Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 34 of 198
Found at i:9927957 original size:28 final size:28
Alignment explanation
Indices: 9927864--9927965 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 28
9927854 CAGTTTTGTT
* *
9927864 TGTGTGGACCACACGAGAGTGTGTGGGC
1 TGTGTGGACCACACGAGGGTGTGTGGTC
* * * *
9927892 CGTGTGTGACACACAGTCTAGGCTAGTTTGGT-
1 TGTGTG-GAC-CACA--CGAGGGT-GTGTGGTC
9927924 TCGTGTGGACCACACGAGGGTGTGTGGTC
1 T-GTGTGGACCACACGAGGGTGTGTGGTC
*
9927953 TGTGTGGGCCACA
1 TGTGTGGACCACA
9927966 TGGGGAAGCC
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
28 22 0.39
29 9 0.16
30 4 0.07
31 4 0.07
32 7 0.12
33 10 0.18
ACGTcount: A:0.17, C:0.20, G:0.38, T:0.25
Consensus pattern (28 bp):
TGTGTGGACCACACGAGGGTGTGTGGTC
Found at i:9927958 original size:61 final size:61
Alignment explanation
Indices: 9927831--9927950 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 61
9927821 TGTACGAGGA
* * *
9927831 CGTGTGTGACACACGGTCTAGGCCAGTTTTGTTTGTGTGGACCACACGAGAGTGTGTGGGC
1 CGTGTGTGACACACAGTCTAGGCCAGTTTGGTTCGTGTGGACCACACGAGAGTGTGTGGGC
* *
9927892 CGTGTGTGACACACAGTCTAGGCTAGTTTGGTTCGTGTGGACCACACGAGGGTGTGTGG
1 CGTGTGTGACACACAGTCTAGGCCAGTTTGGTTCGTGTGGACCACACGAGAGTGTGTGG
9927951 TCTGTGTGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.17, C:0.19, G:0.37, T:0.28
Consensus pattern (61 bp):
CGTGTGTGACACACAGTCTAGGCCAGTTTGGTTCGTGTGGACCACACGAGAGTGTGTGGGC
Found at i:9950575 original size:18 final size:18
Alignment explanation
Indices: 9950531--9950582 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
9950521 CAGCAACTTT
9950531 TTCTTCTTCAGCAACAAC
1 TTCTTCTTCAGCAACAAC
**
9950549 TTCCGCTTC-GACAACAAC
1 TTCTTCTTCAG-CAACAAC
*
9950567 TTCTTCTTCTGCAACA
1 TTCTTCTTCAGCAACA
9950583 TCAATTTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.25, C:0.35, G:0.08, T:0.33
Consensus pattern (18 bp):
TTCTTCTTCAGCAACAAC
Found at i:9984279 original size:19 final size:19
Alignment explanation
Indices: 9984239--9984279 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
9984229 TTGAACTTGA
* *
9984239 AAATTGGACCTGAGATCGT
1 AAATTGGACCTGAGAGCCT
*
9984258 AAATTGGACCTGGGAGCCT
1 AAATTGGACCTGAGAGCCT
9984277 AAA
1 AAA
9984280 ACCAATACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (19 bp):
AAATTGGACCTGAGAGCCT
Found at i:9984628 original size:17 final size:17
Alignment explanation
Indices: 9984606--9984701 Score: 67
Period size: 17 Copynumber: 5.6 Consensus size: 17
9984596 ATTTTAATAG
9984606 TTTAATATTTAATTTAA
1 TTTAATATTTAATTTAA
9984623 TTTAATATTT-ATCTTAA
1 TTTAATATTTAAT-TTAA
* *
9984640 --TAGTATTTTA-TTAA
1 TTTAATATTTAATTTAA
* *
9984654 TTTAGTATTAAAGTGATT-A
1 TTTAATATTTAA-T--TTAA
*
9984673 TCTTAATATTAAATTTAA
1 T-TTAATATTTAATTTAA
9984691 TTTAATATTTA
1 TTTAATATTTA
9984702 CCTTGTAGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 4 0.06
15 7 0.11
16 11 0.17
17 25 0.39
18 2 0.03
19 3 0.05
20 12 0.19
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTAATATTTAATTTAA
Found at i:9984781 original size:23 final size:24
Alignment explanation
Indices: 9984740--9984786 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
9984730 ATAAGATTTA
9984740 ATATTAAATTTAAGATAAA-TGTT
1 ATATTAAATTTAAGATAAAGTGTT
*
9984763 ATATT-AATTTAATATTAAAGTGTT
1 ATATTAAATTTAAGA-TAAAGTGTT
9984787 TAAGTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 9 0.43
24 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (24 bp):
ATATTAAATTTAAGATAAAGTGTT
Found at i:9987146 original size:87 final size:86
Alignment explanation
Indices: 9986984--9987146 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 86
9986974 AACATGCATA
* *
9986984 AGGTTGAGTTCTTACCCTTAATGAATTCATATCCCAAGTTTTAGATGGTCCTATTGAAATGAACT
1 AGGTTGAGTTATTACCCTTAATGAATTCATATCCCAAGTTTTAGATGGTCCTAGTGAAATGAACT
9987049 TGATGAATTCACCAACCTGTG
66 TGATGAATTCACCAACCTGTG
* * * *
9987070 AGGTTGAGTTTATTACTCTTAATGAGTTCATATCCCAAAG-TTTGGGTGGTCCTAGTGAAAT-AG
1 AGGTTGAG-TTATTACCCTTAATGAATTCATATCCC-AAGTTTTAGATGGTCCTAGTGAAATGA-
9987133 ACTTGATGAATTCA
63 ACTTGATGAATTCA
9987147 TCGATTTTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
86 9 0.13
87 56 0.82
88 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (86 bp):
AGGTTGAGTTATTACCCTTAATGAATTCATATCCCAAGTTTTAGATGGTCCTAGTGAAATGAACT
TGATGAATTCACCAACCTGTG
Found at i:9989594 original size:6 final size:7
Alignment explanation
Indices: 9989560--9989592 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
9989550 TTTGAACTAG
9989560 AAAAAAT
1 AAAAAAT
9989567 AAAAAAT
1 AAAAAAT
9989574 AAAAAAT
1 AAAAAAT
9989581 AAAAAAT
1 AAAAAAT
9989588 AAAAA
1 AAAAA
9989593 TAGAATTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:9996008 original size:36 final size:36
Alignment explanation
Indices: 9995967--9996040 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
9995957 TCAAATGTTC
*
9995967 TTTTAGTACCTGAAATAGACCAAAACTTGCTTGGTG
1 TTTTAGTACCTGAAATAGACCAAAACTTGCTTAGTG
*** *
9996003 TTTTAGTGTTTGAAATAGACCAAAACTTTCTTAGTG
1 TTTTAGTACCTGAAATAGACCAAAACTTGCTTAGTG
9996039 TT
1 TT
9996041 GGCTAACTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (36 bp):
TTTTAGTACCTGAAATAGACCAAAACTTGCTTAGTG
Found at i:10002425 original size:12 final size:12
Alignment explanation
Indices: 10002408--10002432 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10002398 ATTATTCTGT
10002408 AAAAATAAAATA
1 AAAAATAAAATA
10002420 AAAAATAAAATA
1 AAAAATAAAATA
10002432 A
1 A
10002433 GCTTGAACAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:10012467 original size:18 final size:18
Alignment explanation
Indices: 10012444--10012482 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
10012434 CATATGAGAT
10012444 GTTATGATTGTGCTATGA
1 GTTATGATTGTGCTATGA
10012462 GTTATGATTGTGCTATGA
1 GTTATGATTGTGCTATGA
10012480 GTT
1 GTT
10012483 TATGTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.05, G:0.28, T:0.46
Consensus pattern (18 bp):
GTTATGATTGTGCTATGA
Found at i:10016458 original size:23 final size:24
Alignment explanation
Indices: 10016432--10016479 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
10016422 GACCACCTCA
*
10016432 AATTGCC-ATTCATTTTTTTAATC
1 AATTGCCTATTCAATTTTTTAATC
* *
10016455 AATTTCCTCTTCAATTTTTTAATC
1 AATTGCCTATTCAATTTTTTAATC
10016479 A
1 A
10016480 GTACAGTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (24 bp):
AATTGCCTATTCAATTTTTTAATC
