Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 4 of 295
Found at i:1016536 original size:14 final size:14
Alignment explanation
Indices: 1016517--1016543 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1016507 AGTGATAAGT
1016517 GACAAGCGACAAGC
1 GACAAGCGACAAGC
1016531 GACAAGCGACAAG
1 GACAAGCGACAAG
1016544 TGATAAGTGG
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:0.44, C:0.26, G:0.30, T:0.00
Consensus pattern (14 bp):
GACAAGCGACAAGC
Found at i:1016613 original size:51 final size:51
Alignment explanation
Indices: 1016531--1016644 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
1016521 AGCGACAAGC
* * *
1016531 GACAAGCGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAGT
*
1016582 GACAAGTGATAAGTGATAAGTAGTAGTTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAGT
1016633 GACAAGTGATAA
1 GACAAGTGATAA
1016645 ATGTGATCAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAGT
Found at i:1020159 original size:49 final size:49
Alignment explanation
Indices: 1020101--1020198 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
1020091 CAAACTTAAA
1020101 TTTTTCGCAAACTTATTTTCGAGTATAACAATTTTGTTTGAACCATTTT
1 TTTTTCGCAAACTTATTTTCGAGTATAACAATTTTGTTTGAACCATTTT
*
1020150 TTTTTCGCAAACTTATTTTCGAGTATAACAGTTTTGTTTGAACCATTTT
1 TTTTTCGCAAACTTATTTTCGAGTATAACAATTTTGTTTGAACCATTTT
1020199 ATATTTTAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (49 bp):
TTTTTCGCAAACTTATTTTCGAGTATAACAATTTTGTTTGAACCATTTT
Found at i:1026886 original size:20 final size:20
Alignment explanation
Indices: 1026848--1026907 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1026838 TATATTTGAA
1026848 ATAAAAAT-TTAATATATTTTT
1 ATAAAAATATTAA-A-ATTTTT
* *
1026869 GTAAAAATATTGAAATTTTT
1 ATAAAAATATTAAAATTTTT
*
1026889 ATAAATATATTAAAATTTT
1 ATAAAAATATTAAAATTTT
1026908 AAATATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 22 0.67
21 8 0.24
22 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (20 bp):
ATAAAAATATTAAAATTTTT
Found at i:1030714 original size:21 final size:21
Alignment explanation
Indices: 1030690--1030730 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1030680 TTATAGTAAG
1030690 TAAATTTTGACAATAATTAGT
1 TAAATTTTGACAATAATTAGT
1030711 TAAATTTTGACAATAATTAG
1 TAAATTTTGACAATAATTAG
1030731 ATCAAGCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (21 bp):
TAAATTTTGACAATAATTAGT
Found at i:1037997 original size:19 final size:19
Alignment explanation
Indices: 1037975--1038013 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1037965 TTTTAAATAG
* *
1037975 ATACACATGTATTAATAAT
1 ATACACATATATAAATAAT
1037994 ATACACATATATAAATAAT
1 ATACACATATATAAATAAT
1038013 A
1 A
1038014 AATAAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (19 bp):
ATACACATATATAAATAAT
Found at i:1038879 original size:15 final size:15
Alignment explanation
Indices: 1038856--1038905 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
1038846 TTTATCAAAT
1038856 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* *
1038871 TTATTTTGATTGAAT
1 TTATATTGATTGAAA
1038886 TTATATTGATTGAAA
1 TTATATTGATTGAAA
1038901 TTATA
1 TTATA
1038906 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:1039569 original size:18 final size:19
Alignment explanation
Indices: 1039548--1039588 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1039538 AATGAAATGA
1039548 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
1039566 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
1039585 GAAA
1 GAAA
1039589 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:1054150 original size:21 final size:21
Alignment explanation
Indices: 1054124--1054179 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1054114 TTATTGGTTT
*
1054124 CTTGCATATTAAGTCAAATTA
1 CTTGCAGATTAAGTCAAATTA
* *
1054145 CTTGCAGATTAGGTCAGATTA
1 CTTGCAGATTAAGTCAAATTA
*
1054166 CTTGTAGATTAAGT
1 CTTGCAGATTAAGT
1054180 AAAGCCACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (21 bp):
CTTGCAGATTAAGTCAAATTA
Found at i:1055576 original size:15 final size:17
Alignment explanation
Indices: 1055556--1055590 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1055546 TTAAAACTTT
1055556 AAATTT-AAA-TAATTC
1 AAATTTAAAATTAATTC
1055571 AAATTTAAAATTAATTC
1 AAATTTAAAATTAATTC
1055588 AAA
1 AAA
1055591 CTGATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 3 0.17
17 9 0.50
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTTAAAATTAATTC
Found at i:1055579 original size:21 final size:22
Alignment explanation
Indices: 1055544--1055584 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1055534 AAACTTGAAG
*
1055544 AATTAAAACTTTAAATTTAAAT
1 AATTAAAACTTTAAAATTAAAT
*
1055566 AATTCAAA-TTTAAAATTAA
1 AATTAAAACTTTAAAATTAA
1055585 TTCAAACTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAAAACTTTAAAATTAAAT
Found at i:1070310 original size:21 final size:21
Alignment explanation
Indices: 1070284--1070329 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1070274 AGCGGTGGCG
* *
1070284 GTGAGATTTGTTACTGTAGCA
1 GTGAGATTGGATACTGTAGCA
*
1070305 GTGAGATTGGATACTGTAGCG
1 GTGAGATTGGATACTGTAGCA
1070326 GTGA
1 GTGA
1070330 AATTAGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.33
Consensus pattern (21 bp):
GTGAGATTGGATACTGTAGCA
Found at i:1071625 original size:21 final size:21
Alignment explanation
Indices: 1071599--1071651 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1071589 AGCGGTGGCG
*
1071599 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
1071620 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
1071641 GTGAGATTAGA
1 GTGAGATTAGA
1071652 AACAGCAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.34, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:1077505 original size:21 final size:21
Alignment explanation
Indices: 1077471--1077511 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1077461 AGACGAGCAA
* * *
1077471 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTAGAGTG
1077492 TACTCCAAAACAGGTAGAGT
1 TACTCCAAAACAGGTAGAGT
1077512 TTGAGCAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTAGAGTG
Found at i:1080055 original size:19 final size:19
Alignment explanation
Indices: 1080031--1080070 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1080021 TTTGAGAAGG
1080031 TTTGAAAA-AAATTATTAAA
1 TTTGAAAATAAATT-TTAAA
*
1080050 TTTGAAAATTAATTTTAAA
1 TTTGAAAATAAATTTTAAA
1080069 TT
1 TT
1080071 AAAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTGAAAATAAATTTTAAA
Found at i:1080076 original size:19 final size:20
Alignment explanation
Indices: 1080040--1080080 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1080030 GTTTGAAAAA
**
1080040 AATTATTAAATTTGAAAATT
1 AATTATTAAATTAAAAAATT
1080060 AATT-TTAAATTAAAAAATT
1 AATTATTAAATTAAAAAATT
1080079 AA
1 AA
1080081 GTCGGCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTATTAAATTAAAAAATT
Found at i:1081378 original size:37 final size:37
Alignment explanation
Indices: 1081334--1081499 Score: 305
Period size: 37 Copynumber: 4.5 Consensus size: 37
1081324 CACTTGTCCC
1081334 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
*
1081371 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1081408 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
* *
1081445 TGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1081482 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
1081500 TAAAGCTATC
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 125 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
Found at i:1081542 original size:52 final size:52
Alignment explanation
Indices: 1081463--1081731 Score: 361
Period size: 52 Copynumber: 5.2 Consensus size: 52
1081453 TAAGTGTAGC
* * **
1081463 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1081516 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
1081568 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* * *
1081614 CACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
1081666 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1081718 CACTTTGTCACTTG
1 CACTTT-TCACTTG
1081732 ATCAGAAGTA
Statistics
Matches: 196, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
46 43 0.22
49 1 0.01
52 137 0.70
53 15 0.08
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:1081629 original size:98 final size:98
Alignment explanation
Indices: 1081463--1081723 Score: 387
