAAAAT-G
1 AAAAATAAATAAAAAATAA
* * *
563560 AAAAATATATATAAAGTAA
1 AAAAATAAATAAAAAATAA
*
563579 ATAAATAAATAAAAAATAA
1 AAAAATAAATAAAAAATAA
563598 AAAGAATAAATCAAAA
1 AAA-AATAAAT-AAAA
563614 GTTGTTACAT
Statistics
Matches: 51, Mismatches: 17, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
18 15 0.29
19 25 0.49
20 7 0.14
21 4 0.08
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAAATAAATAAAAAATAA
Found at i:563982 original size:6 final size:6
Alignment explanation
Indices: 563960--564019 Score: 52
Period size: 6 Copynumber: 9.5 Consensus size: 6
563950 TGCGGGGCCT
*
563960 ATAAAA ATAATA A-AATA ATAATA ATAATA ATAAATA TATATATA TATATATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA AT-AATA -ATA-ATA -ATA-ATA
564012 ATAA-A ATA
1 ATAATA ATA
564020 TTTTTGTAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.18
6 19 0.39
7 8 0.16
8 13 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAATA
Found at i:563988 original size:20 final size:22
Alignment explanation
Indices: 563959--564020 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 22
563949 GTGCGGGGCC
*
563959 TATAAAAATAATAAAATA-ATA
1 TATAATAATAATAAAATATATA
563980 -ATAATAATAAT-AAATATATA
1 TATAATAATAATAAAATATATA
564000 TATATATATATAATAAAATAT
1 TATA-ATA-ATAATAAAATAT
564021 TTTTGTAGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 5 0.14
20 13 0.37
21 3 0.09
22 3 0.09
23 5 0.14
24 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TATAATAATAATAAAATATATA
Found at i:564062 original size:8 final size:8
Alignment explanation
Indices: 564046--564091 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
564036 CAAAAATGAG
564046 TATATACA
1 TATATACA
*
564054 TACATACA
1 TATATACA
*
564062 TATATATA
1 TATATACA
564070 TATATACA
1 TATATACA
*
564078 TATATATA
1 TATATACA
564086 TATATA
1 TATATA
564092 ATGAATAGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (8 bp):
TATATACA
Found at i:564084 original size:4 final size:4
Alignment explanation
Indices: 564046--564091 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
564036 CAAAAATGAG
* * * *
564046 TATA TACA TACA TACA TATA TATA TATA TACA TATA TATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TA
564092 ATGAATAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (4 bp):
TATA
Found at i:564084 original size:16 final size:16
Alignment explanation
Indices: 564046--564091 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
564036 CAAAAATGAG
* *
564046 TATATACATACATACA
1 TATATATATATATACA
564062 TATATATATATATACA
1 TATATATATATATACA
564078 TATATATATATATA
1 TATATATATATATA
564092 ATGAATAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATATATATATACA
Found at i:568086 original size:27 final size:26
Alignment explanation
Indices: 568027--568086 Score: 61
Period size: 27 Copynumber: 2.2 Consensus size: 26
568017 GATCACGAGC
568027 TATTCAAAAAAAATAATATATTAAAAT
1 TATT-AAAAAAAATAATATATTAAAAT
*
568054 TTTTAAAAATAAATAA-ATTATTAATAA-
1 TATTAAAAA-AAATAATA-TATTAA-AAT
568081 TATTAA
1 TATTAA
568087 TATCTATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
26 6 0.21
27 20 0.71
28 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TATTAAAAAAAATAATATATTAAAAT
Found at i:569078 original size:19 final size:18
Alignment explanation
Indices: 569011--569078 Score: 79
Period size: 18 Copynumber: 3.7 Consensus size: 18
569001 TTCATTGAAA
569011 AACCGAAAAACCGAACCG
1 AACCGAAAAACCGAACCG
569029 AACCGAAAAACCCGAACCG
1 AACCGAAAAA-CCGAACCG
569048 TTAA---AAAAACCGAACCG
1 --AACCGAAAAACCGAACCG
569065 AACCGATAAAACCG
1 AACCGA-AAAACCG
569079 GTTTCAGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.05
17 8 0.19
18 16 0.37
19 15 0.35
21 2 0.05
ACGTcount: A:0.50, C:0.31, G:0.15, T:0.04
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:572830 original size:82 final size:82
Alignment explanation
Indices: 572700--572854 Score: 195
Period size: 82 Copynumber: 1.9 Consensus size: 82
572690 ACTATTCAAT
* ** * * **
572700 AGTGAACATTCATATACTCTTACAAACTTCATGTTTGAACCTAGGACCTCAAAGTATTGTAATAA
1 AGTGAACATTCATATACTCTTACAAACGTCATGTTAAAACCTAAGACCTCAAAATATAATAATAA
572765 TCTTTTAATTACTAAAC
66 TCTTTTAATTACTAAAC
* * * *
572782 AGTGAACATTCAT-TCACTTTTACAGACGTCGTGTTAAAACCTAAGACCTTAAAATATAATAATA
1 AGTGAACATTCATAT-ACTCTTACAAACGTCATGTTAAAACCTAAGACCTCAAAATATAATAATA
572846 ATCTTTTAA
65 ATCTTTTAA
572855 CCATTGAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
81 1 0.02
82 60 0.98
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (82 bp):
AGTGAACATTCATATACTCTTACAAACGTCATGTTAAAACCTAAGACCTCAAAATATAATAATAA
TCTTTTAATTACTAAAC
Found at i:573088 original size:20 final size:19
Alignment explanation
Indices: 573063--573106 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
573053 TAAATTAATA
*
573063 TATATTTTAGATATTTTATT
1 TATATTTT-GATAATTTATT
573083 TATA-TTTGATAATTTATT
1 TATATTTTGATAATTTATT
*
573101 TTTATT
1 TATATT
573107 CCCTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 13 0.62
19 4 0.19
20 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TATATTTTGATAATTTATT
Found at i:576310 original size:16 final size:16
Alignment explanation
Indices: 576291--576321 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
576281 AATTGAACAC
*
576291 GAGTTAAATTATTTTT
1 GAGTTAAATAATTTTT
576307 GAGTTAAATAATTTT
1 GAGTTAAATAATTTT
576322 CAAGTCACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (16 bp):
GAGTTAAATAATTTTT
Found at i:582527 original size:21 final size:21
Alignment explanation
Indices: 582503--582548 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
582493 GCTATACTCG
*
582503 CAATAGCGCTCGCTATGACCA
1 CAATAGCGCCCGCTATGACCA
*
582524 CAATAGCGCCCGCTATGACCG
1 CAATAGCGCCCGCTATGACCA
582545 CAAT
1 CAAT
582549 CGTAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (21 bp):
CAATAGCGCCCGCTATGACCA
Found at i:582677 original size:2 final size:2
Alignment explanation
Indices: 582670--582696 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
582660 TCTTTACATG
582670 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
582697 GTCTGGAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:584757 original size:13 final size:13
Alignment explanation
Indices: 584739--584764 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
584729 AATTATTTCA
584739 TTTTTTTAATTTT
1 TTTTTTTAATTTT
584752 TTTTTTTAATTTT
1 TTTTTTTAATTTT
584765 ATTCTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTAATTTT
Found at i:584892 original size:17 final size:19
Alignment explanation
Indices: 584867--584916 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
584857 ATACGTTAGT
584867 AAATGATTAATTTTA-AT-A
1 AAAT-ATTAATTTTAGATAA
584885 AAATATTAAATTTTAGATAA
1 AAATATT-AATTTTAGATAA
*
584905 AAATATCAATTT
1 AAATATTAATTT
584917 AACAGTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
19 7 0.25
20 7 0.25
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (19 bp):
AAATATTAATTTTAGATAA
Found at i:584948 original size:30 final size:31
Alignment explanation
Indices: 584891--584949 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
584881 AATAAAATAT
*
584891 TAAATTTTAGATAAAAATATCAATTTAACAG
1 TAAATTTTAAATAAAAATATCAATTTAACAG
584922 TAAATTTTAAATTAAAAAT-T-AATTTAAC
