Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold84
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: 4163231
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 246351 characters in sequence are not A, C, G, or T
File 10 of 11
Found at i:3684542 original size:19 final size:19
Alignment explanation
Indices: 3684515--3684607 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
3684505 ATATTCCAGC
*
3684515 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
3684534 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
* * * * *
3684553 -A-GTAATTTATTCCAG--C
1 AACTTAATTAACT-AAGATG
*
3684569 AACTTAATTAAATAAGATG
1 AACTTAATTAACTAAGATG
*
3684588 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
3684607 A
1 A
3684608 GTAATTTATT
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
17 10 0.18
18 10 0.18
19 36 0.64
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:3684568 original size:54 final size:54
Alignment explanation
Indices: 3684506--3684630 Score: 223
Period size: 54 Copynumber: 2.3 Consensus size: 54
3684496 CAACAATAAA
* *
3684506 TATTCCAGCAACTAAATTAACTAAGATGAACTTAATTAACTAAGATGAGTAATT
1 TATTCCAGCAACTAAATTAAATAAGATGAACTCAATTAACTAAGATGAGTAATT
*
3684560 TATTCCAGCAACTTAATTAAATAAGATGAACTCAATTAACTAAGATGAGTAATT
1 TATTCCAGCAACTAAATTAAATAAGATGAACTCAATTAACTAAGATGAGTAATT
3684614 TATTCCAGCAACTAAAT
1 TATTCCAGCAACTAAAT
3684631 ACTTATTCAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.31
Consensus pattern (54 bp):
TATTCCAGCAACTAAATTAAATAAGATGAACTCAATTAACTAAGATGAGTAATT
Found at i:3688499 original size:25 final size:24
Alignment explanation
Indices: 3688467--3688550 Score: 87
Period size: 25 Copynumber: 3.4 Consensus size: 24
3688457 AGCTTTAAAC
*
3688467 GGTAAGCTCTTTCGAGCTGAATAGT
1 GGTAAGCTC-TTCGAGCTGAATAAT
* * *
3688492 GGTAAGCTCCTCTGACCTGAATAAC
1 GGTAAGCTCTTC-GAGCTGAATAAT
*
3688517 GGTAAGCTCCTCCGAGCTGAATAAT
1 GGTAAGCT-CTTCGAGCTGAATAAT
*
3688542 AGTAAGCTC
1 GGTAAGCTC
3688551 ATACGATCTA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 3 0.06
25 43 0.90
26 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (24 bp):
GGTAAGCTCTTCGAGCTGAATAAT
Found at i:3705765 original size:16 final size:16
Alignment explanation
Indices: 3705744--3705811 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
3705734 GATTTGCTAT
3705744 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3705760 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
3705776 TACACCTCCAATCCAA
1 TACACCTCTAATCCAA
3705792 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3705808 TACA
1 TACA
3705812 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3707463 original size:12 final size:12
Alignment explanation
Indices: 3707446--3707479 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3707436 AATATAATGA
3707446 TAAATTTTATAT
1 TAAATTTTATAT
*
3707458 TAAATTTAATAT
1 TAAATTTTATAT
*
3707470 TAAATCTTAT
1 TAAATTTTAT
3707480 TAAAATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TAAATTTTATAT
Found at i:3712766 original size:16 final size:16
Alignment explanation
Indices: 3712745--3712775 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3712735 CTATGCATGC
*
3712745 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
3712761 AAAATACAAAAGACA
1 AAAATACAAAAGACA
3712776 TGATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:3727005 original size:413 final size:412
Alignment explanation
Indices: 3726232--3727056 Score: 1623
Period size: 413 Copynumber: 2.0 Consensus size: 412
3726222 CTGTACAGAT
*
3726232 AAATCAGAAGGGTGATTTTACGAAAACTCAGTGTATATTTCCCCATATAGAACAAGCAGACAAAA
1 AAATCAAAAGGGTGATTTTACGAAAACTCAGTGTATATTTCCCCATATAGAACAAGCAGACAAAA
3726297 TGCAGTTACTATCTGGGCTTAAGCCCTTTCGGTACCAGATTCAGTTTCAATTTGGGCCTTACCCT
66 TGCAGTTACTATCTGGGCTTAAGCCCTTTCGGTACCAGATTCAGTTTCAATTTGGGCCTTACCCT
3726362 TTTTAGTACAGAAGCAGTCATGGATTAGGGCCTTGGCCCATTACAGTATCAGTAATCAGTATAGT
131 TTTTAGTACAGAAGCAGTCATGGATTAGGGCCTTGGCCCATTACAGTATCAGTAATCAGTATAGT
3726427 ACCAGATATACAGTCACAAAATCCTACTTAGCTAGCCTCTACACACCATCTCCGTCTAACCCTAC
196 ACCAGATATACAGTCACAAAATCCTACTTAGCTAGCCTCTACACACCATCTCCGTCTAACCCTAC
3726492 ACTCCATATGGGGATATAATCAACCCACCCATCCCTACACTCCAAAAAGTACCGAATGCGGCACT
261 ACTCCATATGGGGATATAATCAACCCACCCATCCCTACACTCCAAAAAGTACCGAATGCGGCACT
3726557 AAACAGTGGTTTGGAACTGAGTTGCCAATAAATTAGGCGGAGGCCTTTCAGTACACTTCCTCCGA
326 AAACAGTGGTTTGGAACTGAGTTGCCAATAAATTAGGCGGAGGCCTTTCAGTACACTTCCTCCGA
3726622 ATAATACCAACCCCCAACCCAA
391 ATAATACCAACCCCCAACCCAA
3726644 AAATCAAAAGGGTGATTTTACGAAAACTCAGTGTATATTTCCCCATATAGAACAAGCAGACAAAA
1 AAATCAAAAGGGTGATTTTACGAAAACTCAGTGTATATTTCCCCATATAGAACAAGCAGACAAAA
*
3726709 TGCAGTTACTGTCTGGGCTTAAGCCCTTTCGGTACCAGATTCAGTTTCAATTTGGGCCTTAGCCC
66 TGCAGTTACTATCTGGGCTTAAGCCCTTTCGGTACCAGATTCAGTTTCAATTTGGGCCTTA-CCC
3726774 TTTTTAGTACAGAAGCAGTCATGGATTAGGGCCTTGGCCCATTACAGTATCAGTAATCAGTATAG
130 TTTTTAGTACAGAAGCAGTCATGGATTAGGGCCTTGGCCCATTACAGTATCAGTAATCAGTATAG
3726839 TACCAGATATACAGTCACAAAATCCTACTTAGCTAGCCTCTACACACCATCTCCGTCTAACCCTA
195 TACCAGATATACAGTCACAAAATCCTACTTAGCTAGCCTCTACACACCATCTCCGTCTAACCCTA
3726904 CACTCCATATGGGGATATAATCAACCCACCCATCCCTACACTCCAAAAAGTACCGAATGCGGCAC
260 CACTCCATATGGGGATATAATCAACCCACCCATCCCTACACTCCAAAAAGTACCGAATGCGGCAC
3726969 TAAACAGTGGTTTGGAACTGAGTTGCCAATAAATTAGGCGGAGGCCTTTCAGTACACTTCCTCCG
325 TAAACAGTGGTTTGGAACTGAGTTGCCAATAAATTAGGCGGAGGCCTTTCAGTACACTTCCTCCG
3727034 AATAATACCAACCCCCAACCCAA
390 AATAATACCAACCCCCAACCCAA
3727057 TGCAATGTAA
Statistics
Matches: 410, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
412 124 0.30
413 286 0.70
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (412 bp):
AAATCAAAAGGGTGATTTTACGAAAACTCAGTGTATATTTCCCCATATAGAACAAGCAGACAAAA
TGCAGTTACTATCTGGGCTTAAGCCCTTTCGGTACCAGATTCAGTTTCAATTTGGGCCTTACCCT
TTTTAGTACAGAAGCAGTCATGGATTAGGGCCTTGGCCCATTACAGTATCAGTAATCAGTATAGT
ACCAGATATACAGTCACAAAATCCTACTTAGCTAGCCTCTACACACCATCTCCGTCTAACCCTAC
ACTCCATATGGGGATATAATCAACCCACCCATCCCTACACTCCAAAAAGTACCGAATGCGGCACT
AAACAGTGGTTTGGAACTGAGTTGCCAATAAATTAGGCGGAGGCCTTTCAGTACACTTCCTCCGA
ATAATACCAACCCCCAACCCAA
Found at i:3727331 original size:17 final size:18
Alignment explanation
Indices: 3727297--3727331 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3727287 CCATGATGTT
*
3727297 CGCCCGTGTAGGCCCACA
1 CGCCCGTGTAGACCCACA
3727315 CGCCCGTGT-GACCCACA
1 CGCCCGTGTAGACCCACA
3727332 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.17, C:0.46, G:0.26, T:0.11
Consensus pattern (18 bp):
CGCCCGTGTAGACCCACA
Found at i:3730161 original size:43 final size:42
Alignment explanation
Indices: 3730073--3730173 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 42
3730063 CAACGTCCCT
* *
3730073 GACGTGGTCTTACATGTAAACACATATCGATGCCACTGTCCCA
1 GACGTGGTCTTACACGTAAACACATATCGATGCAACTGT-CCA
3730116 GACAG-GGTCTTACACGTAAACACA-AGTCGATGCAAACGTGT-CA
1 GAC-GTGGTCTTACACGTAAACACATA-TCGATGC-AAC-TGTCCA
3730159 GACGTGGTCTTACAC
1 GACGTGGTCTTACAC
3730174 AATAACACAT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
42 2 0.04
43 43 0.84
44 3 0.06
45 3 0.06
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.23
Consensus pattern (42 bp):
GACGTGGTCTTACACGTAAACACATATCGATGCAACTGTCCA
Found at i:3755002 original size:42 final size:42
Alignment explanation
Indices: 3754956--3755069 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 42
3754946 GTTCTAAACA
* *
3754956 AAAACCCTTAAGGGTTGAACGGAAGCTCATAAGAGCTGAAC-G
1 AAAACCCTTAAGGGTT-AACGAAAGCTCATAAGAGCTAAACTG
* * *
3754998 AAAACCCATAAGGGTTAAAGTAAAGCTCAAAAGAGCTAAACTG
1 AAAACCCTTAAGGGTTAACG-AAAGCTCATAAGAGCTAAACTG
*
3755041 -AAACCCATT-AGGGTTAAACGAAAACTCAT
1 AAAACCC-TTAAGGGTT-AACGAAAGCTCAT
3755070 GTGAGTTAAC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
41 3 0.05
42 51 0.86
43 5 0.08
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (42 bp):
AAAACCCTTAAGGGTTAACGAAAGCTCATAAGAGCTAAACTG
Found at i:3755007 original size:21 final size:21
Alignment explanation
Indices: 3754956--3755009 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
3754946 GTTCTAAACA
* * *
3754956 AAAACCCTTAAGGGTTGAACG
1 AAAACCCATAAGAGCTGAACG
* * *
3754977 GAAGCTCATAAGAGCTGAACG
1 AAAACCCATAAGAGCTGAACG
3754998 AAAACCCATAAG
1 AAAACCCATAAG
3755010 GGTTAAAGTA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (21 bp):
AAAACCCATAAGAGCTGAACG
Found at i:3758055 original size:197 final size:196
Alignment explanation
Indices: 3757721--3758107 Score: 720
Period size: 197 Copynumber: 2.0 Consensus size: 196
3757711 TTTTGCATCT
*
3757721 TTCTTCGCAAAAAGATATCTCAACGCCGAGTGATTAGTAAAATGGCAACCTTTGCGCCAACAAGA
1 TTCTTCGCAAAAAGATATCTCAACGCCGAGTGATCAGTAAAATGGCAACCTTTGCGCCAACAAGA
* *
3757786 TAAGAACGAAACTTTTCGAAAGTAAAGACTACAGCCAACAATTCTTTCTCTATAGTGGTATAATT
66 TAAGAACGAAACTTGTCGAAAGTAAAGACTACAACCAACAATTCTTTCTCTATAGTGGTATAATT
3757851 GATTTGAGCCTCTGTAAGAGTTTTTCTAGCATAATAGATGGTGTGAAATATTTTTCCCTTACAAC
131 GATTTGAGCCTCTGTAAGAGTTTTTCTAGCATAATAGATGGTGTGAAATATTTTTCCCTTACAAC
3757916 C
196 C
* *
3757917 TTCTTCGCAAAAAGATATCTCAATGCCGAGTGATCAGTAAATATGGCAACCTTTGCGCCGACAAG
1 TTCTTCGCAAAAAGATATCTCAACGCCGAGTGATCAGTAAA-ATGGCAACCTTTGCGCCAACAAG
3757982 ATAAGAACGAAACTTGTCGAAAGTAAAGACTACAACCAACAATTCTTTCTCTATAGTGGTATAAT
65 ATAAGAACGAAACTTGTCGAAAGTAAAGACTACAACCAACAATTCTTTCTCTATAGTGGTATAAT
3758047 TGATTTGAGCCTCTGTAAGAGTTTTTCTAGCATAATAGATGGTGTGAAATATTTTTCCCTT
130 TGATTTGAGCCTCTGTAAGAGTTTTTCTAGCATAATAGATGGTGTGAAATATTTTTCCCTT
3758108 GTGTTGTCCT
Statistics
Matches: 185, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
196 39 0.21
197 146 0.79
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (196 bp):
TTCTTCGCAAAAAGATATCTCAACGCCGAGTGATCAGTAAAATGGCAACCTTTGCGCCAACAAGA
