Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 4 of 255
Found at i:914881 original size:22 final size:23
Alignment explanation
Indices: 914850--914892 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
914840 GGTTTTGCCA
914850 ATTTAGGGTTCTGATTGTTTTTT
1 ATTTAGGGTTCTGATTGTTTTTT
* *
914873 ATTT-GGGTTTTGGTTGTTTT
1 ATTTAGGGTTCTGATTGTTTT
914893 ATGACCAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.09, C:0.02, G:0.26, T:0.63
Consensus pattern (23 bp):
ATTTAGGGTTCTGATTGTTTTTT
Found at i:917728 original size:26 final size:26
Alignment explanation
Indices: 917692--917775 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
917682 TATGAAATTC
917692 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
917718 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
917744 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
917770 TTATCA
1 TTATCA
917776 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:923068 original size:26 final size:26
Alignment explanation
Indices: 923037--923144 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
923027 TGAAATGCCC
*
923037 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
923063 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
923089 ACCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
923115 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
923141 ATCA
1 ATCA
923145 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:923766 original size:16 final size:16
Alignment explanation
Indices: 923745--923780 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
923735 TGAATTACTG
923745 ATTACAACTCTATTCA
1 ATTACAACTCTATTCA
* *
923761 ATTACAGCTCTATTCC
1 ATTACAACTCTATTCA
923777 ATTA
1 ATTA
923781 TAGTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCA
Found at i:946023 original size:131 final size:130
Alignment explanation
Indices: 945703--946034 Score: 364
Period size: 130 Copynumber: 2.5 Consensus size: 130
945693 GATGTTTGGA
* * * * *
945703 AATTCGCGGAATCGTGCCCTAACGTACTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATA
1 AATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATA
* * * * * * **
945768 TCACTTCAAAATTTCACTTATGTCTTTTAAAATCCCTTAAACGAAGGTGATGTGCGATATTTGGC
66 TCCCTTCAAAATTTCACTCAGGTCTTTAAAAATCCCTTAAACGAAGGTAATCTGCGATATTTAAC
* * * * * *
945833 AATTCGTGGAATTGTGCCCTAACGTGTTGGGTTGCAATTGCTCGTTTGCTT-AAAGCAATCAAAT
1 AATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTG-TTCAAAACAATCGAAT
* *
945897 ATCCCTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTGAAACGAAGGTAATACT-CGATGTT
65 ATCCCTTCAAAATTTCACTCAGGTCTT-TAAAAATCCCTT-AAACGAAGGTAAT-CTGCGATATT
*
945961 TAAT
127 TAAC
* * **
945965 AATTCG-GGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTCGTTTGTTCAAAACAATCGAATA
1 AATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATA
*
946029 TTCCTT
66 TCCCTT
946035 TAGGTTTTCA
Statistics
Matches: 165, Mismatches: 32, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
130 77 0.47
131 62 0.38
132 25 0.15
133 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (130 bp):
AATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATA
TCCCTTCAAAATTTCACTCAGGTCTTTAAAAATCCCTTAAACGAAGGTAATCTGCGATATTTAAC
Found at i:952029 original size:21 final size:21
Alignment explanation
Indices: 952005--952046 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
951995 ATATTTACTT
952005 ATTATATAAGTA-TATTATTAA
1 ATTATAT-AGTATTATTATTAA
*
952026 ATTATATATTATTATTATTAA
1 ATTATATAGTATTATTATTAA
952047 GTAAAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTATATAGTATTATTATTAA
Found at i:952216 original size:10 final size:10
Alignment explanation
Indices: 952201--952232 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
952191 TTAATGAAAT
952201 AAAGAAAGAA
1 AAAGAAAGAA
952211 AAAGAATAGAA
1 AAAGAA-AGAA
952222 AAAGAAAGAA
1 AAAGAAAGAA
952232 A
1 A
952233 GGATGAAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:954504 original size:50 final size:51
Alignment explanation
Indices: 954385--954611 Score: 262
Period size: 46 Copynumber: 4.7 Consensus size: 51
954375 TCTGATATGA
* * * *
954385 AATGTGTAAGACCTTGGTTGAAAGATACCATGGCAACGTGATATG-AAATG
1 AATGAGTAAGACCATGGTTGAAAGATACTATGGCAACGTGACATGAAAATG
*
954435 --T--GTAAGACCATGGTTGAAAGATACTATAGCAACGTGACA-GAAAATG
1 AATGAGTAAGACCATGGTTGAAAGATACTATGGCAACGTGACATGAAAATG
* *
954481 AATGAGTAAGACCATAGTTGAAAGACACTATGGCAACGTGACATGAAAA-G
1 AATGAGTAAGACCATGGTTGAAAGATACTATGGCAACGTGACATGAAAATG
* * *
954531 -A--A-TAATACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATG
1 AATGAGTAAGACCATGGTTGAAAGATACTATGGCAACGTGACATGAAAATG
* *
954577 AATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 AATGAGTAAGACCATGGTTGAAAGATACTATGGCA
954612 TCATGTCAAA
Statistics
Matches: 150, Mismatches: 16, Indels: 22
0.80 0.09 0.12
Matches are distributed among these distances:
45 6 0.04
46 72 0.48
47 2 0.01
48 2 0.01
49 2 0.01
50 61 0.41
51 5 0.03
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (51 bp):
AATGAGTAAGACCATGGTTGAAAGATACTATGGCAACGTGACATGAAAATG
Found at i:954554 original size:96 final size:96
Alignment explanation
Indices: 954385--954611 Score: 337
Period size: 96 Copynumber: 2.4 Consensus size: 96
954375 TCTGATATGA
* * * * * * * **
954385 AATGTGTAAGACCTTGGTTGAAAGATACCATGGCAACGTGATATGAAATGTGTAAGACCATGGTT
1 AATGAGTAAGACCATAGTTGAAAGACACTATGGCAACGTGACATGAAAAGAATAAGACCATGGTT
* *
954450 GAAAGATACTATAGCAACGTGACAGAAAATG
66 GAAAGATACCATAGCAACATGACAGAAAATG
*
954481 AATGAGTAAGACCATAGTTGAAAGACACTATGGCAACGTGACATGAAAAGAATAATACCATGGTT
1 AATGAGTAAGACCATAGTTGAAAGACACTATGGCAACGTGACATGAAAAGAATAAGACCATGGTT
*
954546 GAAAGATACCATGGCAACATGACAGAAAATG
66 GAAAGATACCATAGCAACATGACAGAAAATG
954577 AATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 AATGAGTAAGACCATAGTTGAAAGACACTATGGCA
954612 TCATGTCAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 118 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (96 bp):
AATGAGTAAGACCATAGTTGAAAGACACTATGGCAACGTGACATGAAAAGAATAAGACCATGGTT
GAAAGATACCATAGCAACATGACAGAAAATG
Found at i:955666 original size:27 final size:27
Alignment explanation
Indices: 955636--955725 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
955626 TAACAAACGT
955636 ATTTAAAATGAATAATGTGAAAAAGAA
1 ATTTAAAATGAATAATGTGAAAAAGAA
* * * *
955663 ATTTAATATCAACAATGT-ACAAAA-CA
1 ATTTAAAATGAATAATGTGA-AAAAGAA
* * *
955689 ATTAAAAATAGAGT-ATGTGTAAAAGAA
1 ATTTAAAAT-GAATAATGTGAAAAAGAA
955716 ATTTTAAAAT
1 A-TTTAAAAT
955726 AGTTAATGTA
Statistics
Matches: 46, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
26 17 0.37
27 22 0.48
28 7 0.15
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (27 bp):
ATTTAAAATGAATAATGTGAAAAAGAA
Found at i:959516 original size:68 final size:68
Alignment explanation
Indices: 959397--959529 Score: 187
Period size: 68 Copynumber: 2.0 Consensus size: 68
959387 CATGTTTAAA
* *
959397 ATGTCTATCTTAGTCATGTTATCGAAATTTAATATTTTGGTTACGCCTCCATTAAATCACTAATG
1 ATGTCTATCTTAGTCATGTTATCCAAATTTAATATTTTGGTCACGCCTCCATTAAATCACTAATG
959462 CTG
66 CTG
* * ** *
959465 ATGTCTATTTTAGTCATGTTA-CCAAATTTTAATATTTTGGTCATGTTTCCATTAAATCATTAAT
1 ATGTCTATCTTAGTCATGTTATCCAAA-TTTAATATTTTGGTCACGCCTCCATTAAATCACTAAT
959529 G
65 G
959530 GTGACCTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 4 0.07
68 53 0.93
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (68 bp):
ATGTCTATCTTAGTCATGTTATCCAAATTTAATATTTTGGTCACGCCTCCATTAAATCACTAATG
CTG
Found at i:961063 original size:19 final size:20
Alignment explanation
Indices: 961022--961062 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
961012 TATAACATAT
961022 AATTTACAACAAAAAATTAA
1 AATTTACAACAAAAAATTAA
961042 AATTTA-AACAATAAAATTAA
1 AATTTACAACAA-AAAATTAA
961062 A
1 A
961063 TATGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (20 bp):
AATTTACAACAAAAAATTAA
Found at i:962558 original size:13 final size:14
Alignment explanation
Indices: 962542--962583 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
962532 TTTCAATTTT
962542 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
962555 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
