Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_pilon, whole genome shotgun sequence
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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:2145356 original size:10 final size:10
Alignment explanation
Indices: 2145318--2145356 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2145308 TCATCACACT
2145318 AAATTCTCTC
1 AAATTCTCTC
*
2145328 AATTTCTCTC
1 AAATTCTCTC
*
2145338 AACTTCTCTC
1 AAATTCTCTC
*
2145348 AAATACTCT
1 AAATTCTCT
2145357 TATAATCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:2145445 original size:16 final size:17
Alignment explanation
Indices: 2145402--2145446 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
2145392 TTAATATTTT
*
2145402 GTATTTAATTTATTTAA
1 GTATTTAACTTATTTAA
2145419 GTATTTAACTTATTTAA
1 GTATTTAACTTATTTAA
*
2145436 -TATTTTACTTA
1 GTATTTAACTTA
2145447 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (17 bp):
GTATTTAACTTATTTAA
Found at i:2147704 original size:17 final size:16
Alignment explanation
Indices: 2147664--2147716 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
2147654 AGAAAAAATA
2147664 AAATAAT-TTTTAATT
1 AAATAATATTTTAATT
*
2147679 AAATAATATTTTAGTT
1 AAATAATATTTTAATT
2147695 AAATATATATTTTATATT
1 AAATA-ATATTTTA-ATT
2147713 AAAT
1 AAAT
2147717 TAAAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 7 0.21
16 12 0.36
17 8 0.24
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
AAATAATATTTTAATT
Found at i:2150483 original size:15 final size:15
Alignment explanation
Indices: 2150463--2150529 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 15
2150453 GATCCAATCA
*
2150463 CCGAGTCAACTCGAC
1 CCGAGTCAACTCGAT
*
2150478 CCGAGTTAACAT-G-T
1 CCGAGTCAAC-TCGAT
*
2150492 CCGAGTCAACTCAAT
1 CCGAGTCAACTCGAT
*
2150507 CTGAGTCAACTCG-T
1 CCGAGTCAACTCGAT
*
2150521 CTGAGTCAA
1 CCGAGTCAA
2150530 ACCATTGACT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
13 1 0.02
14 19 0.44
15 22 0.51
16 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.22
Consensus pattern (15 bp):
CCGAGTCAACTCGAT
Found at i:2150512 original size:29 final size:29
Alignment explanation
Indices: 2150463--2150529 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
2150453 GATCCAATCA
* *
2150463 CCGAGTCAACTCGACCCGAGTTAACAT-GT
1 CCGAGTCAACTCAACCCGAGTCAAC-TCGT
* *
2150492 CCGAGTCAACTCAATCTGAGTCAACTCGT
1 CCGAGTCAACTCAACCCGAGTCAACTCGT
*
2150521 CTGAGTCAA
1 CCGAGTCAA
2150530 ACCATTGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.22
Consensus pattern (29 bp):
CCGAGTCAACTCAACCCGAGTCAACTCGT
Found at i:2150525 original size:14 final size:15
Alignment explanation
Indices: 2150494--2150529 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
2150484 TAACATGTCC
2150494 GAGTCAACTCAATCT
1 GAGTCAACTCAATCT
*
2150509 GAGTCAACTC-GTCT
1 GAGTCAACTCAATCT
2150523 GAGTCAA
1 GAGTCAA
2150530 ACCATTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (15 bp):
GAGTCAACTCAATCT
Found at i:2161125 original size:21 final size:21
Alignment explanation
Indices: 2161110--2161188 Score: 158
Period size: 21 Copynumber: 3.8 Consensus size: 21
2161100 GTTGATGTGG
2161110 CAGTTCACGGTGTTGACATGA
1 CAGTTCACGGTGTTGACATGA
2161131 CAGTTCACGGTGTTGACATGA
1 CAGTTCACGGTGTTGACATGA
2161152 CAGTTCACGGTGTTGACATGA
1 CAGTTCACGGTGTTGACATGA
2161173 CAGTTCACGGTGTTGA
1 CAGTTCACGGTGTTGA
2161189 AATGGAAGTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
CAGTTCACGGTGTTGACATGA
Found at i:2162448 original size:42 final size:42
Alignment explanation
Indices: 2162384--2162503 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
2162374 TTTCCCCGAA
* *
2162384 TTCCAGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
2162426 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
2162468 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
2162504 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:2162711 original size:21 final size:19
Alignment explanation
Indices: 2162692--2162737 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2162682 TAATTATTAA
2162692 AATATTTAAAATATTTATT
1 AATATTTAAAATATTTATT
*
2162711 AATATTTATAATATATATATT
1 AATATTTA-AA-ATATTTATT
2162732 -ATATTT
1 AATATTT
2162738 TTAATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 8 0.33
21 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTTAAAATATTTATT
Found at i:2162716 original size:19 final size:21
Alignment explanation
Indices: 2162692--2162754 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 21
2162682 TAATTATTAA
*
2162692 AATATTTA-AA-ATATTTATT
1 AATATTTATAATATATATATT
2162711 AATATTTATAATATATATATT
1 AATATTTATAATATATATATT
* *
2162732 -ATATTTTTAATAT-TATATA
1 AATATTTATAATATATATATT
2162751 AATA
1 AATA
2162755 ATCAATTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 13 0.34
20 17 0.45
21 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATTTATAATATATATATT
Found at i:2162723 original size:28 final size:30
Alignment explanation
Indices: 2162693--2162751 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2162683 AATTATTAAA
*
2162693 ATATTTAAAATATTTATTAATATTTATAAT
1 ATATATAAAATATTTATTAATATTTATAAT
**
2162723 ATATATATTATATTT-TTAATATTATATAA
1 ATATATAAAATATTTATTAATATT-TATAA
2162752 ATAATCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
ATATATAAAATATTTATTAATATTTATAAT
Found at i:2162844 original size:28 final size:27
Alignment explanation
Indices: 2162791--2162857 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
2162781 TATTATATTT
*
2162791 TATTTAATAAATATAATAAATTTTTATA
1 TATTTAAT-AATAGAATAAATTTTTATA
2162819 TATTTAATAAT-GAATAATATTATTTATA
1 TATTTAATAATAGAATAA-ATT-TTTATA
*
2162847 T-TTCAATAATA
1 TATTTAATAATA
2162858 TTTTAGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 5 0.15
27 14 0.41
28 15 0.44
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TATTTAATAATAGAATAAATTTTTATA
Found at i:2163103 original size:20 final size:20
Alignment explanation
Indices: 2163025--2163094 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
2163015 TTTCCAGATG
2163025 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2163045 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
2163065 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2163085 TTTTCCAGAA
1 TTTTCCAGAA
2163095 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:2163103 original size:40 final size:40
Alignment explanation
Indices: 2163025--2163103 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
2163015 TTTCCAGATG
* **
2163025 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
2163065 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
2163104 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:2163113 original size:15 final size:15
Alignment explanation
Indices: 2163077--2163143 Score: 109
Period size: 15 Copynumber: 4.5 Consensus size: 15
2163067 TTACAGAAAT
**
2163077 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2163092 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
2163106 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
2163121 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
2163136 GTAATTCA
1 GTAATTCA
2163144 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:2163526 original size:33 final size:32
Alignment explanation
Indices: 2163460--2163563 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 32
2163450 AGCCTCTATC
* *
2163460 GGCTTTG-C-CTCCTCTGCTTCAGCTTCTGCA
1 GGCTTTGCCTCTCCTCTGCTTGAGCTTCTGTA
*
2163490 GGCTTTGCCTCTCCTTCAGCTTGAGCTTCTGTA
1 GGCTTTGCCTCTCC-TCTGCTTGAGCTTCTGTA
* * * *
2163523 GGCTTTGCTTCGGCCTCTGCTGGAGTTTCTGTA
1 GGCTTTGCCTC-TCCTCTGCTTGAGCTTCTGTA
2163556 GGCTTTGC
1 GGCTTTGC
2163564 TTCGGCTTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
30 7 0.11
31 1 0.02
32 4 0.06
33 48 0.77
34 2 0.03
ACGTcount: A:0.07, C:0.30, G:0.25, T:0.38
Consensus pattern (32 bp):
GGCTTTGCCTCTCCTCTGCTTGAGCTTCTGTA
Found at i:2163564 original size:33 final size:33
Alignment explanation
Indices: 2163516--2163580 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2163506 CAGCTTGAGC
*
2163516 TTCTGTAGGCTTTGCTTCGGCCTCTGCTGGAGT
1 TTCTGTAGGCTTTGCTTCGGCCTCTGCCGGAGT
*
2163549 TTCTGTAGGCTTTGCTTCGGCTTCTGCCGGAG
1 TTCTGTAGGCTTTGCTTCGGCCTCTGCCGGAG
2163581 AAGTTTCCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.06, C:0.25, G:0.31, T:0.38
Consensus pattern (33 bp):
TTCTGTAGGCTTTGCTTCGGCCTCTGCCGGAGT
Found at i:2165158 original size:2 final size:2
Alignment explanation
Indices: 2165151--2165201 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2165141 ATTGGGTCGA
*
2165151 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2165193 AT AT AT AT A
1 AT AT AT AT A
2165202 CATTGTGTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2169430 original size:23 final size:23
Alignment explanation
Indices: 2169396--2169497 Score: 141
Period size: 23 Copynumber: 4.4 Consensus size: 23
2169386 GAGTCGAGGG
*
2169396 TTCTACGTGGTCCTTCAGGACAT
1 TTCTACGCGGTCCTTCAGGACAT
2169419 TTCTACGCGGTCCTTCAGGACAT
1 TTCTACGCGGTCCTTCAGGACAT
2169442 TTCTACGCGGTCCTTCAGGACAT
1 TTCTACGCGGTCCTTCAGGACAT
* * * *
2169465 ATCTAAGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCAGGACAT
* *
2169488 TCCTATGCGG
1 TTCTACGCGG
2169498 CACTTTGGTA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCAGGACAT
Found at i:2177765 original size:29 final size:29
Alignment explanation
Indices: 2177722--2177788 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
2177712 GGATTATTAC
*
2177722 ATGAAGTTGGGTTGCAATATTTAAAACCA
1 ATGAAGTTGGGTTGCAAGATTTAAAACCA
*
2177751 GTGAAGTTGGGTTGCAAGATTTAAAACCA
1 ATGAAGTTGGGTTGCAAGATTTAAAACCA
2177780 ATGAAGTTG
1 ATGAAGTTG
