Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold477.1
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: 1033125
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 34335 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:835954 original size:34 final size:33
Alignment explanation
Indices: 835902--836030 Score: 170
Period size: 34 Copynumber: 3.9 Consensus size: 33
835892 ACACAACGTT
835902 ATTTTTTTAAAAAACTAAACCCTAATTTAATTA
1 ATTTTTTTAAAAAACTAAACCCTAATTTAATTA
* *
835935 ATTTTCTTAAAAACTCTAAACCCTAATTTAATTA
1 ATTTTTTTAAAAA-ACTAAACCCTAATTTAATTA
* ** *
835969 ATTTATTTAAAACCCTTAAAACCTAATTTAATT-
1 ATTTTTTTAAAAAAC-TAAACCCTAATTTAATTA
*
836002 ATTTTTTTAAAAAACTAAACCCTAGTTTA
1 ATTTTTTTAAAAAACTAAACCCTAATTTA
836031 TTTTTTAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
32 12 0.15
33 25 0.30
34 45 0.55
ACGTcount: A:0.43, C:0.15, G:0.01, T:0.42
Consensus pattern (33 bp):
ATTTTTTTAAAAAACTAAACCCTAATTTAATTA
Found at i:836140 original size:16 final size:15
Alignment explanation
Indices: 836116--836150 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
836106 TCAAAACACT
*
836116 AACCTTAAACCATAAA
1 AACCATAAACCA-AAA
836132 AACCATAAACCAAAA
1 AACCATAAACCAAAA
836147 AACC
1 AACC
836151 TTAGGGACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.60, C:0.29, G:0.00, T:0.11
Consensus pattern (15 bp):
AACCATAAACCAAAA
Found at i:836691 original size:17 final size:16
Alignment explanation
Indices: 836668--836706 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
836658 CTTCATAAGC
*
836668 ATATATCATTTATTTCA
1 ATATATCA-ATATTTCA
*
836685 TTATATCAATATTTCA
1 ATATATCAATATTTCA
836701 ATATAT
1 ATATAT
836707 TTTATGTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATCAATATTTCA
Found at i:836987 original size:46 final size:46
Alignment explanation
Indices: 836906--837087 Score: 267
Period size: 46 Copynumber: 4.0 Consensus size: 46
836896 TTTGACATGA
* * * * * * * *
836906 TGCCATAGTGTCTTTCAACTATGGTCATACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGACTTACACA-TTTCATATCAGGT
836952 TGCCATGGTATCTTTCAACCATGGACTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGACTTACACATTTCATATCAGGT
836998 TGCCATGGTATCTTTCAACCATGGACTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGACTTACACATTTCATATCAGGT
*
837044 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGACTTACACATTTCATATCAG
837088 AGAGCACACT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 4 0.03
46 122 0.97
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGACTTACACATTTCATATCAGGT
Found at i:838944 original size:29 final size:30
Alignment explanation
Indices: 838887--838954 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
838877 CACCCTTAAA
* * * *
838887 ATATTTGCACTATTAGTCCTTTAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
838917 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
838946 AGTATTTAC
1 A-TATTTAC
838955 TCTTGGGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.49
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:843733 original size:120 final size:120
Alignment explanation
Indices: 843516--843764 Score: 444
Period size: 120 Copynumber: 2.1 Consensus size: 120
843506 TCACAAGCAC
*
843516 ATTAATAGAAAACTGTATAATTTATCCGGATGAAGTATATATTAATAGAAAACTGTATAATTTAC
1 ATTAACAGAAAACTGTATAATTTATCCGGATGAAGTATATATTAATAGAAAACTGTATAATTTAC
* *
843581 CCGGGTAAAGTATGTATTAATAGAAAACTGTATAATTTACCCGGGTAAAGTATGT
66 CCGGGTAAAGTATGTATTAACAGAAAACTGTATAATTTACCCGGATAAAGTATGT
*
843636 ATTAACAGAAAACTGTATAATTTATCCGGATGAAGTATGTATTAATAGAAAACTGTATAATTTAC
1 ATTAACAGAAAACTGTATAATTTATCCGGATGAAGTATATATTAATAGAAAACTGTATAATTTAC
* *
843701 CCGGGTAAAGTATGTATTAACAGAAAATTGTATAATTTACCCGGATGAAGTATGT
66 CCGGGTAAAGTATGTATTAACAGAAAACTGTATAATTTACCCGGATAAAGTATGT
843756 ATTAACAGA
1 ATTAACAGA
843765 TATACTTAAG
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.33
Consensus pattern (120 bp):
ATTAACAGAAAACTGTATAATTTATCCGGATGAAGTATATATTAATAGAAAACTGTATAATTTAC
CCGGGTAAAGTATGTATTAACAGAAAACTGTATAATTTACCCGGATAAAGTATGT
Found at i:843764 original size:40 final size:40
Alignment explanation
Indices: 843516--843760 Score: 382
Period size: 40 Copynumber: 6.1 Consensus size: 40
843506 TCACAAGCAC
* * *
843516 ATTAATAGAAAACTGTATAATTTATCCGGATGAAGTATAT
1 ATTAATAGAAAACTGTATAATTTACCCGGATAAAGTATGT
*
843556 ATTAATAGAAAACTGTATAATTTACCCGGGTAAAGTATGT
1 ATTAATAGAAAACTGTATAATTTACCCGGATAAAGTATGT
*
843596 ATTAATAGAAAACTGTATAATTTACCCGGGTAAAGTATGT
1 ATTAATAGAAAACTGTATAATTTACCCGGATAAAGTATGT
* * *
843636 ATTAACAGAAAACTGTATAATTTATCCGGATGAAGTATGT
1 ATTAATAGAAAACTGTATAATTTACCCGGATAAAGTATGT
*
843676 ATTAATAGAAAACTGTATAATTTACCCGGGTAAAGTATGT
1 ATTAATAGAAAACTGTATAATTTACCCGGATAAAGTATGT
* * *
843716 ATTAACAGAAAATTGTATAATTTACCCGGATGAAGTATGT
1 ATTAATAGAAAACTGTATAATTTACCCGGATAAAGTATGT
843756 ATTAA
1 ATTAA
843761 CAGATATACT
Statistics
Matches: 189, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 189 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (40 bp):
ATTAATAGAAAACTGTATAATTTACCCGGATAAAGTATGT
Found at i:843791 original size:18 final size:18
Alignment explanation
Indices: 843768--843802 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
843758 TAACAGATAT
*
843768 ACTTAAGATCTAGTTGGC
1 ACTTAAAATCTAGTTGGC
843786 ACTTAAAATCTAGTTGG
1 ACTTAAAATCTAGTTGG
843803 ACTACCACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (18 bp):
ACTTAAAATCTAGTTGGC
Found at i:844333 original size:17 final size:17
Alignment explanation
Indices: 844311--844343 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
844301 ATAATGAATG
*
844311 TTATTAACTTATATTTT
1 TTATTAAATTATATTTT
844328 TTATTAAATTATATTT
1 TTATTAAATTATATTT
844344 AATAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAAATTATATTTT
Found at i:844565 original size:16 final size:16
Alignment explanation
Indices: 844544--844616 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
844534 TAAGAATAGT
844544 TATTACAGTTCTATTC
1 TATTACAGTTCTATTC
**
844560 TATTACAACTCTATT-
1 TATTACAGTTCTATTC
844575 TCATTACAGCTT-TATTC
1 T-ATTACAG-TTCTATTC
* * *
844592 AATTACA-TCCCTATTA
1 TATTACAGT-TCTATTC
844608 TATTACAGT
1 TATTACAGT
844617 GAACAAAGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
14 1 0.02
15 1 0.02
16 39 0.91
17 2 0.05
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (16 bp):
TATTACAGTTCTATTC
Found at i:844591 original size:32 final size:32
Alignment explanation
Indices: 844544--844616 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
844534 TAAGAATAGT
* *
844544 TATTACAGTTCTATTCTATTACAACTCTATT-
1 TATTACAGTTCTATTCAATTACAACCCTATTA
*
844575 TCATTACAGCTT-TATTCAATTACATCCCTATTA
1 T-ATTACAG-TTCTATTCAATTACAACCCTATTA
844608 TATTACAGT
1 TATTACAGT
844617 GAACAAAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 2 0.06
32 31 0.86
33 3 0.08
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (32 bp):
TATTACAGTTCTATTCAATTACAACCCTATTA
Found at i:846170 original size:7 final size:7
Alignment explanation
Indices: 846160--846193 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
846150 GATAAATTCA
846160 AAAAAAG
1 AAAAAAG
*
846167 AAAAAAA
1 AAAAAAG
846174 AGAAAAAG
1 A-AAAAAG
846182 AAAAAAG
1 AAAAAAG
846189 AAAAA
1 AAAAA
846194 TATAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:846187 original size:13 final size:13
Alignment explanation
Indices: 846169--846193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
846159 AAAAAAAGAA
846169 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
846182 AAAAAAGAAAAA
1 AAAAAAGAAAAA
846194 TATAATTTTT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:851594 original size:29 final size:29
Alignment explanation
