Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 10 of 125
Found at i:3362154 original size:138 final size:138
Alignment explanation
Indices: 3362001--3362284 Score: 532
Period size: 138 Copynumber: 2.1 Consensus size: 138
3361991 AACTCCCTCT
3362001 AAAATTAAAAAATGTCCATTTAAGCCTTTTAGAAAATTTAAAATTAGTAAAGGTAAAATTCCACT
1 AAAATTAAAAAATGTCCATTTAAGCCTTTTAGAAAATTTAAAATTAGTAAAGGTAAAATTCCACT
*
3362066 TTGGCCTCCTAAAAATGATAATAATTTTATTTAATCCTTTAAAAATTATAAAGATATAGACTATT
66 TTGGCATCCTAAAAATGATAATAATTTTATTTAATCCTTTAAAAATTATAAAGATATAGACTATT
3362131 AAAAATTA
131 AAAAATTA
*
3362139 AAAATTAAAAAATGTCCATTTAAGCCTTTTAGAAAATTTAAAATTAGTAAAGGTAAAATTTCACT
1 AAAATTAAAAAATGTCCATTTAAGCCTTTTAGAAAATTTAAAATTAGTAAAGGTAAAATTCCACT
*
3362204 TTGGCATCCTAAAAATGATAATAATTTTATTTAATCCTTTAAAAATTATAAAGATATAGGCTATT
66 TTGGCATCCTAAAAATGATAATAATTTTATTTAATCCTTTAAAAATTATAAAGATATAGACTATT
3362269 AAAAATTA
131 AAAAATTA
*
3362277 AAATTTAA
1 AAAATTAA
3362285 TTTCCGCCCC
Statistics
Matches: 142, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 142 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (138 bp):
AAAATTAAAAAATGTCCATTTAAGCCTTTTAGAAAATTTAAAATTAGTAAAGGTAAAATTCCACT
TTGGCATCCTAAAAATGATAATAATTTTATTTAATCCTTTAAAAATTATAAAGATATAGACTATT
AAAAATTA
Found at i:3364234 original size:7 final size:7
Alignment explanation
Indices: 3364222--3364251 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3364212 TCTTGATGAA
3364222 AGTGGTG
1 AGTGGTG
3364229 AGTGGTG
1 AGTGGTG
3364236 AGTGGTG
1 AGTGGTG
3364243 AGTGGTG
1 AGTGGTG
3364250 AG
1 AG
3364252 AGACAGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.57, T:0.27
Consensus pattern (7 bp):
AGTGGTG
Found at i:3376103 original size:18 final size:18
Alignment explanation
Indices: 3376080--3376116 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3376070 TTTGTGATTA
3376080 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
3376098 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
3376116 A
1 A
3376117 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:3381981 original size:16 final size:16
Alignment explanation
Indices: 3381960--3381990 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3381950 AGGATTCATA
*
3381960 TAGCTAAATAAATTTT
1 TAGCTAAAGAAATTTT
3381976 TAGCTAAAGAAATTT
1 TAGCTAAAGAAATTT
3381991 AATAAAAGGT
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:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (16 bp):
TAGCTAAAGAAATTTT
Found at i:3394313 original size:43 final size:42
Alignment explanation
Indices: 3394246--3394514 Score: 315
Period size: 43 Copynumber: 6.3 Consensus size: 42
3394236 CGCTAAAGAT
* * *
3394246 AACGCCGCTAAAGAACATGGTCTTTAGTGGCACTTTCTCAACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTC-CCACA
* * * *
3394289 AACGCCGCTAAAGAATACGATCTTTAGCGACGCTTTACCCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-CCCACA
* * * *
3394332 AATGCTGCTAAAGAATATGGTC-TTAGCAGCGCTTTCCTCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCC-CACA
* * *
3394374 AACGCCGCTAAAGAACATGGTTTTTAGCAGCGCATTACCCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCACA
*
3394417 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-TCCCACA
* *
3394460 AACGCCGCTAAAGAACATGGTCTTTAGCAGCGTTTTTCCCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCG-CTTTCCCACA
*
3394503 AACACCGCTAAA
1 AACGCCGCTAAA
3394515 ATTATCAGAT
Statistics
Matches: 195, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.01
42 35 0.18
43 151 0.77
44 7 0.04
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (42 bp):
AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCACA
Found at i:3394474 original size:128 final size:129
Alignment explanation
Indices: 3394246--3394514 Score: 350
Period size: 128 Copynumber: 2.1 Consensus size: 129
3394236 CGCTAAAGAT
* * *
3394246 AACGCCGCTAAAGAACATGGTCTTTAGTGGCACTTTCTCAACAAACGCCGCTAAAGAATACGATC
1 AACGCCGCTAAAGAACATGGTCTTTAGAGGCACTTACTCAACAAACGCCGCTAAAGAACACGATC
* * *
3394311 TTTAGCGACGCTTTACCCACAAATGCTGCTAAAGAATATGGTC-TTAGCAGCG-CTTTCCTCACA
66 TTTAGCGACGCTTTACCCACAAACGCCGCTAAAGAACATGGTCTTTAGCAGCGTCTTTCC-CACA
* * * *
3394374 AACGCCGCTAAAGAACATGGTTTTTAGCAGCGCA-TTAC-CCACAAACGCCGCTAAAGAACATGG
1 AACGCCGCTAAAGAACATGGTCTTTAG-AG-GCACTTACTCAACAAACGCCGCTAAAGAACACGA
* *
3394437 TCTTTAGCGGCGC-TTACCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCAGCGTTTTTCCCA
64 TCTTTAGCGACGCTTTA-CCCACAAACGCCGCTAAAGAACATGGTCTTTAGCAGCGTCTTTCCCA
3394501 CA
128 CA
*
3394503 AACACCGCTAAA
1 AACGCCGCTAAA
3394515 ATTATCAGAT
Statistics
Matches: 123, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
127 3 0.02
128 84 0.68
129 28 0.23
130 8 0.07
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (129 bp):
AACGCCGCTAAAGAACATGGTCTTTAGAGGCACTTACTCAACAAACGCCGCTAAAGAACACGATC
TTTAGCGACGCTTTACCCACAAACGCCGCTAAAGAACATGGTCTTTAGCAGCGTCTTTCCCACA
Found at i:3394478 original size:86 final size:86
Alignment explanation
Indices: 3394246--3394514 Score: 353
Period size: 86 Copynumber: 3.1 Consensus size: 86
3394236 CGCTAAAGAT
* * * * * * *
3394246 AACGCCGCTAAAGAACATGGTCTTTAGTGGCACTTTCTCAACAAACGCCGCTAAAGAATACGATC
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGAACATGGTC
3394311 TTTAGC-GACGCTTTACCCACA
66 TTTAGCAG-CGCTTTACCCACA
* * * * * *
3394332 AATGCTGCTAAAGAATATGGTC-TTAGCAGCGCTTTCCTCACAAACGCCGCTAAAGAACATGGTT
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGAACATGGTC
*
3394396 TTTAGCAGCGCATTACCCACA
66 TTTAGCAGCGCTTTACCCACA
*
3394417 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCCACAAACGCCGCTAAAGAACATGGTC
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGAACATGGTC
* *
3394482 TTTAGCAGCGTTTTTCCCACA
66 TTTAGCAGCGCTTTACCCACA
*
3394503 AACACCGCTAAA
1 AACGCCGCTAAA
3394515 ATTATCAGAT
Statistics
Matches: 156, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
85 69 0.44
86 87 0.56
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (86 bp):
AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGAACATGGTC
TTTAGCAGCGCTTTACCCACA
Found at i:3399951 original size:34 final size:34
Alignment explanation
Indices: 3399913--3399980 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
3399903 TATTCGGTTC
*
3399913 AAAAGAAGCAGGATTTCAACATAACAATCGATTT
1 AAAAGAAGCAAGATTTCAACATAACAATCGATTT
* * * *
3399947 AAAAGAAGTAATATTTTACCATAACAATCGATTT
1 AAAAGAAGCAAGATTTCAACATAACAATCGATTT
3399981 TTAGGATGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (34 bp):
AAAAGAAGCAAGATTTCAACATAACAATCGATTT
Found at i:3400065 original size:73 final size:74
Alignment explanation
Indices: 3399977--3400114 Score: 165
Period size: 74 Copynumber: 1.9 Consensus size: 74
3399967 ATAACAATCG
** *
3399977 ATTTTTAGGATGGAT-ATAATATATATTCAAAGGGAGAAATTG-TAAAAATCTTAAACCTTGGAG
1 ATTTTTAGGATGGATAATAATATATATAAAAAGGGAGAAATTGCAAAAAAT-TTAAACCTT-GAG
3400040 GGTCTACTTAT
64 GGTCTACTTAT
* * * **
3400051 ATTTTTGGGA-GGATAATAGTATATCTAAAAAGGGTTAAATTGCAAAAAATTTAAACCTTGAGGG
1 ATTTTTAGGATGGATAATAATATATATAAAAAGGGAGAAATTGCAAAAAATTTAAACCTTGAGGG
3400115 GCCATGGTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
73 9 0.17
74 39 0.72
75 6 0.11
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.33
Consensus pattern (74 bp):
ATTTTTAGGATGGATAATAATATATATAAAAAGGGAGAAATTGCAAAAAATTTAAACCTTGAGGG
TCTACTTAT
Found at i:3400700 original size:14 final size:14
Alignment explanation
Indices: 3400672--3400712 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3400662 GGAATACAAC
*
3400672 AAATACTAT-AAAT
1 AAATAATATAAAAT
3400685 -AATAATATTAAAAT
1 AAATAATA-TAAAAT
3400699 AAATAATATAAAAT
1 AAATAATATAAAAT
3400713 TATTATAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 6 0.25
13 1 0.04
14 10 0.42
15 7 0.29
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATAATATAAAAT
Found at i:3402779 original size:2 final size:2
Alignment explanation
Indices: 3402772--3402825 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3402762 ATTGATAACA
3402772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3402814 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3402826 TCATTGTTGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3404963 original size:127 final size:127
Alignment explanation
Indices: 3404737--3404982 Score: 483
Period size: 127 Copynumber: 1.9 Consensus size: 127
3404727 AGTGAATTTT
3404737 AGCATTGCTTCCAATTTGTAACAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
1 AGCATTGCTTCCAATTTGTAACAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
3404802 GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAGTTTTTAATATGGTCGC
66 GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAGTTTTTAATATGGTCGC
*
3404864 AGCATTGCTTCCAATTTGTATCAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
1 AGCATTGCTTCCAATTTGTAACAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
3404929 GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAGTTTTTAAT
66 GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAGTTTTTAAT
3404983 GTGGAAGTTC
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 118 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (127 bp):
AGCATTGCTTCCAATTTGTAACAGAACTGGTTTTAATGCCTGTGTTTGAGCTTATTGGAACTGAT
