Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 56 of 135
Found at i:22890214 original size:29 final size:30
Alignment explanation
Indices: 22890161--22890221 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
22890151 ATTTTGTATG
22890161 AATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGCAATTTTTTTGTATGAATATTGT
*
22890191 AATATTGTAA-TTTTTTGTATGAATATTGT
1 AATATTGCAATTTTTTTGTATGAATATTGT
22890220 AA
1 AA
22890222 CGTTTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (30 bp):
AATATTGCAATTTTTTTGTATGAATATTGT
Found at i:22890488 original size:15 final size:15
Alignment explanation
Indices: 22890447--22890488 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
22890437 GTTAACTCAT
*
22890447 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
22890462 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
22890478 TTAAATTTTAT
1 TTAAATTTTAT
22890489 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:22891448 original size:16 final size:15
Alignment explanation
Indices: 22891417--22891460 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
22891407 ACAAAATCAA
22891417 ATAAAATTAAATTAT
1 ATAAAATTAAATTAT
*
22891432 ATAAAAGTTACATTAT
1 ATAAAA-TTAAATTAT
22891448 ATAAAAATTAAAT
1 AT-AAAATTAAAT
22891461 GAGTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAAATTAAATTAT
Found at i:22907356 original size:29 final size:30
Alignment explanation
Indices: 22907320--22907377 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
22907310 GTAAATACCC
* *
22907320 AAAATTTG-AGGGTTAAT-GTGTAAATATG
1 AAAATTTGAAGGATCAATAGTGTAAATATG
22907348 AAAATTTTGAAGGATCAATAGTGTAAATAT
1 AAAA-TTTGAAGGATCAATAGTGTAAATAT
22907378 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 4 0.16
30 7 0.28
31 10 0.40
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAATTTGAAGGATCAATAGTGTAAATATG
Found at i:22909439 original size:57 final size:60
Alignment explanation
Indices: 22909325--22909464 Score: 180
Period size: 57 Copynumber: 2.4 Consensus size: 60
22909315 AATTGACAGT
*
22909325 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAACCCTCCCGAAGAATATGTGTG
1 AAAAAGGATCTAGCCCGGACGGGTGATCC-AT-CTGATATAACCCTCCCGAAAAATATGTG-G
*
22909388 AAAAA-GATCTAGCCCGGACGGGTGAT-C-T-TGATATATCCCTCCCGAAAAATATGTGG
1 AAAAAGGATCTAGCCCGGACGGGTGATCCATCTGATATAACCCTCCCGAAAAATATGTGG
* * *
22909444 AAAATGGATTTAGCTCGGACG
1 AAAAAGGATCTAGCCCGGACG
22909465 AGTAATCCGA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
56 5 0.07
57 38 0.54
59 1 0.01
61 1 0.01
62 21 0.30
63 5 0.07
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (60 bp):
AAAAAGGATCTAGCCCGGACGGGTGATCCATCTGATATAACCCTCCCGAAAAATATGTGG
Found at i:22910571 original size:16 final size:17
Alignment explanation
Indices: 22910550--22910583 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22910540 ACATAATTAT
*
22910550 TAGTAA-AAGGTTAATA
1 TAGTAATAAGGTAAATA
22910566 TAGTAATAAGGTAAATA
1 TAGTAATAAGGTAAATA
22910583 T
1 T
22910584 TAAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
TAGTAATAAGGTAAATA
Found at i:22911511 original size:42 final size:42
Alignment explanation
Indices: 22911451--22911550 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
22911441 CTATATGAAC
* **
22911451 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
* * *
22911493 GGCACTAAGTGTGTGAAATTAAAATGATGATGTTGAATTACA
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
22911535 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
22911551 TACCAAGAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
Found at i:22916019 original size:2 final size:2
Alignment explanation
Indices: 22916012--22916037 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22916002 AGTAAATTGG
22916012 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
22916038 GCGTGGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22935033 original size:12 final size:12
Alignment explanation
Indices: 22935002--22935037 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
22934992 ACTGTGTAAA
* *
22935002 CTCTCTCTCTCT
1 CTCTCTCGCTCG
22935014 CTCTCTCGCTCG
1 CTCTCTCGCTCG
22935026 CTCTCTCGCTCG
1 CTCTCTCGCTCG
22935038 TTCACACAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.11, T:0.39
Consensus pattern (12 bp):
CTCTCTCGCTCG
Found at i:22937280 original size:13 final size:13
Alignment explanation
Indices: 22937262--22937338 Score: 91
Period size: 13 Copynumber: 5.9 Consensus size: 13
22937252 AGTTCTTCAT
22937262 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
22937275 TGCTTTTGGAAAG
1 TGCTTTTGAAAAG
* * *
22937288 TGCTGTGGAGAAG
1 TGCTTTTGAAAAG
* *
22937301 TGCTTTTCAGAAG
1 TGCTTTTGAAAAG
*
22937314 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
22937327 TGCTTTTGAAAA
1 TGCTTTTGAAAA
22937339 TTTTGAGTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 54 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:22940317 original size:64 final size:64
Alignment explanation
Indices: 22940200--22940319 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 64
22940190 GATCAGTATT
* * * * * * *
22940200 GATCCTGCATGTGTTGCGGACATACCGCAGCTCTTTGTAAGTGTTCTATTATATGATCGGTGTG
1 GATCCTGCATATATTGAGGACATACCGCAGCTCTTTATAAGCGTCCGATTATATGATCGGTGTG
*
22940264 GATCCTGCATATATTGAGGACATACCGCAGCTCTTTATGAGCGTCCCGA-TATATGA
1 GATCCTGCATATATTGAGGACATACCGCAGCTCTTTATAAGCGT-CCGATTATATGA
22940320 CTCTTAATGA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
64 45 0.96
65 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (64 bp):
GATCCTGCATATATTGAGGACATACCGCAGCTCTTTATAAGCGTCCGATTATATGATCGGTGTG
Found at i:22947254 original size:12 final size:11
Alignment explanation
Indices: 22947235--22947265 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
22947225 AATTGAAAGC
22947235 TTTTTTTCTCT
1 TTTTTTTCTCT
22947246 TTCTTTTTCTCT
1 TT-TTTTTCTCT
22947258 TTTTTTTC
1 TTTTTTTC
22947266 AGTTTAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:22947463 original size:31 final size:32
Alignment explanation
Indices: 22947397--22947463 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
22947387 AAAAATTGTT
**
22947397 AATAGTCTAGTAACTTAAATGAAAAACTTTTG
1 AATAGTCTAGTAACTTAAATGAAAAACTTCCG
* *
22947429 AATAGTTTAGTGACTTAAATG-AAAACTTCCG
1 AATAGTCTAGTAACTTAAATGAAAAACTTCCG
22947460 AATA
1 AATA
22947464 ACTCAATGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (32 bp):
AATAGTCTAGTAACTTAAATGAAAAACTTCCG
Found at i:22953729 original size:20 final size:21
Alignment explanation
Indices: 22953691--22953730 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
22953681 CCCATTTTTC
*
22953691 ATTCTTTTTTACGTTTAAATTT
1 ATTCTTTTATACG-TTAAATTT
22953713 ATTCTTTTATACG-TAAAT
1 ATTCTTTTATACGTTAAAT
22953731 CTAGAGACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTCTTTTATACGTTAAATTT
Found at i:22958301 original size:65 final size:64
Alignment explanation
Indices: 22958173--22958304 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 64
22958163 AATTTTCAAC
22958173 CCTTAGTAAACTATCAGCTGTGTGGATACTTGAAGTGAATTAAGATACTGAATATTTTATGCAT
1 CCTTAGTAAACTATCAGCTGTGTGGATACTTGAAGTGAATTAAGATACTGAATATTTTATGCAT
*
22958237 CCTTAGTAAACTATCAGCTGTGTGGATACTTGGAAGTGAATTCAGATACTGAATATTTTATGCAT
1 CCTTAGTAAACTATCAGCTGTGTGGATACTT-GAAGTGAATTAAGATACTGAATATTTTATGCAT
22958302 CCT
1 CCT
22958305 AGTTCACTAG
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 31 0.47
65 35 0.53
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (64 bp):
CCTTAGTAAACTATCAGCTGTGTGGATACTTGAAGTGAATTAAGATACTGAATATTTTATGCAT
Found at i:22962106 original size:45 final size:45
Alignment explanation
Indices: 22962055--22962145 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
22962045 AGTTTTTATT
22962055 TCAAACAAAACATTACTAGCTTTAGATGCTAATAAAAATTAAAGC
1 TCAAACAAAACATTACTAGCTTTAGATGCTAATAAAAATTAAAGC
* *
22962100 TCAAACAAAAGATTACTAGCTTTAGATTCTAATAAAAATTAAAGC
1 TCAAACAAAACATTACTAGCTTTAGATGCTAATAAAAATTAAAGC
22962145 T
1 T
22962146 TTATCTAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (45 bp):
TCAAACAAAACATTACTAGCTTTAGATGCTAATAAAAATTAAAGC
Found at i:22973775 original size:13 final size:13
Alignment explanation
Indices: 22973748--22973815 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
22973738 GTATAAGCAC
22973748 TTCATATAACCAT
1 TTCATATAACCAT
* *
22973761 TTCATATATCTAT
1 TTCATATAACCAT
*
22973774 TTCCATATAAACAT
1 TT-CATATAACCAT
** *
22973788 TTTGTATATCCAT
1 TTCATATAACCAT
22973801 TTCATA-ATACCAT
1 TTCATATA-ACCAT
22973814 TT
1 TT
22973816 TCGTTTACTC
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
12 1 0.02
13 30 0.73
14 10 0.24
ACGTcount: A:0.34, C:0.19, G:0.01, T:0.46
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:22973788 original size:27 final size:27
Alignment explanation
Indices: 22973750--22973803 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
22973740 ATAAGCACTT
* *
22973750 CATATAACCATTTCATATATCTATTTC
1 CATATAAACATTTCATATATCCATTTC
**
22973777 CATATAAACATTTTGTATATCCATTTC
1 CATATAAACATTTCATATATCCATTTC
22973804 ATAATACCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (27 bp):
CATATAAACATTTCATATATCCATTTC
Found at i:22973805 original size:53 final size:53
Alignment explanation
Indices: 22973707--22973815 Score: 141
Period size: 53 Copynumber: 2.1 Consensus size: 53
22973697 AAATGTCCCT
* *
22973707 TTTCACATATCTATATTCATATAAATATTTTGTATAAGCACTTCAT-ATAACCA
1 TTTCACATATCTATATTCATATAAACATTTTGTATAACCACTTCATAAT-ACCA
* * *
22973760 TTTCATATATCTAT-TTCCATATAAACATTTTGTATATCCATTTCATAATACCA
1 TTTCACATATCTATATT-CATATAAACATTTTGTATAACCACTTCATAATACCA
22973813 TTT
1 TTT
22973816 TCGTTTACTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 2 0.04
53 45 0.92
54 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (53 bp):
TTTCACATATCTATATTCATATAAACATTTTGTATAACCACTTCATAATACCA
Found at i:22980825 original size:8 final size:8
Alignment explanation
