Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 29
Found at i:3282179 original size:21 final size:21
Alignment explanation
Indices: 3282140--3282180 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3282130 GATAAAAAAT
* * *
3282140 TACCTAAAATATTATTATTTC
1 TACCTAAAACATCAATATTTC
3282161 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
3282181 TTTAACATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:3283847 original size:16 final size:16
Alignment explanation
Indices: 3283826--3283857 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3283816 AATAAATAAG
3283826 CGAACATAAACGAACA
1 CGAACATAAACGAACA
3283842 CGAACATAAACGAACA
1 CGAACATAAACGAACA
3283858 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:3283944 original size:16 final size:16
Alignment explanation
Indices: 3283923--3283977 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
3283913 CATTTAATAA
*
3283923 ATAAACGAACACAAAC
1 ATAAACGAACACGAAC
3283939 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
3283955 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
3283971 ATAAACG
1 ATAAACG
3283978 TTGGAGACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:3285263 original size:27 final size:29
Alignment explanation
Indices: 3285197--3285263 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 29
3285187 GAAGGGAAAG
*
3285197 AGATGAAGCTCTGTCGAATCGTTGCAGTTGA
1 AGATGAAGCTCCGTCGAATCGTTGCA--TGA
3285228 AGACTTGAAGCTCCGTCGAATCGTTGCA-GA
1 AGA--TGAAGCTCCGTCGAATCGTTGCATGA
3285258 A-ATGAA
1 AGATGAA
3285264 AATTGTGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 4 0.12
29 1 0.03
30 3 0.09
31 3 0.09
33 22 0.67
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (29 bp):
AGATGAAGCTCCGTCGAATCGTTGCATGA
Found at i:3285526 original size:24 final size:24
Alignment explanation
Indices: 3285489--3285543 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
3285479 TATTAGGTTA
*
3285489 AACATAAATGAACGCACATAAACG
1 AACATAAATAAACGCACATAAACG
* *
3285513 AACATAACTAAACGCATATAAACG
1 AACATAAATAAACGCACATAAACG
3285537 AACATAA
1 AACATAA
3285544 TCGAACGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.56, C:0.20, G:0.09, T:0.15
Consensus pattern (24 bp):
AACATAAATAAACGCACATAAACG
Found at i:3285550 original size:24 final size:24
Alignment explanation
Indices: 3285489--3285550 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
3285479 TATTAGGTTA
3285489 AACATAAAT-GAACGCACATAAACG
1 AACAT-AATCGAACGCACATAAACG
* *
3285513 AACATAA-CTAAACGCATATAAACG
1 AACATAATC-GAACGCACATAAACG
3285537 AACATAATCGAACG
1 AACATAATCGAACG
3285551 TTCACGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 2 0.06
24 29 0.91
25 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.15
Consensus pattern (24 bp):
AACATAATCGAACGCACATAAACG
Found at i:3285891 original size:26 final size:26
Alignment explanation
Indices: 3285836--3285898 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
3285826 CATTTATTTA
**
3285836 TTTATTTATTAAATTCCTTTTAAATC
1 TTTATTTATTAAATTAATTTTAAATC
* *
3285862 TTTATTTCATTAATTTAATTTT-AATT
1 TTTATTT-ATTAAATTAATTTTAAATC
3285888 TTTA-TTATTAA
1 TTTATTTATTAA
3285899 TCTAGGTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 5 0.16
25 2 0.06
26 14 0.44
27 11 0.34
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTATTTATTAAATTAATTTTAAATC
Found at i:3291620 original size:18 final size:18
Alignment explanation
Indices: 3291593--3291638 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
3291583 ACCTCAGATG
*
3291593 AAAA-AACCCAGAAAGGA
1 AAAACAACCCAAAAAGGA
3291610 AAAACAACCCAAAAAGGA
1 AAAACAACCCAAAAAGGA
3291628 AAAACAACCCA
1 AAAACAACCCA
3291639 TAATAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.65, C:0.24, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAACAACCCAAAAAGGA
Found at i:3293769 original size:54 final size:54
Alignment explanation
Indices: 3293711--3294047 Score: 476
Period size: 54 Copynumber: 6.2 Consensus size: 54
3293701 TTCGTTGCAG
* * * * * * * * **
3293711 TGCACACGTAGTGCCCATACGATCATTCATAAACATATTATGAATTCTGTGGGT
1 TGCACACATAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
*
3293765 TGCACACATAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACATAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * *
3293819 TACATACATAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACATAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * * *
3293873 TACACACATAGTTCCGAAACGGTTATTCATCAACATATGATGAATTCTGTAAAT
1 TGCACACATAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* *
3293927 TGCACACATAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGGGAAT
1 TGCACACATAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* *
3293981 TGCACACATAGTGTCAAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACATAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
3294035 TGCACACATAGTG
1 TGCACACATAGTG
3294048 TCTTTTTGGT
Statistics
Matches: 255, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 255 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (54 bp):
TGCACACATAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
Found at i:3293827 original size:27 final size:27
Alignment explanation
Indices: 3293797--3293882 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
3293787 TTATTCATCA
3293797 ACATATGATGAATTCCGTGAATTACAT
1 ACATATGATGAATTCCGTGAATTACAT
* * *
3293824 ACATAGTG-TCGAA-ACGGT-TATT-CAT
1 ACATA-TGAT-GAATTCCGTGAATTACAT
*
3293849 CAACATATGATGAATTCCGTGAATTACAC
1 --ACATATGATGAATTCCGTGAATTACAT
3293878 ACATA
1 ACATA
3293883 GTTCCGAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 23 0.52
28 8 0.18
29 2 0.05
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (27 bp):
ACATATGATGAATTCCGTGAATTACAT
Found at i:3294395 original size:20 final size:20
Alignment explanation
Indices: 3294367--3294406 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3294357 GTTCCAGGCT
3294367 CCATAGTATCGATACCTCTA
1 CCATAGTATCGATACCTCTA
* * *
3294387 CCATGGTATCTATACTTCTA
1 CCATAGTATCGATACCTCTA
3294407 TACTATGGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (20 bp):
CCATAGTATCGATACCTCTA
Found at i:3294423 original size:22 final size:22
Alignment explanation
Indices: 3294389--3294466 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 22
3294379 TACCTCTACC
* *
3294389 ATGGTATCTATACTTCTATACT
1 ATGGTACCGATACTTCTATACT
*
3294411 ATGGTACCGATACATT-TCT-CT
1 ATGGTACCGATAC-TTCTATACT
* * *
3294432 CA--GTATCGATACTACTACACT
1 -ATGGTACCGATACTTCTATACT
3294453 ATGGTACCGATACT
1 ATGGTACCGATACT
3294467 CCCTTTTGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
19 1 0.02
20 11 0.26
21 4 0.10
22 24 0.57
23 2 0.05
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (22 bp):
ATGGTACCGATACTTCTATACT
Found at i:3300460 original size:11 final size:11
Alignment explanation
Indices: 3300446--3300494 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
3300436 GAAATTTTGG
*
3300446 CTTTTTTGGCT
1 CTTTTTTTGCT
3300457 CTTTTTTTG--
1 CTTTTTTTGCT
3300466 -TTTTTTTGCT
1 CTTTTTTTGCT
*
3300476 TTTTTTTTGC-
1 CTTTTTTTGCT
3300486 CTTTTTTTG
1 CTTTTTTTG
3300495 TTTTTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 8 0.24
10 8 0.24
11 17 0.52
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (11 bp):
CTTTTTTTGCT
Found at i:3300469 original size:19 final size:19
Alignment explanation
Indices: 3300447--3300484 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3300437 AAATTTTGGC
3300447 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGCTCTTTTTTTG
* *
3300466 TTTTTTTGCTTTTTTTTTG
1 TTTTTTGGCTCTTTTTTTG
3300485 CCTTTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.13, T:0.79
Consensus pattern (19 bp):
TTTTTTGGCTCTTTTTTTG
Found at i:3300472 original size:29 final size:28
Alignment explanation
Indices: 3300447--3300510 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
3300437 AAATTTTGGC
3300447 TTTTTTGGCTCTTTTTTTGTTTTTTTGCTT
1 TTTTTTGGC-CTTTTTTTGTTTTTTTGC-T
* *
3300477 TTTTTTTGCCTTTTTTTG-TTTTTTGTT
1 TTTTTTGGCCTTTTTTTGTTTTTTTGCT
3300504 TTTTTTG
1 TTTTTTG
