Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 142 of 196
Found at i:42142285 original size:37 final size:37
Alignment explanation
Indices: 42142244--42142314 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
42142234 ATTCCAAAAA
*
42142244 TAATA-TTATTTTAATA-TATTTAATATTAAATTAAATT
1 TAATACTTAGTTTAATAGTATTT--TATTAAATTAAATT
42142281 TAATACTTAGTTTAATAGTATTTTATTAAATTAA
1 TAATACTTAGTTTAATAGTATTTTATTAAATTAA
42142315 TATTAAAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 16 0.52
38 10 0.32
39 5 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (37 bp):
TAATACTTAGTTTAATAGTATTTTATTAAATTAAATT
Found at i:42142399 original size:21 final size:22
Alignment explanation
Indices: 42142374--42142436 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 22
42142364 ATATAAATAT
42142374 TATATTAATTTAATAAGATTTA
1 TATATTAATTTAATAAGATTTA
*
42142396 -ATATTAAATTTAATCTAATATTTA
1 TATATT-AATTTAA--TAAGATTTA
42142420 TCTATATTAATTTAATA
1 --TATATTAATTTAATA
42142437 TTAAAGTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
21 5 0.15
22 7 0.21
24 10 0.29
26 7 0.21
27 5 0.15
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTAATTTAATAAGATTTA
Found at i:42148527 original size:22 final size:22
Alignment explanation
Indices: 42148501--42148542 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
42148491 ATAAATACTG
*
42148501 TAACATG-GTAATTTTTTTATAA
1 TAACATGAG-AATTGTTTTATAA
42148523 TAACATGAGAATTGTTTTAT
1 TAACATGAGAATTGTTTTAT
42148543 GTAAATGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (22 bp):
TAACATGAGAATTGTTTTATAA
Found at i:42156234 original size:25 final size:26
Alignment explanation
Indices: 42156202--42156256 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
42156192 TTATTAAATT
*
42156202 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
42156227 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
42156252 A-ATAT
1 ATATAT
42156257 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:42156483 original size:45 final size:44
Alignment explanation
Indices: 42156394--42156488 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
42156384 TTACACCTCT
* *
42156394 ATTACATTCAACCAAACACAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGATTTACTATTACACCTCTATTCC
** *
42156438 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACA-CAGATTTACTATTACACCTCTATTCC
42156483 ATTACA
1 ATTACA
42156489 CCTCTAATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGATTTACTATTACACCTCTATTCC
Found at i:42156488 original size:16 final size:16
Alignment explanation
Indices: 42156469--42156536 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
42156459 GATTTGCTAT
* *
42156469 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
*
42156485 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
42156501 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42156517 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42156533 TACA
1 TACA
42156537 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:42156779 original size:15 final size:17
Alignment explanation
Indices: 42156744--42156781 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
42156734 GAATGAAAAG
*
42156744 AAAATTGAAAGATTAGA
1 AAAATAGAAAGATTAGA
42156761 AAAATAGAAAGA-T-GA
1 AAAATAGAAAGATTAGA
42156776 AAAATA
1 AAAATA
42156782 TAATTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 1 0.05
17 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (17 bp):
AAAATAGAAAGATTAGA
Found at i:42167182 original size:28 final size:27
Alignment explanation
Indices: 42167119--42167270 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
42167109 ATATTAAGTC
* * *
42167119 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
42167146 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
42167174 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
42167201 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
42167229 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
42167256 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42167271 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:42167203 original size:55 final size:55
Alignment explanation
Indices: 42167119--42167270 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
42167109 ATATTAAGTC
* * *
42167119 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
42167174 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
42167229 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
42167271 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:42175249 original size:28 final size:27
Alignment explanation
Indices: 42175186--42175337 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
42175176 ATATTAAGTC
* * *
42175186 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
42175213 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
42175241 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
42175268 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
42175296 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
42175323 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42175338 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:42175270 original size:55 final size:55
Alignment explanation
Indices: 42175186--42175337 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
42175176 ATATTAAGTC
* * *
42175186 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
42175241 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
42175296 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
42175338 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:42177243 original size:43 final size:42
Alignment explanation
Indices: 42177177--42177333 Score: 163
Period size: 43 Copynumber: 3.7 Consensus size: 42
42177167 AGCTCGTACA
**
42177177 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATAACG
1 ATGCCAATATCCCAGACATGGTCTTACATGTAATCAAAT-ACG
* * * * *
42177220 ATGCCACTATCCCATACAAGGTCTTACATGAAATCATATACG
1 ATGCCAATATCCCAGACATGGTCTTACATGTAATCAAATACG
* * *
42177262 ATGCCAATGTCTCAGACATGGTCTTACACGTAAATCTCAAAT-CG
1 ATGCCAATATCCCAGACATGGTCTTACATGT-AA--TCAAATACG
* *
42177306 ATGCCAACATCCCAGACGTGGTCTTACA
1 ATGCCAATATCCCAGACATGGTCTTACA
42177334 CGATATCACA
Statistics
Matches: 92, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
42 27 0.29
43 34 0.37
44 26 0.28
45 5 0.05
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (42 bp):
ATGCCAATATCCCAGACATGGTCTTACATGTAATCAAATACG
Found at i:42178343 original size:13 final size:13
Alignment explanation
Indices: 42178325--42178351 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42178315 TACAAACGAT
42178325 AAAATTTTCACAC
1 AAAATTTTCACAC
42178338 AAAATTTTCACAC
1 AAAATTTTCACAC
42178351 A
1 A
42178352 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:42192826 original size:29 final size:30
Alignment explanation
Indices: 42192794--42192868 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
42192784 ATATTACTAT
42192794 AAAAT-TTAATTTTATTGCTATA-TTTTTAA
1 AAAATATT-ATTTTATTGCTATACTTTTTAA
* **
42192823 AAAATATTTTTTTATTTTTATACTTTTTAA
1 AAAATATTATTTTATTGCTATACTTTTTAA
*
42192853 AAAAAATTATTCTTAT
1 AAAATATTATT-TTAT
42192869 ATATTTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 16 0.42
30 18 0.47
31 4 0.11
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (30 bp):
AAAATATTATTTTATTGCTATACTTTTTAA
Found at i:42193737 original size:22 final size:22
Alignment explanation
Indices: 42193706--42193749 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
42193696 TACACCAAAA
*
42193706 TAGGCTTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGGCGCTTTTT
42193728 TAGGCCTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGGCGCTTTTT
42193750 AGCGCCACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.43
Consensus pattern (22 bp):
TAGGCCTTTAGCGGCGCTTTTT
Found at i:42194757 original size:15 final size:17
Alignment explanation
Indices: 42194737--42194774 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
42194727 GATAAGGAAA
42194737 AAAAATTAT-AAAT-AT
1 AAAAATTATAAAATAAT
*
42194752 AAAAATTCTAAAATAAT
1 AAAAATTATAAAATAAT
42194769 AAAAAT
1 AAAAAT
42194775 AAATAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 4 0.20
17 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATTATAAAATAAT
Found at i:42197832 original size:4 final size:4
Alignment explanation
Indices: 42197823--42197859 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
42197813 TTATTTTGCT
42197823 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
42197860 CAATATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:42198075 original size:49 final size:49
Alignment explanation
Indices: 42197980--42198072 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
42197970 CACTAATTAA
* *
42197980 TCCTAAACCCTAAATCGTAAAATAGAAACTCTAAACCCCTAACCCTATC
1 TCCTAAACCCTAAATCATAAAATAAAAACTCTAAACCCCTAACCCTATC
42198029 TCCTAAACCCTAAATCATAAAATAAAAACTCTAAA-CCCTAACCC
1 TCCTAAACCCTAAATCATAAAATAAAAACTCTAAACCCCTAACCC
42198073 CTAACCCTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
48 9 0.21
49 33 0.79
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (49 bp):
TCCTAAACCCTAAATCATAAAATAAAAACTCTAAACCCCTAACCCTATC
Found at i:42198203 original size:14 final size:14
Alignment explanation
Indices: 42198186--42198223 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
42198176 CACTAACTCT
*
42198186 TAACCTCTAAC-ATC
1 TAACCCCTAACTA-C
42198200 TAACCCCTAACTAC
1 TAACCCCTAACTAC
42198214 TAACCCCTAA
1 TAACCCCTAA
42198224 ACCTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (14 bp):
TAACCCCTAACTAC
Found at i:42198973 original size:15 final size:15
Alignment explanation
Indices: 42198938--42198984 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
42198928 TCCCAACCCT
*
42198938 TAAA-CCATAATCGC
1 TAAATCCATAATCCC
42198952 T-AATCCATAATCCC
1 TAAATCCATAATCCC
*
42198966 TAAATCCATACTCCC
1 TAAATCCATAATCCC
42198981 TAAA
1 TAAA
42198985 CCTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.38