Indices: 851494--851581 Score: 176
Period size: 29 Copynumber: 3.0 Consensus size: 29
851484 CAACTTGCAG
851494 CTATACTGACTAGAGGCTAAAAGAAGAGT
1 CTATACTGACTAGAGGCTAAAAGAAGAGT
851523 CTATACTGACTAGAGGCTAAAAGAAGAGT
1 CTATACTGACTAGAGGCTAAAAGAAGAGT
851552 CTATACTGACTAGAGGCTAAAAGAAGAGT
1 CTATACTGACTAGAGGCTAAAAGAAGAGT
851581 C
1 C
851582 ATTTGGCATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (29 bp):
CTATACTGACTAGAGGCTAAAAGAAGAGT
Found at i:854039 original size:18 final size:18
Alignment explanation
Indices: 854004--854038 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
853994 GAGCAATTTA
854004 AACTTTTTATATTCTTTT
1 AACTTTTTATATTCTTTT
*
854022 AACTTTTT-TTTTCTTTT
1 AACTTTTTATATTCTTTT
854039 TTGTTTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (18 bp):
AACTTTTTATATTCTTTT
Found at i:854497 original size:15 final size:15
Alignment explanation
Indices: 854446--854516 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
854436 ACAACACAAT
*
854446 AATATAAGTAATTAA
1 AATATAAATAATTAA
* *
854461 AATAT-AATATTTTA
1 AATATAAATAATTAA
* *
854475 AACATAAATAACTAA
1 AATATAAATAATTAA
854490 AATATAAAATAATGT-A
1 AATAT-AAATAAT-TAA
*
854506 AATAAAAATAA
1 AATATAAATAA
854517 GCATGAGTGT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
14 10 0.23
15 21 0.49
16 11 0.26
17 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:858049 original size:14 final size:15
Alignment explanation
Indices: 858030--858062 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
858020 TTAAATTTGG
858030 ATTTC-AAATTTCAA
1 ATTTCAAAATTTCAA
*
858044 ATTTCAAAATTTTAA
1 ATTTCAAAATTTCAA
858059 ATTT
1 ATTT
858063 ATGATTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTCAAAATTTCAA
Found at i:860881 original size:22 final size:22
Alignment explanation
Indices: 860856--860900 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
860846 GTTCGACTCC
*
860856 TTCCCGTTTAGCGTTCAGCATT
1 TTCCCGTTTAGCATTCAGCATT
860878 TTCCCGTTTAGCATTCAGCATT
1 TTCCCGTTTAGCATTCAGCATT
860900 T
1 T
860901 AGATTAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.42
Consensus pattern (22 bp):
TTCCCGTTTAGCATTCAGCATT
Found at i:873553 original size:61 final size:61
Alignment explanation
Indices: 873458--873583 Score: 243
Period size: 61 Copynumber: 2.1 Consensus size: 61
873448 AAGTTACTGG
*
873458 TAAGTTTAATCTTGAGTGTTAAATGAGGTTGATATTCTTTAATCTACAGTTTATATAAATT
1 TAAGTTTAATCTTGAGTGTTAAATGAGATTGATATTCTTTAATCTACAGTTTATATAAATT
873519 TAAGTTTAATCTTGAGTGTTAAATGAGATTGATATTCTTTAATCTACAGTTTATATAAATT
1 TAAGTTTAATCTTGAGTGTTAAATGAGATTGATATTCTTTAATCTACAGTTTATATAAATT
873580 TAAG
1 TAAG
873584 GTTAGGGAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.45
Consensus pattern (61 bp):
TAAGTTTAATCTTGAGTGTTAAATGAGATTGATATTCTTTAATCTACAGTTTATATAAATT
Found at i:875242 original size:19 final size:18
Alignment explanation
Indices: 875206--875240 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
875196 TGATATCTTA
875206 TTCACATCTACTAAAAAT
1 TTCACATCTACTAAAAAT
*
875224 TTCACATCTATTAAAAA
1 TTCACATCTACTAAAAA
875241 ATCTTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
TTCACATCTACTAAAAAT
Found at i:889119 original size:14 final size:14
Alignment explanation
Indices: 889098--889169 Score: 60
Period size: 14 Copynumber: 5.3 Consensus size: 14
889088 ATATTCAAAC
889098 AATAACAATAAAAT
1 AATAACAATAAAAT
* *
889112 AGTAACAATATAAT
1 AATAACAATAAAAT
*
889126 AATAA-AATAATAAC
1 AATAACAATAA-AAT
* * *
889140 AA-AATAAGAAAAA
1 AATAACAATAAAAT
889153 AATAACAA-AAAAT
1 AATAACAATAAAAT
889166 AATA
1 AATA
889170 TTAAAAAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
13 18 0.39
14 28 0.61
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (14 bp):
AATAACAATAAAAT
Found at i:889129 original size:22 final size:22
Alignment explanation
Indices: 889098--889180 Score: 80
Period size: 22 Copynumber: 3.9 Consensus size: 22
889088 ATATTCAAAC
*
889098 AATAACAATAAAATAGTAACAA
1 AATAACAATAAAATAATAACAA
* *
889120 TATAATAATAAAATAATAACAA
1 AATAACAATAAAATAATAACAA
* * *
889142 AATAAGAAAAAAATAACAA-AA
1 AATAACAATAAAATAATAACAA
* *
889163 AATAATATTAAAA-AATAA
1 AATAACAATAAAATAATAA
889181 ATTTTTTTGT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
20 4 0.08
21 12 0.24
22 34 0.68
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.20
Consensus pattern (22 bp):
AATAACAATAAAATAATAACAA
Found at i:889137 original size:11 final size:11
Alignment explanation
Indices: 889098--889180 Score: 71
Period size: 11 Copynumber: 7.7 Consensus size: 11
889088 ATATTCAAAC
*
889098 AATAACAATAA
1 AATAATAATAA
* *
889109 AATAGTAACAA
1 AATAATAATAA
*
889120 TATAATAATAA
1 AATAATAATAA
*
889131 AATAATAACAA
1 AATAATAATAA
* *
889142 AATAAGAAAAA
1 AATAATAATAA
*
889153 AATAACAA-AA
1 AATAATAATAA
*
889163 AATAATATTAA
1 AATAATAATAA
889174 AA-AATAA
1 AATAATAA
889181 ATTTTTTTGT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
10 12 0.21
11 45 0.79
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.20
Consensus pattern (11 bp):
AATAATAATAA
Found at i:889145 original size:19 final size:19
Alignment explanation
Indices: 889104--889167 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
889094 AAACAATAAC
*
889104 AATAAAATAGTAACAATATAAT
1 AATAAAATAATAAC-A-A-AAT
889126 AATAAAATAATAACAAAAT
1 AATAAAATAATAACAAAAT
* *
889145 AAGAAAAAAATAACAAAA-
1 AATAAAATAATAACAAAAT
889163 AATAA
1 AATAA
889168 TATTAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.11
19 19 0.50
20 1 0.03
21 1 0.03
22 13 0.34
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (19 bp):
AATAAAATAATAACAAAAT
Found at i:895087 original size:21 final size:21
Alignment explanation
Indices: 895061--895111 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
895051 CATATTCCGT
895061 TCCGGTTCAGTTGTTTTGGTG
1 TCCGGTTCAGTTGTTTTGGTG
895082 TCCGGTTCAGTTGTTTTGGTG
1 TCCGGTTCAGTTGTTTTGGTG
895103 TCCGGTTCA
1 TCCGGTTCA
895112 TGTTTTTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.06, C:0.18, G:0.31, T:0.45
Consensus pattern (21 bp):
TCCGGTTCAGTTGTTTTGGTG
Found at i:898412 original size:16 final size:16
Alignment explanation
Indices: 898391--898422 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
898381 GCGTGGAAGA
898391 AAGAGAATAGTTTCAG
1 AAGAGAATAGTTTCAG
898407 AAGAGAATAGTTTCAG
1 AAGAGAATAGTTTCAG
898423 TTGAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (16 bp):
AAGAGAATAGTTTCAG
Found at i:899005 original size:13 final size:13
Alignment explanation
Indices: 898987--899013 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
898977 TCCAGTGATA
898987 TGTCAAACACAAG
1 TGTCAAACACAAG
899000 TGTCAAACACAAG
1 TGTCAAACACAAG
899013 T
1 T
899014 ATTTCAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (13 bp):
TGTCAAACACAAG
Found at i:904190 original size:31 final size:31
Alignment explanation
Indices: 904154--904216 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
904144 TTCCTTATTT
904154 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
*
904185 CCTTTTTGTTTTCATTATTCTCTGTTCCTCC
1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
904216 C
1 C
904217 TTCTCGTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.06, C:0.32, G:0.05, T:0.57
Consensus pattern (31 bp):
CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
Found at i:908572 original size:3 final size:3
Alignment explanation
Indices: 908564--908589 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
908554 TTTATGCTTC
908564 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
908590 TTTTTGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:909043 original size:42 final size:42
Alignment explanation