2177789 TGAAGTGACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (29 bp):
ATGAAGTTGGGTTGCAAGATTTAAAACCA
Found at i:2181562 original size:35 final size:35
Alignment explanation
Indices: 2181491--2181566 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
2181481 GACATGATAT
* * *
2181491 TTCACCAAAAGATGACCTTTCAAAGATCATGTTGC
1 TTCACCAAAAGATGACATTTCAAAGATCACGATGC
2181526 TTCACCAAAAGATG-CATTTCCAAATG-TCACGATGC
1 TTCACCAAAAGATGACATTT-CAAA-GATCACGATGC
2181561 TTCACC
1 TTCACC
2181567 TAAGGGTGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 4 0.11
35 31 0.86
36 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (35 bp):
TTCACCAAAAGATGACATTTCAAAGATCACGATGC
Found at i:2183864 original size:51 final size:53
Alignment explanation
Indices: 2183802--2183910 Score: 186
Period size: 51 Copynumber: 2.1 Consensus size: 53
2183792 ATCGAATAAT
2183802 AAAAGCAGCAACGTTTAGCAAAATTT-AAG-AAAAACTAACAATAATTTTGTA
1 AAAAGCAGCAACGTTTAGCAAAATTTAAAGAAAAAACTAACAATAATTTTGTA
*
2183853 AAAAGCAGCAACGTTTAGCAAAATTTAAAAGAAAAAACTAACAATTATTTTGTA
1 AAAAGCAGCAACGTTTAGCAAAATTT-AAAGAAAAAACTAACAATAATTTTGTA
2183907 AAAA
1 AAAA
2183911 AACATCAGCG
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
51 26 0.48
53 3 0.06
54 25 0.46
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (53 bp):
AAAAGCAGCAACGTTTAGCAAAATTTAAAGAAAAAACTAACAATAATTTTGTA
Found at i:2188683 original size:76 final size:76
Alignment explanation
Indices: 2188601--2188813 Score: 216
Period size: 75 Copynumber: 2.8 Consensus size: 76
2188591 TGTAAATCTA
*
2188601 TATTAAATTCCACAGGTGTAAGTCTGTGATAAGTTTC-TTATTAGAATTATGTGATACTTTCAAT
1 TATTAAATTCCACAGGTGTAAGTCTGTGATAAG-TTCATTATTAGAATTATGTGTTACTTTCAAT
*
2188665 GCTGGAATTATG
65 GCTAGAATTATG
* ** * * * ** * *
2188677 TGTTAAATTTTATAGGCGAAAGTCTGTGAGGAGTTCACTATT-GAAATTATGTGTTAC-TTCAGT
1 TATTAAATTCCACAGGTGTAAGTCTGTGATAAGTTCATTATTAG-AATTATGTGTTACTTTCAAT
*
2188740 GGTAGAATTATG
65 GCTAGAATTATG
* * * ** *
2188752 TATTAAATTCCACTGGTGTGAGTCTATGATAAGTTCATTGCTAGAACTATGTGTTACTTTCA
1 TATTAAATTCCACAGGTGTAAGTCTGTGATAAGTTCATTATTAGAATTATGTGTTACTTTCA
2188814 CTATTGGAGT
Statistics
Matches: 105, Mismatches: 28, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
75 59 0.56
76 46 0.44
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (76 bp):
TATTAAATTCCACAGGTGTAAGTCTGTGATAAGTTCATTATTAGAATTATGTGTTACTTTCAATG
CTAGAATTATG
Found at i:2188856 original size:25 final size:25
Alignment explanation
Indices: 2188828--2188909 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
2188818 TGGAGTTATG
2188828 TTCAATGCTAGAATTATGTGTTACT
1 TTCAATGCTAGAATTATGTGTTACT
* *
2188853 TTCAGTGCTGTTGGAATTATGTGTTACT
1 TTCAATGC---TAGAATTATGTGTTACT
* * *
2188881 TT-AATTGGTAGAACTATGTGCTACT
1 TTCAA-TGCTAGAATTATGTGTTACT
2188906 TTCA
1 TTCA
2188910 CTGGTGCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
25 23 0.51
26 1 0.02
27 1 0.02
28 20 0.44
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (25 bp):
TTCAATGCTAGAATTATGTGTTACT
Found at i:2192681 original size:35 final size:35
Alignment explanation
Indices: 2192640--2192715 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
2192630 AAAACAGTCC
* * *
2192640 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
2192675 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
2192710 TCAATT
1 TCAATT
2192716 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:2193055 original size:16 final size:18
Alignment explanation
Indices: 2193034--2193067 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2193024 ATTTCTTATT
2193034 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
2193050 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
2193068 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:2210177 original size:65 final size:64
Alignment explanation
Indices: 2210035--2210194 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 64
2210025 TGCACTAAGA
* * *
2210035 GTGCATCGATGCATCAAGTGCATTCGATGATTTAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * *
2210099 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATTGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTT-A-AAATAGCCACAGTGCATCGATGCATGGCT
*
2210162 AT
64 -G
* * *
2210164 GTGCATCGATGCATGAAATTCTTTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
2210195 CAATTTAATT
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 32 0.39
65 47 0.57
66 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:2210233 original size:65 final size:63
Alignment explanation
Indices: 2210035--2210236 Score: 173
Period size: 65 Copynumber: 3.1 Consensus size: 63
2210025 TGCACTAAGA
* * *
2210035 GTGCATCGATGCATCAAGTGCATTCGATGATTT-A-AAATAGC-CAGAGTGCATCGATGCATGGC
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAA-ATCTC--AGTGCATCGATGCATGGT
2210097 TG
62 TG
* *
2210099 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATTGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
2210164 -
63 G
* * * **
2210164 GTGCATCGATGCATGAAATTCTTTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
2210227 TG
62 TG
2210229 GTGCATCG
1 GTGCATCG
2210237 GTGTATCACT
Statistics
Matches: 115, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 51 0.44
65 52 0.45
66 5 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:2218932 original size:65 final size:63
Alignment explanation
Indices: 2218778--2218935 Score: 160
Period size: 65 Copynumber: 2.4 Consensus size: 63
2218768 AAATAGTCAG
* *
2218778 AGTGCATCGATGCATGGTTGGTGCATCGATACATCAATTTCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCGATACATCAAATACATTCGATG-TTTCATAAAAT-CTC
* * * * **
2218843 AGTGCATCGGTGCATGGTAT-GTGCATCGATGCATGAAATACTTTCGATG-TTCAATGTAAT-TC
1 AGTGCATCGATGCATGGT-TGGTGCATCGATACATCAAATACATTCGATGTTTC-ATAAAATCTC
2218905 ATGGTGCATCGATGCATGGATTGGTGCATCG
1 A--GTGCATCGATGCATGG-TTGGTGCATCG
2218936 GTGTATCACT
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 21 0.27
65 50 0.64
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATACATCAAATACATTCGATGTTTCATAAAATCTC
Found at i:2227465 original size:23 final size:23
Alignment explanation
Indices: 2227434--2227478 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2227424 CTACTTAGAG
*
2227434 GAGGGAATAAAACATT-AGAGAAT
1 GAGGAAATAAAAC-TTCAGAGAAT
2227457 GAGGAAATAAAACTTCAGAGAA
1 GAGGAAATAAAACTTCAGAGAA
2227479 ATGAACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.53, C:0.07, G:0.24, T:0.16
Consensus pattern (23 bp):
GAGGAAATAAAACTTCAGAGAAT
Found at i:2238930 original size:35 final size:36
Alignment explanation
Indices: 2238884--2238954 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
2238874 ATTGCCCAGA
2238884 GGGAACAGATT-CCCCCCAGGGGGTATC-GATTCCCC
1 GGGAACAGATTCCCCCCCAGGGGGTA-CAGATTCCCC
2238919 GGGAACAGATTCCCCCCCAGGGGGTACAGATTCCCC
1 GGGAACAGATTCCCCCCCAGGGGGTACAGATTCCCC
2238955 CTGCATGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 12 0.35
36 22 0.65
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.15
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCCAGGGGGTACAGATTCCCC
Found at i:2239094 original size:21 final size:21
Alignment explanation
Indices: 2239068--2239109 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2239058 ATTTGAATAT
* *
2239068 TATGAAGGGTTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2239089 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2239110 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2239171 original size:21 final size:21
Alignment explanation
Indices: 2239138--2239177 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2239128 TTTTTGTAGA
*
2239138 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2239160 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2239178 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2244700 original size:11 final size:10
Alignment explanation
Indices: 2244684--2244743 Score: 61
Period size: 11 Copynumber: 5.9 Consensus size: 10
2244674 ATATAATGTA
2244684 TAATATAGTAC
1 TAATATA-TAC
2244695 TAATATAATAC
1 TAATAT-ATAC
*
2244706 TAATATATAA
1 TAATATATAC
2244716 TAATATAT--
1 TAATATATAC
*
2244724 TAATATATAA
1 TAATATATAC
2244734 TAATAATATA
1 TAAT-ATATA
2244744 TAACATAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
8 8 0.18
10 15 0.34
11 20 0.45
12 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (10 bp):
TAATATATAC
Found at i:2244720 original size:3 final size:3
Alignment explanation
Indices: 2244695--2244767 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
2244685 AATATAGTAC
* *
2244695 TAA T-A TAA TAC TAA TATA TAA TAA T-A TAT TAA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA TAA
*
2244740 TATA TAA -CA TAAA TAA TAA TAA TAA TAA
1 TA-A TAA TAA T-AA TAA TAA TAA TAA TAA
2244768 GCTTAATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
2 5 0.09
3 41 0.72
4 11 0.19
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2244727 original size:8 final size:7
Alignment explanation
Indices: 2244674--2244766 Score: 76
Period size: 6 Copynumber: 14.1 Consensus size: 7
2244664 TAAAAATTAA
2244674 ATATAAT
1 ATATAAT
*
2244681 GTATAAT
1 ATATAAT
*
2244688 ATAGTACT
1 ATA-TAAT
2244696 AATATAAT
1 -ATATAAT
*
2244704 A-CTAAT
1 ATATAAT
2244710 ATATAAT
1 ATATAAT
2244717 A-AT-AT
1 ATATAAT
2244722 AT-TAAT
1 ATATAAT
2244728 ATATAAT
1 ATATAAT
2244735 A-ATAAT
1 ATATAAT
*
2244741 ATATAAC
1 ATATAAT
2244748 ATA-AAT
1 ATATAAT
2244754 A-ATAAT
1 ATATAAT
2244760 A-ATAAT
1 ATATAAT
2244766 A
1 A
2244767 AGCTTAATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
5 5 0.07
6 30 0.43
7 26 0.37
8 6 0.09
9 3 0.04
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (7 bp):
ATATAAT
Found at i:2244742 original size:13 final size:13
