Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 177 of 206
Found at i:53875205 original size:49 final size:49
Alignment explanation
Indices: 53875118--53875217 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
53875108 AGGGGTTTGA
*
53875118 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCTAG
1 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
* * *** *
53875167 TTATACTTGAATCCGTGATCGTATAACCATTTTGAACTGGGAGCCCAAG
1 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
53875216 TT
1 TT
53875218 GCAATGCGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (49 bp):
TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
Found at i:53881910 original size:14 final size:14
Alignment explanation
Indices: 53881893--53881920 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53881883 AATATATATT
53881893 AATATATATTAATA
1 AATATATATTAATA
53881907 AATATATATTAATA
1 AATATATATTAATA
53881921 TATGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:53881923 original size:10 final size:10
Alignment explanation
Indices: 53881879--53881911 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
53881869 AAAAACAATT
53881879 TATTAATATA
1 TATTAATATA
53881889 TATTAATATA
1 TATTAATATA
*
53881899 TATTAATAAA
1 TATTAATATA
53881909 TAT
1 TAT
53881912 ATATTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TATTAATATA
Found at i:53886477 original size:49 final size:49
Alignment explanation
Indices: 53886390--53886489 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
53886380 AGGGGTTTGA
*
53886390 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCTAG
1 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
* * *** *
53886439 TTATACTTGAATCCGTGATCGTATAACCATTTTGAACTGGGAGCCCAAG
1 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
53886488 TT
1 TT
53886490 GCAATGCGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (49 bp):
TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
Found at i:53893273 original size:8 final size:10
Alignment explanation
Indices: 53893253--53893283 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
53893243 AAAAACAATT
53893253 TATTAATATA
1 TATTAATATA
53893263 TATTAATATA
1 TATTAATATA
53893273 TATTAATATA
1 TATTAATATA
53893283 T
1 T
53893284 GTAAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATTAATATA
Found at i:53893338 original size:32 final size:33
Alignment explanation
Indices: 53893302--53893386 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
53893292 AACTTTTTCG
* * *
53893302 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGTAAATCTACCAAACACCA
* *
53893334 GAAAATATTTTACA-TAGATTTACCAAACACCA
1 GAAAATATTTTACAGTAAATCTACCAAACACCA
*
53893366 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGTAAATC
53893387 ATTTTATAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
32 37 0.86
33 6 0.14
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.27
Consensus pattern (33 bp):
GAAAATATTTTACAGTAAATCTACCAAACACCA
Found at i:53893417 original size:20 final size:20
Alignment explanation
Indices: 53893379--53893418 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53893369 AATATTTTCC
* *
53893379 AGTAAATCATTTTATAGAAA
1 AGTAAAACATTTTACAGAAA
*
53893399 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
53893419 TCATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:53893433 original size:34 final size:35
Alignment explanation
Indices: 53893367--53893433 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
53893357 CAAACACCAG
* *
53893367 AAAATATTTTCCAGTAAATCATTTTATAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
53893402 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
53893434 CATTTTACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:53893440 original size:14 final size:14
Alignment explanation
Indices: 53893402--53893443 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
53893392 ATAGAAAAGT
*
53893402 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
53893416 AAATCATTTTACGG
1 AAAACATTTTACAG
53893430 AAAACATTTTACAG
1 AAAACATTTTACAG
53893444 CCAAACAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:53897781 original size:49 final size:49
Alignment explanation
Indices: 53897694--53897793 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
53897684 AGGGGTTTGA
*
53897694 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCTAG
1 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
* * *** *
53897743 TTATACTTGAATCCGTGATCGTATAACCATTTTGAACTGGGAGCCCAAG
1 TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
53897792 TT
1 TT
53897794 GCAATGCGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (49 bp):
TTATACTTGAACCCGTGATCGCATAACCACCATCAACTGGGAGCCCAAG
Found at i:53902736 original size:2 final size:2
Alignment explanation
Indices: 53902729--53902754 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53902719 CACATCATTC
53902729 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
53902755 GAATATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53913800 original size:22 final size:22
Alignment explanation
Indices: 53913775--53913827 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
53913765 CAATCCTCTT
* * * *
53913775 TCAATTTTCTCCTATTTTTCTC
1 TCAATTTTCTCATAATTCTCGC
*
53913797 TCAATTCTCTCATAATTCTCGC
1 TCAATTTTCTCATAATTCTCGC
53913819 TCAATTTTC
1 TCAATTTTC
53913828 AATCCTCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.28, G:0.02, T:0.51
Consensus pattern (22 bp):
TCAATTTTCTCATAATTCTCGC
Found at i:53913888 original size:25 final size:23
Alignment explanation
Indices: 53913845--53913901 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
53913835 TTTCAACTCT
53913845 CATTTTTTATTAAAATTGTATTAA
1 CATTTTTTATTAAAATTGT-TTAA
** *
53913869 CATTTTTTAATTAATTTTGTTTTA
1 CATTTTTT-ATTAAAATTGTTTAA
53913893 CGATTTTTT
1 C-ATTTTTT
53913902 TCGTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.61
Consensus pattern (23 bp):
CATTTTTTATTAAAATTGTTTAA
Found at i:53914498 original size:15 final size:16
Alignment explanation
Indices: 53914472--53914507 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
53914462 TGGAGTGGGG
*
53914472 ATTTAGTTTATTTTTT
1 ATTTAGTTTATTTTTA
53914488 ATTTA-TTTATTTTTA
1 ATTTAGTTTATTTTTA
53914503 ATTTA
1 ATTTA
53914508 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
ATTTAGTTTATTTTTA
Found at i:53922469 original size:3 final size:3
Alignment explanation
Indices: 53922463--53922519 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
53922453 GTTGTTGTTT
53922463 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53922511 ATA ATA ATA
1 ATA ATA ATA
53922520 GGATTAAATC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53926629 original size:37 final size:37
Alignment explanation
Indices: 53926548--53926648 Score: 159
Period size: 37 Copynumber: 2.8 Consensus size: 37
53926538 TTTGAGTACT
*
53926548 TCTGATCAAGTGACAAAGTGATAAGT-GCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGCTACACTTA
**
53926584 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGCTACACTTA
*
53926621 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
53926649 TAGCTTCAGC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 24 0.41
37 34 0.59
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (37 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGCTACACTTA
Found at i:53926720 original size:45 final size:46
Alignment explanation
Indices: 53926611--53926734 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
53926601 GTGATAAGTG
*
53926611 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTCA
*
53926657 GCTACACTTATCTGATCAAGTGGTAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTCA
*
53926702 GCTACACTTATCTGATCAAG-GA-CAAGTGATAAG
1 GCTACACTTATCTGATCAAGTGATAAAGTGATAAG
53926735 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 1 0.01
45 21 0.28
46 42 0.57
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTCA
Found at i:53926824 original size:67 final size:67
Alignment explanation
Indices: 53926742--53926875 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
53926732 AAGAGGTCAT
53926742 ATGGCAAAGTGAAAGTGAAGTACTCAAATTTCCATGACCGTTCCTTAATTTTGATCAAGGATGGT
1 ATGGCAAAGTGAAAGTGAAGTACTCAAATTTCCATGACCGTTCCTTAATTTTGATCAAGGATGGT
53926807 AA
66 AA
53926809 ATGGCAAAGTGAAAGTGAAGTACTCAAATTTCCATGACCGTTCCTTAATTTTGATCAAGGATGGT
1 ATGGCAAAGTGAAAGTGAAGTACTCAAATTTCCATGACCGTTCCTTAATTTTGATCAAGGATGGT
53926874 AA
66 AA
53926876 GTGACAAATG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (67 bp):
ATGGCAAAGTGAAAGTGAAGTACTCAAATTTCCATGACCGTTCCTTAATTTTGATCAAGGATGGT
AA
Found at i:53935173 original size:19 final size:19
Alignment explanation
Indices: 53935134--53935192 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
53935124 AACATTTGTA
* *
53935134 CCCTGTTATGTAATTCAGTG
1 CCCTGTT-TGTACTTCGGTG
53935154 CCCTGTTTGTACTTCGGTG
1 CCCTGTTTGTACTTCGGTG
* *
53935173 CCCTGTTTGCACTTTGGTG
1 CCCTGTTTGTACTTCGGTG
53935192 C
1 C
53935193 TTCTGTATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 28 0.80
20 7 0.20
ACGTcount: A:0.10, C:0.25, G:0.24, T:0.41
Consensus pattern (19 bp):
CCCTGTTTGTACTTCGGTG
