Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 7 of 193
Found at i:2487559 original size:36 final size:36
Alignment explanation
Indices: 2487480--2487559 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
2487470 TTCGCACGTG
* * **
2487480 CACATACATACACACATGGACATGCACATACATTCA
1 CACATACATACACACACGGACATGCACACACACACA
* *
2487516 TAAATACATACACACACGTG-CATGCACACACACACA
1 CACATACATACACACACG-GACATGCACACACACACA
2487552 CACATACA
1 CACATACA
2487560 CATTCAAGCA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.16
Consensus pattern (36 bp):
CACATACATACACACACGGACATGCACACACACACA
Found at i:2492556 original size:35 final size:32
Alignment explanation
Indices: 2492501--2492566 Score: 78
Period size: 35 Copynumber: 2.0 Consensus size: 32
2492491 ATAACATTTA
* *
2492501 AACAACAAAAACAACTAAAATAGCAGCAAAAT
1 AACAACAAAAACAACAAAAATAACAGCAAAAT
*
2492533 AACAACAAAAACAATAACAAAAATAACAGTAAAA
1 AACAACAAAAAC---AACAAAAATAACAGCAAAA
2492567 AAAGCACCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 12 0.43
35 16 0.57
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.09
Consensus pattern (32 bp):
AACAACAAAAACAACAAAAATAACAGCAAAAT
Found at i:2494394 original size:2 final size:2
Alignment explanation
Indices: 2494387--2494419 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2494377 TTGCTCTAAA
2494387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2494420 GTTAGCTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2504874 original size:30 final size:31
Alignment explanation
Indices: 2504823--2504884 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
2504813 AAGGTTACAA
2504823 ATTGAACTATTGAAAAGTTTTTATTTAAGTC
1 ATTGAACTATTGAAAAGTTTTTATTTAAGTC
*
2504854 ATTGAACTATTG-AGAGTTTTTATTTAAGTC
1 ATTGAACTATTGAAAAGTTTTTATTTAAGTC
2504884 A
1 A
2504885 CTCAATTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (31 bp):
ATTGAACTATTGAAAAGTTTTTATTTAAGTC
Found at i:2516326 original size:30 final size:28
Alignment explanation
Indices: 2516292--2516351 Score: 68
Period size: 31 Copynumber: 2.1 Consensus size: 28
2516282 CTTCATACTT
*
2516292 TTTA-TTAAAAAAACGATATTCATAATATAA
1 TTTATTTAAAAAAAC-ATA-ACATAATA-AA
*
2516322 TTTATTTAAAGAAACATAACATAATAAA
1 TTTATTTAAAAAAACATAACATAATAAA
2516350 TT
1 TT
2516352 CAAGGATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 7 0.26
30 7 0.26
31 9 0.33
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (28 bp):
TTTATTTAAAAAAACATAACATAATAAA
Found at i:2520472 original size:10 final size:10
Alignment explanation
Indices: 2520440--2520476 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2520430 TCATTCAATC
2520440 TAAAATT-TA
1 TAAAATTATA
2520449 T-AAATTAT-
1 TAAAATTATA
2520457 TAAAATTATA
1 TAAAATTATA
2520467 TAAAATTATA
1 TAAAATTATA
2520477 AAGTCCAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.24
9 9 0.36
10 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TAAAATTATA
Found at i:2525254 original size:6 final size:6
Alignment explanation
Indices: 2525218--2525325 Score: 80
Period size: 6 Copynumber: 18.0 Consensus size: 6
2525208 TTAAATTGAT
* * * *
2525218 TTTAAA TTT--A TTTGAA TTTAGA TTT-AT TTTAAA TTTAAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA-A
* ** *
2525265 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
2525313 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
2525326 AGTCCAAATG
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 49 0.60
7 21 0.26
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:2525274 original size:31 final size:31
Alignment explanation
Indices: 2525233--2525295 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2525223 ATTTATTTGA
* *
2525233 ATTTAGATTTATTTTAAATTTAAAATTAAAT
1 ATTTAAATTTAATTTAAATTTAAAATTAAAT
* *
2525264 ATTTAAATTTAATTTGAATTTAAATTTAAAT
1 ATTTAAATTTAATTTAAATTTAAAATTAAAT
2525295 A
1 A
2525296 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTTAAATTTAATTTAAATTTAAAATTAAAT
Found at i:2525283 original size:11 final size:11
Alignment explanation
Indices: 2525208--2525294 Score: 52
Period size: 11 Copynumber: 7.5 Consensus size: 11
2525198 GACTTTTGAG
* *
2525208 TTAAATTGATT
1 TTAAATTTAAT
2525219 TTAAATTT-AT
1 TTAAATTTAAT
*
2525229 TTGAATTTAGAT
1 TTAAATTTA-AT
*
2525241 TT-ATTTTAAAT
1 TTAAATTT-AAT
*
2525252 TTAAAATTAAATAT
1 TT-AAATT-TA-AT
2525266 TTAAATTTAAT
1 TTAAATTTAAT
*
2525277 TTGAATTTAAAT
1 TTAAATTT-AAT
2525289 TTAAAT
1 TTAAAT
2525295 AAAAATTAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
10 8 0.14
11 24 0.41
12 14 0.24
13 9 0.15
14 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:2525304 original size:48 final size:48
Alignment explanation
Indices: 2525218--2525324 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
2525208 TTAAATTGAT
* ** * *
2525218 TTTAAATTT-ATTTGAATTTAGATTTATTTTAAATTTAAAAT-TAAATA
1 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATATAAA-A
*
2525265 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATATTAAA
1 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATATAAAA
2525313 TTTAACATTTAA
1 TTTAA-ATTTAA
2525325 AAGTCCAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
47 9 0.18
48 33 0.65
49 9 0.18
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.49
Consensus pattern (48 bp):
TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATATAAAA
Found at i:2525315 original size:31 final size:30
Alignment explanation
Indices: 2525245--2525325 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
2525235 TTAGATTTAT
* * *
2525245 TTTAAATTTAAAATTAAATATTTAAATTTAA
1 TTTAAATTTAAATTTAAATA-TAAAATTAAA
*
2525276 TTTGAATTTAAATTTAAATA-AAAATTAAAA
1 TTTAAATTTAAATTTAAATATAAAATT-AAA
2525306 TATTAAATTTAACATTTAAA
1 T-TTAAATTTAA-ATTTAAA
2525326 AGTCCAAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 5 0.12
30 3 0.07
31 27 0.64
32 7 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TTTAAATTTAAATTTAAATATAAAATTAAA
Found at i:2525367 original size:14 final size:14
Alignment explanation
Indices: 2525348--2525379 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2525338 CATGGCCCAC
*
2525348 GGCCCAATTACAAT
1 GGCCCAATTACAAA
2525362 GGCCCAATTACAAA
1 GGCCCAATTACAAA
2525376 GGCC
1 GGCC
2525380 TATTTTTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (14 bp):
GGCCCAATTACAAA
Found at i:2526987 original size:161 final size:163
Alignment explanation
Indices: 2526820--2527127 Score: 451
Period size: 162 Copynumber: 1.9 Consensus size: 163
2526810 AATTTTAATT
** **
2526820 GGTTTATAATTTAGTCCTTTGACTGTTTGACTGTGCCAGAGGTTGCCACGTGTCA-TGTATTGGA
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTGTATTGGA
*
2526884 TTATTTATGCATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCC-CAAATCAACTTTGT
66 TAATTTATGCATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTT-T
*
2526948 -TTTAATTACGAAATTGGCCCCATAATTTTTCGA
130 ATTTAATTACAAAATTGGCCCCATAATTTTTCGA
* * * *
2526981 GGTTTATAAACTGGTCCTTTGACTTTTTGACTGCACCAGAGGTTGCCACGTGTCATTTTTTTGGA
1 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTGTATTGGA
* * * * *
2527046 TAATTTCTGTATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTA
66 TAATTTATGCATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTA
2527111 TTTAATTACAAAATTGG
131 TTTAATTACAAAATTGG
2527128 TCCAAAATTT
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
161 49 0.38
162 54 0.42
163 26 0.20
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (163 bp):
GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTGTATTGGA
TAATTTATGCATTTAGTCCTTTTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTA
TTTAATTACAAAATTGGCCCCATAATTTTTCGA
Found at i:2527197 original size:162 final size:160
Alignment explanation
Indices: 2526855--2527173 Score: 383
Period size: 162 Copynumber: 2.0 Consensus size: 160
2526845 TTTGACTGTG
* *
2526855 CCAGAGGTTGCCACGTGTCATGTATTGGATTATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
1 CCAGAGGCTGCCACGTGTCATGTATTGGATAATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
* * * *
2526920 TTTTAATTTAATCCCAAATCAACTTTGTTTTAATTACGAAATTGGCCCCATAATTTTTCGAGGTT
66 TTTTAATTTAATCCCAAATCAACTTTGTTTTAATTACAAAATTGGCCCCAAAATTTTTCAAGATT
* * * *
2526985 TATAAACTGGTCCTTTGACTTTTTGACTGCA
131 TATAAACTGGTCCCTTGACCTCTGGACT-CA
* * * * * *
2527016 CCAGAGGTTGCCACGTGTCATTTTTTTGGATAATTTCTGTATTTAGTCCTTTTTATTTTTAATTT
1 CCAGAGGCTGCCACGTGTCA-TGTATTGGATAATTTATGCATTTAGTCCTTTTCATTTTTAATTT
* * *
2527081 GTTTTAATTTAATCCTTAAATCGACTTT-TATTTAATTACAAAATTGG-TCCAAAATTTTTTCAA
65 GTTTTAATTTAATCC-CAAATCAACTTTGT-TTTAATTACAAAATTGGCCCCAAAA-TTTTTCAA
*
2527144 GATTT-TCAAATTGGTCCCTTGACCTCTGGA
127 GATTTAT-AAACTGGTCCCTTGACCTCTGGA
2527174 TACCTGTGGG
Statistics
Matches: 135, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
161 20 0.15
162 60 0.44
163 55 0.41
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (160 bp):
