Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 4 of 213
Found at i:1036530 original size:46 final size:46
Alignment explanation
Indices: 1036477--1036745 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
1036467 TAAGTGTAGC
* **
1036477 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
1036523 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1036569 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1036621 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
1036667 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1036719 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1036746 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:1036596 original size:52 final size:52
Alignment explanation
Indices: 1036520--1036739 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
1036510 TAGCTAAAGC
* *
1036520 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1036573 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1036625 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
1036671 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1036723 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
1036740 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:1036642 original size:98 final size:98
Alignment explanation
Indices: 1036477--1036745 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
1036467 TAAGTGTAGC
* * *
1036477 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
1036542 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
1036576 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
1036641 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
1036674 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
1036739 GATCAGA
66 GATCAGA
1036746 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:1039924 original size:49 final size:50
Alignment explanation
Indices: 1039869--1040072 Score: 241
Period size: 49 Copynumber: 4.0 Consensus size: 50
1039859 TTCGTTTTCT
*
1039869 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACA-AATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATAC
* * *
1039918 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACA-TATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATAC
* *
1039967 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACAC-G--T---A-ATCACACA-ATCACATAC
* * *
1040025 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACAT
1040073 GTTCACATGT
Statistics
Matches: 136, Mismatches: 10, Indels: 17
0.83 0.06 0.10
Matches are distributed among these distances:
49 74 0.54
50 7 0.05
51 7 0.05
52 1 0.01
55 1 0.01
56 6 0.04
57 1 0.01
58 39 0.29
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (50 bp):
CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATAC
Found at i:1040039 original size:58 final size:59
Alignment explanation
Indices: 1039953--1040071 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
1039943 TACACGAAAT
1039953 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAT-ATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
1040011 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
1040070 CA
1 CA
1040072 TGTTCACATG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 54 0.90
59 6 0.10
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (59 bp):
CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
Found at i:1040052 original size:28 final size:28
Alignment explanation
Indices: 1039962--1040052 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
1039952 TCACATATCA
1039962 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
* * **
1039990 CTTACACGGAAT-CACATATCACA-CATAT-CA
1 CTTAC-C-G-ATGC-CATAGCCCAGC-TATGGT
1040020 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
1040048 CTTAC
1 CTTAC
1040053 ACGGAATCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 12 0.26
28 13 0.28
29 2 0.04
30 8 0.17
31 12 0.26
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (28 bp):
CTTACCGATGCCATAGCCCAGCTATGGT
Found at i:1041385 original size:37 final size:37
Alignment explanation
Indices: 1041341--1041506 Score: 314
Period size: 37 Copynumber: 4.5 Consensus size: 37
1041331 CACTTGTCCC
*
1041341 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1041378 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1041415 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
*
1041452 TGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1041489 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
1041507 TAAAGCTATC
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 127 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
Found at i:1041523 original size:46 final size:46
Alignment explanation
Indices: 1041470--1041738 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
1041460 TAAGTGTAGC
* **
1041470 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
1041516 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1041562 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1041614 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
1041660 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1041712 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1041739 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:1041589 original size:52 final size:52
Alignment explanation
Indices: 1041513--1041732 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
1041503 TAGCTAAAGC
* *
1041513 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1041566 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1041618 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
1041664 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1041716 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
1041733 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:1041635 original size:98 final size:98
Alignment explanation
Indices: 1041470--1041738 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
1041460 TAAGTGTAGC
* * *
1041470 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
1041535 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
1041569 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
1041634 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
1041667 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
1041732 GATCAGA
66 GATCAGA
1041739 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:1052950 original size:23 final size:21
Alignment explanation
Indices: 1052924--1052974 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
1052914 AGTTATTAAT
1052924 ATTTATATTTTTTTACAATTCAAA
1 ATTTATATTTTTTTA-AA-T-AAA
* *
1052948 TTTTTTATTTTTTTAAATAAA
1 ATTTATATTTTTTTAAATAAA
1052969 ATTTAT
1 ATTTAT
1052975 CATAAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 7 0.30
22 1 0.04
23 2 0.09
24 13 0.57
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTATATTTTTTTAAATAAA
Found at i:1052970 original size:22 final size:24
Alignment explanation
Indices: 1052929--1052972 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1052919 TTAATATTTA
*
1052929 TATTTTTTTACAATTCAAATTTTT
1 TATTTTTTTACAATTAAAATTTTT
1052953 TATTTTTTTA-AA-TAAAATTT
1 TATTTTTTTACAATTAAAATTT
1052973 ATCATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 2 0.11
24 10 0.53
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTTTTTACAATTAAAATTTTT
Found at i:1058805 original size:20 final size:20
Alignment explanation
Indices: 1058780--1058821 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1058770 ACACATCCCT
1058780 AAATTATGAACTTCATTTTA
1 AAATTATGAACTTCATTTTA
1058800 AAATTATGAACTTCATTTTA
1 AAATTATGAACTTCATTTTA
1058820 AA
1 AA
1058822 TTGGTCACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (20 bp):
AAATTATGAACTTCATTTTA
Found at i:1059203 original size:18 final size:18
Alignment explanation