GGCAGTGGAACTTATAATATAAATTAGAAGGAAAATTTCTACCAAGTTTTTAATATGGTCGC
Found at i:3414028 original size:21 final size:21
Alignment explanation
Indices: 3413981--3414021 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3413971 TTATATTAAA
3413981 AGTA-TTTTATACTAATCATT
1 AGTATTTTTATACTAATCATT
*
3414001 AGTATTTTTATATTAATCATT
1 AGTATTTTTATACTAATCATT
3414022 TATATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (21 bp):
AGTATTTTTATACTAATCATT
Found at i:3415491 original size:23 final size:21
Alignment explanation
Indices: 3415443--3415491 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
3415433 AAATTAATGC
3415443 TTTAAAAATATAAAATTATAA
1 TTTAAAAATATAAAATTATAA
* * *
3415464 ATTAATAAATGATGAAATTATAT
1 TTTAA-AAAT-ATAAAATTATAA
3415487 TTTAA
1 TTTAA
3415492 CCTCTCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.18
22 4 0.18
23 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TTTAAAAATATAAAATTATAA
Found at i:3419631 original size:24 final size:24
Alignment explanation
Indices: 3419604--3419650 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3419594 AATTGAACCA
*
3419604 AATTCTATTTTTTAAT-ATATAAAT
1 AATTCTAATTTTT-ATGATATAAAT
*
3419628 AATTTTAATTTTTATGATATAAA
1 AATTCTAATTTTTATGATATAAA
3419651 AATAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
AATTCTAATTTTTATGATATAAAT
Found at i:3420231 original size:23 final size:23
Alignment explanation
Indices: 3420162--3420231 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
3420152 TCATTAACAT
*
3420162 TGTTCGTGAACATATTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* **
3420186 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
3420209 TGTTCGCGAACATGTTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
3420232 GTTAAATGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:3420259 original size:23 final size:23
Alignment explanation
Indices: 3420216--3420260 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3420206 TAATGTTCGC
* *
3420216 GAACATGTTCAATTAAGTTAAAT
1 GAACATGTTCAATGAAATTAAAT
3420239 GAACATGTT-AATGAACATTAAA
1 GAACATGTTCAATGAA-ATTAAA
3420261 CAAACGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (23 bp):
GAACATGTTCAATGAAATTAAAT
Found at i:3421466 original size:22 final size:23
Alignment explanation
Indices: 3421409--3421466 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
3421399 TTATTGTTTA
*
3421409 TTTTTGCTATTTCTGGTGTGTGTG
1 TTTTTACTATTT-TGGTGTGTGTG
*
3421433 TTTTTA-TGTTTTGGTGCTGT-T-
1 TTTTTACTATTTTGGTG-TGTGTG
3421454 TTTTTACTATTTT
1 TTTTTACTATTTT
3421467 AATGCTGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 6 0.21
22 11 0.38
23 7 0.24
24 5 0.17
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.66
Consensus pattern (23 bp):
TTTTTACTATTTTGGTGTGTGTG
Found at i:3421524 original size:25 final size:25
Alignment explanation
Indices: 3421486--3421551 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
3421476 TTTGCTATTA
**
3421486 TTTTTGTTAATGTTTTTGCTGCT-AT
1 TTTTTGTTGTTGTTTTTGCTG-TAAT
3421511 TTTTTGTTGTTG-TTTTGCTGTAAT
1 TTTTTGTTGTTGTTTTTGCTGTAAT
*
3421535 TTTTT-ATGTTGTTTTTG
1 TTTTTGTTGTTGTTTTTG
3421552 TTATTTGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.17
24 20 0.56
25 10 0.28
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.68
Consensus pattern (25 bp):
TTTTTGTTGTTGTTTTTGCTGTAAT
Found at i:3429590 original size:29 final size:29
Alignment explanation
Indices: 3429534--3429591 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3429524 TGATAATTTT
* * *
3429534 AAATTATTAAATATAAACTTCTTTTTTAA
1 AAATTATTAAATACAAAATTCTTATTTAA
*
3429563 AAATTATTAAATACAAAATTGTTATTTAA
1 AAATTATTAAATACAAAATTCTTATTTAA
3429592 TCATATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (29 bp):
AAATTATTAAATACAAAATTCTTATTTAA
Found at i:3430643 original size:18 final size:18
Alignment explanation
Indices: 3430593--3430645 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
3430583 TTTTCTCGAA
*
3430593 ATTATTAAATATAAA-ATT
1 ATTATTTAATATAAACA-T
*
3430611 ATTATTT-A-AT-CACAT
1 ATTATTTAATATAAACAT
3430626 ATTATTTAATATAAACAT
1 ATTATTTAATATAAACAT
3430644 AT
1 AT
3430646 AAGACTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
17 3 0.11
18 12 0.43
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTATTTAATATAAACAT
Found at i:3430705 original size:18 final size:19
Alignment explanation
Indices: 3430670--3430707 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3430660 ATTTACATTA
* *
3430670 TTATTTGATTATATAAAAG
1 TTATTTGATTAAAAAAAAG
3430689 TTATTT-ATTAAAAAAAAG
1 TTATTTGATTAAAAAAAAG
3430707 T
1 T
3430708 ATAATTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (19 bp):
TTATTTGATTAAAAAAAAG
Found at i:3431987 original size:16 final size:19
Alignment explanation
Indices: 3431948--3431987 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 19
3431938 AAATTACATT
3431948 ATTATTTAATTATATAAAA
1 ATTATTTAATTATATAAAA
*
3431967 GTTATTT-ATTA-A-AAAA
1 ATTATTTAATTATATAAAA
3431983 ATTAT
1 ATTAT
3431988 AATTACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 4 0.21
19 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTATTTAATTATATAAAA
Found at i:3434309 original size:14 final size:14
Alignment explanation
Indices: 3434290--3434316 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3434280 AATAACCCTA
3434290 AACCAAAATATGTT
1 AACCAAAATATGTT
3434304 AACCAAAATATGT
1 AACCAAAATATGT
3434317 GAATAACAAA
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:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
AACCAAAATATGTT
Found at i:3434450 original size:47 final size:47
Alignment explanation
Indices: 3434374--3434490 Score: 132
Period size: 47 Copynumber: 2.5 Consensus size: 47
3434364 TAGCAACCAT
* *
3434374 AATCC-AATCAAAATCGAA-ATAACCTTAAATCGAAAATAAAAATCAA
1 AATCCAAATCAAAATCGAATA-AACCCTAAATCAAAAATAAAAATCAA
* * *
3434420 AATCCAAATCAAAATCGAATAAACCCTAAATTAAAAATCACAATCAA
1 AATCCAAATCAAAATCGAATAAACCCTAAATCAAAAATAAAAATCAA
* *
3434467 TAT-CAACATCAAATTCGAATAAAC
1 AATCCAA-ATCAAAATCGAATAAAC
3434491 ACAAAATAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
46 8 0.13
47 52 0.85
48 1 0.02
ACGTcount: A:0.56, C:0.20, G:0.03, T:0.21
Consensus pattern (47 bp):
AATCCAAATCAAAATCGAATAAACCCTAAATCAAAAATAAAAATCAA
Found at i:3434864 original size:30 final size:31
Alignment explanation
Indices: 3434797--3434867 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
3434787 ATTTGATTTC
*
3434797 AGTGACTGTTTTGTCACTTTTCGATAACGTT
1 AGTGACTGTTTTGTAACTTTTCGATAACGTT
3434828 AGTGACTGTTTTGTAACATTTTC-A-AA-GTT
1 AGTGACTGTTTTGTAAC-TTTTCGATAACGTT
3434857 AAGTGACTGTT
1 -AGTGACTGTT
3434868 GTGTTAAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.32
31 17 0.46
32 5 0.14
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.44
Consensus pattern (31 bp):
AGTGACTGTTTTGTAACTTTTCGATAACGTT
Found at i:3435120 original size:18 final size:18
Alignment explanation
Indices: 3435079--3435120 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3435069 GCCCTTAATT
*
3435079 TAATTAGAATCGAACCGA
1 TAATTAGAATCGAACCAA
3435097 TCAATT-GAATCGGAACCAA
1 T-AATTAGAATC-GAACCAA
3435116 TAATT
1 TAATT
3435121 TAAATGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (18 bp):
TAATTAGAATCGAACCAA
Found at i:3435389 original size:16 final size:19
Alignment explanation
Indices: 3435353--3435392 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
3435343 TATTTACGTT
3435353 ATTATTTAATTATATAAAA
1 ATTATTTAATTATATAAAA
3435372 ATTATTT-ATT-TA-AAAA
1 ATTATTTAATTATATAAAA
3435388 ATTAT
1 ATTAT
3435393 AATTACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
18 3 0.14
19 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTATTTAATTATATAAAA
Found at i:3435534 original size:15 final size:16
Alignment explanation
Indices: 3435516--3435548 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3435506 TCCCTCATAT
3435516 TTTCT-CTTCCCTTTC
1 TTTCTCCTTCCCTTTC
3435531 TTTCTCCTTCCCTTTC
1 TTTCTCCTTCCCTTTC
3435547 TT
1 TT
3435549 GCTGTCCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTCTCCTTCCCTTTC
Found at i:3436848 original size:72 final size:73
Alignment explanation
Indices: 3436727--3437073 Score: 308
Period size: 72 Copynumber: 4.7 Consensus size: 73
3436717 AGGTGGGCGT
* * * * * *
3436727 TGAATTGCTACCAAAGCTTTTAGATGGTTCTACAATTGCCAACAG-GATGGGTATGAATATGGAG
1 TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAA-AGAGATGGGTATGAATATGGAG
3436791 -GTGAACAC
65 AGTGAACAC
* * * * * * *
3436799 TGGATTGCTACCATATCCTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAAGACTATGGAGA
1 TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATGAATATGGAGA
3436864 G-GAACAC
66 GTGAACAC
* * * *
3436871 TGAATTGTTACCAAAGCTTGTAGAAGATTCTACAAGTCCTAAAGAGATGGGTCAT-AATACGGAG
1 TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGT-ATGAATATGGA-
*
3436935 GAGTGGAGCA-
64 GAGT-GAACAC
* * * * *
3436945 TCGAATTGATATCAAAGCTTATGGAAGATTCTCCAAGTGCTAAAGAGATGGATATGAAAATGGAG
1 T-GAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATGAATATGGA-
* **
3437010 GAGGAGAACGT
64 GA-GTGAACAC
* * ** * *
