Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 17 of 226
Found at i:6060047 original size:18 final size:19
Alignment explanation
Indices: 6059879--6060033 Score: 114
Period size: 18 Copynumber: 8.3 Consensus size: 19
6059869 CTTCCCTCTT
6059879 CTTCTTCCTTT-TTT-TTTC
1 CTTC-TCCTTTCTTTCTTTC
6059897 TCTTCTCCTTTCCTTTTCTTTC
1 -CTTCTCCTTT-C-TTTCTTTC
*
6059919 CTTCTTTCTTTCTTT-TTT-
1 CTTC-TCCTTTCTTTCTTTC
* *
6059937 CTTCT-C-TT-TTCCTTTT
1 CTTCTCCTTTCTTTCTTTC
*
6059953 CTTCTTC-TTCTTTCTTTC
1 CTTCTCCTTTCTTTCTTTC
6059971 TCTTCTCCTTTCCTTTTCTTTC
1 -CTTCTCCTTT-C-TTTCTTTC
*
6059993 CTTCT-TTTTCTTTCTTTC
1 CTTCTCCTTTCTTTCTTTC
6060011 C-TCTCCTTTCTTTCTTTC
1 CTTCTCCTTTCTTTCTTTC
*
6060029 TTTCT
1 CTTCT
6060034 TTCCCTCTCC
Statistics
Matches: 113, Mismatches: 8, Indels: 30
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.02
15 5 0.04
16 6 0.05
17 7 0.06
18 37 0.33
19 17 0.15
20 8 0.07
21 14 0.12
22 17 0.15
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTCTCCTTTCTTTCTTTC
Found at i:6060214 original size:27 final size:27
Alignment explanation
Indices: 6060184--6060237 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
6060174 TTTTTACAAG
6060184 TTTTTTTTATATATTTTGGTAAATAAA
1 TTTTTTTTATATATTTTGGTAAATAAA
6060211 TTTTTTTTATATATTTTGGTAAATAAA
1 TTTTTTTTATATATTTTGGTAAATAAA
6060238 AAAAAGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (27 bp):
TTTTTTTTATATATTTTGGTAAATAAA
Found at i:6060247 original size:27 final size:27
Alignment explanation
Indices: 6060190--6060262 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
6060180 CAAGTTTTTT
******
6060190 TTATATATTTTGGTAAATAAATTTTTT
1 TTATATATTTTGGTAAATAAAAAAAAG
6060217 TTATATATTTTGGTAAATAAAAAAAAG
1 TTATATATTTTGGTAAATAAAAAAAAG
*
6060244 TTATAACATTTTGGTAAAT
1 TTAT-ATATTTTGGTAAAT
6060263 TTTTATTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 25 0.66
28 13 0.34
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (27 bp):
TTATATATTTTGGTAAATAAAAAAAAG
Found at i:6061001 original size:14 final size:13
Alignment explanation
Indices: 6060975--6061025 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
6060965 GTTTATTTTA
6060975 AATATAATAATAT
1 AATATAATAATAT
6060988 AATATAATTAATAT
1 AATATAA-TAATAT
* *
6061002 AAT-TTACAATAT
1 AATATAATAATAT
*
6061014 AATAAAATAATA
1 AATATAATAATA
6061026 ACATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:6063357 original size:23 final size:23
Alignment explanation
Indices: 6063303--6063351 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
6063293 ACGTTCCAAC
6063303 TTTTT-TTTAAAATTATATTTAA
1 TTTTTATTTAAAATTATATTTAA
*
6063325 TTTTTATTTAAAATT-T-TTTAG
1 TTTTTATTTAAAATTATATTTAA
6063346 TTTTTA
1 TTTTTA
6063352 AATTTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 10 0.40
22 6 0.24
23 9 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTATTTAAAATTATATTTAA
Found at i:6063528 original size:16 final size:16
Alignment explanation
Indices: 6063484--6063535 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
6063474 ATTAATAAGA
6063484 AAAACATTTTTAAAATT
1 AAAA-ATTTTTAAAATT
**
6063501 AAAAATGATTAAAATT
1 AAAAATTTTTAAAATT
*
6063517 ATAAATTTTTAAAAATT
1 AAAAATTTTT-AAAATT
6063534 AA
1 AA
6063536 TTAAATATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAAATTTTTAAAATT
Found at i:6063676 original size:23 final size:21
Alignment explanation
Indices: 6063636--6063683 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6063626 AATTTGACAA
* *
6063636 AAAAATATAAATTTAATAACT
1 AAAAATAAAAATTTAATAAAT
6063657 AAAAATAAAAATATTAAATAAAT
1 AAAAATAAAAAT-TT-AATAAAT
6063680 AAAA
1 AAAA
6063684 CTATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 2 0.09
23 10 0.43
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATAAAAATTTAATAAAT
Found at i:6063941 original size:13 final size:13
Alignment explanation
Indices: 6063920--6063968 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
6063910 CTCCACATCT
* *
6063920 ATTTGATTAATTA
1 ATTTTATTAATTG
6063933 ATTTTATTAATTG
1 ATTTTATTAATTG
*
6063946 ATTTAATTAATTG
1 ATTTTATTAATTG
*
6063959 ATTCTATTAA
1 ATTTTATTAA
6063969 CTGTTTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (13 bp):
ATTTTATTAATTG
Found at i:6078999 original size:24 final size:24
Alignment explanation
Indices: 6078967--6079020 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
6078957 TCTTTCTAGA
6078967 ATATTTAGTATTTATTAGCATAAT
1 ATATTTAGTATTTATTAGCATAAT
6078991 ATATTTAGTATTTATTAGCATAAT
1 ATATTTAGTATTTATTAGCATAAT
*
6079015 TTATTT
1 ATATTT
6079021 GACCTACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
ATATTTAGTATTTATTAGCATAAT
Found at i:6081084 original size:24 final size:24
Alignment explanation
Indices: 6081057--6081103 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6081047 GCTTATAATA
6081057 GGTAGCTCCAAAGAGCAATTAACG
1 GGTAGCTCCAAAGAGCAATTAACG
* *
6081081 GGTAGCTCCGAATAGCAATTAAC
1 GGTAGCTCCAAAGAGCAATTAAC
6081104 AGGAAGTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.19
Consensus pattern (24 bp):
GGTAGCTCCAAAGAGCAATTAACG
Found at i:6081120 original size:24 final size:24
Alignment explanation
Indices: 6081060--6081109 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
6081050 TATAATAGGT
* * * *
6081060 AGCTCCAAAGAGCAATTAACGGGT
1 AGCTCCGAATAGCAATTAACAGGA
6081084 AGCTCCGAATAGCAATTAACAGGA
1 AGCTCCGAATAGCAATTAACAGGA
6081108 AG
1 AG
6081110 TACCGGATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (24 bp):
AGCTCCGAATAGCAATTAACAGGA
Found at i:6081187 original size:26 final size:27
Alignment explanation
Indices: 6081151--6081213 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
6081141 CGAGGACTAA
*
6081151 CGGGAAGCTCACAAAGAGCC-TTTAAT
1 CGGGAAGCTCACAAAGAGCCATATAAT
*
6081177 CGGGAAGCTCACGAAGAGCCATATAAT
1 CGGGAAGCTCACAAAGAGCCATATAAT
*
6081204 -GGGATGCTCA
1 CGGGAAGCTCA
6081214 TAAGAGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 28 0.85
27 5 0.15
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.17
Consensus pattern (27 bp):
CGGGAAGCTCACAAAGAGCCATATAAT
Found at i:6082504 original size:21 final size:21
Alignment explanation
Indices: 6082438--6082504 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
6082428 ATACACCAAT
* *
6082438 AGAAGCTCGTAAGAGCTAAAC
1 AGAAGCTCATAAGAGCTGAAC
* * * * *
6082459 AAAAACTCATAAGAGTTGTAT
1 AGAAGCTCATAAGAGCTGAAC
6082480 AGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCATAAGAGCTGAAC
6082501 AGAA
1 AGAA
6082505 AGTAAAACAC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTGAAC
Found at i:6084418 original size:27 final size:26
Alignment explanation
Indices: 6084371--6084423 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
6084361 TTTTTAAAAA
* ** *
6084371 TAAATTTTAAAATTTTTTTAATTGTT
1 TAAATTTTAAAAATTAATTAAATGTT
6084397 TAAATTTTTAAAAATTAATTAAATGTT
1 TAAA-TTTTAAAAATTAATTAAATGTT
6084424 GATGTGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
TAAATTTTAAAAATTAATTAAATGTT
Found at i:6094070 original size:22 final size:25
Alignment explanation
Indices: 6094045--6094105 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
6094035 TTTTATTGTT
6094045 TTGTTA-TC-ATTTTATTATT-ATA
1 TTGTTACTCTATTTTATTATTAATA
*
6094067 TTGTTACTCTTATTTTATTATTAATT
1 TTGTTACTC-TATTTTATTATTAATA
*
6094093 TTGTTACTATATT
1 TTGTTACTCTATT
6094106 AGAAGTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 6 0.18
23 2 0.06
25 15 0.45
26 10 0.30
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (25 bp):
TTGTTACTCTATTTTATTATTAATA
Found at i:6095122 original size:18 final size:17
Alignment explanation
Indices: 6095105--6095172 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 17
6095095 TAATAATATA
6095105 TTAAAATTTAATTTTA-
1 TTAAAATTTAATTTTAT
* *
6095121 TAAATTAATTTAA-TGTAT
1 TTAA--AATTTAATTTTAT
*
6095139 TTAAAATTTTTAAGTTTAT
1 TTAAAA--TTTAATTTTAT
*
6095158 TTAAAATTAAATTTT
1 TTAAAATTTAATTTT
6095173 TAAATACTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
16 5 0.12
17 10 0.25
18 15 0.38
19 10 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAAATTTAATTTTAT
Found at i:6095356 original size:13 final size:12
Alignment explanation
Indices: 6095314--6095355 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
6095304 ATTGTGCATG
6095314 TTAATTTTAAAT
1 TTAATTTTAAAT
*
6095326 TAAATTTTAAAT
1 TTAATTTTAAAT
6095338 TTAATATTTAAAT
1 TTAAT-TTTAAAT
6095351 TTAAT
1 TTAAT
6095356 AATAACGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAATTTTAAAT
Found at i:6104795 original size:39 final size:37
Alignment explanation
Indices: 6104728--6104820 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
6104718 ACCAGAATGG
* *
6104728 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
6104767 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
6104804 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
6104821 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:6105017 original size:23 final size:24
Alignment explanation
Indices: 6104996--6105040 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
6104986 CACTTTCAAT
* *
6104996 TCAATCATT-TTTC-CACATTCAA
1 TCAATAATTATTTCACAAATTCAA
6105018 TCAATAATTATTTCACAAATTCA
1 TCAATAATTATTTCACAAATTCA
