Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007918.1 Hibiscus syriacus cultivar Beakdansim tig00110321_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: 2302251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1964905 original size:28 final size:28
Alignment explanation
Indices: 1964873--1964948 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 28
1964863 TTATATGACT
* **
1964873 ATATAATAATAATAAAAATAATATTTAA
1 ATATAATAATAATAAAAATAAAACATAA
* *
1964901 ATAT-ATAAACAAGTAAAATTAAAACATAA
1 ATATAAT-AATAA-TAAAAATAAAACATAA
*
1964930 ATA-AACAATAATAAAAATA
1 ATATAATAATAATAAAAATA
1964949 CAATTAGAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
27 9 0.24
28 12 0.32
29 16 0.43
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (28 bp):
ATATAATAATAATAAAAATAAAACATAA
Found at i:1967492 original size:14 final size:14
Alignment explanation
Indices: 1967475--1967598 Score: 60
Period size: 14 Copynumber: 8.9 Consensus size: 14
1967465 TCATTTTGAT
*
1967475 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGA
*
1967489 TTTAA-GTTT-GAA
1 TTTAAGGTTTAGGA
* *
1967501 TTTAGGGTTT-TGA
1 TTTAAGGTTTAGGA
*
1967514 TTTATGGTTTAGGA
1 TTTAAGGTTTAGGA
* *
1967528 TTTAGGGTTCAAGG-
1 TTTAAGGTT-TAGGA
*
1967542 TTTAAGATTGTAGGAA
1 TTTAAGGTT-TAGG-A
* * *
1967558 TTT-AGGATTCAAGT
1 TTTAAGG-TTTAGGA
*
1967572 TTTATGGTTTTAGGA
1 TTTAAGG-TTTAGGA
1967587 TTTAAGGTTTAG
1 TTTAAGGTTTAG
1967599 AGTTCATGGT
Statistics
Matches: 80, Mismatches: 23, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
12 5 0.06
13 18 0.22
14 33 0.41
15 19 0.24
16 5 0.06
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.46
Consensus pattern (14 bp):
TTTAAGGTTTAGGA
Found at i:1967586 original size:30 final size:29
Alignment explanation
Indices: 1967514--1967590 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 29
1967504 AGGGTTTTGA
*
1967514 TTTATGG-TTTAGGATTTAGGGTTCAAGG
1 TTTATGGTTTTAGGATTTAGGATTCAAGG
* * * *
1967542 TTTAAGATTGTAGGAATTTAGGATTCAAGT
1 TTTATGGTTTTAGG-ATTTAGGATTCAAGG
1967572 TTTATGGTTTTAGGATTTA
1 TTTATGGTTTTAGGATTTA
1967591 AGGTTTAGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 5 0.13
29 10 0.26
30 24 0.62
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45
Consensus pattern (29 bp):
TTTATGGTTTTAGGATTTAGGATTCAAGG
Found at i:1967611 original size:21 final size:21
Alignment explanation
Indices: 1967587--1967626 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1967577 GGTTTTAGGA
1967587 TTTAAGGTTTAGAGTTCATGG
1 TTTAAGGTTTAGAGTTCATGG
* *
1967608 TTTAGGGTTTAGGGTTCAT
1 TTTAAGGTTTAGAGTTCAT
1967627 TAAATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (21 bp):
TTTAAGGTTTAGAGTTCATGG
Found at i:1967635 original size:5 final size:5
Alignment explanation
Indices: 1967625--1967663 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
1967615 TTTAGGGTTC
* *
1967625 ATTAA ATTAA ATTAA A-TAA ATTAA ATTCA CTTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
1967664 CAGAATATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:1973648 original size:12 final size:12
Alignment explanation
Indices: 1973631--1973673 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
1973621 GATTATTTCC
*
1973631 TCATCTAAGGTG
1 TCATCTATGGTG
1973643 TCATCTATGGTG
1 TCATCTATGGTG
1973655 TCATCTATGGTG
1 TCATCTATGGTG
*
1973667 TTATCTA
1 TCATCTA
1973674 CAGTAATCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (12 bp):
TCATCTATGGTG
Found at i:1976578 original size:23 final size:23
Alignment explanation
Indices: 1976532--1976585 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1976522 ATGATAAACA
1976532 AACATAAACTAAAATAAATGAACG
1 AACAT-AACTAAAATAAATGAACG
*
1976556 AACATAA-TAAATTAACATGAACG
1 AACATAACTAAAATAA-ATGAACG
1976579 AACATAA
1 AACATAA
1976586 AAAAAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 7 0.25
23 16 0.57
24 5 0.18
ACGTcount: A:0.61, C:0.13, G:0.07, T:0.19
Consensus pattern (23 bp):
AACATAACTAAAATAAATGAACG
Found at i:1981471 original size:15 final size:16
Alignment explanation
Indices: 1981451--1981489 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1981441 GTTTACTTCA
*
1981451 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
1981466 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
1981482 GAATGATT
1 GAATGATT
1981490 TATAAGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:1988047 original size:19 final size:21
Alignment explanation
Indices: 1988012--1988056 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
1988002 AATATTCAAC
1988012 AATAACAAAATCGATAGAAA-
1 AATAACAAAATCGATAGAAAT
1988032 AATAACAAAA-CGATAGAAAT
1 AATAACAAAATCGATAGAAAT
1988052 AATAA
1 AATAA
1988057 TGTTACCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (21 bp):
AATAACAAAATCGATAGAAAT
Found at i:1988637 original size:11 final size:11
Alignment explanation
Indices: 1988612--1988660 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
1988602 TTCCCTATCT
*
1988612 TAATATTTTTA
1 TAATTTTTTTA
1988623 -AATTTTTTTA
1 TAATTTTTTTA
*
1988633 TAATTTTTTTT
1 TAATTTTTTTA
1988644 TAAATTTTTTTA
1 T-AATTTTTTTA
1988656 TAATT
1 TAATT
1988661 CTATACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 9 0.27
11 14 0.42
12 10 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:1988647 original size:23 final size:23
Alignment explanation
Indices: 1988617--1988660 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1988607 TATCTTAATA
1988617 TTTTTAAATTTTTTTATAATTTT
1 TTTTTAAATTTTTTTATAATTTT
1988640 TTTTTAAATTTTTTTATAATT
1 TTTTTAAATTTTTTTATAATT
1988661 CTATACATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTAAATTTTTTTATAATTTT
Found at i:2003571 original size:72 final size:71
Alignment explanation
Indices: 2003444--2003593 Score: 255
Period size: 72 Copynumber: 2.1 Consensus size: 71
2003434 TTAATATATT
* * *
2003444 AAACTGTGATTAACTTTTAAGATTGTTTTTAATCAACAATTAATATGCATAAGTGATACTAATTA
1 AAACTGTGATTAACATTTAAGATTGTTATTAATCAACAATTAATATGCATAAGTGATACTAAGTA
2003509 TAACGA
66 TAACGA
*
2003515 AAACTGTGATTAACATTTAAGATTGGTTATTAGTCAACAATTAATATGCATAAGTGATACTAAGT
1 AAACTGTGATTAACATTTAAGATT-GTTATTAATCAACAATTAATATGCATAAGTGATACTAAGT
2003580 ATAACGA
65 ATAACGA
2003587 AAACTGT
1 AAACTGT
2003594 TAAACAAAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 23 0.31
72 51 0.69
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (71 bp):
AAACTGTGATTAACATTTAAGATTGTTATTAATCAACAATTAATATGCATAAGTGATACTAAGTA
TAACGA
Found at i:2005191 original size:23 final size:23
Alignment explanation
Indices: 2005171--2005217 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2005161 CAATAAACTG
2005171 CTACAGTACAAG-CATCAAAACAA
1 CTACAGTAC-AGTCATCAAAACAA
*
2005194 CTACAGTACAGTCATCAAAGCAA
1 CTACAGTACAGTCATCAAAACAA
2005217 C
1 C
2005218 CAACGTGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.47, C:0.28, G:0.11, T:0.15
Consensus pattern (23 bp):
CTACAGTACAGTCATCAAAACAA
Found at i:2007488 original size:6 final size:6
Alignment explanation
Indices: 2007479--2007509 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2007469 AATAAACAAG
2007479 GGGAAA GGGAAA GGGAAA GGGAAA GGGAAA G
1 GGGAAA GGGAAA GGGAAA GGGAAA GGGAAA G
2007510 AAAGGCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GGGAAA
Found at i:2007581 original size:32 final size:32
Alignment explanation
Indices: 2007538--2007603 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
2007528 GCACCCTTAA
***
2007538 TTTCGGATCCTATTTGCAGCTAGTCCGTTCCG
1 TTTCGGATCCTATCCACAGCTAGTCCGTTCCG
* *
2007570 TTTCGGGTCCTATCCACAGGTAGTCCGTTCCG
1 TTTCGGATCCTATCCACAGCTAGTCCGTTCCG
2007602 TT
1 TT
2007604 ATGCTCAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.12, C:0.29, G:0.23, T:0.36
Consensus pattern (32 bp):
TTTCGGATCCTATCCACAGCTAGTCCGTTCCG
Found at i:2015298 original size:14 final size:14
Alignment explanation
Indices: 2015279--2015318 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2015269 AATGTGAAGT
2015279 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
2015293 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
2015307 AATCTCTGCATA
1 AATCCCTGCATA
2015319 TAGAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:2019012 original size:19 final size:19
Alignment explanation
Indices: 2018985--2019029 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2018975 CTTCAATCAA
* *
2018985 TGCAATCCCAATTACTGTC
1 TGCAGTCCCAATCACTGTC
2019004 TGCAGTCCCAATCACTGTC
1 TGCAGTCCCAATCACTGTC
2019023 TGCAGTC
1 TGCAGTC
2019030 GACCAGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (19 bp):
TGCAGTCCCAATCACTGTC
Found at i:2019231 original size:21 final size:21
Alignment explanation
Indices: 2019205--2019248 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2019195 AAAGCCATAC
*
2019205 GATAATGGTGCATGAATATAT
1 GATAATGATGCATGAATATAT
*
2019226 GATAATGATGCATGAATGTAT
1 GATAATGATGCATGAATATAT
2019247 GA
1 GA
2019249 GGTCTTCGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (21 bp):
GATAATGATGCATGAATATAT
Found at i:2022656 original size:16 final size:16
Alignment explanation
Indices: 2022637--2022670 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2022627 CAATATACGA
2022637 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
2022653 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
2022669 AT
1 AT
2022671 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:2022744 original size:16 final size:18