1 TAAATTTTAAA-TAAAAATATCAATTTAAC
584950 TCATGAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 11 0.42
32 7 0.27
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAATTTTAAATAAAAATATCAATTTAACAG
Found at i:588099 original size:16 final size:16
Alignment explanation
Indices: 588078--588110 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
588068 GTATCTTAGT
588078 TGATATGAAAGTATTA
1 TGATATGAAAGTATTA
*
588094 TGATATGGAAGTATTA
1 TGATATGAAAGTATTA
588110 T
1 T
588111 CTAAGTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (16 bp):
TGATATGAAAGTATTA
Found at i:593173 original size:18 final size:18
Alignment explanation
Indices: 593150--593184 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
593140 ATTTATTGAC
593150 CAATTAATCTAGATCGAT
1 CAATTAATCTAGATCGAT
*
593168 CAATTAATTTAGATCGA
1 CAATTAATCTAGATCGA
593185 ATACTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (18 bp):
CAATTAATCTAGATCGAT
Found at i:597186 original size:122 final size:123
Alignment explanation
Indices: 597045--597276 Score: 403
Period size: 122 Copynumber: 1.9 Consensus size: 123
597035 ATGATTATAA
*
597045 AAAATCATTTAAATTAAAATCAAATATTAAAAAATTATAAATATTTACAATTAAATTTAAATAAA
1 AAAATCATTTAAATTAAAATAAAATATTAAAAAATTATAAATATTTACAATTAAATTTAAATAAA
597110 AACTTAAACAACTCAAATTTTATAAACTCGATTCAATTCA-AAAATATTTTAAGTTTT
66 AACTTAAACAACTCAAATTTTATAAACTCGATTCAATTCACAAAATATTTTAAGTTTT
*
597167 AAAATCATTTAAATTAAAATAAAATATTACAAAATTATAAATATTTACAATTAAATTTAAATAAA
1 AAAATCATTTAAATTAAAATAAAATATTAAAAAATTATAAATATTTACAATTAAATTTAAATAAA
* * * *
597232 AACTTACACAACTCAAATTTTATGAGCTTGATTCAATTCACAAAA
66 AACTTAAACAACTCAAATTTTATAAACTCGATTCAATTCACAAAA
597277 ATAAACTTAA
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
122 99 0.96
123 4 0.04
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (123 bp):
AAAATCATTTAAATTAAAATAAAATATTAAAAAATTATAAATATTTACAATTAAATTTAAATAAA
AACTTAAACAACTCAAATTTTATAAACTCGATTCAATTCACAAAATATTTTAAGTTTT
Found at i:602931 original size:13 final size:13
Alignment explanation
Indices: 602913--602938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
602903 ACATATTTGA
602913 ACAGTCTTCATAT
1 ACAGTCTTCATAT
602926 ACAGTCTTCATAT
1 ACAGTCTTCATAT
602939 GCGCTTCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGTCTTCATAT
Found at i:602978 original size:14 final size:15
Alignment explanation
Indices: 602959--602998 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
602949 AATGGGAAGT
602959 AATCCCTGC-TAATA
1 AATCCCTGCATAATA
602973 AATCCCTGCATAAT-
1 AATCCCTGCATAATA
*
602987 AATCTCTGCATA
1 AATCCCTGCATA
602999 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (15 bp):
AATCCCTGCATAATA
Found at i:615078 original size:47 final size:47
Alignment explanation
Indices: 615024--615449 Score: 755
Period size: 47 Copynumber: 9.1 Consensus size: 47
615014 CGTTCAAGAT
*
615024 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAGA
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
615071 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
* *
615118 AATTATTTTAATGGTTCTTCCCTTTTACAAGTAAAAACAAGATAACA
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
* *
615165 AATTATTTTAATGGTTCTTCCCATCTACAAGGAAAAACAAGAT-AAA
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
*
615211 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAACA
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
*
615258 AATTATTTTAATGGTTATTCCCATTTACAAGTAAAAACAAGATAAAA
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
* *
615305 AATTATTTTAATGGTTCTTCCCTTTTACAAGTAAAAACAAGATAACA
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
*
615352 AATTATTTTAATGGTTCTTCCCATTTACAAGGAAAAACAAGATAAAA
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
615399 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
615446 AATT
1 AATT
615450 TTGATGACCC
Statistics
Matches: 359, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 43 0.12
47 316 0.88
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (47 bp):
AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAA
Found at i:615339 original size:187 final size:188
Alignment explanation
Indices: 615024--615449 Score: 809
Period size: 187 Copynumber: 2.3 Consensus size: 188
615014 CGTTCAAGAT
* *
615024 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAGAAATTATTTTAATGGTTCT
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAAAATTATTTTAATGGTTAT
615089 TCCCATTTACAAGTAAAAACAAGATAAAAAATTATTTTAATGGTTCTTCCCTTTTACAAGTAAAA
66 TCCCATTTACAAGTAAAAACAAGATAAAAAATTATTTTAATGGTTCTTCCCTTTTACAAGTAAAA
615154 ACAAGATAACAAATTATTTTAATGGTTCTTCCCATCTACAAGGAAAAACAAGAT-AAA
131 ACAAGATAACAAATTATTTTAATGGTTCTTCCCATCTACAAGGAAAAACAAGATAAAA
*
615211 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAACAAATTATTTTAATGGTTAT
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAAAATTATTTTAATGGTTAT
615276 TCCCATTTACAAGTAAAAACAAGATAAAAAATTATTTTAATGGTTCTTCCCTTTTACAAGTAAAA
66 TCCCATTTACAAGTAAAAACAAGATAAAAAATTATTTTAATGGTTCTTCCCTTTTACAAGTAAAA
*
615341 ACAAGATAACAAATTATTTTAATGGTTCTTCCCATTTACAAGGAAAAACAAGATAAAA
131 ACAAGATAACAAATTATTTTAATGGTTCTTCCCATCTACAAGGAAAAACAAGATAAAA
615399 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAAAATT
1 AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAAAATT
615450 TTGATGACCC
Statistics
Matches: 234, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
187 181 0.77
188 53 0.23
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (188 bp):
AATTATTTTAATGGTTCTTCCCATTTACAAGTAAAAACAAGATAAAAAATTATTTTAATGGTTAT
TCCCATTTACAAGTAAAAACAAGATAAAAAATTATTTTAATGGTTCTTCCCTTTTACAAGTAAAA
ACAAGATAACAAATTATTTTAATGGTTCTTCCCATCTACAAGGAAAAACAAGATAAAA
Found at i:620905 original size:24 final size:24
Alignment explanation
Indices: 620878--620933 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
620868 ATTATATTAC
*
620878 AAATCTAGG-GAGTGCAAAATTATA
1 AAATCTAGGAG-GTGCAAAATTAGA
620902 AAATCTCAGGAGGTGCAAAATTAGA
1 AAATCT-AGGAGGTGCAAAATTAGA
*
620927 TAATCTA
1 AAATCTA
620934 TTAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.25
25 20 0.71
26 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.25
Consensus pattern (24 bp):
AAATCTAGGAGGTGCAAAATTAGA
Found at i:621901 original size:2 final size:2
Alignment explanation
Indices: 621894--621922 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
621884 TTCCAACATT
621894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
621923 TGAAGGTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:625533 original size:25 final size:25
Alignment explanation
Indices: 625504--625560 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
625494 ATATAAAAAA
625504 GTAAAATTTAGAATAAAACTAAATT
1 GTAAAATTTAGAATAAAACTAAATT
625529 GTAAAATTTAGAATAAAACTAAATT
1 GTAAAATTTAGAATAAAACTAAATT
*
625554 ATAAAAT
1 GTAAAAT
625561 ATTAAACAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.32
Consensus pattern (25 bp):
GTAAAATTTAGAATAAAACTAAATT
Found at i:626074 original size:41 final size:41
Alignment explanation
Indices: 626006--626161 Score: 126
Period size: 41 Copynumber: 3.8 Consensus size: 41
625996 AAAATGAAAC
* * *
626006 TTTAGCGGCGTTTTT-TCAACAAACGCCGTAATAGGGTGGTAA
1 TTTAGCGGCGTTTTTAT--ATAAACGCCGCAATAGGGTCGTAA
