Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 5 of 145
Found at i:2080367 original size:16 final size:16
Alignment explanation
Indices: 2080348--2080380 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2080338 TATCAAACAT
2080348 TTGTTGGATCATGATG
1 TTGTTGGATCATGATG
2080364 TTGTTGGATCATGATG
1 TTGTTGGATCATGATG
2080380 T
1 T
2080381 ACCAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.30, T:0.45
Consensus pattern (16 bp):
TTGTTGGATCATGATG
Found at i:2080729 original size:175 final size:176
Alignment explanation
Indices: 2080438--2080788 Score: 695
Period size: 175 Copynumber: 2.0 Consensus size: 176
2080428 TTGAGTTAAA
2080438 ATGTTGTTATATATGTGGGTTATACTAGGCAGTGGCGAATACAGGAGGGGCTGGCAGGGCCCCGG
1 ATGTTGTTATATATGTGGGTTATACTAGGCAGTGGCGAATACAGGAGGGGCTGGCAGGGCCCCGG
2080503 CCCCTTTAGGGCCATTAAAATTCTAGATTGTAATGGTAAAATTATATTTTAGCCCCTTAAAAATA
66 CCCCTTTAGGGCCATTAAAATTCTAGATTGTAATGGTAAAATTATATTTTAGCCCCTTAAAAATA
2080568 ATAATTTAATTTAATTTAATTCTTTAAAAATTAT-AAGATATAGGC
131 ATAATTTAATTTAATTTAATTCTTTAAAAATTATAAAGATATAGGC
2080613 ATGTTGTTATATATGTGGGTTATACTAGGCAGTGGCGAATACAGGAGGGGCTGGCAGGGCCCCGG
1 ATGTTGTTATATATGTGGGTTATACTAGGCAGTGGCGAATACAGGAGGGGCTGGCAGGGCCCCGG
2080678 CCCCTTTAGGGCCATTAAAATTCTAGATTGTAATGGTAAAATTATATTTTAGCCCCTTAAAAATA
66 CCCCTTTAGGGCCATTAAAATTCTAGATTGTAATGGTAAAATTATATTTTAGCCCCTTAAAAATA
2080743 ATAATTTAATTTAATTTAATTCTTTAAAAATTATAAAGATATAGGC
131 ATAATTTAATTTAATTTAATTCTTTAAAAATTATAAAGATATAGGC
2080789 TATTAAAATG
Statistics
Matches: 175, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
175 164 0.94
176 11 0.06
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.34
Consensus pattern (176 bp):
ATGTTGTTATATATGTGGGTTATACTAGGCAGTGGCGAATACAGGAGGGGCTGGCAGGGCCCCGG
CCCCTTTAGGGCCATTAAAATTCTAGATTGTAATGGTAAAATTATATTTTAGCCCCTTAAAAATA
ATAATTTAATTTAATTTAATTCTTTAAAAATTATAAAGATATAGGC
Found at i:2084725 original size:22 final size:23
Alignment explanation
Indices: 2084700--2084744 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2084690 ACACGATACT
* *
2084700 AATA-CTTTAAGGACTTAATTAA
1 AATATCTTTAAAGACTAAATTAA
*
2084722 AATATTTTTAAAGACTAAATTAA
1 AATATCTTTAAAGACTAAATTAA
2084745 TATTATATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (23 bp):
AATATCTTTAAAGACTAAATTAA
Found at i:2089055 original size:16 final size:16
Alignment explanation
Indices: 2089034--2089096 Score: 55
Period size: 18 Copynumber: 4.1 Consensus size: 16
2089024 TTAAGGAATT
2089034 ATCAAATATATATTTA
1 ATCAAATATATATTTA
2089050 ATC-AA-ATATA-TTA
1 ATCAAATATATATTTA
*
2089063 A--AAAGATATATTATA
1 ATCAAATATATATT-TA
*
2089078 TATTAAATATATATTTA
1 -ATCAAATATATATTTA
2089095 AT
1 AT
2089097 ATGGGTTGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
12 2 0.05
13 9 0.23
14 6 0.15
15 4 0.10
16 6 0.15
17 2 0.05
18 10 0.26
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (16 bp):
ATCAAATATATATTTA
Found at i:2089098 original size:20 final size:21
Alignment explanation
Indices: 2089054--2089098 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2089044 TATTTAATCA
2089054 AATATATTAAAAAGATATATT
1 AATATATTAAAAAGATATATT
* *
2089075 -ATATATTAAATATATAT-TT
1 AATATATTAAAAAGATATATT
2089094 AATAT
1 AATAT
2089099 GGGTTGGGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATATTAAAAAGATATATT
Found at i:2098311 original size:23 final size:23
Alignment explanation
Indices: 2098284--2098338 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2098274 TAATTTGATC
2098284 ATTTTAGTCCCTATACTTTTT-GA
1 ATTTTAGTCCCTATA-TTTTTCGA
*
2098307 ATTTTAGTCCCTGTATTTTTCGA
1 ATTTTAGTCCCTATATTTTTCGA
2098330 ATTTTAGTC
1 ATTTTAGTC
2098339 ATGACCCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.53
Consensus pattern (23 bp):
ATTTTAGTCCCTATATTTTTCGA
Found at i:2104388 original size:38 final size:38
Alignment explanation
Indices: 2104346--2104458 Score: 208
Period size: 38 Copynumber: 3.0 Consensus size: 38
2104336 AAGAGAAGAC
* *
2104346 TATTCTAAAAGAAAGTTTATGCGGAATTTACAAGATCG
1 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATCG
2104384 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATCG
1 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATCG
2104422 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATC
1 TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATC
2104459 CTATACAATT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 73 1.00
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (38 bp):
TATTCTAAAAGAAAGATAATGCGGAATTTACAAGATCG
Found at i:2106748 original size:451 final size:451
Alignment explanation
Indices: 2105906--2106816 Score: 1799
Period size: 451 Copynumber: 2.0 Consensus size: 451
2105896 AAAAATTATG
2105906 ATATTTTTAATTTAATATTTTTTATTAACAATTTTAAACTTAGAAACATAAAATAGTTTTTAATA
1 ATATTTTTAATTTAATATTTTTTATTAACAATTTTAAACTTAGAAACATAAAATAGTTTTTAATA
2105971 TGCACATTATAATTTTAATATAAGCCGATTAAGTCTTAATTTGATTGATATAGACATTACTATCA
66 TGCACATTATAATTTTAATATAAGCCGATTAAGTCTTAATTTGATTGATATAGACATTACTATCA
2106036 ATATAGAAGGACGTGAGTTTGAGTTTGCTGAATGTGTTACAATGATGGCAAAGAACATTTGCATA
131 ATATAGAAGGACGTGAGTTTGAGTTTGCTGAATGTGTTACAATGATGGCAAAGAACATTTGCATA
2106101 TTTTTTGCTAACACACGAAACCATGTTTGAGGTTTTCAATTTGACACTTGTAAATTAACGCTTTA
196 TTTTTTGCTAACACACGAAACCATGTTTGAGGTTTTCAATTTGACACTTGTAAATTAACGCTTTA
2106166 TGGCCCACGTTTTATTGTTTTACTTTTTAAAGTTTTTTGATATATTAATGTAAATTGATTGATCA
261 TGGCCCACGTTTTATTGTTTTACTTTTTAAAGTTTTTTGATATATTAATGTAAATTGATTGATCA
2106231 GGTTCAATTCAAATTTATGTATGAGCGTAACTTAAGCTTATTTAAATTTAGTTCGATTTAAAATA
326 GGTTCAATTCAAATTTATGTATGAGCGTAACTTAAGCTTATTTAAATTTAGTTCGATTTAAAATA
2106296 TAAAATTCAAAATTTATCAAAGTTTACTTATATTTATAAATAATTAATCT-AAATATTTTT
391 TAAAATTCAAAATTTATCAAAGTTTACTTATATTTATAAATAATTAATCTAAAATATTTTT
2106356 AATATTTTTAATTTAATATTTTTTATTAACAATTTTAAACTTAGAAACATAAAATAGTTTTTAAT
1 -ATATTTTTAATTTAATATTTTTTATTAACAATTTTAAACTTAGAAACATAAAATAGTTTTTAAT
2106421 ATGCACATTATAATTTTAATATAAGCCGATTAAGTCTTAATTTGATTGATATAGACATTACTATC
65 ATGCACATTATAATTTTAATATAAGCCGATTAAGTCTTAATTTGATTGATATAGACATTACTATC
2106486 AATATAGAAGGACGTGAGTTTGAGTTTGCTGAATGTGTTACAATGATGGCAAAGAACATTTGCAT
130 AATATAGAAGGACGTGAGTTTGAGTTTGCTGAATGTGTTACAATGATGGCAAAGAACATTTGCAT
2106551 ATTTTTTGCTAACACACGAAACCATGTTTGAGGTTTTCAATTTGACACTTGTAAATTAACGCTTT
195 ATTTTTTGCTAACACACGAAACCATGTTTGAGGTTTTCAATTTGACACTTGTAAATTAACGCTTT
2106616 ATGGCCCACGTTTTATTGTTTTACTTTTTAAAGTTTTTTGATATATTAATGTAAATTGATTGATC
260 ATGGCCCACGTTTTATTGTTTTACTTTTTAAAGTTTTTTGATATATTAATGTAAATTGATTGATC
2106681 AGGTTCAATTCAAATTTATGTATGAGCGTAACTTAAGCTTATTTAAATTTAGTTCGATTTAAAAT
325 AGGTTCAATTCAAATTTATGTATGAGCGTAACTTAAGCTTATTTAAATTTAGTTCGATTTAAAAT
2106746 ATAAAATTCAAAATTTATCAAAGTTTACTTATATTTATAAATAATTAATCTAAAATATTTTT
390 ATAAAATTCAAAATTTATCAAAGTTTACTTATATTTATAAATAATTAATCTAAAATATTTTT
2106808 AT-TTTTTAA
1 ATATTTTTAA
2106817 AATTATTATA
Statistics
Matches: 459, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
450 7 0.02
451 442 0.96
452 10 0.02
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (451 bp):
ATATTTTTAATTTAATATTTTTTATTAACAATTTTAAACTTAGAAACATAAAATAGTTTTTAATA
TGCACATTATAATTTTAATATAAGCCGATTAAGTCTTAATTTGATTGATATAGACATTACTATCA
ATATAGAAGGACGTGAGTTTGAGTTTGCTGAATGTGTTACAATGATGGCAAAGAACATTTGCATA
TTTTTTGCTAACACACGAAACCATGTTTGAGGTTTTCAATTTGACACTTGTAAATTAACGCTTTA
TGGCCCACGTTTTATTGTTTTACTTTTTAAAGTTTTTTGATATATTAATGTAAATTGATTGATCA
GGTTCAATTCAAATTTATGTATGAGCGTAACTTAAGCTTATTTAAATTTAGTTCGATTTAAAATA
TAAAATTCAAAATTTATCAAAGTTTACTTATATTTATAAATAATTAATCTAAAATATTTTT
Found at i:2107992 original size:2 final size:2
Alignment explanation
Indices: 2107985--2108016 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2107975 AAACACATCA
2107985 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2108017 CTTATCTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2118470 original size:15 final size:15
Alignment explanation
Indices: 2118450--2118487 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2118440 GGTAGCAATA
2118450 CAAATAACAACCCT-C
1 CAAATAA-AACCCTAC
*
2118465 CAAATAAAATCCTAC
1 CAAATAAAACCCTAC
2118480 CAAATAAA
1 CAAATAAA
2118488 CTTTCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (15 bp):
CAAATAAAACCCTAC
Found at i:2120317 original size:27 final size:26
Alignment explanation
Indices: 2120282--2120333 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2120272 CTTTGAATAA
*
2120282 TATTCATTTTAATATTTCAATATATTT
1 TATTCATTTTAATATTTAAAT-TATTT
* *
2120309 TATTTATTTTAGTATTTAAATTATT
1 TATTCATTTTAATATTTAAATTATT
2120334 ATCTTGTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTCATTTTAATATTTAAATTATTT
Found at i:2120628 original size:28 final size:28
Alignment explanation
Indices: 2120597--2120663 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
2120587 AAACCCATTC
* *
2120597 ATATTATTTTTATTTTTAAAAAATATTT
1 ATATTATTTTTATATTTAAAAAATATAT
* * * *
2120625 ATATTATATTCATATTTAATAATTATAT
1 ATATTATTTTTATATTTAAAAAATATAT
2120653 ATATTATTTTT
1 ATATTATTTTT
2120664 TAAAATTTCT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATTATTTTTATATTTAAAAAATATAT
Found at i:2126000 original size:2 final size:2
Alignment explanation
Indices: 2125993--2126022 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2125983 TAATTTAAAC