Indices: 908997--909091 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
908987 GTAAATACTG
** *
908997 CTCATATCCCACCTTGGAATAATCCATTCCAGGGATATCCCT
1 CTCATATCCCACCTAAGAATAATCAATTCCAGGGATATCCCT
* ** *
909039 CTCATTTCCCTTCTAAGAATAATCAATTCCGGGGATATCCCT
1 CTCATATCCCACCTAAGAATAATCAATTCCAGGGATATCCCT
*
909081 CTGATATCCCA
1 CTCATATCCCA
909092 TCCCGGTTCG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.31
Consensus pattern (42 bp):
CTCATATCCCACCTAAGAATAATCAATTCCAGGGATATCCCT
Found at i:909231 original size:16 final size:16
Alignment explanation
Indices: 909212--909265 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
909202 CATTCCGAGG
909212 ATATCCCGGCTTAGGT
1 ATATCCCGGCTTAGGT
**
909228 ATATCCCAACTTAGG-
1 ATATCCCGGCTTAGGT
* *
909243 ATAGCCCGGCTGAGGT
1 ATATCCCGGCTTAGGT
909259 ATATCCC
1 ATATCCC
909266 ACCCTGCGGA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (16 bp):
ATATCCCGGCTTAGGT
Found at i:921631 original size:31 final size:31
Alignment explanation
Indices: 921589--921654 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
921579 CTTTTCCAAC
* *
921589 TTTCATTAGTAGAGGAGAGCACCTATGCAAG
1 TTTCATCAGTAGAGGAGAGCACCTATACAAG
921620 TTTCATCAGTAGAGGAGAGCACCTATACAAG
1 TTTCATCAGTAGAGGAGAGCACCTATACAAG
921651 TTTC
1 TTTC
921655 TTTCTTTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (31 bp):
TTTCATCAGTAGAGGAGAGCACCTATACAAG
Found at i:924382 original size:23 final size:22
Alignment explanation
Indices: 924330--924382 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
924320 TCCACGTCTT
*
924330 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
924352 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
924375 TTTCTTTT
1 TTTCTTTT
924383 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:924407 original size:27 final size:27
Alignment explanation
Indices: 924377--924432 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
924367 TTCTTCAATT
924377 TCTTTTTCACTCTCAATCTCTTTTTTC
1 TCTTTTTCACTCTCAATCTCTTTTTTC
* ** *
924404 TCTTTTTCATTCTCTTTTTCTTTTTTC
1 TCTTTTTCACTCTCAATCTCTTTTTTC
924431 TC
1 TC
924433 ACTTGTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (27 bp):
TCTTTTTCACTCTCAATCTCTTTTTTC
Found at i:928163 original size:23 final size:22
Alignment explanation
Indices: 928111--928163 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
928101 TCCTCGTCTT
*
928111 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
928133 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
928156 TTTCTTTT
1 TTTCTTTT
928164 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:934160 original size:31 final size:29
Alignment explanation
Indices: 934116--934176 Score: 88
Period size: 28 Copynumber: 2.0 Consensus size: 29
934106 TATTTATTTG
934116 AAGAGAAAAAAATTCAAAAATAGTAAAAAAAA
1 AAGAGAAAAAAATTC-AAAAT--TAAAAAAAA
934148 AAGAG-AAAAAATTCAAAATTAAAAAAAA
1 AAGAGAAAAAAATTCAAAATTAAAAAAAA
934176 A
1 A
934177 TTTATAGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 10 0.34
30 5 0.17
31 9 0.31
32 5 0.17
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.13
Consensus pattern (29 bp):
AAGAGAAAAAAATTCAAAATTAAAAAAAA
Found at i:935124 original size:6 final size:5
Alignment explanation
Indices: 935100--935156 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
935090 ACGAGAAAAC
*
935100 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
935147 AAAGA AAAGA
1 AAAGA AAAGA
935157 GAGGCAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:935131 original size:15 final size:14
Alignment explanation
Indices: 935100--935156 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
935090 ACGAGAAAAC
935100 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
935116 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
935131 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
935147 AAAGAAAAGA
1 AAAGAAAAGA
935157 GAGGCAAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:935235 original size:13 final size:12
Alignment explanation
Indices: 935204--935235 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
935194 TTGAGAGAAC
*
935204 TTGAAAAGGCCT
1 TTGAAAAAGCCT
935216 TTGAAAAAGCCT
1 TTGAAAAAGCCT
935228 TTGAAAAA
1 TTGAAAAA
935236 TAAAAAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:937134 original size:28 final size:29
Alignment explanation
Indices: 937076--937135 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
937066 TTAATTAAAG
*
937076 TTTTAATGTGTCTTTAGTTGAGGACATAAT
1 TTTTAATGTGTC-TTAGTTGAGAACATAAT
*
937106 TTTTAATGTGTC-TAGTTTTAGAACA-AAT
1 TTTTAATGTGTCTTAG-TTGAGAACATAAT
937134 TT
1 TT
937136 ATTAGCTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.30
29 7 0.26
30 12 0.44
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (29 bp):
TTTTAATGTGTCTTAGTTGAGAACATAAT
Found at i:940903 original size:76 final size:76
Alignment explanation
Indices: 940777--940927 Score: 284
Period size: 76 Copynumber: 2.0 Consensus size: 76
940767 AGTGCAAAAT
*
940777 GAGGCTTAACCTCAGCTCGATCAGCTCAATTTTTGCTCATCTACAGTCAATGAGTTCGTGTGCTC
1 GAGGCTTAACCTCAGCTCGATCAGCTCAATTTTTGCTCATCTACAGTCAATGAGTTCATGTGCTC
940842 AATTCAACGAA
66 AATTCAACGAA
*
940853 GAGGCTTAACCTCAGCTCGATCAGCTCAATTTTTGCTCATCTACAGTCAATGAGTTCATTTGCTC
1 GAGGCTTAACCTCAGCTCGATCAGCTCAATTTTTGCTCATCTACAGTCAATGAGTTCATGTGCTC
940918 AATTCAACGA
66 AATTCAACGA
940928 GCTTGGTGCA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (76 bp):
GAGGCTTAACCTCAGCTCGATCAGCTCAATTTTTGCTCATCTACAGTCAATGAGTTCATGTGCTC
AATTCAACGAA
Found at i:941351 original size:18 final size:18
Alignment explanation
Indices: 941318--941352 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
941308 TTGCTACTGG
*
941318 TTTTAATGTGCCAATTTT
1 TTTTAATGAGCCAATTTT
*
941336 TTTTAATGAGCTAATTT
1 TTTTAATGAGCCAATTT
941353 AATGTGCTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTTAATGAGCCAATTTT
Found at i:942953 original size:30 final size:30
Alignment explanation
Indices: 942929--943025 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
942919 CGAGCTCACT
*
942929 CTTAGCTCATATTCAGCTCACGAGCTAAAC
1 CTTAGCTCAGATTCAGCTCACGAGCTAAAC
* * * * * *
942959 CTTAGCTCAGCTTCAGCTTAGGAGTTTAAT
1 CTTAGCTCAGATTCAGCTCACGAGCTAAAC
* * * *
942989 CTCAGCTCA-ACTTTAGCTCACGAGTTAAAG
1 CTTAGCTCAGA-TTCAGCTCACGAGCTAAAC
943019 CTTAGCT
1 CTTAGCT
943026 GATTTTAGTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (30 bp):
CTTAGCTCAGATTCAGCTCACGAGCTAAAC
Found at i:944679 original size:30 final size:31
Alignment explanation
Indices: 944643--944739 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 31
944633 AGCTCACTCC
*
944643 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
944673 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
*
944703 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
944733 TAGCTCA
1 TAGCTCA
944740 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 49 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:946455 original size:18 final size:18
Alignment explanation
Indices: 946421--946458 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
946411 AAAAAATTCA
*
946421 AAAAAAAATTTCGAAAAG
1 AAAAAAAATCTCGAAAAG
946439 AAAAAAAATCT-GAAAA-
1 AAAAAAAATCTCGAAAAG
946455 AAAA
1 AAAA
946459 GTGTTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 5 0.26
18 10 0.53
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAAAAATCTCGAAAAG
Found at i:947383 original size:9 final size:10
Alignment explanation
Indices: 947369--947414 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 10
947359 TCTTGTAAAG
947369 AGAAAAC-AA
1 AGAAAACAAA
947378 AGAAAACAAA
1 AGAAAACAAA
947388 AGAAAAAGCAAA
1 AG-AAAA-CAAA
*
947400 AGAAGA-AAA
1 AGAAAACAAA
947409 AGAAAA
1 AGAAAA