CCAGAGGCTGCCACGTGTCATGTATTGGATAATTTATGCATTTAGTCCTTTTCATTTTTAATTTG
TTTTAATTTAATCCCAAATCAACTTTGTTTTAATTACAAAATTGGCCCCAAAATTTTTCAAGATT
TATAAACTGGTCCCTTGACCTCTGGACTCA
Found at i:2527419 original size:59 final size:59
Alignment explanation
Indices: 2527267--2527670 Score: 601
Period size: 59 Copynumber: 6.8 Consensus size: 59
2527257 CCTAAAATTT
*
2527267 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCCCGAATC
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTA--CCCCCGAAGC
* * * *
2527328 TTTTAAAATTCCGTTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTGAAGC
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGC
* * * *
2527387 TTTTAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCTCAAAGC
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGC
* * *
2527446 TTCTAAAATTCCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATC
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGC
* * * *
2527505 TTTTAAAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTATCCTCGAAGC
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGC
*** *
2527564 TTCTAAAATTTTGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAGC
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGC
*
2527623 TTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTT
2527671 GCCCTCGGGT
Statistics
Matches: 313, Mismatches: 30, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
59 267 0.85
61 46 0.15
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (59 bp):
TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGC
Found at i:2527565 original size:177 final size:178
Alignment explanation
Indices: 2527267--2527670 Score: 668
Period size: 177 Copynumber: 2.3 Consensus size: 178
2527257 CCTAAAATTT
*
2527267 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCCCGAATCTTTT
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTA-CCCCCCGAATCTTTT
* *
2527332 AAAATTCCGTTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTGAAGCTTTTAAAATT
65 AAAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTGAAGCTTCTAAAATT
* * *
2527397 CCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCTCAAAGC
130 CCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAAGC
*
2527446 TTCTAAAATTCCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTA-CCCCCGAATCTTTTA
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCCGAATCTTTTA
*
2527510 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTA-TCCTCGAAGCTTCTAAAATT
66 AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCT-GAAGCTTCTAAAATT
*** *
2527574 TTGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAGC
130 CCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAAGC
2527623 TTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
2527671 GCCCTCGGGT
Statistics
Matches: 211, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
176 3 0.01
177 161 0.76
179 47 0.22
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (178 bp):
TTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCCGAATCTTTTA
AAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTGAAGCTTCTAAAATTC
CATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAAGC
Found at i:2527699 original size:118 final size:116
Alignment explanation
Indices: 2527267--2527716 Score: 585
Period size: 118 Copynumber: 3.8 Consensus size: 116
2527257 CCTAAAATTT
* * *
2527267 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCCCGAATCTTTT
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTA--CCCTCG--GCTTCT
* * *
2527332 AAAATTCCGTTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTGAAGC
62 AAAATTCCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAAGC
* * *
2527387 TTTTAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCTCAAAGCTTCTAA
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTC--GGCTTCTAA
*
2527452 AATTCCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAATC
64 AATTCCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAAGC
* * *
2527505 TTTTAAAATTCCGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTATCCTCGAAGCTTCTAA
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCG--GCTTCTAA
*** *
2527570 AATTTTGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAGC
64 AATTCCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAAGC
* * * *
2527623 TTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCTCGGGTATCCATA
1 TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGGCT-TCTA-A
* * *
2527688 AGTCCCATTTTTTCACCCCGATTTCATCA
64 AATTCCA-TTTTTAACCCCGATTTCATCA
2527717 TTTATCAATG
Statistics
Matches: 290, Mismatches: 33, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
116 2 0.01
117 3 0.01
118 219 0.76
119 19 0.07
120 47 0.16
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (116 bp):
TTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGGCTTCTAAAA
TTCCATTTTTAACCCCGATTTCATCAAAAATTACCATTTTACCCCCGAAGC
Found at i:2529965 original size:6 final size:6
Alignment explanation
Indices: 2529954--2529984 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2529944 ATATAAATTT
2529954 TATATG TATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG TATATG T
2529985 GTATATGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:2530684 original size:24 final size:24
Alignment explanation
Indices: 2530656--2530718 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
2530646 AGAAATAATC
*
2530656 TTTCAGTTAAACTCTGTTTATGTG
1 TTTCAGTTAAACTCTGTTTATGTA
* *
2530680 TTTCAATTAAACTCTGTTTATTTA
1 TTTCAGTTAAACTCTGTTTATGTA
* *
2530704 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
2530719 TATTACTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATGTA
Found at i:2532682 original size:24 final size:24
Alignment explanation
Indices: 2532649--2532699 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2532639 AGAAATAATA
* *
2532649 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
2532673 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
2532697 TTT
1 TTT
2532700 GAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:2532708 original size:24 final size:24
Alignment explanation
Indices: 2532657--2532711 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2532647 TATTTCAGTT
* *
2532657 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
* *
2532681 AAACTCTATTTATTTGTTTGAGTC
1 AAACTCTATTTATTTGTTTCAATC
2532705 AAACTCT
1 AAACTCT
2532712 TATTACTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAATC
Found at i:2542670 original size:15 final size:16
Alignment explanation
Indices: 2542650--2542682 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2542640 TAGATTTTTT
*
2542650 TTTATATTTTTTA-AA
1 TTTATAATTTTTATAA
2542665 TTTATAATTTTTATAA
1 TTTATAATTTTTATAA
2542681 TT
1 TT
2542683 AAAGCAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATAATTTTTATAA
Found at i:2544585 original size:23 final size:22
Alignment explanation
Indices: 2544531--2544585 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
2544521 ATATTATTTT
*
2544531 ATTAAAATTTTAATAAATGAAA
1 ATTAAAAATTTAATAAATGAAA
* * *
2544553 ATATATAAATTTATTAAATGTTAA
1 AT-TAAAAATTTAATAAATG-AAA
2544577 ATTAAAAAT
1 ATTAAAAAT
2544586 AATATAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.08
23 20 0.77
24 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
ATTAAAAATTTAATAAATGAAA
Found at i:2544599 original size:32 final size:31
Alignment explanation
Indices: 2544550--2544621 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
2544540 TTAATAAATG
*
2544550 AAAAT-ATATAAATTTATTAAATGTTAAA-TTA
1 AAAATAATATAAACTTATT--ATGTTAAATTTA
* *
2544581 AAAATAATATAAACTTATTCTTTTAAATTTA
1 AAAATAATATAAACTTATTATGTTAAATTTA
2544612 AAAATAATAT
1 AAAATAATAT
2544622 GTACAAACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 6 0.17
31 18 0.50
32 12 0.33
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (31 bp):
AAAATAATATAAACTTATTATGTTAAATTTA
Found at i:2545018 original size:2 final size:2
Alignment explanation
Indices: 2545013--2545040 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2545003 TATAAAAAAC
2545013 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
2545041 GCATGCGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2549635 original size:31 final size:31
Alignment explanation
Indices: 2549600--2549660 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2549590 TAGTCACTAA
*
2549600 ATTATTTGAAAA-TTTTCATTTAATTCATTGG
1 ATTATTT-AAAATTTTTCATTTAAATCATTGG
*
2549631 ATTATTTAAAATTTTTTATTTAAATCATTG
1 ATTATTTAAAATTTTTCATTTAAATCATTG
2549661 AGTTGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (31 bp):
ATTATTTAAAATTTTTCATTTAAATCATTGG
Found at i:2550724 original size:20 final size:21
Alignment explanation
Indices: 2550699--2550741 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
2550689 TAAAATTTAT
2550699 AATGTGATTAATA-TTAAAAA