2125993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2126023 TTGGGGTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2128212 original size:26 final size:26
Alignment explanation
Indices: 2128172--2128246 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
2128162 GGATGACGAG
* * *
2128172 GTAAGTTCACGGGCCCAGCTCGCGAT
1 GTAAGTTCGCAGGCCCAGCTCGCAAT
*
2128198 GTAAGTTCGCAGGCCTAGCTCGCAAT
1 GTAAGTTCGCAGGCCCAGCTCGCAAT
**
2128224 GTAAGCTT-GCAGATCCAGCTCGC
1 GTAAG-TTCGCAGGCCCAGCTCGC
2128247 CACAGTCTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 39 0.95
27 2 0.05
ACGTcount: A:0.21, C:0.29, G:0.28, T:0.21
Consensus pattern (26 bp):
GTAAGTTCGCAGGCCCAGCTCGCAAT
Found at i:2138000 original size:34 final size:34
Alignment explanation
Indices: 2137961--2138031 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
2137951 TACTTTTATT
2137961 TTCATTCAATTTGCTATCAATTTTACGATTAATG
1 TTCATTCAATTTGCTATCAATTTTACGATTAATG
2137995 TTCATTCAATTTGCTATCAATTTTACGATTAATG
1 TTCATTCAATTTGCTATCAATTTTACGATTAATG
2138029 TTC
1 TTC
2138032 GAAGTTGGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.48
Consensus pattern (34 bp):
TTCATTCAATTTGCTATCAATTTTACGATTAATG
Found at i:2140415 original size:23 final size:23
Alignment explanation
Indices: 2140372--2140415 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2140362 TTCAACATTT
*
2140372 ATCAATAAATCATGTTTAAACTA
1 ATCAATAAATCATGTTGAAACTA
2140395 ATCACATAAATCATG-TGAAAC
1 ATCA-ATAAATCATGTTGAAAC
2140416 AAGAGGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.30
Consensus pattern (23 bp):
ATCAATAAATCATGTTGAAACTA
Found at i:2148443 original size:27 final size:26
Alignment explanation
Indices: 2148385--2148443 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2148375 ACAAATAAAT
* *
2148385 TAAAATTATAAAAATATTTAAAAAAT
1 TAAAATTATAAAAAAATTTAAAAAAC
*
2148411 TCAAAATTATAAAAAAAGTTTATAAAAC
1 T-AAAATTATAAAAAAA-TTTAAAAAAC
2148439 TAAAA
1 TAAAA
2148444 AATGAATAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 18 0.64
28 9 0.32
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (26 bp):
TAAAATTATAAAAAAATTTAAAAAAC
Found at i:2160880 original size:72 final size:72
Alignment explanation
Indices: 2160763--2160907 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 72
2160753 ACTTCCACGA
*
2160763 TGCTAAATTTCATTTAAGTAAAGAACCCCTTTCCATTCAACAAAAATCTCAAGTGCTGGAGAGAT
1 TGCTAAATTTCATTTAAGTAAAGAACCCCTTTCCATTCAACAAAAATCACAAGTGCTGGAGAGAT
2160828 ACAAAGC
66 ACAAAGC
* * *
2160835 TGCTAAATTTCATTTAAGTAAAGAATCCCTTTCCATTCAATAAAAATCACAAGTGCTGGAGGGAT
1 TGCTAAATTTCATTTAAGTAAAGAACCCCTTTCCATTCAACAAAAATCACAAGTGCTGGAGAGAT
*
2160900 ACAGAGC
66 ACAAAGC
2160907 T
1 T
2160908 TGCTTGACAC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (72 bp):
TGCTAAATTTCATTTAAGTAAAGAACCCCTTTCCATTCAACAAAAATCACAAGTGCTGGAGAGAT
ACAAAGC
Found at i:2172681 original size:22 final size:21
Alignment explanation
Indices: 2172626--2172681 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2172616 TAAAAAAATA
*
2172626 TAAATTTAAA-AGTTTTATAT
1 TAAATTTAAATAATTTTATAT
* *
2172646 TCAAGTTTATATAATTTTATAAT
1 T-AAATTTAAATAATTTTAT-AT
2172669 TAAATTTAAATAA
1 TAAATTTAAATAA
2172682 AATAATCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 7 0.25
22 17 0.61
23 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (21 bp):
TAAATTTAAATAATTTTATAT
Found at i:2172982 original size:2 final size:2
Alignment explanation
Indices: 2172977--2173001 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2172967 TGAATTAGTG
2172977 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 T
2173002 TAGAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2176215 original size:3 final size:3
Alignment explanation
Indices: 2176207--2176233 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2176197 TACGCAACAT
2176207 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
2176234 CCTCAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2186217 original size:7 final size:7
Alignment explanation
Indices: 2186205--2186230 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2186195 GGGGAGTATA
2186205 TGAGATT
1 TGAGATT
2186212 TGAGATT
1 TGAGATT
2186219 TGAGATT
1 TGAGATT
2186226 TGAGA
1 TGAGA
2186231 ACAGATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (7 bp):
TGAGATT
Found at i:2186605 original size:31 final size:31
Alignment explanation
Indices: 2186522--2186618 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
2186512 AAGAGTCTTC
* *
2186522 AAAAATATTGAAGGGTCTAATTAAAAATTTT
1 AAAAATTTTGAAGGGACTAATTAAAAATTTT
* ** * **
2186553 AAAACTTTT-AAATGACTTAATTAGACTTTTT
1 AAAAATTTTGAAGGGAC-TAATTAAAAATTTT
* *
2186584 AAAAATTTTGAAGGGACTAATTCAAAATTTC
1 AAAAATTTTGAAGGGACTAATTAAAAATTTT
2186615 AAAA
1 AAAA
2186619 TTATGCATAA
Statistics
Matches: 48, Mismatches: 16, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
30 4 0.08
31 39 0.81
32 5 0.10
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.36
Consensus pattern (31 bp):
AAAAATTTTGAAGGGACTAATTAAAAATTTT
Found at i:2186907 original size:12 final size:12
Alignment explanation
Indices: 2186890--2186914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2186880 CGGGGCATAA
2186890 AAATTTACTTTC
1 AAATTTACTTTC
2186902 AAATTTACTTTC
1 AAATTTACTTTC
2186914 A
1 A
2186915 TCATTCATCA
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:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTTACTTTC
Found at i:2188198 original size:46 final size:45
Alignment explanation
Indices: 2188092--2188288 Score: 243
Period size: 46 Copynumber: 4.6 Consensus size: 45
2188082 CATATGACCT
*
2188092 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
2188135 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
2188181 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
** *
2188218 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
2188264 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
2188289 AGTACTCAAA
Statistics
Matches: 132, Mismatches: 10, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
37 28 0.21
39 2 0.02
40 3 0.02
41 1 0.01
42 1 0.01
43 10 0.08
44 5 0.04
45 21 0.16
46 61 0.46
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:2188219 original size:37 final size:37
Alignment explanation
Indices: 2188178--2188252 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
2188168 GCTGAAGCTA
2188178 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
* **
2188215 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
2188252 C
1 C
2188253 TAAAACTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
Found at i:2188238 original size:83 final size:83
Alignment explanation
Indices: 2188132--2188288 Score: 251
Period size: 83 Copynumber: 1.9 Consensus size: 83
2188122 AGCTAGGCTA
* *
2188132 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCAC
1 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTATCAC
2188197 TTGATCAGATAAGTGTAG
66 TTGATCAGATAAGTGTAG
**** *
2188215 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCAC
1 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTATCAC
2188280 TTGATCAGA
66 TTGATCAGA
2188289 AGTACTCAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (83 bp):
CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTATCAC
TTGATCAGATAAGTGTAG
Found at i:2193396 original size:24 final size:25
Alignment explanation
Indices: 2193360--2193406 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2193350 TCACAATATA
**
2193360 AAAAATTTTAATAA-ATAAAAAATT
1 AAAAATTAAAATAATATAAAAAATT
2193384 AAAAATTAAAATAATATAAAAAA
1 AAAAATTAAAATAATATAAAAAA
2193407 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAAATTAAAATAATATAAAAAATT
Found at i:2193417 original size:23 final size:21
Alignment explanation
Indices: 2193359--2193419 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
2193349 ATCACAATAT
*
2193359 AAAAAATTTTAATAAATAAAAA
1 AAAAAAATTTAA-AAATAAAAA
*
2193381 ATTAAAAA-TT-AAAATAATATAA
1 A-AAAAAATTTAAAAATAA-A-AA
2193403 AAAAAAATTTAAAAATA
1 AAAAAAATTTAAAAATA
2193420 TGGACGGGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
20 6 0.19
21 7 0.23
22 8 0.26
23 10 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAAATTTAAAAATAAAAA
Found at i:2202495 original size:2 final size:2
Alignment explanation
Indices: 2202488--2202513 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2202478 CCAACCTTCA
2202488 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
2202514 TAATGGAAAC
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:2204667 original size:19 final size:21
Alignment explanation
Indices: 2204629--2204669 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
2204619 TTAGTCCACT
*
2204629 ATTTTTATTTTAGAAGATTTA
1 ATTTTTATTTTAGAAAATTTA
2204650 ATTTTT-TTTTA-AAAATTTA
1 ATTTTTATTTTAGAAAATTTA
2204669 A
1 A
2204670 GTCCAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTTATTTTAGAAAATTTA
Found at i:2205972 original size:14 final size:14
Alignment explanation
Indices: 2205927--2205977 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
2205917 AATCAACCTG
* *
2205927 AACCTTGAATCCTA
1 AACCTCGAACCCTA
* * *
2205941 AACCTCAAACTCTT
1 AACCTCGAACCCTA
2205955 AACCTCGAACCCTA
1 AACCTCGAACCCTA
2205969 AACCT-GAAC
1 AACCTCGAAC
2205978 TTGAACTCCA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.37, C:0.35, G:0.06, T:0.22