3437021 TCAATCGATTTCAAAGCTTATAGAAGATTCTTCAAATGCTAAAGAGATGGGTA
1 TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTA
3437074 AGGATGTGGC
Statistics
Matches: 224, Mismatches: 41, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
71 2 0.01
72 107 0.48
73 5 0.02
74 3 0.01
75 105 0.47
76 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.26
Consensus pattern (73 bp):
TGAATTGATACCAAAGCTTATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATGAATATGGAGA
GTGAACAC
Found at i:3436982 original size:75 final size:73
Alignment explanation
Indices: 3436817--3437073 Score: 272
Period size: 75 Copynumber: 3.5 Consensus size: 73
3436807 TACCATATCC
3436817 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTA-AGACTATGGA-GA-GGAACA-CTGAATTG
1 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATA-A-TATGGAGGAGGGAACATC-GAATTG
* *
3436878 TTACCAAAGCT
63 ATATCAAAGCT
* * * *
3436889 TGTAGAAGATTCTACAAGTCCTAAAGAGATGGGTCATAATACGGAGGAGTGGAGCATCGAATTGA
1 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGT-ATAATATGGAGGAG-GGAACATCGAATTGA
3436954 TATCAAAGCT
64 TATCAAAGCT
* * * * * *
3436964 TATGGAAGATTCTCCAAGTGCTAAAGAGATGGATATGAAAATGGAGGAGGAGAACGTTC-AATCG
1 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTAT-AATATGGAGGAGG-GAAC-ATCGAATTG
*
3437028 ATTTCAAAGCT
63 ATATCAAAGCT
* *
3437039 TATAGAAGATTCTTCAAATGCTAAAGAGATGGGTA
1 TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTA
3437074 AGGATGTGGC
Statistics
Matches: 155, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
72 37 0.24
73 4 0.03
74 4 0.03
75 107 0.69
76 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.25
Consensus pattern (73 bp):
TATAGAAGATTCTACAAGTGCTAAAGAGATGGGTATAATATGGAGGAGGGAACATCGAATTGATA
TCAAAGCT
Found at i:3444418 original size:3 final size:3
Alignment explanation
Indices: 3444410--3444435 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3444400 AGATCTAACA
3444410 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3444436 AGTAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3446548 original size:18 final size:18
Alignment explanation
Indices: 3446517--3446551 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3446507 AATCTTGAAC
* *
3446517 ATACATACATATATATAT
1 ATACACACAGATATATAT
3446535 ATACACACAGATATATA
1 ATACACACAGATATATA
3446552 GGGGAGATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (18 bp):
ATACACACAGATATATAT
Found at i:3447647 original size:32 final size:30
Alignment explanation
Indices: 3447605--3447664 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
3447595 AACCTAAACT
3447605 TGACACTTTTTCTTAA-TTTAGTACGTAAATC
1 TGACACTTTTT-TTAAGTTT-GTACGTAAATC
*
3447636 TGACACCTTTTTTTAAGTTTGTACTTAAA
1 TGACA-CTTTTTTTAAGTTTGTACGTAAA
3447665 CTTTTTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (30 bp):
TGACACTTTTTTTAAGTTTGTACGTAAATC
Found at i:3447935 original size:31 final size:31
Alignment explanation
Indices: 3447904--3448057 Score: 79
Period size: 31 Copynumber: 5.2 Consensus size: 31
3447894 ACTTAAGTAT
*
3447904 CAAATTAGGAAAAAATATCAAGTTCAGGTAT
1 CAAATTAGGAAAAAATATCAAGTTCAGGTAC
* *** *
3447935 C-AATTTGAGTCCAAA-A--AAGTTTAGGTAC
1 CAAATTAG-GAAAAAATATCAAGTTCAGGTAC
* * * *
3447963 CAAATTAAGAAAAAATGTCAAGTACATGTAC
1 CAAATTAGGAAAAAATATCAAGTTCAGGTAC
* ** *
3447994 CAAATTGGGTCAAAA-A--AAGTTTAGGTAC
1 CAAATTAGGAAAAAATATCAAGTTCAGGTAC
** * * *
3448022 CAAATTAAAAAAAAATGTCAAGTTCATGTAT
1 CAAATTAGGAAAAAATATCAAGTTCAGGTAC
3448053 CAAAT
1 CAAAT
3448058 GCTATATTAA
Statistics
Matches: 83, Mismatches: 32, Indels: 16
0.63 0.24 0.12
Matches are distributed among these distances:
28 34 0.41
29 4 0.05
30 6 0.07
31 39 0.47
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (31 bp):
CAAATTAGGAAAAAATATCAAGTTCAGGTAC
Found at i:3447968 original size:59 final size:59
Alignment explanation
Indices: 3447904--3448057 Score: 227
Period size: 59 Copynumber: 2.6 Consensus size: 59
3447894 ACTTAAGTAT
* * * * *
3447904 CAAATTAGGAAAAAATATCAAGTTCAGGTATCAATTTGAGTCCAAAAAAGTTTAGGTAC
1 CAAATTAAGAAAAAATGTCAAGTTCATGTATCAAATTGAGTCAAAAAAAGTTTAGGTAC
* * *
3447963 CAAATTAAGAAAAAATGTCAAGTACATGTACCAAATTGGGTCAAAAAAAGTTTAGGTAC
1 CAAATTAAGAAAAAATGTCAAGTTCATGTATCAAATTGAGTCAAAAAAAGTTTAGGTAC
*
3448022 CAAATTAAAAAAAAATGTCAAGTTCATGTATCAAAT
1 CAAATTAAGAAAAAATGTCAAGTTCATGTATCAAAT
3448058 GCTATATTAA
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 84 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (59 bp):
CAAATTAAGAAAAAATGTCAAGTTCATGTATCAAATTGAGTCAAAAAAAGTTTAGGTAC
Found at i:3448877 original size:6 final size:6
Alignment explanation
Indices: 3448866--3448902 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
3448856 TTTATTTTAA
*
3448866 AAATTT AAATTT AAATTT GAATTT -AATTT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AA
3448903 TATTATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:3448885 original size:31 final size:30
Alignment explanation
Indices: 3448836--3448897 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
3448826 TTTTGAAATT
* * *
3448836 AAATTTATTTTAATTTTGAATTTATTTTAA
1 AAATTTAATTTAAATTTGAATTTAATTTAA
3448866 AAATTTAAATTTAAATTTGAATTTAATTTAA
1 AAATTT-AATTTAAATTTGAATTTAATTTAA
3448897 A
1 A
3448898 TTTAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
AAATTTAATTTAAATTTGAATTTAATTTAA
Found at i:3448895 original size:17 final size:16
Alignment explanation
Indices: 3448831--3448917 Score: 65
Period size: 17 Copynumber: 5.4 Consensus size: 16
3448821 AACCATTTTG
* *
3448831 AAATTAAATTTATTTT
1 AAATTTAATTTAATTT
* *
3448847 AATTTTGAATTTATTTT
1 AAATTT-AATTTAATTT
3448864 AAA---AATTTAAATTT
1 AAATTTAATTT-AATTT
3448878 AAATTTGAATTTAATTT
1 AAATTT-AATTTAATTT
3448895 AAATTTAATATT-ATTAT
1 AAATTTAAT-TTAATT-T
3448912 AAATTT
1 AAATTT
3448918 TAAAAAAAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.08
14 7 0.12
16 10 0.17
17 32 0.54
18 5 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
AAATTTAATTTAATTT
Found at i:3448899 original size:11 final size:11
Alignment explanation
Indices: 3448867--3448903 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
3448857 TTATTTTAAA
3448867 AATTTAAATTT
1 AATTTAAATTT
*
3448878 AAATTTGAATTT
1 -AATTTAAATTT
3448890 AATTTAAATTT
1 AATTTAAATTT
3448901 AAT
1 AAT
3448904 ATTATTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:3448916 original size:23 final size:23
Alignment explanation
Indices: 3448858--3448917 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
3448848 ATTTTGAATT
*
3448858 TATT-TTAAAAATTTAAATTTAA
1 TATTATTATAAATTTAAATTTAA
3448880 -ATTTGAATT-T-AATTTAAATTTAA
1 TA-TT--ATTATAAATTTAAATTTAA
3448903 TATTATTATAAATTT
1 TATTATTATAAATTT
3448918 TAAAAAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 13
0.68 0.02 0.30
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 20 0.67
24 1 0.03
25 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTATTATAAATTTAAATTTAA
Found at i:3449752 original size:17 final size:18
Alignment explanation
Indices: 3449710--3449756 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
3449700 TTATGATTTT
3449710 TTTTAA-AATAATAATAA
1 TTTTAATAATAATAATAA
* *
3449727 TTCTAATAATAATAA-CA
1 TTTTAATAATAATAATAA
3449744 TTTTAATAATAAT
1 TTTTAATAATAAT
3449757 TAAATACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTTAATAATAATAATAA
Found at i:3450145 original size:13 final size:12
Alignment explanation
Indices: 3450130--3450168 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
3450120 ACCAATAAAA
3450130 AAAAAGAAAGGG
1 AAAAAGAAAGGG
3450142 AAAAAGAAAGGG
1 AAAAAGAAAGGG
*
3450154 AAAAAGGAAGGG
1 AAAAAGAAAGGG
3450166 AAA
1 AAA
3450169 CCTTACCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAGGG
Found at i:3450791 original size:30 final size:30
Alignment explanation
Indices: 3450723--3450906 Score: 230
Period size: 30 Copynumber: 6.2 Consensus size: 30
3450713 AAACTGTCCA
*
3450723 AAAATTACATTTTAACTCC-AAAA-TTTTTC
1 AAAATTACATTTTAAC-CCTAAAACTTTTCC
3450752 AAAATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTAACCCTAAAACTTTTCC
* ** *
3450782 AAAAATACATTTCGACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCTAAAACTTTTCC
* *
3450812 AAAATTACATTTTGACCCTAAAACTTTTCT
1 AAAATTACATTTTAACCCTAAAACTTTTCC
* *
3450842 AATATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTAACCCTAAAACTTTTCC
* * *
3450872 AAAAGTACATTTTAACCCTCAAGC-TTTCC
1 AAAATTACATTTTAACCCTAAAACTTTTCC
3450901 AAAATT
1 AAAATT
3450907 CTATTTTTGA
Statistics
Matches: 136, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
28 2 0.01
29 30 0.22
30 104 0.76
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTAAAACTTTTCC
Found at i:3450974 original size:60 final size:58
Alignment explanation
Indices: 3450867--3451002 Score: 129
Period size: 60 Copynumber: 2.3 Consensus size: 58
3450857 CCCTAAAACT
* * * *
3450867 TTTC-CAAAAGTA-CATTTTAACCCTCAAGCTTTCCAAAATTCTATTTTT-GACCTCGGT
1 TTTCACAAAATTACCATTTTAACCCTCAAGCTTTCAAAAATTCCATTTTTAG-CCTC-GA
* * *
3450924 TTTGC-CAAAATTTACCATTTTACCCCTCGAA-CTTTTAAAAATTCCCTTTTTAGCCTCGA
1 TTT-CACAAAA-TTACCATTTTAACCCTC-AAGCTTTCAAAAATTCCATTTTTAGCCTCGA
3450983 TTTCACAAAATTACCATTTT
1 TTTCACAAAATTACCATTTT