TAAGAACGAAACTTGTCGAAAGTAAAGACTACAACCAACAATTCTTTCTCTATAGTGGTATAATT
GATTTGAGCCTCTGTAAGAGTTTTTCTAGCATAATAGATGGTGTGAAATATTTTTCCCTTACAAC
C
Found at i:3763322 original size:21 final size:23
Alignment explanation
Indices: 3763298--3763350 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
3763288 GTGTTGTGGT
3763298 TGCATCT-AATTT-TGGTGTAGA
1 TGCATCTGAATTTATGGTGTAGA
* *
3763319 TGCATCTGACTTTATTGTGTAGA
1 TGCATCTGAATTTATGGTGTAGA
3763342 TGCATCTGA
1 TGCATCTGA
3763351 GGGTGATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 7 0.25
22 4 0.14
23 17 0.61
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (23 bp):
TGCATCTGAATTTATGGTGTAGA
Found at i:3766658 original size:40 final size:39
Alignment explanation
Indices: 3766614--3766728 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 39
3766604 CTGTTTTCAT
* *
3766614 TTCGGTGCCTCTGTTTACACTTTGGTGCCTCTACTTGTGC
1 TTCGGTGCCTCTGTTTACACTTCGGTGCCTCTA-TTATGC
* ** *
3766654 TTCGGTGCCTCTGATTACGGTTCAGTGCCTCTGATTATGC
1 TTCGGTGCCTCTGTTTACACTTCGGTGCCTCT-ATTATGC
* *
3766694 TTCGGTGCCTCTGTTTGCACTTCGGTGGCTCTATT
1 TTCGGTGCCTCTGTTTACACTTCGGTGCCTCTATT
3766729 TGCACTTCGA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
39 3 0.05
40 58 0.94
41 1 0.02
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (39 bp):
TTCGGTGCCTCTGTTTACACTTCGGTGCCTCTATTATGC
Found at i:3766730 original size:20 final size:20
Alignment explanation
Indices: 3766588--3766747 Score: 101
Period size: 20 Copynumber: 8.0 Consensus size: 20
3766578 TTGTATAGGA
* * *
3766588 TTGCATTTCGATGCCTCTGT
1 TTGCACTTCGGTGCCTCTAT
* * *
3766608 TTTCATTTCGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTAT
* * *
3766628 TTACACTTTGGTGCCTCTAC
1 TTGCACTTCGGTGCCTCTAT
**
3766648 TTGTGCTTCGGTGCCTCTGA-
1 TTGCACTTCGGTGCCTCT-AT
* ** *
3766668 TTACGGTTCAGTGCCTCTGAT
1 TTGCACTTCGGTGCCTCT-AT
*
3766689 TATG--CTTCGGTGCCTCTGT
1 T-TGCACTTCGGTGCCTCTAT
*
3766708 TTGCACTTCGGTGGCTCTAT
1 TTGCACTTCGGTGCCTCTAT
*
3766728 TTGCACTTCGATGCTCTCTA
1 TTGCACTTCGGTGC-CTCTA
3766748 GTGTGTTTTG
Statistics
Matches: 111, Mismatches: 23, Indels: 11
0.77 0.16 0.08
Matches are distributed among these distances:
18 2 0.02
19 2 0.02
20 99 0.89
21 7 0.06
22 1 0.01
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.42
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTAT
Found at i:3772154 original size:20 final size:20
Alignment explanation
Indices: 3772131--3772193 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
3772121 AAAATTACAA
3772131 AAAAAATTTAAAATAATTTT
1 AAAAAATTTAAAATAATTTT
*
3772151 AAAAAATTCAAAATAATTTT
1 AAAAAATTTAAAATAATTTT
*
3772171 -TAAAATTTAAAAT-ATTTAT
1 AAAAAATTTAAAATAATTT-T
3772190 AAAA
1 AAAA
3772194 TTCCAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.11
19 12 0.32
20 21 0.57
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAATTTAAAATAATTTT
Found at i:3772201 original size:18 final size:18
Alignment explanation
Indices: 3772133--3772207 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
3772123 AATTACAAAA
* *
3772133 AAAATTTAAAATAATTTTAA
1 AAAATTCAAAAT-A-TTTAT
*
3772153 AAAATTCAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
*
3772172 AAAATTTAAAATATTTAT
1 AAAATTCAAAATATTTAT
*
3772190 AAAATTCCAAAT-TTTAT
1 AAAATTCAAAATATTTAT
3772207 A
1 A
3772208 TTTTTTCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
17 6 0.12
18 15 0.31
19 14 0.29
20 13 0.27
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:3772237 original size:18 final size:18
Alignment explanation
Indices: 3772203--3772239 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3772193 ATTCCAAATT
3772203 TTATATTTTTTCAAAAAA
1 TTATATTTTTTCAAAAAA
*
3772221 TTATGATTTTTTTAAAAAA
1 TTAT-ATTTTTTCAAAAAA
3772240 ATCCTAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
TTATATTTTTTCAAAAAA
Found at i:3772733 original size:38 final size:38
Alignment explanation
Indices: 3772691--3772770 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
3772681 TATTTTTAAC
* *
3772691 TAATAAGTATAAATTAAATTTTAA-TATTTTTAAATATG
1 TAATAAGTAT-AATTAAATTATAATTATTTTTAAATATA
* * *
3772729 TAATAATTCTGATTAAATTATAATTATTTTTAAATATA
1 TAATAAGTATAATTAAATTATAATTATTTTTAAATATA
3772767 TAAT
1 TAAT
3772771 TATCTCAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 11 0.31
38 25 0.69
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (38 bp):
TAATAAGTATAATTAAATTATAATTATTTTTAAATATA
Found at i:3772770 original size:18 final size:18
Alignment explanation
Indices: 3772715--3772773 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
3772705 TAAATTTTAA
*
3772715 TATTTTTAAATATGTAAT
1 TATTTTTAAATATATAAT
*
3772733 AATTCTGATTAAAT-TATAAT
1 TATT-T--TTAAATATATAAT
3772753 TATTTTTAAATATATAAT
1 TATTTTTAAATATATAAT
3772771 TAT
1 TAT
3772774 CTCAACTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 6 0.18
18 12 0.35
19 2 0.06
20 8 0.24
21 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTTTTAAATATATAAT
Found at i:3776435 original size:14 final size:15
Alignment explanation
Indices: 3776416--3776445 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3776406 TAAAGAAAAG
3776416 AAATAAATAAA-GAA
1 AAATAAATAAACGAA
3776430 AAATAAATAAACGAA
1 AAATAAATAAACGAA
3776445 A
1 A
3776446 TAAATTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (15 bp):
AAATAAATAAACGAA
Found at i:3776450 original size:17 final size:16
Alignment explanation
Indices: 3776395--3776450 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
3776385 AAGGGAATAC
*
3776395 AAATAAATAACTAAAG
1 AAATAAATAAATAAAG
*
3776411 AAAAGAAATAAATAAAG
1 -AAATAAATAAATAAAG
3776428 -AA-AAATAAATAAACG
1 AAATAAATAAATAAA-G
3776443 AAATAAAT
1 AAATAAAT
3776451 TGATAAACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 11 0.32
15 3 0.09
16 2 0.06
17 18 0.53
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (16 bp):
AAATAAATAAATAAAG
Found at i:3778176 original size:25 final size:25
Alignment explanation
Indices: 3778121--3778169 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
3778111 TAATTTCAAT
3778121 GATTGGTTTGAAATCATAAGTGGAC
1 GATTGGTTTGAAATCATAAGTGGAC
3778146 GATTGGTTTGAAATCATAAGTGGA
1 GATTGGTTTGAAATCATAAGTGGA
3778170 TGTTTGGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.33
Consensus pattern (25 bp):
GATTGGTTTGAAATCATAAGTGGAC
Found at i:3788098 original size:12 final size:11
Alignment explanation
Indices: 3788071--3788108 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
3788061 GAAAATAGTC
3788071 AAAATTAATA-
1 AAAATTAATAT
3788081 AAAATTAACTAT
1 AAAATTAA-TAT
3788093 AAAATTAAT-T
1 AAAATTAATAT
3788103 AAAATT
1 AAAATT
3788109 CATCATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:3794880 original size:29 final size:29
Alignment explanation
Indices: 3794838--3794898 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
3794828 ATTTATTTAA
3794838 ACAATGAATAAATAAATAAAGTTAATTTC
1 ACAATGAATAAATAAATAAAGTTAATTTC
3794867 ACAATGAATAAATAAATAAAGTTAATTTC
1 ACAATGAATAAATAAATAAAGTTAATTTC
3794896 ACA
1 ACA
3794899 TTTCACTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.30
Consensus pattern (29 bp):
ACAATGAATAAATAAATAAAGTTAATTTC
Found at i:3795033 original size:17 final size:17
Alignment explanation
Indices: 3795013--3795057 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3795003 AGAAAAGTGG
* *
3795013 CATTGTAAGAATGTTTA
1 CATTGCAAGAACGTTTA
*
3795030 CATTGCCAGAACGTTTA
1 CATTGCAAGAACGTTTA
*
3795047 CATTGCCAGAA
1 CATTGCAAGAA
3795058 AGACAACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (17 bp):
CATTGCAAGAACGTTTA
Found at i:3812517 original size:45 final size:45
Alignment explanation
Indices: 3812444--3812604 Score: 155
Period size: 45 Copynumber: 3.6 Consensus size: 45
3812434 ACCACATAGC
* * * *
3812444 ACCACCCTT-ATAGTCAATGATACTCGGTGGAATCAAAACATAGCA
1 ACCA-CCTTCATAATCAATGATACCCGGTGGAATCAAAACACAACA
* * * **
3812489 ACCACCTTCATAATTAGT-AGTACCCGGTGGAACCAGCACACAACA
1 ACCACCTTCATAATCAATGA-TACCCGGTGGAATCAAAACACAACA
* **
3812534 ACCACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACA
1 ACCACCTTCATAATCAATGATACCCGGTGGAATCAAAACACAACA
* * *
3812579 ACCACATTTATAATCAATGGTACCCG
1 ACCACCTTCATAATCAATGATACCCG
3812605 ATAACGTAGT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
44 5 0.05
45 92 0.94
46 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (45 bp):
ACCACCTTCATAATCAATGATACCCGGTGGAATCAAAACACAACA
Found at i:3824189 original size:27 final size:27
Alignment explanation
Indices: 3824154--3824211 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3824144 TTCTCTCAAT
*
3824154 GTTCGCCATACGCACTATT-TCTTCAGA
1 GTTCACCATACGCACTATTCT-TTCAGA
* *
3824181 GTTCACCATATGTACTATTCTTTCAGA
1 GTTCACCATACGCACTATTCTTTCAGA
3824208 GTTC
1 GTTC
3824212 GACATATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (27 bp):
GTTCACCATACGCACTATTCTTTCAGA
Found at i:3824229 original size:27 final size:27
Alignment explanation
Indices: 3824175--3824229 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3824165 GCACTATTTC
* *
3824175 TTCAGAGTTCACCATATGTACTATTCT
1 TTCAGAGTTCACCATATGTACCACTCT
*
3824202 TTCAGAGTTCGA-CATATTTACCACTCT
1 TTCAGAGTTC-ACCATATGTACCACTCT
3824229 T
1 T
3824230 CTCTTTCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.40
Consensus pattern (27 bp):
TTCAGAGTTCACCATATGTACCACTCT
Found at i:3824348 original size:27 final size:27
Alignment explanation
Indices: 3824299--3824425 Score: 157
Period size: 27 Copynumber: 4.7 Consensus size: 27
3824289 CTAGAATGCA
* *
3824299 CCACAAAGGAGTTCC-TTTCCATAGATCG
1 CCACAAAGG-CTTCCATTT-CATAGATTG
*
3824327 CCACAAAGCCTTCCATTTCATAGATTG
1 CCACAAAGGCTTCCATTTCATAGATTG
* *