Consensus pattern (14 bp):
AACCTCGAACCCTA
Found at i:2209471 original size:154 final size:154
Alignment explanation
Indices: 2209182--2209807 Score: 918
Period size: 154 Copynumber: 4.0 Consensus size: 154
2209172 ATATATTTGA
* * * *
2209182 TGTGTGAATTACATTTGTTTTTATTAAGCTTCTTGTAAACGAGTCTTGTTTTTTTTATAATTCAG
1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTG-TTTTTTTATAATTCAG
* *
2209247 TTTACGATTCGTTTTTTCTCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAG
65 TTTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAG
*
2209312 AGTTTTGTGTTGATTTTCAGTGAGT
130 TGTTTTGTGTTGATTTTCAGTGAGT
* *
2209337 TGTGAGAATTACATTTATTTTGATTAAACTTCTTATAAACGAGGCTTGTTTTTTTATAATTCAGT
1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
*
2209402 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAGT
66 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT
2209467 GTTTTGTGTTGATTTTCAGTGAGT
131 GTTTTGTGTTGATTTTCAGTGAGT
**
2209491 TGTGAGAATTACATTTATTTTTTTTAAGCTTCTTATAAACGAGTCTTG-TTTTTTATAATTCAGT
1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
*
2209555 TTACGATTCGTTTTTTTCGCTTTGGTGATTTGGTCGATTGGCTGGTTTTTGAAATGTGAATTTAG
66 TTACGATTCG-TTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAG
* * * *
2209620 TGTTTTGTATTGATGTTAAGTGGGT
130 TGTTTTGTGTTGATTTTCAGTGAGT
**
2209645 TGTGAGAATTACATTTCATTTTGATTAAGCTTCTTATAAACGTTTCTTGTTTTTTTATAATTCAG
1 TGTGAGAATTACATTT-ATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAG
* * * * * *
2209710 TTTAGGATTCAATTTTTT-GCTTTGGTTTG-TTTGGTCGATTGGCTGTTTTTTTAAACGTGAATT
65 TTTACGATTC-GTTTTTTCGCTTTGG--TGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATT
* *
2209773 GAGTGTTTCGTGTTG-TTGTTCAGTGAGT
127 TAGTGTTTTGTGTTGATT-TTCAGTGAGT
2209801 TGTGAGA
1 TGTGAGA
2209808 TTGAGTCAAA
Statistics
Matches: 431, Mismatches: 33, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
153 26 0.06
154 237 0.55
155 78 0.18
156 88 0.20
157 2 0.00
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.50
Consensus pattern (154 bp):
TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT
GTTTTGTGTTGATTTTCAGTGAGT
Found at i:2214483 original size:18 final size:17
Alignment explanation
Indices: 2214453--2214494 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2214443 TTATTGTTTG
2214453 TAATGTTTTTATATTATA
1 TAAT-TTTTTATATTATA
*
2214471 TTATTTTTATATATTATA
1 TAATTTTT-TATATTATA
2214489 TAATTT
1 TAATTT
2214495 GTAACCTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TAATTTTTTATATTATA
Found at i:2221633 original size:2 final size:2
Alignment explanation
Indices: 2221626--2221662 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2221616 CTAATAGTTT
2221626 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2221663 TCATCAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2231735 original size:14 final size:14
Alignment explanation
Indices: 2231713--2231754 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
2231703 AACATTCGGT
*
2231713 GTTTCAAAATTTAA
1 GTTTTAAAATTTAA
2231727 GTTTTAAAATTTAA
1 GTTTTAAAATTTAA
* *
2231741 GGTTTAGAATTTAA
1 GTTTTAAAATTTAA
2231755 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (14 bp):
GTTTTAAAATTTAA
Found at i:2231914 original size:14 final size:14
Alignment explanation
Indices: 2231881--2231916 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2231871 AAGGTATAGT
2231881 GGTTCAAAATTCAA
1 GGTTCAAAATTCAA
* *
2231895 GCTTCAAAATTCAG
1 GGTTCAAAATTCAA
2231909 GGTTCAAA
1 GGTTCAAA
2231917 GCTTCATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (14 bp):
GGTTCAAAATTCAA
Found at i:2242937 original size:32 final size:32
Alignment explanation
Indices: 2242884--2242949 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
2242874 AGTCTCTGTA
*
2242884 TTTTGATAGAATTTAAGATTTAATCCTTATAC
1 TTTTGATAGAATTGAAGATTTAATCCTTATAC
* * *
2242916 TTTTTATAGAATATGAA-ATTTAGTCCTTGTAC
1 TTTTGATAGAAT-TGAAGATTTAATCCTTATAC
2242948 TT
1 TT
2242950 GAAAGGTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 26 0.90
33 3 0.10
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (32 bp):
TTTTGATAGAATTGAAGATTTAATCCTTATAC
Found at i:2253306 original size:2 final size:2
Alignment explanation
Indices: 2253301--2253329 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2253291 ACAATCACTT
2253301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2253330 TTGATAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2254088 original size:75 final size:76
Alignment explanation
Indices: 2253951--2254121 Score: 272
Period size: 75 Copynumber: 2.2 Consensus size: 76
2253941 CATTGTTGTA
* * *
2253951 CTCATTGTTACCATTGTAATAGTTGTTGTTGTTGTTCTGGTTTTCCTTAGTACTCCATCCTTTCT
1 CTCATTGTTACCATTGTAATA--TGTTGTTGCTATTCTGGTTTTCCTTAGTACTCCACCCTTTCT
*
2254016 CAGTGAACATGGC
64 CAGTGAACAAGGC
2254029 CTCATTGTTACCATTGTAATA-GTTGTTGCTATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCA
1 CTCATTGTTACCATTGTAATATGTTGTTGCTATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCA
2254093 GTGAACAAGGC
66 GTGAACAAGGC
*
2254104 CTCGTTGTTACCATTGTA
1 CTCATTGTTACCATTGTA
2254122 GTTGTTGGTT
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
75 67 0.76
78 21 0.24
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (76 bp):
CTCATTGTTACCATTGTAATATGTTGTTGCTATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCA
GTGAACAAGGC
Found at i:2265684 original size:53 final size:56
Alignment explanation
Indices: 2265623--2265833 Score: 200
Period size: 64 Copynumber: 3.6 Consensus size: 56
2265613 TTACAAGCTG
*
2265623 TTTTATTTTATTATTATTTACTTTTTTATTTATTTT-C-A-A-CCTTTCAT-AATTTT
1 TTTTATTTT-TTATTATTTACTTATTTATTTATTTTCCAATAGCCTTTCATGAA-TTT
2265676 TTTTATTTTTTTATTATTTACTTATTTATTTATTATTCCAATTTCAGCCTTTCATGAATTT
1 TTTTA-TTTTTTATTATTTACTTATTTATTTATT-TTCCAA--T-AGCCTTTCATGAATTT
* *
2265737 TTTTATTTTTTATTATTTACTCATTTATTTATTTATTATTGCAATTTTAGCCTTTCATGAATCT
1 TTTTATTTTTTATTATTTA--C--TTATTTATTTATT-TTCCAA---TAGCCTTTCATGAATTT
*
2265801 TTTTA-TTTTTACTCATTTACTTATTTATTTATT
1 TTTTATTTTTTA-TTATTTACTTATTTATTTATT
2265834 ATTGCCCTAC
Statistics
Matches: 138, Mismatches: 4, Indels: 25
0.83 0.02 0.15
Matches are distributed among these distances:
53 28 0.20
54 6 0.04
55 1 0.01
56 1 0.01
60 28 0.20
61 16 0.12
62 4 0.03
63 6 0.04
64 45 0.33
65 3 0.02
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.64
Consensus pattern (56 bp):
TTTTATTTTTTATTATTTACTTATTTATTTATTTTCCAATAGCCTTTCATGAATTT
Found at i:2265749 original size:60 final size:60
Alignment explanation
Indices: 2265656--2265836 Score: 240
Period size: 64 Copynumber: 2.9 Consensus size: 60
2265646 TTTTATTTAT
*
2265656 TTTCAACCTTTCAT-AATTTTTTTTATTTTTTTATTATTTACTTATTTATTTATTATTCCAA
1 TTTCAGCCTTTCATGAA-TTTTTTTA-TTTTTTATTATTTACTTATTTATTTATTATTCCAA
*
2265717 TTTCAGCCTTTCATGAATTTTTTTATTTTTTATTATTTACTCATTTATTTATTTATTATTGCAA
1 TTTCAGCCTTTCATGAATTTTTTTATTTTTTATTATTTA--C--TTATTTATTTATTATTCCAA
* * *
2265781 TTTTAGCCTTTCATGAATCTTTTTA-TTTTTACTCATTTACTTATTTATTTATTATT
1 TTTCAGCCTTTCATGAATTTTTTTATTTTTTA-TTATTTACTTATTTATTTATTATT
2265837 GCCCTACCTT
Statistics
Matches: 109, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
60 30 0.28
61 21 0.19
62 4 0.04
63 6 0.06
64 48 0.44
ACGTcount: A:0.23, C:0.12, G:0.03, T:0.62
Consensus pattern (60 bp):
TTTCAGCCTTTCATGAATTTTTTTATTTTTTATTATTTACTTATTTATTTATTATTCCAA
Found at i:2266021 original size:19 final size:19
Alignment explanation
Indices: 2265997--2266063 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
2265987 AATTTTTATT
2265997 TTTATTTTAAGTTAACTTA
1 TTTATTTTAAGTTAACTTA
**
2266016 TTTATTTT-A-TTATTTTTA
1 TTTATTTTAAGTTA-ACTTA
2266034 TTTTTATTTTAAGTTAACTTA
1 --TTTATTTTAAGTTAACTTA
*
2266055 TCTATTTTA
1 TTTATTTTA
2266064 TTATTATGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 16 0.42
20 8 0.21
21 4 0.11
22 3 0.08
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTATTTTAAGTTAACTTA
Found at i:2266031 original size:39 final size:39
Alignment explanation
Indices: 2265988--2266068 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
2265978 ACATCTTCTA
*
2265988 ATTTTTATTTTTATTTTAAGTTAACTTATTTATTTTATT
1 ATTTTTATTTTTATTTTAAGTTAACTTATCTATTTTATT
2266027 ATTTTTATTTTTATTTTAAGTTAACTTATCTATTTTATT
1 ATTTTTATTTTTATTTTAAGTTAACTTATCTATTTTATT
2266066 ATT
1 ATT
2266069 ATGATTACAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (39 bp):
ATTTTTATTTTTATTTTAAGTTAACTTATCTATTTTATT
Found at i:2274236 original size:18 final size:18
Alignment explanation
Indices: 2274200--2274244 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2274190 CAAAGTTGTT
*
2274200 TTATAAAAAAAAATTAAA
1 TTATAAAAAAAAATAAAA
2274218 TTATAAAAAATAAA-AAAA
1 TTATAAAAAA-AAATAAAA
*
2274236 TAATAAAAA
1 TTATAAAAA
2274245 TGCAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
TTATAAAAAAAAATAAAA
Found at i:2280026 original size:10 final size:10
Alignment explanation
Indices: 2280011--2280048 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2280001 AAAAAAATTC
2280011 TGTTGTTGTT
1 TGTTGTTGTT
2280021 TGTTGTTGTT
1 TGTTGTTGTT
*
2280031 TATTGTTGTT
1 TGTTGTTGTT
2280041 ATGTTGTT
1 -TGTTGTT
2280049 TTGCTACCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 19 0.76
11 6 0.24
ACGTcount: A:0.05, C:0.00, G:0.26, T:0.68
