Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold211
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: 2157208
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 20444 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1046258 original size:30 final size:27
Alignment explanation
Indices: 1046185--1046244 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
1046175 CTGGGTCGTG
* *
1046185 GTAGGATATGATGGGTATGGAGGTTGA
1 GTAGGATATGACGGGTATGGAGGTTAA
1046212 GTAGGATATGACGGGTATGGAGGTTAA
1 GTAGGATATGACGGGTATGGAGGTTAA
1046239 GTAGGA
1 GTAGGA
1046245 AAATATGGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.02, G:0.43, T:0.27
Consensus pattern (27 bp):
GTAGGATATGACGGGTATGGAGGTTAA
Found at i:1050286 original size:16 final size:16
Alignment explanation
Indices: 1050267--1050300 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1050257 ATTTTAACAT
1050267 ATTAAAAAATAA-AAAA
1 ATTAAAAAA-AAGAAAA
1050283 ATTAAAAAAAAGAAAA
1 ATTAAAAAAAAGAAAA
1050299 AT
1 AT
1050301 AAATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
ATTAAAAAAAAGAAAA
Found at i:1050368 original size:21 final size:21
Alignment explanation
Indices: 1050343--1050388 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1050333 TAGAGAAATA
*
1050343 AGAGAATTTAGAAAATTTTAG
1 AGAGAAGTTAGAAAATTTTAG
*
1050364 AGAGAAGTTAGAGAATTTTAG
1 AGAGAAGTTAGAAAATTTTAG
1050385 AGAG
1 AGAG
1050389 TAGAGAGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (21 bp):
AGAGAAGTTAGAAAATTTTAG
Found at i:1050397 original size:21 final size:21
Alignment explanation
Indices: 1050356--1050397 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1050346 GAATTTAGAA
**
1050356 AATTTTAGAGAGAAGTTAGAG
1 AATTTTAGAGAGAAGAGAGAG
*
1050377 AATTTTAGAGAGTAGAGAGAG
1 AATTTTAGAGAGAAGAGAGAG
1050398 TGAAAATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.26
Consensus pattern (21 bp):
AATTTTAGAGAGAAGAGAGAG
Found at i:1051574 original size:18 final size:17
Alignment explanation
Indices: 1051547--1051582 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1051537 ATTAGCATTT
1051547 TAAAAATTAAAAATTAAA
1 TAAAAATTAAAAA-TAAA
*
1051565 TAAAATTTAAAAATAAA
1 TAAAAATTAAAAATAAA
1051582 T
1 T
1051583 TTTTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAATTAAAAATAAA
Found at i:1067486 original size:24 final size:26
Alignment explanation
Indices: 1067444--1067493 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
1067434 AATAATAATC
*
1067444 AAAATTTTAACATATTAAAAAATAAA
1 AAAATTTTAACATAATAAAAAATAAA
1067470 AAAATTTTAA-A-AATAAAAAATAAA
1 AAAATTTTAACATAATAAAAAATAAA
1067494 TATTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 1 0.04
26 10 0.43
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAATTTTAACATAATAAAAAATAAA
Found at i:1067558 original size:21 final size:21
Alignment explanation
Indices: 1067533--1067578 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1067523 TAGAGAAATA
* *
1067533 AGAGAATTTAGAAAATTTTAG
1 AGAGAAATTAAAAAATTTTAG
1067554 AGAGAAATTAAAAAATTTTAG
1 AGAGAAATTAAAAAATTTTAG
1067575 AGAG
1 AGAG
1067579 TAGAGAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (21 bp):
AGAGAAATTAAAAAATTTTAG
Found at i:1069318 original size:15 final size:15
Alignment explanation
Indices: 1069282--1069320 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1069272 TTATATTATT
*
1069282 TTTAATTTTTTTAAA
1 TTTAATCTTTTTAAA
*
1069297 TAT-ATCTTTTTAAA
1 TTTAATCTTTTTAAA
1069311 TTTAATCTTT
1 TTTAATCTTT
1069321 AATATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATCTTTTTAAA
Found at i:1084060 original size:33 final size:33
Alignment explanation
Indices: 1084023--1084092 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
1084013 TTTGAAAGAC
1084023 TTCTTTTTTAATTATTATATTAAATAATATATT
1 TTCTTTTTTAATTATTATATTAAATAATATATT
1084056 TTCTTTTTTAATTATTATATTAAATAATATATT
1 TTCTTTTTTAATTATTATATTAAATAATATATT
1084089 TTCT
1 TTCT
1084093 AATATATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (33 bp):
TTCTTTTTTAATTATTATATTAAATAATATATT
Found at i:1084719 original size:17 final size:17
Alignment explanation
Indices: 1084699--1084732 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1084689 TTTTAACATA
1084699 TTAAAAAATAAAAAAAT
1 TTAAAAAATAAAAAAAT
*
1084716 TTAAAAAATAGAAAAAT
1 TTAAAAAATAAAAAAAT
1084733 AAATATTAAA
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:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
TTAAAAAATAAAAAAAT
Found at i:1084799 original size:21 final size:21
Alignment explanation
Indices: 1084774--1084815 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1084764 TTAGAGAAAT
*
1084774 AAAAGAATTTAGAAAATTTTA
1 AAAAGAAATTAGAAAATTTTA
*
1084795 AAAAGAAATTAGAGAATTTTA
1 AAAAGAAATTAGAAAATTTTA
1084816 GAGAGTAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (21 bp):
AAAAGAAATTAGAAAATTTTA
Found at i:1086456 original size:24 final size:26
Alignment explanation
Indices: 1086406--1086455 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1086396 ATCCAAAGGA
*
1086406 AACCACCATTTTTGACAAAAACAAAAT
1 AACCACAATTTTTGAC-AAAACAAAAT
1086433 AACCACAATTTTTGAC-AAACAAA
1 AACCACAATTTTTGACAAAACAAA
1086456 TGGGTGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
27 15 0.68
ACGTcount: A:0.52, C:0.22, G:0.04, T:0.22
Consensus pattern (26 bp):
AACCACAATTTTTGACAAAACAAAAT
Found at i:1096952 original size:17 final size:17
Alignment explanation
Indices: 1096930--1096963 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1096920 TAGTATTTTA
* *
1096930 AAAATTTTAAATTAAAT
1 AAAATTTAAAAATAAAT
1096947 AAAATTTAAAAATAAAT
1 AAAATTTAAAAATAAAT
1096964 TTTTATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATTTAAAAATAAAT
Found at i:1099825 original size:20 final size:21
Alignment explanation
Indices: 1099782--1099829 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1099772 ACCAAGGAAA
*
1099782 TGTATTGATACATTTTTTTAAT
1 TGTATCGATACA-TTTTTTAAT
*
1099804 TGTATCGATACA-TTTTTCAT
1 TGTATCGATACATTTTTTAAT
1099824 TGTATC
1 TGTATC
1099830 TATCGCAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.54
Consensus pattern (21 bp):
TGTATCGATACATTTTTTAAT
Found at i:1100712 original size:44 final size:44
Alignment explanation
Indices: 1100649--1100737 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1100639 TCATGAGAGA
1100649 AAGAAAAAAGATTTAAGTTTTTTGTTGAAAAACGGGGTTGGAGT
1 AAGAAAAAAGATTTAAGTTTTTTGTTGAAAAACGGGGTTGGAGT
1100693 AAGAAAAAAGATTTAAGTTTTTTGTTGAAAAACGGGGTTGGAGT
1 AAGAAAAAAGATTTAAGTTTTTTGTTGAAAAACGGGGTTGGAGT
1100737 A
1 A
1100738 TCTTTTTGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.31
Consensus pattern (44 bp):
AAGAAAAAAGATTTAAGTTTTTTGTTGAAAAACGGGGTTGGAGT
Found at i:1102012 original size:14 final size:14
Alignment explanation
Indices: 1101993--1102023 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1101983 GATCAATCCA
1101993 GATGAGGGAGTTAC
1 GATGAGGGAGTTAC
1102007 GATGAGGGAGTTAC
1 GATGAGGGAGTTAC
1102021 GAT
1 GAT
1102024 TTTTTGAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.42, T:0.23
Consensus pattern (14 bp):
GATGAGGGAGTTAC
Found at i:1108620 original size:34 final size:34
Alignment explanation
Indices: 1108581--1108669 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 34
1108571 TTTACCTAAT
* *
1108581 ACATCACCTAATATACTTAATATGCTCACTTTAC
1 ACATCACCTAATACACTTAATATGCTCACTTAAC
* *
1108615 ACATCACTTAATACATTTAATATGCTCACTTAAC
1 ACATCACCTAATACACTTAATATGCTCACTTAAC
1108649 ACATCACCT-A-ACACTTAATAT
1 ACATCACCTAATACACTTAATAT
1108670 ATTTACCTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 10 0.20
33 1 0.02
34 38 0.78
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (34 bp):
ACATCACCTAATACACTTAATATGCTCACTTAAC
Found at i:1117864 original size:20 final size:20
Alignment explanation
Indices: 1117839--1117986 Score: 127
Period size: 20 Copynumber: 6.8 Consensus size: 20
1117829 GTAAAAAGAC
1117839 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
1117859 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
1117879 AGAATGTATCGATACATATGGGTATAAGGA
1 AGAATGTATCGATAC--A----T-T---GA
*
1117909 TAGAATGTATCGATATATTGA
1 -AGAATGTATCGATACATTGA
* * *
1117930 AGAATATATCGTTACATTCA
1 AGAATGTATCGATACATTGA
* *
1117950 TA-CATGTATCAATACATTGA