Alignment explanation
Indices: 2022712--2022745 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2022702 TATTAATGTA
2022712 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
2022730 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
2022746 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:2023286 original size:21 final size:23
Alignment explanation
Indices: 2023241--2023287 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2023231 GTGTCACCAA
2023241 TAACATATATCATGATCATGTGT
1 TAACATATATCATGATCATGTGT
* *
2023264 TAACATATGTCA-GATCCTG-GT
1 TAACATATATCATGATCATGTGT
2023285 TAA
1 TAA
2023288 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (23 bp):
TAACATATATCATGATCATGTGT
Found at i:2023418 original size:130 final size:130
Alignment explanation
Indices: 2023214--2023461 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
2023204 AATTTTCTTC
* * *
2023214 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACATATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
2023279 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
2023344 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
2023409 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
2023462 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:2023907 original size:35 final size:35
Alignment explanation
Indices: 2023857--2023932 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
2023847 AATTGAATTT
* *
2023857 AATTGAATTATTTTGGAATTTAGGGTTGAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
* *
2023892 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
2023927 AATTGA
1 AATTGA
2023933 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
Found at i:2025222 original size:25 final size:25
Alignment explanation
Indices: 2025194--2025246 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
2025184 AGTGACATAT
* *
2025194 GAAATTTGTCCCGAA-TGACCGCGTA
1 GAAATTTGCCCCGAAGT-ACCACGTA
2025219 GAAATTTGCCCCGAAGTACCACGTA
1 GAAATTTGCCCCGAAGTACCACGTA
2025244 GAA
1 GAA
2025247 TTGCACCGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (25 bp):
GAAATTTGCCCCGAAGTACCACGTA
Found at i:2025400 original size:24 final size:24
Alignment explanation
Indices: 2025372--2025417 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2025362 AAGAATACAT
* *
2025372 ATATGTCCTGAAGGACCGCGTATA
1 ATATGTCCCGAAGAACCGCGTATA
2025396 ATATGTCCCGAAGAACCGCGTA
1 ATATGTCCCGAAGAACCGCGTA
2025418 GACCCTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (24 bp):
ATATGTCCCGAAGAACCGCGTATA
Found at i:2026400 original size:216 final size:216
Alignment explanation
Indices: 2026026--2026451 Score: 739
Period size: 216 Copynumber: 2.0 Consensus size: 216
2026016 CAAGAGTCAC
* *
2026026 TTCTTACCGTAGTAACTCCTTCATTAACTCATTGCAAGCCAATGTTTGATCAATAATATAAGTAC
1 TTCTTACCGTAGTAACTCCTTCACTAACTCATCGCAAGCCAATGTTTGATCAATAATATAAGTAC
**
2026091 AATTAAATTGCACTCGTCTTAGCCTTGCTTTGATTTGATCATAATTCTTTGATTGTTCCGAAACT
66 AATTAAATTGCACTCACCTTAGCCTTGCTTTGATTTGATCATAATTCTTTGATTGTTCCGAAACT
2026156 TGTTTAGGCTCAATATCTACATAAACATAA-TTTCCGAGATGAATATCAGAAGCCTAAACCTTAT
131 TGTTTAGGCTCAATATCTACATAAACATAACTTT-CGAGATGAATATCAGAAGCCTAAACCTTAT
2026220 AACTTGATGTTAATAACTTCAT
195 AACTTGATGTTAATAACTTCAT
* *
2026242 TTCTTACCGTAGTAACTCCTTCACTGACTCATCGCAAGTCAATGTTTGATCAATAATATAAGTAC
1 TTCTTACCGTAGTAACTCCTTCACTAACTCATCGCAAGCCAATGTTTGATCAATAATATAAGTAC
* * *
2026307 AATTAAATTGCACTCACCTTAGCCTTGCTTTGATTTGATCCTAACTT-TTTGATTGTTCTGGAAC
66 AATTAAATTGCACTCACCTTAGCCTTGCTTTGATTTGATCATAA-TTCTTTGATTGTTCCGAAAC
2026371 TTGTTTAGGCTCAATATCTACATAAACATAACTTTCGAGATGAATATCAGAAGCCTAAACCTTAT
130 TTGTTTAGGCTCAATATCTACATAAACATAACTTTCGAGATGAATATCAGAAGCCTAAACCTTAT
2026436 AACTTGATGTTAATAA
195 AACTTGATGTTAATAA
2026452 ATTAAGCTAG
Statistics
Matches: 199, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
216 194 0.97
217 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (216 bp):
TTCTTACCGTAGTAACTCCTTCACTAACTCATCGCAAGCCAATGTTTGATCAATAATATAAGTAC
AATTAAATTGCACTCACCTTAGCCTTGCTTTGATTTGATCATAATTCTTTGATTGTTCCGAAACT
TGTTTAGGCTCAATATCTACATAAACATAACTTTCGAGATGAATATCAGAAGCCTAAACCTTATA
ACTTGATGTTAATAACTTCAT
Found at i:2027612 original size:3 final size:3
Alignment explanation
Indices: 2027606--2027662 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
2027596 ATCCATTTTT
* *
2027606 TTA TTA TTA TTTA ATA TTA TTA ATA TTA -TA TTA TTTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
2027652 -TA TTT TTA TTA
1 TTA TTA TTA TTA
2027663 ATAAATATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2027637 original size:24 final size:25
Alignment explanation
Indices: 2027605--2027675 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 25
2027595 TATCCATTTT
2027605 TTTATTATTATTTAATATTATTAATA
1 TTTA-TATTATTTAATATTATTAATA
*
2027631 -TTATATTATTTATTATTATT-ATA
1 TTTATATTATTTAATATTATTAATA
* * *
2027654 TTTTTATTAATAAATATTATTA
1 TTTATATTATTTAATATTATTA
2027676 CAAACATGCC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 3 0.08
24 32 0.84
25 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATATTATTTAATATTATTAATA
Found at i:2027643 original size:34 final size:34
Alignment explanation
Indices: 2027605--2027674 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
2027595 TATCCATTTT
*
2027605 TTTATTATTATT-TAATATTATTAATATTATATTA
1 TTTATTATTATTATAATATTATTAATA-AATATTA
* *
2027639 TTTATTATTATTATATTTTTATTAATAAATATTA
1 TTTATTATTATTATAATATTATTAATAAATATTA
2027673 TT
1 TT
2027675 ACAAACATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 20 0.62
35 12 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (34 bp):
TTTATTATTATTATAATATTATTAATAAATATTA
Found at i:2027644 original size:21 final size:20
Alignment explanation
Indices: 2027620--2027673 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
2027610 TATTATTTAA
2027620 TATTATTAATATTATATTATT
1 TATTATTAATATTATATT-TT
2027641 TATTA-T--TATTATATTTT
1 TATTATTAATATTATATTTT
*
2027658 TATTAATAAATATTAT
1 TATT-ATTAATATTAT
2027674 TACAAACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
17 6 0.21
18 10 0.36
20 1 0.04
21 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTATTAATATTATATTTT
Found at i:2029228 original size:107 final size:109
Alignment explanation
Indices: 2029115--2029327 Score: 270
Period size: 108 Copynumber: 2.0 Consensus size: 109
2029105 CATGTTTTAA
* * * * * * *
2029115 TATTTATTTATTTTTCAATAT-TAA-GAAAGGGCAGTCTTAAAATAACTGGATGTCCATTTTTTG
1 TATTTATTTATTTTTCAATATAAAATAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-TTTTCTG
*
2029178 ATATTTTTAAATAAATAAATATTCTATTTATAAAT-TATATAAAT
65 ATATTTCTAAATAAATAAATATTCTATTTATAAATATATATAAAT
* * ** *
2029222 TATTTATTTATTTTTTAATATAAAATAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGA
1 TATTTATTTATTTTTCAATATAAAATAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTCTGA
*
2029287 TATTTCTAAATAAATAAATATTTTATTTATAAATATATATA
66 TATTTCTAAATAAATAAATATTCTATTTATAAATATATATA
2029328 TATATATATA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
107 20 0.22
108 41 0.46
109 28 0.31
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (109 bp):
TATTTATTTATTTTTCAATATAAAATAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTCTGA
TATTTCTAAATAAATAAATATTCTATTTATAAATATATATAAAT
Found at i:2029229 original size:24 final size:23
Alignment explanation
Indices: 2029179--2029232 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
2029169 CATTTTTTGA
*
2029179 TATTTTTAAATAAATAAATATTC
1 TATTTATAAATAAATAAATATTC
*
2029202 TATTTATAAATTATATAAATTATT-
1 TATTTATAAA-TAAATAAA-TATTC
2029226 TATTTAT
1 TATTTAT
2029233 TTTTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 9 0.33
24 14 0.52
25 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATTC
Found at i:2029319 original size:23 final size:23
Alignment explanation
Indices: 2029287--2029330 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2029277 CCTTTTCTGA
*
2029287 TATTTCTAAATAAATAAATATTT
1 TATTTATAAATAAATAAATATTT
* *
2029310 TATTTATAAATATATATATAT
1 TATTTATAAATAAATAAATAT
2029331 ATATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATTT
Found at i:2029326 original size:2 final size:2
Alignment explanation
Indices: 2029314--2029346 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2029304 ATATTTTATT
*
2029314 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2029347 TTTTTCATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2030031 original size:17 final size:17
Alignment explanation
Indices: 2030009--2030042 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2029999 ATGTTATTAA
2030009 AATGACAAAACGTTTTG
1 AATGACAAAACGTTTTG
2030026 AATGACAAAACGTTTTG
1 AATGACAAAACGTTTTG
2030043 GGTTCCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (17 bp):
AATGACAAAACGTTTTG
Found at i:2031044 original size:21 final size:21
Alignment explanation
Indices: 2031019--2031064 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2031009 TTTTAATAAC
2031019 TTTA-TCCTTATGACATATTTT
1 TTTAGTCCTTATGACAT-TTTT
*
2031040 TTTATGTCTTTATGACATTTTT
1 TTTA-GTCCTTATGACATTTTT
2031062 TTT
1 TTT
2031065 CTACCTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 7 0.32
23 11 0.50
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTAGTCCTTATGACATTTTT
Found at i:2031072 original size:22 final size:23
Alignment explanation
Indices: 2031019--2031072 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