Alignment explanation
Indices: 2244697--2244767 Score: 71
Period size: 13 Copynumber: 5.7 Consensus size: 13
2244687 TATAGTACTA
*
2244697 ATATAATACTAAT
1 ATATAATAATAAT
2244710 ATATAATAAT-AT
1 ATATAATAATAAT
2244722 AT-TAATATATAAT
1 ATATAATA-ATAAT
*
2244735 A-ATAATATATAAC
1 ATATAATA-ATAAT
2244748 ATA-AATAATAAT
1 ATATAATAATAAT
2244760 A-ATAATAA
1 ATATAATAA
2244768 GCTTAATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
11 6 0.12
12 16 0.32
13 27 0.54
14 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:2244813 original size:22 final size:22
Alignment explanation
Indices: 2244788--2244927 Score: 112
Period size: 21 Copynumber: 6.4 Consensus size: 22
2244778 TATATATTAC
*
2244788 ATATGTTTTTCAAAAACAATA-T
1 ATAT-TTTTTCAAAAACTATACT
* * *
2244810 ATATGTTTTCAAAAATTATACC
1 ATATTTTTTCAAAAACTATACT
2244832 ATATGTTTTT--AAAACTATACT
1 ATAT-TTTTTCAAAAACTATACT
*
2244853 CTATATTTTTCAAAAACTATA-T
1 ATAT-TTTTTCAAAAACTATACT
* *
2244875 CATATTTTTT-TAAAACTATATT
1 -ATATTTTTTCAAAAACTATACT
* *
2244897 ATATATTTTCAAAAACCATA-T
1 ATATTTTTTCAAAAACTATACT
2244918 ATTATTTTTT
1 A-TATTTTTT
2244928 GACCAAACTA
Statistics
Matches: 95, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
21 49 0.52
22 30 0.32
23 16 0.17
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATTTTTTCAAAAACTATACT
Found at i:2244863 original size:44 final size:43
Alignment explanation
Indices: 2244787--2244912 Score: 157
Period size: 44 Copynumber: 2.9 Consensus size: 43
2244777 ATATATATTA
* * *
2244787 CATATGTTTTTCAAAAACAATA-TATATGTTTTCAAAAATTATAC
1 CATATGTTTTT--AAAACTATATTATATATTTTCAAAAACTATAC
*
2244831 CATATGTTTTTAAAACTATACTCTATAT-TTTTCAAAAACTATAT
1 CATATGTTTTTAAAACTATA-T-TATATATTTTCAAAAACTATAC
*
2244875 CATATTTTTTTAAAACTATATTATATATTTTCAAAAAC
1 CATATGTTTTTAAAACTATATTATATATTTTCAAAAAC
2244913 CATATATTAT
Statistics
Matches: 74, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
42 13 0.18
43 12 0.16
44 44 0.59
45 5 0.07
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (43 bp):
CATATGTTTTTAAAACTATATTATATATTTTCAAAAACTATAC
Found at i:2244927 original size:44 final size:44
Alignment explanation
Indices: 2244809--2244927 Score: 154
Period size: 44 Copynumber: 2.7 Consensus size: 44
2244799 AAAAACAATA
* * *
2244809 TATATGTTTTCAAAAATTATACCATATGTTTTTAAAACTATACTC
1 TATAT-TTTTCAAAAACTATATCATATTTTTTTAAAACTATACTC
2244854 TATATTTTTCAAAAACTATATCATATTTTTTTAAAACTATA-T-
1 TATATTTTTCAAAAACTATATCATATTTTTTTAAAACTATACTC
*
2244896 TATATATTTTCAAAAACCATAT-ATTATTTTTT
1 TATAT-TTTTCAAAAACTATATCA-TATTTTTT
2244928 GACCAAACTA
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
42 6 0.09
43 24 0.35
44 33 0.49
45 5 0.07
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.49
Consensus pattern (44 bp):
TATATTTTTCAAAAACTATATCATATTTTTTTAAAACTATACTC
Found at i:2254200 original size:24 final size:24
Alignment explanation
Indices: 2254171--2254223 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2254161 TGACCCGACT
*
2254171 CCTGATCAGCACCGTTCTGAGACA
1 CCTGATCAGCACCATTCTGAGACA
* * *
2254195 CCTGATCTGTACCATTCTGAGACC
1 CCTGATCAGCACCATTCTGAGACA
2254219 CCTGA
1 CCTGA
2254224 ATATTCACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.25
Consensus pattern (24 bp):
CCTGATCAGCACCATTCTGAGACA
Found at i:2260968 original size:21 final size:21
Alignment explanation
Indices: 2260944--2260985 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2260934 AGTTTATTTT
2260944 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
2260965 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
2260986 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:2261033 original size:33 final size:32
Alignment explanation
Indices: 2260980--2261115 Score: 167
Period size: 33 Copynumber: 4.3 Consensus size: 32
2260970 TTTGTTTCAA
2260980 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
2261012 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
* * *
2261045 TTATCAAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
*
2261077 TTAT-G---TTG-AGTTAATTAAGTATTTGAAT
1 TTATCGAACTTGAAGTT-TTTAAGTATTTGAAT
2261105 TTATCGAACTT
1 TTATCGAACTT
2261116 AAGGTTTGAT
Statistics
Matches: 90, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.03
27 13 0.14
28 6 0.07
29 1 0.01
32 17 0.19
33 50 0.56
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:2261327 original size:21 final size:21
Alignment explanation
Indices: 2261301--2261357 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2261291 TGGAGCGTGG
*
2261301 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
2261322 GGGAATCGGTTCCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
2261343 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
2261358 AAGTGTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:2264905 original size:18 final size:19
Alignment explanation
Indices: 2264858--2264900 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2264848 AATTACCTTA
2264858 TATTTTATATTTTTCGATG
1 TATTTTATATTTTTCGATG
2264877 TATTTTATATTTTTCGATG
1 TATTTTATATTTTTCGATG
2264896 TATTT
1 TATTT
2264901 CTATTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.65
Consensus pattern (19 bp):
TATTTTATATTTTTCGATG
Found at i:2266858 original size:21 final size:21
Alignment explanation
Indices: 2266816--2266858 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2266806 TTACTTGTAA
*
2266816 TTTTATAAACTCAATTTAAAT
1 TTTTATAAACTCAAGTTAAAT
* * *
2266837 TTTTTTAAATTCAAGTTGAAT
1 TTTTATAAACTCAAGTTAAAT
2266858 T
1 T
2266859 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTTATAAACTCAAGTTAAAT
Found at i:2267778 original size:29 final size:29
Alignment explanation
Indices: 2267710--2267906 Score: 180
Period size: 30 Copynumber: 6.6 Consensus size: 29
2267700 TATCCTAAAT
* *
2267710 TTTAAAAATATATTTTATTTTTGTCTTAA
1 TTTAAAAATATATTTTATTTTTATTTTAA
* * *
2267739 CTTATTAAATATATTTTATTTTTATTTTTA
1 TTTA-AAAATATATTTTATTTTTATTTTAA
* * * *
2267769 TTTAAAAATATGTTATATTCTTATTTTAGT
1 TTTAAAAATATATTTTATTTTTATTTTA-A
*
2267799 TTTAAAATATATATTTTATTATTT-TCTTAA
1 TTTAAAA-ATATATTTTATT-TTTATTTTAA
2267829 TTTAAAAAATATATTTTATTTTTATTTTAA
1 TTT-AAAAATATATTTTATTTTTATTTTAA
* * * *
2267859 CTCAAACATATATTTTATTTTTATCTTAA
1 TTTAAAAATATATTTTATTTTTATTTTAA
* * *
2267888 CTTTTAAAATTTATATTAT
1 -TTTAAAAATATATTTTAT
2267907 GAATTTTTAA
Statistics
Matches: 133, Mismatches: 28, Indels: 13
0.76 0.16 0.07
Matches are distributed among these distances:
29 49 0.37
30 64 0.48
31 18 0.14
32 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTAAAAATATATTTTATTTTTATTTTAA
Found at i:2267913 original size:90 final size:90
Alignment explanation
Indices: 2267709--2267913 Score: 211
Period size: 90 Copynumber: 2.3 Consensus size: 90
2267699 ATATCCTAAA
* * * ** * * *
2267709 TTTTAAAA-ATATATTTTAT-TTTTGTCTTAACTTATTAAATATATTTTATTTTTATTTTTATTT
1 TTTTAAAATATATATATTATAATTT-TCTTAATTTAAAAAATATATTTTATTTTTATTTTAACTC
* * *
2267772 AAAAATATGTTATATTCTTATTTTAG
65 AAAAATATATTATATTCTTATTTAAC
* *
2267798 TTTTAAAATATATATTTTATTATTTTCTTAATTTAAAAAATATATTTTATTTTTATTTTAACTCA
1 TTTTAAAATATATATATTATAATTTTCTTAATTTAAAAAATATATTTTATTTTTATTTTAACTCA
* * *
2267863 AACATATATTTTATTTTTATCTTAAC
66 AAAATATATTATATTCTTAT-TTAAC
2267889 TTTTAAAAT-T-TATATTATGAATTTT
1 TTTTAAAATATATATATTAT-AATTTT
2267914 TAATAAAAGT
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
89 15 0.15
90 67 0.69
91 15 0.15
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (90 bp):
TTTTAAAATATATATATTATAATTTTCTTAATTTAAAAAATATATTTTATTTTTATTTTAACTCA
AAAATATATTATATTCTTATTTAAC
Found at i:2273079 original size:72 final size:72
Alignment explanation
Indices: 2273003--2273154 Score: 243
Period size: 72 Copynumber: 2.1 Consensus size: 72
2272993 TCCCATACCT
* * *
2273003 AATATAATGATGCAAATGATATGATAACATAAGTAAGGAAT-TCGTAACATAACATATACATGAA
1 AATATAATGATGCAAATGATATGATAACATAACTAAGGAATAT-GCAACATAAAATATACATGAA
2273067 TTAAGCTA
65 TTAAGCTA
* *
2273075 AATATAATGATGCAAATGATATGATAACATAACTAAGGAATATGCAACATAAAATATGCATTAAT
1 AATATAATGATGCAAATGATATGATAACATAACTAAGGAATATGCAACATAAAATATACATGAAT
2273140 TAAGCTA
66 TAAGCTA
2273147 AATATAAT
1 AATATAAT
2273155 AAGTGGACAT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
72 73 0.99
73 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (72 bp):
AATATAATGATGCAAATGATATGATAACATAACTAAGGAATATGCAACATAAAATATACATGAAT
TAAGCTA
Found at i:2275368 original size:36 final size:35
Alignment explanation
Indices: 2275276--2275390 Score: 171
Period size: 35 Copynumber: 3.3 Consensus size: 35
2275266 TGGCAACCAA
*
2275276 CTTTGAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGTTTTTCAAAGTTTGGTAAATGTTT
2275311 CTTTGAAAATGGTTTTT-AAAGTTTGGTAAATGTTT
1 CTTTGAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
*
2275346 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
2275382 -GTTGAAAAT
1 CTTTGAAAAT
2275391 AGGAATGTGT
Statistics
Matches: 74, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
34 5 0.07
35 42 0.57
36 27 0.36
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:2279529 original size:21 final size:21
Alignment explanation
Indices: 2279505--2279565 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2279495 CCAACTTTGA
2279505 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
2279526 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
2279540 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
2279561 AAATG
1 AAATG
2279566 CTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:2279538 original size:35 final size:35
Alignment explanation
Indices: 2279499--2279613 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
2279489 TGGCAACCAA
2279499 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