1 AATGTGATTAATATTTAAAAA
2550719 AATGTGATTAATATTTAAAAA
1 AATGTGATTAATATTTAAAAA
2550740 AA
1 AA
2550742 AGGATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (21 bp):
AATGTGATTAATATTTAAAAA
Found at i:2555070 original size:21 final size:21
Alignment explanation
Indices: 2555045--2555101 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
2555035 TGTAATTAAG
2555045 ATTACAAATTAAAAAAAAAAA
1 ATTACAAATTAAAAAAAAAAA
2555066 ATTACAAATTAAAAAAAAAAA
1 ATTACAAATTAAAAAAAAAAA
2555087 ATTACAAATTAAAAA
1 ATTACAAATTAAAAA
2555102 GTTATGGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (21 bp):
ATTACAAATTAAAAAAAAAAA
Found at i:2555074 original size:7 final size:7
Alignment explanation
Indices: 2555045--2555101 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
2555035 TGTAATTAAG
*
2555045 ATTACAA
1 ATTAAAA
2555052 ATTAAAA
1 ATTAAAA
**
2555059 AAAAAAA
1 ATTAAAA
*
2555066 ATTACAA
1 ATTAAAA
2555073 ATTAAAA
1 ATTAAAA
**
2555080 AAAAAAA
1 ATTAAAA
*
2555087 ATTACAA
1 ATTAAAA
2555094 ATTAAAA
1 ATTAAAA
2555101 A
1 A
2555102 GTTATGGAAC
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (7 bp):
ATTAAAA
Found at i:2562349 original size:6 final size:6
Alignment explanation
Indices: 2562338--2562372 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2562328 AAGATGGAAA
2562338 GAGGGT GAGGGT GAGGGT GAGGGT GAGGGT GAGGG
1 GAGGGT GAGGGT GAGGGT GAGGGT GAGGGT GAGGG
2562373 AAGGGAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.69, T:0.14
Consensus pattern (6 bp):
GAGGGT
Found at i:2562949 original size:6 final size:6
Alignment explanation
Indices: 2562938--2562978 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
2562928 TCGAATTAAT
2562938 CATCAA CATCAA CATCAA CATCAA CATCAA CATCAA CATCA
1 CATCAA CATCAA CATCAA CATCAA CATCAA CATCAA CATCA
2562979 TTATCCTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (6 bp):
CATCAA
Found at i:2564269 original size:25 final size:25
Alignment explanation
Indices: 2564217--2564275 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
2564207 TTTTGCCCCG
* *
2564217 TAAAAATGATAAAAATTTAATCTTT
1 TAAAAATGATAAAAATATAATCTAT
*
2564242 TAAAAATTATAAAAATAT-ATGCTAT
1 TAAAAATGATAAAAATATAAT-CTAT
2564267 T-AAAATGAT
1 TAAAAATGAT
2564276 GAAATCACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.37
Consensus pattern (25 bp):
TAAAAATGATAAAAATATAATCTAT
Found at i:2568011 original size:17 final size:18
Alignment explanation
Indices: 2567982--2568018 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2567972 AAATTAAGGG
2567982 TTTTCATTTTTGTGGGGC
1 TTTTCATTTTTGTGGGGC
*
2568000 TTTTCA-TTTTGTTGGGC
1 TTTTCATTTTTGTGGGGC
2568017 TT
1 TT
2568019 ATGATTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.05, C:0.11, G:0.24, T:0.59
Consensus pattern (18 bp):
TTTTCATTTTTGTGGGGC
Found at i:2568414 original size:11 final size:11
Alignment explanation
Indices: 2568398--2568424 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2568388 CTTATCTCTT
2568398 TTTTTTTTTTG
1 TTTTTTTTTTG
2568409 TTTTTTTTTTG
1 TTTTTTTTTTG
2568420 TTTTT
1 TTTTT
2568425 GAATCTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:2573246 original size:20 final size:21
Alignment explanation
Indices: 2573207--2573246 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2573197 TCAAAATGAT
*
2573207 AAAATTATATTTTACTATTTAA
1 AAAATTATAATTTAC-ATTTAA
2573229 AAAATTATAATTTA-ATTT
1 AAAATTATAATTTACATTT
2573247 CGACTTCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
22 13 0.76
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAATTATAATTTACATTTAA
Found at i:2577982 original size:16 final size:16
Alignment explanation
Indices: 2577961--2578012 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
2577951 AAAATGAAAA
*
2577961 GAAAATTGGAAGGATG
1 GAAAATTGAAAGGATG
* *
2577977 GAAAATTGAAAGGGTA
1 GAAAATTGAAAGGATG
*
2577993 G-AAATTAAAAGGATG
1 GAAAATTGAAAGGATG
2578008 GAAAA
1 GAAAA
2578013 CATAATTTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (16 bp):
GAAAATTGAAAGGATG
Found at i:2589961 original size:17 final size:17
Alignment explanation
Indices: 2589939--2589977 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2589929 AGGTGGAGAA
* *
2589939 CTTGTTTGTTGAGAGTT
1 CTTGTTTGTAGAGAATT
2589956 CTTGTTTGTAGAGAATT
1 CTTGTTTGTAGAGAATT
2589973 CTTGT
1 CTTGT
2589978 CAAGGTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.08, G:0.26, T:0.51
Consensus pattern (17 bp):
CTTGTTTGTAGAGAATT
Found at i:2590014 original size:41 final size:41
Alignment explanation
Indices: 2589969--2590059 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
2589959 GTTTGTAGAG
2589969 AATTCTTGTCAAGGTAGAGATTGTTAGAATTGAGTAACTAA
1 AATTCTTGTCAAGGTAGAGATTGTTAGAATTGAGTAACTAA
* * * * * * *
2590010 AATTCTTATTATGGTGGAGATTGTTAGAATTGGGTGACTAG
1 AATTCTTGTCAAGGTAGAGATTGTTAGAATTGAGTAACTAA
2590051 AATTCTTGT
1 AATTCTTGT
2590060 TAAAATAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (41 bp):
AATTCTTGTCAAGGTAGAGATTGTTAGAATTGAGTAACTAA
Found at i:2592666 original size:77 final size:77
Alignment explanation
Indices: 2592538--2592680 Score: 268
Period size: 77 Copynumber: 1.9 Consensus size: 77
2592528 GTAGGCCCAC
2592538 AATAGTTTTGGACCGAGATTATCTTATAATAAAGGGCTGAGATTAGCTTATAAATACATATAATA
1 AATAGTTTTGGACCGAGATTATCTTATAATAAAGGGCTGAGATTAGCTTATAAATACATATAATA
2592603 AGTGGCCTAAAT
66 AGTGGCCTAAAT
* *
2592615 AATAGTTTTGGACCGAGATTATCTTATAATAAAGGGCTGGGATTAGGTTATAAATACATATAATA
1 AATAGTTTTGGACCGAGATTATCTTATAATAAAGGGCTGAGATTAGCTTATAAATACATATAATA
2592680 A
66 A
2592681 AGTCCCATAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 64 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (77 bp):
AATAGTTTTGGACCGAGATTATCTTATAATAAAGGGCTGAGATTAGCTTATAAATACATATAATA
AGTGGCCTAAAT
Found at i:2592750 original size:17 final size:19
Alignment explanation
Indices: 2592726--2592773 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
2592716 CCGCATGTCT
2592726 TGTTTTTTTTATTTA-ACA
1 TGTTTTTTTTATTTATACA
*
2592744 T-TTTTTTATA-TTATACA
1 TGTTTTTTTTATTTATACA
*
2592761 TGTTTATTTTATT
1 TGTTTTTTTTATT
2592774 GTTCATGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 3 0.12
17 12 0.50
18 8 0.33
19 1 0.04
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (19 bp):
TGTTTTTTTTATTTATACA
Found at i:2608176 original size:28 final size:29
Alignment explanation
Indices: 2608134--2608234 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 29
2608124 ATTTTTAATT
* * *
2608134 TTTTACAATATTTTACGATTGT-TAAT-A
1 TTTTATAATTTTTTACAATTGTATAATAA
2608161 TCTTTATAATTTTTTACAATTGTATAATAA
1 T-TTTATAATTTTTTACAATTGTATAATAA
* * * *
2608191 TTTTTTATATTTTTTACAGTTCT-TAAAAGA
1 TTTTATA-ATTTTTTACAATTGTATAATA-A
2608221 TTTTA-AATTTTTTA
1 TTTTATAATTTTTTA
2608235 AAAATTTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
27 1 0.02
28 26 0.43
29 14 0.23
30 20 0.33
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (29 bp):
TTTTATAATTTTTTACAATTGTATAATAA
Found at i:2608224 original size:30 final size:31
Alignment explanation
Indices: 2608163--2608224 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
2608153 TGTTAATATC
* *
2608163 TTTATAATTTTTTACAATTGTATAATAATTT
1 TTTATAATTTTTTACAATTCTATAAAAATTT
*
2608194 TTTAT-ATTTTTTACAGTTCT-TAAAAGATTT
1 TTTATAATTTTTTACAATTCTATAAAA-ATTT
2608224 T
1 T
2608225 AAATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.15
30 18 0.67
31 5 0.19
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (31 bp):
TTTATAATTTTTTACAATTCTATAAAAATTT
Found at i:2608976 original size:12 final size:12
Alignment explanation
Indices: 2608961--2608994 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2608951 TAATTTAATA
2608961 TTTAATAATTTT
1 TTTAATAATTTT
*
2608973 TTTATTAATTTT
1 TTTAATAATTTT
2608985 TTTAAATAAT
1 TTT-AATAAT
2608995 CATCTTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAATAATTTT
Found at i:2609697 original size:60 final size:59
Alignment explanation
Indices: 2609553--2609723 Score: 247
Period size: 60 Copynumber: 2.9 Consensus size: 59
2609543 TTAATATAAC
*
2609553 ATTTGGTATCTGAACTTGACATTTTTTTCTAATTTGGTACCTAAAC-TTTTTTGACCCA
1 ATTTGGTACCTGAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTTGACCCA
* * * *
2609611 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGATAGCTAAACTTTTTTTAGACCCA
1 ATTTGGTACCTGAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTT-GACCCA
* *
2609671 ATTTCGTACCTGAACTTAGA-ATTTTTTTCTAATTTGGTACCTAAGCTTTTTTT
1 ATTTGGTACCTGAACTT-GACATTTTTTTCTAATTTGGTACCTAAACTTTTTTT
2609724 TAAGATTCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
58 41 0.41
59 6 0.06
60 50 0.51
61 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTTGACCCA
Found at i:2610012 original size:31 final size:31
Alignment explanation
Indices: 2609967--2610027 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2609957 TAACTTAAAA
* * *