2031009 TTTTAATAAC
2031019 TTTAT-CC-TTATGACATATTTT
1 TTTATACCTTTATGACATATTTT
**
2031040 TTTATGTCTTTATGACAT-TTTT
1 TTTATACCTTTATGACATATTTT
*
2031062 TTTCTACCTTT
1 TTTATACCTTT
2031073 TGGTACACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 13 0.48
23 9 0.33
ACGTcount: A:0.19, C:0.15, G:0.06, T:0.61
Consensus pattern (23 bp):
TTTATACCTTTATGACATATTTT
Found at i:2032059 original size:19 final size:19
Alignment explanation
Indices: 2032035--2032075 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2032025 ACAAAATCGA
2032035 ATTTACATAGTATAAATAG
1 ATTTACATAGTATAAATAG
* *
2032054 ATTTACATTGTATAGATAG
1 ATTTACATAGTATAAATAG
2032073 ATT
1 ATT
2032076 GTAACTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (19 bp):
ATTTACATAGTATAAATAG
Found at i:2032825 original size:2 final size:2
Alignment explanation
Indices: 2032818--2032851 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2032808 TTTGATTCCG
2032818 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2032852 TCCTAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2040197 original size:29 final size:28
Alignment explanation
Indices: 2040164--2040229 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 28
2040154 GTTCATTTAT
2040164 TTAAATTTTAACGA-TGTGAATAGAAAAAA
1 TTAAATTTTAA-GATTGTGAATA-AAAAAA
* *
2040193 TTAAAATTTTTAATATTGTGAATAAAAAGA
1 TT-AAA-TTTTAAGATTGTGAATAAAAAAA
2040223 TTAAATT
1 TTAAATT
2040230 AAAAGAGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
28 2 0.06
29 5 0.16
30 11 0.34
31 14 0.44
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (28 bp):
TTAAATTTTAAGATTGTGAATAAAAAAA
Found at i:2040200 original size:30 final size:30
Alignment explanation
Indices: 2040169--2040227 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
2040159 TTTATTTAAA
2040169 TTTTAACGA-TGTGAATAGAAAAAATTAAAAT
1 TTTTAA-GATTGTGAATA-AAAAAATTAAAAT
* *
2040200 TTTTAATATTGTGAATAAAAAGATTAAA
1 TTTTAAGATTGTGAATAAAAAAATTAAA
2040228 TTAAAAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.36
Consensus pattern (30 bp):
TTTTAAGATTGTGAATAAAAAAATTAAAAT
Found at i:2042081 original size:21 final size:21
Alignment explanation
Indices: 2042055--2042130 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
2042045 TGCGCTACAA
2042055 TTTTTTTTCTTTTGATTTTTG
1 TTTTTTTTCTTTTGATTTTTG
* *
2042076 TTTTTTTT-TATTTGAATGTTG
1 TTTTTTTTCT-TTTGATTTTTG
* *
2042097 ATTTTTTCTTCTTCTAATTTTTG
1 -TTTTTT-TTCTTTTGATTTTTG
*
2042120 GTTTTTTTCTT
1 TTTTTTTTCTT
2042131 ATTAGAATGT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 22 0.50
22 11 0.25
23 9 0.20
24 1 0.02
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.75
Consensus pattern (21 bp):
TTTTTTTTCTTTTGATTTTTG
Found at i:2042083 original size:22 final size:22
Alignment explanation
Indices: 2042055--2042127 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
2042045 TGCGCTACAA
2042055 TTTTTTTTCTTTTGATTTTTGT
1 TTTTTTTTCTTTTGATTTTTGT
* * *
2042077 TTTTTTTT-ATTTGAATGTTGAT
1 TTTTTTTTCTTTTGATTTTTG-T
* * * *
2042099 TTTTTCTTCTTCTAATTTTTGG
1 TTTTTTTTCTTTTGATTTTTGT
2042121 TTTTTTT
1 TTTTTTT
2042128 CTTATTAGAA
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
21 9 0.24
22 22 0.58
23 7 0.18
ACGTcount: A:0.10, C:0.05, G:0.10, T:0.75
Consensus pattern (22 bp):
TTTTTTTTCTTTTGATTTTTGT
Found at i:2042125 original size:24 final size:24
Alignment explanation
Indices: 2042098--2042176 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
2042088 TGAATGTTGA
*
2042098 TTTTTTCTTCTTCTAATTTTTGGT
1 TTTTTTCTTCTTCGAATTTTTGGT
* * ** *
2042122 TTTTTTCTTATTAGAATGTTGAGGA
1 TTTTTTCTTCTTCGAAT-TTTTGGT
* *
2042147 TTTTTTATTCTTCGGATTTTTGGT
1 TTTTTTCTTCTTCGAATTTTTGGT
2042171 TTTTTT
1 TTTTTT
2042177 ATTATATGTA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
24 24 0.59
25 17 0.41
ACGTcount: A:0.13, C:0.08, G:0.14, T:0.66
Consensus pattern (24 bp):
TTTTTTCTTCTTCGAATTTTTGGT
Found at i:2042143 original size:46 final size:45
Alignment explanation
Indices: 2042054--2042181 Score: 152
Period size: 49 Copynumber: 2.8 Consensus size: 45
2042044 CTGCGCTACA
* *
2042054 ATTTTTTTTCTTTTGATTTTT-GTTTTTTTTTATTTGAATGTT-G
1 ATTTTTTTTCTTCTGATTTTTGGTTTTTTTTTATTAGAATGTTGG
*
2042097 ATTTTTTCTTCTTCTAATTTTTGGTTTTTTTCTTATTAGAATGTTGAGG
1 ATTTTTT-TTCTTCTGATTTTTGGTTTTTTT-TTATTAGAATGTT--GG
*
2042146 ATTTTTTATTCTTCGGATTTTTGGTTTTTTTATTAT
1 ATTTTTT-TTCTTCTGATTTTTGGTTTTTTT-TTAT
2042182 ATGTAGAGAT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
43 7 0.10
44 12 0.17
45 8 0.11
46 12 0.17
49 33 0.46
ACGTcount: A:0.14, C:0.05, G:0.12, T:0.68
Consensus pattern (45 bp):
ATTTTTTTTCTTCTGATTTTTGGTTTTTTTTTATTAGAATGTTGG
Found at i:2042872 original size:27 final size:27
Alignment explanation
Indices: 2042834--2042894 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
2042824 TTCTTAAACT
*
2042834 TTAAGTTAAGATCTTTAGAATGAATAA
1 TTAAGATAAGATCTTTAGAATGAATAA
2042861 TTAAGATAAGATCTTTAGAATGAATAA
1 TTAAGATAAGATCTTTAGAATGAATAA
2042888 TTAAGAT
1 TTAAGAT
2042895 GAATTCGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (27 bp):
TTAAGATAAGATCTTTAGAATGAATAA
Found at i:2046689 original size:238 final size:235
Alignment explanation
Indices: 2046327--2046799 Score: 919
Period size: 238 Copynumber: 2.0 Consensus size: 235
2046317 CTATTACAAG
2046327 AAACTAATTTCAGATCAATCGTGCCAAATAAAATTTAATAAAATAGTACAACAAATTTGGATTAG
1 AAACTAATTTCAGATCAATCGTGCCAAATAAAATTTAATAAAATAGTACAACAAATTTGGATTAG
2046392 CAGATTAGTCAATAAAAATCATAACGTTCTACGACACACGGTAAGTCGGTAAGTACTTTCTTCAG
66 CAGATTAGTCAATAAAAATCATAACGTTCTACGACACACGGTAAGTCGGTAAGTACTTTCTTCAG
2046457 AACGAAGCTTCAAAAGAAGAGAAAATAATACCCTTGAAATTAGTGTATCCATTTGGTCTTGAATG
131 AACGAAGCTTCAAAAGAAGAGAAAATAATACCCTTGAAATTAGTGTATCCATTTGGTCTTGAATG
2046522 AGGTCTGCAGGCTTGTTTTCATATACTTATGGTCCAAGTA
196 AGGTCTGCAGGCTTGTTTTCATATACTTATGGTCCAAGTA
2046562 AAACTAATTTCAGATCAATCGTGCCAAATAAAAATTTAATAAATATAGTACAACAAATTTGGATT
1 AAACTAATTTCAGATCAATCGTGCCAAAT-AAAATTTAATAAA-ATAGTACAACAAATTTGGA-T
2046627 TAGCAGATTAGTCAATAAAAATCATAACGTTCTACGACACACGGTAAGTCGGTAAGTACTTTCTT
63 TAGCAGATTAGTCAATAAAAATCATAACGTTCTACGACACACGGTAAGTCGGTAAGTACTTTCTT
2046692 CAGAACGAAGCTTCAAAAGAAGAGAAAATAATACCCTTGAAATTAGTGTATCCATTTGGTCTTGA
128 CAGAACGAAGCTTCAAAAGAAGAGAAAATAATACCCTTGAAATTAGTGTATCCATTTGGTCTTGA
2046757 ATGAGGTCTGCAGGCTTGTTTTCATATACTTATGGTCCAAGTA
193 ATGAGGTCTGCAGGCTTGTTTTCATATACTTATGGTCCAAGTA
2046800 GCGGCTTTTT
Statistics
Matches: 235, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
235 29 0.12
236 13 0.06
237 19 0.08
238 174 0.74
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (235 bp):
AAACTAATTTCAGATCAATCGTGCCAAATAAAATTTAATAAAATAGTACAACAAATTTGGATTAG
CAGATTAGTCAATAAAAATCATAACGTTCTACGACACACGGTAAGTCGGTAAGTACTTTCTTCAG
AACGAAGCTTCAAAAGAAGAGAAAATAATACCCTTGAAATTAGTGTATCCATTTGGTCTTGAATG
AGGTCTGCAGGCTTGTTTTCATATACTTATGGTCCAAGTA
Found at i:2058727 original size:21 final size:22
Alignment explanation
Indices: 2058692--2058758 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
2058682 ACAAGTGTTT
*
2058692 ATATTATATTTTTTTATTTTA-A
1 ATATT-TAATTTTTTATTTTACA
*
2058714 ATATTTAATTTTTT-TGTTACA
1 ATATTTAATTTTTTATTTTACA
* *
2058735 ATGTTTAATATTTTATTTTACA
1 ATATTTAATTTTTTATTTTACA
2058757 AT
1 AT
2058759 CGTTTTAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 4 0.11
21 21 0.55
22 13 0.34
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (22 bp):
ATATTTAATTTTTTATTTTACA
Found at i:2058748 original size:22 final size:22
Alignment explanation
Indices: 2058702--2058763 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
2058692 ATATTATATT
*
2058702 TTTTTATTTTA-AAT-ATTTAA
1 TTTTTATTTTACAATCGTTTAA
2058722 TTTTT-TTGTTACAAT-GTTTAA
1 TTTTTATT-TTACAATCGTTTAA
2058743 TATTTTATTTTACAATCGTTT
1 T-TTTTATTTTACAATCGTTT
2058764 TAAGATTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 2 0.06
20 8 0.22
21 9 0.25
22 11 0.31
23 6 0.17
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTTTATTTTACAATCGTTTAA
Found at i:2066804 original size:19 final size:19
Alignment explanation
Indices: 2066768--2066814 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2066758 TTATATGATT
*
2066768 TATATTAATATTATTTAAA
1 TATATTAATATTAATTAAA
*
2066787 TATATT-ATATTAAATTAAT
1 TATATTAATATT-AATTAAA
*
2066806 TAAATTAAT
1 TATATTAAT
2066815 CTCCATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 16 0.70
20 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATTAATATTAATTAAA
Found at i:2084205 original size:91 final size:91
Alignment explanation
Indices: 2084047--2084226 Score: 263
Period size: 91 Copynumber: 2.0 Consensus size: 91
2084037 AGAGTGCTAT
* *
2084047 TTTTATTCATATTTTAGTACACTACTATCCCATTCTTATATTAAATCAATAGATATAAATTAAAT
1 TTTTATTCATATTTTAATACACTACAATCCCATTCTTATATTAAATCAATAGATATAAATTAAAT
*
2084112 AACCCAAGAATCCTTTAAAATACATA
66 AACCCAAGAATCCTTCAAAATACATA
* * * * * *
2084138 TTTTATTCATATTTTAATATTA-TAGAATCCGATTTTTATATTAAATCAATAGATATGAATTAGA
1 TTTTATTCATATTTTAATA-CACTACAATCCCATTCTTATATTAAATCAATAGATATAAATTAAA
2084202 TAACCCAAGAATCCTTCAAAATACA
65 TAACCCAAGAATCCTTCAAAATACA
2084227 AGACAAGAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 78 0.99
92 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (91 bp):
TTTTATTCATATTTTAATACACTACAATCCCATTCTTATATTAAATCAATAGATATAAATTAAAT
AACCCAAGAATCCTTCAAAATACATA
Found at i:2096615 original size:28 final size:27