3451003 GTCTCCGAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
57 3 0.05
58 17 0.26
59 11 0.17
60 32 0.48
61 3 0.05
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.40
Consensus pattern (58 bp):
TTTCACAAAATTACCATTTTAACCCTCAAGCTTTCAAAAATTCCATTTTTAGCCTCGA
Found at i:3452762 original size:18 final size:18
Alignment explanation
Indices: 3452739--3452776 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3452729 TAATATAGTT
*
3452739 TTATTCG-GTTTATTTGAA
1 TTATTCGAG-TTATTCGAA
3452757 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
3452775 TT
1 TT
3452777 CGAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:3454003 original size:18 final size:19
Alignment explanation
Indices: 3453961--3454005 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3453951 TGACGTTACT
3453961 TTAAAAAGTAATATTTT-A
1 TTAAAAAGTAATATTTTAA
* * *
3453979 GTAAAAAATAATGTTTTAA
1 TTAAAAAGTAATATTTTAA
3453998 TTAAAAAG
1 TTAAAAAG
3454006 GTGTAACGAC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (19 bp):
TTAAAAAGTAATATTTTAA
Found at i:3454961 original size:2 final size:2
Alignment explanation
Indices: 3454954--3455007 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3454944 TTGAATTTTG
3454954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3454996 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3455008 GTATGTAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3455996 original size:20 final size:19
Alignment explanation
Indices: 3455971--3456010 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3455961 TTAATTTTAT
3455971 TATTA-TATTTTATAATAAAA
1 TATTATTATTTT-TAA-AAAA
3455991 TATTATTATTTTTAAAAAA
1 TATTATTATTTTTAAAAAA
3456010 T
1 T
3456011 TAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 8 0.42
21 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTATTATTTTTAAAAAA
Found at i:3456117 original size:20 final size:18
Alignment explanation
Indices: 3456070--3456111 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3456060 ATGACTCCAC
* *
3456070 TAAAATAAAATATATATT
1 TAAATTAAATTATATATT
3456088 TAAATTAAATTATATATT
1 TAAATTAAATTATATATT
3456106 TAAATT
1 TAAATT
3456112 TTAAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAAATTATATATT
Found at i:3456152 original size:99 final size:100
Alignment explanation
Indices: 3456049--3456242 Score: 291
Period size: 100 Copynumber: 1.9 Consensus size: 100
3456039 AAATTGGTGA
* ** * *
3456049 TGCCATTTAAAATGACTCCA-CTAAAATAAAATATATATTTAAATTAAATTATATATTTAAATTT
1 TGCCATTTAAAATGACTCCACCAAAAATAAAATATATAAATAAATTAAACTATATATTTAAATAT
*
3456113 TAAATAATAAATAAAAAAAACAAAAAAATTAATCG
66 TAAATAAAAAATAAAAAAAACAAAAAAATTAATCG
*
3456148 TGCCATTTAATATGACTCCACCAAAAATAAAATATATAAATAAATTAAACTATATATTTAAATAT
1 TGCCATTTAAAATGACTCCACCAAAAATAAAATATATAAATAAATTAAACTATATATTTAAATAT
* **
3456213 TATATAAAAAATAAAAACCACAAAAAAATT
66 TAAATAAAAAATAAAAAAAACAAAAAAATT
3456243 TTAAATTAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 19 0.23
100 65 0.77
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (100 bp):
TGCCATTTAAAATGACTCCACCAAAAATAAAATATATAAATAAATTAAACTATATATTTAAATAT
TAAATAAAAAATAAAAAAAACAAAAAAATTAATCG
Found at i:3460646 original size:99 final size:99
Alignment explanation
Indices: 3460468--3460665 Score: 290
Period size: 99 Copynumber: 2.0 Consensus size: 99
3460458 ACCACTTTAT
* * * **
3460468 ACAGGTATAGTATAAAGTTGAAAAAAAAATACTGGATTGGGATATAGGATCCAAACTGTCATGAC
1 ACAGGTATAGTACAAAGTTGAAAAAAAAATACTGGATTGAGATATAGGATCCAAACTGCCACAAC
**
3460533 ATGCGTACAGGGATAATGAAGTGTATCGAACCTC
66 ATGCACACAGGGATAATGAAGTGTATCGAACCTC
* *
3460567 ACAGGTATAGTACAAAGTTGAAAAAGAAATA-TGGGATTGAGATATGGGATCCAAACTGCCACAA
1 ACAGGTATAGTACAAAGTTGAAAAAAAAATACT-GGATTGAGATATAGGATCCAAACTGCCACAA
*
3460631 CATGCACACATGGATAATGAAGTGTATCGAACCTC
65 CATGCACACAGGGATAATGAAGTGTATCGAACCTC
3460666 CTACAATCGC
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 1 0.01
99 87 0.99
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (99 bp):
ACAGGTATAGTACAAAGTTGAAAAAAAAATACTGGATTGAGATATAGGATCCAAACTGCCACAAC
ATGCACACAGGGATAATGAAGTGTATCGAACCTC
Found at i:3461447 original size:18 final size:18
Alignment explanation
Indices: 3461417--3461483 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
3461407 TAATATTTTT
*
3461417 TAAA-ATTAAAAATAATA
1 TAAATATTATAAATAATA
*
3461434 CAAATATTATAAATCAA-A
1 TAAATATTATAAAT-AATA
3461452 TAAATATTAGGTATAATAATA
1 TAAATATTA--TA-AATAATA
3461473 TAATATATTAT
1 TAA-ATATTAT
3461484 TATTCGAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
17 3 0.08
18 17 0.43
19 2 0.05
20 5 0.12
21 7 0.17
22 6 0.15
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAATATTATAAATAATA
Found at i:3463032 original size:28 final size:28
Alignment explanation
Indices: 3462992--3463053 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
3462982 TACTTTGATT
*
3462992 GACATGAACATTATTGTCAATGAAAGAG
1 GACATGAACATTATTGTCAATGAAAGAA
*
3463020 GACATGAACATTATTGTCAATGCAAGAA
1 GACATGAACATTATTGTCAATGAAAGAA
3463048 GACATG
1 GACATG
3463054 GGTTTGAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (28 bp):
GACATGAACATTATTGTCAATGAAAGAA
Found at i:3463868 original size:23 final size:23
Alignment explanation
Indices: 3463821--3463869 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3463811 TTACATCCAA
* *
3463821 ATACAATTTTAAAAATTATTTTT
1 ATACAATTATAAAAATTATTATT
3463844 ATACAAGTTATAAAAATTA-TATT
1 ATACAA-TTATAAAAATTATTATT
3463867 ATA
1 ATA
3463870 AGCATAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (23 bp):
ATACAATTATAAAAATTATTATT
Found at i:3467304 original size:21 final size:21
Alignment explanation
Indices: 3467270--3467310 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3467260 AATCTCACGA
*
3467270 TTATAATATCTAATGTTATTT
1 TTATAATATCTAATCTTATTT
3467291 TTATAATAAT-TAATCTTATT
1 TTATAAT-ATCTAATCTTATT
3467311 GTAACCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATAATATCTAATCTTATTT
Found at i:3474485 original size:31 final size:31
Alignment explanation
Indices: 3474450--3474515 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
3474440 TTTAAAAATT
3474450 CTATGAATTAACCTAATAATCAAGATATTCA
1 CTATGAATTAACCTAATAATCAAGATATTCA
* *
3474481 CTATGTATTAACTTAATAATCAAGATATTCA
1 CTATGAATTAACCTAATAATCAAGATATTCA
3474512 CTAT
1 CTAT
3474516 TTTAAATGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (31 bp):
CTATGAATTAACCTAATAATCAAGATATTCA
Found at i:3477156 original size:6 final size:6
Alignment explanation
Indices: 3477145--3477176 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3477135 CATACCTCAT
*
3477145 TTCCTC TTCCTC TTCCTC TTCCTC GTCCTC TT
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TT
3477177 TCACGACCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (6 bp):
TTCCTC
Found at i:3477749 original size:24 final size:24
Alignment explanation
Indices: 3477709--3477768 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
3477699 GTAGTTGTGG
*
3477709 TGCTTGTGCTAATAATGATGGCGC
1 TGCTTGTGCTAACAATGATGGCGC
* * * *
3477733 TGTTTGTGCTGACAATGATTGCGG
1 TGCTTGTGCTAACAATGATGGCGC
3477757 TGCTTGTGCTAA
1 TGCTTGTGCTAA
3477769 TACAGGTTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.37
Consensus pattern (24 bp):
TGCTTGTGCTAACAATGATGGCGC
Found at i:3481839 original size:15 final size:16
Alignment explanation
Indices: 3481814--3481843 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3481804 ATTTTTTTTA
3481814 AAAAGCCCCAAAAAAT
1 AAAAGCCCCAAAAAAT
3481830 AAAA-CCCCAAAAAA
1 AAAAGCCCCAAAAAA
3481844 GGAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.27, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAGCCCCAAAAAAT
Found at i:3484306 original size:25 final size:24
Alignment explanation
Indices: 3484273--3484327 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3484263 AAAAATCAAG
* *
3484273 TTTTAAACAATATAATAATTTATAA
1 TTTTGAACAAAAT-ATAATTTATAA
*
3484298 TTTTGAACAAAATATATTTTATAA
1 TTTTGAACAAAATATAATTTATAA
*
3484322 ATTTGA
1 TTTTGA
3484328 TTTCATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
TTTTGAACAAAATATAATTTATAA
Found at i:3484657 original size:17 final size:17
Alignment explanation
Indices: 3484632--3484664 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3484622 TATAAATATA
*
3484632 TTTATATGTATATAATT
1 TTTACATGTATATAATT
3484649 TTTACATGTATATAAT
1 TTTACATGTATATAAT
3484665 ATATATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTACATGTATATAATT
Found at i:3485019 original size:10 final size:10
Alignment explanation
Indices: 3484990--3485019 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3484980 TAAAACTTCA
3484990 TTTTAATATT
1 TTTTAATATT
3485000 TTTTATATATT
1 TTTTA-ATATT
3485011 TTTTAATAT
1 TTTTAATAT
3485020 GCACGATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTAATATT
Found at i:3490220 original size:21 final size:21
Alignment explanation
Indices: 3490196--3490241 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3490186 TCCCACGAGC
*
3490196 TTTAGA-AAATTTTGTAAGAGA
1 TTTAGATAAATTTCGTAAGA-A
*
3490217 TTTA-ATTAATTTCGTAAGAA
1 TTTAGATAAATTTCGTAAGAA
3490237 TTTAG
1 TTTAG