15 16 0.55
ACGTcount: A:0.40, C:0.32, G:0.02, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:42199199 original size:23 final size:23
Alignment explanation
Indices: 42199170--42199224 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
42199160 CCTAACTTTT
*
42199170 AACCCCTAACACATCTAACCCCTA
1 AACCCTTAAC-CATCTAACCCCTA
*
42199194 AACCCTTAACCCTCTAACCCCTA
1 AACCCTTAACCATCTAACCCCTA
42199217 AA-CCTTAA
1 AACCCTTAA
42199225 ATCCCAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 6 0.21
23 14 0.48
24 9 0.31
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.20
Consensus pattern (23 bp):
AACCCTTAACCATCTAACCCCTA
Found at i:42199610 original size:41 final size:41
Alignment explanation
Indices: 42199556--42199791 Score: 321
Period size: 41 Copynumber: 5.8 Consensus size: 41
42199546 TAAAATGCTT
* * *
42199556 TTAGCGGCGCTTCTTAAAAAACGCCCCTAAAGACCAGAGCT
1 TTAGCGGCGCTTCATAAAAAACGCCGCTAAAGACCAGAGCA
* *
42199597 TTAGCGGCGCTTCTTAAAAAACGCTGCTAAAGACCAGAG-A
1 TTAGCGGCGCTTCATAAAAAACGCCGCTAAAGACCAGAGCA
42199637 TTTAGCGGCGCTTCATAAAAAACGCCGCTAAAGACCAGAGCA
1 -TTAGCGGCGCTTCATAAAAAACGCCGCTAAAGACCAGAGCA
* * * *
42199679 TTAGTGGCGCTTCATCAAAAACTCCGCTAAAGACTAGAGCA
1 TTAGCGGCGCTTCATAAAAAACGCCGCTAAAGACCAGAGCA
* * *
42199720 TTAGCGGCGCTTCATCAAAAACACCGCTAAAGACTAGAGCA
1 TTAGCGGCGCTTCATAAAAAACGCCGCTAAAGACCAGAGCA
* * *
42199761 TTAGCGGCGCTTCTTAAAAAACACTGCTAAA
1 TTAGCGGCGCTTCATAAAAAACGCCGCTAAA
42199792 TCCCTAAAAA
Statistics
Matches: 179, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
41 178 0.99
42 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTCATAAAAAACGCCGCTAAAGACCAGAGCA
Found at i:42199960 original size:40 final size:40
Alignment explanation
Indices: 42199837--42199976 Score: 135
Period size: 40 Copynumber: 3.5 Consensus size: 40
42199827 TTTGCGTCGC
* * * * *
42199837 TTTTTGTAAAACGCCGCTAATG-CTCATTTTTAGTGGCG-
1 TTTTTATAAAGCGCCGCTAATGATTGATTTTTAGCGGCGT
* * *
42199875 TTTTTAGAAAAGCGCCGCTAAT-ACTCGATCTTTAGCGGCGT
1 TTTTTA-TAAAGCGCCGCTAATGA-TTGATTTTTAGCGGCGT
*
42199916 TTTTTATATAGCGCCGCTAATGATTGATTTTTAGCGGCGT
1 TTTTTATAAAGCGCCGCTAATGATTGATTTTTAGCGGCGT
42199956 TTTTTATTCAAA-CGCCGCTAA
1 TTTTTA-T-AAAGCGCCGCTAA
42199977 AAGTCTGTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
38 5 0.06
39 13 0.16
40 45 0.55
41 17 0.21
42 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (40 bp):
TTTTTATAAAGCGCCGCTAATGATTGATTTTTAGCGGCGT
Found at i:42202643 original size:16 final size:17
Alignment explanation
Indices: 42202616--42202653 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
42202606 ATAAAAAAAC
42202616 ATATAT-TTTAT-ATTA
1 ATATATGTTTATAATTA
42202631 ATATATGTTTATAATTA
1 ATATATGTTTATAATTA
42202648 A-ATATG
1 ATATATG
42202654 AATATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 10 0.48
17 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
ATATATGTTTATAATTA
Found at i:42204391 original size:4 final size:4
Alignment explanation
Indices: 42204382--42204425 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
42204372 TATATATCAT
42204382 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
42204426 ATAATGTACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:42204990 original size:17 final size:17
Alignment explanation
Indices: 42204968--42205001 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42204958 ATCCACTAAT
*
42204968 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
42204985 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
42205002 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:42209630 original size:17 final size:17
Alignment explanation
Indices: 42209608--42209641 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42209598 ATCCACTAAT
*
42209608 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
42209625 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
42209642 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:42209853 original size:30 final size:30
Alignment explanation
Indices: 42209819--42209878 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
42209809 GTCTACGCCA
*
42209819 CCATCGGCATCTCCTTCTCCTTCCTCTCCG
1 CCATCGGCATCTCCATCTCCTTCCTCTCCG
* *
42209849 CCATCTGCATCTGCATCTCCTTCCTCTCCG
1 CCATCGGCATCTCCATCTCCTTCCTCTCCG
42209879 GTTCCGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.08, C:0.48, G:0.10, T:0.33
Consensus pattern (30 bp):
CCATCGGCATCTCCATCTCCTTCCTCTCCG
Found at i:42212540 original size:18 final size:16
Alignment explanation
Indices: 42212511--42212562 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 16
42212501 AATGAACATG
42212511 TAAAT-AAATAAATAAA
1 TAAATAAAATAAA-AAA
42212527 TAAATAACAATAAAGAAAA
1 TAAATAA-AAT-AA-AAAA
*
42212546 TGAATAAAATAAAAAA
1 TAAATAAAATAAAAAA
42212562 T
1 T
42212563 GTAAGGAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 10 0.32
17 3 0.10
18 6 0.19
19 11 0.35
20 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (16 bp):
TAAATAAAATAAAAAA
Found at i:42214555 original size:29 final size:30
Alignment explanation
Indices: 42214493--42214556 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
42214483 GGGATGGGAG
* *
42214493 GGGAGTAAAAGTTTTTGGGGAAAAGTAGGA
1 GGGAGTAAAAGATTTTGGGGAAAAGTAGAA
*
42214523 GGGAGTAAAA-ATTTTGGGGGAAAGTA-AA
1 GGGAGTAAAAGATTTTGGGGAAAAGTAGAA
42214551 TGGGAG
1 -GGGAG
42214557 AGTAAAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 19 0.63
30 10 0.33
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.22
Consensus pattern (30 bp):
GGGAGTAAAAGATTTTGGGGAAAAGTAGAA
Found at i:42214563 original size:140 final size:144
Alignment explanation
Indices: 42214386--42214660 Score: 364
Period size: 140 Copynumber: 1.9 Consensus size: 144
42214376 GGTTTGGGGA
* * * *
42214386 AGTAAAATTTTTAGGGGAAGTAAATAGGGGGAGTAAAATTTTGGAGAGAAAATATTAAAAAAAAT
1 AGTAAAAATTTTAGGGGAAGTAAATAGGGAGAGTAAAATGTTGAAGAGAAAATATTAAAAAAAAT
*** * * * *
42214451 TGAG-G-GGGGTGGGTTTAGGGTAGATG-GGAG-GTGGGATGGGAGGGGAGTAAAAGTTTTTG-G
66 TG-GTGAGAAATGGATTTAGGGTAGATGAGGAGAATGGGATGGGAGGAGAGTAAAAGTTTTGGAG
42214511 GGAAAAGTAGGAGGG
130 GGAAAAGTAGGAGGG
* *
42214526 AGTAAAAATTTTGGGGGAAAGTAAAT-GGGAGAGTAAAATGTTGAAGGGAAAATATTAAAAAAAA
1 AGTAAAAATTTTAGGGG-AAGTAAATAGGGAGAGTAAAATGTTGAAGAGAAAATATTAAAAAAAA
*
42214590 TTGGTGAGAAATGGATTTTGGGTAGATGAGGAGAATGGGATGGGAGGAGAGTAAAAGTTTTGGAG
65 TTGGTGAGAAATGGATTTAGGGTAGATGAGGAGAATGGGATGGGAGGAGAGTAAAAGTTTTGGAG
42214655 GGAAAA
130 GGAAAA
42214661 TGGAAATAAG
Statistics
Matches: 115, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
139 1 0.01
140 53 0.46
141 24 0.21
142 4 0.03
143 26 0.23
144 7 0.06
ACGTcount: A:0.39, C:0.00, G:0.38, T:0.23
Consensus pattern (144 bp):
AGTAAAAATTTTAGGGGAAGTAAATAGGGAGAGTAAAATGTTGAAGAGAAAATATTAAAAAAAAT
TGGTGAGAAATGGATTTAGGGTAGATGAGGAGAATGGGATGGGAGGAGAGTAAAAGTTTTGGAGG
GAAAAGTAGGAGGG
Found at i:42217029 original size:16 final size:15
Alignment explanation
Indices: 42217008--42217055 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
42216998 GATGTGAATA
42217008 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
42217024 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
42217039 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
42217055 A
1 A
42217056 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:42217031 original size:24 final size:24
Alignment explanation
Indices: 42217004--42217059 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
42216994 TAATGATGTG
*
42217004 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
42217028 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
42217052 AATAATAA
1 AATAATAA
42217060 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:42217038 original size:8 final size:8
Alignment explanation
Indices: 42217004--42217055 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
42216994 TAATGATGTG
*
42217004 AATAATAA
1 AATATTAA
42217012 AATATATAA
1 AATAT-TAA
42217021 AATA-TAA
1 AATATTAA
42217028 AATATTAA
1 AATATTAA
*
42217036 AATATCAA
1 AATATTAA
*
42217044 AATATTAG
1 AATATTAA
42217052 AATA
1 AATA
42217056 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:42217227 original size:20 final size:20
Alignment explanation
Indices: 42217175--42217231 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
42217165 ATACTACATC
*
42217175 AATATGTACATATATAAAAAA
1 AATATGTACATA-ATATAAAA
* * *
42217196 AATACGT-GATAATATTAAA
1 AATATGTACATAATATAAAA
42217215 AATATGTACATAATATA
1 AATATGTACATAATATA
42217232 GTGTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 12 0.43
20 10 0.36
21 6 0.21
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AATATGTACATAATATAAAA
Found at i:42217238 original size:25 final size:25
Alignment explanation
Indices: 42217210--42217258 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
42217200 CGTGATAATA
**
42217210 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATACATACATAATATAGTG
42217235 TTAAAAATACATACATAATATAGT
1 TTAAAAATACATACATAATATAGT
42217259 TAAGATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGTG
Found at i:42217293 original size:27 final size:25
Alignment explanation
Indices: 42217260--42217326 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 25
42217250 TAATATAGTT
42217260 AAGATATATACATAAGATAACATGTAA
1 AAGATATATACATAAGATAACAT-T-A
* * * *
42217287 AATATATATAAATAATATAATATTA
1 AAGATATATACATAAGATAACATTA
42217312 AAGATATATACATAA
1 AAGATATATACATAA
42217327 AATAGTATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 14 0.41
26 1 0.03
27 19 0.56
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (25 bp):
AAGATATATACATAAGATAACATTA
Found at i:42217318 original size:25 final size:25
Alignment explanation
Indices: 42217204--42217419 Score: 134
Period size: 23 Copynumber: 9.0 Consensus size: 25
42217194 AAAATACGTG
* *
42217204 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
42217229 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
42217254 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
42217276 ATAACATGTAAAATATATATAAATAAT
1 ATAATAT-T-AAAGATATATACATAAT