Indices: 22980812--22980864 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
22980802 ATTTTATCTT
22980812 TAATTACC
1 TAATTACC
22980820 TAATTACC
1 TAATTACC
*
22980828 AAATTACC
1 TAATTACC
*
22980836 ---CTACC
1 TAATTACC
22980841 TAATTACC
1 TAATTACC
22980849 TAATTACC
1 TAATTACC
*
22980857 AAATTACC
1 TAATTACC
22980865 CTTACTTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 4 0.11
8 34 0.89
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (8 bp):
TAATTACC
Found at i:22980842 original size:21 final size:21
Alignment explanation
Indices: 22980816--22980856 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
22980806 TATCTTTAAT
22980816 TACCTAATTACCAAATTACCC
1 TACCTAATTACCAAATTACCC
*
22980837 TACCTAATTACCTAATTACC
1 TACCTAATTACCAAATTACC
22980857 AAATTACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.32, G:0.00, T:0.32
Consensus pattern (21 bp):
TACCTAATTACCAAATTACCC
Found at i:23000934 original size:2 final size:2
Alignment explanation
Indices: 23000927--23000955 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23000917 AAAATCGCAA
23000927 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
23000956 TATTTGTTTT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23002663 original size:10 final size:10
Alignment explanation
Indices: 23002631--23002664 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
23002621 AATCAAAGTT
23002631 TTATTATATA
1 TTATTATATA
*
23002641 TTTTTATAT-
1 TTATTATATA
23002650 TTATTATATA
1 TTATTATATA
23002660 TTATT
1 TTATT
23002665 TTCAAACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATATA
Found at i:23003329 original size:114 final size:114
Alignment explanation
Indices: 23003136--23003561 Score: 509
Period size: 114 Copynumber: 3.7 Consensus size: 114
23003126 GCAAAAAGAA
* *
23003136 CCGCAATACATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCATTAGTGGCGCTTA
1 CCGCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGCATTAGTGGCGCTTA
*
23003201 TAC-AAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCG
66 T-CGGAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCG
* * *
23003250 CCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTA
1 CCGCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGCATTAGTGGCGCTTA
* ** * * *
23003315 TCGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTATTGTAAAGCA
66 TCGGAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCG
* * * * *
23003364 CTGCAA-A-ATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCAGTAGTGGCGCTT
1 CCGCAATATATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTAGCATTAGTGGCGCTT
*** ** *
23003427 ATATTAAAACGCCGCTAAATCATAGTATTAGCGGCGAGTAGTGAAAAACG
65 ATCGGAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCG
* * * * * * *
23003477 CCGCAAGATTTTTTAACCAAAATGCAAAGTTTGGTCTTGCGGTATATTAGGC-TTAGTGGCGCTT
1 CCGCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTA-GCATTAGTGGCGCTT
* *
23003541 ATTGGAAAACGCCGCAAAAGA
65 ATCGGAAAACGCCGCTAAAGA
23003562 TTAACCAAAA
Statistics
Matches: 261, Mismatches: 46, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
112 17 0.07
113 78 0.30
114 149 0.57
115 17 0.07
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (114 bp):
CCGCAATATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGCATTAGTGGCGCTTA
TCGGAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCG
Found at i:23003438 original size:227 final size:226
Alignment explanation
Indices: 23003148--23003560 Score: 664
Period size: 227 Copynumber: 1.8 Consensus size: 226
23003138 GCAATACATC
*
23003148 TTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCATTAGTGGCGCTTATACAAAAACGCC
1 TTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCAGTAGTGGCGCTTATACAAAAACGCC
* * *
23003213 GCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGA
66 GCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAACGCCGCAAGATTTCTTAACCAAAACGCAAA
*
23003278 GTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACGCCGCTAAAGCATAGTATT
131 GTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACGCCGCAAAAGCATAGTATT
23003343 AGCGGCGCTTATTGTAAAGCACTGCAAAATA
196 AGCGGCGCTTATTGTAAAGCACTGCAAAATA
* * * **
23003374 TTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCAGTAGTGGCGCTTATATTAAAACGC
1 TTAACCAAAACGCAGAG-TTTGGTCTTGAGGTACACTAGCAGTAGTGGCGCTTATACAAAAACGC
** * *
23003439 CGCTAAATCATAGTATTAGCGGCGAGTAGTGAAAAACGCCGCAAGATTTTTTAACCAAAATGCAA
65 CGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAACGCCGCAAGATTTCTTAACCAAAACGCAA
* * *
23003504 AGTTTGGTCTTGCGGTATATTAGGCTTAGTGGCGCTTATTGGAAAACGCCGCAAAAG
130 AGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACGCCGCAAAAG
23003561 ATTAACCAAA
Statistics
Matches: 169, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
226 16 0.09
227 153 0.91
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (226 bp):
TTAACCAAAACGCAGAGTTTGGTCTTGAGGTACACTAGCAGTAGTGGCGCTTATACAAAAACGCC
GCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAACGCCGCAAGATTTCTTAACCAAAACGCAAA
GTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATCGGAAAACGCCGCAAAAGCATAGTATT
AGCGGCGCTTATTGTAAAGCACTGCAAAATA
Found at i:23003596 original size:74 final size:73
Alignment explanation
Indices: 23003489--23003634 Score: 179
Period size: 74 Copynumber: 2.0 Consensus size: 73
23003479 GCAAGATTTT
* * *
23003489 TTAACCAAAATGCAAAGTTTGGTCTTGCGGTATATTAGGC-TTAGTGGCGCTTAT-TGGAAAACG
1 TTAACCAAAACGCAAAGTTTGGTCTTGAGGTATAGTA-GCATTAGTGGCGCTTATAT-GAAAACG
23003552 CCGCAAAAGA
64 CCGCAAAAGA
** * *
23003562 TTAACCAAAACGCAGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTATATTAAAACGC
1 TTAACCAAAACGCAAAG-TTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTATATGAAAACGC
*
23003627 CGCTAAAG
65 CGCAAAAG
23003635 TATAGTATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
73 16 0.26
74 45 0.73
75 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (73 bp):
TTAACCAAAACGCAAAGTTTGGTCTTGAGGTATAGTAGCATTAGTGGCGCTTATATGAAAACGCC
GCAAAAGA
Found at i:23003669 original size:188 final size:188
Alignment explanation
Indices: 23003340--23003737 Score: 609
Period size: 188 Copynumber: 2.1 Consensus size: 188
23003330 AAAGCATAGT
* * * * *
23003340 ATTAGCGGCGCTTATTGTAAAGCACTGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGTGGCGCTTATTGGAAAACACCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
*
23003405 TATACTAGCAGTAGTGGCGCTTATATTAAAACGCCGCTAAATCATAGTATTAGCGGCGAGTAGTG
66 TATACTAGCAGTAGTGGCGCTTATATTAAAACGCCGCTAAATCATAGTATTAGCGGCGAGTACTG
* * * * *
23003470 AAAAACGCCGCAAGATTTTTTAACCAAAATGCAAAGTTTGGTCTTGCGGTATATTAGG
131 AAAAACGCCGCAAGATTTCTTAACCAAAACGCAAAGTTTGGTCTTGAGGTACATTAAG
* *
23003528 CTTAGTGGCGCTTATTGGAAAACGCCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGTGGCGCTTATTGGAAAACACCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* *
23003593 TATAGTAGCATTAGTGGCGCTTATATTAAAACGCCGCTAAAGT-ATAGTATTAGCGGCGAGTACT
66 TATACTAGCAGTAGTGGCGCTTATATTAAAACGCCGCTAAA-TCATAGTATTAGCGGCGAGTACT
* * *
23003657 GAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTAAG
130 GAAAAACGCCGCAAGATTTCTTAACCAAAACGCAAAGTTTGGTCTTGAGGTACATTAAG
*
23003716 ATTAGTGGCGCTTATTTGAAAA
1 ATTAGTGGCGCTTATTGGAAAA
23003738 TGCCACTAAA
Statistics
Matches: 189, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
188 188 0.99
189 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (188 bp):
ATTAGTGGCGCTTATTGGAAAACACCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
TATACTAGCAGTAGTGGCGCTTATATTAAAACGCCGCTAAATCATAGTATTAGCGGCGAGTACTG
AAAAACGCCGCAAGATTTCTTAACCAAAACGCAAAGTTTGGTCTTGAGGTACATTAAG
Found at i:23003871 original size:113 final size:112
Alignment explanation
Indices: 23003529--23003878 Score: 395
Period size: 114 Copynumber: 3.1 Consensus size: 112
23003519 TATATTAGGC
* *
23003529 TTAGTGGCGCTTATTGGAAAA-CGCCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 TTAGCGGCGCTTATT-GAAAAGCGCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATG
* *
23003593 TATAGTAGCA-TTAGTGGCGCTTATATTAAAACGCCGCTAAAGTATAGTA
64 TATACTAGCAGTTAGTGGCGCTTAT-TTAAAACGCCGCTAAAGCATAGTA
** * * * * *
23003642 TTAGCGGCGAGTACTGAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGG
1 TTAGCGGCGCTTATTGAAAAGCGCCGCAA-A-ATATTAACCAAAACGCAGCGTTTGGTCTTGATG
* * * *
23003707 TACATTA--AGATTAGTGGCGCTTATTTGAAAATGCCACTAAAGCATAGTA
64 TATACTAGCAG-TTAGTGGCGCTTATTT-AAAACGCCGCTAAAGCATAGTA
* * *
23003756 TTAGCGGCGCTTATTGTAAAGCGCCGCAAAATATTAACTAAAATGCAGCGTTTTGGTCTTGATGT
1 TTAGCGGCGCTTATTGAAAAGCGCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATGT
* * *
23003821 ATACTAGCAGTT-GTGGCGCTTATGGTAAAACGCCGCTAAAACATATTA
65 ATACTAGCAGTTAGTGGCGCTTAT-TTAAAACGCCGCTAAAGCATAGTA
23003869 TTAGCGGCGC
1 TTAGCGGCGC
23003879 GTTGTGGGAA
Statistics
Matches: 196, Mismatches: 31, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
112 21 0.11
113 78 0.40
114 79 0.40
115 18 0.09
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (112 bp):
TTAGCGGCGCTTATTGAAAAGCGCCGCAAAATATTAACCAAAACGCAGCGTTTGGTCTTGATGTA
TACTAGCAGTTAGTGGCGCTTATTTAAAACGCCGCTAAAGCATAGTA
Found at i:23003892 original size:113 final size:112
Alignment explanation
Indices: 23003545--23003895 Score: 372
Period size: 113 Copynumber: 3.1 Consensus size: 112
23003535 GCGCTTATTG
* *
23003545 GAAAA-CGCCGCAAAAGATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATAGTAGCA-TTAGT
1 GAAAAGCGCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATGTATACTAGCAGTTAGT
* * *
23003608 GGCGCTTATATTAAAACGCCGCTAAAGTATAGTATTAGCGGCGAGTACT
65 GGCGCTTAT-TTAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTTCT
* * * * * *
23003657 GAAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTA--AGATTA
1 GAAAAGCGCCGCAA-A-ATATTAACCAAAACGCAGCGTTTGGTCTTGATGTATACTAGCAG-TTA
* * *
23003720 GTGGCGCTTATTTGAAAATGCCACTAAAGCATAGTATTAGCGGCGC-TTATT
63 GTGGCGCTTATTT-AAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTT-CT
* * *