Indices: 1059176--1059214 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1059166 TGAAAGGGCC
* *
1059176 ATAAAGAAAAGTAAAATT
1 ATAAAAAAAAATAAAATT
*
1059194 ATAAAAAAAAATTAAATT
1 ATAAAAAAAAATAAAATT
1059212 ATA
1 ATA
1059215 CAATATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
ATAAAAAAAAATAAAATT
Found at i:1061910 original size:12 final size:12
Alignment explanation
Indices: 1061893--1061917 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1061883 AACCGGTCCC
1061893 TGTACGCTAGCA
1 TGTACGCTAGCA
1061905 TGTACGCTAGCA
1 TGTACGCTAGCA
1061917 T
1 T
1061918 AAGGTACACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TGTACGCTAGCA
Found at i:1065795 original size:184 final size:182
Alignment explanation
Indices: 1065457--1065798 Score: 549
Period size: 184 Copynumber: 1.9 Consensus size: 182
1065447 TCTTTGTATA
* *
1065457 TTAGATTAAAGAGCAAATTAATTTTCTGTTAAAAATTTTATCCATTAATACTGTTAAAAACTGGC
1 TTAGATTAAAGAGCAAATAAATTTTCTGTTAAAAATTTTATCCATTAATACTGTTAAAAACTGAC
* *
1065522 ATGGCTAACAGAATAACTAAACAATGACACGTGGCATGCCACATGAACCTCATGCAGACATACAG
66 ATGACTAACAGAATAACTAAACAATGACACGTGGCATGCCACATGAACCTCATGCAGACATACAA
*
1065587 GGACCAATTTTTGACAGAAAAAATGGATGAATTTTTTAACAAAATAATCAAT
131 GGACCAATTTTTAACAGAAAAAATGGATGAATTTTTTAACAAAATAATCAAT
* *
1065639 TTAGATTAAAGAGCAAACTAATATTTTCTGTTAAAAATTTTATCTATTTATACTGTTAAAAACTG
1 TTAGATTAAAGAGCAAA-TAA-ATTTTCTGTTAAAAATTTTATCCATTAATACTGTTAAAAACTG
* * * * *
1065704 ACATGACTAACAGAATAACTTAACAATGACACGTGGCGTGCCACATGTACCTCATGCAGACGTTC
64 ACATGACTAACAGAATAACTAAACAATGACACGTGGCATGCCACATGAACCTCATGCAGACATAC
*
1065769 AAGGACCAATTTTTAACAGCAAAAATGGAT
129 AAGGACCAATTTTTAACAGAAAAAATGGAT
1065799 TTAAAAAACA
Statistics
Matches: 145, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 17 0.12
183 2 0.01
184 126 0.87
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (182 bp):
TTAGATTAAAGAGCAAATAAATTTTCTGTTAAAAATTTTATCCATTAATACTGTTAAAAACTGAC
ATGACTAACAGAATAACTAAACAATGACACGTGGCATGCCACATGAACCTCATGCAGACATACAA
GGACCAATTTTTAACAGAAAAAATGGATGAATTTTTTAACAAAATAATCAAT
Found at i:1068633 original size:51 final size:52
Alignment explanation
Indices: 1068569--1068671 Score: 133
Period size: 51 Copynumber: 2.0 Consensus size: 52
1068559 AGCAGCCGAC
*
1068569 TGACTTGATTCCAAACTTCT-TCCAG-TAATTCCAACTTCTCTTC-TAGATTCAG
1 TGACTTGACTCCAAACTTCTCT-CAGAT-ATTCCAACTTCTCTTCTTA-ATTCAG
*
1068621 TGACTTG-CTCCAAACTTCTCTCAGATATTCCAACTTCTTTTCTTAATTCAG
1 TGACTTGACTCCAAACTTCTCTCAGATATTCCAACTTCTCTTCTTAATTCAG
1068672 CAGCCTGCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
51 35 0.76
52 11 0.24
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (52 bp):
TGACTTGACTCCAAACTTCTCTCAGATATTCCAACTTCTCTTCTTAATTCAG
Found at i:1068681 original size:51 final size:51
Alignment explanation
Indices: 1068578--1068682 Score: 119
Period size: 51 Copynumber: 2.1 Consensus size: 51
1068568 CTGACTTGAT
* *
1068578 TCCAAACTTCTTCCAGTAATTCCAACTTCTCTTCTAGATTCAGTGACTTGC
1 TCCAAACTTCTTCCAGTAATTCCAACTTCTCTTCTAGATTCAGAGACCTGC
*
1068629 TCCAAACTTC-TCTCAG-ATATTCCAACTTCTTTTCTTA-ATTCAGCAG-CCTGC
1 TCCAAACTTCTTC-CAGTA-ATTCCAACTTCTCTTC-TAGATTCAG-AGACCTGC
1068680 TCC
1 TCC
1068683 GACCTCATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
50 3 0.06
51 41 0.87
52 3 0.06
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.37
Consensus pattern (51 bp):
TCCAAACTTCTTCCAGTAATTCCAACTTCTCTTCTAGATTCAGAGACCTGC
Found at i:1074642 original size:15 final size:15
Alignment explanation
Indices: 1074607--1074658 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1074597 TTAAGAATTT
*
1074607 TATTAAATTAT-ATA
1 TATTTAATTATAATA
1074621 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
1074635 TATTTAATAATAAT-
1 TATTTAATTATAATA
1074649 TATGTTAATT
1 TAT-TTAATT
1074659 TAAATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:1075010 original size:45 final size:44
Alignment explanation
Indices: 1074922--1075012 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 44
1074912 ACCTCTATTC
* * *
1074922 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTTCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCATTA
* *
1074966 CATTCAACCAAACA-ATTGATTTGCTATTACACCTCTAATCCATTA
1 CATTCAACCAAACACA-AGA-TTACTATTACACCTCTAATCCATTA
1075011 CA
1 CA
1075013 CCTCTATTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
43 1 0.03
44 16 0.40
45 23 0.57
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCATTA
Found at i:1075012 original size:16 final size:16
Alignment explanation
Indices: 1074991--1075044 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
1074981 TTGATTTGCT
1074991 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
1075007 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
1075023 ATTACGCCTCTAATCC
1 ATTACACCTCTAATCC
*
1075039 AATACA
1 ATTACA
1075045 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.35, G:0.02, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:1076140 original size:19 final size:18
Alignment explanation
Indices: 1076101--1076142 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1076091 ATATAAGTTC
1076101 AAATGTTAAATGAGACGA
1 AAATGTTAAATGAGACGA
*
1076119 AAAT-TTAAATTGAAGACTA
1 AAATGTTAAA-TG-AGACGA
1076138 AAATG
1 AAATG
1076143 ACTTTTTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (18 bp):
AAATGTTAAATGAGACGA
Found at i:1077076 original size:26 final size:26
Alignment explanation
Indices: 1077040--1077103 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
1077030 TAGTTGGCAA
1077040 TGCTTTTGAAAAGTGACGTGAAAAAG
1 TGCTTTTGAAAAGTGACGTGAAAAAG
* *
1077066 TGCTTTCGAAAAGTGACGTGGAAAAG
1 TGCTTTTGAAAAGTGACGTGAAAAAG
1077092 TGCTTTTGAAAA
1 TGCTTTTGAAAA
1077104 ATTTGGTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGACGTGAAAAAG
Found at i:1085002 original size:6 final size:6
Alignment explanation
Indices: 1084991--1085020 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1084981 ACTTTAAAGT
1084991 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
1085021 ACCCATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TTAAAA
Found at i:1092198 original size:31 final size:31
Alignment explanation
Indices: 1092158--1092218 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1092148 TGGACTGGAC
* *
1092158 TAATTTCA-TTCTATTTAAATTATTATTTAAT
1 TAATATCATTTCTATTTAAATT-TAATTTAAT
*
1092189 TAATATCATTTTTATTTAAATTTAATTTAA
1 TAATATCATTTCTATTTAAATTTAATTTAA
1092219 AGATATGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (31 bp):
TAATATCATTTCTATTTAAATTTAATTTAAT
Found at i:1096597 original size:118 final size:118
Alignment explanation
Indices: 1096389--1096625 Score: 447
Period size: 118 Copynumber: 2.0 Consensus size: 118
1096379 TCCGTTCAGA
1096389 TATTGCTAGGCAAAAGGGATTGAGAATATCATACTTCGAAAGGCTTTACAAGCTTAGTCCATTCA
1 TATTGCTAGGCAAAAGGGATTGAGAATATCATACTTCGAAAGGCTTTACAAGCTTAGTCCATTCA
1096454 AGAATGATGATCCAATGTTCATTGCACAGCTTAAGGACCGATCACTTTAGGGC
66 AGAATGATGATCCAATGTTCATTGCACAGCTTAAGGACCGATCACTTTAGGGC
* *
1096507 TATTGCTAGGCAGAAGGGATTGAGAATATCATACTTCGAAAGGCTTTGCAAGCTTAGTCCATTCA
1 TATTGCTAGGCAAAAGGGATTGAGAATATCATACTTCGAAAGGCTTTACAAGCTTAGTCCATTCA
*
1096572 AGAATGATGATCCAATGTTCGTTGCACAGCTTAAGGACCGATCACTTTAGGGC
66 AGAATGATGATCCAATGTTCATTGCACAGCTTAAGGACCGATCACTTTAGGGC
1096625 T
1 T
1096626 GTAAATGAAC
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (118 bp):
TATTGCTAGGCAAAAGGGATTGAGAATATCATACTTCGAAAGGCTTTACAAGCTTAGTCCATTCA
AGAATGATGATCCAATGTTCATTGCACAGCTTAAGGACCGATCACTTTAGGGC
Found at i:1096797 original size:19 final size:17
Alignment explanation
Indices: 1096773--1096817 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 17
1096763 GAGTGTTTAT
1096773 ATTATTTATTTATAATATG
1 ATTATTTATTTAT-AT-TG
1096792 ATTATTAATATTTATATTG
1 ATTATT--TATTTATATTG
1096811 ATTATTT
1 ATTATTT
1096818 TATATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.04
19 14 0.58