962570 ATTTTAAATAATAT
1 ATTTT-AATAATAT
962584 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:962568 original size:16 final size:16
Alignment explanation
Indices: 962546--962582 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
962536 AATTTTATTT
962546 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
962563 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
962578 TAATA
1 TAATA
962583 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:962635 original size:15 final size:15
Alignment explanation
Indices: 962615--962671 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
962605 ATTCAATATT
962615 AATATTTTAATAATA
1 AATATTTTAATAATA
*
962630 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
962649 AATATATTAATAATA
1 AATATTTTAATAATA
962664 AATATTTT
1 AATATTTT
962672 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:965565 original size:30 final size:30
Alignment explanation
Indices: 965517--965574 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
965507 TTGGGCATTT
* * *
965517 CCACATGGGTTGGGCACACGCCCGTATGAG
1 CCACACGGGCTGGCCACACGCCCGTATGAG
*
965547 CCACACGGGCTGGCCACACGCCCTTATG
1 CCACACGGGCTGGCCACACGCCCGTATG
965575 CTAGCCCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.36, G:0.29, T:0.16
Consensus pattern (30 bp):
CCACACGGGCTGGCCACACGCCCGTATGAG
Found at i:965998 original size:11 final size:11
Alignment explanation
Indices: 965984--966023 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
965974 ATTTTTTTCC
965984 TATTTTGCTAT
1 TATTTTGCTAT
*
965995 TATTTTACTAT
1 TATTTTGCTAT
* *
966006 TATGTTGCTAC
1 TATTTTGCTAT
966017 TATTTTG
1 TATTTTG
966024 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:966274 original size:12 final size:12
Alignment explanation
Indices: 966244--966276 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
966234 TATATATTTT
966244 AAAATT-ATATA
1 AAAATTAATATA
966255 AAAA-TAATATA
1 AAAATTAATATA
966266 AAAATTAATAT
1 AAAATTAATAT
966277 GGGCGGGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:967513 original size:13 final size:13
Alignment explanation
Indices: 967495--967519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
967485 CTCTAATCTT
967495 TGTTTTGTGATTG
1 TGTTTTGTGATTG
967508 TGTTTTGTGATT
1 TGTTTTGTGATT
967520 TGGGCGAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (13 bp):
TGTTTTGTGATTG
Found at i:969993 original size:20 final size:21
Alignment explanation
Indices: 969963--970004 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
969953 TATAACATAT
969963 AATTTACAACAATAAAATTAA
1 AATTTACAACAATAAAATTAA
969984 AATTTA-AACAATAAAATTAA
1 AATTTACAACAATAAAATTAA
970004 A
1 A
970005 TATGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTTACAACAATAAAATTAA
Found at i:970194 original size:43 final size:43
Alignment explanation
Indices: 970133--970218 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
970123 TTCACGTTTG
970133 AGGTTCGTTGTTGACCTTCACAACAATATCACCTCTAAGGTAT
1 AGGTTCGTTGTTGACCTTCACAACAATATCACCTCTAAGGTAT
970176 AGGTTCGTTGTTGACCTTCACAACAATATCACCTCTAAGGTAT
1 AGGTTCGTTGTTGACCTTCACAACAATATCACCTCTAAGGTAT
970219 GATCTAGCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (43 bp):
AGGTTCGTTGTTGACCTTCACAACAATATCACCTCTAAGGTAT
Found at i:971425 original size:68 final size:68
Alignment explanation
Indices: 971326--971462 Score: 170
Period size: 68 Copynumber: 2.0 Consensus size: 68
971316 ATGTTTAAAA
* * * *
971326 ATGTTTATCTTAGTCATGTTACTGAAATTTAATATTTTGGCCACGCCTT-CGTTAAATCACTAAT
1 ATGTCTATCTTAGTCACGTTACTCAAATTTAATATTTTAGCCACG-CTTCCGTTAAATCACTAAT
971390 GGTG
65 GGTG
* * * *
971394 ATGTCTATTTTAGTCACGTTAC-CAAATTTTAATATTTTAGTCACGTTTCCGTTAAATTACTAAT
1 ATGTCTATCTTAGTCACGTTACTCAAA-TTTAATATTTTAGCCACGCTTCCGTTAAATCACTAAT
971458 GGTG
65 GGTG
971462 A
1 A
971463 CATTTTTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 5 0.08
68 54 0.92
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (68 bp):
ATGTCTATCTTAGTCACGTTACTCAAATTTAATATTTTAGCCACGCTTCCGTTAAATCACTAATG
GTG
Found at i:975919 original size:15 final size:16
Alignment explanation
Indices: 975870--975912 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
975860 TTTTTATGAA
*
975870 ATTTTTATAATTTTACT
1 ATTTTTATAA-TTTATT
975887 -TTTTTATAATTTATT
1 ATTTTTATAATTTATT
975902 ATTTTTA-AATT
1 ATTTTTATAATT
975913 ATTTATTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTTATAATTTATT
Found at i:977544 original size:19 final size:19
Alignment explanation
Indices: 977513--977562 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
977503 TAAAAAGTGC
*
977513 AAGTGCATACTGGCACACG
1 AAGTGCATCCTGGCACACG
* *
977532 AAGTGTATCCTGGCACATG
1 AAGTGCATCCTGGCACACG
*
977551 AGGTGCATCCTG
1 AAGTGCATCCTG
977563 ACGCATAAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (19 bp):
AAGTGCATCCTGGCACACG
Found at i:979216 original size:27 final size:26
Alignment explanation
Indices: 979156--979217 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
979146 ATTTTATTTT
979156 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * *
979182 ATAATTATTAGGATTATTCAA-ATTTAGG
1 AT-TTTATTAGGATAATT-AATA-TTAAG
979210 ATTTTATT
1 ATTTTATT
979218 TTAATTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 19 0.66
28 8 0.28
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:983037 original size:31 final size:33
Alignment explanation
Indices: 982980--983046 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
982970 CAACCCAATC
* *
982980 TTTCCTTTTCTTTTTTTTCTTTTTATTTATTAT
1 TTTCCTTTTCTTATTTATCTTTTTATTTATTAT
*
983013 TTTCCTTTT-TTATTTAT-TTTTTATTTTTTAT
1 TTTCCTTTTCTTATTTATCTTTTTATTTATTAT
983044 TTT
1 TTT
983047 ATTTTAGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 16 0.52
32 6 0.19
33 9 0.29
ACGTcount: A:0.10, C:0.09, G:0.00, T:0.81
Consensus pattern (33 bp):
TTTCCTTTTCTTATTTATCTTTTTATTTATTAT
Found at i:983045 original size:7 final size:7
Alignment explanation
Indices: 982985--983046 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
982975 CAATCTTTCC
*
982985 TTTTCTT
1 TTTTATT
*
982992 TTTTTTCT
1 TTTTAT-T
983000 TTTTATT
1 TTTTATT
*
983007 TATTATT
1 TTTTATT
*
983014 TTCCTTTTT
1 TT--TTATT
983023 TATTTATT
1 T-TTTATT
983031 TTTTATT
1 TTTTATT
983038 TTTTATT
1 TTTTATT
983045 TT
1 TT
983047 ATTTTAGTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 28 0.62
8 11 0.24
9 5 0.11
10 1 0.02
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTATT
Found at i:983047 original size:19 final size:18
Alignment explanation
Indices: 982999--983051 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
982989 CTTTTTTTTC
*
982999 TTTTTATTTATTATTTTCCT
1 TTTTTATTTATT-TTTT-AT
983019 TTTTTATTTATTTTTTAT
1 TTTTTATTTATTTTTTAT
983037 TTTTTATTTTATTTT
1 TTTTTA-TTTATTTT
983052 AGTTAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 7 0.23
19 12 0.39
20 12 0.39
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTATTTATTTTTTAT
Found at i:983052 original size:24 final size:24
Alignment explanation
Indices: 983000--983052 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
982990 TTTTTTTTCT
983000 TTTTATTTATTATTTTCCTTTTTTA
1 TTTTATTTATTATTTT-CTTTTTTA
*
983025 -TTTATTTTTTATTTT-TTATTTTA
1 TTTTATTTATTATTTTCTT-TTTTA
983048 TTTTA
1 TTTTA
983053 GTTAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 5 0.20
24 18 0.72
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTATTTATTATTTTCTTTTTTA
Found at i:992873 original size:21 final size:21
Alignment explanation
Indices: 992847--992887 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
992837 ATCTGCTCAA
* *
992847 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
992868 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
992888 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:999490 original size:20 final size:20
Alignment explanation
Indices: 999453--999492 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
999443 GAGACGTTGG
*
999453 AATGACTTCAATTCTCAAGA
1 AATGACTTCAAATCTCAAGA
999473 AATGA-TTCAAATCATCAAGA
1 AATGACTTCAAATC-TCAAGA
999493 TCTTTAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (20 bp):