947415 AGAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 15 0.47
10 4 0.12
11 7 0.22
12 6 0.19
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (10 bp):
AGAAAACAAA
Found at i:947407 original size:15 final size:14
Alignment explanation
Indices: 947387--947432 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
947377 AAGAAAACAA
947387 AAGAAAAAGCAAAAG
1 AAGAAAAAG-AAAAG
947402 AAGAAAAAGAAAAAG
1 AAGAAAAAG-AAAAG
*
947417 AAATAAAAAGAAAAG
1 -AAGAAAAAGAAAAG
947432 A
1 A
947433 GAGGCAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 1 0.04
15 19 0.68
16 8 0.29
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (14 bp):
AAGAAAAAGAAAAG
Found at i:947430 original size:21 final size:20
Alignment explanation
Indices: 947365--947432 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
947355 ACATTCTTGT
* * *
947365 AAAGAGAAAACAAAGAAAACA
1 AAAGA-AAAAGAAAAAAAAGA
* *
947386 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGAAAAAAAAG-A
947407 AAAGAAAAAGAAATAAAAAGA
1 AAAGAAAAAGAAA-AAAAAGA
947428 AAAGA
1 AAAGA
947433 GAGGCAAGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.24
21 24 0.63
22 5 0.13
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAAAGA
Found at i:947512 original size:11 final size:12
Alignment explanation
Indices: 947480--947510 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
947470 TTGAGAGAAC
947480 TTGAAAAAGCCT
1 TTGAAAAAGCCT
947492 TTGAAAAAGCCT
1 TTGAAAAAGCCT
947504 TTGAAAA
1 TTGAAAA
947511 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:947521 original size:12 final size:12
Alignment explanation
Indices: 947513--947537 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
947503 TTTGAAAAGC
947513 AAAAAGAAAATG
1 AAAAAGAAAATG
947525 AAAAAGAAAATG
1 AAAAAGAAAATG
947537 A
1 A
947538 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:947534 original size:18 final size:18
Alignment explanation
Indices: 947507--947562 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
947497 AAAGCCTTTG
947507 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
947526 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
947544 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
947561 AA
1 AA
947563 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:947547 original size:30 final size:31
Alignment explanation
Indices: 947513--947594 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
947503 TTTGAAAAGC
*
947513 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
947543 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* *
947573 AAAAAGAAGATGAAAATGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
947595 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.62
31 8 0.19
ACGTcount: A:0.63, C:0.01, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:955042 original size:26 final size:26
Alignment explanation
Indices: 955006--955115 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
954996 TGATACAAAT
955006 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
955032 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
955058 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
955084 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
955110 TGATAA
1 TGATAA
955116 GGATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:957850 original size:16 final size:16
Alignment explanation
Indices: 957820--957849 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
957810 GTTTACAAAA
957820 AAAAACAAAGATTTTC
1 AAAAACAAAGATTTTC
957836 AAAAACAAA-ATTTT
1 AAAAACAAAGATTTT
957850 TTTTGCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAAACAAAGATTTTC
Found at i:958261 original size:10 final size:10
Alignment explanation
Indices: 958246--958272 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
958236 TACTCCTTCA
958246 AGCTCAAATC
1 AGCTCAAATC
958256 AGCTCAAATC
1 AGCTCAAATC
958266 AGCTCAA
1 AGCTCAA
958273 CTTCAACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:958294 original size:10 final size:10
Alignment explanation
Indices: 958246--958294 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
958236 TACTCCTTCA
*
958246 AGCTCAAATC
1 AGCTCAACTC
*
958256 AGCTCAAATC
1 AGCTCAACTC
958266 AGCTCAACTTC
1 AGCTCAAC-TC
* *
958277 AACTCAACTT
1 AGCTCAACTC
958287 AGCTCAAC
1 AGCTCAAC
958295 GAGCTCGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.37, C:0.33, G:0.08, T:0.22
Consensus pattern (10 bp):
AGCTCAACTC
Found at i:965506 original size:24 final size:24
Alignment explanation
Indices: 965474--965638 Score: 224
Period size: 24 Copynumber: 6.9 Consensus size: 24
965464 TCGGTCAAGG
* *
965474 AAATTCGCACACATAGTGCCATGC
1 AAATCCGCACACATAGTGCCATTC
* *
965498 TAACCCGCACACATAGTGCC-TTGC
1 AAATCCGCACACATAGTGCCATT-C
* *
965522 TAATCCGCACACGTAGTGCCATTC
1 AAATCCGCACACATAGTGCCATTC
* *
965546 AAATTCGCACACATAGTGTCATTC
1 AAATCCGCACACATAGTGCCATTC
965570 AAATCCGCACACATAGTGCCATTC
1 AAATCCGCACACATAGTGCCATTC
*
965594 AAATCCGCACACATAGTGCCATTT
1 AAATCCGCACACATAGTGCCATTC
*
965618 AAATCCACACACATAGTGCCA
1 AAATCCGCACACATAGTGCCA
965639 ATGTCATTTC
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
23 1 0.01
24 122 0.98
25 2 0.02
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (24 bp):
AAATCCGCACACATAGTGCCATTC
Found at i:967488 original size:31 final size:31
Alignment explanation
Indices: 967450--967528 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
967440 TTTAACAGTT
*
967450 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
967481 ACTGGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
967512 ACTGGGCCGAAGCCTTA
1 ACTGGGCCGAAGCCTTA
967529 CAGTAAACAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTATCATAAATCATATC
Found at i:967775 original size:25 final size:25
Alignment explanation
Indices: 967747--967816 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
967737 CTCTTTTAAT
967747 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
967772 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
967797 AACTAGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
967817 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 37 0.90
26 4 0.10
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:968656 original size:27 final size:27
Alignment explanation
Indices: 968626--968690 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
968616 GGGCATATTC
968626 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * * *
968653 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
968680 GTCTTTTTACC
1 GTCATTTTACC
968691 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:968692 original size:26 final size:28
Alignment explanation
Indices: 968648--968699 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
968638 TACAAGGGTA
968648 TTACGGTCACTTTACCCTA-TAGGGGCT
1 TTACGGTCACTTTACCCTATTAGGGGCT
**
968675 TTACGGTCTTTTTA-CCTATTAGGGG
1 TTACGGTCACTTTACCCTATTAGGGG
968700 TATTTTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (28 bp):
TTACGGTCACTTTACCCTATTAGGGGCT
Found at i:968849 original size:56 final size:54
Alignment explanation
Indices: 968720--968903 Score: 169
Period size: 54 Copynumber: 3.4 Consensus size: 54
968710 ATTTCATCCT
* * * * *
968720 ACAAGGGTGTTTTGGTAA-ATCTACAAACCAAGGGTATTTCAGTAATTTTGTAA
1 ACAAGGGTATTTTGGTAATTTTTACAAATCAAGGGTATTTCTGTAATTTTGTAA
* * *
968773 ACCAATGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCTGTAATTTTGTAA
1 A-CAAGGGTATTT-TGGTAATTTTTACAAA-TCAAGGGTATTTCTGTAATTTTGTAA
* * * **
968829 ATCAGGGGTATTTTGGTAA-TTTTACAAATTAGGGGTATTT-TGGTAATTTTACAA
1 A-CAAGGGTATTTTGGTAATTTTTACAAATCAAGGGTATTTCT-GTAATTTTGTAA
968883 ACTAAGGGTATTTTGGTAATT
1 AC-AAGGGTATTTTGGTAATT