Period size: 98 Copynumber: 2.6 Consensus size: 98
1081453 TAAGTGTAGC
* *
1081463 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTCCACTT
*
1081528 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* ** *
1081561 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTCCACTT
1081626 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
1081659 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTT
1081724 GTCACTTGAT
Statistics
Matches: 144, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
98 100 0.69
100 1 0.01
104 43 0.30
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:1086772 original size:16 final size:17
Alignment explanation
Indices: 1086732--1086765 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1086722 ACAAAACTGT
1086732 GACACTTTTTCTCGTGA
1 GACACTTTTTCTCGTGA
1086749 GACACTTTTTCTCGTGA
1 GACACTTTTTCTCGTGA
1086766 ACCCTTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (17 bp):
GACACTTTTTCTCGTGA
Found at i:1089442 original size:20 final size:20
Alignment explanation
Indices: 1089403--1089442 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1089393 TAGAACTTAT
*
1089403 AATTTGAAAAGTTAGTTAAA
1 AATTTGAAAAGTTAGATAAA
1089423 AATTTAGAAAAGTT-GATAAA
1 AATTT-GAAAAGTTAGATAAA
1089443 TTTTTTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
AATTTGAAAAGTTAGATAAA
Found at i:1092342 original size:22 final size:21
Alignment explanation
Indices: 1092298--1092382 Score: 64
Period size: 22 Copynumber: 3.9 Consensus size: 21
1092288 TAATTTTCTG
* **
1092298 AATTTTAAATATTATTTGATA
1 AATTTTAAAAATTATTTTTTA
1092319 AATTTTAAAAATTTATTTTTTA
1 AATTTTAAAAA-TTATTTTTTA
** *
1092341 AATAAATAAAAATATTTTTTTATA
1 AAT-TTTAAAAAT-TATTTTT-TA
1092365 ACATTTT-AAAATTATTTT
1 A-ATTTTAAAAATTATTTT
1092383 CAATATTTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
21 10 0.20
22 17 0.34
23 17 0.34
24 4 0.08
25 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (21 bp):
AATTTTAAAAATTATTTTTTA
Found at i:1100486 original size:7 final size:7
Alignment explanation
Indices: 1100474--1100507 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
1100464 ATACAAAGGC
1100474 CCCATAT
1 CCCATAT
1100481 CCCATAT
1 CCCATAT
1100488 CCCATAT
1 CCCATAT
1100495 CCCATAT
1 CCCATAT
1100502 CCCATA
1 CCCATA
1100508 CCCCCCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.26
Consensus pattern (7 bp):
CCCATAT
Found at i:1105953 original size:49 final size:49
Alignment explanation
Indices: 1105874--1105970 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
1105864 TAATTGCTCA
* * * * *
1105874 GTTAACCTTGTTGGTATGCTGATCTGTCTAATAATTAGTTTATTGGTTG
1 GTTAACCTTGCTGGCATGCTGATCTATCTAATAACTAGCTTATTGGTTG
* *
1105923 GTTATCCTTGCTGGCATGCTGATCTATCTAATAACTAGCTTGTTGGTT
1 GTTAACCTTGCTGGCATGCTGATCTATCTAATAACTAGCTTATTGGTT
1105971 TATGCTTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (49 bp):
GTTAACCTTGCTGGCATGCTGATCTATCTAATAACTAGCTTATTGGTTG
Found at i:1106058 original size:51 final size:51
Alignment explanation
Indices: 1105979--1106286 Score: 357
Period size: 51 Copynumber: 6.0 Consensus size: 51
1105969 TTTATGCTTA
* *
1105979 TTAATTGTTCGGTTAACCTTGCTGGCATGTTGATCTGTCTAATAACTAGTT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
*
1106030 TTAATTGTTTGGTTAACCTTGCTAGCATGCTGATCTGTCTAATAACTAGTT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
* * * ** *
1106081 TTAATTATTT-GTTTACACTTGTTGGCATGCTGGCCTGTCTAATAATTAGTT
1 TTAATTGTTTGGTTAAC-CTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
** * * * *
1106132 TTAATTGTTTACTTAACCTTACTGGCATGCTGACCTGTCTAACAATTAGTT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
** * * * * *
1106183 TTAATTGTTTGGTTAACCTTGCCAGTATGTTGATCTGTCTAAAAATTAATT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
** * * *
1106234 TTAATTGTTCAGTTAACCTTGCTGGCGTGCTAATCTATCTAATAACTAGTT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
1106285 TT
1 TT
1106287 TATACTATAG
Statistics
Matches: 216, Mismatches: 39, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
50 5 0.02
51 207 0.96
52 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.44
Consensus pattern (51 bp):
TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
Found at i:1106377 original size:40 final size:40
Alignment explanation
Indices: 1106326--1106450 Score: 160
Period size: 40 Copynumber: 3.1 Consensus size: 40
1106316 CGTTTGAATA
* *
1106326 AAAAACACCGCTACAGATTGAGCATTAGCGGCGCTTTTTG
1 AAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* * * * **
1106366 AAAAACGCCGCTATAGATCAAGCATTAGCTGCGCATTTCA
1 AAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* *
1106406 AAAAACACTGCTATAGATCGACCATTAGCGGCGCTTTTTG
1 AAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
1106446 AAAAA
1 AAAAA
1106451 TGCCAAAAAA
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (40 bp):
AAAAACACCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
Found at i:1106546 original size:40 final size:40
Alignment explanation
Indices: 1106501--1106610 Score: 130
Period size: 40 Copynumber: 2.8 Consensus size: 40
1106491 AGCTTTAGTG
* *
1106501 GCATTAGCAACGCTTTTTGAAAAACACCGCTATAGGTCGA
1 GCATTAGCAACGCTTTCTGAAAAACACCACTATAGGTCGA
* ** * *
1106541 GCATTAGCGACGCTTTCCAAAAAACGCCACTATAGGTTGA
1 GCATTAGCAACGCTTTCTGAAAAACACCACTATAGGTCGA
* * *
1106581 CCATTAGCAGCGCTGTCTGAAAAACACCAC
1 GCATTAGCAACGCTTTCTGAAAAACACCAC
1106611 AAAAAAATTA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (40 bp):
GCATTAGCAACGCTTTCTGAAAAACACCACTATAGGTCGA
Found at i:1106679 original size:155 final size:154
Alignment explanation
Indices: 1106347--1106879 Score: 648
Period size: 155 Copynumber: 3.5 Consensus size: 154
1106337 TACAGATTGA
* *
1106347 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCAAGCATTAGCTG-CGCATTT-CAAAAA
1 GCATTAGCAGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGC-GACGC-TTTCCAAAAA
* * * *
1106410 ACACTGCTATAGATCGACCATTAGCGGCGCTTTTTGAAAAATGCCA-AAAAAAATTAAGCACAAC
64 ACACCGCTATAGGTCGACCATTAGCAGCGC-TTTTGAAAAACGCCACAAAAAAATTAAGCACAAC
* *
1106474 GCCGTCGTTTTATGTTAAGCTTTAGTG
128 GCCATCGTTTTATGTTGAGCTTTAGTG
* * *
1106501 GCATTAGCAACGCTTTTTGAAAAACACCGCTATAGGTCGAGCATTAGCGACGCTTTCCAAAAAAC
1 GCATTAGCAGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGACGCTTTCCAAAAAAC
* * * * *
1106566 GCCACTATAGGTTGACCATTAGCAGCGCTGTCTGAAAAACACCACAAAAAAATTAAGCACAACGC
66 ACCGCTATAGGTCGACCATTAGCAGCGCT-TTTGAAAAACGCCACAAAAAAATTAAGCACAACGC
1106631 CATCGTTTTATGTTGAGCTTTAGTG
130 CATCGTTTTATGTTGAGCTTTAGTG
* * * *
1106656 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATA-AGCCGAGCATTAGCGATGCTTTCCAAAAAA
1 GCATTAGCAGCGCTTTTTGAAAAACGCCGCTATAGA-TCGAGCATTAGCGACGCTTTCC-AAAAA
* * * * *
1106720 ACTCCGCTATAGGTCAACCATTAG-TGCCGCTTTTTAGAAAACGCCAC-AAAAAATTAAACACAA
64 ACACCGCTATAGGTCGACCATTAGCAG-CGCTTTTGA-AAAACGCCACAAAAAAATTAAGCACAA
* *
1106783 CGACATCATTTTATGTTGAGCTTTAGTG
127 CGCCATCGTTTTATGTTGAGCTTTAGTG
* * * ** *
1106811 GTATTAGCAGCGATTTCTGAAAAACGCCGCTATAGAT-GAGCATTAGCGGGGCTTTCTAAAAAAC
1 GCATTAGCAGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGACGCTTTCCAAAAAAC
1106875 ACCGC
66 ACCGC
1106880 AGATAATATT
Statistics
Matches: 326, Mismatches: 44, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
153 16 0.05
154 104 0.32
155 167 0.51
156 39 0.12
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (154 bp):
GCATTAGCAGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGACGCTTTCCAAAAAAC
ACCGCTATAGGTCGACCATTAGCAGCGCTTTTGAAAAACGCCACAAAAAAATTAAGCACAACGCC
ATCGTTTTATGTTGAGCTTTAGTG
Found at i:1107666 original size:276 final size:276
Alignment explanation
Indices: 1107173--1107729 Score: 952
Period size: 276 Copynumber: 2.0 Consensus size: 276
1107163 GTTGACATGG
* *
1107173 GAATTCAGCATGATCTTCATCCTCAAGTACTTTCGAATGGGAAATATCATATGCTGCCTTCTATT
1 GAATTCAGCATGATCTTCATCCCCAAGTACTTTCGAATAGGAAATATCATATGCTGCCTTCTATT
* * * *
1107238 TTTGCAATGTCGAAGAAAGAGAAAGAAGTGCTCTGCATAGTGTTGAAGGATATATAGGTCCCAGA
66 TTTGCAATGTCGAAGAAAGAGAAAAAAATGCTCTGCATAGTATTGAAGGATATAAAGGTCCCAGA
* *
1107303 TGTGTATGCATCAAATATATTTCGATTTGTAAGTCTTAAAGATTAAAGACTATATTCTTTAAAAT
131 TATGTATGCATCAAATATATCTCGATTTGTAAGTCTTAAAGATTAAAGACTATATTCTTTAAAAT
* *
1107368 CACATGATTATCATATCTTGATGCAAGATTTACTACCAGTTGCTTTACGGTGTTGTATGTCAAAA
196 CACATGATTATCACATCTTGATGCAAGATTTACTACCAGTTGCTTTACAGTGTTGTATGTCAAAA
1107433 AAGGTGACGTCTAATA
261 AAGGTGACGTCTAATA
* * *
1107449 GAATTCAGCGTGATCTTCATCCCCAAGTACTTTCGAATAGGAAATATCGTATGCTGCTTTCTATT