3300511 TTTTTTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 7 0.23
28 7 0.23
29 9 0.29
30 8 0.26
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (28 bp):
TTTTTTGGCCTTTTTTTGTTTTTTTGCT
Found at i:3300481 original size:9 final size:8
Alignment explanation
Indices: 3300458--3300518 Score: 61
Period size: 8 Copynumber: 7.0 Consensus size: 8
3300448 TTTTTGGCTC
3300458 TTTTTTTG
1 TTTTTTTG
3300466 TTTTTTTG
1 TTTTTTTG
3300474 CTTTTTTTTTG
1 ---TTTTTTTG
3300485 CCTTTTTTTG
1 --TTTTTTTG
3300495 -TTTTTTG
1 TTTTTTTG
3300502 TTTTTTTTG
1 -TTTTTTTG
3300511 TTTTTTTG
1 TTTTTTTG
3300519 AAAAAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
7 7 0.15
8 16 0.35
9 7 0.15
10 8 0.17
11 8 0.17
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:3300490 original size:19 final size:20
Alignment explanation
Indices: 3300448--3300491 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3300438 AATTTTGGCT
*
3300448 TTTTTGGCTCTTTTTTTG-T
1 TTTTTGGCTCTTTTTTTGCC
* *
3300467 TTTTTTGCTTTTTTTTTGCC
1 TTTTTGGCTCTTTTTTTGCC
3300487 TTTTT
1 TTTTT
3300492 TTGTTTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.77
Consensus pattern (20 bp):
TTTTTGGCTCTTTTTTTGCC
Found at i:3302429 original size:25 final size:25
Alignment explanation
Indices: 3302392--3302467 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
3302382 TACAAAACAA
3302392 GTAA-TAAATAAACATGGAAATAAAG
1 GTAACTAAA-AAACATGGAAATAAAG
* *
3302417 GTAACTAAAAAACA-AGTAATAAAAG
1 GTAACTAAAAAACATGGAAAT-AAAG
*
3302442 GTAACTAAAAATCATAGGAAATAAAG
1 GTAACTAAAAAACAT-GGAAATAAAG
3302468 TTTGACTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 4 0.10
25 26 0.62
26 8 0.19
27 4 0.10
ACGTcount: A:0.61, C:0.07, G:0.14, T:0.18
Consensus pattern (25 bp):
GTAACTAAAAAACATGGAAATAAAG
Found at i:3306811 original size:18 final size:18
Alignment explanation
Indices: 3306785--3306826 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
3306775 CTGTTATTGG
*
3306785 TGTATTGGTTGTATCTTA
1 TGTAATGGTTGTATCTTA
3306803 TGTAATGGTTGTATCTTA
1 TGTAATGGTTGTATCTTA
3306821 TGTAAT
1 TGTAAT
3306827 TTTTCATTAT
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:0.21, C:0.05, G:0.21, T:0.52
Consensus pattern (18 bp):
TGTAATGGTTGTATCTTA
Found at i:3313319 original size:186 final size:184
Alignment explanation
Indices: 3313122--3313614 Score: 833
Period size: 186 Copynumber: 2.7 Consensus size: 184
3313112 AATATATAAT
*
3313122 TATAAATTTTTTAATTAATTAATATTGATATAGGTTTAAAAGTTATTAGATCTTAAATTATTAAT
1 TATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT-GATCTTAAATTATTAAT
** *
3313187 TGGGTTTTAAATTATTTGAACTGAACTCGTATGTTATATATAATATATTTAATATTTTTTAATTT
65 TGGGTTTTAAATGGTTTG-GCTGAACTCGTATGTTATATATAATATATTTAATATTTTTTAATTT
*
3313252 AGAAAAACAGTTTACAATTAATTTAAATAATATATAATTACAAAATAAAAATTTTA
129 AGAAAAACAGTTTACAATTAATTTAAATAATATATAATTACAAAATAAAAAATTTA
*
3313308 TATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCATAAATTATTAAT
1 TATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT-GATCTTAAATTATTAAT
* * *
3313373 TGGGTTTTAAATGGTTTGGGTTAAGTCCGTATGTTATATATAATATATTTAATATTTTTTAATTT
65 TGGGTTTTAAATGGTTTGGCTGAACT-CGTATGTTATATATAATATATTTAATATTTTTTAATTT
*
3313438 AGAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTTA
129 AGAAAAACAGTTTACAATTAATTTAAATAATATATAATTACAAAATAAAAAATTTA
3313494 TATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGATCTTAAATTATTAATT
1 TATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGATCTTAAATTATTAATT
* *
3313559 GGGTTTTAAATGGTTTGGGCTGAGCTCATATGTTATATATAATATATTTAATATTT
66 GGGTTTTAAATGGTTT-GGCTGAACTCGTATGTTATATATAATATATTTAATATTT
3313615 AAAATTTTAT
Statistics
Matches: 288, Mismatches: 17, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
185 66 0.23
186 222 0.77
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (184 bp):
TATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGATCTTAAATTATTAATT
GGGTTTTAAATGGTTTGGCTGAACTCGTATGTTATATATAATATATTTAATATTTTTTAATTTAG
AAAAACAGTTTACAATTAATTTAAATAATATATAATTACAAAATAAAAAATTTA
Found at i:3314219 original size:3 final size:3
Alignment explanation
Indices: 3314211--3314235 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3314201 TCCGTTAACC
3314211 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
3314236 AAATTACTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3321250 original size:21 final size:21
Alignment explanation
Indices: 3321226--3321265 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3321216 AAAAGTAAAG
3321226 GTTAAAAATGAAAGAGAAATA
1 GTTAAAAATGAAAGAGAAATA
*
3321247 GTTAATAATGAAAGAGAAA
1 GTTAAAAATGAAAGAGAAA
3321266 AGAAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (21 bp):
GTTAAAAATGAAAGAGAAATA
Found at i:3331923 original size:20 final size:20
Alignment explanation
Indices: 3331898--3331935 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3331888 TATTTGGCAG
*
3331898 AGGGAATCGATACCCCCATA
1 AGGGAACCGATACCCCCATA
3331918 AGGGAACCGATACCCCCA
1 AGGGAACCGATACCCCCA
3331936 CGGGTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.34, G:0.21, T:0.11
Consensus pattern (20 bp):
AGGGAACCGATACCCCCATA
Found at i:3333682 original size:16 final size:17
Alignment explanation
Indices: 3333648--3333682 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3333638 TAACAAAAAG
3333648 GGGGAGAAGTGTTTTAAA
1 GGGGAGAAGTG-TTTAAA
3333666 GGGGAGAAGTG-TTAAA
1 GGGGAGAAGTGTTTAAA
3333682 G
1 G
3333683 TAAGGGGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
18 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.43, T:0.23
Consensus pattern (17 bp):
GGGGAGAAGTGTTTAAA
Found at i:3338188 original size:33 final size:32
Alignment explanation
Indices: 3338143--3338225 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 32
3338133 TAATGCTTAC
3338143 TTTATTTTTGTTAATTTGGTTGGATTTTT-TTAAA
1 TTTA-TTTTGTTAATTT-GTTGGATTTTTGTT-AA
3338177 TTTATTTTGTTAATATTGTTGGATTTTTGTTAA
1 TTTATTTTGTTAAT-TTGTTGGATTTTTGTTAA
* *
3338210 TATATTTGGTTAATTT
1 TTTATTTTGTTAATTT
3338226 TGTTTATTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
32 2 0.04
33 35 0.78
34 8 0.18
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.64
Consensus pattern (32 bp):
TTTATTTTGTTAATTTGTTGGATTTTTGTTAA
Found at i:3338218 original size:20 final size:20
Alignment explanation
Indices: 3338146--3338212 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
3338136 TGCTTACTTT
3338146 ATTTTTGTTAAT-TTGGTTGG
1 ATTTTTGTTAATATT-GTTGG
3338166 ATTTTT-TTAA-A-T-TT--
1 ATTTTTGTTAATATTGTTGG
3338180 A-TTTTGTTAATATTGTTGG
1 ATTTTTGTTAATATTGTTGG
3338199 ATTTTTGTTAATAT
1 ATTTTTGTTAATAT
3338213 ATTTGGTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
13 4 0.10
14 5 0.13
15 1 0.03
16 3 0.08
17 2 0.05
18 1 0.03
19 5 0.13
20 18 0.46
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (20 bp):
ATTTTTGTTAATATTGTTGG
Found at i:3343656 original size:30 final size:29
Alignment explanation
Indices: 3343592--3343656 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
3343582 GACTAAAATA
* * *
3343592 TAATTTTGAAAGTTTAGTGACCAAAGTAG
1 TAATTTGGAAAATTTAATGACCAAAGTAG
* *
3343621 AAATTTGGAAAATTTCAATGACCAAAGTGG
1 TAATTTGGAAAATTT-AATGACCAAAGTAG
3343651 TAATTT
1 TAATTT
3343657 TCCCCAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (29 bp):
TAATTTGGAAAATTTAATGACCAAAGTAG
Found at i:3344813 original size:26 final size:26
Alignment explanation
Indices: 3344781--3344834 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
3344771 AAAATGAAAC
*
3344781 TAAAAGAAATAGTACCGTAAAAAATA
1 TAAAAGAAATAGTACAGTAAAAAATA
*
3344807 TAAAAGATATAGTACAGTAAAAAATA
1 TAAAAGAAATAGTACAGTAAAAAATA
3344833 TA
1 TA
3344835 GAATAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.22
Consensus pattern (26 bp):
TAAAAGAAATAGTACAGTAAAAAATA
Found at i:3344833 original size:17 final size:17
Alignment explanation
Indices: 3344807--3344847 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3344797 GTAAAAAATA
* *
3344807 TAAAAGATATAGTACAG
1 TAAAAAATATAGAACAG
*
3344824 TAAAAAATATAGAATAG
1 TAAAAAATATAGAACAG
3344841 TAAAAAA
1 TAAAAAA