* *
626048 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGT--
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGGGTCGTAA
* * * *
626087 TTATAGTGGCG-TTTTACAAGAAACGCCGCAA-ATTGGTCGTACA
1 TT-TAGCGGCGTTTTTA-TATAAACGCCGCAATA-GGGTCGTA-A
*
626130 -TTAGTGGCGTTTTTATATAAACGCCGCAATAG
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAG
626162 AGTTGTTTAT
Statistics
Matches: 92, Mismatches: 13, Indels: 19
0.74 0.10 0.15
Matches are distributed among these distances:
39 8 0.09
40 23 0.25
41 38 0.41
42 22 0.24
43 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATATAAACGCCGCAATAGGGTCGTAA
Found at i:626111 original size:40 final size:40
Alignment explanation
Indices: 626067--626199 Score: 171
Period size: 40 Copynumber: 3.3 Consensus size: 40
626057 GTTTTTATAT
626067 AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
1 AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
* * ** * *
626107 AAACGCCGCAAATTG-GTCGTACATTAGTGGCGTTTTTA-TAT
1 AAACGCCGC-AATAGAGTTGTTTA-TAGTGGCG-TTTTACAAG
626148 AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
1 AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
626188 AAACGCCGCAAT
1 AAACGCCGCAAT
626200 TGATTTTAAC
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
39 5 0.07
40 39 0.51
41 27 0.36
42 5 0.07
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (40 bp):
AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
Found at i:626111 original size:81 final size:81
Alignment explanation
Indices: 626049--626198 Score: 282
Period size: 81 Copynumber: 1.9 Consensus size: 81
626039 GGGTGGTAAT
626049 TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGCC
1 TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGCC
*
626114 GCAAATTGGTCGTACA
66 GCAAATGGGTCGTACA
*
626130 TTAGTGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGCC
1 TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGCC
626195 GCAA
66 GCAA
626199 TTGATTTTAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (81 bp):
TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGCC
GCAAATGGGTCGTACA
Found at i:634069 original size:21 final size:21
Alignment explanation
Indices: 634045--634132 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
634035 AGCGGAAAAT
634045 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGC-AGCGGAAGCAGAGAGA
*
634066 GAAGCAGCAGAAGCAGAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
* * *
634087 GAAGCAGTGGCAGCACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
* * * * *
634108 GAGGCATCGGCAGAACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
634129 GAAG
1 GAAG
634133 TAATACATCA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 2 0.04
21 54 0.96
ACGTcount: A:0.43, C:0.15, G:0.40, T:0.02
Consensus pattern (21 bp):
GAAGCAGCGGAAGCAGAGAGA
Found at i:634071 original size:12 final size:12
Alignment explanation
Indices: 634054--634093 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
634044 TGAAGCAAGG
634054 GAAGCAGAGAGA
1 GAAGCAGAGAGA
*
634066 GAAGC--AG-CA
1 GAAGCAGAGAGA
634075 GAAGCAGAGAGA
1 GAAGCAGAGAGA
634087 GAAGCAG
1 GAAGCAG
634094 TGGCAGCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 6 0.26
10 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.47, C:0.12, G:0.40, T:0.00
Consensus pattern (12 bp):
GAAGCAGAGAGA
Found at i:634105 original size:23 final size:22
Alignment explanation
Indices: 634058--634130 Score: 82
Period size: 21 Copynumber: 3.4 Consensus size: 22
634048 GCAAGGGAAG
634058 CAGAGAGAGAAGCA--GCAGAA
1 CAGAGAGAGAAGCATGGCAGAA
*
634078 GCAGAGAGAGAAGCAGTGGCAGCA
1 -CAGAGAGAGAAGCA-TGGCAGAA
634102 CAGAGAGAG--GCATCGGCAGAA
1 CAGAGAGAGAAGCAT-GGCAGAA
634123 CAGAGAGA
1 CAGAGAGA
634131 AGTAATACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
20 1 0.02
21 31 0.67
23 9 0.20
24 5 0.11
ACGTcount: A:0.42, C:0.16, G:0.38, T:0.03
Consensus pattern (22 bp):
CAGAGAGAGAAGCATGGCAGAA
Found at i:634662 original size:43 final size:43
Alignment explanation
Indices: 634487--634719 Score: 164
Period size: 43 Copynumber: 5.4 Consensus size: 43
634477 TTTGTGATAA
* * * * * * **
634487 AAACGCCGCGAAATCTCAAGACATATTGCGGCGTTTGT-AGGA
1 AAACGCCGCTAAATATCAACACCTATTGCGACGTTTGTCTGCC
* * ** * **
634529 AAACACCGCTAAATATCAACATCTCCTGCGACGTTTGTATGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGACGTTTGTCTGCC
* * * * * * * ** *
634572 AAACGACGGTAAAAATAAACATCTACTGCGGCGTTTGTGAAG-A
1 AAACGCCGCTAAATATCAACACCTATTGCGACGTTTGT-CTGCC
* * *
634615 AAACGCCGCTAAACATCAACGCCTATTGCGGCGTTTGTCTGCC
1 AAACGCCGCTAAATATCAACACCTATTGCGACGTTTGTCTGCC
* * *
634658 AAACGCCGTTAAATATCAACACCTATTGCGACGTTTTTCTGCT
1 AAACGCCGCTAAATATCAACACCTATTGCGACGTTTGTCTGCC
634701 AAACGCCGCTAAATATCAA
1 AAACGCCGCTAAATATCAA
634720 TACATCGCCG
Statistics
Matches: 152, Mismatches: 36, Indels: 5
0.79 0.19 0.03
Matches are distributed among these distances:
42 30 0.20
43 120 0.79
44 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGACGTTTGTCTGCC
Found at i:634693 original size:86 final size:85
Alignment explanation
Indices: 634475--634693 Score: 206
Period size: 86 Copynumber: 2.6 Consensus size: 85
634465 CATTTAGCGG
* * * * *
634475 CGTTTGTGAT-AAAAACGCCGCGAAATCTCAAGACATATTGCGGCGTTTGTAGGAAAACACCGCT
1 CGTTTGT-ATGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTAAGAAAACACCGCT
* * *
634539 AAATATCAACATCTCCTGCGA
65 AAACATCAACACCTACTGCGA
* * * * * * *
634560 CGTTTGTATGAAAAACGACGGTAAAAATAAACATCTACTGCGGCGTTTGTGAAGAAAACGCCGCT
1 CGTTTGTATGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-AAGAAAACACCGCT
* * *
634625 AAACATCAACGCCTATTGCGG
65 AAACATCAACACCTACTGCGA
* ** * *
634646 CGTTTGTCTGCCAAACGCCGTTAAATATCAACACCTATTGCGACGTTT
1 CGTTTGTATGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
634694 TTCTGCTAAA
Statistics
Matches: 104, Mismatches: 28, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
84 2 0.02
85 37 0.36
86 65 0.62
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (85 bp):
CGTTTGTATGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTAAGAAAACACCGCTA
AACATCAACACCTACTGCGA
Found at i:637162 original size:24 final size:24
Alignment explanation
Indices: 637135--637190 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
637125 ATTATATTAC
*
637135 AAATCTAGG-GAGTGCAAAATTATA
1 AAATCTAGGAG-GTGCAAAATTAGA
637159 AAATCTCAGGAGGTGCAAAATTAGA
1 AAATCT-AGGAGGTGCAAAATTAGA
*
637184 TAATCTA
1 AAATCTA
637191 TTAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.25
25 20 0.71
26 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.25
Consensus pattern (24 bp):
AAATCTAGGAGGTGCAAAATTAGA
Found at i:637510 original size:13 final size:13
Alignment explanation
Indices: 637492--637518 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
637482 TCATTGACTC
637492 ACAAAAAATTAAA
1 ACAAAAAATTAAA
637505 ACAAAAAATTAAA
1 ACAAAAAATTAAA
637518 A
1 A
637519 TGATTGAAAC
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:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
ACAAAAAATTAAA
Found at i:638155 original size:2 final size:2
Alignment explanation
Indices: 638148--638174 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
638138 TTCCAACATT