3824354 CCACGAAGGCTTCCATTTCATAGAATG
1 CCACAAAGGCTTCCATTTCATAGATTG
* * *
3824381 TCACAAAGGCTTCCATTTCACAAATTG
1 CCACAAAGGCTTCCATTTCATAGATTG
3824408 CCACAAAGGCTTCCATTT
1 CCACAAAGGCTTCCATTT
3824426 TTTTGGTGTG
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
27 75 0.87
28 11 0.13
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (27 bp):
CCACAAAGGCTTCCATTTCATAGATTG
Found at i:3826910 original size:10 final size:10
Alignment explanation
Indices: 3826887--3826916 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
3826877 CATATTGAAC
3826887 ATATTTTCACA
1 ATATTTT-ACA
3826898 ATATTTTACA
1 ATATTTTACA
3826908 ATATTTTAC
1 ATATTTTAC
3826917 CAAGGGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATTTTACA
Found at i:3833638 original size:6 final size:6
Alignment explanation
Indices: 3833627--3833665 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3833617 AGGTTTTTAA
* * *
3833627 AAATGG AAATGG AAACGA AAATGA AAATGG AAATGG AAA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAA
3833666 CTTGCAATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.59, C:0.03, G:0.26, T:0.13
Consensus pattern (6 bp):
AAATGG
Found at i:3837713 original size:6 final size:6
Alignment explanation
Indices: 3837688--3837719 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3837678 TCAAAGTTAT
3837688 TATAAA TA-AAA TAT-AA TATAAA TATAAA TATA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATA
3837720 TTGATATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TATAAA
Found at i:3840346 original size:82 final size:82
Alignment explanation
Indices: 3840209--3840461 Score: 488
Period size: 82 Copynumber: 3.1 Consensus size: 82
3840199 ATTTGTCCTC
*
3840209 ACAATTTCTTGAGCACAAGGACTCAATTCTTCTTGCTAAAGTTGGGATTCCTACATCATTATTTA
1 ACAATTTCTTGAGCACAAGGACTCAATTCTTCCTGCTAAAGTTGGGATTCCTACATCATTATTTA
3840274 CCTCATTGATCAATTTG
66 CCTCATTGATCAATTTG
3840291 ACAATTTCTTGAGCACAAGGACTCAATTCTTCCTGCTAAAGTTGGGATTCCTACATCATTATTTA
1 ACAATTTCTTGAGCACAAGGACTCAATTCTTCCTGCTAAAGTTGGGATTCCTACATCATTATTTA
3840356 CCTCATTGATCAATTTG
66 CCTCATTGATCAATTTG
3840373 ACAATTTCTTGAGCACAAGGACTCAATTCTTCCTGCTAAAGTTGGGATTCCTACATCATTATTTA
1 ACAATTTCTTGAGCACAAGGACTCAATTCTTCCTGCTAAAGTTGGGATTCCTACATCATTATTTA
3840438 CCTCATTGATCAATTTG
66 CCTCATTGATCAATTTG
3840455 ACGAATT
1 AC-AATT
3840462 CAAGGTTGCC
Statistics
Matches: 169, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
82 165 0.98
83 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (82 bp):
ACAATTTCTTGAGCACAAGGACTCAATTCTTCCTGCTAAAGTTGGGATTCCTACATCATTATTTA
CCTCATTGATCAATTTG
Found at i:3842934 original size:20 final size:20
Alignment explanation
Indices: 3842909--3842954 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3842899 TTTCATGGGC
3842909 TTGGGCCGTA-ATGGGCCATG
1 TTGGGCCG-AGATGGGCCATG
*
3842929 TTGGGCCGAGATGGGCCGTG
1 TTGGGCCGAGATGGGCCATG
3842949 -TGGGCC
1 TTGGGCC
3842955 AATGGGCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.11, C:0.22, G:0.46, T:0.22
Consensus pattern (20 bp):
TTGGGCCGAGATGGGCCATG
Found at i:3843247 original size:27 final size:28
Alignment explanation
Indices: 3843216--3843279 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
3843206 AATAACCAAA
* *
3843216 ATACCCCTAAAAGGTA-AAATGACTATT
1 ATACCCCTAAAAGATAGAAATGACCATT
* * *
3843243 TTACCCCTAATAGATAGGAATGACCATT
1 ATACCCCTAAAAGATAGAAATGACCATT
3843271 ATACCCCTA
1 ATACCCCTA
3843280 GAGGTAGGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (28 bp):
ATACCCCTAAAAGATAGAAATGACCATT
Found at i:3843511 original size:25 final size:26
Alignment explanation
Indices: 3843470--3843530 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
3843460 TTTAAAGTAC
* *
3843470 TTTTAAAATAATTTTTTTATTTTTTAT
1 TTTTAAAATAA-TTTTTTAATGTTTAT
3843497 TTTTAAAATAA-TTTTTAATGTTTAT
1 TTTTAAAATAATTTTTTAATGTTTAT
*
3843522 TTTAAAAAT
1 TTTTAAAAT
3843531 GGGCCGGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 20 0.65
27 11 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTAAAATAATTTTTTAATGTTTAT
Found at i:3843771 original size:26 final size:26
Alignment explanation
Indices: 3843735--3843815 Score: 101
Period size: 26 Copynumber: 3.1 Consensus size: 26
3843725 TTTGCCACAT
* *
3843735 ATACTGTTACTAGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* *
3843761 ATACTGATACTGGTAGCTTCGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
3843787 ATACT-ATTACTGGCAGCTTTGCTGTG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
3843813 ATA
1 ATA
3843816 TTGGTGTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 46 0.98
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:3866887 original size:20 final size:20
Alignment explanation
Indices: 3866862--3866900 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3866852 TGAGTTATTT
3866862 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
3866882 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
3866901 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:3877741 original size:18 final size:18
Alignment explanation
Indices: 3877718--3877758 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3877708 ATATTTATGC
3877718 CTTTATTCTGCCTTAGTT
1 CTTTATTCTGCCTTAGTT
* **
3877736 CTTTATTTTGTTTTAGTT
1 CTTTATTCTGCCTTAGTT
3877754 CTTTA
1 CTTTA
3877759 AGAAAAAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.10, T:0.63
Consensus pattern (18 bp):
CTTTATTCTGCCTTAGTT
Found at i:3883494 original size:14 final size:15
Alignment explanation
Indices: 3883471--3883499 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3883461 TGATTAAAGA
3883471 TATTTCTTGAAAAAT
1 TATTTCTTGAAAAAT
3883486 TATTT-TTGAAAAAT
1 TATTTCTTGAAAAAT
3883500 CTTAGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (15 bp):
TATTTCTTGAAAAAT
Found at i:3883640 original size:19 final size:19
Alignment explanation
Indices: 3883618--3883654 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3883608 GCCCAATGAG
3883618 TGAAAATT-AGACCTGAGAT
1 TGAAAATTGAGACC-GAGAT
3883637 TGAAAATTGAGACCGAGA
1 TGAAAATTGAGACCGAGA
3883655 ACCCAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (19 bp):
TGAAAATTGAGACCGAGAT
Found at i:3884089 original size:58 final size:61
Alignment explanation
Indices: 3883976--3884089 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
3883966 TGATTATCTT
*
3883976 AATATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTCTATTAATTTAATAGATTA
1 AATATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATAGATTA
* * *
3884037 AATATTTAATTTAATTTAATATTTTTC-T-T-GATAAGTATTATATTAATTTAATA
1 AATATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATA
3884090 TTAAAGTGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 23 0.47
59 1 0.02
60 1 0.02
61 24 0.49
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (61 bp):
AATATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATAGATTA
Found at i:3884108 original size:58 final size:59
Alignment explanation
Indices: 3883976--3884110 Score: 161
Period size: 58 Copynumber: 2.3 Consensus size: 59
3883966 TGATTATCTT
* *
3883976 AATATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTCTATTAATTTAATAGATTA
1 AATATT-AATTTAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATA-ATTA
*
3884037 AATATTTAATTTAATTTAATATTTTTC-T-T-GATAAGTATTATATTAATTTAAT-ATTA
1 AATA-TTAATTTAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATAATTA
3884093 AAGTGATTAAGTTTAATT
1 AA-T-ATTAA-TTTAATT
3884111 ATAGTTGAAC
Statistics
Matches: 67, Mismatches: 3, Indels: 11
0.83 0.04 0.14
Matches are distributed among these distances:
56 6 0.09
57 5 0.07
58 30 0.45
59 1 0.01
60 1 0.01
61 22 0.33
62 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (59 bp):
AATATTAATTTAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATAATTA
Found at i:3887030 original size:26 final size:26
Alignment explanation
Indices: 3887001--3887050 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3886991 AGATCGGTGG
*
3887001 CGATTCCAATT-TTGATTTTTTAAAGT
1 CGATCCCAATTATT-ATTTTTTAAAGT
*
3887027 CGATCCCCATTATTATTTTTTAAA
1 CGATCCCAATTATTATTTTTTAAA
3887051 TGAAAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (26 bp):
CGATCCCAATTATTATTTTTTAAAGT
Found at i:3887670 original size:22 final size:23
Alignment explanation
Indices: 3887632--3887675 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3887622 TATTGGTTGT
*
3887632 TGATTTTTGTTAATTTA-TTAAG
1 TGATTTTTGATAATTTAGTTAAG
3887654 TGATTTTT-ATAATTTTAGTTAA
1 TGATTTTTGATAA-TTTAGTTAA
3887676 AGGATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.16
22 12 0.63
23 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (23 bp):
TGATTTTTGATAATTTAGTTAAG
Found at i:3891334 original size:14 final size:15
Alignment explanation
Indices: 3891312--3891349 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3891302 TTGATCTATA
3891312 AAATA-ATTAAATT-
1 AAATATATTAAATTG
*
3891325 AAATTTATTAAATTG
1 AAATATATTAAATTG
3891340 AAATATATTA
1 AAATATATTA
3891350 TCATATTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 4 0.19
14 8 0.38
15 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
AAATATATTAAATTG
Found at i:3894247 original size:22 final size:21
Alignment explanation
Indices: 3894204--3894254 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
3894194 TCTCCTTATA
* *
3894204 TATATATGTTTTATAATTATT
1 TATATATGTTATATAATAATT
*
3894225 TATATCATGTTATATTATAATT
1 TATAT-ATGTTATATAATAATT
3894247 TGATATAT
1 T-ATATAT
3894255 ATGTATGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 16 0.64
23 4 0.16
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (21 bp):
TATATATGTTATATAATAATT
Found at i:3903267 original size:9 final size:9