Found at i:10017663 original size:22 final size:22
Alignment explanation
Indices: 10017613--10017655 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
10017603 TTTATTGTTC
10017613 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
10017635 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
10017656 TAGCCATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:10034066 original size:19 final size:19
Alignment explanation
Indices: 10034024--10034066 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
10034014 ATGCAAGCAA
*
10034024 CAAGCTTAACCGAATTCTC
1 CAAGCTTAACCGAATGCTC
* *
10034043 TAAGCTTAATCGAATGCTC
1 CAAGCTTAACCGAATGCTC
10034062 CAAGC
1 CAAGC
10034067 CTTTTTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.26
Consensus pattern (19 bp):
CAAGCTTAACCGAATGCTC
Found at i:10045339 original size:23 final size:24
Alignment explanation
Indices: 10045313--10045365 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
10045303 GCATGATTAG
10045313 TAATTAGTTAAGTTAATT-AAATA
1 TAATTAGTTAAGTTAATTAAAATA
*
10045336 TAATTAGTTAAGTTAATTAAAATT
1 TAATTAGTTAAGTTAATTAAAATA
10045360 TAATTA
1 TAATTA
10045366 ACCATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (24 bp):
TAATTAGTTAAGTTAATTAAAATA
Found at i:10057241 original size:22 final size:22
Alignment explanation
Indices: 10057213--10057294 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
10057203 CACAGGTGAA
10057213 GTACTAAGCTCTCATGTTTAAC
1 GTACTAAGCTCTCATGTTTAAC
10057235 GTACTAAGCTCTCATGTTTAAC
1 GTACTAAGCTCTCATGTTTAAC
* * * **
10057257 GAACTAAACCCTCATGGCTAAC
1 GTACTAAGCTCTCATGTTTAAC
10057279 GTACTAAGCTCTCATG
1 GTACTAAGCTCTCATG
10057295 GCTCTTGTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (22 bp):
GTACTAAGCTCTCATGTTTAAC
Found at i:10066894 original size:24 final size:24
Alignment explanation
Indices: 10066867--10066915 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
10066857 CGCAAGGCCA
*
10066867 TGTGGTCGCCCGTGCGGTAAGCCG
1 TGTGGTCGCCCGTGCGATAAGCCG
* *
10066891 TGTGGTCGCCTGTGCGATAGGCCG
1 TGTGGTCGCCCGTGCGATAAGCCG
10066915 T
1 T
10066916 ATGGCTGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.08, C:0.27, G:0.41, T:0.24
Consensus pattern (24 bp):
TGTGGTCGCCCGTGCGATAAGCCG
Found at i:10067841 original size:13 final size:13
Alignment explanation
Indices: 10067823--10067847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10067813 TATTTTAATA
10067823 TTATTTTGTGTGT
1 TTATTTTGTGTGT
10067836 TTATTTTGTGTG
1 TTATTTTGTGTG
10067848 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:10069535 original size:41 final size:42
Alignment explanation
Indices: 10069478--10069593 Score: 182
Period size: 41 Copynumber: 2.8 Consensus size: 42
10069468 AAATTATTCA
*
10069478 GACTATATGTCTAGCAGGCTAAGTGTCGGTGAACTAAATC-G
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTAAATCAG
*
10069519 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTAAATCAG
* *
10069561 G-CTATAGGCCTAGCAGGCTAAGTGCCGGTGAAC
1 GACTATATGTCTAGCAGGCTAAGTGCCGGTGAAC
10069594 GAAACTAGAC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 68 0.97
42 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (42 bp):
GACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTAAATCAG
Found at i:10069607 original size:41 final size:41
Alignment explanation
Indices: 10069477--10069613 Score: 170
Period size: 41 Copynumber: 3.3 Consensus size: 41
10069467 AAAATTATTC
* *
10069477 AGACTATATGTCTAGCAGGCTAAGTGTCGGTGAACTAAA-T
1 AGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACGAAACT
* *
10069517 CGGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACTGAATC-
1 -AGACTATATGTCTAGCAGGCTAAGTGCCGGTGAAC-GAAACT
* * *
10069559 AGGCTATAGGCCTAGCAGGCTAAGTGCCGGTGAACGAAACT
1 AGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACGAAACT
*
10069600 AGACTATAAGTCTA
1 AGACTATATGTCTA
10069614 TTAGGTGAAG
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (41 bp):
AGACTATATGTCTAGCAGGCTAAGTGCCGGTGAACGAAACT
Found at i:10071958 original size:155 final size:154
Alignment explanation
Indices: 10071664--10071976 Score: 459
Period size: 155 Copynumber: 2.0 Consensus size: 154
10071654 GAGAGAGCCT
*** *
10071664 AATTTGACGTATCAAATTACGGTAGATCATATACACAATTATGCAGTTCGTCACAAGTATTAGAA
1 AATTTGACGTATCAAATTACAACAAATCATATACACAATTATGCAGTTCGTCACAAGTATTAGAA
* **
10071729 TATTAAACAATTAATTATTTAATTATTCTAATTGACAAGGCAAATATTCTAAGTTATTAAATACC
66 TATTAAACAATTAATTATTTAATTATTCTAATAGACAAAACAAATATTCTAAGTTATTAAATACC
*
10071794 TGTCAAATATTTAACAAACCGGAAC
131 TGTCAAATATCTAAC-AACCGGAAC
* * *
10071819 AATTTGACGTATCAAATTATAACAAATCGTATACACAATTATGTAGTTCGTCACAAGTATTAGAA
1 AATTTGACGTATCAAATTACAACAAATCATATACACAATTATGCAGTTCGTCACAAGTATTAGAA
* *
10071884 TATTAAACAATTACA-TATTTAATTATTCTGATAGACAAAACAAATATTCTAAGTTATTAAAT-T
66 TATTAAACAATTA-ATTATTTAATTATTCTAATAGACAAAACAAATATTCTAAGTTATTAAATAC
*
10071947 CTAGTCGAATATCTAACAACCGGAAC
130 CT-GTCAAATATCTAACAACCGGAAC
10071973 AATT
1 AATT
10071977 GTAATTCAAA
Statistics
Matches: 142, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
154 15 0.11
155 126 0.89
156 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (154 bp):
AATTTGACGTATCAAATTACAACAAATCATATACACAATTATGCAGTTCGTCACAAGTATTAGAA
TATTAAACAATTAATTATTTAATTATTCTAATAGACAAAACAAATATTCTAAGTTATTAAATACC
TGTCAAATATCTAACAACCGGAAC
Found at i:10073405 original size:158 final size:158
Alignment explanation
Indices: 10073231--10073701 Score: 703
Period size: 158 Copynumber: 3.0 Consensus size: 158
10073221 CTAACTCCAT
* *
10073231 TGTGCAACAATTCACTCTCACATATGTAATATATGTAA-GTCAAATTAAGTTTTAATTAAGGAAT
1 TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAA-GAAT
10073295 TTTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAAT
65 TTTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAAT
10073360 TTCGGTTGCCACAACGAAATACTTCTATA
130 TTCGGTTGCCACAACGAAATACTTCTATA
10073389 TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAAGAATT
1 TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAAGAATT
* * *
10073454 TTTTATTATTAACATTATATACGATATTATTTATTATAAAATATGATCTTATTATAAAATAAATT
66 TTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATT
* * ** * *
10073519 CCAGTTATCGCAAGGAAATACTTCTATA
131 TCGGTTGCCACAACGAAATACTTCTATA
** * * *
10073547 TGTGCTGCTATCTACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAA-TAGT