3344848 ATTAGTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.22
Consensus pattern (17 bp):
TAAAAAATATAGAACAG
Found at i:3353811 original size:21 final size:21
Alignment explanation
Indices: 3353763--3353815 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3353753 ATGGAGAAAA
*
3353763 AGAAGAAGAAGAAGAAGGATG
1 AGAAGAAGAAGAAGAAGAATG
3353784 AGAAGAAGAAGAAGAAGAACT-
1 AGAAGAAGAAGAAGAAGAA-TG
*
3353805 AGTAGAAGAAG
1 AGAAGAAGAAG
3353816 GATTAATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.34, T:0.06
Consensus pattern (21 bp):
AGAAGAAGAAGAAGAAGAATG
Found at i:3353815 original size:3 final size:3
Alignment explanation
Indices: 3353757--3353802 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
3353747 AAAAGAATGG
* *
3353757 AGA AAA AGA AGA AGA AGA AGA AGGA TG- AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA
3353802 A
1 A
3353803 CTAGTAGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.92
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:3354785 original size:26 final size:25
Alignment explanation
Indices: 3354717--3354891 Score: 80
Period size: 24 Copynumber: 6.7 Consensus size: 25
3354707 TTTTTAGTGC
* *
3354717 TTTTAATAAAATATAAATTATTAA-AA
1 TTTTAAT--AATATATATTATTAATTA
3354743 TATTTAA-AATATA-ATTATTAATTA
1 T-TTTAATAATATATATTATTAATTA
3354767 TTTTAATAATAT-TA-TATTATATT-
1 TTTTAATAATATATATTATTA-ATTA
*
3354790 TGTTTAATATTATACTAATATATTCAATTA
1 T-TTTAATAATATA-T-AT-TATT-AATTA
* * *
3354820 TATT-ATAATA-ATATAATCAATTA
1 TTTTAATAATATATATTATTAATTA
3354843 TATTATAATAATATATGA-TATTATATTTTTA
1 T-TT-TAATAATATAT-ATTATTA-A---TTA
*
3354874 TGTTAATAATATATATTA
1 TTTTAATAATATATATTA
3354892 ATAAAATTTA
Statistics
Matches: 116, Mismatches: 10, Indels: 43
0.69 0.06 0.25
Matches are distributed among these distances:
23 25 0.22
24 30 0.26
25 3 0.03
26 9 0.08
27 12 0.10
28 8 0.07
29 22 0.19
30 3 0.03
31 4 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTTAATAATATATATTATTAATTA
Found at i:3354832 original size:23 final size:23
Alignment explanation
Indices: 3354796--3354858 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
3354786 TATTTGTTTA
*
3354796 ATATTATACTAATATATTCAATT
1 ATATTATAATAATATATTCAATT
*
3354819 ATATTATAATAATATAATCAATT
1 ATATTATAATAATATATTCAATT
3354842 ATATTATAATAATATAT
1 ATATTATAATAATATAT
3354859 GATATTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATTATAATAATATATTCAATT
Found at i:3354865 original size:23 final size:22
Alignment explanation
Indices: 3354796--3354869 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 22
3354786 TATTTGTTTA
*
3354796 ATATTATACTAATATATTCAATT
1 ATATTATAATAATATA-TCAATT
3354819 ATATTATAATAATATAATCAATT
1 ATATTATAATAATAT-ATCAATT
*
3354842 ATATTATAATAATATATGATATT
1 ATATTATAATAATATATCA-ATT
3354865 ATATT
1 ATATT
3354870 TTTATGTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
22 3 0.06
23 43 0.91
24 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (22 bp):
ATATTATAATAATATATCAATT
Found at i:3355312 original size:21 final size:21
Alignment explanation
Indices: 3355288--3355328 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3355278 TATATATAAT
*
3355288 ATTTTAAAAATAATAATATTG
1 ATTTTAAAAATAACAATATTG
* *
3355309 ATTTTTATAATAACAATATT
1 ATTTTAAAAATAACAATATT
3355329 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTTTAAAAATAACAATATTG
Found at i:3355336 original size:21 final size:21
Alignment explanation
Indices: 3355296--3355336 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3355286 ATATTTTAAA
*
3355296 AATAATAATATTGATTTTTAT
1 AATAACAATATTGATTTTTAT
3355317 AATAACAATATT-ATTATTTA
1 AATAACAATATTGATT-TTTA
3355337 GTCTATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AATAACAATATTGATTTTTAT
Found at i:3357176 original size:11 final size:11
Alignment explanation
Indices: 3357160--3357187 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3357150 GGTTTATAGT
3357160 GTTTTATCAAA
1 GTTTTATCAAA
3357171 GTTTTATCAAA
1 GTTTTATCAAA
3357182 GTTTTA
1 GTTTTA
3357188 GGATTGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (11 bp):
GTTTTATCAAA
Found at i:3358677 original size:13 final size:14
Alignment explanation
Indices: 3358645--3358680 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3358635 TTCAAAAATA
3358645 TATTAAAAATACGT
1 TATTAAAAATACGT
*
3358659 TATTAAAAATATGT
1 TATTAAAAATACGT
3358673 T-TTAAAAA
1 TATTAAAAA
3358681 GTTATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (14 bp):
TATTAAAAATACGT
Found at i:3358718 original size:57 final size:57
Alignment explanation
Indices: 3358654--3358761 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
3358644 ATATTAAAAA
* *
3358654 TACGTTATTAAAAATATGTTTTAAAAAGT-TA-TATT-ATAATTTTAAATTTTTTAAATT
1 TACGTTATTAAAAATA--TATTAAAAA-TATATTATTGATAATTATAAATTTTTTAAATT
3358711 TACGTTATTAAAAATATATTAAAAATATATTATTGATAATTATAAATTTTT
1 TACGTTATTAAAAATATATTAAAAATATATTATTGATAATTATAAATTTTT
3358762 AAAAATATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
54 1 0.02
55 10 0.22
56 4 0.09
57 31 0.67
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (57 bp):
TACGTTATTAAAAATATATTAAAAATATATTATTGATAATTATAAATTTTTTAAATT
Found at i:3358732 original size:11 final size:11
Alignment explanation
Indices: 3358716--3358772 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
3358706 AAATTTACGT
3358716 TATTAAAAATA
1 TATTAAAAATA
3358727 TATTAAAAATA
1 TATTAAAAATA
***
3358738 TATTATTGATA
1 TATTAAAAATA
*
3358749 -ATTATAAAT-
1 TATTAAAAATA
*
3358758 TTTTAAAAATA
1 TATTAAAAATA
3358769 TATT
1 TATT
3358773 TTTAAATGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 14 0.39
11 22 0.61
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:3358834 original size:23 final size:23
Alignment explanation
Indices: 3358808--3358882 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
3358798 AGGTTCAAAT
* *
3358808 TCGAGTTTGAGTTCGAGCTTGAA
1 TCGAGTTTGAGTTCGAGTTTTAA
** **
3358831 TCGAGTTCAAAATCGAGTTTTAA
1 TCGAGTTTGAGTTCGAGTTTTAA
*
3358854 TCGAGCTTGAGTCTCGAGTTTTAA
1 TCGAGTTTGAGT-TCGAGTTTTAA
3358878 TCGAG
1 TCGAG
3358883 CTCTTAATTT
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 24 0.60
24 16 0.40
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (23 bp):
TCGAGTTTGAGTTCGAGTTTTAA
Found at i:3363001 original size:31 final size:32
Alignment explanation
Indices: 3362966--3363028 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
3362956 TAATTTGCCG
*
3362966 CCCATGTTTCCAACCACCC-AGTTGCCAAAGA
1 CCCATGGTTCCAACCACCCAAGTTGCCAAAGA
* *
3362997 CCCATGGTTCCAGCCGCCCAAGTTGCCAAAGA
1 CCCATGGTTCCAACCACCCAAGTTGCCAAAGA
3363029 ATTTTGCAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.27, C:0.38, G:0.17, T:0.17
Consensus pattern (32 bp):
CCCATGGTTCCAACCACCCAAGTTGCCAAAGA
Found at i:3376144 original size:29 final size:30
Alignment explanation
Indices: 3376075--3376133 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3376065 AATTTAAGGC
3376075 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
3376106 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
3376134 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:3376314 original size:21 final size:21
Alignment explanation
Indices: 3376270--3376367 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
3376260 AATACAATTA
***
3376270 GTGCATCGATGCATC-CTTCT
1 GTGCATCGATGCATCAAGGCT
3376290 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
3376311 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
3376332 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
*
3376353 GTGCATCAATGCATC
1 GTGCATCGATGCATC
3376368 CTGCTATGCA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
20 15 0.21
21 58 0.79
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.27
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:3376578 original size:13 final size:13
Alignment explanation
Indices: 3376560--3376605 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
3376550 AAACACATTC
3376560 CAAGCTATAAATA
1 CAAGCTATAAATA
3376573 CAAGCTATAAATA
1 CAAGCTATAAATA
*
3376586 CAAGTTATAAATA
1 CAAGCTATAAATA
3376599 CAAGCTA
1 CAAGCTA