638148 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
638175 TGAAGGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:640647 original size:22 final size:22
Alignment explanation
Indices: 640615--640656 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
640605 ATTTTTTCTG
* *
640615 AAAAAATAAATTAAACTCTTCA
1 AAAAAAAAAATTAAAATCTTCA
640637 AAAAAAAAAATTAAAATCTT
1 AAAAAAAAAATTAAAATCTT
640657 AATTTAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAAAAAAATTAAAATCTTCA
Found at i:641788 original size:25 final size:25
Alignment explanation
Indices: 641759--641815 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
641749 ATATAAAAAA
*
641759 GTAAAATTTAGAATAAAATTAAATT
1 GTAAAATTTAGAATAAAACTAAATT
641784 GTAAAATTTAGAATAAAACTAAATT
1 GTAAAATTTAGAATAAAACTAAATT
*
641809 ATAAAAT
1 GTAAAAT
641816 ATTAAACAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (25 bp):
GTAAAATTTAGAATAAAACTAAATT
Found at i:642275 original size:41 final size:41
Alignment explanation
Indices: 642207--642362 Score: 117
Period size: 41 Copynumber: 3.8 Consensus size: 41
642197 AAAATAAAAC
* *
642207 TTTAGCGGCGTTTTT-TCAACAAACGCCGCAATAGGGTGGTAA
1 TTTAGCGGCGTTTTTAT--ATAAACGCCGCAATAGGGTCGTAA
* *
642249 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGT--
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGGGTCGTAA
* * * * * *
642288 TTATAGTGGC-ATTTTACAAGAAACACCGCAA-ATTGGTCGTACA
1 TT-TAGCGGCGTTTTTA-TATAAACGCCGCAATA-GGGTCGTA-A
*
642331 -TTAGTGGCGTTTTTATATAAACGCCGCAATAG
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAG
642363 AGTTGTTTAT
Statistics
Matches: 89, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
39 8 0.09
40 21 0.24
41 37 0.42
42 22 0.25
43 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATATAAACGCCGCAATAGGGTCGTAA
Found at i:642367 original size:81 final size:81
Alignment explanation
Indices: 642250--642399 Score: 273
Period size: 81 Copynumber: 1.9 Consensus size: 81
642240 GGGTGGTAAT
642250 TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCATTTTACAAGAAACACC
1 TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCATTTTACAAGAAACACC
642315 GCAAATTGGTCGTACA
66 GCAAATTGGTCGTACA
* * *
642331 TTAGTGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGCC
1 TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCATTTTACAAGAAACACC
642396 GCAA
66 GCAA
642400 TTGATTTTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (81 bp):
TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCATTTTACAAGAAACACC
GCAAATTGGTCGTACA
Found at i:642379 original size:40 final size:41
Alignment explanation
Indices: 642213--642400 Score: 163
Period size: 40 Copynumber: 4.6 Consensus size: 41
642203 AAACTTTAGC
* * * * *
642213 GGCGTTTTTTCAACAAACGCCGCAATAGGGTGGTAATT-TAGC
1 GGCGTTTTTACAAGAAACGCCGCAATAGAGTTGT--TTATAGT
* *
642255 GGCGTTTTTA-TATAAACGCCGCAATAGAGTTGTTTATAGT
1 GGCGTTTTTACAAGAAACGCCGCAATAGAGTTGTTTATAGT
* * * * **
642295 GGC-ATTTTACAAGAAACACCGCAAATTG-GTCGTACATTAGT
1 GGCGTTTTTACAAGAAACGCCGC-AATAGAGTTGTTTA-TAGT
* *
642336 GGCGTTTTTA-TATAAACGCCGCAATAGAGTTGTTTATAGT
1 GGCGTTTTTACAAGAAACGCCGCAATAGAGTTGTTTATAGT
642376 GGCG-TTTTACAAGAAACGCCGCAAT
1 GGCGTTTTTACAAGAAACGCCGCAAT
642401 TGATTTTAAC
Statistics
Matches: 115, Mismatches: 24, Indels: 16
0.74 0.15 0.10
Matches are distributed among these distances:
39 12 0.10
40 45 0.39
41 44 0.38
42 14 0.12
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (41 bp):
GGCGTTTTTACAAGAAACGCCGCAATAGAGTTGTTTATAGT
Found at i:650332 original size:21 final size:21
Alignment explanation
Indices: 650308--650416 Score: 85
Period size: 21 Copynumber: 5.2 Consensus size: 21
650298 AGCGGAAAAT
650308 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGC-AGCGGAAGCAGAGAGA
*
650329 GAAGCAGCAGAAGCAGAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
* * *
650350 GAAGCAGTGGCAGCACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
* * * * *
650371 GAGGCAGCAGCAGAACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
* * * *
650392 GAGGCAGCGGCAGAACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
650413 GAAG
1 GAAG
650417 TAATACATCA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
20 2 0.03
21 74 0.97
ACGTcount: A:0.43, C:0.16, G:0.40, T:0.01
Consensus pattern (21 bp):
GAAGCAGCGGAAGCAGAGAGA
Found at i:650334 original size:12 final size:12
Alignment explanation
Indices: 650317--650356 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
650307 TGAAGCAAGG
650317 GAAGCAGAGAGA
1 GAAGCAGAGAGA
*
650329 GAAGC--AG-CA
1 GAAGCAGAGAGA
650338 GAAGCAGAGAGA
1 GAAGCAGAGAGA
650350 GAAGCAG
1 GAAGCAG
650357 TGGCAGCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 6 0.26
10 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.47, C:0.12, G:0.40, T:0.00
Consensus pattern (12 bp):
GAAGCAGAGAGA
Found at i:650390 original size:44 final size:42
Alignment explanation
Indices: 650321--650414 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
650311 GCAAGGGAAG
* *
650321 CAGAGAGAGAAGCAGCAGAAGCAGAGAGAGAAGCAGTGGCAGCA
1 CAGAGAGAGAAGCAGCAGAAGCAGAGAGAG--GCAGCGGCAGAA
*
650365 CAGAGAGAGGCAGCAGCAGAA-CAGAGAGAGGCAGCGGCAGAA
1 CAGAGAGA-GAAGCAGCAGAAGCAGAGAGAGGCAGCGGCAGAA
650407 CAGAGAGA
1 CAGAGAGA
650415 AGTAATACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
42 18 0.39
44 17 0.37
45 11 0.24
ACGTcount: A:0.43, C:0.17, G:0.39, T:0.01
Consensus pattern (42 bp):
CAGAGAGAGAAGCAGCAGAAGCAGAGAGAGGCAGCGGCAGAA
Found at i:650934 original size:86 final size:85
Alignment explanation
Indices: 650797--650977 Score: 200
Period size: 86 Copynumber: 2.1 Consensus size: 85
650787 CAAGACATAT
* * * *
650797 TGCGGCGTTTGTAGGAAAACGCCGCTAAATATCAACATCTCCTCCGACGTTTGTATGAAAAACGA
1 TGCGGCGTTTGTAAGAAAACGCCGCTAAACATCAACACCTACTCCGACGTTTGTATGAAAAACGA
*
650862 CGGTAAAAATAAACATCTAC
66 CGGTAAAAATAAACACCTAC
* * * * * **
650882 TGCGGCGTTTGTGAAGAAAACGCCGCTAAACATCAACGCCTATTGCGGCGTTTGTCTGCCAAACG
1 TGCGGCGTTTGT-AAGAAAACGCCGCTAAACATCAACACCTACTCCGACGTTTGTATGAAAAACG
* * * * *
650947 TCGTTAAATATCAACACCTAT
65 ACGGTAAAAATAAACACCTAC
650968 TGCGGCGTTT
1 TGCGGCGTTT
650978 TTCTGCTAAA
Statistics
Matches: 78, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
85 12 0.15
86 66 0.85
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (85 bp):
TGCGGCGTTTGTAAGAAAACGCCGCTAAACATCAACACCTACTCCGACGTTTGTATGAAAAACGA
CGGTAAAAATAAACACCTAC
Found at i:650983 original size:43 final size:43
Alignment explanation
Indices: 650771--651003 Score: 173
Period size: 43 Copynumber: 5.4 Consensus size: 43
650761 TTTGTGATAA
* * * * * **
650771 AAACGCCGCGAAATCTCAAGACATATTGCGGCGTTTGT-AGGA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGCC
* ** * * * **
650813 AAACGCCGCTAAATATCAACATCTCCTCCGACGTTTGTATGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGCC
* * * * * * ** *
650856 AAACGACGGTAAAAATAAACATCTACTGCGGCGTTTGTGAAG-A
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-CTGCC
* *
650899 AAACGCCGCTAAACATCAACGCCTATTGCGGCGTTTGTCTGCC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGCC
* * * *
650942 AAACGTCGTTAAATATCAACACCTATTGCGGCGTTTTTCTGCT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGCC
650985 AAACGCCGCTAAATATCAA
1 AAACGCCGCTAAATATCAA
651004 TACATCGCCG