6105041 CACATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (24 bp):
TCAATAATTATTTCACAAATTCAA
Found at i:6105034 original size:22 final size:23
Alignment explanation
Indices: 6104990--6105040 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
6104980 TTCTCACACT
*
6104990 TTCAATTCAATCATTTTTCCACA
1 TTCAATTCAATAATTTTTCCACA
*
6105013 TTCAA-TCAATAATTATTTCACAAA
1 TTCAATTCAATAATT-TTTC-CACA
6105037 TTCA
1 TTCA
6105041 CACATTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 9 0.38
24 7 0.29
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (23 bp):
TTCAATTCAATAATTTTTCCACA
Found at i:6105783 original size:28 final size:28
Alignment explanation
Indices: 6105751--6105807 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
6105741 ACTTAATTCC
6105751 ATCAAAACTTTGTTTTAAAGCTTTTAAA
1 ATCAAAACTTTGTTTTAAAGCTTTTAAA
6105779 ATCAAAACTTTGTTTTAAAGCTTTTAAA
1 ATCAAAACTTTGTTTTAAAGCTTTTAAA
6105807 A
1 A
6105808 CATTATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (28 bp):
ATCAAAACTTTGTTTTAAAGCTTTTAAA
Found at i:6105962 original size:16 final size:17
Alignment explanation
Indices: 6105941--6105974 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6105931 TTGGCTATTC
*
6105941 TGTTTCT-TTCTTCTTT
1 TGTTTCTCTTATTCTTT
6105957 TGTTTCTCTTATTCTTT
1 TGTTTCTCTTATTCTTT
6105974 T
1 T
6105975 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.03, C:0.18, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCTCTTATTCTTT
Found at i:6106182 original size:14 final size:17
Alignment explanation
Indices: 6106163--6106199 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
6106153 ATTTATTTCT
6106163 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
6106177 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
6106194 TAATAT
1 TAATAT
6106200 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:6111166 original size:21 final size:21
Alignment explanation
Indices: 6111124--6111166 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
6111114 TTCAGTATAC
*
6111124 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
6111145 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
6111166 A
1 A
6111167 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:6112277 original size:39 final size:37
Alignment explanation
Indices: 6112210--6112302 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
6112200 ACCAGAATGG
* *
6112210 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
6112249 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
6112286 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
6112303 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:6112498 original size:24 final size:26
Alignment explanation
Indices: 6112446--6112514 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
6112436 ACATATATTC
**
6112446 TCAATTCAATCACAATTTCTCACACTT
1 TCAATTCAATCA-TTTTTCTCACACTT
6112473 TCAATTCAATCATTTTTC-CACA-TT
1 TCAATTCAATCATTTTTCTCACACTT
*
6112497 TCAA-TCAATAATTATTTC
1 TCAATTCAATCATT-TTTC
6112515 ACAAATTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 8 0.21
24 10 0.26
25 4 0.11
26 4 0.11
27 12 0.32
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (26 bp):
TCAATTCAATCATTTTTCTCACACTT
Found at i:6112517 original size:23 final size:24
Alignment explanation
Indices: 6112459--6112517 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
6112449 ATTCAATCAC
*
6112459 AATTTCTCACACTTTCAATTCAAT
1 AATTTTTCACACTTTCAATTCAAT
*
6112483 CATTTTTC-CACATTTCAA-TCAAT
1 AATTTTTCACAC-TTTCAATTCAAT
6112506 AATTATTTCACA
1 AATT-TTTCACA
6112518 AATTCACACA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 11 0.38
24 16 0.55
25 2 0.07
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTTTTCACACTTTCAATTCAAT
Found at i:6113427 original size:17 final size:16
Alignment explanation
Indices: 6113395--6113428 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
6113385 TTGGCTATTC
*
6113395 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
6113411 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
6113428 T
1 T
6113429 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:6113476 original size:14 final size:14
Alignment explanation
Indices: 6113417--6113467 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
6113407 CTTTTGTTTC
*
6113417 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
6113430 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
6113445 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
6113459 TTTTATTTC
1 TTTTATTTC
6113468 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:6113636 original size:14 final size:17
Alignment explanation
Indices: 6113617--6113653 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
6113607 ATTTATTTCT
6113617 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
6113631 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
6113648 TAATAT
1 TAATAT
6113654 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:6113952 original size:24 final size:26
Alignment explanation
Indices: 6113925--6113980 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
6113915 GGACTCAATT
*
6113925 TACTAA-GA-CGGAGGCTCGATATTA
1 TACTAACGAGCGGAGGCCCGATATTA
6113949 TACTAATCGATGCGGAGGCCCGATATTA
1 TACTAA-CGA-GCGGAGGCCCGATATTA
6113977 TACT
1 TACT
6113981 TTTTCGATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 6 0.22
26 2 0.07
28 19 0.70
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (26 bp):
TACTAACGAGCGGAGGCCCGATATTA
Found at i:6115182 original size:17 final size:17
Alignment explanation
Indices: 6115149--6115182 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6115139 CACCTTTTGC
**
6115149 TTTATTTTTCATTTTTT
1 TTTATTTTTCACGTTTT
6115166 TTTATTTTTCACGTTTT
1 TTTATTTTTCACGTTTT
6115183 AAGAAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTATTTTTCACGTTTT
Found at i:6116631 original size:21 final size:21
Alignment explanation
Indices: 6116598--6116639 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6116588 TCATAAATTT
* * *
6116598 TTTTACATCATATAATTAAAA
1 TTTTAAATAATATAATAAAAA
6116619 TTTTAAATAATATAATAAAAA
1 TTTTAAATAATATAATAAAAA
6116640 AACTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTAAATAATATAATAAAAA
Found at i:6145425 original size:25 final size:26
Alignment explanation
Indices: 6145397--6145454 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 26
6145387 CATCAAAATC
6145397 TATTTTCTTTA-GAAATATAA-ATTAA
1 TATTTTCTTTATGAAA-ATAATATTAA
*
6145422 TATTTTTTTTATGAAAATAATTATTAA
1 TATTTTCTTTATGAAAATAA-TATTAA
6145449 TATTTT
1 TATTTT
6145455 TAAGAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 14 0.48
26 4 0.14
27 11 0.38
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (26 bp):
TATTTTCTTTATGAAAATAATATTAA
Found at i:6145439 original size:27 final size:25
Alignment explanation
Indices: 6145397--6145455 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
6145387 CATCAAAATC
*
6145397 TATTTTCTTTAGAAAT-ATAAATTAA
1 TATTTTTTTTAGAAATAAT-AATTAA
*
6145422 TATTTTTTTTATGAAAATAATTATTAA
1 TATTTTTTTTA-G-AAATAATAATTAA
6145449 TATTTTT
1 TATTTTT
6145456 AAGAAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 10 0.34
26 1 0.03
27 16 0.55
28 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (25 bp):
TATTTTTTTTAGAAATAATAATTAA
Found at i:6146236 original size:40 final size:40
Alignment explanation
Indices: 6146164--6146242 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
6146154 ACTGTTCATG
* *
6146164 CCACGTCAGCAAATCGCGTCCTAGAGGGCGCGATTTCCTT
1 CCACGTCAGCAAATCGCGTCCTACAGGACGCGATTTCCTT
6146204 CCACGTCAGCAAATCGC-T-CTGACATGGACGCGATTTCCT
1 CCACGTCAGCAAATCGCGTCCT-ACA-GGACGCGATTTCCT
6146243 GCGCGTACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 2 0.06
39 3 0.09
40 30 0.86
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.23
Consensus pattern (40 bp):
CCACGTCAGCAAATCGCGTCCTACAGGACGCGATTTCCTT
Found at i:6146325 original size:30 final size:30
Alignment explanation
Indices: 6146286--6146354 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
6146276 GATTTCGCGG
* *
6146286 AAAATGGCCCATTCCGGTAAATAATT-AAAA
1 AAAACGGCCCATTCCGATAAAT-ATTGAAAA
* * *
6146316 AAACCGGCCCATTTCGATAAATTTTGAAAA
1 AAAACGGCCCATTCCGATAAATATTGAAAA
6146346 AAAACGGCC
1 AAAACGGCC
6146355 TTTTTTGGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.22
Consensus pattern (30 bp):
AAAACGGCCCATTCCGATAAATATTGAAAA
Found at i:6152976 original size:18 final size:17
Alignment explanation
Indices: 6152936--6153000 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 17
6152926 AATTAATTAT
* *
6152936 TTTTTTATATTTAAAAA
1 TTTTTTATATTTTATAA
6152953 TATTTTTATAATTTTATAA
1 T-TTTTTAT-ATTTTATAA
* *
6152972 -TTTTTATTTTTTTTGAA
1 TTTTTTATATTTTAT-AA
6152989 TTTTTTATATTT
1 TTTTTTATATTT
6153001 AAAATTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 5 0.13
17 10 0.26
18 17 0.44
19 7 0.18
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTTTATATTTTATAA
Found at i:6160511 original size:87 final size:86
Alignment explanation
Indices: 6160402--6160874 Score: 342
Period size: 87 Copynumber: 5.4 Consensus size: 86
6160392 ACTAATGCCT
* * *