20 2 0.08
21 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTATTTATTTATATTG
Found at i:1100350 original size:21 final size:18
Alignment explanation
Indices: 1100321--1100370 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 18
1100311 TATACCTAAA
1100321 AAAAACAAATCTCAGATTTC
1 AAAAACAAATC-CA-ATTTC
1100341 AAAAATCAAAATCCAATTTC
1 AAAAA-C-AAATCCAATTTC
1100361 AATAAACAAA
1 AA-AAACAAA
1100371 AGGGAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.11
20 13 0.48
21 6 0.22
22 5 0.19
ACGTcount: A:0.58, C:0.18, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAACAAATCCAATTTC
Found at i:1101112 original size:24 final size:26
Alignment explanation
Indices: 1101056--1101116 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
1101046 GATATGATCA
* *
1101056 ATAAAACATCAAATTGATGTAATAAAT
1 ATAAAACAT-ATATTGATGTAACAAAT
*
1101083 ACAAAACATATA-TGAT-TAACAAAT
1 ATAAAACATATATTGATGTAACAAAT
1101107 ATAAAA-ATAT
1 ATAAAACATAT
1101117 TACAATAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 4 0.13
24 12 0.40
25 4 0.13
26 2 0.07
27 8 0.27
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (26 bp):
ATAAAACATATATTGATGTAACAAAT
Found at i:1103482 original size:17 final size:17
Alignment explanation
Indices: 1103460--1103493 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1103450 AAGCGTTGAA
1103460 GAAAGAAATAAATAGGG
1 GAAAGAAATAAATAGGG
* *
1103477 GAAAGAATTATATAGGG
1 GAAAGAAATAAATAGGG
1103494 ACCTCAACGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.29, T:0.18
Consensus pattern (17 bp):
GAAAGAAATAAATAGGG
Found at i:1104868 original size:23 final size:24
Alignment explanation
Indices: 1104841--1104888 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1104831 AAAGGAAAGT
1104841 TTAAAGAACATAAAA-GAAAAAAA
1 TTAAAGAACATAAAATGAAAAAAA
** *
1104864 TTAAATTACTTAAAATGAAAAAAA
1 TTAAAGAACATAAAATGAAAAAAA
1104888 T
1 T
1104889 ATGGGATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (24 bp):
TTAAAGAACATAAAATGAAAAAAA
Found at i:1105734 original size:19 final size:19
Alignment explanation
Indices: 1105702--1105761 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
1105692 ATTTTGTAAA
1105702 AAAATATAAAAATATATTAG
1 AAAATAT-AAAATATATTAG
* *
1105722 AAAATTTAAAATAT-TGTAA
1 AAAATATAAAATATAT-TAG
1105741 AAAATATAAAA-ATATTAG
1 AAAATATAAAATATATTAG
1105759 AAA
1 AAA
1105762 TTGTAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.24
19 20 0.59
20 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAATATAAAATATATTAG
Found at i:1105752 original size:27 final size:29
Alignment explanation
Indices: 1105708--1105773 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 29
1105698 TAAAAAAATA
1105708 TAAAAATATATTAGAAAAT-TTAAAATATTG
1 TAAAAA-ATATTAGAAAATATTAAAA-ATTG
*
1105738 TAAAAAATA-TA-AAAATATTAGAAATTG
1 TAAAAAATATTAGAAAATATTAAAAATTG
1105765 TAAAAAATA
1 TAAAAAATA
1105774 AATTTAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
27 18 0.53
28 7 0.21
29 3 0.09
30 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (29 bp):
TAAAAAATATTAGAAAATATTAAAAATTG
Found at i:1105771 original size:20 final size:19
Alignment explanation
Indices: 1105729--1105797 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
1105719 TAGAAAATTT
* * *
1105729 AAAATATTGTAAAAAATATA
1 AAAATATTG-AAATAGTAAA
*
1105749 AAAATATTAGAAATTGTAAA
1 AAAATATT-GAAATAGTAAA
* *
1105769 AAATAAATTTAAATAGTAAA
1 AAA-ATATTGAAATAGTAAA
1105789 AAAATATTG
1 AAAATATTG
1105798 TATCCTAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.11
20 29 0.76
21 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
AAAATATTGAAATAGTAAA
Found at i:1106051 original size:3 final size:3
Alignment explanation
Indices: 1106043--1106076 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1106033 TAAATAAATT
1106043 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1106077 GTTTGAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1106627 original size:3 final size:3
Alignment explanation
Indices: 1106621--1106647 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1106611 TATTATTATT
1106621 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1106648 CACACTATAT
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:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:1107611 original size:14 final size:14
Alignment explanation
Indices: 1107592--1107619 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1107582 AACCCTGCTT
1107592 ATTTTATATTAATA
1 ATTTTATATTAATA
1107606 ATTTTATATTAATA
1 ATTTTATATTAATA
1107620 TTAATATTAA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTATATTAATA
Found at i:1112014 original size:55 final size:55
Alignment explanation
Indices: 1111930--1112038 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
1111920 GATCTATGGG
* *
1111930 CATGAGTAAACTTATTCATGAGTTAAGTTATTTGTCCAAACTCGAAGGATTGCTT
1 CATGAGTAAACTTATTCACGAGTTAAGTTATTTGTCCAAACTAGAAGGATTGCTT
*
1111985 CATGAGTAAGCTTATTCACGAGTTAAGTTATTTGTCCAAACTAGAAGGATTGCT
1 CATGAGTAAACTTATTCACGAGTTAAGTTATTTGTCCAAACTAGAAGGATTGCT
1112039 CGAAATATGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (55 bp):
CATGAGTAAACTTATTCACGAGTTAAGTTATTTGTCCAAACTAGAAGGATTGCTT
Found at i:1113704 original size:16 final size:16
Alignment explanation
Indices: 1113685--1113717 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1113675 TTAAACTTGA
*
1113685 TTAAGCTCAAATTTAT
1 TTAAGCTCAAACTTAT
1113701 TTAAGCTCAAACTTAT
1 TTAAGCTCAAACTTAT
1113717 T
1 T
1113718 CATATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (16 bp):
TTAAGCTCAAACTTAT
Found at i:1122058 original size:41 final size:39
Alignment explanation
Indices: 1122013--1122105 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 39
1122003 ATCAAAGAAT
** * *
1122013 AAATTAGTTCTATTAAAAATTTCATCAATTTCTACGGTTAA
1 AAATTAGTTCTATTAAAAA--AAATCAATTTCTAAGATTAA
*
1122054 AAATTAGTTCTA-TAAAAAAAATCAATTTCTAATATTAA
1 AAATTAGTTCTATTAAAAAAAATCAATTTCTAAGATTAA
*
1122092 AAATTGGTTCTATT
1 AAATTAGTTCTATT
1122106 CATTATTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 26 0.58
39 1 0.02
40 6 0.13
41 12 0.27
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (39 bp):
AAATTAGTTCTATTAAAAAAAATCAATTTCTAAGATTAA
Found at i:1122180 original size:41 final size:41
Alignment explanation
Indices: 1122013--1122191 Score: 120
Period size: 41 Copynumber: 4.5 Consensus size: 41
1122003 ATCAAAGAAT
* **
1122013 AAATTAGTTCTATTAAAAATT-TCATCAATTTCTACGGTTAA
1 AAATTAGTTCTATTAAAAATTAT-ATCAATTTCCAATGTTAA
* * *
1122054 AAATTAGTTCTA-TAAAAA--AAATCAATTTCTAATATTAA
1 AAATTAGTTCTATTAAAAATTATATCAATTTCCAATGTTAA
* * ** * * * * *
1122092 AAATTGGTTCTATTCATTATTATACGCTAGTT-CAAAG--AGC
1 AAATTAGTTCTATTAAAAATTATA-TCAATTTCCAATGTTA-A
* *
1122132 AAATTAGTTCTATTAAAAATTCTATCAATTTCCACTGTTAA
1 AAATTAGTTCTATTAAAAATTATATCAATTTCCAATGTTAA
*
1122173 AAATTAGTTCTATAAAAAA
1 AAATTAGTTCTATTAAAAA
1122192 ATAGTTTAAT
Statistics
Matches: 101, Mismatches: 28, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
38 26 0.26
39 8 0.08
40 28 0.28
41 34 0.34
42 5 0.05
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (41 bp):
AAATTAGTTCTATTAAAAATTATATCAATTTCCAATGTTAA
Found at i:1128637 original size:32 final size:32
Alignment explanation
Indices: 1128598--1128668 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
1128588 TATGGGTTAT
*
1128598 ACAACAAACACATATTTAAAACTCAAAACCCA
1 ACAACAAAAACATATTTAAAACTCAAAACCCA
1128630 ACAACAAAAACATATTTAAAACTCAAAACCCA
1 ACAACAAAAACATATTTAAAACTCAAAACCCA
1128662 ACAACAA
1 ACAACAA
1128669 TAATTAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (32 bp):
ACAACAAAAACATATTTAAAACTCAAAACCCA
Found at i:1129479 original size:18 final size:18
Alignment explanation
Indices: 1129458--1129501 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1129448 TTTTATATAA
* *
1129458 AAATAAATTTAATACATT
1 AAATAAATTAAAAACATT
*