3376606 AGGACACTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (13 bp):
CAAGCTATAAATA
Found at i:3379365 original size:27 final size:27
Alignment explanation
Indices: 3379334--3379388 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3379324 TGATTTTTCC
3379334 AATAAGTTTTAAAATGTCAAATTTAAT
1 AATAAGTTTTAAAATGTCAAATTTAAT
3379361 AATAAGTTTTAAAATGTCAAATTTAAT
1 AATAAGTTTTAAAATGTCAAATTTAAT
3379388 A
1 A
3379389 CTTATTCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (27 bp):
AATAAGTTTTAAAATGTCAAATTTAAT
Found at i:3379800 original size:21 final size:21
Alignment explanation
Indices: 3379774--3379830 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
3379764 AGGGTGTCCA
* *
3379774 AGTGCATTCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
*
3379795 AGTGCATCCATGCATCCCTAC
1 AGTGCATCCATGCACCCCTAC
3379816 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3379831 TCAAACACCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:3379880 original size:20 final size:20
Alignment explanation
Indices: 3379855--3379924 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
3379845 CAATTAGTGC
*
3379855 ATCGATGCATCCTTCTGTGT
1 ATCGATGCATCCTACTGTGT
** *
3379875 ATCGATGCATCAAGACTGTGC
1 ATCGATGCATC-CTACTGTGT
* *
3379896 ATCGATACATCCTGCTGTGT
1 ATCGATGCATCCTACTGTGT
*
3379916 ATCCATGCA
1 ATCGATGCA
3379925 CGAAGGCTGC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (20 bp):
ATCGATGCATCCTACTGTGT
Found at i:3379899 original size:21 final size:20
Alignment explanation
Indices: 3379851--3379906 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
3379841 AATGCAATTA
***
3379851 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCAGACT
*
3379871 GTGTATCGATGCATCAAGACT
1 GTGCATCGATGCATC-AGACT
*
3379892 GTGCATCGATACATC
1 GTGCATCGATGCATC
3379907 CTGCTGTGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCAGACT
Found at i:3380107 original size:32 final size:34
Alignment explanation
Indices: 3380045--3380107 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
3380035 AAAAATCATC
* *
3380045 GTTCTAGCTTATCCCGTGTAAAAGCTAGGGAAAG
1 GTTCTAGCTTAGCCCGTGTAAAAACTAGGGAAAG
*
3380079 GTTCTAGTTTAGCCCG-G-AAAAACTAGGGA
1 GTTCTAGCTTAGCCCGTGTAAAAACTAGGGA
3380108 GTTGTAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 11 0.42
33 1 0.04
34 14 0.54
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (34 bp):
GTTCTAGCTTAGCCCGTGTAAAAACTAGGGAAAG
Found at i:3382098 original size:21 final size:21
Alignment explanation
Indices: 3382083--3382137 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
3382073 GATTAGGTGC
3382083 CCTTGGTCCTGCATTAGGCAG
1 CCTTGGTCCTGCATTAGGCAG
3382104 CCTTGGTCCTGCATTAGGCAG
1 CCTTGGTCCTGCATTAGGCAG
*
3382125 CCTTGTTCCTGCA
1 CCTTGGTCCTGCA
3382138 GTAGTAGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.13, C:0.31, G:0.25, T:0.31
Consensus pattern (21 bp):
CCTTGGTCCTGCATTAGGCAG
Found at i:3384246 original size:21 final size:21
Alignment explanation
Indices: 3384222--3384316 Score: 70
Period size: 21 Copynumber: 4.4 Consensus size: 21
3384212 AACAATTCTC
3384222 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAATCCT
* *
3384243 TTCATGAAAAGGTTAAGCAT-TT
1 TTCATGAAAAGATTAA--ATCCT
* *
3384265 TTCATCAAAAGGA-TAAGTCCT
1 TTCATGAAAA-GATTAAATCCT
* *
3384286 TTAATTG-AAAGATTAAGTCCT
1 TTCA-TGAAAAGATTAAATCCT
3384307 TTCATCGAAA
1 TTCAT-GAAA
3384317 GGTCTTAACC
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
20 4 0.07
21 34 0.60
22 16 0.28
23 3 0.05
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (21 bp):
TTCATGAAAAGATTAAATCCT
Found at i:3384929 original size:21 final size:21
Alignment explanation
Indices: 3384877--3384936 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
3384867 CGATTAAAGA
* *
3384877 CTTATCCTTTTGATGAAAAGTG
1 CTTAACCTTTTAATG-AAAGTG
*
3384899 CTTAACCTTTTCATGAAAG-G
1 CTTAACCTTTTAATGAAAGTG
*
3384919 CTGTAATCTTTTAATGAA
1 CT-TAACCTTTTAATGAA
3384937 GAGAATTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.09
21 17 0.52
22 13 0.39
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
CTTAACCTTTTAATGAAAGTG
Found at i:3385501 original size:210 final size:211
Alignment explanation
Indices: 3385134--3385553 Score: 817
Period size: 210 Copynumber: 2.0 Consensus size: 211
3385124 GGCATCATAT
3385134 TATTTTTTAGACTAACTCTACAAAGGTTGTCAATAAAGTTCAGCGCGGGATAACAATATTTCCAC
1 TATTTTTTAGACTAACTCTACAAAGGTTGTCAATAAAGTTCAGCGCGGGATAACAATATTTCCAC
3385199 TTAGGCTTTCTATTCCAGGATGCTCATGTTCTCTTGTATTCTAATGTACATTTTACTGTCCATCA
66 TTAGGCTTTCTATTCCAGGATGCTCATGTTCTCTTGTATTCTAATGTACATTTTACTGTCCATCA
3385264 TAATCCTAGAACATGTAATCTAGTTGCGCACAAGTTAGCATCATGGGCACCTA-GTTTGGGAGTT
131 TAATCCTAGAACATGTAATCTAGTTGCGCACAAGTTAGCATCATGGGCACCTAGGTTTGGGAGTT
3385328 CTTTGTTTTTTTTTTA
196 CTTTGTTTTTTTTTTA
3385344 TATTATTTTAGACTAACTCTACAAAGGTTGTCAATAAAG-TCAGCGCGGGATAACAATATTTCCA
1 TATT-TTTTAGACTAACTCTACAAAGGTTGTCAATAAAGTTCAGCGCGGGATAACAATATTTCCA
3385408 CTTAGGCTTTCTATTCCAGGATGCTCATGTTCTCTTGTATTCTAATGTACATTTTACTGTCCATC
65 CTTAGGCTTTCTATTCCAGGATGCTCATGTTCTCTTGTATTCTAATGTACATTTTACTGTCCATC
3385473 ATAATCCTAGAACATGTAATCTAGTTGCGCACAAGTTAGCATCATGGGCACCTAGGTTTGGGAGT
130 ATAATCCTAGAACATGTAATCTAGTTGCGCACAAGTTAGCATCATGGGCACCTAGGTTTGGGAGT
3385538 TCTTTGTTTTTTTTTT
195 TCTTTGTTTTTTTTTT
3385554 TTTGACTTGG
Statistics
Matches: 208, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
210 148 0.71
211 60 0.29
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (211 bp):
TATTTTTTAGACTAACTCTACAAAGGTTGTCAATAAAGTTCAGCGCGGGATAACAATATTTCCAC
TTAGGCTTTCTATTCCAGGATGCTCATGTTCTCTTGTATTCTAATGTACATTTTACTGTCCATCA
TAATCCTAGAACATGTAATCTAGTTGCGCACAAGTTAGCATCATGGGCACCTAGGTTTGGGAGTT
CTTTGTTTTTTTTTTA
Found at i:3386806 original size:24 final size:24
Alignment explanation
Indices: 3386770--3386817 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3386760 ACAAAGGAAA
3386770 AAACACATATTTCCTTCTTATTAT
1 AAACACATATTTCCTTCTTATTAT
* *
3386794 AAACGCATGTTTCCTTCTTATTAT
1 AAACACATATTTCCTTCTTATTAT
3386818 TTCACACACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (24 bp):
AAACACATATTTCCTTCTTATTAT
Found at i:3393218 original size:23 final size:24
Alignment explanation
Indices: 3393170--3393220 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
3393160 TCATAAATTT
3393170 CATAAACATAAGCATGCTAGACAA
1 CATAAACATAAGCATGCTAGACAA
*
3393194 CATAAACA-AAG-ATGCATAGATAA
1 CATAAACATAAGCATGC-TAGACAA
3393217 CATA
1 CATA
3393221 TATATTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 4 0.16
23 13 0.52
24 8 0.32
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (24 bp):
CATAAACATAAGCATGCTAGACAA
Found at i:3394245 original size:6 final size:6
Alignment explanation
Indices: 3394234--3394262 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3394224 ATAAAACATA
3394234 ATAATT ATAATT ATAATT ATAATT ATAAT
1 ATAATT ATAATT ATAATT ATAATT ATAAT
3394263 GAGCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:3397779 original size:2 final size:2
Alignment explanation
Indices: 3397772--3397800 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3397762 GTTATATGTG
3397772 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
3397801 TCTTGTTTCA
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:3416940 original size:21 final size:22
Alignment explanation
Indices: 3416900--3416951 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
3416890 GGGCTTGTAC
*
3416900 TTAATAATGTTATTTTTTATTTT
1 TTAATAATATTA-TTTTTATTTT
3416923 TTAATAATATTA-TTTTATTTT
1 TTAATAATATTATTTTTATTTT
*
3416944 TCAATAAT
1 TTAATAAT
3416952 GGTGTGACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 16 0.59
23 11 0.41
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTAATAATATTATTTTTATTTT
Found at i:3417009 original size:12 final size:12
Alignment explanation
Indices: 3416992--3417039 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
3416982 AAATGAGTTA
3416992 TTAAAATAAAAT
1 TTAAAATAAAAT
3417004 TTAAAAT-AAAT
1 TTAAAATAAAAT
*
3417015 ATT-AAATATAATT
1 -TTAAAATA-AAAT
3417028 TTAAAATAAAAT
1 TTAAAATAAAAT