1 -AGAATGTATCGATACATTGA
1117970 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
1117987 CTGAGTACCT
Statistics
Matches: 103, Mismatches: 12, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
19 1 0.01
20 77 0.75
21 3 0.03
22 1 0.01
24 1 0.01
25 1 0.01
26 1 0.01
27 1 0.01
29 1 0.01
30 2 0.02
31 14 0.14
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1117914 original size:71 final size:71
Alignment explanation
Indices: 1117791--1117966 Score: 235
Period size: 71 Copynumber: 2.5 Consensus size: 71
1117781 TTTTAACTAG
*
1117791 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATACGGGTAAAAAGACAGAATGTATCGATACAT
1117856 TGAAGA
66 TGAAGA
* * * * * *
1117862 ATGTATCGATACATTGAAGAATGTATCGATACATATGGGTATAAGGATAGAATGTATCGATATAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATACGGGTAAAAAGACAGAATGTATCGATACAT
1117927 TGAAGA
66 TGAAGA
* * * * * *
1117933 ATATATCGTTACATTCATACATGTATCAATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACAT
1117967 TGAAGAATGT
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30
Consensus pattern (71 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATACGGGTAAAAAGACAGAATGTATCGATACAT
TGAAGA
Found at i:1118448 original size:49 final size:47
Alignment explanation
Indices: 1118353--1118476 Score: 133
Period size: 49 Copynumber: 2.6 Consensus size: 47
1118343 ATGAGAGGAT
* * **
1118353 TGCCAATGTGCTAATTCAAGGCCAGCGACATTGGATTAAGGGAAAAG
1 TGCCAATGTGCTGATTCAAGGCCAGTGACATTGGATTAAGAAAAAAG
* *
1118400 TGGACCAATGTACTGATTCAAGGCCAGTGACATTGGGCTTAA-AAAAAAG
1 T-G-CCAATGTGCTGATTCAAGGCCAGTGACATT-GGATTAAGAAAAAAG
* * *
1118449 TGCCAATATGCTGATTCAATGCTAGTGA
1 TGCCAATGTGCTGATTCAAGGCCAGTGA
1118477 TGTCAGACAG
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
47 23 0.36
48 2 0.03
49 33 0.52
50 6 0.09
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (47 bp):
TGCCAATGTGCTGATTCAAGGCCAGTGACATTGGATTAAGAAAAAAG
Found at i:1118711 original size:32 final size:28
Alignment explanation
Indices: 1118558--1119104 Score: 576
Period size: 28 Copynumber: 18.6 Consensus size: 28
1118548 CACTAACTTG
*
1118558 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1118586 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1118614 TGTGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1118642 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1118670 TGTGGGCTTTGAAATGGGTTGCCACCGACTT
1 TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
1118701 GTGTGGGCTTTGAAATGGGTTGCCA-TCGACTT
1 -TGTGGGCTTTGAAA-GGG-TGCCACT-GAC-T
* * *
1118733 GTGTGGGCTTTGAAATAGGTTACCACCGACTT
1 -TGTGGGCTTTG-AA-AGGGTGCCACTGAC-T
* *
1118765 GTGTGGGCTTTCAAATGGGTTGCCACCGACT
1 -TGTGGGCTTTGAAA-GGG-TGCCACTGACT
* *
1118796 TGTATGGGCTTTTAAATGGGTTGCCACCGACTT
1 TG--TGGGCTTTGAAA-GGG-TGCCACTGAC-T
*
1118829 GTGTGGGCTTTCAAATGGGTTGCCACTGACTT
1 -TGTGGGCTTTGAAA-GGG-TGCCACTGAC-T
*
1118861 GTGTGGGCTTTGAAAGAGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1118890 AGTGGACTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1118918 TGTGGGCTTTGAAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1118946 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1118975 TGTGGGCTTTAAAAAGAGTGCCACTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
* *
1119004 TATGGGCTTTGAAAGGGTGCCA-TGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1119031 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1119059 CGTGGGCTTTGAAAAGAGTACCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1119088 TGTGGGCTTTGAAAGGG
1 TGTGGGCTTTGAAAGGG
1119105 ATGAACATTC
Statistics
Matches: 460, Mismatches: 41, Indels: 36
0.86 0.08 0.07
Matches are distributed among these distances:
27 25 0.05
28 183 0.40
29 77 0.17
30 22 0.05
31 8 0.02
32 137 0.30
33 5 0.01
34 3 0.01
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:1118789 original size:96 final size:91
Alignment explanation
Indices: 1118553--1119072 Score: 473
Period size: 96 Copynumber: 5.9 Consensus size: 91
1118543 GGTTCCACTA
* *
1118553 ACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA--GGATGCCACTGAC-T-
1 ACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
*
1118614 TGTGGGCTTTGAAA-AGG-TGCCACTG
66 TGTGGGCTTTGAAATGGGTTGCCAC-G
1118639 AC-T-TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 ACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1118702 TGTGGGCTTTGAAATGGGTTGCCATCG
66 TGTGGGCTTTGAAATGGGTTGCCA-CG
* * * *
1118729 ACTTGTGTGGGCTTTGAAATAGGTTACCACCGACTTGTGTGGGCTTTCAAATGGGTTGCCACCGA
1 ACTTGTGTGGGCTTTG-AA-AGGATGCCACTGAC-T-TGTGGGCTTTGAAATGGGTTGCCACCGA
* *
1118794 CTTGTATGGGCTTTTAAATGGGTTGCCACCG
62 CTTGTGTGGGCTTTGAAATGGGTTGCCA-CG
* * * *
1118825 ACTTGTGTGGGCTTTCAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAA-GAG-TGCCACTGA
1 ACTTGTGTGGGCTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTGAAATGGGTTGCCACCGA
* * *
1118888 C-T-AGTGGACTTTGAAA-GGG-TGCCACTA
62 CTTGTGTGGGCTTTGAAATGGGTTGCCAC-G
* * * * *
1118915 AC-T-TGTGGGCTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGAG-TGCCACTGAC-T-
1 ACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* * *
1118975 TGTGGGCTTTAAAAAGAG-TGCCACTG
66 TGTGGGCTTTGAAATGGGTTGCCAC-G
* * * *
1119001 AC-T-TATGGGCTTTGAAAGGGTGCCA-TGATTTGTGGGCTTTGAAA-GGG-TGCCACTGAC-T-
1 ACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
*
1119059 CGTGGGCTTTGAAA
66 TGTGGGCTTTGAAA
1119073 AGAGTACCAT
Statistics
Matches: 381, Mismatches: 35, Indels: 38
0.84 0.08 0.08
Matches are distributed among these distances:
84 81 0.21
85 44 0.12
86 57 0.15
87 1 0.00
88 27 0.07
89 4 0.01
90 15 0.04
91 5 0.01
92 21 0.06
93 3 0.01
94 21 0.06
95 5 0.01
96 97 0.25
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (91 bp):
ACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTG
TGTGGGCTTTGAAATGGGTTGCCACG
Found at i:1120341 original size:20 final size:18
Alignment explanation
Indices: 1120318--1120370 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
1120308 TCTAGACCCC
1120318 TTTCTTTTTTTTGCTATTTT
1 TTTCTTTTTTTTG-T-TTTT
1120338 TTTCTTGGTTTTTTGTTTTT
1 TTTCTT--TTTTTTGTTTTT
*
1120358 TTTATTTTATTTT
1 TTTCTTTT-TTTT
1120371 TTTGGGTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.07
19 4 0.14
20 15 0.52
21 1 0.03
22 7 0.24
ACGTcount: A:0.06, C:0.06, G:0.08, T:0.81
Consensus pattern (18 bp):
TTTCTTTTTTTTGTTTTT
Found at i:1134390 original size:31 final size:32
Alignment explanation
Indices: 1134352--1134426 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
1134342 TGCATTGAAA
1134352 AATGTATCGATACAT-CCGGGTAAAAAGATAG
1 AATGTATCGATACATACCGGGTAAAAAGATAG
** *
1134383 AATGTATCGATACATATTGGGTAAAAGGATAG
1 AATGTATCGATACATACCGGGTAAAAAGATAG
1134415 AATGTATCGATA
1 AATGTATCGATA
1134427 TATTGAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 15 0.38
32 25 0.62
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (32 bp):
AATGTATCGATACATACCGGGTAAAAAGATAG
Found at i:1134438 original size:20 final size:20
Alignment explanation
Indices: 1134413--1134489 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1134403 GTAAAAGGAT
*
1134413 AGAATGTATCGATATATTGA
1 AGAATGTATCGATACATTGA
* *
1134433 AGAATGTATCAATACATTCA
1 AGAATGTATCGATACATTGA
*
1134453 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
1134473 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
1134490 CTAGATACCT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1138603 original size:26 final size:26
Alignment explanation
Indices: 1138541--1138605 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 26
1138531 TTAAAATAAT
* ** *
1138541 ATAAAAAATTTTAAAATTATTTTTAT
1 ATAAAAAATTTTATAATTAAATTTAA
*
1138567 AT-AAATA-TTTATAATTAAATTTAA
1 ATAAAAAATTTTATAATTAAATTTAA
1138591 ATAAAAAATTTTATA
1 ATAAAAAATTTTATA
1138606 TTTTAAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
24 15 0.48
25 8 0.26
26 8 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAAAAAATTTTATAATTAAATTTAA
Found at i:1138616 original size:181 final size:183
Alignment explanation
Indices: 1138269--1138597 Score: 502
Period size: 181 Copynumber: 1.8 Consensus size: 183
1138259 ATACAGTTAG
* *
1138269 AGGTCATCATGGGCTGACCTAGAACTTCAATATTTTTATCTTTACCTTAGCCCAAGATCGTTTGA
1 AGGTCATCATGGGCCGACCTAGAACTTCAATATTTTTATCTTTACCTTAGCCCAAGATCGCTTGA
* * * *