Alignment explanation
Indices: 3903253--3903388 Score: 94
Period size: 9 Copynumber: 15.1 Consensus size: 9
3903243 CAGTAGTTCA
3903253 ACTAATAAT
1 ACTAATAAT
*
3903262 ACTAATACT
1 ACTAATAAT
* *
3903271 ACTACTACT
1 ACTAATAAT
* *
3903280 ACTACTACT
1 ACTAATAAT
* *
3903289 ACTACTACT
1 ACTAATAAT
*
3903298 ACTACTAAT
1 ACTAATAAT
*
3903307 AATAATAAT
1 ACTAATAAT
*
3903316 AATAATAAT
1 ACTAATAAT
*
3903325 AATAATAAT
1 ACTAATAAT
*
3903334 AATAATAAT
1 ACTAATAAT
*
3903343 AATAATAAT
1 ACTAATAAT
* *
3903352 AATAATAGT
1 ACTAATAAT
*
3903361 AAC-AGTAAT
1 -ACTAATAAT
**
3903370 AAAAATAAT
1 ACTAATAAT
3903379 ACTAATAAT
1 ACTAATAAT
3903388 A
1 A
3903389 AATAATAATG
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
8 1 0.01
9 110 0.98
10 1 0.01
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (9 bp):
ACTAATAAT
Found at i:3903273 original size:3 final size:3
Alignment explanation
Indices: 3903261--3903304 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3903251 CAACTAATAA
*
3903261 TAC TAA TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
3903305 ATAATAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:3903309 original size:3 final size:3
Alignment explanation
Indices: 3903303--3903397 Score: 136
Period size: 3 Copynumber: 31.3 Consensus size: 3
3903293 CTACTACTAC
3903303 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
3903351 TAA TAA TAG TAA CAG TAA TAA AAA TAA TAC TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
3903397 T
1 T
3903398 GAACCAAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
3 78 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3903438 original size:11 final size:10
Alignment explanation
Indices: 3903304--3903449 Score: 99
Period size: 9 Copynumber: 14.4 Consensus size: 10
3903294 TACTACTACT
3903304 AATAATAAT-
1 AATAATAATA
3903313 AATAATAAT-
1 AATAATAATA
3903322 AATAATAAT-
1 AATAATAATA
3903331 AATAATAAT-
1 AATAATAATA
3903340 AATAATAAT-
1 AATAATAATA
3903349 AATAATAATA
1 AATAATAATA
* *
3903359 GTAACAGTAATA
1 --AATAATAATA
3903371 AA-AATAAT-
1 AATAATAATA
*
3903379 ACTAATAATA
1 AATAATAATA
3903389 AATAATAATGAA
1 AATAATAAT--A
* *
3903401 CCAAAAATCATA
1 --AATAATAATA
*
3903413 ATTAGAGTAATA
1 AATA-A-TAATA
3903425 AATAATATATA
1 AATAATA-ATA
*
3903436 AATTATAATA
1 AATAATAATA
3903446 AATA
1 AATA
3903450 GGGAAAGGCC
Statistics
Matches: 112, Mismatches: 13, Indels: 23
0.76 0.09 0.16
Matches are distributed among these distances:
8 1 0.01
9 56 0.50
10 20 0.18
11 11 0.10
12 17 0.15
14 7 0.06
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (10 bp):
AATAATAATA
Found at i:3912991 original size:20 final size:20
Alignment explanation
Indices: 3912966--3913018 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3912956 GGAAAAGACG
3912966 GCCTAGGGTGATATCACACA
1 GCCTAGGGTGATATCACACA
* **
3912986 GCCTAGGGTGACATCACATG
1 GCCTAGGGTGATATCACACA
*
3913006 GCCTAGAGTGATA
1 GCCTAGGGTGATA
3913019 GGGTGATATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (20 bp):
GCCTAGGGTGATATCACACA
Found at i:3918133 original size:14 final size:14
Alignment explanation
Indices: 3918113--3918151 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
3918103 TCAAACAAAC
*
3918113 AAAAAATTAAAATG
1 AAAAAATTAAAATA
*
3918127 TAAAAATT-AAATA
1 AAAAAATTAAAATA
3918140 AAAAAATTAAAA
1 AAAAAATTAAAA
3918152 AATAGCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAAAATTAAAATA
Found at i:3920843 original size:12 final size:12
Alignment explanation
Indices: 3920826--3920850 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3920816 TGAGGGATAT
3920826 GATGGAAGAAGA
1 GATGGAAGAAGA
3920838 GATGGAAGAAGA
1 GATGGAAGAAGA
3920850 G
1 G
3920851 GCAACAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GATGGAAGAAGA
Found at i:3953160 original size:14 final size:15
Alignment explanation
Indices: 3953131--3953163 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3953121 AAGTGAGTAA
3953131 AAAAGAATGAAAAAG
1 AAAAGAATGAAAAAG
3953146 AAAAGAATG-AAAAG
1 AAAAGAATGAAAAAG
3953160 AAAA
1 AAAA
3953164 ATACTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
AAAAGAATGAAAAAG
Found at i:3953164 original size:15 final size:14
Alignment explanation
Indices: 3953129--3953164 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
3953119 CAAAGTGAGT
3953129 AAAAAAGAATGAAA
1 AAAAAAGAATGAAA
3953143 AAGAAAAGAATGAAA
1 AA-AAAAGAATGAAA
3953158 AGAAAAA
1 A-AAAAA
3953165 TACTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 17 0.85
16 1 0.05
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (14 bp):
AAAAAAGAATGAAA
Found at i:3963644 original size:31 final size:31
Alignment explanation
Indices: 3963608--3963678 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
3963598 AAGAAAAGAT
**
3963608 AATAGTTCAGC-GACTTAAATAAAAACTTTTG
1 AATAGTTCA-CTGACTTAAATAAAAACTTTCA
*
3963639 AATAGTTCACTGGCTTAAATAAAAACTTTCA
1 AATAGTTCACTGACTTAAATAAAAACTTTCA
3963670 AATAGTTCA
1 AATAGTTCA
3963679 ATAACTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (31 bp):
AATAGTTCACTGACTTAAATAAAAACTTTCA
Found at i:3965155 original size:175 final size:175
Alignment explanation
Indices: 3964859--3965201 Score: 614
Period size: 175 Copynumber: 2.0 Consensus size: 175
3964849 ATGCCCTAAC
3964859 AACAAACATGGATCTCTTTGATCTTTTCTAGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
1 AACAAACATGGATCTCTTTGATCTTTTCTAGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
* * *
3964924 GCTAAAGTCCCCACACCTTTGCTAGTATGGTTGTTATTTGAAGTGATTTGAATAATTAACGGGAA
66 GCTAAAGTCCCCACACCTTTGCTAGCACGGTTGTTATTTGAAGTGATTTAAATAATTAACGGGAA
*
3964989 TCTGTGGTGATTAGAGGTACTCATGGTCGGGTCAGGCCAAGTTTG
131 TCTGTGGTGATTAGAGGTACTCATGGCCGGGTCAGGCCAAGTTTG
*
3965034 AACAAACATGGATCTCTTTGATCTTTTCTGGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
1 AACAAACATGGATCTCTTTGATCTTTTCTAGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
*
3965099 GCTAAAGTCCCCACACCTTTGCTAGCACGGTTGTTATTTGAAGTGCTTTAAATAATTAACGGGAA
66 GCTAAAGTCCCCACACCTTTGCTAGCACGGTTGTTATTTGAAGTGATTTAAATAATTAACGGGAA
* *
3965164 TCTGTGGTGATTAGAGGTGCTCATGGCCGGGTCGGGCC
131 TCTGTGGTGATTAGAGGTACTCATGGCCGGGTCAGGCC
3965202 GGGTTTGAGC
Statistics
Matches: 160, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
175 160 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (175 bp):
AACAAACATGGATCTCTTTGATCTTTTCTAGATATTTACTTTAGCAGACTTGAGGCTTATTGCAT
GCTAAAGTCCCCACACCTTTGCTAGCACGGTTGTTATTTGAAGTGATTTAAATAATTAACGGGAA
TCTGTGGTGATTAGAGGTACTCATGGCCGGGTCAGGCCAAGTTTG
Found at i:3965828 original size:20 final size:20
Alignment explanation
Indices: 3965805--3965845 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3965795 AAATAACATA
3965805 ATATAAAGTATTATAAACTT
1 ATATAAAGTATTATAAACTT
3965825 ATATAAAGTATTATAAACTT
1 ATATAAAGTATTATAAACTT
3965845 A
1 A
3965846 AAATGGCTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
ATATAAAGTATTATAAACTT
Found at i:3970466 original size:22 final size:22
Alignment explanation
Indices: 3970425--3970467 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3970415 ACACCAAAAC
* **
3970425 AGGCTTTTAGCGGCGTTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
3970447 AGGCCTTTAGCGGCACTTTTT
1 AGGCCTTTAGCGGCACTTTTT
3970468 AGCGCTGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTT
Found at i:3970615 original size:43 final size:43
Alignment explanation
Indices: 3970568--3970775 Score: 265
Period size: 43 Copynumber: 4.8 Consensus size: 43
3970558 CTAAATAATG
* * *
3970568 TGTTCTTTAGTGACACTTTTCTCACAAACGCCGCTAATGGTCA
1 TGTTCTTTAGTGGCGCTTTTCTCACAAACGCCGCTAAAGGTCA
* *
3970611 TGTTCTTTAGCGGCGCATTTCTCACAAACGCCGCTAAAGGTCA
1 TGTTCTTTAGTGGCGCTTTTCTCACAAACGCCGCTAAAGGTCA
* * * *
3970654 TGTTCTTTAATGGCACCTCTT-TCACAAACGCTGCTAAAGGTCA
1 TGTTCTTTAGTGGC-GCTTTTCTCACAAACGCCGCTAAAGGTCA
* * *
3970697 TGTTCTTTAATGACGCTTTTCTCACAAACGCCGCTAAAGTTCA
1 TGTTCTTTAGTGGCGCTTTTCTCACAAACGCCGCTAAAGGTCA
* **
3970740 TGTTCTTTAGCGGCGCTTCCCTCACAAACGCCGCTA
1 TGTTCTTTAGTGGCGCTTTTCTCACAAACGCCGCTA
3970776 TTGTCTGATG
Statistics
Matches: 142, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 4 0.03
43 135 0.95
44 3 0.02
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (43 bp):
TGTTCTTTAGTGGCGCTTTTCTCACAAACGCCGCTAAAGGTCA
Found at i:3972995 original size:25 final size:24
Alignment explanation
Indices: 3972964--3973042 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
3972954 TGATATATAT
3972964 TTATGTATTAGGTAAATTATGTAAG
1 TTATGTATTA-GTAAATTATGTAAG
*
3972989 TTATGTATTA-TAGAAGTCATGTAAG
1 TTATGTATTAGTA-AA-TTATGTAAG
**
3973014 TTATGTATTATGTAAGCTATGTAAG
1 TTATGTATTA-GTAAATTATGTAAG
3973039 TTAT
1 TTAT
3973043 TTAAGTTACG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 39 0.85
26 1 0.02
27 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (24 bp):
TTATGTATTAGTAAATTATGTAAG
Found at i:3973069 original size:34 final size:33
Alignment explanation
Indices: 3973031--3973138 Score: 83
Period size: 34 Copynumber: 3.1 Consensus size: 33
3973021 TTATGTAAGC
*
3973031 TATGTAAGTTATTTAAGTTACGTAAGTTGTGTAT
1 TATGTAAGTTATTTAA-TTAAGTAAGTTGTGTAT
* * * *
3973065 TATGTTAGTTATGT-ACTATGTAAGTTATGTGTAT
1 TATGTAAGTTATTTAATTAAGTAAG-T-TGTGTAT
* *
3973099 TATGTATGTTATGTATAATATTAATTAAGTTGTGTAT
1 TATGTAAGTTAT-T-T-A-ATTAAGTAAGTTGTGTAT
3973136 TAT
1 TAT
3973139 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
32 7 0.12
33 2 0.04
34 29 0.51
36 1 0.02
37 10 0.18
38 1 0.02
39 7 0.12
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.50
Consensus pattern (33 bp):
TATGTAAGTTATTTAATTAAGTAAGTTGTGTAT
Found at i:3973114 original size:9 final size:9
Alignment explanation
Indices: 3972935--3973113 Score: 105