*
42217303 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * *
42217328 ATAGTA-T-AATATATATACGTAAT
1 ATAATATTAAAGATATATACATAAT
* *
42217351 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
42217374 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
42217396 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
42217419 A
1 A
42217420 ACAAAAAAAG
Statistics
Matches: 151, Mismatches: 27, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
21 4 0.03
22 27 0.18
23 45 0.30
24 10 0.07
25 45 0.30
26 1 0.01
27 19 0.13
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:42218055 original size:30 final size:30
Alignment explanation
Indices: 42217905--42218079 Score: 237
Period size: 30 Copynumber: 5.8 Consensus size: 30
42217895 TAGGTACAAG
* *
42217905 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
42217935 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
*
42217965 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
42217995 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
42218025 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
42218055 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
42218080 TGAGAAAAGT
Statistics
Matches: 131, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
29 2 0.02
30 129 0.98
ACGTcount: A:0.21, C:0.04, G:0.49, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:42220577 original size:82 final size:80
Alignment explanation
Indices: 42220471--42220634 Score: 283
Period size: 82 Copynumber: 2.0 Consensus size: 80
42220461 TTAGGATGTT
* *
42220471 TGCCAATTAAGACCAACACAATAAAAACACTTGAGCTGGTAAAACACAACGAATTGCTCACAAGT
1 TGCCAATTAACACCAACACAATAAAAACACTTGAGCTAGTAAAACACAACGAATTGCTCACAAGT
42220536 GCTTGTAGGAAAAAGA
66 GCTTGTAGG-AAAAGA
*
42220552 TGCCAATTAAACACCCACACAATAAAAACACTTGAGCTAGTAAAACACAACGAATTGCTCACAAG
1 TGCCAATT-AACACCAACACAATAAAAACACTTGAGCTAGTAAAACACAACGAATTGCTCACAAG
42220617 TGCTTGTAGGAAAAGA
65 TGCTTGTAGGAAAAGA
42220633 TG
1 TG
42220635 AAGAATTGAA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
81 16 0.20
82 63 0.80
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (80 bp):
TGCCAATTAACACCAACACAATAAAAACACTTGAGCTAGTAAAACACAACGAATTGCTCACAAGT
GCTTGTAGGAAAAGA
Found at i:42221455 original size:17 final size:18
Alignment explanation
Indices: 42221423--42221457 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42221413 TGAAATTTAT
*
42221423 CAAGTTTTATTTCAAAAA
1 CAAGCTTTATTTCAAAAA
42221441 CAAGCTTTA-TTCAAAAA
1 CAAGCTTTATTTCAAAAA
42221458 TATTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (18 bp):
CAAGCTTTATTTCAAAAA
Found at i:42222132 original size:37 final size:35
Alignment explanation
Indices: 42222091--42222175 Score: 82
Period size: 35 Copynumber: 2.4 Consensus size: 35
42222081 AGTTTTTATG
* * *
42222091 ATTTAGTCCCTGAAATCTAAATTTTCATTATTCTATA
1 ATTTAGTCCCTAAAAGC-AAATTTTC-TTATTCTACA
* * *
42222128 ATTTAATCCTTAAAAGCATATTTTCTTATTCTACA
1 ATTTAGTCCCTAAAAGCAAATTTTCTTATTCTACA
*
42222163 ATTCAGT-CCTAAA
1 ATTTAGTCCCTAAA
42222176 TCCCATTTTG
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
34 5 0.13
35 14 0.36
36 7 0.18
37 13 0.33
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.44
Consensus pattern (35 bp):
ATTTAGTCCCTAAAAGCAAATTTTCTTATTCTACA
Found at i:42226190 original size:22 final size:22
Alignment explanation
Indices: 42226163--42226208 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
42226153 ATAATGTATT
*
42226163 TTTTAAA-AAAGATATTTAAAAA
1 TTTTAAAGAAA-ATATATAAAAA
42226185 TTTTAAAGAAAATATATAAAAA
1 TTTTAAAGAAAATATATAAAAA
42226207 TT
1 TT
42226209 ATATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
TTTTAAAGAAAATATATAAAAA
Found at i:42226241 original size:18 final size:17
Alignment explanation
Indices: 42226218--42226269 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
42226208 TATATATTTT
42226218 TAAATTTAAAAGAAATTA
1 TAAATTTAAAA-AAATTA
42226236 TAAA-TTAAAAAAATATA
1 TAAATTTAAAAAAAT-TA
**
42226253 TGTATTTAAAAAAATTA
1 TAAATTTAAAAAAATTA
42226270 AAAAAATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 4 0.13
17 12 0.40
18 14 0.47
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (17 bp):
TAAATTTAAAAAAATTA
Found at i:42228989 original size:14 final size:14
Alignment explanation
Indices: 42228936--42229009 Score: 69
Period size: 14 Copynumber: 5.2 Consensus size: 14
42228926 TTTCTTCTTA
* *
42228936 AATTCTCAATCTTC
1 AATTTTCAATTTTC
* * *
42228950 AATTTCCAGTTTTT
1 AATTTTCAATTTTC
42228964 AATTTT-ATATTTTC
1 AATTTTCA-ATTTTC
42228978 AATTTTCAATTTTC
1 AATTTTCAATTTTC
*
42228992 AAATTTTTAATTTTC
1 -AATTTTCAATTTTC
42229007 AAT
1 AAT
42229010 CCTCAATTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
13 1 0.02
14 33 0.69
15 14 0.29
ACGTcount: A:0.30, C:0.14, G:0.01, T:0.55
Consensus pattern (14 bp):
AATTTTCAATTTTC
Found at i:42228997 original size:29 final size:29
Alignment explanation
Indices: 42228966--42229029 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
42228956 CAGTTTTTAA
42228966 TTTTATATTTTCAATTTTCAATTTTCAAAT
1 TTTTA-ATTTTCAATTTTCAATTTTCAAAT
** *
42228996 TTTTAATTTTCAATCCTCAATTCTCAAAT
1 TTTTAATTTTCAATTTTCAATTTTCAAAT
42229025 ATTTT
1 -TTTT
42229030 TTTAAGTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTAATTTTCAATTTTCAATTTTCAAAT
Found at i:42228998 original size:15 final size:15
Alignment explanation
Indices: 42228972--42229008 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42228962 TTAATTTTAT
42228972 ATTTTC-AATTTTCA
1 ATTTTCAAATTTTCA
*
42228986 ATTTTCAAATTTTTA
1 ATTTTCAAATTTTCA
42229001 ATTTTCAA
1 ATTTTCAA
42229009 TCCTCAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTCAAATTTTCA
Found at i:42229015 original size:22 final size:22
Alignment explanation
Indices: 42228972--42229015 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42228962 TTAATTTTAT
**
42228972 ATTTTCAATTTTCAATTTTCAA
1 ATTTTCAATTTTCAATCCTCAA
*
42228994 ATTTTTAATTTTCAATCCTCAA
1 ATTTTCAATTTTCAATCCTCAA
42229016 TTCTCAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTCAATTTTCAATCCTCAA
Found at i:42235914 original size:24 final size:24
Alignment explanation
Indices: 42235882--42235957 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
42235872 TGTTTTCTGT
42235882 TTAAGTGCTCTTCGGAGCTTCCCG
1 TTAAGTGCTCTTCGGAGCTTCCCG
*
42235906 TTAAGTGCTCTTCGGAGCTACCCG
1 TTAAGTGCTCTTCGGAGCTTCCCG
* * *
42235930 ATATAG-GCTCTTTGTGAGCTTCCTG
1 TTA-AGTGCTCTTCG-GAGCTTCCCG
42235955 TTA
1 TTA
42235958 CACGGCTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 32 0.73
25 12 0.27
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.36
Consensus pattern (24 bp):
TTAAGTGCTCTTCGGAGCTTCCCG
Found at i:42238826 original size:19 final size:19
Alignment explanation
Indices: 42238802--42238841 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42238792 CTGCACCTGC
*
42238802 ACCTGATATAATTGCTGGT
1 ACCTGATATAATTACTGGT
* *
42238821 ACCTGATGTGATTACTGGT
1 ACCTGATATAATTACTGGT
42238840 AC
1 AC
42238842 TTTTTCTCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (19 bp):
ACCTGATATAATTACTGGT
Found at i:42238871 original size:36 final size:36
Alignment explanation
Indices: 42238831--42238905 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
42238821 ACCTGATGTG
*
42238831 ATTACTGGTACTTTTTCTCTCTTTGATACTGATATA
1 ATTACTGGTAATTTTTCTCTCTTTGATACTGATATA
42238867 ATTACTGGTAATTTTTCTCTCTTTGATACTGATATA
1 ATTACTGGTAATTTTTCTCTCTTTGATACTGATATA
42238903 ATT
1 ATT
42238906 GCTTTGATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.51
Consensus pattern (36 bp):
ATTACTGGTAATTTTTCTCTCTTTGATACTGATATA
Found at i:42240478 original size:158 final size:158
Alignment explanation
Indices: 42240249--42240571 Score: 540
Period size: 158 Copynumber: 2.0 Consensus size: 158
42240239 AAATGACCAA
42240249 AAAAAAATCAATTATTTACATAAATGATCCTGGTTCAAAAACAATAACTTAAATGACCTGAAATG
1 AAAAAAATCAATTATTTACATAAATGATCCTGGTTCAAAAACAATAACTTAAATGACCTGAAATG
*
42240314 ACCAGTAAAATTAGGTAAGAGAGACTAAATGGTTGGCACCAATATTTTTTTCTAACACAATCATT
66 ACCAGTAAAATTAGGTAAGAGAGACTAAATGGCTGGCACCAATATTTTTTTCTAACACAATCATT
42240379 GTTTTGTGTGATGATTGTGTCAGTGGTT
131 GTTTTGTGTGATGATTGTGTCAGTGGTT
* ** *
42240407 AAAAAAATTAATTATTTGTATAAATGAT-CTCGGTTCAAAAACAATAACTTAAATGACTTGAAAT
1 AAAAAAATCAATTATTTACATAAATGATCCT-GGTTCAAAAACAATAACTTAAATGACCTGAAAT
* * **
42240471 GATCAGTAAAATTGGGTAAGAGAGACTAAATGGCTGGCACCAATATTTTTTTCTAACACAATTGT
65 GACCAGTAAAATTAGGTAAGAGAGACTAAATGGCTGGCACCAATATTTTTTTCTAACACAATCAT
*
42240536 TGTTTTGTTTGATGATTGTGTCAGTGGTT
130 TGTTTTGTGTGATGATTGTGTCAGTGGTT
42240565 AAAAAAA
1 AAAAAAA
42240572 ATTTGGGTGC
Statistics
Matches: 154, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
157 2 0.01
158 152 0.99
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (158 bp):
AAAAAAATCAATTATTTACATAAATGATCCTGGTTCAAAAACAATAACTTAAATGACCTGAAATG
ACCAGTAAAATTAGGTAAGAGAGACTAAATGGCTGGCACCAATATTTTTTTCTAACACAATCATT
GTTTTGTGTGATGATTGTGTCAGTGGTT
Found at i:42241580 original size:75 final size:75
Alignment explanation
Indices: 42241492--42241639 Score: 217
Period size: 75 Copynumber: 2.0 Consensus size: 75
42241482 CCACTTCTCC
* * * ***
42241492 AATTTTATTATTATTGTTTTTGAATCAGGGTCATTTATGTAAATAATTAATATTTTGGA-TCATT
1 AATTTTACTATTATTGTTTTTAAACCAAAATCATTTATGTAAATAATTAAT-TTTTGGAGTCATT
42241556 TGGGTAAAACT
65 TGGGTAAAACT
*
42241567 AATTTTACTATTATTGTTTTTAAACCAAAATCATTTATGTAAATAATTAATTTTTTGAGTCATTT
1 AATTTTACTATTATTGTTTTTAAACCAAAATCATTTATGTAAATAATTAATTTTTGGAGTCATTT
42241632 GGGTAAAA
66 GGGTAAAA
42241640 TAGCCATTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 6 0.09
75 59 0.91
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (75 bp):
AATTTTACTATTATTGTTTTTAAACCAAAATCATTTATGTAAATAATTAATTTTTGGAGTCATTT
GGGTAAAACT
Found at i:42243904 original size:4 final size:4
Alignment explanation
Indices: 42243897--42243949 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
42243887 TTTACTTTTC
* * * *
42243897 TATG TATG TATG TATG TATG TACG TACG TATG TATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