Consensus pattern (10 bp):
TGTTGTTGTT
Found at i:2280141 original size:18 final size:19
Alignment explanation
Indices: 2280104--2280144 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2280094 ATTGTTTGGA
**
2280104 TATTGTATAATTTTTGTTT
1 TATTGTATAATTTTACTTT
2280123 TATTGT-TAATTTTACTTT
1 TATTGTATAATTTTACTTT
2280141 TATT
1 TATT
2280145 TTAGAGGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.68
Consensus pattern (19 bp):
TATTGTATAATTTTACTTT
Found at i:2284312 original size:20 final size:21
Alignment explanation
Indices: 2284287--2284348 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 21
2284277 TAAAATATAA
2284287 ATTTTGAAATTTTT-ACAAA-T
1 ATTTTGAAATTTTTGA-AAATT
2284307 ATTTTG-AATTTTTGAAAATT
1 ATTTTGAAATTTTTGAAAATT
2284327 ATTTTGAATTATTTTTAGAAAA
1 ATTTTGAA--ATTTTT-GAAAA
2284349 AGATAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 10 0.28
20 14 0.39
21 1 0.03
23 6 0.17
24 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.52
Consensus pattern (21 bp):
ATTTTGAAATTTTTGAAAATT
Found at i:2284318 original size:19 final size:20
Alignment explanation
Indices: 2284287--2284336 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2284277 TAAAATATAA
2284287 ATTTTGAAATTTTT-ACAAA-T
1 ATTTTG-AATTTTTGA-AAATT
2284307 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
2284327 ATTTTGAATT
1 ATTTTGAATT
2284337 ATTTTTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:2284927 original size:21 final size:21
Alignment explanation
Indices: 2284901--2284941 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2284891 CTTAACAGGA
2284901 TAGCTGACGTGGCCAGTTAAC
1 TAGCTGACGTGGCCAGTTAAC
*
2284922 TAGCTGATGTGGCCAGTTAA
1 TAGCTGACGTGGCCAGTTAA
2284942 TTTGCCATGT
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:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (21 bp):
TAGCTGACGTGGCCAGTTAAC
Found at i:2285048 original size:21 final size:21
Alignment explanation
Indices: 2285010--2285049 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2285000 CTTCTCTATG
*
2285010 TCTTTCTTCTTTTTCTTCTCA
1 TCTTTCTTCTTTTGCTTCTCA
2285031 TCTTTC-TCTTTATGCTTCT
1 TCTTTCTTCTTT-TGCTTCT
2285050 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.05, C:0.28, G:0.03, T:0.65
Consensus pattern (21 bp):
TCTTTCTTCTTTTGCTTCTCA
Found at i:2285911 original size:11 final size:11
Alignment explanation
Indices: 2285891--2286059 Score: 89
Period size: 11 Copynumber: 16.4 Consensus size: 11
2285881 TAAAAATTAA
2285891 AAAAAGTATTTT
1 AAAAA-TATTTT
2285903 AAAAATATTTT
1 AAAAATATTTT
2285914 --AAA-A--TT
1 AAAAATATTTT
* *
2285920 AAAAAAATTTA
1 AAAAATATTTT
2285931 AAAAAGTATTTT
1 AAAAA-TATTTT
*
2285943 AAAAA-AATTT
1 AAAAATATTTT
*
2285953 AAAAAAATTTT
1 AAAAATATTTT
*
2285964 -TAAA-A--TT
1 AAAAATATTTT
2285971 AAAAA-ATTTT
1 AAAAATATTTT
* *
2285981 AAAAA-AGTAT
1 AAAAATATTTT
2285991 AAAAAGTATTTT
1 AAAAA-TATTTT
* *
2286003 AAAAAGATTTA
1 AAAAATATTTT
*
2286014 AAAAAAATTTT
1 AAAAATATTTT
*
2286025 AAAAATA---A
1 AAAAATATTTT
2286033 AAAAAGTATTTT
1 AAAAA-TATTTT
*
2286045 AAAAGTATTTT
1 AAAAATATTTT
2286056 AAAA
1 AAAA
2286060 TTTAAAAATA
Statistics
Matches: 122, Mismatches: 19, Indels: 33
0.70 0.11 0.19
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 13 0.11
9 7 0.06
10 27 0.22
11 45 0.37
12 26 0.21
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:2285931 original size:10 final size:10
Alignment explanation
Indices: 2285914--2286029 Score: 85
Period size: 10 Copynumber: 11.2 Consensus size: 10
2285904 AAAATATTTT
2285914 AAAA-TTAAA
1 AAAATTTAAA
2285923 AAAATTTAAA
1 AAAATTTAAA
2285933 AAAGTATTTTAAA
1 AAA--A-TTTAAA
2285946 AAAATTTAAA
1 AAAATTTAAA
**
2285956 AAAATTT-TT
1 AAAATTTAAA
2285965 AAAA-TTAAA
1 AAAATTTAAA
*
2285974 AAATTTTAAA
1 AAAATTTAAA
* *
2285984 AAAGTATAAA
1 AAAATTTAAA
*
2285994 AAGTATTTTAAA
1 AA--AATTTAAA
*
2286006 AAGATTTAAAA
1 AAAATTT-AAA
2286017 AAAATTTTAAA
1 AAAA-TTTAAA
2286028 AA
1 AA
2286030 TAAAAAAAGT
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
8 2 0.02
9 11 0.13
10 39 0.46
11 12 0.14
12 12 0.14
13 9 0.11
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:2285936 original size:40 final size:42
Alignment explanation
Indices: 2285864--2285957 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 42
2285854 ACCAAAAATT
2285864 TATTTTAAAAATTAAACTAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAC-AAAAATTAAAAAAAGTATTTTAAAAA
*
2285908 TATTTTAAAATT-AA-AAAAATTTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAACAAAAATTAAAAAAAGTATTTTAAAAA
* *
2285948 AATTTAAAAA
1 TATTTTAAAA
2285958 AATTTTTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
40 33 0.70
42 2 0.04
43 6 0.13
44 6 0.13
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (42 bp):
TATTTTAAAATTAAACAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:2286037 original size:42 final size:40
Alignment explanation
Indices: 2285969--2286081 Score: 133
Period size: 38 Copynumber: 2.8 Consensus size: 40
2285959 ATTTTTAAAA
*
2285969 TTAAAAAATTTTAAAAAAGTATAAAAAGTATTTTAAAAAG-AT
1 TTAAAAAATTTT-AAAAA-TAAAAAAAGTATTTT-AAAAGTAT
2286011 TTAAAAAAAATTTTAAAAATAAAAAAAGTATTTTAAAAGTAT
1 TT--AAAAAATTTTAAAAATAAAAAAAGTATTTTAAAAGTAT
* *
2286053 TT-TAAAA-TTTAAAAATAAAAAAAATATTT
1 TTAAAAAATTTTAAAAATAAAAAAAGTATTT
2286082 ATTATTCGGG
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
38 21 0.32
39 4 0.06
41 5 0.08
42 20 0.31
43 5 0.08
44 10 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (40 bp):
TTAAAAAATTTTAAAAATAAAAAAAGTATTTTAAAAGTAT
Found at i:2286563 original size:17 final size:17
Alignment explanation
Indices: 2286541--2286580 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2286531 TTCCATTTTC
2286541 TCTTCTTCTTATCTTAT
1 TCTTCTTCTTATCTTAT
* * *
2286558 TCTTCTTTTTCTCTTCT
1 TCTTCTTCTTATCTTAT
2286575 TCTTCT
1 TCTTCT
2286581 ACTGCCCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.68
Consensus pattern (17 bp):
TCTTCTTCTTATCTTAT
Found at i:2296806 original size:21 final size:21
Alignment explanation
Indices: 2296780--2296824 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2296770 AGCTACTTGT
*
2296780 ATAGCAAGT-ATGAGATTTGAA
1 ATAGCAAGTGATGAGAATT-AA
2296801 ATAGCAAGTGATGAGAATTAA
1 ATAGCAAGTGATGAGAATTAA
2296822 ATA
1 ATA
2296825 TGTTATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (21 bp):
ATAGCAAGTGATGAGAATTAA
Found at i:2297359 original size:20 final size:22
Alignment explanation
Indices: 2297334--2297373 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2297324 GAATTATCGT
2297334 TTTGA-TATGTTTT-AATTGTA
1 TTTGATTATGTTTTGAATTGTA
*
2297354 TTTGATTGTGTTTTGAATTG
1 TTTGATTATGTTTTGAATTG
2297374 GTTGAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (22 bp):
TTTGATTATGTTTTGAATTGTA
Found at i:2305501 original size:3 final size:3
Alignment explanation
Indices: 2305493--2305525 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2305483 AAACTGTGGG
*
2305493 TCT TCT TCT TCT TCT TCT TC- TCT TCC TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2305526 GCGTGTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:2306627 original size:34 final size:34
Alignment explanation
Indices: 2306579--2306643 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2306569 TTACTATTCA
2306579 ATTTAAAACAAAATAATAAT-ATTAATTTAAAATG
1 ATTTAAAACAAAATAA-AATAATTAATTTAAAATG
** *
2306613 ATTTAAAAGTAAATAAAATAATTAGTTTAAA
1 ATTTAAAACAAAATAAAATAATTAATTTAAA
2306644 TATATAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 24 0.89
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (34 bp):
ATTTAAAACAAAATAAAATAATTAATTTAAAATG
Found at i:2323421 original size:14 final size:15
Alignment explanation
Indices: 2323404--2323432 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2323394 ATATAGTAGC
2323404 AAAACAG-AAGAAAA
1 AAAACAGCAAGAAAA
2323418 AAAACAGCAAGAAAA
1 AAAACAGCAAGAAAA
2323433 CAACAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAACAGCAAGAAAA
Found at i:2329656 original size:9 final size:9
Alignment explanation
Indices: 2329642--2329717 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
2329632 AAATAAAATT
2329642 AAAATTATA
1 AAAATTATA
2329651 AAAATT-TA
1 AAAATTATA
2329659 AAAA-TATTA
1 AAAATTA-TA
2329668 TAAAA-TATA
1 -AAAATTATA
* *
2329677 AAAAATCTA
1 AAAATTATA
*
2329686 ATAAATTGTAA
1 A-AAATTAT-A
*
2329697 AAAAATATA
1 AAAATTATA
*
2329706 AAAATAATA
1 AAAATTATA
2329715 AAA
1 AAA
2329718 CTTGTTTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
7 1 0.02
8 10 0.19
9 25 0.46
10 16 0.30
11 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:2329667 original size:19 final size:18
Alignment explanation
Indices: 2329642--2329710 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
2329632 AAATAAAATT
2329642 AAAATTATAAAAATTTAA
1 AAAATTATAAAAATTTAA
*
2329660 AAATATTAT-AAAATATAA
1 AAA-ATTATAAAAATTTAA
*
2329678 AAAATCTA-ATAAATTGTAA
1 AAAAT-TATAAAAATT-TAA
*
2329697 AAAAATATAAAAAT
1 AAAATTATAAAAAT
2329711 AATAAAACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 2 0.05
18 22 0.54
19 17 0.41
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (18 bp):
AAAATTATAAAAATTTAA
Found at i:2329697 original size:26 final size:25
Alignment explanation