1129476 AAATAAATTAAAAATATT
1 AAATAAATTAAAAACATT
1129494 AAATAAAT
1 AAATAAAT
1129502 GTTTTCTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAAATTAAAAACATT
Found at i:1129480 original size:9 final size:9
Alignment explanation
Indices: 1129458--1129501 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
1129448 TTTTATATAA
1129458 AAATAAATT
1 AAATAAATT
* *
1129467 TAATACATT
1 AAATAAATT
1129476 AAATAAATT
1 AAATAAATT
1129485 AAA-AATATT
1 AAATAA-ATT
1129494 AAATAAAT
1 AAATAAAT
1129502 GTTTTCTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 25 0.86
10 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATAAATT
Found at i:1130804 original size:9 final size:9
Alignment explanation
Indices: 1130792--1130843 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
1130782 GAATGTTTAG
1130792 TTTAAAATT
1 TTTAAAATT
1130801 TTTAAAA-T
1 TTTAAAATT
*
1130809 TTT-AAATA
1 TTTAAAATT
1130817 TTTAATTAATAT
1 TTTAA--AAT-T
1130829 TTTAAAATT
1 TTTAAAATT
1130838 TTTAAA
1 TTTAAA
1130844 GGGTTTGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
7 3 0.08
8 7 0.19
9 15 0.42
10 3 0.08
11 3 0.08
12 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TTTAAAATT
Found at i:1130830 original size:20 final size:19
Alignment explanation
Indices: 1130792--1130838 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1130782 GAATGTTTAG
1130792 TTTAAAATTT--TTAAAAT
1 TTTAAAATTTAATTAAAAT
*
1130809 TTTAAATATTTAATTAATAT
1 TTTAAA-ATTTAATTAAAAT
1130829 TTTAAAATTT
1 TTTAAAATTT
1130839 TTAAAGGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 6 0.23
18 4 0.15
19 4 0.15
20 12 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAATTTAATTAAAAT
Found at i:1133973 original size:27 final size:27
Alignment explanation
Indices: 1133941--1134006 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 27
1133931 TAAGTTTTGG
1133941 GTTTAATTAATTTTTTTAAAATTAAGA
1 GTTTAATTAATTTTTTTAAAATTAAGA
* * *
1133968 GTTTAATCAGAATTTTTTTTAAATTGAGA
1 GTTTAAT--TAATTTTTTTAAAATTAAGA
*
1133997 TTTTAATTAA
1 GTTTAATTAA
1134007 AAATTTTGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 9 0.28
29 23 0.72
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (27 bp):
GTTTAATTAATTTTTTTAAAATTAAGA
Found at i:1134012 original size:30 final size:29
Alignment explanation
Indices: 1133949--1134048 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 29
1133939 GGGTTTAATT
* *
1133949 AATTTTTTTAAAATTAAGAGTTTAATCAG
1 AATTTTTTTAAAATTAAGAGTTTAATAAA
* * *
1133978 AATTTTTTTTAAATTGAGATTTTAATTAAA
1 AATTTTTTTAAAATTAAGAGTTTAA-TAAA
*** ** *
1134008 AATTTTGAGAAAATTGTGAGATTAAT-AA
1 AATTTTTTTAAAATTAAGAGTTTAATAAA
*
1134036 AATCTTTTTAAAA
1 AATTTTTTTAAAA
1134049 AAACAAGAGA
Statistics
Matches: 54, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
28 11 0.20
29 23 0.43
30 20 0.37
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (29 bp):
AATTTTTTTAAAATTAAGAGTTTAATAAA
Found at i:1134013 original size:29 final size:30
Alignment explanation
Indices: 1133949--1134013 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
1133939 GGGTTTAATT
*
1133949 AATTTTTTTAAAATTAAGAGTTTAATC-AG
1 AATTTTTTTAAAATTAAGAGTTTAATCAAA
* * * *
1133978 AATTTTTTTTAAATTGAGATTTTAATTAAA
1 AATTTTTTTAAAATTAAGAGTTTAATCAAA
1134008 AATTTT
1 AATTTT
1134014 GAGAAAATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (30 bp):
AATTTTTTTAAAATTAAGAGTTTAATCAAA
Found at i:1135910 original size:10 final size:10
Alignment explanation
Indices: 1135881--1135910 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1135871 ACAATTTCTG
*
1135881 TTCTTTTTTC
1 TTCTTTTTTT
1135891 TTCTTTTTTT
1 TTCTTTTTTT
1135901 TTCTTTTTTT
1 TTCTTTTTTT
1135911 AATCTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:1136281 original size:51 final size:52
Alignment explanation
Indices: 1136226--1136324 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 52
1136216 TATTTGAAAA
* *
1136226 AAATTAAAC-TATGAAGCCAAG-TTCACGTACCTAATTGGACAA-AAAAATATC
1 AAATTAAACAT-TGAAACCAAGATT-ACGTACCTAACTGGACAATAAAAATATC
* *
1136277 AAATTAAACATTGAAACTAAGATTAGGTACCTAACTGGACAATAAAAA
1 AAATTAAACATTGAAACCAAGATTACGTACCTAACTGGACAATAAAAA
1136325 AAACTTTGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
51 33 0.80
52 8 0.20
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.23
Consensus pattern (52 bp):
AAATTAAACATTGAAACCAAGATTACGTACCTAACTGGACAATAAAAATATC
Found at i:1141069 original size:21 final size:21
Alignment explanation
Indices: 1141038--1141093 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
1141028 CCGGCCCATT
1141038 TTTATTTTTAAAAATTAAAAAA
1 TTTA-TTTTAAAAATTAAAAAA
1141060 TTTATTTT-AAAATTAAAAAA
1 TTTATTTTAAAAATTAAAAAA
*
1141080 ATTATTTTAAAAAT
1 TTTATTTTAAAAAT
1141094 ATTGTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 19 0.59
21 9 0.28
22 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTATTTTAAAAATTAAAAAA
Found at i:1141131 original size:40 final size:41
Alignment explanation
Indices: 1141068--1141154 Score: 122
Period size: 40 Copynumber: 2.1 Consensus size: 41
1141058 AATTTATTTT
* * * *
1141068 AAAATTAAAAAAATTATTTTAAAAATATTGTAAAATTAAAA
1 AAAATAAAAAAAAGTATTGTAAAAATATTGTAAAATAAAAA
*
1141109 AAAATAAAAAAAAGTA-TGTAAAAATATTTTAAAATAAAAA
1 AAAATAAAAAAAAGTATTGTAAAAATATTGTAAAATAAAAA
1141149 AAAATA
1 AAAATA
1141155 TTTATTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 27 0.66
41 14 0.34
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (41 bp):
AAAATAAAAAAAAGTATTGTAAAAATATTGTAAAATAAAAA
Found at i:1159128 original size:14 final size:14
Alignment explanation
Indices: 1159109--1159139 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1159099 GTTATCTGTG
*
1159109 TATTCGTATTTTGT
1 TATTCGTATTTGGT
1159123 TATTCGTATTTGGT
1 TATTCGTATTTGGT
1159137 TAT
1 TAT
1159140 CCGTGTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.61
Consensus pattern (14 bp):
TATTCGTATTTGGT
Found at i:1171806 original size:23 final size:23
Alignment explanation
Indices: 1171776--1171821 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1171766 AGTGTGATTT
*
1171776 AATTTGAGAATTTGGACCATATC
1 AATTTGAGAATATGGACCATATC
1171799 AATTTGAGAATATGGACCATATC
1 AATTTGAGAATATGGACCATATC
1171822 TATAACTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (23 bp):
AATTTGAGAATATGGACCATATC
Found at i:1180724 original size:21 final size:22
Alignment explanation
Indices: 1180699--1180751 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1180689 AAATGATAAT
1180699 TTAAATATTAAAATA-AAAAAA
1 TTAAATATTAAAATAGAAAAAA
* *
1180720 TTAAATATCAAAATAGAAATAA
1 TTAAATATTAAAATAGAAAAAA
*
1180742 TAAAAT-TTAA
1 TTAAATATTAA
1180752 TTCTAAGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
TTAAATATTAAAATAGAAAAAA
Found at i:1187385 original size:3 final size:3
Alignment explanation
Indices: 1187377--1187404 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1187367 AAAATAAGTA
1187377 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1187405 AGAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1190822 original size:26 final size:28
Alignment explanation
Indices: 1190773--1190825 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
1190763 GATAATCATA
1190773 ATTAATATATCAATAAATAAAATTTTAT
1 ATTAATATATCAATAAATAAAATTTTAT
* *
1190801 ATTAA-ATAT-AATAATTACAATTTTA
1 ATTAATATATCAATAAATAAAATTTTA
1190826 AAGTATGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 4 0.17
28 5 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTAATATATCAATAAATAAAATTTTAT
Found at i:1191284 original size:3 final size:3
Alignment explanation
Indices: 1191276--1191300 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1191266 CCTTCGCAAA
1191276 CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG C
1191301 TCGCTTTGCT
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:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1195555 original size:30 final size:31