AATGACTTCAAATCTCAAGA
Found at i:1015418 original size:16 final size:18
Alignment explanation
Indices: 1015383--1015419 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1015373 ATGTAATCAG
1015383 GAAAAGAAAAGTAAACAA
1 GAAAAGAAAAGTAAACAA
*
1015401 GAAAA-AAAAG-AAAGAA
1 GAAAAGAAAAGTAAACAA
1015417 GAA
1 GAA
1015420 CCGATTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (18 bp):
GAAAAGAAAAGTAAACAA
Found at i:1026930 original size:14 final size:14
Alignment explanation
Indices: 1026894--1026937 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1026884 GATTTAAAAT
1026894 TTATAAAATATTCAAA
1 TTATAAAATA-T-AAA
*
1026910 GTATAAAATATAAA
1 TTATAAAATATAAA
*
1026924 TTATAAATTATAAA
1 TTATAAAATATAAA
1026938 AAAGAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 15 0.60
15 1 0.04
16 9 0.36
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (14 bp):
TTATAAAATATAAA
Found at i:1029469 original size:18 final size:18
Alignment explanation
Indices: 1029443--1029499 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
1029433 TACGACCATT
*
1029443 TACGGTACTATTCACATA
1 TACGGTACTATTCACGTA
*
1029461 TACGATACTATTCACGTA
1 TACGGTACTATTCACGTA
*
1029479 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
1029497 TAC
1 TAC
1029500 AGTAGTTGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:1033564 original size:11 final size:11
Alignment explanation
Indices: 1033544--1033597 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
1033534 TAGAATATAC
*
1033544 CCCATTCCTTG
1 CCCATACCTTG
1033555 CCCATACCTTG
1 CCCATACCTTG
*
1033566 CCCATACCTTT
1 CCCATACCTTG
*
1033577 CCCATACC-TA
1 CCCATACCTTG
1033587 CCCATACCTTG
1 CCCATACCTTG
1033598 GAAAGGTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.19, C:0.46, G:0.06, T:0.30
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:1043916 original size:23 final size:22
Alignment explanation
Indices: 1043871--1043916 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1043861 CAACCAATCC
*
1043871 AATTCAGCATATTTTCAAGATA
1 AATTCAGCATATTTTCAAAATA
1043893 AATTCATGCATATTTAT-AAAATA
1 AATTCA-GCATATTT-TCAAAATA
1043916 A
1 A
1043917 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (22 bp):
AATTCAGCATATTTTCAAAATA
Found at i:1048377 original size:17 final size:17
Alignment explanation
Indices: 1048355--1048388 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1048345 ATCCACTAAT
*
1048355 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1048372 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1048389 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1053016 original size:17 final size:17
Alignment explanation
Indices: 1052994--1053027 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1052984 ATCCACTAAT
*
1052994 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1053011 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1053028 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1061930 original size:30 final size:31
Alignment explanation
Indices: 1061894--1061962 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
1061884 GGTTTCATTT
* *
1061894 CAGTCACTCAAC-TTTTGAAAAA-TAACAAAA
1 CAGTCACT-AACGTTATAAAAAAGTAACAAAA
*
1061924 CAGTCACTAACGTTATAAAAAAGTGACAAAA
1 CAGTCACTAACGTTATAAAAAAGTAACAAAA
1061955 CAGTCACT
1 CAGTCACT
1061963 GACTAACAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 16 0.47
31 15 0.44
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (31 bp):
CAGTCACTAACGTTATAAAAAAGTAACAAAA
Found at i:1062101 original size:3 final size:3
Alignment explanation
Indices: 1062093--1062128 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1062083 TTTAACAGAG
*
1062093 GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1062129 CAGTTACTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1063044 original size:18 final size:18
Alignment explanation
Indices: 1063023--1063059 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1063013 AGCCAGTAAT
1063023 TTTCTTCTTCTTCTTCTC
1 TTTCTTCTTCTTCTTCTC
* *
1063041 TTTCTTTTTCTTTTTCTC
1 TTTCTTCTTCTTCTTCTC
1063059 T
1 T
1063060 AGCCCTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCTTCTTCTTCTTCTC
Found at i:1063625 original size:28 final size:28
Alignment explanation
Indices: 1063572--1063628 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1063562 TTTTCCTAAA
* *
1063572 TATTATTTTTATCTAAATTATTATTTTT
1 TATTATTTTTATCTAAAATATCATTTTT
1063600 TATTATTTTTAT-TAAAAATATCATTTTT
1 TATTATTTTTATCT-AAAATATCATTTTT
1063628 T
1 T
1063629 CCTAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (28 bp):
TATTATTTTTATCTAAAATATCATTTTT
Found at i:1065855 original size:35 final size:35
Alignment explanation
Indices: 1065816--1065883 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1065806 AGGAAAGTAG
* *
1065816 GGTCAAATCCTCAAAGATTGGATTGCTACAACTAA
1 GGTCAAATCCTCAAAGACTAGATTGCTACAACTAA
**
1065851 GGTCAAATCCTCAGCGACTAGATTGCTACAACT
1 GGTCAAATCCTCAAAGACTAGATTGCTACAACT
1065884 TCTTGTTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (35 bp):
GGTCAAATCCTCAAAGACTAGATTGCTACAACTAA
Found at i:1069499 original size:98 final size:95
Alignment explanation
Indices: 1069333--1069525 Score: 230
Period size: 98 Copynumber: 2.0 Consensus size: 95
1069323 TAAACTAAAT
* * * **
1069333 CCTAAGCACTTAAAAATAAAAAATCCTAAACCCTAATTCCATAAACCCTAATCTTAACACTACTC
1 CCTAAACACTTAAAAATAAAAAATCCTAAACCCTAATTCCATAAACCCTAACCCTAACACTAAAC
*
1069398 ACTTAAAAATT-TAAAAACCCT-AAACCCTAA
66 ACTT-AAAATTATAAAAA-ACTAAAACCCTAA
* **
1069428 CCTAAACACTTAAAAAATAAAAAAATCCATAAACCTTAATTTTATAAACCCTAACCCTAAC-CTT
1 CCTAAACACTT-AAAAAT-AAAAAATCC-TAAACCCTAATTCCATAAACCCTAACCCTAACAC-T
1069492 AAACACTTAAAATTATAAAAAACTAAAACCCTAA
62 AAACACTTAAAATTATAAAAAACTAAAACCCTAA
1069526 TTTTACTAGA
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
95 10 0.12
96 6 0.07
97 18 0.22
98 49 0.59
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.24
Consensus pattern (95 bp):
CCTAAACACTTAAAAATAAAAAATCCTAAACCCTAATTCCATAAACCCTAACCCTAACACTAAAC
ACTTAAAATTATAAAAAACTAAAACCCTAA
Found at i:1072126 original size:18 final size:16
Alignment explanation
Indices: 1072103--1072137 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1072093 ATAAAAAATA
1072103 TTAATTAAAATATATAAT
1 TTAATT-AAATA-ATAAT
1072121 TTAATTAAATAATAAT
1 TTAATTAAATAATAAT
1072137 T
1 T
1072138 AGTGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATTAAATAATAAT
Found at i:1075066 original size:10 final size:10
Alignment explanation
Indices: 1075053--1075110 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
1075043 TTATTAAAAA
1075053 TATATATTTT
1 TATATATTTT
1075063 TATATATTTT
1 TATATATTTT
1075073 TA-ATAATTTT
1 TATAT-ATTTT
*
1075083 TAAAT-TTTT
1 TATATATTTT
*
1075092 TAAATGA-TTT
1 TATAT-ATTTT
1075102 TATAT-TTTT
1 TATATATTTT
1075111 CAAAATTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
9 14 0.33
10 26 0.62
11 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TATATATTTT
Found at i:1075083 original size:20 final size:19
Alignment explanation
Indices: 1075058--1075119 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1075048 AAAAATATAT
1075058 ATTTTTATATATTTTTAATA
1 ATTTTTATAT-TTTTTAATA
* *
1075078 ATTTTTAAATTTTTTAAATG
1 ATTTTTATATTTTTT-AATA
*
1075098 A-TTTTATATTTTTCAA-A
1 ATTTTTATATTTTTTAATA
1075115 ATTTT
1 ATTTT
1075120 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.03
18 5 0.14
19 16 0.46
20 13 0.37
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTATATTTTTTAATA
Found at i:1076257 original size:29 final size:30
Alignment explanation
Indices: 1076222--1076279 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1076212 TGTGGTCCAA
1076222 TGTGCAATGTTATACATG-AAATTTGATTT
1 TGTGCAATGTTATACATGTAAATTTGATTT
* *
1076251 TGTGCAATTTTATACATGTTAATTTGATT
1 TGTGCAATGTTATACATGTAAATTTGATT
1076280 CAATTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (30 bp):
TGTGCAATGTTATACATGTAAATTTGATTT
Found at i:1081523 original size:149 final size:154
Alignment explanation
Indices: 1081192--1081602 Score: 573
Period size: 149 Copynumber: 2.7 Consensus size: 154