42243945 TATG T
1 TATG T
42243950 GTTGTGTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.43
Consensus pattern (4 bp):
TATG
Found at i:42244367 original size:31 final size:31
Alignment explanation
Indices: 42244308--42244368 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
42244298 TACAATTTAG
*
42244308 TTATTAAACTATTCAAAAGTTTTCATTTAAA
1 TTATTAAACTATTCAAAAATTTTCATTTAAA
* *
42244339 TTATTGAATTATTCAAAAAATTTT-ATTTAA
1 TTATTAAACTATTC-AAAAATTTTCATTTAA
42244369 GTTAATGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (31 bp):
TTATTAAACTATTCAAAAATTTTCATTTAAA
Found at i:42247109 original size:8 final size:9
Alignment explanation
Indices: 42247082--42247107 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42247072 CACGTTCACC
42247082 GGGTAAAAA
1 GGGTAAAAA
42247091 GGGTAAAAA
1 GGGTAAAAA
42247100 GGGTAAAA
1 GGGTAAAA
42247108 GGAAGAGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.35, T:0.12
Consensus pattern (9 bp):
GGGTAAAAA
Found at i:42247442 original size:6 final size:6
Alignment explanation
Indices: 42247431--42247493 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
42247421 TGCAAGATCC
42247431 CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT
1 CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT
42247479 CTGCTT CTGCTT CTG
1 CTGCTT CTGCTT CTG
42247494 ATACTAACTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.00, C:0.33, G:0.17, T:0.49
Consensus pattern (6 bp):
CTGCTT
Found at i:42247610 original size:15 final size:15
Alignment explanation
Indices: 42247601--42247635 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42247591 ACCAGCTCCT
42247601 CCTCCTCCAGCACCA
1 CCTCCTCCAGCACCA
* *
42247616 CCTCCTGCGGCACCA
1 CCTCCTCCAGCACCA
42247631 CCTCC
1 CCTCC
42247636 CAAAGCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.60, G:0.11, T:0.14
Consensus pattern (15 bp):
CCTCCTCCAGCACCA
Found at i:42251881 original size:24 final size:23
Alignment explanation
Indices: 42251814--42251881 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
42251804 AATTTATTTT
42251814 ATATATTTTTC-TTTATA-TATA
1 ATATATTTTTCTTTTATAGTATA
* **
42251835 ATATTTATTTTTGTAGTATTAGTATA
1 ATA--TATTTTTCTTTTA-TAGTATA
42251861 ATATATTTTTCTTTCTATAGT
1 ATATATTTTTCTTT-TATAGT
42251882 TGCTACTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
21 3 0.09
23 7 0.20
24 14 0.40
25 4 0.11
26 7 0.20
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (23 bp):
ATATATTTTTCTTTTATAGTATA
Found at i:42252601 original size:35 final size:35
Alignment explanation
Indices: 42252553--42252621 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
42252543 TAATTTGAAT
* *
42252553 ATTTTATATTTATC-TCAAATAATATTAATGTTATA
1 ATTTTAGAATTATCTTCAAATAAT-TTAATGTTATA
* *
42252588 ATTTTAGAATTATCTTCAATTTATTTAATGTTAT
1 ATTTTAGAATTATCTTCAAATAATTTAATGTTAT
42252622 TGTTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (35 bp):
ATTTTAGAATTATCTTCAAATAATTTAATGTTATA
Found at i:42253414 original size:14 final size:14
Alignment explanation
Indices: 42253391--42253457 Score: 58
Period size: 14 Copynumber: 5.2 Consensus size: 14
42253381 TATATTTACG
42253391 CTACTATTA-T-TA
1 CTACTATTATTATA
42253403 -TACTATTATTATA
1 CTACTATTATTATA
42253416 CTACTATTATGTATA
1 CTACTATTAT-TATA
**
42253431 -TA-TA-T-TTACG
1 CTACTATTATTATA
42253441 CTACTATTATTATA
1 CTACTATTATTATA
42253455 CTA
1 CTA
42253458 TTAGTTCCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
10 2 0.05
11 11 0.26
12 4 0.09
13 5 0.12
14 17 0.40
15 4 0.09
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.49
Consensus pattern (14 bp):
CTACTATTATTATA
Found at i:42253425 original size:25 final size:25
Alignment explanation
Indices: 42253383--42253460 Score: 99
Period size: 25 Copynumber: 3.1 Consensus size: 25
42253373 TTTTGGTATA
42253383 TATTTACGCTACTATTATTATACTAT
1 TATTTAC-CTACTATTATTATACTAT
42253409 TATTATA-CTACTATTATGTATA-TA-
1 TATT-TACCTACTATTAT-TATACTAT
42253433 TATTTACGCTACTATTATTATACTAT
1 TATTTAC-CTACTATTATTATACTAT
42253459 TA
1 TA
42253461 GTTCCTCCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
23 2 0.04
24 8 0.17
25 24 0.52
26 10 0.22
27 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (25 bp):
TATTTACCTACTATTATTATACTAT
Found at i:42253460 original size:11 final size:11
Alignment explanation
Indices: 42253392--42253425 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
42253382 ATATTTACGC
42253392 TACTATTATTA
1 TACTATTATTA
42253403 TACTATTATTA
1 TACTATTATTA
*
42253414 TACTACTATTA
1 TACTATTATTA
42253425 T
1 T
42253426 GTATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (11 bp):
TACTATTATTA
Found at i:42253474 original size:50 final size:50
Alignment explanation
Indices: 42253379--42253488 Score: 152
Period size: 50 Copynumber: 2.2 Consensus size: 50
42253369 AGACTTTTGG
*
42253379 TATATATTTACGCTACTATTATTATACTATTATTATACTACTATTA-TGT
1 TATATATTTACGCTACTATTATTATACTATTAGTATACTACTATTATTGT
* *
42253428 ATATATATTTACGCTACTATTATTATACTATTAGT-TCCTCCTTATTATTGT
1 -TATATATTTACGCTACTATTATTATACTATTAGTATACTAC-TATTATTGT
*
42253479 TATATTTTTA
1 TATATATTTA
42253489 TTTATATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
49 4 0.07
50 47 0.87
51 3 0.06
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.53
Consensus pattern (50 bp):
TATATATTTACGCTACTATTATTATACTATTAGTATACTACTATTATTGT
Found at i:42253599 original size:29 final size:29
Alignment explanation
Indices: 42253566--42253625 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
42253556 ATATCTTTGC
* *
42253566 ACCTTAT-TATATATATATATGTTTTCTAT
1 ACCTTATATATACATATATAT-TTTTATAT
42253595 ACCTTATATATACATATATATTTTTATAT
1 ACCTTATATATACATATATATTTTTATAT
42253624 AC
1 AC
42253626 ATATTCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.52
Consensus pattern (29 bp):
ACCTTATATATACATATATATTTTTATAT
Found at i:42253604 original size:28 final size:28
Alignment explanation
Indices: 42253566--42253622 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
42253556 ATATCTTTGC
* *
42253566 ACCTTATTATATATATATATGTTTTCTAT
1 ACCTTATTATATACATATATATTTT-TAT
42253595 ACCTTA-TATATACATATATATTTTTAT
1 ACCTTATTATATACATATATATTTTTAT
42253622 A
1 A
42253623 TACATATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 4 0.15
28 16 0.62
29 6 0.23
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.53
Consensus pattern (28 bp):
ACCTTATTATATACATATATATTTTTAT
Found at i:42253731 original size:16 final size:16
Alignment explanation
Indices: 42253695--42253733 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42253685 TTAATTTGTA
42253695 TATATATACATACTTT
1 TATATATACATACTTT
* **
42253711 CATATATACATGTTTT
1 TATATATACATACTTT
42253727 TATATAT
1 TATATAT
42253734 TTCTATTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (16 bp):
TATATATACATACTTT
Found at i:42255438 original size:19 final size:19
Alignment explanation
Indices: 42255401--42255442 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
42255391 ATGTTATAAT
42255401 TATAGGAAATCTAAAATTA
1 TATAGGAAATCTAAAATTA
*
42255420 CTATAGTAAATCT-AAATTA
1 -TATAGGAAATCTAAAATTA
42255439 TATA
1 TATA
42255443 ATTTAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 11 0.52
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (19 bp):
TATAGGAAATCTAAAATTA
Found at i:42259134 original size:12 final size:12
Alignment explanation
Indices: 42259113--42259147 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
42259103 GTGAAAAACA
42259113 TACATAAAAATG
1 TACATAAAAATG
* *
42259125 TCCATCAAAATG
1 TACATAAAAATG
42259137 TACATAAAAAT
1 TACATAAAAAT
42259148 ACATATGGCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (12 bp):
TACATAAAAATG
Found at i:42264795 original size:120 final size:120
Alignment explanation
Indices: 42264557--42265023 Score: 884
Period size: 120 Copynumber: 3.9 Consensus size: 120
42264547 ACTAGCATCA
*
42264557 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAACATTAATTATTAAGAA-TTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
42264621 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
42264676 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
42264741 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
42264796 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
42264861 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
* *
42264916 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
42264981 AATTATATA-TTGTAATTAAAATATATTTAATAATAATTATGTT
66 AATTATATAGTT-TAATTAAAATATATTTAATAATAATTATGTT
42265024 TAAATATGAT
Statistics
Matches: 343, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
119 58 0.17
120 285 0.83
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (120 bp):
ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
Found at i:42265220 original size:44 final size:45
Alignment explanation
Indices: 42265171--42265261 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
42265161 ACCTCTATTC
* * *
42265171 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
42265215 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
42265260 CA
1 CA
42265262 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:42265263 original size:16 final size:16
Alignment explanation
Indices: 42265242--42265310 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
42265232 GATTAGCTAT
42265242 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42265258 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
42265275 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
42265291 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
42265307 TACA
1 TACA
42265311 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:42265284 original size:33 final size:32
Alignment explanation
Indices: 42265242--42265310 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
42265232 GATTAGCTAT
42265242 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
42265275 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
42265307 TACA
1 TACA
42265311 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:42276758 original size:5 final size:5