2609967 AAAAAGTGTCAAGTTTAGATATCAAATTAGG
1 AAAAAGTATCAAGTTTAAATACCAAATTAGG
*
2609998 AAAAAGTATTAAGTTTAAATACCAAATTAG
1 AAAAAGTATCAAGTTTAAATACCAAATTAG
2610028 ATAAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.30
Consensus pattern (31 bp):
AAAAAGTATCAAGTTTAAATACCAAATTAGG
Found at i:2610041 original size:32 final size:31
Alignment explanation
Indices: 2609977--2610041 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
2609967 AAAAAGTGTC
* * **
2609977 AAGTTTAGATATCAAATTAGGAAAAAGTATT
1 AAGTTTAAATACCAAATTAGGAAAAAAAATT
*
2610008 AAGTTTAAATACCAAATTAGATAAAAAAAATT
1 AAGTTTAAATACCAAATTAG-GAAAAAAAATT
2610040 AA
1 AA
2610042 ATATCAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (31 bp):
AAGTTTAAATACCAAATTAGGAAAAAAAATT
Found at i:2610049 original size:26 final size:25
Alignment explanation
Indices: 2610012--2610074 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
2610002 AGTATTAAGT
*
2610012 TTAAATACCAAATTAGATAAAAAAAA
1 TTAAATATCAAATTAGA-AAAAAAAA
*
2610038 TTAAATATCAAATTAGAAAAAAATA
1 TTAAATATCAAATTAGAAAAAAAAA
*
2610063 TCAAAT-TCAAAT
1 TTAAATATCAAAT
2610075 ACCAGATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 6 0.18
25 12 0.35
26 16 0.47
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (25 bp):
TTAAATATCAAATTAGAAAAAAAAA
Found at i:2628926 original size:6 final size:6
Alignment explanation
Indices: 2628908--2629003 Score: 67
Period size: 6 Copynumber: 16.0 Consensus size: 6
2628898 TTAAATTGAT
* * *
2628908 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTT-AA TTTGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
2628952 TTTAAA TTTAAA -TAAAA TATTAAAA TATTAAA TTTAACA TTAAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TT-AAA T-TTAAA TTTAA-A TT-TAAA TTTAAA
2629004 GCCCAGTGTC
Statistics
Matches: 72, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
4 4 0.06
5 12 0.17
6 36 0.50
7 11 0.15
8 9 0.12
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:2628938 original size:17 final size:15
Alignment explanation
Indices: 2628912--2628962 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 15
2628902 ATTGATTTTA
2628912 AATTTATTTAAATTT
1 AATTTATTTAAATTT
2628927 AGATTTATTTTAAATTT
1 A-ATTTA-TTTAAATTT
2628944 AATTTGAATTTAAATTT
1 AATTT--ATTTAAATTT
2628961 AA
1 AA
2628963 ATAAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.03
16 9 0.28
17 21 0.66
18 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (15 bp):
AATTTATTTAAATTT
Found at i:2628953 original size:11 final size:11
Alignment explanation
Indices: 2628898--2628962 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
2628888 GACTTTTGAG
* *
2628898 TTAAATTGATT
1 TTAAATTTAAT
2628909 TTAAATTT-AT
1 TTAAATTTAAT
2628919 TTAAATTTAGAT
1 TTAAATTTA-AT
*
2628931 TT-ATTTTAAAT
1 TTAAATTT-AAT
2628942 TT-AATTTGAAT
1 TTAAATTT-AAT
2628953 TTAAATTTAA
1 TTAAATTTAA
2628963 ATAAAATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
10 9 0.20
11 26 0.58
12 10 0.22
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:2629002 original size:20 final size:19
Alignment explanation
Indices: 2628955--2629003 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2628945 ATTTGAATTT
*
2628955 AAATTTAAATAAAATATTA
1 AAATTTAAATAAAACATTA
**
2628974 AAATATTAAATTTAACATTAA
1 AAAT-TTAAATAAAACATT-A
2628995 AAATTTAAA
1 AAATTTAAA
2629004 GCCCAGTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.16
20 16 0.64
21 5 0.20
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTTAAATAAAACATTA
Found at i:2629214 original size:20 final size:20
Alignment explanation
Indices: 2629167--2629225 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
2629157 CACGTGCCTA
* *
2629167 CTGCTGCTGGCCACCAACTC
1 CTGCTGCTGACCACCAGCTC
*
2629187 CAT-TTGCTGACCACCAGCTC
1 C-TGCTGCTGACCACCAGCTC
*
2629207 CTGCTGCTGCTCCACCAGC
1 CTGCTGCTG-ACCACCAGC
2629226 CGCCTGCTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 21 0.68
21 9 0.29
ACGTcount: A:0.15, C:0.44, G:0.19, T:0.22
Consensus pattern (20 bp):
CTGCTGCTGACCACCAGCTC
Found at i:2629712 original size:3 final size:3
Alignment explanation
Indices: 2629704--2629739 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2629694 TGAAAGACAT
*
2629704 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2629740 AAAAAAACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2630850 original size:30 final size:30
Alignment explanation
Indices: 2630812--2630980 Score: 241
Period size: 30 Copynumber: 5.6 Consensus size: 30
2630802 AATTATCCAG
2630812 AAAA-TACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
2630841 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
2630871 AAAATTATATTTTTGACCCCGAAACTTTACC
1 AAAATTACA-TTTTGACCCCAAAACTTTTCC
* * *
2630902 AAAATTATATTTTGACCCTAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
2630932 GAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
2630962 AAAATTACATTTTAACCCC
1 AAAATTACATTTTGACCCC
2630981 GATTTCACCG
Statistics
Matches: 125, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
29 4 0.03
30 93 0.74
31 28 0.22
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:2630915 original size:61 final size:60
Alignment explanation
Indices: 2630812--2630980 Score: 241
Period size: 61 Copynumber: 2.8 Consensus size: 60
2630802 AATTATCCAG
2630812 AAAA-TACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * * * * *
2630871 AAAATTATATTTTTGACCCCGAAACTTTACCAAAATTATATTTTGACCCTAAAACTTTTCT
1 AAAATTACA-TTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
* * *
2630932 GAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTAACCCC
1 AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCC
2630981 GATTTCACCG
Statistics
Matches: 94, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
59 4 0.04
60 37 0.39
61 53 0.56
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (60 bp):
AAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:2631011 original size:30 final size:30
Alignment explanation
Indices: 2630962--2631190 Score: 152
Period size: 30 Copynumber: 7.7 Consensus size: 30
2630952 AAACTTTTCC
2630962 AAAATTA-CATTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTAACCCCGATTTCACCG
* * * **
2630991 AAAATTACCGTTTTACCCCCGA-ATC-CTTT
1 AAAATTACCATTTTAACCCCGATTTCAC-CG
2631020 AAAATT-CCATTTTTAACCCCGATTTCACCG
1 AAAATTACCA-TTTTAACCCCGATTTCACCG
* ** ** *
2631050 AAAATTACCATTTTACCCCCGA-AGCTTCT
1 AAAATTACCATTTTAACCCCGATTTCACCG
* *
2631079 AAAATT-CCATTTTTAACCCTGATTTCACCA
1 AAAATTACCA-TTTTAACCCCGATTTCACCG
** ** *
2631109 AAAATTACCATTTT-ACCCTCGA-AGCTTCT
1 AAAATTACCATTTTAACCC-CGATTTCACCG
* *
2631138 AAAATT-CTATTTTTTAACCCCGATTTCACCA
1 AAAATTACCA--TTTTAACCCCGATTTCACCG
*
2631169 AAAATTACCATTTTACCCCCGA
1 AAAATTACCATTTTAACCCCGA
2631191 ATCTTTTAAA
Statistics
Matches: 148, Mismatches: 37, Indels: 29
0.69 0.17 0.14
Matches are distributed among these distances:
28 8 0.05
29 56 0.38
30 63 0.43
31 19 0.13
32 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.34
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGATTTCACCG
Found at i:2631034 original size:59 final size:59
Alignment explanation
Indices: 2630962--2631247 Score: 400
Period size: 59 Copynumber: 4.9 Consensus size: 59
2630952 AAACTTTTCC
* * * *
2630962 AAAATTACA-TTTTAACCCCGATTTCACCGAAAATTACCGTTTTACCCCCGAATCCTT-T
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAA-GCTTCT
*
2631020 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCT
* *
2631079 AAAATTCCATTTTTAACCCTGATTTCACCAAAAATTACCATTTTACCCTCGAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCT
* *
2631138 AAAATTCTATTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTT-T
1 AAAATTCCA-TTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCT
* * * *
2631197 TAAATTCCATTTTTTAACCCCGATTACACC-AAAATTATCATTTTGCCCCCG
1 AAAATTCCA-TTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCG
2631248 GGTATCCATA
Statistics
Matches: 210, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
58 30 0.14
59 135 0.64
60 45 0.21
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCT
Found at i:2631240 original size:29 final size:29
Alignment explanation
Indices: 2630960--2631240 Score: 152
Period size: 29 Copynumber: 9.6 Consensus size: 29
2630950 TAAAACTTTT
2630960 CCAAAATTA-CATTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTAACCCCGATTTCA
* * * * *
2630988 CCGAAAATTACCGTTTTACCCCCGAATCCT
1 CC-AAAATTACCATTTTAACCCCGATTTCA
**
2631018 TTAAAATT-CCATTTTTAACCCCGATTTCA
1 CCAAAATTACCA-TTTTAACCCCGATTTCA
* *
2631047 CCGAAAATTACCATTTTACCCCCGAAGCTT--
1 CC-AAAATTACCATTTTAACCCCG-A-TTTCA
* *
2631077 CTAAAATT-CCATTTTTAACCCTGATTTCA
1 CCAAAATTACCA-TTTTAACCCCGATTTCA
*
2631106 CCAAAAATTACCATTTT-ACCCTCGAAGCTT--
1 CC-AAAATTACCATTTTAACCC-CG-A-TTTCA
* *
2631136 CTAAAATT-CTATTTTTTAACCCCGATTTCA
1 CCAAAATTACCA--TTTTAACCCCGATTTCA
* * *
2631166 CCAAAAATTACCATTTTACCCCCGA-ATCT