3490242 TAATTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.43
Consensus pattern (21 bp):
TTTAGATAAATTTCGTAAGAA
Found at i:3490247 original size:19 final size:21
Alignment explanation
Indices: 3490203--3490247 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3490193 AGCTTTAGAA
* *
3490203 AATTTTGTAAGAGATTTAATT
1 AATTTCGTAAGAGATTTAAGT
3490224 AATTTCGTAAGA-ATTT-AGT
1 AATTTCGTAAGAGATTTAAGT
3490243 AATTT
1 AATTT
3490248 TAGTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
21 11 0.50
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (21 bp):
AATTTCGTAAGAGATTTAAGT
Found at i:3492119 original size:23 final size:21
Alignment explanation
Indices: 3492076--3492120 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
3492066 TTTTTCTAAT
*
3492076 TTAAAACTTTAGGTTCATTTG
1 TTAAAACTTCAGGTTCATTTG
*
3492097 TTAAAACTGTCAGAGTTCTTTTG
1 TTAAAACT-TCAG-GTTCATTTG
3492120 T
1 T
3492121 GTTGTGTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.47
Consensus pattern (21 bp):
TTAAAACTTCAGGTTCATTTG
Found at i:3492943 original size:27 final size:28
Alignment explanation
Indices: 3492911--3492975 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
3492901 CCGCCACCAA
* **
3492911 AACCCGAACCGCT-GGCGGAAACGCCAC
1 AACCCGAACCGATCGGAAGAAACGCCAC
*
3492938 AACCCGAACC-ATCGGAAGAAATGCCAC
1 AACCCGAACCGATCGGAAGAAACGCCAC
3492965 AACCCGAACCG
1 AACCCGAACCG
3492976 GCGGTTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.35, C:0.38, G:0.22, T:0.05
Consensus pattern (28 bp):
AACCCGAACCGATCGGAAGAAACGCCAC
Found at i:3492985 original size:27 final size:26
Alignment explanation
Indices: 3492911--3492993 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 26
3492901 CCGCCACCAA
**
3492911 AACCCGAACCGCTGGCGGAAACGCCAC
1 AACCCGAACCGC-GGAAGAAACGCCAC
* *
3492938 AACCCGAACCATCGGAAGAAATGCCAC
1 AACCCGAACC-GCGGAAGAAACGCCAC
** *
3492965 AACCCGAACCGGCGGTTGAAACACCAC
1 AACCCGAACC-GCGGAAGAAACGCCAC
3492992 AA
1 AA
3492994 GCTGATGTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
27 44 0.98
28 1 0.02
ACGTcount: A:0.36, C:0.36, G:0.22, T:0.06
Consensus pattern (26 bp):
AACCCGAACCGCGGAAGAAACGCCAC
Found at i:3493113 original size:12 final size:12
Alignment explanation
Indices: 3493095--3493157 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
3493085 CAGATGTCCA
3493095 AACATATGCTCC
1 AACATATGCTCC
* *
3493107 GACATATCCTCC
1 AACATATGCTCC
**
3493119 AATTTATGCTCC
1 AACATATGCTCC
* *
3493131 AACGTATGC-CGG
1 AACATATGCTC-C
3493143 AACATATGCTCC
1 AACATATGCTCC
3493155 AAC
1 AAC
3493158 GTATCCTCGA
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
11 1 0.03
12 36 0.95
13 1 0.03
ACGTcount: A:0.30, C:0.32, G:0.13, T:0.25
Consensus pattern (12 bp):
AACATATGCTCC
Found at i:3493126 original size:24 final size:24
Alignment explanation
Indices: 3493099--3493184 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 24
3493089 TGTCCAAACA
* * *
3493099 TATGCTCCGACATATCCTCCAATT
1 TATGCTCCAACGTATCCTCGAATT
* **
3493123 TATGCTCCAACGTATGCC-GGAACA
1 TATGCTCCAACGTAT-CCTCGAATT
3493147 TATGCTCCAACGTATCCTCGAATT
1 TATGCTCCAACGTATCCTCGAATT
*
3493171 TATGCTCCGACGTA
1 TATGCTCCAACGTA
3493185 CGCTACAAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 2 0.04
24 46 0.92
25 2 0.04
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (24 bp):
TATGCTCCAACGTATCCTCGAATT
Found at i:3494371 original size:27 final size:29
Alignment explanation
Indices: 3494318--3494371 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
3494308 TTTAATTCAA
* *
3494318 AAAAGTAGAGAGATTAAATTTTTAAAACT
1 AAAAGCAGAGAGATTAAATTTTCAAAACT
3494347 AAAAGCAGAGAGATT-AA-TTTCAAAA
1 AAAAGCAGAGAGATTAAATTTTCAAAA
3494372 TTACGAAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 2 0.09
29 14 0.61
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.26
Consensus pattern (29 bp):
AAAAGCAGAGAGATTAAATTTTCAAAACT
Found at i:3499657 original size:17 final size:20
Alignment explanation
Indices: 3499618--3499657 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
3499608 ACCAATTTTA
*
3499618 AATTTCTTATAAAAATATTT
1 AATTTCTTATAAAAATATCT
3499638 AATTTC-TA-AAAAATA-CT
1 AATTTCTTATAAAAATATCT
3499655 AAT
1 AAT
3499658 GCTCTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 2 0.11
20 6 0.32
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTCTTATAAAAATATCT
Found at i:3506203 original size:17 final size:19
Alignment explanation
Indices: 3506171--3506207 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
3506161 TTTATTATAA
3506171 ATTTTGATCATATATATTT
1 ATTTTGATCATATATATTT
3506190 ATTTTGAT-AT-TATATTT
1 ATTTTGATCATATATATTT
3506207 A
1 A
3506208 AAATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 2 0.11
19 8 0.44
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTTGATCATATATATTT
Found at i:3506997 original size:20 final size:18
Alignment explanation
Indices: 3506959--3506997 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
3506949 ATAATTATTA
*
3506959 AATTCGATTAATTACCCG
1 AATTCGATTAATTAACCG
3506977 AATTCGAATTGAATTAACCG
1 AATTCG-ATT-AATTAACCG
3506997 A
1 A
3506998 TAACCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (18 bp):
AATTCGATTAATTAACCG
Found at i:3507430 original size:40 final size:41
Alignment explanation
Indices: 3507356--3507432 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
3507346 AGAAAATTGG
*
3507356 AATTTCTCATTAAATCTTTCAAAAGTTTTTAATTTTTTGAT
1 AATTTCTCATTAAATCTTTCAAAAGTTTTAAATTTTTTGAT
*
3507397 AATTT-TCGTTAAATCTTT-AAAA-TATTTGAAATTTTT
1 AATTTCTCATTAAATCTTTCAAAAGT-TTT-AAATTTTT
3507433 AATTAGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 1 0.03
39 7 0.22
40 19 0.59
41 5 0.16
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (41 bp):
AATTTCTCATTAAATCTTTCAAAAGTTTTAAATTTTTTGAT
Found at i:3513318 original size:24 final size:24
Alignment explanation
Indices: 3513290--3513336 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3513280 TCATCAGCTT
*
3513290 GTAAGAGCTAAACATTCTTGGCTC
1 GTAAGAGCTAAACATTCTGGGCTC
*
3513314 GTAAGAGCTAACCATTCTGGGCT
1 GTAAGAGCTAAACATTCTGGGCT
3513337 AAATGTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
GTAAGAGCTAAACATTCTGGGCTC
Found at i:3514547 original size:99 final size:99
Alignment explanation
Indices: 3514361--3514611 Score: 276
Period size: 99 Copynumber: 2.5 Consensus size: 99
3514351 TGAGTGTTAC
* * *
3514361 ATACTTTATCCTTCTAGAATTTATTTTTGGCTACTGACTTACAATGTATCAATACATCAATCTTA
1 ATACTTTACCCCTCTAGAAATTATTTTTGGCTACTGACTTACAATGTATCAATACATCAATCTTA
* *
3514426 AGGACTAATATCAATACCTTGATACATGGTATCA
66 AGGACTAATATAAATACCTTGATAAATGGTATCA
* * * *
3514460 ATACTTTACCCCTCTAGAAATTATTTTTGGCTATTGTCTTGA-AATGTA-CTAATTCATCAATTT
1 ATACTTTACCCCTCTAGAAATTATTTTTGGCTACTGACTT-ACAATGTATC-AATACATCAATCT
** * ** *
3514523 TGGGGAC-ATGTATAAATATTTTGATAAATGGTATTA
64 TAAGGACTA-ATATAAATACCTTGATAAATGGTATCA
* * * *
3514559 ATACTTTACCCCTTTA-AAAGTATTTTGGGCTACAGACTTACAATGTATCAATA
1 ATACTTTACCCCTCTAGAAATTATTTTTGGCTACTGACTTACAATGTATCAATA
3514612 TACCAGTCTT
Statistics
Matches: 125, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
97 1 0.01
98 29 0.23
99 94 0.75
100 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (99 bp):
ATACTTTACCCCTCTAGAAATTATTTTTGGCTACTGACTTACAATGTATCAATACATCAATCTTA
AGGACTAATATAAATACCTTGATAAATGGTATCA
Found at i:3545416 original size:17 final size:17
Alignment explanation
Indices: 3545385--3545422 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3545375 GCATATAAAT
3545385 AAAATTTTATATAAC-A
1 AAAATTTTATATAACTA
*
3545401 AAAATTATTATTTAACTA
1 AAAATT-TTATATAACTA
3545419 AAAA
1 AAAA
3545423 AAATCTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 8 0.42
18 5 0.26
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATTTTATATAACTA
Found at i:3548175 original size:6 final size:6
Alignment explanation
Indices: 3548160--3548197 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
3548150 ATTAACATAC
3548160 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA
3548198 GGTATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:3583729 original size:16 final size:15
Alignment explanation
Indices: 3583704--3583733 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3583694 GTAAAAAATA
3583704 ATATAAATTTATAAT
1 ATATAAATTTATAAT
3583719 ATATAATATTTATAA
1 ATATAA-ATTTATAA
3583734 GAAAGAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAAATTTATAAT
Found at i:3592841 original size:55 final size:55
Alignment explanation
Indices: 3592735--3592841 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 55
3592725 ACTAAAACAT
* *
3592735 ATTTTTTAGTCATCCAGCTATGAAAAATTACAAAATGGTCACGCAATTATTCGTA
1 ATTTTTTAGTCATCCAACTATGAAAAATTACAAAATGGTCACGCAACTATTCGTA
* * ** * **
3592790 ATTTTTTTGTCATTCAACTATGAAATGTTATAAAATGGTCACTTAACTATTC
1 ATTTTTTAGTCATCCAACTATGAAAAATTACAAAATGGTCACGCAACTATTC
3592842 AATTTTATCT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (55 bp):
ATTTTTTAGTCATCCAACTATGAAAAATTACAAAATGGTCACGCAACTATTCGTA
Found at i:3593584 original size:18 final size:18
Alignment explanation
Indices: 3593561--3593598 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3593551 AATCAATATT
3593561 TTTTAAATAAA-AAACATG