1 TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAAGAATT
* * * *
10073611 TTTTATTATTAAGTTTATATAATATATTAATTATTATAAAATATGACCTTATTATGAAATAAATT
66 TTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATT
* * * *
10073676 TCGATTGCTACAATGGAATACTTCTA
131 TCGGTTGCCACAACGAAATACTTCTA
10073702 CAATATCTTA
Statistics
Matches: 280, Mismatches: 32, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
157 77 0.28
158 182 0.65
159 21 0.08
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (158 bp):
TGTGCAACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTAAGAATT
TTTTATTATTAAGATTATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATT
TCGGTTGCCACAACGAAATACTTCTATA
Found at i:10074579 original size:12 final size:12
Alignment explanation
Indices: 10074562--10074591 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
10074552 TTGTGGAATG
10074562 GTTTCAGATTGA
1 GTTTCAGATTGA
10074574 GTTTCAGATTGA
1 GTTTCAGATTGA
10074586 GTTTCA
1 GTTTCA
10074592 TAAGTGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (12 bp):
GTTTCAGATTGA
Found at i:10075382 original size:13 final size:13
Alignment explanation
Indices: 10075366--10075415 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
10075356 GGGGGTAGGA
10075366 TTCTGTATATTTG
1 TTCTGTATATTTG
*
10075379 TTCTGCATATTTG
1 TTCTGTATATTTG
* *
10075392 TATCTGTATATGTA
1 T-TCTGTATATTTG
10075406 TT-TGTATATT
1 TTCTGTATATT
10075416 AAAGGATTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 7 0.23
13 14 0.45
14 10 0.32
ACGTcount: A:0.20, C:0.08, G:0.14, T:0.58
Consensus pattern (13 bp):
TTCTGTATATTTG
Found at i:10087764 original size:17 final size:18
Alignment explanation
Indices: 10087738--10087777 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
10087728 ATTAAGAATA
* *
10087738 TATAATATATTAT-TTAT
1 TATAAAATATGATCTTAT
10087755 TATAAAATATGATCTTAT
1 TATAAAATATGATCTTAT
10087773 TATAA
1 TATAA
10087778 CATAAATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TATAAAATATGATCTTAT
Found at i:10087920 original size:155 final size:157
Alignment explanation
Indices: 10087662--10087968 Score: 469
Period size: 155 Copynumber: 2.0 Consensus size: 157
10087652 TCCAATGTGT
*
10087662 TACTATCCACTCTCACATATGAAATATATAAAGGTCAAATTAAGTTTTAATTAAGAATTTTTTAT
1 TACTATCCACTCTCACATATGAAATATATAAAGGTCAAATTAAGCTTTAATTAAGAATTTTTTAT
* * * *
10087727 TATTAAGAATATATAATATATTATTTATTATAAAATATGATCTTATTATAACATAAAT-TCCGAT
66 TATTAAGAATATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATCT-CGAC
*
10087791 TGCCGCAATGAAATACTTCTATATGTAC
130 CGCCGCAATGAAATACTTCTATATGTAC
* *
10087819 TACTATCCACTCTCACATATGTAATATATATAAGGTCAAATTAAGCTTTAATTAA-TA-TTTTT-
1 TACTATCCACTCTCACATATGAAATATATA-AAGGTCAAATTAAGCTTTAATTAAGAATTTTTTA
** *
10087881 TTATTAAGTTTATATAAGATATTAATTATTATAAAATATGATCTTGTTATAAAATAAATCTCGAC
65 TTATTAAGAATATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATCTCGAC
10087946 CGCCGCAATGAAATACTTCTATA
130 CGCCGCAATGAAATACTTCTATA
10087969 ATATTTTATA
Statistics
Matches: 137, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
155 78 0.57
156 6 0.04
157 30 0.22
158 23 0.17
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (157 bp):
TACTATCCACTCTCACATATGAAATATATAAAGGTCAAATTAAGCTTTAATTAAGAATTTTTTAT
TATTAAGAATATATAAGATATTAATTATTATAAAATATGATCTTATTATAAAATAAATCTCGACC
GCCGCAATGAAATACTTCTATATGTAC
Found at i:10088985 original size:12 final size:12
Alignment explanation
Indices: 10088968--10089001 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
10088958 AGGGGAAAAC
10088968 AGGCATAGGCCT
1 AGGCATAGGCCT
* *
10088980 AGGCATAAGCGT
1 AGGCATAGGCCT
10088992 AGGCATAGGC
1 AGGCATAGGC
10089002 ATAAGGAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.21, G:0.35, T:0.15
Consensus pattern (12 bp):
AGGCATAGGCCT
Found at i:10092463 original size:18 final size:17
Alignment explanation
Indices: 10092440--10092482 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
10092430 ATAATCATAT
10092440 ATTTTAATGA-TATAATAA
1 ATTTTAAT-ATTATAAT-A
10092458 ATTTTAATATTTATAATA
1 ATTTTAATA-TTATAATA
10092476 ATTTTAA
1 ATTTTAA
10092483 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTTAATATTATAATA
Found at i:10092474 original size:19 final size:17
Alignment explanation
Indices: 10092450--10092486 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
10092440 ATTTTAATGA
10092450 TATAATAAATTTTAATATT
1 TATAAT-AATTTTAA-ATT
10092469 TATAATAATTTTAAATT
1 TATAATAATTTTAAATT
10092486 T
1 T
10092487 TAAATAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATAATAATTTTAAATT
Found at i:10092620 original size:23 final size:23
Alignment explanation
Indices: 10092564--10092613 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
10092554 TTAGTATTAA
*
10092564 ATTTTA-TAGTATAAAATATGAAT
1 ATTTTACTAATAT-AAATATGAAT
*
10092587 ATTTTACTAATATAAATATGAGT
1 ATTTTACTAATATAAATATGAAT
10092610 ATTT
1 ATTT
10092614 GTTTAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (23 bp):
ATTTTACTAATATAAATATGAAT
Found at i:10092763 original size:17 final size:18
Alignment explanation
Indices: 10092737--10092776 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
10092727 ATTAAGAATA
* *
10092737 TATAATATATTAT-TTAT
1 TATAAAATATGATCTTAT
10092754 TATAAAATATGATCTTAT
1 TATAAAATATGATCTTAT
10092772 TATAA
1 TATAA
10092777 CATAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TATAAAATATGATCTTAT
Found at i:10092879 original size:157 final size:158
Alignment explanation
Indices: 10092651--10093128 Score: 705
Period size: 157 Copynumber: 3.0 Consensus size: 158
10092641 CTTTTCTAAC
* *
10092651 TCTA-ATGTGCTACTATCCACTCCCACATATGTAGTATATGT-AGGTCAAATTAAGTTTTAATTA
1 TCTATATGTGCTACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTA
* * *
10092714 AGATTTTTTTATTATTAAGAATATATAATATATTATTTATTATAAAATATGATCTTATTATAACA
66 AGATTTTTTTATTATTAAGATTATATAAGATATTATTTATTATAAAATATGATCTTATTATAAAA
* * *
10092779 TAAATTTTGGTTGTCACAATGAAATACT
131 TAAATTTCGGTTGCCGCAATGAAATACT
* *** *
10092807 TCTATATGTGCTACTATCCACTCTCACATATGTAATGTATGTAACACCAAATTAAGTTTTAAATA
1 TCTATATGTGCTACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTA
* *
10092872 AGA-TTTTTTATTATTAAGATTATATAAGATTATGA-TTATTATAAAATATGATCTCATTATAAA
66 AGATTTTTTTATTATTAAGATTATATAAGA-TATTATTTATTATAAAATATGATCTTATTATAAA
10092935 ATAAATTTCGGTTGCCGCAATGAAATACT
130 ATAAATTTCGGTTGCCGCAATGAAATACT
* *