1 CC-AAAATTACCATTTTAACCCCGATTTCA
*** *
2631195 TTTAAATT-CCATTTTTTAACCCCGATTACA
1 CCAAAATTACCA--TTTTAACCCCGATTTCA
*
2631225 CCAAAATTATCATTTT
1 CCAAAATTACCATTTT
2631241 GCCCCCGGGT
Statistics
Matches: 185, Mismatches: 42, Indels: 51
0.67 0.15 0.18
Matches are distributed among these distances:
27 5 0.03
28 17 0.09
29 70 0.38
30 67 0.36
31 20 0.11
32 6 0.03
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (29 bp):
CCAAAATTACCATTTTAACCCCGATTTCA
Found at i:2633257 original size:22 final size:22
Alignment explanation
Indices: 2633196--2633284 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 22
2633186 CTAGCGCGCT
* *
2633196 TACTGTTTCGCACTTTGTGTGCC
1 TACTGATT-GCACTATGTGTGCC
**
2633219 TACTGATTTGCGTTATGTGTGCC
1 TACTGA-TTGCACTATGTGTGCC
*
2633242 TACTTATTGCACTATGTGTGCC
1 TACTGATTGCACTATGTGTGCC
*
2633264 TACTGGATTGCACTGTGTGTG
1 TACT-GATTGCACTATGTGTG
2633285 GTTACTGTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 18 0.33
23 35 0.64
24 2 0.04
ACGTcount: A:0.13, C:0.20, G:0.25, T:0.42
Consensus pattern (22 bp):
TACTGATTGCACTATGTGTGCC
Found at i:2635034 original size:14 final size:14
Alignment explanation
Indices: 2634984--2635034 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
2634974 ATCTTAAATA
2634984 TTTTTA-AATTATT
1 TTTTTATAATTATT
*
2634997 TTTTTATAAATATGTT
1 TTTTTAT-AAT-TATT
2635013 TATTTTATAATTATT
1 T-TTTTATAATTATT
2635028 TTTTTAT
1 TTTTTAT
2635035 TTTGGGTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 6 0.19
14 6 0.19
15 7 0.22
16 7 0.22
17 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTTTATAATTATT
Found at i:2635552 original size:3 final size:3
Alignment explanation
Indices: 2635544--2635571 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2635534 TGCCATAATT
2635544 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2635572 AATAGAGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2635928 original size:6 final size:6
Alignment explanation
Indices: 2635919--2635964 Score: 58
Period size: 6 Copynumber: 7.3 Consensus size: 6
2635909 ACGGAAAGAG
2635919 AAACAA AAACAA AAACAA AAACAA AAA-AA TAGACACAA AAACAA AA
1 AAACAA AAACAA AAACAA AAACAA AAACAA -A-A-ACAA AAACAA AA
2635965 CATGATCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 2 0.06
6 28 0.78
7 2 0.06
8 2 0.06
9 2 0.06
ACGTcount: A:0.80, C:0.15, G:0.02, T:0.02
Consensus pattern (6 bp):
AAACAA
Found at i:2637495 original size:2 final size:2
Alignment explanation
Indices: 2637488--2637512 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2637478 GGGTCAGAAT
2637488 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
2637513 TGAGTGAAGA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2645190 original size:31 final size:29
Alignment explanation
Indices: 2645145--2645207 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 29
2645135 TAACCATTTT
* * *
2645145 AATAACTTATATTTTAAATATTTTTAAAATA
1 AATAAATTAAATTTT-AACATTTTTAAAA-A
*
2645176 AATAAATTAAATTTTTACATTTTTAAAAA
1 AATAAATTAAATTTTAACATTTTTAAAAA
2645205 AAT
1 AAT
2645208 CAAAATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.14
30 11 0.39
31 13 0.46
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
AATAAATTAAATTTTAACATTTTTAAAAA
Found at i:2645228 original size:83 final size:81
Alignment explanation
Indices: 2645096--2645251 Score: 181
Period size: 85 Copynumber: 1.9 Consensus size: 81
2645086 TAAAGGGTCA
* * *
2645096 AAATTAAATTGTAATTTTTATAATAATAAAAATATAATTTAACCATTTTAATAA-CTTATATTTT
1 AAATTAAATTGTAATTTTTAAAAAAATAAAAATATAATTT-A-CATTTTAATAATCTTAAATTTT
2645160 AAATATTTTTAAAATAAAT
64 AAA-ATTTTTAAAATAAAT
* * * *
2645179 AAATTAAATTTTTACATTTTTAAAAAAATCAAAATATAATTT-CATTTTTACTAATTTTAAATTT
1 AAATTAAA-TTGTA-ATTTTTAAAAAAATAAAAATATAATTTACA-TTTTAATAATCTTAAATTT
2645243 TAAAATTTT
63 TAAAATTTT
2645252 AAACAAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
82 2 0.03
83 21 0.34
84 15 0.24
85 24 0.39
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (81 bp):
AAATTAAATTGTAATTTTTAAAAAAATAAAAATATAATTTACATTTTAATAATCTTAAATTTTAA
AATTTTTAAAATAAAT
Found at i:2646560 original size:16 final size:15
Alignment explanation
Indices: 2646533--2646574 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2646523 CTCTATTATC
2646533 GAAAATATTTTAAAA
1 GAAAATATTTTAAAA
*
2646548 GAAAATAATTTTAATA
1 GAAAAT-ATTTTAAAA
*
2646564 TAAAATATTTT
1 GAAAATATTTT
2646575 CTTTCACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
GAAAATATTTTAAAA
Found at i:2651201 original size:16 final size:15
Alignment explanation
Indices: 2651160--2651206 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2651150 TTAATTTTTT
* *
2651160 TTTGAATATTTTAAG
1 TTTGGATATTTTAAA
2651175 TTTGGATATTTTAAA
1 TTTGGATATTTTAAA
*
2651190 TTTTGATAATTTTAAA
1 TTTGGAT-ATTTTAAA
2651206 T
1 T
2651207 GTGATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (15 bp):
TTTGGATATTTTAAA
Found at i:2652488 original size:28 final size:28
Alignment explanation
Indices: 2652430--2652481 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
2652420 GATCGTTAGG
*
2652430 TTTTATTTTATTTTTGATTTGACGTTCA
1 TTTTATGTTATTTTTGATTTGACGTTCA
*
2652458 TTTTATGTT-TTTTTGTTTTG-CGTT
1 TTTTATGTTATTTTTGATTTGACGTT
2652482 TGCATTTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 10 0.45
28 8 0.36
ACGTcount: A:0.12, C:0.06, G:0.13, T:0.69
Consensus pattern (28 bp):
TTTTATGTTATTTTTGATTTGACGTTCA
Found at i:2660846 original size:67 final size:67
Alignment explanation
Indices: 2660727--2660883 Score: 206
Period size: 67 Copynumber: 2.3 Consensus size: 67
2660717 CTAGACCTAA
* * * * * * *
2660727 AACTGATGCTTAACTATAAAATTTTACGAGCATTTTATCTTAGTAACTTATGCCTGCTGCTAACC
1 AACTGATGCTTAGCTATAAAAATTTACAAGCATTTTATATCAGTAACCTATGCCTGCTGCCAACC
2660792 TG
66 TG
* *
2660794 AACTGATGCTTAGCTATAAAAATTTACAAGCATTTTGTATCAGTAGCCTATGCCTGCTGCCAACC
1 AACTGATGCTTAGCTATAAAAATTTACAAGCATTTTATATCAGTAACCTATGCCTGCTGCCAACC
2660859 TG
66 TG
**
2660861 AGACCAATGCTTAGCTATAAAAA
1 A-ACTGATGCTTAGCTATAAAAA
2660884 AATTTCATGC
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 59 0.76
68 19 0.24
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (67 bp):
AACTGATGCTTAGCTATAAAAATTTACAAGCATTTTATATCAGTAACCTATGCCTGCTGCCAACC
TG
Found at i:2667299 original size:34 final size:34
Alignment explanation
Indices: 2667260--2667326 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
2667250 GAAGTGTTAC
*
2667260 ATAACAATCGATTTAAAAAAAATAATACTCTAAT
1 ATAACAATCGATTCAAAAAAAATAATACTCTAAT
* * *
2667294 ATAACAGTCGATTCAAAAAAAGTAATATTCTAA
1 ATAACAATCGATTCAAAAAAAATAATACTCTAA
2667327 CATGACATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (34 bp):
ATAACAATCGATTCAAAAAAAATAATACTCTAAT
Found at i:2672284 original size:13 final size:13
Alignment explanation
Indices: 2672263--2672297 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2672253 GTAGTCGAGA
*
2672263 AGTTGTTCTAAGG
1 AGTTTTTCTAAGG
2672276 AGTTTTTCTAAGG
1 AGTTTTTCTAAGG
2672289 AGTTATTTC
1 AGTT-TTTC
2672298 AAAAAGTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.46
Consensus pattern (13 bp):
AGTTTTTCTAAGG
Found at i:2677885 original size:4 final size:4
Alignment explanation
Indices: 2677876--2677902 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2677866 TGCAACACCA
2677876 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
2677903 AACTCACTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2680367 original size:16 final size:17
Alignment explanation
Indices: 2680343--2680383 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2680333 GTTATATTTC
*
2680343 AAAAGAAAATAT-TAGT
1 AAAAGAAAAAATATAGT
*
2680359 AAAATAAAAAATATAGT
1 AAAAGAAAAAATATAGT
2680376 AAAAGAAA
1 AAAAGAAA
2680384 TAAGTGGCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (17 bp):
AAAAGAAAAAATATAGT
Found at i:2683071 original size:395 final size:395
Alignment explanation
Indices: 2682341--2683132 Score: 1431
Period size: 395 Copynumber: 2.0 Consensus size: 395
2682331 ATGAGATTGC
* *
2682341 TGCTATTGGTGTGATTGTGCGAAATGAGGATGCTTGTGTAGTTGCTGCTTTGGATGAGAAGGTGG
1 TGCTATTGGTGTGATTGTGCAAAATGAGGATGCTTGTGTAGTTGCTGCTTTGGATGAAAAGGTGG
*
2682406 TTGTCGAGGAGGTGGTGGAGGTTGAAGCTTTAGCTGTGATGAAAGGCATTTTATGGGCTGAGAAG
66 TTGTCGAGGAGGTGGTGGAGGTTGAAGCTTTAGCTGGGATGAAAGGCATTTTATGGGCTGAGAAG
2682471 CAAGGGTACAGGCATATTATTGTTGAAACTGATTCTGAAATTGTGTATAGAGTTTTTAATGGGGA
131 CAAGGGTACAGGCATATTATTGTTGAAACTGATTCTGAAATTGTGTATAGAGTTTTTAATGGGGA
* *
2682536 TTGGGTTTGCAATTTTTGGAAGATCCATTCATAATTACAGGTTTTTCTATCTCACAATTTTTGAA
196 TTGAGTTTGCAATTTTTCGAAGATCCATTCATAATTACAGGTTTTTCTATCTCACAATTTTTGAA
* *
2682601 TTGTGTTCCAGGAAAAATTGGAAGAGAAGCTAATAAAGTGGCTGACAGGTGTGCTCACCTTACTT
261 TTGTGTTCCAAGAAAAATTGGAAGAGAAGATAATAAAGTGGCTGACAGGTGTGCTCACCTTACTT
* * *
2682666 TGAAGGGGATGTGCCTCTATGGTCGGGTTAGTGAAGCCCCATCCTCTCTGGTTTCGGTGTTGAGG