6160402 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTCAACCAGGGAGATAGAATTACGGCTT
1 AGGGAGATAAAATCTGACATCTTCAATCTACTCCACTGT-AACCAGGGAGATAGAATTACGGCTT
*
6160467 CAATGTACTCCACTGTAACCAC
65 CAATCTACTCCACTGTAACCAC
* * * *
6160489 AGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCAC--TAATGCCTAGGGAGATAGAATTACGGC
1 AGGGAGATAAAATCTGACATCTTCAATCTACTCCACTGTAA--CC-AGGGAGATAGAATTACGGC
*
6160552 TTCAATATACTCCACTGTAACCAC
63 TTCAATCTACTCCACTGTAACCAC
* * * * *
6160576 AGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCAC--TAATGCCTAGGGAGATA-AGATCTGAA
1 AGGGAGATAAAATCTGACATCTTCAATCTACTCCACTGTAA--CC-AGGGAGATAGA-AT-T-AC
** * *
6160638 ATCTTCAATCTATTCCACTGCCAA-C-C
60 GGCTTCAATCTACTCCACTG-TAACCAC
* ** * * * *
6160664 AGGGAGATAGAAT-T-ACGGCTTCAATGTACTCCACTGTAACCACGGGGAGGTA-AAATCCGCCA
1 AGGGAGATAAAATCTGACATCTTCAATCTACTCCACTGTAACCA--GGGAGATAGAATTACG---
* * * *
6160726 TCTTCGATCTGCTCCAC--TAATGCC-T
61 GCTTCAATCTACTCCACTGTAA--CCAC
* * * * *
6160751 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCTGGGAGATAGAATTACGGCTT
1 AGGGAGATAAAATCTGACATCTTCAATCTACTCCACTG-TAACCAGGGAGATAGAATTACGGCTT
*
6160816 CAATGTACTCCACTGTAACCAC
65 CAATCTACTCCACTGTAACCAC
* * *
6160838 AGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACT
1 AGGGAGATAAAATCTGACATCTTCAATCTACTCCACT
6160875 ACTGCTTAGG
Statistics
Matches: 307, Mismatches: 55, Indels: 48
0.75 0.13 0.12
Matches are distributed among these distances:
84 4 0.01
85 3 0.01
86 35 0.11
87 192 0.63
88 27 0.09
89 40 0.13
90 6 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (86 bp):
AGGGAGATAAAATCTGACATCTTCAATCTACTCCACTGTAACCAGGGAGATAGAATTACGGCTTC
AATCTACTCCACTGTAACCAC
Found at i:6160527 original size:131 final size:132
Alignment explanation
Indices: 6160213--6160541 Score: 552
Period size: 132 Copynumber: 2.5 Consensus size: 132
6160203 ATTGGAGTCG
* * ** * *
6160213 CCACCGTAACCTCAGGGAGGTAAAATTTGCCATCTTCGATCTGCTCCACTACCGCTTAAGGAGAT
1 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
* *
6160278 AATATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGGGATAAAATTACTGGCTTCAATGTA
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAAAATTACTGGCTTCAATGTA
6160343 CT
131 CT
6160345 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
1 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
* *
6160410 AAGATCTGAAATCTTCAATCTATTCCACTGTCAACCAGGGAGATAGAATTAC-GGCTTCAATGTA
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAAAATTACTGGCTTCAATGTA
6160474 CT
131 CT
*
6160476 CCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
1 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
6160541 A
66 A
6160542 GAATTACGGC
Statistics
Matches: 186, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
131 79 0.42
132 107 0.58
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (132 bp):
CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAAAATTACTGGCTTCAATGTA
CT
Found at i:6160624 original size:131 final size:130
Alignment explanation
Indices: 6160489--6160910 Score: 607
Period size: 131 Copynumber: 3.2 Consensus size: 130
6160479 CTGTAACCAC
* ** * *
6160489 AGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT-AATGCCTAGGGAGATAGAATTACGGCT
1 AGGGAGATAAAATCTGAAATCTTCAATCTACTCCACTCAA--CCTAGGGAGATAGAATTACGGCT
* *
6160553 TCAATATACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGC
64 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGC
6160618 CT
129 CT
* *
6160620 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC-AGGGAGATAGAATTACGGCT
1 AGGGAGATAAAATCTGAAATCTTCAATCTACTCCACT--CAACCTAGGGAGATAGAATTACGGCT
* * *
6160684 TCAATGTACTCCACTGTAACCACGGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAATGC
64 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGC
6160749 CT
129 CT
* *
6160751 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCT-GGGAGATAGAATTACGGCT
1 AGGGAGATAAAATCTGAAATCTTCAATCTACTCCACT--CAACCTAGGGAGATAGAATTACGGCT
*
6160815 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTGC
64 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGC
*
6160880 TT
129 CT
* *
6160882 AGGGAAATAAGATCTGAAATCTTCAATCT
1 AGGGAGATAAAATCTGAAATCTTCAATCT
6160911 TTTAAATTGC
Statistics
Matches: 271, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
131 267 0.99
132 2 0.01
134 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (130 bp):
AGGGAGATAAAATCTGAAATCTTCAATCTACTCCACTCAACCTAGGGAGATAGAATTACGGCTTC
AATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCT
Found at i:6160634 original size:218 final size:219
Alignment explanation
Indices: 6160314--6160760 Score: 824
Period size: 218 Copynumber: 2.0 Consensus size: 219
6160304 ACTGCCAACC
* * *
6160314 AGGGGGATAAAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
1 AGGGAGATAAAATTACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
*
6160379 TTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTCAA
66 TTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
*
6160444 CCAGGGAGATAGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT
131 CCAGGGAGATAGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCAT
6160509 CTTCGATCTGCTCCACTAATGCCT
196 CTTCGATCTGCTCCACTAATGCCT
*
6160533 AGGGAGATAGAATTAC-GGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
1 AGGGAGATAAAATTACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
6160597 TTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
66 TTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
*
6160662 CCAGGGAGATAGAATTACGGCTTCAATGTACTCCACTGTAACCACGGGGAGGTAAAATCCGCCAT
131 CCAGGGAGATAGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCAT
6160727 CTTCGATCTGCTCCACTAATGCCT
196 CTTCGATCTGCTCCACTAATGCCT
6160751 AGGGAGATAA
1 AGGGAGATAA
6160761 GATCTGAAAT
Statistics
Matches: 220, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
218 206 0.94
219 14 0.06
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (219 bp):
AGGGAGATAAAATTACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
TTCGATCTGCTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA
CCAGGGAGATAGAATTACGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCAT
CTTCGATCTGCTCCACTAATGCCT
Found at i:6160800 original size:44 final size:44
Alignment explanation
Indices: 6160272--6160910 Score: 173
Period size: 44 Copynumber: 14.6 Consensus size: 44
6160262 TACCGCTTAA
* * *
6160272 GGAGATAATATCTGAAATCTTCAATCTATTCCACTGCCAA-CCAG
1 GGAGATAAGATCTGAAATCTTCAATCTACTCCACTG-CAACCCTG
* * * * * *
6160316 GGGGATAAAATTACTG---GCTTCAATGTACTCCACTGTAACCTCAG
1 GGAGATAAGA-T-CTGAAATCTTCAATCTACTCCACTGCAACC-CTG
* * ** * * *
6160360 GGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT--AATGCCTAG
1 GGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCAA-CCCT-G
* *
6160404 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTCAA-CCAG
1 GGAGATAAGATCTGAAATCTTCAATCTACTCCACTG-CAACCCTG
*** * * *
6160448 GGAGAT-AGAAT-T-ACGGCTTCAATGTACTCCACTGTAACCACAG
1 GGAGATAAG-ATCTGAAATCTTCAATCTACTCCACTGCAACC-CTG
* * ** * * *
6160491 GGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT--AATGCCTAG
1 GGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCAA-CCCT-G
*** * * *
6160535 GGAGAT-AGAAT-T-ACGGCTTCAATATACTCCACTGTAACCACAG
1 GGAGATAAG-ATCTGAAATCTTCAATCTACTCCACTGCAACC-CTG
* * ** * * *
6160578 GGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT--AATGCCTAG
1 GGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCAA-CCCT-G
* *
6160622 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA-CCAG
1 GGAGATAAGATCTGAAATCTTCAATCTACTCCACTG-CAACCCTG
*** * * *
6160666 GGAGAT-AGAAT-T-ACGGCTTCAATGTACTCCACTGTAACCACGG
1 GGAGATAAG-ATCTGAAATCTTCAATCTACTCCACTGCAACC-CTG
* * * ** * * *
6160709 GGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT--AATGCCTAG
1 GGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCAA-CCCT-G
*
6160753 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAA-CCTG
1 GGAGATAAGATCTGAAATCTTCAATCTACTCCACTG-CAACCCTG
*** * * *
6160797 GGAGAT-AGAAT-T-ACGGCTTCAATGTACTCCACTGTAACCACAG
1 GGAGATAAG-ATCTGAAATCTTCAATCTACTCCACTGCAACC-CTG
* * ** * * ** *
6160840 GGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAC-TGCTTAG
1 GGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCAACCCT-G
*
6160884 GGAAATAAGATCTGAAATCTTCAATCT
1 GGAGATAAGATCTGAAATCTTCAATCT
6160911 TTTAAATTGC
Statistics
Matches: 427, Mismatches: 118, Indels: 100
0.66 0.18 0.16
Matches are distributed among these distances:
41 6 0.01
42 74 0.17
43 78 0.18
44 177 0.41
45 83 0.19
46 3 0.01
47 6 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (44 bp):
GGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCAACCCTG
Found at i:6160865 original size:349 final size:350
Alignment explanation
Indices: 6160213--6160886 Score: 1179
Period size: 349 Copynumber: 1.9 Consensus size: 350
6160203 ATTGGAGTCG
* * * *
6160213 CCACCGTAACCTCAGGGAGGTAAAATTTGCCATCTTCGATCTGCTCCACTACCGCTTAAGGAGAT
1 CCACCGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAACGCCTAAGGAGAT
* *
6160278 AATATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGGGATAAAATTACTGGCTTCAATGTA
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAAAATTACTGGCTTCAATGTA
* *
6160343 CTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAG
131 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAG
*
6160408 ATAAGATCTGAAATCTTCAATCTATTCCACTGTCAACCAGGGAGATAGAATTACGGCTTCAATGT
196 ATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGT
*
6160473 ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGA
261 ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGA
6160538 GATAGAATTACGGCTTCAATATACT
326 GATAGAATTACGGCTTCAATATACT
* * *
6160563 CCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
1 CCACCGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAACGCCTAAGGAGAT
*
6160628 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTAC-GGCTTCAATGTA
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAAAATTACTGGCTTCAATGTA
*
6160692 CTCCACTGTAACCACGGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAG
131 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAG
*
6160757 ATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCTGGGAGATAGAATTACGGCTTCAATGT
196 ATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGT
* *
6160822 ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTGCTTAGGGA
261 ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGA
6160887 AATAAGATCT
Statistics
Matches: 306, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
349 199 0.65
350 107 0.35
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (350 bp):
CCACCGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAACGCCTAAGGAGAT
AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAAAATTACTGGCTTCAATGTA
CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAG
ATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGT
ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGA
GATAGAATTACGGCTTCAATATACT
Found at i:6162384 original size:8 final size:8
Alignment explanation
Indices: 6162362--6162400 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
6162352 CCTTAGCCTC
6162362 TCCATTTT
1 TCCATTTT
*
6162370 TAC-TTTT
1 TCCATTTT
6162377 TCCATTTT
1 TCCATTTT
6162385 T-CATTTT
1 TCCATTTT
6162392 TCCATTTT
1 TCCATTTT
6162400 T
1 T
6162401 ATTTTTTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.67
Consensus pattern (8 bp):
TCCATTTT
Found at i:6162421 original size:16 final size:15
Alignment explanation
Indices: 6162362--6162422 Score: 72
Period size: 15 Copynumber: 4.0 Consensus size: 15
6162352 CCTTAGCCTC
*
6162362 TCCATTTTTACTTTT
1 TCCATTTTTATTTTT
6162377 TCCATTTTTCA-TTTT
1 TCCATTTTT-ATTTTT
6162392 TCCATTTTTATTTTT
1 TCCATTTTTATTTTT
6162407 TCACATCTTTT-TTTTT
1 TC-CAT-TTTTATTTTT
6162423 GCAACTCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.02
15 28 0.67
16 9 0.21
17 4 0.10
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (15 bp):
TCCATTTTTATTTTT
Found at i:6162901 original size:1 final size:1
Alignment explanation
Indices: 6162895--6163018 Score: 77
Period size: 1 Copynumber: 124.0 Consensus size: 1
6162885 CCGGTAGAGG
* * * * * * * * * * *
6162895 TTTTTTTGTTTCTTTTTATTTTTTGTTTTTTGTTCTTTTTTTGTTCTCTTTTTTTTCTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * *
6162960 TCTCTTTTTTTTATTTTTTTGTTTTTTATTTTTGTTTTTTTGTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6163019 AATTGAATCT
Statistics
Matches: 85, Mismatches: 38, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 85 1.00
ACGTcount: A:0.02, C:0.06, G:0.06, T:0.85
Consensus pattern (1 bp):
T
Found at i:6162936 original size:11 final size:11
Alignment explanation
Indices: 6162895--6163018 Score: 102
Period size: 10 Copynumber: 11.5 Consensus size: 11
6162885 CCGGTAGAGG
6162895 TTTTTTTGTTTC
1 TTTTTTTG-TTC
*
6162907 TTTTTATT-TTT
1 TTTTT-TTGTTC
6162918 TGTTTTTTGTTC
1 T-TTTTTTGTTC
6162930 TTTTTTTGTTC
1 TTTTTTTGTTC
6162941 TCTTTTTT-TTC
1 T-TTTTTTGTTC
*
6162952 TTTTTTT-CTC
1 TTTTTTTGTTC
*
6162962 TCTTTTTT-TTA
1 T-TTTTTTGTTC
6162973 TTTTTTTGTT-
1 TTTTTTTGTTC
*
6162983 TTTTATTT-TTG
1 TTTT-TTTGTTC
6162994 TTTTTTTGTT-
1 TTTTTTTGTTC
6163004 TTTTTTTGTT-
1 TTTTTTTGTTC
6163014 TTTTT
1 TTTTT
6163019 AATTGAATCT
Statistics
Matches: 98, Mismatches: 5, Indels: 20
0.80 0.04 0.16
Matches are distributed among these distances:
10 39 0.40
11 39 0.40
12 18 0.18
13 2 0.02
ACGTcount: A:0.02, C:0.06, G:0.06, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTTC
Found at i:6162971 original size:21 final size:21
Alignment explanation
Indices: 6162897--6163018 Score: 99
Period size: 23 Copynumber: 5.8 Consensus size: 21
6162887 GGTAGAGGTT
* *
6162897 TTTTTGTTTCTTTTTATTTTTTG
1 TTTTT-TTTCTTTTT-TTTTCTC
6162920 TTTTTTGTTCTTTTTTTGTTCTC
1 TTTTTT-TTCTTTTTTT-TTCTC
*
6162943 TTTTTTTTCTTTTTTTCTCTC
1 TTTTTTTTCTTTTTTTTTCTC
*
6162964 TTTTTTTTATTTTTTTGTT-T-
1 TTTTTTTTCTTTTTTT-TTCTC
* * *
6162984 TTTATTTT-TGTTTTTTTGT-
1 TTTTTTTTCTTTTTTTTTCTC
*
6163003 TTTTTTTTGTTTTTTT
1 TTTTTTTTCTTTTTTT
6163019 AATTGAATCT
Statistics
Matches: 85, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
18 2 0.02
19 14 0.16
20 13 0.15
21 20 0.24
22 14 0.16
23 22 0.26
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.84
Consensus pattern (21 bp):
TTTTTTTTCTTTTTTTTTCTC
Found at i:6166193 original size:40 final size:39
Alignment explanation
Indices: 6166109--6166331 Score: 272
Period size: 40 Copynumber: 5.6 Consensus size: 39
6166099 TTGAATGATG
* * * *
6166109 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
6166149 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
6166189 TCCGGGCTAAGCCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
6166227 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
6166266 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
6166307 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
6166332 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
38 34 0.21
39 38 0.23
40 81 0.50
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:6166353 original size:79 final size:78
Alignment explanation
Indices: 6166109--6166364 Score: 243
Period size: 79 Copynumber: 3.3 Consensus size: 78
6166099 TTGAATGATG
* * * * * * *
6166109 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATTT
** *
6166174 GTGCGAGAT-ACTAAT
64 GAACGAG-TGACTAAA
* * *
6166189 TCCGGGCTAAG-CCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGA
* *
6166253 GCGAGTTACTAAA
66 ACGAGTGACTAAA
*
6166266 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
*
6166330 TGAACGAG-GAGCTATA
63 TGAACGAGTGA-CTAAA
* *
6166346 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
6166365 TACGTGATTT
Statistics
Matches: 153, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
76 1 0.01
77 35 0.23
78 26 0.17
79 54 0.35
80 37 0.24
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGA
ACGAGTGACTAAA
Found at i:6174140 original size:40 final size:40
Alignment explanation
Indices: 6174056--6174279 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
6174046 TTGAATGATG
* * * *
6174056 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
6174096 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
6174136 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6174174 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6174214 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
6174255 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6174280 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 25 0.15
39 19 0.12
40 111 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:6174274 original size:80 final size:80
Alignment explanation
Indices: 6174056--6174279 Score: 296
Period size: 78 Copynumber: 2.8 Consensus size: 80
6174046 TTGAATGATG
* * * * *
6174056 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
6174119 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
6174136 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
6174198 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
6174214 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
6174279 G
66 G
6174280 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 2 0.02
78 49 0.39
79 25 0.20
80 49 0.39
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:6178434 original size:3 final size:3
Alignment explanation
Indices: 6178426--6178484 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
6178416 ACATACATGC
* *
6178426 AAT AAT AAT -AT AGT AAT AATT AAA AAT AAAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT -AAT AAT AAT AAT AAT AAT
* *
6178471 CAT AAT AAA AAT AA
1 AAT AAT AAT AAT AA
6178485 ACTAAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
2 3 0.07
3 35 0.80
4 6 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:6178461 original size:17 final size:17
Alignment explanation
Indices: 6178439--6178478 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6178429 AATAATATAG
6178439 TAATAATTAAAAATAA-A
1 TAATAA-TAAAAATAACA
*
6178456 TAATAATAATAATAACA
1 TAATAATAAAAATAACA
6178473 TAATAA
1 TAATAA
6178479 AAATAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TAATAATAAAAATAACA
Found at i:6178476 original size:31 final size:27
Alignment explanation
Indices: 6178426--6178485 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 27
6178416 ACATACATGC