Indices: 2329633--2329698 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
2329623 CTCCTACAAA
* *
2329633 AATAAAATTAAAATTATAAAAATTT
1 AATAAATTTAAAATTATAAAAATCT
*
2329658 AA-AAATATTATAAAATATAAAAAATCT
1 AATAAAT-TTA-AAATTAT-AAAAATCT
2329685 AATAAATTGTAAAA
1 AATAAATT-TAAAA
2329699 AAATATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
24 3 0.09
25 5 0.15
26 6 0.18
27 13 0.39
28 6 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
AATAAATTTAAAATTATAAAAATCT
Found at i:2331732 original size:16 final size:18
Alignment explanation
Indices: 2331713--2331750 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2331703 TTAATTTTTT
2331713 TAAATTA-TAAAA-AATA
1 TAAATTATTAAAATAATA
2331729 TAAATTATTAAAATAATA
1 TAAATTATTAAAATAATA
2331747 -AAAT
1 TAAAT
2331751 CATATATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAATTATTAAAATAATA
Found at i:2335618 original size:28 final size:28
Alignment explanation
Indices: 2335586--2335648 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
2335576 AACAGGCTTA
*
2335586 ATTATAAAATTGCATACATAATATATAT
1 ATTATAAAAATGCATACATAATATATAT
*
2335614 ATTATAAAAATGCATATATAATATATAT
1 ATTATAAAAATGCATACATAATATATAT
2335642 ATATATA
1 AT-TATA
2335649 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (28 bp):
ATTATAAAAATGCATACATAATATATAT
Found at i:2335632 original size:2 final size:2
Alignment explanation
Indices: 2335627--2335661 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2335617 ATAAAAATGC
2335627 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2335662 TGTTTTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2339188 original size:37 final size:37
Alignment explanation
Indices: 2339147--2339219 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
2339137 TTGTTTCGAG
*
2339147 TGTTGTTTCAGAGCTCGTCGTTGTCGTCTCCTCCTCA
1 TGTTGTTTCAGAGCTCGTCGTTGTCGTCTCCCCCTCA
2339184 TGTTGTTTCAGAGCTCGTCGTTGTCGTCTCCCCCTC
1 TGTTGTTTCAGAGCTCGTCGTTGTCGTCTCCCCCTC
2339220 CCCTGCCATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.07, C:0.32, G:0.22, T:0.40
Consensus pattern (37 bp):
TGTTGTTTCAGAGCTCGTCGTTGTCGTCTCCCCCTCA
Found at i:2348028 original size:19 final size:19
Alignment explanation
Indices: 2347983--2348029 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
2347973 TTTTCTTTTT
2347983 CATAGTTTCTGCTTTGAGTA
1 CATAGTTT-TGCTTTGAGTA
2348003 -A-AGTTTTGACTTTGA-TA
1 CATAGTTTTG-CTTTGAGTA
2348020 CATAGTTTTG
1 CATAGTTTTG
2348030 TAGGCCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
19 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (19 bp):
CATAGTTTTGCTTTGAGTA
Found at i:2350167 original size:21 final size:21
Alignment explanation
Indices: 2350138--2350181 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2350128 TGGATTAGTA
*
2350138 TTTTGTATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
2350159 TTTTATATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
2350180 TT
1 TT
2350182 AGCAGAAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTATATGAATATTGTAATT
Found at i:2350402 original size:38 final size:38
Alignment explanation
Indices: 2350360--2350441 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
2350350 AAAAAGTCAG
2350360 TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
* *
2350398 TTATAATTAAACTTTTAATAAGATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
2350436 TTATAA
1 TTATAA
2350442 ACTTTATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
Found at i:2350553 original size:27 final size:27
Alignment explanation
Indices: 2350515--2350579 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
2350505 TACTAATATA
*
2350515 TTCATTGGCGCCTCTCTATGAGGCATC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
2350542 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
2350569 TTCATTAGCGC
1 TTCATTGGCGC
2350580 TTACCTGGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.14, C:0.31, G:0.23, T:0.32
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:2355186 original size:41 final size:43
Alignment explanation
Indices: 2355106--2355186 Score: 112
Period size: 41 Copynumber: 1.9 Consensus size: 43
2355096 AGGCCCGTAA
* * *
2355106 TAAATATATATTTTTTGTTTTTATTTTTAATTTTAAAATACTT
1 TAAAAATAAATTTTTTGTTATTATTTTTAATTTTAAAATACTT
*
2355149 TAAAAATAAATTTTTT-TTATT-TTTTTATTTTTAAAATA
1 TAAAAATAAATTTTTTGTTATTATTTTTAATTTTAAAATA
2355187 ATTTTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 16 0.47
42 4 0.12
43 14 0.41
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (43 bp):
TAAAAATAAATTTTTTGTTATTATTTTTAATTTTAAAATACTT
Found at i:2356483 original size:20 final size:20
Alignment explanation
Indices: 2356458--2356517 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
2356448 TTGTAATTTT
2356458 ATTATGATTTAAATTATTCA
1 ATTATGATTTAAATTATTCA
** **
2356478 ATTATGATCAAAGATATAATTTT
1 ATTATGATTTAA-AT-T-ATTCA
2356501 ATTATGATTTAAATTAT
1 ATTATGATTTAAATTAT
2356518 CGAATTTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
20 12 0.39
21 3 0.10
22 3 0.10
23 13 0.42
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (20 bp):
ATTATGATTTAAATTATTCA
Found at i:2362908 original size:11 final size:11
Alignment explanation
Indices: 2362874--2362943 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
2362864 TTTTTTTTAC
*
2362874 TATTTTGTTGT
1 TATTTTGTTAT
*
2362885 TGCTTTT-TTAT
1 T-ATTTTGTTAT
2362896 TATTTTGTTAT
1 TATTTTGTTAT
***
2362907 TATTTCACTAT
1 TATTTTGTTAT
* **
2362918 TATGTTACTAT
1 TATTTTGTTAT
2362929 TATTTTGTTAT
1 TATTTTGTTAT
2362940 TATT
1 TATT
2362944 ATTTGGATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
10 4 0.09
11 38 0.83
12 4 0.09
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.67
Consensus pattern (11 bp):
TATTTTGTTAT
Found at i:2362909 original size:14 final size:14
Alignment explanation
Indices: 2362892--2362947 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2362882 TGTTGCTTTT
2362892 TTATTATTTTGTTA
1 TTATTATTTTGTTA
2362906 TTATTTCACTATTATGTTA
1 TTA-TT-A-T-TT-TGTTA
*
2362925 CTATTATTTTGTTA
1 TTATTATTTTGTTA
2362939 TTATTATTT
1 TTATTATTT
2362948 GGATATTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
15 4 0.11
16 2 0.06
17 2 0.06
18 4 0.11
19 7 0.20
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.66
Consensus pattern (14 bp):
TTATTATTTTGTTA
Found at i:2370283 original size:3 final size:3
Alignment explanation
Indices: 2370270--2370396 Score: 245
Period size: 3 Copynumber: 42.0 Consensus size: 3
2370260 ATTTTTTAAA
2370270 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2370316 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2370364 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2370397 TATTATTATT
Statistics
Matches: 123, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 120 0.98
4 3 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2372361 original size:21 final size:20
Alignment explanation
Indices: 2372332--2372385 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
2372322 AATAATAAAA
*
2372332 TAAATAAATAAATCATGAAGT
1 TAAAAAAATAAATC-TGAAGT
* * *
2372353 TAAAAAAATAACTCTTAATT
1 TAAAAAAATAAATCTGAAGT
2372373 TAAAGAAAATAAA
1 TAAA-AAAATAAA
2372386 AGTAATCATC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (20 bp):
TAAAAAAATAAATCTGAAGT
Found at i:2396363 original size:16 final size:16
Alignment explanation
Indices: 2396342--2396393 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
2396332 TTTGGTTCGC
*
2396342 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
2396358 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
2396374 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
2396390 TGTA
1 TGTA
2396394 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:2396440 original size:45 final size:44
Alignment explanation
Indices: 2396374--2396464 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
2396364 GGATTAGAGG
* *
2396374 TGTAATGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
2396419 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
2396463 TG
1 TG
2396465 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:2399150 original size:20 final size:20
Alignment explanation
Indices: 2399120--2399157 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2399110 GTTAAAAATA
2399120 ATTATCATTTTCATCATTTGG
1 ATTATCATTTTCAT-ATTTGG
2399141 ATTA-CATTTTCATATTT
1 ATTATCATTTTCATATTT
2399158 TAATCCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTATCATTTTCATATTTGG
Found at i:2405130 original size:33 final size:32
Alignment explanation
Indices: 2405080--2405146 Score: 116
Period size: 33 Copynumber: 2.1 Consensus size: 32
2405070 ACCATAAAGC
*
2405080 TTATATTTCGTTTAGTTAAAATTTCAGTGCAT
1 TTATATTTAGTTTAGTTAAAATTTCAGTGCAT
2405112 TTATATTTAGTTTTAGTTAAAATTTCAGTGCAT
1 TTATATTTAG-TTTAGTTAAAATTTCAGTGCAT
2405145 TT
1 TT
2405147 CTTATCCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 9 0.27
33 24 0.73
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.52
Consensus pattern (32 bp):
TTATATTTAGTTTAGTTAAAATTTCAGTGCAT
Found at i:2413225 original size:163 final size:163
Alignment explanation
Indices: 2412955--2413281 Score: 654
Period size: 163 Copynumber: 2.0 Consensus size: 163
2412945 CATTATGCTA
2412955 TAACTTTTAAGGGGAAAAAACAACTGATGTATCTTGATAGAAGTTATCTCCTGTTGTAACAGTGT