326 TGAAGGGGATGTGCCTCTATGGTCGGGTTAGTGAACCCCCATCCTCTCTGGTTTCGATATTGAGG
2682731 AGTGA
391 AGTGA
*
2682736 TGCTATTGGTGTGATTGTGCAAAATGATGATGCTTGTGTAGTTGCTGCTTTGGATGAAAAGGTGG
1 TGCTATTGGTGTGATTGTGCAAAATGAGGATGCTTGTGTAGTTGCTGCTTTGGATGAAAAGGTGG
* *
2682801 TTGTCGAGGAGGTGGTGGAGGTTGAAGCTTTAGCTGGGGTGAAAGGCATTTTATGGGTTGAGAAG
66 TTGTCGAGGAGGTGGTGGAGGTTGAAGCTTTAGCTGGGATGAAAGGCATTTTATGGGCTGAGAAG
* *
2682866 CAAGGGTACAGTCATATTATTGTTGAAACTGATTCTGAAATTGTGTATAGAGTTTTTAATGGTGA
131 CAAGGGTACAGGCATATTATTGTTGAAACTGATTCTGAAATTGTGTATAGAGTTTTTAATGGGGA
*
2682931 TTGAGTTTGCAATTTTTCGAAGATCCATTCATACTTACAGGTTTTTCTATCTCACAATTTTTGAA
196 TTGAGTTTGCAATTTTTCGAAGATCCATTCATAATTACAGGTTTTTCTATCTCACAATTTTTGAA
*
2682996 TTGTGTTCCAAGAAAAATTGGAAGAGAAGATAATAAAGTGGTTGACAGGTGTGCTCACCTTACTT
261 TTGTGTTCCAAGAAAAATTGGAAGAGAAGATAATAAAGTGGCTGACAGGTGTGCTCACCTTACTT
2683061 TGAAGGGGATGTGCCTCTATGGTCGGGTTAGTGAACCCCCATCCTCTCTGGTTTCGATATTGAGG
326 TGAAGGGGATGTGCCTCTATGGTCGGGTTAGTGAACCCCCATCCTCTCTGGTTTCGATATTGAGG
2683126 AGTGA
391 AGTGA
2683131 TG
1 TG
2683133 GCCTTCTTGC
Statistics
Matches: 380, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
395 380 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.34
Consensus pattern (395 bp):
TGCTATTGGTGTGATTGTGCAAAATGAGGATGCTTGTGTAGTTGCTGCTTTGGATGAAAAGGTGG
TTGTCGAGGAGGTGGTGGAGGTTGAAGCTTTAGCTGGGATGAAAGGCATTTTATGGGCTGAGAAG
CAAGGGTACAGGCATATTATTGTTGAAACTGATTCTGAAATTGTGTATAGAGTTTTTAATGGGGA
TTGAGTTTGCAATTTTTCGAAGATCCATTCATAATTACAGGTTTTTCTATCTCACAATTTTTGAA
TTGTGTTCCAAGAAAAATTGGAAGAGAAGATAATAAAGTGGCTGACAGGTGTGCTCACCTTACTT
TGAAGGGGATGTGCCTCTATGGTCGGGTTAGTGAACCCCCATCCTCTCTGGTTTCGATATTGAGG
AGTGA
Found at i:2688930 original size:26 final size:26
Alignment explanation
Indices: 2688893--2688955 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
2688883 TTTATTGAGG
*
2688893 CTATTAGTTTATCAATAAA-TAATATT
1 CTATTAATTTATCAATAAATTAATA-T
* *
2688919 TTATTAATTTATCGATAAATTAATAT
1 CTATTAATTTATCAATAAATTAATAT
2688945 CTATTAATTTA
1 CTATTAATTTA
2688956 GAGAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 27 0.84
27 5 0.16
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.49
Consensus pattern (26 bp):
CTATTAATTTATCAATAAATTAATAT
Found at i:2689142 original size:33 final size:33
Alignment explanation
Indices: 2689065--2689142 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
2689055 CATGTATCAA
* ***
2689065 AGTTAATTGGTTCATGTAACCAAAAAAAGAGTT
1 AGTTAATTGGTTCATGTAACCAAAAAAAAAAAG
*
2689098 AATTAATTGGTTCATGTAACCAAAAAGAAAAAAG
1 AGTTAATTGGTTCATGTAACCAAAAA-AAAAAAG
2689132 AGTTAA-TGGTT
1 AGTTAATTGGTT
2689143 TCAAAATCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 30 0.79
34 8 0.21
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (33 bp):
AGTTAATTGGTTCATGTAACCAAAAAAAAAAAG
Found at i:2697663 original size:47 final size:47
Alignment explanation
Indices: 2697594--2697697 Score: 190
Period size: 47 Copynumber: 2.2 Consensus size: 47
2697584 TAGGCTAGTG
2697594 GCCATGCTTTTACTTGAAACTACTACAATCTATATTTAAAAGTAATA
1 GCCATGCTTTTACTTGAAACTACTACAATCTATATTTAAAAGTAATA
*
2697641 GCCATGCTTTTACTTGAAACTACTACCATCTATATTTAAAAGTAATA
1 GCCATGCTTTTACTTGAAACTACTACAATCTATATTTAAAAGTAATA
*
2697688 CCCATGCTTT
1 GCCATGCTTT
2697698 CATCAGGGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.37
Consensus pattern (47 bp):
GCCATGCTTTTACTTGAAACTACTACAATCTATATTTAAAAGTAATA
Found at i:2697689 original size:22 final size:22
Alignment explanation
Indices: 2697621--2697689 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
2697611 AACTACTACA
2697621 ATCTATATTTAAAAGTAATAGCC
1 ATCTATATTTAAAAGTAATA-CC
* * * * *
2697644 ATGCTTTTACTTGAAACTACTACC
1 AT-C-TATATTTAAAAGTAATACC
2697668 ATCTATATTTAAAAGTAATACC
1 ATCTATATTTAAAAGTAATACC
2697690 CATGCTTTCA
Statistics
Matches: 34, Mismatches: 10, Indels: 5
0.69 0.20 0.10
Matches are distributed among these distances:
22 14 0.41
23 3 0.09
24 5 0.15
25 12 0.35
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.36
Consensus pattern (22 bp):
ATCTATATTTAAAAGTAATACC
Found at i:2698504 original size:28 final size:28
Alignment explanation
Indices: 2698460--2698534 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
2698450 ATATTTATAT
*
2698460 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTAAATAATTTTA
* **
2698488 TATATT-TTTTATTTATTAAATTTTTTTA
1 TATATTATTTTA-ATATTAAATAATTTTA
* *
2698516 TATAATTATCTTAACATTA
1 TAT-ATTATTTTAATATTA
2698535 TTTTAATGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 5 0.14
28 21 0.57
29 7 0.19
30 4 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (28 bp):
TATATTATTTTAATATTAAATAATTTTA
Found at i:2700147 original size:60 final size:60
Alignment explanation
Indices: 2700054--2700175 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
2700044 GAGGATGATG
2700054 TTTATCCTAAGAAACCCGAGTTCGAACACCTGTGTATGCAAGGTGTGTGTTGTCAAAGGA
1 TTTATCCTAAGAAACCCGAGTTCGAACACCTGTGTATGCAAGGTGTGTGTTGTCAAAGGA
2700114 TTTATCCTAAGAAACCCGAGTTCGAACACCTGTGTATGCAAGGTGTGTGTTGTCAAAGGA
1 TTTATCCTAAGAAACCCGAGTTCGAACACCTGTGTATGCAAGGTGTGTGTTGTCAAAGGA
2700174 TT
1 TT
2700176 AAGAAAGCAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (60 bp):
TTTATCCTAAGAAACCCGAGTTCGAACACCTGTGTATGCAAGGTGTGTGTTGTCAAAGGA
Found at i:2712020 original size:29 final size:30
Alignment explanation
Indices: 2711980--2712203 Score: 149
Period size: 29 Copynumber: 7.7 Consensus size: 30
2711970 ACCCAGGGGC
*
2711980 AAAATGGTAATTATTGTGAAATCGGGGTTA
1 AAAATGGTAATTTTTGTGAAATCGGGGTTA
* ** *
2712010 AAAATGG-AATTTTTGAGAGTTCGGAG-T-
1 AAAATGGTAATTTTTGTGAAATCGGGGTTA
2712037 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGGTAATTTTT-GTGAAATCGGGGTTA
* *
2712068 AAAATGG-AA-TTTTG-GAAAGTTCGAAGG--C
1 AAAATGGTAATTTTTGTGAAA--TCG-GGGTTA
2712096 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGGTAATTTTT-GTGAAATCGGGGTTA
* *
2712127 AAAATGG-AA-TTTTG-GAAAGTTTGGGGGT-
1 AAAATGGTAATTTTTGTGAAA--TCGGGGTTA
* *
2712155 AAAATAGTAA-TTTTG-GAAGTTTCGGGGTT-
1 AAAATGGTAATTTTTGTGAA--ATCGGGGTTA
2712184 AAAAT-GTAATTTTT-TGAAAT
1 AAAATGGTAATTTTTGTGAAAT
2712204 TTTGGAGTCC
Statistics
Matches: 154, Mismatches: 20, Indels: 43
0.71 0.09 0.20
Matches are distributed among these distances:
27 16 0.10
28 27 0.18
29 71 0.46
30 21 0.14
31 15 0.10
32 4 0.03
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTTGTGAAATCGGGGTTA
Found at i:2712057 original size:58 final size:58
Alignment explanation
Indices: 2711980--2712168 Score: 281
Period size: 59 Copynumber: 3.2 Consensus size: 58
2711970 ACCCAGGGGC
* * *
2711980 AAAATGGTAATTATT-GTGAAATCGGGGTTAAAAATGGAATTTTTGAGAGTTCGGAGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGAGT
* *
2712037 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAAGGC
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGA-GT
* *
2712096 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCGGAGT
*
2712155 AAAATAGTAATTTT
1 AAAATGGTAATTTT
2712169 GGAAGTTTCG
Statistics
Matches: 119, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
57 14 0.12
58 37 0.31
59 65 0.55
60 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGAGT
Found at i:2712129 original size:59 final size:59
Alignment explanation
Indices: 2711977--2712147 Score: 283
Period size: 59 Copynumber: 2.9 Consensus size: 59
2711967 GATACCCAGG
* * * *
2711977 GGCAAAATGGTAATTATT-GTGAAATCGGGGTTAAAAATGGAATTTTTGAGAGTTCGGA
1 GGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAA
*
2712035 -GTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAA
1 GGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAA
2712093 GGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
1 GGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
2712148 TGGGGGTAAA
Statistics
Matches: 105, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
57 15 0.14
58 37 0.35
59 53 0.50
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
GGCAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAA
Found at i:2714051 original size:35 final size:35
Alignment explanation
Indices: 2714012--2714105 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 35
2714002 GTAATTGGAC
* * *
2714012 ATTTAAATTTATAA-TAATTTTAAATTTGAAAGCAA
1 ATTTAAATTTA-AATTAAATTTAAATTTAAAAACAA
* *
2714047 ATTTAAACTTAAATTAAATTTAAATTTAAAAATAA
1 ATTTAAATTTAAATTAAATTTAAATTTAAAAACAA
**
2714082 ATTTAAACTTTAAAACAAATTTAA
1 ATTTAAA-TTTAAATTAAATTTAA
2714106 TCTTAAGATA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 2 0.04
35 34 0.69
36 13 0.27
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (35 bp):
ATTTAAATTTAAATTAAATTTAAATTTAAAAACAA
Found at i:2714053 original size:18 final size:17
Alignment explanation
Indices: 2714012--2714123 Score: 91
Period size: 18 Copynumber: 6.4 Consensus size: 17
2714002 GTAATTGGAC
* *
2714012 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAACAA
* *
2714029 TTTTAAATTTGAAAGCAA
1 ATTTAAATTT-AAAACAA