23003771 GTAAAGCGCCGCAAAATATTAACTAAAATGCAGCGTTTTGGTCTTGATGTATACTAGCAGTT-GT
1 GAAAAGCGCCGCAAAATATTAACCAAAACGCAGCG-TTTGGTCTTGATGTATACTAGCAGTTAGT
* * * *
23003835 GGCGCTTATGGTAAAACGCCGCTAAAACATATTATTAGCGGCGCGTTGT
65 GGCGCTTAT-TTAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTTCT
**
23003884 GGGAAGCGCCGC
1 GAAAAGCGCCGC
23003896 TAGATTATTA
Statistics
Matches: 197, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
112 21 0.11
113 79 0.40
114 79 0.40
115 18 0.09
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (112 bp):
GAAAAGCGCCGCAAAATATTAACCAAAACGCAGCGTTTGGTCTTGATGTATACTAGCAGTTAGTG
GCGCTTATTTAAAACGCCGCTAAAGCATAGTATTAGCGGCGCGTTCT
Found at i:23008550 original size:21 final size:20
Alignment explanation
Indices: 23008525--23008590 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
23008515 CAACTTAAAA
*
23008525 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCA-CAGCGAGAGAAG
23008546 CAGAGGCTACAGCGAGAGAAG
1 CAGAGGC-ACAGCGAGAGAAG
* *
23008567 TAGAGGCCACAGTGAGAGAAG
1 CAGAGG-CACAGCGAGAGAAG
23008588 CAG
1 CAG
23008591 CGAGAGAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 37 0.95
22 2 0.05
ACGTcount: A:0.36, C:0.18, G:0.41, T:0.05
Consensus pattern (20 bp):
CAGAGGCACAGCGAGAGAAG
Found at i:23009558 original size:42 final size:42
Alignment explanation
Indices: 23009464--23009734 Score: 350
Period size: 43 Copynumber: 6.4 Consensus size: 42
23009454 GTTTGTGAAG
*
23009464 TAAGCGCCG-TGAAAGAACACT-A-CTTTTAGCGGTGTTTTTTTCC
1 TAAGCGCCGCT-AAAGAACA-TGATC-TTTAGCGGCGTTTTTTT-C
*
23009507 TAAGCGCCGCTAAAGAACATGATCTTTTGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
*
23009549 TAAGCGCCGCTAAAGAACATGATCTTTTGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-C
*
23009592 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * *
23009634 CAAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTCCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TC
* * * *
23009677 TAAGCGCCGCTAAAGAATATGACCTTTAGCAGCGTTTTTTCTG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TC
*
23009720 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
23009735 TTAGCGACGT
Statistics
Matches: 209, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
42 82 0.39
43 125 0.60
44 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:23009595 original size:85 final size:85
Alignment explanation
Indices: 23009464--23009734 Score: 377
Period size: 85 Copynumber: 3.2 Consensus size: 85
23009454 GTTTGTGAAG
*
23009464 TAAGCGCCG-TGAAAGAACACT-A-CTTTTAGCGGTGTTTTTTTCCTAAGCGCCGCTAAAGAACA
1 TAAGCGCCGCT-AAAGAACA-TGATCTTTT-GCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACA
*
23009526 TGATCTTTTGCGGCGTTTTTTTC
63 TGATCTTTAGCGGCGTTTTTTTC
23009549 TAAGCGCCGCTAAAGAACATGATCTTTTGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATGATCTTTTGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGA
*
23009614 TCTTTAGCGGCGTTTTTTCC
66 TCTTTAGCGGCGTTTTTTTC
* * * * *
23009634 CAAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTCCCTAAGCGCCGCTAAAGAATATGA
1 TAAGCGCCGCTAAAGAACATGATCTTTTGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGA
* * *
23009699 CCTTTAGCAGCGTTTTTTCTG
66 TCTTTAGCGGCGTTTTTT-TC
*
23009720 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
23009735 TTAGCGACGT
Statistics
Matches: 168, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
84 1 0.01
85 148 0.88
86 19 0.11
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (85 bp):
TAAGCGCCGCTAAAGAACATGATCTTTTGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGA
TCTTTAGCGGCGTTTTTTTC
Found at i:23019900 original size:12 final size:12
Alignment explanation
Indices: 23019883--23019920 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
23019873 AAAAAAGTGA
23019883 GGCATTGGCAAT
1 GGCATTGGCAAT
*
23019895 GGCATTGGCAAA
1 GGCATTGGCAAT
23019907 GGCATTGGGCAAT
1 GGCATT-GGCAAT
23019920 G
1 G
23019921 CATGATGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (12 bp):
GGCATTGGCAAT
Found at i:23032383 original size:3 final size:3
Alignment explanation
Indices: 23032375--23032431 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
23032365 ATTGGTAACA
23032375 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
23032421 ATT ATT ATT AT
1 ATT ATT ATT AT
23032432 ATGTTAAAGC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23041594 original size:15 final size:12
Alignment explanation
Indices: 23041561--23041596 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
23041551 CTTTCCGGCA
23041561 ATCCTTCTTCTC
1 ATCCTTCTTCTC
23041573 ATCCTTCTTCTC
1 ATCCTTCTTCTC
23041585 ATCCTTCTTCTC
1 ATCCTTCTTCTC
23041597 CTCTTTTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.42, G:0.00, T:0.50
Consensus pattern (12 bp):
ATCCTTCTTCTC
Found at i:23046650 original size:3 final size:3
Alignment explanation
Indices: 23046639--23046679 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
23046629 AAAATCCAAA
23046639 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
23046680 CAAGCAAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23052125 original size:13 final size:13
Alignment explanation
Indices: 23052107--23052134 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
23052097 AGTTTATCGG
23052107 AATTATTATAATT
1 AATTATTATAATT
23052120 AATTATTATAATT
1 AATTATTATAATT
23052133 AA
1 AA
23052135 GATTTTGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTATTATAATT
Found at i:23062935 original size:24 final size:25
Alignment explanation
Indices: 23062902--23062962 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
23062892 ATGAAACAAC
*
23062902 AAAAAGAAAATA-TATTCTAAAAAG
1 AAAAAGAAAATACTAATCTAAAAAG
* *
23062926 GAAAAGAAAA-ACCTAATCTAAAAAT
1 AAAAAGAAAATA-CTAATCTAAAAAG
23062951 AAAAAGAAAATA
1 AAAAAGAAAATA
23062963 AACAAAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 9 0.30
25 19 0.63
26 1 0.03
ACGTcount: A:0.69, C:0.07, G:0.08, T:0.16
Consensus pattern (25 bp):
AAAAAGAAAATACTAATCTAAAAAG
Found at i:23062972 original size:16 final size:16
Alignment explanation
Indices: 23062951--23062981 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23062941 ATCTAAAAAT
*
23062951 AAAAAGAAAATAAACA
1 AAAAAGAAAAGAAACA
23062967 AAAAAGAAAAGAAAC
1 AAAAAGAAAAGAAAC
23062982 TTAACGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.06, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAGAAACA
Found at i:23066834 original size:69 final size:69
Alignment explanation
Indices: 23066723--23066852 Score: 242
Period size: 69 Copynumber: 1.9 Consensus size: 69
23066713 TGGGATGCTA
* *
23066723 AAACTATGCTATGATCATGTAGAATAATGATTTCAAGCTATAACCAAAGTTTGCATGAAGCCGAG
1 AAACTATGCTATGATCATGTAGAATAATGAATCCAAGCTATAACCAAAGTTTGCATGAAGCCGAG
23066788 ATAG
66 ATAG
23066792 AAACTATGCTATGATCATGTAGAATAATGAATCCAAGCTATAACCAAAGTTTGCATGAAGC
1 AAACTATGCTATGATCATGTAGAATAATGAATCCAAGCTATAACCAAAGTTTGCATGAAGC
23066853 ATATCTGAAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (69 bp):
AAACTATGCTATGATCATGTAGAATAATGAATCCAAGCTATAACCAAAGTTTGCATGAAGCCGAG
ATAG
Found at i:23072030 original size:15 final size:15
Alignment explanation
Indices: 23072010--23072039 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23072000 CATATTTCAC
*
23072010 TTAATATTATATAAA
1 TTAATATAATATAAA
23072025 TTAATATAATATAAA
1 TTAATATAATATAAA
23072040 AATTATTTAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAATATAATATAAA
Found at i:23073306 original size:3 final size:3
Alignment explanation
Indices: 23073300--23073328 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
23073290 AAAAAAAAAT
23073300 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
23073329 GCATGTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:23079987 original size:25 final size:24
Alignment explanation
Indices: 23079952--23080008 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
23079942 TATATTACAT
* *
23079952 ATAC-AAATAATTTTATTTATTTA
1 ATACAAAATAATTTGATGTATTTA
23079975 ATACAAAAGTAATTTGATGTATTTA
1 ATACAAAA-TAATTTGATGTATTTA
*
23080000 ATAAAAAAT
1 ATACAAAAT
23080009 TCTCGGCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.14
24 4 0.14
25 21 0.72
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (24 bp):
ATACAAAATAATTTGATGTATTTA
Found at i:23089475 original size:334 final size:334
Alignment explanation
Indices: 23088866--23089533 Score: 1327
Period size: 334 Copynumber: 2.0 Consensus size: 334
23088856 GGTTTTTTTT
23088866 CACTCAAATAATATAAAATAATTAAATAAATATTGAAATGGGATAAATGTAATATAGTAAAAAAT
1 CACTCAAATAATATAAAATAATTAAATAAATATTGAAATGGGATAAATGTAATATAGTAAAAAAT
23088931 TTAGAATTGTCTGACTAATCGGCGGCACTACTCTCTCTAGCCACTGGTCACATCAAATTTTTAAA
66 TTAGAATTGTCTGACTAATCGGCGGCACTACTCTCTCTAGCCACTGGTCACATCAAATTTTTAAA
23088996 AAAAAAATTATAAGTATAGGCTGATCAATTGACGGCATTAGACTAAAATGTGATAACTTAAAATA
131 AAAAAAATTATAAGTATAGGCTGATCAATTGACGGCATTAGACTAAAATGTGATAACTTAAAATA
23089061 TTTAGAGATAAATTTGCCATTTTGGTTGATAAGCCTTAAAAGTGTGACCTAGCAGCTTGGTGGTA
196 TTTAGAGATAAATTTGCCATTTTGGTTGATAAGCCTTAAAAGTGTGACCTAGCAGCTTGGTGGTA
23089126 TCAAACTTCAAATAGTGTAAATTGTTTCATAAATCCCCTTGTTTATTATTATTATTTATTTCCCT
261 TCAAACTTCAAATAGTGTAAATTGTTTCATAAATCCCCTTGTTTATTATTATTATTTATTTCCCT
23089191 TCAATACAA
326 TCAATACAA
23089200 CACTCAAATAATATAAAATAATTAAATAAATATTGAAATGGGATAAATGTAATATAGTAAAAAAT
1 CACTCAAATAATATAAAATAATTAAATAAATATTGAAATGGGATAAATGTAATATAGTAAAAAAT
23089265 TTAGAATTGTCTGACTAATCGGCGGCACTACTCTCTCTAGCCACTGGTCACATCAAATTTTTAAA
66 TTAGAATTGTCTGACTAATCGGCGGCACTACTCTCTCTAGCCACTGGTCACATCAAATTTTTAAA
23089330 AAAAAAATTATAAGTATAGGCTGATCAATTGACGGCATTAGACTAAAATGTGATAACTTAAAATA
131 AAAAAAATTATAAGTATAGGCTGATCAATTGACGGCATTAGACTAAAATGTGATAACTTAAAATA
23089395 TTTAGAGATAAATTTGCCATTTTGGTTGATAAGCCTTAAAAGTGTGACCTAGCAGCTTGGTGGTA
196 TTTAGAGATAAATTTGCCATTTTGGTTGATAAGCCTTAAAAGTGTGACCTAGCAGCTTGGTGGTA
*
23089460 TCAAACTTCAAATAGTGTAAATTGTTTCATAAATCCTCTTGTTTATTATTATTATTTATTTCCCT