Found at i:53935224 original size:20 final size:19
Alignment explanation
Indices: 53935151--53935232 Score: 85
Period size: 19 Copynumber: 4.2 Consensus size: 19
53935141 ATGTAATTCA
* *
53935151 GTGCCCTGTTTGTACTTCG
1 GTGCCCTGTTTGCACTTTG
53935170 GTGCCCTGTTTGCACTTTG
1 GTGCCCTGTTTGCACTTTG
* *
53935189 GTGCTTCTGTATGCACATTT-
1 GTGC-CCTGTTTGCAC-TTTG
*
53935209 GTGCCCTGTTTAGCACCTTG
1 GTGCCCTGTTT-GCACTTTG
53935229 GTGC
1 GTGC
53935233 TCCTTGATAC
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
19 28 0.54
20 21 0.40
21 3 0.06
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.40
Consensus pattern (19 bp):
GTGCCCTGTTTGCACTTTG
Found at i:53939481 original size:29 final size:30
Alignment explanation
Indices: 53939442--53939510 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
53939432 CGAATAATTT
*
53939442 AATGATGAAATTGTAAC-TTCTTTTAGTTA
1 AATGATCAAATTGTAACTTTCTTTTAGTTA
*
53939471 AATGATCAAATTGTAACTTTTTTTTAGTTA
1 AATGATCAAATTGTAACTTTCTTTTAGTTA
*
53939501 AATAATCAAA
1 AATGATCAAA
53939511 ACAAAAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 16 0.44
30 20 0.56
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.43
Consensus pattern (30 bp):
AATGATCAAATTGTAACTTTCTTTTAGTTA
Found at i:53939703 original size:2 final size:2
Alignment explanation
Indices: 53939696--53939735 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
53939686 TTCAGCATGC
53939696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53939736 TATCATATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53944250 original size:21 final size:21
Alignment explanation
Indices: 53944226--53944266 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53944216 CAACCAAAAA
53944226 AGAAAACAAAAAAACCCTAGC
1 AGAAAACAAAAAAACCCTAGC
* *
53944247 AGAAAACAGAAGAACCCTAG
1 AGAAAACAAAAAAACCCTAG
53944267 GCGCCGTTCC
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:0.59, C:0.22, G:0.15, T:0.05
Consensus pattern (21 bp):
AGAAAACAAAAAAACCCTAGC
Found at i:53946217 original size:111 final size:110
Alignment explanation
Indices: 53946015--53946297 Score: 426
Period size: 111 Copynumber: 2.6 Consensus size: 110
53946005 AAGGAAAATG
* *
53946015 TTTTAAAATAAGGCAATATTTCGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
* * * * *
53946080 TTGATTTTTCTCGTCCAACCATATGGCTTAATATCCTTTTAAAAC
66 TTGATTTTCCTCGTCAAACCAAATGGCTTAATATCCTTCTAAAAA
53946125 TTTTAAGAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
1 TTTTAA-AATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
*
53946190 GTTGATTTTCCTCGTTAAACCAAATGGCTTAATATCCTTCTAAAAA
65 GTTGATTTTCCTCGTCAAACCAAATGGCTTAATATCCTTCTAAAAA
* * * * *
53946236 TTTCAAAATAAGGCAATGTTTTGCATTT-GGAAATTCGAG-GAACGTGCCCTAAGGTGTTGGGT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGT
53946298 TTCGGTTTCT
Statistics
Matches: 159, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
108 20 0.13
109 11 0.07
110 27 0.17
111 101 0.64
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (110 bp):
TTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
TTGATTTTCCTCGTCAAACCAAATGGCTTAATATCCTTCTAAAAA
Found at i:53947445 original size:69 final size:69
Alignment explanation
Indices: 53947262--53947434 Score: 222
Period size: 69 Copynumber: 2.5 Consensus size: 69
53947252 GTGTAATGCT
* * * *
53947262 ATAGCTTGGCTATGGCAACCAATAGAGTCCATCTAGATAGTAAACACGAGGATTTCAGGGTGAAA
1 ATAGCTTGGCTATGACAACCAATAGAGTCCATCAAGATAGTAAACACGAAGATTTCAAGGTGAAA
53947327 GACC
66 GACC
* * *
53947331 ATAG-TTCGGCTATGACAACCAATAGAGTCCACCAGGATAGTAAACACGAAGATTTCAAGGTGTA
1 ATAGCTT-GGCTATGACAACCAATAGAGTCCATCAAGATAGTAAACACGAAGATTTCAAGGTGAA
***
53947395 ATTTC
65 AGACC
* *
53947400 ATAGCTTAGCTATGACAACCAATAGAGTCTATCAA
1 ATAGCTTGGCTATGACAACCAATAGAGTCCATCAA
53947435 AACATTAAAC
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
68 2 0.02
69 84 0.95
70 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (69 bp):
ATAGCTTGGCTATGACAACCAATAGAGTCCATCAAGATAGTAAACACGAAGATTTCAAGGTGAAA
GACC
Found at i:53952525 original size:24 final size:25
Alignment explanation
Indices: 53952476--53952526 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
53952466 CTCACTTGAA
*
53952476 CTTCCCGATATATGGCTATTCGGAG
1 CTTCCCGATATATGGCTATTCAGAG
* *
53952501 CTTCCCGTTA-ATGGCTCTTCAGAG
1 CTTCCCGATATATGGCTATTCAGAG
53952525 CT
1 CT
53952527 ACCCATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (25 bp):
CTTCCCGATATATGGCTATTCAGAG
Found at i:53952539 original size:24 final size:24
Alignment explanation
Indices: 53952487--53952539 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
53952477 TTCCCGATAT
* * *
53952487 ATGGCTATTCGGAGCTTCCCGTTA
1 ATGGCTATTCAGAGCTACCCATTA
*
53952511 ATGGCTCTTCAGAGCTACCCATTA
1 ATGGCTATTCAGAGCTACCCATTA
*
53952535 TTGGC
1 ATGGC
53952540 CCACATGAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (24 bp):
ATGGCTATTCAGAGCTACCCATTA
Found at i:53963454 original size:6 final size:6
Alignment explanation
Indices: 53963445--53963493 Score: 71
Period size: 6 Copynumber: 8.0 Consensus size: 6
53963435 CAGCAGCAGA
* *
53963445 AACAAC AACACC AACACC AACACC AACACC AACACC AACCACC ACCACC
1 AACACC AACACC AACACC AACACC AACACC AACACC AA-CACC AACACC
53963494 TTGTGGGTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
6 35 0.88
7 5 0.12
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (6 bp):
AACACC
Found at i:53963696 original size:24 final size:24
Alignment explanation
Indices: 53963644--53963698 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
53963634 GAGCGGTGAG
* *
53963644 GGAACAGGAAGGGATACCAGAGCTA
1 GGAAGAGGAAGGGATACCAAAGC-A
53963669 -GAAGAGGAAGGAGATACCAAAG-A
1 GGAAGAGGAAGG-GATACCAAAGCA
53963692 GGAAGAG
1 GGAAGAG
53963699 AAAAAAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.62
25 9 0.35
ACGTcount: A:0.45, C:0.11, G:0.38, T:0.05
Consensus pattern (24 bp):
GGAAGAGGAAGGGATACCAAAGCA
Found at i:53966913 original size:22 final size:22
Alignment explanation
Indices: 53966885--53966934 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
53966875 AGAAAAAGAA
**
53966885 AATTTTAATTTTTTTTTTTTAC
1 AATTTTAATTTTTTACTTTTAC
* *
53966907 AATTTTAGTTTTTTACTTTTCC
1 AATTTTAATTTTTTACTTTTAC
53966929 AATTTT
1 AATTTT
53966935 CTTTCCACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (22 bp):
AATTTTAATTTTTTACTTTTAC
Found at i:53968939 original size:2 final size:2
Alignment explanation
Indices: 53968932--53968959 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53968922 AGAAAACTCC
53968932 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
53968960 GGTTGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:53979352 original size:23 final size:25
Alignment explanation
Indices: 53979326--53979374 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
53979316 ATAATATGTT
* *
53979326 ATTTTATGTGTAATTA-T-AAATAA
1 ATTTTAGGTATAATTATTAAAATAA
53979349 ATTTTAGGTATAATTATTAAAATAA
1 ATTTTAGGTATAATTATTAAAATAA
53979374 A
1 A
53979375 ATATATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 1 0.05
25 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (25 bp):
ATTTTAGGTATAATTATTAAAATAA
Found at i:53980018 original size:15 final size:15
Alignment explanation
Indices: 53979998--53980027 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53979988 AAAACCCCGA
*
53979998 AACCCGAAAATAATG
1 AACCCGAAAACAATG
53980013 AACCCGAAAACAATG
1 AACCCGAAAACAATG
53980028 TAAACACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.23, G:0.13, T:0.10
Consensus pattern (15 bp):
AACCCGAAAACAATG
Found at i:53986544 original size:105 final size:101
Alignment explanation
Indices: 53986366--53986563 Score: 252
Period size: 105 Copynumber: 1.9 Consensus size: 101
53986356 AATTGACGGA
* * * * *
53986366 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGTTGGGCTATGACATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAGACCATAGCTGGGATATGACATTCTAA
* * *
53986431 TGAAAAGACCATAATTGGGTTTTGGCACCTTGAACG
66 TGAAAAGACCATAACTAGGTTATGGCACCTTGAACG
* *
53986467 TAAGACCATGGTTGGACCATGGCAGTATATATACATGTGTAAGATCATAGCTGGGATATGACATT
1 TAAGACCATGGTTGGACCATGGCA--ATATATA-A-ATGTAAGACCATAGCTGGGATATGACATT
* *
53986532 CTGATGATAAGACCATAACTAGGTTATGGCAC
62 CTAATGAAAAGACCATAACTAGGTTATGGCAC
53986564 TACAAATGTA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
101 24 0.30
103 5 0.06
104 1 0.01
105 51 0.63
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAGACCATAGCTGGGATATGACATTCTAA
TGAAAAGACCATAACTAGGTTATGGCACCTTGAACG
Found at i:53986593 original size:105 final size:105
Alignment explanation
Indices: 53986399--53986595 Score: 234
Period size: 105 Copynumber: 1.9 Consensus size: 105
53986389 AATGTTTAAA
* * * * * * **
53986399 TGTAAGACCATAGTTGGGCTATGACATTTTAATGAAAAGACCATAATTGGGTTTTGGCACCTTGA
1 TGTAAGACCATAGCTGGGATATGACATTCTAATGAAAAGACCATAACTAGGTTATGGCACCTCAA
**
53986464 ACGTAAGACCATGGTTGGACCATGGCAGTATATATACATG
66 ACGTAAGACCATGGCAGGACCATGGCAGTATATATACATG
* * *
53986504 TGTAAGATCATAGCTGGGATATGACATTCTGATGATAAGACCATAACTAGGTTATGGCA-CTACA
1 TGTAAGACCATAGCTGGGATATGACATTCTAATGAAAAGACCATAACTAGGTTATGGCACCT-CA
* **
53986568 AATGTAAGACCATGGCAGGGTCATGGCA
65 AACGTAAGACCATGGCAGGACCATGGCA
53986596 ATGCATGTGT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