1081182 TTTCTTTGTC
* * *
1081192 GGTTTTATATCAATTTTAGGTACCAAAACAGTAATCTATCTTATCCCATTCGA-TTGAATTGGAT
1 GGTTTCATATCAATTTTAGGTGCCAAAACAGTAATCTATATTATCCCATTCGATTTG-ATTGGAT
* * *
1081256 TTGAATTCTAGTTTATTTAACTTTTTAAAATTTATTTTTTATATATTCAAAAAGATTTGTACTAT
65 TTGAATTCGAGTTTATTAAACTTTTTAAAATTTATTTTTTACATATTCAAAAAGATTTGTACTAT
1081321 GTTTATATGCGAAATGTGCATATGAGGATT
130 G-TTATAT----AATGTGCATATGAGGATT
* * *
1081351 GGTTTCATATCAGTTTTAGGTGCCAAAACAGTACTCTATATTATCCCATTAGATTTGATTGGATT
1 GGTTTCATATCAATTTTAGGTGCCAAAACAGTAATCTATATTATCCCATTCGATTTGATTGGATT
* *
1081416 TAAATTCGAGTTTATTAAACTTTTTAAAACTTATTTTTTACATATTC-AAAAGATTTGTACTATG
66 TGAATTCGAGTTTATTAAACTTTTTAAAATTTATTTTTTACATATTCAAAAAGATTTGTACTATG
1081480 -T-T-T-ATGTGCATATGAGGATT
131 TTATATAATGTGCATATGAGGATT
* * * *
1081500 GGTTTCATATCATTTTTAAGTGCCAAAACAGTAATCTTTGTTATCCCATTCGATTTGATTGGATT
1 GGTTTCATATCAATTTTAGGTGCCAAAACAGTAATCTATATTATCCCATTCGATTTGATTGGATT
* *
1081565 TGAATTCGAGTTTATTAAATTTTTTAAAGTTTATTTTT
66 TGAATTCGAGTTTATTAAACTTTTTAAAATTTATTTTT
1081603 GGGTAAATTG
Statistics
Matches: 230, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
149 110 0.48
154 1 0.00
155 1 0.00
156 1 0.00
158 17 0.07
159 97 0.42
160 3 0.01
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (154 bp):
GGTTTCATATCAATTTTAGGTGCCAAAACAGTAATCTATATTATCCCATTCGATTTGATTGGATT
TGAATTCGAGTTTATTAAACTTTTTAAAATTTATTTTTTACATATTCAAAAAGATTTGTACTATG
TTATATAATGTGCATATGAGGATT
Found at i:1082955 original size:17 final size:17
Alignment explanation
Indices: 1082933--1082966 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1082923 ATCCACTAAT
*
1082933 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1082950 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1082967 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1087594 original size:17 final size:17
Alignment explanation
Indices: 1087572--1087605 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1087562 ATCCACTAAT
*
1087572 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1087589 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1087606 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1088533 original size:99 final size:99
Alignment explanation
Indices: 1088362--1088540 Score: 340
Period size: 99 Copynumber: 1.8 Consensus size: 99
1088352 AGACTTGGAC
* *
1088362 AGAGGTTGAGGGAGAGGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCATAGAGAATG
1 AGAGGTTGAGGGAGAAGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCACAGAGAATG
1088427 CCCAATCATCTTTTTATTACACCAACAAGGAGAA
66 CCCAATCATCTTTTTATTACACCAACAAGGAGAA
1088461 AGAGGTTGAGGGAGAAGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCACAGAGAATG
1 AGAGGTTGAGGGAGAAGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCACAGAGAATG
1088526 CCCAATCATCTTTTT
66 CCCAATCATCTTTTT
1088541 TTTCGACCCT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
99 78 1.00
ACGTcount: A:0.45, C:0.11, G:0.28, T:0.16
Consensus pattern (99 bp):
AGAGGTTGAGGGAGAAGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCACAGAGAATG
CCCAATCATCTTTTTATTACACCAACAAGGAGAA
Found at i:1088979 original size:30 final size:30
Alignment explanation
Indices: 1088945--1089004 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1088935 TTGTTATTGT
* *
1088945 ATTAACTTATATTTTTATA-TATTTTCAAAG
1 ATTAAATTA-ATTTTTATACTATTTTAAAAG
*
1088975 ATTAAATTAATTTTTTTACTATTTTAAAAG
1 ATTAAATTAATTTTTATACTATTTTAAAAG
1089005 GTCAAAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (30 bp):
ATTAAATTAATTTTTATACTATTTTAAAAG
Found at i:1093977 original size:21 final size:21
Alignment explanation
Indices: 1093951--1093993 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1093941 GATAAAAATG
1093951 ATAACTCAAGGAAGAATAGCT
1 ATAACTCAAGGAAGAATAGCT
1093972 ATAACTCAAGGAAGAATAGCT
1 ATAACTCAAGGAAGAATAGCT
1093993 A
1 A
1093994 CCAACACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.19
Consensus pattern (21 bp):
ATAACTCAAGGAAGAATAGCT
Found at i:1098481 original size:21 final size:20
Alignment explanation
Indices: 1098456--1098498 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1098446 TTCGAACCGA
1098456 TTTTAT-AATCTTTTAAGTAAT
1 TTTTATGAAT-TTTTAA-TAAT
1098477 TTTTATGAATTTTTAATAAT
1 TTTTATGAATTTTTAATAAT
1098497 TT
1 TT
1098499 ATTTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 12 0.57
22 3 0.14
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTATGAATTTTTAATAAT
Found at i:1100697 original size:6 final size:6
Alignment explanation
Indices: 1100688--1100715 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1100678 GAACCATCAC
1100688 CACCCA CACCCA CACCCA CACCCA CACC
1 CACCCA CACCCA CACCCA CACCCA CACC
1100716 ACCAGCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCCA
Found at i:1101293 original size:15 final size:15
Alignment explanation
Indices: 1101248--1101355 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
1101238 CCAATATCTC
1101248 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1101263 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
1101278 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1101293 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
1101308 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1101323 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
1101338 GATACCCATATCTTT
1 GATACCCATATCTTT
1101353 GAT
1 GAT
1101356 TTTCCATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:1101362 original size:30 final size:30
Alignment explanation
Indices: 1101238--1101361 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
1101228 TTTTATTATG
*
1101238 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
1101269 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
1101299 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
1101329 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
1101359 CCA
1 CCA
1101362 TAAATATGGA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 83 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:1105985 original size:15 final size:15
Alignment explanation
Indices: 1105940--1106047 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
1105930 CCAATATCTC
1105940 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1105955 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
1105970 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1105985 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
1106000 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1106015 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
1106030 GATACCCATATCTTT
1 GATACCCATATCTTT
1106045 GAT
1 GAT
1106048 TTTCCATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:1106054 original size:30 final size:30
Alignment explanation
Indices: 1105930--1106053 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
1105920 TTTTATTATG
*
1105930 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
1105961 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
1105991 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
1106021 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
1106051 CCA
1 CCA
1106054 TAAATATGGA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 83 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:1106492 original size:157 final size:157
Alignment explanation
Indices: 1106206--1106517 Score: 425
Period size: 157 Copynumber: 2.0 Consensus size: 157
1106196 TTTCTTCGTC
* * *
1106206 GGTTTTATATCAATTTTAGGTACCAAAACAGTAATCTATGTTATCCCATTCGATTGAATTGGATT
1 GGTTTTATATCAATTTTAGGTACCAAAACAGTAAACTATATTATCCCATACGATTGAATTGGATT
* * * *
1106271 TGAACTGGAGTTTATTTAACTTTTTAAACCTTTTTTTTATATATTCAAAAGATTTATACTATGTT
66 TGAACTCGAGTTAATTAAACTTTTTAAACCTTTTTTTTATATATTCAAAAAATTTATACTATGTT
*
1106336 TATATGCAAAATGTGCATATGAGGATT
131 TATATGCAAAATGTGCATATAAGGATT
* * *
1106363 GGTTTTATATCATTTTTAGGTATCC-AAACAGTAAACTATATTAT-CC-TAGGATTGGATTGGAT
1 GGTTTTATATCAATTTTAGGTA-CCAAAACAGTAAACTATATTATCCCATACGATTGAATTGGAT
* * * *
1106425 TTGAATTCGAGTTAATTAAAGTTTTTTAAA-GTTTATCTTTTATATATTCAAAAAATTTGTACTA