1138334 CAACTCATTTCATAATTCAAAATAATATTAAAAATTTTAAAATTATTTTTACATGAATATTTATA
66 AAACTCATTTCACAATTCAAAATAATATAAAAAATTTTAAAATTATTTTTACATAAATATTTATA
1138399 ATTAAATTTAAATAAAAATAATTTTTTAAAAAATAAATGAGACATATGTTTAA
131 ATTAAATTTAAATAAAAATAATTTTTTAAAAAATAAATGAGACATATGTTTAA
* * * * *
1138452 AGGTCATCA-GGGCCGACCTAGGACTTGAAT-TTTTTTTTTTTACCTT-GACCTAAGATCGCTTG
1 AGGTCATCATGGGCCGACCTAGAACTTCAATATTTTTATCTTTACCTTAG-CCCAAGATCGCTTG
* * *
1138514 AAAACTCATTTTACAATTTAAAATAATATAAAAAATTTTAAAATTATTTTTATATAAATATTTAT
65 AAAACTCATTTCACAATTCAAAATAATATAAAAAATTTTAAAATTATTTTTACATAAATATTTAT
1138579 AATTAAATTTAAATAAAAA
130 AATTAAATTTAAATAAAAA
1138598 ATTTTATATT
Statistics
Matches: 131, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
180 1 0.01
181 103 0.79
182 18 0.14
183 9 0.07
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (183 bp):
AGGTCATCATGGGCCGACCTAGAACTTCAATATTTTTATCTTTACCTTAGCCCAAGATCGCTTGA
AAACTCATTTCACAATTCAAAATAATATAAAAAATTTTAAAATTATTTTTACATAAATATTTATA
ATTAAATTTAAATAAAAATAATTTTTTAAAAAATAAATGAGACATATGTTTAA
Found at i:1139762 original size:13 final size:14
Alignment explanation
Indices: 1139736--1139769 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1139726 TTTTTCAAAT
1139736 TTTTAAAAATATAA
1 TTTTAAAAATATAA
1139750 TTTTAAAAA-ATAA
1 TTTTAAAAATATAA
1139763 TTATTAA
1 TT-TTAA
1139770 GATAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:1142224 original size:9 final size:9
Alignment explanation
Indices: 1142202--1142236 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1142192 TGTGTTTATA
1142202 TATTTAATT
1 TATTTAATT
* *
1142211 GATTTGATT
1 TATTTAATT
1142220 TATTTAATT
1 TATTTAATT
1142229 TATTTAAT
1 TATTTAAT
1142237 CAATTTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:1142770 original size:18 final size:17
Alignment explanation
Indices: 1142744--1142807 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
1142734 TTTTTAAAAT
1142744 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1142761 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
1142778 ATTTT-TA-TTATATAA
1 ATTTTATATTTATATAA
*
1142793 ATTTTA-ATATATATA
1 ATTTTATATTTATATA
1142808 TTTATTGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 9 0.22
16 6 0.15
17 11 0.28
18 6 0.15
19 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1142797 original size:14 final size:14
Alignment explanation
Indices: 1142753--1142810 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1142743 TATTTTATAT
1142753 TTATATAAATTTTAA
1 TTATATAAATTTT-A
*
1142768 TATATTAATAATTTTTA
1 T-TA-T-ATAAATTTTA
1142785 TTATATAAATTTTA
1 TTATATAAATTTTA
* *
1142799 ATATATATATTT
1 TTATATAAATTT
1142811 ATTGTAATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 19 0.53
15 2 0.06
16 4 0.11
17 3 0.08
18 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:1142808 original size:18 final size:17
Alignment explanation
Indices: 1142744--1142807 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 17
1142734 TTTTTAAAAT
*
1142744 ATTTTATATTTATATAA
1 ATTTTATATATATATAA
1142761 ATTTTA-ATATAT-TAATA
1 ATTTTATATATATAT-A-A
1142778 ATTTT-TAT-TATATAA
1 ATTTTATATATATATAA
1142793 ATTTTA-ATATATATA
1 ATTTTATATATATATA
1142808 TTTATTGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
15 9 0.22
16 16 0.40
17 15 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATATATATAA
Found at i:1145214 original size:3 final size:3
Alignment explanation
Indices: 1145201--1145237 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
1145191 ACAATAAAGA
1145201 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1145238 TTCTTGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1147234 original size:39 final size:40
Alignment explanation
Indices: 1147190--1147267 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 40
1147180 TTAAATTTGG
*
1147190 TAAAATGAATATTAA-TTTGA-A-AATATAAAATTTATAATA
1 TAAAATAAATA-TAATTTTGAGAGAATATAAAATTT-TAATA
*
1147229 TAAAATAAATATAATTTTGAGAGAATATAATATTTTAAT
1 TAAAATAAATATAATTTTGAGAGAATATAAAATTTTAAT
1147268 TCACATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 3 0.09
39 15 0.44
40 5 0.15
41 11 0.32
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (40 bp):
TAAAATAAATATAATTTTGAGAGAATATAAAATTTTAATA
Found at i:1148713 original size:19 final size:19
Alignment explanation
Indices: 1148672--1148714 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1148662 GCTCTATCAA
* *
1148672 TTTTTTTTGTTGAATCTTT
1 TTTTTTTTGTTAAATCTTC
1148691 TTTTTTTTGTCTAAAT-TTC
1 TTTTTTTTGT-TAAATCTTC
1148710 TTTTT
1 TTTTT
1148715 AAAATTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (19 bp):
TTTTTTTTGTTAAATCTTC
Found at i:1148760 original size:19 final size:19
Alignment explanation
Indices: 1148736--1148793 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1148726 TTTTTATTCA
1148736 AATCTTCTCAAAAATAATT
1 AATCTTCTCAAAAATAATT
1148755 AATC-T-TC--AAAT--TT
1 AATCTTCTCAAAAATAATT
1148768 AATCTTCTCAAAAATAATT
1 AATCTTCTCAAAAATAATT
1148787 AATCTTC
1 AATCTTC
1148794 ATTCCAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 6 0.18
14 1 0.03
15 6 0.18
17 6 0.18
18 1 0.03
19 13 0.39
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
AATCTTCTCAAAAATAATT
Found at i:1150124 original size:2 final size:2
Alignment explanation
Indices: 1150110--1150175 Score: 52
Period size: 2 Copynumber: 34.5 Consensus size: 2
1150100 GAGGAGCCAG
* *
1150110 AT AT AT -T AG AT AT AT AT ACT A- AA AT CAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT
*
1150152 A- AT AT -T AT AT GT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1150176 CTAAATTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
1 5 0.10
2 43 0.83
3 4 0.08
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1150152 original size:25 final size:24
Alignment explanation
Indices: 1150110--1150180 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 24
1150100 GAGGAGCCAG
*
1150110 ATATAT-TAGATATATATACTAAA
1 ATATATATATATATATATACTAAA
* **
1150133 ATCATATATATATATATATAATATT
1 AT-ATATATATATATATATACTAAA
*
1150158 ATATGTATAT-TATATATACTAAA
1 ATATATATATATATATATACTAAA
1150181 TTTATATTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 12 0.32
24 11 0.29
25 15 0.39
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (24 bp):
ATATATATATATATATATACTAAA
Found at i:1150166 original size:16 final size:17
Alignment explanation
Indices: 1150110--1150175 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
1150100 GAGGAGCCAG
1150110 ATATAT-TAGATATATAT
1 ATATATATA-ATATATAT
* *
1150127 ACTA-AAATCATATATAT
1 A-TATATATAATATATAT
1150144 ATATATATAATAT-TAT
1 ATATATATAATATATAT
* *
1150160 ATGTATATTATATATA
1 ATATATATAATATATA
1150176 CTAAATTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 16 0.41
17 20 0.51
18 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATATATAATATATAT
Found at i:1150174 original size:18 final size:20
Alignment explanation
Indices: 1150112--1150173 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
1150102 GGAGCCAGAT
* *
1150112 ATATTAGATATATATACTAAA
1 ATATTATATATATATA-TATA
1150133 ATCA-TATATATATATATATA
1 AT-ATTATATATATATATATA
*
1150153 ATATTATATGTATATTATATA
1 ATATTATATATATA-TATATA
1150174 TACTAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.40
21 19 0.54
22 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
ATATTATATATATATATATA
Found at i:1151569 original size:33 final size:31
Alignment explanation
Indices: 1151515--1151594 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 31
1151505 TATAACATAA
*
1151515 ATATAATAAAAATAATTAAATATATTAAAATTT
1 ATATAAT-ATAATAATTAAA-ATATTAAAATTT
*
1151548 ATATAATATAATTATTAAAATATTAAAATTT
1 ATATAATATAATAATTAAAATATTAAAATTT
1151579 ATTATAA-ATATATAAT
1 A-TATAATATA-ATAAT
1151595 ATTTTAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 16 0.38
32 19 0.45
33 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
ATATAATATAATAATTAAAATATTAAAATTT
Found at i:1151574 original size:31 final size:32
Alignment explanation
Indices: 1151515--1151639 Score: 101
Period size: 31 Copynumber: 3.7 Consensus size: 32
1151505 TATAACATAA
*
1151515 ATATAATAAAAATAATTAAATATATTAAAATTT
1 ATATAAT-ATAATAATTAAATATATTAAAATTT
*
1151548 ATATAATATAATTATTAAA-ATATTAAAATTT