3417040 AAAATTAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
11 8 0.27
12 14 0.47
13 8 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAATAAAAT
Found at i:3417040 original size:25 final size:24
Alignment explanation
Indices: 3416974--3417044 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
3416964 TTATATTGTA
**
3416974 AAATTTTAAAATGAGTTATTAAAAT
1 AAATTTTAAAAT-AAATATTAAAAT
*
3416999 AAAATTTAAAATAAATATT-AAAT
1 AAATTTTAAAATAAATATTAAAAT
3417022 ATAATTTTAAAATAAA-A-TAAAAT
1 A-AATTTTAAAATAAATATTAAAAT
3417045 TAGTAAAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 1 0.03
23 10 0.25
24 18 0.45
25 11 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
AAATTTTAAAATAAATATTAAAAT
Found at i:3417452 original size:14 final size:14
Alignment explanation
Indices: 3417433--3417462 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3417423 AAGTGCACAT
3417433 TTGTTAGACTGCTG
1 TTGTTAGACTGCTG
3417447 TTGTTAGACTGCTG
1 TTGTTAGACTGCTG
3417461 TT
1 TT
3417463 AAAGAACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.27, T:0.47
Consensus pattern (14 bp):
TTGTTAGACTGCTG
Found at i:3417486 original size:26 final size:27
Alignment explanation
Indices: 3417456--3417509 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3417446 GTTGTTAGAC
*
3417456 TGCTGTTAAAG-AACATGCACGTGTAT
1 TGCTGTTAAAGAAACATGCACATGTAT
*
3417482 TGCTGTTAAAGAAATATGCACATGTAT
1 TGCTGTTAAAGAAACATGCACATGTAT
3417509 T
1 T
3417510 CAATAAGCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (27 bp):
TGCTGTTAAAGAAACATGCACATGTAT
Found at i:3418810 original size:69 final size:69
Alignment explanation
Indices: 3418699--3418837 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
3418689 GATTCATTCT
*
3418699 GATGATAAAACAACACCTCATTCTTCTTCAGGGAATGAGGGTCCCCGAGCTTTTGAGCAAAGTCA
1 GATGATAAAACAACACCTCATTCTTCTTCAGGGAATGAGGGTCCCCGAGCTTCTGAGCAAAGTCA
3418764 AATA
66 AATA
3418768 GATGATAAAACAACACCTCATTCTTCTTCAGGGAATGAGGGTCCCCGAGCTTCTGAGCAAAGTCA
1 GATGATAAAACAACACCTCATTCTTCTTCAGGGAATGAGGGTCCCCGAGCTTCTGAGCAAAGTCA
3418833 AATA
66 AATA
3418837 G
1 G
3418838 TAGTTAATCA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (69 bp):
GATGATAAAACAACACCTCATTCTTCTTCAGGGAATGAGGGTCCCCGAGCTTCTGAGCAAAGTCA
AATA
Found at i:3419116 original size:35 final size:36
Alignment explanation
Indices: 3419070--3419208 Score: 156
Period size: 35 Copynumber: 3.9 Consensus size: 36
3419060 GAATACGTCA
**
3419070 AACGGAAGGAAGTATCGTTACTTTCGATTCAAG-TG
1 AACGGAAGGAAGTATCGACACTTTCGATTCAAGATG
* * * *
3419105 AACGGAAGGAAGCATCGGCACTTTCGATTCTAGAAG
1 AACGGAAGGAAGTATCGACACTTTCGATTCAAGATG
* *
3419141 AACGAAAGGAAGTATCGACACTTTCGATTCAAGTTG
1 AACGGAAGGAAGTATCGACACTTTCGATTCAAGATG
* * **
3419177 AACGGAAAGAGGCGTC-ACACTTTCGATTCAAG
1 AACGGAAGGAAGTATCGACACTTTCGATTCAAG
3419209 TGTTCATCTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
35 45 0.52
36 42 0.48
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (36 bp):
AACGGAAGGAAGTATCGACACTTTCGATTCAAGATG
Found at i:3419198 original size:71 final size:71
Alignment explanation
Indices: 3419070--3419205 Score: 193
Period size: 71 Copynumber: 1.9 Consensus size: 71
3419060 GAATACGTCA
* ** * *
3419070 AACGGAAGGAAGTATCGTTACTTTCGATTCAAGTGAACGGAAGGAAGCATCGGCACTTTCGATTC
1 AACGAAAGGAAGTATCGACACTTTCGATTCAAGTGAACGGAAAGAAGCATCGACACTTTCGATTC
3419135 TAGAAG
66 TAGAAG
* *
3419141 AACGAAAGGAAGTATCGACACTTTCGATTCAAGTTGAACGGAAAGAGGCGTC-ACACTTTCGATT
1 AACGAAAGGAAGTATCGACACTTTCGATTCAAG-TGAACGGAAAGAAGCATCGACACTTTCGATT
3419205 C
65 C
3419206 AAGTGTTCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 42 0.74
72 15 0.26
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (71 bp):
AACGAAAGGAAGTATCGACACTTTCGATTCAAGTGAACGGAAAGAAGCATCGACACTTTCGATTC
TAGAAG
Found at i:3421230 original size:35 final size:36
Alignment explanation
Indices: 3421191--3421263 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
3421181 GATCACTAAT
*
3421191 GGAAAATGATG-AAGACTTAATGTATTATTGAAAAC
1 GGAAAATGACGAAAGACTTAATGTATTATTGAAAAC
* *
3421226 GGAAAATGACGAAAAGACTTAATGTGTTATTGAGAAC
1 GGAAAATGACG-AAAGACTTAATGTATTATTGAAAAC
3421263 G
1 G
3421264 AAGCATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 10 0.30
37 23 0.70
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (36 bp):
GGAAAATGACGAAAGACTTAATGTATTATTGAAAAC
Found at i:3423811 original size:5 final size:5
Alignment explanation
Indices: 3423797--3423855 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
3423787 GTTAAAAGAG
* *
3423797 AAAAT AAAAAT AAAAC AAAAT AAAAT AATAAT -AAAT AAAAGT GAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAA-T AAAAT
*
3423844 ATAAT AAAAT AA
1 AAAAT AAAAT AA
3423856 TAAATAATAG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
4 3 0.07
5 29 0.66
6 12 0.27
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:3423816 original size:11 final size:11
Alignment explanation
Indices: 3423797--3423862 Score: 57
Period size: 10 Copynumber: 6.2 Consensus size: 11
3423787 GTTAAAAGAG
3423797 AAAATAAAAAT
1 AAAATAAAAAT
*
3423808 AAAA-CAAAAT
1 AAAATAAAAAT
*
3423818 AAAATAATAAT
1 AAAATAAAAAT
*
3423829 -AAATAAAAGT
1 AAAATAAAAAT
* *
3423839 GAAAT-ATAAT
1 AAAATAAAAAT
3423849 AAAATAATAAAT
1 AAAATAA-AAAT
3423861 AA
1 AA
3423863 TAGTACTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
10 24 0.57
11 13 0.31
12 5 0.12
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:3423833 original size:31 final size:31
Alignment explanation
Indices: 3423798--3423858 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3423788 TTAAAAGAGA
3423798 AAATAAAAATAAAACAAAATAAAATAATAAT
1 AAATAAAAATAAAACAAAATAAAATAATAAT
* * * *
3423829 AAATAAAAGTGAAATATAATAAAATAATAA
1 AAATAAAAATAAAACAAAATAAAATAATAA
3423859 ATAATAGTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (31 bp):
AAATAAAAATAAAACAAAATAAAATAATAAT
Found at i:3423853 original size:21 final size:21
Alignment explanation
Indices: 3423797--3423855 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
3423787 GTTAAAAGAG
* *
3423797 AAAATAAAAATAAAACAAAAT
1 AAAATAATAATAAAATAAAAT
3423818 AAAATAATAAT-AAATAAAAGT
1 AAAATAATAATAAAATAAAA-T
*
3423839 GAAAT-ATAATAAAATAA
1 AAAATAATAATAAAATAA
3423856 TAAATAATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAATAATAATAAAATAAAAT
Found at i:3423927 original size:18 final size:18
Alignment explanation
Indices: 3423906--3423948 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3423896 GTTGTTTTTA
* *
3423906 AAATGAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
3423924 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
3423942 AAATAAA
1 AAATAAA
3423949 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:3425065 original size:5 final size:4
Alignment explanation
Indices: 3425019--3425063 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
3425009 AAAAATAACA
* *
3425019 AAAT GAAT AAAT AAAT AAAT AAAT AAAT GAAAAG AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AAA
3425064 ATGACATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 32 0.91
6 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:3433972 original size:18 final size:18
Alignment explanation
Indices: 3433951--3433993 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3433941 GTTGTTTTTA
* *
3433951 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
3433969 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
3433987 AAATAAA
1 AAATAAA
3433994 TAATCTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:3435101 original size:22 final size:22
Alignment explanation
Indices: 3435073--3435124 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3435063 ACCCCTAAAA
*
3435073 AAATAAAAATAACAAAATG-AAT
1 AAATAAAAA-AACAAAAAGAAAT
* *
3435095 AAATAAATAAATAAAAAGAAAT
1 AAATAAAAAAACAAAAAGAAAT
3435117 AAATAAAA
1 AAATAAAA
3435125 TGGCATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (22 bp):
AAATAAAAAAACAAAAAGAAAT
Found at i:3435194 original size:34 final size:30
Alignment explanation
Indices: 3435152--3435228 Score: 73
Period size: 34 Copynumber: 2.3 Consensus size: 30
3435142 ATAATAATAT
*