Statistics
Matches: 151, Mismatches: 37, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
42 30 0.20
43 119 0.79
44 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGCC
Found at i:651713 original size:16 final size:15
Alignment explanation
Indices: 651672--651709 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
651662 AAATGTTATT
651672 TATTATTTATAATTAA
1 TATTA-TTATAATTAA
651688 TATTATTATAA-TAA
1 TATTATTATAATTAA
651702 TATT-TTAT
1 TATTATTAT
651710 TATATTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 7 0.32
15 6 0.27
16 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTATTATAATTAA
Found at i:653439 original size:24 final size:24
Alignment explanation
Indices: 653412--653467 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
653402 ATTATATTAC
*
653412 AAATCTAGG-GAGTGCAAAATTATA
1 AAATCTAGGAG-GTGCAAAATTAGA
653436 AAATCTCAGGAGGTGCAAAATTAGA
1 AAATCT-AGGAGGTGCAAAATTAGA
*
653461 TAATCTA
1 AAATCTA
653468 TTAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.25
25 20 0.71
26 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.25
Consensus pattern (24 bp):
AAATCTAGGAGGTGCAAAATTAGA
Found at i:656905 original size:21 final size:21
Alignment explanation
Indices: 656879--656919 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
656869 ATTTTTTCTG
* *
656879 AAAAAATAAATTAAACTCTTC
1 AAAAAAAAAATTAAAATCTTC
656900 AAAAAAAAAATTAAAATCTT
1 AAAAAAAAAATTAAAATCTT
656920 AATTTAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAAAAAATTAAAATCTTC
Found at i:658051 original size:25 final size:25
Alignment explanation
Indices: 658022--658078 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
658012 ATATAAAAAA
*
658022 GTAAAATTTAGAATAAAATTAAATT
1 GTAAAATTTAGAATAAAACTAAATT
658047 GTAAAATTTAGAATAAAACTAAATT
1 GTAAAATTTAGAATAAAACTAAATT
*
658072 ATAAAAT
1 GTAAAAT
658079 ATTAAACAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (25 bp):
GTAAAATTTAGAATAAAACTAAATT
Found at i:658278 original size:2 final size:2
Alignment explanation
Indices: 658267--658309 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
658257 CAATCTAAAT
*
658267 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
658308 TA
1 TA
658310 AATAAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:658622 original size:41 final size:41
Alignment explanation
Indices: 658548--658791 Score: 207
Period size: 41 Copynumber: 6.0 Consensus size: 41
658538 AAAATGAAAC
* * * *
658548 TTTAGCGGCGTTTTT-TCAACAAATGCCGCAATAGGGTGGTAA
1 TTTAGCGGCGTTTTTAT--ATAAACGCCGCAATAGAGTTGTAA
*
658590 TTTAGCGGCGTTTTTATATAAACGCCGTAATAGAGTTGT--
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTAA
* * * * *
658629 TTATAGTGGCGTTTTCTAAAAAAACACCGCAATAGAGTAGTAA
1 TT-TAGCGGCGTTTT-TATATAAACGCCGCAATAGAGTTGTAA
*
658672 TTTAGCGGCGTTTTTATATAAACACCGCAATAGAGTTGT--
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTAA
* * * * *
658711 TTATAGTGGCG-TTTTACAAGAAACGCCGCAAATTG-GTCGTACA
1 TT-TAGCGGCGTTTTTA-TATAAACGCCGC-AATAGAGTTGTA-A
*
658754 -TTAGTGGCGTTTTTATATAAACGCCGCAATAGAGTTGT
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGT
658792 TTATAGTGGC
Statistics
Matches: 164, Mismatches: 25, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
39 9 0.05
40 35 0.21
41 85 0.52
42 32 0.20
43 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTAA
Found at i:658740 original size:40 final size:40
Alignment explanation
Indices: 658609--658823 Score: 197
Period size: 41 Copynumber: 5.3 Consensus size: 40
658599 GTTTTTATAT
* *
658609 AAACGCCGTAATAGAGTTGTTTATAGTGGCGTTTT-CTAAAA
1 AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTAC--AAG
* * * * *
658650 AAACACCGCAATAGAGTAGTAATT-TAGCGGCGTTTTTA-TAT
1 AAACGCCGCAATAGAGTTGT--TTATAGTGGCG-TTTTACAAG
*
658691 AAACACCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
1 AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
* * ** * *
658731 AAACGCCGCAAATTG-GTCGTACATTAGTGGCGTTTTTA-TAT
1 AAACGCCGC-AATAGAGTTGTTTA-TAGTGGCG-TTTTACAAG
658772 AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
1 AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
658812 AAACGCCGCAAT
1 AAACGCCGCAAT
658824 TGATTTTAAC
Statistics
Matches: 140, Mismatches: 23, Indels: 23
0.75 0.12 0.12
Matches are distributed among these distances:
39 12 0.09
40 46 0.33
41 64 0.46
42 12 0.09
43 6 0.04
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (40 bp):
AAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAG
Found at i:658781 original size:81 final size:82
Alignment explanation
Indices: 658554--658822 Score: 359
Period size: 81 Copynumber: 3.3 Consensus size: 82
658544 AAACTTTAGC
* * * * * *
658554 GGCGTTTTTTCAACAAATGCCGC-AATAGGGTGGTAATTTAGCGGCGTTTTTATATAAACGCCGT
1 GGCG-TTTTACAAGAAACGCCGCAAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGC
658618 AATAGAGTTGTTTATAGT
65 AATAGAGTTGTTTATAGT
* * *
658636 GGCGTTTT-CTAAAAAAACACCGC-AATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACACCG
1 GGCGTTTTAC--AAGAAACGCCGCAAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCG
658699 CAATAGAGTTGTTTATAGT
64 CAATAGAGTTGTTTATAGT
* * *
658718 GGCGTTTTACAAGAAACGCCGCAAATTG-GTCGTACA-TTAGTGGCGTTTTTATATAAACGCCGC
1 GGCGTTTTACAAGAAACGCCGCAAATAGAGTAGTA-ATTTAGCGGCGTTTTTATATAAACGCCGC
658781 AATAGAGTTGTTTATAGT
65 AATAGAGTTGTTTATAGT
658799 GGCGTTTTACAAGAAACGCCGCAA
1 GGCGTTTTACAAGAAACGCCGCAA
658823 TTGATTTTAA
Statistics
Matches: 169, Mismatches: 13, Indels: 11
0.88 0.07 0.06
Matches are distributed among these distances:
80 1 0.01
81 86 0.51
82 81 0.48
83 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (82 bp):
GGCGTTTTACAAGAAACGCCGCAAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGCA
ATAGAGTTGTTTATAGT
Found at i:666721 original size:21 final size:22
Alignment explanation
Indices: 666695--666759 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 22
666685 AGCGGAAAAT
666695 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGCAAGCGGAAGCAGAGAGA
*
666716 GCAGC-AGCGGAAGCAGAGAGA
1 GAAGCAAGCGGAAGCAGAGAGA
* * *
666737 GAAGC-AGTGGCAGCACAGAGA
1 GAAGCAAGCGGAAGCAGAGAGA
666758 GA
1 GA
666760 GACAGCGGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 2 0.05
21 36 0.95
ACGTcount: A:0.42, C:0.15, G:0.42, T:0.02
Consensus pattern (22 bp):
GAAGCAAGCGGAAGCAGAGAGA
Found at i:666769 original size:21 final size:22
Alignment explanation
Indices: 666708--666780 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 22
666698 GCAAGGGAAG
*
666708 CAGAGAGAGCAGCAGCGGAAGCA
1 CAGAGAGAG-AGCAGCGGCAGCA
* *
666731 GAGAGAGA-AGCAGTGGCAGCA
1 CAGAGAGAGAGCAGCGGCAGCA
*
666752 CAGAGAGAGA-CAGCGGCAGAA
1 CAGAGAGAGAGCAGCGGCAGCA
666773 CAGAGAGA
1 CAGAGAGA
666781 AGTAATATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
21 35 0.81
22 1 0.02
23 7 0.16
ACGTcount: A:0.41, C:0.18, G:0.40, T:0.01
Consensus pattern (22 bp):
CAGAGAGAGAGCAGCGGCAGCA
Found at i:667285 original size:128 final size:129
Alignment explanation
Indices: 667114--667356 Score: 307
Period size: 129 Copynumber: 1.9 Consensus size: 129
667104 CATACATTTA
*
667114 GCGGCGTTTGTGATAAAAACGCCGCGAAATCTCAAGACATATTGCGGCGTTTGT-AGGAAAACGC
1 GCGGCGTTTGTGATAAAAACGCCGCGAAATCTCAAGACATATTGCGGCGTTTGTCAGCAAAACGC
* *