Alignment explanation
Indices: 2096583--2096643 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 27
2096573 TTAAAGCGTG
*
2096583 ATATTTAAATTTAAATAATTAATATATAAT
1 ATATTTAAACTT-AA-AATTAATATAT-AT
*
2096613 ATTTTTAAACTTAAAATTAATATATAT
1 ATATTTAAACTTAAAATTAATATATAT
2096640 ATAT
1 ATAT
2096644 ATATTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.18
28 11 0.39
29 2 0.07
30 10 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATTTAAACTTAAAATTAATATATAT
Found at i:2098320 original size:3 final size:3
Alignment explanation
Indices: 2098312--2098354 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
2098302 CCTTATCAGC
*
2098312 CTT CTT CTT CTT CTT CTT TTT CTT CTT C-T CTTT CTT C-T CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CT
2098355 GTTGCAGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.83
4 2 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:2102271 original size:17 final size:16
Alignment explanation
Indices: 2102251--2102290 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2102241 GACAAAGCTT
2102251 AATTGATAAGATTTTTA
1 AATTGA-AAGATTTTTA
**
2102268 AATTGAATTATTTTTA
1 AATTGAAAGATTTTTA
2102284 AATTGAA
1 AATTGAA
2102291 TTGTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (16 bp):
AATTGAAAGATTTTTA
Found at i:2102280 original size:16 final size:16
Alignment explanation
Indices: 2102261--2102302 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
2102251 AATTGATAAG
2102261 ATTTTTAAATTGAATT
1 ATTTTTAAATTGAATT
2102277 ATTTTTAAATTGAATT
1 ATTTTTAAATTGAATT
*
2102293 -GTTTTAAATT
1 ATTTTTAAATT
2102303 AGTACTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
ATTTTTAAATTGAATT
Found at i:2102401 original size:30 final size:30
Alignment explanation
Indices: 2102367--2102425 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2102357 AGTTCACATC
2102367 TTATTCTATT-TAATA-TTTAATGAAAATGAT
1 TTATT-TATTATAATATTTTAAT-AAAATGAT
2102397 TTATTTATTATAATATTTTAATAAAATGA
1 TTATTTATTATAATATTTTAATAAAATGA
2102426 CCAAATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 17 0.63
31 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (30 bp):
TTATTTATTATAATATTTTAATAAAATGAT
Found at i:2102831 original size:2 final size:2
Alignment explanation
Indices: 2102824--2102856 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2102814 TCATGAACAC
*
2102824 GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2102857 GGGGGAGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2105129 original size:33 final size:30
Alignment explanation
Indices: 2105068--2105144 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 30
2105058 TTGGCTCAAT
* *
2105068 TACAGGCTGTTCAGTTACAACTGGCTCAGC
1 TACAGGCTGTTCAGTTACAACCGACTCAGC
*
2105098 TACAGGTTGTTCAGATATAACAACCGACTCAGC
1 TACAGGCTGTTCAG-T-T-ACAACCGACTCAGC
*
2105131 TTCAGGCTGTTCAG
1 TACAGGCTGTTCAG
2105145 GTGCACGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 13 0.33
31 1 0.03
32 1 0.03
33 24 0.62
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (30 bp):
TACAGGCTGTTCAGTTACAACCGACTCAGC
Found at i:2110802 original size:3 final size:3
Alignment explanation
Indices: 2110794--2110826 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2110784 CAAGAGAAAG
2110794 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2110827 TCTCAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2112403 original size:45 final size:45
Alignment explanation
Indices: 2112305--2112480 Score: 212
Period size: 45 Copynumber: 3.9 Consensus size: 45
2112295 CGAAGGGCGA
* * * * *
2112305 TCGA-TCCATTTCTCTTCTACACGATACCGAACTGGACTAGAAGG
1 TCGATTCCATTTCTCTTCGACATGATACCGAACAGGACTCGATGG
* * *
2112349 -CTTAGTCCATTTCTCTTCAACATGATACCGAACAGGACTCGATGG
1 TC-GATTCCATTTCTCTTCGACATGATACCGAACAGGACTCGATGG
* *
2112394 TCGATTCCATTTCTCTTCGCCATGACACCGAACAGGACTCGATGG
1 TCGATTCCATTTCTCTTCGACATGATACCGAACAGGACTCGATGG
* * *
2112439 TCGATTCCCTTTCTCTTCGCCATGATACCAAACAGGACTCGA
1 TCGATTCCATTTCTCTTCGACATGATACCGAACAGGACTCGA
2112481 GCTCTTCCGC
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
43 1 0.01
44 1 0.01
45 112 0.97
46 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (45 bp):
TCGATTCCATTTCTCTTCGACATGATACCGAACAGGACTCGATGG
Found at i:2129360 original size:17 final size:18
Alignment explanation
Indices: 2129335--2129368 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2129325 TTTGTTTTAA
*
2129335 TAATGTTGAGAT-TCTAG
1 TAATCTTGAGATCTCTAG
2129352 TAATCTTGAGATCTCTA
1 TAATCTTGAGATCTCTA
2129369 CTTCGAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (18 bp):
TAATCTTGAGATCTCTAG
Found at i:2134533 original size:3 final size:3
Alignment explanation
Indices: 2134525--2134576 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
2134515 TTTTTGTATA
** * *
2134525 TAT TAT TAT TAT CGT TAT T-T TAAT TAT TAT TAT TAG CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
2134570 TAT TAT T
1 TAT TAT T
2134577 TAACTTACAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2138171 original size:29 final size:30
Alignment explanation
Indices: 2138119--2138176 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
2138109 TATTTTCATG
2138119 TACTAACTTATTTTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTTCTCTTTTGTTTGTGTA
2138149 TACTAACTTA-TTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTTCTCTTTTGTTTGTGT
2138177 CATTTTGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.60
Consensus pattern (30 bp):
TACTAACTTATTTTCTCTTTTGTTTGTGTA
Found at i:2140245 original size:25 final size:22
Alignment explanation
Indices: 2140202--2140258 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 22
2140192 AAGATCAAAC
*
2140202 CAAAGAAAAAAAAAACAAAGAG
1 CAAAGAAAAAAAAAACAAAAAG
*
2140224 CAAAGAAAAAAATCAAAGCAAAAAT
1 CAAAGAAAAAAA--AAA-CAAAAAG
2140249 CAAAGAAAAA
1 CAAAGAAAAA
2140259 GCAAAGAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 12 0.40
24 3 0.10
25 15 0.50
ACGTcount: A:0.75, C:0.11, G:0.11, T:0.04
Consensus pattern (22 bp):
CAAAGAAAAAAAAAACAAAAAG
Found at i:2140246 original size:13 final size:12
Alignment explanation
Indices: 2140224--2140271 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
2140214 AAACAAAGAG
2140224 CAAAGAAAAAAAT
1 CAAAG-AAAAAAT
*
2140237 CAAAGCAAAAAT
1 CAAAGAAAAAAT
*
2140249 CAAAG-AAAAAG
1 CAAAGAAAAAAT
2140260 CAAAGAACAAAA
1 CAAAGAA-AAAA
2140272 GAGGACAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.32
12 12 0.39
13 9 0.29
ACGTcount: A:0.73, C:0.12, G:0.10, T:0.04
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:2140257 original size:11 final size:11
Alignment explanation
Indices: 2140231--2140266 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2140221 GAGCAAAGAA
2140231 AAAAATCAAAG
1 AAAAATCAAAG
2140242 CAAAAATCAAAG
1 -AAAAATCAAAG
*
2140254 AAAAAGCAAAG
1 AAAAATCAAAG
2140265 AA
1 AA
2140267 CAAAAGAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.72, C:0.11, G:0.11, T:0.06
Consensus pattern (11 bp):
AAAAATCAAAG
Found at i:2140270 original size:25 final size:24
Alignment explanation
Indices: 2140202--2140271 Score: 58
Period size: 25 Copynumber: 2.9 Consensus size: 24
2140192 AAGATCAAAC
*
2140202 CAAAGAAAAA-AAA-AACAAAGAG
1 CAAAGAAAAACAAAGAACAAAAAG
*
2140224 CAAAGAAAAA-AATCA-AAGCAAAAAT
1 CAAAGAAAAACAA--AGAA-CAAAAAG
2140249 CAAAGAAAAAGCAAAGAACAAAA
1 CAAAGAAAAA-CAAAGAACAAAA
2140272 GAGGACAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 12 0.30
24 3 0.08
25 21 0.52
26 2 0.05
27 2 0.05
ACGTcount: A:0.74, C:0.11, G:0.11, T:0.03
Consensus pattern (24 bp):
CAAAGAAAAACAAAGAACAAAAAG
Found at i:2141437 original size:4 final size:4
Alignment explanation
Indices: 2141428--2141473 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
2141418 GATCGAGAAA
* *
2141428 ACAT ACAT ACAT ACAA ACAT ATAT AC-- ACAT ACAT ACAT A-AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2141473 A
1 A
2141474 AAATTTGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 2 0.06
3 3 0.09
4 30 0.86
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:2141459 original size:18 final size:17
Alignment explanation
Indices: 2141436--2141471 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2141426 AAACATACAT
2141436 ACATACAAACATATATAC
1 ACATACAAACATA-ATAC
*
2141454 ACATACATACATAATAC
1 ACATACAAACATAATAC
2141471 A
1 A
2141472 TAAAATTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (17 bp):
ACATACAAACATAATAC
Found at i:2142151 original size:36 final size:35
Alignment explanation
Indices: 2142076--2142208 Score: 117
Period size: 36 Copynumber: 3.7 Consensus size: 35
2142066 GTTTCACATT
* * ** *
2142076 AAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAAA
1 AAACAAATTTG-TCTCGCTTGAGA-CAATTTCTCTAA
2142113 AAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
1 AAACAAA-TTTGTCTCGCTTGAGACAATTTCTCTAA
** * *
2142149 AAACAAATTTTGTCTCATTTGAGACTATATCT-T-A
1 AAACAAA-TTTGTCTCGCTTGAGACAATTTCTCTAA
*
2142183 AAGCAAATTTCGTCTCGCTTGAGACA
1 AAACAAATTT-GTCTCGCTTGAGACA
2142209 TTTTTCCTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
33 3 0.04
34 19 0.24
35 1 0.01
36 36 0.45
37 18 0.22
38 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (35 bp):
AAACAAATTTGTCTCGCTTGAGACAATTTCTCTAA
Found at i:2142597 original size:29 final size:29
Alignment explanation
Indices: 2142555--2142653 Score: 139
Period size: 29 Copynumber: 3.5 Consensus size: 29
2142545 TTTCTCTTGA