104 2 0.03
105 73 0.97
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGATATGACATTCTAATGAAAAGACCATAACTAGGTTATGGCACCTCAA
ACGTAAGACCATGGCAGGACCATGGCAGTATATATACATG
Found at i:53987899 original size:20 final size:20
Alignment explanation
Indices: 53987876--53987913 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53987866 TATTAATACC
53987876 TTTTATTTAGTATCGATAAA
1 TTTTATTTAGTATCGATAAA
*
53987896 TTTTATTTGGTATCGATA
1 TTTTATTTAGTATCGATA
53987914 TCTCTAGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTTATTTAGTATCGATAAA
Found at i:53989030 original size:22 final size:22
Alignment explanation
Indices: 53988970--53989034 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
53988960 AAAGTATTAG
* *
53988970 AAAAAGAAACAGAGATAGAAAT
1 AAAAAGAAAAAGAGAAAGAAAT
* * * * *
53988992 GAAAACAGAACGGGAAAGAAAT
1 AAAAAGAAAAAGAGAAAGAAAT
53989014 AAAAAGAAAAAGAGAAAGAAA
1 AAAAAGAAAAAGAGAAAGAAA
53989035 GAAAGGAGAA
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.69, C:0.05, G:0.22, T:0.05
Consensus pattern (22 bp):
AAAAAGAAAAAGAGAAAGAAAT
Found at i:53989963 original size:41 final size:39
Alignment explanation
Indices: 53989902--53990038 Score: 111
Period size: 40 Copynumber: 3.5 Consensus size: 39
53989892 CTTTGAGTCA
*
53989902 ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTCG
1 ATGAGACACTGGGTGCCAATTTACTACTTCGGATT-A-TCG
* * *
53989943 ATGAGGCACTGGGTGCCAA-TT-C-ACTT-TGATTTAGCCG
1 ATGAGACACTGGGTGCCAATTTACTACTTCGGA-TTA-TCG
* * * *
53989980 ATGAGACACTAGGTGTCAATTTATTACTTCGAATTATCTG
1 ATGAGACACTGGGTGCCAATTTACTACTTCGGATTATC-G
**
53990020 ATGAGGTACTGGGTGCCAA
1 ATGAGACACTGGGTGCCAA
53990039 ACTGGTGTGT
Statistics
Matches: 74, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
37 21 0.28
38 8 0.11
39 2 0.03
40 25 0.34
41 18 0.24
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (39 bp):
ATGAGACACTGGGTGCCAATTTACTACTTCGGATTATCG
Found at i:53991392 original size:17 final size:17
Alignment explanation
Indices: 53991370--53991404 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
53991360 CTATCTCCAA
53991370 GCCTCCTTATTTCAATG
1 GCCTCCTTATTTCAATG
*
53991387 GCCTCCTTTTTTCAATG
1 GCCTCCTTATTTCAATG
53991404 G
1 G
53991405 TGCAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (17 bp):
GCCTCCTTATTTCAATG
Found at i:53993456 original size:26 final size:27
Alignment explanation
Indices: 53993403--53993456 Score: 65
Period size: 30 Copynumber: 1.9 Consensus size: 27
53993393 CATCGAATAT
*
53993403 GAAAAGGGATGGTTTCGACCATTGATTAAA
1 GAAAAGAGATGGTTTCGACC--T-ATTAAA
53993433 GAAAAGAGATGGTTTCGACC-ATTA
1 GAAAAGAGATGGTTTCGACCTATTA
53993457 TTTAGCACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.17
30 19 0.83
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (27 bp):
GAAAAGAGATGGTTTCGACCTATTAAA
Found at i:54002642 original size:33 final size:32
Alignment explanation
Indices: 54002601--54002761 Score: 117
Period size: 33 Copynumber: 4.8 Consensus size: 32
54002591 CAGTGTTTAT
54002601 ATGTAAGACCATAGCTGAGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGAGCTATGGCATTCTG
* * * * *
54002633 ATGATAAGACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAGCTGAGCTATGGCATTCTG
* * * * * *
54002666 AACGTAAGACCATGGTTG-GACCATGGCAGTGTTTAT
1 -ATGTAAGACCATAGCTGAG-CTATGGCA-T-TCT-G
*
54002702 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGAGCTATGGCATTCTG
* * *
54002734 ATGATAAGACCATAACTAAGTTATGGCA
1 ATG-TAAGACCATAGCTGAGCTATGGCA
54002762 CTACGAATGT
Statistics
Matches: 97, Mismatches: 24, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
32 7 0.07
33 63 0.65
34 3 0.03
35 23 0.24
36 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGAGCTATGGCATTCTG
Found at i:54002758 original size:101 final size:101
Alignment explanation
Indices: 54002583--54002773 Score: 337
Period size: 101 Copynumber: 1.9 Consensus size: 101
54002573 TGACGGATAA
54002583 GACCATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGCATTCTGATGATAAGACCATAA
1 GACCATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGCATTCTGATGATAAGACCATAA
** *
54002648 CTGGGTTATGGCACTATGAACGTAAGACCATGGTTG
66 CTAAGTTATGGCACTACGAACGTAAGACCATGGTTG
*
54002684 GACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAA
1 GACCATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGCATTCTGATGATAAGACCATAA
*
54002749 CTAAGTTATGGCACTACGAATGTAA
66 CTAAGTTATGGCACTACGAACGTAA
54002774 AGGACGAATT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 85 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (101 bp):
GACCATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGCATTCTGATGATAAGACCATAA
CTAAGTTATGGCACTACGAACGTAAGACCATGGTTG
Found at i:54005885 original size:18 final size:17
Alignment explanation
Indices: 54005852--54005890 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
54005842 TTTTATAAAT
54005852 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
54005870 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
54005887 TGTG
1 TGTG
54005891 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:54006143 original size:23 final size:23
Alignment explanation
Indices: 54006116--54006214 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
54006106 AGTGTTATTG
*
54006116 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
54006139 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
54006162 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
54006185 AACAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
54006208 ATCAGTG
1 ATCAGTG
54006215 TTGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:54007968 original size:22 final size:23
Alignment explanation
Indices: 54007926--54007971 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
54007916 AATTTAACTG
*
54007926 TCATTTCATCTATGATTTACTTA
1 TCATTTCACCTATGATTTACTTA
54007949 TCATTTCACCTAT-ATTTACTTA
1 TCATTTCACCTATGATTTACTTA
54007971 T
1 T
54007972 AAATAAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.26, C:0.20, G:0.02, T:0.52
Consensus pattern (23 bp):
TCATTTCACCTATGATTTACTTA
Found at i:54009157 original size:43 final size:43
Alignment explanation
Indices: 54009096--54009258 Score: 192
Period size: 43 Copynumber: 3.8 Consensus size: 43
54009086 CAATCCCAAC
*
54009096 GTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACT
1 GTCCCAGACGTGGTCTTACATGTAAACACATATCGATGCCACT
* * * *
54009139 GTCCCAGACAG-GGTCTTACA-CTAATCAAATA-CGATGCCAAT
1 GTCCCAGAC-GTGGTCTTACATGTAAACACATATCGATGCCACT
*
54009180 GTCCCAGACATGGTCTTACATGTAAACACA-AGTCGATGCCAAC-
1 GTCCCAGACGTGGTCTTACATGTAAACACATA-TCGATGCC-ACT
* *
54009223 GTCCCAGACGTGGTCTTACACGAAAACACATATCGA
1 GTCCCAGACGTGGTCTTACATGTAAACACATATCGA
54009259 AATCTTATGT
Statistics
Matches: 102, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
41 28 0.27
42 15 0.15
43 56 0.55
44 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (43 bp):
GTCCCAGACGTGGTCTTACATGTAAACACATATCGATGCCACT
Found at i:54011152 original size:15 final size:15
Alignment explanation
Indices: 54011129--54011163 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54011119 TTTCTATGCC
* *
54011129 ATTGATGTATTTATT
1 ATTGTTGTAATTATT
54011144 ATTGTTGTAATTATT
1 ATTGTTGTAATTATT
54011159 ATTGT
1 ATTGT
54011164 AGCATTGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (15 bp):
ATTGTTGTAATTATT
Found at i:54016462 original size:20 final size:20
Alignment explanation
Indices: 54016439--54016476 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54016429 TATCAATACC
54016439 TTTTATTTGGTATCGATAAA
1 TTTTATTTGGTATCGATAAA
*
54016459 TTTTCTTTGGTATCGATA
1 TTTTATTTGGTATCGATA
54016477 TCTCTAGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (20 bp):
TTTTATTTGGTATCGATAAA
Found at i:54029799 original size:16 final size:16
Alignment explanation
Indices: 54029778--54029810 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54029768 ATGGGTCCAT
54029778 TCATCCACCATGTGGA
1 TCATCCACCATGTGGA
54029794 TCATCCACCATGTGGA
1 TCATCCACCATGTGGA
54029810 T
1 T
54029811 GATTTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (16 bp):
TCATCCACCATGTGGA
Found at i:54038067 original size:18 final size:20
Alignment explanation
Indices: 54038025--54038084 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
54038015 ATGGGGTTAG
* *
54038025 AAGGGAAAAGGAAAAAAATGA
1 AAGGAAAAAAGAAAAAAAT-A
*
54038046 AAGG-AAATAGAAAAAAAT-
1 AAGGAAAAAAGAAAAAAATA
54038064 AAGGAAAAAAG-AAAAAATA
1 AAGGAAAAAAGAAAAAAATA
54038083 AA
1 AA
54038085 AAAATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.32
19 7 0.21
20 12 0.35
21 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (20 bp):
AAGGAAAAAAGAAAAAAATA
Found at i:54057047 original size:132 final size:132
Alignment explanation
Indices: 54056805--54057066 Score: 425
Period size: 132 Copynumber: 2.0 Consensus size: 132
54056795 TATGAACTTC
* * *
54056805 CTAAACATTCAAAATGCTTACTTTGTTTCGTTTTCTATTTCTGTAGTGGTTATTTTGCAGAACAT
1 CTAAACATTCAAAATGCTTACTCTGTTTCGTTTTCTATTTCTATAGTGGTTATTTTGCAGAACAC
* *
54056870 GTCGACTGGATCACCTTGGAGCTCAAACTACCCAGCTTCTGACTCGGTAGACTTTTAAATGTTCT
66 GTCGACTGGATCACCTCGGAGCTCAAACTACCCAGCTTCTGACTCGGTAGACTTTTAAACGTTCT
54056935 TA
131 TA
* * *