1 TAACTTTTAAGGGGAAAAAACAACTGATGTATCTTGATAGAAGTTATCTCCTGTTGTAACAGTGT
2413020 TAATTTTTTTTTTCTGTTTATTGGTATCACCAGGTAGCATAGATTAGATAGATATTCTGTTACTG
66 TAATTTTTTTTTTCTGTTTATTGGTATCACCAGGTAGCATAGATTAGATAGATATTCTGTTACTG
2413085 TTAATGACCAGTTTCCTTTTACTTCAAATTTGT
131 TTAATGACCAGTTTCCTTTTACTTCAAATTTGT
2413118 TAACTTTTAAGGGGAAAAAACAACTGATGTATCTTGATAGAAGTTATCTCCTGTTGTAACAGTGT
1 TAACTTTTAAGGGGAAAAAACAACTGATGTATCTTGATAGAAGTTATCTCCTGTTGTAACAGTGT
2413183 TAATTTTTTTTTTCTGTTTATTGGTATCACCAGGTAGCATAGATTAGATAGATATTCTGTTACTG
66 TAATTTTTTTTTTCTGTTTATTGGTATCACCAGGTAGCATAGATTAGATAGATATTCTGTTACTG
2413248 TTAATGACCAGTTTCCTTTTACTTCAAATTTGT
131 TTAATGACCAGTTTCCTTTTACTTCAAATTTGT
2413281 T
1 T
2413282 CTGAGTTTTG
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.43
Consensus pattern (163 bp):
TAACTTTTAAGGGGAAAAAACAACTGATGTATCTTGATAGAAGTTATCTCCTGTTGTAACAGTGT
TAATTTTTTTTTTCTGTTTATTGGTATCACCAGGTAGCATAGATTAGATAGATATTCTGTTACTG
TTAATGACCAGTTTCCTTTTACTTCAAATTTGT
Found at i:2419429 original size:5 final size:5
Alignment explanation
Indices: 2419419--2419452 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
2419409 AATATTGCTT
2419419 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
2419453 GTAGTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:2431833 original size:13 final size:13
Alignment explanation
Indices: 2431815--2431841 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2431805 TGACTATTCA
2431815 TCTACATGAGGAG
1 TCTACATGAGGAG
2431828 TCTACATGAGGAG
1 TCTACATGAGGAG
2431841 T
1 T
2431842 TGTGACTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (13 bp):
TCTACATGAGGAG
Found at i:2434232 original size:23 final size:23
Alignment explanation
Indices: 2434202--2434247 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2434192 ACTTTTTATC
2434202 TTCAAGTCTCTCCACTCTTCATA
1 TTCAAGTCTCTCCACTCTTCATA
*
2434225 TTCAAGTCTCTTCACTCTTCATA
1 TTCAAGTCTCTCCACTCTTCATA
2434248 ACTTTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.33, G:0.04, T:0.41
Consensus pattern (23 bp):
TTCAAGTCTCTCCACTCTTCATA
Found at i:2435127 original size:47 final size:49
Alignment explanation
Indices: 2435073--2435199 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 49
2435063 GCACAATTTA
2435073 TTTTCTTTCTCAGTCTTTTCTTTGCTTGAAACCCAAAAT-CC-TATCCC
1 TTTTCTTTCTCAGTCTTTTCTTTGCTTGAAACCCAAAATCCCATATCCC
*
2435120 TTTTCTTTCTCA-TACTTTTCTTTGCTTGAAACCCAAAATCCCATGTCCC
1 TTTTCTTTCTCAGT-CTTTTCTTTGCTTGAAACCCAAAATCCCATATCCC
* *
2435169 TTTTCTTTCTCGGTCTTTTCGTTGCTTGAAA
1 TTTTCTTTCTCAGTCTTTTCTTTGCTTGAAA
2435200 AAAATATTCA
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
46 1 0.01
47 37 0.51
48 2 0.03
49 32 0.44
50 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.09, T:0.46
Consensus pattern (49 bp):
TTTTCTTTCTCAGTCTTTTCTTTGCTTGAAACCCAAAATCCCATATCCC
Found at i:2442196 original size:43 final size:42
Alignment explanation
Indices: 2442124--2442238 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 42
2442114 ATCTGCTAAA
* *
2442124 TTAGTGGCG-TTTTTCACAAACGCCACTAAAGAACATGGAC-T
1 TTAGTGGCGCTTTTACACAAACGCCGCTAAAGAACAT-GACAT
* *
2442165 TTAGTGGCGCTTTTACTAAAAACGCCGCTAAAGAATATGACAT
1 TTAGTGGCGCTTTTAC-ACAAACGCCGCTAAAGAACATGACAT
*
2442208 TTAGTGGCGCTTTTCCCACAAACGCCGCTAA
1 TTAGTGGCGCTTTT-ACACAAACGCCGCTAA
2442239 GCCACTAAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
41 9 0.14
42 8 0.12
43 46 0.72
44 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (42 bp):
TTAGTGGCGCTTTTACACAAACGCCGCTAAAGAACATGACAT
Found at i:2459924 original size:421 final size:421
Alignment explanation
Indices: 2459140--2459982 Score: 1670
Period size: 421 Copynumber: 2.0 Consensus size: 421
2459130 TATTATAAAA
2459140 ACTATTTTTAAAAATTAAAATTATTGAAATTATTAAAAATATAAAATATATATTATTATATTAAA
1 ACTATTTTTAAAAATTAAAATTATTGAAATTATTAAAAATATAAAATATATATTATTATATTAAA
2459205 GATGGGTTGCTGAATATTGACTTTGGTTGCACCATAAAAAGCCGAACCACATGCATCAAACGTGT
66 GATGGGTTGCTGAATATTGACTTTGGTTGCACCATAAAAAGCCGAACCACATGCATCAAACGTGT
2459270 AATGTGAGCAAATAAAAGAATCATAACATAAAAAAGGTAAATACCTAATTAAAGTAATAAACTAA
131 AATGTGAGCAAATAAAAGAATCATAACATAAAAAAGGTAAATACCTAATTAAAGTAATAAACTAA
2459335 TGCCTGTATTTTTCACATATCTTATTGGAGCATAATCACTAATAAATTACAAAAAAGGGTACTAA
196 TGCCTGTATTTTTCACATATCTTATTGGAGCATAATCACTAATAAATTACAAAAAAGGGTACTAA
2459400 ATAAAAAATTAATTATCCATAATATTAATTAATGAATATGCAAACCATATATATAAAAACTAATT
261 ATAAAAAATTAATTATCCATAATATTAATTAATGAATATGCAAACCATATATATAAAAACTAATT
2459465 AAATTGAATTAATAATTAAATAGTACCCCTAAAGAAACATTAATACTAGGTGAAAAATTTTACAA
326 AAATTGAATTAATAATTAAATAGTACCCCTAAAGAAACATTAATACTAGGTGAAAAATTTTACAA
2459530 TTTATTGCCTCTCTAAATCTTGCACACTATC
391 TTTATTGCCTCTCTAAATCTTGCACACTATC
2459561 ACTATTTTTAAAAATTAAAATTATTGAAATTATTAAAAATATAAAATATATATTATTATATTAAA
1 ACTATTTTTAAAAATTAAAATTATTGAAATTATTAAAAATATAAAATATATATTATTATATTAAA
2459626 GATGGGTTGCTGAATTATTGACTTT-GTTGCACCATAAAAAGCCGAACCACATGCATCAAACGTG
66 GATGGGTTGCTGAA-TATTGACTTTGGTTGCACCATAAAAAGCCGAACCACATGCATCAAACGTG
2459690 TAATGTGAGCAAATAAAAGAATCATAACATAAAAAAGGTAAATACCTAATTAAAGTAATAAACTA
130 TAATGTGAGCAAATAAAAGAATCATAACATAAAAAAGGTAAATACCTAATTAAAGTAATAAACTA
2459755 ATGCCTGTATTTTTCACATATCTTATTGGAGCATAATCACTAATAAATTACAAAAAAGGGTACTA
195 ATGCCTGTATTTTTCACATATCTTATTGGAGCATAATCACTAATAAATTACAAAAAAGGGTACTA
2459820 AATAAAAAATTAATTATCCATAATATTAATTAATGAATATGCAAACCATATATATAAAAACTAAT
260 AATAAAAAATTAATTATCCATAATATTAATTAATGAATATGCAAACCATATATATAAAAACTAAT
2459885 TAAATTGAATTAATAATTAAATAGTACCCCTAAAGAAACATTAATACTAGGTGAAAAATTTTACA
325 TAAATTGAATTAATAATTAAATAGTACCCCTAAAGAAACATTAATACTAGGTGAAAAATTTTACA
2459950 ATTTATTGCCTCTCTAAATCTTGCACACTATC
390 ATTTATTGCCTCTCTAAATCTTGCACACTATC
2459982 A
1 A
2459983 AATATTTCAT
Statistics
Matches: 421, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
421 411 0.98
422 10 0.02
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (421 bp):
ACTATTTTTAAAAATTAAAATTATTGAAATTATTAAAAATATAAAATATATATTATTATATTAAA
GATGGGTTGCTGAATATTGACTTTGGTTGCACCATAAAAAGCCGAACCACATGCATCAAACGTGT
AATGTGAGCAAATAAAAGAATCATAACATAAAAAAGGTAAATACCTAATTAAAGTAATAAACTAA
TGCCTGTATTTTTCACATATCTTATTGGAGCATAATCACTAATAAATTACAAAAAAGGGTACTAA
ATAAAAAATTAATTATCCATAATATTAATTAATGAATATGCAAACCATATATATAAAAACTAATT
AAATTGAATTAATAATTAAATAGTACCCCTAAAGAAACATTAATACTAGGTGAAAAATTTTACAA
TTTATTGCCTCTCTAAATCTTGCACACTATC
Found at i:2460874 original size:2 final size:2
Alignment explanation
Indices: 2460867--2460893 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2460857 GGTGAATTGT
2460867 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2460894 TTAGAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2463177 original size:45 final size:43
Alignment explanation
Indices: 2463126--2463221 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 43
2463116 CACAAGTAGA
*
2463126 GTTAGTGGTTGACAAGTGTCCTATATAGGGGTATAATAAAATAAG
1 GTTAGTGGTTAACAAGTGTCCTATA-A-GGGTATAATAAAATAAG
* *
2463171 GTTAGTGTGGTTAACAAGTGTCGTATAAGGGTATAATAAAATAGG
1 GTTA--GTGGTTAACAAGTGTCCTATAAGGGTATAATAAAATAAG
2463216 GTTAGT
1 GTTAGT
2463222 ATTTAGTGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
43 2 0.04
45 24 0.52
46 1 0.02
47 19 0.41
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.32
Consensus pattern (43 bp):
GTTAGTGGTTAACAAGTGTCCTATAAGGGTATAATAAAATAAG
Found at i:2475806 original size:212 final size:210
Alignment explanation
Indices: 2475509--2476084 Score: 803
Period size: 212 Copynumber: 2.7 Consensus size: 210
2475499 CATCTCATGT
* * *
2475509 TTTAAAATTGTTTATTGGATGCATGAGTCCACTTCACAGTCATTTTTTTATTTGTTAGCCTGTAC
1 TTTAAAATTGTTTACTGGATGCA--AGTCAACTTCACATTCA-TTTTTTATTTGTTAGCCTGTAC
* * *
2475574 ATTGGATTTGTTGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTGAATAAAGGAGAGAAGACT
63 ATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACT
* * *
2475639 AGTAAGAAAAACCAGGAAAGCAAAGACGCTGAGTGAGTGGATTATTCTTTTATTTTTCAGTTATC
128 AGTAAGAAAAACCAGGAAAGCAAAGACGCTGAGTGAGTGGATAATTCTTTTATTTTTCAATCATC
* *
2475704 TCATGTTCAATCTTTTGC
193 TCATCTTCAAGCTTTTGC
* *
2475722 TTTGAAATTGTTTACTGGACGTGCAAGTCAACTTCACATTCATTTTTTATTTGTTAGCCTGTATA
1 TTTAAAATTGTTTACTGGA--TGCAAGTCAACTTCACATTCATTTTTTATTTGTTAGCCTGTACA
* *
2475787 TTGTATCTGTTGCAGGTTGGGTGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGACTA
64 TTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTA
** * *
2475852 GTAAGAAAAATAAGGAATGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTCAATCATCT
129 GTAAGAAAAACCAGGAAAGCAAAGACGCTGAGTGAGTGGATAATTCTTTTATTTTTCAATCATCT
2475917 CATCTTCAAGCTTTTGC
194 CATCTTCAAGCTTTTGC
* * * * *
2475934 TTTAAAATTGTTTGCTGGATGCATAACTCAACTTAACATTCTTTTTTTTTTAATTTATTAGCCTG
1 TTTAAAATTGTTTACTGGATGC--AAGTCAACTTCACATTC---ATTTTTT-ATTTGTTAGCCTG
**
2475999 TACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTC-GACCCTAAATATTGGAGAGAA
60 TACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAG-CCCTAAATAAAGGAGAGAA
2476063 GACTAGTAAGAAAAACCAGGAA
124 GACTAGTAAGAAAAACCAGGAA
2476085 GGTAAAGCCG
Statistics
Matches: 322, Mismatches: 32, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
210 3 0.01
212 187 0.58
213 32 0.10
215 10 0.03
216 90 0.28
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (210 bp):
TTTAAAATTGTTTACTGGATGCAAGTCAACTTCACATTCATTTTTTATTTGTTAGCCTGTACATT
GTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGT
AAGAAAAACCAGGAAAGCAAAGACGCTGAGTGAGTGGATAATTCTTTTATTTTTCAATCATCTCA
TCTTCAAGCTTTTGC
Found at i:2480776 original size:15 final size:15
Alignment explanation
Indices: 2480758--2480787 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2480748 CTCTCTGCCC
2480758 TTCTCCTCCACCTCT
1 TTCTCCTCCACCTCT
*
2480773 TTCTCCTCCCCCTCT
1 TTCTCCTCCACCTCT
2480788 CTCAGTCAAA
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:0.57, G:0.00, T:0.40
Consensus pattern (15 bp):
TTCTCCTCCACCTCT
Found at i:2484384 original size:30 final size:31
Alignment explanation
Indices: 2484345--2484405 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
2484335 GGAGATGGGA
*
2484345 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
2484376 TGGG-AGGGAGTAAAAATTTTGGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
2484406 AAAATGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:2484631 original size:9 final size:9
Alignment explanation
Indices: 2484617--2484653 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2484607 TATAGTTTGA
2484617 TATTCGAAT
1 TATTCGAAT
2484626 TATTCGAAT
1 TATTCGAAT
*
2484635 TATTCGAGT
1 TATTCGAAT
2484644 TATTCGAAT
1 TATTCGAAT
2484653 T
1 T
2484654 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:2486305 original size:4 final size:4
Alignment explanation
Indices: 2486296--2486352 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
2486286 CAATGACAAG
2486296 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2486344 ATAC ATAC A
1 ATAC ATAC A
2486353 ACCCTTTTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:2496663 original size:19 final size:19
Alignment explanation
Indices: 2496612--2496664 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
2496602 TAACTTTTAT
2496612 TTTTCAAAATTTTTATAAAA
1 TTTTCAAAA-TTTTATAAAA
*
2496632 TTTTGC-AATTTTTATAAATA
1 TTTT-CAAAATTTTATAAA-A
2496652 TTTT-AAAATTTTA
1 TTTTCAAAATTTTA
2496665 AGTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 16 0.57
20 11 0.39
21 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTTCAAAATTTTATAAAA
Found at i:2498543 original size:105 final size:102
Alignment explanation
Indices: 2498419--2498624 Score: 256
Period size: 105 Copynumber: 2.0 Consensus size: 102
2498409 TATTTTTTTC
2498419 GGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTA-AAA-AATAAATTGAAAA-TTTTTTTCGTG
1 GGTGCTGGCCTGTCAATGGCCGGCA-CC--CAGTACAAATAATAAA---AAAATTTTTTTTCGTG
2498481 TCAAAATTAGATATAAATATACGAAAAAAATAAAAAAAATTTG
60 TCAAAATTAGATATAAATATACGAAAAAAATAAAAAAAATTTG
* ** *
2498524 GGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTTAAAAAAATTCTTTTTTTTGTGTCA
1 GGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAA-TAATAAAAAAA-T-TTTTTTTCGTGTCA
* *
2498589 GAATTAGATATAAATATACGCAAAAAATAAAAAAAA
63 AAATTAGATATAAATATACGAAAAAAATAAAAAAAA
2498625 AAAATTTTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
102 9 0.10
103 3 0.03
104 2 0.02
105 75 0.84
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (102 bp):
GGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATAATAAAAAAATTTTTTTTCGTGTCAAAA
TTAGATATAAATATACGAAAAAAATAAAAAAAATTTG
Found at i:2499516 original size:29 final size:29
Alignment explanation
Indices: 2499450--2499516 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
2499440 ACTTTGTAAT
*
2499450 ATTTAAAAATATAAGGACTAAATTCTTAA
1 ATTTAAAAATATAAGAACTAAATTCTTAA
**
2499479 AAATAAAAATATACA-AACTAAATTC-TAA
1 ATTTAAAAATATA-AGAACTAAATTCTTAA
2499507 ATTTACAAAA
1 ATTTA-AAAA
2499517 AATATATAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 6 0.19
29 24 0.77
30 1 0.03
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (29 bp):
ATTTAAAAATATAAGAACTAAATTCTTAA
Found at i:2500390 original size:99 final size:97
Alignment explanation
Indices: 2500077--2500449 Score: 513
Period size: 96 Copynumber: 3.8 Consensus size: 97
2500067 AAAAAAAATT
* * *
2500077 TACTGGGTGCCGGCCATTAACAGGCCAGCACCCAAA-TTTTTTTTATTTTTTCGTATATTTATAT
1 TACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTATTTTTTTGTATATTTATAT
***
2500141 CTGATTCTGACAC-AA--AAATTTTAAATTTG
66 CTGATTCTGACACGAATTTTTTTTTAAATTTG
*
2500170 TACTAGGTGCCGGCCATTGACAGGCCATCACCCAAATTTTTTTTTATTTTTTTGTATATTTATAT
1 TACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTATTTTTTTGTATATTTATAT
*
2500235 CTGATTCTGACACG-ATTTTTTTTAAAATTTG
66 CTGATTCTGACACGAATTTTTTTTTAAATTTG
* * *
2500266 TACTAGGTGCCTGCCATTGACAGGCCAGCACTCAAATTTTTTATTATTTTTTTCGTATATTTATA
1 TACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTATTTTTTT-GTATATTTATA
*
2500331 TCTGATTCTGATACGGAATTTTTTTTTAAATTTG
65 TCTGATTCTGACAC-GAATTTTTTTTTAAATTTG
* *
2500365 TACTGGGTGCTGGCCATTGACAGGCCAGCACCCAAAAATTTTTATTTTTATTTTTTTGTATATTT
1 TACTAGGTGCCGGCCATTGACAGGCCAGCACCC--AAA-TTTT-TTTTTATTTTTTTGTATATTT
* *
2500430 ATATCTAATTCTCACACGAA
62 ATATCTGATTCTGACACGAA
2500450 AAAAAAAGAA
Statistics
Matches: 247, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
93 33 0.13
94 41 0.17
96 59 0.24
97 24 0.10
98 1 0.00
99 45 0.18
101 6 0.02
102 26 0.11
103 12 0.05
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (97 bp):
TACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTATTTTTTTGTATATTTATAT
CTGATTCTGACACGAATTTTTTTTTAAATTTG
Found at i:2500499 original size:112 final size:111
Alignment explanation
Indices: 2500350--2500641 Score: 330
Period size: 112 Copynumber: 2.6 Consensus size: 111
2500340 GATACGGAAT
2500350 TTTTTTTTAAATTTGTACTGGGTG-CTGGCCATTGACAGGCCAGCACCCAAAAAT-TTTTATTTT
1 TTTTTTTTAAATTTGTACTGGGTGTC-GGCCATTGACAGGCCAGCACCCAAAAATATTTT-TTTT
** * *
2500413 TA-TTTTTTTGTATATTTATATCTAATTCTCACACGAAAAAAAAAGAAAA
64 TACTTTTTTCATATACTGATATCTAATTCTCACACG--AAAAAAAGAAAA
* *
2500462 TTTTTTTTAAATTTGTACTGGGTGTCGCCCATTGACAGGCCAGCACCAAAAAATATTTTTTTTTA
1 TTTTTTTTAAATTTGTACTGGGTGTCGGCCATTGACAGGCCAGCACCCAAAAATATTTTTTTTTA
* * * ***
2500527 CTTTTTTCATATACTGATATTTGATTCTGACACGAAAAAAATTTAA
66 CTTTTTTCATATACTGATATCTAATTCTCACACGAAAAAAAGAAAA
* * *
2500573 TTTTTTTT--A-CTGT--TGGGTGTAGGCCATTGACAGGCCAGCACCCAAAAAAAACTTTTTTTT
1 TTTTTTTTAAATTTGTACTGGGTGTCGGCCATTGACAGGCCAGCACCC-AAAAATA-TTTTTTTT
*
2500633 TCCTTTTTT
64 TACTTTTTT
2500642 TTCTTTTTGC
Statistics
Matches: 157, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
106 27 0.17
107 6 0.04
108 19 0.12
109 1 0.01
111 17 0.11
112 56 0.36
113 31 0.20
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (111 bp):
TTTTTTTTAAATTTGTACTGGGTGTCGGCCATTGACAGGCCAGCACCCAAAAATATTTTTTTTTA
CTTTTTTCATATACTGATATCTAATTCTCACACGAAAAAAAGAAAA
Found at i:2506932 original size:24 final size:24
Alignment explanation
Indices: 2506900--2506955 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
2506890 ATAGTTGTGT
2506900 TTATTTTAAGAAAAACAGTGATGG
1 TTATTTTAAGAAAAACAGTGATGG
2506924 TTATTTTAAGAAAAACAGTGATGG
1 TTATTTTAAGAAAAACAGTGATGG
2506948 TTATTTTA
1 TTATTTTA
2506956 TATATCTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (24 bp):
TTATTTTAAGAAAAACAGTGATGG
Found at i:2508744 original size:22 final size:22
Alignment explanation
Indices: 2508702--2508746 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2508692 TATAACAAGA
**
2508702 TTTTAATTTAACATGTTTAATT
1 TTTTAATTTAACATGAATAATT
2508724 TTTTAATTTAAC-TCGAATAATT
1 TTTTAATTTAACAT-GAATAATT
2508746 T
1 T
2508747 AACTCGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACATGAATAATT
Found at i:2508746 original size:14 final size:14
Alignment explanation
Indices: 2508727--2508753 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2508717 TTTAATTTTT
2508727 TAATTTAACTCGAA
1 TAATTTAACTCGAA
2508741 TAATTTAACTCGA
1 TAATTTAACTCGA
2508754 TTCGATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
TAATTTAACTCGAA
Found at i:2510301 original size:48 final size:48
Alignment explanation
Indices: 2510230--2510325 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
2510220 CGATGACACG
2510230 TTTCTCCGGAACAGCCTGTGCATATCCAAGAGTGGCACCAACTGACCA
1 TTTCTCCGGAACAGCCTGTGCATATCCAAGAGTGGCACCAACTGACCA
*
2510278 TTTCTCTGGAACAGCCTGTGCATATCCAAGAGTGGCACCAACTGACCA
1 TTTCTCCGGAACAGCCTGTGCATATCCAAGAGTGGCACCAACTGACCA
2510326 CCCAATTGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (48 bp):
TTTCTCCGGAACAGCCTGTGCATATCCAAGAGTGGCACCAACTGACCA
Found at i:2514364 original size:64 final size:64
Alignment explanation
Indices: 2514281--2514681 Score: 379
Period size: 64 Copynumber: 6.3 Consensus size: 64
2514271 AAACCGGGCT
* * * *
2514281 ACACCGAAAAGCA-ATACAAAC-AAAGACCACTGTTGTCTTCAATGAGAAAGCAATGAAACTCTA
1 ACACCCAAAAGCATA-ACAAACGAAAGACCACTGTTGTCTGCAATGAAAAAGCAAT-AAACCCTA
2514344 A
64 A
* * * *
2514345 ACACCCAAAAGCATAACAAACGAAAG-CCACTGTTGTGTGCAAATAAAAAAG-AGTAAACCCCAA
1 ACACCCAAAAGCATAACAAACGAAAGACCACTGTTGTCTGC-AATGAAAAAGCAATAAACCCTAA
* * * ** * * *
2514408 ACACTCAAAAGCATTACAAAC-AAAGACCAGTACTGTCTTCAATGAGAAAGCAATGAAACCCTAG
1 ACACCCAAAAGCATAACAAACGAAAGACCACTGTTGTCTGCAATGAAAAAGCAAT-AAACCCTAA
* * * **
2514472 ACACCCAAAAGCATAACAAACGAAAG-CCACTGTTGTATGCAAATAAAAAAG-AGTAAACCCCGA
1 ACACCCAAAAGCATAACAAACGAAAGACCACTGTTGTCTGC-AATGAAAAAGCAATAAACCCTAA
* * * * * *
2514535 ACACTCAAAAGCATTACAAAC-AAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAA
1 ACACCCAAAAGCATAACAAACGAAAGACCACTGTTGTCTGCAATGAAAAAGCAAT-AAACCCTAA
* * ** * *