1 GAATTCAGCATGATCTTCATCCCCAAGTACTTTCGAATAGGAAATATCATATGCTGCCTTCTATT
* *
1107514 TTTGCAATGTCGAAGAAAGAGAAAAAAATGTTCTGCATGGTATTGAAGGATATAAAGGTCCCAGA
66 TTTGCAATGTCGAAGAAAGAGAAAAAAATGCTCTGCATAGTATTGAAGGATATAAAGGTCCCAGA
1107579 TATGTATGCATCAAATATATCTCGATTTGTAAGTCTTAAAGATTAAAGACTATATTCTTTAAAAT
131 TATGTATGCATCAAATATATCTCGATTTGTAAGTCTTAAAGATTAAAGACTATATTCTTTAAAAT
* *
1107644 CACATGATTATCACATCTTGATGCAAGATTTACTGCCAGTTGCTTTACAGTGTTGTATGTTAAAA
196 CACATGATTATCACATCTTGATGCAAGATTTACTACCAGTTGCTTTACAGTGTTGTATGTCAAAA
1107709 AAGGTGACGTCTAATA
261 AAGGTGACGTCTAATA
*
1107725 TAATT
1 GAATT
1107730 GAACTATCCA
Statistics
Matches: 263, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
276 263 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (276 bp):
GAATTCAGCATGATCTTCATCCCCAAGTACTTTCGAATAGGAAATATCATATGCTGCCTTCTATT
TTTGCAATGTCGAAGAAAGAGAAAAAAATGCTCTGCATAGTATTGAAGGATATAAAGGTCCCAGA
TATGTATGCATCAAATATATCTCGATTTGTAAGTCTTAAAGATTAAAGACTATATTCTTTAAAAT
CACATGATTATCACATCTTGATGCAAGATTTACTACCAGTTGCTTTACAGTGTTGTATGTCAAAA
AAGGTGACGTCTAATA
Found at i:1110530 original size:14 final size:14
Alignment explanation
Indices: 1110506--1110540 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1110496 TTAAATATTT
1110506 ATAAT-GTTTAATC
1 ATAATGGTTTAATC
*
1110519 ATAATGGTTTAATT
1 ATAATGGTTTAATC
1110533 ATAATGGT
1 ATAATGGT
1110541 ATATTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (14 bp):
ATAATGGTTTAATC
Found at i:1111299 original size:43 final size:43
Alignment explanation
Indices: 1111260--1111498 Score: 239
Period size: 43 Copynumber: 5.6 Consensus size: 43
1111250 TAGAAAAGTA
*
1111260 CCGCTAAAAGTCACGTTCTTTAGCGGCATTTGTATGAAAAGCG
1 CCGCTAAAAGTCACGTTCTTTAGCGGCGTTTGTATGAAAAGCG
* * *
1111303 CCGCTATAAGTTACGTTCTTTAGCGGCGTTTTTGA-GAAAAGCG
1 CCGCTAAAAGTCACGTTCTTTAGCGGCGTTTGT-ATGAAAAGCG
* ** * *
1111346 CCGCTAAAGGTCATTTTCTTTAACGGCGTTTGTATGAAATGCG
1 CCGCTAAAAGTCACGTTCTTTAGCGGCGTTTGTATGAAAAGCG
* ** * * *
1111389 CCGTTAAAAGTCATATTCTTTAACGGCATTTTTGA-GAAAAGCG
1 CCGCTAAAAGTCACGTTCTTTAGCGGCGTTTGT-ATGAAAAGCG
* * * * * *
1111432 TCGCTAAAGGTCACATTCTTTAGCAGCGTTTGTGTGAACAGCG
1 CCGCTAAAAGTCACGTTCTTTAGCGGCGTTTGTATGAAAAGCG
* *
1111475 CCGCTAGAGGTCACGTTCTTTAGC
1 CCGCTAAAAGTCACGTTCTTTAGC
1111499 TAGGGGTGAG
Statistics
Matches: 161, Mismatches: 31, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
42 1 0.01
43 158 0.98
44 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (43 bp):
CCGCTAAAAGTCACGTTCTTTAGCGGCGTTTGTATGAAAAGCG
Found at i:1111390 original size:86 final size:85
Alignment explanation
Indices: 1111236--1111498 Score: 301
Period size: 86 Copynumber: 3.1 Consensus size: 85
1111226 TCTGCTAAAA
* * ** * * *
1111236 TTAGTGGCGTTTTTTAGAAAAGTACCGCTAAAAGTCACGTTCTTTAGCGGCATTTGTATGAAAAG
1 TTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCACATTCTTTAGCGGCGTTTGTATG-AAAG
* *
1111301 CGCCGCTATAAGTTACGTTCT
65 CGCCGCTAAAAGTCACGTTCT
** *
1111322 TTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCATTTTCTTTAACGGCGTTTGTATGAAATG
1 TTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCACATTCTTTAGCGGCGTTTGTATGAAA-G
* **
1111387 CGCCGTTAAAAGTCATATTCT
65 CGCCGCTAAAAGTCACGTTCT
* * * * *
1111408 TTAACGGCATTTTTGAGAAAAGCGTCGCTAAAGGTCACATTCTTTAGCAGCGTTTGTGTGAACAG
1 TTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCACATTCTTTAGCGGCGTTTGTATGAA-AG
* *
1111473 CGCCGCTAGAGGTCACGTTCT
65 CGCCGCTAAAAGTCACGTTCT
1111494 TTAGC
1 TTAGC
1111499 TAGGGGTGAG
Statistics
Matches: 147, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
85 3 0.02
86 143 0.97
87 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (85 bp):
TTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCACATTCTTTAGCGGCGTTTGTATGAAAGC
GCCGCTAAAAGTCACGTTCT
Found at i:1111475 original size:129 final size:129
Alignment explanation
Indices: 1111264--1111496 Score: 308
Period size: 129 Copynumber: 1.8 Consensus size: 129
1111254 AAAGTACCGC
* * * * *
1111264 TAAAAGTCACGTTCTTTAGCGGCATTTGTATGAAAAGCGCCGCTATAAGTTACGTTCTTTAGCGG
1 TAAAAGTCACATTCTTTAACGGCATTTGTATGAAAAGCGCCGCTATAAGTCACATTCTTTAGCAG
* **
1111329 CGTTTTTGAGAAAAGCGCCGCTAAAGGTCATTTTCTTTAACGGCGTTTGTATGAAATGCGCCGT
66 CGTTTGTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAACGGCGTTTGTATGAAATGCGCCGT
* * *
1111393 TAAAAGTCATATTCTTTAACGGCATTTTTGA-GAAAAGCGTCGCTA-AAGGTCACATTCTTTAGC
1 TAAAAGTCACATTCTTTAACGGCATTTGT-ATGAAAAGCGCCGCTATAA-GTCACATTCTTTAGC
* * *
1111456 AGCGTTTGTGTGAACAGCGCCGCTAGAGGTCACGTTCTTTA
64 AGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTA
1111497 GCTAGGGGTG
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
128 2 0.02
129 85 0.97
130 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (129 bp):
TAAAAGTCACATTCTTTAACGGCATTTGTATGAAAAGCGCCGCTATAAGTCACATTCTTTAGCAG
CGTTTGTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAACGGCGTTTGTATGAAATGCGCCGT
Found at i:1112310 original size:67 final size:68
Alignment explanation
Indices: 1112201--1112341 Score: 169
Period size: 67 Copynumber: 2.1 Consensus size: 68
1112191 ATAACTAATT
* * * *
1112201 TTAATTGTTTTGGTTAATCTTGCTAACATGCTGATCTGTCTAATAATT-AGTTTGTTGGTTCATG
1 TTAATTGTTTTGGTTAATCTTGCTAACATGCTAACCTGTCTAATAATTGA-TTTATTAGTTCATG
*
1112265 CTTG
65 CTTA
* ** * *
1112269 TTAATTG-TTTGGTTGATCTTGCTGGCCTGCTAACCTGTCTAATAATTGATTTATTAGTTTATGC
1 TTAATTGTTTTGGTTAATCTTGCTAACATGCTAACCTGTCTAATAATTGATTTATTAGTTCATGC
1112333 TTA
66 TTA
1112336 TTAATT
1 TTAATT
1112342 TCTCGGTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
67 54 0.87
68 8 0.13
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (68 bp):
TTAATTGTTTTGGTTAATCTTGCTAACATGCTAACCTGTCTAATAATTGATTTATTAGTTCATGC
TTA
Found at i:1122122 original size:64 final size:64
Alignment explanation
Indices: 1122021--1122151 Score: 226
Period size: 64 Copynumber: 2.0 Consensus size: 64
1122011 AGGTCATCCA
* * *
1122021 TTAATAAGAGTCTCAACTAAGTTGGGGAATTACTAAAAAAAGATCAATTTTTAACAAAAATAAG
1 TTAATAAGAGACTCAACTAAGTTAGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
*
1122085 TTAATCAGAGACTCAACTAAGTTAGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
1 TTAATAAGAGACTCAACTAAGTTAGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
1122149 TTA
1 TTA
1122152 TATGAATATG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (64 bp):
TTAATAAGAGACTCAACTAAGTTAGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
Found at i:1129042 original size:21 final size:22
Alignment explanation
Indices: 1129017--1129057 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1129007 TTATTATTTT
1129017 ATAATAAAAATA-GAAAAATAA
1 ATAATAAAAATAGGAAAAATAA
*
1129038 ATAATCAAAATAGGAAAAAT
1 ATAATAAAAATAGGAAAAAT
1129058 TAGTTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (22 bp):
ATAATAAAAATAGGAAAAATAA
Found at i:1137989 original size:30 final size:29
Alignment explanation
Indices: 1137953--1138023 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
1137943 ACAAATGAAT
* **
1137953 CTAAATTTTTAAATTTGAAATGTAGAGAGA
1 CTAAATTTCTAAAAATGAAA-GTAGAGAGA
*
1137983 CTAAATTTCTAAAAATGAAAGTATAGAGA
1 CTAAATTTCTAAAAATGAAAGTAGAGAGA
*
1138012 TTAAA-TTCTAAA
1 CTAAATTTCTAAA
1138024 TATACAGAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 7 0.19
29 12 0.33
30 17 0.47
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.34
Consensus pattern (29 bp):
CTAAATTTCTAAAAATGAAAGTAGAGAGA
Found at i:1141345 original size:21 final size:21
Alignment explanation
Indices: 1141303--1141345 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1141293 ACTAATACGT
**
1141303 ATTTATGTCTGTAATCTGTAA
1 ATTTATGTCTGTAATCCATAA
* *
1141324 ATTTATGTTTGTTATCCATAA
1 ATTTATGTCTGTAATCCATAA
1141345 A
1 A
1141346 AATAAAACAA
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:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (21 bp):
ATTTATGTCTGTAATCCATAA
Found at i:1146188 original size:40 final size:39
Alignment explanation
Indices: 1146138--1146217 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 39
1146128 GAAGATTTGT
* *
1146138 TTCAGTTGTTACCCTACTGCTTAGGGGGTAAGATCTGTAA
1 TTCAGCTGTTACCCTACTGCTTAGGGGATAAGAT-TGTAA
1146178 TTCAGCTGTTACCCTACTGCTTAGGGGATAAGATTGTAA
1 TTCAGCTGTTACCCTACTGCTTAGGGGATAAGATTGTAA
1146217 T
1 T
1146218 CTTCGATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 6 0.16
40 32 0.84
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (39 bp):
TTCAGCTGTTACCCTACTGCTTAGGGGATAAGATTGTAA