Alignment explanation
Indices: 1195520--1195583 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1195510 TATAAAATGG
1195520 TCATTGAACTA-TTAAAAGTTTTTATTTAAA
1 TCATTGAACTATTTAAAAGTTTTTATTTAAA
*
1195550 TCATTGACCTATTTAAAAGTTTTTATTTAAA
1 TCATTGAACTATTTAAAAGTTTTTATTTAAA
1195581 TCA
1 TCA
1195584 CTTGGATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 10 0.31
31 22 0.69
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (31 bp):
TCATTGAACTATTTAAAAGTTTTTATTTAAA
Found at i:1197308 original size:3 final size:3
Alignment explanation
Indices: 1197302--1197331 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1197292 AGAAGAAGAA
*
1197302 GAT GAT GAT GAT GAT GAA GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1197332 ATTGTGGATT
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:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:1197880 original size:25 final size:25
Alignment explanation
Indices: 1197816--1197882 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
1197806 CCACAAAATT
1197816 AGAAGTTTATAATTTAATTTCTTAAA
1 AGAA-TTTATAATTTAATTTCTTAAA
* * *
1197842 AGAATTTAAAATTTTATTTCTCTCAA
1 AGAATTTATAATTTAATTTCT-TAAA
*
1197868 A-AATTTATGATTTAA
1 AGAATTTATAATTTAA
1197883 AATGGGGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 26 0.76
26 8 0.24
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (25 bp):
AGAATTTATAATTTAATTTCTTAAA
Found at i:1211495 original size:13 final size:13
Alignment explanation
Indices: 1211477--1211513 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1211467 TTTAATAAAA
1211477 TTATAAATTTTTT
1 TTATAAATTTTTT
*
1211490 TTATAAATTTTGT
1 TTATAAATTTTTT
1211503 TTAT-AATTTTT
1 TTATAAATTTTT
1211514 ATGATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATAAATTTTTT
Found at i:1215037 original size:27 final size:28
Alignment explanation
Indices: 1215007--1215060 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
1214997 TAAGCACTCG
1215007 TAAATATAGTCAAAT-ATATATTATTGT
1 TAAATATAGTCAAATAATATATTATTGT
*
1215034 TAAATATAGTTAAATAAATATATTATT
1 TAAATATAGTCAAAT-AATATATTATT
1215061 ATCGAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
29 10 0.42
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (28 bp):
TAAATATAGTCAAATAATATATTATTGT
Found at i:1215068 original size:29 final size:27
Alignment explanation
Indices: 1215008--1215069 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
1214998 AAGCACTCGT
* *
1215008 AAATATAGTCAAATATATATTATTGTT
1 AAATATAGTCAAATATATATTATTATC
*
1215035 AAATATAGTTAAATAAATATATTATTATC
1 AAATATAGTCAAAT--ATATATTATTATC
*
1215064 GAATAT
1 AAATAT
1215070 TATGTTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.45
29 16 0.55
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (27 bp):
AAATATAGTCAAATATATATTATTATC
Found at i:1232939 original size:15 final size:16
Alignment explanation
Indices: 1232921--1232951 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1232911 TATAATAAAA
1232921 AGTTTTAAG-ATTTTT
1 AGTTTTAAGTATTTTT
1232936 AGTTTTAAGTATTTTT
1 AGTTTTAAGTATTTTT
1232952 CAGAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (16 bp):
AGTTTTAAGTATTTTT
Found at i:1244080 original size:142 final size:141
Alignment explanation
Indices: 1243804--1244084 Score: 447
Period size: 142 Copynumber: 2.0 Consensus size: 141
1243794 ATTTGATACC
* * *
1243804 TTAAGCTAAGTTCATTAGAACTAGCCTAGAATTTCAAAAATTAGGCACGGCATAGCCAGCAAATC
1 TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAGCAAATC
** *
1243869 AGTTCTTAACCTCTCATTTGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCAAT
66 AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCAAC
1243934 TTCAATTAACT
131 TTCAATTAACT
* *
1243945 TTAAGCTAAGTTCAGTTAAAACTAGCCTAGAGTTTCAAAAAATAGGCACTACATAGCCAAG-AAA
1 TTAAGCTAAGTTCA-TTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCC-AGCAAA
* *
1244009 TCAGTTCTTAACCTCTCATCCGCCATGATTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCA
64 TCAGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCA
1244074 ACTTCAATTAA
129 ACTTCAATTAA
1244085 AACTAGCTTA
Statistics
Matches: 128, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
141 14 0.11
142 112 0.88
143 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (141 bp):
TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAGCAAATC
AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCAAC
TTCAATTAACT
Found at i:1244902 original size:26 final size:26
Alignment explanation
Indices: 1244853--1244902 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1244843 TTAATATTTA
* *
1244853 ATAATTTTGTATATTTTATACTTATT
1 ATAATTTTATATATATTATACTTATT
1244879 ATAATTTTATATATAATTAT-CTTA
1 ATAATTTTATATAT-ATTATACTTA
1244903 ATATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (26 bp):
ATAATTTTATATATATTATACTTATT
Found at i:1244910 original size:24 final size:24
Alignment explanation
Indices: 1244850--1244910 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
1244840 AATTTAATAT
* *
1244850 TTAATAATTTTGTATAT-TTTATAC
1 TTAATAATTTTATATATAATTAT-C
1244874 TTATTATAATTTTATATATAATTATC
1 TTA--ATAATTTTATATATAATTATC
*
1244900 TTAATATTTTT
1 TTAATAATTTT
1244911 TAATGTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 10 0.32
26 17 0.55
27 4 0.13
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (24 bp):
TTAATAATTTTATATATAATTATC
Found at i:1247618 original size:6 final size:6
Alignment explanation
Indices: 1247607--1247653 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
1247597 CTCTAAACAG
1247607 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACAT
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACAT
1247654 GAAGGTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:1250428 original size:30 final size:31
Alignment explanation
Indices: 1250394--1250453 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1250384 AAACCTTTTA
*
1250394 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
1250424 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
1250454 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:1250734 original size:17 final size:17
Alignment explanation
Indices: 1250714--1250760 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1250704 CACATTTTAT
1250714 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
1250731 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
1250749 A-TATTTATATTA
1 ATTATTTATATTA
1250761 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:1253359 original size:26 final size:26
Alignment explanation
Indices: 1253321--1253372 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1253311 TTACTATGAA
1253321 AATAATAAAGGTTAAAATACAAACACT
1 AATAATAAAGGTTAAAAT-CAAACACT
* *
1253348 AATAA-AAAGGTTGAAATCTAACACT
1 AATAATAAAGGTTAAAATCAAACACT
1253373 TAGACAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.23
Consensus pattern (26 bp):
AATAATAAAGGTTAAAATCAAACACT
Found at i:1258162 original size:15 final size:16
Alignment explanation
Indices: 1258144--1258181 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1258134 TTAAAAATAA
1258144 AAAAATACATT-AATT
1 AAAAATACATTAAATT
1258159 AAAAATA-ATTAAATT
1 AAAAATACATTAAATT
1258174 -AAAATACA
1 AAAAATACA
1258182 AAAACAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATACATTAAATT
Found at i:1262771 original size:19 final size:21
Alignment explanation
Indices: 1262732--1262772 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1262722 ATTATATTCT
*
1262732 ATATTTTATTCTTAGTTTTAA
1 ATATTTTACTCTTAGTTTTAA
1262753 ATATTTTACT-TTA-TTTTAA
1 ATATTTTACTCTTAGTTTTAA
1262772 A
1 A
1262773 AAAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 3 0.16
21 9 0.47
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (21 bp):
ATATTTTACTCTTAGTTTTAA
Found at i:1274338 original size:122 final size:123