2142555 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
2142584 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
* * *
2142613 AAATATCTTTGAG-TCGTTTCTTTTGAA-
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
2142640 AAAAAACTTTGAGT
1 AAAAATCTTTGAGT
2142654 CTATTTATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
27 11 0.18
28 12 0.19
29 39 0.63
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCTTTTGAAT
Found at i:2142664 original size:28 final size:27
Alignment explanation
Indices: 2142605--2142668 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
2142595 AGTTTGTTCC
* * * *
2142605 TTTTGAATAAATATCTTTGAGTCGTTTC
1 TTTTGAA-AAAAAACTTTGAGTCATTTA
2142633 TTTTGAAAAAAAACTTTGAGTCTATTTA
1 TTTTGAAAAAAAACTTTGAGTC-ATTTA
2142661 TTTTGAAA
1 TTTTGAAA
2142669 CAAAGTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (27 bp):
TTTTGAAAAAAAACTTTGAGTCATTTA
Found at i:2142665 original size:56 final size:56
Alignment explanation
Indices: 2142551--2142668 Score: 132
Period size: 56 Copynumber: 2.1 Consensus size: 56
2142541 ACAGTTTCTC
* * * * *
2142551 TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAATCTTTGAGTTCGTTCCTTTTGAATAAAAAACTTGGAGTCTATTCATT
* * *
2142607 TTGAATAAATATCTTTGAG-TCGTTTCTTTTGAA-AAAAAACTTTGAGTCTATTTATT
1 TTGAA-AAA-ATCTTTGAGTTCGTTCCTTTTGAATAAAAAACTTGGAGTCTATTCATT
2142663 TTGAAA
1 TTGAAA
2142669 CAAAGTTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
55 1 0.02
56 27 0.52
57 15 0.29
58 9 0.17
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (56 bp):
TTGAAAAAATCTTTGAGTTCGTTCCTTTTGAATAAAAAACTTGGAGTCTATTCATT
Found at i:2142742 original size:52 final size:52
Alignment explanation
Indices: 2142664--2142767 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
2142654 CTATTTATTT
*
2142664 TGAAACAAAGTTTTATCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTATATCTCTTGAGACAATTT-GTGAAAAAATCTTTGAGTC
*
2142716 TGAAACAAAGTTTTGTATCTCTTGAGACAATTTGTGAAAAAAATCTTTGAGT
1 TGAAACAAAGTTTTATATCTCTTGAGACAATTTGTG-AAAAAATCTTTGAGT
2142768 TGTTTCTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
51 3 0.06
52 31 0.65
53 14 0.29
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (52 bp):
TGAAACAAAGTTTTATATCTCTTGAGACAATTTGTGAAAAAATCTTTGAGTC
Found at i:2142863 original size:67 final size:67
Alignment explanation
Indices: 2142754--2142908 Score: 242
Period size: 67 Copynumber: 2.3 Consensus size: 67
2142744 AATTTGTGAA
* *
2142754 AAAAATCTTTGAG-TTGTTTCTTTGGAAACAAAATTCTTTCTCTTTTAAGATAGTTTCTTTTGAA
1 AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATAATTTCTTTTGAA
2142818 AC
66 AC
*
2142820 AAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATT-TTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTT-TCTCTCTTAAGATAATTTCTTTTGA
2142884 AAC
65 AAC
* *
2142887 AAAAATCTTTGAATCTGTTTCT
1 AAAAATCTTTGAGTTTGTTTCT
2142909 CTTAAAATGA
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
66 15 0.18
67 67 0.82
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (67 bp):
AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATAATTTCTTTTGAA
AC
Found at i:2143192 original size:120 final size:117
Alignment explanation
Indices: 2143009--2143229 Score: 263
Period size: 120 Copynumber: 1.9 Consensus size: 117
2142999 TTAACAAAAT
* * *
2143009 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTAATTAAAAAC
1 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATTAAAAA-
2143074 TAACTTTTGAGATT-GTTTCATTTGAAAC-AAATTTGGTCTTACTTAAGATGTAATC
65 T--C-TTTGAG-TTGGTTTCATTTGAAACAAAATTTGGTCTTACTTAAGATGTAATC
** *
2143129 CATCTTTGAGTCTATTTCTTTTGAAACAAAAT-TT-TATCTCTTAAAGACAATTTCT-TTTGAAA
1 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTAATT-AAA
* *
2143191 AATCTTTGAGTTGGTTTCCTTTGAAACAAAATTTTGTCT
63 AATCTTTGAGTTGGTTTCATTTGAAACAAAATTTGGTCT
2143230 CTCGAGATAA
Statistics
Matches: 88, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
115 2 0.02
116 19 0.22
117 11 0.12
119 10 0.11
120 42 0.48
121 4 0.05
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (117 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATTAAAAAT
CTTTGAGTTGGTTTCATTTGAAACAAAATTTGGTCTTACTTAAGATGTAATC
Found at i:2143719 original size:35 final size:37
Alignment explanation
Indices: 2143653--2143732 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 37
2143643 TGTTTCTTTG
* * *
2143653 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT-
1 GAAACAAAATTAAACATCTTTGAAACTGTTTCCCTTA
2143689 GAAACAAAA-TAAACATCTTTGAGAAC-GTTTCCCTTA
1 GAAACAAAATTAAACATCTTTGA-AACTGTTTCCCTTA
*
2143725 AAAACAAA
1 GAAACAAA
2143733 TTTTGTCTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 20 0.53
36 18 0.47
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (37 bp):
GAAACAAAATTAAACATCTTTGAAACTGTTTCCCTTA
Found at i:2144066 original size:40 final size:40
Alignment explanation
Indices: 2144011--2144376 Score: 200
Period size: 40 Copynumber: 8.6 Consensus size: 40
2144001 TGGCCAGTAG
* *
2144011 TCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATC
* * ** * *
2144051 TCCTCATCACGTAGGAGTCGTGTCAACCATTGGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCC---CCA-GACCAGATC
* * * *
2144094 ATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATTGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCATC-CC--CAGA----CCAGATC
* * *
2144142 TCTTCATCACGTATGAGCCGTGCCATTCCCCAGACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCA-TCCCCAGACCAGATC
* * * *
2144183 TCCTCATCACGTATGAGCTGTGTCATCCCCTGACCAGATT
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATC
* * * *
2144223 TCCTCATCACGTAGGAACCGGGTCA-CCCTTAGATAACCAG-TAG
1 TCCTCATCACGTAGGAGCCGTGTCATCCC-CAG---ACCAGAT-C
* * * *
2144266 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 TCCTCATCACGTAGGAGCCGTGTCATC-CC--CAGA---CCAGATC
* * *
2144312 TCTTCATCACGTATGAGCCGTGTCATTCCCC-GACCAGAGC
1 TCCTCATCACGTAGGAGCCGTGTCA-TCCCCAGACCAGATC
*
2144352 TCTTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAGCCGTGTCA
2144377 CCTTTAGACG
Statistics
Matches: 253, Mismatches: 46, Indels: 54
0.72 0.13 0.15
Matches are distributed among these distances:
39 3 0.01
40 89 0.35
41 28 0.11
42 1 0.00
43 34 0.13
44 30 0.12
45 6 0.02
46 31 0.12
47 28 0.11
48 3 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATC
Found at i:2144192 original size:41 final size:40
Alignment explanation
Indices: 2144135--2144235 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 40
2144125 TTTAGATTGG
* *
2144135 CCAGAACTCTTCATCACGTATGAGCCGTGCCATTCCCCAGA
1 CCAGATCTCCTCATCACGTATGAGCCGTGCCA-TCCCCAGA
* * *
2144176 CCAGATCTCCTCATCACGTATGAGCTGTGTCATCCCCTGA
1 CCAGATCTCCTCATCACGTATGAGCCGTGCCATCCCCAGA
*
2144216 CCAGATTTCCTCATCACGTA
1 CCAGATCTCCTCATCACGTA
2144236 GGAACCGGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
40 26 0.48
41 28 0.52
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.26
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTATGAGCCGTGCCATCCCCAGA
Found at i:2144301 original size:171 final size:170
Alignment explanation
Indices: 2144011--2144376 Score: 556
Period size: 172 Copynumber: 2.1 Consensus size: 170
2144001 TGGCCAGTAG
* * ** *
2144011 TCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGTCGTGTCA
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAACCGGGTCA
*
2144076 ACCATTGGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATTGGCCAGAA
66 ACCATTAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA-TGGCCAGAA
*
2144141 CTCTTCATCACGTATGAGCCGTGCCATTCCCCAGACCAGATC
130 CTCTTCATCACGTATGAGCCGTGCCATTCCCC-GACCAGAGC
* * * *
2144183 TCCTCATCACGTATGAGCTGTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTC-
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAACCGGGTCA
* *
2144247 ACCCTTAGATAACCAG-TAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAA
66 ACCATTAGATAACCAGCCA-TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAA
*
2144311 CTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGAGC
130 CTCTTCATCACGTATGAGCCGTGCCATTCCCCGACCAGAGC
*
2144352 TCTTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAGCCGTGTCA
2144377 CCTTTAGACG
Statistics
Matches: 176, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
169 30 0.17
170 41 0.23
171 50 0.28
172 55 0.31
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (170 bp):
TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAACCGGGTCA
ACCATTAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
TCTTCATCACGTATGAGCCGTGCCATTCCCCGACCAGAGC
Found at i:2144403 original size:43 final size:43
Alignment explanation
Indices: 2144042--2144418 Score: 166
Period size: 40 Copynumber: 8.8 Consensus size: 43
2144032 GTCATCCCCA
* * * * * *
2144042 GACCAGATCTCCTCATCACGTAGGAGTCGTGTCAACCATTGGAT
1 GACCAGAACTCTTCATCACGTAGGAGCCGTGTC-ACCTTTAGAC
* * * * *
2144086 AACCAG-CCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATT
1 GACCAGAAC-TCTTCATCACGTAGGAGCCGTG---TCACCTTTAGA-C
* * * ***
2144133 GGCCAGAACTCTTCATCACGTATGAGCCGTG---CCATTCCCC
1 GACCAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGAC
* * * * **
2144173 AGACCAGATCTCCTCATCACGTATGAGCTGTGTCATCCCCT----
1 -GACCAGAACTCTTCATCACGTAGGAGCCGTGTCA-CCTTTAGAC
** * * * * *
2144214 GACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGAT
1 GACCAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGAC
* * * * * *
2144257 AACCAGTAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGAT
1 GACCAGAACTCTTCATCACGTAGGAGCCGTG---TCACCTTTAGAC
* * ***
2144303 GGCCAGAACTCTTCATCACGTATGAGCCGTGTCA---TTCCCC
1 GACCAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGAC
*
2144343 GACCAGAGCTCTTCATCACGTAGGAGCCGTGTCACCTTTAGAC
1 GACCAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGAC
* *
2144386 GACCCA-AACTCTTCATCACGTATGAGCAGTGTC
1 GA-CCAGAACTCTTCATCACGTAGGAGCCGTGTC
2144419 GTCCCCAACA
Statistics
Matches: 256, Mismatches: 55, Indels: 45
0.72 0.15 0.13
Matches are distributed among these distances:
39 4 0.02
40 62 0.24
41 31 0.12
43 59 0.23
44 28 0.11
45 3 0.01
46 42 0.16
47 26 0.10
48 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (43 bp):
GACCAGAACTCTTCATCACGTAGGAGCCGTGTCACCTTTAGAC
Found at i:2144581 original size:3 final size:3
Alignment explanation
Indices: 2144573--2144620 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
2144563 TTTTTGTATA
* * * *
2144573 TAT TAT TAT TAT CAT TAT T-T AAT TAT TAT TAT TAG CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2144620 T
1 T
2144621 TAACTTACAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
2 1 0.03
3 35 0.97
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2148987 original size:26 final size:26
Alignment explanation
Indices: 2148956--2149005 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2148946 AAGGAAAGAA
*
2148956 TAAAATTACCATTAAAGGAAGATGAT
1 TAAAATGACCATTAAAGGAAGATGAT
**
2148982 TAAAATGGTCATTAAAGGAAGATG
1 TAAAATGACCATTAAAGGAAGATG
2149006 GGAGATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (26 bp):
TAAAATGACCATTAAAGGAAGATGAT
Found at i:2163581 original size:27 final size:26
Alignment explanation
Indices: 2163534--2163586 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
2163524 CCCTCGAGCC
2163534 TCCATCCCCAAATCCTCCCCTCTCTCG
1 TCCATCCCCAAATCCTCCCCTC-CTCG
* *
2163561 TCCATTCCC-AATCTCTTCCCTCCTCG
1 TCCATCCCCAAATC-CTCCCCTCCTCG
2163587 CCGTTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.13, C:0.53, G:0.04, T:0.30
Consensus pattern (26 bp):
TCCATCCCCAAATCCTCCCCTCCTCG
Found at i:2168534 original size:15 final size:15
Alignment explanation
Indices: 2168514--2168543 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2168504 TTGTGCTTCT
2168514 GGCCTGCTCCATCTC
1 GGCCTGCTCCATCTC
*
2168529 GGCCTGCTCCCTCTC
1 GGCCTGCTCCATCTC
2168544 ATCAGGTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.50, G:0.20, T:0.27
Consensus pattern (15 bp):
GGCCTGCTCCATCTC
Found at i:2168667 original size:27 final size:26
Alignment explanation
Indices: 2168620--2168672 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
2168610 CCCTCGAGCC
2168620 TCCATCCCCAAATCCTCCCCTCTCTCG
1 TCCATCCCCAAATCCTCCCCTC-CTCG
* *
2168647 TCCATTCCC-AATCTCTTCCCTCCTCG
1 TCCATCCCCAAATC-CTCCCCTCCTCG
2168673 CCGTTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.13, C:0.53, G:0.04, T:0.30
Consensus pattern (26 bp):
TCCATCCCCAAATCCTCCCCTCCTCG
Found at i:2176397 original size:19 final size:19
Alignment explanation
Indices: 2176373--2176428 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 19
2176363 TTTACCTCAC
2176373 TAACCCTTTTATTTTTTGT
1 TAACCCTTTTATTTTTTGT
2176392 TAACCCTTTTATTTTTTGT
1 TAACCCTTTTATTTTTTGT
* *
2176411 T--CTCTTTTATTTTGTGT
1 TAACCCTTTTATTTTTTGT
2176428 T
1 T
2176429 CATCGTTTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.43
19 20 0.57
ACGTcount: A:0.12, C:0.14, G:0.07, T:0.66
Consensus pattern (19 bp):
TAACCCTTTTATTTTTTGT
Found at i:2177082 original size:26 final size:26
Alignment explanation
Indices: 2177064--2177133 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
2177054 ATTTTGTTAT
2177064 TTTTCTTTACATTCACATTATTTTTCC
1 TTTT-TTTACATTCACATTATTTTTCC
2177091 TTTTTTTACATTCACATTATTTTTCC
1 TTTTTTTACATTCACATTATTTTTCC
2177117 TTTTTTTACATTCACAT
1 TTTTTTTACATTCACAT
2177134 GTCTTATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 39 0.91
27 4 0.09
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTTTTACATTCACATTATTTTTCC
Found at i:2179231 original size:45 final size:45
Alignment explanation
Indices: 2179177--2179268 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
2179167 GGGCCATCAT
2179177 TCATTTAAAGGAAATTTACAGCACAACTTAAGTCAAGAAAAGTTG
1 TCATTTAAAGGAAATTTACAGCACAACTTAAGTCAAGAAAAGTTG
2179222 TCATTTAAAGGAAATTTACAGCACAACTTAAGTCAAGAAAAGTTG
1 TCATTTAAAGGAAATTTACAGCACAACTTAAGTCAAGAAAAGTTG
2179267 TC
1 TC
2179269 TGTCAACAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (45 bp):
TCATTTAAAGGAAATTTACAGCACAACTTAAGTCAAGAAAAGTTG
Found at i:2179459 original size:106 final size:108
Alignment explanation
Indices: 2179269--2179501 Score: 312
Period size: 106 Copynumber: 2.2 Consensus size: 108
2179259 AAAAGTTGTC
* * * *
2179269 TGTCAACAAACAACTTTCCAATTTCATTCAGAGTCTATTTCAACTTCGCAGCGAAGAAAATTGGA
1 TGTCAACAAACAACTTTCCAA-TT-ATTCAGAGCCAATTTCAACTTCACAACGAAGAAAATTGGA
* *
2179334 CTTCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGT
64 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
2179379 TGTCAACAAACAAC-TTCTCAA-T-TTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGGAC
1 TGTCAACAAACAACTTTC-CAATTATTCAGAGCCAATTTCAACTTCACAACGAAGAAAATTGGAC
*
2179441 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGT
65 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
2179485 TGTCAATAAACAA-TTTC
1 TGTCAACAAACAACTTTC
2179502 AACTTCACAG
Statistics
Matches: 110, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
106 89 0.81
108 1 0.01
109 3 0.03
110 17 0.15
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (108 bp):
TGTCAACAAACAACTTTCCAATTATTCAGAGCCAATTTCAACTTCACAACGAAGAAAATTGGACT
CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:2179474 original size:43 final size:43
Alignment explanation
Indices: 2179413--2179560 Score: 142
Period size: 43 Copynumber: 3.4 Consensus size: 43
2179403 CAGAGCCAAT
* *
2179413 TTCAACTTTACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
** * * * * *
2179456 TTCAACTTCACGACGAAGGGATCGCTGG-TTGTCA-ATAA-ACAAT
1 TTCAACTTCACGACGAA-GGAT-ATTGGACT-CCAGACAACGCAAG
2179499 TTCAACTTCAC-AGCGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGA-CGAAGGATATTGGACTCCAGACAACGCAAG
*
2179542 TTCAACTTCACGATGAAGG
1 TTCAACTTCACGACGAAGG
2179561 GACCGCTGGT
Statistics
Matches: 80, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
41 5 0.06
42 9 0.11
43 52 0.65
44 9 0.11
45 5 0.06
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:2179554 original size:86 final size:86
Alignment explanation
Indices: 2179409--2179615 Score: 344
Period size: 86 Copynumber: 2.4 Consensus size: 86
2179399 ATTTCAGAGC
* *
2179409 CAATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
2179474 GGATCGCTGGTTGTCAATAAA
66 GGACCGCTGGTTGTCAATAAA
*
2179495 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
2179560 GGACCGCTGGTTGTCAATAAA
66 GGACCGCTGGTTGTCAATAAA
*
2179581 CAACTTTCAACTTCAC-GACGGAGGATATTGGACTC
1 CAA-TTTCAACTTCACAG-CGAAGGATATTGGACTC
2179616 GGAACAATGC
Statistics
Matches: 114, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
86 86 0.75
87 28 0.25
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (86 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAATAAA
Found at i:2180254 original size:85 final size:83
Alignment explanation
Indices: 2179792--2180330 Score: 540
Period size: 83 Copynumber: 6.5 Consensus size: 83
2179782 ATATCCAACT
* * *
2179792 CGAGAA-GGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA
1 CGAGAAGGGCTATCTGCCACCAAAGACCCTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCA
* *
2179853 TTTACAGCATAACTCAAGG
65 TTTGCAGCATAACTTAAGG
* * * * * *
2179872 CTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
1 CGAGAAGGGCTATCTGCCACC-AAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACATCA
* *
2179937 TTTGCAGCATAGCTTAAGT
65 TTTGCAGCATAACTTAAGG
* * * *
2179956 CGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCA
1 CGAGAAGGGCTATCTGCCACCAAAGACCCTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCA
* * *
2180018 TTTACAACATAACTCAAGG
65 TTTGCAGCATAACTTAAGG
* * * * * ** *
2180037 CTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGTTCAGCTCTAAGGCACATCAT
1 CGAGAAGGGCTATCTGCCACCAAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACATCAT
* *
2180102 TTGCACCATAACTTAGGG
66 TTGCAGCATAACTTAAGG
* * * * *
2180120 CTAGAAGGGTTATCTACCAACC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAAT-
1 CGAGAAGGGCTATCTGCC-ACCAAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCAC-ATC
* **
2180183 ATTTGCAGCATAGCTTAAAT
64 ATTTGCAGCATAACTTAAGG
* *
2180203 CGAGAAGAGCTATCTGCCATCCAAAAGACCCTCGAGTTCGATTACACTCAGCTCCGAGGCACATC
1 CGAGAAGGGCTATCTGCCA-CC-AAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACATC
* *
2180268 ATTTGCAGCATAGCTTAAGT
64 ATTTGCAGCATAACTTAAGG
2180288 CGAGAAGGGCTATCTGCCAGCCAAAGA-CCTGACGAGTTCGATT
1 CGAGAAGGGCTATCTGCCA-CCAAAGACCCT--CGAGTTCGATT
2180331 TTATTCAGCT
Statistics
Matches: 381, Mismatches: 61, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
80 30 0.08
81 49 0.13
82 1 0.00
83 110 0.29
84 81 0.21
85 110 0.29
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (83 bp):
CGAGAAGGGCTATCTGCCACCAAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACATCAT
TTGCAGCATAACTTAAGG
Found at i:2180341 original size:85 final size:83
Alignment explanation
Indices: 2179792--2180330 Score: 547
Period size: 85 Copynumber: 6.5 Consensus size: 83