Found at i:1146486 original size:44 final size:45
Alignment explanation
Indices: 1146299--1146893 Score: 513
Period size: 44 Copynumber: 13.5 Consensus size: 45
1146289 GGGAGGTAAA
* * ** * * *
1146299 ATCTGCCATCTTCGATCTGCTTCGTTGCCAAATACAGGAAGGCAAG
1 ATCTGCTATCTTCGATCTACTTCACTACC-AATATAGGAAGACAAG
* * * * * *
1146345 ATCTGC-ATCCTCAATCTA-TTCCACTGTCAAATACAGG--GATAAG
1 ATCTGCTATCTTCGATCTACTT-CACT-ACCAATATAGGAAGACAAG
* * * *
1146388 ATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * * *
1146433 ATTTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
1146476 ACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * *
1146520 ATCTACT-TCCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTAT-CTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
1146565 ATCTG-TATTTTCGATCCACTTC-CTACCAATATAGGAAGACAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
1146608 ATCAGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
1146652 ATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
1146697 ATCTGC-ATCTTCGATCCATTTC-CTACCAATATAGGAAGACAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
1146740 ATCAGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
1146784 ATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
1146829 ATCTGC-ATCTTCGATCCA-TTC-CTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
*
1146871 ATCAGCTATCTTCGATCTACTTC
1 ATCTGCTATCTTCGATCTACTTC
1146894 TTGCCCGGGA
Statistics
Matches: 434, Mismatches: 96, Indels: 40
0.76 0.17 0.07
Matches are distributed among these distances:
42 22 0.05
43 94 0.22
44 216 0.50
45 95 0.22
46 7 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
Found at i:1146595 original size:132 final size:132
Alignment explanation
Indices: 1146385--1146893 Score: 851
Period size: 132 Copynumber: 3.9 Consensus size: 132
1146375 ATACAGGGAT
* * * * * *
1146385 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATTTGTATCTTGGATCC
1 AAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
* * * *
1146450 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGACAGGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
1146515 AC
131 AC
* * * *
1146517 AAGATCTACT-TCCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATTTTCGATC
1 AAGATCTGCTCT-CTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATC
1146581 CACTTCCTACCAATATAGGAAGACAGGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAA
65 CACTTCCTACCAATATAGGAAGACAGGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAA
1146646 GAC
130 GAC
1146649 AAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
*
1146714 ATTTCCTACCAATATAGGAAGACAGGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGACAGGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
1146779 AC
131 AC
1146781 AAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
*
1146846 A-TTCCTACCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTC
66 ACTTCCTACCAATATAGGAAGACAGGATCAGCTATCTTCGATCTACTTC
1146894 TTGCCCGGGA
Statistics
Matches: 358, Mismatches: 17, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
131 47 0.13
132 310 0.87
133 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
AAGATCTGCTCTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
ACTTCCTACCAATATAGGAAGACAGGATCAGCTATCTTCGATCTACTTCACGCCAATACATGAAG
AC
Found at i:1147070 original size:42 final size:42
Alignment explanation
Indices: 1146971--1147122 Score: 155
Period size: 42 Copynumber: 3.5 Consensus size: 42
1146961 CTGCTTGCTG
* * *
1146971 CCAATACAGGAAGGCAAGATCTGCAATCTTCGATCTACTTCGCCA
1 CCAATACAGGAA-GAAAGATCTGTAA-CTTCGATCTACTTC-ACA
** *
1147016 CCAATATGGGAAGAAAGATCTGTAACTTCGATCCACTTC-CTA
1 CCAATACAGGAAGAAAGATCTGTAACTTCGATCTACTTCAC-A
* *
1147058 CCAATATAGGAAGATAGATCTGCT-ACTTCGATCTACTTCACA
1 CCAATACAGGAAGAAAGATCTG-TAACTTCGATCTACTTCACA
*
1147100 CCAATACATGAAGACAAGATCTG
1 CCAATACAGGAAGA-AAGATCTG
1147123 CTTTCTTGAC
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.01
42 48 0.52
43 22 0.24
44 11 0.12
45 10 0.11
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (42 bp):
CCAATACAGGAAGAAAGATCTGTAACTTCGATCTACTTCACA
Found at i:1148046 original size:1 final size:1
Alignment explanation
Indices: 1148040--1148069 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1148030 GCCTCTCCCC
1148040 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1148070 AGGCAAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1171001 original size:11 final size:11
Alignment explanation
Indices: 1170985--1171009 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1170975 CCTTAGGGGT
1170985 TTTTTTTTTTG
1 TTTTTTTTTTG
1170996 TTTTTTTTTTG
1 TTTTTTTTTTG
1171007 TTT
1 TTT
1171010 AAATAAATTA
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:1172300 original size:12 final size:12
Alignment explanation
Indices: 1172278--1172306 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1172268 TAATAATAAA
1172278 TTAAT-GTTTAT
1 TTAATAGTTTAT
1172289 TTAATAGTTTAT
1 TTAATAGTTTAT
1172301 TTAATA
1 TTAATA
1172307 TAATAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
TTAATAGTTTAT
Found at i:1173619 original size:3 final size:3
Alignment explanation
Indices: 1173611--1173637 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1173601 TTGAGACAAA
1173611 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1173638 TGACTAACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1173696 original size:28 final size:30
Alignment explanation
Indices: 1173637--1173696 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
1173627 TTATTATTAT
* *
1173637 TTGACTAACTGACTTTATTACATTTACTTA
1 TTGACTAACTGAATTTATTACATTTACATA
1173667 TTGACTAA-TGAATTT-TTA-ACTTTACATA
1 TTGACTAACTGAATTTATTACA-TTTACATA
1173695 TT
1 TT
1173697 ATGTTGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 12 0.44
29 6 0.22
30 8 0.30
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (30 bp):
TTGACTAACTGAATTTATTACATTTACATA
Found at i:1175898 original size:13 final size:13
Alignment explanation
Indices: 1175880--1175908 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1175870 TTTAGATGAT
1175880 TTTCCTTTCTGCC
1 TTTCCTTTCTGCC
1175893 TTTCCTTTCTGCC
1 TTTCCTTTCTGCC
1175906 TTT
1 TTT
1175909 GTGATGTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.34, G:0.07, T:0.59
Consensus pattern (13 bp):
TTTCCTTTCTGCC
Found at i:1181042 original size:22 final size:23
Alignment explanation
Indices: 1181015--1181071 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1181005 TTTAATATTT
*
1181015 TAAAAATTATATTTTTACTATCA
1 TAAAAATTACATTTTTACTATCA
*
1181038 TAAAAATTACATTTTTACTATTA
1 TAAAAATTACATTTTTACTATCA
1181061 TAAAAATTACA
1 TAAAAATTACA
1181072 ATTTAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAAATTACATTTTTACTATCA
Found at i:1185377 original size:16 final size:16
Alignment explanation
Indices: 1185337--1185382 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1185327 GTGAAATGAT
1185337 TTGGATAAAAATATAAA
1 TTGGATAAAAA-ATAAA
*
1185354 TTCG---AAAAATAAA
1 TTGGATAAAAAATAAA
1185367 TTGGATAAAAAATAAA
1 TTGGATAAAAAATAAA
1185383 ACTTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
13 8 0.33
14 4 0.17
16 9 0.38
17 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (16 bp):
TTGGATAAAAAATAAA
Found at i:1188877 original size:19 final size:19
Alignment explanation
Indices: 1188839--1188879 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1188829 ATCAGCATGA
*
1188839 GGTACACGTGTTATTATTT
1 GGTACACGTGTTACTATTT
*
1188858 GGTACACGTGTTACTGTTT
1 GGTACACGTGTTACTATTT
1188877 GGT
1 GGT
1188880 TATTTCCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (19 bp):
GGTACACGTGTTACTATTT
Found at i:1194397 original size:16 final size:16
Alignment explanation
Indices: 1194362--1194394 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1194352 TTAATTTTTT
*
1194362 AATTTAAAATATATAA
1 AATTCAAAATATATAA
1194378 AATTCAAAAT-TATAA
1 AATTCAAAATATATAA
1194393 AA
1 AA
1194395 ATTATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTCAAAATATATAA
Found at i:1195230 original size:6 final size:7
Alignment explanation
Indices: 1195213--1195237 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1195203 ATTAACATAA
1195213 AAAAAAT
1 AAAAAAT
1195220 AAAAAAT
1 AAAAAAT
1195227 AAAAAAT
1 AAAAAAT
1195234 AAAA
1 AAAA
1195238 CATAGGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1211173 original size:13 final size:14
Alignment explanation
