Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 8 of 126
Found at i:2702517 original size:16 final size:16
Alignment explanation
Indices: 2702496--2702545 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2702486 TGATGGAGAT
2702496 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
2702512 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
2702527 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
2702542 ATTA
1 ATTA
2702546 GCTAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:2708546 original size:60 final size:60
Alignment explanation
Indices: 2708473--2708589 Score: 234
Period size: 60 Copynumber: 1.9 Consensus size: 60
2708463 AAGTCAGTGT
2708473 TGAACTTAACATCACTGTCATTTTATTCAACAATTCTAATCAGTGATCACATTCGACTGC
1 TGAACTTAACATCACTGTCATTTTATTCAACAATTCTAATCAGTGATCACATTCGACTGC
2708533 TGAACTTAACATCACTGTCATTTTATTCAACAATTCTAATCAGTGATCACATTCGAC
1 TGAACTTAACATCACTGTCATTTTATTCAACAATTCTAATCAGTGATCACATTCGAC
2708590 CTCAATTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.35
Consensus pattern (60 bp):
TGAACTTAACATCACTGTCATTTTATTCAACAATTCTAATCAGTGATCACATTCGACTGC
Found at i:2716861 original size:3 final size:3
Alignment explanation
Indices: 2716853--2716895 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
2716843 AACCCAATAC
* * *
2716853 AAG AAG AAG AAT AAG AAG AAG AAG ACG AAG AAG GAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2716896 CTGAGGAGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.63, C:0.02, G:0.33, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:2717697 original size:3 final size:3
Alignment explanation
Indices: 2717691--2717724 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2717681 ATATTATTTT
2717691 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2717725 AAGGTTGAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2721100 original size:16 final size:16
Alignment explanation
Indices: 2721072--2721102 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2721062 AATTTCTAGC
2721072 TAAATTATATTTTTTT
1 TAAATTATATTTTTTT
2721088 TAAA-TATATTTTTTT
1 TAAATTATATTTTTTT
2721103 ATTGTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TAAATTATATTTTTTT
Found at i:2722088 original size:17 final size:17
Alignment explanation
Indices: 2722053--2722088 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2722043 ATAGATATGA
*
2722053 AATGAATACCCTTAATC
1 AATGAATACCCGTAATC
*
2722070 AATGAATACCCGTATTC
1 AATGAATACCCGTAATC
2722087 AA
1 AA
2722089 ACATTAGAAT
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:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (17 bp):
AATGAATACCCGTAATC
Found at i:2722368 original size:3 final size:3
Alignment explanation
Indices: 2722355--2722391 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2722345 ATTATCTATG
*
2722355 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2722392 CTAAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2725816 original size:36 final size:35
Alignment explanation
Indices: 2725767--2725835 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
2725757 CAAGTTGGCG
* * *
2725767 AGTTGAGTGAAGTCCTTTGTGTTCTCTCTTTAGGTA
1 AGTTGAGTAAAGTCC-TCGTGTCCTCTCTTTAGGTA
*
2725803 AGTTGGGTAAAGTCCTCGTGTCCTCTCTTTAGG
1 AGTTGAGTAAAGTCCTCGTGTCCTCTCTTTAGG
2725836 CAACACATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 16 0.55
36 13 0.45
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (35 bp):
AGTTGAGTAAAGTCCTCGTGTCCTCTCTTTAGGTA
Found at i:2731738 original size:23 final size:23
Alignment explanation
Indices: 2731712--2731886 Score: 228
Period size: 23 Copynumber: 7.5 Consensus size: 23
2731702 GAACACTAGC
*
2731712 GTGCTCTCTGATTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
2731735 GTGCTCTCTGTTTAGCAC-GTAT
1 GTGCTCTCTGTTTAGCACTGTGT
2731757 CGTGCTCTCTGTTTAGCACTGTGT
1 -GTGCTCTCTGTTTAGCACTGTGT
*
2731781 GTGCTCTCTGTTTAGCAC-GTCT
1 GTGCTCTCTGTTTAGCACTGTGT
*
2731803 CGTGCTCTCTGTTATTAGCACTTTGT
1 -GTGCTCTCTG-T-TTAGCACTGTGT
* * *
2731829 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
2731852 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
2731875 GTGCTCTCTGTT
1 GTGCTCTCTGTT
2731887 GCCCAGCACT
Statistics
Matches: 133, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.05
23 104 0.78
24 4 0.03
25 17 0.13
26 2 0.02
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (23 bp):
GTGCTCTCTGTTTAGCACTGTGT
Found at i:2731859 original size:71 final size:68
Alignment explanation
Indices: 2731715--2731934 Score: 239
Period size: 71 Copynumber: 3.1 Consensus size: 68
2731705 CACTAGCGTG
* * * * *
2731715 CTCTCTGATTAGCACTGTGTGTGCTCTCTG-TTTAGCACGTATCGTGCTCTCTGTTTAGCACTGT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTTAGCAC-TTTTGTGCTCTCTG-TTAGTACTTT
*
2731779 GTGTG
64 GTGTA
*
2731784 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTTTGTGTGCTCTCTGATTAGTACT
1 CTCTCTGTTTAGCACTGTGT-GTGCTCTCTGTT-TTAGCACTTT-TGTGCTCTCTG-TTAGTACT
2731848 TTGTGTA
62 TTGTGTA
** *
2731855 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTCAGTACTT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTT--TTAGCACTTTTGTGCTCTCTGTT-AGTACTT
*
2731920 CG-GTA
63 TGTGTA
2731925 CTCTCTGTTT
1 CTCTCTGTTT
2731935 GTTCCGTTTA
Statistics
Matches: 130, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
68 3 0.02
69 24 0.18
70 18 0.14
71 75 0.58
72 10 0.08
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (68 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTTAGCACTTTTGTGCTCTCTGTTAGTACTTTGT
GTA
Found at i:2731874 original size:94 final size:92
Alignment explanation
Indices: 2731711--2731886 Score: 266
Period size: 94 Copynumber: 1.9 Consensus size: 92
2731701 GGAACACTAG
*
2731711 CGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTATCGTGCTCTCTGTTTAGCAC
1 CGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTATCGTGCTCTCTGTTTAGCAC
2731776 TGTGTGTGCTCTCTGTTTAGCACGTCT
66 TGTGTGTGCTCTCTGTTTAGCACGTCT
* * *
2731803 CGTGCTCTCTGTTATTAGCACTTTGTGTGCTCTCTGATTAGTAC-T-TTGTGTACTCTCTGTTTA
1 CGTGCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACGTATCGTG--CTCTCTGTTTA
2731866 GCACTGTGTGTGCTCTCTGTT
62 GCACTGTGTGTGCTCTCTGTT
2731887 GCCCAGCACT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
92 15 0.20
93 1 0.01
94 60 0.79
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (92 bp):
CGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTATCGTGCTCTCTGTTTAGCAC
TGTGTGTGCTCTCTGTTTAGCACGTCT
Found at i:2734936 original size:35 final size:35
Alignment explanation
Indices: 2734897--2734967 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
2734887 TTTTGATGAC
2734897 TTTTAGAAAATTCTCTAATTGGATTTTAATGCGTA
1 TTTTAGAAAATTCTCTAATTGGATTTTAATGCGTA
*
2734932 TTTTAGAAAATTCTCTTATTGGATTTTAATGCGTA
1 TTTTAGAAAATTCTCTAATTGGATTTTAATGCGTA
2734967 T
1 T
2734968 GTTCTCTCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (35 bp):
TTTTAGAAAATTCTCTAATTGGATTTTAATGCGTA
Found at i:2755535 original size:2 final size:2
Alignment explanation
Indices: 2755528--2755577 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2755518 TAAATAACAT
2755528 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2755570 TA TA TA TA
1 TA TA TA TA
2755578 AATAAAGTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2761481 original size:40 final size:41
Alignment explanation
Indices: 2761405--2761481 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
2761395 CGACTTGCTT
2761405 CAAAATATGAGTTAATAATTAAAAAATTAAATAGGAGGCTC
1 CAAAATATGAGTTAATAATTAAAAAATTAAATAGGAGGCTC
2761446 CAAAATATGAGTTAATAATT-AAAAATTAAATAGGAG
1 CAAAATATGAGTTAATAATTAAAAAATTAAATAGGAG
2761482 ATTGTGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 16 0.44
41 20 0.56
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.27
Consensus pattern (41 bp):
CAAAATATGAGTTAATAATTAAAAAATTAAATAGGAGGCTC
Found at i:2765088 original size:20 final size:22
Alignment explanation
Indices: 2765054--2765094 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2765044 AGGCCCAACT
*
2765054 CAAATGTATTGATA-CCTTTCA
1 CAAATGTATTAATACCCTTTCA
2765075 CAAA-GTATTAATACCCTTTC
1 CAAATGTATTAATACCCTTTC
2765095 TGGTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (22 bp):
CAAATGTATTAATACCCTTTCA
Found at i:2767435 original size:57 final size:58
Alignment explanation
Indices: 2767373--2767491 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 58
2767363 ACTCATCAAC
*
2767373 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAA-AACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
* *
2767430 AAACTAAACCCAAATATTTTTAAACCCAAATATAGTTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
2767488 AAAC
1 AAAC
2767492 AACTCATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
57 45 0.78
58 13 0.22
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
Found at i:2776117 original size:17 final size:15
Alignment explanation
Indices: 2776089--2776127 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
2776079 AATTTGAGAG
*
2776089 TTTTATTTTATTTTAT
1 TTTTATTATATTTT-T
2776105 TTATTATTATATTTTT
1 TT-TTATTATATTTTT
2776121 TTTTATT
1 TTTTATT
2776128 TTTTGGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTATATTTTT
Found at i:2776130 original size:10 final size:10
Alignment explanation
Indices: 2776089--2776131 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
2776079 AATTTGAGAG
*
2776089 TTTTATTTTA
1 TTTTATTTTT
2776099 TTTTATTTATT
1 TTTTATTT-TT
*
2776110 ATTATATTTTT
1 -TTTTATTTTT
2776121 TTTTATTTTT
1 TTTTATTTTT
2776131 T
1 T
2776132 GGGCTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 18 0.64
11 3 0.11
12 7 0.25
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:2779750 original size:15 final size:15
Alignment explanation
Indices: 2779725--2779758 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2779715 CAACGTTGGG
2779725 ATAAT-ATTAAATAT
1 ATAATAATTAAATAT
2779739 ATAATAATTAAATAT
1 ATAATAATTAAATAT
2779754 A-AATA
1 ATAATA
2779759 CAATGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATAATTAAATAT
Found at i:2788053 original size:31 final size:30
Alignment explanation
Indices: 2788013--2788071 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
2788003 GGGTGAAAAG
*
2788013 GAAAAAAAAAGAAGAGAAAAATAAAATATAA
1 GAAAAAAAAAGAAAAGAAAAA-AAAATATAA
* *
2788044 GAAATAAAAAGAAAATAAAAAAAAATAT
1 GAAAAAAAAAGAAAAGAAAAAAAAATAT
2788072 TCGATGCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (30 bp):
GAAAAAAAAAGAAAAGAAAAAAAAATATAA
Found at i:2789843 original size:29 final size:30
Alignment explanation
Indices: 2789800--2789858 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
2789790 GAATTGAATC
2789800 AAATCAAAACTTCATGTATA-AGATTGCACA
1 AAATCAAAACTTCATGTATACA-ATTGCACA
2789830 AAATCAAAA-TTCATGTATACAATTGCACA
1 AAATCAAAACTTCATGTATACAATTGCACA
2789859 TTAAACCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.27
Consensus pattern (30 bp):
AAATCAAAACTTCATGTATACAATTGCACA
Found at i:2789877 original size:31 final size:29
Alignment explanation
Indices: 2789804--2789879 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 29
2789794 TGAATCAAAT
*
2789804 CAAAACTTCATGTATAAGATTGCACAAAAT
1 CAAAA-TTCATGTATAAGATTGCACAAAAC
2789834 CAAAATTCATGTATACA-ATTGCACATTAAAC
1 CAAAATTCATGTATA-AGATTGCACA--AAAC
* *
2789865 CATAGTTCATGTATA
1 CAAAATTCATGTATA
2789880 GTTTTGAGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 18 0.45
30 6 0.15
31 16 0.40
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (29 bp):
CAAAATTCATGTATAAGATTGCACAAAAC
Found at i:2791866 original size:9 final size:9
Alignment explanation
Indices: 2791854--2791897 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
2791844 ATTATTTTTT
2791854 AAATTTAAA
1 AAATTTAAA
2791863 AAATTTAAA
1 AAATTTAAA
*
2791872 AAATATAAA
1 AAATTTAAA
2791881 ATAATTTTTAAA
1 A-AA--TTTAAA
2791893 AAATT
1 AAATT
2791898 CTGATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 20 0.67
10 2 0.07
11 2 0.07
12 6 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATTTAAA
Found at i:2807871 original size:14 final size:14
Alignment explanation
Indices: 2807847--2807893 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2807837 AAATTTTATA
2807847 ACTTAAA-TTCAAC
1 ACTTAAATTTCAAC
*
2807860 ACTTAAATTTCAAT
1 ACTTAAATTTCAAC
*
2807874 ACTTAATTTGTCAAC
1 ACTTAAATT-TCAAC
2807889 ACTTA
1 ACTTA
2807894 TTTTTTCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 7 0.24
14 13 0.45
15 9 0.31
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (14 bp):
ACTTAAATTTCAAC
Found at i:2807896 original size:14 final size:14
Alignment explanation