*
6178426 AATAATAATATAGTAATAATTAAAAATA
1 AATAATAATATAATAATAA-TAAAAATA
6178454 AATAATAATAATAATAACATAATAAAAATA
1 AATAATAAT-ATAAT-A-ATAATAAAAATA
6178484 AA
1 AA
6178486 CTAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.32
29 4 0.14
30 11 0.39
31 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (27 bp):
AATAATAATATAATAATAATAAAAATA
Found at i:6178483 original size:17 final size:16
Alignment explanation
Indices: 6178450--6178484 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
6178440 AATAATTAAA
*
6178450 AATAAATAATAATAAT
1 AATAAATAATAAAAAT
6178466 AATAACATAATAAAAAT
1 AATAA-ATAATAAAAAT
6178483 AA
1 AA
6178485 ACTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATAATAAAAAT
Found at i:6182124 original size:20 final size:20
Alignment explanation
Indices: 6182099--6182141 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
6182089 GTTACCCTCC
6182099 AAAAAACACTTAAAACGTGA
1 AAAAAACACTTAAAACGTGA
6182119 AAAAAACACTTAAAACGTGA
1 AAAAAACACTTAAAACGTGA
6182139 AAA
1 AAA
6182142 CATTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAAAACACTTAAAACGTGA
Found at i:6183886 original size:27 final size:27
Alignment explanation
Indices: 6183851--6183906 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
6183841 TCAATTTTAA
*
6183851 TGGTGCCAATAAAAATGGCACCATTGG
1 TGGTGCCAATAAAAATAGCACCATTGG
* * *
6183878 TGGTGCCAATGAGAATAGCACCGTTGG
1 TGGTGCCAATAAAAATAGCACCATTGG
6183905 TG
1 TG
6183907 TCGCCATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (27 bp):
TGGTGCCAATAAAAATAGCACCATTGG
Found at i:6199746 original size:19 final size:20
Alignment explanation
Indices: 6199716--6199756 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
6199706 AAATTTTGAG
*
6199716 AAATTATTATTTATTTTTTA
1 AAATTATTATTTATCTTTTA
6199736 AAATT-TTATTTATCTTTTA
1 AAATTATTATTTATCTTTTA
6199755 AA
1 AA
6199757 GAAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTATTTATCTTTTA
Found at i:6204881 original size:3 final size:3
Alignment explanation
Indices: 6204873--6204903 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6204863 AACTAGCCCT
6204873 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6204904 ATATAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6205054 original size:41 final size:42
Alignment explanation
Indices: 6205004--6205084 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
6204994 CTATTTTCTG
*
6205004 GACTAATATAA-AAACATAGTGAAACATCACATCTAATTTAT
1 GACTAATATAACAAACATAATGAAACATCACATCTAATTTAT
* * *
6205045 GACTCATATAACAAACATAATGAAACATCACTTTTAATTT
1 GACTAATATAACAAACATAATGAAACATCACATCTAATTT
6205085 GGCAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (42 bp):
GACTAATATAACAAACATAATGAAACATCACATCTAATTTAT
Found at i:6206928 original size:37 final size:37
Alignment explanation
Indices: 6206863--6206971 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
6206853 TACATATGAT
* *
6206863 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
6206898 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
6206935 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
6206972 AAAAGCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:6206988 original size:46 final size:46
Alignment explanation
Indices: 6206935--6207255 Score: 399
Period size: 52 Copynumber: 6.6 Consensus size: 46
6206925 TAAGTGTAGC
* **
6206935 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCAAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
6206981 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
6207027 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
6207079 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
6207131 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
6207183 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
6207229 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
6207256 AGTACTCAAA
Statistics
Matches: 258, Mismatches: 10, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
46 113 0.44
49 1 0.00
50 1 0.00
51 3 0.01
52 140 0.54
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:6207058 original size:52 final size:52
Alignment explanation
Indices: 6206978--6207249 Score: 412
Period size: 52 Copynumber: 5.3 Consensus size: 52
6206968 TAGCAAAAGC
* * *
6206978 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
6207031 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
6207083 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
6207135 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
6207187 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
6207233 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
6207250 ATCAGAAGTA
Statistics
Matches: 202, Mismatches: 10, Indels: 14
0.89 0.04 0.06
Matches are distributed among these distances:
46 43 0.21
50 1 0.00
52 143 0.71
53 15 0.07
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:6207143 original size:104 final size:98
Alignment explanation
Indices: 6206935--6207249 Score: 468
Period size: 104 Copynumber: 3.1 Consensus size: 98
6206925 TAAGTGTAGC
* * * *
6206935 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCAAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCAGAAGCTATCACTTATCACTTTGTCACT
6207000 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
6207034 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAACCGAAGCTATCACTTATCACTTTTCACTTG
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCAGAAGCTATCACTTATCAC---T---TTG
* *
6207099 TCACTTGATCAGATAAGTGTAACCGAAGCTATCACTTAT
60 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
6207138 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCAGAAGCTATCACTTATCACTTTGTCACTT
6207203 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
6207236 CACTTTGTCACTTG
1 CACTTT-TCACTTG
6207250 ATCAGAAGTA
Statistics
Matches: 195, Mismatches: 14, Indels: 14
0.87 0.06 0.06
Matches are distributed among these distances:
98 87 0.45
99 15 0.08
101 2 0.01
104 91 0.47
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCAGAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:6208522 original size:45 final size:45
Alignment explanation
Indices: 6208472--6208735 Score: 411
Period size: 45 Copynumber: 5.9 Consensus size: 45
6208462 CTGGCCATGG
* * * * *
6208472 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
6208517 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
6208562 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6208607 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
6208652 TGCTTCTTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
6208697 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
6208736 TCCACCTCTT
Statistics
Matches: 203, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 203 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:6208870 original size:16 final size:16
Alignment explanation
Indices: 6208849--6208880 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6208839 CATTCTGCAT
6208849 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
6208865 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
6208881 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:6211616 original size:19 final size:18
Alignment explanation
Indices: 6211592--6211640 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
6211582 TTTCAATCAC
6211592 TTTTTTTTAATTTCGAATT
1 TTTTTTTTAATTTC-AATT
**
6211611 TTTTTTTTGAATTTCTCTT
1 TTTTTTTT-AATTTCAATT
6211630 TTTTTTTTAAT
1 TTTTTTTTAAT
6211641 ACCGAATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 18 0.67
20 6 0.22
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTTTTTAATTTCAATT
Found at i:6212452 original size:45 final size:45
Alignment explanation
Indices: 6212403--6212665 Score: 411
Period size: 45 Copynumber: 5.9 Consensus size: 45
6212393 CCGGCCATGG
* * * * *
6212403 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
6212448 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
6212493 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6212538 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6212583 TGCTT-CTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
6212627 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
6212666 TCCACCTCTT
Statistics
Matches: 203, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
44 44 0.22
45 159 0.78
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:6212646 original size:134 final size:135
Alignment explanation
Indices: 6212403--6212665 Score: 420
Period size: 134 Copynumber: 2.0 Consensus size: 135
6212393 CCGGCCATGG
* * * *
6212403 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
**
6212468 TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGG
66 TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCACAAATTATGCATGATGTTGG
6212533 CCAAA
131 CCAAA
* *
6212538 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTT-CTCAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
* * *
6212602 TGAATTATGCATGATGTTGGTCAAATGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
66 TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCACAAATTATGCATGATGTTG
6212666 TCCACCTCTT