10092964 TCTATATGTGCTACTATCCACTCTTACATATGTAATATATGTAAGGTCAAATTAAGCTTTAATTA
1 TCTATATGTGCTACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTA
* *
10093029 ATATTTTTATTATTATTAAGTTTATATAAGATATTAATTT-TTATAAAATATGATCTTATTATAA
66 AGATTTTT-TTATTATTAAGATTATATAAGATATT-ATTTATTATAAAATATGATCTTATTATAA
* *
10093093 AATAAATTTCGATTGCCGCAATGAAATTCT
129 AATAAATTTCGGTTGCCGCAATGAAATACT
10093123 TCTATA
1 TCTATA
10093129 ACATTTTATA
Statistics
Matches: 287, Mismatches: 28, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
156 4 0.01
157 170 0.59
158 32 0.11
159 79 0.28
160 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.42
Consensus pattern (158 bp):
TCTATATGTGCTACTATCCACTCTCACATATGTAATATATGTAAGGTCAAATTAAGTTTTAATTA
AGATTTTTTTATTATTAAGATTATATAAGATATTATTTATTATAAAATATGATCTTATTATAAAA
TAAATTTCGGTTGCCGCAATGAAATACT
Found at i:10092921 original size:16 final size:16
Alignment explanation
Indices: 10092889--10092937 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
10092879 TTATTATTAA
*
10092889 GATTA-TATAAGATTAT
1 GATTATTATAA-AATAT
10092905 GATTATTATAAAATAT
1 GATTATTATAAAATAT
10092921 GATCTCATTATAAAATA
1 GAT-T-ATTATAAAATA
10092938 AATTTCGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.41
17 6 0.21
18 11 0.38
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (16 bp):
GATTATTATAAAATAT
Found at i:10093079 original size:17 final size:18
Alignment explanation
Indices: 10093042--10093079 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
10093032 TTTTTATTAT
*
10093042 TATTAAGTTTATATAAGA
1 TATTAAGTTTATATAAAA
*
10093060 TATTAA-TTTTTATAAAA
1 TATTAAGTTTATATAAAA
10093077 TAT
1 TAT
10093080 GATCTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TATTAAGTTTATATAAAA
Found at i:10096006 original size:27 final size:26
Alignment explanation
Indices: 10095987--10096425 Score: 443
Period size: 27 Copynumber: 16.4 Consensus size: 26
10095977 GGGTATAATA
10095987 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
10096014 GTCATTTTATCATAT-GGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
*
10096040 GTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTT-G
* * * *
10096067 ATCATTTTATCCTATAGGGGTAATTAG
1 GTCATTTTACCCTATGGGGGT-ATTTG
*
10096094 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
*
10096121 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
10096148 ATCATTTTACCCTATAGGGGTATTTAG
1 GTCATTTTACCCTATGGGGGTATTT-G
* * * *
10096175 TTCATTTTACCCTCTAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTT-G
*
10096202 GTCA-TTTACCATATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* *
10096228 GTCATTTTATCTTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* * *
10096254 GCCATTTTACCCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTT-G
*
10096281 GTCATTTTACCCTATTGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
* *
10096308 GTCATTTTACCTTATGGGCGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
10096335 GTCATTTTACCTTATCGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
10096362 ATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTT-G
* *
10096389 GTTATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTA-TTTG
10096416 GTCATTTTAC
1 GTCATTTTAC
10096426 TTATTTTGGG
Statistics
Matches: 349, Mismatches: 51, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
25 3 0.01
26 66 0.19
27 271 0.78
28 9 0.03
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGGTATTTG
Found at i:10096114 original size:54 final size:52
Alignment explanation
Indices: 10095987--10096425 Score: 495
Period size: 54 Copynumber: 8.2 Consensus size: 52
10095977 GGGTATAATA
* * *
10095987 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGTATTTAG
** * *
10096040 GTCATTTTACCCTATGGGGGTATTTCAATCATTTTATCCTATAGGGGTAATTAG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTAT-GGGGTATTTAG
*
10096094 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATG-GGGTATTTAG
* * * *
10096148 ATCATTTTACCCTATAGGGGTATTTAGTTCATTTTACCCTCTAGGGGTATTTCA-
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTAT-GGGGTATTT-AG
* * * * *
10096202 GTCA-TTTACCATATGGGGGTATTTTGGTCATTTTATCTTATGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGGTATTTAG
* * *
10096254 GCCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATTGGGGTATTTTG
1 GTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTA-TGGGGTATTTAG
* * *
10096308 GTCATTTTACCTTATGGGCGTATTTCGGTCATTTTACCTTATCGGGGTATTTCG
1 GTCATTTTACCCTATGGG-GTATTTCGGTCATTTTACCCTAT-GGGGTATTTAG
* * *
10096362 ATCATTTTACCCTATGAGGGTATTTCGGTTATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATG-GGGTATTTAG
10096416 GTCATTTTAC
1 GTCATTTTAC
10096426 TTATTTTGGG
Statistics
Matches: 331, Mismatches: 43, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
52 13 0.04
53 103 0.31
54 212 0.64
55 3 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (52 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGGGGTATTTAG
Found at i:10096142 original size:81 final size:80
Alignment explanation
Indices: 10095987--10096425 Score: 528
Period size: 81 Copynumber: 5.5 Consensus size: 80
10095977 GGGTATAATA
* * * *
10095987 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTTTGGTCATTTTACCC
1 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCC
* *
10096052 TATGGGGGTATTTCA
66 TATGAGGGTATTTCG
* * * *
10096067 ATCATTTTATCCTATAGGGGTAATTAGGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACC
10096132 CTATGAGGGTATTTCG
65 CTATGAGGGTATTTCG
* * * * *
10096148 ATCATTTTACCCTATAGGGGTATTTAGTTCATTTTACCCTCTAGGGGTATTTCAGTCA-TTTACC
1 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTACC
* * *
10096212 ATATGGGGGTATTTTG
65 CTATGAGGGTATTTCG
* * * *
10096228 GTCATTTTATCTTAT-GGGGTATTTCGGCCATTTTACCCTATGAGGGTATTTCAGTCATTTTACC
1 GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACC
*
10096292 CTATTG-GGGTATTTTG
65 CTA-TGAGGGTATTTCG
* * *
10096308 GTCATTTTACCTTAT-GGGCGTATTTCGGTCATTTTACCTTATCGGGGTATTTCGATCATTTTAC
1 GTCATTTTACCCTATAGGG-GTATTTCGGTCATTTTACCCTAT-GGGGTATTTCGGTCATTTTAC
10096372 CCTATGAGGGTATTTCG
64 CCTATGAGGGTATTTCG
* *
10096389 GTTATTTTACCCTAT-GAGGGTATTTTGGTCATTTTAC
1 GTCATTTTACCCTATAG-GGGTATTTCGGTCATTTTAC
10096426 TTATTTTGGG
Statistics
Matches: 316, Mismatches: 35, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
78 1 0.00
79 36 0.11
80 103 0.33
81 173 0.55
82 3 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (80 bp):
GTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCC
TATGAGGGTATTTCG
Found at i:10096368 original size:214 final size:215
Alignment explanation
Indices: 10095973--10096401 Score: 636
Period size: 214 Copynumber: 2.0 Consensus size: 215
10095963 ATTTAATCTC
*
10095973 CTAGGGGTATAATAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTT
1 CTAGGGGTATAATAGTCATTTTACCATATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTT
* * * *
10096038 TGGTCATTTTACCCTATGGGGGTATTTCAATCATTTTATCCTATAGGGGTAATTAGGTCATTTTA
66 CGGCCATTTTACCCTATGAGGGTATTTCAATCATTTTACCCTATAGGGGTAATTAGGTCATTTTA
10096103 CCCTATAGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTAT-AGGG
131 CCCTATAGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATGA-GG
10096167 GTATTT-AGTTCATTTTACCCT
195 GTATTTCAGTT-ATTTTACCCT
* * *
10096188 CTAGGGGTAT-TTCAGTCA-TTTACCATATGGGGGTATTTTGGTCATTTTATCTTATGGGGTATT
1 CTAGGGGTATAAT-AGTCATTTTACCATATGGGGGTATTTCGGTCATTTTATCATATGGGGTATT
* * * *
10096251 TCGGCCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATTGGGGTATTTTGGTCATTTT
65 TCGGCCATTTTACCCTATGAGGGTATTTCAATCATTTTACCCTATAGGGGTAATTAGGTCATTTT
* *
10096316 ACCTTAT-GGGCGTATTTCGGTCATTTTACCTTATCG-GGGTATTTCGATCATTTTACCCTATGA
130 ACCCTATAGGG-GTATTTCGGTCATTTTACCCTAT-GAGGGTATTTCGATCATTTTACCCTATGA
*
10096379 GGGTATTTCGGTTATTTTACCCT
193 GGGTATTTCAGTTATTTTACCCT
10096402 ATGAGGGTAT
Statistics
Matches: 194, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
213 3 0.02
214 171 0.88
215 20 0.10
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (215 bp):
CTAGGGGTATAATAGTCATTTTACCATATGGGGGTATTTCGGTCATTTTATCATATGGGGTATTT
CGGCCATTTTACCCTATGAGGGTATTTCAATCATTTTACCCTATAGGGGTAATTAGGTCATTTTA
CCCTATAGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATGAGGG
TATTTCAGTTATTTTACCCT
Found at i:10099183 original size:27 final size:26
Alignment explanation
Indices: 10099127--10099183 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
10099117 GTTAACACTT
* *
10099127 AAAACCTAAAGAATTTAAAGTTCATC
1 AAAACCTAAAGAAATTAAAGTGCATC
* * *
10099153 AAAACACTAAATAAATTAATGTGCATG
1 AAAAC-CTAAAGAAATTAAAGTGCATC
10099180 AAAA
1 AAAA
10099184 ATGTATGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (26 bp):
AAAACCTAAAGAAATTAAAGTGCATC
Found at i:10115241 original size:267 final size:266
Alignment explanation
Indices: 10114761--10115320 Score: 832
Period size: 267 Copynumber: 2.1 Consensus size: 266
10114751 CTTATCGCCT
* ** * *
10114761 CAACGTTGCAATGGAAAAGATTGAAGCCACAACGACGAATCTTATTTTCCTGGCGTTGTAGCGGA
1 CAACATTGCAATTTAAAAGAATGAAGCCACAACGACGAATCTTATTTTCCTGGCATTGTAGCGGA
* * * * *
10114826 GCAGATTGAAGCCACAACAACGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTGAACTGG
66 GCAAATTAAAGCCACAACAACGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTAAAATAG
** * *
10114891 AGCGGATTAAAGCTGTGGGCAGTGAATCCTATCTCTTTGGCATTACAGTGGAGCAGATTGAAACC
131 AGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTACAATAGAGCAGATTGAAACC
* * * *
10114956 ACGACGGTGAATCTTACTCCCCTGGCGATGTAGTGGAACAAATTGAAGCTACGACGGCGATTCTT
196 ACGACAGTGAATCTTACTCCCCTGGCGATGTAGTAGAACAAATTAAAGCTACGACGGCGAATCTT
10115021 GTTTCC
261 GTTTCC
* *
10115027 ACAACATTGCAATTTAAAAGAATGAAGCCACAACGGCGAATCTTATTTTCCTGGTATTGTAGCGG
1 -CAACATTGCAATTTAAAAGAATGAAGCCACAACGACGAATCTTATTTTCCTGGCATTGTAGCGG
***
10115092 AGCAAATTAAAGCCACAACGGTGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTAAAATA
65 AGCAAATTAAAGCCACAACAACGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTAAAATA
*
10115157 GTGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTACAATAGAGCAGATTGAAAC
130 GAGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTACAATAGAGCAGATTGAAAC
* * * *
10115222 CACGGCAGTGAATCTTACTCCCCTGGCGGTGTAGTAGAACAGATTAAAGCTACGATGGCGAATCT
195 CACGACAGTGAATCTTACTCCCCTGGCGATGTAGTAGAACAAATTAAAGCTACGACGGCGAATCT
10115287 TGTTTCC
260 TGTTTCC
* *
10115294 CTAACATTGCAATTTGAAAGACTGAAG
1 C-AACATTGCAATTTAAAAGAATGAAG
10115321 ATGGCAAATC
Statistics
Matches: 262, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
266 1 0.00
267 261 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (266 bp):
CAACATTGCAATTTAAAAGAATGAAGCCACAACGACGAATCTTATTTTCCTGGCATTGTAGCGGA
GCAAATTAAAGCCACAACAACGAATCTTATCTCCCTGGCGTTAAGGCTTGGATTAGCTAAAATAG
AGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTACAATAGAGCAGATTGAAACC
ACGACAGTGAATCTTACTCCCCTGGCGATGTAGTAGAACAAATTAAAGCTACGACGGCGAATCTT
GTTTCC
Found at i:10115385 original size:44 final size:44
Alignment explanation
Indices: 10115325--10115447 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 44
10115315 CTGAAGATGG
*
10115325 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* ** *
10115369 -ATAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCA
1 CA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
* * *
10115413 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGAT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
10115448 CGCATCTAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
43 7 0.11
44 58 0.88
45 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCA
Found at i:10115477 original size:78 final size:78
Alignment explanation
Indices: 10115390--10115559 Score: 322
Period size: 78 Copynumber: 2.2 Consensus size: 78
10115380 TCCCTGAAGT
*
10115390 TGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
1 TGCAGTGGAGTGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCT
10115455 AGTCTTATCTCCC
66 AGTCTTATCTCCC
*
10115468 TGCAGTGGAGTAGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCT
1 TGCAGTGGAGTGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCT
10115533 AGTCTTATCTCCC
66 AGTCTTATCTCCC
10115546 TGCAGTGGAGTGGA
1 TGCAGTGGAGTGGA
10115560 GTAGACTAAG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (78 bp):
TGCAGTGGAGTGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCT
AGTCTTATCTCCC
Found at i:10115540 original size:40 final size:40
Alignment explanation
Indices: 10115417--10115543 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
10115407 AAATCACAGA
10115417 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
1 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * * ** *
10115457 TCTTATCTCCCTGCAG-TGGAGTAGATTAAAAT--CA-C-AG
1 TCTTATCTCTCTGAAGTTGCAG-AGA-GCAGATCGCATCTAG
*
10115494 ATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCTAG
1 -TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
10115535 TCTTATCTC
1 TCTTATCTC
10115544 CCTGCAGTGG
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
37 5 0.08
38 17 0.26
39 12 0.18
40 26 0.40
41 5 0.08
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (40 bp):
TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
Found at i:10115637 original size:45 final size:44
Alignment explanation
Indices: 10115533--10115649 Score: 125
Period size: 45 Copynumber: 2.7 Consensus size: 44
10115523 GATCGCATCT
* *
10115533 AGTCTTATCTCCCTGCAG-TGGAGTGGAGTAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA
* *
10115576 AGTCTTATC-CCTCTGAAGTTGCAGTGGTGTAGACTGAAG-ATGGCGA
1 AGTCTTATCTCC-CTGAAGTTGCAGTGGAGTAGACT-AAGTA-AGC-A
*
10115622 A-TCTTATCTCCCTGAAGTTGCAGCGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
10115650 CAGATTAAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.03
43 14 0.23
44 15 0.24
45 27 0.44
46 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA
Found at i:10116494 original size:17 final size:16
Alignment explanation
Indices: 10116462--10116502 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
10116452 AAGGTTGATA
*
10116462 TTTGTTTTGTTTCTTT
1 TTTGTTTTGATTCTTT
10116478 TTTGTTGTTGATTCTTT
1 TTTGTT-TTGATTCTTT
*
10116495 TTTATTTT
1 TTTGTTTT
10116503 CGTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.05, C:0.05, G:0.12, T:0.78
Consensus pattern (16 bp):
TTTGTTTTGATTCTTT
Found at i:10125935 original size:18 final size:19
Alignment explanation
Indices: 10125912--10125950 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
10125902 AACTTATCCT
*
10125912 TAAATTAATTT-TTTTATA
1 TAAATTAATTTGTTGTATA
*
10125930 TAAATTTATTTGTTGTATA
1 TAAATTAATTTGTTGTATA
10125949 TA
1 TA
10125951 TTTTTCACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TAAATTAATTTGTTGTATA
Found at i:10126826 original size:20 final size:18
Alignment explanation
Indices: 10126789--10126840 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
10126779 TATGGTTCGA
10126789 GTTTGAGGTTTAGGATTTAAG
1 GTTT-AGGTTT-GGATTT-AG
*
10126810 GTTTAGTGTTTGGATTTAT
1 GTTTAG-GTTTGGATTTAG
10126829 GTTTAGGTTTGG
1 GTTTAGGTTTGG
10126841 GGTTTGGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 8 0.28
21 8 0.28
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (18 bp):
GTTTAGGTTTGGATTTAG
Found at i:10138631 original size:6 final size:6
Alignment explanation
Indices: 10138622--10138652 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
10138612 CTTGTGCTTG
*
10138622 TTCTTA TTCTTA TTCTTA TTCGTA TTCTTA T
1 TTCTTA TTCTTA TTCTTA TTCTTA TTCTTA T
10138653 ACTTGTACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.03, T:0.65
Consensus pattern (6 bp):
TTCTTA
Found at i:10139095 original size:13 final size:14
Alignment explanation
Indices: 10139065--10139095 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10139055 GAGCACGCAT
10139065 AAAACATAACTTTA
1 AAAACATAACTTTA
*
10139079 AAAACATAACTTGA
1 AAAACATAACTTTA
10139093 AAA
1 AAA
10139096 TAGAGTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAACATAACTTTA
Found at i:10139663 original size:27 final size:27
Alignment explanation
Indices: 10139633--10139707 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
10139623 ATTCTAGAGT
10139633 TCGCCAAACCAACTGGTGAACCCCAAC
1 TCGCCAAACCAACTGGTGAACCCCAAC
* * **
10139660 TCGCCAAACCAATTGGCGAACCTTAAC
1 TCGCCAAACCAACTGGTGAACCCCAAC
10139687 TCGCCAAACCAACTGGTGAAC
1 TCGCCAAACCAACTGGTGAAC
10139708 ACAACTAGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.33, C:0.36, G:0.16, T:0.15
Consensus pattern (27 bp):
TCGCCAAACCAACTGGTGAACCCCAAC
Found at i:10141433 original size:42 final size:42
Alignment explanation
Indices: 10141349--10141433 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
10141339 TGCACTTTTG
** * *
10141349 AACCACACGGCCAGGGACATGGGCATGTGCCCAGGCCGTGTA
1 AACCACACGGCCAAAGACATGGGCATGTGCACAGGCCATGTA
* * * *
10141391 AACCACACGGGCAAAGACATGGGCATGTGTATAGGTCATGTA
1 AACCACACGGCCAAAGACATGGGCATGTGCACAGGCCATGTA
10141433 A
1 A
10141434 CTTACTGGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.29, C:0.25, G:0.31, T:0.15
Consensus pattern (42 bp):
AACCACACGGCCAAAGACATGGGCATGTGCACAGGCCATGTA
Found at i:10141536 original size:105 final size:104
Alignment explanation
Indices: 10141312--10141536 Score: 260
Period size: 105 Copynumber: 2.2 Consensus size: 104
10141302 GGCATTGGTG
* * *
10141312 TGTGTCTAGGCCATGTAACTCACTGTTTGCACTTTTGAACCACACGGCCAGGGACATGGGCATGT
1 TGTGTCTAGGCCATGTAACTCACTGTTTGCACTTTAGAACCACACAGCCAGGGACATAGGCATGT
10141377 GCCCAGGCCGTGTAAACCACACGGGCAAAGACATGGGCA
66 GCCCAGGCCGTGTAAACCACACGGGCAAAGACATGGGCA
* * *
10141416 TGTGTATAGGTCATGTAACTTACTGGTTATG-A-TTTAGAACCACACAAG-CAGGTGACATAGGC
1 TGTGTCTAGGCCATGTAACTCACT-GTT-TGCACTTTAGAACCACAC-AGCCAGG-GACATAGGC
* * * * * *
10141478 GTGTG-CCTGAGCCGTGTGAGCCACACGGGCAAGGACATGGGCT
62 ATGTGCCCAG-GCCGTGTAAACCACACGGGCAAAGACATGGGCA
*
10141521 TGTGTCCAGGCCATGT
1 TGTGTCTAGGCCATGT
10141537 GGCATATGAA
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
104 40 0.40
105 59 0.58
106 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (104 bp):
TGTGTCTAGGCCATGTAACTCACTGTTTGCACTTTAGAACCACACAGCCAGGGACATAGGCATGT
GCCCAGGCCGTGTAAACCACACGGGCAAAGACATGGGCA
Found at i:10144912 original size:21 final size:21
Alignment explanation
Indices: 10144871--10144910 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
10144861 TTTGTTTATT
10144871 TTAATTAATGCTTTAATTTTA
1 TTAATTAATGCTTTAATTTTA
*
10144892 TTAATTTAT-CTTTAATTTT
1 TTAATTAATGCTTTAATTTT
10144911 TAACAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TTAATTAATGCTTTAATTTTA
Found at i:10156992 original size:45 final size:43
Alignment explanation
Indices: 10156941--10157040 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 43
10156931 AGTCATGTTT
* * *
10156941 TTACTCATTTACATCATGACACCGTAGCATCTTTTAGCTATGGTC
1 TTACTCATTT--ATCATGACACCATAGCATCTCTCAGCTATGGTC
**
10156986 TTACTCATCCTTATCATGATGCCATAGCATCTCTCAGCTATGGTC
1 TTACTCAT--TTATCATGACACCATAGCATCTCTCAGCTATGGTC
10157031 TTACTCATTT
1 TTACTCATTT
10157041 TCAGCGTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
43 2 0.04
45 44 0.92
47 2 0.04
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (43 bp):
TTACTCATTTATCATGACACCATAGCATCTCTCAGCTATGGTC