1 TTTTAAA-AAATAAACATG
*
3593579 TTTTAAAAAATAAAGATG
1 TTTTAAAAAATAAACATG
3593597 TT
1 TT
3593599 AATAGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (18 bp):
TTTTAAAAAATAAACATG
Found at i:3593962 original size:197 final size:198
Alignment explanation
Indices: 3593608--3593976 Score: 431
Period size: 197 Copynumber: 1.9 Consensus size: 198
3593598 TAATAGTTTT
* *
3593608 AAAAAATGTGCATAATTTTCTTTTAATAATCTCATTACATGTCTTGATCATATATGTTTTTTTTA
1 AAAAAATGTGCATAATTTTCTTTGAATAATCTCATTACATGTCTTGATCATATA-GTTTTTTTAA
** * * * * * * *
3593673 CACAATATTTAGAACCATCCATAACTCCTCTTCAACTCATAAATAAAAGGATAATGTAGTTCAAT
65 CACAATACCTAAAACCATCCATAACTCATCTTCAACTCATAAATAAAAGCATAATGCACTCCAAC
* * **
3593738 GCACTCAAACCCATTTTTTTTTGCATTGACAACAATACTCATGCCAATTGAGCTAAAACTCAATC
130 GCACTCAAACCCACTTTCTCGTGCATTGACAACAATACTCATGCCAATTGAGCTAAAACTCAATC
3593803 AACA
195 AACA
* * *
3593807 AAAAAACTGTGCATAATTTT-TTTGAATAGTTTCATTACATGTTTTGATCATATA-TTTTTTTAA
1 AAAAAA-TGTGCATAATTTTCTTTGAATAATCTCATTACATGTCTTGATCATATAGTTTTTTTAA
* * * * * **
3593870 TATAATACCTAAAACTA-CTTATAGCTCAT-TTCCAACTCATAAATAGGAGCATAATGCACTCCA
65 CACAATACCTAAAACCATC-CATAACTCATCTT-CAACTCATAAATAAAAGCATAATGCACTCCA
* *
3593933 ACGCACTCAAACTCACTTTCTCGTGCATTGACAACAATGCTCAT
128 ACGCACTCAAACCCACTTTCTCGTGCATTGACAACAATACTCAT
3593977 TTTAATTAAA
Statistics
Matches: 140, Mismatches: 27, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
196 3 0.02
197 88 0.63
199 36 0.26
200 13 0.09
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (198 bp):
AAAAAATGTGCATAATTTTCTTTGAATAATCTCATTACATGTCTTGATCATATAGTTTTTTTAAC
ACAATACCTAAAACCATCCATAACTCATCTTCAACTCATAAATAAAAGCATAATGCACTCCAACG
CACTCAAACCCACTTTCTCGTGCATTGACAACAATACTCATGCCAATTGAGCTAAAACTCAATCA
ACA
Found at i:3601524 original size:29 final size:31
Alignment explanation
Indices: 3601481--3601541 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
3601471 TGACATGATT
*
3601481 GACTTAATTGA-TTTTT-ATTATTTTACGAG
1 GACTTAATTGATTTTTTAATTATTTTAAGAG
3601510 GACTTAATT-ATTTTTTTAATTATTTTAAGAG
1 GACTTAATTGA-TTTTTTAATTATTTTAAGAG
3601541 G
1 G
3601542 GATTGAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 1 0.04
29 9 0.32
30 5 0.18
31 13 0.46
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.52
Consensus pattern (31 bp):
GACTTAATTGATTTTTTAATTATTTTAAGAG
Found at i:3601649 original size:14 final size:14
Alignment explanation
Indices: 3601630--3601659 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3601620 AACTACACTT
3601630 ATGGTTACTCTAAA
1 ATGGTTACTCTAAA
3601644 ATGGTTACTCTAAA
1 ATGGTTACTCTAAA
3601658 AT
1 AT
3601660 AGAGTTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (14 bp):
ATGGTTACTCTAAA
Found at i:3602493 original size:17 final size:17
Alignment explanation
Indices: 3602471--3602507 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3602461 GTTTTTCCTA
*
3602471 AAATTTAAACTTAATAT
1 AAATTTAAACTTAAAAT
*
3602488 AAATTTAAATTTAAAAT
1 AAATTTAAACTTAAAAT
3602505 AAA
1 AAA
3602508 AATTAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAACTTAAAAT
Found at i:3603606 original size:23 final size:23
Alignment explanation
Indices: 3603562--3603606 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3603552 TCAAAAAGTT
*
3603562 TTTTAAATAAAGTGAAATAAAAG
1 TTTTAAATAAAGTAAAATAAAAG
3603585 TTTTAAATAAAG-AAAATGAAAA
1 TTTTAAATAAAGTAAAAT-AAAA
3603607 AGAAACCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (23 bp):
TTTTAAATAAAGTAAAATAAAAG
Found at i:3604437 original size:30 final size:30
Alignment explanation
Indices: 3604362--3604458 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
3604352 AAAAACTATT
*
3604362 TTTTGACCCTAAAAC-TTTAAAAATTTACA
1 TTTTGACCCCAAAACTTTTAAAAATTTACA
* * **
3604391 TTTTAACCTCTGAACTTTTAAAAA-TTACTA
1 TTTTGACCCCAAAACTTTTAAAAATTTAC-A
* **
3604421 TTTTGACCCCCAAACTTTCCAAAATTT-CA
1 TTTTGACCCCAAAACTTTTAAAAATTTACA
3604450 TTTTTGACC
1 -TTTTGACC
3604459 TCGATTTCAC
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
29 15 0.28
30 36 0.68
31 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (30 bp):
TTTTGACCCCAAAACTTTTAAAAATTTACA
Found at i:3604519 original size:54 final size:54
Alignment explanation
Indices: 3604426--3604592 Score: 178
Period size: 54 Copynumber: 3.0 Consensus size: 54
3604416 TACTATTTTG
* *
3604426 ACCCCCAAACTTTCCAAAATT-TCATTTTTGACCTCGATTTCACCAAAAATTACC
1 ACCCCCGAACCTTCCAAAATTCT-ATTTTTGACCTCGATTTCACCAAAAATTACC
* *
3604480 A-CCTCGAACCTTCCAAAATTCTATTTTTTGACCTCGATTTCATCAAAAATTACC
1 ACCCCCGAACCTTCCAAAATTCTA-TTTTTGACCTCGATTTCACCAAAAATTACC
* * * *
3604534 ATTTTACCCCCGAACCTTCCAAAATCCCA-TTTTAACCCCGATTTCACCAAAAATTACC
1 -----ACCCCCGAACCTTCCAAAATTCTATTTTTGACCTCGATTTCACCAAAAATTACC
3604592 A
1 A
3604593 TTTTACACCC
Statistics
Matches: 95, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
53 18 0.19
54 31 0.33
58 26 0.27
59 1 0.01
60 19 0.20
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (54 bp):
ACCCCCGAACCTTCCAAAATTCTATTTTTGACCTCGATTTCACCAAAAATTACC
Found at i:3604585 original size:58 final size:58
Alignment explanation
Indices: 3604475--3604661 Score: 221
Period size: 58 Copynumber: 3.2 Consensus size: 58
3604465 TCACCAAAAA
* * *
3604475 TTACCACCTCGAACCTTCCAAAATTCTATTTTTTGACCTCGATTTCATCAAAAATTACCATT
1 TTACC-CC-CGAACCTTCCAAAATTCCA--TTTTAACCTCGATTTCACCAAAAATTACCATT
* *
3604537 TTACCCCCGAACCTTCCAAAATCCCATTTTAACCCCGATTTCACCAAAAATTACCATT
1 TTACCCCCGAACCTTCCAAAATTCCATTTTAACCTCGATTTCACCAAAAATTACCATT
* * * * * * *
3604595 TTACACCCAAACTTTCCAAAATTTCATTTTAACCTCAATTTTACAAAAAATTACCATT
1 TTACCCCCGAACCTTCCAAAATTCCATTTTAACCTCGATTTCACCAAAAATTACCATT
*
3604653 TTGCCCCCG
1 TTACCCCCG
3604662 GGTGTCCAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
58 84 0.78
60 17 0.16
61 2 0.02
62 5 0.05
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (58 bp):
TTACCCCCGAACCTTCCAAAATTCCATTTTAACCTCGATTTCACCAAAAATTACCATT
Found at i:3604596 original size:30 final size:29
Alignment explanation
Indices: 3604505--3604654 Score: 87
Period size: 30 Copynumber: 5.1 Consensus size: 29
3604495 AAATTCTATT
* * *
3604505 TTTTGACCTCGATTTCATCAAAAATTACCA
1 TTTTAACCCCGATTT-ACCAAAAATTACCA
* * *
3604535 TTTTACCCCCGAACCTT-CC-AAAA-TCCCA
1 TTTTAACCCCG-A-TTTACCAAAAATTACCA
3604563 TTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTAACCCCGATTT-ACCAAAAATTACCA
** *
3604593 TTTTACACCCAAACTTT-CC-AAAATT-TCA
1 TTTTA-ACCCCGA-TTTACCAAAAATTACCA
* * *
3604621 TTTTAACCTCAATTTTACAAAAAATTACCA
1 TTTTAACCCCGA-TTTACCAAAAATTACCA
3604651 TTTT
1 TTTT
3604655 GCCCCCGGGT
Statistics
Matches: 92, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
26 2 0.02
27 9 0.10
28 24 0.26
29 20 0.22
30 26 0.28
31 6 0.07
32 5 0.05
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.35
Consensus pattern (29 bp):
TTTTAACCCCGATTTACCAAAAATTACCA
Found at i:3604615 original size:29 final size:29
Alignment explanation
Indices: 3604525--3604625 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 29
3604515 GATTTCATCA
* * *
3604525 AAAATTACCATTTTACCCCCGAACCTTCC
1 AAAATTACCATTTTACACCCAAACTTTCC
* **
3604554 AAAA-TCCCATTTTA-ACCCCGA-TTTCACC
1 AAAATTACCATTTTACACCCAAACTTT--CC
3604582 AAAAATTACCATTTTACACCCAAACTTTCC
1 -AAAATTACCATTTTACACCCAAACTTTCC
*
3604612 AAAATT-TCATTTTA
1 AAAATTACCATTTTA
3604626 ACCTCAATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
26 2 0.04
27 4 0.07
28 18 0.32
29 14 0.25
30 11 0.19
31 5 0.09
32 3 0.05
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACACCCAAACTTTCC
Found at i:3613068 original size:72 final size:69
Alignment explanation
Indices: 3612916--3613055 Score: 221
Period size: 72 Copynumber: 2.0 Consensus size: 69
3612906 AAAACAAAAA
*
3612916 TTCAAATAGAAGAATAGAAAACAGCTCCTGTTCTTAGCTTTTTTTTTTTTTTTTTAAATTATAAG
1 TTCAAATAGAAGAATAGAAAACAGCTCCTGTTCTTAGC---TTTCTTTTTTTTTTAAATTATAAG
*
3612981 AGGAGGG
63 AAGAGGG
3612988 TTCAAATAGAAGAATAGAAAACAGCTCCTGTTCTTAGC-TTCTTTTTTTTTT-AATTATAAGAAG
1 TTCAAATAGAAGAATAGAAAACAGCTCCTGTTCTTAGCTTTCTTTTTTTTTTAAATTATAAGAAG
3613051 AGGG
66 AGGG
3613055 T
1 T
3613056 AAAATCTTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
67 16 0.24
68 12 0.18
72 38 0.58
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (69 bp):
TTCAAATAGAAGAATAGAAAACAGCTCCTGTTCTTAGCTTTCTTTTTTTTTTAAATTATAAGAAG
AGGG
Found at i:3614388 original size:6 final size:6
Alignment explanation
Indices: 3614361--3614412 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
3614351 GGCTAGGACT
* * *
3614361 TTTAAA GTTTAAA -TTAAT TTTAAA TTTAAA TTT-AT TTTAGA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3614408 TTTAA
1 TTTAA
3614413 TCAAATTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
5 8 0.22
6 23 0.62
7 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:3614410 original size:17 final size:17
Alignment explanation
Indices: 3614360--3614411 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
3614350 GGGCTAGGAC
*
3614360 TTTTAAAGTTTAAATTAA
1 TTTTAAA-TTTAAATTTA
3614378 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
3614395 TTTTAGATTTAAATTTA
1 TTTTAAATTTAAATTTA
3614412 ATCAAATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 25 0.78
18 7 0.22