1 ATATAATATAATAATTAAATATATTAAAATTT
* * **
1151579 ATTATAAATATATAATATTTTAAATATAATTATAATAA
1 A-TAT--A-ATATAATA-ATTAAATAT-ATTAAAATTT
1151617 ATATAA-ATATATAATATAAATAT
1 ATATAATATA-ATAAT-TAAATAT
1151640 TCAAATTATT
Statistics
Matches: 75, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
31 13 0.17
32 13 0.17
33 11 0.15
34 12 0.16
35 8 0.11
36 5 0.07
37 5 0.07
38 8 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
ATATAATATAATAATTAAATATATTAAAATTT
Found at i:1151600 original size:21 final size:20
Alignment explanation
Indices: 1151537--1151600 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
1151527 TAATTAAATA
*
1151537 TATTAAAATTTATATAATATAAT
1 TATTAAAA--TATATAATAT-TT
*
1151560 TATTAAAATAT-TAA-AATT
1 TATTAAAATATATAATATTT
1151578 TATTATAAATATATAATATTT
1 TATTA-AAATATATAATATTT
1151599 TA
1 TA
1151601 AATATAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.17
19 7 0.20
20 6 0.17
21 8 0.23
23 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTAAAATATATAATATTT
Found at i:1151789 original size:23 final size:23
Alignment explanation
Indices: 1151761--1151815 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
1151751 TATTTATCTG
1151761 ATTA-AAAT-ATTTAAAATAAAA
1 ATTATAAATAATTTAAAATAAAA
* *
1151782 ATTATAAATAATTTTAAATTAAA
1 ATTATAAATAATTTAAAATAAAA
1151805 ATT-T-AATAATT
1 ATTATAAATAATT
1151816 ATAATTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 11 0.37
22 5 0.17
23 14 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTATAAATAATTTAAAATAAAA
Found at i:1151804 original size:24 final size:22
Alignment explanation
Indices: 1151762--1151824 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
1151752 ATTTATCTGA
*
1151762 TTAA-AATATTTAAAATAAAAAT
1 TTAATAAT-TTTAAATTAAAAAT
1151784 TATAAATAATTTTAAATT-AAAAT
1 T-T-AATAATTTTAAATTAAAAAT
*
1151807 TTAATAATTAT-AATTAAA
1 TTAATAATTTTAAATTAAA
1151825 TTAAGTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 4 0.11
21 10 0.29
22 2 0.06
23 7 0.20
24 9 0.26
25 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAATAATTTTAAATTAAAAAT
Found at i:1152599 original size:21 final size:20
Alignment explanation
Indices: 1152550--1152602 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1152540 TGGTTGTTTT
*
1152550 ATTAAAATTATTTTTTATATA
1 ATTAAAA-TATTTTTAATATA
* *
1152571 ATAAAAATATTTTTAATTTA
1 ATTAAAATATTTTTAATATA
1152591 ATTATAAATATT
1 ATTA-AAATATT
1152603 AATTAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAAAATATTTTTAATATA
Found at i:1153151 original size:12 final size:13
Alignment explanation
Indices: 1153133--1153171 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1153123 TTTTAAATTA
1153133 AATTTTTTTATTT
1 AATTTTTTTATTT
1153146 AATTTTTTTATTT
1 AATTTTTTTATTT
*
1153159 AATTTTTTAATTT
1 AATTTTTTTATTT
1153172 GATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
AATTTTTTTATTT
Found at i:1153430 original size:19 final size:19
Alignment explanation
Indices: 1153406--1153444 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1153396 GTAATATAAT
*
1153406 TTAAATATTAATTTTATTA
1 TTAAATATTAATTATATTA
* *
1153425 TTAAATTTTTATTATATTA
1 TTAAATATTAATTATATTA
1153444 T
1 T
1153445 AATTATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAAATATTAATTATATTA
Found at i:1153519 original size:25 final size:25
Alignment explanation
Indices: 1153405--1153529 Score: 92
Period size: 25 Copynumber: 4.8 Consensus size: 25
1153395 AGTAATATAA
* * *
1153405 TTTAAATATTAATTTTATTATTAAAT
1 TTTAATTATTTATATTA-TATTAAAT
*
1153431 TTTTATTATATTATAATTATATTTAAAAT
1 TTTAATTAT-TTAT-ATTATA-TT-AAAT
* * *
1153460 ATTAATAATTAATATTATA-TAAAT
1 TTTAATTATTTATATTATATTAAAT
* *
1153484 TTTAAAATATTTATATTATATTACAT
1 TTT-AATTATTTATATTATATTAAAT
*
1153510 TTTAATTATTT-TTTTATATT
1 TTTAATTATTTATATTATATT
1153530 TTAACTTTCG
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
24 14 0.18
25 21 0.27
26 14 0.18
27 11 0.14
28 8 0.10
29 10 0.13
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTAATTATTTATATTATATTAAAT
Found at i:1159600 original size:15 final size:15
Alignment explanation
Indices: 1159582--1159637 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1159572 TTATTTATAA
1159582 AAATAATATAA-ATTT
1 AAATAATA-AATATTT
1159597 AAATAATAAATATTT
1 AAATAATAAATATTT
*
1159612 AAA-ATTAAATTTATTAT
1 AAATAATAAA--TATT-T
1159629 AAATAATAA
1 AAATAATAA
1159638 TTATACTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 7 0.21
15 15 0.44
16 4 0.12
17 4 0.12
18 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATAATAAATATTT
Found at i:1161525 original size:31 final size:32
Alignment explanation
Indices: 1161471--1161533 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1161461 TTTTGAATAG
1161471 GAATTATTCTGAATAGGAGCTATT-TTCTACAA
1 GAATTATTCTGAATAGGAGCTATTCTT-TACAA
*
1161503 GAATTATTTTGAATA-GAGCTATTCTTTACAA
1 GAATTATTCTGAATAGGAGCTATTCTTTACAA
1161534 TAGTGATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (32 bp):
GAATTATTCTGAATAGGAGCTATTCTTTACAA
Found at i:1161565 original size:15 final size:16
Alignment explanation
Indices: 1161545--1161579 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1161535 AGTGATTATA
*
1161545 AACAAGAGTT-TTCTT
1 AACAAGAGTTGTTCTG
1161560 AACAAGAGTTGTTCTG
1 AACAAGAGTTGTTCTG
1161576 AACA
1 AACA
1161580 TAAGATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (16 bp):
AACAAGAGTTGTTCTG
Found at i:1164958 original size:208 final size:208
Alignment explanation
Indices: 1164561--1164978 Score: 730
Period size: 208 Copynumber: 2.0 Consensus size: 208
1164551 ATAAGTCATG
1164561 ACCATCATATTAAAAGTTTAAATTCTATAATATATATTCAAATATAAACTTAAAATTACATTACA
1 ACCATCATATTAAAAGTTTAAATTCTATAATATATATTCAAATATAAACTTAAAATTACATTACA
1164626 TTTAACTATAATTAAAAAAATTAACAAAATAAAATAAAGTAAAATGAAAACGTATATATTATAAC
66 TTTAACTATAATTAAAAAAATTAACAAAATAAAATAAAGTAAAATGAAAACGTATATATTATAAC
* * *
1164691 TCACCATCTCAAATAATCATGAAAGACTTAACGAAAAGAATAATACAAAACTAAAAAAAAGTAAA
131 TCACCACCTCAAATAATCATGAAAGACTTAACAAAAAGAATAATAAAAAACTAAAAAAAAGTAAA
1164756 ATCGAAAAAAATT
196 ATCGAAAAAAATT
* *
1164769 ACCATCATATTAAAAGTTTAAATTCTATAATATATCTTCAAATATAGACTTAAAATTACATTACA
1 ACCATCATATTAAAAGTTTAAATTCTATAATATATATTCAAATATAAACTTAAAATTACATTACA
* *
1164834 TTTAACTATAATTAAAAAAATTAACAAAATAAAATAAAGTAAAATGAAAAATGTATATATTATGA
66 TTTAACTATAATTAAAAAAATTAACAAAATAAAATAAAGTAAAATG-AAAACGTATATATTATAA
* *
1164899 CTCATCACCTCAAATAATCATGAAAGA-TATAATAAAAAGAATAATAAAAAACTAAAAAAAAGTA
130 CTCACCACCTCAAATAATCATGAAAGACT-TAACAAAAAGAATAATAAAAAACTAAAAAAAAGTA
1164963 AAATCGAAAAAAATT
194 AAATCGAAAAAAATT
1164978 A
1 A
1164979 TAAGATCTAA
Statistics
Matches: 199, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
208 110 0.55
209 89 0.45
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (208 bp):
ACCATCATATTAAAAGTTTAAATTCTATAATATATATTCAAATATAAACTTAAAATTACATTACA
TTTAACTATAATTAAAAAAATTAACAAAATAAAATAAAGTAAAATGAAAACGTATATATTATAAC
TCACCACCTCAAATAATCATGAAAGACTTAACAAAAAGAATAATAAAAAACTAAAAAAAAGTAAA
ATCGAAAAAAATT
Found at i:1165063 original size:2 final size:2
Alignment explanation
Indices: 1165054--1165146 Score: 80
Period size: 2 Copynumber: 51.5 Consensus size: 2
1165044 AATAAACAAA
*
1165054 AT AT -T AT AT AT -T AT AT AT AT TT AT AT -T A- AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1165091 AT AT AT -T AT AT A- AT AT AT A- AC AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1165129 AT GT AT AT A- AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1165147 ACAAAAAACA
Statistics
Matches: 75, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
1 10 0.13
2 65 0.87
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1165066 original size:7 final size:7
Alignment explanation
Indices: 1165054--1165137 Score: 77
Period size: 7 Copynumber: 12.4 Consensus size: 7
1165044 AATAAACAAA
1165054 ATATTAT
1 ATATTAT
1165061 ATATTAT
1 ATATTAT
1165068 ATA-TAT
1 ATATTAT
*
1165074 TTA-TAT
1 ATATTAT
*
1165080 -TAATAT
1 ATATTAT
1165086 ATATTAT
1 ATATTAT
1165093 ATATTAT
1 ATATTAT
*
1165100 ATAATAT
1 ATATTAT
**
1165107 ATAACAT
1 ATATTAT
*
1165114 ATAATAT
1 ATATTAT
1165121 ATA-TAT
1 ATATTAT
1165127 ATATGTAT
1 ATAT-TAT
1165135 ATA
1 ATA
1165138 AAATATATAA
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
5 2 0.03
6 17 0.25
7 43 0.63