Period size: 9 Copynumber: 21.0 Consensus size: 9
3972925 ACTATAAATG
3972935 AGTTATGTA
1 AGTTATGTA
3972944 AGTTATGATA
1 AGTTATG-TA
* * *
3972954 TGATATAT-
1 AGTTATGTA
*
3972962 ATTTATGT-
1 AGTTATGTA
*
3972970 A-TTAGGTA
1 AGTTATGTA
*
3972978 AATTATGTA
1 AGTTATGTA
3972987 AGTTATGT-
1 AGTTATGTA
3972995 A-TTATAG-A
1 AGTTAT-GTA
*
3973003 AGTCATGTA
1 AGTTATGTA
3973012 AGTTATGT-
1 AGTTATGTA
3973020 A-TTATGTA
1 AGTTATGTA
*
3973028 AGCTATGTA
1 AGTTATGTA
*
3973037 AGTTATTTA
1 AGTTATGTA
*
3973046 AGTTACGTA
1 AGTTATGTA
*
3973055 AGTTGTGT-
1 AGTTATGTA
*
3973063 A-TTATGTT
1 AGTTATGTA
3973071 AGTTATGT-
1 AGTTATGTA
*
3973079 A-CTATGTA
1 AGTTATGTA
*
3973087 AGTTATGTGT
1 AGTTATGT-A
3973097 A-TTATGTA
1 AGTTATGTA
*
3973105 TGTTATGTA
1 AGTTATGTA
3973114 TAATATTAAT
Statistics
Matches: 130, Mismatches: 25, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
7 25 0.19
8 16 0.12
9 82 0.63
10 7 0.05
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
AGTTATGTA
Found at i:3973330 original size:25 final size:25
Alignment explanation
Indices: 3973314--3973360 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3973304 GTTGTGTATA
*
3973314 ATGTTAGTTATCAAAGTTATGTACT
1 ATGTAAGTTATCAAAGTTATGTACT
*
3973339 ATGTAAGTTAT-TAAGTTATGTA
1 ATGTAAGTTATCAAAGTTATGTA
3973361 AGTTGTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (25 bp):
ATGTAAGTTATCAAAGTTATGTACT
Found at i:3973348 original size:16 final size:16
Alignment explanation
Indices: 3973327--3973403 Score: 75
Period size: 16 Copynumber: 4.5 Consensus size: 16
3973317 TTAGTTATCA
*
3973327 AAGTTATGTACTATGT
1 AAGTTATGTATTATGT
3973343 AAGTTAT-TAAGTTATGT
1 AAGTTATGT-A-TTATGT
*
3973360 AAGTTGTGTATTATGT
1 AAGTTATGTATTATGT
3973376 AAGTTATTATGTTATTATGT
1 AAG---TTATG-TATTATGT
3973396 AAGTTATG
1 AAGTTATG
3973404 CAAGTTTATA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
15 1 0.02
16 17 0.33
17 17 0.33
18 1 0.02
19 4 0.08
20 11 0.22
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.48
Consensus pattern (16 bp):
AAGTTATGTATTATGT
Found at i:3973364 original size:9 final size:9
Alignment explanation
Indices: 3973296--3973409 Score: 64
Period size: 9 Copynumber: 13.2 Consensus size: 9
3973286 NNNNNNNNNN
3973296 TTATGTAAG
1 TTATGTAAG
*
3973305 TTGTGT-A-
1 TTATGTAAG
* *
3973312 TAATGTTAG
1 TTATGTAAG
**
3973321 TTATCAAAG
1 TTATGTAAG
3973330 TTATGT-A-
1 TTATGTAAG
*
3973337 CTATGTAAG
1 TTATGTAAG
3973346 TTAT-TAAG
1 TTATGTAAG
3973354 TTATGTAAG
1 TTATGTAAG
*
3973363 TTGTGT-A-
1 TTATGTAAG
3973370 TTATGTAAG
1 TTATGTAAG
*
3973379 TTAT-TATG
1 TTATGTAAG
3973387 TTATTATGTAAG
1 ---TTATGTAAG
*
3973399 TTATGCAAG
1 TTATGTAAG
3973408 TT
1 TT
3973410 TATATATAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
7 14 0.18
8 17 0.22
9 40 0.51
11 4 0.05
12 3 0.04
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3973364 original size:33 final size:33
Alignment explanation
Indices: 3973327--3973390 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
3973317 TTAGTTATCA
3973327 AAGTTATGTACTATGTAAGTTATTAAGTTATGT
1 AAGTTATGTACTATGTAAGTTATTAAGTTATGT
* * *
3973360 AAGTTGTGTATTATGTAAGTTATTATGTTAT
1 AAGTTATGTACTATGTAAGTTATTAAGTTAT
3973391 TATGTAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (33 bp):
AAGTTATGTACTATGTAAGTTATTAAGTTATGT
Found at i:3975098 original size:84 final size:84
Alignment explanation
Indices: 3974902--3975091 Score: 301
Period size: 84 Copynumber: 2.3 Consensus size: 84
3974892 TTCATGAAGC
* * * * *
3974902 GAAACGGTGCCGCATTGACAAACATTAATTCACTCTTGCGGCGTTTGCTTAAAAAATGCCACTAT
1 GAAACGGCGCCGCTTTGGCAAACATTAATTCACTCTTGCGGCGTTTGCCTAAAAAACGCCACTAT
3974967 AAGATTTTATTCTAGTAGA
66 AAGATTTTATTCTAGTAGA
* *
3974986 GAAACGACGCCG-TATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTA
1 GAAACGGCGCCGCT-TTGGCAAACATTAATTCACTCTTGCGGCGTTTGCCTAAAAAACGCCACTA
3975050 TAAGATTTTATTCTAGTAGA
65 TAAGATTTTATTCTAGTAGA
3975070 GAAACGGCGCCGCTTTGGCAAA
1 GAAACGGCGCCGCTTTGGCAAA
3975092 TTTTAATAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
84 95 0.99
85 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (84 bp):
GAAACGGCGCCGCTTTGGCAAACATTAATTCACTCTTGCGGCGTTTGCCTAAAAAACGCCACTAT
AAGATTTTATTCTAGTAGA
Found at i:3975108 original size:84 final size:84
Alignment explanation
Indices: 3974910--3975116 Score: 265
Period size: 84 Copynumber: 2.5 Consensus size: 84
3974900 GCGAAACGGT
* * ** * * *
3974910 GCCGCATTGACAAACATTAATTCACTCTTGCGGCGTTTGCTTAAAAAATGCCACTATAAGATTTT
1 GCCGTATTGGCAAACATTAATAAACTCTTGCGGCGTTTTCCTAAAAAACGCCACTATAAGATTTT
3974975 ATTCTAGTAGAGAAACGAC
66 ATTCTAGTAGAGAAACGAC
**
3974994 GCCGTATTGGCAAACATTAATTCACTCTTGCGGCGTTTTCCTAAAAAACGCCACTATAAGATTTT
1 GCCGTATTGGCAAACATTAATAAACTCTTGCGGCGTTTTCCTAAAAAACGCCACTATAAGATTTT
*
3975059 ATTCTAGTAGAGAAACGGC
66 ATTCTAGTAGAGAAACGAC
** *
3975078 GCCGCT-TTGGCAAATTTTAATAAA-TCCTTGCAGCGTTTT
1 GCCG-TATTGGCAAACATTAATAAACT-CTTGCGGCGTTTT
3975117 TATTAAAATC
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
83 1 0.01
84 108 0.98
85 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (84 bp):
GCCGTATTGGCAAACATTAATAAACTCTTGCGGCGTTTTCCTAAAAAACGCCACTATAAGATTTT
ATTCTAGTAGAGAAACGAC
Found at i:3975633 original size:82 final size:81
Alignment explanation
Indices: 3975540--3975781 Score: 286
Period size: 82 Copynumber: 2.9 Consensus size: 81
3975530 TATAAAGAAC
* *
3975540 TTATTTAATATATAAATTAAAAAGTACTAATTAATCTAAATCTTAAACCCTAACCTGACCCCAAA
1 TTATTTAATATATAAATTAAAAA-CACTAATTAATCTAAATCCTAAACCCTAACCTGACCCCAAA
3975605 TCCCTAACACCTAAACT
65 TCCCTAACACCTAAACT
* **
3975622 TTATTTAATATATAAATTAACAAACACTAATTAATCTAAATCCTAAACCCTGAGCCTGACCTGGA
1 TTATTTAATATATAAATTAA-AAACACTAATTAATCTAAATCCTAAACCCT-AACCTGACC-CCA
* *
3975687 ATCCCTACCCTAACCCCTAAACT
63 A---AT-CCCTAACACCTAAACT
* * * * * **
3975710 TTAGTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGATCCTGAAT
1 TTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTAACCTGACCCCAAAT
3975775 CCCTAAC
66 CCCTAAC
3975782 CCTTAACCCC
Statistics
Matches: 136, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
81 7 0.05
82 46 0.34
83 11 0.08
84 2 0.01
85 1 0.01
86 6 0.04
87 29 0.21
88 34 0.25
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (81 bp):
TTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTAACCTGACCCCAAAT
CCCTAACACCTAAACT
Found at i:3975723 original size:88 final size:85
Alignment explanation
Indices: 3975544--3975874 Score: 330
Period size: 95 Copynumber: 3.8 Consensus size: 85
3975534 AAGAACTTAT
* * ** *
3975544 TTAATATATAAATTAAAAAGTACTAATTAATCTAAATCTTAAACCCTAACCTGACCCCAA---AT
1 TTAATATATAAATTAAAAA-CACTAATTAATCTAAATCCTAAACCCTAACCTGACCTGAATCCCT
* *
3975606 -CCCTAACACCTAAACTTTAT
65 ACCCTAACCCCTAAACTTTAG
*
3975626 TTAATATATAAATTAACAAACACTAATTAATCTAAATCCTAAACCCTGAGCCTGACCTGGAATCC
1 TTAATATATAAATTAA-AAACACTAATTAATCTAAATCCTAAACCCT-AACCTGACCT-GAATCC
3975691 CTACCCTAACCCCTAAACTTTAG
63 CTACCCTAACCCCTAAACTTTAG
* * *
3975714 TTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCATAACCCGATCCTGAATCCCT
1 TTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTAACCTGA-CCTGAATCCCT
* *
3975779 AACCCTTAACCCCTATCCCTTAAACATTAT
65 -ACCC-TAA---C---CCC-TAAACTTTAG
* * * *
3975809 TTAATATAT-AATTAAAACATACTAATTAATCTAAACCCTAAACTCTAACCTGACATCGAATCCC
1 TTAATATATAAATTAAAA-ACACTAATTAATCTAAATCCTAAACCCTAACCTGACCT-GAATCCC
3975873 TA
64 TA
3975875 AACCATAAAT
Statistics
Matches: 211, Mismatches: 19, Indels: 26
0.82 0.07 0.10
Matches are distributed among these distances:
82 41 0.19
83 11 0.05
84 2 0.01
86 13 0.06
87 36 0.17
88 37 0.18
91 1 0.00
94 14 0.07
95 56 0.27
ACGTcount: A:0.42, C:0.26, G:0.04, T:0.29
Consensus pattern (85 bp):
TTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAACCCTAACCTGACCTGAATCCCTA
CCCTAACCCCTAAACTTTAG
Found at i:3975887 original size:15 final size:15
Alignment explanation
Indices: 3975867--3975969 Score: 74
Period size: 15 Copynumber: 7.1 Consensus size: 15
3975857 CCTGACATCG
3975867 AATCCCTAAACCATA
1 AATCCCTAAACCATA
*
3975882 AATCCCTAAACCTTA
1 AATCCCTAAACCATA
3975897 AATCCCT-AACC-T-
1 AATCCCTAAACCATA
* * *
3975909 AACCCCTAACCCCTA
1 AATCCCTAAACCATA
* *
3975924 AA-CCTTAAATCACATT
1 AATCCCTAAA-C-CATA
3975940 AA-CCCTTAAACCA-A
1 AATCCC-TAAACCATA
*
3975954 AATCCCTAATCCATA
1 AATCCCTAAACCATA
3975969 A
1 A
3975970 TCCTTAATTC
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.09
13 4 0.06
14 18 0.26
15 31 0.44
16 7 0.10
17 4 0.06
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (15 bp):
AATCCCTAAACCATA
Found at i:3976333 original size:114 final size:114
Alignment explanation
Indices: 3976118--3976812 Score: 948
Period size: 114 Copynumber: 6.1 Consensus size: 114
3976108 CGGCGCATCC
* * *
3976118 TCAAAAACGCCGCTAATGCACTGAGCATTAGCGGCGCTTTATTAAAAAACGCCACTAAATCCCCG
1 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATT-AAAAACGCCGCTAAATCCCCG
* * *
3976183 AAAGCTAAGAAAACGGCGTCATTGGGCTTAGG-TTTTTTGCGGCGCTTT-
65 AAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTA
* * *
3976231 TCCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGC-GTACTTAAAAACGCCGCTAAATCCTC
1 T-CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTA-TTAAAAACGCCGCTAAATCCCC
* * *
3976295 GAAAGCTCAGAAAACGGCGTCATTGGGCTTATGTTTTTTTGTGGCCCTTTA
64 GAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTA
* * * *
3976346 TCAAAAACGCCACTAAAGCCCTGAGCACTAGCGGCGC-TTACTTGAAAACGCCGCTAAATCCCCA
1 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTA-TTAAAAACGCCGCTAAATCCCCG
* * *
3976410 AAAGCTAAGAAAACGGCGTCGTTGGACTTAGGTTTTTTTGTGTCGCTTTA
65 AAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTA
* *