Indices: 1211155--1211185 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1211145 ATATTTTAGG
1211155 AAAAAC-AAAAATA
1 AAAAACAAAAAATA
1211168 AAAAACAAAAAATA
1 AAAAACAAAAAATA
1211182 AAAA
1 AAAA
1211186 TATATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (14 bp):
AAAAACAAAAAATA
Found at i:1219539 original size:35 final size:36
Alignment explanation
Indices: 1219477--1219550 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 36
1219467 TATAATTTTT
1219477 TAATATTTTTTTAAAAAAATTCATAAA-TATTTTTAAA
1 TAATATTTTTTT-AAAAAATTCATAAATTA-TTTTAAA
* **
1219514 TAATATTTTTTT-AAGAATTTTTAAATTATTTTAAA
1 TAATATTTTTTTAAAAAATTCATAAATTATTTTAAA
1219549 TA
1 TA
1219551 TACAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 19 0.58
36 2 0.06
37 12 0.36
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
TAATATTTTTTTAAAAAATTCATAAATTATTTTAAA
Found at i:1226293 original size:17 final size:17
Alignment explanation
Indices: 1226271--1226307 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1226261 TAAAATCAAC
1226271 AAATTAGTGTTAAAATA
1 AAATTAGTGTTAAAATA
1226288 AAATTAGTGTTAAAATA
1 AAATTAGTGTTAAAATA
1226305 AAA
1 AAA
1226308 AATTGTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (17 bp):
AAATTAGTGTTAAAATA
Found at i:1234811 original size:20 final size:20
Alignment explanation
Indices: 1234779--1234821 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1234769 TTCAAAATAA
1234779 TTATTTTAGGTTG-AGATTAT
1 TTATTTTAGGTTGAAG-TTAT
1234799 TTATTTT-GAGTTGAAGTTAT
1 TTATTTTAG-GTTGAAGTTAT
1234819 TTA
1 TTA
1234822 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.05
20 18 0.86
21 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (20 bp):
TTATTTTAGGTTGAAGTTAT
Found at i:1234882 original size:39 final size:40
Alignment explanation
Indices: 1234799--1234884 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 40
1234789 TTGAGATTAT
* *
1234799 TTATTTTGAGTTGAAGTTATTTAAATTTTTTTATTTTCATA
1 TTATTTTGAGTT-AAGTTATTTAAATTATTTCATTTTCATA
* *
1234840 TTATTTTGAGTT-ATTTATTTAAATTATTTCATGTTTGA-A
1 TTATTTTGAGTTAAGTTATTTAAATTATTTCAT-TTTCATA
1234879 TTATTT
1 TTATTT
1234885 AAGGTTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
39 24 0.60
40 4 0.10
41 12 0.30
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (40 bp):
TTATTTTGAGTTAAGTTATTTAAATTATTTCATTTTCATA
Found at i:1241092 original size:8 final size:8
Alignment explanation
Indices: 1241079--1241107 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1241069 TTATGTTTAG
1241079 TATATTAT
1 TATATTAT
1241087 TATATTAT
1 TATATTAT
1241095 TATATTAT
1 TATATTAT
1241103 TATAT
1 TATAT
1241108 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:1241140 original size:5 final size:5
Alignment explanation
Indices: 1241130--1241166 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
1241120 TTATGTTTTA
1241130 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1241167 AAACTAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:1242453 original size:15 final size:15
Alignment explanation
Indices: 1242433--1242489 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
1242423 CGATGAATTT
*
1242433 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
1242448 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
1242463 ATTGAAATTATATTG
1 ATTGAAATTATATTG
1242478 ATTG-AATTATAT
1 ATTGAAATTATAT
1242490 AATATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 8 0.21
15 31 0.79
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:1242894 original size:23 final size:23
Alignment explanation
Indices: 1242864--1242950 Score: 65
Period size: 21 Copynumber: 4.0 Consensus size: 23
1242854 GCTTTATCGA
*
1242864 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTCATGTGTCGTATT
* * *
1242887 TCAGGCACCTCGTGTGTTGTA--
1 TCAGGCACTTCATGTGTCGTATT
* *
1242908 TCAGGCACATCGTGTGTCGT-TT
1 TCAGGCACTTCATGTGTCGTATT
* * *
1242930 T-AGACACTTTATTTGTCGTAT
1 TCAGGCACTTCATGTGTCGTAT
1242951 ACTGATCAGG
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
21 31 0.62
22 2 0.04
23 17 0.34
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (23 bp):
TCAGGCACTTCATGTGTCGTATT
Found at i:1244303 original size:13 final size:13
Alignment explanation
Indices: 1244287--1244311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1244277 ATATTCCCAC
1244287 ATTATTTTGTATG
1 ATTATTTTGTATG
1244300 ATTATTTTGTAT
1 ATTATTTTGTAT
1244312 ATAAATGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
ATTATTTTGTATG
Found at i:1247544 original size:28 final size:28
Alignment explanation
Indices: 1247513--1247574 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1247503 TAGTATAATC
* * *
1247513 GATTAACTGTTTGAAATTAAAATACCGA
1 GATTAACCGTTTCAAATTAAAATACAGA
*
1247541 GATTAACCGTTTCAAATTAAAATATAGA
1 GATTAACCGTTTCAAATTAAAATACAGA
1247569 GATTAA
1 GATTAA
1247575 ATCTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (28 bp):
GATTAACCGTTTCAAATTAAAATACAGA
Found at i:1252017 original size:11 final size:11
Alignment explanation
Indices: 1252001--1252030 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1251991 CAATAATTAC
1252001 ATATATATATA
1 ATATATATATA
1252012 ATATATATATA
1 ATATATATATA
1252023 ATATATAT
1 ATATATAT
1252031 TTTGATTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATATATATA
Found at i:1252510 original size:17 final size:17
Alignment explanation
Indices: 1252471--1252512 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1252461 TGATGAAAAC
*
1252471 ATTTTTTATTGTTTTCT
1 ATTTTTTATTATTTTCT
*
1252488 AATTTTTATATATTTT-T
1 ATTTTTTAT-TATTTTCT
1252505 ATTTTTTA
1 ATTTTTTA
1252513 AAAATCATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTTTATTATTTTCT
Found at i:1261867 original size:19 final size:19
Alignment explanation
Indices: 1261843--1261881 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1261833 AACTTAAAAT
1261843 CTCAATCCATGAGGATAAG
1 CTCAATCCATGAGGATAAG
1261862 CTCAATCCATGAGGATAAG
1 CTCAATCCATGAGGATAAG
1261881 C
1 C
1261882 CCATGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (19 bp):
CTCAATCCATGAGGATAAG
Found at i:1262705 original size:72 final size:72
Alignment explanation
Indices: 1262588--1262800 Score: 372
Period size: 72 Copynumber: 3.0 Consensus size: 72
1262578 GAGCAAGAAA
*
1262588 AGACCCCTTACTATAGTAAGGGGCCCTTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1 AGACCCCTTACTATAGTAAGGGGCCATTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1262653 ATACCTC
66 ATACCTC
* * * * *
1262660 AGACCCCTTACTATAGTAAGGGGCCTTTTCTTCCAAGATGCCGGGTGCACAAGAACGCCCAACCT
1 AGACCCCTTACTATAGTAAGGGGCCATTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1262725 ATACCTC
66 ATACCTC
1262732 AGACCCCTTACTATAGTAAGGGGCCATTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1 AGACCCCTTACTATAGTAAGGGGCCATTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
1262797 ATAC
66 ATAC
1262801 AAGAGATTTC
Statistics
Matches: 131, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 131 1.00
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.21
Consensus pattern (72 bp):
AGACCCCTTACTATAGTAAGGGGCCATTTCTTGCAGGATGCCGGGTGCGCAGGAACGCCCAACCT
ATACCTC
Found at i:1266402 original size:23 final size:24
Alignment explanation
Indices: 1266371--1266415 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1266361 TTCGAGAATT
*
1266371 ATTTGAATAAATAATTA-AAAATA
1 ATTTAAATAAATAATTAGAAAATA
*
1266394 ATTTAAATAAGTAATTAGAAAA
1 ATTTAAATAAATAATTAGAAAA
1266416 GACTTGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (24 bp):
ATTTAAATAAATAATTAGAAAATA
Found at i:1272565 original size:180 final size:177
Alignment explanation
Indices: 1272068--1272761 Score: 760
Period size: 180 Copynumber: 4.0 Consensus size: 177
1272058 CAAAGCTGTC
* *
1272068 AAAAATGACCCAATTTCTAAATTAAAACAAATAGAAATACAAAGTACACAATTTTTTTCAAATAC
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAATACAAAGTAAAC-ATTTTTTTCAAATAC
* * * * * *
1272133 CCTTTGTACATTTTTTTTATAAACCTTATTAATTATTTA-AACTTTTTCCAGTACTTTCTCAGGA
65 CCTTTGTACAATTTTTAT-TAAACCTTATTAATT-TCTACAAC-TTCTCCACTACTTTCTCAGCA
*
1272197 AACAAACACCAAATAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCC-A
127 AACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
* * * * *
1272247 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAACACAAAGCAAGCA-CTTCTTCAAATAC
1 AAAAATGACCCAATTTCTAAATTAAAACACATAG-AAATACAAAGTAAACATTTTTTTCAAATAC
* * * * * * *