8 6 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (7 bp):
ATATTAT
Found at i:1165833 original size:20 final size:19
Alignment explanation
Indices: 1165792--1165830 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1165782 TATAAATATT
*
1165792 ATATTTATAAAAAAATTTA
1 ATATTTATAAAAAAATTAA
*
1165811 ATATTTATTAAAAAATTAA
1 ATATTTATAAAAAAATTAA
1165830 A
1 A
1165831 ATAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATTTATAAAAAAATTAA
Found at i:1165838 original size:25 final size:26
Alignment explanation
Indices: 1165776--1165839 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 26
1165766 TTAGATTAAT
* *
1165776 TTAAAATATAAATATTATATTTATAAA
1 TTAAAATA-AAATATTATATTAAAAAA
**
1165803 --AAAATTTAATATT-TATTAAAAAA
1 TTAAAATAAAATATTATATTAAAAAA
1165826 TTAAAATAAAATAT
1 TTAAAATAAAATAT
1165840 AAAAATAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
23 8 0.28
24 6 0.21
25 15 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAAAATAAAATATTATATTAAAAAA
Found at i:1169237 original size:24 final size:24
Alignment explanation
Indices: 1169227--1169309 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
1169217 TGCGTGTGCG
* * *
1169227 TGTGCGTGTGCCTGTGCCTGGGCA
1 TGTGCGTGTGCGTGTGCATGCGCA
*
1169251 TGCGCGTGTGCGTGTGCATGCGCA
1 TGTGCGTGTGCGTGTGCATGCGCA
*
1169275 TGTGCCTGTGCGTGTGCATGCGCA
1 TGTGCGTGTGCGTGTGCATGCGCA
*
1169299 TGTGCATGTGC
1 TGTGCGTGTGC
1169310 ATTTGCGAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.07, C:0.24, G:0.40, T:0.29
Consensus pattern (24 bp):
TGTGCGTGTGCGTGTGCATGCGCA
Found at i:1169299 original size:6 final size:6
Alignment explanation
Indices: 1169201--1169311 Score: 87
Period size: 6 Copynumber: 18.5 Consensus size: 6
1169191 GGCAAAGGAA
* * * * * * * *
1169201 CATGCG CATGTG CGTGTG CGTGTG CGTGTG CGTGTG CCTGTG CCTGGG
1 CATGTG CATGTG CATGTG CATGTG CATGTG CATGTG CATGTG CATGTG
* * * * * * *
1169249 CATGCG CGTGTG CGTGTG CATGCG CATGTG CCTGTG CGTGTG CATGCG
1 CATGTG CATGTG CATGTG CATGTG CATGTG CATGTG CATGTG CATGTG
1169297 CATGTG CATGTG CAT
1 CATGTG CATGTG CAT
1169312 TTGCGAGTAC
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.08, C:0.23, G:0.40, T:0.29
Consensus pattern (6 bp):
CATGTG
Found at i:1169545 original size:21 final size:20
Alignment explanation
Indices: 1169499--1169567 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 20
1169489 ATTATTAAAA
1169499 AATATAA-AAATATAATATTTTA
1 AATATAATAAATATAATA---TA
*
1169521 AATATAATTATAAT-TTATATA
1 AATATAA-TA-AATATAATATA
1169542 AATAT-ATAAATATAATATA
1 AATATAATAAATATAATATA
1169561 AATATAA
1 AATATAA
1169568 ATATGGAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
18 3 0.08
19 13 0.32
20 2 0.05
21 7 0.17
22 7 0.17
24 5 0.12
25 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATAATAAATATAATATA
Found at i:1169571 original size:25 final size:25
Alignment explanation
Indices: 1169471--1169571 Score: 82
Period size: 25 Copynumber: 3.8 Consensus size: 25
1169461 TTAAAATTTT
1169471 TATAATATAAATTATTAAAT-TATTAAA
1 TATAATATAAA-TA-TAAATATA-TAAA
* *
1169498 -A-AATATAAAAATATAATATTTTAAA
1 TATAATATAAATATA-AATA-TATAAA
1169523 TATAATTATAATTTATATAAATATATAAA
1 TATAA-TATAA---ATATAAATATATAAA
1169552 TATAATATAAATATAAATAT
1 TATAATATAAATATAAATAT
1169572 GGAGCAGCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
23 2 0.03
24 4 0.07
25 22 0.36
26 3 0.05
27 2 0.03
28 10 0.16
29 10 0.16
30 4 0.07
31 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TATAATATAAATATAAATATATAAA
Found at i:1170309 original size:25 final size:25
Alignment explanation
Indices: 1170269--1170337 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
1170259 TATGATAATT
*
1170269 AAATATTTTTATATTATATATATTTC
1 AAATA-TTTTATATTATATAAATTTC
*
1170295 AAATATTTTATATTAATATAAATTTT
1 AAATATTTTATATT-ATATAAATTTC
**
1170321 AAA-AAATTATATTATAT
1 AAATATTTTATATTATAT
1170338 TTTAATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 4 0.11
25 17 0.45
26 17 0.45
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
AAATATTTTATATTATATAAATTTC
Found at i:1170319 original size:26 final size:26
Alignment explanation
Indices: 1170269--1170319 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1170259 TATGATAATT
*
1170269 AAATATTTTTATATTATATATATTTC
1 AAATATTTTTATATTATATAAATTTC
1170295 AAATA-TTTTATATTAATATAAATTT
1 AAATATTTTTATATT-ATATAAATTT
1170320 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
AAATATTTTTATATTATATAAATTTC
Found at i:1171224 original size:21 final size:22
Alignment explanation
Indices: 1171183--1171224 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1171173 ATTGATTTAC
1171183 TAAAATAAAATTTTAAATATTT
1 TAAAATAAAATTTTAAATATTT
1171205 TAAAA-AATAATTTT-AATATT
1 TAAAATAA-AATTTTAAATATT
1171225 AAATAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATAAAATTTTAAATATTT
Found at i:1171245 original size:16 final size:19
Alignment explanation
Indices: 1171217--1171264 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1171207 AAAAATAATT
*
1171217 TTAATATTA-AATAAAT-A
1 TTAATAATATAATAAATAA
1171234 TT-A-AATATAATAAATAA
1 TTAATAATATAATAAATAA
1171251 TTAATAATATAATA
1 TTAATAATATAATA
1171265 TATTTAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 3 0.12
16 8 0.31
17 5 0.19
18 1 0.04
19 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATAATATAATAAATAA
Found at i:1171939 original size:20 final size:20
Alignment explanation
Indices: 1171892--1171939 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1171882 AATTTTTTAA
1171892 TTTTTAGTTTTATATTAAATT
1 TTTTTA-TTTTATATTAAATT
* *
1171913 ATATTATTTTATTATT-AATT
1 TTTTTATTTTA-TATTAAATT
1171933 TTTTTAT
1 TTTTTAT
1171940 AGATGATAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTATTTTATATTAAATT
Found at i:1172536 original size:2 final size:2
Alignment explanation
Indices: 1172531--1172564 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1172521 TATATGTGTG
*
1172531 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1172565 CAAGCTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1174347 original size:22 final size:22
Alignment explanation
Indices: 1174307--1174348 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1174297 TTGATTTACG
1174307 ATTAAGTTAAATTAAAAAATCC
1 ATTAAGTTAAATTAAAAAATCC
*
1174329 ATTAA-TTCAATTAATAAAAT
1 ATTAAGTTAAATTAA-AAAAT
1174349 TACAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
ATTAAGTTAAATTAAAAAATCC
Found at i:1176430 original size:14 final size:14
Alignment explanation
Indices: 1176402--1176443 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1176392 ATATAAATAA
1176402 AAATAATTAATTAT
1 AAATAATTAATTAT
1176416 AAAT-ATTAATATAT
1 AAATAATTAAT-TAT
1176430 AAAAATAATTAATT
1 --AAATAATTAATT
1176444 TTTAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.25
14 7 0.29
16 5 0.21
17 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATAATTAATTAT
Found at i:1176776 original size:18 final size:17
Alignment explanation
Indices: 1176741--1176786 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
1176731 ATATTTTATT
*
1176741 TAATTTTATTTAAAATA
1 TAATTATATTTAAAATA
1176758 TACATTCATATTT-AAATA
1 TA-ATT-ATATTTAAAATA
1176776 TAATTATATTT
1 TAATTATATTT
1176787 CTTATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.23
17 5 0.19
18 10 0.38
19 5 0.19
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTATATTTAAAATA
Found at i:1177369 original size:19 final size:19
Alignment explanation
Indices: 1177345--1177386 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1177335 AGTACGTTAA
1177345 AGTTTATATGTGAGTTTGG
1 AGTTTATATGTGAGTTTGG
1177364 AGTTTATATGTGAGTTTGG
1 AGTTTATATGTGAGTTTGG
1177383 -GTTT
1 AGTTT
1177387 GATTTTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (19 bp):
AGTTTATATGTGAGTTTGG
Found at i:1177640 original size:16 final size:16
Alignment explanation
Indices: 1177621--1177656 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1177611 AATTATCTTT
1177621 AATTATTATTAAATTA
1 AATTATTATTAAATTA
*
1177637 AATTATTATTAAGTTA
1 AATTATTATTAAATTA
1177653 AATT
1 AATT
1177657 TTAATTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:1178044 original size:25 final size:25
Alignment explanation
Indices: 1178010--1178067 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