Found at i:10159724 original size:43 final size:44
Alignment explanation
Indices: 10159572--10159729 Score: 185
Period size: 43 Copynumber: 3.6 Consensus size: 44
10159562 TGTGGCTTCG
* * * * * *
10159572 TCCATAACCTATATGGTAGCTTATCTG-CAAAATTGGTGGTTTA
1 TCCACAACCTACATGGTAGCTTGTTTGTGAATATTGGTGGTTTA
* * * *
10159615 TCCACAACCTACATGGTAACCTGTCTGTGAATATTGGTGGCTTCA
1 TCCACAACCTACATGGTAGCTTGTTTGTGAATATTGGTGG-TTTA
* *
10159660 TCCACAACCTACATGGCAGCTTGTTTGTGAGT-TTGGTGGTTTA
1 TCCACAACCTACATGGTAGCTTGTTTGTGAATATTGGTGGTTTA
10159703 TCCACAACCTACATGGTAGCTTGTTTG
1 TCCACAACCTACATGGTAGCTTGTTTG
10159730 CAAATAGTGG
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
43 51 0.52
44 17 0.17
45 30 0.31
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (44 bp):
TCCACAACCTACATGGTAGCTTGTTTGTGAATATTGGTGGTTTA
Found at i:10163649 original size:22 final size:22
Alignment explanation
Indices: 10163621--10163664 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
10163611 CATCAAGATC
10163621 AAGATAAGTTTGATTTACTTTA
1 AAGATAAGTTTGATTTACTTTA
10163643 AAGATAAGTTTGATTTACTTTA
1 AAGATAAGTTTGATTTACTTTA
10163665 TGACTCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (22 bp):
AAGATAAGTTTGATTTACTTTA
Found at i:10163681 original size:30 final size:30
Alignment explanation
Indices: 10163647--10163707 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
10163637 ACTTTAAAGA
10163647 TAAGTTTGATTTACTTTATGACTCTAATTT
1 TAAGTTTGATTTACTTTATGACTCTAATTT
10163677 TAAGTTTGATTTACTTTATGACTCTAATTT
1 TAAGTTTGATTTACTTTATGACTCTAATTT
10163707 T
1 T
10163708 TACTAGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (30 bp):
TAAGTTTGATTTACTTTATGACTCTAATTT
Found at i:10163919 original size:26 final size:25
Alignment explanation
Indices: 10163874--10163927 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
10163864 ATTCCATCTC
10163874 TTTATTTTTACTTTCTTCTCTCTTTT
1 TTTATTTTTACTTTCTTCTCT-TTTT
*
10163900 TTTATTTTTA-TTTTTATCTCTTTTT
1 TTTATTTTTACTTTCT-TCTCTTTTT
10163925 TTT
1 TTT
10163928 CTATAAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTATTTTTACTTTCTTCTCTTTTT
Found at i:10163924 original size:24 final size:26
Alignment explanation
Indices: 10163874--10163926 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
10163864 ATTCCATCTC
*
10163874 TTTATTTTTACTTTCTTCTCTCTTTT
1 TTTATTTTTACTTTCTTATCTCTTTT
10163900 TTTATTTTTA-TTT-TTATCTCTTTT
1 TTTATTTTTACTTTCTTATCTCTTTT
10163924 TTT
1 TTT
10163927 TCTATAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 13 0.50
25 3 0.12
26 10 0.38
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTATTTTTACTTTCTTATCTCTTTT
Found at i:10164870 original size:21 final size:20
Alignment explanation
Indices: 10164833--10164871 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
10164823 AATATAAATC
* *
10164833 TATTTATTAAATGTTATTTT
1 TATTTATAAAATATTATTTT
10164853 TATTTAATAAAATATTATT
1 TATTT-ATAAAATATTATT
10164872 AATAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTTATAAAATATTATTTT
Found at i:10167987 original size:31 final size:28
Alignment explanation
Indices: 10167924--10167991 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 28
10167914 AATACAATTC
* *
10167924 TTTATTATTATTTTTTTCTTTTTTTTCT
1 TTTATTCTTATTTTTTTCTTTTTTTTCA
10167952 TTTATTCTTACTTTTTTTCTTCTCTCTTTT-A
1 TTTATTCTTA-TTTTTTTCTT-T-T-TTTTCA
10167983 TTTATTCTT
1 TTTATTCTT
10167992 TCTTCTTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 9 0.26
29 10 0.29
30 1 0.03
31 10 0.29
32 4 0.12
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTATTCTTATTTTTTTCTTTTTTTTCA
Found at i:10168792 original size:6 final size:6
Alignment explanation
Indices: 10168781--10168825 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
10168771 AAAATAAAGA
*
10168781 AAATAT AAATAT AAATAT AAATAAA AAATAT AAATA- AAATA- AAAT
1 AAATAT AAATAT AAATAT AAAT-AT AAATAT AAATAT AAATAT AAAT
10168826 TGGGTTGCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 9 0.25
6 22 0.61
7 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (6 bp):
AAATAT
Found at i:10168798 original size:12 final size:11
Alignment explanation
Indices: 10168774--10168825 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
10168764 ATGCAAGAAA
*
10168774 ATAAAGAAAAT
1 ATAAATAAAAT
10168785 ATAAATATAAAT
1 ATAAATA-AAAT
10168797 ATAAATAAAAAAT
1 ATAAAT--AAAAT
10168810 ATAAATAAAAT
1 ATAAATAAAAT
10168821 A-AAAT
1 ATAAAT
10168826 TGGGTTGCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 4 0.11
11 12 0.32
12 10 0.27
13 10 0.27
14 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:10168801 original size:23 final size:24
Alignment explanation
Indices: 10168780--10168825 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
10168770 GAAAATAAAG
10168780 AAAATATAAATATAAATATAAATAA
1 AAAATATAAATA-AAATATAAATAA
10168805 AAAATATAAATAAAATA-AAAT
1 AAAATATAAATAAAATATAAAT
10168826 TGGGTTGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATATAAATAAAATATAAATAA
Found at i:10168811 original size:13 final size:13
Alignment explanation
Indices: 10168780--10168819 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
10168770 GAAAATAAAG
10168780 AAAATATAAAT-A
1 AAAATATAAATAA
*
10168792 TAAATATAAATAA
1 AAAATATAAATAA
10168805 AAAATATAAATAA
1 AAAATATAAATAA
10168818 AA
1 AA
10168820 TAAAATTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAATATAAATAA
Found at i:10168811 original size:19 final size:18
Alignment explanation
Indices: 10168774--10168824 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
10168764 ATGCAAGAAA
* *
10168774 ATAAAGAAAAT-ATAAAT
1 ATAAATAAAATAAAAAAT
10168791 ATAAATATAAATAAAAAAT
1 ATAAATA-AAATAAAAAAT
10168810 ATAAATAAAATAAAA
1 ATAAATAAAATAAAA
10168825 TTGGGTTGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 6 0.20
18 12 0.40
19 12 0.40
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
ATAAATAAAATAAAAAAT
Found at i:10180410 original size:30 final size:31
Alignment explanation
Indices: 10180366--10180431 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
10180356 TAGTAAAAAT
*
10180366 AAAATTGTACTTTAATTCTTTAAAAACGATA
1 AAAATTGTAATTTAATTCTTTAAAAACGATA
* **
10180397 AAAATT-TAATTTAATTTTTTAAAAATTATA
1 AAAATTGTAATTTAATTCTTTAAAAACGATA
10180427 AAAAT
1 AAAAT
10180432 ACAAACTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
AAAATTGTAATTTAATTCTTTAAAAACGATA