1272311 CGTTTGCAGAATATTTTA-TAAACCTTACTAATTTGTACAACTTCCCCTCTACTTTCTCAGCAAA
65 CCTTTGTACAAT-TTTTATTAAACCTTATTAATTTCTACAACTTCTCCACTACTTTCTCAGCAAA
* * * *
1272375 CAAACACCAAGTAATGGCGGGTAATTAAAGAGTACCACAAAACCGCCAA
129 CAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
* * * *
1272424 AAAAAGGACCCAATTTCTAATTTAAAACACATACAAAGTACAAAGTAAACATTTTTTTTCTAATA
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAA-TACAAAGTAAACA-TTTTTTTCAAATA
* *
1272489 CCCTTTGTATAATTTTTATTAAACCTTATTAATTTCAACAACTTCTCCGACTACTTTCTCAGCAA
64 CCCTTTGTACAATTTTTATTAAACCTTATTAATTTCTACAACTTCTCC-ACTACTTTCTCAGCAA
* * *
1272554 ACAAACACCAAGTAATGGTGAGTAATTAAAAAGCACCTCAAAGCTGCCAA
128 ACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
*
1272604 AAAAATGACCCAATTTCTAAATTCAAACACATAG----A-AAA-T--AC---TTTTTCAAATACC
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAATACAAAGTAAACATTTTTTTCAAATACC
* * * *
1272658 CTTTGCT-C-ATTTTT-TTATGAACCTTATTAAATTGT-TAACTTTTCCCACTACTTTCTCAGCA
66 CTTTG-TACAATTTTTATTA--AACCTTATTAATTTCTACAACTTCT-CCACTACTTTCTCAGCA
* * *
1272719 AACAAACACCAAGTAATGATGGCTAACTAAAGAGTACCTCAAA
127 AACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAA
1272762 CAAGGCCATC
Statistics
Matches: 437, Mismatches: 65, Indels: 39
0.81 0.12 0.07
Matches are distributed among these distances:
165 3 0.01
166 64 0.15
167 32 0.07
168 1 0.00
171 2 0.00
173 1 0.00
174 3 0.01
175 1 0.00
176 66 0.15
177 59 0.14
178 24 0.05
179 82 0.19
180 99 0.23
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (177 bp):
AAAAATGACCCAATTTCTAAATTAAAACACATAGAAATACAAAGTAAACATTTTTTTCAAATACC
CTTTGTACAATTTTTATTAAACCTTATTAATTTCTACAACTTCTCCACTACTTTCTCAGCAAACA
AACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
Found at i:1283808 original size:3 final size:3
Alignment explanation
Indices: 1283800--1283824 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1283790 ACTTAATCTC
1283800 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1283825 CTTTGCCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1295786 original size:21 final size:22
Alignment explanation
Indices: 1295760--1295808 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1295750 TTTAGTGAAT
1295760 TATTATTTAATGATTAA-AAAA
1 TATTATTTAATGATTAATAAAA
* **
1295781 TATTATTTTATTTTTAATAAAA
1 TATTATTTAATGATTAATAAAA
1295803 TATTAT
1 TATTAT
1295809 AAATAAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TATTATTTAATGATTAATAAAA
Found at i:1296487 original size:167 final size:170
Alignment explanation
Indices: 1296207--1296520 Score: 573
Period size: 167 Copynumber: 1.9 Consensus size: 170
1296197 AATAAGTTAT
*
1296207 TTTTAGTTATTGTACATTTCAAAATTTAAATTTTAATCATGATCCAAACAATACTTATTAAATAT
1 TTTTAGTCATTGTACATTTCAAAATTTAAATTTTAATCATGATCCAAACAATACTTATTAAATAT
1296272 GTTTGGTTAAATTTTGTAATGTATCTTACGCTATGCTAAAATTAGATTTAGTCTATATTCGGGAT
66 GTTTGGTTAAATTTTGTAATGTATCTTACGCTATGCTAAAATTAGATTTAGTCTATATT-GGGAT
1296337 GTAGATAAGGGCACGCACCCCCATCCAATGGTAAATATGCC
130 GTAGATAAGGGCACGCACCCCCATCCAATGGTAAATATGCC
1296378 TTTTAGTCATTGTACATTT-AAAATTTAAATTTTAATCATGAT-CAAACAATAC-T-TTAAATAT
1 TTTTAGTCATTGTACATTTCAAAATTTAAATTTTAATCATGATCCAAACAATACTTATTAAATAT
1296439 GTTTGGTTAAATTTTGTAATGTATCTTACGCTATGCTAAAATTAGATTTAGTCTATATTGGGATG
66 GTTTGGTTAAATTTTGTAATGTATCTTACGCTATGCTAAAATTAGATTTAGTCTATATTGGGATG
*
1296504 TAGATAAGGGCATGCAC
131 TAGATAAGGGCACGCAC
1296521 GTAAATATGC
Statistics
Matches: 141, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
166 22 0.16
167 67 0.48
168 1 0.01
169 10 0.07
170 23 0.16
171 18 0.13
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (170 bp):
TTTTAGTCATTGTACATTTCAAAATTTAAATTTTAATCATGATCCAAACAATACTTATTAAATAT
GTTTGGTTAAATTTTGTAATGTATCTTACGCTATGCTAAAATTAGATTTAGTCTATATTGGGATG
TAGATAAGGGCACGCACCCCCATCCAATGGTAAATATGCC
Found at i:1310772 original size:19 final size:19
Alignment explanation
Indices: 1310750--1310788 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1310740 TAGATAGATG
1310750 ATAATTGAATTAAGGTTGT
1 ATAATTGAATTAAGGTTGT
1310769 ATAATTGAATTAAGGTTGT
1 ATAATTGAATTAAGGTTGT
1310788 A
1 A
1310789 CTCTTTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (19 bp):
ATAATTGAATTAAGGTTGT
Found at i:1311795 original size:22 final size:22
Alignment explanation
Indices: 1311767--1311810 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1311757 AGGCCCCAAT
1311767 GTTGGAATAATTGATTAGTTTA
1 GTTGGAATAATTGATTAGTTTA
1311789 GTTGGAATAATTGATTAGTTTA
1 GTTGGAATAATTGATTAGTTTA
1311811 AGTCCTAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (22 bp):
GTTGGAATAATTGATTAGTTTA
Found at i:1316444 original size:3 final size:3
Alignment explanation
Indices: 1316436--1316480 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1316426 AGTATAAAGG
1316436 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1316481 ACTGTGAGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1318454 original size:38 final size:38
Alignment explanation
Indices: 1318341--1318456 Score: 144
Period size: 38 Copynumber: 3.1 Consensus size: 38
1318331 ATTCTTACAT
* * * *
1318341 TAAATCGATAAATCCAATTCAATCTAAAATATAAAAGA
1 TAAATCAATAAATCTAATTCAATCCAAAATATAAAAGG
* *
1318379 TTAATCAATAAAT-TCAATTCAATTCAAAATATAAAAGG
1 TAAATCAATAAATCT-AATTCAATCCAAAATATAAAAGG
* *
1318417 TAAATCAATAAATCTGATTCGATCCAAAATATAAAAGG
1 TAAATCAATAAATCTAATTCAATCCAAAATATAAAAGG
1318455 TA
1 TA
1318457 GAATAAAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
38 65 0.98
39 1 0.02
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (38 bp):
TAAATCAATAAATCTAATTCAATCCAAAATATAAAAGG
Found at i:1318789 original size:31 final size:33
Alignment explanation
Indices: 1318754--1318825 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
1318744 TTAGTCCTTA
1318754 AAGTTTAAACCCTAAAATGAGAA-TA-ATTGTC
1 AAGTTTAAACCCTAAAATGAGAATTATATTGTC
** ** *
1318785 AAGTTTAGGCTTTAATATGAGAATTATATTGTC
1 AAGTTTAAACCCTAAAATGAGAATTATATTGTC
1318818 AAGTTTAA
1 AAGTTTAA
1318826 GGATTAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 18 0.55
32 2 0.06
33 13 0.39
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (33 bp):
AAGTTTAAACCCTAAAATGAGAATTATATTGTC
Found at i:1318833 original size:33 final size:31
Alignment explanation
Indices: 1318770--1318833 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 31
1318760 AAACCCTAAA
*
1318770 ATGAGAATAATTGTCAAGTTTAGGCTTTAAT
1 ATGAGAATAATTGTCAAGTTTAGGCATTAAT
1318801 ATGAGAATTATATTGTCAAGTTTAAGG-ATTAAT
1 ATGAGAA-TA-ATTGTCAAGTTT-AGGCATTAAT
1318834 TTGGACCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.24
32 2 0.07
33 17 0.59
34 3 0.10
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.39
Consensus pattern (31 bp):
ATGAGAATAATTGTCAAGTTTAGGCATTAAT
Found at i:1320227 original size:18 final size:18
Alignment explanation
Indices: 1320177--1320227 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1320167 GGAAAAAAAA
* *
1320177 TAGTAATAATAAAAGGGT
1 TAGTAATAATAGAGGGGT
* *
1320195 TAGTTCATCAT-GAGGGGT
1 TAG-TAATAATAGAGGGGT
1320213 TAGTAATAATAGAGG
1 TAGTAATAATAGAGG
1320228 CACTTGGTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.29
Consensus pattern (18 bp):
TAGTAATAATAGAGGGGT
Found at i:1321494 original size:18 final size:18
Alignment explanation
Indices: 1321458--1321496 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1321448 ATTATATCAG
1321458 TAAAATTTAATTCGAATT
1 TAAAATTTAATTCGAATT
*
1321476 TAAATATTTAATTCGATTT
1 TAAA-ATTTAATTCGAATT
1321495 TA
1 TA
1321497 TTATAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
TAAAATTTAATTCGAATT
Found at i:1327707 original size:19 final size:19
Alignment explanation
Indices: 1327677--1327747 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
1327667 TTAGAAATTT
1327677 TTTTGAAATTTTTATAAATA
1 TTTT-AAATTTTTATAAATA
* *
1327697 TTTTGAA-TTTTAAAAATTA
1 TTTTAAATTTTTATAAA-TA
1327716 TTTTAAATTTTT-TAAAATAA
1 TTTTAAATTTTTAT-AAAT-A
1327736 TTTTAAATTTTT
1 TTTTAAATTTTT
1327748 GTTGAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
18 8 0.19
19 11 0.26
20 24 0.56
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTAAATTTTTATAAATA
Found at i:1327707 original size:39 final size:39
Alignment explanation
Indices: 1327664--1327746 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 39
1327654 CTTTACATAT
* * *
1327664 ATTTTAGAAATTTTTTTGAAA-TTTTTATAAAT-ATTTTGA
1 ATTTTAAAAATTATTTT-AAATTTTTTA-AAATAATTTTAA
1327703 ATTTTAAAAATTATTTTAAATTTTTTAAAATAATTTTAA