Indices: 2807854--2807913 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
2807844 ATAACTTAAA
*
2807854 TTCAACACTTAAAT
1 TTCAACACTTAATT
*
2807868 TTCAATACTTAATT
1 TTCAACACTTAATT
*
2807882 TGTCAACACTTATTTT
1 T-TCAACACTTA-ATT
* *
2807898 TTCAGCACTCAATT
1 TTCAACACTTAATT
2807912 TT
1 TT
2807914 ACAGTCTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 17 0.46
15 17 0.46
16 3 0.08
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (14 bp):
TTCAACACTTAATT
Found at i:2812521 original size:27 final size:27
Alignment explanation
Indices: 2812491--2812544 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2812481 AATTAAATAC
*
2812491 AAAAAATAAAAATGTTTCATTTCTCAT
1 AAAAAATAAAAATGTGTCATTTCTCAT
2812518 AAAAAATAAAAATGTGTCATTTCTCAT
1 AAAAAATAAAAATGTGTCATTTCTCAT
2812545 CATTATAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (27 bp):
AAAAAATAAAAATGTGTCATTTCTCAT
Found at i:2812727 original size:2 final size:2
Alignment explanation
Indices: 2812715--2812778 Score: 78
Period size: 2 Copynumber: 32.5 Consensus size: 2
2812705 ATAGATTGTT
* * *
2812715 TA TA T- TA TA TA TA TG TA TA T- TA TA TA TGA TA TA TA TA TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
2812756 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2812779 GAGAGATATC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 2 0.04
2 51 0.93
3 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2812752 original size:24 final size:24
Alignment explanation
Indices: 2812715--2812779 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
2812705 ATAGATTGTT
2812715 TATAT-TATATATATGTATATTATA
1 TATATATATATATATGTATA-TATA
*
2812739 TATGATATATATATGTGTATATATA
1 TAT-ATATATATATATGTATATATA
2812764 TATATATATATATATG
1 TATATATATATATATG
2812780 AGAGATATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 15 0.41
25 9 0.24
26 13 0.35
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (24 bp):
TATATATATATATATGTATATATA
Found at i:2813939 original size:3 final size:3
Alignment explanation
Indices: 2813931--2813960 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2813921 GGTTGTACGT
2813931 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2813961 TAGAGAGAGA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2821362 original size:28 final size:27
Alignment explanation
Indices: 2821318--2821371 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2821308 TCCATGTTGA
*
2821318 TTTTTTTGAAAATTTTATTAACTTTTAT
1 TTTTTTTGAAAATTTTA-TAAATTTTAT
*
2821346 TTTTTTTG-AATTATTTATAAATTTTA
1 TTTTTTTGAAAAT-TTTATAAATTTTA
2821372 AATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTTTTGAAAATTTTATAAATTTTAT
Found at i:2821575 original size:23 final size:22
Alignment explanation
Indices: 2821543--2821597 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2821533 AAATTTAACT
2821543 TAAAAA-ATAAAAATTAAATTGAC
1 TAAAAATATAAAAATTAAA--GAC
**
2821566 -AAAAATATAATTATTAAAGAC
1 TAAAAATATAAAAATTAAAGAC
2821587 TAAAAATATAA
1 TAAAAATATAA
2821598 TTATGCTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 3 0.11
22 15 0.54
23 10 0.36
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (22 bp):
TAAAAATATAAAAATTAAAGAC
Found at i:2824746 original size:229 final size:229
Alignment explanation
Indices: 2824345--2824799 Score: 757
Period size: 229 Copynumber: 2.0 Consensus size: 229
2824335 TCATAGAATT
*
2824345 AATGTAAGGTTGCTTATATTTGGCATGATTAAATTAATTAGAGAAAATCACAGTCTAATCAACTC
1 AATGTAAGGTTGCTTATATTTGGCATGATTAAATTAATTAGACAAAATCACAGTCTAATCAACTC
* * *
2824410 AATAATACAAAAACATTGAGAAGAAAGGCACATGTATTTATTTTCTCCAGAGATTTTCTTATCAC
66 AATAATACAAAAACATTGAGAAGAAAGGCACATGCATTTATTTTCTCCAGAGATCTTCTCATCAC
* *
2824475 TTTATGCATGAAATATATGTAATTTGCTAATTATGGATAGAATTTGAGAGGAATATTACCTTCTT
131 TTTATGCATGAAATATATGCAATTTGCTAATTATGGATAGAATTTGAGAAGAATATTACCTTCTT
*
2824540 TAGTTTACTGGTGCTTGATTAAAACAACTAAGAA
196 TACTTTACTGGTGCTTGATTAAAACAACTAAGAA
* *
2824574 AATGTAAGGTTGCTTATATTTGGCATGATTATATTAATTAGACAAAATCACAGTGTAATCAACTC
1 AATGTAAGGTTGCTTATATTTGGCATGATTAAATTAATTAGACAAAATCACAGTCTAATCAACTC
** * *
2824639 AATAATACAAAGGCATTGAGAAGAAAGGCACATGCATTTATTTTCTCCAGGGATCTTCTCATTAC
66 AATAATACAAAAACATTGAGAAGAAAGGCACATGCATTTATTTTCTCCAGAGATCTTCTCATCAC
* *
2824704 TTTATGCATGAAATATATGCAATTTGCTAATTATGGATAGAATTTGAGAAGAATATTGCCTTGTT
131 TTTATGCATGAAATATATGCAATTTGCTAATTATGGATAGAATTTGAGAAGAATATTACCTTCTT
* *
2824769 TACTTTACTGGTGCTTTATTAAAACTACTAA
196 TACTTTACTGGTGCTTGATTAAAACAACTAA
2824800 TTCTTAGTTA
Statistics
Matches: 209, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
229 209 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (229 bp):
AATGTAAGGTTGCTTATATTTGGCATGATTAAATTAATTAGACAAAATCACAGTCTAATCAACTC
AATAATACAAAAACATTGAGAAGAAAGGCACATGCATTTATTTTCTCCAGAGATCTTCTCATCAC
TTTATGCATGAAATATATGCAATTTGCTAATTATGGATAGAATTTGAGAAGAATATTACCTTCTT
TACTTTACTGGTGCTTGATTAAAACAACTAAGAA
Found at i:2842023 original size:29 final size:29
Alignment explanation
Indices: 2841980--2842037 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2841970 AGAATTGAAT
* *
2841980 TAAAATAAAATTTTATATATAAAATTACA
1 TAAAATAAAATTTTAGATATAAAAATACA
*
2842009 TAAAATTAAAA-TTTAGGTATAAAAATACA
1 TAAAA-TAAAATTTTAGATATAAAAATACA
2842038 CATTAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (29 bp):
TAAAATAAAATTTTAGATATAAAAATACA
Found at i:2842034 original size:30 final size:31
Alignment explanation
Indices: 2841980--2842049 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
2841970 AGAATTGAAT
*
2841980 TAAAA-TAAAATTTTATATATAAAAT-TACA
1 TAAAATTAAAATTTTATATATAAAATACACA
2842009 TAAAATTAAAA-TTTAGGTATA-AAAATACACA
1 TAAAATTAAAATTTTA--TATATAAAATACACA
*
2842040 TTAAATTAAA
1 TAAAATTAAA
2842050 GTTCATGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 9 0.26
30 10 0.29
31 16 0.46
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (31 bp):
TAAAATTAAAATTTTATATATAAAATACACA
Found at i:2852000 original size:85 final size:86
Alignment explanation
Indices: 2851898--2852062 Score: 233
Period size: 86 Copynumber: 1.9 Consensus size: 86
2851888 AGGTAAATTT
* * * * *
2851898 TTGTTCATTTTCTTTTCAAATAGATGAATTTTAGT-TCTATATTTTTAAAAATTTAAATTTTAAT
1 TTGTCCATTTTCTTTTCAAATAGATCAATTTTAATATCTATACTCTTAAAAATTTAAATTTTAAT
2851962 CTTGACTTGGTAACAAGTAAA
66 CTTGACTTGGTAACAAGTAAA
* ** * *
2851983 TTGTCCATTTTCTTTTCAAATTGATCAATTTTAATATCTATACTCTTAGTATTTTAAATTTTGAT
1 TTGTCCATTTTCTTTTCAAATAGATCAATTTTAATATCTATACTCTTAAAAATTTAAATTTTAAT
2852048 CTTGACTTGGTAACA
66 CTTGACTTGGTAACA
2852063 GTTAAACTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
85 31 0.45
86 38 0.55
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (86 bp):
TTGTCCATTTTCTTTTCAAATAGATCAATTTTAATATCTATACTCTTAAAAATTTAAATTTTAAT
CTTGACTTGGTAACAAGTAAA
Found at i:2852666 original size:131 final size:132
Alignment explanation
Indices: 2852431--2852693 Score: 404
Period size: 131 Copynumber: 2.0 Consensus size: 132
2852421 TTAAGACTAA
* * * *
2852431 ATGTTATTGTCTTTAAAAGAAGATTTGCATTGTGTTGGTTGTCAGTCGATGTCGTTTATGAAAAG
1 ATGTTATTGGCTTTAAAAGAAGACTAGCATTGTGTTGGTTGTCAGTCAATGTCGTTTATGAAAAG
*
2852496 TCTTGCCTTCTTGATCCCCACTCCCCATATCGGCATAACCCTATCTCTATATTAAAGCTCACATT
66 TCTTGCCTTCTTGATCCCCACTCCCCATAGCGGCATAACCCTATCTCTATATTAAAGCTCACATT
2852561 TG
131 TG
2852563 ATGTTATTGGCTTTAAAAGAAGACTAGCATTGTG-TGGTTGTCAGTCAATGTC-TTCTATGAAAA
1 ATGTTATTGGCTTTAAAAGAAGACTAGCATTGTGTTGGTTGTCAGTCAATGTCGTT-TATGAAAA
* * * * * *
2852626 GTCTTGCCTTCTTGGTCCCCACTCTCCATGGCGGTATAACCCTGTCTCTATGTTAAAGCTCACAT
65 GTCTTGCCTTCTTGATCCCCACTCCCCATAGCGGCATAACCCTATCTCTATATTAAAGCTCACAT
2852691 TTG
130 TTG
2852694 TCTTAGTCTT
Statistics
Matches: 119, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
130 2 0.02
131 86 0.72
132 31 0.26
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (132 bp):
ATGTTATTGGCTTTAAAAGAAGACTAGCATTGTGTTGGTTGTCAGTCAATGTCGTTTATGAAAAG
TCTTGCCTTCTTGATCCCCACTCCCCATAGCGGCATAACCCTATCTCTATATTAAAGCTCACATT
TG
Found at i:2871106 original size:11 final size:11
Alignment explanation
Indices: 2871092--2871150 Score: 91
Period size: 11 Copynumber: 5.2 Consensus size: 11
2871082 TTTTTTGAAC
2871092 TTTTCAATTTT
1 TTTTCAATTTT
2871103 TTTTCAAACTTTT
1 TTTTC-AA-TTTT
*
2871116 TTTTTAATTTT
1 TTTTCAATTTT
2871127 TTTTCAATTTT
1 TTTTCAATTTT
2871138 TTTTCAATTTT
1 TTTTCAATTTT
2871149 TT
1 TT
2871151 AAGAACATGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
11 32 0.73
12 4 0.09
13 8 0.18
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTCAATTTT
Found at i:2871112 original size:20 final size:19
Alignment explanation
Indices: 2871078--2871115 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2871068 TAAATAAACT
*
2871078 AATTTTTTTTGAACTTTTC
1 AATTTTTTTTAAACTTTTC
2871097 AATTTTTTTTCAAACTTTT
1 AATTTTTTTT-AAACTTTT
2871116 TTTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.63
Consensus pattern (19 bp):
AATTTTTTTTAAACTTTTC
Found at i:2876653 original size:14 final size:14
Alignment explanation
Indices: 2876636--2876667 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2876626 AAATAAAAGG
2876636 GAAAAATTAAATTA
1 GAAAAATTAAATTA
2876650 GAAAAATTAAATTA
1 GAAAAATTAAATTA
2876664 -AAAA
1 GAAAA
2876668 TGCAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (14 bp):
GAAAAATTAAATTA
Found at i:2877791 original size:25 final size:23
Alignment explanation
Indices: 2877763--2877808 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2877753 GTTGGATCCA
2877763 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATT-TAAAAA-ATAATTTG
*
2877788 AATTAAATTTAAATAATAATT
1 AATTAAATTTAAAAAATAATT
2877809 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTTG
Found at i:2879760 original size:89 final size:92
Alignment explanation
Indices: 2879656--2879843 Score: 283
Period size: 92 Copynumber: 2.1 Consensus size: 92
2879646 TGAATAAAAG
* * *
2879656 TTTTTTTACATCATTTATAT-A-A-TATTAGAAAGGTATAATAATAAAAATAGTCCCTAACGTTT
1 TTTTTTTACACCATTTATATAATATTATTAGAAAGGTATAATAACAAAAATAGTCCCTAACATTT
*
2879718 AGGTGTTGGATCACTTTAACTCTTAAT
66 AGGTGTCGGATCACTTTAACTCTTAAT
* *
2879745 TTTTTTTACACCATTTATATAATATTATTAGAAAGGTATAATGACAAAAATAGTCTCTAACATTT
1 TTTTTTTACACCATTTATATAATATTATTAGAAAGGTATAATAACAAAAATAGTCCCTAACATTT
* *
2879810 AGGTGTCGGGTCACTTTGACTCTTAAT
66 AGGTGTCGGATCACTTTAACTCTTAAT
2879837 TTTTTTT
1 TTTTTTT
2879844 GAAGTACTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
89 19 0.22
90 1 0.01
91 1 0.01
92 67 0.76
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (92 bp):
TTTTTTTACACCATTTATATAATATTATTAGAAAGGTATAATAACAAAAATAGTCCCTAACATTT
AGGTGTCGGATCACTTTAACTCTTAAT
Found at i:2886015 original size:115 final size:115
Alignment explanation
Indices: 2885883--2886111 Score: 415
Period size: 115 Copynumber: 2.0 Consensus size: 115
2885873 CAAAAGAACG
* *
2885883 AAGAGTACAAAAGATAGAGATAAAAAATTAAACC-CTGAAAACCTGAAAACAAAGAACCCTCAAA
1 AAGAGTACAAAAGATAGAGATAAAAAATTAAACCTC-GAAAACCCGAAAACAAAAAACCCTCAAA
2885947 ACGTAAACACTAAATTCTCCAAAAGTGTTAGGAGTTCTAAACTCTAATGCA
65 ACGTAAACACTAAATTCTCCAAAAGTGTTAGGAGTTCTAAACTCTAATGCA
2885998 AAGAGTACAAAAGATAGAGATAAAAAATTAAACCTCGAAAACCCGAAAACAAAAAACCCTCAAAA
1 AAGAGTACAAAAGATAGAGATAAAAAATTAAACCTCGAAAACCCGAAAACAAAAAACCCTCAAAA
*
2886063 TGTAAACACTAAATTCTCCAAAAGTGTTAGGAGTTCTAAACTCTAATGC
66 CGTAAACACTAAATTCTCCAAAAGTGTTAGGAGTTCTAAACTCTAATGC
2886112 GTATTTATCT
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
115 109 0.99
116 1 0.01
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.19
Consensus pattern (115 bp):
AAGAGTACAAAAGATAGAGATAAAAAATTAAACCTCGAAAACCCGAAAACAAAAAACCCTCAAAA
CGTAAACACTAAATTCTCCAAAAGTGTTAGGAGTTCTAAACTCTAATGCA
Found at i:2886233 original size:24 final size:24
Alignment explanation
Indices: 2886193--2886326 Score: 205
Period size: 24 Copynumber: 5.6 Consensus size: 24
2886183 TAGACTACTA
*
2886193 AGAGTTTGATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
* *
2886217 AGAATTTAATTGAAACAAATAAAT
1 AGAGTTTAATTGAAACAAATAAAC
*
2886241 AGAGTTTAATTCAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
2886265 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
2886289 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
2886313 AGAGTTTAACTGAA
1 AGAGTTTAATTGAA
2886327 TGATTATTTC
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 101 1.00
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:2891309 original size:30 final size:29
Alignment explanation
Indices: 2891256--2891312 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
2891246 TTTTAGTCTC
2891256 TATACTTTTAGAATTTTAATTTTAATCCA
1 TATACTTTTAGAATTTTAATTTTAATCCA
*
2891285 TATATTTTTAGAATTTTAAATTTTAATC
1 TATACTTTTAGAATTTT-AATTTTAATC
2891313 TTGACTTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (29 bp):