54056937 CTAAGCATTCAAAATGCTTACTCTGTTTCGTTTTTTATTTCTATAGTGGTTATTTTGCGGAACAC
1 CTAAACATTCAAAATGCTTACTCTGTTTCGTTTTCTATTTCTATAGTGGTTATTTTGCAGAACAC
* * *
54057002 GTCGATTGGATCACCTCGGAGCTCAAACTATCTAGCTTCTGACTCGGTAGACTTTTAAACGTTCT
66 GTCGACTGGATCACCTCGGAGCTCAAACTACCCAGCTTCTGACTCGGTAGACTTTTAAACGTTCT
54057067 AGACTCAGTT
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 119 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.39
Consensus pattern (132 bp):
CTAAACATTCAAAATGCTTACTCTGTTTCGTTTTCTATTTCTATAGTGGTTATTTTGCAGAACAC
GTCGACTGGATCACCTCGGAGCTCAAACTACCCAGCTTCTGACTCGGTAGACTTTTAAACGTTCT
TA
Found at i:54058792 original size:2 final size:2
Alignment explanation
Indices: 54058785--54058810 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54058775 ATGAAATTGA
54058785 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54058811 GTATGTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54059935 original size:19 final size:20
Alignment explanation
Indices: 54059911--54059957 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
54059901 TTAAGGTTAG
* *
54059911 TTAATTAAGCTTATTTA-AA
1 TTAATTAAGATTAGTTAGAA
*
54059930 TTAATTAAGATTAGTTAGAT
1 TTAATTAAGATTAGTTAGAA
54059950 TTAATTAA
1 TTAATTAA
54059958 AGTATATAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (20 bp):
TTAATTAAGATTAGTTAGAA
Found at i:54063926 original size:51 final size:50
Alignment explanation
Indices: 54063857--54063960 Score: 172
Period size: 51 Copynumber: 2.1 Consensus size: 50
54063847 CCTAATGTTG
54063857 AATAATATGAATGATATGTTTAGGTACTTATGTAAATGAATTGAAGTGCAA
1 AATAATATGAATGATATGTTTAGGTACTTATGT-AATGAATTGAAGTGCAA
* * *
54063908 AATAGTATGAATGGTATGTTTAGGTACTTATGTAATGAATTGAAGTGTAA
1 AATAATATGAATGATATGTTTAGGTACTTATGTAATGAATTGAAGTGCAA
54063958 AAT
1 AAT
54063961 GGATATGTGC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
50 19 0.38
51 31 0.62
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (50 bp):
AATAATATGAATGATATGTTTAGGTACTTATGTAATGAATTGAAGTGCAA
Found at i:54068000 original size:90 final size:90
Alignment explanation
Indices: 54067882--54068121 Score: 306
Period size: 90 Copynumber: 2.7 Consensus size: 90
54067872 ATTTTAGCCC
* *
54067882 GTATTATTTGTTGGTCG-ATTTTTATATTTTCGTATATCAGTTTTGTAAAATGTTTGTTTTATTT
1 GTATTATTTGTTGGTCGAATTTTT-TATTTTCGTATATCAGTTTTGTAAAATGTTCGTATTATTT
* *
54067946 TTGGATCTGTAAA-AATATCTTAGTT-T
65 TTGGATCTGTAAATAAAAT-TTA-TTCG
* * * *
54067972 GTATTATTTGTCGATCGAATTTTTTATTTTCGTATATCAATTTTCTAAAATGTTCGTATTATTTT
1 GTATTATTTGTTGGTCGAATTTTTTATTTTCGTATATCAGTTTTGTAAAATGTTCGTATTATTTT
*
54068037 TGTATCTGTAAATAAAATTTATTCG
66 TGGATCTGTAAATAAAATTTATTCG
* * * * *
54068062 GTATTATTTGTTGGTTGAATTATATATTTTCGTATATTAGTTTTGTAGAATGTTCGTATT
1 GTATTATTTGTTGGTCGAATTTTTTATTTTCGTATATCAGTTTTGTAAAATGTTCGTATT
54068122 TTCTTATATA
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
89 2 0.02
90 117 0.91
91 10 0.08
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.54
Consensus pattern (90 bp):
GTATTATTTGTTGGTCGAATTTTTTATTTTCGTATATCAGTTTTGTAAAATGTTCGTATTATTTT
TGGATCTGTAAATAAAATTTATTCG
Found at i:54068190 original size:15 final size:15
Alignment explanation
Indices: 54068170--54068198 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54068160 TTGTTCGAAT
54068170 TATTTTTTTACTTAA
1 TATTTTTTTACTTAA
54068185 TATTTTTTTACTTA
1 TATTTTTTTACTTA
54068199 TCTATGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTTTACTTAA
Found at i:54070445 original size:22 final size:22
Alignment explanation
Indices: 54070419--54070471 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
54070409 GGTGGTCGGT
54070419 GGTGGTCGACGGTGGAACTTAC
1 GGTGGTCGACGGTGGAACTTAC
*** * *
54070441 GGTGGTCGGTTGTGGAGCTTGC
1 GGTGGTCGACGGTGGAACTTAC
54070463 GGTGGTCGA
1 GGTGGTCGA
54070472 ACAGTTGGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.11, C:0.15, G:0.47, T:0.26
Consensus pattern (22 bp):
GGTGGTCGACGGTGGAACTTAC
Found at i:54070904 original size:51 final size:52
Alignment explanation
Indices: 54070841--54071248 Score: 248
Period size: 51 Copynumber: 7.1 Consensus size: 52
54070831 TTTTTATTCC
*
54070841 TTTTTAATTAAAATCTATCTATTCAATTATTTTT-ATTTATACTTTAAATAT
1 TTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAAATAT
*
54070892 TTTTTAATTAAAATCGATCTATTCGATTATTTTTAATTTATACTTTGATTAAAATTTTTAT
1 TTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATAC--T--TT-AAA----TAT
* * *
54070953 TTTTTAATAAAAATATATCTATTCGATTATTTTT-ATTTATACTTAAATTAATTTTTATT
1 TTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATAC-T---TTAA---ATA-T
* * *
54071012 CTTTTTAATAAAAATATATCTATTCGTTTATTATTTAATTTATACTTTAATTGATTTTTATT
1 -TTTTTAATTAAAATCTATCTATTCGATTATT-TTTAATTTATACTTTAA---A----TA-T
* ** * *
54071074 CTTTTTAATTAAAATCTATATATTTTATTATTTTTAATTTATAGTTT-ATTCA-
1 -TTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAAAT-AT
* *
54071126 TTTTTAATTAAAATCTATCTATTCAATTATTTTTAATATATACTTTAATTAATTTTTTTATTCT
1 TTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTT-A--AA------TA---T
* *
54071190 TTTTTAATTAAAATCTATCTATTCCATTATTTTTTGATTTATACTTTAAATAAT
1 TTTTTAATTAAAATCTATCTATTCGATTA-TTTTTAATTTATACTTTAAAT-AT
54071244 TTTTT
1 TTTTT
54071249 TATTTATTCT
Statistics
Matches: 291, Mismatches: 27, Indels: 75
0.74 0.07 0.19
Matches are distributed among these distances:
51 73 0.25
52 8 0.03
53 1 0.00
54 8 0.03
55 1 0.00
56 3 0.01
57 4 0.01
58 8 0.03
59 5 0.02
60 43 0.15
61 53 0.18
62 40 0.14
64 29 0.10
65 15 0.05
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (52 bp):
TTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAAATAT
Found at i:54070976 original size:112 final size:116
Alignment explanation
Indices: 54070825--54071248 Score: 472
Period size: 112 Copynumber: 3.6 Consensus size: 116
54070815 TTTTTTATAC
54070825 TTAAAATTTTTATTCCTTTTTAATTAAAATCTATCTATTCAATTATTTTT-ATTTATACTTTAAA
1 TTAAAATTTTTATT-CTTTTTAATTAAAATCTATCTATTCAATTATTTTTAATTTATACTTTAAA
* *
54070889 T-ATTTTTTAATTAAAATCGATCTATTCGATTATTTTTAATTTATACTTTGA
65 TAATTTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAA
* * *
54070940 TTAAAATTTTTA-T-TTTTTAATAAAAATATATCTATTCGATTATTTTT-ATTTATAC-TTAAAT
1 TTAAAATTTTTATTCTTTTTAATTAAAATCTATCTATTCAATTATTTTTAATTTATACTTTAAA-
* * *
54071001 TAATTTTTATTCTTTTTAATAAAAATATATCTATTCGTTTATTATTTAATTTATACTTTAA
65 T-A-----A-T-TTTTTAATTAAAATCTATCTATTCGATTATT-TTTAATTTATACTTTAA
* * ** * *
54071062 TT--GATTTTTATTCTTTTTAATTAAAATCTATATATTTTATTATTTTTAATTTATAGTTT-ATT
1 TTAAAATTTTTATTCTTTTTAATTAAAATCTATCTATTCAATTATTTTTAATTTATACTTTAAAT
* * *
54071124 CA-TTTTTAATTAAAATCTATCTATTCAATTATTTTTAATATATACTTTAA
66 AATTTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAA
** * *
54071174 TTAATTTTTTTATTCTTTTTTAATTAAAATCTATCTATTCCATTATTTTTTGATTTATACTTTAA
1 TTAAAATTTTTATTC-TTTTTAATTAAAATCTATCTATTCAATTA-TTTTTAATTTATACTTTAA
54071239 ATAATTTTTT
64 ATAATTTTTT
54071249 TATTTATTCT
Statistics
Matches: 257, Mismatches: 31, Indels: 39
0.79 0.09 0.12
Matches are distributed among these distances:
111 5 0.02
112 58 0.23
113 27 0.11
114 10 0.04
115 38 0.15
116 16 0.06
117 3 0.01
118 5 0.02
119 1 0.00
120 8 0.03
121 28 0.11
122 48 0.19
123 8 0.03
124 2 0.01
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (116 bp):
TTAAAATTTTTATTCTTTTTAATTAAAATCTATCTATTCAATTATTTTTAATTTATACTTTAAAT
AATTTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAA
Found at i:54070995 original size:60 final size:60
Alignment explanation
Indices: 54070891--54071247 Score: 376
Period size: 62 Copynumber: 6.0 Consensus size: 60
54070881 ACTTTAAATA
* *
54070891 TTTTTTAATTAAAATCGATCTATTCGATTATTTTTAATTTATACTTTGATTAAAATTTTTA-
1 TTTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAATT--AATTTTTAT
* * *
54070952 TTTTTTAATAAAAATATATCTATTCGATTATTTTT-ATTTATACTTAAATTAATTTTTAT
1 TTTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAATTAATTTTTAT
* * * *
54071011 TCTTTTTAATAAAAATATATCTATTCGTTTATTATTTAATTTATACTTTAATTGATTTTTAT
1 T-TTTTTAATTAAAATCTATCTATTCGATTATT-TTTAATTTATACTTTAATTAATTTTTAT
* ** * *
54071073 TCTTTTTAATTAAAATCTATATATTTTATTATTTTTAATTTATA--GT--TT-A--TTCA-
1 T-TTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAATTAATTTTTAT
* *
54071126 -TTTTTAATTAAAATCTATCTATTCAATTATTTTTAATATATACTTTAATTAATTTTTTTATT
1 TTTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAATTAA--TTTTTA-T
* * *
54071188 CTTTTTTAATTAAAATCTATCTATTCCATTATTTTTTGATTTATACTTTAAATAATTTTT
1 -TTTTTTAATTAAAATCTATCTATTCGATTA-TTTTTAATTTATACTTTAATTAATTTTT
54071248 TTATTTATTC
Statistics
Matches: 252, Mismatches: 26, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
51 38 0.15
53 1 0.00
54 3 0.01
55 2 0.01
56 2 0.01
57 2 0.01
58 8 0.03
59 2 0.01
60 46 0.18
61 46 0.18
62 49 0.19
63 5 0.02
64 28 0.11
65 20 0.08
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (60 bp):
TTTTTTAATTAAAATCTATCTATTCGATTATTTTTAATTTATACTTTAATTAATTTTTAT
Found at i:54071116 original size:21 final size:22
Alignment explanation
Indices: 54071092--54071134 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
54071082 TTAAAATCTA
*
54071092 TATATTTTATT-ATTTTTAATT
1 TATAGTTTATTCATTTTTAATT
54071113 TATAGTTTATTCATTTTTAATT
1 TATAGTTTATTCATTTTTAATT
54071135 AAAATCTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TATAGTTTATTCATTTTTAATT