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
134 72 0.62
135 45 0.38
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (135 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
TGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCACAAATTATGCATGATGTTGG
CCAAA
Found at i:6216384 original size:45 final size:45
Alignment explanation
Indices: 6216313--6216576 Score: 411
Period size: 45 Copynumber: 5.9 Consensus size: 45
6216303 TCGGCCGTGG
* * * * *
6216313 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
6216358 TGCTTTCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
6216403 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6216448 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6216493 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
6216538 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
6216577 TCCACCTCTT
Statistics
Matches: 203, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 203 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:6216707 original size:16 final size:16
Alignment explanation
Indices: 6216688--6216719 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6216678 AACATTCTAT
6216688 TTAAACAACAACAGCA
1 TTAAACAACAACAGCA
*
6216704 TTAAACAACAGCAGCA
1 TTAAACAACAACAGCA
6216720 AAACACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.25, G:0.09, T:0.12
Consensus pattern (16 bp):
TTAAACAACAACAGCA
Found at i:6218505 original size:19 final size:20
Alignment explanation
Indices: 6218471--6218517 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6218461 ACTCTTAAAA
*
6218471 TTTTAGAAATTATTATTTATT
1 TTTTA-AAATTATTATTTATC
*
6218492 TTTTAAAATT-TTATTTCTC
1 TTTTAAAATTATTATTTATC
6218511 TTTTAAA
1 TTTTAAA
6218518 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 5 0.21
21 5 0.21
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTAAAATTATTATTTATC
Found at i:6223717 original size:41 final size:42
Alignment explanation
Indices: 6223667--6223747 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
6223657 TTTTTGACTC
* * *
6223667 GACTAATATAA-AAATATAGTGAAAGATCACATCTAATTTAT
1 GACTAATATAACAAACATAATGAAACATCACATCTAATTTAT
*
6223708 GACTCATATAACAAACATAATGAAACATCACATCTAATTT
1 GACTAATATAACAAACATAATGAAACATCACATCTAATTT
6223748 GGCAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (42 bp):
GACTAATATAACAAACATAATGAAACATCACATCTAATTTAT
Found at i:6224973 original size:19 final size:20
Alignment explanation
Indices: 6224943--6224983 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
6224933 AAATTTTGAG
*
6224943 AAATTATTATTTATTTTTTA
1 AAATTATTATTTATCTTTTA
*
6224963 AAATT-TTATTTCTCTTTTA
1 AAATTATTATTTATCTTTTA
6224982 AA
1 AA
6224984 GTAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTATTTATCTTTTA
Found at i:6228031 original size:82 final size:82
Alignment explanation
Indices: 6227944--6228107 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 82
6227934 TTAGTACATA
*
6227944 AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAATA-TGTTTTTTCCAAG
1 AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAA-ACTGTTTTTTCCAAA
6228008 GATTCAAAAGCATTTTCT
65 GATTCAAAAGCATTTTCT
* * *
6228026 AAACACATTAAATTATAAATAATGGTTAAAAATGTGACTTGACTTTAAAACTGTTTTTTTCAAAG
1 AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAAACTGTTTTTTCCAAAG
6228091 ATTCAAAAGCATTTTCT
66 ATTCAAAAGCATTTTCT
6228108 TACTTCTGAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 1 0.01
82 76 0.99
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (82 bp):
AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAAACTGTTTTTTCCAAAG
ATTCAAAAGCATTTTCT
Found at i:6231519 original size:21 final size:21
Alignment explanation
Indices: 6231493--6231533 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6231483 AGACGAGCAA
* *
6231493 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
6231514 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
6231534 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:6235085 original size:7 final size:7
Alignment explanation
Indices: 6235073--6235099 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
6235063 CGATCATCAA
6235073 ATTATAG
1 ATTATAG
6235080 ATTATAG
1 ATTATAG
6235087 ATTATAG
1 ATTATAG
6235094 ATTATA
1 ATTATA
6235100 AGTTCATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (7 bp):
ATTATAG
Found at i:6237347 original size:33 final size:34
Alignment explanation
Indices: 6237309--6237394 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 34
6237299 TATGATCTGA
6237309 TTGAAACACGAGAATTTAAAAAAAACGAAAA-TT
1 TTGAAACACGAGAATTTAAAAAAAACGAAAATTT
** *
6237342 TTGAAACACGAGAATTTTTTGAAAACACGAAAATTT
1 TTGAAACACGAGAA--TTTAAAAAAAACGAAAATTT
* *
6237378 TTGAAACAAGAAAATTT
1 TTGAAACACGAGAATTT
6237395 TTTGAAAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 14 0.31
34 3 0.07
35 14 0.31
36 14 0.31
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (34 bp):
TTGAAACACGAGAATTTAAAAAAAACGAAAATTT
Found at i:6237369 original size:19 final size:18
Alignment explanation
Indices: 6237340--6237462 Score: 139
Period size: 18 Copynumber: 6.9 Consensus size: 18
6237330 AAAACGAAAA
6237340 TTTTG-AAACACGAGAATT
1 TTTTGAAAACACGA-AATT
*
6237358 TTTTGAAAACACGAAAAT
1 TTTTGAAAACACGAAATT
*
6237376 TTTTG-AAACAAGAAAATT
1 TTTTGAAAACACG-AAATT
*
6237394 TTTTGAAAACATGAAATT
1 TTTTGAAAACACGAAATT
*
6237412 TTTTTAAAACAC-AAAGTT
1 TTTTGAAAACACGAAA-TT
6237430 TTTT--AAACACGAGAATT
1 TTTTGAAAACACGA-AATT
6237447 TTTTGAAAACACGAAA
1 TTTTGAAAACACGAAA
6237463 ACACAAAAGT
Statistics
Matches: 91, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.07
17 16 0.18
18 47 0.52
19 22 0.24
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (18 bp):
TTTTGAAAACACGAAATT
Found at i:6237617 original size:54 final size:54
Alignment explanation
Indices: 6237497--6237618 Score: 138
Period size: 54 Copynumber: 2.3 Consensus size: 54
6237487 TTTTAAAAAA
* * * *
6237497 AAAACAAGAAAATTTTGAAAGACGGGAATTTTTTTTGAAAACACAAATTTTTTT
1 AAAACACGAAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAATTTTTTT
** * * *
6237551 TTAGCACAAAAATTTTGAAACACTAGAA-TTTTTCTGAAAACACTAAATTTTTTT
1 AAAACACGAAAATTTTGAAACACGAGAATTTTTTCTGAAAACAC-AAATTTTTTT
*
6237605 AAAATACGAAAATT
1 AAAACACGAAAATT
6237619 GTGATAAATT
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
53 14 0.26
54 39 0.74
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (54 bp):
AAAACACGAAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAATTTTTTT
Found at i:6238421 original size:7 final size:7
Alignment explanation
Indices: 6238409--6238433 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6238399 ATATATATAA
6238409 TTTTTTC
1 TTTTTTC
6238416 TTTTTTC
1 TTTTTTC
6238423 TTTTTTC
1 TTTTTTC
6238430 TTTT
1 TTTT
6238434 CTTTCTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:6238435 original size:19 final size:20
Alignment explanation
Indices: 6238411--6238451 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6238401 ATATATAATT
6238411 TTTTCTTT-T-TTCTTTTTTC
1 TTTTCTTTCTCTT-TTTTTTC
6238430 TTTTCTTTCTCTTTTTTTTC
1 TTTTCTTTCTCTTTTTTTTC
6238450 TT
1 TT
6238452 CGGGCCGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 10 0.50
21 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTCTTTCTCTTTTTTTTC
Found at i:6238444 original size:18 final size:19
Alignment explanation
Indices: 6238411--6238446 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6238401 ATATATAATT
*
6238411 TTTTCTTTTTTCTTTTTTC
1 TTTTCTTTTCTCTTTTTTC
6238430 TTTTC-TTTCTCTTTTTT
1 TTTTCTTTTCTCTTTTTT
6238447 TTCTTCGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTCTTTTCTCTTTTTTC
Found at i:6238603 original size:23 final size:23
Alignment explanation
Indices: 6238576--6238633 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
6238566 TTCTCCCTTC
**
6238576 TTTTTCCTTTTGGTTGCTGTTTT
1 TTTTTCCTTTTACTTGCTGTTTT
*
6238599 TTTTTCTTTTTTACTTGCTGTTTT
1 TTTTTC-CTTTTACTTGCTGTTTT
*
6238623 TTTTTTCTTTT
1 TTTTTCCTTTT
6238634 TTGCTTGTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.02, C:0.12, G:0.10, T:0.76
Consensus pattern (23 bp):
TTTTTCCTTTTACTTGCTGTTTT
Found at i:6238610 original size:24 final size:25
Alignment explanation
Indices: 6238583--6238640 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
6238573 TTCTTTTTCC
*
6238583 TTTTGGTTGCTG-TTTTTTTTTCTT
1 TTTTGCTTGCTGTTTTTTTTTTCTT
*
6238607 TTTTACTTGCTGTTTTTTTTTTCTT
1 TTTTGCTTGCTGTTTTTTTTTTCTT
6238632 TTTTGCTTG
1 TTTTGCTTG
6238641 TTGCCTTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.02, C:0.10, G:0.14, T:0.74
Consensus pattern (25 bp):
TTTTGCTTGCTGTTTTTTTTTTCTT
Found at i:6238907 original size:23 final size:23
Alignment explanation
Indices: 6238859--6238909 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
6238849 GTGAGGGCCC
* **
6238859 TTTTGCTGCTGTTTTCTTGGTGT
1 TTTTGCTGCTATTTTCTTCATGT
*
6238882 TTTTGCTGCTATTTTCTTTCATTT
1 TTTTGCTGCTATTTTC-TTCATGT
6238906 TTTT
1 TTTT
6238910 TTACTTTCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.04, C:0.14, G:0.16, T:0.67
Consensus pattern (23 bp):
TTTTGCTGCTATTTTCTTCATGT
Found at i:6240179 original size:12 final size:12
Alignment explanation