1178000 TATTTTTAAA
1178010 CAAAGATAATATA-ATATATTAATAT
1 CAAAGATAATATATATA-ATTAATAT
*
1178035 CAAAGTTAATATATATAATTAAT-T
1 CAAAGATAATATATATAATTAATAT
*
1178059 TAAAGATAA
1 CAAAGATAA
1178068 GTTAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 8 0.28
25 18 0.62
26 3 0.10
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (25 bp):
CAAAGATAATATATATAATTAATAT
Found at i:1179291 original size:34 final size:33
Alignment explanation
Indices: 1179251--1179331 Score: 94
Period size: 36 Copynumber: 2.4 Consensus size: 33
1179241 TTTAATATAA
1179251 ATTAATTAAATTTTA-AAAATTTAATAAATAATAT
1 ATTAATTAAATTTTATAAAA-TTAA-AAATAATAT
*
1179285 ATTAATTATTATTTTTTATAAAATTAAAAATAATAT
1 ATTAATTA--A-ATTTTATAAAATTAAAAATAATAT
1179321 -TTAATTAAATT
1 ATTAATTAAATT
1179332 GAAAAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
32 2 0.05
33 1 0.02
34 8 0.20
35 7 0.17
36 10 0.24
37 9 0.22
38 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTAATTAAATTTTATAAAATTAAAAATAATAT
Found at i:1179625 original size:11 final size:11
Alignment explanation
Indices: 1179609--1179657 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1179599 TTATTACTCT
1179609 TTATTTATAAA
1 TTATTTATAAA
* *
1179620 TTATTTTTAAT
1 TTATTTATAAA
1179631 TTATTTATAAA
1 TTATTTATAAA
1179642 TTA--TATAAA
1 TTATTTATAAA
1179651 TTTATTT
1 -TTATTT
1179658 TTATTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 6 0.19
10 3 0.10
11 21 0.68
12 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:1186889 original size:47 final size:47
Alignment explanation
Indices: 1186837--1186926 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
1186827 ACAAAAAAAA
*
1186837 AATGACCAAATGAATGCAAGAAATGTCATGAAAATTCCTATGTCATG
1 AATGACCAAATGAATGCAAGAAATGTCACGAAAATTCCTATGTCATG
*
1186884 AATGACCAAATGATTGCAAGAAATGTCACGAAAATTCCTATGT
1 AATGACCAAATGAATGCAAGAAATGTCACGAAAATTCCTATGT
1186927 TATGGAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.26
Consensus pattern (47 bp):
AATGACCAAATGAATGCAAGAAATGTCACGAAAATTCCTATGTCATG
Found at i:1209162 original size:22 final size:23
Alignment explanation
Indices: 1209134--1209185 Score: 97
Period size: 22 Copynumber: 2.3 Consensus size: 23
1209124 CATGTTAAAT
1209134 ATGCATGAAACATAAT-AAAAAA
1 ATGCATGAAACATAATAAAAAAA
1209156 ATGCATGAAACATAATAAAAAAA
1 ATGCATGAAACATAATAAAAAAA
1209179 ATGCATG
1 ATGCATG
1209186 GTCAAAGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (23 bp):
ATGCATGAAACATAATAAAAAAA
Found at i:1210147 original size:20 final size:20
Alignment explanation
Indices: 1210100--1210174 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1210090 AAAAAGACAT
*
1210100 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1210119 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1210140 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1210160 AATGTATCGATACAT
1 AATGTATCGATACAT
1210175 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1210168 original size:40 final size:39
Alignment explanation
Indices: 1210097--1210174 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1210087 GGTAAAAAGA
* *
1210097 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1210136 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1210175 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1210603 original size:13 final size:13
Alignment explanation
Indices: 1210585--1210613 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1210575 TTTGAGGCAA
1210585 TGTATCGATACAT
1 TGTATCGATACAT
1210598 TGTATCGATACAT
1 TGTATCGATACAT
1210611 TGT
1 TGT
1210614 TGTCGCAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1213886 original size:20 final size:20
Alignment explanation
Indices: 1213837--1213894 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1213827 AAAAAAAGAC
1213837 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
* *
1213857 AGAATATATCGATACATTCAT
1 AGAATGTATCGATACATT-AA
*
1213878 A-CATGTATCGATACATT
1 AGAATGTATCGATACATT
1213895 TCCCATCACC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:1214016 original size:18 final size:19
Alignment explanation
Indices: 1213975--1214046 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
1213965 ATGTATTAGA
* *
1213975 ATGTATTGATACATTCATAC
1 ATGTATCGATACATTGA-AC
1213995 ATGTATCGATACATTG-AC
1 ATGTATCGATACATTGAAC
*
1214013 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAA-C
1214033 ATGTATCGATACAT
1 ATGTATCGATACAT
1214047 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
18 18 0.38
19 1 0.02
20 28 0.60
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACATTGAAC
Found at i:1214921 original size:17 final size:19
Alignment explanation
Indices: 1214899--1214948 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1214889 AAAAATATGA
1214899 AATAAATATAATATT-T-T
1 AATAAATATAATATTATAT
1214916 AATAAATATAA-ATTAGTAT
1 AATAAATATAATATTA-TAT
1214935 AATAAATATAATAT
1 AATAAATATAATAT
1214949 AATTAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.10
17 11 0.38
18 1 0.03
19 12 0.41
20 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AATAAATATAATATTATAT
Found at i:1214969 original size:33 final size:33
Alignment explanation
Indices: 1214899--1214981 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 33
1214889 AAAAATATGA
* *
1214899 AATAAATATAATATTTTAATAAATATAAATTAGTAT
1 AATAAATATAATA---TAATAAAAATAAATTAATAT
1214935 AATAAATATAATATAATTAAAAAT-AATTAATAT
1 AATAAATATAATATAA-TAAAAATAAATTAATAT
* *
1214968 AATATATATTATAT
1 AATAAATATAATAT
1214982 TTATATATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 23 0.55
34 6 0.14
36 13 0.31
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (33 bp):
AATAAATATAATATAATAAAAATAAATTAATAT
Found at i:1215551 original size:20 final size:20
Alignment explanation
Indices: 1215528--1215602 Score: 58
Period size: 20 Copynumber: 4.1 Consensus size: 20
1215518 CTAAATTTTG
1215528 ATATATTAATTATTTATATT
1 ATATATTAATTATTTATATT
1215548 ATATA--AA-T-TTTA-A--
1 ATATATTAATTATTTATATT
*
1215561 A-ATATTTATATATTTATATT
1 ATATATTAAT-TATTTATATT
* *
1215581 ATATTTTAATTTTTTATATT
1 ATATATTAATTATTTATATT
1215601 AT
1 AT
1215603 TTAAATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
12 3 0.07
13 1 0.02
14 1 0.02
15 1 0.02
16 5 0.12
17 5 0.12
18 3 0.07
20 17 0.40
21 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATATTAATTATTTATATT
Found at i:1215555 original size:32 final size:33
Alignment explanation
Indices: 1215503--1215584 Score: 105
Period size: 32 Copynumber: 2.5 Consensus size: 33
1215493 CGTATTTAAG
* * *
1215503 ATAT-TTTATAATTATCTAAATTTTGATATATTA
1 ATATATTTAT-ATTATATAAATTTTAAAATATTA
*
1215536 AT-TATTTATATTATATAAATTTTAAAATATTT
1 ATATATTTATATTATATAAATTTTAAAATATTA
1215568 ATATATTTATATTATAT
1 ATATATTTATATTATAT
1215585 TTTAATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 22 0.51
33 21 0.49
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (33 bp):
ATATATTTATATTATATAAATTTTAAAATATTA
Found at i:1215887 original size:16 final size:17
Alignment explanation
Indices: 1215858--1215904 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1215848 ATGTACTATG
*
1215858 ATATAA-ATATAATAT-
1 ATATAATATAAAATATA
1215873 ATAATAAT-TAAAATATA
1 AT-ATAATATAAAATATA
1215890 ATATAATATAAAATA
1 ATATAATATAAAATA
1215905 ATTAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 2 0.07
16 16 0.59
17 9 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAATATAAAATATA
Found at i:1215895 original size:26 final size:26
Alignment explanation
Indices: 1215858--1216044 Score: 107
Period size: 26 Copynumber: 7.0 Consensus size: 26
1215848 ATGTACTATG
*
1215858 ATATAAATATAATATATAATAATTAAA
1 ATAT-AATATAATATAAAATAATTAAA
1215885 ATATAATATAATATAAAATAATTAAA
1 ATATAATATAATATAAAATAATTAAA
* * *
1215911 ATATGATATGAATATTTAAATATTTTAAA
1 ATATAATAT-AATA-TAAAATA-ATTAAA
* * * *
1215940 AT-TTATATTATA-AAAATTATTAAT
1 ATATAATATAATATAAAATAATTAAA
* * * *
1215964 ATATTAAAAT-TTATAAAAAAAATTTTAA
1 ATA-TAATATAATAT-AAAATAA-TTAAA
1215992 ATATAATTATAATAT-AAA-AATTATAA
1 ATATAA-TATAATATAAAATAATTA-AA
*
1216018 ATATGACATA-AATATATAAATTATTAA
1 ATAT-A-ATATAATATA-AAATAATTAA
1216045 TTTTATTTAA
Statistics
Matches: 123, Mismatches: 21, Indels: 31
0.70 0.12 0.18
Matches are distributed among these distances:
24 6 0.05
25 8 0.07
26 46 0.37
27 25 0.20
28 24 0.20
29 14 0.11
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.40
Consensus pattern (26 bp):
ATATAATATAATATAAAATAATTAAA
Found at i:1215971 original size:32 final size:31
Alignment explanation
Indices: 1215929--1216021 Score: 92
Period size: 32 Copynumber: 3.2 Consensus size: 31
1215919 TGAATATTTA
*
1215929 AATATTTTAAAATTTATATTATAAAAATTATT
1 AATATATTAAAATTTATA-TATAAAAATTATT
*
1215961 AATATATTAAAATTTATA-AAAAAAATT-TT
1 AATATATTAAAATTTATATATAAAAATTATT
*
1215990 AA-ATA-T--AA-TTATAATATAAAAATTATA
1 AATATATTAAAATTTAT-ATATAAAAATTATT
1216017 AATAT
1 AATAT
1216022 GACATAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
24 4 0.08
25 3 0.06
26 8 0.15
27 4 0.08
28 5 0.09
29 4 0.08
30 8 0.15
32 17 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
AATATATTAAAATTTATATATAAAAATTATT
Found at i:1215987 original size:30 final size:31
Alignment explanation
Indices: 1215925--1215996 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
1215915 GATATGAATA
* *
1215925 TTTAAATATTTTAAAATTTATATTATAAAAAT
1 TTTAAATATATTAAAATTTATA-TAAAAAAAT
1215957 TATT-AATATATTAAAATTTATA-AAAAAAAT
1 T-TTAAATATATTAAAATTTATATAAAAAAAT
1215987 TTTAAATATA
1 TTTAAATATA
1215997 ATTATAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 2 0.06
30 14 0.39
32 18 0.50
33 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTAAATATATTAAAATTTATATAAAAAAAT
Found at i:1216015 original size:14 final size:14
Alignment explanation
Indices: 1215936--1216017 Score: 64
Period size: 14 Copynumber: 5.9 Consensus size: 14
1215926 TTAAATATTT
* *
1215936 TAAAATTTATATTA
1 TAAAAATTATAATA
1215950 TAAAAATTATTAATA
1 TAAAAATTA-TAATA
1215965 TATTAAAATTTATAA-A
1 TA--AAAA-TTATAATA
*
1215981 -AAAAATTTTAA-A
1 TAAAAATTATAATA
*
1215993 T-ATAATTATAATA
1 TAAAAATTATAATA
1216006 TAAAAATTATAA
1 TAAAAATTATAA
1216018 ATATGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
12 14 0.25
13 6 0.11
14 17 0.31
15 7 0.13
16 1 0.02
17 7 0.13
18 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAAATTATAATA
Found at i:1222573 original size:4 final size:4
Alignment explanation
Indices: 1222566--1222590 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1222556 TATATATGTA
1222566 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
1222591 TAGGAGAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1223673 original size:2 final size:2
Alignment explanation
Indices: 1223655--1223694 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1223645 TCTTACGTGC
* *
1223655 AT AT AG AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1223695 CATTAATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1225845 original size:24 final size:24
Alignment explanation
Indices: 1225774--1225845 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
1225764 TTAATATTAA
* *
1225774 CTAATATCAACTATTAACTAGAAC
1 CTAATATTAATTATTAACTAGAAC
1225798 C--ATATTATATT-TGTCAAC-AGAAC
1 CTAATATTA-ATTAT-T-AACTAGAAC
1225821 CTAATATTAATTATTAACTAGAAC
1 CTAATATTAATTATTAACTAGAAC
1225845 C
1 C
1225846 AAACATTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
22 6 0.15
23 12 0.31
24 14 0.36
25 7 0.18
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (24 bp):
CTAATATTAATTATTAACTAGAAC
Found at i:1226735 original size:50 final size:50
Alignment explanation
Indices: 1226678--1226778 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
1226668 TTTTCAATGC
1226678 CATCAAAAGAAGGATGGGTTTGAAATTTATGATTAAAATCTAAAAACTGA
1 CATCAAAAGAAGGATGGGTTTGAAATTTATGATTAAAATCTAAAAACTGA
1226728 CATCAAAAGAAGGATGGGTTTGAAATTTATGATTAAAATCTAAAAACTGA
1 CATCAAAAGAAGGATGGGTTTGAAATTTATGATTAAAATCTAAAAACTGA
1226778 C
1 C
1226779 GATGACTCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.28
Consensus pattern (50 bp):
CATCAAAAGAAGGATGGGTTTGAAATTTATGATTAAAATCTAAAAACTGA
Found at i:1228433 original size:2 final size:2
Alignment explanation
Indices: 1228420--1228449 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1228410 AATGTACTTC
*
1228420 AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1228450 GTTACTTCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1229774 original size:2 final size:2
Alignment explanation
Indices: 1229767--1229807 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1229757 AAACACTAGG
1229767 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1229808 GAAGTTACAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1230780 original size:17 final size:16
Alignment explanation
Indices: 1230760--1230813 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
1230750 AAAAAAATTA
1230760 AAATAATTATTTATATT
1 AAATAA-TATTTATATT
**
1230777 AAATAATA-AAATA-T
1 AAATAATATTTATATT
1230791 AGAAT-ATATTTATATT
1 A-AATAATATTTATATT
1230807 AAATAAT
1 AAATAAT
1230814 TATTAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
14 5 0.17
15 12 0.41
16 6 0.21
17 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AAATAATATTTATATT
Found at i:1230808 original size:110 final size:104
Alignment explanation
Indices: 1230694--1230917 Score: 260
Period size: 104 Copynumber: 2.1 Consensus size: 104
1230684 TTAGATTCAA
1230694 ATTAAATAATTATTAAGAAAATTTGATTAAAATAT-G-TATATATATAATAAAAATTTAAAAAAA
1 ATTAAATAATTATT----AAATTTG-TTAAAATATAGCTATAT-T-TAATAAAAA-TTAAAAAAA
1230757 TTAAAA-TAATTATTTATATTAAATAATAAAATATAG-AA-TATATTTAT
58 TTAAAATTAA--ATTTATATTAAA-AATAAAATATAGAAACTATATTTAT
* * * *
1230804 ATTAAATAATTATTAAATTTGTTAAATTATAGCTATGTTTAATAATAATTAAAAATATTAAAATT
1 ATTAAATAATTATTAAATTTGTTAAAATATAGCTATATTTAATAAAAATTAAAAAAATTAAAATT
* *
1230869 AAATTTATATTAAAAATAAAATTTTGAAACTATATTTAT
66 AAATTTATATTAAAAATAAAATATAGAAACTATATTTAT
1230908 ATTAAATAAT
1 ATTAAATAAT
1230918 AAATATATAT
Statistics
Matches: 103, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
102 10 0.10
103 14 0.14
104 33 0.32
105 19 0.18
106 9 0.09
107 4 0.04
110 14 0.14
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (104 bp):
ATTAAATAATTATTAAATTTGTTAAAATATAGCTATATTTAATAAAAATTAAAAAAATTAAAATT
AAATTTATATTAAAAATAAAATATAGAAACTATATTTAT
Found at i:1230890 original size:18 final size:17
Alignment explanation
Indices: 1230858--1230892 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1230848 ATAATTAAAA
*
1230858 ATATTAAAATTAAATTT
1 ATATTAAAATAAAATTT
1230875 ATATTAAAAATAAAATTT
1 ATATT-AAAATAAAATTT
1230893 TGAAACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATTAAAATAAAATTT
Found at i:1230890 original size:31 final size:33
Alignment explanation
Indices: 1230749--1230953 Score: 109
Period size: 31 Copynumber: 6.1 Consensus size: 33
1230739 AATAAAAATT
*
1230749 TAAAAAAATTAAAA-TAATTATTTATATTAAATAA
1 TAAAAATATTAAAATTAA--ATTTATATTAAATAA
* *
1230783 T-AAAATA-TAGAA-TATATTTATATTAAATAA
1 TAAAAATATTAAAATTAAATTTATATTAAATAA
* * * * ** *
1230813 TTATTAAATTTGTTAAATTATAGCTATGTTTAATAATAA
1 -TA-AAAATAT-TAAAATTAAATTTAT-ATT-A-AATAA
1230852 TTAAAAATATTAAAATTAAATTTATATTAAA-AA
1 -TAAAAATATTAAAATTAAATTTATATTAAATAA
* * * *
1230885 T-AAAATTTTGAAACTATATTTATATTAAATAA
1 TAAAAATATTAAAATTAAATTTATATTAAATAA
* * *
1230917 TAAATATATATTAAAATTAGA-GTATGTTAAATAA
1 TAAA-A-ATATTAAAATTAAATTTATATTAAATAA
1230951 TAA
1 TAA
1230954 TCAAAATAAT
Statistics
Matches: 131, Mismatches: 27, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
30 15 0.11
31 25 0.19
32 10 0.08
33 13 0.10
34 18 0.14
35 14 0.11
36 9 0.07
37 13 0.10
38 6 0.05
39 8 0.06
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (33 bp):
TAAAAATATTAAAATTAAATTTATATTAAATAA
Found at i:1230954 original size:102 final size:103
Alignment explanation
Indices: 1230739--1230959 Score: 261
Period size: 104 Copynumber: 2.1 Consensus size: 103
1230729 GTATATATAT
*
1230739 AATAAAAATTTAAAAAAATTAAAATAATTATTTATATTAAATAATAAAATATAGAATATATTTAT
1 AATAATAA-TTAAAAAAATTAAAATAA-TATTTATATTAAATAATAAAATATAGAATATATTTAT
* * * * * *
1230804 ATTAAATAATTATTAAATTTGTTAAATTATAGCTATGTTT
64 ATTAAATAATAAATAAATATGTAAAATTAGAGCTATGTTA
* * *
1230844 AATAATAATTAAAAATATTAAAATTAA-ATTTATATTAAA-AATAAAATTTTGAAACTATATTTA
1 AATAATAATTAAAAAAATTAAAA-TAATATTTATATTAAATAATAAAATATAG-AA-TATATTTA
*
1230907 TATTAAATAATAAATATATAT-TAAAATTAGAG-TATGTTA
63 TATTAAATAATAAATAAATATGTAAAATTAGAGCTATGTTA
*
1230946 AATAATAATCAAAA
1 AATAATAATTAAAA
1230960 TAATAATTAT