TATACTTTTAGAATTTTAATTTTAATCCA
Found at i:2893230 original size:59 final size:59
Alignment explanation
Indices: 2893157--2893308 Score: 243
Period size: 59 Copynumber: 2.6 Consensus size: 59
2893147 TTTGGATACC
* *
2893157 CGAGGGCAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAAATGGAATTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGCT-AAAAATGGAATTTTGGAAAGTT
* *
2893216 CGAGGGTAAAATGGTAATTTTTGATGAAATTGGGGCTAAAAATGGAATTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGCTAAAAATGGAATTTTGGAAAGTT
*
2893275 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGG
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGG
2893309 TGTCGAAACC
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
59 69 0.81
60 16 0.19
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.30
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGCTAAAAATGGAATTTTGGAAAGTT
Found at i:2893236 original size:29 final size:28
Alignment explanation
Indices: 2893164--2893308 Score: 115
Period size: 30 Copynumber: 4.9 Consensus size: 28
2893154 ACCCGAGGGC
2893164 AAAATGGTAATTTTGGTGAAA-TCGGGGTT
1 AAAATGGTAATTTT-GTGAAATTCGGGG-T
2893193 AAAAAATGG-AATTTTG-GAAAGTTCGAGGGT
1 --AAAATGGTAATTTTGTGAAA-TTCG-GGGT
2893223 AAAATGGTAATTTTTGATGAAATT-GGGGCT
1 AAAATGGTAA-TTTTG-TGAAATTCGGGG-T
2893253 AAAAATGG-AATTTTG-GAAAGTTCGGGGGT
1 -AAAATGGTAATTTTGTGAAA-TTC-GGGGT
2893282 AAAATGGTAATTTTTGGTGAAA-TCGGG
1 AAAATGGTAA-TTTT-GTGAAATTCGGG
2893309 TGTCGAAACC
Statistics
Matches: 98, Mismatches: 0, Indels: 34
0.74 0.00 0.26
Matches are distributed among these distances:
27 4 0.04
28 20 0.20
29 17 0.17
30 29 0.30
31 20 0.20
32 8 0.08
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAATGGTAATTTTGTGAAATTCGGGGT
Found at i:2894532 original size:29 final size:29
Alignment explanation
Indices: 2894498--2894920 Score: 208
Period size: 29 Copynumber: 14.5 Consensus size: 29
2894488 ACCCGGGGGC
*
2894498 AAAATGGTAATTTTGGTAAAATCGAGGTT
1 AAAATGGTAATTTTGGTAAAATCGAGGGT
* *
2894527 AAAATGG-AATTTTGG-AAAGTTTTG-GGGT
1 AAAATGGTAATTTTGGTAAA--ATCGAGGGT
* * * * *
2894555 AAAATGATAATTTTTGGTGAAGTCGTGGTT
1 AAAATGGTAA-TTTTGGTAAAATCGAGGGT
*
2894585 AAAAATGG-AATTTTGG-AAAGTTC-AGGGGT
1 -AAAATGGTAATTTTGGTAAA-ATCGA-GGGT
* *
2894614 AAAATGGTAATTTTTAGTAAAATCGAGGTT
1 AAAATGGTAA-TTTTGGTAAAATCGAGGGT
*
2894644 AAAAATGG-AATTTT--AAAAGATTCGAGGGT
1 -AAAATGGTAATTTTGGTAAA-A-TCGAGGGT
*
2894673 AAAATGGTAATTTTCGGTGAAATCG-GGGTT
1 AAAATGGTAATTTT-GGTAAAATCGAGGG-T
*
2894703 AAAAATGG-AATTTT--AAAAGATTCGAGGGT
1 -AAAATGGTAATTTTGGTAAA-A-TCGAGGGT
* * *
2894732 AAAATGGTAATTTTCGGTGAAATTTG-GGTT
1 AAAATGGTAATTTT-GGT-AAAATCGAGGGT
*
2894762 AAAAAT-GTAATTTTGG-AAAGTTCGAGGGT
1 -AAAATGGTAATTTTGGTAAA-ATCGAGGGT
* *
2894791 AAAATGGTAATTTTTGGTGAAACCG-GGGTT
1 AAAATGGTAA-TTTTGGTAAAATCGAGGG-T
* **
2894821 AAAAATGG-AATTTTGG-AAAGTTTAGGGGT
1 -AAAATGGTAATTTTGGTAAAATCGA-GGGT
*
2894850 -AAATGGTAATTTTTGGTGAAATCGA-GGT
1 AAAATGGTAA-TTTTGGTAAAATCGAGGGT
* * *
2894878 AAAAATGG-AATTTTAG-AAGATTCGGGGGT
1 -AAAATGGTAATTTTGGTAA-AATCGAGGGT
2894907 AAAATGGTAATTTT
1 AAAATGGTAATTTT
2894921 TGGAAGTTTT
Statistics
Matches: 302, Mismatches: 44, Indels: 96
0.68 0.10 0.22
Matches are distributed among these distances:
27 18 0.06
28 73 0.24
29 92 0.30
30 71 0.24
31 43 0.14
32 2 0.01
33 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTAAAATCGAGGGT
Found at i:2894600 original size:59 final size:59
Alignment explanation
Indices: 2894493--2894923 Score: 540
Period size: 59 Copynumber: 7.4 Consensus size: 59
2894483 TGGATACCCG
* * *
2894493 GGGGCAAAATGGTAA-TTTTGGTAAAATCGAGGTT-AAAATGGAATTTTGGAAAGTTTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTC
* * *
2894550 GGGGTAAAATGATAATTTTTGGTGAAGTCGTGGTTAAAAATGGAATTTTGGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTC
* * * *
2894608 AGGGGTAAAATGGTAATTTTTAGTAAAATCGAGGTTAAAAATGGAATTTT-AAAAGATTC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTC
* * * *
2894667 GAGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTT-AAAAGATTC
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTC
* * *
2894726 GAGGGTAAAATGGTAATTTTCGGTGAAATTTG-GGTTAAAAATGTAATTTTGGAAAG-TTC
1 G-GGGTAAAATGGTAATTTTTGGTGAAA-TCGAGGTTAAAAATGGAATTTTGGAAAGTTTC
* * *
2894785 GAGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTC
* *
2894845 GGGGT-AAATGGTAATTTTTGGTGAAATCGAGG-TAAAAATGGAATTTTAG-AAGATTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTC
2894901 GGGGGTAAAATGGTAATTTTTGG
1 -GGGGTAAAATGGTAATTTTTGG
2894924 AAGTTTTGGG
Statistics
Matches: 334, Mismatches: 29, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
56 5 0.01
57 34 0.10
58 65 0.19
59 221 0.66
60 9 0.03
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTC
Found at i:2895349 original size:161 final size:161
Alignment explanation
Indices: 2895051--2895390 Score: 556
Period size: 161 Copynumber: 2.1 Consensus size: 161
2895041 AGGCATCCAG
* * * *
2895051 CAGTCAAAGGATTAAATTGTAAATCTTGAAAAATTCTTGGCCCAATTTCGTAATTAAATAAAAGT
1 CAGTCAAAGGACTAAATTATAAACCATGAAAAATTCTTGGCCCAATTTCGTAATTAAATAAAAGT
2895116 TGATTTAGGGATTAAATTAAAACAAATTAAAAATAAAAGGACTAAATGCATAAATAAGCCAAAAA
66 TGATTTAGGGATTAAATTAAAACAAATTAAAAATAAAAGGACTAAATGCATAAATAAGCCAAAAA
2895181 GTGACACGTGGCAGCCCCTGGTACAGTCAAA
131 GTGACACGTGGCAGCCCCTGGTACAGTCAAA
* *
2895212 CAGTCAAAGGACTAATTTATAAACCATGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAGT
1 CAGTCAAAGGACTAAATTATAAACCATGAAAAATTCTTGGCCCAATTTCGTAATTAAATAAAAGT
* ** * *
2895277 TGATTTGGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGCATAAATAATCCAAAA
66 TGATTTAGGGATTAAATTAAAACAAATTAAAAAT-AAAAGGACTAAATGCATAAATAAGCCAAAA
*
2895342 A-TGACACGTGGCAGCCTCTGGTACAGTCAAA
130 AGTGACACGTGGCAGCCCCTGGTACAGTCAAA
2895373 CAGTCAAAGGACTAAATT
1 CAGTCAAAGGACTAAATT
2895391 GAAAAGCAAT
Statistics
Matches: 165, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
161 138 0.84
162 27 0.16
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (161 bp):
CAGTCAAAGGACTAAATTATAAACCATGAAAAATTCTTGGCCCAATTTCGTAATTAAATAAAAGT
TGATTTAGGGATTAAATTAAAACAAATTAAAAATAAAAGGACTAAATGCATAAATAAGCCAAAAA
GTGACACGTGGCAGCCCCTGGTACAGTCAAA
Found at i:2896788 original size:20 final size:20
Alignment explanation
Indices: 2896750--2896788 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2896740 CAGGGCATGG
*
2896750 TGGAGCTTGGTGGTGGCAGA
1 TGGAGCTTGGTGGTAGCAGA
2896770 TGGAGC-TGGTGGTCAGCAG
1 TGGAGCTTGGTGGT-AGCAG
2896789 CAGCATAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.15, C:0.13, G:0.49, T:0.23
Consensus pattern (20 bp):
TGGAGCTTGGTGGTAGCAGA
Found at i:2896972 original size:17 final size:17
Alignment explanation
Indices: 2896952--2897016 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 17
2896942 TTAATATTAT
* *
2896952 TTTAAATTAAGTTTAAA
1 TTTAAAATAAATTTAAA
2896969 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
*
2896986 --T-AAGTAAATTTAAA
1 TTTAAAATAAATTTAAA
*
2897000 TTTAAGATAAATTTAAA
1 TTTAAAATAAATTTAAA
2897017 AATGAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 12 0.30
15 1 0.03
16 1 0.03
17 26 0.65
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:2896979 original size:11 final size:11
Alignment explanation
Indices: 2896965--2897035 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
2896955 AAATTAAGTT
2896965 TAAATTTAAAA
1 TAAATTTAAAA
2896976 TAAATTT-AAA
1 TAAATTTAAAA
* *
2896986 T-AA-GTAAATT
1 TAAATTTAAA-A
*
2896996 TAAATTTAAGA
1 TAAATTTAAAA
2897007 TAAATTTAAAAA
1 TAAATTT-AAAA
*
2897019 TGAATTTAAAA
1 TAAATTTAAAA
*
2897030 TTAATT
1 TAAATT
2897036 CAAACTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
8 1 0.02
9 4 0.09
10 5 0.11
11 25 0.53
12 12 0.26
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:2897001 original size:31 final size:29
Alignment explanation
Indices: 2896936--2897033 Score: 99
Period size: 31 Copynumber: 3.3 Consensus size: 29
2896926 ATTGGATTTA
* * * * *
2896936 TTAAATTTAATAT-TATTTTAAATTAAGT
1 TTAAATTTAAAATAAATTTAAAAATAAAT
2896964 TTAAATTTAAAATAAATTTAAATAAGTAAAT
1 TTAAATTTAAAATAAATTTAAA-AA-TAAAT
* *
2896995 TTAAATTTAAGATAAATTTAAAAATGAAT
1 TTAAATTTAAAATAAATTTAAAAATAAAT
*
2897024 TTAAAATTAA
1 TTAAATTTAA
2897034 TTCAAACTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.20
29 19 0.32
30 3 0.05
31 25 0.42
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (29 bp):
TTAAATTTAAAATAAATTTAAAAATAAAT
Found at i:2897505 original size:37 final size:37
Alignment explanation
Indices: 2897384--2897949 Score: 378
Period size: 37 Copynumber: 15.5 Consensus size: 37
2897374 AAATGATGCT
* * *
2897384 ACTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCC
1 ACTC-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
* * * *
2897422 AACTCTACTTCAATTTTAAGCAGATGAAG--TTGATGT-T
1 -ACTCTACTTCAA-TTTCAG-AGATGAAGACTTGTTATCC
*
2897459 ACTCTTACTTCAGTTTCAGAGATGAAGACTTGTTATCC
1 ACTC-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
* * * * *
2897497 ACTCTACTTCAATTTTAAGCGGATGAAG--TTGATGT-T
1 ACTCTACTTCAA-TTTCAG-AGATGAAGACTTGTTATCC
2897533 ACTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCC
1 ACTC-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
* * * * *
2897571 ACTCTACTTCAATTTTAAGCGGATGAAG--TTGATGT-T
1 ACTCTACTTCAA-TTTCAG-AGATGAAGACTTGTTATCC
* * *
2897607 ACTCTTACTTCAATTTCAAAGATAAAGACTTGATATCC
1 ACTC-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
* * *
2897645 AGTTTTACTTCAATTTCAAGAGGATAGGAA-ACGATGTTA--C
1 A-CTCTACTTCAATTTC-AGA-GAT--GAAGAC-TTGTTATCC
*
2897685 TCT-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
1 ACTCTACTTCAATTTCAGAGATGAAGACTTGTTATCC
* * *
2897721 AACTCTACTTCAATTTCAAGAGGATGAAG--TTGATGT-T
1 -ACTCTACTTCAATTTC-AGA-GATGAAGACTTGTTATCC
2897758 ACTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCC
1 ACTC-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
* * *
2897796 AACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
1 -ACTCTACTTCAATTTCAGAGATGAAGACTTGTTATCC
* * *
2897829 TCT-TACTTCAATTTCAGAGATAAAGACGTGTTATCC
1 ACTCTACTTCAATTTCAGAGATGAAGACTTGTTATCC
* * *
2897865 ACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
1 ACTCTACTTCAATTTCAGAGATGAAGACTTGTTATCC
* * *
2897897 TCT-TACTTCAATTTCAGAGATAAAGACATGTTATCC
1 ACTCTACTTCAATTTCAGAGATGAAGACTTGTTATCC
2897933 ACTCTACTTCAATTTCA
1 ACTCTACTTCAATTTCA
2897950 AGCGGATAGG
Statistics
Matches: 411, Mismatches: 68, Indels: 98
0.71 0.12 0.17
Matches are distributed among these distances:
31 26 0.06
32 20 0.05
33 3 0.01
34 12 0.03
35 33 0.08
36 52 0.13
37 120 0.29
38 85 0.21
39 34 0.08
40 18 0.04
41 2 0.00
42 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (37 bp):
ACTCTACTTCAATTTCAGAGATGAAGACTTGTTATCC
Found at i:2897531 original size:74 final size:74
Alignment explanation
Indices: 2897325--2897956 Score: 808
Period size: 74 Copynumber: 8.6 Consensus size: 74
2897315 GCTCTTCAGG
* * * * *
2897325 GAGATAAAGACTTTGCTATCCAACTTTACTTCAATTTCTAGAGGATAGGAA-ATGATGCTACTCT
1 GAGATAAAGAC-TTGTTATCC-ACTCTACTTCAATTTCAAGAGGAT--GAAGTTGATGTTACTCT
2897389 TACTTCAATTTCA
62 TACTTCAATTTCA
* * *
2897402 GAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTTAAGCA-GATGAAGTTGATGTTACTCTTA
1 GAGATAAAGACTTGTTATCC-ACTCTACTTCAATTTCAAG-AGGATGAAGTTGATGTTACTCTTA
*
2897466 CTTCAGTTTCA
64 CTTCAATTTCA
* * *
2897477 GAGATGAAGACTTGTTATCCACTCTACTTCAATTTTAAGCGGATGAAGTTGATGTTACTCTTACT
1 GAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGAGGATGAAGTTGATGTTACTCTTACT
2897542 TCAATTTCA
66 TCAATTTCA
* * *
2897551 GAGATGAAGACTTGTTATCCACTCTACTTCAATTTTAAGCGGATGAAGTTGATGTTACTCTTACT
1 GAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGAGGATGAAGTTGATGTTACTCTTACT
2897616 TCAATTTCA
66 TCAATTTCA
* * * * **
2897625 AAGATAAAGACTTGATATCCAGTTTTACTTCAATTTCAAGAGGATAGGAA-ACGATGTTACTCTT
1 GAGATAAAGACTTGTTATCCA-CTCTACTTCAATTTCAAGAGGAT--GAAGTTGATGTTACTCTT
2897689 ACTTCAATTTCA
63 ACTTCAATTTCA
*
2897701 GAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAAGTTGATGTTACTCTTAC
1 GAGATAAAGACTTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAAGTTGATGTTACTCTTAC
2897766 TTCAATTTCA
65 TTCAATTTCA
* *
2897776 GAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG-T--TG---CTCTTAC
1 GAGATAAAGACTTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAAGTTGATGTTACTCTTAC
2897835 TTCAATTTCA
65 TTCAATTTCA
* *
2897845 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG-T--TG---CTCTTACT
1 GAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGAGGATGAAGTTGATGTTACTCTTACT
2897904 TCAATTTCA
66 TCAATTTCA
* *
2897913 GAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGCGGAT
1 GAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGAGGAT
2897957 AGGAAATGAT
Statistics
Matches: 512, Mismatches: 35, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
68 90 0.18
69 35 0.07
72 2 0.00
74 150 0.29
75 131 0.26
76 89 0.17
77 15 0.03
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (74 bp):
GAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGAGGATGAAGTTGATGTTACTCTTACT
TCAATTTCA
Found at i:2897839 original size:31 final size:31
Alignment explanation
Indices: 2897801--2897912 Score: 125
Period size: 31 Copynumber: 3.4 Consensus size: 31
2897791 TATCCAACTC
2897801 TACTTCAATTTCAAGAGGATGACGTTGCTCT
1 TACTTCAATTTCAAGAGGATGACGTTGCTCT
** * * *
2897832 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT
2897868 CTACTTCAATTTCAAGAGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACGTTGCTCT
2897900 TACTTCAATTTCA
1 TACTTCAATTTCA
2897913 GAGATAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
31 26 0.40
32 11 0.17
33 1 0.02
34 2 0.03
35 1 0.02
36 11 0.17
37 13 0.20
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (31 bp):
TACTTCAATTTCAAGAGGATGACGTTGCTCT
Found at i:2906866 original size:30 final size:31
Alignment explanation
Indices: 2906824--2907278 Score: 177
Period size: 29 Copynumber: 15.5 Consensus size: 31
2906814 ACCCGGGGGC
* *
2906824 AAAATGGTAATTTTTGGGGAAATCGGGGTTA
1 AAAATGGTAATTTTAGGAGAAATCGGGGTTA
* ** *
2906855 AAAATGG-AATTTTAGAAG-CTTCGGGGGT-
1 AAAATGGTAATTTTAGGAGAAATCGGGGTTA
* * *
2906883 AAAATGGTAATTATCGGTGAAATC-GGGTTA
1 AAAATGGTAATTTTAGGAGAAATCGGGGTTA
* *** *
2906913 AAAATGG-AATTTTAGAAGCTTTAGGGG-T-
1 AAAATGGTAATTTTAGGAGAAATCGGGGTTA
* *
2906941 AAAATGGTAAGTTTTCGGTGAAATCGGGGTTA
1 AAAATGGTAA-TTTTAGGAGAAATCGGGGTTA
* ** **
2906973 AAAATGG-AATTTTA-AAGATTTAAGGG-T-
1 AAAATGGTAATTTTAGGAGAAATCGGGGTTA
*
2907000 AAAATGGTAATTTTTA-GTGAAATCGGGGTT-
1 AAAATGGTAA-TTTTAGGAGAAATCGGGGTTA
* *
2907030 AAAATAG-AATTTTA--AAAAGATTCAGGGG-T-
1 AAAATGGTAATTTTAGGAGAA-A-TC-GGGGTTA
*
2907059 AAAATGGTAATTTT-TGATGAAATCGGGGTTA
1 AAAATGGTAATTTTAGGA-GAAATCGGGGTTA
* ** * *
2907090 AAAATGG-AATTTTAGAAG-CTTAGGGGGT-
1 AAAATGGTAATTTTAGGAGAAATCGGGGTTA
* *
2907118 AAAATGGTAATGTTT-CGTGAAATCGGGGGTTA
1 AAAATGGTAAT-TTTAGGAGAAATC-GGGGTTA
* ** * *
2907150 AAAATAG-AATTTTAAAAG-ATTCGGGGGT-
1 AAAATGGTAATTTTAGGAGAAATCGGGGTTA
* *
2907178 -AAATGGTAATTTT-TGATAAAATCGGGGTTA
1 AAAATGGTAATTTTAGGA-GAAATCGGGGTTA
* * ** *
2907208 AAAATAG-AATTTTAGAAG-CTTCGGGGGT-
1 AAAATGGTAATTTTAGGAGAAATCGGGGTTA
*
2907236 AAAATGGTAA-TTTACGGTGAAATC-GGGTTA
1 AAAATGGTAATTTTA-GGAGAAATCGGGGTTA
2907266 AAAATGG-AATTTT
1 AAAATGGTAATTTT
2907279 GTAAGTTTCG
Statistics
Matches: 302, Mismatches: 84, Indels: 77
0.65 0.18 0.17
Matches are distributed among these distances:
27 15 0.05
28 46 0.15
29 101 0.33
30 90 0.30
31 35 0.12
32 15 0.05
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTAGGAGAAATCGGGGTTA
Found at i:2906887 original size:59 final size:59
Alignment explanation
Indices: 2906817--2907309 Score: 638
Period size: 59 Copynumber: 8.4 Consensus size: 59
2906807 TATGGATACC
* *
2906817 CGGGGGCAAAATGGTAATTTTTGGGGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* *
2906876 CGGGGGTAAAATGGTAATTATCGGTGAAATC-GGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
** * *
2906934 TAGGGGTAAAATGGTAAGTTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTA-AAGATT
1 CGGGGGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
*** * * * *
2906993 TAAGGGTAAAATGGTAATTTTTAGTGAAATCGGGGTT-AAAATAGAATTTTAAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-AGAAGCTT
* *
2907052 CAGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * * * * *
2907111 AGGGGGTAAAATGGTAATGTTTCGTGAAATCGGGGGTTAAAAATAGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTAGAAGCTT
* * *
2907171 CGGGGGT-AAATGGTAATTTTTGATAAAATCGGGGTTAAAAATAGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
** *
2907229 CGGGGGTAAAATGGTAATTTACGGTGAAATC-GGGTTAAAAATGGAATTTT-GTAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGCTT
*
2907287 CGAGGGTAAAATGGTAATTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
2907310 AAATTTTGGG
Statistics
Matches: 383, Mismatches: 43, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
57 13 0.03
58 137 0.36
59 170 0.44
60 63 0.16
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
Found at i:2907386 original size:30 final size:29
Alignment explanation
Indices: 2907281--2907409 Score: 111
Period size: 30 Copynumber: 4.4 Consensus size: 29
2907271 GGAATTTTGT
* * *
2907281 AAGTTTCGAGGGTAAAATGGTAATTTTTG-A
1 AAGTTTAG-GGGTAAAAT-ATAATTTTGGAA
* * *
2907311 AA-TTTTGGGGTCAAATATAACTTTGGAA
1 AAGTTTAGGGGTAAAATATAATTTTGGAA
*
2907339 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTAGGGGT-AAAATATAATTTTGGAA
* *
2907369 AAGTTTCAGGGGTAAAATGTAATTTTTGGAT
1 AAGTTT-AGGGGTAAAATATAA-TTTTGGAA
2907400 AA-TTTAGGGG
1 AAGTTTAGGGG
2907410 CTTACAAAGT
Statistics
Matches: 84, Mismatches: 10, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
27 7 0.08
28 11 0.13
29 18 0.21
30 34 0.40
31 14 0.17
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
AAGTTTAGGGGTAAAATATAATTTTGGAA
Found at i:2909044 original size:6 final size:6
Alignment explanation
Indices: 2909005--2909123 Score: 95
Period size: 6 Copynumber: 20.2 Consensus size: 6
2908995 CTTTGGACTC
* * ** *
2909005 TTAAATT TTTAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA-
1 TTAAA-T TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
2909054 TTAAAT TTAAAT ATTAAAT TTAAAT TTAAA- ATAAAT CTAAAT TTAAA-
1 TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
2909101 -TAAAT TTAAA- ATCAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT T
2909124 CAAAAGTCCA
Statistics
Matches: 90, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
4 4 0.04
5 11 0.12
6 60 0.67
7 15 0.17
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:2909057 original size:17 final size:17
Alignment explanation
Indices: 2909037--2909123 Score: 85
Period size: 17 Copynumber: 5.4 Consensus size: 17
2909027 TAATTTTTAT
2909037 TTAAATTTAAATTCAAA
1 TTAAATTTAAATTCAAA
2909054 TTAAATTTAAA-T---A
1 TTAAATTTAAATTCAAA
*
2909067 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTCAAA
* * *
2909084 ATAAATCTAAATTTAAA
1 TTAAATTTAAATTCAAA
* *
2909101 -TAAATTTAAAATCAAT
1 TTAAATTTAAATTCAAA
2909117 TTAAATT
1 TTAAATT
2909124 CAAAAGTCCA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
13 12 0.20
14 1 0.02
16 13 0.22
17 33 0.56
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAATTCAAA
Found at i:2909126 original size:11 final size:11
Alignment explanation
Indices: 2909035--2909123 Score: 83
Period size: 11 Copynumber: 7.8 Consensus size: 11
2909025 TTTAATTTTT
2909035 ATTTAAATTTAA
1 ATTTAAA-TTAA
*
2909047 ATTCAAATTAA
1 ATTTAAATTAA
2909058 ATTTAAATATTAA
1 ATTT-AA-ATTAA
2909071 ATTTAAATTTAA
1 ATTTAAA-TTAA
*
2909083 A-ATAAATCTAA
1 ATTTAAAT-TAA
2909094 ATTTAAA-TAA
1 ATTTAAATTAA
* *
2909104 ATTTAAAATCA
1 ATTTAAATTAA
2909115 ATTTAAATT
1 ATTTAAATT
2909124 CAAAAGTCCA
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
10 11 0.17
11 26 0.40
12 19 0.29
13 9 0.14
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:2909488 original size:68 final size:68
Alignment explanation
Indices: 2909399--2910126 Score: 1185
Period size: 68 Copynumber: 10.5 Consensus size: 68
2909389 AAGACTTTGC
2909399 TATCCAACTCTACTT-ATATTTC-AGGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAG
1 TATCC-ACTCTACTTCA-ATTTCAAGG-GGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAG
2909462 ACATGT
63 ACATGT
* * *
2909468 TATCCACTCTACTTCAATTTCAAAGGGACGATGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
2909533 TGT
66 TGT
*
2909536 TATCCACTCTACTTCAATTTCAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
2909601 TGT
66 TGT
*
2909604 TATCCACTCTACTTCTACTTCGATTTCAAGGGG-CGACGTTGCTCTTACTTCAATTTCAGAGATG
1 TATCCACTCTACTTC-A-----ATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
2909668 AAGACATGT
60 AAGACATGT
*
2909677 TATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
2909742 TGT
66 TGT
2909745 TATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCCACTCTACTTCAATTTC-AAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
2909810 ATGT
65 ATGT
*
2909814 TATCCACTCTACTTCACTTCAATTTC-AGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 TATCCA--CT-C-T-ACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
2909878 AGACATGC
61 AGACATGT
*
2909886 TATCCAGTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
2909951 TGT
66 TGT
2909954 TATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCCACTCTACTTCAATTTC-AAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
2910019 ATGT
65 ATGT
*
2910023 TATCCACTCTACTTCAATTTCAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
*
2910088 TGC
66 TGT
2910091 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
2910127 AGATCTGCAA
Statistics
Matches: 625, Mismatches: 17, Indels: 35
0.92 0.03 0.05
Matches are distributed among these distances:
67 22 0.04
68 340 0.54
69 131 0.21
70 1 0.00
71 2 0.00
72 51 0.08
73 56 0.09
74 22 0.04
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (68 bp):
TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
TGT
Found at i:2909852 original size:209 final size:210
Alignment explanation
Indices: 2909416--2910126 Score: 1251
Period size: 209 Copynumber: 3.4 Consensus size: 210
2909406 CTCTACTTAT
* *
2909416 ATTTC-AGGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTAC
1 ATTTCAAGG-GGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGCTATCCACTCTAC
* * *
2909480 TTCAATTTCAAAGGGACGATGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTC
65 TTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTC
*
2909545 TACTTCAATTTC-AAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCC
130 TACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCC
*
2909609 ACTCTACTTCTACTTCG
195 ACTCTACTTC-ACTTCA
*
2909626 ATTTCAAGGGG-CGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACT
1 ATTTCAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGCTATCCACTCTACT
*
2909690 TCGATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCT
66 TCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCT
2909755 ACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCA
131 ACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCA
2909820 CTCTACTTCACTTCA
196 CTCTACTTCACTTCA
*
2909835 ATTTC-AGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGCTATCCAGTCTACT
1 ATTTCAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGCTATCCACTCTACT
2909899 TCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCT
66 TCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCT
2909964 ACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCA
131 ACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCA
2910029 --CT-C-T-ACTTCA
196 CTCTACTTCACTTCA
2910039 ATTTCAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGCTATCCACTCTACT
1 ATTTCAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGCTATCCACTCTACT
2910104 TCAATTTCAAGGGGATGACGTTG
66 TCAATTTCAAGGGGATGACGTTG
2910127 AGATCTGCAA
Statistics
Matches: 486, Mismatches: 11, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
204 11 0.02
205 82 0.17
206 1 0.00
207 2 0.00
208 5 0.01
209 314 0.65
210 68 0.14
211 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (210 bp):
ATTTCAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGCTATCCACTCTACT
TCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCT
ACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCA
CTCTACTTCACTTCA
Found at i:2909921 original size:277 final size:279
Alignment explanation
Indices: 2909399--2910106 Score: 1188
Period size: 277 Copynumber: 2.5 Consensus size: 279
2909389 AAGACTTTGC
2909399 TATCCAACTCTACTT-ATATTTC-AGGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAG
1 TATCC-ACTCTACTTCA-ATTTCAAGG-GGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAG
*
2909462 ACATGTTATCCACTCTACTTCAATTTCAAA-GGGACGATGTTGCTCTTACTTCAATTTCAGAGAT
63 ACATGTTATCCACTCTACTTCAATTTCAAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGAT
2909526 GAAGACATGTTATCCA--CT-C-T-ACTTCAATTTCAAGGGGACGACGTTGCTCTTACTTCAATT
128 GAAGACATGTTATCCACTCTACTTCACTTCAATTTCAAGGGGACGACGTTGCTCTTACTTCAATT
*
2909586 TCAGAGATGAAGACATGTTATCCACTCTACTTCTACTTCGATTTCAAGGGGCGACGTTGCTCTTA
193 TCAGAGATGAAGACATGCTATCCACTCTACTTCTA---C-ATTTCAAGGGGCGACGTTGCTCTTA
2909651 CTTCAATTTCAGAGATGAAGACATGT
254 CTTCAATTTCAGAGATGAAGACATGT
*
2909677 TATCCACTCTACTTCGATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
*
2909742 TGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAA
66 TGTTATCCACTCTACTTCAATTTCAAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAA
2909807 GACATGTTATCCACTCTACTTCACTTCAATTTC-AGGGGACGACGTTGCTCTTACTTCAATTTCA
131 GACATGTTATCCACTCTACTTCACTTCAATTTCAAGGGGACGACGTTGCTCTTACTTCAATTTCA
* *
2909871 GAGATGAAGACATGCTATCCAGTCTACTTC-A-ATTTCAAGGGGATGACGTTGCTCTTACTTCAA
196 GAGATGAAGACATGCTATCCACTCTACTTCTACATTTCAAGGGG-CGACGTTGCTCTTACTTCAA
2909934 TTTCAGAGATGAAGACATGT
260 TTTCAGAGATGAAGACATGT
2909954 TATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCCACTCTACTTCAATTTC-AAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
2910019 ATGTTATCCACTCTACTTCAATTTC-AAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGA
65 ATGTTATCCACTCTACTTCAATTTCAAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
2910083 AGACATGCTATCCACTCTACTTCA
130 AGACATGTTATCCACTCTACTTCA
2910107 ATTTCAAGGG
Statistics
Matches: 411, Mismatches: 9, Indels: 21
0.93 0.02 0.05
Matches are distributed among these distances:
276 11 0.03
277 201 0.49
278 124 0.30
280 2 0.00
281 2 0.00
282 60 0.15
283 11 0.03
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (279 bp):
TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACA
TGTTATCCACTCTACTTCAATTTCAAAGGGGACGACGTTGCTCTTACTTCAATTTCAGAGATGAA
GACATGTTATCCACTCTACTTCACTTCAATTTCAAGGGGACGACGTTGCTCTTACTTCAATTTCA
GAGATGAAGACATGCTATCCACTCTACTTCTACATTTCAAGGGGCGACGTTGCTCTTACTTCAAT
TTCAGAGATGAAGACATGT
Found at i:2922142 original size:59 final size:59
Alignment explanation
Indices: 2922047--2922536 Score: 648
Period size: 59 Copynumber: 8.4 Consensus size: 59
2922037 TATGGATACC
* * * * *
2922047 CGGGGGAAAAATGGT-ATTTTCGGTGAAATCGAGGTTAAAAACGGATTTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* * *
2922105 CGAGGGTAAAATGGTAATTTTCGGGGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* * * *
2922164 TGGGGGTAAAATGGTAATTATCGGTGAAATTGGGG-TAAAAATGGAACTTTAAAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* *
2922222 TGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* *
2922281 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAACA--GAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAA-ATGGAATTTTAAAAGCTT
* * *
2922339 CGGGGGTAAAATGGTAATTTTTGATGAAATC-GGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* * *** *
2922397 CGGGGGTAAAATGGTAATTTTCGGTAAAATTGGGGTTAAAAAACAAAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTT-AAAAATGGAATTTTAAAAGCTT
* ** *
2922457 CGGGGGTAAAATGGTAATTTTCGGTGAAATCTGGGTTAAAAATGGAATTTTGTAAGTTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
* *
2922516 TGGGGGTAAAATTGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
2922537 TGAAAATTTT
Statistics
Matches: 383, Mismatches: 42, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
56 1 0.00
57 9 0.02
58 152 0.40
59 169 0.44
60 52 0.14
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGCTT
Found at i:2922221 original size:117 final size:117
Alignment explanation
Indices: 2922047--2922536 Score: 662
Period size: 117 Copynumber: 4.2 Consensus size: 117
2922037 TATGGATACC
* * * * * * *
2922047 CGGGGGAAAAATGGT-ATTTTCGGTGAAATCGAGGTTAAAAACGGATTTTTAGAAGCTTCGAGGG
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCG-GGGTAAAAACAGAATTTTAAAAGATTCGGGGG
*
2922111 TAAAATGGTAATTTTCGGGGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
65 TAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * * ** * * *
2922164 TGGGGGTAAAATGGTAATTATCGGTGAAATTGGGGTAAAAATGGAACTTTAAAAGCTTTGGGGGT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAACAGAATTTTAAAAGATTCGGGGGT
* *
2922229 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
66 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* *
2922281 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAACAGAATTTTAAAAGATTCGGGGGT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAACAGAATTTTAAAAGATTCGGGGGT
* *
2922346 AAAATGGTAATTTTTGATGAAATC-GGGTTAAAAATGGAATTTTAGAAGCTT
66 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * *
2922397 CGGGGGTAAAATGGTAATTTTCGGTAAAATTGGGGTTAAAAAACAAAATTTTAAAAGATTCGGGG
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGG-T-AAAAACAGAATTTTAAAAGATTCGGGG
* *
2922462 GTAAAATGGTAATTTTCGGTGAAATCTGGGTTAAAAATGGAATTTT-GTAAGTTT
64 GTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGCTT
* *
2922516 TGGGGGTAAAATTGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
2922537 TGAAAATTTT
Statistics
Matches: 330, Mismatches: 38, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
116 57 0.17
117 166 0.50
118 64 0.19
119 43 0.13
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (117 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAACAGAATTTTAAAAGATTCGGGGGT
AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
Found at i:2922477 original size:29 final size:29
Alignment explanation
Indices: 2922195--2922477 Score: 157
Period size: 29 Copynumber: 9.7 Consensus size: 29
2922185 CGGTGAAATT
* * *
2922195 GGGGTAAAAATGG-AACTTTAAAAGCTTTG
1 GGGGT-AAAATGGTAATTTTAAAAGATTCG
**** *
2922224 GGGGTAAAATGGTAATTTTCGGTGAAATCG
1 GGGGTAAAATGGTAATTTTAAAAG-ATTCG
*
2922254 GGGTTAAAAATGG-AATTTTAAAAGATTCG
1 GGGGT-AAAATGGTAATTTTAAAAGATTCG
**** *
2922283 GGGGTAAAATGGTAATTTTTGGTGAAATCG
1 GGGGTAAAATGGTAATTTTAAAAG-ATTCG
* **
2922313 GGGTTAAAACAG-AATTTTAAAAGATTCG
1 GGGGTAAAATGGTAATTTTAAAAGATTCG
** * *
2922341 GGGGTAAAATGGTAATTTTTGATGAAATC-
1 GGGGTAAAATGGTAATTTTAAAAG-ATTCG
* * *
2922370 GGGTTAAAAATGG-AATTTTAGAAGCTTCG
1 GGGGT-AAAATGGTAATTTTAAAAGATTCG
*
2922399 GGGGTAAAATGGTAATTTTCGGTAAA-ATT-G
1 GGGGTAAAATGGTAATTTT---AAAAGATTCG
* ****
2922429 GGGTTAAAAAACAAAATTTTAAAAGATTCG
1 GGGGT-AAAATGGTAATTTTAAAAGATTCG
2922459 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
2922478 CGGTGAAATC
Statistics
Matches: 183, Mismatches: 55, Indels: 32
0.68 0.20 0.12
Matches are distributed among these distances:
28 39 0.21
29 77 0.42
30 46 0.25
31 19 0.10
32 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTAAAAGATTCG
Found at i:2922534 original size:29 final size:29
Alignment explanation
Indices: 2922495--2922591 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 29
2922485 ATCTGGGTTA
* *
2922495 AAAATGGAA-TTTTGTAAGTTTTGGGGGT
1 AAAATGTAACTTTTGAAAGTTTTGGGGGT
* * *
2922523 AAAATTGTAATTTTTGAAAATTTTGGGGTT
1 AAAA-TGTAACTTTTGAAAGTTTTGGGGGT
* * *
2922553 AAAATATAACTTTGGAAAAGTTTCGGGGGT
1 AAAATGTAACTTTTG-AAAGTTTTGGGGGT
2922583 AAAATGTAA
1 AAAATGTAA
2922592 TTTCTGGACA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
28 4 0.07
29 12 0.22
30 39 0.71
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAATGTAACTTTTGAAAGTTTTGGGGGT
Found at i:2922552 original size:59 final size:56
Alignment explanation
Indices: 2922047--2922594 Score: 446
Period size: 59 Copynumber: 9.4 Consensus size: 56
2922037 TATGGATACC
* * * * * * *
2922047 CGGGGGAAAAATGGT-ATTTTCGGTGAAATCGAGGTTAAAAACGGATTTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTT---TGAAATTGGGGTTAAAAATGGAATTTTAAAAGATT
* * * * *
2922105 CGAGGGTAAAATGGTAATTTTCGGGGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTT---TGAAATTGGGGTTAAAAATGGAATTTTAAAAGATT
* * * *
2922164 TGGGGGTAAAATGGTAATTATCGGTGAAATTGGGG-TAAAAATGGAACTTTAAAAGCTT
1 CGGGGGTAAAATGGTAATT-T--TTGAAATTGGGGTTAAAAATGGAATTTTAAAAGATT
* *
2922222 TGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTT---TGAAATTGGGGTTAAAAATGGAATTTTAAAAGATT
*
2922281 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAACA--GAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAA-TTTT--TGAAATTGGGGTTAAAA-ATGGAATTTTAAAAGATT
* * * *
2922339 CGGGGGTAAAATGGTAATTTTTGATGAAATCGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGA--AATTGGGGTTAAAAATGGAATTTTAAAAGATT
* ***
2922397 CGGGGGTAAAATGGTAATTTTCGGTAAAATTGGGGTTAAAAAACAAAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTT---TGAAATTGGGGTT-AAAAATGGAATTTTAAAAGATT
** *
2922457 CGGGGGTAAAATGGTAATTTTCGGTGAAATCT-GGGTTAAAAATGGAATTTTGTAAGTTT
1 CGGGGGTAAAATGGTAATTTT---TGAAAT-TGGGGTTAAAAATGGAATTTTAAAAGATT
* * * *
2922516 TGGGGGTAAAATTGTAATTTTTGAAAATTTTGGGGTTAAAATAT--AACTTTGGAAAAGTTT
1 CGGGGGTAAAATGGTAATTTTTG-AAA--TTGGGGTTAAAA-ATGGAA-TTT-TAAAAGATT
2922576 CGGGGGTAAAAT-GTAATTT
1 CGGGGGTAAAATGGTAATTT
2922595 CTGGACAATT
Statistics
Matches: 420, Mismatches: 44, Indels: 51
0.82 0.09 0.10
Matches are distributed among these distances:
55 3 0.01
56 3 0.01
57 19 0.05
58 132 0.31
59 184 0.44
60 76 0.18
61 3 0.01
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (56 bp):
CGGGGGTAAAATGGTAATTTTTGAAATTGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:2922909 original size:162 final size:162
Alignment explanation
Indices: 2922692--2923005 Score: 470
Period size: 162 Copynumber: 1.9 Consensus size: 162
2922682 ATTTGAAAAT
* *
2922692 CTTGAAAAATTTTTGGACCAATTTTGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
1 CTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
* * *
2922757 AATTAAAAATAGAAAGGACTAAATGAAGAAATAATCCAA-AGAATGACACGTGGCAACCTCTGGT
66 AATAAAAAATAAAAAGGACTAAATGAAGAAATAATCCAATA-AATGACACGTGGCAACCTCTGGC
*
2922821 GCAGTCAAACAGTCAAAGGACTAGTTTATAAAC
130 ACAGTCAAACAGTCAAAGGACTAGTTTATAAAC
* * **
2922854 CTTGAAAAATTATTGGGCCAATTTCGTAATTAAA-ATAAAGTTGATTTGGGGATTAAATTAAAAC
1 CTTGAAAAATTATTGGACCAATTTCGTAATTAAATA-AAAGTCGATTTAAGGATTAAATTAAAAC
* * *
2922918 AAATAAAAAATAAAAAGGACTAAATGCATAAATAATCCAATACATGACACGTGGCAACCTCTGGC
65 AAATAAAAAATAAAAAGGACTAAATGAAGAAATAATCCAATAAATGACACGTGGCAACCTCTGGC
*
2922983 ATAGTCAAACAGTCAAAGGACTA
130 ACAGTCAAACAGTCAAAGGACTA
2923006 AATTACAAAC
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
161 1 0.01
162 134 0.99
163 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (162 bp):
CTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
AATAAAAAATAAAAAGGACTAAATGAAGAAATAATCCAATAAATGACACGTGGCAACCTCTGGCA
CAGTCAAACAGTCAAAGGACTAGTTTATAAAC
Found at i:2923085 original size:162 final size:161
Alignment explanation
Indices: 2922738--2923088 Score: 395
Period size: 162 Copynumber: 2.2 Consensus size: 161
2922728 AAAGTCGATT
* *
2922738 TAAGGATTAAATTAAAACAAATTAAAAATAGAAAGGACTAAATGAAGAAATAATCCAAAGAATGA
1 TAAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGAAGAAATAATCCAAAGAATGA
** ** * **
2922803 CACGTGGCAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATT
66 CACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTACAAACCTT-AAAAATTACA
* * * * **
2922868 GGGCCAATTTCGTAATTAAAATAAAGTTGATT
130 GGGCAAATTTCGCAAATAAAATAAAGATGACA
** * * *
2922900 TGGGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGCATAAATAATCCAATA-CATG
1 TAAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGAAGAAATAATCCAA-AGAATG
*
2922964 ACACGTGGCAACCTCTGGCATAGTCAAACAGTCAAAGGACTAAATTACAAACCAATT-AAAATTA
65 ACACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTACAAACC--TTAAAAATTA
*
2923028 CAGGGCAAATTT-GCAAATAATTAA-AAAGATGCCA
128 CAGGGCAAATTTCGCAAATAA--AATAAAGATGACA
* * *
2923062 TAAGGACTAAATTGAAGCAAATAAAAA
1 TAAGGATTAAATTAAAACAAATAAAAA
2923089 TGCGGAAGGA
Statistics
Matches: 157, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
161 6 0.04
162 146 0.93
163 3 0.02
164 2 0.01
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.23
Consensus pattern (161 bp):
TAAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGAAGAAATAATCCAAAGAATGA
CACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTACAAACCTTAAAAATTACAG
GGCAAATTTCGCAAATAAAATAAAGATGACA
Found at i:2924235 original size:18 final size:15
Alignment explanation
Indices: 2924175--2924230 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
2924165 GCAGGTTTAA
*
2924175 TGGTGGTGGCAGGGC
1 TGGTGGTGGCAGAGC
2924190 ATGGTGGAT-G--GAGC
1 -TGGTGG-TGGCAGAGC
2924204 TGGTGGTGGCAGAGC
1 TGGTGGTGGCAGAGC
2924219 TGGTGGTGGCAG
1 TGGTGGTGGCAG
2924231 CAGAGGCACG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 1 0.03
13 7 0.20
14 3 0.09
15 16 0.46
16 7 0.20
17 1 0.03
ACGTcount: A:0.12, C:0.11, G:0.55, T:0.21
Consensus pattern (15 bp):
TGGTGGTGGCAGAGC
Found at i:2924415 original size:6 final size:6
Alignment explanation
Indices: 2924376--2924495 Score: 88
Period size: 6 Copynumber: 20.2 Consensus size: 6
2924366 CTTTGGACTC
* * ** *
2924376 TTAAATT TTTAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA-
1 TTAAA-T TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
2924425 TTAAAT TTAAATAT TTAAAT TTAAAT TTAAA- ATAAAT CTAAAT TTAAA-
1 TTAAAT TT-AA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
2924473 -TAAAT TTAAA- ATCAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT T
2924496 CAAAAGTCCA
Statistics
Matches: 90, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
4 4 0.04
5 11 0.12
6 58 0.64
7 13 0.14
8 4 0.04