* **
2714047 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAACAA
*
2714064 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAACAA
2714082 ATTTAAACTTTAAAACAA
1 ATTTAAA-TTTAAAACAA
* *
2714100 ATTT-AATCTTAAGATAA
1 ATTTAAAT-TTAAAACAA
2714117 ATTTAAA
1 ATTTAAA
2714124 ATGGGTTTGG
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
16 1 0.01
17 36 0.47
18 37 0.48
19 3 0.04
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:2714069 original size:6 final size:6
Alignment explanation
Indices: 2714045--2714095 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
2714035 ATTTGAAAGC
* **
2714045 AAATTT AAACTT AAA-TT AAATTT AAATTT AAAAAT AAATTT AAACTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA-TTT
2714093 AAA
1 AAA
2714096 ACAAATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
5 5 0.13
6 27 0.71
7 6 0.16
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (6 bp):
AAATTT
Found at i:2714088 original size:53 final size:52
Alignment explanation
Indices: 2714012--2714123 Score: 147
Period size: 53 Copynumber: 2.1 Consensus size: 52
2714002 GTAATTGGAC
* * *
2714012 ATTTAAATTTATAATAATTTTAAA-TTTGAAAGCAAATTTAAACTTAA-ATTAA
1 ATTTAAATTTAAAATAAATTTAAACTTT-AAAACAAATTTAAACTTAAGA-TAA
*
2714064 ATTTAAATTTAAAAATAAATTTAAACTTTAAAACAAATTTAATCTTAAGATAA
1 ATTTAAATTT-AAAATAAATTTAAACTTTAAAACAAATTTAAACTTAAGATAA
2714117 ATTTAAA
1 ATTTAAA
2714124 ATGGGTTTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
52 10 0.19
53 39 0.74
54 4 0.08
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (52 bp):
ATTTAAATTTAAAATAAATTTAAACTTTAAAACAAATTTAAACTTAAGATAA
Found at i:2714117 original size:35 final size:35
Alignment explanation
Indices: 2714024--2714123 Score: 60
Period size: 35 Copynumber: 2.8 Consensus size: 35
2714014 TTAAATTTAT
* * * *
2714024 AATAATTTTAAATTTGAAAGCAAATTTAAACTT-AA
1 AATAAATTTAAACTT-AAAACAAATTTAAATTTAAA
* * *
2714059 ATTAAATTTAAATTTAAAAATAAATTTAAACTTT-AA
1 AATAAATTTAAACTT-AAAACAAATTTAAA-TTTAAA
* * * *
2714095 AACAAATTTAATCTTAAGATAAATTTAAA
1 AATAAATTTAAACTTAAAACAAATTTAAA
2714124 ATGGGTTTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
35 38 0.72
36 15 0.28
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (35 bp):
AATAAATTTAAACTTAAAACAAATTTAAATTTAAA
Found at i:2715162 original size:22 final size:22
Alignment explanation
Indices: 2715126--2715186 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
2715116 CGATCTAAGG
2715126 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
2715147 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
2715169 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
2715187 GGAAGTCGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 11 0.30
22 25 0.68
23 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:2715177 original size:15 final size:16
Alignment explanation
Indices: 2715152--2715181 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2715142 GAATTAAAAA
2715152 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
2715168 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
2715182 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:2721298 original size:35 final size:35
Alignment explanation
Indices: 2721258--2721327 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
2721248 AATAACCAAA
* * * * * *
2721258 ACATAAATTTGCTAATAGTTTAGTGATATTAAGTG
1 ACATAAACTTACTAACAGTTCAATGACATTAAGTG
2721293 ACATAAACTTACTAACAGTTCAATGACATTAAGTG
1 ACATAAACTTACTAACAGTTCAATGACATTAAGTG
2721328 TAGTTTACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (35 bp):
ACATAAACTTACTAACAGTTCAATGACATTAAGTG
Found at i:2725535 original size:22 final size:21
Alignment explanation
Indices: 2725488--2725535 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
2725478 CTTAAAAATA
*
2725488 ATAAATTTTTTATTTAATCTT
1 ATAAATTTTTTATTTAATATT
* * *
2725509 TTAAATTTTTATTTTTACTATT
1 ATAAATTTTT-TATTTAATATT
2725531 ATAAA
1 ATAAA
2725536 AATTACAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
ATAAATTTTTTATTTAATATT
Found at i:2728650 original size:23 final size:24
Alignment explanation
Indices: 2728598--2728651 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
2728588 TTTTTGATAA
*
2728598 TTATAAAAATATATTATATATTTG
1 TTATAAAAAAATATTATATATTTG
* * *
2728622 -TGTAAAAAAATCTTA-ATTTTTG
1 TTATAAAAAAATATTATATATTTG
2728644 TTATAAAA
1 TTATAAAA
2728652 TCAAATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (24 bp):
TTATAAAAAAATATTATATATTTG
Found at i:2728651 original size:22 final size:24
Alignment explanation
Indices: 2728598--2728651 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
2728588 TTTTTGATAA
2728598 TTATAAAAATATATTATATATTTG
1 TTATAAAAATATATTATATATTTG
* *
2728622 TGTA-AAAAA-ATCTTA-ATTTTTG
1 T-TATAAAAATATATTATATATTTG
2728644 TTATAAAA
1 TTATAAAA
2728652 TCAAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.08
22 11 0.42
23 5 0.19
24 6 0.23
25 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (24 bp):
TTATAAAAATATATTATATATTTG
Found at i:2730060 original size:32 final size:33
Alignment explanation
Indices: 2730014--2730076 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
2730004 TTTGAAGTTT
2730014 ACTTACAATTATTTTCAAAAGAAGAAACAGTAA
1 ACTTACAATTATTTTCAAAAGAAGAAACAGTAA
*
2730047 ACTT-CAATTATTTTTAAAAGAAGAAACAGT
1 ACTTACAATTATTTTCAAAAGAAGAAACAGT
2730077 CTTTTTAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (33 bp):
ACTTACAATTATTTTCAAAAGAAGAAACAGTAA
Found at i:2748052 original size:34 final size:34
Alignment explanation
Indices: 2747993--2748060 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
2747983 TAGTTGAAAC
2747993 CAAAATAAAATTTTATTTCACATATTCTCAACCCT
1 CAAAATAAAATTTTATTTCACATATTCTC-ACCCT
**
2748028 CAAAATAAAA-TTTATTTCGTATATTCTCACCCT
1 CAAAATAAAATTTTATTTCACATATTCTCACCCT
2748061 ACTATTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 5 0.16
34 16 0.52
35 10 0.32
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.38
Consensus pattern (34 bp):
CAAAATAAAATTTTATTTCACATATTCTCACCCT
Found at i:2751283 original size:16 final size:18
Alignment explanation
Indices: 2751244--2751277 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2751234 TAAGTTTATA
2751244 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
2751261 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
2751278 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:2752404 original size:15 final size:16
Alignment explanation
Indices: 2752376--2752410 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2752366 AAACCCTTAT
2752376 TTATAAAATCTGTATA
1 TTATAAAATCTGTATA
*
2752392 TTAT-AAATTTGTATA
1 TTATAAAATCTGTATA
2752407 TTAT
1 TTAT
2752411 TTTTTACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (16 bp):
TTATAAAATCTGTATA
Found at i:2754198 original size:23 final size:24
Alignment explanation
Indices: 2754167--2754214 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
2754157 GACTTAAATT
2754167 TTAATATT-CGACAAAATAAAAACA
1 TTAATATTCCGA-AAAATAAAAACA
*
2754191 TTAA-ATTCCTAAAAATAAAAACA
1 TTAATATTCCGAAAAATAAAAACA
2754214 T
1 T
2754215 GGAGATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.27
Consensus pattern (24 bp):
TTAATATTCCGAAAAATAAAAACA
Found at i:2760178 original size:30 final size:29
Alignment explanation
Indices: 2760144--2760203 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
2760134 TAATTTAAAA
* * *
2760144 AAAATTAGATCAAGTCAAAATTTCATGTAT
1 AAAATTACATAAAATCAAAATTT-ATGTAT
*
2760174 AAAATTACATAAAATCAAAGTTTATGTAT
1 AAAATTACATAAAATCAAAATTTATGTAT
2760203 A
1 A
2760204 GATTTGGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (29 bp):
AAAATTACATAAAATCAAAATTTATGTAT
Found at i:2762366 original size:17 final size:18
Alignment explanation
Indices: 2762335--2762370 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2762325 AACTGGTTCG
*
2762335 ATTTAAAAAATATTAAAA
1 ATTTAAAAAACATTAAAA
2762353 ATTT-AAAAACATTAAAA
1 ATTTAAAAAACATTAAAA
2762370 A
1 A
2762371 AAGTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTTAAAAAACATTAAAA
Found at i:2762371 original size:19 final size:19
Alignment explanation
Indices: 2762336--2762386 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
2762326 ACTGGTTCGA
*
2762336 TTTAAAAAA-TATTAAAAA-
1 TTTAAAAAATTA-AAAAAAG
2762354 TTTAAAAACATTAAAAAAAG
1 TTTAAAAA-ATTAAAAAAAG
*
2762374 TTTTAAAAATTAA
1 TTTAAAAAATTAA
2762387 TTCAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 8 0.29
19 11 0.39
20 9 0.32
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
TTTAAAAAATTAAAAAAAG
Found at i:2763141 original size:12 final size:13
Alignment explanation
Indices: 2763115--2763150 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
2763105 TTAAATCAAG
2763115 TTTTTCAAAAGTA
1 TTTTTCAAAAGTA
2763128 TTTTTCAAAA-TA
1 TTTTTCAAAAGTA
*
2763140 TTTTTTAAAAG
1 TTTTTCAAAAG