2179782 ATATCCAACT
** * *
2179792 CGAGAA-GGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA
1 CGAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCA
* *
2179853 TTTACAGCATAACTCAAGG
65 TTTGCAGCATAACTTAAGG
* * * * *
2179872 CTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
1 CGAGAAGGGCTATCTGCCACC-AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCA
* *
2179937 TTTGCAGCATAGCTTAAGT
65 TTTGCAGCATAACTTAAGG
** * * *
2179956 CGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCA
1 CGAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCA
* * *
2180018 TTTACAACATAACTCAAGG
65 TTTGCAGCATAACTTAAGG
* * * * ** *
2180037 CTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGTTCAGCTCTAAGGCACATCAT
1 CGAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCAT
* *
2180102 TTGCACCATAACTTAGGG
66 TTGCAGCATAACTTAAGG
* * * *
2180120 CTAGAAGGGTTATCTACCAACC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAAT-
1 CGAGAAGGGCTATCTGCC-ACCAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCAC-ATC
* **
2180183 ATTTGCAGCATAGCTTAAAT
64 ATTTGCAGCATAACTTAAGG
* * *
2180203 CGAGAAGAGCTATCTGCCATCCAAAAGACCCTCGAGTTCGATTACACTCAGCTCCGAGGCACATC
1 CGAGAAGGGCTATCTGCCA-CC-AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATC
* *
2180268 ATTTGCAGCATAGCTTAAGT
64 ATTTGCAGCATAACTTAAGG
*
2180288 CGAGAAGGGCTATCTGCCAGCCAAAGACCTGACGAGTTCGATT
1 CGAGAAGGGCTATCTGCCA-CCAAAGACCT-TCGAGTTCGATT
2180331 TTATTCAGCT
Statistics
Matches: 380, Mismatches: 63, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
80 30 0.08
81 49 0.13
82 1 0.00
83 107 0.28
84 83 0.22
85 110 0.29
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (83 bp):
CGAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCAT
TTGCAGCATAACTTAAGG
Found at i:2180582 original size:16 final size:15
Alignment explanation
Indices: 2180561--2180604 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2180551 TATTTTTATT
2180561 TTTATTGTATTATTTA
1 TTTATT-TATTATTTA
2180577 TTTATTTAATTATTTA
1 TTTATTT-ATTATTTA
*
2180593 ATTA-TTATTATT
1 TTTATTTATTATT
2180605 ATTATTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 6 0.23
15 3 0.12
16 17 0.65
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTATTTATTATTTA
Found at i:2180584 original size:8 final size:8
Alignment explanation
Indices: 2180569--2180598 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2180559 TTTTTATTGT
2180569 ATTATTTA
1 ATTATTTA
*
2180577 TTTATTTA
1 ATTATTTA
2180585 ATTATTTA
1 ATTATTTA
2180593 ATTATT
1 ATTATT
2180599 ATTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
ATTATTTA
Found at i:2189158 original size:4 final size:4
Alignment explanation
Indices: 2189149--2189174 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2189139 ATATAGGTAC
2189149 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
2189175 AAAATACGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:2194976 original size:51 final size:50
Alignment explanation
Indices: 2194908--2195004 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 50
2194898 ATTATAATGA
* *
2194908 TTTTTATATTTAATTACTGATATTTGATGTATTATCCACTAAACATTATT
1 TTTTTATATTTAATTACTGATATTCGATCTATTATCCACTAAACATTATT
* * *
2194958 TTTTTCATATTTAATTACTGATGTTCGATCTATTATCGATTAAACAT
1 TTTTT-ATATTTAATTACTGATATTCGATCTATTATCCACTAAACAT
2195005 GATTAAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 5 0.12
51 36 0.88
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (50 bp):
TTTTTATATTTAATTACTGATATTCGATCTATTATCCACTAAACATTATT
Found at i:2195612 original size:6 final size:6
Alignment explanation
Indices: 2195601--2195639 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2195591 ATCAAAAAAG
* * *
2195601 GAAGCC GAAGCC GAAGCC GAATCC GAATCC GAATCC GAA
1 GAAGCC GAAGCC GAAGCC GAAGCC GAAGCC GAAGCC GAA
2195640 TCGGAAGAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (6 bp):
GAAGCC
Found at i:2195618 original size:12 final size:12
Alignment explanation
Indices: 2195601--2195639 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2195591 ATCAAAAAAG
*
2195601 GAAGCCGAAGCC
1 GAAGCCGAATCC
2195613 GAAGCCGAATCC
1 GAAGCCGAATCC
*
2195625 GAATCCGAATCC
1 GAAGCCGAATCC
2195637 GAA
1 GAA
2195640 TCGGAAGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (12 bp):
GAAGCCGAATCC
Found at i:2195632 original size:18 final size:18
Alignment explanation
Indices: 2195605--2195646 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2195595 AAAAAGGAAG
2195605 CCGAAGCCGAAGCCGAAT
1 CCGAAGCCGAAGCCGAAT
* *
2195623 CCGAATCCGAATCCGAAT
1 CCGAAGCCGAAGCCGAAT
*
2195641 CGGAAG
1 CCGAAG
2195647 AGCCTGAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.31, G:0.26, T:0.10
Consensus pattern (18 bp):
CCGAAGCCGAAGCCGAAT
Found at i:2195640 original size:6 final size:6
Alignment explanation
Indices: 2195605--2195641 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
2195595 AAAAAGGAAG
* *
2195605 CCGAAG CCGAAG CCGAAT CCGAAT CCGAAT CCGAAT C
1 CCGAAT CCGAAT CCGAAT CCGAAT CCGAAT CCGAAT C
2195642 GGAAGAGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.32, C:0.35, G:0.22, T:0.11
Consensus pattern (6 bp):
CCGAAT
Found at i:2198889 original size:13 final size:13
Alignment explanation
Indices: 2198883--2198907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2198873 TAAATTATTC
2198883 TTTTAAATAATAT
1 TTTTAAATAATAT
2198896 TTTTAAATAATA
1 TTTTAAATAATA
2198908 AAAATTGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTAAATAATAT
Found at i:2208722 original size:40 final size:40
Alignment explanation
Indices: 2208678--2208763 Score: 122
Period size: 38 Copynumber: 2.2 Consensus size: 40
2208668 TTCGTTATTA
***
2208678 TATCTCTTTTGTGGATGCATTCACAAGGCATACATGGTTT
1 TATCTCTTTTGAAAATGCATTCACAAGGCATACATGGTTT
*
2208718 TATCTC--TTGAAAATGCATTCACAAGGCGTACATGGTTT
1 TATCTCTTTTGAAAATGCATTCACAAGGCATACATGGTTT
2208756 TATCTCTT
1 TATCTCTT
2208764 GAAAAGTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 34 0.85
40 6 0.15
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (40 bp):
TATCTCTTTTGAAAATGCATTCACAAGGCATACATGGTTT
Found at i:2208737 original size:38 final size:38
Alignment explanation
Indices: 2208692--2208768 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
2208682 TCTTTTGTGG
2208692 ATGCATTCACAAGGCATACATGGTTTTATCTCTTGAAA
1 ATGCATTCACAAGGCATACATGGTTTTATCTCTTGAAA
*
2208730 ATGCATTCACAAGGCGTACATGGTTTTATCTCTTGAAA
1 ATGCATTCACAAGGCATACATGGTTTTATCTCTTGAAA
2208768 A
1 A
2208769 GTAAAGATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (38 bp):
ATGCATTCACAAGGCATACATGGTTTTATCTCTTGAAA
Found at i:2213850 original size:27 final size:27
Alignment explanation
Indices: 2213788--2213854 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 27
2213778 CCTAAACCCG
2213788 AACCCGACCCGAATATCACATTAAAAAA
1 AACCCGACCCGAATATCACATT-AAAAA
2213816 AACCCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGAATATCACA-TTAAAAA
2213843 AACCCGACCCGA
1 AACCCGACCCGA
2213855 CCCGAACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.42
28 20 0.53
29 2 0.05
ACGTcount: A:0.45, C:0.34, G:0.09, T:0.12
Consensus pattern (27 bp):
AACCCGACCCGAATATCACATTAAAAA
Found at i:2213973 original size:241 final size:234
Alignment explanation
Indices: 2213585--2214037 Score: 721
Period size: 241 Copynumber: 1.9 Consensus size: 234
2213575 ACCCGACTCA
*
2213585 ACCCGAATATCACACTTAAAAAACCCGACCGACCCGAACAAAATAAAGTTTCATCCGATCCGACC
1 ACCCGAATATCACACTTAAAAAACCCGACCGACCCGAACAAAATAAAGTTTCAT-C-ACCCGACC
*
2213650 CGAATATATGAATTAAAAATCCGACCCGACCCGAAATAATAAAAATTATTTTTATTTAATAAAAA
64 CGAATATATGAATTAAAAACCCGACCCGACCCGAAATAATAAAAATTATTTTTATTTAATAAAAA
*
2213715 TAGTAACTTAATCCGACCCGACCCGAATTATATATATTTTTGGGTCGGTCCGGTTTTTTTCACCC
129 TAGTAACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGG-TTTTTTCACCC
2213780 TAAACCCGAACCCGACCCGAATATCACATTAAAAAAAACCCG
193 TAAACCCGAACCCGACCCGAATATCACATTAAAAAAAACCCG
* *
2213822 ACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTTAT-ACCCGTCCC
1 ACCCGAATATCACACTTAAAAAACCCGA-CCGACCCGAACAAAATAAAGTTTCATCACCCGACCC
2213886 GAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAAT
65 GAATATATGAATT--AAA---AACCCGACCCGACCCGAAATAAT-AAAAATTATTTTTATTTAAT
* *
2213951 -AAAATCAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTTT
124 AAAAAT-AGTAACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTT
*
2214015 CACCCTAAACCCGAACCTGACCC
188 CACCCTAAACCCGAACCCGACCC
2214038 ATCCCGAATA
Statistics
Matches: 200, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
235 20 0.10
237 31 0.16
238 25 0.12
240 55 0.28
241 69 0.34
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (234 bp):
ACCCGAATATCACACTTAAAAAACCCGACCGACCCGAACAAAATAAAGTTTCATCACCCGACCCG
AATATATGAATTAAAAACCCGACCCGACCCGAAATAATAAAAATTATTTTTATTTAATAAAAATA
GTAACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTCACCCTAA
ACCCGAACCCGACCCGAATATCACATTAAAAAAAACCCG
Found at i:2218301 original size:229 final size:227
Alignment explanation
Indices: 2217891--2218339 Score: 790
Period size: 229 Copynumber: 2.0 Consensus size: 227
2217881 GTAAATTATC
* * *
2217891 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
2217956 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
2218021 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
2218086 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