667178 CGCTAAATATCAACATCT-TCTGCGGCGTTTGTATGAAAAACGCCGGTAAAAATAAACATCTACT
66 CGCTAAATATCAACACCTAT-TGCGGCGTTTGTATGAAAAACGCCGCTAAAAATAAACATCTACT
* * * *
667242 GCGGCGTTTGTGA-AGAAAACGCCGCTAAA-CATCAACGTC-TATTGCGGCGTTTGTCTGCCAAA
1 GCGGCGTTTGTGATA-AAAACGCCGCGAAATC-TCAA-GACATATTGCGGCGTTTGTCAGCAAAA
* * * * *
667304 CGTCGTTAAATATCAACACCTATTGCGGCGTTTTTCTGCAAAACGCCGCTAAA
63 CGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGAAAAACGCCGCTAAA
667357 TATCAACACT
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
127 2 0.02
128 45 0.46
129 50 0.51
130 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (129 bp):
GCGGCGTTTGTGATAAAAACGCCGCGAAATCTCAAGACATATTGCGGCGTTTGTCAGCAAAACGC
CGCTAAATATCAACACCTATTGCGGCGTTTGTATGAAAAACGCCGCTAAAAATAAACATCTACT
Found at i:667294 original size:86 final size:85
Alignment explanation
Indices: 667156--667364 Score: 249
Period size: 86 Copynumber: 2.4 Consensus size: 85
667146 CAAGACATAT
*
667156 TGCGGCGTTTGTAGGAAAACGCCGCTAAATATCAACATCTTCTGCGGCGTTTGTATGAAAAACGC
1 TGCGGCGTTTGTAAGAAAACGCCGCTAAATATCAACATCTTCTGCGGCGTTTGTATGAAAAACGC
*
667221 CGGTAAAAATAAACATCTAC
66 CGGTAAAAATAAACACCTAC
* * * **
667241 TGCGGCGTTTGTGAAGAAAACGCCGCTAAACATCAACGTCTAT-TGCGGCGTTTGTCTGCCAAAC
1 TGCGGCGTTTGT-AAGAAAACGCCGCTAAATATCAACATCT-TCTGCGGCGTTTGTATGAAAAAC
* * * * *
667305 GTCGTTAAATATCAACACCTAT
64 GCCGGTAAAAATAAACACCTAC
* **
667327 TGCGGCGTTTTTCTGCAAAACGCCGCTAAATATCAACA
1 TGCGGCGTTTGTAAG-AAAACGCCGCTAAATATCAACA
667365 CTTATTGCGA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
85 13 0.12
86 90 0.87
87 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (85 bp):
TGCGGCGTTTGTAAGAAAACGCCGCTAAATATCAACATCTTCTGCGGCGTTTGTATGAAAAACGC
CGGTAAAAATAAACACCTAC
Found at i:667371 original size:86 final size:84
Alignment explanation
Indices: 667114--667373 Score: 231
Period size: 86 Copynumber: 3.0 Consensus size: 84
667104 CATACATTTA
** * * * *
667114 GCGGCGTTTGTGAT-AAAAACGCCGCG-AAATCTCAAGACATATTGCGGCGTTTGTAGGAAAACG
1 GCGGCGTTTGT-ATGAAAAACGCCG-GTAAAAATAAACACCTATTGCGGCGTTTTTA-GAAAACG
*
667177 CCGCTAAATATCAACATCTT-CT
63 CCGCTAAATATCAACA-CTTATT
* * *
667199 GCGGCGTTTGTATGAAAAACGCCGGTAAAAATAAACATCTACTGCGGCGTTTGTGAAGAAAACGC
1 GCGGCGTTTGTATGAAAAACGCCGGTAAAAATAAACACCTATTGCGGCGTTT-T-TAGAAAACGC
* *
667264 CGCTAAACATCAAC-GTCTATT
64 CGCTAAATATCAACACT-TATT
* ** * * * * *
667285 GCGGCGTTTGTCTGCCAAACGTCGTTAAATATCAACACCTATTGCGGCGTTTTTCTGCAAAACGC
1 GCGGCGTTTGTATGAAAAACGCCGGTAAAAATAAACACCTATTGCGGCGTTTTT-AG-AAAACGC
667350 CGCTAAATATCAACACTTATT
64 CGCTAAATATCAACACTTATT
667371 GCG
1 GCG
667374 ACATTTTTTT
Statistics
Matches: 141, Mismatches: 25, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
84 4 0.03
85 43 0.30
86 92 0.65
87 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (84 bp):
GCGGCGTTTGTATGAAAAACGCCGGTAAAAATAAACACCTATTGCGGCGTTTTTAGAAAACGCCG
CTAAATATCAACACTTATT
Found at i:667381 original size:43 final size:43
Alignment explanation
Indices: 667129--667373 Score: 194
Period size: 43 Copynumber: 5.7 Consensus size: 43
667119 GTTTGTGATA
* * * * * * *
667129 AAAACGCCGCGAAATCTCAAGACATATTGCGGCGTTTGT-AGG
1 AAAACGCCGCTAAATATCAACACTTATTGCGGCGTTTTTCTGC
* * * *
667171 AAAACGCCGCTAAATATCAACATCTT-CTGCGGCGTTTGTATGA
1 AAAACGCCGCTAAATATCAACA-CTTATTGCGGCGTTTTTCTGC
* * * * ***
667214 AAAACGCCGGTAAAAATAAACA-TCTACTGCGGCGTTTGTGAAG-
1 AAAACGCCGCTAAATATCAACACT-TATTGCGGCGTTT-TTCTGC
* * *
667257 AAAACGCCGCTAAACATCAAC-GTCTATTGCGGCGTTTGTCTGC
1 AAAACGCCGCTAAATATCAACACT-TATTGCGGCGTTTTTCTGC
* * * *
667300 CAAACGTCGTTAAATATCAACACCTATTGCGGCGTTTTTCTGC
1 AAAACGCCGCTAAATATCAACACTTATTGCGGCGTTTTTCTGC
667343 AAAACGCCGCTAAATATCAACACTTATTGCG
1 AAAACGCCGCTAAATATCAACACTTATTGCG
667374 ACATTTTTTT
Statistics
Matches: 163, Mismatches: 32, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.01
42 33 0.20
43 127 0.78
44 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (43 bp):
AAAACGCCGCTAAATATCAACACTTATTGCGGCGTTTTTCTGC
Found at i:674081 original size:52 final size:52
Alignment explanation
Indices: 673995--674135 Score: 164
Period size: 51 Copynumber: 2.8 Consensus size: 52
673985 CTTGGATTTG
* * * *
673995 CTTTTCTTCTTCTTCTTTTTCTCTTTGTCA---TCTTTATCTGATTTCTTTT
1 CTTTTTTTCTTCTTCTTCTCCTCCTTGTCATCTTCTTTATCTGATTTCTTTT
674044 CTTTTTTTCTTCTTCTTCTCCTCCTTGTCATCTTCTTTATCTGATTTCTTTT
1 CTTTTTTTCTTCTTCTTCTCCTCCTTGTCATCTTCTTTATCTGATTTCTTTT
** ** **
674096 CTTCCTTT-TTCTTCTTCTCCTTGTCATCATCTTCTTTATC
1 CTTTTTTTCTTCTTCTTCTCCTCCTTGTCATCTTCTTTATC
674136 CAGTTTATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 26 0.33
51 28 0.35
52 25 0.32
ACGTcount: A:0.06, C:0.27, G:0.04, T:0.63
Consensus pattern (52 bp):
CTTTTTTTCTTCTTCTTCTCCTCCTTGTCATCTTCTTTATCTGATTTCTTTT
Found at i:674147 original size:51 final size:52
Alignment explanation
Indices: 674025--674162 Score: 131
Period size: 51 Copynumber: 2.7 Consensus size: 52
674015 CTCTTTGTCA
* * * * **
674025 TCTTTATCTGATTTCTTTTCTT-TTTTTCTTCTTCTTCTCCTCCTTGTCATCT
1 TCTTTATCAGATTTATTTTCTTCCTTCT-TTCTTCTTCTCCTCCTCATCATCT
* * **
674077 TCTTTATCTGATTTCTTTTCTTCCTT-TTTCTTCTTCTCCTTGTCATCATCT
1 TCTTTATCAGATTTATTTTCTTCCTTCTTTCTTCTTCTCCTCCTCATCATCT
*
674128 TCTTTATCCAG-TTTATTTTCTTTCTTCTTT-TTCTT
1 TCTTTAT-CAGATTTATTTTCTTCCTTCTTTCTTCTT
674163 TTTTCCATCT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
51 45 0.60
52 28 0.37
53 2 0.03
ACGTcount: A:0.07, C:0.25, G:0.04, T:0.64
Consensus pattern (52 bp):
TCTTTATCAGATTTATTTTCTTCCTTCTTTCTTCTTCTCCTCCTCATCATCT
Found at i:675957 original size:22 final size:22
Alignment explanation
Indices: 675940--676006 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
675930 CTCGTATAAA
675940 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
675962 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
675984 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
676006 T
1 T
676007 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:676267 original size:30 final size:31
Alignment explanation
Indices: 676226--676285 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
676216 TAGACATAGT
*
676226 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
676256 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
676286 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:676342 original size:29 final size:29
Alignment explanation
Indices: 676300--676371 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
676290 TTTTCTGCAT
**
676300 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
676329 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
676358 ATTCATGTCATGTA
1 ATTCATGTCATGTA
676372 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:676813 original size:68 final size:68
Alignment explanation
Indices: 676674--676825 Score: 207
Period size: 68 Copynumber: 2.2 Consensus size: 68
676664 TTTTTCTCAT
* * * * *
676674 GGGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTAGAATATCATATACGA
676739 TGA
66 TGA
* * * *
676742 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTAGAA-ATCATATTCGT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTAGAATATCATATACGA
676806 TGA
66 TGA
*
676809 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
676826 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 27 0.36