2279534 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGCTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
2279569 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
2279605 -GTTGAAAAT
1 CTTTGAAAAT
2279614 AGGAATGGGT
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 5 0.07
35 42 0.57
36 27 0.36
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2280707 original size:44 final size:43
Alignment explanation
Indices: 2280657--2280777 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 43
2280647 CCCCTTTGGC
*
2280657 GTGAACAAGATGGTTCAACT-TCATTGCATGAACTT-GG-TTCCCAT
1 GTGAACATGATGGTTCAACTATC-TT-CATGAA-TTAGGATT-CCAT
**
2280701 GTGAACATGATGGTTCGGCTATCTTCATGAATTAGGATTCCAT
1 GTGAACATGATGGTTCAACTATCTTCATGAATTAGGATTCCAT
*
2280744 GTGAACATGATGGTTCAACTACCTTCATGGAATT
1 GTGAACATGATGGTTCAACTATCTTCAT-GAATT
2280778 GAATTTACAC
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
42 2 0.03
43 37 0.55
44 26 0.39
45 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (43 bp):
GTGAACATGATGGTTCAACTATCTTCATGAATTAGGATTCCAT
Found at i:2281470 original size:71 final size:72
Alignment explanation
Indices: 2281393--2281542 Score: 205
Period size: 71 Copynumber: 2.1 Consensus size: 72
2281383 TCTCCAGCCT
* * * * *
2281393 AATATAATAATACAAATGATATGATAATATAAGTACGGAATG-CGTAATATAACATATGCA-TGA
1 AATATAATAATACAAATGATACGATAACATAAGTAAGGAATGAC-TAACATAACATATGCATTAA
2281456 TTAAGCTA
65 TTAAGCTA
* * *
2281464 AATATAATGATGCAAATGATACGATAACATAAGTAAGGAATGACTAACGTAACATATGCATTAAT
1 AATATAATAATACAAATGATACGATAACATAAGTAAGGAATGACTAACATAACATATGCATTAAT
2281529 TAAGCTA
66 TAAGCTA
2281536 AATATAA
1 AATATAA
2281543 GAGGTGGACA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 51 0.74
72 18 0.26
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (72 bp):
AATATAATAATACAAATGATACGATAACATAAGTAAGGAATGACTAACATAACATATGCATTAAT
TAAGCTA
Found at i:2283185 original size:21 final size:21
Alignment explanation
Indices: 2283134--2283185 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
2283124 TAAAATGGTT
2283134 TAAATGATTTTTAGAATATTA
1 TAAATGATTTTTAGAATATTA
** * * * *
2283155 TTTATTATTTTTGGGATTTTA
1 TAAATGATTTTTAGAATATTA
2283176 TAAATGATTT
1 TAAATGATTT
2283186 ATAAGTTGAC
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (21 bp):
TAAATGATTTTTAGAATATTA
Found at i:2289429 original size:20 final size:20
Alignment explanation
Indices: 2289406--2289456 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2289396 CACGGAATGT
* *
2289406 AAGATTATCAGTGTGAATAA
1 AAGATTACCAGTGGGAATAA
2289426 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
2289446 AAGATTACCAG
1 AAGATTACCAG
2289457 GGAATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:2289461 original size:18 final size:18
Alignment explanation
Indices: 2289406--2289462 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 18
2289396 CACGGAATGT
*
2289406 AAGATTATCAGTGTGAATAA
1 AAGATTACCAG-G-GAATAA
2289426 AAGATTACCAGTGGGAATAA
1 AAGATTACCA--GGGAATAA
2289446 AAGATTACCAGGGAATA
1 AAGATTACCAGGGAATA
2289463 TGATTACTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 7 0.21
20 25 0.74
21 1 0.03
22 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (18 bp):
AAGATTACCAGGGAATAA
Found at i:2289639 original size:36 final size:38
Alignment explanation
Indices: 2289598--2289684 Score: 110
Period size: 36 Copynumber: 2.4 Consensus size: 38
2289588 TATAATATTA
2289598 AAAATTATAAAATATTTATAT-ATTTCTTTAAAAAATT
1 AAAATTATAAAATATTTATATAATTTCTTTAAAAAATT
* *
2289635 -AAATTCAT--AATATTTATATAATTTTTTTATAAAATT
1 AAAATT-ATAAAATATTTATATAATTTCTTTAAAAAATT
*
2289671 AAAAATATAAAATA
1 AAAATTATAAAATA
2289685 GGTTTAATGA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
35 11 0.26
36 21 0.50
37 6 0.14
38 4 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (38 bp):
AAAATTATAAAATATTTATATAATTTCTTTAAAAAATT
Found at i:2304773 original size:23 final size:23
Alignment explanation
Indices: 2304747--2304807 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2304737 CTCATATAAA
*
2304747 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* * *
2304770 TGCACCGTAGTGCCGCGTAGAGT
1 TGCACCGTAGTGCCACATAGAAT
2304793 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
2304808 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:2305002 original size:103 final size:103
Alignment explanation
Indices: 2304823--2305143 Score: 624
Period size: 103 Copynumber: 3.1 Consensus size: 103
2304813 TAATGTCCAT
2304823 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
2304888 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2304926 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2304991 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2305029 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
2305094 GACTTCACACATGTTCCAAATAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2305132 AAGGACCACATA
1 AAGGACCACATA
2305144 GACCCTCGAC
Statistics
Matches: 216, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 216 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2309933 original size:89 final size:89
Alignment explanation
Indices: 2309753--2310120 Score: 384
Period size: 90 Copynumber: 4.1 Consensus size: 89
2309743 CCAGAACTAC
* * * * * *
2309753 ATCCGTAAGGCTTACCCTCAGCACACAGCAAAAAGGGAGCCAACCTAAAGATATACCTTGGGGCC
1 ATCCGT-AGGGTTACCTTCAGCACACAG--TAAAGGGAACCAACCTAAAGATATGCCTTGGGGCT
* * * *
2309818 TAT-AGAACTACCCAAGGATATTCTTAG
63 TATGGGCA-TACCCAAGGGTATCCTTAG
* *
2309845 ATCCGTAGGGTTACCTTCAGCACACAGTAAAGGGAACCAACCTAAGGATATGGCTTGGGGCTTAT
1 ATCCGTAGGGTTACCTTCAGCACACAGTAAAGGGAACCAACCTAAAGATATGCCTTGGGGCTTAT
*
2309910 GGGCATACCTAAGGGTATCCTTAG
66 GGGCATACCCAAGGGTATCCTTAG
* * **
2309934 ATCCTTAGGGTTACCTTAAGCACACAACAAATGGGAACCAACCTAAAGATATGCCTTGGGG-TCT
1 ATCCGTAGGGTTACCTTCAGCACACAGTAAA-GGGAACCAACCTAAAGATATGCCTTGGGGCT-T
*
2309998 ATGGGCCTACCCAAGGGTATCCTTAG
64 ATGGGCATACCCAAGGGTATCCTTAG
* * * **
2310024 ATCCGTAGGGTTACCTT-ATGCACAAAGTAAAAGGGAACCAATCTAAGGATATGCCTTGGGGCCA
1 ATCCGTAGGGTTACCTTCA-GCACACAGT-AAAGGGAACCAACCTAAAGATATGCCTTGGGGCTT
** * *
2310088 ATATGCCTACCCAAGGATATCCTTA-
64 ATGGGCATACCCAAGGGTATCCTTAG
2310113 AGTCCGTA
1 A-TCCGTA
2310121 AGGTCTTACC
Statistics
Matches: 237, Mismatches: 32, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
89 78 0.33
90 131 0.55
91 22 0.09
92 6 0.03
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (89 bp):
ATCCGTAGGGTTACCTTCAGCACACAGTAAAGGGAACCAACCTAAAGATATGCCTTGGGGCTTAT
GGGCATACCCAAGGGTATCCTTAG
Found at i:2312605 original size:16 final size:17
Alignment explanation
Indices: 2312574--2312611 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2312564 GTCAACGGTA
*
2312574 GTCAATGTCGGTCAACG
1 GTCAATGTCAGTCAACG
2312591 GTCAATG-CAGTCAACG
1 GTCAATGTCAGTCAACG
*
2312607 ATCAA
1 GTCAA
2312612 CGGTCAACGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (17 bp):
GTCAATGTCAGTCAACG
Found at i:2317383 original size:20 final size:22
Alignment explanation
Indices: 2317337--2317384 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
2317327 GGTTCAAACA
*
2317337 TGAAGTGTTTGAGCTTAATTGAG
1 TGAA-TGTTTGAGCTTAATTAAG
2317360 TGAATGTTTG-GCTTAA-TAAG
1 TGAATGTTTGAGCTTAATTAAG
2317380 TGAAT
1 TGAAT
2317385 TATGGGCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 6 0.25
22 6 0.25
23 4 0.17
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (22 bp):
TGAATGTTTGAGCTTAATTAAG
Found at i:2318098 original size:22 final size:22
Alignment explanation
Indices: 2318073--2318115 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2318063 AAATGAACAT
*
2318073 AGAAGATATATATG-ATAATATA
1 AGAAGA-AGATATGAATAATATA
*
2318095 AGAATAAGATATGAATAATAT
1 AGAAGAAGATATGAATAATAT
2318116 GATATGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (22 bp):
AGAAGAAGATATGAATAATATA
Found at i:2323029 original size:21 final size:21
Alignment explanation
Indices: 2322963--2323054 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
2322953 TCGATATCGC
* * *
2322963 TGGTATCCATATCGGATAAAT
1 TGGTATCCATACCAGATGAAT
* ** *
2322984 TGTTATCCATACC-GGGGGAT
1 TGGTATCCATACCAGATGAAT
*
2323004 TGGTATCCATACCAGATGAGT
1 TGGTATCCATACCAGATGAAT
*
2323025 TGGTATCCATACCAGATGAAC
1 TGGTATCCATACCAGATGAAT
2323046 TGGTATCCA
1 TGGTATCCA
2323055 CACTGAAGAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 15 0.26
21 42 0.74
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (21 bp):
TGGTATCCATACCAGATGAAT
Found at i:2332504 original size:18 final size:18
Alignment explanation
Indices: 2332470--2332520 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
2332460 ATTTTTAGTA
*
2332470 AATTTTTAATTTATTTTT
1 AATTTTTAAATTATTTTT
2332488 AATTTTTAAA--ATTTTT
1 AATTTTTAAATTATTTTT
* *
2332504 TATTTATTATATTATTT
1 AATTT-TTAAATTATTT
2332521 AGATGGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.37
17 4 0.15
18 9 0.33
19 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
AATTTTTAAATTATTTTT
Found at i:2332520 original size:28 final size:27
Alignment explanation
Indices: 2332457--2332520 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
2332447 ATTTTTCAAC
2332457 TTTATTTTTAGTAAATTTTTAATTTATT
1 TTTATTTTTAG-AAATTTTTAATTTATT
*
2332485 TTTAATTTTTA-AAATTTTTTATTTATT
1 TTT-ATTTTTAGAAATTTTTAATTTATT
2332512 ATATTATTT
1 -T-TTATTT
2332521 AGATGGTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 15 0.47
28 8 0.25
29 9 0.28
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTATTTTTAGAAATTTTTAATTTATT
Found at i:2335320 original size:3 final size:3
Alignment explanation
Indices: 2335312--2335342 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2335302 AGGGATCTTT