Indices: 6240162--6240186 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6240152 GGTATTCATT
6240162 CGGTTAACCGAC
1 CGGTTAACCGAC
6240174 CGGTTAACCGAC
1 CGGTTAACCGAC
6240186 C
1 C
6240187 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:6240690 original size:30 final size:30
Alignment explanation
Indices: 6240656--6240727 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
6240646 CCGAAAAAAT
6240656 TCGGTTAACCGACCGATTAACCGAATTCGG
1 TCGGTTAACCGACCGATTAACCGAATTCGG
6240686 TCGGTTAACCGACCGATTAACCGAATTCGG
1 TCGGTTAACCGACCGATTAACCGAATTCGG
6240716 TCGGTTAACCGA
1 TCGGTTAACCGA
6240728 ATTTTTTCGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (30 bp):
TCGGTTAACCGACCGATTAACCGAATTCGG
Found at i:6240695 original size:18 final size:18
Alignment explanation
Indices: 6240672--6240730 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
6240662 AACCGACCGA
6240672 TTAACCGAATTCGGTCGG
1 TTAACCGAATTCGGTCGG
*
6240690 TTAACCG-A--C---CGA
1 TTAACCGAATTCGGTCGG
6240702 TTAACCGAATTCGGTCGG
1 TTAACCGAATTCGGTCGG
6240720 TTAACCGAATT
1 TTAACCGAATT
6240731 TTTTCGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
12 9 0.27
13 1 0.03
15 2 0.06
17 1 0.03
18 20 0.61
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (18 bp):
TTAACCGAATTCGGTCGG
Found at i:6246193 original size:21 final size:21
Alignment explanation
Indices: 6246153--6246210 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
6246143 TTCCAAAAGG
*
6246153 CAAAACGGTAGAAATGTAGGGA
1 CAAAACGGTA-AAATATAGGGA
*
6246175 CAAAACGGTAAAATATAGGGG
1 CAAAACGGTAAAATATAGGGA
*
6246196 CAAAAAGGATAAAAT
1 CAAAACGG-TAAAAT
6246211 TCTATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.52, C:0.09, G:0.26, T:0.14
Consensus pattern (21 bp):
CAAAACGGTAAAATATAGGGA
Found at i:6250555 original size:33 final size:33
Alignment explanation
Indices: 6250508--6250571 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
6250498 GGGTGGAGGC
6250508 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
1 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
* * * *
6250541 GGTGGAGTCTGCATGGTTTTTGGAGGTGGAG
1 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAG
6250572 GCGGCAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.16, C:0.09, G:0.47, T:0.28
Consensus pattern (33 bp):
GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
Found at i:6254920 original size:14 final size:14
Alignment explanation
Indices: 6254901--6254930 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6254891 ATATGCAAGT
6254901 AAAAAAAATGTACA
1 AAAAAAAATGTACA
6254915 AAAAAAAATGTACA
1 AAAAAAAATGTACA
6254929 AA
1 AA
6254931 TAAATCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAAAAAATGTACA
Found at i:6277915 original size:14 final size:14
Alignment explanation
Indices: 6277896--6277934 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
6277886 ATTATGTGTT
6277896 TTATTTAATTTTAA
1 TTATTTAATTTTAA
**
6277910 TTATTTGTTTTTAA
1 TTATTTAATTTTAA
*
6277924 TTTTTTAATTT
1 TTATTTAATTT
6277935 ACAATAAGTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTATTTAATTTTAA
Found at i:6279312 original size:22 final size:23
Alignment explanation
Indices: 6279274--6279328 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
6279264 GAAAATGGGA
*
6279274 AAAAT-AAAAGTTAAAATAACAT
1 AAAATAAAAAATTAAAATAACAT
** *
6279296 AAAATAAAAAATT-AAATTGCTT
1 AAAATAAAAAATTAAAATAACAT
6279318 AAAATAAAAAA
1 AAAATAAAAAA
6279329 ATATAGGAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (23 bp):
AAAATAAAAAATTAAAATAACAT
Found at i:6279894 original size:224 final size:223
Alignment explanation
Indices: 6279451--6279899 Score: 792
Period size: 224 Copynumber: 2.0 Consensus size: 223
6279441 AAAATGTTAC
* * * *
6279451 AACATGATAACATAAGTGATTTAAACGTAGCATTTCAAATATAAGTGACTAAAATATAACCTGAG
1 AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
6279516 GCAAACAAAAGTGATTATTTTAGTAGTTTACCCTTTTTTTGAATTATATAATATTAATAACTATT
66 GCAAACAAAAGTGATTATTTTAGTAGTTTACCCTTTTTTTGAATTATATAATATTAATAACTATT
*
6279581 TACGGGAAATAACAAATTAAGTTTAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAGC
131 TACGGAAAATAACAAATTAAGTTTAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAGC
* *
6279646 TAAATTCCTAACGACTATTAGGGCCCTA
196 TAAATTCCTAACGACTACTAGGGCCATA
*
6279674 AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAGCCTGAG
1 AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
*
6279739 GCAAACAAAAGTGATTATTTTAGTAGTTTATCCTTTTTTTTGAATTATATAATATTAATAACTAT
66 GCAAACAAAAGTGATTATTTTAGTAGTTTA-CCCTTTTTTTGAATTATATAATATTAATAACTAT
6279804 TTACGGAAAATAACAAATTAAG-TTAAAAAAATTGTATAAATCGACCTTAAAGATAATATTGGAA
130 TTACGGAAAATAACAAATTAAGTTTAAAAAAA-TGTATAAATCGACCTTAAAGATAATATTGGAA
6279868 GCTAAATTCCTAACGACTACTAGGGCCATA
194 GCTAAATTCCTAACGACTACTAGGGCCATA
6279898 AA
1 AA
6279900 TTGACGGTGC
Statistics
Matches: 215, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
223 99 0.46
224 116 0.54
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.32
Consensus pattern (223 bp):
AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
GCAAACAAAAGTGATTATTTTAGTAGTTTACCCTTTTTTTGAATTATATAATATTAATAACTATT
TACGGAAAATAACAAATTAAGTTTAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAGC
TAAATTCCTAACGACTACTAGGGCCATA
Found at i:6287630 original size:14 final size:15
Alignment explanation
Indices: 6287607--6287636 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6287597 TAAATTTAAT
6287607 TAAATAAATTAAAAA
1 TAAATAAATTAAAAA
6287622 TAAAT-AATTAAAAA
1 TAAATAAATTAAAAA
6287636 T
1 T
6287637 TTGAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATAAATTAAAAA
Found at i:6289852 original size:22 final size:24
Alignment explanation
Indices: 6289813--6289866 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
6289803 TTTCTTCCCC
6289813 TTCTTCTTCTAGTCTCTT-TCTCTGT
1 TTCTT-TTCTAGTCTCTTCT-TCTGT
*
6289838 TTCTTTTCT-GT-TCTTCTTTTGT
1 TTCTTTTCTAGTCTCTTCTTCTGT
6289860 TTCTTTT
1 TTCTTTT
6289867 TCTTTTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 15 0.56
23 3 0.11
24 4 0.15
25 5 0.19
ACGTcount: A:0.02, C:0.22, G:0.07, T:0.69
Consensus pattern (24 bp):
TTCTTTTCTAGTCTCTTCTTCTGT
Found at i:6290073 original size:5 final size:5
Alignment explanation
Indices: 6290054--6290122 Score: 76
Period size: 5 Copynumber: 14.4 Consensus size: 5
6290044 TCAGTTTATT
6290054 TAATA T-ATAA TAATA TAATA TAAT- TAATA TAATA TAATA TAATA T-ATAA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT-A
*
6290103 TAAAA TAATA T-AT- TAATA TA
1 TAATA TAATA TAATA TAATA TA
6290123 TTTAAAACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
3 1 0.02
4 12 0.22
5 39 0.71
6 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:6290086 original size:22 final size:21
Alignment explanation
Indices: 6290057--6290122 Score: 86
Period size: 19 Copynumber: 3.3 Consensus size: 21
6290047 GTTTATTTAA
6290057 TATATAATAATATAATATAAT
1 TATATAATAATATAATATAAT
6290078 TA-AT-ATAATATAATATAA-
1 TATATAATAATATAATATAAT
*
6290096 TATATAATAAAATAATAT-AT
1 TATATAATAATATAATATAAT
6290116 TAATATA
1 T-ATATA
6290123 TTTAAAACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 2 0.05
19 17 0.43
20 14 0.35
21 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATATAATAATATAATATAAT
Found at i:6294925 original size:18 final size:18
Alignment explanation
Indices: 6294898--6294946 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
6294888 TAAAAAATTC
6294898 AAATATTAAAATTAG-AAA
1 AAATA-TAAAATTAGTAAA
* *
6294916 AAATTATAAAAATCGTAAA
1 AAA-TATAAAATTAGTAAA
6294935 AAATATAAAATT
1 AAATATAAAATT
6294947 TTATAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATATAAAATTAGTAAA
Found at i:6294926 original size:9 final size:9
Alignment explanation
Indices: 6294914--6295009 Score: 70
Period size: 9 Copynumber: 10.4 Consensus size: 9
6294904 TAAAATTAGA
6294914 AAAAATTAT
1 AAAAATTAT
**
6294923 AAAAATCGT
1 AAAAATTAT
*
6294932 AAAAAATAT
1 AAAAATTAT
*
6294941 AAAATTTTAT
1 AAAA-ATTAT
*
6294951 AAAATTTTAT
1 AAAA-ATTAT
*
6294961 AAAAATCAT
1 AAAAATTAT
6294970 AAAAA-TAT
1 AAAAATTAT
6294978 ATAAAATATAT
1 A-AAAAT-TAT
*
6294989 AGAAA-TAT
1 AAAAATTAT
*
6294997 GAAAATTAT
1 AAAAATTAT
6295006 AAAA
1 AAAA
6295010 TTTTATAAAT
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
8 9 0.13
9 35 0.51
10 20 0.29
11 4 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6294926 original size:71 final size:72
Alignment explanation
Indices: 6294829--6294965 Score: 167
Period size: 72 Copynumber: 1.9 Consensus size: 72
6294819 CTCCTACTTT
*
6294829 TATTAAAAATTAGAAAAAAAACT-AAAATC-AATAAAACTAT-AAATATTATTAAATTTTAATAA
1 TATTAAAAATTAGAAAAAAAACTAAAAATCGAA-AAAA-TATAAAATATTATAAAATTTT-ATAA
6294891 AAAATTCAAA
63 AAAATTCAAA
* *
6294901 TATT-AAAATTAGAAAAAATTA-TAAAAATCGTAAAAAATATAAAATTTTATAAAATTTTATAAA
1 TATTAAAAATTAGAAAAAA-AACTAAAAATCG-AAAAAATATAAAATATTATAAAATTTTATAAA
6294964 AA
64 AA
6294966 TCATAAAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
71 15 0.26
72 21 0.37
73 19 0.33
74 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (72 bp):
TATTAAAAATTAGAAAAAAAACTAAAAATCGAAAAAATATAAAATATTATAAAATTTTATAAAAA
ATTCAAA
Found at i:6294935 original size:19 final size:19