968904 CTATCCTACA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
53 3 0.03
54 48 0.46
55 17 0.16
56 37 0.35
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (54 bp):
ACAAGGGTATTTTGGTAATTTTTACAAATCAAGGGTATTTCTGTAATTTTGTAA
Found at i:968857 original size:27 final size:27
Alignment explanation
Indices: 968721--968903 Score: 147
Period size: 27 Copynumber: 6.7 Consensus size: 27
968711 TTTCATCCTA
* * * *
968721 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
** ** *
968748 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
968775 CAATGGTATTTCT-ATAATTTTTAGAAAGT
1 CAAGGGTATTT-TGGTAA-TTTTACAAA-T
**
968804 CAAGGGTATTTCT-GTAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
*
968831 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
968858 TAGGGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
968884 CTAAGGGTATTTTGGTAATT
1 C-AAGGGTATTTTGGTAATT
968904 CTATCCTACA
Statistics
Matches: 128, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.01
27 98 0.77
28 14 0.11
29 15 0.12
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:968918 original size:27 final size:26
Alignment explanation
Indices: 968807--968945 Score: 118
Period size: 27 Copynumber: 5.2 Consensus size: 26
968797 AGAAAGTCAA
**
968807 GGGTATTTCT-GTAATTTTGTAAATCAG
1 GGGTATTT-TGGTAATTTTACAAA-CAG
*
968834 GGGTATTTTGGTAATTTTACAAATTAG
1 GGGTATTTTGGTAATTTTACAAA-CAG
*
968861 GGGTATTTTGGTAATTTTACAAACTAA
1 GGGTATTTTGGTAATTTTACAAAC-AG
* **
968888 GGGTATTTTGGTAATTCTATCCTACAG
1 GGGTATTTTGGTAATTTTA-CAAACAG
** * * *
968915 GGGTATTTCAGTAATTTCACAATCAA
1 GGGTATTTTGGTAATTTTACAAACAG
968941 GGGTA
1 GGGTA
968946 AAACGGTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
26 9 0.10
27 80 0.87
28 3 0.03
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTACAAACAG
Found at i:968973 original size:27 final size:27
Alignment explanation
Indices: 968935--969107 Score: 213
Period size: 27 Copynumber: 6.4 Consensus size: 27
968925 GTAATTTCAC
* * *
968935 AATCAAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
968962 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTCTGTA
*
968989 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* * *
969016 AATCAAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* *
969043 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
969070 AATCGAGGGTAAAATGGTAATTATGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* *
969097 AGTCGGGGGTA
1 AATCGAGGGTA
969108 CTTTGGTTAT
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
26 1 0.01
27 128 0.98
28 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTGTA
Found at i:970400 original size:17 final size:17
Alignment explanation
Indices: 970378--970410 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
970368 CCCACTTAAT
*
970378 ATATTATAACTTATTTA
1 ATATTATAACATATTTA
970395 ATATTATAACATATTT
1 ATATTATAACATATTT
970411 CAATTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTATAACATATTTA
Found at i:973123 original size:12 final size:12
Alignment explanation
Indices: 973106--973130 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
973096 TTTGAGTAAT
973106 GAAACGGAATAA
1 GAAACGGAATAA
973118 GAAACGGAATAA
1 GAAACGGAATAA
973130 G
1 G
973131 CATTTAATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (12 bp):
GAAACGGAATAA
Found at i:973526 original size:40 final size:40
Alignment explanation
Indices: 973443--973662 Score: 259
Period size: 40 Copynumber: 5.5 Consensus size: 40
973433 ACCCAAGTAT
* * * *
973443 CTTCGGGATTTAG-CCGGATATAGCCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
** * *
973481 CTTCGGGTTTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
973521 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
973561 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
973601 CTTC-GGATTTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
973641 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
973663 CATTCGAATA
Statistics
Matches: 154, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
38 12 0.08
39 19 0.12
40 119 0.77
41 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:978115 original size:27 final size:27
Alignment explanation
Indices: 978085--978424 Score: 380
Period size: 27 Copynumber: 12.6 Consensus size: 27
978075 TTAGTTTACC
978085 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
978112 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
978139 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
978166 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
978193 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
978220 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
978247 AAATTACCAAAATACCACTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
978274 AAATT-CCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
978300 AAATTATCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
** * * *
978327 AAATTACCAAAATAAACCTGATTTATG
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
978354 AAATTACTAAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*** **
978381 AAATTATGGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*
978408 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
978425 TTAATTTATA
Statistics
Matches: 263, Mismatches: 47, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
26 28 0.11
27 233 0.89
28 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:978493 original size:27 final size:27
Alignment explanation
Indices: 978463--978603 Score: 120
Period size: 27 Copynumber: 5.2 Consensus size: 27
978453 CGATTTACAA
**
978463 AATTACCGAAACACGTCTATAGGGTAG
1 AATTACCGAAACACCCCTATAGGGTAG
*
978490 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAACACCCCTATAGGGTAG
* * * * *
978517 AATTATCGCAATACCCTTGTAGGGTAG
1 AATTACCGAAACACCCCTATAGGGTAG
** * * *
978544 AATTATTGAAATACCCTTGTAGGGTAG
1 AATTACCGAAACACCCCTATAGGGTAG
** * * *
978571 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAACACCCCTATAGGGTAG
978598 AATTAC
1 AATTAC
978604 TGAGATACCT
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 101 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (27 bp):
AATTACCGAAACACCCCTATAGGGTAG
Found at i:978604 original size:27 final size:27
Alignment explanation
Indices: 978482--978612 Score: 165
Period size: 27 Copynumber: 4.9 Consensus size: 27
978472 AACACGTCTA
* *
978482 TAGGGTAGAATTACCGAAATACCCCTA
1 TAGGGTAGAATTACTGAAATACCCCTG
* *
978509 TAGGGTAGAATTA-TCGCAATACCCTTG
1 TAGGGTAGAATTACT-GAAATACCCCTG
* *
978536 TAGGGTAGAATTATTGAAATACCCTTG
1 TAGGGTAGAATTACTGAAATACCCCTG
*
978563 TAGGGTAGAATTACTAAAATACCCCTG
1 TAGGGTAGAATTACTGAAATACCCCTG
* *
978590 TAGGGTGGAATTACTGAGATACC
1 TAGGGTAGAATTACTGAAATACC
978613 TTTTGGGGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
27 90 0.99
28 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (27 bp):
TAGGGTAGAATTACTGAAATACCCCTG
Found at i:979109 original size:22 final size:22
Alignment explanation
Indices: 979057--979121 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
979047 TTAAAGCCTT
* *
979057 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
979079 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
979101 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
979122 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:979318 original size:26 final size:27
Alignment explanation
Indices: 979280--979353 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
979270 ATTCTGTTAA
*
979280 GTGGCT-TTGCCACATTATCTGT-TCTG
1 GTGGCTCTT-CCACAATATCTGTATCTG
979306 GTGGCTCTTCCACAATATCTGTATCTG
1 GTGGCTCTTCCACAATATCTGTATCTG
*
979333 GTGACTCTGT-CACAATATCTG
1 GTGGCTCT-TCCACAATATCTG