3976460 TAAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCTGCTAAATCCCCGA
1 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGA
3976525 AAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT-TGTG-GC---A
66 AAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTG-GCGCTTTA
* * *
3976570 TAAAAAACGTCGCTAAAGCCCTGAGCATTAGCGTCGC-TTACTTAAAAACGCCGCTAAATCCCCG
1 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTA-TTAAAAACGCCGCTAAATCCCCG
* *
3976634 AAAGCTCAGAAAACGTCGTCGTTGGGCTTAGGTTTGTTTGTGGCGCTTTA
65 AAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTA
* *
3976684 TCAAAAACGCTGCTAAAGCCCTGAGCATTAGTGGCGCTTTATTAAAAACGCCGCTAAATCCCCGA
1 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGA
* *
3976749 AAGCTC-GAAAAACGGCGTCGTTGGGCTTAGG-TATTTTGCGGCGCGTTT-
66 AAGCTCAG-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGC-TTTA
*
3976797 TCGAAAACGCCGCTAA
1 TCAAAAACGCCGCTAA
3976813 TGCTTATTTT
Statistics
Matches: 519, Mismatches: 48, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
109 3 0.01
110 96 0.18
111 4 0.01
113 81 0.16
114 328 0.63
115 7 0.01
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (114 bp):
TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGA
AAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTA
Found at i:3976692 original size:224 final size:225
Alignment explanation
Indices: 3976120--3976785 Score: 959
Period size: 224 Copynumber: 2.9 Consensus size: 225
3976110 GCGCATCCTC
* * *
3976120 AAAAACGCCGCTAATGCACTGAGCATTAGCGGCGCTTTA-TTAAAAAACGCCACTAAATCCCCGA
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC-TTACTT-AAAAACGCCGCTAAATCCCCGA
* * *
3976184 AAGCTAAGAAAACGGCGTCATTGGGCTTAGGTTTTTTGCGGCGCTTT-TCCAAAAATGCCGCTAA
64 AAGCTAAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTAT-CAAAAACGCCGCTAA
* *
3976248 AGCCCTGAGCATTAGCGGCGC-GTACTTAAAAACGCCGCTAAATCCTCGAAAGCTCAGAAAACGG
128 AGCCCTGAGCATTAGCGGCGCTTTA-TTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGG
* * *
3976312 CGTCATTGGGCTTATG-TTTTTTTGTGGCCCTTTATC
192 CGTCGTTGGGCTTAGGTTTTTTTTGTGG-CC--TATA
* * * *
3976348 AAAAACGCCACTAAAGCCCTGAGCACTAGCGGCGCTTACTTGAAAACGCCGCTAAATCCCCAAAA
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAA
* * *
3976413 GCTAAGAAAACGGCGTCGTTGGACTTAGGTTTTTTTGTGTCGCTTTATAAAAAACGCCGCTAAAG
66 GCTAAGAAAACGGCGTCGTTGGGCTTAGG-TTTTTTGTGGCGCTTTATCAAAAACGCCGCTAAAG
*
3976478 CCCTGAGCATTAGCGGCGCTTTATTAAAAACGCTGCTAAATCCCCGAAAGCTCAGAAAACGGCGT
130 CCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGT
3976543 CGTTGGGCTTAGGTTTTTTTTGTGG-C-ATA
195 CGTTGGGCTTAGGTTTTTTTTGTGGCCTATA
* *
3976572 AAAAACGTCGCTAAAGCCCTGAGCATTAGCGTCGCTTACTTAAAAACGCCGCTAAATCCCCGAAA
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAA
* * *
3976637 GCTCAGAAAACGTCGTCGTTGGGCTTAGGTTTGTTTGTGGCGCTTTATCAAAAACGCTGCTAAAG
66 GCTAAGAAAACGGCGTCGTTGGGCTTAGGTTT-TTTGTGGCGCTTTATCAAAAACGCCGCTAAAG
*
3976702 CCCTGAGCATTAGTGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTC-GAAAAACGGCG
130 CCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCAG-AAAACGGCG
*
3976766 TCGTTGGGCTTAGGTATTTT
194 TCGTTGGGCTTAGGTTTTTT
3976786 GCGGCGCGTT
Statistics
Matches: 397, Mismatches: 34, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
223 4 0.01
224 195 0.49
227 52 0.13
228 132 0.33
229 14 0.04
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (225 bp):
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAA
GCTAAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTATCAAAAACGCCGCTAAAGC
CCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
GTTGGGCTTAGGTTTTTTTTGTGGCCTATA
Found at i:3976740 original size:338 final size:341
Alignment explanation
Indices: 3976120--3976785 Score: 993
Period size: 338 Copynumber: 2.0 Consensus size: 341
3976110 GCGCATCCTC
*
3976120 AAAAACGCCGCTAATGCACTGAGCATTAGCGGCGCTTTATTAAAAAACGCCACTAAATCCCCGAA
1 AAAAACGCCGCTAAAGCACTGAGCATTAGCGGCGCTTTATTAAAAAACGCCACTAAATCCCCGAA
* * *
3976185 AGCTAAGAAAACGGCGTCATTGGGCTTAGGTTTTTTGCGGCGCTTTTCCAAAAATGCCGCTAAAG
66 AGCTAAGAAAACGGCGTCATTGGGCTTAGGTTTTTTGCGGCGC-TATCAAAAAACGCCGCTAAAG
*
3976250 CCCTGAGCATTAGCGGCGCGTACTTAAAAACGCCGCTAAATCCTCGAAAGCTCAGAAAACGGCGT
130 CCCTGAGCATTAGCGGCGCGTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGT
* *
3976315 CATTGGGCTTATGTTTTTTTGTGGCCCTTTATCAAAAACGCCACTAAAGCCCTGAGCACTAGCGG
195 CATTGGGCTTAGGTTTGTTTGTGGCCCTTTATCAAAAACGCCACTAAAGCCCTGAGCACTAGCGG
* *
3976380 CGCTTACTTGAAAACGCCGCTAAATCCCCAAAAGCTA-AGAAAACGGCGTCGTTGGACTTAGGTT
260 CGCTTACTTAAAAACGCCGCTAAATCCCCAAAAGCTAGA-AAAACGGCGTCGTTGGACTTAGGTA
3976444 TTTTTGTGTCGCTTTATA
324 TTTTTGTGTCGCTTTATA
* **
3976462 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATT-AAAAACGCTGCTAAATCCCCGAA
1 AAAAACGCCGCTAAAGCACTGAGCATTAGCGGCGCTTTATTAAAAAACGCCACTAAATCCCCGAA
* * ** *
3976526 AGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTTGTG-GC-AT-AAAAAACGTCGCTAAAG
66 AGCTAAGAAAACGGCGTCATTGGGCTTAGGTTTTTTGCG-GCGCTATCAAAAAACGCCGCTAAAG
* * *
3976588 CCCTGAGCATTAGCGTCGCTTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGTCGT
130 CCCTGAGCATTAGCGGCGCGTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGT
* * ** * *
3976653 CGTTGGGCTTAGGTTTGTTTGTGGCGCTTTATCAAAAACGCTGCTAAAGCCCTGAGCATTAGTGG
195 CATTGGGCTTAGGTTTGTTTGTGGCCCTTTATCAAAAACGCCACTAAAGCCCTGAGCACTAGCGG
* * *
3976718 CGCTTTA-TTAAAAACGCCGCTAAATCCCCGAAAGCTCGAAAAACGGCGTCGTTGGGCTTAGGTA
260 CGC-TTACTTAAAAACGCCGCTAAATCCCCAAAAGCTAGAAAAACGGCGTCGTTGGACTTAGGTA
3976782 TTTT
324 TTTT
3976786 GCGGCGCGTT
Statistics
Matches: 292, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
338 189 0.65
339 5 0.02
341 58 0.20
342 40 0.14
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (341 bp):
AAAAACGCCGCTAAAGCACTGAGCATTAGCGGCGCTTTATTAAAAAACGCCACTAAATCCCCGAA
AGCTAAGAAAACGGCGTCATTGGGCTTAGGTTTTTTGCGGCGCTATCAAAAAACGCCGCTAAAGC
CCTGAGCATTAGCGGCGCGTACTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTC
ATTGGGCTTAGGTTTGTTTGTGGCCCTTTATCAAAAACGCCACTAAAGCCCTGAGCACTAGCGGC
GCTTACTTAAAAACGCCGCTAAATCCCCAAAAGCTAGAAAAACGGCGTCGTTGGACTTAGGTATT
TTTGTGTCGCTTTATA
Found at i:3983188 original size:27 final size:28
Alignment explanation
Indices: 3983137--3983191 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 28
3983127 CTGGGCCTTC
3983137 CCACACGGGCTGGACACATGGCCATGTGAG
1 CCACACGGGCT-G-CACATGGCCATGTGAG
3983167 CCACACGGGCT-CACATGGCCATGTG
1 CCACACGGGCTGCACATGGCCATGTG
3983192 CCAGATCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 14 0.56
30 11 0.44
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.15
Consensus pattern (28 bp):
CCACACGGGCTGCACATGGCCATGTGAG
Found at i:3984278 original size:6 final size:6
Alignment explanation
Indices: 3984267--3984309 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
3984257 TTGATTTAGC
* *
3984267 TATTTT TATTTT TATTTT TA--TT TATTTT TAATTT AATTTT TAT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TAT
3984310 ATGTTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 4 0.13
6 27 0.87
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:3984286 original size:22 final size:22
Alignment explanation
Indices: 3984261--3984308 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3984251 ATTCTATTGA
* *
3984261 TTTAGCTATTTTTATTTTTATT
1 TTTAGCTATTTTTAATTTAATT
**
3984283 TTTATTTATTTTTAATTTAATT
1 TTTAGCTATTTTTAATTTAATT
3984305 TTTA
1 TTTA
3984309 TATGTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTAGCTATTTTTAATTTAATT
Found at i:3984305 original size:16 final size:16
Alignment explanation
Indices: 3984271--3984305 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3984261 TTTAGCTATT
* *
3984271 TTTATTTTTATTTTTA
1 TTTATTTTTAATTTAA
3984287 TTTATTTTTAATTTAA
1 TTTATTTTTAATTTAA
3984303 TTT
1 TTT
3984306 TTATATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATTTTTAATTTAA
Found at i:3984309 original size:22 final size:22
Alignment explanation
Indices: 3984267--3984309 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3984257 TTGATTTAGC
* *
3984267 TATTTTTATTTTTATTTTTATT
1 TATTTTTAATTTAATTTTTATT
3984289 TATTTTTAATTTAATTTTTAT
1 TATTTTTAATTTAATTTTTAT
3984310 ATGTTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (22 bp):
TATTTTTAATTTAATTTTTATT
Found at i:3986817 original size:12 final size:12
Alignment explanation
Indices: 3986800--3986824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3986790 CCTTATACAC
3986800 ATTACACATTGA
1 ATTACACATTGA
3986812 ATTACACATTGA
1 ATTACACATTGA
3986824 A
1 A
3986825 ATTAGATTTT
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:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:4003634 original size:50 final size:51
Alignment explanation
Indices: 4003564--4003700 Score: 186
Period size: 50 Copynumber: 2.7 Consensus size: 51
4003554 TATCATTCGA
* * * *
4003564 TACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAA-CTTTTCGG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCGG
* * *
4003614 TTCACGTAGTAGGCTGCACATAGTACTACACACGTGACCAAAGCCTTCCGG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCGG
* *
4003665 TACACATAGTAGCCTGCACATAGTGCAACACACGTG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTG
4003701 TTTATAGACG
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 37 0.50
51 37 0.50
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCGG
Found at i:4010545 original size:25 final size:26
Alignment explanation
Indices: 4010516--4010570 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
4010506 AAATTTTCTC
*
4010516 AAAATTTTACCG-GGGTAAAATTGTT
1 AAAATTTTAACGAGGGTAAAATTGTT
4010541 AAAATTTTAACGAGGGTAAAATTGTT
1 AAAATTTTAACGAGGGTAAAATTGTT
4010567 AAAA
1 AAAA
4010571 ACTTTACTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (26 bp):