2335312 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2335343 GTTATTATAT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2336244 original size:20 final size:19
Alignment explanation
Indices: 2336194--2336249 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2336184 GACCAATAAT
2336194 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
2336213 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
2336233 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
2336250 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:2336385 original size:22 final size:22
Alignment explanation
Indices: 2336333--2336450 Score: 73
Period size: 22 Copynumber: 5.2 Consensus size: 22
2336323 CAAAGAAACT
2336333 AAAA-ATAT-AATGAAAATAA-A
1 AAAATATATAAAT-AAAATAATA
*
2336353 TAAATAGTATAAATAAAATAATA
1 AAAATA-TATAAATAAAATAATA
*
2336376 AAAATATATATATATAAAT-ATA
1 AAAATATATAAATA-AAATAATA
* ** *
2336398 AAAATGTATGTATAACATAATA
1 AAAATATATAAATAAAATAATA
*
2336420 AAATACTAAATAGTAATAATAATAATA
1 AAA-A-TATATA--AATAA-AATAATA
2336447 AAAA
1 AAAA
2336451 AATGAAAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
20 3 0.04
21 4 0.05
22 38 0.50
23 14 0.18
24 3 0.04
26 5 0.07
27 9 0.12
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAATATATAAATAAAATAATA
Found at i:2336677 original size:12 final size:12
Alignment explanation
Indices: 2336660--2336713 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
2336650 AAAAAATTAT
*
2336660 AATAAATAAATA
1 AATAAATATATA
2336672 AATAAA-ATATA
1 AATAAATATATA
*
2336683 ATTAAATATATA
1 AATAAATATATA
*
2336695 CATATATATATATA
1 -A-ATAAATATATA
2336709 AATAA
1 AATAA
2336714 TAAGGGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 9 0.26
12 14 0.41
13 2 0.06
14 9 0.26
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAAATATATA
Found at i:2336678 original size:23 final size:23
Alignment explanation
Indices: 2336644--2336690 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
2336634 ACGCAAAGAA
2336644 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
2336667 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
2336690 A
1 A
2336691 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:2337201 original size:37 final size:37
Alignment explanation
Indices: 2337108--2337209 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
2337098 ATGCTTGTGG
* * ** * *
2337108 ATCCTATCATTAGGAGTTTAAATAATAGTATAACTCT
1 ATCCTATTATTAGGAGTTTGAATCCTAGAAAAACTCT
* *
2337145 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAATTCT
1 ATCCTATTATTAGGAGTTTGAATCCTAGAAAAACTCT
2337182 ATCCTATTATTAGGAGTTTGAATCCTAG
1 ATCCTATTATTAGGAGTTTGAATCCTAG
2337210 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTATTAGGAGTTTGAATCCTAGAAAAACTCT
Found at i:2338146 original size:106 final size:106
Alignment explanation
Indices: 2337962--2339233 Score: 1953
Period size: 106 Copynumber: 12.0 Consensus size: 106
2337952 GCATTGTTCC
* * * * *
2337962 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
** * * *
2338026 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*** * * *
2338068 GAGTCCAATATCCTTTTTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
2338133 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
2338174 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGAACTGAAATTAAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
2338239 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2338280 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
2338345 CCAGCGG----TTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2338382 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
2338447 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** * *
2338488 GAGTCCAATATCTTTCGCAGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
2338553 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2338594 GAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
2338659 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2338700 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTATTCACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
2338765 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCCTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2338806 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
2338871 CCAGCGGTCCCTTCTTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2338912 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
2338977 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2339018 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
2339083 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2339124 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * *
2339189 CCAGTC-GTCCCTCCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2339230 GAGT
1 GAGT
2339234 GGCACGATAT
Statistics
Matches: 1082, Mismatches: 78, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
102 98 0.09
106 982 0.91
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2340868 original size:19 final size:19
Alignment explanation
Indices: 2340846--2340899 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2340836 TTGATTTTTG
2340846 TTCTTTCTTTTTTTTTGTT
1 TTCTTTCTTTTTTTTTGTT
* *
2340865 TTC-TTCTTTTTTGCTTCTT
1 TTCTTTCTTTTTT-TTTGTT
*
2340884 TTCTTT-TTTGTTTTTG
1 TTCTTTCTTTTTTTTTG
2340900 CCCTTTTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 11 0.39
19 15 0.54
20 2 0.07
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (19 bp):
TTCTTTCTTTTTTTTTGTT
Found at i:2340893 original size:16 final size:15
Alignment explanation
Indices: 2340849--2340897 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
2340839 ATTTTTGTTC
*
2340849 TTTCTTTTTTTTTGT
1 TTTCTTCTTTTTTGT
2340864 TTTCTTCTTTTTTGCT
1 TTTCTTCTTTTTTG-T
2340880 TCTT-TTCTTTTTTGT
1 T-TTCTTCTTTTTTGT
2340895 TTT
1 TTT
2340898 TGCCCTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 2 0.06
15 15 0.48
16 12 0.39
17 2 0.06
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTCTTCTTTTTTGT
Found at i:2345368 original size:20 final size:19
Alignment explanation
Indices: 2345318--2345373 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2345308 GACCAATAAT
2345318 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
2345337 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
2345357 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
2345374 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:2345511 original size:22 final size:22
Alignment explanation
Indices: 2345459--2345527 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
2345449 CAAAGAAACT
*
2345459 AAAAATAT-AATGAAAATAAATA
1 AAAAATATAAATAAAAAT-AATA
* *
2345481 AATAGTATAAATAAAAATAATA
1 AAAAATATAAATAAAAATAATA
*
2345503 AAAAATATATATAAAAAT-ATA
1 AAAAATATAAATAAAAATAATA
2345524 AAAA
1 AAAA
2345528 TGTGTGTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 7 0.17
22 25 0.62
23 8 0.20
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (22 bp):
AAAAATATAAATAAAAATAATA
Found at i:2345815 original size:23 final size:23
Alignment explanation
Indices: 2345781--2345827 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
2345771 ACACAAAGAA
2345781 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
2345804 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
2345827 A
1 A
2345828 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:2346287 original size:37 final size:37
Alignment explanation
Indices: 2346246--2346338 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
2346236 ATGCTTGTGG
* * *
2346246 ATCCTATCTTTAGGAGTTTAAATAATAGTATAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
2346283 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
2346320 ATCATATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
2346339 GAATCCTAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:2348790 original size:2 final size:2
Alignment explanation
Indices: 2348783--2348853 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
2348773 GGGGTTAGTT
2348783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2348825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2348854 GCATGTATGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2351882 original size:16 final size:16
Alignment explanation
Indices: 2351858--2351897 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2351848 TTAGAGGACG
2351858 AAAATATATTATTAATAA
1 AAAATATA-TA-TAATAA
2351876 AAAATATATATAATAA
1 AAAATATATATAATAA
*
2351892 ATAATA
1 AAAATA
2351898 ATTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 2 0.10
18 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATATATAATAA
Found at i:2352475 original size:18 final size:17
Alignment explanation
Indices: 2352437--2352475 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2352427 AATCTAATTG
*
2352437 TTGGTGTGTTGGTTTAA
1 TTGGTGTGTTGGGTTAA
*
2352454 TTGGTGTGGTTGGGTTAT
1 TTGGTGT-GTTGGGTTAA
2352472 TTGG
1 TTGG
2352476 CAGTTAGCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.08, C:0.00, G:0.41, T:0.51
Consensus pattern (17 bp):
TTGGTGTGTTGGGTTAA
Found at i:2353376 original size:2 final size:2
Alignment explanation
Indices: 2353369--2353400 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2353359 CACATACATT
2353369 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2353401 CACACAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2357003 original size:5 final size:5
Alignment explanation
Indices: 2356993--2357017 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2356983 GAACCTAAGA
2356993 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
2357018 CTTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:2357433 original size:33 final size:32