68 47 0.64
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTAGAATATCATATACGA
TGA
Found at i:676835 original size:21 final size:21
Alignment explanation
Indices: 676805--676847 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
676795 ATCATATTCG
* *
676805 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
676826 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
676847 T
1 T
676848 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:676837 original size:67 final size:67
Alignment explanation
Indices: 676675--676847 Score: 197
Period size: 68 Copynumber: 2.6 Consensus size: 67
676665 TTTTCTCATG
* * * *
676675 GGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCC-CCCCTGGGGGTACCGATTCCCCTCAAGCAATCTAGAATATCATATACGAT
*
676740 GAG
65 GAA
* * * *
676743 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTAGAA-ATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTAGAATATCATATACGAT
676807 GAA
65 GAA
* *
676810 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
676848 AGCCCGAAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
65 6 0.07
67 39 0.43
68 44 0.48
69 2 0.02
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTAGAATATCATATACGATG
AA
Found at i:694805 original size:31 final size:31
Alignment explanation
Indices: 694767--694834 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
694757 GTTTAAATTT
694767 TGTTTTAGTTAGTATTTTAACTATTTAGATA
1 TGTTTTAGTTAGTATTTTAACTATTTAGATA
*
694798 TGTTTTAGTTAGTGTTTTAACTATTTAGATA
1 TGTTTTAGTTAGTATTTTAACTATTTAGATA
694829 TGTTTT
1 TGTTTT
694835 GATTTACTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (31 bp):
TGTTTTAGTTAGTATTTTAACTATTTAGATA
Found at i:698737 original size:11 final size:12
Alignment explanation
Indices: 698723--698772 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 12
698713 TAATAATAAA
698723 AATATTAATATAAT
1 AATATT-ATAT-AT
*
698737 AATATTA-ATAA
1 AATATTATATAT
698748 AATA-TATATAT
1 AATATTATATAT
698759 AATATATATATAT
1 AATAT-TATATAT
698772 A
1 A
698773 TAATAATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
10 2 0.06
11 12 0.39
12 2 0.06
13 9 0.29
14 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATTATATAT
Found at i:698745 original size:9 final size:8
Alignment explanation
Indices: 698712--698779 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 8
698702 ACATGAGAAA
698712 ATAATAAT
1 ATAATAAT
698720 A-AA-AAT
1 ATAATAAT
698726 AT--TAAT
1 ATAATAAT
698732 ATAATAAT
1 ATAATAAT
698740 AT--TAAT
1 ATAATAAT
*
698746 AAAAT-AT
1 ATAATAAT
698753 ATATATAAT
1 ATA-ATAAT
698762 ATATATATAT
1 ATA-ATA-AT
698772 ATAATAAT
1 ATAATAAT
698780 TACCTTGGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
6 14 0.29
7 6 0.12
8 12 0.24
9 12 0.24
10 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:698960 original size:33 final size:34
Alignment explanation
Indices: 698917--698994 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 34
698907 AGTCCTACTT
* * *
698917 GGACTTAAATACT-TCAGTTTTAGTGTTTTAATA
1 GGACTCAAATACTGTCAGTTTTAGTATTTCAATA
* *
698950 TGACTCAAATA-TGTTAGTTTTAGTATTTCAATA
1 GGACTCAAATACTGTCAGTTTTAGTATTTCAATA
698983 GGACTCAAATAC
1 GGACTCAAATAC
698995 GTTGATTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 1 0.03
33 36 0.97
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (34 bp):
GGACTCAAATACTGTCAGTTTTAGTATTTCAATA
Found at i:699097 original size:24 final size:24
Alignment explanation
Indices: 699050--699113 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
699040 GGGGCCTATA
* *
699050 AAAATAAAAATAAA-AAATTTAAT
1 AAAATAATAATAAATAAATTAAAT
699073 AATAATAATAATAAATAAA-TAAAT
1 AA-AATAATAATAAATAAATTAAAT
699097 -AAAT-ATAATATAATAAA
1 AAAATAATAATA-AATAAA
699114 ATGTTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 6 0.17
22 9 0.25
23 3 0.08
24 15 0.42
25 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATAATAATAAATAAATTAAAT
Found at i:699104 original size:14 final size:14
Alignment explanation
Indices: 699074--699113 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
699064 AAATTTAATA
699074 ATAATAATAATAAAT
1 ATAAT-ATAATAAAT
699089 A-AATA-AATAAAT
1 ATAATATAATAAAT
699101 ATAATATAATAAA
1 ATAATATAATAAA
699114 ATGTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.35
13 5 0.22
14 9 0.39
15 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATATAATAAAT
Found at i:699629 original size:83 final size:81
Alignment explanation
Indices: 699454--699703 Score: 250
Period size: 83 Copynumber: 3.1 Consensus size: 81
699444 AATGGAATCA
* * * * *
699454 AACTCGAAGGT-C-T-TTGGCATATAACCCTTCTTGCCTTGAGCTATGATACAAATGATGGTGCC
1 AACTCGAAGGTCCTTGTTGACAGATAACCCTTCTAGCCTTGAG-TATG-TATAAATGA-CGTGCC
** *
699516 TTTG-AGCTGATTGAAGTCG
63 -TTGAAGCTGAGCGTAGTCG
*
699535 AACTCGGAGGTCCTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGACGTGCCT
1 AACTCGAAGGTCCTTGTTGACAGATAACCCTTCTAGCCTTGAG-TATG-TATAAATGACGTGCCT
699600 TGAAGCTGAGCGTAGTCG
64 TGAAGCTGAGCGTAGTCG
* * * * *
699618 AACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTT--G-A-G--TAAATGATGTGTCTTG
1 AACTCGAAGGTCCTTGTTGACAGATAACCCTTCTAGCCTTGAGTATGTATAAATGACGTGCCTTG
699677 AAGCTGAGCGTAGTCG
66 AAGCTGAGCGTAGTCG
699693 AACTCGAAGGT
1 AACTCGAAGGT
699704 TTGATGTTTC
Statistics
Matches: 147, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
75 40 0.27
78 1 0.01
79 1 0.01
81 11 0.07
82 4 0.03
83 54 0.37
84 36 0.24
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (81 bp):
AACTCGAAGGTCCTTGTTGACAGATAACCCTTCTAGCCTTGAGTATGTATAAATGACGTGCCTTG
AAGCTGAGCGTAGTCG
Found at i:699748 original size:29 final size:29
Alignment explanation
Indices: 699713--699768 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
699703 TTTGATGTTT
*
699713 CAAGAGAAACATTTTCAAAGGTTTTTTTC
1 CAAGAGAAACAATTTCAAAGGTTTTTTTC
* *
699742 CAAGAGAAACAATTTCGAGGGTTTTTT
1 CAAGAGAAACAATTTCAAAGGTTTTTT
699769 GTGTTTCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (29 bp):
CAAGAGAAACAATTTCAAAGGTTTTTTTC
Found at i:699922 original size:37 final size:36
Alignment explanation
Indices: 699770--699976 Score: 219
Period size: 37 Copynumber: 5.8 Consensus size: 36
699760 GGGTTTTTTG
* *
699770 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAATTT
* * *
699806 TGTTTCAAAAGAAACTGTCTC-A-ATA-A-AAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAATTT
* * * *
699838 AG-TTCTAAAAGAAACTGTCTTAAGGGAGACGAAA-TT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGAC-AAATTT
*
699874 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-ATTT
* *
699911 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-ATTT
*
699948 TGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA
699977 GAATAGTGAG
Statistics
Matches: 148, Mismatches: 14, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
31 3 0.02
32 20 0.14
33 2 0.01
34 2 0.01
35 4 0.03
36 44 0.30
37 73 0.49
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAATTT
Found at i:701299 original size:32 final size:32
Alignment explanation
Indices: 701194--701300 Score: 126
Period size: 32 Copynumber: 3.3 Consensus size: 32
701184 ATTGAATTCC
* * * *
701194 CAAATATGCCCCAATATTCGATATTGAATC-T
1 CAAAAATGCCCCAACATTTGATGTTGAATCTT
* *