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:3615238 original size:16 final size:16
Alignment explanation
Indices: 3615213--3615244 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3615203 AGCATTAAAG
3615213 ATATTATTAATAATAA
1 ATATTATTAATAATAA
*
3615229 ATATTTTTAATAATAA
1 ATATTATTAATAATAA
3615245 TAAATGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTATTAATAATAA
Found at i:3615244 original size:19 final size:19
Alignment explanation
Indices: 3615220--3615284 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
3615210 AAGATATTAT
3615220 TAATAATAAATATTTTTAA
1 TAATAATAAATATTTTTAA
*
3615239 TAATAATAAATGTTTTACTAA
1 TAATAATAAATATTTT--TAA
3615260 TAATAATATTAATA--TTTAA
1 TAATAATA--AATATTTTTAA
3615279 TAATAA
1 TAATAA
3615285 AAAAAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 24 0.60
21 13 0.32
23 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
TAATAATAAATATTTTTAA
Found at i:3615260 original size:18 final size:19
Alignment explanation
Indices: 3615220--3615284 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 19
3615210 AAGATATTAT
*
3615220 TAATAATAAATATTTTTAA
1 TAATAATAAATAGTTTTAA
*
3615239 TAATAATAAAT-GTTTTAC
1 TAATAATAAATAGTTTTAA
*
3615257 TAATAATAATATTAATATTTAA
1 TAATAATAA-A-TAGT-TTTAA
3615279 TAATAA
1 TAATAA
3615285 AAAAAGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 14 0.37
19 12 0.32
20 1 0.03
21 1 0.03
22 10 0.26
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
TAATAATAAATAGTTTTAA
Found at i:3616442 original size:30 final size:29
Alignment explanation
Indices: 3616366--3616719 Score: 189
Period size: 29 Copynumber: 12.1 Consensus size: 29
3616356 ATTTATAGGT
** * * *
3616366 CCCCAAACAGTCCATAAATTGCATTTTGA
1 CCCCAAACTTTCCAAAAATTCCATTTTAA
* * **
3616395 CCCTAAAATTTTAAAAAATTCCATTTTTAA
1 CCCCAAACTTTCCAAAAATTCCA-TTTTAA
* * *
3616425 CCCCAAAATTGCCAAAAATTACCA-TTTAC
1 CCCCAAACTTTCCAAAAATT-CCATTTTAA
*
3616454 CCCCAAACTTTCC-AAAATTCTATTTTAA
1 CCCCAAACTTTCCAAAAATTCCATTTTAA
* * *
3616482 CCCC-GATTTTACCAAAAATTACCATTTTAC
1 CCCCAAACTTT-CCAAAAATT-CCATTTTAA
* *
3616512 CCCCGAACTTTCC-AAAATTCCATTTTTGAT
1 CCCCAAACTTTCCAAAAATTCCA-TTTT-AA
*
3616542 CCCGAAAC-TTCCAAAAATTACCATTTT-A
1 CCCCAAACTTTCCAAAAATT-CCATTTTAA
*
3616570 CCCCTGAACTTTCC-AAAATTCCATTTTAA
1 CCCC-AAACTTTCCAAAAATTCCATTTTAA
* *
3616599 CCTC-GA-TTTCACCAAAAATTACCATTTT-A
1 CCCCAAACTTT--CCAAAAATT-CCATTTTAA
* * *
3616628 CCCCTGAACCTTCC-AAAATTTCATTTTTAA
1 CCCC-AAACTTTCCAAAAATTCCA-TTTTAA
* *
3616658 CCTC-AA-TTTCACCAAAATTACCATTTT-A
1 CCCCAAACTTTC-CAAAAATT-CCATTTTAA
* *
3616686 CCCCTAAA-TTTTCTAAAATTCCATTTTCAA
1 CCCC-AAACTTTCCAAAAATTCCATTTT-AA
3616716 CCCC
1 CCCC
3616720 GATTTCACCA
Statistics
Matches: 253, Mismatches: 42, Indels: 59
0.71 0.12 0.17
Matches are distributed among these distances:
26 3 0.01
27 10 0.04
28 47 0.19
29 100 0.40
30 80 0.32
31 11 0.04
32 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCCAAACTTTCCAAAAATTCCATTTTAA
Found at i:3616479 original size:58 final size:58
Alignment explanation
Indices: 3616409--3616748 Score: 393
Period size: 58 Copynumber: 5.8 Consensus size: 58
3616399 AAAATTTTAA
* * **
3616409 AAAATTCCATTTTTAACCCCAAAATTGCCAAAAATTACCA-TTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTAACCCC-AATTTACCAAAAATTACCATTTTACCCCTGAACTTTCC
* * *
3616467 AAAATTCTA-TTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCCGAACTTTCC
1 AAAATTCCATTTTTAACCCC-AATTTACCAAAAATTACCATTTTACCCCTGAACTTTCC
* * *
3616525 AAAATTCCATTTTTGATCCCGAAACTT-CCAAAAATTACCATTTTACCCCTGAACTTTCC
1 AAAATTCCATTTTT-AACCC-CAATTTACCAAAAATTACCATTTTACCCCTGAACTTTCC
* * *
3616584 AAAATTCCA-TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTGAACCTTCC
1 AAAATTCCATTTTTAACCCCAATTT-ACCAAAAATTACCATTTTACCCCTGAACTTTCC
* * * * *
3616642 AAAATTTCATTTTTAACCTCAATTTCACC-AAAATTACCATTTTACCCCTAAATTTTCT
1 AAAATTCCATTTTTAACCCCAATTT-ACCAAAAATTACCATTTTACCCCTGAACTTTCC
* * *
3616700 AAAATTCCATTTTCAACCCCGATTTCACCAAAAATTACCATTTTGCCCC
1 AAAATTCCATTTTTAACCCCAATTT-ACCAAAAATTACCATTTTACCCC
3616749 CGGGTATCCA
Statistics
Matches: 245, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
56 3 0.01
57 29 0.12
58 126 0.51
59 80 0.33
60 7 0.03
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCCAATTTACCAAAAATTACCATTTTACCCCTGAACTTTCC
Found at i:3616597 original size:117 final size:115
Alignment explanation
Indices: 3616409--3616750 Score: 472
Period size: 117 Copynumber: 2.9 Consensus size: 115
3616399 AAAATTTTAA
*
3616409 AAAATTCCATTTTTAACCCCAAAATTGCCAAAAATTACCA-TTTACCCCCAAACTTTCCAAAATT
1 AAAATTCCATTTTTAA-CCCAAAATT-CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATT
* * *
3616473 CTATTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCCGAACTTTCC
64 CCATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACCTTCC
* * *
3616525 AAAATTCCATTTTTGATCCCGAAACTTCCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATT
1 AAAATTCCATTTTT-AACCC-AAAATTCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATT
* *
3616590 CCATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTGAACCTTCC
64 CCATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACCTTCC
* * * * *
3616642 AAAATTTCATTTTTAACCTC-AATTTCACCAAAATTACCATTTTACCCCTAAATTTTCTAAAATT
1 AAAATTCCATTTTTAACC-CAAAATTC-CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATT
*
3616706 CCATTTTCAACCCCGATTTCACCAAAAATTACCATTTTGCCCCCG
64 CCATTTT-AACCCCGATTTCACCAAAAATTACCATTTTACCCCCG
3616751 GGTATCCAAA
Statistics
Matches: 201, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
115 5 0.02
116 73 0.36
117 123 0.61
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (115 bp):
AAAATTCCATTTTTAACCCAAAATTCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCC
ATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACCTTCC
Found at i:3628678 original size:76 final size:76
Alignment explanation
Indices: 3628453--3629272 Score: 1288
Period size: 76 Copynumber: 10.8 Consensus size: 76
3628443 ATCAGACCGC
* * *
3628453 AGCAAGATCATTCCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACA-TTTTTATCTCTGA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA-AGTCTTTATCTCTGA
3628516 AATTGAAGTAAG
65 AATTGAAGTAAG
* * *
3628528 ACCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
3628592 ATTGAAGTAAG
66 ATTGAAGTAAG
* * *
3628603 AGCAAGATCATTTCGTATTCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
3628668 ATTGAAGTAAG
66 ATTGAAGTAAG
** * * *
3628679 AGCAAGATCGTTTCCCGTCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
* *
3628744 ATTAAAGTAAA
66 ATTGAAGTAAG
* *
3628755 AGCAAGATCTTTTCCTATCCGT-TTGAAATTGAAGTAGAGTTGGATAACAAGCCTTTATCTCTGA
1 AGCAAGATCGTTTCCTATCC-TCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
3628819 AATTGAAGTAAG
65 AATTGAAGTAAG
* *
3628831 AGCAAGATTGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
3628896 ATTGAAGTAAG
66 ATTGAAGTAAG
*
3628907 AGCAAGATCGTTTCCTATCCTATTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
3628972 ATTGAAGTAAG
66 ATTGAAGTAAG
* * ** *
3628983 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
3629048 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
3629059 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
3629124 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
3629135 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTTTGAA
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
3629200 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * *
3629211 AGCAAGATCGTTTCCCATCTTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCT
1 AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCT
3629273 CTGAAGAGCA
Statistics
Matches: 684, Mismatches: 57, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
75 105 0.15
76 578 0.85
77 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (76 bp):
AGCAAGATCGTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
ATTGAAGTAAG
Found at i:3629579 original size:6 final size:6
Alignment explanation
Indices: 3629541--3629620 Score: 62
Period size: 6 Copynumber: 13.8 Consensus size: 6
3629531 GGCTTGGGCT
* **
3629541 TTTAAA GTTTAAA -TTAAT TTTAAA TTT-GT TTTAAA TTTAAA TTT--A
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
3629586 TCTTAAA TTTAAA TTT-AT TTTAGA TTTAAA TTTAA
1 T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
3629621 TCAAATTCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
4 2 0.04
5 13 0.23
6 34 0.60
7 8 0.14
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:3629579 original size:17 final size:17
Alignment explanation
Indices: 3629554--3629619 Score: 96
Period size: 17 Copynumber: 3.9 Consensus size: 17
3629544 AAAGTTTAAA
* *
3629554 TTAATTTTAAATTTGTT
1 TTAAATTTAAATTTATT
*
3629571 TTAAATTTAAATTTATC
1 TTAAATTTAAATTTATT
3629588 TTAAATTTAAATTTATT
1 TTAAATTTAAATTTATT
*
3629605 TTAGATTTAAATTTA
1 TTAAATTTAAATTTA
3629620 ATCAAATTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (17 bp):
TTAAATTTAAATTTATT
Found at i:3629582 original size:28 final size:29
Alignment explanation
Indices: 3629540--3629595 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
3629530 GGGCTTGGGC
*
3629540 TTTTAAAGTTTAAATTAATTTTAAATTTG