65 TTGAACTCGAGTTAATTAAA-CTTTTTAAACCTTT-T-TTTTATATATTCAAAAAATTTATACTA
1106489 TGTTTATATGCAAAATGTGCATATAAGGA
127 TGTTTATATGCAAAATGTGCATATAAGGA
1106518 CAAGAATCAC
Statistics
Matches: 136, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
155 32 0.24
156 11 0.08
157 91 0.67
158 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (157 bp):
GGTTTTATATCAATTTTAGGTACCAAAACAGTAAACTATATTATCCCATACGATTGAATTGGATT
TGAACTCGAGTTAATTAAACTTTTTAAACCTTTTTTTTATATATTCAAAAAATTTATACTATGTT
TATATGCAAAATGTGCATATAAGGATT
Found at i:1109161 original size:37 final size:37
Alignment explanation
Indices: 1109105--1109178 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1109095 GTATGCAACG
*
1109105 TGATTGTATTTCTTAACTACAACCCAAGGGCTAAAGC
1 TGATCGTATTTCTTAACTACAACCCAAGGGCTAAAGC
* *
1109142 TGATCGTATTTCTTGACTACAACCCCAGGGCTAAAGC
1 TGATCGTATTTCTTAACTACAACCCAAGGGCTAAAGC
1109179 AAAACTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (37 bp):
TGATCGTATTTCTTAACTACAACCCAAGGGCTAAAGC
Found at i:1176996 original size:1 final size:1
Alignment explanation
Indices: 1176990--1177041 Score: 104
Period size: 1 Copynumber: 52.0 Consensus size: 1
1176980 AATTTCTATC
1176990 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1177042 CCTCTACTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1177620 original size:24 final size:24
Alignment explanation
Indices: 1177588--1177645 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
1177578 TGGGTTACAC
* *
1177588 GATCATGTGGTAGGCCATGTGACA
1 GATCGTGTGGTAGGCCATGCGACA
*
1177612 GATCGTGTGGTAGGCCATGCGGCA
1 GATCGTGTGGTAGGCCATGCGACA
1177636 GATCGTGTGG
1 GATCGTGTGG
1177646 GTCACACGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.17, G:0.40, T:0.24
Consensus pattern (24 bp):
GATCGTGTGGTAGGCCATGCGACA
Found at i:1177660 original size:41 final size:41
Alignment explanation
Indices: 1177615--1177789 Score: 156
Period size: 41 Copynumber: 4.3 Consensus size: 41
1177605 TGTGACAGAT
*
1177615 CGTGTGGTAGGCCATGCGGCAGATCGTGTGGGTCACACGAC
1 CGTGTGGTAGGCCATGTGGCAGATCGTGTGGGTCACACGAC
*** * * * *
1177656 CGTGTGGTAGGTGGTGTGGTAGAACGTGTCGGTCACAGGAC
1 CGTGTGGTAGGCCATGTGGCAGATCGTGTGGGTCACACGAC
* * * * * * * * *
1177697 CATATAGTAAGCCATTTAGCAGACCGTGTGTGTCACACGAA
1 CGTGTGGTAGGCCATGTGGCAGATCGTGTGGGTCACACGAC
* * *
1177738 CATGTGGTAGG-C-TGTGGTAGATCGTGTGGGTCACATGAC
1 CGTGTGGTAGGCCATGTGGCAGATCGTGTGGGTCACACGAC
1177777 CGTGTGGTAGGCC
1 CGTGTGGTAGGCC
1177790 GTATGGCAAA
Statistics
Matches: 99, Mismatches: 34, Indels: 3
0.73 0.25 0.02
Matches are distributed among these distances:
39 30 0.30
40 2 0.02
41 67 0.68
ACGTcount: A:0.20, C:0.19, G:0.37, T:0.24
Consensus pattern (41 bp):
CGTGTGGTAGGCCATGTGGCAGATCGTGTGGGTCACACGAC
Found at i:1184448 original size:76 final size:74
Alignment explanation
Indices: 1184319--1184493 Score: 248
Period size: 76 Copynumber: 2.4 Consensus size: 74
1184309 AGAAACCCTT
*
1184319 GGGGAATC-GCACTTAGCAACCCCCTTCACCTTTAAAATACGGTGGGATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAA-CCCCTTCACCTTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1184383 CCAATGAATC
65 CCAATGAATC
* * *
1184393 GGGGAATCAGCACTTAGCAACTCCCTTTA-TTATTCAAGATACGGTGGAATCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGCAAC-CCCTTCACCT-TT-AAAATACGGTGGAATCAGCACTTAGCAAC
1184457 CACCAATGAATC
63 CACCAATGAATC
*
1184469 -GGGAATCAACACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
1184494 GGGGAATCAG
Statistics
Matches: 92, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
74 15 0.16
75 38 0.41
76 39 0.42
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (74 bp):
GGGGAATCAGCACTTAGCAACCCCTTCACCTTTAAAATACGGTGGAATCAGCACTTAGCAACCAC
CAATGAATC
Found at i:1216233 original size:26 final size:26
Alignment explanation
Indices: 1216204--1216310 Score: 187
Period size: 26 Copynumber: 4.1 Consensus size: 26
1216194 TGGTACAAAT
1216204 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1216230 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1216256 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1216282 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1216308 TGA
1 TGA
1216311 CGGGCATTTC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1220387 original size:41 final size:40
Alignment explanation
Indices: 1220342--1220509 Score: 124
Period size: 41 Copynumber: 4.2 Consensus size: 40
1220332 ACTATGTACA
* *
1220342 TCACACGGTCGTATGGTAGGCCTTGTGGCAGACCGCGTAGG
1 TCACACGG-CGTATGGTAAGCCTTGTGGCAGACCGTGTAGG
* *
1220383 TCACACGAC-TATGTGTTAAGCCTTGTGGCAGACCATGTAGG
1 TCACACGGCGTATG-G-TAAGCCTTGTGGCAGACCGTGTAGG
* * * * * ** *
1220424 TCACACAGCCGTGTGGTAAGCCCTGTGGGAAATAGTATAGG
1 TCACAC-GGCGTATGGTAAGCCTTGTGGCAGACCGTGTAGG
* * * * *
1220465 TCACACGGCGTGTGGTAGGCCATGTGGTAGATCGTGT-GG
1 TCACACGGCGTATGGTAAGCCTTGTGGCAGACCGTGTAGG
*
1220504 CCACAC
1 TCACAC
1220510 AGCCTGGTCA
Statistics
Matches: 102, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
39 11 0.11
40 26 0.25
41 59 0.58
42 3 0.03
43 3 0.03
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (40 bp):
TCACACGGCGTATGGTAAGCCTTGTGGCAGACCGTGTAGG
Found at i:1220583 original size:22 final size:22
Alignment explanation
Indices: 1220558--1220606 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
1220548 TGGGCCCATT
1220558 TTGGGCAATTTGTTGGCCCCGG
1 TTGGGCAATTTGTTGGCCCCGG
*
1220580 TT-GGCAATTTGTTGGCCCCGT
1 TTGGGCAATTTGTTGGCCCCGG
1220601 TTGGGC
1 TTGGGC
1220607 TAAAAGTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.08, C:0.22, G:0.35, T:0.35
Consensus pattern (22 bp):
TTGGGCAATTTGTTGGCCCCGG
Found at i:1225231 original size:17 final size:18
Alignment explanation
Indices: 1225197--1225231 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1225187 CCATGTGACC
*
1225197 TGCCCGTTTGGACCCACA
1 TGCCCGTGTGGACCCACA
1225215 TGCCCGTGTGG-CCCACA
1 TGCCCGTGTGGACCCACA
1225232 CGGCCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.40, G:0.26, T:0.20
Consensus pattern (18 bp):
TGCCCGTGTGGACCCACA
Found at i:1229329 original size:18 final size:18
Alignment explanation
Indices: 1229306--1229351 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1229296 GAAGAAGTGA
*
1229306 AAGATACACCCAAAACAG
1 AAGATACACCCAAAAAAG
*
1229324 AAGATAAACCCAAAAAAG
1 AAGATACACCCAAAAAAG
*
1229342 AAGATCCACC
1 AAGATACACC
1229352 AAAGCCCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.57, C:0.26, G:0.11, T:0.07
Consensus pattern (18 bp):
AAGATACACCCAAAAAAG
Found at i:1230466 original size:5 final size:5
Alignment explanation
Indices: 1230449--1230479 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1230439 AATATTAACA
1230449 TTATT TCTATT TTATT TTATT TTATT TTATT
1 TTATT T-TATT TTATT TTATT TTATT TTATT
1230480 AATAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:1231042 original size:17 final size:16
Alignment explanation
Indices: 1231011--1231041 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1231001 TAGTATAATA
1231011 AAATATTTTAAAAAAT
1 AAATATTTTAAAAAAT
1231027 AAATATTTTAAAAAA
1 AAATATTTTAAAAAA
1231042 AGAGACACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATTTTAAAAAAT
Found at i:1231642 original size:19 final size:19
Alignment explanation
Indices: 1231607--1231664 Score: 82
Period size: 20 Copynumber: 3.1 Consensus size: 19
1231597 TTATTTAAAA
1231607 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
1231625 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
*
1231644 TGAAAAATATTTGGAATTTT
1 T-ATAAATATTTGGAATTTT
1231664 T
1 T
1231665 TCTATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
18 7 0.20
19 11 0.31
20 17 0.49
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.53
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:1232042 original size:57 final size:57
Alignment explanation
Indices: 1231977--1232090 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
1231967 TGGTTAAGGA
1231977 AGTCAACTTATTATAATAGTATTATGGGAAGGTAAAATATACATGTTCCAGCACCAT
1 AGTCAACTTATTATAATAGTATTATGGGAAGGTAAAATATACATGTTCCAGCACCAT
* * *
1232034 AGTCAACTTATTATGATAGTATTATGGGAAGGTAATATATGCATGTTCCAGCACCAT
1 AGTCAACTTATTATAATAGTATTATGGGAAGGTAAAATATACATGTTCCAGCACCAT