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:2924428 original size:17 final size:17
Alignment explanation
Indices: 2924408--2924495 Score: 85
Period size: 17 Copynumber: 5.4 Consensus size: 17
2924398 TAATTTTTAT
2924408 TTAAATTTAAATTCAAA
1 TTAAATTTAAATTCAAA
*
2924425 TTAAATTTAAA-T--AT
1 TTAAATTTAAATTCAAA
*
2924439 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTCAAA
* * *
2924456 ATAAATCTAAATTTAAA
1 TTAAATTTAAATTCAAA
* *
2924473 -TAAATTTAAAATCAAT
1 TTAAATTTAAATTCAAA
2924489 TTAAATT
1 TTAAATT
2924496 CAAAAGTCCA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.20
15 1 0.02
16 13 0.22
17 33 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAATTCAAA
Found at i:2928928 original size:58 final size:58
Alignment explanation
Indices: 2928901--2929389 Score: 600
Period size: 58 Copynumber: 8.4 Consensus size: 58
2928891 TGGATACCCG
* *
2928901 GGGGCAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTCA
*
2928958 GAGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTCA
* *
2929016 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-AAAAGATTC-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAG-TTCA
** * *
2929074 GAGGGTAAAATGGTAATTTTCAGTGAAATCGAGGTTAAAATGGAATTTT-AAAAGATTCA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAG-TTCA
* * ** *
2929133 GGGGTAAAATGGTAATTTTCGATGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTT-T
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTCA
* *
2929191 GAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-AAAAGATTC-
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAG-TTCA
** *
2929250 GAGGGTAAAATGGTAATTTTCAGTGAAATCGGGGTTAAAATGGAATTTT-AAAAGATTCA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAG-TTCA
* * **
2929309 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTTG-AAGATTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAG-TTCA
2929368 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
2929390 AAGTTTCGGG
Statistics
Matches: 389, Mismatches: 30, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
57 13 0.03
58 188 0.48
59 184 0.47
60 4 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTCA
Found at i:2928931 original size:29 final size:29
Alignment explanation
Indices: 2928899--2929386 Score: 232
Period size: 29 Copynumber: 16.7 Consensus size: 29
2928889 TTTGGATACC
*
2928899 CGGGGGCAAAATGGTAATTTTGGTGAAAT
1 CGGGGGTAAAATGGTAATTTTGGTGAAAT
*
2928928 CGGGGTTAAAATGG-AATTTT-G-GAAAGTT
1 CGGGGGTAAAATGGTAATTTTGGTGAAA--T
** *
2928956 TAGAGGTAAAATGGTAATTTTTGGTGAAAT
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAAT
*
2928986 CGGGGTTAAAATGG-AATTTT-G-GAAAGTT
1 CGGGGGTAAAATGGTAATTTTGGTGAAA--T
*
2929014 CAGGGGTAAAATGGTAATTTTTGGTGAAAT
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAAT
* * **
2929044 CGAGGTTAAAAATGG-AATTTT--AAAAGATT
1 CGGGGGT-AAAATGGTAATTTTGGTGAA-A-T
* *
2929073 CGAGGGTAAAATGGTAATTTTCAGTGAAAT
1 CGGGGGTAAAATGGTAATTTT-GGTGAAAT
* * **
2929103 CGAGGTTAAAATGG-AATTTT--AAAAGATT
1 CGGGGGTAAAATGGTAATTTTGGTGAA-A-T
* *
2929131 CAGGGGTAAAATGGTAATTTTCGATGAAAT
1 CGGGGGTAAAATGGTAATTTT-GGTGAAAT
** *
2929161 TAGGGTTAAAAATGG-AATTTT-G-GAAAGTT
1 CGGGGGT-AAAATGGTAATTTTGGTGAAA--T
* *
2929190 TGAGGGTAAAATGGTAATTTTTGGTGAAAT
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAAT
* * **
2929220 CGAGGTTAAAAATGG-AATTTT--AAAAGATT
1 CGGGGGT-AAAATGGTAATTTTGGTGAA-A-T
* *
2929249 CGAGGGTAAAATGGTAATTTTCAGTGAAAT
1 CGGGGGTAAAATGGTAATTTT-GGTGAAAT
* **
2929279 CGGGGTTAAAATGG-AATTTT--AAAAGATT
1 CGGGGGTAAAATGGTAATTTTGGTGAA-A-T
*
2929307 CAGGGGTAAAATGGTAATTTTTGGTGAAAT
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAAT
* *
2929337 CGAGGTTAAAAATGG-AATTTT--TGAAGATT
1 CGGGGGT-AAAATGGTAATTTTGGTGAA-A-T
*
2929366 TGGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
2929387 TGGAAGTTTC
Statistics
Matches: 355, Mismatches: 55, Indels: 98
0.70 0.11 0.19
Matches are distributed among these distances:
26 12 0.03
27 16 0.05
28 90 0.25
29 94 0.26
30 88 0.25
31 35 0.10
32 20 0.06
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (29 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAAT
Found at i:2929100 original size:117 final size:118
Alignment explanation
Indices: 2928901--2929389 Score: 658
Period size: 117 Copynumber: 4.2 Consensus size: 118
2928891 TGGATACCCG
* * * * *
2928901 GGGGCAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTTAGA-GGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTGAAAAGATTCGAGGGTA
* *
2928964 AAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAG-TTCA
66 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-AAAAGATTCA
2929016 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-AAAAGATTCGAGGGT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGAAAAGATTCGAGGGT
**
2929080 AAAATGGTAATTTTCAGTGAAATCGAGGTT-AAAATGGAATTTTAAAAGATTCA
65 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCA
* * * * *
2929133 GGGGTAAAATGGTAATTTTCGATGAAAT-TAGGGTTAAAAATGGAATTTTGGAAAG-TTTGAGGG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGA-GGTT-AAAATGGAATTTTGAAAAGATTCGAGGG
2929196 TAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTC-
64 TAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCA
** *
2929250 GAGGGTAAAATGGTAATTTTCAGTGAAATCGGGGTTAAAATGGAATTTT-AAAAGATTC-AGGGG
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTGAAAAGATTCGA-GGG
** **
2929313 TAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTTGAAGATTTG
64 TAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCA
2929368 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
2929390 AAGTTTCGGG
Statistics
Matches: 335, Mismatches: 27, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
115 14 0.04
116 36 0.11
117 229 0.68
118 56 0.17
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (118 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTGAAAAGATTCGAGGGTA
AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCA
Found at i:2929223 original size:176 final size:176
Alignment explanation
Indices: 2928906--2929389 Score: 773
Period size: 176 Copynumber: 2.8 Consensus size: 176
2928896 ACCCGGGGGC
* * * *
2928906 AAAATGGTAATTTT-GGTGAAATCGGGGTTAAAATGGAATTTTGGAAAG-TTTAGAGGTAAAATG
1 AAAATGGTAATTTTCAGTGAAATCGGGGTTAAAATGGAATTTT-AAAAGATTCAGGGGTAAAATG
** *
2928969 GTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAG-TTCAGGGGTAAAATGGTAAT
65 GTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGA-GGGTAAAATGGTAAT
2929032 TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCGAGGGT
129 TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCGAGGGT
*
2929080 AAAATGGTAATTTTCAGTGAAATCGAGGTTAAAATGGAATTTTAAAAGATTCAGGGGTAAAATGG
1 AAAATGGTAATTTTCAGTGAAATCGGGGTTAAAATGGAATTTTAAAAGATTCAGGGGTAAAATGG
* *
2929145 TAATTTTCGATGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTT
66 TAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTT
2929210 TTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCGAGGGT
131 TTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCGAGGGT
2929256 AAAATGGTAATTTTCAGTGAAATCGGGGTTAAAATGGAATTTTAAAAGATTCAGGGGTAAAATGG
1 AAAATGGTAATTTTCAGTGAAATCGGGGTTAAAATGGAATTTTAAAAGATTCAGGGGTAAAATGG
* * *
2929321 TAATTTTTGGTGAAA-TCGAGGTTAAAAATGGAATTTTTG-AAGATTTGGGGGTAAAATGGTAAT
66 TAATTTTTGGTGAAATTAG-GGTTAAAAATGGAATTTTGGAAAG-TTTGAGGGTAAAATGGTAAT
2929384 TTTTGG
129 TTTTGG
2929390 AAGTTTCGGG
Statistics
Matches: 288, Mismatches: 16, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
174 18 0.06
175 64 0.22
176 203 0.70
177 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (176 bp):
AAAATGGTAATTTTCAGTGAAATCGGGGTTAAAATGGAATTTTAAAAGATTCAGGGGTAAAATGG
TAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAATTT
TTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCGAGGGT
Found at i:2929711 original size:162 final size:162
Alignment explanation
Indices: 2929520--2929858 Score: 516
Period size: 162 Copynumber: 2.1 Consensus size: 162
2929510 CATCCAGCAG
* * * * ** *
2929520 TCAAAGGATTAAATTGTAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGA
1 TCAAAGGACTAAATTATAAACCATGAAAAATTCTTGGGCCAATTTCATAATTAAATAAAAGTTCA
* *
2929585 TTTGGGGATTAAATTAAGACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAGT
66 TTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAAT
2929650 GACACGTGGCAGCCCCTGGTACAGTCAAACAA
131 GACACGTGGCAGCCCCTGGTACAGTCAAACAA
*
2929682 TCAAAGGACTAATTTATAAACCATGAAAAATTCTTGGGCCAATTTCATAATTAAATAAAAGTTCA
1 TCAAAGGACTAAATTATAAACCATGAAAAATTCTTGGGCCAATTTCATAATTAAATAAAAGTTCA
*** * *
2929747 TTTGGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGTATAAATAATCCAAAAAAT
66 TTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAAT
* * *
2929812 GACATGTGGCAGCCTCTGGTACAGTCAAACAG
131 GACACGTGGCAGCCCCTGGTACAGTCAAACAA
2929844 TCAAAGGACTAAATT
1 TCAAAGGACTAAATT
2929859 GAAAAGTAAT
Statistics
Matches: 158, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
162 158 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (162 bp):
TCAAAGGACTAAATTATAAACCATGAAAAATTCTTGGGCCAATTTCATAATTAAATAAAAGTTCA
TTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCAAAAAAT
GACACGTGGCAGCCCCTGGTACAGTCAAACAA
Found at i:2930735 original size:3 final size:3
Alignment explanation
Indices: 2930727--2930756 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2930717 TTTTATTGCT
2930727 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2930757 ATGTTTCTCA
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:2931444 original size:17 final size:17
Alignment explanation
Indices: 2931424--2931490 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
2931414 TTAATATTAT
* *
2931424 TTTAAATTAAGTTTAAA
1 TTTAAAATAAATTTAAA
2931441 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
*
2931458 --T-AAGTAAATTTAAA
1 TTTAAAATAAATTTAAA
* *
2931472 TTTAAGATAAATTAAAA
1 TTTAAAATAAATTTAAA
2931489 TT
1 TT
2931491 AATTCAAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
14 12 0.29
15 1 0.02
16 1 0.02
17 27 0.66
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:2931625 original size:30 final size:29
Alignment explanation
Indices: 2931583--2931685 Score: 86
Period size: 31 Copynumber: 3.5 Consensus size: 29
2931573 GTTCGGGGCT
2931583 AAAATGGTAATTTTGGGTGAAATCGAGATTA
1 AAAATGGTAATTTT-GGTGAAATCGAG-TTA
* ** ***
2931614 AAAATGG-AATTTTTG-GAAAGTTTAGGGG
1 AAAATGGTAATTTTGGTGAAA-TCGAGTTA
2931642 AAAATGGTAATTTTTGGTGAAATCGAGGTTA
1 AAAATGGTAA-TTTTGGTGAAATCGA-GTTA
2931673 AAAATGG-AATTTT
1 AAAATGGTAATTTT
2931686 TTTGAGAGTT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
28 11 0.20
29 10 0.18
30 15 0.27
31 19 0.35
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATCGAGTTA
Found at i:2931646 original size:59 final size:59
Alignment explanation
Indices: 2931555--2931893 Score: 456
Period size: 59 Copynumber: 5.7 Consensus size: 59
2931545 ATCGGGGTTG
* * * *
2931555 AAAATAGAATTTTGGAAAG-TTCGGGGCTAAAATGGTAATTTTGGGTGAAATCGAGATTA
1 AAAATGGAATTTTGGAGAGTTTAGGGG-TAAAATGGTAATTTTTGGTGAAATCGAGATTA
* *
2931614 AAAATGGAATTTTTGGAAAGTTTAGGGG-AAAATGGTAATTTTTGGTGAAATCGAGGTTA
1 AAAATGGAA-TTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGATTA
* * *
2931673 AAAATGGAATTTTTTTGAGAGTTTGGGGGTAAAATGGTAATTTTTTGGTAAAATC-AGGATTAA
1 AAAATGGAA--TTTTGGAGAGTTTAGGGGTAAAATGGTAA-TTTTTGGTGAAATCGA-GATT-A
2931736 AAAATGGAATTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGATTA
1 AAAATGGAATTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGATTA
*
2931795 AAAATGGAATTTTGGAGAGTTTAGGGGT-AAATGGTAATTTTTGGTGAAATCGAGGTT-
1 AAAATGGAATTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGATTA
* *
2931852 AAAATGGAGTTTTTGAGAGTTT-GGGGTTAAAATGGTAATTTT
1 AAAATGGAATTTTGGAGAGTTTAGGGG-TAAAATGGTAATTTT
2931894 GGGAAGTTTC
Statistics
Matches: 255, Mismatches: 15, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
56 4 0.02
57 21 0.08
58 41 0.16
59 75 0.29
60 43 0.17
61 45 0.18
62 16 0.06
63 10 0.04
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (59 bp):
AAAATGGAATTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGATTA
Found at i:2931779 original size:122 final size:118
Alignment explanation
Indices: 2931555--2931893 Score: 456
Period size: 122 Copynumber: 2.9 Consensus size: 118
2931545 ATCGGGGTTG
* * * * *
2931555 AAAATAGAATTTTGGAAAGTTCGGGGCTAAAATGGTAATTTTGGGTGAAATC-GAGATTAAAAAT
1 AAAATGGAATTTTGGAGAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCAG-GATTAAAAAT
* *
2931619 GGAATTTTTGGAAAGTTTAGGGG-AAAATGGTAATTTTTGGTGAAATCGAGGTTA
65 GGAA-TTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGATTA
* *