2763151 CGTTTCTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTTTCAAAAGTA
Found at i:2764453 original size:2 final size:2
Alignment explanation
Indices: 2764446--2764481 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2764436 TCAACAATAC
2764446 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
2764482 GAAAAGAGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2771409 original size:29 final size:30
Alignment explanation
Indices: 2771343--2771409 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 30
2771333 ATTTCGAGCT
*
2771343 ATTTAA-ATTAAATAAATTATTAAAATTTC
1 ATTTAATATTAAAAAAATTATTAAAATTTC
**
2771372 ATAAAAATATTAAAAAAATTA-T-AAATTTC
1 AT-TTAATATTAAAAAAATTATTAAAATTTC
2771401 AATTTAATA
1 -ATTTAATA
2771410 AAATTTTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
29 13 0.43
30 5 0.17
31 12 0.40
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (30 bp):
ATTTAATATTAAAAAAATTATTAAAATTTC
Found at i:2794754 original size:25 final size:25
Alignment explanation
Indices: 2794695--2794757 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
2794685 TTTAGCACTG
2794695 CTTTTGAAAAGTACTTTTAAAAAGT
1 CTTTTGAAAAGTACTTTTAAAAAGT
* * * *
2794720 GTTGTGGAAAAGTGC-TTTAAGAAGT
1 CTT-TTGAAAAGTACTTTTAAAAAGT
2794745 ACTTTTGAAAAGT
1 -CTTTTGAAAAGT
2794758 TTGGTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
25 19 0.63
26 11 0.37
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (25 bp):
CTTTTGAAAAGTACTTTTAAAAAGT
Found at i:2795038 original size:33 final size:35
Alignment explanation
Indices: 2794943--2795039 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
2794933 TTAATATTTT
*
2794943 AATATATAAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
2794978 AATTAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AA-T-ATATAAATTATATTTTAAATATTTAATTAAGC
2795011 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
2795040 ATATAACCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 7 0.14
33 12 0.24
34 8 0.16
35 6 0.12
36 4 0.08
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:2796155 original size:22 final size:22
Alignment explanation
Indices: 2796130--2796178 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2796120 ATATCTTCAT
*
2796130 GAATTCTTAAAAGTTTCTGTAA
1 GAATTCTTAAAAGTTTCTCTAA
* * *
2796152 GAATTCTTCATAGTTTCTCTTA
1 GAATTCTTAAAAGTTTCTCTAA
2796174 GAATT
1 GAATT
2796179 TCTAATACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (22 bp):
GAATTCTTAAAAGTTTCTCTAA
Found at i:2796857 original size:63 final size:63
Alignment explanation
Indices: 2796784--2796911 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
2796774 GAATATATTG
2796784 AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCATAGTGTA
1 AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCATAGTGTA
* *
2796847 AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAATTAAGATTATAATCATGGTGTA
1 AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCATAGTGTA
2796910 AG
1 AG
2796912 GTGGTAATCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (63 bp):
AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCATAGTGTA
Found at i:2815211 original size:5 final size:5
Alignment explanation
Indices: 2815201--2815228 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2815191 TACATTCTAA
2815201 ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATA
2815229 GTTGAGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:2828049 original size:24 final size:22
Alignment explanation
Indices: 2828015--2828071 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
2828005 TTAACCGTTC
* *
2828015 AATTATTAAATCAAACAAGATTAA
1 AATT-TTAAATCAAAAAAAATT-A
*
2828039 AATTTTGAAATTAAAAAAAATTA
1 AATTTT-AAATCAAAAAAAATTA
2828062 AATTTTAAAT
1 AATTTTAAAT
2828072 ATACAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 4 0.14
23 9 0.31
24 16 0.55
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
AATTTTAAATCAAAAAAAATTA
Found at i:2828840 original size:36 final size:37
Alignment explanation
Indices: 2828800--2828878 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
2828790 TTTTTTTTTT
* *
2828800 TTCTTTTTATCAG-AGTTTGAATCTGGGTTTTTGGGG
1 TTCTTTTCATCAGTAGCTTGAATCTGGGTTTTTGGGG
**
2828836 TTCTTTTCATTTGTAGCTTGAATCTGGGTTTTTGGGG
1 TTCTTTTCATCAGTAGCTTGAATCTGGGTTTTTGGGG
*
2828873 TACTTT
1 TTCTTT
2828879 CATTTGCAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 10 0.27
37 27 0.73
ACGTcount: A:0.13, C:0.10, G:0.25, T:0.52
Consensus pattern (37 bp):
TTCTTTTCATCAGTAGCTTGAATCTGGGTTTTTGGGG
Found at i:2842852 original size:29 final size:27
Alignment explanation
Indices: 2842786--2842852 Score: 62
Period size: 31 Copynumber: 2.3 Consensus size: 27
2842776 GAGTTTTACG
* *
2842786 TGTATAATTGCATCAAATTAAAATTTA
1 TGTATAATTGCATCAAATCAAAATTCA
* *
2842813 TGTATACAATTGCACATTAAATCAAAGTTCA
1 TGTAT--AATTG--CATCAAATCAAAATTCA
2842844 TGTATAATT
1 TGTATAATT
2842853 TTGAGATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.16
29 9 0.28
31 18 0.56
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (27 bp):
TGTATAATTGCATCAAATCAAAATTCA
Found at i:2848864 original size:30 final size:32
Alignment explanation
Indices: 2848802--2848864 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
2848792 GGAGAAGAAG
* * *
2848802 AAGTATAAACATATTGGGTCATTTATGCAAAA
1 AAGTATAAACATATTGGATAATTTATGAAAAA
*
2848834 AAGTA-AAA-ATATTGGATAATTTATTAAAAA
1 AAGTATAAACATATTGGATAATTTATGAAAAA
2848864 A
1 A
2848865 CGAAAAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 19 0.70
31 3 0.11
32 5 0.19
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.32
Consensus pattern (32 bp):
AAGTATAAACATATTGGATAATTTATGAAAAA
Found at i:2869308 original size:23 final size:23
Alignment explanation
Indices: 2869271--2869318 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2869261 TACAAAATGC
2869271 TATTGATTAATAAAAATATTATT
1 TATTGATTAATAAAAATATTATT
*
2869294 TATTGTATTAA-AAAATTATTATT
1 TATTG-ATTAATAAAAATATTATT
2869317 TA
1 TA
2869319 AAATAATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
TATTGATTAATAAAAATATTATT
Found at i:2870897 original size:25 final size:24
Alignment explanation
Indices: 2870861--2870959 Score: 99
Period size: 24 Copynumber: 4.0 Consensus size: 24
2870851 ACTGAGTTCC
*
2870861 AAAAATTTAGCTCATACGAGCCCAA
1 AAAAA-TTAGCTCATACGAGCCCAG
*
2870886 ACAAAATTAGCTCATACAAGCCCAG
1 A-AAAATTAGCTCATACGAGCCCAG
* ** *
2870911 ATAGGTTAGCTCTTACGAGCCCAG
1 AAAAATTAGCTCATACGAGCCCAG
* * *
2870935 ATAAGTTAGCTCATTCGAGCCCAG
1 AAAAATTAGCTCATACGAGCCCAG
2870959 A
1 A
2870960 CAGAGTTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
24 40 0.63
25 19 0.30
26 4 0.06
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (24 bp):
AAAAATTAGCTCATACGAGCCCAG
Found at i:2878074 original size:2 final size:2
Alignment explanation
Indices: 2878067--2878094 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2878057 GAATTCAATG
2878067 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2878095 ACTTTCATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2882886 original size:16 final size:15
Alignment explanation
Indices: 2882865--2882894 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2882855 TCAACTTGAT
2882865 TTGGACAGATAAATTA
1 TTGGACAGA-AAATTA
2882881 TTGGACAGAAAATT
1 TTGGACAGAAAATT
2882895 TTGCAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (15 bp):
TTGGACAGAAAATTA
Found at i:2888302 original size:113 final size:113
Alignment explanation
Indices: 2888177--2888406 Score: 372
Period size: 113 Copynumber: 2.0 Consensus size: 113
2888167 TTCTTCTTCC
* * *
2888177 CTTTTGATTCCAATATATTTAGTTATAAATCTGTCTCAAAGCTTGAATCTTTAAAA-CTCATTAA
1 CTTTTGATTCCAATATATTTAGTTACAAACCTATCTCAAAGCTTGAATCTTTAAAACCT-ATTAA
*
2888241 CCAAAAGATTCAATATATTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
65 CCAAAAGATTCAATATATTTGGTTCCAATATCTTCTTCCCATTAAGTTT
*
2888290 CTTTTGATTCCAATATCTTTAGTTACAAACCTATCTCAAAGCTTGAATCTTTAAAACCTATTAAC
1 CTTTTGATTCCAATATATTTAGTTACAAACCTATCTCAAAGCTTGAATCTTTAAAACCTATTAAC
* * *
2888355 CAAAAGATTTAATATTTTTGGTTCCAATATCTTCTTCCCATTACGTTT
66 CAAAAGATTCAATATATTTGGTTCCAATATCTTCTTCCCATTAAGTTT
2888403 CTTT
1 CTTT
2888407 AGGTTAATAG
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
113 106 0.98
114 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (113 bp):
CTTTTGATTCCAATATATTTAGTTACAAACCTATCTCAAAGCTTGAATCTTTAAAACCTATTAAC
CAAAAGATTCAATATATTTGGTTCCAATATCTTCTTCCCATTAAGTTT
Found at i:2890757 original size:12 final size:12
Alignment explanation
Indices: 2890740--2890764 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2890730 AACTTAATCC
2890740 ATAAACACCTCT
1 ATAAACACCTCT
2890752 ATAAACACCTCT
1 ATAAACACCTCT
2890764 A
1 A
2890765 AATTGATTGC
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:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAACACCTCT
Done.