2514599 ACACCCAAAGGAATAACAAACGAAA-ACCACTGTTGTCTGCAAACAAAAAGGAGTAAACCCTAA
1 ACACCCAAAAGCATAACAAACGAAAGACCACTGTTGTCTGCAATGAAAAAGCAATAAACCCTAA
*
2514662 ACACCCAAAAGCATTACAAA
1 ACACCCAAAAGCATAACAAA
2514682 TGTGATTTCT
Statistics
Matches: 266, Mismatches: 59, Indels: 25
0.76 0.17 0.07
Matches are distributed among these distances:
62 24 0.09
63 100 0.38
64 114 0.43
65 28 0.11
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.15
Consensus pattern (64 bp):
ACACCCAAAAGCATAACAAACGAAAGACCACTGTTGTCTGCAATGAAAAAGCAATAAACCCTAA
Found at i:2514513 original size:127 final size:127
Alignment explanation
Indices: 2514287--2514681 Score: 646
Period size: 127 Copynumber: 3.1 Consensus size: 127
2514277 GGCTACACCG
* * * *
2514287 AAAAGCAATACAAACAAAGACCACTGTTGTCTTCAATGAGAAAGCAATGAAACTCTAAACACCCA
1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
*
2514352 AAAGCATAACAAACGAAAGCCACTGTTGTGTGCAAATAAAAAAGAGTAAACCCCAAACACTC
66 AAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTC
* *
2514414 AAAAGCATTACAAACAAAGACCAGTACTGTCTTCAATGAGAAAGCAATGAAACCCTAGACACCCA
1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
*
2514479 AAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCGAACACTC
66 AAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTC
2514541 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
* * * * * * * *
2514606 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAACAAAAAGGAGTAAACCCTAAACACCC
66 AAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTC
2514668 AAAAGCATTACAAA
1 AAAAGCATTACAAA
2514682 TGTGATTTCT
Statistics
Matches: 249, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 249 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.15
Consensus pattern (127 bp):
AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
AAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTC
Found at i:2514908 original size:10 final size:10
Alignment explanation
Indices: 2514895--2515050 Score: 59
Period size: 9 Copynumber: 16.4 Consensus size: 10
2514885 TTTTTAAGAC
2514895 TTATTAAAAA
1 TTATTAAAAA
2514905 TTA-TAAAAA
1 TTATTAAAAA
* *
2514914 -TATTTGAACA
1 TTA-TTAAAAA
*
2514924 -TATTAAAGA
1 TTATTAAAAA
2514933 -T-TTATAAAA
1 TTATTA-AAAA
2514942 TTATTAAAAA
1 TTATTAAAAA
2514952 TT-TTAAAAAA
1 TTATT-AAAAA
* *
2514962 TT-GTGAAAA
1 TTATTAAAAA
*
2514971 TCATTTAAAAA
1 TTA-TTAAAAA
2514982 TT-TTAAAAA
1 TTATTAAAAA
*
2514991 -GATTAAAAA
1 TTATTAAAAA
* * *
2515000 ATGTAAAAAA
1 TTATTAAAAA
**
2515010 TTATTTGAAA
1 TTATTAAAAA
*
2515020 TT-TATAAGAA
1 TTAT-TAAAAA
2515030 TT-TT-AAAA
1 TTATTAAAAA
2515038 TT-TTAAAAA
1 TTATTAAAAA
2515047 TTAT
1 TTAT
2515051 AATATATTTT
Statistics
Matches: 109, Mismatches: 24, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
8 12 0.11
9 44 0.40
10 44 0.40
11 9 0.08
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.39
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:2514946 original size:19 final size:18
Alignment explanation
Indices: 2514901--2514959 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
2514891 AGACTTATTA
2514901 AAAATTA-TAAAAATATTT
1 AAAATTATTAAAAAT-TTT
* *
2514919 GAACA-TATTAAAGATTTAT
1 -AAAATTATTAAAAATTT-T
2514938 AAAATTATTAAAAATTTT
1 AAAATTATTAAAAATTTT
2514956 AAAA
1 AAAA
2514960 AATTGTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 12 0.36
19 21 0.64
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAATTATTAAAAATTTT
Found at i:2514988 original size:39 final size:39
Alignment explanation
Indices: 2514932--2515037 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
2514922 CATATTAAAG
*
2514932 ATTTATAAAATTATTAAAAATTTTAAAAAATTGT-GAAAATC
1 ATTTA-AAAATT-TTAAAAATTTTAAAAAA-TGTAAAAAATC
** *
2514973 ATTTAAAAATTTTAAAAAGATTAAAAAATGTAAAAAATT
1 ATTTAAAAATTTTAAAAATTTTAAAAAATGTAAAAAATC
* *
2515012 ATTT-GAAATTTATAAGAATTTTAAAA
1 ATTTAAAAATTT-TAAAAATTTTAAAA
2515038 TTTTAAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
38 9 0.16
39 35 0.64
40 6 0.11
41 5 0.09
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.38
Consensus pattern (39 bp):
ATTTAAAAATTTTAAAAATTTTAAAAAATGTAAAAAATC
Found at i:2516146 original size:12 final size:12
Alignment explanation
Indices: 2516129--2516163 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
2516119 CCAAAACAGG
2516129 CTTTTAGCGGCA
1 CTTTTAGCGGCA
2516141 CTTTTAGCGGCA
1 CTTTTAGCGGCA
2516153 CTTTTAGCGGC
1 CTTTTAGCGGC
2516164 GTTTGGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.14, C:0.26, G:0.26, T:0.34
Consensus pattern (12 bp):
CTTTTAGCGGCA
Found at i:2516280 original size:40 final size:40
Alignment explanation
Indices: 2516236--2516314 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
2516226 AAGGCTAGCA
* *
2516236 TTAGCTGCGTTTCT-GAAAAAGTGCCGCTATAGATCGAGCG
1 TTAGCGGCGTTTCTCGAAAAA-TGACGCTATAGATCGAGCG
* *
2516276 TTAGCGGCGTTTTTCGAAAAATGACGCTATAGTTCGAGC
1 TTAGCGGCGTTTCTCGAAAAATGACGCTATAGATCGAGC
2516315 ATAAAACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 28 0.82
41 6 0.18
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (40 bp):
TTAGCGGCGTTTCTCGAAAAATGACGCTATAGATCGAGCG
Found at i:2516727 original size:43 final size:43
Alignment explanation
Indices: 2516692--2516901 Score: 330
Period size: 43 Copynumber: 4.9 Consensus size: 43
2516682 CGTTTATAAA
* *
2516692 AAAAGCACCGCTAAAAGTCATGATCTATAGTGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
*
2516735 AAAAGCGCCGCTAAAAGTCATGATCTATAGCTGCGTTTGTGGG
1 AAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
* * *
2516778 AGAAGCGCCGCTAAAAGTCATGATCTATAACGGCGTTTGTTGG
1 AAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
*
2516821 AGAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
* * *
2516864 AAAAGCACCGCTAAAAGTCATGATCTATAACGACGTTT
1 AAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTT
2516902 ATTTCTAAAA
Statistics
Matches: 154, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 154 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.25
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGG
Found at i:2519668 original size:14 final size:13
Alignment explanation
Indices: 2519651--2519694 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
2519641 AACATTAGAT
2519651 TTTAAGATTTATAG
1 TTTAAGATTTA-AG
2519665 TTTAAGATTTAAG
1 TTTAAGATTTAAG
*
2519678 TTTTAGAGTTTTAAG
1 -TTTA-AGATTTAAG
2519693 TT
1 TT
2519695 GAGATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 2 0.07
14 17 0.63
15 8 0.30
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTTAAGATTTAAG
Found at i:2526370 original size:31 final size:31
Alignment explanation
Indices: 2526311--2526370 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2526301 TAGACTTTTT
* * **
2526311 TTTTGAAAAATTAATAGTTAAATCTAATTCC
1 TTTTAAAAAATTAAAAGCAAAATCTAATTCC
*
2526342 TTTTAAAAAATTAAAAGCAAAATTTAATT
1 TTTTAAAAAATTAAAAGCAAAATCTAATT
2526371 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (31 bp):
TTTTAAAAAATTAAAAGCAAAATCTAATTCC
Found at i:2527288 original size:29 final size:29
Alignment explanation
Indices: 2527231--2527288 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2527221 TAAGGATACC
* *
2527231 TTGGCTAAAACTATCTTCTTTTTCTTTAT
1 TTGGCTAAAAATATCTTCTTTTTCGTTAT
* * *
2527260 TTGGCTAAAAATATGTTGTTTTTGGTTAT
1 TTGGCTAAAAATATCTTCTTTTTCGTTAT
2527289 ATTTGATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.53
Consensus pattern (29 bp):
TTGGCTAAAAATATCTTCTTTTTCGTTAT
Found at i:2529666 original size:15 final size:15
Alignment explanation
Indices: 2529648--2529689 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2529638 AATAAAAAAT
2529648 ATATAAAAATATTAA
1 ATATAAAAATATTAA
* *
2529663 ATATTAAAATAATAA
1 ATATAAAAATATTAA
*
2529678 A-ATATAAATATT
1 ATATAAAAATATT
2529690 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATAAAAATATTAA
Found at i:2529676 original size:28 final size:29
Alignment explanation
Indices: 2529609--2529676 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
2529599 TAAAATAATG
* *
2529609 TTAAAATGATTATATAAAAAATTTCAATAA
1 TTAAAAT-AATATATAAAAAATTTAAATAA
*
2529639 ATAAAA-AATATAT-AAAAATATTAAAT-A
1 TTAAAATAATATATAAAAAAT-TTAAATAA
2529666 TTAAAATAATA
1 TTAAAATAATA
2529677 AAATATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 12 0.38
28 15 0.47
30 5 0.16
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
TTAAAATAATATATAAAAAATTTAAATAA
Found at i:2530945 original size:24 final size:24
Alignment explanation
Indices: 2530915--2530960 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2530905 AAATAAATTT
2530915 AAAATAAAAAACTAT-TATATTTTA
1 AAAATAAAAAA-TATATATATTTTA
2530939 AAAATAAAAAATATATATATTT
1 AAAATAAAAAATATATATATTT
2530961 AATATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAATATATATATTTTA
Found at i:2530961 original size:23 final size:23
Alignment explanation
Indices: 2530911--2530962 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
2530901 AAGTAAATAA
2530911 ATTT-AAAATAAAAAACTATTAT
1 ATTTAAAAATAAAAAACTATTAT
2530933 ATTTTAAAAATAAAAAA-TATATAT
1 A-TTTAAAAATAAAAAACTAT-TAT
2530957 ATTTAA
1 ATTTAA
2530963 TATTTTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 1 0.04
23 11 0.41
24 15 0.56
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTTAAAAATAAAAAACTATTAT
Done.