Alignment explanation
Indices: 2357345--2357443 Score: 96
Period size: 32 Copynumber: 3.0 Consensus size: 32
2357335 CCAATTAGAT
* *
2357345 ATATTTTAATATTCAAATTTAAATAGATAATA
1 ATATCTTAATATTCAAAATTAAATAGATAATA
* *
2357377 ATATCTTTAT-TTGAAATATTTAAA-AG-TATATA
1 ATATCTTAATATTCAAA-A-TTAAATAGATA-ATA
2357409 ATTATCGTTAATATTCAAAATTAAATAGATAATA
1 A-TATC-TTAATATTCAAAATTAAATAGATAATA
2357443 A
1 A
2357444 ATACATTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
31 7 0.13
32 14 0.26
33 14 0.26
34 11 0.21
35 7 0.13
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (32 bp):
ATATCTTAATATTCAAAATTAAATAGATAATA
Found at i:2362131 original size:12 final size:12
Alignment explanation
Indices: 2362114--2362139 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2362104 ATCCTTAGGG
2362114 TACTAATATGTC
1 TACTAATATGTC
2362126 TACTAATATGTC
1 TACTAATATGTC
2362138 TA
1 TA
2362140 TGTGTAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (12 bp):
TACTAATATGTC
Found at i:2371083 original size:20 final size:19
Alignment explanation
Indices: 2371054--2371093 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
2371044 TTTATTATGT
2371054 ATATAATAATAATAATATAA
1 ATATAATAATAAT-ATATAA
*
2371074 ATATATTAATAATATATAA
1 ATATAATAATAATATATAA
2371093 A
1 A
2371094 AACATCACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAATAATAATATATAA
Found at i:2378113 original size:39 final size:39
Alignment explanation
Indices: 2378049--2378124 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
2378039 GTATATCTCG
* *
2378049 TACAATACATCATTATTCTTATAATTAGGTGTCTATCCA
1 TACAATACATCACTATTCTTATAATTAGATGTCTATCCA
* *
2378088 TACAATACATCACTA-TCTCTGTAATTAGATGTGTATC
1 TACAATACATCACTATTCT-TATAATTAGATGTCTATC
2378125 TGGTGCAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.09
39 29 0.91
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (39 bp):
TACAATACATCACTATTCTTATAATTAGATGTCTATCCA
Found at i:2378175 original size:40 final size:40
Alignment explanation
Indices: 2378090--2378183 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 40
2378080 TCTATCCATA
* * ***
2378090 CAATACATCACTATCTCTGTAATTAGATGTGTATCTGGTG
1 CAATACATCACCATCTCTGTAATTAGATATGTATCAAATG
* *
2378130 CAATACATCACCATCTTTGTAGTTAGATATGTATCAAATG
1 CAATACATCACCATCTCTGTAATTAGATATGTATCAAATG
*
2378170 TAATACATCACCAT
1 CAATACATCACCAT
2378184 TATTGTAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (40 bp):
CAATACATCACCATCTCTGTAATTAGATATGTATCAAATG
Found at i:2378215 original size:40 final size:40
Alignment explanation
Indices: 2378171--2378290 Score: 109
Period size: 40 Copynumber: 3.0 Consensus size: 40
2378161 TATCAAATGT
2378171 AATACATCACCATTATTGTAATTAAGTTTGTATCCCGTAC
1 AATACATCACCATTATTGTAATTAAGTTTGTATCCCGTAC
* * * ***
2378211 AATACATCACC-GTATATGTAATTAGGTTTATATCTTATAC
1 AATACATCACCATTAT-TGTAATTAAGTTTGTATCCCGTAC
* * * * *
2378251 AATATATCATCATGT-TTGTAGTTGAGTGTGTATCCCGTAC
1 AATACATCACCAT-TATTGTAATTAAGTTTGTATCCCGTAC
2378291 GTACGAGTCA
Statistics
Matches: 60, Mismatches: 17, Indels: 6
0.72 0.20 0.07
Matches are distributed among these distances:
39 3 0.05
40 55 0.92
41 1 0.02
42 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (40 bp):
AATACATCACCATTATTGTAATTAAGTTTGTATCCCGTAC
Found at i:2379748 original size:17 final size:17
Alignment explanation
Indices: 2379723--2379762 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2379713 GTATGTTGTT
*
2379723 CATTAAAGCATGCATTA
1 CATTTAAGCATGCATTA
* *
2379740 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTA
2379757 CATTTA
1 CATTTA
2379763 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTA
Found at i:2379789 original size:17 final size:17
Alignment explanation
Indices: 2379769--2379827 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
2379759 TTTAGGGAAG
2379769 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
2379786 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
2379802 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
2379819 TAGTTCATT
1 TAGTTCATT
2379828 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:2381427 original size:46 final size:46
Alignment explanation
Indices: 2381347--2381435 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 46
2381337 CTTGTCATAA
2381347 ATTTAATTACTTAATAACACATAAAAAAATTTACTTCTTATGTATG
1 ATTTAATTACTTAATAACACATAAAAAAATTTACTTCTTATGTATG
* *
2381393 ATTTAATTACTTAATAACATAT-ATAAAATGTTACTTCTTATGT
1 ATTTAATTACTTAATAACACATAAAAAAAT-TTACTTCTTATGT
2381436 CTTCATACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 6 0.15
46 34 0.85
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (46 bp):
ATTTAATTACTTAATAACACATAAAAAAATTTACTTCTTATGTATG
Found at i:2382538 original size:3 final size:3
Alignment explanation
Indices: 2382530--2382560 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2382520 CCCTTTTCCA
2382530 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2382561 TTTATCAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2383577 original size:131 final size:132
Alignment explanation
Indices: 2383325--2383695 Score: 448
Period size: 131 Copynumber: 2.8 Consensus size: 132
2383315 TAATTTTAAG
* * * *
2383325 AGAGAAAACGATAATGTCTAATTATTTCCAATCGAAAATAAATGACATTTCA-AGCCTTAAAACA
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATA-CCTTAAAGCA
*
2383389 ATCATTTATTACTCCAATCGAAATGAAGTGATATTACTATT-TCATCTTAAAATTCAATATCGAT
65 ATCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTCTCATCTTAAAATTCAATATCGAT
*
2383453 TCG
130 TCA
** * * * *
2383456 ATTGGAAACAATAATATCTAATGATTTCCAATAGAGAATAAATGATC-TCTCATACCTTAAAGCA
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGA-CATCTCATACCTTAAAGCA
* * * * * *
2383520 GTCATTTATTGCTCCAATCGAAATGAAGAGATATCACCATTCT-GTCTTTAAAA-TCAATATTGA
65 ATCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTCTCATC-TTAAAATTCAATATCGA
2383583 TTCA
129 TTCA
* *
2383587 AGAGAAAACGATAATAT-TGAATTATTTCCAATCGAGAATAAATGACATGTCATGCCTTAAAGCA
1 AGAGAAAACGATAATATCT-AATTATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAGCA
* * * *
2383651 TTCATTTATTACTCCAACCTAAATGAAAAGATATTACTATTCTCA
65 ATCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTCTCA
2383696 ATATCGATTC
Statistics
Matches: 199, Mismatches: 34, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
130 2 0.01
131 188 0.94
132 9 0.05
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (132 bp):
AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAGCAA
TCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTCTCATCTTAAAATTCAATATCGATT
CA
Found at i:2386106 original size:15 final size:15
Alignment explanation
Indices: 2386086--2386120 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2386076 AATGTTTTTT
2386086 AATAAT-AATAAAATA
1 AATAATAAATAAAA-A
2386101 AATAATAAATAAAAA
1 AATAATAAATAAAAA
2386116 AATAA
1 AATAA
2386121 AAAAATGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAATAAATAAAAA
Found at i:2386523 original size:139 final size:139
Alignment explanation
Indices: 2386356--2387001 Score: 965
Period size: 139 Copynumber: 4.7 Consensus size: 139
2386346 TGGATGAGAA
* * *
2386356 AAGGTTGAAAAAGTTCTTATCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCAGTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* * * * *
2386421 GAACTATCC-GTAGGAAGTATTGATCCCTTGAGTGAGGTGTTGCTGATTCAACTCCATATATGAT
66 GAACTCTCCACT-GGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATATGAT
2386485 GAATCGAGCT
130 GAATCGAGCT
* * * *
2386495 ATGGTTGAACAAGTTCTTATCATTATGAACTTTTTCTCCCTCATAGGATGAGTTTTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* *
2386560 GAACCCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTAGCTGATTCAACTCCATATATGATG
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATATGATG
*
2386625 AAACGAGCT
131 AATCGAGCT
* * * *
2386634 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGATTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* * *
2386699 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTTAACTCCATATGTGAGG
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATATGATG
2386764 AATCGAGCT
131 AATCGAGCT
* * *
2386773 AAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTC-CCCTTCATCGGATGAGTTCTTATTATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCC-TCATCGGATGAGTTCTTCTCATTA
* * *
2386837 TGAACTCTCCACTGGAAATGTTGATCCCTCGAGTAAGGTGTTGTTGATTCAACTCCATATGTGAT
65 TGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATATGAT
*
2386902 AAATCGAGCT
130 GAATCGAGCT
* * *
2386912 AAGGTTGAACAAGTTC-TCTCATTATGAACTTCTTCTCCCTCATCAGATGATTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
2386976 GAACTCTCCACTGGAAATGTTGATCC
66 GAACTCTCCACTGGAAATGTTGATCC
2387002 AAGGTTGAAC
Statistics
Matches: 460, Mismatches: 44, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
138 68 0.15
139 391 0.85
140 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (139 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATATGATG
AATCGAGCT
Found at i:2387041 original size:91 final size:90
Alignment explanation
Indices: 2386912--2387090 Score: 295
Period size: 91 Copynumber: 2.0 Consensus size: 90
2386902 AAATCGAGCT
* * *
2386912 AAGGTTGAACAAGTTCTCTCATTATGAACTTCTTCTCCCTCATCAGATGATTTCTTCTCATTATG
1 AAGGTTGAACAAGTTCTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTATTATCATTATG
2386977 AACTCTCCACTGGAAATGTTGATCC
66 AACTCTCCACTGGAAATGTTGATCC
* **
2387002 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTATCATTAT
1 AAGGTTGAACAAGTTC-TCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTATTATCATTAT
2387067 GAACTCTCCACTGGAAATGTTGAT
65 GAACTCTCCACTGGAAATGTTGAT
2387091 TGGTTTATCC
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 16 0.20