701225 CAAAAAATGCCCCAACATTTTATGTTAAATCTT
1 C-AAAAATGCCCCAACATTTGATGTTGAATCTT
*
701258 AAAAAATGCCCCAACATTTGATGTTGAATCTT
1 CAAAAATGCCCCAACATTTGATGTTGAATCTT
*
701290 CAAAGATGCCC
1 CAAAAATGCCC
701301 TCATTGTTCC
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
31 1 0.02
32 61 0.97
33 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.30
Consensus pattern (32 bp):
CAAAAATGCCCCAACATTTGATGTTGAATCTT
Found at i:702336 original size:69 final size:69
Alignment explanation
Indices: 702211--702348 Score: 206
Period size: 69 Copynumber: 2.0 Consensus size: 69
702201 TGTCTCTCTC
* * * *
702211 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCAGAAATAATTATGCTTGATCAATC
702276 TCAT
66 TCAT
*
702280 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAATGATTC-GAAAATAATTATGCTTGATCAAT
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCAG-AAATAATTATGCTTGATCAAT
*
702344 TTCAT
65 CTCAT
702349 AGTTTGAATC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
68 1 0.02
69 61 0.98
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCAGAAATAATTATGCTTGATCAATC
TCAT
Found at i:702450 original size:26 final size:27
Alignment explanation
Indices: 702421--702473 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
702411 TTTTTTCTTC
*
702421 ATTTTTCCTTTG-TTTTTTCTCTTTTT
1 ATTTTTCATTTGTTTTTTTCTCTTTTT
*
702447 ATTTTTTATTTGTTTTTTTCTCTTTTT
1 ATTTTTCATTTGTTTTTTTCTCTTTTT
702474 TTTCTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.06, C:0.11, G:0.04, T:0.79
Consensus pattern (27 bp):
ATTTTTCATTTGTTTTTTTCTCTTTTT
Found at i:702452 original size:38 final size:38
Alignment explanation
Indices: 702409--702484 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
702399 TCTTGTCTTC
*
702409 TTTTTTTTCTTCATTTTTCCT-TTGTTTTTTCTCTTTTTA
1 TTTTTTAT-TTCATTTTTCCTCTT-TTTTTTCTCTTTTTA
** *
702448 TTTTTTATTTGTTTTTTTCTCTTTTTTTTCTCTTTTT
1 TTTTTTATTTCATTTTTCCTCTTTTTTTTCTCTTTTT
702485 GTTCTTGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 23 0.72
39 9 0.28
ACGTcount: A:0.04, C:0.13, G:0.03, T:0.80
Consensus pattern (38 bp):
TTTTTTATTTCATTTTTCCTCTTTTTTTTCTCTTTTTA
Found at i:702473 original size:11 final size:11
Alignment explanation
Indices: 702459--702489 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
702449 TTTTTATTTG
702459 TTTTTTTCTCT
1 TTTTTTTCTCT
702470 TTTTTTTCTCT
1 TTTTTTTCTCT
*
702481 TTTTGTTCT
1 TTTTTTTCT
702490 TGATTGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:702484 original size:12 final size:12
Alignment explanation
Indices: 702404--702484 Score: 60
Period size: 12 Copynumber: 6.6 Consensus size: 12
702394 ATGCATCTTG
702404 TCTTCTTTTTTT-
1 TCTT-TTTTTTTC
**
702416 TCTTCATTTTTC
1 TCTTTTTTTTTC
702428 -CTTTGTTTTTTC
1 TCTTT-TTTTTTC
*
702440 TCTTTTTATTTTT
1 TCTTTTT-TTTTC
*
702453 TATTTGTTTTTT-
1 TCTTT-TTTTTTC
702465 TCTCTTTTTTTTC
1 TCT-TTTTTTTTC
702478 TCTTTTT
1 TCTTTTT
702485 GTTCTTGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
11 8 0.15
12 24 0.44
13 21 0.38
14 2 0.04
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (12 bp):
TCTTTTTTTTTC
Found at i:705410 original size:24 final size:25
Alignment explanation
Indices: 705374--705428 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
705364 ATGAGAAAAG
705374 AATAATAAAAAATAT-TA-ATATAAT
1 AATAATAAAAAATATATATATAT-AT
* *
705398 AATATTAATAAATATATATATATAT
1 AATAATAAAAAATATATATATATAT
705423 AATAAT
1 AATAAT
705429 TACCTCGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 13 0.50
25 9 0.35
26 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AATAATAAAAAATATATATATATAT
Found at i:705603 original size:33 final size:33
Alignment explanation
Indices: 705566--705641 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
705556 AGTCCTACTT
705566 GGACTCAAATGC-TTCAGTTTTAGTGTTTCAATA
1 GGACTCAAATGCGTT-AGTTTTAGTGTTTCAATA
*
705599 GGACTCAAATGCGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATGCGTTAGTTTTAGTGTTTCAATA
*
705632 GGAGTCAAAT
1 GGACTCAAAT
705642 ACTTTGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 38 0.95
34 2 0.05
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (33 bp):
GGACTCAAATGCGTTAGTTTTAGTGTTTCAATA
Found at i:705736 original size:31 final size:31
Alignment explanation
Indices: 705701--705760 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
705691 GGCTTGCAAA
705701 AATAAAAAATAAAAAAAT-TAATAATAATAAT
1 AATAAAAAATAAAAAAATATAAT-ATAATAAT
* *
705732 AATAATAAATAAATAAATATAATATAATA
1 AATAAAAAATAAAAAAATATAATATAATA
705761 TTTTTGTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (31 bp):
AATAAAAAATAAAAAAATATAATATAATAAT
Found at i:705915 original size:2 final size:2
Alignment explanation
Indices: 705904--705939 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
705894 TATTAAAAAA
*
705904 AT AT AA AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
705940 CTTATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:709457 original size:57 final size:57
Alignment explanation
Indices: 709369--709482 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
709359 CTTTAGAGAA
*
709369 GGCACGATTACCTGACCACGTCTCTCATTTTAAATAAAGGCCTTATTGGTCTACATT
1 GGCACGATTACCTGACCACGTCTCTCATTTTAAATAAAGGCCTTATTGATCTACATT
*
709426 GGCACGATTACCTGACCACGTCTCTCATTTTAAATAAAGGCCTTGTTGATCTACATT
1 GGCACGATTACCTGACCACGTCTCTCATTTTAAATAAAGGCCTTATTGATCTACATT
709483 TGAAAACCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (57 bp):
GGCACGATTACCTGACCACGTCTCTCATTTTAAATAAAGGCCTTATTGATCTACATT
Found at i:710181 original size:29 final size:29
Alignment explanation
Indices: 710139--710198 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
710129 TAAAGTTACC
* *
710139 TTTTTGGTCAAAATAGGTATTTAAAGTAT
1 TTTTTGGTCAAAATAGGTACTTAAAATAT
*
710168 TTTTTTGTCAAAATAGGTACTTAAAATAT
1 TTTTTGGTCAAAATAGGTACTTAAAATAT
710197 TT
1 TT
710199 AATTTTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (29 bp):
TTTTTGGTCAAAATAGGTACTTAAAATAT
Found at i:713392 original size:111 final size:111
Alignment explanation
Indices: 713255--713476 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
713245 ATTATAAAAA
*
713255 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
713320 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
713366 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
713431 AATTAAAACGTTAAAATGTTACCGTATCAATAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
713477 ATGATTTCTA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:713581 original size:17 final size:18
Alignment explanation
Indices: 713538--713578 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
713528 GAATTATATT
713538 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
713555 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
713573 ATTAAA
1 AGTAAA
713579 TACATAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:713632 original size:12 final size:10
Alignment explanation
Indices: 713618--713658 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
713608 ACATTAAAAA
*
713618 GAGAGTATTT
1 GAGAGAATTT
713628 GAGAGAAATTT
1 GAGAG-AATTT
713639 -AGAGAATTT
1 GAGAGAATTT
713648 GAGAGAATTT
1 GAGAGAATTT
713658 G
1 G
713659 GTGTAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Done.