1232091 TCTTTTTAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (57 bp):
AGTCAACTTATTATAATAGTATTATGGGAAGGTAAAATATACATGTTCCAGCACCAT
Found at i:1243525 original size:27 final size:27
Alignment explanation
Indices: 1243494--1243617 Score: 104
Period size: 27 Copynumber: 4.6 Consensus size: 27
1243484 GGATTACTTA
* *
1243494 ATGTTTATTGTCCCGGCGGACTACCCT
1 ATGTTTATTGTCCAGGCGGACTACCCC
* * *
1243521 GTGTTTATTGTCCAAGTGGACTACCCC
1 ATGTTTATTGTCCAGGCGGACTACCCC
* * * *
1243548 ATTTTTATTGTCCTGACAGACTACCCC
1 ATGTTTATTGTCCAGGCGGACTACCCC
* * * * *
1243575 ATATTTATTGTCCTGGTGAACTACCGC
1 ATGTTTATTGTCCAGGCGGACTACCCC
*
1243602 ATTTTTATTGTTCCAG
1 ATGTTTATTG-TCCAG
1243618 TGGACTCTAT
Statistics
Matches: 76, Mismatches: 20, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
27 72 0.95
28 4 0.05
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (27 bp):
ATGTTTATTGTCCAGGCGGACTACCCC
Found at i:1243560 original size:54 final size:54
Alignment explanation
Indices: 1243497--1243612 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
1243487 TTACTTAATG
* * ** * *
1243497 TTTATTGTCCCGGCGGACTACCCTGTGTTTATTGTCCAAGTGGACTACCCCATT
1 TTTATTGTCCCGACAGACTACCCCATATTTATTGTCCAAGTGAACTACCCCATT
* ** *
1243551 TTTATTGTCCTGACAGACTACCCCATATTTATTGTCCTGGTGAACTACCGCATT
1 TTTATTGTCCCGACAGACTACCCCATATTTATTGTCCAAGTGAACTACCCCATT
1243605 TTTATTGT
1 TTTATTGT
1243613 TCCAGTGGAC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (54 bp):
TTTATTGTCCCGACAGACTACCCCATATTTATTGTCCAAGTGAACTACCCCATT
Found at i:1244027 original size:3 final size:3
Alignment explanation
Indices: 1244021--1244085 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
1244011 ATCTAAGATT
* ** *
1244021 TTA TTA TTA TTAA TTA TTA GTA TGG TT- TTA -TA TTA -AA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1244064 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
1244086 AATATTAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1249926 original size:23 final size:23
Alignment explanation
Indices: 1249897--1250067 Score: 211
Period size: 23 Copynumber: 7.4 Consensus size: 23
1249887 CCCTTTAATA
*
1249897 AATGTTATGCAAACCCCTTAGTG
1 AATGTTATGCGAACCCCTTAGTG
*
1249920 AATGTTATGCGAACCCCTTAATG
1 AATGTTATGCGAACCCCTTAGTG
* * *
1249943 AATGTTGTGCGAACCCCTTACTA
1 AATGTTATGCGAACCCCTTAGTG
**
1249966 AATGTTATGCGAACATCTTAGTG
1 AATGTTATGCGAACCCCTTAGTG
*
1249989 AATGTTATGTGAA-CCCTTCAGTG
1 AATGTTATGCGAACCCCTT-AGTG
*
1250012 AATGTTATGCGAACCCCTTAGTA
1 AATGTTATGCGAACCCCTTAGTG
* *
1250035 AATATTATGTGAACCCCTT-GATG
1 AATGTTATGCGAACCCCTTAG-TG
1250058 AATGTTATGC
1 AATGTTATGC
1250068 AAATCTTGTT
Statistics
Matches: 125, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.03
23 116 0.93
24 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (23 bp):
AATGTTATGCGAACCCCTTAGTG
Found at i:1250014 original size:69 final size:69
Alignment explanation
Indices: 1249885--1250067 Score: 235
Period size: 69 Copynumber: 2.6 Consensus size: 69
1249875 GTACCGCACG
* *
1249885 ACCCCTTTAATAAATGTTATGCAAACCCCTTAGTGAATGTTATGCGAACCCCTTAATGAATGTTG
1 ACCCC-TTAATAAATGTTATGCGAACCCCTTAGTGAATGTTATGCGAACCCCTTAATGAATGTTA
1249950 TGCGA
65 TGCGA
* ** * *
1249955 ACCCCTTACTAAATGTTATGCGAACATCTTAGTGAATGTTATGTGAA-CCCTTCAGTGAATGTTA
1 ACCCCTTAATAAATGTTATGCGAACCCCTTAGTGAATGTTATGCGAACCCCTT-AATGAATGTTA
1250019 TGCGA
65 TGCGA
* * *
1250024 ACCCCTTAGTAAATATTATGTGAACCCCTT-GATGAATGTTATGC
1 ACCCCTTAATAAATGTTATGCGAACCCCTTAG-TGAATGTTATGC
1250068 AAATCTTGTT
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
68 6 0.06
69 87 0.89
70 5 0.05
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (69 bp):
ACCCCTTAATAAATGTTATGCGAACCCCTTAGTGAATGTTATGCGAACCCCTTAATGAATGTTAT
GCGA
Found at i:1250649 original size:26 final size:27
Alignment explanation
Indices: 1250579--1250653 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
1250569 TCAAGAACAA
*
1250579 TATTAGATTAAATTTAATATTAAATCC
1 TATTAAATTAAATTTAATATTAAATCC
** * *
1250606 TATTAAATT-AATAAAATATT-TAT-G
1 TATTAAATTAAATTTAATATTAAATCC
1250630 TATTTAAATTAAATTTAATATTAA
1 TA-TTAAATTAAATTTAATATTAA
1250654 GATAATCATT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
24 2 0.05
25 9 0.24
26 18 0.49
27 8 0.22
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (27 bp):
TATTAAATTAAATTTAATATTAAATCC
Found at i:1250733 original size:17 final size:17
Alignment explanation
Indices: 1250698--1250730 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1250688 TTAAGATAAG
*
1250698 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
1250715 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
1250731 ATAATATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:1252540 original size:25 final size:25
Alignment explanation
Indices: 1252506--1252554 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1252496 TGATCCTTTT
* *
1252506 AACTATTATGTGAACCCTTTTGTAA
1 AACTATTATGCGAACCCTTATGTAA
*
1252531 AACTGTTATGCGAACCCTTATGTA
1 AACTATTATGCGAACCCTTATGTA
1252555 TAATGTACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (25 bp):
AACTATTATGCGAACCCTTATGTAA
Found at i:1252632 original size:25 final size:25
Alignment explanation
Indices: 1252567--1252634 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
1252557 ATGTACTGCA
* * *
1252567 AACATTCATACGAACCCTCATTCTG
1 AACATTCATGCGAACCTTCAATCTG
* * *
1252592 AACACTCATGTGAACCTTCAATGTG
1 AACATTCATGCGAACCTTCAATCTG
*
1252617 AACATTCATGCCAACCTT
1 AACATTCATGCGAACCTT
1252635 ATCTACGAGC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.28
Consensus pattern (25 bp):
AACATTCATGCGAACCTTCAATCTG
Found at i:1253157 original size:47 final size:46
Alignment explanation
Indices: 1253093--1253219 Score: 128
Period size: 47 Copynumber: 2.7 Consensus size: 46
1253083 CAACAGTTTT
* *
1253093 TCTGCTTGACCAGTGGTTTATCCACAATTAATTTTAGTCAGCAACCA
1 TCTGCTCGACTAGTGGTTTATCCACAATT-ATTTTAGTCAGCAACCA
* * * * * **
1253140 TCTGTTTGATTAGTGGTTTATCCATGAAATATTTTAGTCAGCAGTCA
1 TCTGCTCGACTAGTGGTTTATCCA-CAATTATTTTAGTCAGCAACCA
* *
1253187 TTTGCTCGACTAGTGGTTCATCCACAATGTATT
1 TCTGCTCGACTAGTGGTTTATCCACAAT-TATT
1253220 AACAGCTTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
46 2 0.03
47 59 0.92
48 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (46 bp):
TCTGCTCGACTAGTGGTTTATCCACAATTATTTTAGTCAGCAACCA
Found at i:1263575 original size:21 final size:21
Alignment explanation
Indices: 1263549--1263589 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1263539 ATCTGCTCAA
* *
1263549 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1263570 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1263590 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1269214 original size:28 final size:26
Alignment explanation
Indices: 1269161--1269223 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 26
1269151 ATTAGATTTG
1269161 TAAAA-AAAATTATAAATATTGTTAA
1 TAAAATAAAATTATAAATATTGTTAA
* *
1269186 TAAAATAAAATTTTAAATTATATTTTAA
1 TAAAATAAAATTATAAA-TAT-TGTTAA
*
1269214 TTAAATAAAA
1 TAAAATAAAA
1269224 ATTAATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.16
26 10 0.31
27 3 0.09
28 14 0.44
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
TAAAATAAAATTATAAATATTGTTAA
Found at i:1269224 original size:29 final size:27
Alignment explanation
Indices: 1269161--1269227 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
1269151 ATTAGATTTG
1269161 TAAA-AAAAATTATAAATATTGTTAAT
1 TAAATAAAAATTATAAATATTGTTAAT
* * *
1269187 AAAAT-AAAATTTTAAATTATATTTTAAT
1 TAAATAAAAATTATAAA-TAT-TGTTAAT
1269215 TAAATAAAAATTA
1 TAAATAAAAATTA
1269228 ATTTTGATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 13 0.41
27 3 0.09
28 10 0.31
29 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (27 bp):
TAAATAAAAATTATAAATATTGTTAAT
Found at i:1277973 original size:12 final size:12
Alignment explanation
Indices: 1277953--1277981 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1277943 TCTGTGTGTG
1277953 TTTCCTTTTTTT
1 TTTCCTTTTTTT
1277965 TTT-CTTTTTTT
1 TTTCCTTTTTTT
1277976 TTTCCT
1 TTTCCT
1277982 CTTTGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTCCTTTTTTT
Found at i:1278719 original size:30 final size:31
Alignment explanation
Indices: 1278656--1278724 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
1278646 TTATTATTCC
* *
1278656 ATTTGGTACTTATATTTAGTTTTAATGTTTA
1 ATTTGGTACTTATATTTAGTTTCAATATTTA
*
1278687 ATTTGGTACTTGA-GTTT-GTTTCAATATTTA
1 ATTTGGTACTT-ATATTTAGTTTCAATATTTA
*
1278717 ATTCGGTA
1 ATTTGGTA
1278725 TATAAACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 18 0.55
31 14 0.42
32 1 0.03
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.54
Consensus pattern (31 bp):
ATTTGGTACTTATATTTAGTTTCAATATTTA
Found at i:1289814 original size:3 final size:3
Alignment explanation
Indices: 1289806--1289838 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1289796 TGTACTTGTT
1289806 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1289839 ACTCAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1291219 original size:29 final size:29
Alignment explanation
Indices: 1291157--1291219 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
1291147 TAAGGAATAC
* *
1291157 AAATTTCTTTTTTTTGTCATCTAATTATT
1 AAATTTCTTTTTTCTGTCATCTAATCATT
*
1291186 TAATTT-TTTCTTTCTGATCATC-AATCATT
1 AAATTTCTTT-TTTCTG-TCATCTAATCATT
1291215 AAATT
1 AAATT
1291220 ATTAACGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.11
29 20 0.71
30 5 0.18
ACGTcount: A:0.27, C:0.13, G:0.03, T:0.57
Consensus pattern (29 bp):
AAATTTCTTTTTTCTGTCATCTAATCATT
Found at i:1291911 original size:15 final size:15
Alignment explanation
Indices: 1291870--1291912 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1291860 TTCTATGTAA
* *
1291870 AAATATATTAAATAT
1 AAATATATAAAAAAT
* *
1291885 ATATAAATAAAAAAT
1 AAATATATAAAAAAT
1291900 AAATATATAAAAA
1 AAATATATAAAAA
1291913 CCTCAAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATATAAAAAAT
Found at i:1298618 original size:2 final size:2
Alignment explanation
Indices: 1298613--1298657 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1298603 CCCCCCCTCC
1298613 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1298655 CT C
1 CT C
1298658 ACACACACCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1311612 original size:20 final size:20
Alignment explanation
Indices: 1311560--1311612 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
1311550 CTATACCTTT
1311560 GAAA-TTTAAAAAAGGAAAA
1 GAAATTTTAAAAAAGGAAAA
** *
1311579 -AAATTGAAAAAAAAGAAAA
1 GAAATTTTAAAAAAGGAAAA
1311598 GAAATTTTAATAAAA
1 GAAATTTTAA-AAAA
1311613 ATACCCATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 3 0.12
19 12 0.46
20 7 0.27
21 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (20 bp):
GAAATTTTAAAAAAGGAAAA
Found at i:1313018 original size:17 final size:16
Alignment explanation
Indices: 1313007--1313048 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1312997 TAAATATAAT
1313007 TTTATAAAAAATTTAAGA
1 TTTATAAAAAA-TTAA-A
1313025 -TTA-AAAAAATTAAA
1 TTTATAAAAAATTAAA
1313039 TTTATAAAAA
1 TTTATAAAAA
1313049 CAAAAATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 7 0.32
16 11 0.50
17 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TTTATAAAAAATTAAA
Found at i:1320954 original size:16 final size:17
Alignment explanation
Indices: 1320930--1320974 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
1320920 TCGATCAAAC
1320930 TAATTTTTTAATTTTAA
1 TAATTTTTTAATTTTAA
* *
1320947 T-TTTTTTTAAATTTAA
1 TAATTTTTTAATTTTAA
1320963 TAATTTTTTAAT
1 TAATTTTTTAAT
1320975 CTAATCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTTTAATTTTAA
Found at i:1320959 original size:17 final size:17
Alignment explanation
Indices: 1320933--1320971 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
1320923 ATCAAACTAA
1320933 TTTTTTAATTT-TAATT
1 TTTTTTAATTTATAATT
1320949 TTTTTTAAATTTAATAATT
1 TTTTTT-AATTT-ATAATT
1320968 TTTT
1 TTTT
1320972 AATCTAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
19 9 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTTAATTTATAATT
Found at i:1339988 original size:21 final size:22
Alignment explanation
Indices: 1339947--1339988 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
1339937 ATAAAAAATC
1339947 TATTTAGAAAAAAGGTCAAATTT
1 TATTTAGAAAAAAGG-CAAATTT
1339970 TATTTA-AAATAAAGG-AAAT
1 TATTTAGAAA-AAAGGCAAAT
1339989 ATTTCCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (22 bp):
TATTTAGAAAAAAGGCAAATTT
Found at i:1344699 original size:16 final size:17
Alignment explanation
Indices: 1344675--1344714 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1344665 ATATATATAT
* *
1344675 AAAGTAAAAGAA-ATAA
1 AAAGAAAAAGAATAGAA
1344691 AAAGAAAAAGAATAGAA
1 AAAGAAAAAGAATAGAA
1344708 AAAGAAA
1 AAAGAAA
1344715 GAAAGGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (17 bp):
AAAGAAAAAGAATAGAA
Found at i:1344709 original size:11 final size:10
Alignment explanation
Indices: 1344681--1344718 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
1344671 ATATAAAGTA
1344681 AAAGAAATAA-
1 AAAGAAA-AAG
1344691 AAAGAAAAAG
1 AAAGAAAAAG
1344701 AATAGAAAAAG
1 AA-AGAAAAAG
1344712 AAAGAAA
1 AAAGAAA
1344719 GGATGAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.08
10 14 0.54
11 10 0.38
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:1344778 original size:17 final size:16
Alignment explanation
Indices: 1344743--1344782 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1344733 AGAGAGCAGG
* *
1344743 GGAAAGAAAGAAGGAA
1 GGAAAAAAAGAAAGAA
1344759 GGAAAAAAAGGAAAGAA
1 GGAAAAAAA-GAAAGAA
1344776 GGAAAAA
1 GGAAAAA
1344783 GGGAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
GGAAAAAAAGAAAGAA
Found at i:1347137 original size:46 final size:46
Alignment explanation
Indices: 1346810--1347131 Score: 500
Period size: 46 Copynumber: 7.0 Consensus size: 46
1346800 AGTGTGCTCT
** *
1346810 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGAAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* **
1346856 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
*
1346902 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
1346948 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATTGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
**
1346994 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1347040 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
1347086 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1347132 ATGACAGAAA
Statistics
Matches: 256, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 256 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:1347144 original size:138 final size:138
Alignment explanation
Indices: 1346825--1347131 Score: 578
Period size: 138 Copynumber: 2.2 Consensus size: 138
1346815 ATGAAATGTG
* *
1346825 TAAGACCATGGTTGAAAGATACCATGGAAACCTAATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
*
1346890 TACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
66 TACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
1346955 GAAAAGAA
131 GAAAAGAA
*
1346963 TAAGACCATGGTTGAAAGATACCATTGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1347028 TACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
66 TACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
1347093 GAAAAGAA
131 GAAAAGAA
1347101 TAAGACCATGGTTGAAAGATACCATGGCAAC
1 TAAGACCATGGTTGAAAGATACCATGGCAAC
1347132 ATGACAGAAA
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 164 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (138 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
TACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
GAAAAGAA
Found at i:1347178 original size:50 final size:49
Alignment explanation
Indices: 1346825--1347184 Score: 371
Period size: 46 Copynumber: 7.7 Consensus size: 49
1346815 ATGAAATGTG
* * * * *
1346825 TAAGACCATGGTTGAAAGATACCATGGAAACCTAATATGAAATG--TG-
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATGA
* * *
1346871 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATG-A--A
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATGA
*
1346917 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAG-A--A
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATGA
* * * *
1346963 TAAGACCATGGTTGAAAGATACCATTGCAACCTGATATGAAATG--TG-
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATGA
* * *
1347009 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATG-A--A
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATGA
*
1347055 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAG-A--A
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATGA
1347101 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAATGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAA-GAATGA
* * * * *
1347150 GTAAGATCATAGTTGAAAGACACTATGGCATCATG
1 -TAAGACCATGGTTGAAAGATACCATGGCAACATG
1347185 TCAAAGATAA
Statistics
Matches: 284, Mismatches: 19, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
45 5 0.02
46 248 0.87
47 1 0.00
49 1 0.00
50 29 0.10
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (49 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATGA
Found at i:1350586 original size:13 final size:14
Alignment explanation
Indices: 1350568--1350597 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1350558 TTTGTTCAAA
1350568 TTTTATA-TTTAAT
1 TTTTATATTTTAAT
1350581 TTTTATATTTTAAT
1 TTTTATATTTTAAT
1350595 TTT
1 TTT
1350598 GATACCTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATATTTTAAT
Found at i:1354631 original size:20 final size:20
Alignment explanation
Indices: 1354606--1354667 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
1354596 TTTAGAAAAT
*
1354606 TTTAAAAATATATAAATTTA
1 TTTAAAAATATATAAAATTA
*
1354626 TTTAAAAA-ATTTAAAATTA
1 TTTAAAAATATATAAAATTA
* * *
1354645 TTAAAAAATATACAAAATAA
1 TTTAAAAATATATAAAATTA
1354665 TTT
1 TTT
1354668 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTAAAAATATATAAAATTA
Found at i:1354640 original size:19 final size:19
Alignment explanation
Indices: 1354606--1354656 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
1354596 TTTAGAAAAT
*
1354606 TTTAAAAATATATAAATTTA
1 TTTAAAAA-ATATAAAATTA
*
1354626 TTTAAAAAATTTAAAATTA
1 TTTAAAAAATATAAAATTA
1354645 -TTAAAAAATATA
1 TTTAAAAAATATA
1354657 CAAAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 11 0.39
19 9 0.32
20 8 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAAAAATATAAAATTA
Found at i:1355560 original size:25 final size:25
Alignment explanation
Indices: 1355532--1355581 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1355522 TGTATAAAGA
1355532 GATTTCAACTCAAAATATTACGACT
1 GATTTCAACTCAAAATATTACGACT
1355557 GATTTCAACTCAAAATATTACGACT
1 GATTTCAACTCAAAATATTACGACT
1355582 ATCTTTAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (25 bp):
GATTTCAACTCAAAATATTACGACT
Found at i:1358575 original size:21 final size:22
Alignment explanation
Indices: 1358525--1358575 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1358515 TAGATTAACG
* *
1358525 ATAATTATTTGCGTTAAATATT
1 ATAATTATATGCGCTAAATATT
*
1358547 ATAA-TATATGTGCTAAAT-TT
1 ATAATTATATGCGCTAAATATT
1358567 ATAATTATA
1 ATAATTATA
1358576 CACATAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 6 0.24
21 15 0.60
22 4 0.16
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (22 bp):
ATAATTATATGCGCTAAATATT
Found at i:1359021 original size:35 final size:35
Alignment explanation
Indices: 1358981--1359054 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
1358971 TAATTAAGGA
* *
1358981 ACATTCAAGTGTAATTCAGCCTGCAGATGAACAAG
1 ACATTCAAGTGTAATTCAGCCTGCAAAAGAACAAG
**
1359016 ACATTCAAGTGTGCTTCAGCCTGCAAAAGAACAAG
1 ACATTCAAGTGTAATTCAGCCTGCAAAAGAACAAG
1359051 ACAT
1 ACAT
1359055 ATCAGTTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (35 bp):
ACATTCAAGTGTAATTCAGCCTGCAAAAGAACAAG
Found at i:1359357 original size:44 final size:45
Alignment explanation
Indices: 1359309--1359401 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 45
1359299 ATGAATTTAA
* * *
1359309 TTTAATCGTTTTAT-TTTTTATTTTGAAGGAAATAATATTA-CATT
1 TTTAATCGATTTATCTTTTT-TTTTGAAGCAAATAAAATTATCATT
* *
1359353 TTTAATTGATTTATCTTTTTTTTTGAAGCAAATAAAATTATTATT
1 TTTAATCGATTTATCTTTTTTTTTGAAGCAAATAAAATTATCATT
1359398 TTTA
1 TTTA
1359402 GTTTAAGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 30 0.71
45 12 0.29
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (45 bp):
TTTAATCGATTTATCTTTTTTTTTGAAGCAAATAAAATTATCATT
Found at i:1363548 original size:53 final size:53
Alignment explanation
Indices: 1363490--1363597 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
1363480 GATGATGTAC
1363490 AGGAGAAAGATTGGTTGGGATAGTTGAAATGAAAAATGAGAAGGTCTATTTAT
1 AGGAGAAAGATTGGTTGGGATAGTTGAAATGAAAAATGAGAAGGTCTATTTAT
1363543 AGGAGAAAGATTGGTTGGGATAGTTGAAATGAAAAATGAGAAGGTCTATTTAT
1 AGGAGAAAGATTGGTTGGGATAGTTGAAATGAAAAATGAGAAGGTCTATTTAT
1363596 AG
1 AG
1363598 TTGAAATTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.40, C:0.02, G:0.31, T:0.28
Consensus pattern (53 bp):
AGGAGAAAGATTGGTTGGGATAGTTGAAATGAAAAATGAGAAGGTCTATTTAT
Found at i:1372492 original size:25 final size:24
Alignment explanation
Indices: 1372453--1372500 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1372443 TATAATAATA
*
1372453 ATAATAAGTAGTATAAAAGTAAAAC
1 ATAATAAATAGTATAAAA-TAAAAC
* *
1372478 ATAATAAATATTATATAATAAAA
1 ATAATAAATAGTATAAAATAAAA
1372501 TATATGGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (24 bp):
ATAATAAATAGTATAAAATAAAAC
Found at i:1372604 original size:20 final size:20
Alignment explanation
Indices: 1372557--1372621 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
1372547 TATATGTAAA
*
1372557 AATAATATGTATAAATAA-AT
1 AATAATATATATAAA-AATAT
*
1372577 ATATAATATATGTAAAAATAT
1 A-ATAATATATATAAAAATAT
*
1372598 AATAATATATATATAAATAAT
1 AATAATATATATAAAAAT-AT
1372619 AAT
1 AAT
1372622 TATGAGAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AATAATATATATAAAAATAT
Found at i:1372613 original size:31 final size:34
Alignment explanation
Indices: 1372547--1372613 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 34
1372537 AATGAAAATT
1372547 TATATGTAAAAATAATATGTATAAATAAATATATAA
1 TATATGTAAAAATAATA--TATAAATAAATATATAA
*
1372583 TATATGTAAAAAT-ATA-AT-AATATATATATAA
1 TATATGTAAAAATAATATATAAATAAATATATAA
1372614 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 12 0.40
32 2 0.07
35 3 0.10
36 13 0.43
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.37
Consensus pattern (34 bp):
TATATGTAAAAATAATATATAAATAAATATATAA
Found at i:1375843 original size:15 final size:16
Alignment explanation
Indices: 1375823--1375852 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1375813 AAATATAAAC
1375823 ATACAATT-AAAAGAA
1 ATACAATTCAAAAGAA
1375838 ATACAATTCAAAAGA
1 ATACAATTCAAAAGA
1375853 TAATTTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (16 bp):
ATACAATTCAAAAGAA
Found at i:1378030 original size:47 final size:47
Alignment explanation
Indices: 1377966--1378076 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
1377956 GACCTTGAGT
*
1377966 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * * *
1378013 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCTGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
1378060 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
1378077 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:1381681 original size:20 final size:20
Alignment explanation
Indices: 1381649--1381686 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1381639 TGTTTCACAT
1381649 TCATATAACTAATATTTATA
1 TCATATAACTAATATTTATA
*
1381669 TCAT-TAACATAATTTTTA
1 TCATATAAC-TAATATTTA
1381687 ACTTAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TCATATAACTAATATTTATA
Found at i:1386624 original size:32 final size:32
Alignment explanation
Indices: 1386578--1386638 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1386568 AATAAGTTAT
1386578 GTATAATAATATAAT-ATGAATAAAATAAGGAA
1 GTATAATAATATAATAAT-AATAAAATAAGGAA
*
1386610 GTATAA-AATAATAATAATAATATAATAAG
1 GTATAATAAT-ATAATAATAATAAAATAAG
1386639 TATTTTGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 3 0.12
32 21 0.81
33 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.30
Consensus pattern (32 bp):
GTATAATAATATAATAATAATAAAATAAGGAA
Done.