AAAATTTTAACGAGGGTAAAATTGTT
Found at i:4010582 original size:26 final size:26
Alignment explanation
Indices: 4010528--4010586 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
4010518 AATTTTACCG
*
4010528 GGGTAAAATTGTTAAAATTTTAACGA
1 GGGTAAAATTGTTAAAACTTTAACGA
*
4010554 GGGTAAAATTGTTAAAAACTTT-ACTA
1 GGGTAAAATTGTT-AAAACTTTAACGA
4010580 GGGTAAA
1 GGGTAAA
4010587 TTTGGGATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.32
Consensus pattern (26 bp):
GGGTAAAATTGTTAAAACTTTAACGA
Found at i:4027424 original size:20 final size:18
Alignment explanation
Indices: 4027388--4027429 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
4027378 AATTTAAAAC
*
4027388 TTAATTAACCTTTATTAA
1 TTAATTAACCTTAATTAA
4027406 TTAATATAATCCTTAATTAA
1 TTAAT-TAA-CCTTAATTAA
4027426 TTAA
1 TTAA
4027430 ACTTAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 13 0.62
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAATTAACCTTAATTAA
Found at i:4028175 original size:24 final size:24
Alignment explanation
Indices: 4028148--4028204 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
4028138 AAACCTAATT
*
4028148 CTAATCAAA-GTCAAATATATTATG
1 CTAAT-AAATGTCAAACATATTATG
* *
4028172 CTAATAAATGTTAAACATATTATA
1 CTAATAAATGTCAAACATATTATG
*
4028196 CTCATAAAT
1 CTAATAAAT
4028205 ACTAAATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (24 bp):
CTAATAAATGTCAAACATATTATG
Found at i:4028210 original size:24 final size:24
Alignment explanation
Indices: 4028164--4028210 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
4028154 AAAGTCAAAT
* **
4028164 ATATTATGCTAATAAATGTTAAAC
1 ATATTATACTAATAAATACTAAAC
*
4028188 ATATTATACTCATAAATACTAAA
1 ATATTATACTAATAAATACTAAA
4028211 TCTTCTAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (24 bp):
ATATTATACTAATAAATACTAAAC
Found at i:4032648 original size:43 final size:42
Alignment explanation
Indices: 4032491--4032648 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 42
4032481 TTCCGATATA
*
4032491 TGATTTCGTGTAAGACCACGTCTGGGAC-GTTGGCATCG-ATT
1 TGATTACGTGTAAGACCACGTCTGGGACAG-TGGCATCGTATT
* * * * * *
4032532 TGAGATTTACGTGTAAGACCATGTTTGGGACATTAGCATTGTATA
1 T--GA-TTACGTGTAAGACCACGTCTGGGACAGTGGCATCGTATT
* * *
4032577 TGATTTCGTGTAAGACC-CTATCTAGGACAGTGGCATCGTTATT
1 TGATTACGTGTAAGACCAC-GTCTGGGACAGTGGCATCG-TATT
*
4032620 TGATTACATGTAAGACCACGTCTGGGACA
1 TGATTACGTGTAAGACCACGTCTGGGACA
4032649 TTGGTATTGT
Statistics
Matches: 89, Mismatches: 20, Indels: 14
0.72 0.16 0.11
Matches are distributed among these distances:
41 1 0.01
42 26 0.29
43 30 0.34
44 29 0.33
45 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (42 bp):
TGATTACGTGTAAGACCACGTCTGGGACAGTGGCATCGTATT
Found at i:4035591 original size:24 final size:24
Alignment explanation
Indices: 4035564--4035610 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4035554 AAACCTAATT
4035564 CTAATCAAA-GTAAAATATATTATG
1 CTAAT-AAATGTAAAATATATTATG
*
4035588 CTAATAAATGTTAAATATATTAT
1 CTAATAAATGTAAAATATATTAT
4035611 ATTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:4035626 original size:24 final size:24
Alignment explanation
Indices: 4035576--4035627 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
4035566 AATCAAAGTA
* **
4035576 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
* *
4035600 AAATATATTATATTCATAAATACT
1 AAATATATTATACTAATAAATACT
4035624 AAAT
1 AAAT
4035628 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:4038223 original size:8 final size:8
Alignment explanation
Indices: 4038212--4038245 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
4038202 ACATTAATTT
4038212 TTTAAAAA
1 TTTAAAAA
4038220 TTTAAAAA
1 TTTAAAAA
4038228 TATTAAAAAA
1 T-TT-AAAAA
4038238 TTTAAAAA
1 TTTAAAAA
4038246 CATTAGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 14 0.58
9 4 0.17
10 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TTTAAAAA
Found at i:4038238 original size:18 final size:18
Alignment explanation
Indices: 4038215--4038250 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4038205 TTAATTTTTT
*
4038215 AAAAATTTAAAAATATTA
1 AAAAATTTAAAAACATTA
4038233 AAAAATTTAAAAACATTA
1 AAAAATTTAAAAACATTA
4038251 GATTGACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATTTAAAAACATTA
Found at i:4048474 original size:12 final size:12
Alignment explanation
Indices: 4048457--4048487 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4048447 TGCCCCACAC
4048457 GCCGTGTGCTAG
1 GCCGTGTGCTAG
4048469 GCCGTGTGCTAG
1 GCCGTGTGCTAG
*
4048481 GTCGTGT
1 GCCGTGT
4048488 AACTCAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.42, T:0.29
Consensus pattern (12 bp):
GCCGTGTGCTAG
Found at i:4051421 original size:13 final size:13
Alignment explanation
Indices: 4051389--4051426 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
4051379 TCTCCAATTC
4051389 TTCT-TCTTCTTT
1 TTCTCTCTTCTTT
4051401 TTCGTCTCTTCTTT
1 TTC-TCTCTTCTTT
4051415 TTCTCTCTTCTT
1 TTCTCTCTTCTT
4051427 CTTTTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.12
13 10 0.42
14 11 0.46
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (13 bp):
TTCTCTCTTCTTT
Found at i:4052346 original size:5 final size:5
Alignment explanation
Indices: 4052332--4052369 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
4052322 ACAACTAAAG
* *
4052332 CTTTA CTTTA ATTTA CTTTA CTTTA CTTTA ATTTA CTT
1 CTTTA CTTTA CTTTA CTTTA CTTTA CTTTA CTTTA CTT
4052370 ATGCATTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.61
Consensus pattern (5 bp):
CTTTA
Found at i:4052348 original size:10 final size:10
Alignment explanation
Indices: 4052333--4052369 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
4052323 CAACTAAAGC
4052333 TTTACTTTAA
1 TTTACTTTAA
*
4052343 TTTACTTTAC
1 TTTACTTTAA
4052353 TTTACTTTAA
1 TTTACTTTAA
4052363 TTTACTT
1 TTTACTT
4052370 ATGCATTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTACTTTAA
Found at i:4053160 original size:31 final size:32
Alignment explanation
Indices: 4053116--4053180 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
4053106 TTCTCAAAAG
*
4053116 AAAAGTTACCAAGCCACAAACCAA-AAATAATT
1 AAAAATTACCAAGCCA-AAACCAATAAATAATT
* *
4053148 AAAAATTA-CAAGCGAAAACCAATAAATACTT
1 AAAAATTACCAAGCCAAAACCAATAAATAATT
4053179 AA
1 AA
4053181 TAATACTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 7 0.24
31 15 0.52
32 7 0.24
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.17
Consensus pattern (32 bp):
AAAAATTACCAAGCCAAAACCAATAAATAATT
Found at i:4054136 original size:31 final size:31
Alignment explanation
Indices: 4054098--4054162 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
4054088 ATTGTTTAAC
4054098 TTTTTATCATATATAACATGATATTTAACAT
1 TTTTTATCATATATAACATGATATTTAACAT
4054129 TTTTTATCATATATAACATGATATTTAACAT
1 TTTTTATCATATATAACATGATATTTAACAT
4054160 TTT
1 TTT
4054163 ATATGTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (31 bp):
TTTTTATCATATATAACATGATATTTAACAT
Found at i:4054163 original size:29 final size:29
Alignment explanation
Indices: 4054092--4054164 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 29
4054082 TCAAAAATTG
*
4054092 TTTAACTTTTTATCATATATAACATGATA
1 TTTAACATTTTATCATATATAACATGATA
4054121 TTTAACATTTTTTATCATATATAACATGATA
1 TTTAACA--TTTTATCATATATAACATGATA
4054152 TTTAACATTTTAT
1 TTTAACATTTTAT
4054165 ATGTTTAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 12 0.29
31 29 0.71
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTAACATTTTATCATATATAACATGATA
Found at i:4057767 original size:19 final size:19
Alignment explanation
Indices: 4057687--4057760 Score: 103
Period size: 19 Copynumber: 3.9 Consensus size: 19
4057677 ATACACCTCA
4057687 TGTGCCAGGATGCACTTCG
1 TGTGCCAGGATGCACTTCG
* * *
4057706 TGTGTCAGTATACACTTCG
1 TGTGCCAGGATGCACTTCG
*
4057725 TGTGCTAGGATGCACTTCG
1 TGTGCCAGGATGCACTTCG
*
4057744 TGTGCCAGTATGCACTT
1 TGTGCCAGGATGCACTT
4057761 TATGTGCTAG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (19 bp):
TGTGCCAGGATGCACTTCG
Found at i:4057768 original size:38 final size:38
Alignment explanation
Indices: 4057677--4057770 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 38
4057667 ATGCGCTCGG
* * *
4057677 ATACACCTCATGTGCCAGGATGCACTTCGTGTGTCAGT
1 ATACACTTCATGTGCTAGGATGCACTTCGTGTGCCAGT
*
4057715 ATACACTTCGTGTGCTAGGATGCACTTCGTGTGCCAGT
1 ATACACTTCATGTGCTAGGATGCACTTCGTGTGCCAGT
* *
4057753 ATGCACTTTATGTGCTAG
1 ATACACTTCATGTGCTAG
4057771 TTTACAATCT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (38 bp):
ATACACTTCATGTGCTAGGATGCACTTCGTGTGCCAGT
Found at i:4061216 original size:43 final size:44
Alignment explanation
Indices: 4061168--4061254 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
4061158 GGGTAAATCA
* *
4061168 AACAACCCATGTTTATCTTCTT-CTGTTTTT-AAATTCTTTTTTC
1 AACAACCCAAGATTATCTT-TTCCTGTTTTTAAAATTCTTTTTTC
*
4061211 AACAACCCAAGATTATCTTTTCCTTTTTTTAAAATTCTTTTTTC
1 AACAACCCAAGATTATCTTTTCCTGTTTTTAAAATTCTTTTTTC
4061255 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 2 0.05
43 24 0.62
44 13 0.33
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.52
Consensus pattern (44 bp):
AACAACCCAAGATTATCTTTTCCTGTTTTTAAAATTCTTTTTTC
Found at i:4064228 original size:33 final size:32
Alignment explanation
Indices: 4064186--4064387 Score: 111
Period size: 33 Copynumber: 5.6 Consensus size: 32
4064176 TCCCCCAAGG
4064186 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCC-GAATCATTGGT
*
4064219 GGTTGCTAAGTGCTGATTCCACCGCAACTTGAATGTGAAAG-
1 GGTTGCTAAGTGCTGATT-C-CCG-AA--T-CAT-TG---GT
4064260 GGTTTGCTAAGTGCTGATTTCCCGAATCATTGGT
1 GG-TTGCTAAGTGCTGA-TTCCCGAATCATTGGT
* * *
4064294 GGCTGCTTAGTGCTGATTCCACCGTATC-TTGAATGT