Alignment explanation
Indices: 6294913--6295080 Score: 68
Period size: 21 Copynumber: 8.8 Consensus size: 19
6294903 TTAAAATTAG
6294913 AAAAAATTATAAAAATCGT
1 AAAAAATTATAAAAATCGT
**
6294932 AAAAAA-TAT-AAAATTTT
1 AAAAAATTATAAAAATCGT
* *
6294949 ATAAAATTTTATAAAAATCAT
1 A-AAAA-ATTATAAAAATCGT
*
6294970 -AAAAA-TATATAAAAT-AT
1 AAAAAATTATA-AAAATCGT
* *
6294987 ATAGAAA-TATGAAAAT--T
1 A-AAAAATTATAAAAATCGT
* * *
6295004 ATAAAATTTTATAAATTCGT
1 AAAAAATTATA-AAAATCGT
6295024 AAGAAAATTATACAAAAT-GT
1 AA-AAAATTATA-AAAATCGT
**
6295044 AAAGAAA-TATAAATTTCGT
1 AAA-AAATTATAAAAATCGT
6295063 AAAAAAAATTATAAAAAT
1 --AAAAAATTATAAAAAT
6295081 TATTGTACCA
Statistics
Matches: 111, Mismatches: 21, Indels: 32
0.68 0.13 0.20
Matches are distributed among these distances:
16 3 0.03
17 17 0.15
18 24 0.22
19 24 0.22
20 15 0.14
21 28 0.25
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Found at i:6294951 original size:10 final size:10
Alignment explanation
Indices: 6294938--6294964 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
6294928 TCGTAAAAAA
6294938 TATAAAATTT
1 TATAAAATTT
6294948 TATAAAATTT
1 TATAAAATTT
6294958 TATAAAA
1 TATAAAA
6294965 ATCATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TATAAAATTT
Found at i:6295058 original size:55 final size:54
Alignment explanation
Indices: 6294914--6295056 Score: 157
Period size: 56 Copynumber: 2.6 Consensus size: 54
6294904 TAAAATTAGA
6294914 AAAAATTATAAAAATCGTAAA-AAATATAAAATTTTATAAAATTTTATAAAAATCAT
1 AAAAATTATAAAAAT-GTAAAGAAATATAAAA--TTATAAAATTTTATAAAAATCAT
* * * *
6294970 AAAAA-TATATAAAATATATAGAAATATGAAAATTATAAAATTTTAT-AAATTCGT
1 AAAAATTATA-AAAATGTAAAGAAATAT-AAAATTATAAAATTTTATAAAAATCAT
6295024 AAGAAAATTATACAAAATGTAAAGAAATATAAA
1 -A-AAAATTATA-AAAATGTAAAGAAATATAAA
6295057 TTTCGTAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
54 6 0.08
55 22 0.30
56 23 0.31
57 23 0.31
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (54 bp):
AAAAATTATAAAAATGTAAAGAAATATAAAATTATAAAATTTTATAAAAATCAT
Found at i:6295309 original size:19 final size:20
Alignment explanation
Indices: 6295275--6295330 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
6295265 AAAAAAAATC
*
6295275 TACTTTTTAAT-GAATTTAA
1 TACTTTTTAATAAAATTTAA
*
6295294 -ATTTTTTAATAAAATTTAA
1 TACTTTTTAATAAAATTTAA
*
6295313 TACTTTTT-CTAAAATTTA
1 TACTTTTTAATAAAATTTA
6295331 TTTTTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.29
19 16 0.52
20 6 0.19
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (20 bp):
TACTTTTTAATAAAATTTAA
Found at i:6295508 original size:89 final size:85
Alignment explanation
Indices: 6295358--6295564 Score: 242
Period size: 89 Copynumber: 2.4 Consensus size: 85
6295348 TAATAAGAGC
* * *
6295358 AGGGGCTTAATTGC-TTTTTTGAAAATTTTTGAGGGTCTTTTTGATACATTTTGAAAGTTCAAGT
1 AGGGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAA--
* *
6295422 AT-C-CAATTGAGTGAGAAAAAAA
63 ATGCTCAATTAAGTG-CAAAAAAA
*
6295444 GTAGGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATGCATTTTAAAAGTTCAA
1 --AGGGGCTTAATTGCTTTTTTTGAA-AAGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAA
6295509 ATGCTCAATTAAGTGCAAAAAAA
63 ATGCTCAATTAAGTGCAAAAAAA
* **
6295532 A-GGGCTTAATTGTTTTTTTTTTAAAGTTTGAGG
1 AGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGG
6295565 AATTTTTACA
Statistics
Matches: 106, Mismatches: 9, Indels: 12
0.83 0.07 0.09
Matches are distributed among these distances:
84 10 0.09
85 19 0.18
86 1 0.01
87 2 0.02
88 22 0.21
89 50 0.47
90 2 0.02
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (85 bp):
AGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAATG
CTCAATTAAGTGCAAAAAAA
Found at i:6296316 original size:14 final size:15
Alignment explanation
Indices: 6296293--6296322 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6296283 TAAATTTAAT
6296293 TAAATCAATTAAAAA
1 TAAATCAATTAAAAA
6296308 TAAAT-AATTAAAAA
1 TAAATCAATTAAAAA
6296322 T
1 T
6296323 TTGAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATCAATTAAAAA
Found at i:6296940 original size:12 final size:11
Alignment explanation
Indices: 6296869--6296950 Score: 61
Period size: 11 Copynumber: 7.9 Consensus size: 11
6296859 AAAATTTTAA
6296869 TTTTAAAATAT
1 TTTTAAAATAT
*
6296880 TTTAAAAATACT
1 TTTTAAAATA-T
* *
6296892 TTTT-TATTAT
1 TTTTAAAATAT
6296902 TTTT--AA-A-
1 TTTTAAAATAT
6296909 TTTTAAAATAT
1 TTTTAAAATAT
6296920 TTTTAAAATACT
1 TTTTAAAATA-T
*
6296932 TTTT-TAA-AT
1 TTTTAAAATAT
6296941 TTTTAAAATA
1 TTTTAAAATA
6296951 AATTTTTAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
7 4 0.07
8 1 0.02
9 8 0.14
10 9 0.16
11 25 0.45
12 9 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:6296947 original size:39 final size:40
Alignment explanation
Indices: 6296863--6296947 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 40
6296853 TAAAAAAAAA
*
6296863 TTTT-AATTTTAAAATATTTTAAAAATACTTTTTTATTAT
1 TTTTAAATTTTAAAATATTTTAAAAATACTTTTTTATAAT
*
6296902 TTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA-AAT
1 TTTTAAATTTTAAAATATTTTAAAAATACTTTTTTATAAT
6296941 TTTTAAA
1 TTTTAAA
6296948 ATAAATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 13 0.30
40 30 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (40 bp):
TTTTAAATTTTAAAATATTTTAAAAATACTTTTTTATAAT
Found at i:6296956 original size:21 final size:21
Alignment explanation
Indices: 6296918--6296958 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6296908 ATTTTAAAAT
**
6296918 ATTTTTAAAATACTTTTTTAA
1 ATTTTTAAAATAAATTTTTAA
6296939 ATTTTTAAAATAAATTTTTA
1 ATTTTTAAAATAAATTTTTA
6296959 GTATTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTAA
Found at i:6296970 original size:31 final size:29
Alignment explanation
Indices: 6296848--6296970 Score: 83
Period size: 32 Copynumber: 4.0 Consensus size: 29
6296838 AAATATATTT
* * *
6296848 ATTTTTAAAAAAAAATTTTA-ATTTTAAA
1 ATTTTTAAAATAAATTTTTATATTTTTAA
**
6296876 ATATTTTAAAAATACTTTTTTATTATTTTTAA
1 AT-TTTT-AAAATAAATTTTTA-TATTTTTAA
6296908 A-TTTTAAAAT--ATTTTTAAAATACTTTTTTAA
1 ATTTTTAAAATAAATTTTT---ATA--TTTTTAA
6296939 ATTTTTAAAATAAATTTTTAGTATTTATTAA
1 ATTTTTAAAATAAATTTTTA-TATTT-TTAA
6296970 A
1 A
6296971 AAATGGGCCG
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
27 5 0.07
28 2 0.03
29 11 0.15
30 18 0.24
31 14 0.19
32 19 0.25
34 6 0.08
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.54
Consensus pattern (29 bp):
ATTTTTAAAATAAATTTTTATATTTTTAA
Found at i:6300896 original size:20 final size:21
Alignment explanation
Indices: 6300871--6300910 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6300861 TTTTTTTTTA
6300871 TAAATTTGTA-AAAA-TATTAT
1 TAAATTT-TATAAAAGTATTAT
6300891 TAAATTTTATAAAAGTATTA
1 TAAATTTTATAAAAGTATTA
6300911 AATAAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 11 0.61
21 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
TAAATTTTATAAAAGTATTAT
Found at i:6308735 original size:23 final size:19
Alignment explanation
Indices: 6308684--6308735 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 19
6308674 ATTGAGTAGG
6308684 TATATTAAACAAGTTAATA
1 TATATTAAACAAGTTAATA
6308703 TATATATAAACAATTGTATAATAA
1 TATAT-TAAACAA--GT-TAAT-A
6308727 TATATTAAA
1 TATATTAAA
6308736 ACAAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 5 0.18
20 7 0.25
22 2 0.07
23 8 0.29
24 6 0.21
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (19 bp):
TATATTAAACAAGTTAATA
Found at i:6308812 original size:3 final size:3
Alignment explanation
Indices: 6308777--6308860 Score: 64
Period size: 3 Copynumber: 27.3 Consensus size: 3
6308767 ATAAGAAAAC
* * * * *
6308777 ATA ATA CTA ACA ATA GTA TTA ATA A-A TATA ATA ATA GTA A-A GATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA
*
6308822 ATA ATG ATA ATA ATA ATA ATA ACTAA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A-T-A ATA ATA ATA ATA A
6308861 ATTACTAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
2 2 0.03
3 56 0.88
4 4 0.06
5 2 0.03
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:6316229 original size:12 final size:13
Alignment explanation
Indices: 6316203--6316231 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6316193 TTTTTGAAAA
6316203 TTATGAGGATTTT
1 TTATGAGGATTTT
6316216 TTATGAGG-TTTT
1 TTATGAGGATTTT
6316228 TTAT
1 TTAT
6316232 TAAAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (13 bp):
TTATGAGGATTTT
Found at i:6321540 original size:9 final size:9
Alignment explanation
Indices: 6321523--6321559 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
6321513 TGATTTTTCA
6321523 AATTCGAAT
1 AATTCGAAT
*
6321532 AACTCGAAT
1 AATTCGAAT
6321541 AATTCGAAT
1 AATTCGAAT
6321550 AATTCGAAT
1 AATTCGAAT
6321559 A
1 A
6321560 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6321636 original size:21 final size:21
Alignment explanation
Indices: 6321595--6321637 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
6321585 ACCCTAAACT
* *
6321595 CTCAAACCTTTTTATTTTTCC
1 CTCAAAACTTTTTATTCTTCC
6321616 CTCAAAAC-TTTTACTTCTTCC
1 CTCAAAACTTTTTA-TTCTTCC
6321637 C
1 C
6321638 ACTTCCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.47
Consensus pattern (21 bp):
CTCAAAACTTTTTATTCTTCC
Done.