979354 ATAACTGAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 18 0.42
27 24 0.56
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (27 bp):
GTGGCTCTTCCACAATATCTGTATCTG
Found at i:979527 original size:6 final size:6
Alignment explanation
Indices: 979493--979661 Score: 132
Period size: 6 Copynumber: 27.3 Consensus size: 6
979483 TTGCATTCAC
* * * *
979493 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATACTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
979543 -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* *
979593 ATTCTG ATTCTG ATTCTA ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG
979642 ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
979662 AATGTTTCTT
Statistics
Matches: 132, Mismatches: 16, Indels: 30
0.74 0.09 0.17
Matches are distributed among these distances:
5 8 0.06
6 102 0.77
7 18 0.14
8 4 0.03
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:979539 original size:31 final size:31
Alignment explanation
Indices: 979493--979604 Score: 197
Period size: 31 Copynumber: 3.6 Consensus size: 31
979483 TTGCATTCAC
979493 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
*
979525 ATACTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
979556 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
979587 ATTCTGATTCTGATTCTG
1 ATTCTGATTTTGATTCTG
979605 ATTCTAATTC
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
31 71 0.92
32 6 0.08
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:979600 original size:43 final size:43
Alignment explanation
Indices: 979547--979659 Score: 172
Period size: 43 Copynumber: 2.6 Consensus size: 43
979537 ATTCTGTTAC
* * * *
979547 CTGATACTGATTCTGATTTTGATTCTGTTACCTGATACTGATT
1 CTGATTCTGATTCTGATTCTAATTCTGTCACCTGATACTGATT
*
979590 CTGATTCTGATTCTGATTCTAATTCTGTCACCTGATTCTGATT
1 CTGATTCTGATTCTGATTCTAATTCTGTCACCTGATACTGATT
*
979633 CTGATTCTGATTCTGATTCTAGTTCTG
1 CTGATTCTGATTCTGATTCTAATTCTG
979660 ATAATGTTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (43 bp):
CTGATTCTGATTCTGATTCTAATTCTGTCACCTGATACTGATT
Found at i:979625 original size:37 final size:36
Alignment explanation
Indices: 979516--979652 Score: 161
Period size: 37 Copynumber: 3.7 Consensus size: 36
979506 ATTCTGTTAC
* * * *
979516 CTGATACTGATACTGATTTTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGATTCTGATTCTG-TACCTGATT
*
979553 CTGATTCTGATTTTGATTCTG-TTACCTGATA-CTGATT
1 CTGATTCTGATTCTGATTCTGATT--CTG-TACCTGATT
*
979590 CTGATTCTGATTCTGATTCTAATTCTGTCACCTGATT
1 CTGATTCTGATTCTGATTCTGATTCTGT-ACCTGATT
979627 CTGATTCTGATTCTGATTCTGATTCT
1 CTGATTCTGATTCTGATTCTGATTCT
979653 AGTTCTGATA
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
35 1 0.01
36 6 0.07
37 72 0.84
38 7 0.08
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (36 bp):
CTGATTCTGATTCTGATTCTGATTCTGTACCTGATT
Found at i:982634 original size:119 final size:120
Alignment explanation
Indices: 982460--982699 Score: 419
Period size: 119 Copynumber: 2.0 Consensus size: 120
982450 ACAAATGCGG
**
982460 CCCTAATGTCTAGGCCGGGTTTGGGGTGTTACAAATCATATACCTTAAGTGTACTACTTGAGCCT
1 CCCTAATGTCTAGGCCAAGTTTGGGGTGTTACAAATCATATACCTTAAGTGTACTACTTGAGCCT
982525 TCATCAGGATTTCAAAGATTCAATGGATATATAACTCTTGACTTGGCATAAAAAT
66 TCATCAGGATTTCAAAGATTCAATGGATATATAACTCTTGACTTGGCATAAAAAT
* * *
982580 CCCTAATGTCTAGGCCAAG-TTGGGGTGTTACAAATCATATATCTTGAGTGTACTACTTGGGCCT
1 CCCTAATGTCTAGGCCAAGTTTGGGGTGTTACAAATCATATACCTTAAGTGTACTACTTGAGCCT
*
982644 TCATCAGGATTTCAAAGATTCAATGGATATATAACTCTTGACTTGGCATGAAAAT
66 TCATCAGGATTTCAAAGATTCAATGGATATATAACTCTTGACTTGGCATAAAAAT
982699 C
1 C
982700 TTGAGATAAA
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
119 97 0.85
120 17 0.15
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (120 bp):
CCCTAATGTCTAGGCCAAGTTTGGGGTGTTACAAATCATATACCTTAAGTGTACTACTTGAGCCT
TCATCAGGATTTCAAAGATTCAATGGATATATAACTCTTGACTTGGCATAAAAAT
Found at i:987296 original size:17 final size:17
Alignment explanation
Indices: 987263--987296 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
987253 GATGATGAAA
* *
987263 AAAAAGAAAAGAGAAAG
1 AAAAAGAAAAAAAAAAG
987280 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
987297 GAAAGGCTCT
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:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:988613 original size:40 final size:40
Alignment explanation
Indices: 988558--988657 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
988548 ATGATAACCG
* *
988558 GGCTAAGTCCCGAAGGCGTTTGCGCTAATGACTAGT-TCCA
1 GGCTAAGTCCCGAAGGCATTTGCGCGAATGACTA-TATCCA
* * * *
988598 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGCGCGAATGACTATATCCA
*
988638 GGCTATGTCCCGAAGGCATT
1 GGCTAAGTCCCGAAGGCATT
988658 CGAGCGAGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
39 1 0.02
40 51 0.98
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGCGCGAATGACTATATCCA
Found at i:988665 original size:40 final size:40
Alignment explanation
Indices: 988555--988692 Score: 113
Period size: 40 Copynumber: 3.5 Consensus size: 40
988545 TGGATGATAA
* * * * *
988555 CCGGGCTAAGTCCCGAAGGCGTTTGCGCTAATGA-CTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTCGAGCGAGT-ATCTA-TAT
* * *
988595 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGT-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGAGCGAGTAT-CTATAT
*
988635 CCGGGCTATGTCCCGAAGGCATTCGAGCGAGTATCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGAGCGAGTATCTATAT
* * *
988675 -CTGGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
988693 TACTTGGCTT
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
39 15 0.19
40 65 0.80
41 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAGCGAGTATCTATAT
Found at i:991672 original size:43 final size:42
Alignment explanation
Indices: 991622--991720 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 42
991612 TCCCATACGT
*
991622 GGTCTTACATGTAATCA-ACTATCGATG-CAACTGTCCCAGACAG
1 GGTCTTACATGTAATCATA-TA-CGATGCCAA-TGTCCCAGACAC
* * *
991665 GGTCTTACACGAAATCATATACGATGCCGATGTCCCAGACAC
1 GGTCTTACATGTAATCATATACGATGCCAATGTCCCAGACAC
991707 GGTCTTACATGTAA
1 GGTCTTACATGTAA
991721 ACCACAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
42 28 0.58
43 19 0.40
44 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
GGTCTTACATGTAATCATATACGATGCCAATGTCCCAGACAC
Found at i:996465 original size:64 final size:64
Alignment explanation
Indices: 996384--996567 Score: 167
Period size: 67 Copynumber: 2.8 Consensus size: 64
996374 AGACATTATG
* * * *
996384 ATGTAGCTAGGTTGCATGGGTGATACTATGTGTACACCATGTAGACCAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
996448 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
996513 AA
63 AA
* * * * *
996515 AT-TGGCTAGGTCACATGGGCGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG-ACAAGAGAGC
996568 CAAACTATAT
Statistics
Matches: 95, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 20 0.21
65 7 0.07
66 17 0.18
67 31 0.33
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:998812 original size:17 final size:17
Alignment explanation
Indices: 998779--998812 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
998769 GATGATGAAA
* *
998779 AAAAAGAAAAGAGAAAG
1 AAAAAGAAAAAAAAAAG
998796 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
998813 GAAAGGCTCT
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:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:1000129 original size:40 final size:40
Alignment explanation
Indices: 1000074--1000173 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
1000064 ATGATAACCG
* *
1000074 GGCTAAGTCCCGAAGGCGTTTGCGCTAATGACTAGT-TCCA
1 GGCTAAGTCCCGAAGGCATTTGCGCGAATGACTA-TATCCA
* * * *