2931673 AAAATGGAATTTTTTTGAGAGTTTGGGGGTAAAATGGTAATTTTTTGGTAAAATCAGGATTAAAA
1 AAAATGGAA--TTTTGGAGAGTTTGGGGGTAAAATGGTAA-TTTTTGGTGAAATCAGGATT-AAA
2931738 AATGGAATTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGATTA
62 AATGGAATTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGATTA
*
2931795 AAAATGGAATTTTGGAGAGTTTAGGGGT-AAATGGTAATTTTTGGTGAAATCGAGG-TT-AAAAT
1 AAAATGGAATTTTGGAGAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATC-AGGATTAAAAAT
* *
2931857 GGAGTTTTTGAGAGTTT-GGGGTTAAAATGGTAATTTT
65 GGAATTTTGGAGAGTTTAGGGG-TAAAATGGTAATTTT
2931894 GGGAAGTTTC
Statistics
Matches: 199, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
115 4 0.02
116 35 0.18
118 23 0.12
119 12 0.06
120 42 0.21
121 33 0.17
122 50 0.25
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (118 bp):
AAAATGGAATTTTGGAGAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGATTAAAAATG
GAATTTTGGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGATTA
Found at i:2931864 original size:29 final size:30
Alignment explanation
Indices: 2931582--2931893 Score: 150
Period size: 30 Copynumber: 10.5 Consensus size: 30
2931572 AGTTCGGGGC
* *
2931582 TAAAATGGTAATTTTGGGTGAAATCGAGAT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGT
** *
2931612 TAAAAATGG-AATTTTT-G-GAAAGTTTAGGG
1 T-AAAATGGTAATTTTTGGTGAAA-TCGAGGT
*
2931641 GAAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGT
* * * * *
2931671 TAAAAATGG-AATTTTT-TTGAGAGTTTGGGGG
1 T-AAAATGGTAATTTTTGGTGA-A-ATCGAGGT
*
2931702 TAAAATGGTAATTTTTTGGTAAAATC-AGGAT
1 TAAAATGGTAA-TTTTTGGTGAAATCGAGG-T
* * ** *
2931733 TAAAAAATGG-AA-TTTTGGAG-AGTTTAGGGG
1 T--AAAATGGTAATTTTTGGTGAAATCGA-GGT
*
2931763 TAAAATGGTAATTTTTGGTGAAATCGAGAT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGT
* * ** *
2931793 TAAAAATGG-AA-TTTTGGAG-AGTTTAGGGG
1 T-AAAATGGTAATTTTTGGTGAAATCGA-GGT
2931822 T-AAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGT
* * ** * *
2931851 TAAAATGG-AGTTTTT-GAGAGTTTGGGGT
1 TAAAATGGTAATTTTTGGTGAAATCGAGGT
2931879 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
2931894 GGGAAGTTTC
Statistics
Matches: 206, Mismatches: 50, Indels: 53
0.67 0.16 0.17
Matches are distributed among these distances:
27 6 0.03
28 39 0.19
29 48 0.23
30 57 0.28
31 39 0.19
32 8 0.04
33 9 0.04
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGTGAAATCGAGGT
Found at i:2933899 original size:11 final size:11
Alignment explanation
Indices: 2933885--2933975 Score: 62
Period size: 11 Copynumber: 8.5 Consensus size: 11
2933875 GTTTTATAAT
*
2933885 TTTAATTTTAA
1 TTTAAATTTAA
2933896 TTTAAATTTAA
1 TTTAAATTTAA
**
2933907 GGTAAATTTAA
1 TTTAAATTTAA
* *
2933918 -AT-AATTAAA
1 TTTAAATTTAA
2933927 TTTAAATTTAA
1 TTTAAATTTAA
**
2933938 GATAAATTTAAA
1 TTTAAATTT-AA
*
2933950 TTTAAA-TAAA
1 TTTAAATTTAA
* *
2933960 TTTAAAATCAA
1 TTTAAATTTAA
2933971 TTTAA
1 TTTAA
2933976 CTTTTAAATT
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
9 6 0.10
10 10 0.16
11 41 0.65
12 6 0.10
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:2933905 original size:6 final size:6
Alignment explanation
Indices: 2933877--2933965 Score: 71
Period size: 6 Copynumber: 15.0 Consensus size: 6
2933867 TTAAATTTGT
* * **
2933877 TTTATAA TTTTAA TTTTAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
2933927 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2933966 ATCAATTTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 17
0.75 0.07 0.19
Matches are distributed among these distances:
4 5 0.07
5 6 0.09
6 47 0.69
7 4 0.06
8 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:2933932 original size:31 final size:32
Alignment explanation
Indices: 2933894--2933965 Score: 110
Period size: 31 Copynumber: 2.2 Consensus size: 32
2933884 TTTTAATTTT
* *
2933894 AATTTAAATTTAAGGTAAATTTAAA-TAATTA
1 AATTTAAATTTAAGATAAATTTAAATTAAATA
2933925 AATTTAAATTTAAGATAAATTTAAATTTAAATA
1 AATTTAAATTTAAGATAAATTTAAA-TTAAATA
2933958 AATTTAAA
1 AATTTAAA
2933966 ATCAATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 24 0.65
33 13 0.35
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (32 bp):
AATTTAAATTTAAGATAAATTTAAATTAAATA
Found at i:2933967 original size:17 final size:17
Alignment explanation
Indices: 2933894--2933965 Score: 98
Period size: 17 Copynumber: 4.5 Consensus size: 17
2933884 TTTTAATTTT
*
2933894 AATTTAAATTTAAGGTA
1 AATTTAAATTTAAGATA
*
2933911 AATTTAAA--TAA-TTA
1 AATTTAAATTTAAGATA
2933925 AATTTAAATTTAAGATA
1 AATTTAAATTTAAGATA
2933942 AATTTAAATTTAA-ATA
1 AATTTAAATTTAAGATA
2933958 AATTTAAA
1 AATTTAAA
2933966 ATCAATTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 14 0.28
17 23 0.46
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (17 bp):
AATTTAAATTTAAGATA
Found at i:2935549 original size:2 final size:2
Alignment explanation
Indices: 2935542--2935570 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2935532 TTACATGTAT
2935542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2935571 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2935812 original size:76 final size:75
Alignment explanation
Indices: 2935673--2935870 Score: 289
Period size: 76 Copynumber: 2.7 Consensus size: 75
2935663 CAAGGAGAAA
*
2935673 ACTTGATATCCAGCTTTACTTCAATTTCAA--G--AGGAAATGATCTTGTTCTTACTTCAATTTC
1 ACTTGATATCCAGCTTTACTTCAATTTCAAGCGATAGGAAATGATCTTGCTCTTACTTCAATTTC
*
2935734 AGAGATCAAG
66 AGAGATAAAG
*
2935744 ACTTGATATCCAGCTTTACTTCAATTTCAAGCGAATAGGAAAAGATCTTGCTCTTACTTCAATTT
1 ACTTGATATCCAGCTTTACTTCAATTTCAAGCG-ATAGGAAATGATCTTGCTCTTACTTCAATTT
2935809 CAGAGATAAAG
65 CAGAGATAAAG
* * *
2935820 ACGTGTTATCCA-CTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCT
1 ACTTGATATCCAGCTTTACTTCAATTTCAAGC-GATAGGAAATGATCTTGCT
2935871 GCGGTCTGAT
Statistics
Matches: 114, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
71 30 0.26
73 1 0.01
75 35 0.31
76 48 0.42
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (75 bp):
ACTTGATATCCAGCTTTACTTCAATTTCAAGCGATAGGAAATGATCTTGCTCTTACTTCAATTTC
AGAGATAAAG
Found at i:2954086 original size:59 final size:59
Alignment explanation
Indices: 2953979--2954441 Score: 730
Period size: 59 Copynumber: 7.9 Consensus size: 59
2953969 TATGGATACC
* * *
2953979 CGGGGGCAAAATGGTAATTTT-GGTGTAATCGGGATTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * *
2954037 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * *
2954096 CGGGGGTAAAATGGTAATTTTTGGTGAAGTCGGGGTTAAAAATGGAATTTTAAAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
2954155 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * * *
2954214 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * *
2954273 CAGGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGAAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
2954332 CGGGGGTAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAGAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
2954391 CGGGGGTAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGTAATTTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTT
2954442 GGAAAAGTTT
Statistics
Matches: 376, Mismatches: 28, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
58 20 0.05
59 356 0.95
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:2954530 original size:29 final size:27
Alignment explanation
Indices: 2954427--2954530 Score: 82
Period size: 30 Copynumber: 3.5 Consensus size: 27
2954417 AAATCGGGGT
*
2954427 TAAAAATGTAATTTTGGAAAAGTTTTGGGG
1 TAAAAATG--ATTTTGGAAAAG-TTTCGGG
*
2954457 TTAAAATATAATTTTGGAAAAGTTTCGGGG
1 -TAAAA-ATGATTTTGGAAAAGTTTC-GGG
*
2954487 TTAAAATGTAATTTTGGAAAAGTTTCGGG
1 TAAAAATG--ATTTTGGAAAAGTTTCGGG
*
2954516 TCGAAAGATGATTTT
1 T--AAAAATGATTTT
2954531 TAGACATTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
28 2 0.03
29 16 0.26
30 31 0.51
31 10 0.16
32 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (27 bp):
TAAAAATGATTTTGGAAAAGTTTCGGG
Found at i:2954858 original size:161 final size:162
Alignment explanation
Indices: 2954623--2954950 Score: 450
Period size: 161 Copynumber: 2.0 Consensus size: 162
2954613 ACTAATTTGA
* *
2954623 AAACTTTGAAAAATTTTCGGACCAATTTTGTAATTAACTAAGAGTTAATTTAAGGACTAAATTAA
1 AAACCTTGAAAAATTTTCGGACCAATTTCGTAATTAACTAAGAGTTAATTTAAGGACTAAATTAA
* * *
2954688 AATAAATTAAAAATAAAAGGGACTAAATGCAGAAATAAGCC-AAAAATTGACACGTGGCAACCTC
66 AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCGAAAAA-TGACACATGGCAACCTC
* **
2954752 TGGTGCAGTCAAACAGTCAAAGGACTAGTTTAT
130 TGGTACAGTCAAACAGTCAAAGGACTAAATTAT
* * *
2954785 AAACCTTGAAAAATTATT-GGGCCAATTTCGTAATTAAAAC-AA-AGTTGATTT-AGGATTAAAT
1 AAACCTTGAAAAATT-TTCGGACCAATTTCGTAATT--AACTAAGAGTTAATTTAAGGACTAAAT
* * * *
2954846 TAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCGAAACATGACACATGGCAATC
63 TAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCGAAAAATGACACATGGCAACC
2954911 TCTGGTACAGTCAAACAGTCAAAGGACTAAATTAT
128 TCTGGTACAGTCAAACAGTCAAAGGACTAAATTAT
2954946 AAACC
1 AAACC
2954951 AATTAAAATT
Statistics
Matches: 147, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
161 99 0.67
162 41 0.28
163 4 0.03
164 3 0.02
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.26
Consensus pattern (162 bp):
AAACCTTGAAAAATTTTCGGACCAATTTCGTAATTAACTAAGAGTTAATTTAAGGACTAAATTAA
AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCGAAAAATGACACATGGCAACCTCT
GGTACAGTCAAACAGTCAAAGGACTAAATTAT
Found at i:2955023 original size:161 final size:160
Alignment explanation
Indices: 2954674--2955023 Score: 404
Period size: 161 Copynumber: 2.2 Consensus size: 160
2954664 GAGTTAATTT
* *
2954674 AAGGACTAAATTAAAATAAATTAAAAATAAAAGGGACTAAATGCAGAAATAAGCCAAAAATTGAC
1 AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
* * ** **
2954739 ACGTGGCAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATTG
66 ACATGGCAACCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTT-AAAAATTACAG
* * * * **
2954804 GGCCAATTTCGTAATTAAAACAAAGTTGATT
130 GGCAAATTTCGCAAATAAAACAAAGATGAAA
* * * * *
2954835 TAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAATCCGAAACA-TGA
1 AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCC-AAAAATTGA
*
2954899 CACATGGCAATCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCAATT-AAAATTAC
65 CACATGGCAACCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACC--TTAAAAATTAC
2954963 AGGGCAAATTT-GCAAATAATTAA-AAAGATGCAAA
128 AGGGCAAATTTCGCAAATAA--AACAAAGATG-AAA
* *
2954997 AAGGACTAAATTGAAGCAAA-TAAAAAT
1 AAGGACTAAATTAAAACAAATTAAAAAT
2955024 GCGGAAGGAT
Statistics
Matches: 159, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
160 6 0.04
161 128 0.81
162 23 0.14
163 2 0.01
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (160 bp):
AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
ACATGGCAACCTCTGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTTAAAAATTACAGG
GCAAATTTCGCAAATAAAACAAAGATGAAA
Found at i:2955753 original size:25 final size:25
Alignment explanation
Indices: 2955719--2955768 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2955709 TTTTTTATTT
2955719 ATTAATAATTAATAATATCATTAAA
1 ATTAATAATTAATAATATCATTAAA
* * *
2955744 ATTATTAATTAATGATATTATTAAA
1 ATTAATAATTAATAATATCATTAAA
2955769 TGTTATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTAATAATTAATAATATCATTAAA
Found at i:2956268 original size:20 final size:21
Alignment explanation
Indices: 2956236--2956275 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2956226 CAGGGCATGG
*
2956236 TGGAGCTTGGTGGTCAGCAGA
1 TGGAGCTTGGTGGCCAGCAGA
2956257 TGGAGC-TGGTGGCCAGCAG
1 TGGAGCTTGGTGGCCAGCAG
2956276 CAGTAGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.20
Consensus pattern (21 bp):
TGGAGCTTGGTGGCCAGCAGA
Found at i:2956474 original size:6 final size:6
Alignment explanation
Indices: 2956435--2956548 Score: 76
Period size: 6 Copynumber: 19.2 Consensus size: 6
2956425 CTTTGGACTC
* * ** *
2956435 TTAAATT TTTAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA-
1 TTAAA-T TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
2956484 TTAAAT TTAAATAT TTAAAT TTAAA- ATAAAT CTAAAT TTAAA- -TAAAT
1 TTAAAT TT-AA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
2956531 TTAAA- ATCAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT T
2956549 CAAAAGTCCA
Statistics
Matches: 84, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
4 4 0.05
5 11 0.13
6 52 0.62
7 13 0.15
8 4 0.05
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:2956487 original size:11 final size:12
Alignment explanation
Indices: 2956469--2956552 Score: 63
Period size: 11 Copynumber: 7.2 Consensus size: 12
2956459 ATTTTTATTT
2956469 AAATTTAAATTC
1 AAATTTAAATTC
*
2956481 AAA-TTAAATTTA
1 AAATTTAAA-TTC
*
2956493 AATATTTAAATTT