Found at i:54071188 original size:64 final size:65
Alignment explanation
Indices: 54071118--54071252 Score: 218
Period size: 64 Copynumber: 2.1 Consensus size: 65
54071108 TAATTTATAG
*
54071118 TTTATTCATTTTTAATTAAAATCTATCTATTCAATTA-TTTTTAATATATACTTTAATTAATTTT
1 TTTATTCATTTTTAATTAAAATCTATCTATTCAATTATTTTTTAATATATACTTTAAATAATTTT
* * * *
54071182 TTTATTCTTTTTTAATTAAAATCTATCTATTCCATTATTTTTTGATTTATACTTTAAATAATTTT
1 TTTATTCATTTTTAATTAAAATCTATCTATTCAATTATTTTTTAATATATACTTTAAATAATTTT
54071247 TTTATT
1 TTTATT
54071253 TATTCTTTGC
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
64 35 0.54
65 30 0.46
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.60
Consensus pattern (65 bp):
TTTATTCATTTTTAATTAAAATCTATCTATTCAATTATTTTTTAATATATACTTTAAATAATTTT
Found at i:54073886 original size:14 final size:14
Alignment explanation
Indices: 54073864--54073899 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
54073854 ATCTCAAAAC
54073864 AATATAAATTTAGAA
1 AATATAAATTTA-AA
54073879 AA-ATAAATTTAAA
1 AATATAAATTTAAA
54073892 AATATAAA
1 AATATAAA
54073900 CTGATAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 14 0.70
15 2 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AATATAAATTTAAA
Found at i:54079086 original size:6 final size:7
Alignment explanation
Indices: 54079069--54079095 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
54079059 TATCATCCAT
54079069 AAAAAAG
1 AAAAAAG
54079076 AAAAAAG
1 AAAAAAG
54079083 AAAAAAG
1 AAAAAAG
54079090 AAAAAA
1 AAAAAA
54079096 TCCTTTTTAT
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:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:54080049 original size:17 final size:18
Alignment explanation
Indices: 54080018--54080051 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54080008 AATTTAATTT
54080018 TAATTAAATTATTTAAAC
1 TAATTAAATTATTTAAAC
*
54080036 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
54080052 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAC
Found at i:54081492 original size:2 final size:2
Alignment explanation
Indices: 54081485--54081519 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
54081475 TCCTTAAATT
* *
54081485 TA TA TA TA TA TT TA AA 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 TA TA TA T
54081520 TTTTATACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54081499 original size:18 final size:18
Alignment explanation
Indices: 54081478--54081513 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54081468 CTATAAATCC
*
54081478 TTAAATTTATATATATAT
1 TTAAATATATATATATAT
54081496 TTAAATATATATATATAT
1 TTAAATATATATATATAT
54081514 ATATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAATATATATATATAT
Found at i:54081526 original size:12 final size:12
Alignment explanation
Indices: 54081482--54081526 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
54081472 AAATCCTTAA
54081482 ATTTATATATAT
1 ATTTATATATAT
*
54081494 ATTTAAATATAT
1 ATTTATATATAT
*
54081506 ATATATATATAT
1 ATTTATATATAT
*
54081518 ATTTTTATA
1 ATTTATATA
54081527 CTTTTTAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:54085856 original size:18 final size:20
Alignment explanation
Indices: 54085833--54085880 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
54085823 AATTTGTTAG
54085833 AAAAAAAAAAGATTGA-A-A
1 AAAAAAAAAAGATTGAGATA
* *
54085851 AAAAAACAAAGGTTGATGATA
1 AAAAAAAAAAGATTGA-GATA
54085872 AAAAAAAAA
1 AAAAAAAAA
54085881 CTCAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 14 0.58
20 1 0.04
21 9 0.38
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAAGATTGAGATA
Found at i:54086341 original size:11 final size:11
Alignment explanation
Indices: 54086327--54086372 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
54086317 CTTTTTGGGC
54086327 AATTTTCGGGT
1 AATTTTCGGGT
54086338 AA--TTCGGGT
1 AATTTTCGGGT
54086347 AATTTTCGGGT
1 AATTTTCGGGT
54086358 AATTTTCGGGT
1 AATTTTCGGGT
54086369 AATT
1 AATT
54086373 CAATTAATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.27
11 24 0.73
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (11 bp):
AATTTTCGGGT
Found at i:54086345 original size:9 final size:9
Alignment explanation
Indices: 54086331--54086425 Score: 66
Period size: 9 Copynumber: 10.2 Consensus size: 9
54086321 TTGGGCAATT
54086331 TTCGGGTAA
1 TTCGGGTAA
54086340 TTCGGGTAA
1 TTCGGGTAA
54086349 TTTTCGGGTAA
1 --TTCGGGTAA
54086360 TTTTCGGGTAA
1 --TTCGGGTAA
***
54086371 TTCAATTAA
1 TTCGGGTAA
*
54086380 TTCGGTTAA
1 TTCGGGTAA
* *
54086389 TTCAGTTAA
1 TTCGGGTAA
*
54086398 -TCAGGTAA
1 TTCGGGTAA
**
54086406 TTCTTGTAA
1 TTCGGGTAA
54086415 TTCGGGTAA
1 TTCGGGTAA
54086424 TT
1 TT
54086426 TTTAACCAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
8 7 0.10
9 45 0.62
11 20 0.28
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:54086352 original size:20 final size:21
Alignment explanation
Indices: 54086327--54086372 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
54086317 CTTTTTGGGC
54086327 AATTTTCGGGTAA-TTCGGGT
1 AATTTTCGGGTAATTTCGGGT
54086347 AATTTTCGGGTAATTTTCGGGT
1 AATTTTCGGGTAA-TTTCGGGT
54086369 AATT
1 AATT
54086373 CAATTAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (21 bp):
AATTTTCGGGTAATTTCGGGT
Found at i:54086381 original size:31 final size:31
Alignment explanation
Indices: 54086318--54086381 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
54086308 AACACCGAAC
* **
54086318 TTTTTGGGCAATTTTCGGGTAATTCGGGTAA
1 TTTTCGGGCAATTTTCGGGTAATTCAAGTAA
* *
54086349 TTTTCGGGTAATTTTCGGGTAATTCAATTAA
1 TTTTCGGGCAATTTTCGGGTAATTCAAGTAA
54086380 TT
1 TT
54086382 CGGTTAATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.45
Consensus pattern (31 bp):
TTTTCGGGCAATTTTCGGGTAATTCAAGTAA
Found at i:54091437 original size:30 final size:30
Alignment explanation
Indices: 54091375--54091444 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
54091365 TATCATTTGG
*
54091375 TAAAAACT-AAAATTTTAAAATTCAAAAGA
1 TAAAAACTAAAAATTATAAAATTCAAAAGA
* * *
54091404 TAAAAAACTAAAAATTATCAAATT-TAAATA
1 T-AAAAACTAAAAATTATAAAATTCAAAAGA
54091434 TAAAAACTAAA
1 TAAAAACTAAA
54091445 TTTACAACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 11 0.31
30 12 0.34
31 12 0.34
ACGTcount: A:0.64, C:0.07, G:0.01, T:0.27
Consensus pattern (30 bp):
TAAAAACTAAAAATTATAAAATTCAAAAGA
Found at i:54109441 original size:2 final size:2
Alignment explanation
Indices: 54109434--54109462 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54109424 GAAAATACAT
54109434 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
54109463 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:54115403 original size:16 final size:17
Alignment explanation
Indices: 54115370--54115409 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
54115360 CATAAAATAG
54115370 TTTAAATAAATAAATTT
1 TTTAAATAAATAAATTT
*
54115387 TTTAATTAAAT-AATTT
1 TTTAAATAAATAAATTT
*
54115403 TCTAAAT
1 TTTAAAT
54115410 CTGATTCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAAATAAATAAATTT
Found at i:54125853 original size:38 final size:38
Alignment explanation
Indices: 54125811--54125883 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
54125801 TATTAATATT
*
54125811 TTTTCAAAATTTAGT-AGTTTGTAATTTTTTAAAATCGC
1 TTTTCAAAATTTA-TCACTTTGTAATTTTTTAAAATCGC
* *
54125849 TTTTCAGAATTTATCACTTTTTAATTTTTTAAAAT
1 TTTTCAAAATTTATCACTTTGTAATTTTTTAAAAT
54125884 ATTGATTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.03
38 30 0.97
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (38 bp):
TTTTCAAAATTTATCACTTTGTAATTTTTTAAAATCGC
Found at i:54127580 original size:50 final size:49
Alignment explanation
Indices: 54127526--54127650 Score: 126
Period size: 50 Copynumber: 2.5 Consensus size: 49
54127516 ATTCGGAAAT
* * * **
54127526 GCTCATAAGAGCACATAAACAGGAAGCTCTTTCGAGCCATATAACGGGAA
1 GCTCATAAGAGC-CATAAACAAGAAGCTCATTCGAACCATATAACAAGAA
* * **
54127576 GCTCAGT-TGAGCCATGTAACAAGAAGCTCATTCGAACTGTATAACAAGAA
1 GCTCA-TAAGAGCCAT-AAACAAGAAGCTCATTCGAACCATATAACAAGAA
*
54127626 GCTCATAAGAGCCATAATCAAGAAG
1 GCTCATAAGAGCCATAAACAAGAAG
54127651 TTTAAGCGAG
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
49 12 0.20
50 47 0.78
51 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (49 bp):
GCTCATAAGAGCCATAAACAAGAAGCTCATTCGAACCATATAACAAGAA
Found at i:54127587 original size:25 final size:26
Alignment explanation
Indices: 54127534--54127630 Score: 85
Period size: 25 Copynumber: 3.8 Consensus size: 26
54127524 ATGCTCATAA
*
54127534 GAGCACATA-AACAGGAAGCTC-TTTC
1 GAGC-CATATAACAGGAAGCTCAGTTC
*
54127559 GAGCCATATAACGGGAAGCTCAGTT-
1 GAGCCATATAACAGGAAGCTCAGTTC
* *
54127584 GAGCCATGTAACAAGAAGCTCA-TTC
1 GAGCCATATAACAGGAAGCTCAGTTC
* ** *
54127609 GAACTGTATAACAAGAAGCTCA
1 GAGCCATATAACAGGAAGCTCA
54127631 TAAGAGCCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
24 6 0.10
25 52 0.87
26 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
GAGCCATATAACAGGAAGCTCAGTTC
Found at i:54130115 original size:43 final size:41
Alignment explanation
Indices: 54130046--54130136 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 41
54130036 TTGCATATCA
* **
54130046 ATAAAAAAATTAATTTTTTTTAAAGTTTAAATAAAAAATTAAT