1000114 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGCGCGAATGACTATATCCA
*
1000154 GGCTATGTCCCGAAGGCATT
1 GGCTAAGTCCCGAAGGCATT
1000174 CGAGCGAGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
39 1 0.02
40 51 0.98
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGCGCGAATGACTATATCCA
Found at i:1000181 original size:40 final size:40
Alignment explanation
Indices: 1000071--1000208 Score: 113
Period size: 40 Copynumber: 3.5 Consensus size: 40
1000061 TGGATGATAA
* * * * *
1000071 CCGGGCTAAGTCCCGAAGGCGTTTGCGCTAATGA-CTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTCGAGCGAGT-ATCTA-TAT
* * *
1000111 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGT-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGAGCGAGTAT-CTATAT
*
1000151 CCGGGCTATGTCCCGAAGGCATTCGAGCGAGTATCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGAGCGAGTATCTATAT
* * *
1000191 -CTGGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
1000209 TACTTGGCTT
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
39 15 0.19
40 65 0.80
41 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAGCGAGTATCTATAT
Found at i:1003188 original size:43 final size:42
Alignment explanation
Indices: 1003138--1003236 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 42
1003128 TCCCATACGT
*
1003138 GGTCTTACATGTAATCA-ACTATCGATG-CAACTGTCCCAGACAG
1 GGTCTTACATGTAATCATA-TA-CGATGCCAA-TGTCCCAGACAC
* * *
1003181 GGTCTTACACGAAATCATATACGATGCCGATGTCCCAGACAC
1 GGTCTTACATGTAATCATATACGATGCCAATGTCCCAGACAC
1003223 GGTCTTACATGTAA
1 GGTCTTACATGTAA
1003237 ACCACAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
42 28 0.58
43 19 0.40
44 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
GGTCTTACATGTAATCATATACGATGCCAATGTCCCAGACAC
Found at i:1011772 original size:68 final size:66
Alignment explanation
Indices: 1011700--1011871 Score: 179
Period size: 67 Copynumber: 2.6 Consensus size: 66
1011690 CATCATGTGT
* * * *
1011700 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCACATGCGTGATACTAGTGAAGGACACCA
1011763 TGTAG
62 TGTAG
** * *
1011768 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCACATGCGTGGTTCTAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCACATGCGTGATACTA-GTGAAGGACACCATGT
1011833 AG
65 AG
* * *
1011835 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCACATG
1011872 GGCGGTACTG
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 18 0.20
67 32 0.36
68 13 0.14
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCACATGCGTGATACTAGTGAAGGACACCATGTA
G
Found at i:1015519 original size:19 final size:19
Alignment explanation
Indices: 1015495--1015534 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1015485 TTTCATTCTC
*
1015495 AAACATGGTATACAATTCA
1 AAACATAGTATACAATTCA
1015514 AAACATAGTATACAATTCA
1 AAACATAGTATACAATTCA
1015533 AA
1 AA
1015535 CGTACCTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (19 bp):
AAACATAGTATACAATTCA
Found at i:1015775 original size:44 final size:43
Alignment explanation
Indices: 1015636--1015799 Score: 153
Period size: 43 Copynumber: 3.8 Consensus size: 43
1015626 CAGAAAGCTC
* * * *
1015636 ATACAATGCCAACGTCCTAGACGTGGCCTTACATGT-AATCAA
1 ATACGATGCCAACATCCTAGACGTGGTCTTACACGTAAATCAA
* *
1015678 ATACCGATGCC-ACTATCCCAGA--TAGGATCTTACAC-AAAATCAA
1 ATA-CGATGCCAAC-ATCCTAGACGT-GG-TCTTACACGTAAATCAA
1015721 ATACGATGCCAACATCCTAGACGTGGTCTTACACGTAAATCATA
1 ATACGATGCCAACATCCTAGACGTGGTCTTACACGTAAATCA-A
*
1015765 AGT-CGATGCCAACGT-CTCAGACGTGGTCTTACACG
1 A-TACGATGCCAACATCCT-AGACGTGGTCTTACACG
1015800 ATAACACATA
Statistics
Matches: 101, Mismatches: 9, Indels: 22
0.77 0.07 0.17
Matches are distributed among these distances:
41 1 0.01
42 29 0.29
43 39 0.39
44 31 0.31
45 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (43 bp):
ATACGATGCCAACATCCTAGACGTGGTCTTACACGTAAATCAA
Found at i:1017850 original size:15 final size:15
Alignment explanation
Indices: 1017830--1017860 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1017820 AATTATGAAA
1017830 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
1017845 GATATGTTTTGTATT
1 GATATGTTTTGGATT
1017860 G
1 G
1017861 GAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:1018517 original size:55 final size:56
Alignment explanation
Indices: 1018433--1018541 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 56
1018423 CATGGCTTCG
1018433 ATATATGTGTACGAGAAAGACCACGTTTAAT-CATTGGCATCGATATGTGATTTCA
1 ATATATGTGTACGAGAAAGACCACGTTTAATACATTGGCATCGATATGTGATTTCA
* * *
1018488 ATATATGTGTGCGAGTAAGACCACGTTTAATACTTTGGCATCGATATGTGATTT
1 ATATATGTGTACGAGAAAGACCACGTTTAATACATTGGCATCGATATGTGATTT
1018542 TGATATGTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
55 29 0.58
56 21 0.42
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (56 bp):
ATATATGTGTACGAGAAAGACCACGTTTAATACATTGGCATCGATATGTGATTTCA
Found at i:1018548 original size:13 final size:13
Alignment explanation
Indices: 1018530--1018554 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1018520 CTTTGGCATC
1018530 GATATGTGATTTT
1 GATATGTGATTTT
1018543 GATATGTGATTT
1 GATATGTGATTT
1018555 GTAACATCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (13 bp):
GATATGTGATTTT
Found at i:1025870 original size:33 final size:33
Alignment explanation
Indices: 1025828--1025891 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
1025818 TTAATAGATG
1025828 AAAGTATCATTGGTCTGTTTGGGTTAAATTCGA
1 AAAGTATCATTGGTCTGTTTGGGTTAAATTCGA
1025861 AAAGTATCATTGGTCTGTTTGGGTTAAATTC
1 AAAGTATCATTGGTCTGTTTGGGTTAAATTC
1025892 AACATTGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (33 bp):
AAAGTATCATTGGTCTGTTTGGGTTAAATTCGA
Found at i:1028133 original size:27 final size:27
Alignment explanation
Indices: 1028111--1028334 Score: 340
Period size: 27 Copynumber: 8.3 Consensus size: 27
1028101 CAATTTGTAA
* *
1028111 AATTACCGTTTTACCCTTGATTTATAG
1 AATTACCATTTTACCCTCGATTTATAG
*
1028138 AATTACCATTTTACCCTCGATTTACAG
1 AATTACCATTTTACCCTCGATTTATAG
* *
1028165 AATTATCATTTTACCCTCGATTTACAG
1 AATTACCATTTTACCCTCGATTTATAG
1028192 AATTACCATTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTATAG
*
1028219 AATTACCGTTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTATAG
* *
1028246 AATTACCGTTTTACCCTCGATTTACAG
1 AATTACCATTTTACCCTCGATTTATAG
* * *
1028273 AATTACCATTTTACCCTCAATTTACAA
1 AATTACCATTTTACCCTCGATTTATAG
*
1028300 AATTACTATTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTATAG
1028327 AATTACCA
1 AATTACCA
1028335 AAATACCCTT
Statistics
Matches: 181, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 181 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
AATTACCATTTTACCCTCGATTTATAG
Found at i:1028177 original size:54 final size:54
Alignment explanation
Indices: 1028111--1028361 Score: 340
Period size: 54 Copynumber: 4.6 Consensus size: 54
1028101 CAATTTGTAA
* * *
1028111 AATTACCGTTTTACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAG
1 AATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
* *
1028165 AATTATCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
* * *
1028219 AATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAG
1 AATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
* * * *
1028273 AATTACCATTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
*** * * *
1028327 AATTACCAAAATACCCTTGGTTTACAAAATTACCA
1 AATTACCATTTTACCCTCGATTTACAGAATTACCA
1028362 AAATATCCTT
Statistics
Matches: 173, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 173 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.39
Consensus pattern (54 bp):
AATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
Found at i:1028214 original size:81 final size:81