3435152 TATATATATTTTCAAAAAATGCTTTCAAAATCATA
1 TATATATATTTTC--AAAATGCTTTCAAAA--A-C
*
3435187 TAGTATATATTTTCAAAATGTTTTCAAAAAC
1 TA-TATATATTTTCAAAATGCTTTCAAAAAC
3435218 TATACTATATT
1 TATA-TATATT
3435229 AATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 2 0.05
31 8 0.21
32 1 0.03
34 14 0.37
35 2 0.05
36 11 0.29
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (30 bp):
TATATATATTTTCAAAATGCTTTCAAAAAC
Found at i:3447244 original size:21 final size:21
Alignment explanation
Indices: 3447220--3447266 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3447210 ATTGACCATG
*
3447220 ACAATGCTTACATGACAATTC
1 ACAATGCTTACATGACAATAC
* *
3447241 ACAAAGCTTACATGGCAATAC
1 ACAATGCTTACATGACAATAC
3447262 ACAAT
1 ACAAT
3447267 ATTAATGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (21 bp):
ACAATGCTTACATGACAATAC
Found at i:3448921 original size:18 final size:19
Alignment explanation
Indices: 3448898--3448933 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3448888 TTGTAAAATT
3448898 GTTTAAAAAAT-ATTTTAG
1 GTTTAAAAAATAATTTTAG
*
3448916 GTTTAAAACATAATTTTA
1 GTTTAAAAAATAATTTTA
3448934 CACTTTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (19 bp):
GTTTAAAAAATAATTTTAG
Found at i:3449157 original size:13 final size:14
Alignment explanation
Indices: 3449139--3449172 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
3449129 TAAGATTTTC
3449139 TTTGAAAATCA-TT
1 TTTGAAAATCATTT
3449152 TTTG-AAATCATTT
1 TTTGAAAATCATTT
3449165 TTTGAAAA
1 TTTGAAAA
3449173 CTACTCCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 10 0.53
14 3 0.16
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (14 bp):
TTTGAAAATCATTT
Found at i:3450942 original size:13 final size:13
Alignment explanation
Indices: 3450920--3450988 Score: 70
Period size: 13 Copynumber: 5.3 Consensus size: 13
3450910 TCCTAATGGG
3450920 CAAT-TTTGAAAA
1 CAATGTTTGAAAA
* **
3450932 CTATGTTTGAAGGG
1 CAATGTTTGAA-AA
3450946 CAAT-TTTGAAAA
1 CAATGTTTGAAAA
*
3450958 CTATGTTTGAAAA
1 CAATGTTTGAAAA
3450971 CAATGTTTGAAAA
1 CAATGTTTGAAAA
3450984 TCAAT
1 -CAAT
3450989 ATGGAGCTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
12 6 0.13
13 32 0.71
14 7 0.16
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.35
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:3450946 original size:26 final size:26
Alignment explanation
Indices: 3450917--3450968 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3450907 AAATCCTAAT
3450917 GGGCAATTTTGAAAACTATGTTTGAA
1 GGGCAATTTTGAAAACTATGTTTGAA
3450943 GGGCAATTTTGAAAACTATGTTTGAA
1 GGGCAATTTTGAAAACTATGTTTGAA
3450969 AACAATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (26 bp):
GGGCAATTTTGAAAACTATGTTTGAA
Found at i:3450979 original size:26 final size:26
Alignment explanation
Indices: 3450920--3450983 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
3450910 TCCTAATGGG
**
3450920 CAATTTTGAAAACTATGTTTGAAGGG
1 CAATTTTGAAAACTATGTTTGAAGAA
3450946 CAATTTTGAAAACTATGTTTGAA-AA
1 CAATTTTGAAAACTATGTTTGAAGAA
3450971 CAATGTTTGAAAA
1 CAAT-TTTGAAAA
3450984 TCAATATGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 4 0.11
26 31 0.89
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (26 bp):
CAATTTTGAAAACTATGTTTGAAGAA
Found at i:3451506 original size:21 final size:21
Alignment explanation
Indices: 3451477--3451548 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
3451467 CAAGACATAC
*
3451477 ATCGGTGCACCTTCATAGTGT
1 ATCGATGCACCTTCATAGTGT
** * *
3451498 ATCGATGCATATTCAAGAGATGC
1 ATCGATGCACCTTC-ATAG-TGT
*
3451521 ATCGATAC-CCTTTCATAGTGT
1 ATCGATGCACC-TTCATAGTGT
3451542 ATCGATG
1 ATCGATG
3451549 TGTATCGATG
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
21 19 0.51
22 6 0.16
23 12 0.32
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
ATCGATGCACCTTCATAGTGT
Found at i:3451512 original size:44 final size:44
Alignment explanation
Indices: 3451449--3451548 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
3451439 AAACCCGACG
* *
3451449 AGTGTATCGATGCACATTCAAGACATACATCGGTGCACC-TTCAT
1 AGTGTATCGATGCACATTCAAGACATACATCGATAC-CCTTTCAT
* * *
3451493 AGTGTATCGATGCATATTCAAGAGATGCATCGATACCCTTTCAT
1 AGTGTATCGATGCACATTCAAGACATACATCGATACCCTTTCAT
3451537 AGTGTATCGATG
1 AGTGTATCGATG
3451549 TGTATCGATG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
43 2 0.04
44 48 0.96
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGACATACATCGATACCCTTTCAT
Found at i:3459330 original size:15 final size:15
Alignment explanation
Indices: 3459310--3459354 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3459300 ACATAAATTA
3459310 TATTTTTATTATAAT
1 TATTTTTATTATAAT
3459325 TA-TTTTAGTTAT--T
1 TATTTTTA-TTATAAT
3459338 TATATTTTATTATAAT
1 TAT-TTTTATTATAAT
3459354 T
1 T
3459355 TAAATAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.12
14 9 0.36
15 11 0.44
16 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTTTTATTATAAT
Found at i:3459370 original size:29 final size:28
Alignment explanation
Indices: 3459308--3459386 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 28
3459298 TAACATAAAT
** *
3459308 TATAT-TTTTATTATAATTATTTTAGTTA
1 TATATATTTTATTATAATTA-AATAGATA
*
3459336 TTTATATTTTATTATAATTTAAATAGATA
1 TATATATTTTATTATAA-TTAAATAGATA
* *
3459365 TATATAATATA-TATAATTAAAT
1 TATATATTTTATTATAATTAAAT
3459387 TTAAAAATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
27 6 0.14
28 9 0.21
29 24 0.57
30 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (28 bp):
TATATATTTTATTATAATTAAATAGATA
Found at i:3459399 original size:21 final size:23
Alignment explanation
Indices: 3459365--3459422 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
3459355 TAAATAGATA
*
3459365 TATATAATATATATAATTA-AATT
1 TATAAAATA-ATATAATTATAATT
*
3459388 TA-AAAATAATATATTTATAATT
1 TATAAAATAATATAATTATAATT
*
3459410 TATAATATAATAT
1 TATAAAATAATAT
3459423 CTAAAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 8 0.27
22 11 0.37
23 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATAAAATAATATAATTATAATT
Found at i:3459419 original size:23 final size:22
Alignment explanation
Indices: 3459367--3459422 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
3459357 AATAGATATA
3459367 TATAATAT-ATATAATTAAATT
1 TATAATATAATATAATTAAATT
* *
3459388 TA-AAAATAATATATTTATAATT
1 TATAATATAATATAATTA-AATT
3459410 TATAATATAATAT
1 TATAATATAATAT
3459423 CTAAAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 4 0.14
21 10 0.34
22 6 0.21
23 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATAATATAATATAATTAAATT
Found at i:3459512 original size:14 final size:15
Alignment explanation
Indices: 3459493--3459521 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3459483 CTTAAACTCA
3459493 ACTTTTAAAA-TATT
1 ACTTTTAAAAGTATT
3459507 ACTTTTAAAAGTATT
1 ACTTTTAAAAGTATT
3459522 TTTTCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (15 bp):
ACTTTTAAAAGTATT
Found at i:3459537 original size:13 final size:13
Alignment explanation
Indices: 3459495--3459545 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
3459485 TAAACTCAAC
3459495 TTTTAAAATATTAC-
1 TTTTAAAA-A-TACT
* *
3459509 TTTTAAAAGTATT
1 TTTTAAAAATACT
*
3459522 TTTTCAAAATACT
1 TTTTAAAAATACT
3459535 TTTTAAAAATA
1 TTTTAAAAATA
3459546 ATGTCAAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 2 0.07
13 20 0.67
14 8 0.27
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (13 bp):
TTTTAAAAATACT
Found at i:3467924 original size:14 final size:14
Alignment explanation
Indices: 3467905--3467953 Score: 71
Period size: 15 Copynumber: 3.4 Consensus size: 14
3467895 ATGTTCTTTG
*
3467905 TCTTTTCTTTTTTT
1 TCTTTTCCTTTTTT
3467919 TCTTTTCCCTTTTTT
1 TCTTTT-CCTTTTTT
3467934 TCTTTATCCTTTTTT
1 TCTTT-TCCTTTTTT
3467949 TCTTT
1 TCTTT
3467954 ATCTCTACTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 6 0.19
15 25 0.78
16 1 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (14 bp):
TCTTTTCCTTTTTT
Found at i:3467933 original size:15 final size:15
Alignment explanation
Indices: 3467913--3467956 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
3467903 TGTCTTTTCT