1 ATAAAAAAATTAAATTCCTTTAAAG-TTAAA-AAAAAATTAAT
**
54130089 ATAAAAAATATTAAATTCCTTT-AAGTTCGAAAAAAATTAAT
1 ATAAAAAA-ATTAAATTCCTTTAAAGTTAAAAAAAAATTAAT
*
54130130 ATCAAAA
1 ATAAAAA
54130137 TTTGAAAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
41 17 0.41
42 3 0.07
43 11 0.27
44 10 0.24
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.36
Consensus pattern (41 bp):
ATAAAAAAATTAAATTCCTTTAAAGTTAAAAAAAAATTAAT
Found at i:54130231 original size:60 final size:59
Alignment explanation
Indices: 54130111--54130434 Score: 355
Period size: 60 Copynumber: 5.5 Consensus size: 59
54130101 AAATTCCTTT
* * *
54130111 AAGTTCG-A-AAAAAATTAATATCAAAATTTGAAAGTTGGAAGAAAAAAAAGTTTTTTA
1 AAGTTCGAATAAAAAATTAATATCAAAATTTGAAAGTTAGAAGAAAACAAAGTTTTTAA
* ** *
54130168 AAGTTCGAATAAAAAATTAATGTCAAAATTTGTTAGTAAGAAGAAAACCAAAGTTTTTAA
1 AAGTTCGAATAAAAAATTAATATCAAAATTTGAAAGTTAGAAGAAAA-CAAAGTTTTTAA
* * * *
54130228 AAGTTTGAATTAAAAAAATTAATATAAAAATTTGTAAGTTAGAAGAAAAAGAAAGTTTTTAA
1 AAGTTCGAA-T-AAAAAATTAATATCAAAATTTGAAAGTTAGAAG-AAAACAAAGTTTTTAA
*
54130290 AAGTTCGAATAAAAAATTAACATCAAAATTTGAAAGTTAGAAGAAAA-ATAATGTTTTTATA
1 AAGTTCGAATAAAAAATTAATATCAAAATTTGAAAGTTAGAAGAAAACA-AA-GTTTTTA-A
* * *
54130351 AAATTTGAATAAAAAATTAATATCAAAATTT----G---GAAGAAATACAAAGTTTTTTA
1 AAGTTCGAATAAAAAATTAATATCAAAATTTGAAAGTTAGAAGAAA-ACAAAGTTTTTAA
54130404 AAGTTCGAATAAAGAAA-TAATATCAAAATTT
1 AAGTTCGAATAAA-AAATTAATATCAAAATTT
54130435 ATAACTGAAA
Statistics
Matches: 232, Mismatches: 23, Indels: 28
0.82 0.08 0.10
Matches are distributed among these distances:
53 26 0.11
54 16 0.07
55 3 0.01
56 1 0.00
57 8 0.03
58 2 0.01
59 38 0.16
60 55 0.24
61 31 0.13
62 48 0.21
63 4 0.02
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (59 bp):
AAGTTCGAATAAAAAATTAATATCAAAATTTGAAAGTTAGAAGAAAACAAAGTTTTTAA
Found at i:54130334 original size:122 final size:120
Alignment explanation
Indices: 54130118--54130434 Score: 400
Period size: 122 Copynumber: 2.7 Consensus size: 120
54130108 TTTAAGTTCG
*
54130118 AAAAAAATTAATATCAAAATTTGAAAGTTGGAAGAAAAAAAAGTTTTTTAAAGTTCGAATAAAAA
1 AAAAAAATTAATATCAAAATTTGTAAGTT-GAAGAAAAAAAAGTTTTTTAAAGTTCGAATAAAAA
* ** * *
54130183 ATTAATGTCAAAATTTGTTAGTAAGAAGAAAACCAAAGTTTTTA-AAAGTTTGAATT
65 ATTAATATCAAAATTTGAAAGTAAGAAGAAAAACAAAGTTTTTATAAAATTTGAA-T
* *
54130239 AAAAAAATTAATATAAAAATTTGTAAGTTAGAAGAAAAAGAAAGTTTTTAAAAGTTCGAATAAAA
1 AAAAAAATTAATATCAAAATTTGTAAGTT-GAAGAAAAA-AAAGTTTTTTAAAGTTCGAATAAAA
* * * *
54130304 AATTAACATCAAAATTTGAAAGTTAGAAGAAAAATAATGTTTTTATAAAATTTGAAT
64 AATTAATATCAAAATTTGAAAGTAAGAAGAAAAACAAAGTTTTTATAAAATTTGAAT
*
54130361 -AAAAAATTAATATCAAAA-TT-T--G--GAAGAAATACAAAGTTTTTTAAAGTTCGAATAAAGA
1 AAAAAAATTAATATCAAAATTTGTAAGTTGAAGAAA-AAAAAGTTTTTTAAAGTTCGAATAAA-A
54130419 AA-TAATATCAAAATTT
64 AATTAATATCAAAATTT
54130435 ATAACTGAAA
Statistics
Matches: 175, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
114 43 0.25
115 4 0.02
117 1 0.01
119 1 0.01
120 2 0.01
121 53 0.30
122 62 0.35
123 9 0.05
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (120 bp):
AAAAAAATTAATATCAAAATTTGTAAGTTGAAGAAAAAAAAGTTTTTTAAAGTTCGAATAAAAAA
TTAATATCAAAATTTGAAAGTAAGAAGAAAAACAAAGTTTTTATAAAATTTGAAT
Found at i:54130387 original size:54 final size:53
Alignment explanation
Indices: 54130329--54130434 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
54130319 TTGAAAGTTA
* * *
54130329 GAAGAAAAATAATGTTTTTATAAAATTTGAATAAA-AAATTAATATCAAAATTTG
1 GAAGAAAAACAAAGTTTTT-TAAAATTCGAATAAAGAAA-TAATATCAAAATTTG
* *
54130383 GAAGAAATACAAAGTTTTTTAAAGTTCGAATAAAGAAATAATATCAAAATTT
1 GAAGAAAAACAAAGTTTTTTAAAATTCGAATAAAGAAATAATATCAAAATTT
54130435 ATAACTGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
53 27 0.59
54 19 0.41
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (53 bp):
GAAGAAAAACAAAGTTTTTTAAAATTCGAATAAAGAAATAATATCAAAATTTG
Found at i:54131720 original size:170 final size:171
Alignment explanation
Indices: 54131437--54131776 Score: 556
Period size: 170 Copynumber: 2.0 Consensus size: 171
54131427 ACAACGAATC
* * * *
54131437 AGATGAGTACTTCGAGGATCGTACCCAGGGGAGGTGAGCACTAAATTAACCCTAACCTAAGCACA
1 AGATGAGTACTTCGAAGATCATACCCAAGGGAGGCGAGCACTAAATTAACCCTAACCTAAGCACA
*
54131502 AATAGAGCTAATTAGTACTTTAAATAAATTCTATTATGAATCAACATAAAGAAAGA-TTTTTGGT
66 AATAGAGCTAATTAGTACTTTAAATAAATTCTATTATGAATAAACATAAAGAAAGATTTTTTGGT
*
54131566 ATTTTTGTAAATAAGGAATAAAATAATATAAAGAAAAAGAA
131 ATTTTTGTAAATAAAGAATAAAATAATATAAAGAAAAAGAA
* * * * *
54131607 AGATGAGTGCTTCGAATATCATACCTAAGGGAGGCGAGCACTAGATTAACCCTAACCTTAGCACA
1 AGATGAGTACTTCGAAGATCATACCCAAGGGAGGCGAGCACTAAATTAACCCTAACCTAAGCACA
*
54131672 AATAGAGCTAATTAGTACTTTAAATAAATTCTATTATGAATAAACATAAAGAAAGATTTTTTTGT
66 AATAGAGCTAATTAGTACTTTAAATAAATTCTATTATGAATAAACATAAAGAAAGATTTTTTGGT
*
54131737 ATTTTTGTAAATAAAGAATAAATTAATATAAAGAAAAAGA
131 ATTTTTGTAAATAAAGAATAAAATAATATAAAGAAAAAGA
54131777 CTTTGGGAAA
Statistics
Matches: 156, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
170 111 0.71
171 45 0.29
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (171 bp):
AGATGAGTACTTCGAAGATCATACCCAAGGGAGGCGAGCACTAAATTAACCCTAACCTAAGCACA
AATAGAGCTAATTAGTACTTTAAATAAATTCTATTATGAATAAACATAAAGAAAGATTTTTTGGT
ATTTTTGTAAATAAAGAATAAAATAATATAAAGAAAAAGAA
Found at i:54138982 original size:15 final size:13
Alignment explanation
Indices: 54138938--54138988 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 13
54138928 GTGTGCCAAT
54138938 TTTTAATTATTTTTA
1 TTTTAATTA--TTTA
54138953 TTTTAATTA-TTA
1 TTTTAATTATTTA
54138965 TTTTAATTTATTTAA
1 TTTTAA-TTATTT-A
*
54138980 TTTTCATTA
1 TTTTAATTA
54138989 GATACCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 9 0.28
13 3 0.09
14 5 0.16
15 15 0.47
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAATTATTTA
Found at i:54144214 original size:19 final size:19
Alignment explanation
Indices: 54144190--54144228 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
54144180 CAATTGAGGG
*
54144190 TAATTAGCTATTTAATTGA
1 TAATTAGATATTTAATTGA
54144209 TAATTAGATATTTAATTGA
1 TAATTAGATATTTAATTGA
54144228 T
1 T
54144229 CATAGGCCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (19 bp):
TAATTAGATATTTAATTGA
Found at i:54152558 original size:24 final size:24
Alignment explanation
Indices: 54152522--54152568 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
54152512 ATAAACTAAG
* * *
54152522 GACAATTGGATGGTGATGATAATA
1 GACAAGTGGATGGTAATAATAATA
*
54152546 GACAAGTGTATGGTAATAATAAT
1 GACAAGTGGATGGTAATAATAAT
54152569 TACATGTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (24 bp):
GACAAGTGGATGGTAATAATAATA
Found at i:54152747 original size:41 final size:38
Alignment explanation
Indices: 54152693--54152831 Score: 121
Period size: 41 Copynumber: 3.7 Consensus size: 38
54152683 AAATGAAAGA
*
54152693 AAAAGAAACAAAGAAACAAAACGGAGAACGAAACAGGGAG
1 AAAAGAAACAAAGAAACAAAAC-GA-AATGAAACAGGGAG
* * *
54152733 AAAAGAAAGGAAAGAAAGAAAA-TAAATG-AA-A--GA-
1 AAAAGAAA-CAAAGAAACAAAACGAAATGAAACAGGGAG
54152766 AAAAGAAACAAAGAAACAAAACAGATAATGAAACAGGGAG
1 AAAAGAAACAAAGAAACAAAAC-GA-AATGAAACAGGGAG
* *
54152806 AAAAGAAAGGAAAGAAAGAAAA-GAAA
1 AAAAGAAA-CAAAGAAACAAAACGAAA
54152832 CAGAAGCTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
32 11 0.14
33 8 0.10
34 3 0.04
35 4 0.05
36 3 0.04
37 3 0.04
38 5 0.06
39 5 0.06
40 16 0.20
41 22 0.28
ACGTcount: A:0.68, C:0.06, G:0.22, T:0.03
Consensus pattern (38 bp):
AAAAGAAACAAAGAAACAAAACGAAATGAAACAGGGAG
Found at i:54152779 original size:73 final size:73
Alignment explanation
Indices: 54152678--54152827 Score: 273
Period size: 73 Copynumber: 2.1 Consensus size: 73
54152668 AAGAATAAAC
*
54152678 AAAATAAATGAAAGAAAAAGAAACAAAGAAACAAAACGGAGAACGAAACAGGGAGAAAAGAAAGG
1 AAAATAAATGAAAGAAAAAGAAACAAAGAAACAAAACAGAGAACGAAACAGGGAGAAAAGAAAGG
54152743 AAAGAAAG
66 AAAGAAAG
* *
54152751 AAAATAAATGAAAGAAAAAGAAACAAAGAAACAAAACAGATAATGAAACAGGGAGAAAAGAAAGG
1 AAAATAAATGAAAGAAAAAGAAACAAAGAAACAAAACAGAGAACGAAACAGGGAGAAAAGAAAGG
54152816 AAAGAAAG
66 AAAGAAAG
54152824 AAAA
1 AAAA
54152828 GAAACAGAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.69, C:0.06, G:0.21, T:0.04
Consensus pattern (73 bp):
AAAATAAATGAAAGAAAAAGAAACAAAGAAACAAAACAGAGAACGAAACAGGGAGAAAAGAAAGG
AAAGAAAG
Found at i:54153277 original size:17 final size:18
Alignment explanation
Indices: 54153255--54153288 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54153245 TAAATGAGTT
54153255 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
54153272 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
54153289 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:54153634 original size:12 final size:10
Alignment explanation
Indices: 54153604--54153637 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
54153594 GGTTAATTGA
54153604 TTTGGGTGTG
1 TTTGGGTGTG
54153614 TTTGGGTGTG
1 TTTGGGTGTG
*
54153624 TTTGGGAGTG
1 TTTGGGTGTG
54153634 TTTG
1 TTTG
54153638 AAAAGCCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (10 bp):
TTTGGGTGTG
Found at i:54155266 original size:27 final size:26
Alignment explanation
Indices: 54155244--54155432 Score: 179
Period size: 27 Copynumber: 7.1 Consensus size: 26
54155234 CAAAATAGCT
*
54155244 CCATAAGGTAGAATGACTGAAATACC