Alignment explanation
Indices: 1028111--1028361 Score: 358
Period size: 81 Copynumber: 3.1 Consensus size: 81
1028101 CAATTTGTAA
* * * *
1028111 AATTACCGTTTTACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCATTT
1 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
1028176 TACCCTCGATTTACAG
66 TACCCTCGATTTACAG
* *
1028192 AATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTT
1 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
1028257 TACCCTCGATTTACAG
66 TACCCTCGATTTACAG
* * * * ***
1028273 AATTACCATTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGATTTATAGAATTACCAAAA
1 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
* * *
1028338 TACCCTTGGTTTACAA
66 TACCCTCGATTTACAG
1028354 AATTACCA
1 AATTACCA
1028362 AAATATCCTT
Statistics
Matches: 152, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 152 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.39
Consensus pattern (81 bp):
AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
TACCCTCGATTTACAG
Found at i:1028341 original size:27 final size:27
Alignment explanation
Indices: 1028122--1028511 Score: 191
Period size: 27 Copynumber: 14.4 Consensus size: 27
1028112 ATTACCGTTT
* ***
1028122 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCAAAA
* * ***
1028149 TACCCTCGATTTACAGAATTATCATTT
1 TACCCTCGATTTATAGAATTACCAAAA
* ***
1028176 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCAAAA
****
1028203 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCAAAA
****
1028230 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCAAAA
* ***
1028257 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCAAAA
* * * * ***
1028284 TACCCTCAATTTACAAAATTACTATTT
1 TACCCTCGATTTATAGAATTACCAAAA
1028311 TACCCTCGATTTATAGAATTACCAAAA
1 TACCCTCGATTTATAGAATTACCAAAA
* * * *
1028338 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAGAATTACCAAAA
* * * *
1028365 TATCCTTGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-TAGAATTACCAAAA
* * * *
1028392 TACCC-CTAGTTTGTAAAATTACTAAAA
1 TACCCTCGA-TTTATAGAATTACCAAAA
* * *
1028419 TACCC-CTGGTTTGTAAAATTACCAAAA
1 TACCCTC-GATTTATAGAATTACCAAAA
* *
1028446 TACCCCTGGCTTGTA-A-AATTACCAAAA
1 TA-CCCTCGATT-TATAGAATTACCAAAA
* * *
1028473 TACCCAT-GATTTGT-GAAATTATCGAAA
1 TACCC-TCGATTTATAG-AATTACCAAAA
*
1028500 TACTCTCGATTT
1 TACCCTCGATTT
1028512 GTAAAATATC
Statistics
Matches: 308, Mismatches: 43, Indels: 24
0.82 0.11 0.06
Matches are distributed among these distances:
25 1 0.00
26 10 0.03
27 288 0.94
28 8 0.03
29 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCAAAA
Found at i:1028385 original size:54 final size:54
Alignment explanation
Indices: 1028327--1028559 Score: 204
Period size: 54 Copynumber: 4.3 Consensus size: 54
1028317 CGATTTATAG
* ** * *
1028327 AATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATATCCTTGATCAGTAA
1 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATCAGTAA
* * * **
1028381 AATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCCTGGTTTGTAA
1 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATCAGTAA
* * ** *
1028435 AATTACCAAAATACCCCTGGCTTGTAAAATTACCAAAATACCCATGATTTGTGA
1 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATCAGTAA
* * * * * * *
1028489 AATTATCGAAATA-CTCTCGATTTGTAAAA-TATCGAAATACCCCTG-T-AGGGTAG
1 AATTACCAAAATACCCCT-GGTTTGTAAAATTACCAAAATACCCCTGATCA--GTAA
*
1028542 AATTACCGAAATACCCCT
1 AATTACCAAAATACCCCT
1028560 ATAAGGTAGA
Statistics
Matches: 146, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
52 1 0.01
53 30 0.21
54 115 0.79
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (54 bp):
AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATCAGTAA
Found at i:1028486 original size:81 final size:81
Alignment explanation
Indices: 1028318--1028502 Score: 212
Period size: 81 Copynumber: 2.3 Consensus size: 81
1028308 TTTTACCCTC
* * * * *
1028318 GATTTATAGAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATATCCTTGATCAGTAAAA
1 GATTTGTAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTGGATCAGTAAAA
*
1028383 TTACCAAAATACCCCT
66 TTACCAAAATACCCAT
* ** * *
1028399 -AGTTTGTAAAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGCT-TGTAA
1 GA-TTTGTAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAAAATA-CCCTGGATCAGTAA
1028462 AATTACCAAAATACCCAT
64 AATTACCAAAATACCCAT
* * *
1028480 GATTTGTGAAATTATCGAAATAC
1 GATTTGTAAAATTACCAAAATAC
1028503 TCTCGATTTG
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
80 1 0.01
81 79 0.92
82 6 0.07
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (81 bp):
GATTTGTAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTGGATCAGTAAAA
TTACCAAAATACCCAT
Found at i:1028513 original size:81 final size:80
Alignment explanation
Indices: 1028377--1028533 Score: 194
Period size: 81 Copynumber: 1.9 Consensus size: 80
1028367 TCCTTGATCA
* *
1028377 GTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCCTGGTTTGTAAAATTACC
1 GTAAAATTACCAAAATACCCATAGTTTGTAAAATTACTAAAATACCCCTGATTTGTAAAA-TACC
1028442 AAAATACCCCTGGCTT
65 AAAATACCCCTGGCTT
* * *
1028458 GTAAAATTACCAAAATACCCAT-GATTTGTGAAATTA-TCGAAATA-CTCTCGATTTGTAAAATA
1 GTAAAATTACCAAAATACCCATAG-TTTGTAAAATTACT-AAAATACCCCT-GATTTGTAAAATA
* *
1028520 TCGAAATACCCCTG
63 CCAAAATACCCCTG
1028534 TAGGGTAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
80 19 0.29
81 47 0.71
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (80 bp):
GTAAAATTACCAAAATACCCATAGTTTGTAAAATTACTAAAATACCCCTGATTTGTAAAATACCA
AAATACCCCTGGCTT
Found at i:1028559 original size:27 final size:27
Alignment explanation
Indices: 1028521--1028711 Score: 256
Period size: 27 Copynumber: 7.0 Consensus size: 27
1028511 TGTAAAATAT
1028521 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
1028548 CGAAATACCCCTATAAGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
1028575 CGAAATACACCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
1028602 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * * * *
1028629 TGAAATACCCTTATAGGGGAAAAATAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
1028656 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * *
1028683 CGAGATACCCTTGTGGGGTAAAAATTAC
1 CGAAATACCCCTGTAGGGT-AGAATTAC
1028711 C
1 C
1028712 ATTTTGCCCC
Statistics
Matches: 141, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 133 0.94
28 8 0.06
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (27 bp):
CGAAATACCCCTGTAGGGTAGAATTAC
Found at i:1028961 original size:25 final size:25
Alignment explanation
Indices: 1028914--1029007 Score: 120
Period size: 25 Copynumber: 3.8 Consensus size: 25
1028904 AGGAAGTGCT
1028914 AAAAGGG-TTATG-CCCAGTTTACCG
1 AAAAGGGCTT-TGCCCCAGTTTACCG
* *
1028938 AGAAGGGCTTTGCCGCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* * *
1028963 AAAAGGGCTTTTCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
1028988 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
1029008 ATTAAAAGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
24 8 0.13
25 52 0.87
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:1029020 original size:24 final size:25
Alignment explanation
Indices: 1028926--1029020 Score: 81
Period size: 25 Copynumber: 3.8 Consensus size: 25
1028916 AAGGGTTATG
* *
1028926 CCCAGTTTACCGAGAAG-GGCTTTGC
1 CCCAGTTTATC-AAAAGAGGCTTTGC
* * *
1028951 CGCAGTTTACCGAAAAG-GGCTTTTC
1 CCCAGTTTATC-AAAAGAGGCTTTGC
1028976 CCCAGTTTATCAAAA-AGGGCTTTGC
1 CCCAGTTTATCAAAAGA-GGCTTTGC
*
1029001 CCCAG-TTATTAAAAGAGGCT
1 CCCAGTTTATCAAAAGAGGCT
1029021 AGGTCTCCAG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
24 16 0.27
25 44 0.73
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
CCCAGTTTATCAAAAGAGGCTTTGC
Done.