Alignment explanation
Indices: 1274068--1274329 Score: 314
Period size: 122 Copynumber: 2.1 Consensus size: 123
1274058 ATTAGGCAAG
* * * * * * *
1274068 AGATTTTTGAATTTGGGTCAGATCGAATTGACTTAAATTCGAATTAGACATTCCCATTGATTGAA
1 AGATTTTTGAATTTGGGTAAGATCAAACTAACTTAAATTCGAATTAAACATTCCCATTAATTAAA
* * *
1274133 ATACTCTTCTAACCTTTTCAAGTCTGATCAAAACCTATAAAAATCAAACATTGGATGA
66 ATACTCTTCTAACCCTTTCAAGTCTGATCAAAACCTATAAAAATCAAACATTGAATAA
* * * * *
1274191 A-ACTTTTAAATTTGGATAAGATCAAACTAACTTGAATTCGAATTAAACATTCTCATTAATTAAA
1 AGATTTTTGAATTTGGGTAAGATCAAACTAACTTAAATTCGAATTAAACATTCCCATTAATTAAA
* * ** *
1274255 ATACTC-TCTAACCCTTT-AAGTTTGATCTAAAGTTATAAAAATCAAACTTTGAATAAA
66 ATACTCTTCTAACCCTTTCAAGTCTGATCAAAACCTATAAAAATCAAACATTGAAT-AA
1274312 AGATTTTTGAATTTGGGT
1 AGATTTTTGAATTTGGGT
1274330 TATTTCAAAT
Statistics
Matches: 114, Mismatches: 23, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
120 31 0.27
121 12 0.11
122 70 0.61
123 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (123 bp):
AGATTTTTGAATTTGGGTAAGATCAAACTAACTTAAATTCGAATTAAACATTCCCATTAATTAAA
ATACTCTTCTAACCCTTTCAAGTCTGATCAAAACCTATAAAAATCAAACATTGAATAA
Found at i:1279033 original size:16 final size:16
Alignment explanation
Indices: 1279012--1279042 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1279002 TTTATTCAGA
*
1279012 TCATTTCATGTTTAAG
1 TCATTTCAGGTTTAAG
1279028 TCATTTCAGGTTTAA
1 TCATTTCAGGTTTAA
1279043 ATTATTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (16 bp):
TCATTTCAGGTTTAAG
Found at i:1279049 original size:16 final size:16
Alignment explanation
Indices: 1279011--1279049 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1279001 ATTTATTCAG
*
1279011 ATCATTTCATGTTTAA
1 ATCATTTCAGGTTTAA
*
1279027 GTCATTTCAGGTTTAA
1 ATCATTTCAGGTTTAA
*
1279043 ATTATTT
1 ATCATTT
1279050 TGGGCTTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (16 bp):
ATCATTTCAGGTTTAA
Found at i:1280063 original size:31 final size:31
Alignment explanation
Indices: 1280028--1280088 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1280018 CTCAATGACA
*
1280028 TAAATAAAAACTTTTGAATAGTTTACTGATT
1 TAAATAAAAACTTTTGAATAATTTACTGATT
* *
1280059 TAAATGAAAACTTTTGAATAATTTAGTGAT
1 TAAATAAAAACTTTTGAATAATTTACTGAT
1280089 CATTTTGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (31 bp):
TAAATAAAAACTTTTGAATAATTTACTGATT
Found at i:1288663 original size:18 final size:17
Alignment explanation
Indices: 1288630--1288668 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1288620 TTTTATAAAT
1288630 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1288648 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1288665 TGTG
1 TGTG
1288669 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:1288921 original size:23 final size:23
Alignment explanation
Indices: 1288895--1288969 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
1288885 GTGTTATTGA
1288895 TCAGTGGTAGCTTCGGCTACAAT
1 TCAGTGGTAGCTTCGGCTACAAT
* *
1288918 TCAGTGGTAGCTACGGTTACATAT
1 TCAGTGGTAGCTTCGGCTACA-AT
*
1288942 T-AGTGGTAACTTCGGCTAC-AT
1 TCAGTGGTAGCTTCGGCTACAAT
1288963 ATCAGTG
1 -TCAGTG
1288970 TGGCATTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 2 0.05
22 1 0.02
23 38 0.86
24 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACAAT
Found at i:1293307 original size:13 final size:13
Alignment explanation
Indices: 1293289--1293333 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1293279 AAGGGAAAAT
1293289 AATAAAATATTTG
1 AATAAAATATTTG
**
1293302 AATAAAATAAAT-
1 AATAAAATATTTG
1293314 AATAAAATATTTG
1 AATAAAATATTTG
1293327 AATAAAA
1 AATAAAA
1293334 AGAGAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (13 bp):
AATAAAATATTTG
Found at i:1293343 original size:25 final size:25
Alignment explanation
Indices: 1293285--1293333 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1293275 TTAAAAGGGA
1293285 AAATAATAAAATATTTGAATAAAAT
1 AAATAATAAAATATTTGAATAAAAT
1293310 AAATAATAAAATATTTGAATAAAA
1 AAATAATAAAATATTTGAATAAAA
1293334 AGAGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
AAATAATAAAATATTTGAATAAAAT
Found at i:1294436 original size:2 final size:2
Alignment explanation
Indices: 1294431--1294459 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1294421 GGCAAGTGGT
1294431 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1294460 AGGGTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1295034 original size:31 final size:31
Alignment explanation
Indices: 1294985--1295117 Score: 112
Period size: 31 Copynumber: 4.4 Consensus size: 31
1294975 AAAAAAGATT
*
1294985 AGATACCAAATTAAGAAAAAGAGTCAAGTTC
1 AGATACCAAATTAGGAAAAAGAGTCAAGTTC
* * * * *
1295016 AGGTACCAGATTAGGAAAACGTGTCAAGTTT
1 AGATACCAAATTAGGAAAAAGAGTCAAGTTC
* * * *
1295047 GGGTACCAAATT-GGACCAAAA-A--AAAGTTT
1 AGATACCAAATTAGGA--AAAAGAGTCAAGTTC
* *
1295076 AGATACCAAATTAGGAAAACGTGTCAAGTTC
1 AGATACCAAATTAGGAAAAAGAGTCAAGTTC
1295107 AGATACCAAAT
1 AGATACCAAAT
1295118 GTCATAAATT
Statistics
Matches: 79, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
28 3 0.04
29 16 0.20
30 6 0.08
31 51 0.65
32 3 0.04
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (31 bp):
AGATACCAAATTAGGAAAAAGAGTCAAGTTC
Found at i:1295487 original size:51 final size:51
Alignment explanation
Indices: 1295383--1295494 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 51
1295373 TGTTGCGAGC
* * * **
1295383 TAAATTTGTT-AATCAAGATGAAATTGACATAATGTGTAAATATTGTGGGT
1 TAAATTTGTTAAATCAAGATGAAATTAACAAAATGTGTAAATATTGAGCAT
*
1295433 TAAATTTGTTAAATCAATAT-AGAATTAACAAAATGTGTAAACT-TTGAGCAT
1 TAAATTTGTTAAATCAAGATGA-AATTAACAAAATGTGTAAA-TATTGAGCAT
1295484 TAAATTTGTTA
1 TAAATTTGTTA
1295495 TTATACCAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
50 11 0.21
51 41 0.77
52 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (51 bp):
TAAATTTGTTAAATCAAGATGAAATTAACAAAATGTGTAAATATTGAGCAT
Found at i:1299205 original size:41 final size:41
Alignment explanation
Indices: 1299160--1299251 Score: 184
Period size: 41 Copynumber: 2.2 Consensus size: 41
1299150 GAAATCTTTT
1299160 AAATTTCCCTGCCTTCGATCATAAAAAGTAAGAAAAAAGAA
1 AAATTTCCCTGCCTTCGATCATAAAAAGTAAGAAAAAAGAA
1299201 AAATTTCCCTGCCTTCGATCATAAAAAGTAAGAAAAAAGAA
1 AAATTTCCCTGCCTTCGATCATAAAAAGTAAGAAAAAAGAA
1299242 AAATTTCCCT
1 AAATTTCCCT
1299252 CATTTTCTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (41 bp):
AAATTTCCCTGCCTTCGATCATAAAAAGTAAGAAAAAAGAA
Found at i:1318112 original size:23 final size:24
Alignment explanation
Indices: 1318084--1318128 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1318074 TTTTTTCTCT
*
1318084 TTTCCTTCTCTTCT-TTCTCCCCA
1 TTTCCTTCTCCTCTCTTCTCCCCA
*
1318107 TTTCCTTTTCCTCTCTTCTCCC
1 TTTCCTTCTCCTCTCTTCTCCC
1318129 TTTCACAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTCCTTCTCCTCTCTTCTCCCCA
Found at i:1325503 original size:21 final size:21
Alignment explanation
Indices: 1325477--1325516 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1325467 GTAAGTTTAA
*
1325477 TTTAATTTAAT-TTAATTATCT
1 TTTAATATAATATT-ATTATCT
1325498 TTTAATATAATATTATTAT
1 TTTAATATAATATTATTAT
1325517 TTGATTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATATAATATTATTATCT
Found at i:1326658 original size:15 final size:15
Alignment explanation
Indices: 1326633--1326698 Score: 53
Period size: 16 Copynumber: 4.3 Consensus size: 15
1326623 CAAAAAATCA
1326633 AAAAACT-AAACTCG
1 AAAAACTCAAACTCG
*
1326647 AAAAACTCAAACCTGG
1 AAAAACTCAAA-CTCG
* * * *
1326663 ACAAATTCCAACTCAT
1 AAAAACTCAAACTC-G
*
1326679 AAAAATTCAAACTCG
1 AAAAACTCAAACTCG
1326694 AAAAA
1 AAAAA
1326699 ACTTAGACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
14 7 0.17
15 10 0.25
16 23 0.57
ACGTcount: A:0.55, C:0.23, G:0.06, T:0.17
Consensus pattern (15 bp):
AAAAACTCAAACTCG
Found at i:1331969 original size:12 final size:12
Alignment explanation