261 TCAAACTTCAAATAGTGTAAATTGTTTCATAAATCCCCTTGTTTATTATTATTATTTATTTCCCT
23089525 TCAATACAA
326 TCAATACAA
23089534 AAAAAAAAAA
Statistics
Matches: 333, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 333 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (334 bp):
CACTCAAATAATATAAAATAATTAAATAAATATTGAAATGGGATAAATGTAATATAGTAAAAAAT
TTAGAATTGTCTGACTAATCGGCGGCACTACTCTCTCTAGCCACTGGTCACATCAAATTTTTAAA
AAAAAAATTATAAGTATAGGCTGATCAATTGACGGCATTAGACTAAAATGTGATAACTTAAAATA
TTTAGAGATAAATTTGCCATTTTGGTTGATAAGCCTTAAAAGTGTGACCTAGCAGCTTGGTGGTA
TCAAACTTCAAATAGTGTAAATTGTTTCATAAATCCCCTTGTTTATTATTATTATTTATTTCCCT
TCAATACAA
Found at i:23089636 original size:15 final size:15
Alignment explanation
Indices: 23089618--23089682 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
23089608 AACTAAAATT
23089618 TATTTTTCAAAAAAA
1 TATTTTTCAAAAAAA
*
23089633 TATTTGTTC-AAATAA
1 TATTT-TTCAAAAAAA
* *** *
23089648 TCTTTTTTGTAAAAT
1 TATTTTTCAAAAAAA
*
23089663 TATTTTTCAAAAAAT
1 TATTTTTCAAAAAAA
23089678 TATTT
1 TATTT
23089683 GAACGGGAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
14 2 0.05
15 33 0.87
16 3 0.08
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (15 bp):
TATTTTTCAAAAAAA
Found at i:23094458 original size:24 final size:24
Alignment explanation
Indices: 23094421--23094482 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
23094411 TGATCCCCAT
23094421 ATTTTTTTCGTTTTAAGTAATTTAA
1 ATTTTTTTC-TTTTAAGTAATTTAA
* **
23094446 ATTTTTTTCTTTTATGTTCTTTAA
1 ATTTTTTTCTTTTAAGTAATTTAA
* *
23094470 ACTTTCTTCTTTT
1 ATTTTTTTCTTTT
23094483 TTTTCCATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.66
Consensus pattern (24 bp):
ATTTTTTTCTTTTAAGTAATTTAA
Found at i:23094616 original size:14 final size:14
Alignment explanation
Indices: 23094599--23094632 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
23094589 TCATCATTTG
23094599 CCTATAACCAAAAC
1 CCTATAACCAAAAC
23094613 CCTATAACCAAAAC
1 CCTATAACCAAAAC
23094627 CC-ATAA
1 CCTATAA
23094633 ACTCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:23097926 original size:17 final size:16
Alignment explanation
Indices: 23097906--23097939 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23097896 ATGAATATAG
23097906 AGAAAAAGAAGGAAATA
1 AGAAAAA-AAGGAAATA
*
23097923 AGAAAAAATGGAAATA
1 AGAAAAAAAGGAAATA
23097939 A
1 A
23097940 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (16 bp):
AGAAAAAAAGGAAATA
Found at i:23126496 original size:24 final size:23
Alignment explanation
Indices: 23126467--23126515 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23126457 TTTTTTGTAT
*
23126467 TTTTAATTTGTTGAAAAATATTTA
1 TTTTAATAT-TTGAAAAATATTTA
* *
23126491 TTTTAATATTTGTAATATATTTA
1 TTTTAATATTTGAAAAATATTTA
23126514 TT
1 TT
23126516 GTATTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
TTTTAATATTTGAAAAATATTTA
Found at i:23126513 original size:23 final size:22
Alignment explanation
Indices: 23126482--23126545 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
23126472 ATTTGTTGAA
*
23126482 AAATATTTATTTTAATATTTGT
1 AAATATTTATTTTTATATTTGT
*
23126504 AATATATTTATTGTATTATATTTTT
1 AA-ATATTTATT-T-TTATATTTGT
23126529 AAA-ATTTATTTTTATAT
1 AAATATTTATTTTTATAT
23126546 AAAAAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
21 6 0.16
22 3 0.08
23 16 0.43
24 2 0.05
25 10 0.27
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (22 bp):
AAATATTTATTTTTATATTTGT
Found at i:23133351 original size:3 final size:3
Alignment explanation
Indices: 23133343--23133395 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
23133333 GGCGGCAATC
23133343 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
23133391 TCT TC
1 TCT TC
23133396 CTAGCTACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:23142008 original size:11 final size:11
Alignment explanation
Indices: 23141994--23142114 Score: 242
Period size: 11 Copynumber: 11.0 Consensus size: 11
23141984 TATTTATTAG
23141994 TTATTATTATA
1 TTATTATTATA
23142005 TTATTATTATA
1 TTATTATTATA
23142016 TTATTATTATA
1 TTATTATTATA
23142027 TTATTATTATA
1 TTATTATTATA
23142038 TTATTATTATA
1 TTATTATTATA
23142049 TTATTATTATA
1 TTATTATTATA
23142060 TTATTATTATA
1 TTATTATTATA
23142071 TTATTATTATA
1 TTATTATTATA
23142082 TTATTATTATA
1 TTATTATTATA
23142093 TTATTATTATA
1 TTATTATTATA
23142104 TTATTATTATA
1 TTATTATTATA
23142115 GTAAAGTAAC
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 110 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATTATTATA
Found at i:23142505 original size:21 final size:21
Alignment explanation
Indices: 23142480--23142547 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
23142470 TGTTTTTGAG
23142480 TACTGAATTGAATTGTGAAGT
1 TACTGAATTGAATTGTGAAGT
* *
23142501 TACTGAA-T--ATTGTTATGT
1 TACTGAATTGAATTGTGAAGT
* * *
23142519 GTACTGCATTGAACTGTGAAAT
1 -TACTGAATTGAATTGTGAAGT
23142541 TACTGAA
1 TACTGAA
23142548 GTAATGAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 2 0.06
21 13 0.37
22 6 0.17
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (21 bp):
TACTGAATTGAATTGTGAAGT
Found at i:23142523 original size:40 final size:40
Alignment explanation
Indices: 23142440--23142547 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
23142430 TTGAGACTGA
* * * * *
23142440 TACTGAATTGCATTATGAAATATTGAATATTGTTTTTGAG
1 TACTGAATTGAATTGTGAATTACTGAATATTGTTTATGAG
*
23142480 TACTGAATTGAATTGTGAAGTTACTGAATATTG-TTATGTG
1 TACTGAATTGAATTGTGAA-TTACTGAATATTGTTTATGAG
* *
23142520 TACTGCATTGAACTGTGAAATTACTGAA
1 TACTGAATTGAATTGTG-AATTACTGAA
23142548 GTAATGAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 45 0.78
41 13 0.22
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.41
Consensus pattern (40 bp):
TACTGAATTGAATTGTGAATTACTGAATATTGTTTATGAG
Found at i:23142818 original size:45 final size:45
Alignment explanation
Indices: 23142751--23142846 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 45
23142741 CCGACTACTA
* *
23142751 TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
1 TTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTATTACCG
* *
23142796 TTACTGTTACAGATTC-AGCACTTTGTGTGTTGAATACTATTACTG
1 TTACTGTTACAGATTCGA-CACTTTGTGTGTCGAATACTATTACCG
23142841 TTACTG
1 TTACTG
23142847 CTACCGTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (45 bp):
TTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTATTACCG
Found at i:23145521 original size:22 final size:22
Alignment explanation
Indices: 23145462--23145523 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
23145452 GATAACATTG
** *
23145462 AATTTTAAAG-GTTTTTCCTAT
1 AATTTTAAAGAGTTTTTTTTAA
*
23145483 ATTTTTAAA-A-TTATTTTTTAA
1 AATTTTAAAGAGTT-TTTTTTAA
23145504 AATTTTAAAGAGTTTTTTTT
1 AATTTTAAAGAGTTTTTTTT
23145524 CATATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 2 0.06
21 21 0.66
22 7 0.22
23 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (22 bp):
AATTTTAAAGAGTTTTTTTTAA
Found at i:23145530 original size:22 final size:21
Alignment explanation
Indices: 23145463--23145531 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
23145453 ATAACATTGA
**
23145463 ATTTTAAAG-GTTTTTCCTAT
1 ATTTTAAAGAGTTTTTTTTAT
*
23145483 ATTTTTAAA-A-TTATTTTTTAAA
1 A-TTTTAAAGAGTT-TTTTTT-AT
23145505 ATTTTAAAGAGTTTTTTTTCAT
1 ATTTTAAAGAGTTTTTTTT-AT
23145527 ATTTT
1 ATTTT
23145532 TTTTATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 3 0.08
21 18 0.47
22 15 0.39
23 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.59
Consensus pattern (21 bp):
ATTTTAAAGAGTTTTTTTTAT
Found at i:23146729 original size:43 final size:42
Alignment explanation
Indices: 23146680--23146906 Score: 226
Period size: 43 Copynumber: 5.2 Consensus size: 42
23146670 TTATTTTTAA
* *
23146680 AAACGCCGCTAAAAGTCATATTCTTTAGTGGCGCTTTATACAC
1 AAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTT-TACAC
* *
23146723 AAACGCCGCTAAAGGTCGTGTTCCGACCTTTAGCGGCGCTTTTAACAC
1 AAACGCCGCTAAAAGTCATGTT-----CTTTAGCGGCGCTTTT-ACAC
* * * *
23146771 AAACGCCGCTAAAGGTCATATTTTTTGGCGGCGCTTTTA-AC
1 AAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTTTACAC
* *
23146812 ATTAAAGCCGCT-AAAGTTCATGTTCTTTAGCGGCGCTTCTAACAC
1 A--AACGCCGCTAAAAG-TCATGTTCTTTAGCGGCGCTT-TTACAC
23146857 AAACGCCGCT-AAAGCTCATGTTCTTTAGCGGCGCTTTTTACAC
1 AAACGCCGCTAAAAG-TCATGTTCTTTAGCGGCGC-TTTTACAC
23146900 AAACGCC
1 AAACGCC
23146907 ACTATTTATT
Statistics
Matches: 155, Mismatches: 17, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
41 3 0.02
42 4 0.03
43 102 0.66
44 4 0.03
45 3 0.02
47 1 0.01
48 38 0.25
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (42 bp):
AAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTTTACAC
Found at i:23146888 original size:86 final size:85
Alignment explanation
Indices: 23146680--23146902 Score: 261
Period size: 86 Copynumber: 2.5 Consensus size: 85
23146670 TTATTTTTAA
* * *
23146680 AAACGCCGCTAAAAGTCATATTCTTTAGTGGCGCTTTATACACAAACGCCGCTAAAGGTCGTGTT
1 AAACGCCGCT-AAAGTCATATTCTTTAGCGGCGCTTT-TACACAAAAGCCGCTAAAGGTCATGTT
*
23146745 CCGACCTTTAGCGGCGCTTTTAACAC
64 ----CCTTTAGCGGCGCTTCTAACAC
* * *
23146771 AAACGCCGCTAAAGGTCATATTTTTTGGCGGCGCTTTTA-ACATTAAAGCCGCTAAAGTTCATGT
1 AAACGCCGCTAAA-GTCATATTCTTTAGCGGCGCTTTTACACA--AAAGCCGCTAAAGGTCATGT
23146835 T-CTTTAGCGGCGCTTCTAACAC
63 TCCTTTAGCGGCGCTTCTAACAC
*
23146857 AAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTTTACACAAA
1 AAACGCCGCTAAAG-TCATATTCTTTAGCGGCGC-TTTTACACAAA
23146903 CGCCACTATT
Statistics
Matches: 116, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
85 1 0.01
86 51 0.44
87 5 0.04
88 3 0.03
89 3 0.03
90 5 0.04
91 48 0.41
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (85 bp):
AAACGCCGCTAAAGTCATATTCTTTAGCGGCGCTTTTACACAAAAGCCGCTAAAGGTCATGTTCC
TTTAGCGGCGCTTCTAACAC
Found at i:23147263 original size:21 final size:21
Alignment explanation
Indices: 23147239--23147306 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
23147229 TGCTCTACTT
23147239 TGCTTCTCTCGCTGCAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
*
23147260 TGCTTCTCTCGCTGCAACCTC
1 TGCTTCTCTCGCTGCAGCCTC
* * *
23147281 TGTTTCCCTCGCTGCCGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
23147302 TGCTT
1 TGCTT
23147307 TAAGTTGTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.35
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCAGCCTC
Found at i:23148431 original size:41 final size:41
Alignment explanation
Indices: 23148380--23148768 Score: 599
Period size: 41 Copynumber: 9.5 Consensus size: 41
23148370 GCGTTTTTTA
* *
23148380 AAAAAGCGCCGCTAAAGGCCTGAGAA-A-TAGCGGCGCAT-CAAT
1 AAAAA-CGCCGCTAAA-GCC-CAGAACATTAGCGGCGCTTAC-AT
*
23148422 AAAAACGCCGCTAAAGTCCAGAACATTAGCGGCGCTTAC-T
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
*
23148462 AAAAAACGCCGCTAAATCCCAGAACATTAGCGGCGCTTACAT
1 -AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
23148504 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTGA-AT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTT-ACAT
23148545 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
23148586 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* *
23148627 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGTTTAGAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* *
23148668 AAAAATGCCGCTAAAGCCTAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* *
23148709 AAAAACACCGCTAAAGCTCAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
23148750 AAAAACGCCGCTAAAGCCC
1 AAAAACGCCGCTAAAGCCC
23148769 CCGAAAAGTC
Statistics
Matches: 322, Mismatches: 18, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
39 4 0.01
40 5 0.02
41 305 0.95
42 8 0.02
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.15
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
Found at i:23148477 original size:123 final size:121
Alignment explanation
Indices: 23148328--23148768 Score: 556
Period size: 123 Copynumber: 3.6 Consensus size: 121
23148318 TAATTTTTTT
* * * * * * ***
23148328 GCGGCGCTTTC-TAAAAATGCCACTAAATGAAGAGCATTAGTGGCG-TTTTTTAAAAAAGCGCCG
1 GCGGCGCTTACATAAAAACGCCGCTAAATGCAGAACATTAGCGGCGCTTACAT-AAAAA-CGCCG
* *
23148391 CTAAAGGCCTGAGAA-A-TAGCGGCGCATCAATAAAAACGCCGCTAAAGTCCAGAACATTA
64 CTAAA-GCC-CAGAACATTAGCGGCGCTTCAATAAAAACGCCGCTAAAG-CCAGAACATTA
*
23148450 GCGGCGCTTAC-TAAAAAACGCCGCTAAATCCCAGAACATTAGCGGCGCTTACATAAAAACGCCG
1 GCGGCGCTTACAT-AAAAACGCCGCTAAAT-GCAGAACATTAGCGGCGCTTACATAAAAACGCCG
*
23148514 CTAAAGCCCAGAACATTAGCGGCGCTTGAATAAAAACGCCGCTAAAGCCCAGAACATTA
64 CTAAAGCCCAGAACATTAGCGGCGCTTCAATAAAAACGCCGCTAAAG-CCAGAACATTA
23148573 GCGGCGCTTACATAAAAACGCCGCTAAA-GCCCAGAACATTAGCGGCGCTTACATAAAAACGCCG
1 GCGGCGCTTACATAAAAACGCCGCTAAATG--CAGAACATTAGCGGCGCTTACATAAAAACGCCG
* *
23148637 CTAAAGCCCAGAACATTAGCGGCG-TTTAGATAAAAATGCCGCTAAAGCCTAGAACATTA
64 CTAAAGCCCAGAACATTAGCGGCGCTTCA-ATAAAAACGCCGCTAAAGCC-AGAACATTA
*
23148696 GCGGCGCTTACATAAAAACACCGCTAAA-GCTCAGAACATTAGCGGCGCTTACATAAAAACGCCG
1 GCGGCGCTTACATAAAAACGCCGCTAAATG--CAGAACATTAGCGGCGCTTACATAAAAACGCCG
23148760 CTAAAGCCC
64 CTAAAGCCC
23148769 CCGAAAAGTC
Statistics
Matches: 290, Mismatches: 19, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
121 4 0.01
122 20 0.07
123 244 0.84
124 19 0.07
125 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (121 bp):
GCGGCGCTTACATAAAAACGCCGCTAAATGCAGAACATTAGCGGCGCTTACATAAAAACGCCGCT
AAAGCCCAGAACATTAGCGGCGCTTCAATAAAAACGCCGCTAAAGCCAGAACATTA
Found at i:23168827 original size:6 final size:6
Alignment explanation
Indices: 23168794--23168824 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
23168784 GAATGAAAGC
*
23168794 GGCGTT GGCGTT GGCGTT GGCGTT GACGTT G
1 GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT G
23168825 ACGATGGGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.16, G:0.48, T:0.32
Consensus pattern (6 bp):
GGCGTT
Found at i:23174731 original size:30 final size:29
Alignment explanation
Indices: 23174695--23174761 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
23174685 ATAATTTGTG
* *
23174695 AAAATTAAACCAAATCAAAATTTCATATAT
1 AAAATTAAACAAAATCAAAA-CTCATATAT
* *
23174725 AAAATTACACAAAATTAAAACTCATATAT
1 AAAATTAAACAAAATCAAAACTCATATAT
*
23174754 AATATTAA
1 AAAATTAA
23174762 CATTACATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (29 bp):
AAAATTAAACAAAATCAAAACTCATATAT
Found at i:23175593 original size:3 final size:3
Alignment explanation
Indices: 23175585--23175613 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
23175575 AAATATAAAT
23175585 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
23175614 TTAAGTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:23178675 original size:40 final size:40
Alignment explanation
Indices: 23178630--23178711 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
23178620 CGTTTCTTTT
23178630 ATGTAAAAATAGACTCAATAATCTTTCATTTACTATCTCA
1 ATGTAAAAATAGACTCAATAATCTTTCATTTACTATCTCA
*
23178670 ATGTAATAATAGACTCAATAATCTTTCATTTACTATCTCA
1 ATGTAAAAATAGACTCAATAATCTTTCATTTACTATCTCA
23178710 AT
1 AT
23178712 CACCCTCTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (40 bp):
ATGTAAAAATAGACTCAATAATCTTTCATTTACTATCTCA
Found at i:23179085 original size:48 final size:48
Alignment explanation
Indices: 23179013--23179220 Score: 236
Period size: 48 Copynumber: 4.3 Consensus size: 48
23179003 TCGGAATAAA
* * * * * *
23179013 AACAGATTTCTCGGTGGCTTGCACACAGTCCGTACCACCTTTGTGTAAT
1 AACAGA-TTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
* * * *
23179062 AACAGATTCTCGGTGGCCGGCACATAGTCCGTGCCACCCTTGTATCTT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
* * *
23179110 AACCGGTTATTGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
* * * **
23179158 TACAGAATATCAGTGGCCTGCACACAGTCCGTGCCACCCTTGTGCCAT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
*
23179206 AACAGAATATCGGTG
1 AACAGATTATCGGTG
23179221 CGCATAGTAG
Statistics
Matches: 134, Mismatches: 25, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
48 128 0.96
49 6 0.04
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (48 bp):
AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
Found at i:23193453 original size:29 final size:29
Alignment explanation
Indices: 23193411--23193477 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
23193401 GAAGAGGTAG
23193411 AGAACTTGTTCGTTGAGAGTTCGCGATGA
1 AGAACTTGTTCGTTGAGAGTTCGCGATGA
*
23193440 AGAACTTGTTCGTTGAGATTTCGCGATGA
1 AGAACTTGTTCGTTGAGAGTTCGCGATGA
23193469 AGAACTTGT
1 AGAACTTGT
23193478 GTCAAGGTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.33
Consensus pattern (29 bp):
AGAACTTGTTCGTTGAGAGTTCGCGATGA
Found at i:23210845 original size:18 final size:17
Alignment explanation
Indices: 23210818--23210853 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
23210808 TATATACAAT
23210818 TTAATCTCAAAAAACACA
1 TTAATCTC-AAAAACACA
*
23210836 TTAATGTCAAAAACACA
1 TTAATCTCAAAAACACA
23210853 T
1 T
23210854 CAAAACCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (17 bp):
TTAATCTCAAAAACACA
Found at i:23210912 original size:98 final size:99
Alignment explanation
Indices: 23210742--23210942 Score: 343
Period size: 98 Copynumber: 2.1 Consensus size: 99
23210732 CATTAATCGA
* * * *
23210742 GTCAAAAACACATCAAAACTAACCTAAATATGTGTCTAACTAATGTACCCTCATTGGTACCACAA
1 GTCAAAAACACATCAAAACCAACCTAAATATGTGCCGAACCAATGTACCCTCATTGGTACCACAA
23210807 TTATATACAATTTAATCTCAAAAAACACATTAAT
66 TTATATACAATTTAATCTCAAAAAACACATTAAT
23210841 GTCAAAAACACATCAAAACCAACCT-AATATGTGCCGAACCAATGTACCCTCATTGGTACCACAA
1 GTCAAAAACACATCAAAACCAACCTAAATATGTGCCGAACCAATGTACCCTCATTGGTACCACAA
*
23210905 TTATATACAATTTAATCTCAAAATACACATTAAT
66 TTATATACAATTTAATCTCAAAAAACACATTAAT
23210939 -TCAA
1 GTCAA
23210943 TTCATCAACT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 4 0.04
98 69 0.71
99 24 0.25
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (99 bp):
GTCAAAAACACATCAAAACCAACCTAAATATGTGCCGAACCAATGTACCCTCATTGGTACCACAA
TTATATACAATTTAATCTCAAAAAACACATTAAT
Found at i:23216553 original size:23 final size:23
Alignment explanation
Indices: 23216502--23216560 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
23216492 TAGCCTTTGA
* *
23216502 CCGAACGACAATGTATTTCATTC
1 CCGAACGATAGTGTATTTCATTC
**
23216525 TTGAACGATAGTGTATTTCATTC
1 CCGAACGATAGTGTATTTCATTC
23216548 CCGAACGAGTAGT
1 CCGAACGA-TAGT
23216561 CCCAGTAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (23 bp):
CCGAACGATAGTGTATTTCATTC
Found at i:23226848 original size:12 final size:12
Alignment explanation
Indices: 23226831--23226855 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23226821 CAGCAGAAAG
23226831 GAGTGAAGAGAA
1 GAGTGAAGAGAA
23226843 GAGTGAAGAGAA
1 GAGTGAAGAGAA
23226855 G
1 G
23226856 GCATTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGTGAAGAGAA
Found at i:23235949 original size:21 final size:21
Alignment explanation
Indices: 23235909--23235950 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23235899 ATTTTTAATC
* *
23235909 TTTAAATTGATATCTGAATTT
1 TTTAAATTAATATCTAAATTT
*
23235930 TTTAAATTAATATTTAAATTT
1 TTTAAATTAATATCTAAATTT
23235951 ATTTCAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAAATTAATATCTAAATTT
Found at i:23235981 original size:52 final size:52
Alignment explanation
Indices: 23235884--23235982 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 52
23235874 AATATATCAT
* * * * * *
23235884 TTAATATTTAAATTTATTTTTAATCTTTAAATTGATATCTGAATTTTTTAAA
1 TTAATATTTAAATTTATTTTCAATATTTAAATTAAAATATAAATTTTTTAAA
*
23235936 TTAATATTTAAATTTA-TTTCAATATTTAAATTAAAATATAAAATTTT
1 TTAATATTTAAATTTATTTTCAATATTTAAATTAAAATATAAATTTTT
23235983 CAATTTTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 24 0.60
52 16 0.40
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (52 bp):
TTAATATTTAAATTTATTTTCAATATTTAAATTAAAATATAAATTTTTTAAA
Found at i:23236258 original size:18 final size:18
Alignment explanation