2218119 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
2218184 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
2218249 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
2218314 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
2218340 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 40 0.19
229 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:2218428 original size:20 final size:20
Alignment explanation
Indices: 2218405--2218454 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2218395 CGATATACCA
2218405 GGTAAAATTATGATAAAACC
1 GGTAAAATTATGATAAAACC
*
2218425 GGTAACAA-AATGATAAAACC
1 GGTAA-AATTATGATAAAACC
2218445 GGTAAAATTA
1 GGTAAAATTA
2218455 AAAGTGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (20 bp):
GGTAAAATTATGATAAAACC
Found at i:2218595 original size:20 final size:19
Alignment explanation
Indices: 2218572--2218618 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2218562 CGATATAACA
*
2218572 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
2218592 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
2218612 GGTAAAA
1 GGTAAAA
2218619 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:2222528 original size:183 final size:184
Alignment explanation
Indices: 2222188--2223037 Score: 1613
Period size: 183 Copynumber: 4.7 Consensus size: 184
2222178 CTTTCAACAT
*
2222188 ATTATAAT-AAATAGATAATTTTGTAATATAACC-GTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
2222251 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
2222316 AATGTGTCGATACGATTTCAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
2222370 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
2222435 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
2222499 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
2222553 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
2222618 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
2222683 AATGTGTCGATACAATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
2222736 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
2222801 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
2222865 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
2222919 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
2222984 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTC-GTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
2223038 CCATTTAAAA
Statistics
Matches: 659, Mismatches: 5, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
182 44 0.07
183 503 0.76
184 112 0.17
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:2225613 original size:23 final size:23
Alignment explanation
Indices: 2225587--2225649 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2225577 ATAGGTAAAC
*
2225587 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2225610 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2225633 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
2225650 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2225657 original size:23 final size:23
Alignment explanation
Indices: 2225587--2225659 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2225577 ATAGGTAAAC
* * **
2225587 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
2225610 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
2225633 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
2225656 ATAT
1 ATAT
2225660 GTAAAGTGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:2226048 original size:22 final size:23
Alignment explanation
Indices: 2226015--2226076 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
2226005 ATAGGTAAAC
*
2226015 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2226038 ATAT-ATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2226060 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
2226077 ATGGTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 19 0.54
23 16 0.46
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2226084 original size:23 final size:22
Alignment explanation
Indices: 2226015--2226091 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
2226005 ATAGGTAAAC
* **
2226015 ATATGATGTAATAGGTAGCCCTT
1 ATAT-ATGTAATAGGTATCGGTT
*
2226038 ATATATGTAATAGGTATCGTTT
1 ATATATGTAATAGGTATCGGTT
2226060 ATATAATGTAATAGGTAAT-GGTT
1 ATAT-ATGTAATAGGT-ATCGGTT
2226083 ATAT-TGTAA
1 ATATATGTAA
2226092 AGTGTCTATC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.10
22 19 0.40
23 22 0.46
24 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (22 bp):
ATATATGTAATAGGTATCGGTT
Found at i:2227486 original size:23 final size:23
Alignment explanation
Indices: 2227451--2227510 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
2227441 ATCAAATAAA
* *
2227451 ATAATAAATTAGGTAACGTTTAT
1 ATAATAAAATAGGTAACGGTTAT
** *
2227474 ATAATGTAATAGGTAGCGGTTAT
1 ATAATAAAATAGGTAACGGTTAT
2227497 ATAATAAAATAGGT
1 ATAATAAAATAGGT
2227511 TAATTACTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.35
Consensus pattern (23 bp):
ATAATAAAATAGGTAACGGTTAT
Found at i:2227573 original size:23 final size:23
Alignment explanation
Indices: 2227547--2227597 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2227537 AATAACATAT
* **
2227547 TAGGTAGCGTTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
2227570 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
2227593 TAGGT
1 TAGGT
2227598 TAATTACTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:2227577 original size:87 final size:87
Alignment explanation
Indices: 2227431--2227649 Score: 366
Period size: 87 Copynumber: 2.5 Consensus size: 87
2227421 ATTATTTAAA
* * * * * *
2227431 TGGAAATATTATCAAATAAAATAATAAATTAGGTAACGTTTATATAATGTAATAGGTAGCGGTTA
1 TGGAAATATTATCAAGTACAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCTTA
2227496 TATAATAAAATAGGTTAATTAC
66 TATAATAAAATAGGTTAATTAC
*
2227518 TGGAAATATTATCAAGCACAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCTTA
1 TGGAAATATTATCAAGTACAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCTTA
2227583 TATAATAAAATAGGTTAATTAC
66 TATAATAAAATAGGTTAATTAC
*
2227605 TGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATAT
1 TGGAAATATTATCAAGTACAATAACATATTAGGTAGCGTTTATAT
2227650 TGACCTACTA
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 123 1.00
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.34
Consensus pattern (87 bp):
TGGAAATATTATCAAGTACAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCTTA
TATAATAAAATAGGTTAATTAC
Found at i:2228090 original size:198 final size:199
Alignment explanation
Indices: 2227662--2228327 Score: 849
Period size: 198 Copynumber: 3.4 Consensus size: 199
2227652 ACCTACTATA
* ** *
2227662 TCATAAAATCGATATATTTATACC-GGTAACATTACAAATTTACCTATTACATTATAATTTTCGG
1 TCATAAAACCGATATATTTATACCGGGT-ACATTGTAAATTTACCTATTACATTATAATTATCGG
* *
2227726 TTTCGATGTTTTTGGGATTGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCGTT
65 TTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTT
* * * *
2227789 GGACATTCATTCTGG-AAAAAGTATCGACACAAACTTAAAACGTGTCAATATATTATGTAGGCCT
129 GGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCT
2227853 ATTTTC
194 ATTTTC
* * ** * *
2227859 TCATAAAACCGGTATATTTCTATTGGGTACATTGTAAATTTACCTATTACATTGTAATTGTCGGT
1 TCATAAAACCGATATATTTATACCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGT
* * * * *
2227924 TTTGAT-TTTTTGGGATCGATACTTTTAATAAATATATCGACACTTTATGTGTTCACTTCGTTGG
66 TTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGG
* *
2227988 ACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAAACTTAT
131 ACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTAT
2228053 TTTC
196 TTTC
* ** * *
2228057 TCATAAAACCGATATATTTCTACCGAATACATTGTAAATTTACCTATTACATTGTAATTATTGGT
1 TCATAAAACCGATATATTTATACCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGT
* * * *
2228122 TTCAATGTTTTTAGGATCGATACTTTTAATAAATGTATCGACATTTTATGCGTGCACCTCGTTTG
66 TTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGG
* * *** * *
2228187 TCATTCATTCTGGACAAAATGTATCGACA-ATTTTTAAATTTGGGTCGATACATTATGTAGACCT
131 ACATTCATTCTGGA-AAAAAGTATCGACACAAACTTAAA-ATGTGTCGATACATTATGTAGACCT
*
2228251 ATTCTC
194 ATTTTC
* * * * *
2228257 TCATAAAACCGGTATATTTATACTGGTTACATTGTAAATTTAACTATTATATTATAATTATCGGT
1 TCATAAAACCGATATATTTATACCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGT
2228322 TTCGAT
66 TTCGAT
2228328 ATAACATATG
Statistics
Matches: 404, Mismatches: 58, Indels: 11
0.85 0.12 0.02
Matches are distributed among these distances:
195 3 0.01
196 15 0.04
197 102 0.25
198 114 0.28
199 70 0.17
200 100 0.25
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (199 bp):
TCATAAAACCGATATATTTATACCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGT
TTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGG
ACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACCTAT
TTTC
Found at i:2228471 original size:31 final size:30
Alignment explanation
Indices: 2228430--2228515 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
2228420 TTATAATAAA
*
2228430 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
2228460 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
*
2228490 TTATAAAATTATAGAT-ATAAT-ATTTT
1 TAATAAAA-TATA-ATAATAATAATTTT
2228516 AATAATGGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 2 0.04
30 28 0.58
31 16 0.33
32 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Done.