3467913 TTTTTTTCTTT-TCCC
1 TTTTTTTCTTTAT-CC
3467928 TTTTTTTCTTTATCC
1 TTTTTTTCTTTATCC
3467943 TTTTTTTCTTTATC
1 TTTTTTTCTTTATC
3467957 TCTACTCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTTTCTTTATCC
Found at i:3468338 original size:25 final size:25
Alignment explanation
Indices: 3468288--3468336 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
3468278 ATATAAATGC
3468288 ATTTCTTTTAACTTTTTATAAATTTG
1 ATTTCTTTT-ACTTTTTATAAATTTG
3468314 ATTTCTTTT-CTTTTT-TAATATTT
1 ATTTCTTTTACTTTTTATAA-ATTT
3468337 TGGTTGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.14
24 10 0.45
26 9 0.41
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTCTTTTACTTTTTATAAATTTG
Found at i:3468774 original size:28 final size:28
Alignment explanation
Indices: 3468732--3468825 Score: 100
Period size: 28 Copynumber: 3.3 Consensus size: 28
3468722 GTAGTGATTA
3468732 TAAAAATATAGGTTGTTATTGTAATATG
1 TAAAAATATAGGTTGTTATTGTAATATG
*
3468760 TAAAAATAT-GAGTTGTTATTGTAATTTG
1 TAAAAATATAG-GTTGTTATTGTAATATG
* *** * *
3468788 TAAAAAGTATATGCCATTATTGTAATTTA
1 TAAAAA-TATAGGTTGTTATTGTAATATG
3468817 TAAAAATAT
1 TAAAAATAT
3468826 TTGTTTTCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
27 1 0.02
28 34 0.60
29 22 0.39
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (28 bp):
TAAAAATATAGGTTGTTATTGTAATATG
Found at i:3468837 original size:29 final size:28
Alignment explanation
Indices: 3468729--3468973 Score: 170
Period size: 29 Copynumber: 8.5 Consensus size: 28
3468719 AATGTAGTGA
**
3468729 TTATAAAAATATAGGT-TGTTATTGTAAT
1 TTATAAAAATATTTGTCT-TTATTGTAAT
* * **
3468757 ATGTAAAAATATGAGT-TGTTATTGTAAT
1 TTATAAAAATATTTGTCT-TTATTGTAAT
* * * *
3468785 TTGTAAAAAGTATATGCCATTATTGTAAT
1 TTATAAAAA-TATTTGTCTTTATTGTAAT
* * *
3468814 TTATAAAAATATTTGTTTTCTATTTTAAA
1 TTATAAAAATATTTGTCTT-TATTGTAAT
* *
3468843 TTATAAAAAGAGTTGTCCTTTATTGTAAT
1 TTATAAAAATATTTGT-CTTTATTGTAAT
* * * *
3468872 TTATAAGAAGATTTATCTTCTATTATAAT
1 TTATAAAAATATTTGTCTT-TATTGTAAT
* *
3468901 TTATAAAAAGATTTGTCCATTATTGTAAT
1 TTATAAAAATATTTGT-CTTTATTGTAAT
* * *
3468930 TTATAAAAATCTTTGTCCTTAAATGTAAT
1 TTATAAAAATATTTGT-CTTTATTGTAAT
*
3468959 TAATAAAAAATATTT
1 TTAT-AAAAATATTT
3468974 AATTTTAATT
Statistics
Matches: 174, Mismatches: 36, Indels: 12
0.78 0.16 0.05
Matches are distributed among these distances:
28 41 0.24
29 120 0.69
30 13 0.07
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (28 bp):
TTATAAAAATATTTGTCTTTATTGTAAT
Found at i:3468946 original size:87 final size:87
Alignment explanation
Indices: 3468805--3468964 Score: 196
Period size: 87 Copynumber: 1.8 Consensus size: 87
3468795 TATATGCCAT
* * ** * * *
3468805 TATTGTAATTTATAAAAATATTTGTTTTCTATTTTAAATTATAAAAAGAGTTGTCCTTTATTGTA
1 TATTATAATTTATAAAAAGATTTGTCATCTATTGTAAATTATAAAAAGAGTTGTCCTTAAATGTA
*
3468870 ATTTATAAGAAGATTTATCTTC
66 ATTAATAAGAAGATTTATCTTC
* ***
3468892 TATTATAATTTATAAAAAGATTTGTCCAT-TATTGTAATTTATAAAAATCTTTGTCCTTAAATGT
1 TATTATAATTTATAAAAAGATTTGT-CATCTATTGTAAATTATAAAAAGAGTTGTCCTTAAATGT
3468956 AATTAATAA
65 AATTAATAA
3468965 AAAATATTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
87 59 0.98
88 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.47
Consensus pattern (87 bp):
TATTATAATTTATAAAAAGATTTGTCATCTATTGTAAATTATAAAAAGAGTTGTCCTTAAATGTA
ATTAATAAGAAGATTTATCTTC
Found at i:3468967 original size:58 final size:58
Alignment explanation
Indices: 3468776--3468946 Score: 218
Period size: 58 Copynumber: 2.9 Consensus size: 58
3468766 TATGAGTTGT
* * *
3468776 TATTGTAATTTGTAAAAAGTATATG-CCATTATTGTAATTTATAAAAATATTTGTTTTC
1 TATTGTAATTTATAAAAAG-ATTTGTCCATTATTGTAATTTATAAAAATATTTGTCTTC
* * * * * * *
3468834 TATTTTAAATTATAAAAAGAGTTGTCCTTTATTGTAATTTATAAGAAGATTTATCTTC
1 TATTGTAATTTATAAAAAGATTTGTCCATTATTGTAATTTATAAAAATATTTGTCTTC
* *
3468892 TATTATAATTTATAAAAAGATTTGTCCATTATTGTAATTTATAAAAATCTTTGTC
1 TATTGTAATTTATAAAAAGATTTGTCCATTATTGTAATTTATAAAAATATTTGTC
3468947 CTTAAATGTA
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
57 3 0.03
58 91 0.97
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.47
Consensus pattern (58 bp):
TATTGTAATTTATAAAAAGATTTGTCCATTATTGTAATTTATAAAAATATTTGTCTTC
Found at i:3473873 original size:21 final size:20
Alignment explanation
Indices: 3473829--3473902 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
3473819 GCAGCCTTCG
*
3473829 TGCATGGATGCACAACAAGA
1 TGCATCGATGCACAACAAGA
**
3473849 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAA-CAAGA
*
3473870 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACA-ACAAGA
3473890 TGCATCGATGCAC
1 TGCATCGATGCAC
3473903 TAAGTGCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 29 0.62
21 17 0.36
22 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAACAAGA
Found at i:3474100 original size:29 final size:30
Alignment explanation
Indices: 3474068--3474137 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
3474058 GAAATATTTT
3474068 AAAAC-TTTTAATAAATTCAATT-AAGTCCA
1 AAAACATTTT-ATAAATTCAATTCAAGTCCA
* **
3474097 AAAACATTTTGTAAATTTGATTCAAGTCCA
1 AAAACATTTTATAAATTCAATTCAAGTCCA
3474127 AAAACCATTTT
1 AAAA-CATTTT
3474138 GCCTTAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.40
30 15 0.43
31 6 0.17
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (30 bp):
AAAACATTTTATAAATTCAATTCAAGTCCA
Found at i:3481013 original size:22 final size:22
Alignment explanation
Indices: 3480946--3481028 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
3480936 TTGGTGCAGA
* *
3480946 GGGAATCGA-TCCCCCCC-CTAA
1 GGGAACCGATTCCCCCCCAC-AG
**
3480967 GGGAACCGATTCCCCCTTTGA-AG
1 GGGAACCGATTCCCCC--CCACAG
3480990 GGGAACCGATTCCCCCCCACAG
1 GGGAACCGATTCCCCCCCACAG
* *
3481012 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
3481029 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
21 9 0.18
22 23 0.47
23 17 0.35
ACGTcount: A:0.23, C:0.40, G:0.23, T:0.14
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCCACAG
Found at i:3482980 original size:9 final size:8
Alignment explanation
Indices: 3482957--3483008 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
3482947 TTGTTTCAAC
3482957 TTTTTGGA
1 TTTTTGGA
3482965 TATTTTGGA
1 T-TTTTGGA
3482974 TTGTTT-GA
1 TT-TTTGGA
3482982 TTTTGTGGA
1 TTTT-TGGA
*
3482991 TTGTTGGA
1 TTTTTGGA
3482999 -TTTTGGA
1 TTTTTGGA
3483006 TTT
1 TTT
3483009 ATGAATAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (8 bp):
TTTTTGGA
Found at i:3482992 original size:17 final size:17
Alignment explanation
Indices: 3482960--3483003 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3482950 TTTCAACTTT
3482960 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
3482977 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
3482994 TTGGATTTTG
1 TTGGATTTTG
3483004 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:3484817 original size:21 final size:20
Alignment explanation
Indices: 3484773--3484846 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
3484763 GCAGCCTTCG
*
3484773 TGCATGGATGCACAACAAGA
1 TGCATCGATGCACAACAAGA
**
3484793 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAA-CAAGA
*
3484814 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACA-ACAAGA
3484834 TGCATCGATGCAC
1 TGCATCGATGCAC
3484847 TAAGTGCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 29 0.62
21 17 0.36
22 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAACAAGA
Found at i:3485044 original size:29 final size:30
Alignment explanation
Indices: 3485012--3485081 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
3485002 GAAATATTTT
3485012 AAAAC-TTTTAATAAATTCAATT-AAGTCCA
1 AAAACATTTT-ATAAATTCAATTCAAGTCCA
* *
3485041 AAAACATTTTGTAAATTCGATTCAAGTCCA
1 AAAACATTTTATAAATTCAATTCAAGTCCA
3485071 AAAACCATTTT
1 AAAA-CATTTT
3485082 GCCTTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 15 0.42
30 15 0.42
31 6 0.17
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (30 bp):
AAAACATTTTATAAATTCAATTCAAGTCCA
Found at i:3485070 original size:30 final size:30
Alignment explanation
Indices: 3485023--3485082 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