1 AA-ATTTAAATTC
*
2956506 AAA-ATAAA-TC
1 AAATTTAAATTC
2956516 TAAATTTAAA-T-
1 -AAATTTAAATTC
*
2956527 AAATTTAAAATC
1 AAATTTAAATTC
2956539 -AATTTAAATTC
1 AAATTTAAATTC
2956550 AAA
1 AAA
2956553 AGTCCAAGCC
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
10 10 0.17
11 23 0.40
12 15 0.26
13 5 0.09
14 5 0.09
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATTTAAATTC
Found at i:2956499 original size:25 final size:25
Alignment explanation
Indices: 2956471--2956520 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2956461 TTTTATTTAA
* *
2956471 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
2956496 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
2956521 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:2956502 original size:31 final size:31
Alignment explanation
Indices: 2956464--2956527 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
2956454 TTTTAATTTT
*
2956464 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
2956495 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
2956526 TA
1 TA
2956528 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:2956548 original size:17 final size:16
Alignment explanation
Indices: 2956465--2956535 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
2956455 TTTAATTTTT
2956465 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
2956483 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
2956496 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
2956513 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
2956529 ATTTAAA
1 ATTTAAA
2956536 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:2957965 original size:28 final size:27
Alignment explanation
Indices: 2957933--2957994 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
2957923 TGAAAACGGG
*
2957933 AATTTTGGATACCCG-GGGGTAGAATGGT
1 AATTTTGG--ACCCGAGGGGTAAAATGGT
*
2957961 AATTTTGGACTCGTAGGGGTAAAATGGT
1 AATTTTGGACCCG-AGGGGTAAAATGGT
2957989 AATTTT
1 AATTTT
2957995 TGGTGAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.13
28 26 0.87
ACGTcount: A:0.27, C:0.08, G:0.31, T:0.34
Consensus pattern (27 bp):
AATTTTGGACCCGAGGGGTAAAATGGT
Found at i:2958008 original size:29 final size:30
Alignment explanation
Indices: 2957976--2958136 Score: 137
Period size: 30 Copynumber: 5.5 Consensus size: 30
2957966 TGGACTCGTA
2957976 GGGGT-AAAATGGTAATTTTTGGTGAAATC
1 GGGGTAAAAATGGTAATTTTTGGTGAAATC
*
2958005 GGGGTCAAAAATGG-AA-TTTT-G-GAAAGTTTA
1 GGGGT-AAAAATGGTAATTTTTGGTGAAA---TC
2958035 GGGGT-AAAATGGTAATTTTTGGTGAAATC
1 GGGGTAAAAATGGTAATTTTTGGTGAAATC
*
2958064 GAGGTTAAAAATGG-AA-TTTT-G-GAAAGTTC
1 G-GGGTAAAAATGGTAATTTTTGGTGAAA--TC
*
2958093 GAGGGT-AAAACGGTAATTTTTGGTGAAATC
1 G-GGGTAAAAATGGTAATTTTTGGTGAAATC
*
2958123 GGGTTAAAAATGGT
1 GGGGTAAAAATGGT
2958137 GTTTTGGAAA
Statistics
Matches: 107, Mismatches: 7, Indels: 35
0.72 0.05 0.23
Matches are distributed among these distances:
27 8 0.07
28 15 0.14
29 29 0.27
30 31 0.29
31 16 0.15
32 8 0.07
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (30 bp):
GGGGTAAAAATGGTAATTTTTGGTGAAATC
Found at i:2958039 original size:30 final size:29
Alignment explanation
Indices: 2958005--2958170 Score: 89
Period size: 30 Copynumber: 5.7 Consensus size: 29
2957995 TGGTGAAATC
2958005 GGGGTCAAAAATGGAATTTTGGAAAGTTTA
1 GGGGT-AAAAATGGAATTTTGGAAAGTTTA
**
2958035 GGGGT-AAAATGGTAATTTTTGGTGAAA-TCGA
1 GGGGTAAAAATGG-AA-TTTT-G-GAAAGTTTA
* *
2958066 -GGTTAAAAATGGAATTTTGGAAAG-TTC
1 GGGGTAAAAATGGAATTTTGGAAAGTTTA
* *
2958093 GAGGGT-AAAACGGTAATTTTTGGTGAAA---TC
1 G-GGGTAAAAATGG-AA-TTTT-G-GAAAGTTTA
* **
2958123 GGGTTAAAAATGGTGTTTTGGAAAGTTTA
1 GGGGTAAAAATGGAATTTTGGAAAGTTTA
2958152 GGGGT-AAAATGGTAATTTT
1 GGGGTAAAAATGG-AATTTT
2958171 TAGACAGTTC
Statistics
Matches: 103, Mismatches: 16, Indels: 35
0.67 0.10 0.23
Matches are distributed among these distances:
26 4 0.04
27 5 0.05
28 25 0.24
29 23 0.22
30 27 0.26
31 11 0.11
32 8 0.08
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTGGAAAGTTTA
Found at i:2958041 original size:59 final size:59
Alignment explanation
Indices: 2957974--2958171 Score: 319
Period size: 59 Copynumber: 3.4 Consensus size: 59
2957964 TTTGGACTCG
*
2957974 TAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTT
1 TAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
*
2958033 TAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAG-T
1 TAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* * **
2958091 TCGAGGGTAAAACGGTAATTTTTGGTGAAATC-GGGTTAAAAATGGTGTTTTGGAAAGTT
1 TAG-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
2958150 TAGGGGTAAAATGGTAATTTTT
1 TAGGGGTAAAATGGTAATTTTT
2958172 AGACAGTTCA
Statistics
Matches: 128, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
58 43 0.34
59 85 0.66
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (59 bp):
TAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:2958607 original size:21 final size:21
Alignment explanation
Indices: 2958581--2958623 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2958571 ACGCCATTCC
*
2958581 AAACAACAAAATAAAAAACAA
1 AAACAACAAAACAAAAAACAA
* *
2958602 AAACAACACAACAAAAATCAA
1 AAACAACAAAACAAAAAACAA
2958623 A
1 A
2958624 TAAACGAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.77, C:0.19, G:0.00, T:0.05
Consensus pattern (21 bp):
AAACAACAAAACAAAAAACAA
Found at i:2958905 original size:58 final size:58
Alignment explanation
Indices: 2958826--2958945 Score: 181
Period size: 58 Copynumber: 2.1 Consensus size: 58
2958816 AAAAGGAGTT
*
2958826 GTTTATGAGTGTTATTTAAGAATAAAATTATAAT-TGAGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTAT-ATCTGAGTTTAAAAATATTTGGGTTTA
* *
2958884 GTTTATGAGTATT-TTTGAAGAATGAAATTATATCTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTATTATTT-AAGAATAAAATTATATCTGAGTTTAAAAATATTTGGGTTTA
2958942 GTTT
1 GTTT
2958946 GTTGATGGGT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
57 5 0.09
58 52 0.91
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (58 bp):
GTTTATGAGTATTATTTAAGAATAAAATTATATCTGAGTTTAAAAATATTTGGGTTTA
Found at i:2959204 original size:23 final size:23
Alignment explanation
Indices: 2959161--2959205 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2959151 AAAAAAATTC
**
2959161 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
2959184 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
2959206 ATTTGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:2962078 original size:16 final size:15
Alignment explanation
Indices: 2962059--2962108 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
2962049 AATTTTATGA
2962059 TTATATTATTTATATT
1 TTATATTATTTA-ATT
*
2962075 TTATCATTTTTTAATT
1 TTAT-ATTATTTAATT
* *
2962091 TTATATAATTAAATT
1 TTATATTATTTAATT
2962106 TTA
1 TTA
2962109 AAACCTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 11 0.38
16 11 0.38
17 7 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATATTATTTAATT
Found at i:2966746 original size:59 final size:58
Alignment explanation
Indices: 2966652--2967025 Score: 507
Period size: 59 Copynumber: 6.3 Consensus size: 58
2966642 TTGGATATCC
* *
2966652 AGGGGCAAAATGGTAATTTTTTGGTGAAATCGGGGTTAAAAATGGAAATTTGGAAAGTTT
1 AGGGGTAAAATGGTAA-TTTTTGGTGAAAT-GGGGTTAAAAATGGAATTTTGGAAAGTTT
*
2966712 AGGGGTAAAATGGTAACTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAA-TGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * * *
2966771 AGGGATAAAATGGTAA-TTTTAGTTAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAA-TGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * *
2966829 AGGGATAAAATGGTAATTTTTGGTTAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAA-TGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * * * *
2966888 AGGGGTGAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGGATTTTGGGAAGTTC
1 AGGGGTAAAATGGTAATTTTTGGTGAAA-TGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * **
2966947 GGGGGTAAAATAGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAAT-GGGGTTAAAAATGGAATTTTGGAAAGTTT
2967006 AGGGGTAAAATGGTAATTTT
1 AGGGGTAAAATGGTAATTTT
2967026 GGGACCATCC
Statistics
Matches: 280, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
58 54 0.19
59 210 0.75
60 16 0.06
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (58 bp):
AGGGGTAAAATGGTAATTTTTGGTGAAATGGGGTTAAAAATGGAATTTTGGAAAGTTT
Found at i:2966965 original size:29 final size:29
Alignment explanation
Indices: 2966933--2967029 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
2966923 TAAAAATGGG
*
2966933 ATTTTGGGAAGTTCGGGGGTAAAATAGTA
1 ATTTTGGGAAGTTCAGGGGTAAAATAGTA
* * * *
2966962 ATTTTTGGTGAA-ATCAAGGTTAAAA-ATGGA
1 A-TTTTGG-GAAGTTCAGGGGTAAAATA-GTA
* * *
2966992 ATTTTGGAAAGTTTAGGGGTAAAATGGTA
1 ATTTTGGGAAGTTCAGGGGTAAAATAGTA
2967021 ATTTTGGGA
1 ATTTTGGGA
2967030 CCATCCAGGG
Statistics
Matches: 50, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
28 2 0.04
29 27 0.54
30 18 0.36
31 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (29 bp):
ATTTTGGGAAGTTCAGGGGTAAAATAGTA
Found at i:2968906 original size:17 final size:17
Alignment explanation
Indices: 2968886--2968961 Score: 61
Period size: 17 Copynumber: 4.5 Consensus size: 17
2968876 AATTCAATTT
2968886 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
2968903 TAAATTCAAATTT-T-A
1 TAAATTTAAATTTATAA
*
2968918 TGCAAATTTAAATTCGA-AA
1 T--AAATTTAAATT-TATAA
*
2968937 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTATAA
2968953 CTAAATTTA
1 -TAAATTTA
2968962 TATCTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
15 3 0.06
16 7 0.15
17 35 0.74
19 2 0.04
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:2972848 original size:22 final size:23
Alignment explanation
Indices: 2972806--2972848 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2972796 ATTAACATTT
2972806 ATAATTAAACATATCATTTTATC
1 ATAATTAAACATATCATTTTATC
*
2972829 ATAATTAATCATA-CATTTTA
1 ATAATTAAACATATCATTTTA
2972849 AAATTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAATTAAACATATCATTTTATC
Found at i:2975004 original size:12 final size:12
Alignment explanation
Indices: 2974989--2975014 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2974979 ATTTAGATAT
2974989 AAGTTTACATTC
1 AAGTTTACATTC
2975001 AAGTTTACATTC
1 AAGTTTACATTC
2975013 AA
1 AA
2975015 CTTCTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (12 bp):
AAGTTTACATTC
Found at i:2977232 original size:28 final size:31
Alignment explanation
Indices: 2977198--2977262 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2977188 AATGATCTTT
2977198 CAACTATTTG-AT-TTT-TTTTTGGGTC-AC
1 CAACTATTTGAATCTTTCTTTTTGGGTCTAC
*
2977225 CTAACTATTTGAATCTTTCTTTTTTGGTCTAC
1 C-AACTATTTGAATCTTTCTTTTTGGGTCTAC
2977257 CAACTA
1 CAACTA
2977263 ATGAAAAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.03
28 9 0.28
29 2 0.06
30 3 0.09
31 14 0.44
32 3 0.09
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (31 bp):
CAACTATTTGAATCTTTCTTTTTGGGTCTAC
Found at i:2977372 original size:21 final size:21
Alignment explanation
Indices: 2977347--2977412 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 21
2977337 AAAGGATCAA
2977347 AGAAAAGCAAAATTGAAAAAG
1 AGAAAAGCAAAATTGAAAAAG
**
2977368 AG-AAAG-ATTAAATT-ATCAA-
1 AGAAAAGCA--AAATTGAAAAAG
2977387 AGAAAAGCAAAATTGAAAAAG
1 AGAAAAGCAAAATTGAAAAAG
2977408 AGAAA
1 AGAAA
2977413 GATTAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
19 8 0.23
20 14 0.40
21 13 0.37
ACGTcount: A:0.65, C:0.05, G:0.17, T:0.14
Consensus pattern (21 bp):
AGAAAAGCAAAATTGAAAAAG
Found at i:2977397 original size:40 final size:40
Alignment explanation
Indices: 2977342--2977422 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
2977332 AAGTGAAAGG
2977342 ATCAAAGAAAAGCAAAATTGAAAAAGAGAAAGATTAAATT
1 ATCAAAGAAAAGCAAAATTGAAAAAGAGAAAGATTAAATT
2977382 ATCAAAGAAAAGCAAAATTGAAAAAGAGAAAGATTAAATT
1 ATCAAAGAAAAGCAAAATTGAAAAAGAGAAAGATTAAATT
2977422 A
1 A
2977423 CACAATGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.63, C:0.05, G:0.15, T:0.17
Consensus pattern (40 bp):
ATCAAAGAAAAGCAAAATTGAAAAAGAGAAAGATTAAATT
Found at i:2977407 original size:19 final size:20
Alignment explanation
Indices: 2977345--2977413 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 20
2977335 TGAAAGGATC
2977345 AAAGA-AAAGCAAAATTGAA
1 AAAGAGAAAGCAAAATTGAA
*
2977364 AAAGAGAAAG-ATTAAATT-ATC
1 AAAGAGAAAGCA--AAATTGA-A
2977385 AAAGA-AAAGCAAAATTGAA
1 AAAGAGAAAGCAAAATTGAA
2977404 AAAGAGAAAG
1 AAAGAGAAAG
2977414 ATTAAATTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
19 16 0.39
20 14 0.34
21 11 0.27
ACGTcount: A:0.65, C:0.04, G:0.17, T:0.13
Consensus pattern (20 bp):
AAAGAGAAAGCAAAATTGAA
Done.