1 ATTTTAAAAATTATTTTAAATTTTTTAAAATAATTTTAA
1327742 ATTTT
1 ATTTT
1327747 TGTTGAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
38 7 0.18
39 32 0.82
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (39 bp):
ATTTTAAAAATTATTTTAAATTTTTTAAAATAATTTTAA
Found at i:1327865 original size:19 final size:19
Alignment explanation
Indices: 1327828--1327865 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1327818 CGAATTATGA
*
1327828 AATTCGAATTAACTCAAAT
1 AATTCGAATTAACTAAAAT
1327847 AATTCGAA-TAACTTAAAAT
1 AATTCGAATTAAC-TAAAAT
1327866 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (19 bp):
AATTCGAATTAACTAAAAT
Found at i:1329447 original size:13 final size:14
Alignment explanation
Indices: 1329429--1329468 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
1329419 ATTGAAAGTC
1329429 TTTTTAATAAATA-
1 TTTTTAATAAATAT
1329442 TTTTTAA-AAATAT
1 TTTTTAATAAATAT
1329455 TTTTTAAGTAAATA
1 TTTTTAA-TAAATA
1329469 AAAATTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
15 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TTTTTAATAAATAT
Found at i:1330540 original size:29 final size:29
Alignment explanation
Indices: 1330447--1330548 Score: 109
Period size: 29 Copynumber: 3.5 Consensus size: 29
1330437 ATGTGTATAT
*
1330447 TATATGCGAGCCTATATGTGAACCTTAGAA
1 TATATGCAAGCCTATATGTGAACCTTA-AA
**
1330477 T-TATGCAAGGTTATATGTGAACCTTAAGA
1 TATATGCAAGCCTATATGTGAACCTTAA-A
* * *
1330506 -ACATGCAAGCCTACATGTGAACCCTAAA
1 TATATGCAAGCCTATATGTGAACCTTAAA
*
1330534 TATATGCGAGCCTAT
1 TATATGCAAGCCTAT
1330549 GTGCGAAACC
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
28 2 0.03
29 55 0.95
30 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (29 bp):
TATATGCAAGCCTATATGTGAACCTTAAA
Found at i:1332586 original size:24 final size:24
Alignment explanation
Indices: 1332551--1332619 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
1332541 GGTCAACATT
*
1332551 GGCACTAAGTGTGCGGATTTGAAA
1 GGCACTATGTGTGCGGATTTGAAA
* * *
1332575 GGCACTATGTGTGAGGAATTGAAT
1 GGCACTATGTGTGCGGATTTGAAA
*
1332599 GGCACTATGTGTGCTGATTTG
1 GGCACTATGTGTGCGGATTTG
1332620 GATGTCAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.30
Consensus pattern (24 bp):
GGCACTATGTGTGCGGATTTGAAA
Found at i:1341792 original size:14 final size:15
Alignment explanation
Indices: 1341765--1341795 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1341755 TTATTTTTAC
1341765 AAATTTTCAAAAAAT
1 AAATTTTCAAAAAAT
1341780 AAATTTT-AAAAAAT
1 AAATTTTCAAAAAAT
1341794 AA
1 AA
1341796 TACGAACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTTTCAAAAAAT
Found at i:1348696 original size:3 final size:3
Alignment explanation
Indices: 1348683--1348712 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1348673 TGATGATGAT
*
1348683 GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1348713 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1359596 original size:30 final size:30
Alignment explanation
Indices: 1359562--1359621 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1359552 CAAATGGTCA
1359562 TTGAACTATTTAAAAGTTTTCATTTAAGTC
1 TTGAACTATTTAAAAGTTTTCATTTAAGTC
* *
1359592 TTGAACTATTTGAAAGTTTTTATTTAAGTC
1 TTGAACTATTTAAAAGTTTTCATTTAAGTC
1359622 ACTAGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (30 bp):
TTGAACTATTTAAAAGTTTTCATTTAAGTC
Found at i:1365421 original size:14 final size:13
Alignment explanation
Indices: 1365380--1365430 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 13
1365370 TTGCATCTAC
1365380 TTCAAA-ATTAAA
1 TTCAAATATTAAA
*
1365392 TAT-AAATAAT-AA
1 T-TCAAATATTAAA
1365404 TTCAAATATCTAAA
1 TTCAAATAT-TAAA
1365418 TTCAAATATTAAA
1 TTCAAATATTAAA
1365431 AAATATCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.03
12 12 0.38
13 8 0.25
14 11 0.34
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (13 bp):
TTCAAATATTAAA
Found at i:1366109 original size:22 final size:22
Alignment explanation
Indices: 1366084--1366132 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1366074 TTAATATTTG
*
1366084 AAATTT-TTTAAATAAAATTAAA
1 AAATTTATTT-AATAAAATGAAA
*
1366106 AAATTTATTTACTAAAATGAAA
1 AAATTTATTTAATAAAATGAAA
1366128 AAATT
1 AAATT
1366133 GCATGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATTTATTTAATAAAATGAAA
Found at i:1367084 original size:21 final size:21
Alignment explanation
Indices: 1367060--1367100 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1367050 CAAAAAGAAC
1367060 TTTATTTTATTTAAAGGTTCA
1 TTTATTTTATTTAAAGGTTCA
*
1367081 TTTATTTTGTTTAAAGGTTC
1 TTTATTTTATTTAAAGGTTC
1367101 GACCAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (21 bp):
TTTATTTTATTTAAAGGTTCA
Found at i:1371023 original size:60 final size:59
Alignment explanation
Indices: 1370955--1371107 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 59
1370945 TCATCTAGTT
* * *
1370955 ACCAAAAAGGAAAAATTA-AATAGTT-AGATGACTATTTTATAATTTTTCATAGTTAGATG
1 ACCAAAAAAG-AAAATTACAATAGTTGAG-TGACTATTTTATAACTTTTCATAATTAGATG
* * * *
1371014 ACTAAAAAAGAAATTTACTAATAGTTGAGTGACTATTTTGTCACTTTTCATAATTAGATG
1 ACCAAAAAAGAAAATTAC-AATAGTTGAGTGACTATTTTATAACTTTTCATAATTAGATG
*
1371074 ACC-AAAAAG-AAATATACCAATAGTTGGGTGACTA
1 ACCAAAAAAGAAAAT-TA-CAATAGTTGAGTGACTA
1371108 CTAGTGTAGT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
58 9 0.11
59 31 0.39
60 37 0.47
61 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (59 bp):
ACCAAAAAAGAAAATTACAATAGTTGAGTGACTATTTTATAACTTTTCATAATTAGATG
Found at i:1379440 original size:16 final size:15
Alignment explanation
Indices: 1379413--1379480 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 15
1379403 TTAAAAAATT
1379413 AATTATAAAAAATTATA
1 AATTATAAAAAA-TA-A
*
1379430 AA-AATATAAAAATATA
1 AATTATA-AAAAATA-A
*
1379446 AATTATAAAAAATTA
1 AATTATAAAAAATAA
1379461 AATTATAAAAAATTAA
1 AATTATAAAAAA-TAA
1379477 AATT
1 AATT
1379481 TCATCCGGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
15 13 0.30
16 21 0.48
17 10 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATTATAAAAAATAA
Found at i:1379455 original size:33 final size:31
Alignment explanation
Indices: 1379399--1379460 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 31
1379389 TAGTAAAAGT
*
1379399 AAAATTAAAAAATTAATTATAAAAAATTATA
1 AAAATTAAAAAATAAATTATAAAAAATTATA
1379430 AAAATATAAAAATATAAATTATAAAAAATTA
1 AAAAT-TAAAAA-ATAAATTATAAAAAATTA
1379461 AATTATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 5 0.18
32 6 0.21
33 17 0.61
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (31 bp):
AAAATTAAAAAATAAATTATAAAAAATTATA
Found at i:1379477 original size:15 final size:15
Alignment explanation
Indices: 1379404--1379477 Score: 96
Period size: 15 Copynumber: 4.8 Consensus size: 15
1379394 AAAGTAAAAT
1379404 TAAAAAATT-AATTA
1 TAAAAAATTAAATTA
**
1379418 TAAAAAATTATAAAAA
1 TAAAAAATTA-AATTA
1379434 TATAAAAATATAAATTA
1 TA-AAAAAT-TAAATTA
1379451 TAAAAAATTAAATTA
1 TAAAAAATTAAATTA
1379466 TAAAAAATTAAA
1 TAAAAAATTAAA
1379478 ATTTCATCCG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.17
15 19 0.37
16 11 0.21
17 11 0.21
18 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAAATTAAATTA
Found at i:1380629 original size:11 final size:11
Alignment explanation
Indices: 1380613--1380637 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1380603 AAAAAATCAT
1380613 AATTATAATAA
1 AATTATAATAA
1380624 AATTATAATAA
1 AATTATAATAA
1380635 AAT
1 AAT
1380638 ATGAAAAAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTATAATAA
Found at i:1380631 original size:17 final size:16
Alignment explanation
Indices: 1380599--1380632 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1380589 GTGATGGTAT
1380599 TTATAAAAAATCATAA
1 TTATAAAAAATCATAA
*
1380615 TTATAATAAAATTATAA
1 TTATAA-AAAATCATAA
1380632 T
1 T
1380633 AAAATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TTATAAAAAATCATAA
Found at i:1382136 original size:3 final size:3
Alignment explanation
Indices: 1382128--1382157 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1382118 GTGGGGTCTT
1382128 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1382158 CCTGCTAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1382207 original size:27 final size:27
Alignment explanation
Indices: 1382169--1382224 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1382159 CTGCTAGACT
1382169 CATAGCCAAAACTTCCCAACTTAACCC
1 CATAGCCAAAACTTCCCAACTTAACCC
*
1382196 CATAGCCAAAACTTCCCAGCTTAACCC