Statistics
Matches: 101, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
102 29 0.29
103 23 0.23
104 39 0.39
105 10 0.10
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (103 bp):
AATAATAATTAAAAAAATTAAAATAATATTTATATTAAATAATAAAATATAGAATATATTTATAT
TAAATAATAAATAAATATGTAAAATTAGAGCTATGTTA
Found at i:1231000 original size:15 final size:13
Alignment explanation
Indices: 1230968--1231016 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
1230958 AATAATAATT
1230968 ATATTAAAAAATA
1 ATATTAAAAAATA
1230981 A-ATTAATAAAATAA
1 ATATTAA-AAAAT-A
1230995 ATATTAAAAAA-A
1 ATATTAAAAAATA
*
1231007 TTATTAAAAA
1 ATATTAAAAA
1231017 TTTGGAGGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 15 0.47
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATTAAAAAATA
Found at i:1231016 original size:12 final size:13
Alignment explanation
Indices: 1230975--1231015 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 13
1230965 ATTATATTAA
*
1230975 AAAATAAATTAAT
1 AAAATAAATTATT
1230988 AAAATAAA-TATT
1 AAAATAAATTATT
1231000 AAAA-AAATTATT
1 AAAATAAATTATT
1231012 AAAA
1 AAAA
1231016 ATTTGGAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 3 0.12
12 15 0.58
13 8 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATAAATTATT
Found at i:1231432 original size:10 final size:10
Alignment explanation
Indices: 1231391--1231432 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
1231381 TAATCTTATC
1231391 AAATATAAAA
1 AAATATAAAA
*
1231401 AAATTTAAAA
1 AAATATAAAA
1231411 AAATTATAAAA
1 AAA-TATAAAA
1231422 AACATATAAAA
1 AA-ATATAAAA
1231433 TAACTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 12 0.43
11 15 0.54
12 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATATAAAA
Found at i:1233331 original size:13 final size:14
Alignment explanation
Indices: 1233308--1233336 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1233298 TATTATTCAA
1233308 ATTTAAATATAAAT
1 ATTTAAATATAAAT
1233322 ATTT-AATATAAAT
1 ATTTAAATATAAAT
1233335 AT
1 AT
1233337 ATATTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTAAATATAAAT
Found at i:1233418 original size:20 final size:19
Alignment explanation
Indices: 1233395--1233437 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1233385 TTATATTTTT
*
1233395 ATATTATATAATATATATAA
1 ATATTA-ATAATAAATATAA
*
1233415 ATA-TAATATTAAATATAA
1 ATATTAATAATAAATATAA
1233433 ATATT
1 ATATT
1233438 TTAAAAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 14 0.70
19 3 0.15
20 3 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTAATAATAAATATAA
Found at i:1233435 original size:13 final size:13
Alignment explanation
Indices: 1233400--1233437 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1233390 TTTTTATATT
1233400 ATATAATATATATAA
1 ATATAA-ATAT-TAA
1233415 ATAT-AATATTAA
1 ATATAAATATTAA
1233427 ATATAAATATT
1 ATATAAATATT
1233438 TTAAAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 10 0.45
14 1 0.05
15 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAAATATTAA
Found at i:1234825 original size:53 final size:53
Alignment explanation
Indices: 1234745--1234852 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
1234735 ACATGGCGAC
1234745 ATTGGTGTGGAGATATAATCACAAATTTCCCATCAACTTGGTGCAATGAACCA
1 ATTGGTGTGGAGATATAATCACAAATTTCCCATCAACTTGGTGCAATGAACCA
* *
1234798 ATTGGTGTGGAGATATAATCACAAATTTCCCATCAGCTTGGTGCATTGAACCA
1 ATTGGTGTGGAGATATAATCACAAATTTCCCATCAACTTGGTGCAATGAACCA
1234851 AT
1 AT
1234853 GGCAAAGGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (53 bp):
ATTGGTGTGGAGATATAATCACAAATTTCCCATCAACTTGGTGCAATGAACCA
Found at i:1239035 original size:17 final size:17
Alignment explanation
Indices: 1239009--1239042 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1238999 CGATAATTCG
* *
1239009 TATATTTATTTTGTATT
1 TATATATATTTTCTATT
1239026 TATATATATTTTCTATT
1 TATATATATTTTCTATT
1239043 ATGATCATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TATATATATTTTCTATT
Found at i:1240470 original size:9 final size:11
Alignment explanation
Indices: 1240445--1240480 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1240435 TAACAGTTCA
1240445 TATATTTATAT
1 TATATTTATAT
*
1240456 TATATTTATTT
1 TATATTTATAT
*
1240467 TATTTTTATAT
1 TATATTTATAT
1240478 TAT
1 TAT
1240481 TTAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1241549 original size:21 final size:21
Alignment explanation
Indices: 1241524--1241563 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1241514 TTTTAAATAT
1241524 ATTTATTATTAACAAACATCA
1 ATTTATTATTAACAAACATCA
*
1241545 ATTTATTATTAATAAACAT
1 ATTTATTATTAACAAACAT
1241564 ATCATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTATTATTAACAAACATCA
Found at i:1241622 original size:23 final size:22
Alignment explanation
Indices: 1241571--1241622 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1241561 CATATCATTT
* * *
1241571 AATTAGTTTATTTTTAAATAAG
1 AATTAATTTACTTTTAAAAAAG
*
1241593 AATTAATTTACTTTTAAAAAAT
1 AATTAATTTACTTTTAAAAAAG
1241615 AATATAAT
1 AAT-TAAT
1241623 ACATTTATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
AATTAATTTACTTTTAAAAAAG
Found at i:1241866 original size:15 final size:15
Alignment explanation
Indices: 1241846--1241882 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1241836 ACATGCCAAA
1241846 TATAAAAATTTAATT
1 TATAAAAATTTAATT
1241861 TATAAAAATTTAATT
1 TATAAAAATTTAATT
*
1241876 TTTAAAA
1 TATAAAA
1241883 TATTAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAAAAATTTAATT
Found at i:1243562 original size:26 final size:26
Alignment explanation
Indices: 1243533--1243589 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1243523 AAATTTAATT
1243533 ATAAAATTATAAAT-AT-TAATATAAAA
1 ATAAAATT-TAAATAATATAATAT-AAA
* *
1243559 ATAATATTTAAATAATATAATGTAAA
1 ATAAAATTTAAATAATATAATATAAA
1243585 ATAAA
1 ATAAA
1243590 TTCTTTGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
26 16 0.62
27 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
ATAAAATTTAAATAATATAATATAAA
Found at i:1244385 original size:2 final size:2
Alignment explanation
Indices: 1244378--1244420 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1244368 AAGAGCTTTC
* * * *
1244378 TA TA TA TA CA TA TG TA CA TA TA TA TG 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
1244420 T
1 T
1244421 GGTCTAATGC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1244947 original size:17 final size:18
Alignment explanation
Indices: 1244918--1244951 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1244908 TATCAAGTAA
1244918 ATTTAATAAATAAATAAT
1 ATTTAATAAATAAATAAT
1244936 ATTTAA-AAATAAATAA
1 ATTTAATAAATAAATAA
1244952 ACATTGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTTAATAAATAAATAAT
Found at i:1253483 original size:23 final size:23
Alignment explanation
Indices: 1253445--1253503 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1253435 AATTATTTAA
* *
1253445 TATATTATTAAA-ATAT-TATTT
1 TATATAATTAAATTTATATATTT
1253466 T-TAT-ATTAATATTTATATATTT
1 TATATAATTAA-ATTTATATATTT
1253488 TATATAATTAAATTTA
1 TATATAATTAAATTTA
1253504 AATAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 5 0.16
20 4 0.12
21 4 0.12
22 6 0.19
23 8 0.25
24 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATAATTAAATTTATATATTT
Found at i:1256109 original size:12 final size:11
Alignment explanation
Indices: 1256087--1256162 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1256077 AGAGAAAGAA
*
1256087 GAGAGAGGAGG
1 GAGATAGGAGG
1256098 GATGATAGGAGG
1 GA-GATAGGAGG
*
1256110 AGAGACAGGA--
1 -GAGATAGGAGG
*
1256120 GAGATAGTA--
1 GAGATAGGAGG
1256129 GAGATAGGAGG
1 GAGATAGGAGG
1256140 GATGATAGGAGG
1 GA-GATAGGAGG
*
1256152 AGAGACAGGAG
1 -GAGATAGGAG
1256163 ACATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1256138 original size:42 final size:42
Alignment explanation
Indices: 1256077--1256195 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1256067 TAGCCCTCAA
* *
1256077 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1256119 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * *
1256161 AGACATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1256196 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.43, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Done.