Indices: 23236235--23236271 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
23236225 GTAGTAAAAA
23236235 AAAAAAAAAAAAGCCACT
1 AAAAAAAAAAAAGCCACT
23236253 AAAAAAAAAAAAGCCACT
1 AAAAAAAAAAAAGCCACT
23236271 A
1 A
23236272 CCCTCTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.73, C:0.16, G:0.05, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAAAAGCCACT
Found at i:23243064 original size:31 final size:30
Alignment explanation
Indices: 23243026--23243132 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 30
23243016 TTAGGAAGTC
*
23243026 CTTATTTGAGCACTTTCAAAAAGGTCTGGCT
1 CTTATTTGAGCACTTTC-AAAAGGTTTGGCT
* * *
23243057 CTTATTTGAGCACTTCCCAAATGTTTTGGC-
1 CTTATTTGAGCACTT-TCAAAAGGTTTGGCT
* *
23243087 CATTACTTGAGCACTTT-GAAAGGTTTGGCT
1 C-TTATTTGAGCACTTTCAAAAGGTTTGGCT
23243117 -TTCATTTGAGCACTTT
1 CTT-ATTTGAGCACTTT
23243133 TGTAAAGGTT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.03
29 21 0.34
30 1 0.02
31 37 0.60
32 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
CTTATTTGAGCACTTTCAAAAGGTTTGGCT
Found at i:23245827 original size:6 final size:6
Alignment explanation
Indices: 23245782--23245823 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
23245772 AAGCAGAGCT
* * *
23245782 GGCACT GGCACT GGCACC GGCACC GGCACC GGCACC AGCACC
1 GGCACC GGCACC GGCACC GGCACC GGCACC GGCACC GGCACC
23245824 AGCAAAGTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.19, C:0.45, G:0.31, T:0.05
Consensus pattern (6 bp):
GGCACC
Found at i:23256112 original size:17 final size:18
Alignment explanation
Indices: 23256071--23256114 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
23256061 TTTATCAAAT
* *
23256071 AAATTATTAAAAATTTAT
1 AAATAATTAAAAATTTAA
23256089 AAA-AATTAAAAA-TTAA
1 AAATAATTAAAAATTTAA
23256105 AAATAATTAA
1 AAATAATTAA
23256115 GCTGATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 14 0.61
18 3 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAATTAAAAATTTAA
Found at i:23257188 original size:32 final size:32
Alignment explanation
Indices: 23257150--23257210 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
23257140 TAATCAGTAT
*
23257150 GAGTTATCAAATTAAAATAATTAATTTATCAC
1 GAGTTATCAAATTAAAATAATCAATTTATCAC
* *
23257182 GAGTTATTAAATTAAAGTAATCAATTTAT
1 GAGTTATCAAATTAAAATAATCAATTTAT
23257211 AAATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (32 bp):
GAGTTATCAAATTAAAATAATCAATTTATCAC
Found at i:23258497 original size:16 final size:17
Alignment explanation
Indices: 23258470--23258502 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
23258460 TTTGAGTACT
*
23258470 AAATTAAAAATATATAA
1 AAATTAAAAATAAATAA
23258487 AAATT-AAAATAAATAA
1 AAATTAAAAATAAATAA
23258503 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATTAAAAATAAATAA
Found at i:23261295 original size:16 final size:14
Alignment explanation
Indices: 23261272--23261322 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
23261262 CGAGAGGAAA
23261272 GAAAATTGGAAGGAT
1 GAAAATT-GAAGGAT
23261287 GAAAGATTGAAGGAT
1 GAAA-ATTGAAGGAT
*
23261302 AGAAAACTAGAAGGAT
1 -GAAAA-TTGAAGGAT
23261318 GAAAA
1 GAAAA
23261323 ACATAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 17 0.53
16 15 0.47
ACGTcount: A:0.53, C:0.02, G:0.29, T:0.16
Consensus pattern (14 bp):
GAAAATTGAAGGAT
Found at i:23272320 original size:3 final size:3
Alignment explanation
Indices: 23272312--23272348 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
23272302 TTCCAAAGTA
23272312 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
23272349 TAACTTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23274481 original size:9 final size:9
Alignment explanation
Indices: 23274467--23274494 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
23274457 TAATTTGACA
23274467 TTTTTAAAT
1 TTTTTAAAT
23274476 TTTTTAAAT
1 TTTTTAAAT
23274485 TTTTTAAAT
1 TTTTTAAAT
23274494 T
1 T
23274495 AACTCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:23274577 original size:11 final size:11
Alignment explanation
Indices: 23274561--23274587 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
23274551 AAAAAATATC
23274561 AAATTAAATTA
1 AAATTAAATTA
23274572 AAATTAAATTA
1 AAATTAAATTA
23274583 AAATT
1 AAATT
23274588 CTAGTGAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATTAAATTA
Found at i:23287098 original size:17 final size:17
Alignment explanation
Indices: 23287072--23287105 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23287062 CAGGGGACGT
*
23287072 GTCAGCAAATCGCGTCC
1 GTCAGAAAATCGCGTCC
23287089 GTCAGAAAATCGCGTCC
1 GTCAGAAAATCGCGTCC
23287106 TCGTAGGCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (17 bp):
GTCAGAAAATCGCGTCC
Found at i:23287623 original size:44 final size:43
Alignment explanation
Indices: 23287574--23287750 Score: 117
Period size: 39 Copynumber: 4.3 Consensus size: 43
23287564 TACAAAGTAG
23287574 TATTTAAATATTAAACTGGTAAAAATAAAATTTAATAACTGTAA
1 TATTTAAATATTAAACTGGTAAAAATAAAATTT-ATAACTGTAA
* * *
23287618 TATTTAAATA-TAAA-TAGT---ATTTAAATATTA-AACTGGTAA
1 TATTTAAATATTAAACTGGTAAAAATAAAAT-TTATAACT-GTAA
* * * * * * * *
23287657 AAATAAAAT-TTAATAACT-GTAATATTTAAA--TATAA--ATAG
1 TATTTAAATATT-A-AACTGGTAAAAATAAAATTTATAACTGTAA
23287696 TATTTAAATATTAAACTGGTAAAAATAAAATTTAATAACTGTAA
1 TATTTAAATATTAAACTGGTAAAAATAAAATTT-ATAACTGTAA
23287740 TATTTAAATAT
1 TATTTAAATAT
23287751 AAATAGTATT
Statistics
Matches: 100, Mismatches: 16, Indels: 34
0.67 0.11 0.23
Matches are distributed among these distances:
38 8 0.08
39 36 0.36
40 5 0.05
41 7 0.07
42 10 0.10
43 4 0.04
44 30 0.30
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (43 bp):
TATTTAAATATTAAACTGGTAAAAATAAAATTTATAACTGTAA
Found at i:23287781 original size:61 final size:61
Alignment explanation
Indices: 23287562--23287770 Score: 400
Period size: 61 Copynumber: 3.4 Consensus size: 61
23287552 TGATTGAAGC
*
23287562 AATACAAAGTAGTATTTAAATATTAAACTGGTAAAAATAAAATTTAATAACTGTAATATTTA
1 AATATAAA-TAGTATTTAAATATTAAACTGGTAAAAATAAAATTTAATAACTGTAATATTTA
23287624 AATATAAATAGTATTTAAATATTAAACTGGTAAAAATAAAATTTAATAACTGTAATATTTA
1 AATATAAATAGTATTTAAATATTAAACTGGTAAAAATAAAATTTAATAACTGTAATATTTA
23287685 AATATAAATAGTATTTAAATATTAAACTGGTAAAAATAAAATTTAATAACTGTAATATTTA
1 AATATAAATAGTATTTAAATATTAAACTGGTAAAAATAAAATTTAATAACTGTAATATTTA
23287746 AATATAAATAGTATTTAAATATTAA
1 AATATAAATAGTATTTAAATATTAA
23287771 TTAGATAAAA
Statistics
Matches: 146, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
61 139 0.95
62 7 0.05
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (61 bp):
AATATAAATAGTATTTAAATATTAAACTGGTAAAAATAAAATTTAATAACTGTAATATTTA
Found at i:23297945 original size:3 final size:3
Alignment explanation
Indices: 23297861--23297926 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
23297851 ATATATATAG
*
23297861 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23297909 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
23297927 ATATAGCAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:23299563 original size:44 final size:44
Alignment explanation
Indices: 23299468--23299751 Score: 246
Period size: 44 Copynumber: 6.3 Consensus size: 44
23299458 AAGACTCGTA
* * * *
23299468 TCTTCGATCTACTTCACTGCCACTACAGGAAGACAAGATCTGCTT
1 TCTTCAATCTACTTCAC-GCCAATACATGAAGACAAGATCTACTT
* *
23299513 TCTTCAATCTACTTCACGCTAATACATGAAGACAAGATCTATTT
1 TCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCTACTT
* * * * * * *
23299557 TATTCAATCTGCTTTACGCCAATACATAAAGATAAGATTTACTC
1 TCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCTACTT
* * * * *** * * *
23299601 TCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTA
1 TCTTCAATCTACTTC-ACGCCAATACATGAAGACAAGATCTACTT
* *
23299646 TC-TCTAATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTTT
1 TCTTC-AATCTACTTCACGCCAATACATGAAGACAAGATCTA---CTT
* *
23299693 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCTACTT
**
23299737 TCTTGGATCTACTTC
1 TCTTCAATCTACTTC
23299752 GCCACCAGTA
Statistics
Matches: 188, Mismatches: 45, Indels: 13
0.76 0.18 0.05
Matches are distributed among these distances:
44 106 0.56
45 44 0.23
47 36 0.19
48 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (44 bp):
TCTTCAATCTACTTCACGCCAATACATGAAGACAAGATCTACTT
Found at i:23299672 original size:133 final size:137
Alignment explanation
Indices: 23299518--23299825 Score: 383
Period size: 136 Copynumber: 2.3 Consensus size: 137
23299508 TGCTTTCTTC
* * *
23299518 AATCTACTTCACGCTAATACATGAAGACAAGATCTA-TTTTATTCAATCTGCTTTACGCCAATAC
1 AATCTACTTCACGCTAGTACATGAAGACAAGATCTATTTTTATTCAATCTACTTCACGCCAATAC
* * * *
23299582 ATAAAGATAAGATTTACTCTCTTCGATCTACTTCGCCACCAGTATGGG--AAGGCAAG-ATCTAG
66 ATAAAGACAAGATCTACTCTCTTCGATCTACTTCGCCACCAGTATGGGACAAGAC-AGCATCTAC
23299644 T-ATCTCT
130 TGATCTCT
* * *
23299651 AATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTTTTCTTCGATCTACTTCACGCCAAT
1 AATCTACTTCACGCTAGTACATGAAGACAAGATCTA--TTTTTATTCAATCTACTTCACGCCAAT
* * * * * *
23299716 ACATGAAGACAAGATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGACAAGATCAGCTTTT
64 ACATAAAGACAAGATCTACTCTCTTCGATCTACTTCGCCACCAGTATGGGACAAGA-CAGCATCT
*
23299781 TCTGATCTCT
128 ACTGATCTCT
*
23299791 GATCTACTTCACGCTAGTACATGAAGACAAGATCT
1 AATCTACTTCACGCTAGTACATGAAGACAAGATCT
23299826 GTTATCTTTC
Statistics
Matches: 148, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
133 34 0.23
136 66 0.45
138 5 0.03
139 4 0.03
140 39 0.26
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (137 bp):
AATCTACTTCACGCTAGTACATGAAGACAAGATCTATTTTTATTCAATCTACTTCACGCCAATAC
ATAAAGACAAGATCTACTCTCTTCGATCTACTTCGCCACCAGTATGGGACAAGACAGCATCTACT
GATCTCT
Found at i:23300173 original size:134 final size:135
Alignment explanation
Indices: 23299922--23300190 Score: 522
Period size: 134 Copynumber: 2.0 Consensus size: 135
23299912 TGATGAACCT
23299922 AATTATGCCTAGTGATTAGGATGTCATGATCAAATGAATCAAATGCTCCTAACTAGACGTGTGTG