1 CATAGCCAAAACTTCCCAACTTAACCC
1382223 CA
1 CA
1382225 CATACATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.41, G:0.05, T:0.18
Consensus pattern (27 bp):
CATAGCCAAAACTTCCCAACTTAACCC
Found at i:1386011 original size:17 final size:17
Alignment explanation
Indices: 1385989--1386029 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1385979 GATTTGATCA
*
1385989 ATTTAAATCTT-ATTTTG
1 ATTTAAATCTTGA-ATTG
1386006 ATTTAAA-CTTGAATTG
1 ATTTAAATCTTGAATTG
1386022 ATTTAAAT
1 ATTTAAAT
1386030 TCAAAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (17 bp):
ATTTAAATCTTGAATTG
Found at i:1391763 original size:24 final size:25
Alignment explanation
Indices: 1391716--1391763 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1391706 ATTAAAATTG
* *
1391716 TAAGTGGATATTATTTTTTTAAATAA
1 TAAGTGGATA-TATTTATTCAAATAA
1391742 TAAGTGGATA-ATTTATTCAAAT
1 TAAGTGGATATATTTATTCAAAT
1391764 TACTAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
26 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
TAAGTGGATATATTTATTCAAATAA
Found at i:1394259 original size:21 final size:21
Alignment explanation
Indices: 1394224--1394264 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1394214 TTTGTAATGT
* *
1394224 TATTAATTCATTTATGTTTTA
1 TATTAATTCAATTATATTTTA
*
1394245 TATTAATTTAATTATATTTT
1 TATTAATTCAATTATATTTT
1394265 GTAACTGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTAATTCAATTATATTTTA
Found at i:1402785 original size:21 final size:21
Alignment explanation
Indices: 1402761--1402811 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1402751 GGCTCAAACA
1402761 TATTATTT-TTAATATT-TTATT
1 TATTATTTATT-AT-TTATTATT
1402782 TATTATTTATTATTTATTATT
1 TATTATTTATTATTTATTATT
1402803 TATTATTTA
1 TATTATTTA
1402812 GTCATTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTATTTATTATTTATTATT
Found at i:1402789 original size:7 final size:7
Alignment explanation
Indices: 1402777--1402811 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
1402767 TTTTAATATT
1402777 TTATTTA
1 TTATTTA
1402784 TTATTTA
1 TTATTTA
1402791 TTATTTA
1 TTATTTA
1402798 TTATTTA
1 TTATTTA
1402805 TTATTTA
1 TTATTTA
1402812 GTCATTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTTA
Found at i:1403270 original size:22 final size:23
Alignment explanation
Indices: 1403242--1403288 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1403232 AATTTAAATT
1403242 ATAATAAAAGTGTAATTTAACATGG
1 ATAA-AAAA-TGTAATTTAACATGG
*
1403267 ATAAAAAATGTCATTTAACATG
1 ATAAAAAATGTAATTTAACATG
1403289 CACGGATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 4 0.19
25 4 0.19
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (23 bp):
ATAAAAAATGTAATTTAACATGG
Found at i:1404120 original size:32 final size:32
Alignment explanation
Indices: 1404066--1404126 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1404056 CTGACCCACA
* * * *
1404066 AAACCCAATACACAGAAGCCCAAACCCCTTAC
1 AAACCCAAAACACAAAACCCCAAAACCCTTAC
*
1404098 AAACCCAAAACTCAAAACCCCAAAACCCT
1 AAACCCAAAACACAAAACCCCAAAACCCT
1404127 AATCAGCCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.48, C:0.41, G:0.03, T:0.08
Consensus pattern (32 bp):
AAACCCAAAACACAAAACCCCAAAACCCTTAC
Found at i:1405222 original size:20 final size:21
Alignment explanation
Indices: 1405180--1405224 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1405170 TTTTGTTGTT
*
1405180 TATTCTTATTTTCTTATTAAA
1 TATTCTTATTATCTTATTAAA
1405201 TATTCTTATTAT-TTA-TATAA
1 TATTCTTATTATCTTATTA-AA
1405221 TATT
1 TATT
1405225 AGTACCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 11 0.50
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTCTTATTATCTTATTAAA
Found at i:1405259 original size:3 final size:3
Alignment explanation
Indices: 1405253--1405313 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
1405243 ATTGTTCTTC
*
1405253 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1405301 TTA TTA TGTA TTA
1 TTA TTA T-TA TTA
1405314 GTTTATGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1405545 original size:15 final size:15
Alignment explanation
Indices: 1405512--1405550 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1405502 TTTAATGTCG
*
1405512 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
1405528 TATTATATATTTTCA
1 TATTATATATTTTAA
1405543 TATTATAT
1 TATTATAT
1405551 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:1409663 original size:16 final size:16
Alignment explanation
Indices: 1409644--1409675 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1409634 AAAATTTTCT
1409644 ATTCAAATCATTTTAA
1 ATTCAAATCATTTTAA
*
1409660 ATTCACATCATTTTAA
1 ATTCAAATCATTTTAA
1409676 CTTGTTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTCAAATCATTTTAA
Found at i:1411771 original size:16 final size:17
Alignment explanation
Indices: 1411750--1411787 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1411740 TTTTGGATTC
1411750 GAGTTTAAGTT-ATTTT
1 GAGTTTAAGTTAATTTT
1411766 GAGTTTAAGTTAATTTT
1 GAGTTTAAGTTAATTTT
*
1411783 TAGTT
1 GAGTT
1411788 CGAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
GAGTTTAAGTTAATTTT
Found at i:1412019 original size:17 final size:17
Alignment explanation
Indices: 1411999--1412034 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1411989 TCACTTTGAG
*
1411999 TTCAAATTTACTCAGGT
1 TTCAAATTTACTCAAGT
*
1412016 TTCAAGTTTACTCAAGT
1 TTCAAATTTACTCAAGT
1412033 TT
1 TT
1412035 GTTAGTTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (17 bp):
TTCAAATTTACTCAAGT
Found at i:1415398 original size:24 final size:24
Alignment explanation
Indices: 1415371--1415422 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1415361 TTAGTAAGTC
*
1415371 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1415395 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1415419 AAAT
1 AAAT
1415423 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1417367 original size:24 final size:24
Alignment explanation
Indices: 1417340--1417391 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1417330 TTAGTAAGTC
*
1417340 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1417364 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1417388 AAAT
1 AAAT
1417392 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1419464 original size:38 final size:38
Alignment explanation
Indices: 1419390--1419464 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
1419380 CGGCATTTAA
*
1419390 GAGAAAAATAACTATAAACCCTAAAAAATAATATTATT
1 GAGAAAAATAACTATAAACCCTAAAAAATAACATTATT
* * * *
1419428 GAGAAAATTAACTATAAACCTTAAAAATTGACATTAT
1 GAGAAAAATAACTATAAACCCTAAAAAATAACATTAT
1419465 AAAAAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.55, C:0.11, G:0.07, T:0.28
Consensus pattern (38 bp):
GAGAAAAATAACTATAAACCCTAAAAAATAACATTATT
Found at i:1419473 original size:38 final size:38
Alignment explanation
Indices: 1419393--1419474 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
1419383 CATTTAAGAG
* **
1419393 AAAAA-TAACTATAAACCCTAAAAAATAATATTATTGA
1 AAAAATTAACTATAAACCCTAAAAAATAACATTATAAA
* * * *
1419430 GAAAATTAACTATAAACCTTAAAAATTGACATTATAAA
1 AAAAATTAACTATAAACCCTAAAAAATAACATTATAAA
1419468 AAAAATT
1 AAAAATT
1419475 TACACTTTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
37 4 0.11
38 32 0.89
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.28
Consensus pattern (38 bp):
AAAAATTAACTATAAACCCTAAAAAATAACATTATAAA
Found at i:1420398 original size:11 final size:11
Alignment explanation
Indices: 1420382--1420410 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1420372 ATTATATTAA
1420382 ATAATTTAAAT
1 ATAATTTAAAT
1420393 ATAATTTAAAT
1 ATAATTTAAAT
1420404 AT-ATTTA
1 ATAATTTA
1420411 TTTTTTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATAATTTAAAT
Found at i:1422456 original size:3 final size:3
Alignment explanation
Indices: 1422441--1422532 Score: 53
Period size: 3 Copynumber: 30.7 Consensus size: 3
1422431 CTTACTTCCT
* * * * *
1422441 TCA TCA TCC TCA TCA TCG TCA TCG TCA TC- TCCA TCT TCA TCT TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA TCA TCA
* * * * * *
1422486 TCC TCA TCA TCC TCG TCC TCA TCC TCG TCCA -CA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA TCA TCA TCA
1422531 TC
1 TC
1422533 TCCTATCTCT
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
2 3 0.05
3 61 0.92
4 2 0.03
ACGTcount: A:0.20, C:0.41, G:0.04, T:0.35
Consensus pattern (3 bp):
TCA
Done.