1 GGTTGCTAAGTGCTGATT-C-CCGAATCATTG---GT
*
4064330 GAAAGGCGTTGCTAAGTGTTGATTCGCCGAATCATTGGT
1 -----G-GTTGCTAAGTGCTGATTC-CCGAATCATTGGT
*
4064369 GGTTGCTAAGTTCTGATTC
1 GGTTGCTAAGTGCTGATTC
4064388 TACCGTATCT
Statistics
Matches: 132, Mismatches: 12, Indels: 50
0.68 0.06 0.26
Matches are distributed among these distances:
32 2 0.02
33 51 0.39
34 11 0.08
35 4 0.03
36 4 0.03
37 3 0.02
38 3 0.02
39 4 0.03
40 2 0.02
41 13 0.10
42 33 0.25
43 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCGAATCATTGGT
Found at i:4064273 original size:75 final size:74
Alignment explanation
Indices: 4064182--4064465 Score: 406
Period size: 75 Copynumber: 3.8 Consensus size: 74
4064172 TGATTCCCCC
* *
4064182 AAGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGCAAC
1 AAGGGGTTGCTAAGTGCTGATTCCC-GAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
4064247 TTGAATGTGA
65 TTGAATGTGA
* * *
4064257 AAGGGTTTGCTAAGTGCTGATTTCCCGAATCATTGGTGGCTGCTTAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGA-TTCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
4064322 TTGAATGTGA
65 TTGAATGTGA
* * * *
4064332 AAGGCGTTGCTAAGTGTTGATTCGCCGAATCATTGGTGGTTGCTAAGTTCTGATTCTACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTC-CCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
4064397 TTTGAATGTGA
65 -TTGAATGTGA
* * * *
4064408 AAGGGGTTGCTAATTGTTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCA
1 AAGGGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCA
4064466 TCGAGTAACG
Statistics
Matches: 187, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
74 3 0.02
75 118 0.63
76 65 0.35
77 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.33
Consensus pattern (74 bp):
AAGGGGTTGCTAAGTGCTGATTCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
TGAATGTGA
Found at i:4071757 original size:27 final size:26
Alignment explanation
Indices: 4071721--4071771 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
4071711 GAATATAAAG
4071721 GGGGTTGCTAAGTGCTGATTTCCCCAA
1 GGGGTTGCTAAGTGCTGA-TTCCCCAA
*
4071748 GGGGTTGCTAAGTGTTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
4071772 GAATCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:4071792 original size:33 final size:33
Alignment explanation
Indices: 4071750--4071990 Score: 185
Period size: 33 Copynumber: 6.7 Consensus size: 33
4071740 TTCCCCAAGG
4071750 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
* * *
4071783 GGTTGCTAAGTGTTGATTCGACCGTAACTTGAATATGAAAGG
1 GGTTGCTAAGTGTTGATTC-CCCG-AA--T-CAT-TG---GT
* *
4071825 GGTTGCTAAGTGCTAATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
* * *
4071858 GGTTGCTAAGTGCTGATTCCACCGTATCTTGAATGTGAACGG
1 GGTTGCTAAGTGTTGATTCC-CCGAATC----AT-TG---GT
*
4071900 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
* * *
4071933 GGTTGCTAAGTGTTTATTCCTCGAATCACTGGT
1 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
* *
4071966 GGTTGCTAAATGTTGAATCCACCGA
1 GGTTGCTAAGTGTTGATTCC-CCGA
4071991 GTAACAGATA
Statistics
Matches: 168, Mismatches: 21, Indels: 37
0.74 0.09 0.16
Matches are distributed among these distances:
33 86 0.51
34 12 0.07
35 2 0.01
36 4 0.02
37 5 0.03
38 5 0.03
39 4 0.02
40 2 0.01
41 9 0.05
42 39 0.23
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
Found at i:4071869 original size:75 final size:75
Alignment explanation
Indices: 4071746--4071952 Score: 342
Period size: 75 Copynumber: 2.8 Consensus size: 75
4071736 TGATTTCCCC
* *
4071746 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCGACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCGTAAC
4071811 TTGAATATGA
66 TTGAATATGA
* * *
4071821 AAGGGGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCGTAAC
*
4071886 TTGAATGTGA
66 TTGAATATGA
* *
4071896 ACGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTTATTCC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCC
4071953 TCGAATCACT
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 122 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCGTAAC
TTGAATATGA
Found at i:4073519 original size:35 final size:35
Alignment explanation
Indices: 4073462--4073578 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
4073452 ACTCTATATT
** *
4073462 TTGGTGTGTTTCGGTTGTATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* * *
4073497 TTGGTGTTTTTTGGAGGGATTAGCTCTTATGAGCG
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* * *
4073532 TTGGTGTGTTTCGGATGGACTGGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
*
4073567 TCTAGTGTGTTT
1 T-TGGTGTGTTT
4073579 GGGTAGTTTG
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 59 0.87
36 9 0.13
ACGTcount: A:0.14, C:0.11, G:0.32, T:0.44
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
Found at i:4076087 original size:20 final size:20
Alignment explanation
Indices: 4076062--4076103 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4076052 TATATAGCAT
4076062 TGGGTGCCAATTTGAGGCAC
1 TGGGTGCCAATTTGAGGCAC
4076082 TGGGTGCCAATTTGAGGCAC
1 TGGGTGCCAATTTGAGGCAC
4076102 TG
1 TG
4076104 AGACACTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (20 bp):
TGGGTGCCAATTTGAGGCAC
Found at i:4079903 original size:15 final size:16
Alignment explanation
Indices: 4079850--4079908 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 16
4079840 GCTTTTTTGC
* *
4079850 TCCT-TTTTAATTTCA
1 TCCTATTTTATTTTTA
*
4079865 TCCTATTTCATTTTTA
1 TCCTATTTTATTTTTA
*
4079881 T-TTATTTTATTTTTA
1 TCCTATTTTATTTTTA
4079896 TCCT-TTTTATTTT
1 TCCTATTTTATTTT
4079909 ATTCTTGTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 26 0.72
16 10 0.28
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (16 bp):
TCCTATTTTATTTTTA
Found at i:4080381 original size:3 final size:3
Alignment explanation
Indices: 4080368--4080445 Score: 61
Period size: 3 Copynumber: 25.3 Consensus size: 3
4080358 TACTTTTTTA
* * *
4080368 TAT TAT T-T TAT TAT TAT CAT TAT TAT ATAG TAT TAT TAAT TGAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT T-AT T-AT TAT
* *
4080415 T-T TAT TAT TTT TAT TAT TATT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
4080446 GTATTCATTA
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
2 4 0.07
3 46 0.78
4 9 0.15
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:4080443 original size:10 final size:10
Alignment explanation
Indices: 4080364--4080456 Score: 66
Period size: 10 Copynumber: 9.1 Consensus size: 10
4080354 ATCATACTTT
4080364 TTTA-TATTA
1 TTTATTATTA
4080373 TTTTATTATTA
1 -TTTATTATTA
*
4080384 -TCATTATTA
1 TTTATTATTA
* *
4080393 TATAGTATTA
1 TTTATTATTA
* *
4080403 TTAATTGAATA
1 TTTATT-ATTA
4080414 TTTTATTATT-
1 -TTTATTATTA
4080424 TTTATTATTA
1 TTTATTATTA
*
4080434 TTTCTTATTA
1 TTTATTATTA
4080444 TTGTATTCATTA
1 TT-TATT-ATTA
4080456 T
1 T
4080457 AATATTGGCA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
9 17 0.27
10 24 0.38
11 13 0.20
12 10 0.16
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTATTATTA
Found at i:4083386 original size:11 final size:11
Alignment explanation
Indices: 4083370--4083395 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4083360 AAATATATAA
4083370 TAAAATAATTT
1 TAAAATAATTT
4083381 TAAAATAATTT
1 TAAAATAATTT
4083392 TAAA
1 TAAA
4083396 TTATTCTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAAATAATTT
Found at i:4092064 original size:9 final size:9
Alignment explanation
Indices: 4092050--4092089 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
4092040 GGAAAGGGAG
*
4092050 GGTGGTAGT
1 GGTGGTAGA
*
4092059 GGTGGTGGA
1 GGTGGTAGA
4092068 GGTGGTAGA
1 GGTGGTAGA
*
4092077 GGTGGCAGA
1 GGTGGTAGA
4092086 GGTG
1 GGTG
4092090 TTTGTTTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.15, C:0.03, G:0.60, T:0.23
Consensus pattern (9 bp):
GGTGGTAGA
Found at i:4097837 original size:52 final size:52
Alignment explanation
Indices: 4097769--4097873 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
4097759 ATAATTGAAC
*
4097769 TCATATTAGTTCTAAGAAGTAAAAGTATGATTGAGAGAGTGTTAAATTGTAT
1 TCATATTAGTTCTAAGAAGTAAAAGTATCATTGAGAGAGTGTTAAATTGTAT
4097821 TCATATTAGTTCTAAGAAGTAAAAGTATCATTGAGAGAGTGTTAAATTGTAT
1 TCATATTAGTTCTAAGAAGTAAAAGTATCATTGAGAGAGTGTTAAATTGTAT
4097873 T
1 T
4097874 TTATTTATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (52 bp):
TCATATTAGTTCTAAGAAGTAAAAGTATCATTGAGAGAGTGTTAAATTGTAT
Found at i:4100125 original size:25 final size:25
Alignment explanation
Indices: 4100084--4100135 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
4100074 ATTTGTATAA
*
4100084 ACTAAATTGATTAATTGAACTAAAT
1 ACTAAATTAATTAATTGAACTAAAT
*
4100109 ACTAAATTAATTGATTGAACTAAAT
1 ACTAAATTAATTAATTGAACTAAAT
4100134 AC
1 AC
4100136 ATTCAGGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.35
Consensus pattern (25 bp):
ACTAAATTAATTAATTGAACTAAAT
Found at i:4100198 original size:14 final size:14
Alignment explanation
Indices: 4100179--4100210 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4100169 TTGTTTTATT
*
4100179 GAAAATGGTTTCTG
1 GAAAATGATTTCTG
4100193 GAAAATGATTTCTG
1 GAAAATGATTTCTG
4100207 GAAA
1 GAAA
4100211 GTGACTTTTC
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:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:4107013 original size:22 final size:22
Alignment explanation
Indices: 4106987--4107040 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
4106977 TTGACTTGGG
*
4106987 TATCGCAATACCTAAACACGGA
1 TATCGCAATACCTAAACACGAA
*
4107009 TATCGCAATACCTAAACTCGAA
1 TATCGCAATACCTAAACACGAA
*
4107031 TATTGCAATA
1 TATCGCAATA
4107041 GATAAGACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (22 bp):
TATCGCAATACCTAAACACGAA
Done.