1 CCATAAGGTAAAATGACTGAAATACC
* *
54155270 CCATAGGGTAAAAT-AATCGAAATACC
1 CCATAAGGTAAAATGACT-GAAATACC
*
54155296 CTCATAAGATAAAATGACTGAAATACC
1 C-CATAAGGTAAAATGACTGAAATACC
*
54155323 CC-TATAGGATAAAATGA-TCAAAATACCC
1 CCATA-AGG-TAAAATGACT-GAAATA-CC
*
54155351 CCAT-AGGATAAAATGACCGAAATACCC
1 CCATAAGG-TAAAATGACTGAAATA-CC
* *
54155378 CCATAGGGTAGAATGACTGAAATACCC
1 CCATAAGGTAAAATGACTGAAATA-CC
**
54155405 CCATAAGGTAAAATGACTGTTATACC
1 CCATAAGGTAAAATGACTGAAATACC
54155431 CC
1 CC
54155433 TAGGAGATGA
Statistics
Matches: 136, Mismatches: 17, Indels: 20
0.79 0.10 0.12
Matches are distributed among these distances:
25 4 0.03
26 29 0.21
27 94 0.69
28 8 0.06
29 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (26 bp):
CCATAAGGTAAAATGACTGAAATACC
Found at i:54155361 original size:54 final size:54
Alignment explanation
Indices: 54155227--54155434 Score: 242
Period size: 54 Copynumber: 3.9 Consensus size: 54
54155217 AAAATAGGTG
* * * *
54155227 AAATGACCAAAATAGCTCCATAAGGTAGAATGACTGAAATACCCC-ATAGGGTA
1 AAATGATCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCTATAGGGTA
* * * * *
54155280 AAATAATCGAAATACCCTCATAAGATAAAATGACTGAAATACCCCTATAGGATA
1 AAATGATCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCTATAGGGTA
* *
54155334 AAATGATCAAAATACCCCCAT-AGGATAAAATGACCGAAATACCCCCATAGGGTA
1 AAATGATCAAAATACCCCCATAAGG-TAAAATGACTGAAATACCCCTATAGGGTA
* * **
54155388 GAATGA-CTGAAATACCCCCATAAGGTAAAATGACTGTTATACCCCTA
1 AAATGATC-AAAATACCCCCATAAGGTAAAATGACTGAAATACCCCTA
54155435 GGAGATGAAA
Statistics
Matches: 129, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
53 40 0.31
54 86 0.67
55 3 0.02
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (54 bp):
AAATGATCAAAATACCCCCATAAGGTAAAATGACTGAAATACCCCTATAGGGTA
Found at i:54155446 original size:81 final size:81
Alignment explanation
Indices: 54155244--54155448 Score: 231
Period size: 81 Copynumber: 2.5 Consensus size: 81
54155234 CAAAATAGCT
* * * *
54155244 CCATAAGGTAGAATGACTGAAATACCCCATAGGG-TAAAATAATCGAAATACCCTCATAAGATAA
1 CCATAAGGTAAAATGACTGAAATACCCCATAGGGATAAAATGACCGAAATACCCCCATAAGATAA
54155308 AATGACTGAAATACCC
66 AATGACTGAAATACCC
* * * *
54155324 CTAT-AGGATAAAATGA-TCAAAATACCCCCATA-GGATAAAATGACCGAAATACCCCCATAGGG
1 CCATAAGG-TAAAATGACT-GAAATA-CCCCATAGGGATAAAATGACCGAAATACCCCCATAAGA
*
54155386 TAGAATGACTGAAATACCC
63 TAAAATGACTGAAATACCC
** *
54155405 CCATAAGGTAAAATGACTGTTATACCCC-TAGGAGATGAAATGAC
1 CCATAAGGTAAAATGACTGAAATACCCCATAGG-GATAAAATGAC
54155449 TGTTATGGCC
Statistics
Matches: 103, Mismatches: 14, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
79 6 0.06
80 22 0.21
81 71 0.69
82 4 0.04
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (81 bp):
CCATAAGGTAAAATGACTGAAATACCCCATAGGGATAAAATGACCGAAATACCCCCATAAGATAA
AATGACTGAAATACCC
Found at i:54161338 original size:21 final size:22
Alignment explanation
Indices: 54161314--54161381 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 22
54161304 ATGGAAACCT
54161314 ATAAAGGTTGAAC-GAAAGCTC
1 ATAAAGGTTGAACAGAAAGCTC
*
54161335 AT-AAGAGCTGAACAGAAA-CTC
1 ATAAAG-GTTGAACAGAAAGCTC
* * *
54161356 ATAAGGGTTAAACTG-AAGCTC
1 ATAAAGGTTGAACAGAAAGCTC
54161377 A-AAAG
1 ATAAAG
54161382 AGCTGAACTG
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
20 8 0.22
21 23 0.62
22 6 0.16
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.18
Consensus pattern (22 bp):
ATAAAGGTTGAACAGAAAGCTC
Found at i:54161376 original size:42 final size:42
Alignment explanation
Indices: 54161307--54161410 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
54161297 GTGCTAAATG
* * * *
54161307 GAAACCTATAAAGGTTGAAC-GAAAGCTCATAAGAGCTGAACA
1 GAAACCCATAAGGGTTAAACTG-AAGCTCAAAAGAGCTGAACA
* *
54161349 GAAACTCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACT
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACA
*
54161391 GAAACCCATTAGGGTTAAAC
1 GAAACCCATAAGGGTTAAAC
54161411 AGAAACTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 52 0.98
43 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.18
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACA
Found at i:54161390 original size:21 final size:21
Alignment explanation
Indices: 54161329--54161393 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
54161319 GGTTGAACGA
*
54161329 AAGCTCATAAGAGCTGAACAG
1 AAGCTCATAAGAGCTGAACTG
* * * *
54161350 AAACTCATAAGGGTTAAACTG
1 AAGCTCATAAGAGCTGAACTG
*
54161371 AAGCTCAAAAGAGCTGAACTG
1 AAGCTCATAAGAGCTGAACTG
54161392 AA
1 AA
54161394 ACCCATTAGG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
AAGCTCATAAGAGCTGAACTG
Found at i:54161510 original size:11 final size:11
Alignment explanation
Indices: 54161494--54161518 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54161484 TGAACCTCAG
54161494 TTTACCTTCAA
1 TTTACCTTCAA
54161505 TTTACCTTCAA
1 TTTACCTTCAA
54161516 TTT
1 TTT
54161519 CTCCTTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTACCTTCAA
Found at i:54167309 original size:27 final size:26
Alignment explanation
Indices: 54167263--54167338 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 26
54167253 TTTTCTTATC
* *
54167263 ACAATTTCACTCC-AGTAAAATTTTA
1 ACAATTTTACCCCTAGTAAAATTTTA
54167288 ACAATTTTACCCCTTAGTAAAATTTTA
1 ACAATTTTACCCC-TAGTAAAATTTTA
* * *
54167315 ACGATTTTTCCCCTGGTAAAATTT
1 ACAATTTTACCCCTAGTAAAATTT
54167339 CAAGAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
25 11 0.25
26 10 0.23
27 23 0.52
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (26 bp):
ACAATTTTACCCCTAGTAAAATTTTA
Found at i:54167504 original size:18 final size:17
Alignment explanation
Indices: 54167481--54167514 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54167471 AGCACTGCAA
54167481 ATTTCCAATTTCAATTTC
1 ATTTCC-ATTTCAATTTC
*
54167499 ATTTCCATTTCCATTT
1 ATTTCCATTTCAATTT
54167515 TTGGAAACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTCCATTTCAATTTC
Found at i:54176595 original size:134 final size:135
Alignment explanation
Indices: 54176412--54176678 Score: 464
Period size: 136 Copynumber: 2.0 Consensus size: 135
54176402 GTCACACTTG
54176412 AATTTATTACTCATCTCAACTTACATAATTTCCATGAATCAACATATCAAGATATTG-ATATATA
1 AATTTATTACTCATCTCAACTTACATAATTTCCATGAATCAACATATCAAGATATTGAATATATA
* *
54176476 TACATTTCATGATACATATCATTCTTTTACTGTTTCTTCATATACATATATCATCCACGACAACT
66 TACATTTCATGATACATATCATTCTTTTACTGTTTCTTCAAATACATATATCATCCAAGACAACT
54176541 CCTGA
131 CCTGA
* * *
54176546 AATTTATTACTCGTTTTAACTTACATAATTTCCATGAATCAACATATCAAGATATTGATATATAT
1 AATTTATTACTCATCTCAACTTACATAATTTCCATGAATCAACATATCAAGATATTGA-ATATAT
*
54176611 ATACATTTCATGATACGTATCATTCTTTTACTGTTTCTTCAAATACATATATCATCCAAGACAAC
65 ATACATTTCATGATACATATCATTCTTTTACTGTTTCTTCAAATACATATATCATCCAAGACAAC
54176676 TCC
130 TCC
54176679 CGATAACTTA
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
134 54 0.43
136 71 0.57
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (135 bp):
AATTTATTACTCATCTCAACTTACATAATTTCCATGAATCAACATATCAAGATATTGAATATATA
TACATTTCATGATACATATCATTCTTTTACTGTTTCTTCAAATACATATATCATCCAAGACAACT
CCTGA
Found at i:54176806 original size:21 final size:21
Alignment explanation
Indices: 54176782--54176869 Score: 61
Period size: 21 Copynumber: 4.2 Consensus size: 21
54176772 TCGTAGGAGC
*
54176782 TAAACGGAAACCCATAAGGGT
1 TAAACGGAAACCCATAAGAGT
* * * *
54176803 TAAACAGAAGCTCA-ATAGAGC
1 TAAACGGAAACCCATA-AGAGT
* * *
54176824 TGAACGGAAACCCATTAGGGT
1 TAAACGGAAACCCATAAGAGT
* * *
54176845 TGAACGGAAACTCATATGAGT
1 TAAACGGAAACCCATAAGAGT
54176866 TAAA
1 TAAA
54176870 AAAAAGCTCA
Statistics
Matches: 48, Mismatches: 17, Indels: 4
0.70 0.25 0.06
Matches are distributed among these distances:
20 1 0.02
21 47 0.98
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (21 bp):
TAAACGGAAACCCATAAGAGT
Found at i:54176813 original size:42 final size:42
Alignment explanation
Indices: 54176725--54176845 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
54176715 ATATGTATAT
* ** * * **
54176725 GAAGCTC-ATGAGAGTTAAACAAAAACTCATAAGGGTTGAATG
1 GAAGCTCAAT-AGAGCTAAACGGAAACCCATAAGGGTTAAACA
*
54176767 GAAGCTC-GTAGGAGCTAAACGGAAACCCATAAGGGTTAAACA
1 GAAGCTCAATA-GAGCTAAACGGAAACCCATAAGGGTTAAACA
* *
54176809 GAAGCTCAATAGAGCTGAACGGAAACCCATTAGGGTT
1 GAAGCTCAATAGAGCTAAACGGAAACCCATAAGGGTT
54176846 GAACGGAAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 63 0.95
43 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.18
Consensus pattern (42 bp):
GAAGCTCAATAGAGCTAAACGGAAACCCATAAGGGTTAAACA
Found at i:54180944 original size:25 final size:23
Alignment explanation
Indices: 54180916--54180962 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
54180906 TATGAGCATC
*
54180916 CTGATATAGGCTCTTTGTGAACTTT
1 CTGATAT-GGCTCATT-TGAACTTT
54180941 CTGATATGGCTCATTTGAACTT
1 CTGATATGGCTCATTTGAACTT
54180963 CCTATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (23 bp):
CTGATATGGCTCATTTGAACTTT
Found at i:54196567 original size:19 final size:18
Alignment explanation
Indices: 54196522--54196575 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
54196512 AATAAAATAA
*
54196522 AATAAAATAA-AACAATT
1 AATAAAATAATAATAATT
* *
54196539 -TTAAAATAATAATTATT
1 AATAAAATAATAATAATT
54196556 AATAAAATTAATAATAATT
1 AATAAAA-TAATAATAATT
54196575 A