1 AATTATGCCTAGTGATTAGGATGTCATGATCAAATGAATCAAATGCTCCTAACTAGACGTGTGTG
23299987 AATGACATTTGAATGTTATGTCATGAAAAATGAATATTGAATGTTTAAAGTCATTATTGCTCATT
66 AATGACATTTGAATGTTATGTCATGAAAAATGAATATTGAATGTTTAAAGTCATTATTGCTCATT
23300052 AAGGC
131 AAGGC
23300057 AATTATGCCT-GTGATTAGGATGTCATGATCAAATGAATCAAATGCTCCTAACTAGACGTGTGTG
1 AATTATGCCTAGTGATTAGGATGTCATGATCAAATGAATCAAATGCTCCTAACTAGACGTGTGTG
*
23300121 AATGACATTTGAATGTTATGTTATGAAAAATGAATATTGAATGTTTAAAGTCATTATTGCTCATT
66 AATGACATTTGAATGTTATGTCATGAAAAATGAATATTGAATGTTTAAAGTCATTATTGCTCATT
23300186 AAGGC
131 AAGGC
23300191 TTCCTTTGTG
Statistics
Matches: 133, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
134 123 0.92
135 10 0.08
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (135 bp):
AATTATGCCTAGTGATTAGGATGTCATGATCAAATGAATCAAATGCTCCTAACTAGACGTGTGTG
AATGACATTTGAATGTTATGTCATGAAAAATGAATATTGAATGTTTAAAGTCATTATTGCTCATT
AAGGC
Found at i:23301736 original size:47 final size:49
Alignment explanation
Indices: 23301637--23301778 Score: 195
Period size: 51 Copynumber: 2.9 Consensus size: 49
23301627 AGCCTCTCCA
*
23301637 TTTTTTTTT-ACTC-AAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTCTTT
1 TTTTTTTTTGACTCAAAGGC-CCCTTTGTAGGGTTTCACCTTGGTCTC-TT
23301686 TTTTTTTTTGACTCAAAGAGCCCCTTTGTAGGGTTTCACCTTGG-C-CTT
1 TTTTTTTTTGACTCAAAG-GCCCCTTTGTAGGGTTTCACCTTGGTCTCTT
*
23301734 TTTTTTTTTGACTCAAA-GCGCCCTTTGTAGGCTTTCACCTTGGTC
1 TTTTTTTTTGACTCAAAGGC-CCCTTTGTAGGGTTTCACCTTGGTC
23301779 CCACCTTTTA
Statistics
Matches: 86, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
46 2 0.02
47 22 0.26
48 20 0.23
49 10 0.12
50 5 0.06
51 25 0.29
52 2 0.02
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.46
Consensus pattern (49 bp):
TTTTTTTTTGACTCAAAGGCCCCTTTGTAGGGTTTCACCTTGGTCTCTT
Found at i:23307649 original size:3 final size:3
Alignment explanation
Indices: 23307565--23307630 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
23307555 ATATATATAG
*
23307565 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23307613 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
23307631 ATATAGCAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:23311283 original size:35 final size:37
Alignment explanation
Indices: 23311225--23311297 Score: 114
Period size: 35 Copynumber: 2.0 Consensus size: 37
23311215 ATAAACACAA
23311225 AAAAATATTTTAAAAATAAAAAATAAAAAATAT-TTT
1 AAAAATATTTTAAAAATAAAAAATAAAAAATATATTT
* *
23311261 AAAAGTATTTT-AAAATTAAAAATAAAAAATATATTT
1 AAAAATATTTTAAAAATAAAAAATAAAAAATATATTT
23311297 A
1 A
23311298 TTAAATTCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 20 0.59
36 14 0.41
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (37 bp):
AAAAATATTTTAAAAATAAAAAATAAAAAATATATTT
Found at i:23317971 original size:58 final size:59
Alignment explanation
Indices: 23317876--23317994 Score: 195
Period size: 58 Copynumber: 2.0 Consensus size: 59
23317866 TTGTTGTTCA
23317876 AAAGTATTGTTGAGATAAAAAGCGCTTTTGGAACTATAATATTAAATGGG-CAATTTTT
1 AAAGTATTGTTGAGATAAAAAGCGCTTTTGGAACTATAATATTAAATGGGTCAATTTTT
* * * *
23317934 AAAGTATTGTTGATATAAAAAGCGCTTTTGGACCTATAATGTTAAATGGGTCATTTTTT
1 AAAGTATTGTTGAGATAAAAAGCGCTTTTGGAACTATAATATTAAATGGGTCAATTTTT
23317993 AA
1 AA
23317995 GTTAGAAGTA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
58 47 0.84
59 9 0.16
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (59 bp):
AAAGTATTGTTGAGATAAAAAGCGCTTTTGGAACTATAATATTAAATGGGTCAATTTTT
Found at i:23319977 original size:9 final size:9
Alignment explanation
Indices: 23319963--23320012 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
23319953 GTAGTGATTC
23319963 AATTTGGTT
1 AATTTGGTT
*
23319972 AATTTGGGT
1 AATTTGGTT
*
23319981 AATTTGGGT
1 AATTTGGTT
*
23319990 AATTCGGTT
1 AATTTGGTT
*
23319999 AATTCGGTT
1 AATTTGGTT
23320008 AATTT
1 AATTT
23320013 TTAACCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (9 bp):
AATTTGGTT
Found at i:23322659 original size:66 final size:67
Alignment explanation
Indices: 23322561--23322694 Score: 261
Period size: 66 Copynumber: 2.0 Consensus size: 67
23322551 TTTGTTTATA
23322561 TATATATATATATATATTCAACATGGCAAGCTTAGAACTTTTGGGGTTAAAATGATGGGTTTAGC
1 TATATATATATATATATTCAACATGGCAAGCTTAGAACTTTTGGGGTTAAAATGATGGGTTTAGC
23322626 AT
66 AT
23322628 TATATATATA-ATATATTCAACATGGCAAGCTTAGAACTTTTGGGGTTAAAATGATGGGTTTAGC
1 TATATATATATATATATTCAACATGGCAAGCTTAGAACTTTTGGGGTTAAAATGATGGGTTTAGC
23322692 AT
66 AT
23322694 T
1 T
23322695 TAGTAACTCT
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 57 0.85
67 10 0.15
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (67 bp):
TATATATATATATATATTCAACATGGCAAGCTTAGAACTTTTGGGGTTAAAATGATGGGTTTAGC
AT
Found at i:23328750 original size:61 final size:62
Alignment explanation
Indices: 23328637--23328755 Score: 179
Period size: 61 Copynumber: 1.9 Consensus size: 62
23328627 ACTATTTTAA
* *
23328637 TAAATTTAATTTAATATTTATCTTGATTAGTATTTTATACATTTAATATTAATATGAGATAT
1 TAAATTTAATTTAATATTTATCTTGAATAGTATTTTATACATTTAAAATTAATATGAGATAT
* *
23328699 TAAATTTGATTTAATATTTATCTT-AATAGTATTTTATTA-ATTTAAAATTAATGTGAG
1 TAAATTTAATTTAATATTTATCTTGAATAGTATTTTA-TACATTTAAAATTAATATGAG
23328756 TAATTTCAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 27 0.52
62 25 0.48
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.51
Consensus pattern (62 bp):
TAAATTTAATTTAATATTTATCTTGAATAGTATTTTATACATTTAAAATTAATATGAGATAT
Found at i:23332047 original size:6 final size:6
Alignment explanation
Indices: 23332036--23332060 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
23332026 CCTAACTGTT
23332036 CAAAGA CAAAGA CAAAGA CAAAGA C
1 CAAAGA CAAAGA CAAAGA CAAAGA C
23332061 GGGAGCTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.20, G:0.16, T:0.00
Consensus pattern (6 bp):
CAAAGA
Found at i:23338784 original size:21 final size:21
Alignment explanation
Indices: 23338760--23338804 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
23338750 GATCCAAGCT
*
23338760 CCAGATCTGCTTCCATTGATC
1 CCAGACCTGCTTCCATTGATC
23338781 CCAGACCTGCTTCCATTGATC
1 CCAGACCTGCTTCCATTGATC
23338802 CCA
1 CCA
23338805 ACTATAGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.38, G:0.13, T:0.29
Consensus pattern (21 bp):
CCAGACCTGCTTCCATTGATC
Found at i:23338836 original size:66 final size:66
Alignment explanation
Indices: 23338717--23338849 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
23338707 TCCAAGCTCT
* * * *
23338717 AGACCTGCTTCCATCGATCCTAATTATAGAGCAGATCCAAGCTCCAGATCTGCTTCCATTGATCC
1 AGACCTGCTTCCATCGATCCCAACTATAGAGCAGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
23338782 C
66 C
* * ** *
23338783 AGACCTGCTTCCATTGATCCCAACTATAGAGCGGATCCGGGCTCTAGAGCTGCTCCCATTGATCC
1 AGACCTGCTTCCATCGATCCCAACTATAGAGCAGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
23338848 C
66 C
23338849 A
1 A
23338850 ATTATAGAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (66 bp):
AGACCTGCTTCCATCGATCCCAACTATAGAGCAGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
C
Found at i:23338842 original size:45 final size:45
Alignment explanation
Indices: 23338787--23338949 Score: 220
Period size: 45 Copynumber: 3.6 Consensus size: 45
23338777 GATCCCAGAC
* * *
23338787 CTGCTTCCATTGATCCCAACTATAGAGCGGATCCGGGCTCTAGAG
1 CTGCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG
*
23338832 CTGCTCCCATTGATCCCAATTATAGAGTGGATCCGAGCTCTAGAG
1 CTGCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG
* * * * *
23338877 -TCGCTTCCATTGACCCCAATTATAGAGCGGATCCAAGCGCTAGAA
1 CT-GCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG
*
23338922 CTGCTCCGATTGATCCCAATTATAGAGC
1 CTGCTCCCATTGATCCCAATTATAGAGC
23338950 TGCTCCAGAG
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 101 0.98
46 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (45 bp):
CTGCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG
Found at i:23339423 original size:15 final size:15
Alignment explanation
Indices: 23339399--23339429 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23339389 CAGCAATTTA
23339399 TAATCATATTTGAAC
1 TAATCATATTTGAAC
*
23339414 TAATCGTATTTGAAC
1 TAATCATATTTGAAC
23339429 T
1 T
23339430 GTGGATGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (15 bp):
TAATCATATTTGAAC
Found at i:23352279 original size:103 final size:104
Alignment explanation
Indices: 23352149--23352355 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 104
23352139 TTAAATCGGA
23352149 TTTTTATAATTTTAAGGGGGTCAAAGTACAATTTTACTTTTACTAATTTAAATTTTTTTTAAAAA
1 TTTTTATAATTTTAAGGGGGTCAAAGTACAATTTTACTTTTACTAATTTAAATTTTTTTTAAAAA
23352214 TTTAAGAGCCTAATTAAATAATAATTTTACATTTTATGG
66 TTTAAGAGCCTAATTAAATAATAATTTTACATTTTATGG
23352253 TTTTTATAA-TTTAAGGGGGTCAAAGTACAATTTTACTTTTACTAATTTAAATTTTTTTTAAAAA
1 TTTTTATAATTTTAAGGGGGTCAAAGTACAATTTTACTTTTACTAATTTAAATTTTTTTTAAAAA
23352317 TTTAAGAGCCTAATTAAATAATAATTTTACATTTTATGG
66 TTTAAGAGCCTAATTAAATAATAATTTTACATTTTATGG
23352356 GAGGCCGGGC
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 94 0.91
104 9 0.09
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (104 bp):
TTTTTATAATTTTAAGGGGGTCAAAGTACAATTTTACTTTTACTAATTTAAATTTTTTTTAAAAA
TTTAAGAGCCTAATTAAATAATAATTTTACATTTTATGG
Found at i:23355584 original size:93 final size:94
Alignment explanation
Indices: 23355424--23355611 Score: 369
Period size: 93 Copynumber: 2.0 Consensus size: 94
23355414 CAATAACGTA
23355424 AGTGACTAAAACGTAACATTTCAAATATAAATAAAAAAATATAATTTAAGACAAATAAAAATAAT
1 AGTGACTAAAACGTAACATTTCAAATATAAATAAAAAAATATAATTTAAGACAAATAAAAATAAT
23355489 TATTTTTATAATTTTCCCTAAAAATAAAT
66 TATTTTTATAATTTTCCCTAAAAATAAAT
23355518 AGTGACTAAAA-GTAACATTTCAAATATAAATAAAAAAATATAATTTAAGACAAATAAAAATAAT
1 AGTGACTAAAACGTAACATTTCAAATATAAATAAAAAAATATAATTTAAGACAAATAAAAATAAT
23355582 TATTTTTATAATTTTCCCTAAAAATAAAT
66 TATTTTTATAATTTTCCCTAAAAATAAAT
23355611 A
1 A
23355612 TATCATGTGC
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 83 0.88
94 11 0.12