91 66 0.80
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (90 bp):
AAGGTTGAACAAGTTCTCTCATTATGAACTTCTTCTCCCTCATCAGATGAGTTATTATCATTATG
AACTCTCCACTGGAAATGTTGATCC
Found at i:2387908 original size:239 final size:236
Alignment explanation
Indices: 2387472--2387979 Score: 636
Period size: 239 Copynumber: 2.1 Consensus size: 236
2387462 GCCATGATTG
* *
2387472 AAAGACTTACT-AGTGGTCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTATTTTTTCTT
1 AAAGACTTACTGA-TGGCCCGAAGGACTTACTAAGTAAGAAAATTTGGAAATCGTATTTTTTCTT
* * *
2387536 TCAAAAATCTCAATTTCCAAAAAAGAATAAAAAACTTTGGAAATCATTTTCTCATTTTTTTTTCA
65 TCAAAAAACTCAATTTCCAAAAAAGAATAAAAAACTTTGGAAATCACTTTCTCA--TTATTTTCA
** *
2387601 AAAATCATGTGAAAACATGTTACCTGAAGGTCTTATGGATGGCCTGAAGAACTTATTATCTTGCT
128 AAAATCATGTGAAAACATGCCACCTGAAGGTCTTATGGATGGCCTGAAGAACTTATCATCTTGCT
* * *
2387666 CGAATGACGTATAGATGACCCGAAGGATTTAAGCATCATGCTCA
193 CGAAAGACATATAGATGACCCGAAGAATTTAAGCATCATGCTCA
*
2387710 AAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAAATTTGGAAATTGT-TTTCTTAAT-
1 AAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAAATTTGGAAATCGTATTT-TT--TC
* * * *
2387773 TTTTAAAAAAC-CAATTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTCA-TAT
63 TTTCAAAAAACTCAATTTCCAAAAAAGA-AT-AA--A-AAACTTTGGAAATCACTTTCTCATTAT
* * *
2387836 TTT-GAAAATCTTGTGAAAACAT-CCAGCCTGAAGGTCTTATGGATGG-CTCGAAGGACTTATCA
123 TTTCAAAAATCATGTGAAAACATGCCA-CCTGAAGGTCTTATGGATGGCCT-GAAGAACTTATCA
* *
2387898 TCTTGCTCGAAAGACATATAGATGACCTGAAGAATTTAAGCATCATGCTCG
186 TCTTGCTCGAAAGACATATAGATGACCCGAAGAATTTAAGCATCATGCTCA
* *
2387949 AAAGACTTATTGATGGCCCGATGGACTTACT
1 AAAGACTTACTGATGGCCCGAAGGACTTACT
2387980 CATCAAGAAA
Statistics
Matches: 236, Mismatches: 23, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
237 3 0.01
238 68 0.29
239 134 0.57
240 8 0.03
242 1 0.00
243 22 0.09
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (236 bp):
AAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAAATTTGGAAATCGTATTTTTTCTTT
CAAAAAACTCAATTTCCAAAAAAGAATAAAAAACTTTGGAAATCACTTTCTCATTATTTTCAAAA
ATCATGTGAAAACATGCCACCTGAAGGTCTTATGGATGGCCTGAAGAACTTATCATCTTGCTCGA
AAGACATATAGATGACCCGAAGAATTTAAGCATCATGCTCA
Found at i:2387984 original size:42 final size:41
Alignment explanation
Indices: 2387871--2387984 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
2387861 GCCTGAAGGT
* * *
2387871 CTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* * * * * *
2387912 CATATAGATGACCTGAAGAATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGA
* *
2387954 CTTATTGATGGCCCGATGGACTTACTCATCA
1 CTTATAGATGGCCCGAAGGACTTA-TCATCA
2387985 AGAAACCCTT
Statistics
Matches: 54, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
41 17 0.31
42 37 0.69
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:2388155 original size:53 final size:53
Alignment explanation
Indices: 2388038--2388648 Score: 636
Period size: 53 Copynumber: 11.7 Consensus size: 53
2388028 TTACAATTAT
* * * *
2388038 CATCAAGAAACCCCTAAAAATTAGGCTTAGATTCTTTAAAAATTAATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTT-CAAATTCATTTGAAAA
* * *
2388092 CATCAAGAAACCCTTGAAAATCAGGTTTAGCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * * * * *
2388145 TATCAAGAAACCCTTAAAAATTAGGTTTAGCTTTTTTTTTAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGC---TTCTTTCAAATTCATTTGAAAA
* *
2388201 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATGCATTTCAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * * * *
2388254 CATCAAAAAACCCCTAAAAATTAAGCTTAACTT-ATTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* *
2388306 CATCAAGAAACCCTTGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
*
2388359 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * * * *
2388412 CATCAAGAAACCCCTCAAAATTAGGCTTAGCTACTTTAAAAATTCA--AG-AAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTT-CAAATTCATTTGAAAA
* ** * ** * ***
2388463 C-CCCTGAAA---ATAAAGCTTA-GCTT--CTT-TCAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * * * *
2388508 TATCAAGAAACCCCTGAAAATCAGGCTTAACTTCTTTCAAGTTCATCTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* *
2388561 CATCAAGAAACCTCT-AAAATCAGGCTTAGCTTCTTTCAAAATTCATTTAAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTC-AAATTCATTTGAAAA
* * * *
2388614 TATCAAGAAACCCTTGAAAATTAGGCTTAGCTTCT
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCT
2388649 AAAAAATCAC
Statistics
Matches: 464, Mismatches: 75, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
42 8 0.02
43 1 0.00
44 3 0.01
45 3 0.01
46 9 0.02
47 6 0.01
49 5 0.01
50 9 0.02
51 4 0.01
52 68 0.15
53 244 0.53
54 57 0.12
56 47 0.10
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
Found at i:2388473 original size:41 final size:42
Alignment explanation
Indices: 2388414--2388499 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 42
2388404 TTTGAAAACA
* *
2388414 TCAAGAAACCCCTCAAAATTAGGCTTAGCTACTTT-AAAAAT
1 TCAAGAAACCCCTCAAAATAAAGCTTAGCTACTTTCAAAAAT
* *
2388455 TCAAGAAACCCCTGAAAATAAAGCTTAGCTTCTTTCAAAAAT
1 TCAAGAAACCCCTCAAAATAAAGCTTAGCTACTTTCAAAAAT
2388497 TCA
1 TCA
2388500 TTTGAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 31 0.77
42 9 0.22
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (42 bp):
TCAAGAAACCCCTCAAAATAAAGCTTAGCTACTTTCAAAAAT
Found at i:2388535 original size:149 final size:146
Alignment explanation
Indices: 2388308--2388605 Score: 470
Period size: 149 Copynumber: 2.0 Consensus size: 146
2388298 TTTGAAAACA
* * *
2388308 TCAAGAAACCCTTGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCC
1 TCAAGAAACCCCTGAAAATAAAGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCC
* * *
2388373 TGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCTCAAAATTAGGC
66 TGAAAATCAGGCTTAACTTCTTTCAAATTCATCTGAAAACATCAAGAAACCCCT-AAAATCAGGC
2388438 TTAGCTACTTTAAAAAT
130 TTAGCTACTTTAAAAAT
*
2388455 TCAAGAAACCCCTGAAAATAAAGCTTAGCTTCTTTCAAAAATTCATTTGAAAATATCAAGAAACC
1 TCAAGAAACCCCTGAAAATAAAGCTTAGCTTCTTTC--AAATTCATTTGAAAACATCAAGAAACC
* *
2388520 CCTGAAAATCAGGCTTAACTTCTTTCAAGTTCATCTGAAAACATCAAGAAACCTCTAAAATCAGG
64 CCTGAAAATCAGGCTTAACTTCTTTCAAATTCATCTGAAAACATCAAGAAACCCCTAAAATCAGG
* *
2388585 CTTAGCTTCTTTCAAAAT
129 CTTAGCTACTTTAAAAAT
2388603 TCA
1 TCA
2388606 TTTAAAAATA
Statistics
Matches: 138, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
147 33 0.24
148 27 0.20
149 78 0.57
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (146 bp):
TCAAGAAACCCCTGAAAATAAAGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCC
TGAAAATCAGGCTTAACTTCTTTCAAATTCATCTGAAAACATCAAGAAACCCCTAAAATCAGGCT
TAGCTACTTTAAAAAT
Found at i:2388544 original size:202 final size:205
Alignment explanation
Indices: 2388038--2388645 Score: 775
Period size: 202 Copynumber: 2.9 Consensus size: 205
2388028 TTACAATTAT
* * *
2388038 CATCAAGAAACCCCTAAAAATTAGGCTTAGATTCTTT-AAAAATTAATTTGAAAACATCAAGAAA
1 CATCAAGAAACCCCTAAAAATTAAGCTTAGCTTCTTTCAAAAATTCATTTGAAAACATCAAGAAA
* * * *
2388102 CCCTTGAAAATCAGGTTTAGCTTCTTTCAAATTCATTTGAAAATATCAAGAAACCCTTAAAAATT
66 CCCTTGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCT-AAAATC
* * * *
2388167 AGGTTTAGCTTTTTTTTTAAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATCAGGCTTAGC
130 AGGCTTAGC---TTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAG-
2388232 TTCTTTCAAATGCATTTCAAAA
191 --C--T--AA-GCATTTCAAAA
* * *
2388254 CATCAAAAAACCCCTAAAAATTAAGCTTAACTT-ATTC--AAATTCATTTGAAAACATCAAGAAA
1 CATCAAGAAACCCCTAAAAATTAAGCTTAGCTTCTTTCAAAAATTCATTTGAAAACATCAAGAAA
2388316 CCCTTGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATC
66 CCCTTGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCT-AAAATC
*
2388381 AGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCTCAAAATTAGGCTTAGCT-A
130 AGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTAA
2388445 -C-TTT-AAAA
195 GCATTTCAAAA
* * *
2388453 -ATTCAAGAAACCCCTGAAAATAAAGCTTAGCTTCTTTCAAAAATTCATTTGAAAATATCAAGAA
1 CA-TCAAGAAACCCCTAAAAATTAAGCTTAGCTTCTTTCAAAAATTCATTTGAAAACATCAAGAA
* * * * *
2388517 ACCCCTGAAAATCAGGCTTAACTTCTTTCAAGTTCATCTGAAAACATCAAGAAACCTCTAAAATC
65 ACCCTTGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCTAAAATC
* * * *
2388582 AGGCTTAGCTTCTTTCAAAATTCATTTAAAAATATCAAGAAACCCTTGAAAATTAGGCTTAGCT
130 AGGCTTAGCTTCTTTC-AAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCT
2388646 TCTAAAAAAT
Statistics
Matches: 355, Mismatches: 31, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
198 1 0.00
199 31 0.09
200 6 0.02
201 23 0.06
202 120 0.34
203 1 0.00
206 1 0.00
208 1 0.00
211 48 0.14
214 92 0.26
215 2 0.01
216 29 0.08
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (205 bp):
CATCAAGAAACCCCTAAAAATTAAGCTTAGCTTCTTTCAAAAATTCATTTGAAAACATCAAGAAA
CCCTTGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCTAAAATCA
GGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCTAAG
CATTTCAAAA
Found at i:2391505 original size:14 final size:14
Alignment explanation
Indices: 2391486--2391512 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2391476 ATTAATATAT
2391486 AACCTAAACTAAAA
1 AACCTAAACTAAAA
2391500 AACCTAAACTAAA
1 AACCTAAACTAAA
2391513 TCTAAGCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.22, G:0.00, T:0.15
Consensus pattern (14 bp):
AACCTAAACTAAAA
Found at i:2392923 original size:110 final size:108
Alignment explanation
Indices: 2392780--2393086 Score: 347
Period size: 110 Copynumber: 2.8 Consensus size: 108
2392770 AATGACGAGA
* * *
2392780 CAACTCCCTATTTCTTCAGGGAGTATA-AGACTCGAACAATCTTCAGTAAAA-GTTTCTTCTCCC
1 CAACTCCATA-TTCTTCAGGGAGTATAGA-ACTCGAACAATCTTCA-TAAAACGGTTCTGCTCCC
* *
2392843 TATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAACGGGT
63 TATTCATTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAAC-GGT
** *
2392890 CCGCTCCATATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGTTCTGCTCTCTA
1 CAACTCCATATTC-TTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGTTCTGCTCCCTA
*
2392955 TTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGT
65 TTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGT
* * * * *
2392999 CAACTCCCTATTCTATCAGAGAGTATAGGACTCAAACAATCTTCA-ACAAACGGGTAC-GCTCCC
1 CAACTCCATATTCT-TCAGGGAGTATAGAACTCGAACAATCTTCATA-AAAC-GGTTCTGCTCCC
*
2393062 TATT-TTATCAGAGAGTATAGAACTC
63 TATTCAT-TCAGAGAGTATAGAACTC
2393087 TATCTTCATA
Statistics
Matches: 171, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
108 3 0.02
109 79 0.46
110 87 0.51
111 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (108 bp):
CAACTCCATATTCTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGTTCTGCTCCCTAT
TCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGT
Found at i:2393080 original size:55 final size:54
Alignment explanation
Indices: 2392783--2393086 Score: 287
Period size: 55 Copynumber: 5.6 Consensus size: 54
2392773 GACGAGACAA
* * ** * * **
2392783 CTCCCTATTTCTTCAGGGAGTATA-AGACTCGAACAATCTTCAGTAAAAGTTTCTT
1 CTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACG-GTCAG
* * * *
2392838 CTCCCTATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAACGGGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAAC-GGTCAG
* * * *
2392893 CTCCATATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGGTTCTG
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGG-TCAG
* *
2392948 CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGTCAA
1 CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGTCAG
* *
2393002 CTCCCTATT-CTATCAGAGAGTATAGGACTCAAACAATCTTCAACAAACGGGT-ACG
1 CTCCCTATTCCT-TCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC-GGTCA-G
*
2393057 CTCCCTATT-TTATCAGAGAGTATAGAACTC
1 CTCCCTATTCCT-TCAGAGAGTATAGAACTC
2393087 TATCTTCATA
Statistics
Matches: 219, Mismatches: 22, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
53 2 0.01
54 48 0.22
55 166 0.76
56 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (54 bp):
CTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGTCAG
Found at i:2393144 original size:36 final size:37
Alignment explanation
Indices: 2393099--2393208 Score: 132
Period size: 37 Copynumber: 3.0 Consensus size: 37
2393089 TCTTCATAAA
*
2393099 ATGAGTTTGCTTCACTACTCTTCCGTGAAGGCTTATG-
1 ATGA-TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGT
**
2393136 ATGATTTGCTTCACTACTCTTCTATGAAGGCTTAAGT
1 ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGT
* * * * *
2393173 TTGAATTGCTTCACTGCTCTTTCGTGAAAGCTTAAG
1 ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
2393209 ATTGACTTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
36 29 0.47
37 33 0.53
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (37 bp):
ATGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGT
Found at i:2393193 original size:37 final size:36
Alignment explanation
Indices: 2393105--2393210 Score: 122
Period size: 36 Copynumber: 2.9 Consensus size: 36
2393095 TAAAATGAGT
* * *
2393105 TTGCTTCACTACTCTTCCGTGAAGGCTTATGATGAT
1 TTGCTTCACTACTCTTCCATGAAGGCTTAAGATGAA
* *
2393141 TTGCTTCACTACTCTTCTATGAAGGCTTAAGTTTGAA
1 TTGCTTCACTACTCTTCCATGAAGGCTTAAG-ATGAA
* * * *
2393178 TTGCTTCACTGCTCTTTCGTGAAAGCTTAAGAT
1 TTGCTTCACTACTCTTCCATGAAGGCTTAAGAT
2393211 TGACTTGTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 29 0.50
37 29 0.50
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.40
Consensus pattern (36 bp):
TTGCTTCACTACTCTTCCATGAAGGCTTAAGATGAA
Found at i:2394516 original size:7 final size:7
Alignment explanation
Indices: 2394506--2394696 Score: 69
Period size: 7 Copynumber: 26.4 Consensus size: 7
2394496 ATTTTTCTCT
2394506 TTTTTCA
1 TTTTTCA
2394513 TTTTT-A
1 TTTTTCA
*
2394519 TTTCTC-
1 TTTTTCA
*
2394525 TTTCTTCT
1 TTT-TTCA
2394533 TTTTTCA
1 TTTTTCA
*
2394540 TTTTTTA
1 TTTTTCA
2394547 TTTTTTTCCA
1 --TTTTT-CA
**
2394557 TTTCCCA
1 TTTTTCA
*
2394564 TTTTCCA
1 TTTTTCA
2394571 TTTTT--
1 TTTTTCA
2394576 TTCCTTTCTA
1 TT--TTTC-A
2394586 TTTTTTCA
1 -TTTTTCA
2394594 TCATTTTTCA
1 ---TTTTTCA
2394604 TTTTTCA
1 TTTTTCA
2394611 -TTTT--
1 TTTTTCA
*
2394615 TTTCTCA
1 TTTTTCA
*
2394622 TTTTTCT
1 TTTTTCA
2394629 TTTCTTC-
1 TTT-TTCA
*
2394636 TTTTTCT
1 TTTTTCA
2394643 TCTTTTCA
1 T-TTTTCA
2394651 TTTTT--
1 TTTTTCA
*
2394656 TTTATCA
1 TTTTTCA
2394663 TTTTTTCA
1 -TTTTTCA
2394671 TTTTTCA
1 TTTTTCA
*
2394678 TTTTTTTCT
1 --TTTTTCA
2394687 TTTTTCA
1 TTTTTCA
2394694 TTT
1 TTT
2394697 ATTCTTCAAG
Statistics
Matches: 141, Mismatches: 18, Indels: 50
0.67 0.09 0.24
Matches are distributed among these distances:
5 9 0.06
6 15 0.11
7 70 0.50
8 22 0.16
9 15 0.11
10 8 0.06
11 2 0.01
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:2394600 original size:25 final size:26
Alignment explanation
Indices: 2394564--2394626 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 26
2394554 CCATTTCCCA
*
2394564 TTTTC-CATTTTTTTCCTTTCT-A-TT
1 TTTTCTCA-TTTTTTCATTTCTCATTT
*
2394588 TTTTCATCA-TTTTTCATTTTTCATTT
1 TTTTC-TCATTTTTTCATTTCTCATTT
2394614 TTTTCTCATTTTT
1 TTTTCTCATTTTT
2394627 CTTTTCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
24 15 0.47
25 4 0.12
26 13 0.41
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTTCTCATTTTTTCATTTCTCATTT
Found at i:2394607 original size:17 final size:16
Alignment explanation
Indices: 2394587--2394694 Score: 71
Period size: 17 Copynumber: 6.5 Consensus size: 16
2394577 TCCTTTCTAT
2394587 TTTTTCATCATTTTTCA
1 TTTTTCATC-TTTTTCA
*
2394604 TTTTTCATTTTTTTCTCA
1 TTTTTCA-TCTTTT-TCA
2394622 TTTTTC-T-TTTCTTC-
1 TTTTTCATCTTT-TTCA
*
2394636 TTTTTCTTC-TTTTCA
1 TTTTTCATCTTTTTCA
*
2394651 TTTTTTTTATCATTTTTTCA
1 --TTTTTCATC--TTTTTCA
* *
2394671 TTTTTCATTTTTTTCT
1 TTTTTCATCTTTTTCA
2394687 TTTTTCAT
1 TTTTTCAT
2394695 TTATTCTTCA
Statistics
Matches: 74, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
14 9 0.12
15 8 0.11
16 16 0.22
17 18 0.24
18 17 0.23
20 6 0.08
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTCATCTTTTTCA
Found at i:2394614 original size:6 final size:7
Alignment explanation
Indices: 2394594--2394696 Score: 74
Period size: 7 Copynumber: 14.9 Consensus size: 7
2394584 TATTTTTTCA
2394594 TCATTTT
1 TCATTTT
2394601 TCATTTT
1 TCATTTT
2394608 TCA-TTT
1 TCATTTT
*
2394614 T--TTTC
1 TCATTTT
2394619 TCATTTT
1 TCATTTT
*
2394626 TCTTTTCT
1 TCATTT-T
2394634 TC-TTTT
1 TCATTTT
*
2394640 TCTTCTTT
1 TCAT-TTT
2394648 TCATTTT
1 TCATTTT
*
2394655 T--TTTA
1 TCATTTT
2394660 TCATTTTT
1 TCA-TTTT
2394668 TCATTTT
1 TCATTTT
2394675 TCATTTTTT
1 TCA--TTTT
*
2394684 TCTTTTT
1 TCATTTT
2394691 TCATTT
1 TCATTT
2394697 ATTCTTCAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
5 7 0.09
6 7 0.09
7 42 0.55
8 15 0.19
9 6 0.08
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (7 bp):
TCATTTT
Found at i:2394624 original size:11 final size:10
Alignment explanation
Indices: 2394604--2394675 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
2394594 TCATTTTTCA
2394604 TTTTTCATTT
1 TTTTTCATTT
2394614 TTTTCTCATTTT
1 TTTT-TCA-TTT
*
2394626 TCTTTTC-TTC
1 T-TTTTCATTT
2394636 TTTTTC--TT
1 TTTTTCATTT
*
2394644 CTTTTCATTT
1 TTTTTCATTT
*
2394654 TTTTT-ATCAT
1 TTTTTCAT-TT
2394664 TTTTTCATTT
1 TTTTTCATTT
2394674 TT
1 TT
2394676 CATTTTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
8 6 0.12
9 7 0.14
10 22 0.45
11 5 0.10
12 6 0.12
13 3 0.06
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:2407759 original size:12 final size:12
Alignment explanation
Indices: 2407742--2407806 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
2407732 CATCTTAAAA
2407742 TTTTTTATCTTT
1 TTTTTTATCTTT
2407754 TTTTTTAT-TTT
1 TTTTTTATCTTT
*
2407765 TTTACTTA-CTTT
1 TTT-TTTATCTTT
2407777 TTCTTTTATTCTTT
1 TT-TTTTA-TCTTT
* *
2407791 CTTTTCTCTCTTT
1 -TTTTTTATCTTT
2407804 TTT
1 TTT
2407807 ATTTTTGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
11 6 0.14
12 22 0.51
13 6 0.14
14 7 0.16
15 2 0.05
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTATCTTT
Found at i:2411704 original size:4 final size:4
Alignment explanation
Indices: 2411682--2411725 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
2411672 TTCGAACATA
* *
2411682 AAAT AAAAT ACAT ACAT AAAT AAAT AAAT AAAT AAAT AAA- AAAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2411726 TAGCGGTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
3 3 0.08
4 29 0.81
5 4 0.11
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2416120 original size:18 final size:19
Alignment explanation
Indices: 2416097--2416139 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
2416087 CAGTAATCAT
2416097 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
2416115 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
2416135 ATTCC
1 ATTCC
2416140 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:2416127 original size:20 final size:20
Alignment explanation
Indices: 2416102--2416139 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2416092 ATCATATTCC
2416102 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
2416122 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2416140 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2419681 original size:15 final size:16
Alignment explanation
Indices: 2419654--2419683 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2419644 CATAAAACTG
2419654 GAAAATCAATCATCGT
1 GAAAATCAATCATCGT
2419670 GAAAAT-AATCATCG
1 GAAAATCAATCATCG
2419684 ATGGAAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (16 bp):
GAAAATCAATCATCGT
Done.