1 TTTTAAAGTTTAAATTAATCTTAAATTTG
*
3629569 TTTTAAA-TTTAAATTTATCTTAAATTT
1 TTTTAAAGTTTAAATTAATCTTAAATTT
3629596 AAATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTAAAGTTTAAATTAATCTTAAATTTG
Found at i:3629612 original size:11 final size:11
Alignment explanation
Indices: 3629548--3629613 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
3629538 GCTTTTAAAG
*
3629548 TTTAAATTAAT
1 TTTAAATTTAT
*
3629559 TTTAAATTTGT
1 TTTAAATTTAT
*
3629570 TTTAAATTTAAA
1 TTTAAATTT-AT
** * *
3629582 TTTATCTTAAA
1 TTTAAATTTAT
3629593 TTTAAATTTAT
1 TTTAAATTTAT
*
3629604 TTTAGATTTA
1 TTTAAATTTA
3629614 AATTTAATCA
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
11 36 0.86
12 6 0.14
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:3630671 original size:30 final size:28
Alignment explanation
Indices: 3630622--3630692 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 28
3630612 AAAATTTTAG
3630622 AAATTCCATTTTTGA-CCTCGAAAC-TTCCAA
1 AAATTCCA-TTTT-ACCCTCG-AACTTTCC-A
3630652 AAATTACCATTTTACCCTCGAACTTTCCA
1 AAATT-CCATTTTACCCTCGAACTTTCCA
3630681 AAATTCCATTTT
1 AAATTCCATTTT
3630693 TAATCCCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
28 7 0.18
29 10 0.26
30 18 0.47
31 3 0.08
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (28 bp):
AAATTCCATTTTACCCTCGAACTTTCCA
Found at i:3630685 original size:29 final size:29
Alignment explanation
Indices: 3630637--3630784 Score: 89
Period size: 29 Copynumber: 5.1 Consensus size: 29
3630627 CCATTTTTGA
3630637 CCTCGAAAC-TTCCAAAAATTACCATTTTAC
1 CCTCG-AACTTTCC-AAAATTACCATTTTAC
*
3630667 CCTCGAACTTTCCAAAATT-CCATTTTTAAT
1 CCTCGAACTTTCCAAAATTACCA-TTTT-AC
* *
3630697 CC-CG-A-TTTCACCAAAACTACCATTTTTC
1 CCTCGAACTTT--CCAAAATTACCATTTTAC
* *
3630725 CC-CTAAACTTTCCAAAATT-CCATTTTTAA
1 CCTC-GAACTTTCCAAAATTACCA-TTTTAC
*
3630754 CATCG-A-TTTCACCAAAATTACCATTTTAC
1 CCTCGAACTTT--CCAAAATTACCATTTTAC
3630783 CC
1 CC
3630785 CTAAATTTTC
Statistics
Matches: 92, Mismatches: 12, Indels: 29
0.69 0.09 0.22
Matches are distributed among these distances:
27 6 0.07
28 11 0.12
29 52 0.57
30 20 0.22
31 3 0.03
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.34
Consensus pattern (29 bp):
CCTCGAACTTTCCAAAATTACCATTTTAC
Found at i:3630739 original size:58 final size:57
Alignment explanation
Indices: 3630651--3630828 Score: 223
Period size: 58 Copynumber: 3.1 Consensus size: 57
3630641 GAAACTTCCA
* *
3630651 AAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAATCCCGATTTCACC
1 AAAACTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAA-CCCGATTTCACC
* *
3630709 AAAACTACCATTTTTCCCCTAAACTTTCCAAAATTCCATTTTTAACATCGATTTCACC
1 AAAACTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAAC-CCGATTTCACC
* * * * * *
3630767 AAAATTACCATTTTACCCCTAAATTTTCTAAAATTCTATTTTCAACCCTGATTTCACG
1 AAAACTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCC-GATTTCACC
3630825 AAAA
1 AAAA
3630829 ATTATCATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
57 2 0.02
58 99 0.94
59 4 0.04
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (57 bp):
AAAACTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCGATTTCACC
Found at i:3647441 original size:32 final size:32
Alignment explanation
Indices: 3647400--3647469 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
3647390 TTTGGTTCGC
*
3647400 TGTAATGGAATAGAAGTGTAATGGAATAGAGT
1 TGTAATGGAATAGAACTGTAATGGAATAGAGT
3647432 TGTAATGGAATAGAACTGTAATGGAATAGAGT
1 TGTAATGGAATAGAACTGTAATGGAATAGAGT
3647464 TGTAAT
1 TGTAAT
3647470 CAGTAATTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.40, C:0.01, G:0.29, T:0.30
Consensus pattern (32 bp):
TGTAATGGAATAGAACTGTAATGGAATAGAGT
Found at i:3647467 original size:16 final size:16
Alignment explanation
Indices: 3647400--3647469 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
3647390 TTTGGTTCGC
3647400 TGTAATGGAATAGAAG-
1 TGTAATGGAATAG-AGT
3647416 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGT
**
3647432 TGTAATGGAATAGAAC
1 TGTAATGGAATAGAGT
3647448 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGT
3647464 TGTAAT
1 TGTAAT
3647470 CAGTAATTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
15 2 0.04
16 47 0.96
ACGTcount: A:0.40, C:0.01, G:0.29, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:3647709 original size:58 final size:59
Alignment explanation
Indices: 3647640--3647785 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 59
3647630 AATTTTAATG
* *
3647640 ATTATTATTAAATATAATTTAATAAAAATATTAAT-TAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAAT-ATGTAATTTAATAATATTTTTAACATA
* *
3647698 ATTATTATTAAATACAATTTAAT-AAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATGTAATTTAATAATATTTTTAACATA
* *
3647756 CTTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
3647786 TATAATATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
56 2 0.03
57 19 0.25
58 39 0.51
59 9 0.12
60 7 0.09
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATGTAATTTAATAATATTTTTAACATA
Found at i:3647788 original size:25 final size:24
Alignment explanation
Indices: 3647759--3647809 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
3647749 TAATATACTT
*
3647759 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
3647784 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
3647808 AT
1 AT
3647810 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:3653668 original size:20 final size:20
Alignment explanation
Indices: 3653635--3653674 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3653625 TATCTCGACC
3653635 AAAATATATCATAT-TATAA
1 AAAATATATCATATATATAA
*
3653654 AAAATAATATTATATATATAA
1 AAAAT-ATATCATATATATAA
3653675 TCTAATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATATATCATATATATAA
Found at i:3655068 original size:20 final size:19
Alignment explanation
Indices: 3655040--3655077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3655030 ACATAATATA
*
3655040 TCCTTTGTGTTTTAATTACT
1 TCCTATGTGTTTT-ATTACT
3655060 TCCTATGTGTTTTATTAC
1 TCCTATGTGTTTTATTAC
3655078 ATAATCGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.58
Consensus pattern (19 bp):
TCCTATGTGTTTTATTACT
Found at i:3656084 original size:29 final size:30
Alignment explanation
Indices: 3656017--3656081 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
3656007 TTAATAGTTT
* *
3656017 ATTTTTATAATTTTTAAAGAATTAAATTAA
1 ATTTTTATTATTTTTAAAGAATTAAAATAA
3656047 ATTTTTATTATTTTTAAA-AATTAAAATATA
1 ATTTTTATTATTTTTAAAGAATTAAAATA-A
3656077 ATTTT
1 ATTTT
3656082 ATTTTTACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
ATTTTTATTATTTTTAAAGAATTAAAATAA
Found at i:3660817 original size:19 final size:19
Alignment explanation
Indices: 3660793--3660833 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3660783 AATTTAACAG
* *
3660793 GGTTTATTGTTTGGATGGT
1 GGTTTATTGATTGGATAGT
3660812 GGTTTATTGATTGGATAGT
1 GGTTTATTGATTGGATAGT
3660831 GGT
1 GGT
3660834 ACTGATAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.49
Consensus pattern (19 bp):
GGTTTATTGATTGGATAGT
Found at i:3668771 original size:21 final size:20
Alignment explanation
Indices: 3668717--3668767 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
3668707 TTATAAATTT
* * *
3668717 TTTATTTAATAATAAAAATC
1 TTTAGTTAATAATAAAGAGC
3668737 TTTAGTATAATAATAAAGAGC
1 TTTAGT-TAATAATAAAGAGC
3668758 TTTAGTTAAT
1 TTTAGTTAAT
3668768 TAATCAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (20 bp):
TTTAGTTAATAATAAAGAGC
Found at i:3668776 original size:21 final size:21
Alignment explanation
Indices: 3668723--3668776 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3668713 ATTTTTTATT
* *
3668723 TAATAATAAAAATCTTTAGTA
1 TAATAATAAAGAGCTTTAGTA
3668744 TAATAATAAAGAGCTTTAGT-
1 TAATAATAAAGAGCTTTAGTA
*
3668764 TAATTAATCAAGA
1 TAA-TAATAAAGA
3668777 AATAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (21 bp):
TAATAATAAAGAGCTTTAGTA
Found at i:3672200 original size:29 final size:29
Alignment explanation
Indices: 3672168--3672449 Score: 211
Period size: 29 Copynumber: 9.7 Consensus size: 29
3672158 TGACTTTCGA
3672168 GGGTAAAAAT-GTAATTTTTGGTGAAATCG
1 GGGTAAAAATGGTAA-TTTTGGTGAAATCG
* *
3672197 GGGTCGAAAAT-G-AGATTTTAG-GAAATTCG
1 GGGT-AAAAATGGTA-ATTTTGGTGAAA-TCG
3672226 AGGAGT-AAAATGGTAATTTTGGTGAAATCG
1 -GG-GTAAAAATGGTAATTTTGGTGAAATCG
* *
3672256 GGGTTAAAAATGG-GATTTT-G-GAAGTTCG
1 GGG-TAAAAATGGTAATTTTGGTGAA-ATCG
*
3672284 AGGGTAAAAATGGTAATTTTTGGTGAAACCG
1 -GGGTAAAAATGGTAA-TTTTGGTGAAATCG
*
3672315 GGGTTAAAATGGT-ATTTT-G-GAAAGTTCG
1 GGGTAAAAATGGTAATTTTGGTGAAA--TCG
*
3672343 GGGT-AAAATGGTAATTTTTGGTGAAACCG
1 GGGTAAAAATGGTAA-TTTTGGTGAAATCG
*
3672372 GGGTTAAAATGGT-ATTTT-G-GAAAGTTCG
1 GGGTAAAAATGGTAATTTTGGTGAAA--TCG
3672400 GGGT-AAAATGGTAATTTTTGGTGAAATCG
1 GGGTAAAAATGGTAA-TTTTGGTGAAATCG
*
3672429 GGGTTAAAAATGG-GATTTTGG
1 GGG-TAAAAATGGTAATTTTGG
3672450 AAGTTTAGGG
Statistics
Matches: 209, Mismatches: 13, Indels: 62
0.74 0.05 0.22
Matches are distributed among these distances:
26 8 0.04
27 21 0.10
28 40 0.19
29 58 0.28
30 54 0.26
31 25 0.12
32 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGGTAATTTTGGTGAAATCG
Done.