1 A
54196576 TTTAAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 8 0.28
17 5 0.17
18 5 0.17
19 11 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAAATAATAATAATT
Found at i:54204559 original size:20 final size:21
Alignment explanation
Indices: 54204512--54204559 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
54204502 ATATAAAATA
*
54204512 ATTAATTTTATAATAATATTT
1 ATTAATTTTATAAAAATATTT
54204533 ATT-ATTTTA-AAAAATAATTT
1 ATTAATTTTATAAAAAT-ATTT
54204553 -TTAATTT
1 ATTAATTT
54204560 ATTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTAATTTTATAAAAATATTT
Found at i:54206194 original size:88 final size:88
Alignment explanation
Indices: 54206045--54206208 Score: 265
Period size: 88 Copynumber: 1.9 Consensus size: 88
54206035 TGATTCCACC
* * *
54206045 GTTCCTAGTACTAACATTCCGTGCGGACTTCAGGCCTGCTGGACATGTGTTTCATTCTGGGTTGC
1 GTTCCTAGTACTAACATTCCGTGCGGACTTCAGGCATGCTGGACACGTGTTTCACTCTGGGTTGC
*
54206110 CTGCGGAGCACGCGGTCCTTTCT
66 CTACGGAGCACGCGGTCCTTTCT
** *
54206133 GTTCCTAGTACTAACATTTTGTGTGGACTTCAGGCATGCTGGACACGTGTTTCACTCTGGGTTGC
1 GTTCCTAGTACTAACATTCCGTGCGGACTTCAGGCATGCTGGACACGTGTTTCACTCTGGGTTGC
54206198 CTACGGAGCAC
66 CTACGGAGCAC
54206209 AAGGCCCCCC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 69 1.00
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.32
Consensus pattern (88 bp):
GTTCCTAGTACTAACATTCCGTGCGGACTTCAGGCATGCTGGACACGTGTTTCACTCTGGGTTGC
CTACGGAGCACGCGGTCCTTTCT
Found at i:54207269 original size:105 final size:101
Alignment explanation
Indices: 54207120--54207317 Score: 272
Period size: 105 Copynumber: 1.9 Consensus size: 101
54207110 ACACTCGTAA
** *
54207120 TGCCATAACCCAATTATGGTCTTATCATCAGGATGCCATAGCCCAGCTATGGTCTTACACGT-AT
1 TGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTTACA-GTCAA
54207184 ACATTTACTGCCATGGTCCAACCATGGTCTTATGTTTAAGG
65 ACA--T--TGCCATGGTCCAACCATGGTCTTATGTTTAAGG
* * * * *
54207225 TGCCATAACCTAGTTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTATGGTCTTACATTCAAA
1 TGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTTACAGTCAAA
54207290 CATTGCCATGGTCCAACCATGGTCTTAT
66 CATTGCCATGGTCCAACCATGGTCTTAT
54207318 CCGTCAATTC
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
101 25 0.30
103 1 0.01
104 1 0.01
105 57 0.68
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (101 bp):
TGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGCTATGGTCTTACAGTCAAA
CATTGCCATGGTCCAACCATGGTCTTATGTTTAAGG
Found at i:54211831 original size:13 final size:13
Alignment explanation
Indices: 54211813--54211858 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
54211803 TTTGACTAGG
54211813 GTCACACAGCCGT
1 GTCACACAGCCGT
54211826 GTCACACAGCCGT
1 GTCACACAGCCGT
* *
54211839 GTCATACAGCCAT
1 GTCACACAGCCGT
54211852 GTCACAC
1 GTCACAC
54211859 GCCCGTGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.26, C:0.37, G:0.20, T:0.17
Consensus pattern (13 bp):
GTCACACAGCCGT
Found at i:54211842 original size:26 final size:26
Alignment explanation
Indices: 54211813--54211866 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
54211803 TTTGACTAGG
*
54211813 GTCACACAGCCGTGTCACACAG-CCGT
1 GTCACACAGCCATGTCACAC-GCCCGT
*
54211839 GTCATACAGCCATGTCACACGCCCGT
1 GTCACACAGCCATGTCACACGCCCGT
54211865 GT
1 GT
54211867 GCTAGGCCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.19
Consensus pattern (26 bp):
GTCACACAGCCATGTCACACGCCCGT
Found at i:54213621 original size:42 final size:42
Alignment explanation
Indices: 54213569--54213651 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
54213559 AGGCCGTACA
* *
54213569 GAAGCACATAAGTA-CTAAACAGAAACCCG-TAATGGTTAAACG
1 GAAGCACATAAG-AGCTAAAC-GAAAACCGATAAGGGTTAAACG
*
54213611 GAAGCTCATAAGAGCTAAACGAAAACCGATAAGGGTTAAAC
1 GAAGCACATAAGAGCTAAACGAAAACCGATAAGGGTTAAAC
54213652 TTCAGCTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 8 0.22
42 28 0.78
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (42 bp):
GAAGCACATAAGAGCTAAACGAAAACCGATAAGGGTTAAACG
Found at i:54213659 original size:42 final size:42
Alignment explanation
Indices: 54213613--54213694 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
54213603 GTTAAACGGA
* * *
54213613 AGCTCATAAGAGCTAAAC-GAAAACCGATAAGGGTTAAACTTC
1 AGCTCAAAAGAGCTAAACTG-AAACCCAGAAGGGTTAAACTTC
*
54213655 AGCTCAAAAGAGCTGAACTGAAACCCAGAAGGGTTAAACT
1 AGCTCAAAAGAGCTAAACTGAAACCCAGAAGGGTTAAACT
54213695 GAAACTCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (42 bp):
AGCTCAAAAGAGCTAAACTGAAACCCAGAAGGGTTAAACTTC
Found at i:54213711 original size:21 final size:21
Alignment explanation
Indices: 54213603--54213739 Score: 82
Period size: 21 Copynumber: 6.6 Consensus size: 21
54213593 ACCCGTAATG
* *
54213603 GTTAAACGGAAGCTCATAAGA
1 GTTAAACTGAAACTCATAAGA
* *
54213624 GCTAAAC-GAAAAC-CGATAAGG
1 GTTAAACTG-AAACTC-ATAAGA
** * *
54213645 GTTAAACTTCAGCTCAAAAGA
1 GTTAAACTGAAACTCATAAGA
* * * * *
54213666 GCTGAACTGAAACCCAGAAGG
1 GTTAAACTGAAACTCATAAGA
*
54213687 GTTAAACTGAAACTCATATGA
1 GTTAAACTGAAACTCATAAGA
* *
54213708 GTT-AATTGAAGCTCATAAGA
1 GTTAAACTGAAACTCATAAGA
*
54213728 GCTAAACTGAAA
1 GTTAAACTGAAA
54213740 GAAAACACGG
Statistics
Matches: 82, Mismatches: 29, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
20 18 0.22
21 63 0.77
22 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
GTTAAACTGAAACTCATAAGA
Found at i:54221235 original size:14 final size:14
Alignment explanation
Indices: 54221216--54221248 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54221206 AAACTTTAAC
54221216 ATTACT-AACTCATA
1 ATTACTAAACT-ATA
54221230 ATTACTAAACTATA
1 ATTACTAAACTATA
54221244 ATTAC
1 ATTAC
54221249 AAATAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTACTAAACTATA
Found at i:54222655 original size:76 final size:76
Alignment explanation
Indices: 54222565--54222780 Score: 306
Period size: 76 Copynumber: 2.8 Consensus size: 76
54222555 CGATAGTAGA
* * * *
54222565 TGTGCCCTGCACTAGTCGAATAAATTGACAAAGATTTGCACCCAACACTAGTCAGATTAACTGAC
1 TGTGCCCAGCACTAGTTGAATAAATTGACAAAGATTTGCACCTAGCACTAGTCAGATTAACTGAC
54222630 GATATTAATTG
66 GATATTAATTG
* * * * *
54222641 TGTGCCCAGGACTAGTTGAATAAATCGACAAAGATTTACACCTAGCCCTAGTCTGATTAACTGAC
1 TGTGCCCAGCACTAGTTGAATAAATTGACAAAGATTTGCACCTAGCACTAGTCAGATTAACTGAC
54222706 GATATTAATTG
66 GATATTAATTG
* * * * *
54222717 TGTGCCCAACACTAGTTGAATAAATTGACAAAGACTTGCGCCTAGCACTAGTCGGATAAACTGA
1 TGTGCCCAGCACTAGTTGAATAAATTGACAAAGATTTGCACCTAGCACTAGTCAGATTAACTGA
54222781 TGATCACATA
Statistics
Matches: 122, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 122 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (76 bp):
TGTGCCCAGCACTAGTTGAATAAATTGACAAAGATTTGCACCTAGCACTAGTCAGATTAACTGAC
GATATTAATTG
Found at i:54235320 original size:11 final size:13
Alignment explanation
Indices: 54235304--54235337 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
54235294 AATTTTACGG
54235304 AAAAATTTCG-T-
1 AAAAATTTCGTTC
54235315 AAAAATTTCGTTC
1 AAAAATTTCGTTC
54235328 AAAAATTTCG
1 AAAAATTTCG
54235338 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:54236528 original size:103 final size:103
Alignment explanation
Indices: 54236346--54236653 Score: 481
Period size: 103 Copynumber: 3.0 Consensus size: 103
54236336 ATTGAATATG
* * * * *
54236346 AAGGGGTTGTTAAGTGCTGATTCCCTGACTCATTGGTGGTTGCTAAGTGCTGATTCCACAGTATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
54236411 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
54236449 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
54236514 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCTCC
66 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * *
54236552 AAGGGGTTGCTAAGTGTTGATTCCCCGAATGATTGGTGGTTGCTAAGTGCTGATTACACCATATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
54236617 TTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCC
54236654 GAATCACTGG
Statistics
Matches: 188, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 188 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:54241242 original size:21 final size:21
Alignment explanation
Indices: 54241216--54241257 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54241206 TATAATAATT
54241216 TAAAAATTACT-AAAATAAAAA
1 TAAAAA-TACTAAAAATAAAAA
*
54241237 TAAAAATATTAAAAATAAAAA
1 TAAAAATACTAAAAATAAAAA
54241258 ATTAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAATACTAAAAATAAAAA
Found at i:54241251 original size:16 final size:14
Alignment explanation
Indices: 54241227--54241263 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
54241217 AAAAATTACT
54241227 AAAA-TAAAAATAA
1 AAAATTAAAAATAA
54241240 AAATATTAAAAATAA
1 AAA-ATTAAAAATAA
54241255 AAAATTAAA
1 AAAATTAAA
54241264 TAAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 7 0.32
15 12 0.55
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATTAAAAATAA
Found at i:54241269 original size:16 final size:15
Alignment explanation
Indices: 54241231--54241263 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
54241221 ATTACTAAAA
54241231 TAAAAATAAAAATAT
1 TAAAAATAAAAATAT
54241246 TAAAAATAAAAA-AT
1 TAAAAATAAAAATAT
54241260 TAAA
1 TAAA
54241264 TAAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAATAAAAATAT
Done.