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (94 bp):
AGTGACTAAAACGTAACATTTCAAATATAAATAAAAAAATATAATTTAAGACAAATAAAAATAAT
TATTTTTATAATTTTCCCTAAAAATAAAT
Found at i:23366217 original size:27 final size:26
Alignment explanation
Indices: 23366166--23366218 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
23366156 GTAAAAAAAC
*
23366166 TTTAAAATTCTATATAAAAGATTTTT
1 TTTAAAATTCTATATAAAACATTTTT
23366192 TTTAAAATTACTATATAAAAC-TTTTT
1 TTTAAAATT-CTATATAAAACATTTTT
23366218 T
1 T
23366219 ACTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTAAAATTCTATATAAAACATTTTT
Found at i:23378551 original size:6 final size:6
Alignment explanation
Indices: 23378540--23378574 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
23378530 AGATAATTTA
23378540 ATATGT ATATGT ATATGT ATATGT ATATGT ATATG
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATG
23378575 CATGCATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (6 bp):
ATATGT
Found at i:23395420 original size:4 final size:4
Alignment explanation
Indices: 23395411--23395525 Score: 70
Period size: 4 Copynumber: 25.2 Consensus size: 4
23395401 CAGAAGGAGG
*
23395411 GAAA GAAA GAAA GAAA TGAGAG GAAA GAAA GAAAA TGAAA GGAAAA GAGAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA G-AAA -GAAA -G-AAA GA-AA
23395462 GAAAA GGAAA GAAA GGAGAA GAAAA GGAGAA GAGAA GAAA -AAA GAAA GAAA
1 G-AAA -GAAA GAAA -GA-AA G-AAA -GA-AA GA-AA GAAA GAAA GAAA GAAA
*
23395513 GAAG GAAA GAAA G
1 GAAA GAAA GAAA G
23395526 GGAAAGGAGA
Statistics
Matches: 92, Mismatches: 5, Indels: 28
0.74 0.04 0.22
Matches are distributed among these distances:
3 3 0.03
4 43 0.47
5 33 0.36
6 13 0.14
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:23395438 original size:18 final size:18
Alignment explanation
Indices: 23395411--23395515 Score: 73
Period size: 18 Copynumber: 5.9 Consensus size: 18
23395401 CAGAAGGAGG
23395411 GAAA-GAAAGAAAGAAAT
1 GAAAGGAAAGAAAGAAAT
*
23395428 GAGAGGAAAGAAAGAAAAT
1 GAAAGGAAAGAAAG-AAAT
*
23395447 GAAAGGAAA-AGAG-AA-
1 GAAAGGAAAGAAAGAAAT
23395462 GAAAAGGAAAGAAAGGAGAA-
1 G-AAAGGAAAGAAA-GA-AAT
23395482 GAAAAGGAGAAGAGAAGAAA-
1 G-AAAGGA-AAGA-AAGAAAT
23395502 -AAA-GAAAGAAAGAA
1 GAAAGGAAAGAAAGAA
23395516 GGAAAGAAAG
Statistics
Matches: 75, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
15 6 0.08
16 14 0.19
17 7 0.09
18 16 0.21
19 12 0.16
20 12 0.16
21 6 0.08
22 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (18 bp):
GAAAGGAAAGAAAGAAAT
Found at i:23395457 original size:6 final size:5
Alignment explanation
Indices: 23395434--23395512 Score: 52
Period size: 5 Copynumber: 15.4 Consensus size: 5
23395424 AAATGAGAGG
* * * * *
23395434 AAAG- AAAGA AAATGA AAGGA AAAGA GAAGA AAAGG AAAGA AAGGA GAAGA
1 AAAGA AAAGA AAA-GA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
* * *
23395484 AAAGGA GAAGA GAAGA AAAAA GAAAGA AA
1 AAA-GA AAAGA AAAGA AAAGA -AAAGA AA
23395513 GAAGGAAAGA
Statistics
Matches: 57, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
4 4 0.07
5 41 0.72
6 12 0.21
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (5 bp):
AAAGA
Found at i:23395489 original size:11 final size:11
Alignment explanation
Indices: 23395439--23395494 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
23395429 AGAGGAAAGA
*
23395439 AAGAAAATGA-
1 AAGAAAAGGAG
23395449 AAGGAAAA-GAG
1 AA-GAAAAGGAG
23395460 AAGAAAAGGA-
1 AAGAAAAGGAG
23395470 AAG-AAAGGAG
1 AAGAAAAGGAG
23395480 AAGAAAAGGAG
1 AAGAAAAGGAG
23395491 AAGA
1 AAGA
23395495 GAAGAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.15
10 15 0.37
11 20 0.49
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (11 bp):
AAGAAAAGGAG
Found at i:23395492 original size:31 final size:30
Alignment explanation
Indices: 23395410--23395580 Score: 99
Period size: 30 Copynumber: 5.7 Consensus size: 30
23395400 GCAGAAGGAG
* *
23395410 GGAAAGAAA-GAAAG-AAATGAG-AGGAAA
1 GGAAAGAAAGGAAAGAAAAGGAGAAGAAAA
*
23395437 -GAAAGAAAATGAAAGGAAAA-GAGAAGAAAA
1 GGAAAG-AAAGGAAA-GAAAAGGAGAAGAAAA
*
23395467 GGAAAGAAAGGAGAAGAAAAGGAGAAGAGAA
1 GGAAAGAAAGGA-AAGAAAAGGAGAAGAAAA
*
23395498 -GAAA-AAA-GAAAGAAAGAAGGA-AAGAAAG
1 GGAAAGAAAGGAAAG-AA-AAGGAGAAGAAAA
* * * *
23395526 GGAAAGGAGAAGAGAAAAAAAAAGAAGAACAAGA
1 GGAAA-GA-AAG-G-AAAGAAAAGGAGAAGAAAA
* *
23395560 GGGAAGAAAGGAAAAAAAAGG
1 GGAAAGAAAGGAAAGAAAAGG
23395581 GAAAAATGTA
Statistics
Matches: 114, Mismatches: 12, Indels: 33
0.72 0.08 0.21
Matches are distributed among these distances:
26 5 0.04
27 6 0.05
28 13 0.11
29 16 0.14
30 31 0.27
31 18 0.16
32 5 0.04
33 6 0.05
34 11 0.10
35 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.01
Consensus pattern (30 bp):
GGAAAGAAAGGAAAGAAAAGGAGAAGAAAA
Found at i:23395538 original size:16 final size:14
Alignment explanation
Indices: 23395417--23395538 Score: 56
Period size: 16 Copynumber: 8.3 Consensus size: 14
23395407 GAGGGAAAGA
*
23395417 AAGAAAGAAATGAG
1 AAGAAAGAAAGGAG
* *
23395431 AGGAAAGAAA-GAA
1 AAGAAAGAAAGGAG
*
23395444 AATGAAAGGAAAAGAG
1 AA-GAAA-GAAAGGAG
23395460 AAGAAAAGGAAA-GA-
1 AAG-AAA-GAAAGGAG
23395474 AAGGAGAAGAAAAGGAG
1 AA-GA-AAG-AAAGGAG
**
23395491 AAGAGAAGAAAAAAG
1 AAGA-AAGAAAGGAG
23395506 AAAGAAAG-AAGGA-
1 -AAGAAAGAAAGGAG
23395519 AAGAAAGGGAAAGGAG
1 AAGAAA--GAAAGGAG
23395535 AAGA
1 AAGA
23395539 GAAAAAAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 26
0.72 0.07 0.22
Matches are distributed among these distances:
12 6 0.07
13 3 0.03
14 21 0.24
15 26 0.30
16 28 0.33
17 2 0.02
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02
Consensus pattern (14 bp):
AAGAAAGAAAGGAG
Found at i:23395554 original size:18 final size:19
Alignment explanation
Indices: 23395442--23395554 Score: 67
Period size: 20 Copynumber: 5.8 Consensus size: 19
23395432 GGAAAGAAAG
*
23395442 AAAATGAAAGGAA-AAGAGA
1 AAAAAGAAA-GAAGAAGAGA
*
23395461 AGAAAAGGAAAGAA-AGGAGA
1 A-AAAA-GAAAGAAGAAGAGA
*
23395481 AGAAAAG-GAGAAG-AGAAGA
1 A-AAAAGAAAGAAGAAG-AGA
23395500 AAAAAGAAAGAAAGAAG-GA
1 AAAAAGAAAG-AAGAAGAGA
*
23395519 AAGAAAGGGAAAGGAGAAGAGA
1 AA-AAA--GAAAGAAGAAGAGA
23395541 AAAAA-AAAGAAGAA
1 AAAAAGAAAGAAGAA
23395555 CAAGAGGGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 23
0.72 0.07 0.22
Matches are distributed among these distances:
18 18 0.24
19 12 0.16
20 23 0.30
21 14 0.18
22 9 0.12
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (19 bp):
AAAAAGAAAGAAGAAGAGA
Found at i:23395614 original size:19 final size:20
Alignment explanation
Indices: 23395590--23395628 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
23395580 GGAAAAATGT
23395590 AATTTTATTTATAA-ATTTG
1 AATTTTATTTATAATATTTG
* *
23395609 AATTTTTTTTGTAATATTTG
1 AATTTTATTTATAATATTTG
23395629 TGTGTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
AATTTTATTTATAATATTTG
Found at i:23403286 original size:19 final size:21
Alignment explanation
Indices: 23403262--23403300 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
23403252 ACTAAAACAA
*
23403262 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
23403281 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
23403301 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:23403460 original size:27 final size:27
Alignment explanation
Indices: 23403422--23403497 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
23403412 GTAATACGAG
*
23403422 TGGTGCCGCCAATTAGTA-TGGCACCAT
1 TGGTGCCGCCAA-TAGCATTGGCACCAT
* *
23403449 TGGTGCCGCCAATGGCATTGGCACCGT
1 TGGTGCCGCCAATAGCATTGGCACCAT
* *
23403476 TGGTGCCGCCAACACCATTGGC
1 TGGTGCCGCCAATAGCATTGGC
23403498 GTGACCAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 3 0.07
27 39 0.93
ACGTcount: A:0.18, C:0.30, G:0.29, T:0.22
Consensus pattern (27 bp):
TGGTGCCGCCAATAGCATTGGCACCAT
Found at i:23403574 original size:26 final size:26
Alignment explanation
Indices: 23403543--23403613 Score: 108
Period size: 26 Copynumber: 2.7 Consensus size: 26
23403533 TTGGTTTTGT
23403543 TTATATATTTTGGTAAATAAAAAAAAG
1 TTATATATTTTGGTAAAT-AAAAAAAG
23403570 -TATATATTTTGGTAAATAAAAAAAG
1 TTATATATTTTGGTAAATAAAAAAAG
*
23403595 TTGTAATATTTTGGTAAAT
1 TTAT-ATATTTTGGTAAAT
23403614 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 8 0.20
26 19 0.46
27 14 0.34
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (26 bp):
TTATATATTTTGGTAAATAAAAAAAG
Found at i:23413031 original size:46 final size:46
Alignment explanation
Indices: 23412961--23413099 Score: 217
Period size: 46 Copynumber: 3.0 Consensus size: 46
23412951 ACAATGCTAT
*
23412961 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
* *
23413007 AACTCAATATGGTTTTCGTT-ACTGAAATATCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTC-TTCACTGAAATACCATACCTACGTTTCAC
* *
23413053 AACTCAGTATGGTTTTCTTCACTAAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
23413099 A
1 A
23413100 CTTTATCATG
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
45 2 0.02
46 80 0.95
47 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
Found at i:23417265 original size:111 final size:111
Alignment explanation
Indices: 23417071--23417294 Score: 439
Period size: 111 Copynumber: 2.0 Consensus size: 111
23417061 GATCACCTTG
23417071 AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
1 AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
23417136 GTTATCACCCTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
66 GTTATCACCCTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
23417182 AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
1 AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
*
23417247 GTTATCACCTTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
66 GTTATCACCCTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
23417293 AA
1 AA
23417295 TGTCTTAGTG
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (111 bp):
AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
GTTATCACCCTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
Done.