Indices: 1331952--1331978 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1331942 AATCAAGAGG
1331952 TATATATACATA
1 TATATATACATA
1331964 TATATATACATA
1 TATATATACATA
1331976 TAT
1 TAT
1331979 CTCAATGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATATACATA
Found at i:1352336 original size:15 final size:15
Alignment explanation
Indices: 1352305--1352337 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1352295 AATATATAAT
1352305 TATATTAAATTAGAA
1 TATATTAAATTAGAA
1352320 TATATATAAATTA-AA
1 TATAT-TAAATTAGAA
1352335 TAT
1 TAT
1352338 CAAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATTAAATTAGAA
Found at i:1356269 original size:12 final size:11
Alignment explanation
Indices: 1356252--1356285 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1356242 GCTTAAAGTG
1356252 AAAGAAAGACAA
1 AAAGAAAGA-AA
1356264 AAAGAAAGAAA
1 AAAGAAAGAAA
*
1356275 AAAAAAAGAAA
1 AAAGAAAGAAA
1356286 TTAAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:1356291 original size:15 final size:15
Alignment explanation
Indices: 1356251--1356285 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1356241 AGCTTAAAGT
*
1356251 GAAAGAAAGACAAAAA
1 GAAAGAAA-AAAAAAA
1356267 GAAAGAAAAAAAAAA
1 GAAAGAAAAAAAAAA
1356282 GAAA
1 GAAA
1356286 TTAAAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAAAAAAA
Found at i:1359234 original size:31 final size:32
Alignment explanation
Indices: 1359199--1359259 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1359189 CATGTTAAGC
*
1359199 ACATGTGTCTATAATCTTGTA-CATTTGGTTA
1 ACATGTGTCCATAATCTTGTATCATTTGGTTA
* *
1359230 ACATGTGTCCATACTGTTGTATCATTTGGT
1 ACATGTGTCCATAATCTTGTATCATTTGGT
1359260 AAGGTGAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (32 bp):
ACATGTGTCCATAATCTTGTATCATTTGGTTA
Found at i:1361574 original size:11 final size:11
Alignment explanation
Indices: 1361550--1361619 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
1361540 CACAAACTAA
1361550 TCCTCTTAAATT
1 TCCTC-TAAATT
*
1361562 TCCTCTGAATT
1 TCCTCTAAATT
*
1361573 TCCTCTAAAAT
1 TCCTCTAAATT
*
1361584 TCCTCTCAATT
1 TCCTCTAAATT
*
1361595 TGCTCTCAAA-T
1 TCCTCT-AAATT
*
1361606 TCCTTCCAAATT
1 TCC-TCTAAATT
1361618 TC
1 TC
1361620 TCTCAAATCT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 34 0.74
12 12 0.26
ACGTcount: A:0.24, C:0.30, G:0.03, T:0.43
Consensus pattern (11 bp):
TCCTCTAAATT
Found at i:1361622 original size:22 final size:22
Alignment explanation
Indices: 1361550--1361627 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
1361540 CACAAACTAA
* *
1361550 TCCTCTTAAATTTCCTCTGAATT
1 TCCTCTCAAA-TTCCTCTCAATT
*
1361573 TCCTCTAAAATTCCTCTCAATT
1 TCCTCTCAAATTCCTCTCAATT
*
1361595 TGCTCTCAAATTCCT-TCCAAATT
1 TCCTCTCAAATTCCTCT-C-AATT
1361618 T-CTCTCAAAT
1 TCCTCTCAAAT
1361628 CTATATTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 1 0.02
22 34 0.69
23 14 0.29
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (22 bp):
TCCTCTCAAATTCCTCTCAATT
Found at i:1361626 original size:11 final size:11
Alignment explanation
Indices: 1361569--1361627 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
1361559 ATTTCCTCTG
*
1361569 AATTTCCTCTAA
1 AATTT-CTCTCA
*
1361581 AATTCCTCTC-
1 AATTTCTCTCA
1361591 AATTTGCTCTCA
1 AATTT-CTCTCA
*
1361603 AATTCCT-TCCA
1 AATTTCTCT-CA
1361614 AATTTCTCTCA
1 AATTTCTCTCA
1361625 AAT
1 AAT
1361628 CTATATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
10 5 0.13
11 24 0.63
12 9 0.24
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.41
Consensus pattern (11 bp):
AATTTCTCTCA
Found at i:1361686 original size:51 final size:51
Alignment explanation
Indices: 1361587--1361686 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
1361577 CTAAAATTCC
*
1361587 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCTATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
* * * *
1361638 TCTCAATTTGCTCTCAAGTTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTTC-CAAATTTCTCTCAAATCCATATTT
1361687 TTAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.05
51 41 0.95
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:1363473 original size:18 final size:18
Alignment explanation
Indices: 1363440--1363478 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1363430 AAGTGTGTTC
**
1363440 CCTAGCCTTTTTATGTAT
1 CCTAGCCTTTACATGTAT
*
1363458 CCTAGCCTTTACATGTTT
1 CCTAGCCTTTACATGTAT
1363476 CCT
1 CCT
1363479 TTTTCGAGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.28, G:0.10, T:0.46
Consensus pattern (18 bp):
CCTAGCCTTTACATGTAT
Found at i:1364038 original size:14 final size:13
Alignment explanation
Indices: 1364021--1364069 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
1364011 TTAATTGACA
1364021 AACCTTAAACCCTT
1 AACCTTAAACCC-T
*
1364035 AACCTAAAAGCCCT
1 AACCTTAAA-CCCT
1364049 AACCTT-AACCCT
1 AACCTTAAACCCT
1364061 AACTCTTAA
1 AAC-CTTAA
1364070 CTTAAAAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 7 0.23
13 5 0.17
14 15 0.50
15 3 0.10
ACGTcount: A:0.39, C:0.35, G:0.02, T:0.24
Consensus pattern (13 bp):
AACCTTAAACCCT
Found at i:1364079 original size:21 final size:21
Alignment explanation
Indices: 1364055--1364181 Score: 146
Period size: 21 Copynumber: 6.0 Consensus size: 21
1364045 CCCTAACCTT
*
1364055 AACCCTAACTCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
1364076 AACCGTAACCCTTAAATTAAA
1 AACCCTAACCCTTAACTTAAA
* *
1364097 AACCCTAAACCTTTAACTTTAA
1 AACCCT-AACCCTTAACTTAAA
* * * *
1364119 AATCGTAACCCTTAAATAAAA
1 AACCCTAACCCTTAACTTAAA
* *
1364140 AACCCTAACACTTAAGTTAAA
1 AACCCTAACCCTTAACTTAAA
1364161 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
1364182 TATAATTTGA
Statistics
Matches: 85, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
21 69 0.81
22 16 0.19
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:1364126 original size:43 final size:42
Alignment explanation
Indices: 1364055--1364181 Score: 166
Period size: 43 Copynumber: 3.0 Consensus size: 42
1364045 CCCTAACCTT
*
1364055 AACCCTAACTCTTAACTTAAAAACCGTAACCCTTAAATTAAA
1 AACCCTAACACTTAACTTAAAAACCGTAACCCTTAAATTAAA
* * *
1364097 AACCCTAA-ACCTTTAACTTTAAAATCGTAACCCTTAAATAAAA
1 AACCCTAACA-C-TTAACTTAAAAACCGTAACCCTTAAATTAAA
* * *
1364140 AACCCTAACACTTAAGTTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAACACTTAACTTAAAAACCGTAACCCTTAAATTAAA
1364182 TATAATTTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
42 34 0.47
43 37 0.51
44 1 0.01
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (42 bp):
AACCCTAACACTTAACTTAAAAACCGTAACCCTTAAATTAAA
Found at i:1367090 original size:28 final size:29
Alignment explanation
Indices: 1367066--1367123 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
1367056 AAATAAATTT
*
1367066 AATATATATAAATTAA-AATATTAAAATA
1 AATATAAATAAATTAACAATATTAAAATA
*
1367094 AATTTAAATAAATTAACAATATTAAAATA
1 AATATAAATAAATTAACAATATTAAAATA
1367123 A
1 A
1367124 GTTGAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (29 bp):
AATATAAATAAATTAACAATATTAAAATA
Found at i:1367115 original size:29 final size:28
Alignment explanation
Indices: 1367073--1367170 Score: 110
Period size: 29 Copynumber: 3.5 Consensus size: 28
1367063 TTTAATATAT
*
1367073 ATAAATTAAAATATTAAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
*
1367101 ATAAATTAACAATATTAAAATAAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
* * *
1367130 ATGAATTAAAGATGTTAAAAT-ATTTGAA
1 ATAAATTAAA-ATATTAAAATAAATTGAA
*
1367158 AGAAA-TAAAATAT
1 ATAAATTAAAATAT
1367171 CTATATAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.05
27 4 0.07
28 19 0.32
29 34 0.57
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:1367486 original size:3 final size:3
Alignment explanation
Indices: 1367480--1367535 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
1367470 CAATAATAGC
* * * *
1367480 AAT AAT AGT AAT AAT ATT AAT AAT AAT GAA- AGT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