3485013 AAACTTTTAA
3485023 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
*
3485052 TAAATTCGATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
3485083 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:3486396 original size:19 final size:20
Alignment explanation
Indices: 3486353--3486400 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3486343 TCTAAATCCT
*
3486353 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
3486373 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
3486392 TTTTCAAAA
1 TTTTCAAAA
3486401 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:3487944 original size:29 final size:29
Alignment explanation
Indices: 3487923--3487980 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
3487913 AAACTTTGAA
*
3487923 TAAATTTAATT-AAATCCAAAAACATTTTG
1 TAAATTCAATTCAAATCCAAAAACA-TTTG
*
3487952 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAATCCAAAAA-CATTT
3487981 TGCCTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 13 0.52
31 2 0.08
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAATCCAAAAACATTTG
Found at i:3487973 original size:30 final size:30
Alignment explanation
Indices: 3487923--3487982 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
3487913 AAACTTTGAA
*
3487923 TAAATTTAATTAAATCCAAAAA-CATTTTG
1 TAAATTCAATTAAATCCAAAAACCATTTTG
*
3487952 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAATCCAAAAACCATTTTG
3487983 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAATCCAAAAACCATTTTG
Found at i:3488044 original size:21 final size:21
Alignment explanation
Indices: 3488018--3488064 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3488008 GTTCAACAGG
3488018 TATCAATACTCTAAGTAATGT
1 TATCAATACTCTAAGTAATGT
*
3488039 TATCAATACTCTGAGTAATGT
1 TATCAATACTCTAAGTAATGT
3488060 TATCA
1 TATCA
3488065 GCATTGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (21 bp):
TATCAATACTCTAAGTAATGT
Found at i:3489394 original size:77 final size:79
Alignment explanation
Indices: 3489258--3489415 Score: 198
Period size: 77 Copynumber: 2.0 Consensus size: 79
3489248 CCCGAATATA
* ** *
3489258 TTAAGTAAACATTAAAAGAATGTAATTTTGATTACAACTATTTTAATTGATATTTAATTTGGAA-
1 TTAAATAAACATTAAAAGAATGTAATTAAGATTACAACTACTTTAATTGATATTTAATTT-GAAT
3489322 TAATTAAATAAGATT
65 TAATTAAATAAGATT
* * *
3489337 TTAAATAAACATT-AAAGATTGTAATTAAGATTATAAGT-CTTTAA-TGTATATTTAATTTGAAT
1 TTAAATAAACATTAAAAGAATGTAATTAAGATTACAACTACTTTAATTG-ATATTTAATTTGAAT
*
3489399 TAATTAAATATGATT
65 TAATTAAATAAGATT
3489414 TT
1 TT
3489416 TTATTAATTC
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
76 5 0.07
77 32 0.46
78 20 0.29
79 12 0.17
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (79 bp):
TTAAATAAACATTAAAAGAATGTAATTAAGATTACAACTACTTTAATTGATATTTAATTTGAATT
AATTAAATAAGATT
Found at i:3500534 original size:18 final size:18
Alignment explanation
Indices: 3500493--3500536 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3500483 TAAGTGTGTT
* *
3500493 GTTCATTT-AAGCATGTA
1 GTTCATTTAAAGAATCTA
*
3500510 TTTCATTTAAAGAATCTA
1 GTTCATTTAAAGAATCTA
3500528 GTTCATTTA
1 GTTCATTTA
3500537 GGGAAGTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (18 bp):
GTTCATTTAAAGAATCTA
Found at i:3500621 original size:35 final size:35
Alignment explanation
Indices: 3500543--3500622 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
3500533 TTTAGGGAAG
* * *
3500543 TAGTTCATTTATGCATATTTAGATCATTTAGTAAGT
1 TAGTTCATTCATGCA-ATTTAGATCATTGAATAAGT
* *
3500579 TACTTCATTCATGC-ATTTAGTTCATTGAATAAAGT
1 TAGTTCATTCATGCAATTTAGATCATTGAAT-AAGT
3500614 TAGTTCATT
1 TAGTTCATT
3500623 AATTAAACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
34 13 0.35
35 12 0.32
36 12 0.32
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.46
Consensus pattern (35 bp):
TAGTTCATTCATGCAATTTAGATCATTGAATAAGT
Found at i:3500636 original size:17 final size:17
Alignment explanation
Indices: 3500596--3500666 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
3500586 TTCATGCATT
*
3500596 TAGTTCATTGAA-TAAAGT
1 TAGTTCATT-AATTAAA-C
3500614 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
3500631 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
3500648 TAGTTCATTTATTAGAC
1 TAGTTCATTAATTAAAC
3500665 TA
1 TA
3500667 ACTCTTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 33 0.72
18 13 0.28
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:3501894 original size:9 final size:9
Alignment explanation
Indices: 3501880--3501921 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
3501870 CGGGTTTAAT
*
3501880 AAAAAAACAA
1 AAAAAAA-AG
3501890 AAAAAAAAG
1 AAAAAAAAG
*
3501899 AGAAAAAAG
1 AAAAAAAAG
3501908 AAAAAAAAG
1 AAAAAAAAG
3501917 AAAAA
1 AAAAA
3501922 TTTAAAGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.88, C:0.02, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:3501913 original size:16 final size:15
Alignment explanation
Indices: 3501888--3501921 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3501878 ATAAAAAAAC
*
3501888 AAAAAAAAAAGAGAA
1 AAAAAAAAAAAAGAA
3501903 AAAAGAAAAAAAAGAA
1 AAAA-AAAAAAAAGAA
3501919 AAA
1 AAA
3501922 TTTAAAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:3502869 original size:15 final size:15
Alignment explanation
Indices: 3502849--3502894 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
3502839 AGAAATTCAA
3502849 AAAATGATGAGAGTG
1 AAAATGATGAGAGTG
***
3502864 AAAATGATGATTTTG
1 AAAATGATGAGAGTG
3502879 AAAATGATGAGAGTG
1 AAAATGATGAGAGTG
3502894 A
1 A
3502895 CATCGTCCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (15 bp):
AAAATGATGAGAGTG
Found at i:3504153 original size:17 final size:17
Alignment explanation
Indices: 3504082--3504153 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 17
3504072 ATTCATGCAT
3504082 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
* *
3504099 GTTAGTTCATTAAATAAA
1 -CTAGTTCATTAATTAAA
* * *
3504117 CTACTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
3504134 CTAGTTCATTTATTAGA
1 CTAGTTCATTAATTAAA
3504151 CTA
1 CTA
3504154 ACTCTTAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 30 0.70
18 13 0.30
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:3506585 original size:24 final size:24
Alignment explanation
Indices: 3506523--3506599 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
3506513 TGTAAAAGGT
*
3506523 TGAATATA-AAATGA-ATTTATCA
1 TGAATATATATATGATATTTATCA
** *
3506545 TTGGTTATTATATATGATGTTTATCA
1 -TGAATA-TATATATGATATTTATCA
3506571 TGAATATATATATGATATTTATCA
1 TGAATATATATATGATATTTATCA
3506595 TGAAT
1 TGAAT
3506600 GTTATTACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
23 4 0.09
24 24 0.55
25 9 0.20
26 7 0.16
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (24 bp):
TGAATATATATATGATATTTATCA
Found at i:3506911 original size:86 final size:86
Alignment explanation
Indices: 3506752--3506915 Score: 231
Period size: 86 Copynumber: 1.9 Consensus size: 86
3506742 ATATCAGATA
** *
3506752 GTACTAAAGGATACCTAGTACGGGTCAGTACTAAAGGAAACCTAGTGTTGATGGTGGGCATGACC
1 GTACTAAAGGATACCTAGTACGGGTCAGTACTAAAGGAAACCTAGTGTTGATGAAGGACATGACC
* *
3506817 TTATGTGTCATATTTGGGATC
66 TCACGTGTCATATTTGGGATC
* * *
3506838 GTACTAAAGGATATCTAGTGCGGGTCAGTACTAAAGGATACCTAGT-TCTGATGAAGGACATGAC
1 GTACTAAAGGATACCTAGTACGGGTCAGTACTAAAGGAAACCTAGTGT-TGATGAAGGACATGAC
*
3506902 CTCCCGTGTCATAT
65 CTCACGTGTCATAT
3506916 CAGTTTAGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 1 0.01
86 67 0.99
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (86 bp):
GTACTAAAGGATACCTAGTACGGGTCAGTACTAAAGGAAACCTAGTGTTGATGAAGGACATGACC
TCACGTGTCATATTTGGGATC
Found at i:3509344 original size:12 final size:13
Alignment explanation
Indices: 3509316--3509358 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
3509306 TATTTTATTC
* *
3509316 TCATTTTCCACTT
1 TCATATTCCATTT
3509329 TCATATT-CATTT
1 TCATATTCCATTT
*
3509341 TCATATTCCATGT
1 TCATATTCCATTT
3509354 TCATA
1 TCATA
3509359 ATAAATACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.23, C:0.23, G:0.02, T:0.51
Consensus pattern (13 bp):
TCATATTCCATTT
Done.