Alignment explanation
Indices: 42276748--42276795 Score: 87
Period size: 5 Copynumber: 9.6 Consensus size: 5
42276738 ACAATATCAC
*
42276748 AAAAT AAAAT AAAAT AAAAT TAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
42276796 TCGAGACAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:42299613 original size:25 final size:25
Alignment explanation
Indices: 42299579--42299628 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42299569 GTAAAGTTTG
42299579 GATGGGAGATGTCTTGGATCTGAAA
1 GATGGGAGATGTCTTGGATCTGAAA
42299604 GATGGGAGATGTCTTGGATCTGAAA
1 GATGGGAGATGTCTTGGATCTGAAA
42299629 CTACTTACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.36, T:0.28
Consensus pattern (25 bp):
GATGGGAGATGTCTTGGATCTGAAA
Found at i:42303155 original size:18 final size:17
Alignment explanation
Indices: 42303113--42303155 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
42303103 TTTTTAAGTT
*
42303113 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
42303130 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
42303148 TATAATTT
1 TATAATTT
42303156 AGAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:42304347 original size:183 final size:183
Alignment explanation
Indices: 42304039--42304408 Score: 722
Period size: 183 Copynumber: 2.0 Consensus size: 183
42304029 CATAGAGACT
*
42304039 TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTTGGTATCGAGTTTAGGGACTAAATTGAATAAA
1 TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTCGGTATCGAGTTTAGGGACTAAATTGAATAAA
42304104 TTAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATAA
66 TTAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATAA
42304169 CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTTAAATGA
131 CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTTAAATGA
42304222 TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTCGGTATCGAGTTTAGGGACTAAATTGAATAAA
1 TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTCGGTATCGAGTTTAGGGACTAAATTGAATAAA
*
42304287 TTAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATGA
66 TTAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATAA
42304352 CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTTAAATGA
131 CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTTAAATGA
42304405 TATT
1 TATT
42304409 TTTATTAATA
Statistics
Matches: 185, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 185 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (183 bp):
TATTAGTAGGAGCATGTGGTTAATTTAAAAGTTCGGTATCGAGTTTAGGGACTAAATTGAATAAA
TTAAAAAATTATAGGAATTAAAATGCAAGTATTCCATTTTTATTTTGATGAAAAAGACTTGATAA
CAATTTTACCATTACTTAAAAAAATCAATAGTTTTACGATGGCTTTTAAATGA
Found at i:42305733 original size:3 final size:3
Alignment explanation
Indices: 42305725--42305750 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42305715 TAAAGTAAAG
42305725 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
42305751 GAGATAAAAT
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:42311934 original size:39 final size:41
Alignment explanation
Indices: 42311861--42311950 Score: 121
Period size: 39 Copynumber: 2.2 Consensus size: 41
42311851 TAAAAAATAT
* * *
42311861 TTATATTAAAAAACATTACCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAACATCACAATAAATATAATAAATATTTTA
*
42311902 TTATATTAAAAAACA-CA-AATAAATATAATAAATATTTTG
1 TTATATTAAAAAACATCACAATAAATATAATAAATATTTTA
*
42311941 TTGTATTAAA
1 TTATATTAAA
42311951 TATAATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 28 0.64
40 1 0.02
41 15 0.34
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAACATCACAATAAATATAATAAATATTTTA
Found at i:42313362 original size:21 final size:20
Alignment explanation
Indices: 42313307--42313363 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
42313297 AAATTCAAAA
42313307 TTATTTTAGTTTTTTATTTAT
1 TTATTTTA-TTTTTTATTTAT
* * *
42313328 TTCTTTTGTCTTTTTATTTCT
1 TTATTTTAT-TTTTTATTTAT
42313349 TTATTTATATTTTTT
1 TTATTT-TATTTTTT
42313364 TTGTCAAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (20 bp):
TTATTTTATTTTTTATTTAT
Found at i:42313472 original size:10 final size:10
Alignment explanation
Indices: 42313459--42313530 Score: 67
Period size: 10 Copynumber: 7.1 Consensus size: 10
42313449 AATATTAAAA
42313459 TATATATTTT
1 TATATATTTT
* *
42313469 TATATATGTA
1 TATATATTTT
42313479 TATATATTTT
1 TATATATTTT
*
42313489 TA-ATAATTT
1 TATATATTTT
42313498 TA-ATGATTTT
1 TATAT-ATTTT
*
42313508 TAAAATAATTTT
1 T-ATAT-ATTTT
42313520 TATATATTTT
1 TATATATTTT
42313530 T
1 T
42313531 GAAATTTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
9 10 0.20
10 29 0.57
11 4 0.08
12 8 0.16
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (10 bp):
TATATATTTT
Found at i:42313519 original size:31 final size:31
Alignment explanation
Indices: 42313484--42313544 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
42313474 ATGTATATAT
42313484 ATTTTTA-ATAATTTT-AATGATTTTTAAAATA
1 ATTTTTATATAATTTTGAA--ATTTTTAAAATA
*
42313515 ATTTTTATATATTTTTGAAATTTTTAAAAT
1 ATTTTTATATAATTTTGAAATTTTTAAAAT
42313545 TTAAAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 18 0.67
32 7 0.26
33 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (31 bp):
ATTTTTATATAATTTTGAAATTTTTAAAATA
Found at i:42313529 original size:21 final size:20
Alignment explanation
Indices: 42313479--42313529 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
42313469 TATATATGTA
*
42313479 TATATATTTTTAATAATTTT
1 TATATATTTTAAATAATTTT
*
42313499 AATGAT-TTTTAAAATAATTTT
1 TAT-ATATTTT-AAATAATTTT
42313520 TATATATTTT
1 TATATATTTT
42313530 TGAAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TATATATTTTAAATAATTTT
Found at i:42321649 original size:13 final size:14
Alignment explanation
Indices: 42321626--42321668 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
42321616 AATATTTAAA
42321626 AATATTAAAATATT
1 AATATTAAAATATT
42321640 AATA-TAAAATATT
1 AATATTAAAATATT
* *
42321653 ATATTTTTAAATATT
1 A-ATATTAAAATATT
42321668 A
1 A
42321669 TTAAACTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 6 0.24
15 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTAAAATATT
Found at i:42321738 original size:13 final size:12
Alignment explanation
Indices: 42321719--42321781 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
42321709 TAAATTATAT
42321719 TAATTATATTAA
1 TAATTATATTAA
42321731 TAATT-TATTATA
1 TAATTATATTA-A
42321743 TAATTA-ATATAA
1 TAATTATAT-TAA
*
42321755 TTAATTATTTTAA
1 -TAATTATATTAA
42321768 TAAATTAT-TTAA
1 T-AATTATATTAA
42321780 TA
1 TA
42321782 TTTCAATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
11 6 0.14
12 20 0.45
13 17 0.39
14 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATTATATTAA
Found at i:42321740 original size:25 final size:22
Alignment explanation
Indices: 42321703--42321768 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 22
42321693 ATATTTAGTC
*
42321703 ATATAATAAATTATATTAATTA
1 ATATAATTAATTATATTAATTA
*
42321725 TATTAATAATTTATTATA-TAATTA
1 -A-T-ATAATTAATTATATTAATTA
*
42321749 ATATAATTAATTATTTTAAT
1 ATATAATTAATTATATTAAT
42321769 AAATTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 11 0.31
22 5 0.14
23 2 0.06
24 7 0.19
25 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATAATTAATTATATTAATTA
Found at i:42321744 original size:37 final size:37
Alignment explanation
Indices: 42321703--42321776 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
42321693 ATATTTAGTC
*
42321703 ATATAATAAAT-TATATTAATTATATTAATAATTTATT
1 ATATAATAAATATA-ATTAATTATATTAATAAATTATT
* *
42321740 ATATAATTAATATAATTAATTATTTTAATAAATTATT
1 ATATAATAAATATAATTAATTATATTAATAAATTATT
42321777 TAATATTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
ATATAATAAATATAATTAATTATATTAATAAATTATT
Found at i:42321750 original size:16 final size:17
Alignment explanation
Indices: 42321711--42321780 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
42321701 TCATATAATA
42321711 AATTATATTAATTATATT
1 AATTA-ATTAATTATATT
*
42321729 AA-TAATTTATTATA-T
1 AATTAATTAATTATATT
42321744 AATTAATATAATTA-ATT
1 AATTAAT-TAATTATATT
* *
42321761 ATTTTAATAAATTAT-TT
1 A-ATTAATTAATTATATT
42321778 AAT
1 AAT
42321781 ATTTCAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
15 3 0.07
16 15 0.36
17 17 0.40
18 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTAATTAATTATATT
Found at i:42321832 original size:16 final size:16
Alignment explanation
Indices: 42321797--42321829 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
42321787 ATTTTAATTT
42321797 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
42321813 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
42321828 AA
1 AA
42321830 ATATTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:42321883 original size:15 final size:15
Alignment explanation
Indices: 42321865--42321921 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
42321855 ATTCAATATT
42321865 AATATTTTAACAATA
1 AATATTTTAACAATA
*
42321880 AATATTTATTACAATTATA
1 AATATTT-TAAC-A--ATA
* *
42321899 AATATATTAATAATA
1 AATATTTTAACAATA
42321914 AATATTTT
1 AATATTTT
42321922 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 3 0.09
17 2 0.06
18 2 0.06
19 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAACAATA
Found at i:42326666 original size:98 final size:98
Alignment explanation
Indices: 42326487--42326671 Score: 266
Period size: 98 Copynumber: 1.9 Consensus size: 98
42326477 CTTTATTCTG
*
42326487 CTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAG
1 CTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGAGAG
*
42326552 ATAAAATTATCGGCTTCAATCTGATGTGATCTA
66 ATAAAATTATCAGCTTCAATCTGATGTGATCTA
* * *
42326585 CTCTACTGTAACTTCAGTGAGATAAGATCCT-TTATTTTAATCCACTCCACTGTAACTTCAGAGA
1 CTCTACTGTAACTTCAGAGAGATAAGAT-CTGTGATTTTAATCCACTCCACTGCAACTTCAGAGA
* **
42326649 GTTAGGATTA-CTAGCTTCAATCT
65 GATAAAATTATC-AGCTTCAATCT
42326672 ACTCCGTTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
97 1 0.01
98 74 0.96
99 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (98 bp):
CTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGAGAG
ATAAAATTATCAGCTTCAATCTGATGTGATCTA
Found at i:42326676 original size:44 final size:44
Alignment explanation
Indices: 42326629--42327712 Score: 393
Period size: 44 Copynumber: 24.6 Consensus size: 44
42326619 TTTTAATCCA
* * * *
42326629 CTCCACTGTAACTTCAGAGAGTTAGGATTACTAGCTTCAATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATTACTAGCTTCAATCTG
** * *
42326673 CTCCGTTATAATCTT-AGGGAGATAAGATCT-CTGGCTTCAATCTG
1 CTCCACTGTAA-CTTCAGGGAGATAAGAT-TACTAGCTTCAATCTG
* * * * ** *
42326717 CTCCACTGTAACCTCAAGGAGATAAGATCTGA-AATTCTTCGGTCTA
1 CTCCACTGTAACTTCAGGGAGATAAGAT-T-ACTA-GCTTCAATCTG
* * * *
42326763 CTCCACTGTAACCTCAGGGAGATAAGA-T-CT-GATGCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATTACTAGCTTCAATCTG
** * ** * * *
42326804 CTCTGCTGTAACTTCAGAGAGATAAGATCTTTTA-TTTTAATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGAT-TACTAGCTTCAATCTG
*
42326848 CTCCACTGTAA-TCTCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * * * * *
42326892 CTCCGCTGTAA-TCTCAGGGAGATAAGA--CCT-GATACGATATA
1 CTCCACTGTAACT-TCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * * * *
42326933 CTCTACTGTAACTTCAGAGAGATAAGATTATTTA-TTTTAATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGATTA-CTAGCTTCAATCTG
* *
42326977 CTCCACTGCAA-TCTCAGGGAGATAAGATTACTAGCTTCAATCTA
1 CTCCACTGTAACT-TCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * * * *
42327021 CTCCGCTGTAA-TCTCAGGGAGATAAGA--CCT-GATACGATCTA
1 CTCCACTGTAACT-TCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * * *
42327062 CTCTACTGTAACTTCAGAGAGATAAGATT-CTTTA-TTTTAATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGATTAC--TAGCTTCAATCTG
*
42327106 CTCCACTGTAA-TCTCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATTACTAGCTTCAATCTG
** * * * * *
42327150 CTCTGCTGTAA-TCTCAGGGAGATAAGA--CCT-GATACGATCTA
1 CTCCACTGTAACT-TCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * * * *
42327191 CTCTACTGTAACTTCAGAGAGATAAGATTATTTA-TTTTAATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGATTA-CTAGCTTCAATCTG
*
42327235 CTCCACTGTAA-TCTCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * * **
42327279 CTCCGCTGTAA-TCTCAGGGAGATAAGACTT-GT-GATTTTAATCCA
1 CTCCACTGTAACT-TCAGGGAGATAAGA-TTACTAG-CTTCAATCTG
* *
42327323 CTCCACTGCAACTTCAGGGAGAT-AGAATTA-TCGGCTTCAATCTGATGTG
1 CTCCACTGTAACTTCAGGGAGATAAG-ATTACT-AGCTTCAATC-----TG
* * * * **
42327372 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTA-TTTTAATCCA
1 --CT-C-C-ACTGTAACTTCAGGGAGATAAGAT--TACTAGCTTCAATCTG
* * * * *
42327421 CTCCACTATAACTTCAGAGAGTTAGGATTACTAGCTTCAATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATTACTAGCTTCAATCTG
* ** * * * * *
42327465 CTTCGTTATAA-TCTCAGGGAGATAAGATCTGA-AATTCTTCAGTCTA
1 CTCCACTGTAACT-TCAGGGAGATAAGAT-T-ACTA-GCTTCAATCTG
* * * * * *
42327511 CTCCACTGTAACCTCAGGGAGATAAG---ACTTGATGCGATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * ** *
42327552 CTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTTAAT-TCG
1 CTCCACTGTAACTTCAGGGAGATAAGAT--TACTAGCTTCAATCT-G
* * *
42327597 CTCCACTGTAACTTCAGGGAGATAGGA-TAGT-GTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATTACTAG-CTTCAATCTG
* ** * * *
42327640 CTCCGCTGTAA-TCTCAGGGAGATAAGATCTAAAATTCTTCAGTCTA
1 CTCCACTGTAACT-TCAGGGAGATAAGAT-TACTA-GCTTCAATCTG
*
42327686 CTCCACTGTAACCTCAGGGAGATAAGA
1 CTCCACTGTAACTTCAGGGAGATAAGA
42327713 CCTGATGCGA
Statistics
Matches: 764, Mismatches: 196, Indels: 158
0.68 0.18 0.14
Matches are distributed among these distances:
41 147 0.19
42 13 0.02
43 54 0.07
44 378 0.49
45 42 0.05
46 95 0.12
47 2 0.00
51 2 0.00
52 1 0.00
53 1 0.00
54 25 0.03
55 2 0.00
56 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGAGATAAGATTACTAGCTTCAATCTG
Found at i:42326941 original size:85 final size:86
Alignment explanation
Indices: 42326681--42327305 Score: 332
Period size: 85 Copynumber: 7.2 Consensus size: 86
42326671 TACTCCGTTA
* * * *
42326681 TAATCTTAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACCTCAAGGAGATAAGAT
1 TAATCTCAGGGAGATAAGAT-TACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
* * *
42326745 -CTGAAATTCTTCGGTCTACTCCACTG
65 CCTG--A---TACGATATACTCCACTG
* * * * ** *
42326771 TAACCTCAGGGAGATAAGA-T-CT-GATGCGATCTGCTCTGCTGTAA-CTTCAGAGAGATAAGAT
1 TAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT
** *** *
42326832 -CTTTTATTTTAATCCGCTCCACTG
65 CCTGATACGAT-AT--ACTCCACTG
* *
42326856 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-C
1 TAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATC
*
42326920 CTGATACGATATACTCTACTG
66 CTGATACGATATACTCCACTG
* * * * * *
42326941 TAA-CTTCAGAGAGATAAGATTATTTA-TTTTAATCCGCTCCACTGCAATCTCAGGGAGATAAGA
1 TAATC-TCAGGGAGATAAGATTA-CTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGA
* * * * * *
42327004 TTACTAGCTTCAATCTACTCCGCTG
64 -TCCT-GATACGATATACTCCACTG
* * * * * * *
42327029 TAATCTCAGGGAGATAAGA--CCT-GATACGATCTACTCTACTGTAA-CTTCAGAGAGATAAGAT
1 TAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT
* * *** *
42327090 TCT-TTATTTTAATCCGCTCCACTG
65 CCTGATACGAT-AT--ACTCCACTG
* **
42327114 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGA-C
1 TAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATC
* *
42327178 CTGATACGATCTACTCTACTG
66 CTGATACGATATACTCCACTG
* * * * * *
42327199 TAA-CTTCAGAGAGATAAGATTATTTA-TTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGA
1 TAATC-TCAGGGAGATAAGATTA-CTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGA
* * * * * * *
42327262 TTACTAGCTTCAATCTGCTCCGCTG
64 -TCCT-GATACGATATACTCCACTG
42327287 TAATCTCAGGGAGATAAGA
1 TAATCTCAGGGAGATAAGA
42327306 CTTGTGATTT
Statistics
Matches: 404, Mismatches: 100, Indels: 64
0.71 0.18 0.11
Matches are distributed among these distances:
82 4 0.01
83 2 0.00
84 6 0.01
85 190 0.47
86 6 0.01
87 45 0.11
88 130 0.32
89 4 0.01
90 17 0.04
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (86 bp):
TAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATC
CTGATACGATATACTCCACTG
Found at i:42326942 original size:129 final size:129
Alignment explanation
Indices: 42326763--42327306 Score: 964
Period size: 129 Copynumber: 4.2 Consensus size: 129
42326753 CTTCGGTCTA
* * * * * *
42326763 CTCCACTGTAACCTCAGGGAGATAAGATCTGATGCGATCTGCTCTGCTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
42326828 AGATCT-TTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
66 AGAT-TATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
*
42326892 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATATACTCTACTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
* * *
42326957 AGATTATTTATTTTAATCCGCTCCACTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTA
66 AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
42327021 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
*
42327086 AGATTCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
66 AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
*
42327150 CTCTGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
42327215 AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
66 AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
42327279 CTCCGCTGTAATCTCAGGGAGATAAGAC
1 CTCCGCTGTAATCTCAGGGAGATAAGAC
42327307 TTGTGATTTT
Statistics
Matches: 396, Mismatches: 18, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
128 1 0.00
129 395 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (129 bp):
CTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
AGATTATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
Found at i:42327527 original size:46 final size:46
Alignment explanation
Indices: 42327477--42327717 Score: 184
Period size: 46 Copynumber: 5.4 Consensus size: 46
42327467 TCGTTATAAT
42327477 CTCAGGGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAAC
1 CTCAGGGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAAC
* * *
42327523 CTCAGGGAGATAAGA-CTTG--ATGC--GA-TCTACTCTACTGTAAC
1 CTCAGGGAGATAAGATC-TGAAATTCTTCAGTCTACTCCACTGTAAC
* * ** * * * *
42327564 TTCAGAGAGATAAGATCCT-TTATTTTTAATTC-GCTCCACTGTAAC
1 CTCAGGGAGATAAGAT-CTGAAATTCTTCAGTCTACTCCACTGTAAC
* * * * * *
42327609 TTCAGGGAGATAGGA--T--AGTGTCTTC-GATCTGCTCCGCTGTAAT
1 CTCAGGGAGATAAGATCTGAAAT-TCTTCAG-TCTACTCCACTGTAAC
*
42327652 CTCAGGGAGATAAGATCTAAAATTCTTCAGTCTACTCCACTGTAAC
1 CTCAGGGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAAC
*
42327698 CTCAGGGAGATAAGACCTGA
1 CTCAGGGAGATAAGATCTGA
42327718 TGCGATCTAC
Statistics
Matches: 152, Mismatches: 27, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
41 29 0.19
42 8 0.05
43 27 0.18
44 3 0.02
45 27 0.18
46 55 0.36
47 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (46 bp):
CTCAGGGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTGTAAC
Found at i:42327657 original size:43 final size:43
Alignment explanation
Indices: 42327371--42327841 Score: 187
Period size: 44 Copynumber: 10.8 Consensus size: 43
42327361 AATCTGATGT
* * * * * *
42327371 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTT
1 GATCTACTCCACTGTAACTTCAGGGAGATAAGATACTGT-CTTC
* * * * * *
42327415 AATCCACTCCACTATAACTTCAGAGAGTTAGGATTACTAG-CTTC
1 GATCTACTCCACTGTAACTTCAGGGAGATAAGA-TACT-GTCTTC
* * ** *
42327459 AATCTACTTCGTTATAA-TCTCAGGGAGATAAGAT-CTGAAATTCTTC
1 GATCTACTCCACTGTAACT-TCAGGGAGATAAGATACTG----TCTTC
* * *
42327505 -AGTCTACTCCACTGTAACCTCAGGGAGATAAG--ACT-TGATGC
1 GA-TCTACTCCACTGTAACTTCAGGGAGATAAGATACTGT-CTTC
* * * * * *
42327546 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTT
1 GATCTACTCCACTGTAACTTCAGGGAGATAAGATAC--TGTCTTC
* * * *
42327591 AAT-TCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTC
1 GATCT-ACTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTC
* * *
42327634 GATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGAT-CTAAAATTCTTC
1 GATCTACTCCACTGTAACT-TCAGGGAGATAAGATACT----GTCTTC
* * * *
42327680 -AGTCTACTCCACTGTAACCTCAGGGAGATAAGA-CCTG-ATGC
1 GA-TCTACTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTC
** ** * * * * *
42327721 GATCTACTCTGCTGTAACTTCATAGAGGTAAGATCCTTTATTTT
1 GATCTACTCCACTGTAACTTCAGGGAGATAAGATACTGT-CTTC
* ** * *
42327765 AATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTC
1 GATCTACTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTC
*
42327808 GATCTACTCCGCTGTAA-TCTCAGGGAGATAAGAT
1 GATCTACTCCACTGTAACT-TCAGGGAGATAAGAT
42327842 CTCTAATATT
Statistics
Matches: 313, Mismatches: 81, Indels: 67
0.68 0.18 0.15
Matches are distributed among these distances:
40 1 0.00
41 57 0.18
42 10 0.03
43 63 0.20
44 83 0.27
45 36 0.12
46 63 0.20
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (43 bp):
GATCTACTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTC
Found at i:42327662 original size:175 final size:174
Alignment explanation
Indices: 42327364--42327843 Score: 773
Period size: 175 Copynumber: 2.7 Consensus size: 174
42327354 CGGCTTCAAT
* * *
42327364 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * * * * *
42327429 TAACTTCAGAGAGTTAGGATTACTAG-CTTCAATCTACTTCGTTATAATCTCAGGGAGATAAGAT
66 TAACTTCAGGGAGATAGGA-TAGT-GTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGAT
*
42327493 CTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
129 CTAAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
* *
42327539 TTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTTAATTCGCTCCACT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTA-TTTTAATCCGCTCCACT
*
42327604 GTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
65 GTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGATC
42327669 TAAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
130 TAAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
* * *
42327714 CTGATGCGATCTACTCTGCTGTAACTTCATAGAGGTAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
42327779 TAACTTCAGGGAGATAGGATAGTGTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGATCT
66 TAACTTCAGGGAGATAGGATAGTGTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGATCT
42327844 CTAATATTTA
Statistics
Matches: 283, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
174 82 0.29
175 169 0.60
176 32 0.11
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (174 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAACTTCAGGGAGATAGGATAGTGTCTTCGATCTACTCCGCTGTAATCTCAGGGAGATAAGATCT
AAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
Found at i:42327840 original size:87 final size:86
Alignment explanation
Indices: 42327371--42327842 Score: 393
Period size: 87 Copynumber: 5.4 Consensus size: 86
42327361 AATCTGATGT
** *
42327371 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAACTTC
1 GATCTACTCCGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAACTTC
* *
42327436 AGAGAGTTAGGATTACTAGCTTC
66 AGGGAGATAGGA-TACT-GCTTC
* * * * * ** * *
42327459 AATCTACTTCGTTATAA-TCTCAGGGAGATAAGAT-CTGAAATTCTTCAGTCTACTCCACTGTAA
1 GATCTACTCCGCTGTAACT-TCAGAGAGATAAGATCCT-TTATT-TT-AATCCACTCCACTGTAA
* * * *
42327522 CCTCAGGGAGATA--AGACTTGATGC
62 CTTCAGGGAGATAGGATAC-TGCTTC
** * *
42327546 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTTAATTCGCTCCACTGTAACTT
1 GATCTACTCCGCTGTAACTTCAGAGAGATAAGATCCTTTA-TTTTAATCCACTCCACTGTAACTT
*
42327611 CAGGGAGATAGGATAGTGTCTTC
65 CAGGGAGATAGGATACTG-CTTC
* * ** * *
42327634 GATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGAT-CTAAAATTCTTCAGTCTACTCCACTGTAA
1 GATCTACTCCGCTGTAACT-TCAGAGAGATAAGATCCT-TTATT-TT-AATCCACTCCACTGTAA
* * * * *
42327697 CCTCAGGGAGATAAGA-CCTGATGC
62 CTTCAGGGAGATAGGATACTGCTTC
* * * *
42327721 GATCTACTCTGCTGTAACTTCATAGAGGTAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTC
1 GATCTACTCCGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAACTTC
*
42327786 AGGGAGATAGGATAGTGTCTTC
66 AGGGAGATAGGATACTG-CTTC
*
42327808 GATCTACTCCGCTGTAA-TCTCAGGGAGATAAGATC
1 GATCTACTCCGCTGTAACT-TCAGAGAGATAAGATC
42327843 TCTAATATTT
Statistics
Matches: 292, Mismatches: 72, Indels: 41
0.72 0.18 0.10
Matches are distributed among these distances:
85 28 0.10
86 30 0.10
87 106 0.36
88 75 0.26
89 29 0.10
90 24 0.08
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (86 bp):
GATCTACTCCGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAACTTC
AGGGAGATAGGATACTGCTTC
Found at i:42329084 original size:7 final size:7
Alignment explanation
Indices: 42329072--42329118 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
42329062 TTAGCCTCTC
42329072 CATTTTT
1 CATTTTT
42329079 CA-TTTT
1 CATTTTT
42329085 CATTTTT
1 CATTTTT
*
42329092 CATGTTT
1 CATTTTT
*
42329099 CA-TTCT
1 CATTTTT
42329105 CATTTTT
1 CATTTTT
42329112 CATTTTT
1 CATTTTT
42329119 TTTGACTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 10 0.29
7 24 0.71
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.66
Consensus pattern (7 bp):
CATTTTT
Found at i:42329090 original size:13 final size:13
Alignment explanation
Indices: 42329072--42329118 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
42329062 TTAGCCTCTC
42329072 CATTTTTCATTTT
1 CATTTTTCATTTT
42329085 CATTTTTCATGTTT
1 CATTTTTCAT-TTT
*
42329099 CA-TTCTCATTTTT
1 CATTTTTCA-TTTT
42329112 CATTTTT
1 CATTTTT
42329119 TTTGACTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 20 0.69
14 9 0.31
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.66
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:42329101 original size:20 final size:20
Alignment explanation
Indices: 42329076--42329114 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42329066 CCTCTCCATT
*
42329076 TTTCATTTTCATTTTTCATG
1 TTTCATTCTCATTTTTCATG
42329096 TTTCATTCTCATTTTTCAT
1 TTTCATTCTCATTTTTCAT
42329115 TTTTTTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTCATTCTCATTTTTCATG
Found at i:42330085 original size:7 final size:7
Alignment explanation
Indices: 42330075--42330105 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42330065 TTTAATTTTT
42330075 TTTCTTC
1 TTTCTTC
42330082 TTTCTTC
1 TTTCTTC
42330089 TTTCTTC
1 TTTCTTC
42330096 TTTCTTC
1 TTTCTTC
42330103 TTT
1 TTT
42330106 TTGTTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCTTC
Found at i:42330127 original size:15 final size:15
Alignment explanation
Indices: 42330103--42330141 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
42330093 TTCTTTCTTC
*
42330103 TTTTTGTTTTTG-TT
1 TTTTTATTTTTGATT
42330117 TTTTTATTTTTGATT
1 TTTTTATTTTTGATT
42330132 TTTTTATTTT
1 TTTTTATTTT
42330142 CATTTTGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (15 bp):
TTTTTATTTTTGATT
Found at i:42330146 original size:14 final size:15
Alignment explanation
Indices: 42330115--42330147 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
42330105 TTTGTTTTTG
*
42330115 TTTTTTTATTTTTGA
1 TTTTTTTATTTTTCA
42330130 TTTTTTTA-TTTTCA
1 TTTTTTTATTTTTCA
42330144 TTTT
1 TTTT
42330148 GACTTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTTTATTTTTCA
Found at i:42336669 original size:12 final size:12
Alignment explanation
Indices: 42336643--42336676 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
42336633 TTATTGTCGT
42336643 TTTATTCA-ATA
1 TTTATTCATATA
*
42336654 TTTATTCATTTA
1 TTTATTCATATA
42336666 TTTATTCATAT
1 TTTATTCATAT
42336677 GTTCGTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATTCATATA
Found at i:42340687 original size:35 final size:36
Alignment explanation
Indices: 42340638--42340737 Score: 98
Period size: 35 Copynumber: 2.8 Consensus size: 36
42340628 AAAAAAAAGG
*
42340638 GAAGAAAAATGAAAAAATTCAAAATCAAAGTA-AAAAA
1 GAAG-AAAATGAAAAAATTCAAAATCAAA-AACAAAAA
* *
42340675 -ACGAAAATGAAAAATCAATCAAAATCAAAAACAAAAA
1 GAAGAAAATGAAAAA--ATTCAAAATCAAAAACAAAAA
* *
42340712 GAAGAAAAAGTAAAAATT-AAAATCAA
1 GAAGAAAATGAAAAAATTCAAAATCAA
42340738 GGTCAAAGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
35 19 0.37
36 5 0.10
37 17 0.33
38 11 0.21
ACGTcount: A:0.70, C:0.08, G:0.09, T:0.13
Consensus pattern (36 bp):
GAAGAAAATGAAAAAATTCAAAATCAAAAACAAAAA
Found at i:42340734 original size:45 final size:44
Alignment explanation
Indices: 42340685--42340772 Score: 108
Period size: 47 Copynumber: 2.0 Consensus size: 44
42340675 ACGAAAATGA
*
42340685 AAAATCAA-TCAAA-ATCAAAAACAAAAAGAAGAAAAAGTAAAAATT
1 AAAATCAAGTCAAAGA-CAAAAAAAAAAAG-AGAAAAAG-AAAAATT
*
42340730 AAAATCAAGGTCAAAGAGAAAAAAAAAAAGAGAAAAAGAAAAA
1 AAAATCAA-GTCAAAGACAAAAAAAAAAAGAGAAAAAGAAAAA
42340773 GAGAGGCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 13 0.34
46 8 0.21
47 16 0.42
48 1 0.03
ACGTcount: A:0.73, C:0.07, G:0.11, T:0.09
Consensus pattern (44 bp):
AAAATCAAGTCAAAGACAAAAAAAAAAAGAGAAAAAGAAAAATT
Found at i:42340777 original size:16 final size:14
Alignment explanation
Indices: 42340742--42340776 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
42340732 AATCAAGGTC
42340742 AAAGAGAAAAAAAA
1 AAAGAGAAAAAAAA
*
42340756 AAAGAGAAAAAGAA
1 AAAGAGAAAAAAAA
42340770 AAAGAGA
1 AAAGAGA
42340777 GGCCAAGGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAGAGAAAAAAAA
Found at i:42343748 original size:128 final size:128
Alignment explanation
Indices: 42342745--42343730 Score: 1675
Period size: 128 Copynumber: 7.7 Consensus size: 128
42342735 ATTAGTGAAT
* * * * *
42342745 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGACGATGGCGAATCTTATCTTCCTC
1 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATC-T--TC
* * * * *
42342810 AGGAGTAGGGAAACAGATTTAAGCCACAAGTTCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
63 AAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGA
42342875 A
128 A
*
42342876 ATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
1 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
**
42342941 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTAAAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
42343004 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
1 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
42343069 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
* * *
42343132 ATTACAGATCTTGCCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
1 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
*
42343197 TGTAAGGAAGCATATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
42343260 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
1 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
*
42343325 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTAGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
* *
42343388 ATTGCAGATCTTGTCTTCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTAAAG
1 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
* * *
42343453 TGTAAGGAAGAAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGTAGTGAAATAGGTTGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
* * *
42343516 ATTGTAGATCTTGTCTCCCTAAGAAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
1 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
* * *
42343581 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGCCAGCAATGAAATAGGTTGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
42343644 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
1 ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
*
42343709 TGTAAGGAAGCAGATTGAAGCC
66 TGTAAGGAAGCAGATTTAAGCC
42343731 GATAATCCTG
Statistics
Matches: 813, Mismatches: 42, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
128 757 0.93
130 1 0.00
131 55 0.07
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (128 bp):
ATTGCAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAA
Found at i:42343960 original size:44 final size:44
Alignment explanation
Indices: 42343741--42343980 Score: 168
Period size: 44 Copynumber: 5.5 Consensus size: 44
42343731 GATAATCCTG
* * *
42343741 TCTCCCTGAAGTTGTAGTGGAACGGATTAAAGTAATAGATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAATAGATCTTA
* * * * * *
42343785 TCTCTCTGAAGTTGCAGTAGAGTGGATCGTA-TCA-AG-TCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAATAGATCTTA
* ** * * * * *
42343826 TCCCCCTGAAGTCACAGTGGGGCAGACTGAAG-AAGCAAATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAA-TAGATCTTA
* * *
42343870 TCTCCCT-AAGGTTGCAGTGGAGCAGATTGAAGTCGATA-ATCCTA
1 TCTCCCTGAA-GTTGCAGTGGAGCGGATTGAAGT-AATAGATCTTA
* * * *
42343914 TCTCCATGAAGTTGTAGTGGAACGGATTAAAGTAATAGATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAATAGATCTTA
* * *
42343958 TCTCTCTGAAGTAGCAGTAGAGC
1 TCTCCCTGAAGTTGCAGTGGAGC
42343981 AGAACGCATC
Statistics
Matches: 144, Mismatches: 43, Indels: 18
0.70 0.21 0.09
Matches are distributed among these distances:
41 26 0.18
42 2 0.01
43 8 0.06
44 104 0.72
45 3 0.02
46 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGTAATAGATCTTA
Found at i:42354238 original size:20 final size:20
Alignment explanation
Indices: 42354191--42354246 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
42354181 CATTGATTTA
42354191 TTTTT-TTTATTT-CTAGTTG
1 TTTTTATTT-TTTGCTAGTTG
42354210 TACTTTTATTTTTTGCTAGTTG
1 T--TTTTATTTTTTGCTAGTTG
*
42354232 TTTTTATTTTATGCT
1 TTTTTATTTTTTGCT
42354247 GAGACTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 7 0.22
22 11 0.34
ACGTcount: A:0.12, C:0.07, G:0.11, T:0.70
Consensus pattern (20 bp):
TTTTTATTTTTTGCTAGTTG
Found at i:42357844 original size:28 final size:28
Alignment explanation
Indices: 42357812--42357866 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
42357802 ACACTTATCA
*
42357812 TATTTCATATGT-TTTTAGAACTTTTTTT
1 TATTTCATAT-TCTTTTAGAACTCTTTTT
*
42357840 TATTTCATGTTCTTTTAGAACTCTTTT
1 TATTTCATATTCTTTTAGAACTCTTTT
42357867 ATAAAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.62
Consensus pattern (28 bp):
TATTTCATATTCTTTTAGAACTCTTTTT
Found at i:42359952 original size:37 final size:37
Alignment explanation
Indices: 42359902--42359975 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
42359892 AAAGGCAGAG
42359902 AAAGAAAAAAAAAGAATTTGTATCGATTTTCTTTTCT
1 AAAGAAAAAAAAAGAATTTGTATCGATTTTCTTTTCT
42359939 AAAGAAAAAAAAAGAATTTGTATCGATTTTCTTTTCT
1 AAAGAAAAAAAAAGAATTTGTATCGATTTTCTTTTCT
42359976 TTTTGTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (37 bp):
AAAGAAAAAAAAAGAATTTGTATCGATTTTCTTTTCT
Found at i:42370984 original size:21 final size:21
Alignment explanation
Indices: 42370960--42371056 Score: 106
Period size: 21 Copynumber: 4.6 Consensus size: 21
42370950 TAACCCTAAT
*
42370960 CCTAACACTTAACTTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
*
42370981 CCTAACCCTTCAA-TTAAAAAT
1 CCTAACCCTT-AACTTAAAAAC
*
42371002 ACTAACCCTTAACTTAAAAATC
1 CCTAACCCTTAACTTAAAAA-C
* *
42371024 CCAAACCCTAAACTTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
* *
42371045 CATAAACCTTAA
1 CCTAACCCTTAA
42371057 ACCCTAAACC
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.03
21 41 0.66
22 19 0.31
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
CCTAACCCTTAACTTAAAAAC
Found at i:42371055 original size:43 final size:42
Alignment explanation
Indices: 42370967--42371056 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 42
42370957 AATCCTAACA
* * * *
42370967 CTTAACTTAAAAACCCTAACCCTTCAATTAAAAATACTAACC
1 CTTAACTTAAAAACCCAAACCCTTAAATTAAAAACACTAAAC
42371009 CTTAACTTAAAAATCCCAAACCC-TAAACTTAAAAAC-CATAAAC
1 CTTAACTTAAAAA-CCCAAACCCTTAAA-TTAAAAACAC-TAAAC
42371052 CTTAA
1 CTTAA
42371057 ACCCTAAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 17 0.41
43 24 0.59
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (42 bp):
CTTAACTTAAAAACCCAAACCCTTAAATTAAAAACACTAAAC
Found at i:42371059 original size:29 final size:29
Alignment explanation
Indices: 42371026--42371085 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
42371016 TAAAAATCCC
*
42371026 AAACCCTAAACTTAAAAACCATAAACCTT
1 AAACCCTAAACCTAAAAACCATAAACCTT
*
42371055 AAACCCTAAACCTAAAAACCATAACCCTT
1 AAACCCTAAACCTAAAAACCATAAACCTT
42371084 AA
1 AA
42371086 CTTAAAAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (29 bp):
AAACCCTAAACCTAAAAACCATAAACCTT
Found at i:42371064 original size:14 final size:15
Alignment explanation
Indices: 42371026--42371085 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
42371016 TAAAAATCCC
42371026 AAACCCTAAA-CTTAA
1 AAACCCTAAACCTT-A
*
42371041 AAACCATAAACCTT-
1 AAACCCTAAACCTTA
*
42371055 AAACCCTAAACCTAA
1 AAACCCTAAACCTTA
* *
42371070 AAACCATAACCCTTA
1 AAACCCTAAACCTTA
42371085 A
1 A
42371086 CTTAAAAACC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 12 0.32
15 22 0.59
16 3 0.08
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (15 bp):
AAACCCTAAACCTTA
Found at i:42371073 original size:22 final size:22
Alignment explanation
Indices: 42371048--42371472 Score: 229
Period size: 22 Copynumber: 19.8 Consensus size: 22
42371038 TAAAAACCAT
42371048 AAACCTTAAACCCTAAACCTAA
1 AAACCTTAAACCCTAAACCTAA
* * *
42371070 AAACCAT-AACCCTTAACTTAA
1 AAACCTTAAACCCTAAACCTAA
*
42371091 AAACCTCAAACCCTAAACCTAA
1 AAACCTTAAACCCTAAACCTAA
* * *
42371113 AAA-CAT-AGCCCTTAACCTAA
1 AAACCTTAAACCCTAAACCTAA
* * *
42371133 AAACCCTAAACTCTAAACTTAA
1 AAACCTTAAACCCTAAACCTAA
** *
42371155 AAACCTTAAACCCTAAAAAT-T
1 AAACCTTAAACCCTAAACCTAA
* * * *
42371176 TAGCTTTAAAACCCT-AACCT-T
1 AAACCTT-AAACCCTAAACCTAA
* * *
42371197 AATCC-T-AACCCTTAACTTAA
1 AAACCTTAAACCCTAAACCTAA
* * *
42371217 AAACCCT-AACACTTAAA-TTAA
1 AAACCTTAAAC-CCTAAACCTAA
* * *
42371238 AAATGC-T-AACCCTTAACTTAA
1 AAA-CCTTAAACCCTAAACCTAA
**
42371259 AAACCCCAAACCCTAAACCTAA
1 AAACCTTAAACCCTAAACCTAA
* * *
42371281 AAACCATAAACCTTAAACTTAA
1 AAACCTTAAACCCTAAACCTAA
* *
42371303 AAATCC-CAAACTCTAAA-CTAAA
1 AAA-CCTTAAACCCTAAACCT-AA
* *
42371325 AAACCTTAAACCTTAAA-CTTA
1 AAACCTTAAACCCTAAACCTAA
** *
42371346 AAACCCCAAACACTAAACCTAA
1 AAACCTTAAACCCTAAACCTAA
* * *
42371368 AAACAC-T-AACCTTTAACTTAA
1 AAAC-CTTAAACCCTAAACCTAA
*
42371389 AAACCTTAAACCCTAAATC-ATA
1 AAACCTTAAACCCTAAACCTA-A
* * *
42371411 AAACCCTAAACCTTAAACTTAA
1 AAACCTTAAACCCTAAACCTAA
* *
42371433 AAACCATGAACCCTAAACCTAA
1 AAACCTTAAACCCTAAACCTAA
*
42371455 AAACCTTAAACCTTAAAC
1 AAACCTTAAACCCTAAAC
42371473 TTTAAAATCC
Statistics
Matches: 304, Mismatches: 78, Indels: 42
0.72 0.18 0.10
Matches are distributed among these distances:
18 6 0.02
19 4 0.01
20 26 0.09
21 85 0.28
22 179 0.59
23 4 0.01
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.22
Consensus pattern (22 bp):
AAACCTTAAACCCTAAACCTAA
Found at i:42371347 original size:6 final size:7
Alignment explanation
Indices: 42371325--42371500 Score: 69
Period size: 7 Copynumber: 24.3 Consensus size: 7
42371315 CTAAACTAAA
42371325 AAACCTT
1 AAACCTT
42371332 AAACCTT
1 AAACCTT
42371339 AAA-CTT
1 AAACCTT
**
42371345 AAAACCCC
1 -AAACCTT
42371353 AAACAC-T
1 AAAC-CTT
*
42371360 AAACCTAA
1 AAACCT-T
42371368 AAACAC-T
1 AAAC-CTT
42371375 -AACCTT
1 AAACCTT
*
42371381 TAA-CTT
1 AAACCTT
42371387 AAAAACCTT
1 --AAACCTT
*
42371396 AAACCCT
1 AAACCTT
* *
42371403 AAATCATA
1 AAA-CCTT
*
42371411 AAACCCT
1 AAACCTT
42371418 AAACCTT
1 AAACCTT
42371425 AAA-CTT
1 AAACCTT
*
42371431 AAAAACCAT
1 --AAACCTT
* *
42371440 GAACCCT
1 AAACCTT
*
42371447 AAACCTAA
1 AAACCT-T
42371455 AAACCTT
1 AAACCTT
42371462 AAACCTT
1 AAACCTT
*
42371469 AAACTTT
1 AAACCTT
42371476 AAAATCC-T
1 -AAA-CCTT
42371484 AAACCTT
1 AAACCTT
42371491 AAAACCTT
1 -AAACCTT
42371499 AA
1 AA
42371501 CTTAAAAACC
Statistics
Matches: 126, Mismatches: 23, Indels: 40
0.67 0.12 0.21
Matches are distributed among these distances:
5 1 0.01
6 16 0.13
7 70 0.56
8 32 0.25
9 7 0.06
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.23
Consensus pattern (7 bp):
AAACCTT
Found at i:42371459 original size:37 final size:36
Alignment explanation
Indices: 42371418--42371518 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 36
42371408 ATAAAACCCT
42371418 AAACCTTAAACTTAAAAACCATGAACCCTAAACCTAA
1 AAACCTTAAACTTAAAAACCAT-AACCCTAAACCTAA
**** * * *
42371455 AAACCTTAAACCTTAAACTTTAAAATCCTAAACCTTA
1 AAACCTTAAA-CTTAAAAACCATAACCCTAAACCTAA
*
42371492 AAACCTT-AACTTAAAAACCCTAACCCT
1 AAACCTTAAACTTAAAAACCATAACCCT
42371519 TAAGTTAAAT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
35 11 0.22
36 2 0.04
37 29 0.59
38 7 0.14
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.24
Consensus pattern (36 bp):
AAACCTTAAACTTAAAAACCATAACCCTAAACCTAA
Done.