1367525 AAT TAT AAT AA
1 AAT AAT AAT AA
1367536 AAACAACAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 40 0.93
4 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1367500 original size:9 final size:9
Alignment explanation
Indices: 1367471--1367527 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
1367461 TAATATTATC
*
1367471 AATAATAGC
1 AATAATAGT
1367480 AATAATAGT
1 AATAATAGT
*
1367489 AATAATATT
1 AATAATAGT
*
1367498 AATAATAAT
1 AATAATAGT
*
1367507 GAA-AGTAGT
1 -AATAATAGT
*
1367516 AATAATAAT
1 AATAATAGT
1367525 AAT
1 AAT
1367528 TATAATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 2 0.05
9 35 0.90
10 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32
Consensus pattern (9 bp):
AATAATAGT
Found at i:1367515 original size:27 final size:30
Alignment explanation
Indices: 1367459--1367534 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 30
1367449 TATATAAGCA
1367459 AATAATATT-ATCAATAATAGCAATAATAGT
1 AATAATATTAAT-AATAATAGCAATAATAGT
*
1367489 AATAATATTAATAATAAT-G-AA-AGTAGT
1 AATAATATTAATAATAATAGCAATAATAGT
* *
1367516 AATAATAATAATTATAATA
1 AATAATATTAATAATAATA
1367535 AAAACAACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 21 0.51
28 2 0.05
29 1 0.02
30 15 0.37
31 2 0.05
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.34
Consensus pattern (30 bp):
AATAATATTAATAATAATAGCAATAATAGT
Found at i:1378554 original size:31 final size:32
Alignment explanation
Indices: 1378519--1378579 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1378509 CATGTTAAGC
1378519 ACATGTGTCAATAATCTTGTA-CATTTGGTTA
1 ACATGTGTCAATAATCTTGTATCATTTGGTTA
* * *
1378550 ACATGTTTCCATACTCTTGTATCATTTGGT
1 ACATGTGTCAATAATCTTGTATCATTTGGT
1378580 AAGGTGAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (32 bp):
ACATGTGTCAATAATCTTGTATCATTTGGTTA
Found at i:1383256 original size:7 final size:8
Alignment explanation
Indices: 1383239--1383265 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1383229 CACTATCATC
1383239 TTTTTATT
1 TTTTTATT
1383247 TTTTTATT
1 TTTTTATT
1383255 TTTTTATT
1 TTTTTATT
1383263 TTT
1 TTT
1383266 CTGGCATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:1388633 original size:39 final size:39
Alignment explanation
Indices: 1388574--1388655 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
1388564 TTGCAAGTTG
1388574 CCAATAATTAACACACTGTTACTGCCCTGCCCAAAGCTA
1 CCAATAATTAACACACTGTTACTGCCCTGCCCAAAGCTA
* * * *
1388613 CCAATAATTAACACAGTGTTAGTGGCTTGCCCAAAGCTA
1 CCAATAATTAACACACTGTTACTGCCCTGCCCAAAGCTA
1388652 CCAA
1 CCAA
1388656 AGAAAGTGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.23
Consensus pattern (39 bp):
CCAATAATTAACACACTGTTACTGCCCTGCCCAAAGCTA
Found at i:1415222 original size:12 final size:12
Alignment explanation
Indices: 1415205--1415246 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1415195 CAAGGATAAA
1415205 AATAAATAAATG
1 AATAAATAAATG
*
1415217 AATAAATGAATG
1 AATAAATAAATG
*
1415229 TAA-AAATAAATA
1 -AATAAATAAATG
1415241 AATAAA
1 AATAAA
1415247 ATAGAGCAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (12 bp):
AATAAATAAATG
Found at i:1425470 original size:18 final size:18
Alignment explanation
Indices: 1425429--1425503 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
1425419 ACCGTTTACG
* **
1425429 GTACTATTTACGTATATG
1 GTACTATTCACGTATACA
* * *
1425447 GCACTATTTACATATACA
1 GTACTATTCACGTATACA
*
1425465 GTACTATTCACGTATACG
1 GTACTATTCACGTATACA
*
1425483 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
1425501 GTA
1 GTA
1425504 GTTGGGATTG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:1425478 original size:36 final size:36
Alignment explanation
Indices: 1425429--1425503 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
1425419 ACCGTTTACG
* * *
1425429 GTACTATTTACGTATATGGCACTATTTACATATACA
1 GTACTATTCACGTATACGGCACTATTCACATATACA
* * *
1425465 GTACTATTCACGTATACGGTACTGTTCACGTATACA
1 GTACTATTCACGTATACGGCACTATTCACATATACA
1425501 GTA
1 GTA
1425504 GTTGGGATTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (36 bp):
GTACTATTCACGTATACGGCACTATTCACATATACA
Found at i:1432360 original size:24 final size:23
Alignment explanation
Indices: 1432294--1432367 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 23
1432284 AAAAAGGGGT
*
1432294 GATAAATAATAATGAAATAATAATA
1 GATAAATAA-AATG-AATAATAATG
*
1432319 GATAACA-AAATATCAATAATAATG
1 GATAA-ATAAA-ATGAATAATAATG
1432343 GCATAAATAAAATGAATAACTAATG
1 G-ATAAATAAAATGAATAA-TAATG
1432368 AAAGAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
24 19 0.46
25 21 0.51
26 1 0.02
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.26
Consensus pattern (23 bp):
GATAAATAAAATGAATAATAATG
Found at i:1441193 original size:13 final size:13
Alignment explanation
Indices: 1441175--1441200 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1441165 AAAGTGCGAG
1441175 CCTGTTGAAGACA
1 CCTGTTGAAGACA
1441188 CCTGTTGAAGACA
1 CCTGTTGAAGACA
1441201 ATATGCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CCTGTTGAAGACA
Found at i:1445650 original size:141 final size:141
Alignment explanation
Indices: 1445398--1445743 Score: 660
Period size: 141 Copynumber: 2.5 Consensus size: 141
1445388 TCCTTAATAA
*
1445398 TGCAAGTTGCCAATGA-GGGAGTGGTTTCCACACAAAAGACAAGAATTTCCTTTCATCTGTCAT-
1 TGCAAGTTGCCAATGAGGGGAATGGTTTCCACACAAAAGACAAGAATTTCCTTTCATCTGTCATA
1445461 ACTCTCAGCATGCCAAACTGGAATTCAGACTTTAGAATAAAATTCAGGTTTTAAAATTGCAGATT
66 ACTCTCAGCATGCCAAACTGGAATTCAGACTTTAGAATAAAATTCAGGTTTTAAAATTGCAGATT
1445526 CACTGGTTGAT
131 CACTGGTTGAT
1445537 TGCAAGTTGCCAATGAGGGGAATGGTTTCCACACAAAAGACAAGAATTTCCTTTCATCTGTCATA
1 TGCAAGTTGCCAATGAGGGGAATGGTTTCCACACAAAAGACAAGAATTTCCTTTCATCTGTCATA
*
1445602 ACTCTCAGCTTGCCAAACTGGAATTCAGACTTTAGAATAAAATTCAGGTTTTAAAATTGCAGATT
66 ACTCTCAGCATGCCAAACTGGAATTCAGACTTTAGAATAAAATTCAGGTTTTAAAATTGCAGATT
1445667 CACTGGTTGAT
131 CACTGGTTGAT
1445678 TGCAAGTTGCCAATGAGGGGAATGGTTTCCACACAAAAGACAAGAATTTCCTTTCATCTGTCATA
1 TGCAAGTTGCCAATGAGGGGAATGGTTTCCACACAAAAGACAAGAATTTCCTTTCATCTGTCATA
1445743 A
66 A
1445744 ATAAATATCA
Statistics
Matches: 203, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
139 16 0.08
140 46 0.23
141 141 0.69
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (141 bp):
TGCAAGTTGCCAATGAGGGGAATGGTTTCCACACAAAAGACAAGAATTTCCTTTCATCTGTCATA
ACTCTCAGCATGCCAAACTGGAATTCAGACTTTAGAATAAAATTCAGGTTTTAAAATTGCAGATT
CACTGGTTGAT
Found at i:1446126 original size:34 final size:36
Alignment explanation
Indices: 1446079--1446147 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 36
1446069 TGGAAAAAAT
* *
1446079 ATTTTATTGAAAACATA-TAAATTTAA-TTTAATTTA
1 ATTTTATTAAAAACATAGT-AACTTAATTTTAATTTA
1446114 ATTTT-TTAAAAACATAGTAACTTAATTTTAATTT
1 ATTTTATTAAAAACATAGTAACTTAATTTTAATTT
1446148 TGAATAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (36 bp):
ATTTTATTAAAAACATAGTAACTTAATTTTAATTTA
Found at i:1447451 original size:73 final size:73
Alignment explanation
Indices: 1447332--1447590 Score: 500
Period size: 73 Copynumber: 3.5 Consensus size: 73
1447322 TATTATTATT
*
1447332 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1447397 ATTTTAAG
66 ATTTTAAG
*
1447405 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1447470 ATTTTAAG
66 ATTTTAAG
1447478 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1447543 ATTTTAAG
66 ATTTTAAG
1447551 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1447591 GTCAAGTTGT
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 185 1.00
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:1451814 original size:3 final size:3
Alignment explanation
Indices: 1451806--1451831 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1451796 ATCACATGTT
1451806 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1451832 TGGATGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.