Found at i:10184802 original size:69 final size:68
Alignment explanation
Indices: 10184703--10184956 Score: 305
Period size: 69 Copynumber: 3.7 Consensus size: 68
10184693 TTTACAGTTA
* * **
10184703 GAGCTTTACTCTCG-TCAACTATGTTGGAGGTCGCGGTTCTTCACCTAAGAACAATGATTTTACA
1 GAGCTTTGCTCTCGCT-AACTATGTTGGAGGTCGCGGCTCTTCACCTAAGAACCTTGATTTTACA
10184767 ACTG
65 ACTG
* * *
10184771 GAAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCGGCTCTTCACCTGTA-AACCTTGATTTTAC
1 G-AGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCACCT-AAGAACCTTGATTTTAC
10184835 AACTAG
64 AACT-G
* * * ** * *
10184841 GAGCTTTGCTCTTGCTAACTATGTTGGAGGTTGCGGCTCTTCGCCTGTGAACCTTGATTTTATAG
1 GAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCACCTAAGAACCTTGATTTTACAA
10184906 CTGG
66 CT-G
* *
10184910 GAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCGCCTA
1 GAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCACCTA
10184957 TTTTACAGCT
Statistics
Matches: 162, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
68 1 0.01
69 157 0.97
70 4 0.02
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (68 bp):
GAGCTTTGCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCACCTAAGAACCTTGATTTTACAA
CTG
Found at i:10185009 original size:59 final size:59
Alignment explanation
Indices: 10184897--10185015 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 59
10184887 GTGAACCTTG
* * ** *
10184897 ATTTTATAGCTGGGAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCGGCTCTTCGCCT
1 ATTTTACAGCTGAGAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCAACTCTTCACCT
* * * *
10184956 ATTTTACAGCTGAGAGTTTTTCTCTTGTTAACTATGTTGGAGGTCGCAACTCTTCACCT
1 ATTTTACAGCTGAGAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCAACTCTTCACCT
10185015 A
1 A
10185016 CAAATCTTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38
Consensus pattern (59 bp):
ATTTTACAGCTGAGAGCTTTCCTCTCGCTAACTATGTTGGAGGTCGCAACTCTTCACCT
Found at i:10185070 original size:69 final size:69
Alignment explanation
Indices: 10184987--10185168 Score: 211
Period size: 69 Copynumber: 2.6 Consensus size: 69
10184977 CTCTTGTTAA
* * ** * * *
10184987 CTATGTTGGAGGTCGCAACTCTTCACCTACAAATCTTAATTTTATAGTTGGGAGCTTTGTTTTTG
1 CTATGTTGGAGGTCGCAACTCTTCACCTACAAACCTTGATTTTATAACTGGGAGCTTTGCTCTAG
10185052 CTAG
66 CTAG
* * * * * *
10185056 CTGTGTTGGAGGTCGTAGCTATTCACCTGCTAACCTTGATTTTATAACTGGGAGCTTTGCTCTAG
1 CTATGTTGGAGGTCGCAACTCTTCACCTACAAACCTTGATTTTATAACTGGGAGCTTTGCTCTAG
10185121 CTAG
66 CTAG
* * * *
10185125 CTATGTTGGAGGTCACGATTCTTCACCTACGAACCTTGATTTTA
1 CTATGTTGGAGGTCGCAACTCTTCACCTACAAACCTTGATTTTA
10185169 CAAATGATAG
Statistics
Matches: 91, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 91 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (69 bp):
CTATGTTGGAGGTCGCAACTCTTCACCTACAAACCTTGATTTTATAACTGGGAGCTTTGCTCTAG
CTAG
Found at i:10197750 original size:18 final size:17
Alignment explanation
Indices: 10197716--10197754 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
10197706 TTAAGTGAAA
**
10197716 AACTAGAAACAGGGTTT
1 AACTAGAAACAAAGTTT
10197733 AACTAGAAAACAAAGTTT
1 AACTAG-AAACAAAGTTT
10197751 AACT
1 AACT
10197755 GGTAGAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (17 bp):
AACTAGAAACAAAGTTT
Found at i:10203790 original size:20 final size:22
Alignment explanation
Indices: 10203754--10203794 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
10203744 AATGGTTTTA
10203754 ATAAAATAAATTTAAATAATAT
1 ATAAAATAAATTTAAATAATAT
10203776 ATAAAA-AAA-TTAAATAATA
1 ATAAAATAAATTTAAATAATA
10203795 ATGAAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATAAAATAAATTTAAATAATAT
Found at i:10206793 original size:2 final size:2
Alignment explanation
Indices: 10206786--10206814 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10206776 AAGCTGCTTC
10206786 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
10206815 CCTTTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:10219069 original size:2 final size:2
Alignment explanation
Indices: 10219062--10219087 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10219052 TTATGCATGC
10219062 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
10219088 GAGTTGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10226664 original size:33 final size:33
Alignment explanation
Indices: 10226619--10226689 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
10226609 GCTAATGTAC
* * * * *
10226619 TCCAATGTATCTAATTTATATTACAAATTTTGT
1 TCCAATGAATCTAATTTAAATTAAAAAGTTGGT
10226652 TCCAATGAATCTAATTTAAATTAAAAAGTTGGT
1 TCCAATGAATCTAATTTAAATTAAAAAGTTGGT
10226685 TCCAA
1 TCCAA
10226690 GTTTGTTACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (33 bp):
TCCAATGAATCTAATTTAAATTAAAAAGTTGGT
Found at i:10226710 original size:44 final size:44
Alignment explanation
Indices: 10226647--10226756 Score: 175
Period size: 44 Copynumber: 2.5 Consensus size: 44
10226637 TATTACAAAT
*
10226647 TTTGTTCCAATGAATCTAATTTAAATTAAAAAGTTGGTTCCAAG
1 TTTGTTACAATGAATCTAATTTAAATTAAAAAGTTGGTTCCAAG
* *
10226691 TTTGTTACAATGAATCTAATTTAAATTACATAGTTGGTTCCAAG
1 TTTGTTACAATGAATCTAATTTAAATTAAAAAGTTGGTTCCAAG
* *
10226735 TTTGGTGCAATGAATCTAATTT
1 TTTGTTACAATGAATCTAATTT
10226757 CTGCATGTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.41
Consensus pattern (44 bp):
TTTGTTACAATGAATCTAATTTAAATTAAAAAGTTGGTTCCAAG
Found at i:10232811 original size:14 final size:14
Alignment explanation
Indices: 10232775--10232813 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
10232765 GCTTAATAAA
10232775 TTATGACATATGCT
1 TTATGACATATGCT
* * *
10232789 TAATAACATATGGT
1 TTATGACATATGCT
10232803 TTATGACATAT
1 TTATGACATAT
10232814 AAACTAATGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (14 bp):
TTATGACATATGCT
Found at i:10233030 original size:16 final size:16
Alignment explanation
Indices: 10233002--10233034 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10232992 ATAAAGTAGA
10233002 TTATATATATATATAT
1 TTATATATATATATAT
10233018 TTATAGTAT-TATATAT
1 TTATA-TATATATATAT
10233034 T
1 T
10233035 ATGATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATATATATATATAT
Found at i:10233033 original size:22 final size:21
Alignment explanation
Indices: 10233005--10233046 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
10232995 AAGTAGATTA
10233005 TATATATATAT-ATTTATAGTAT
1 TATATAT-TATGATTT-TAGTAT
10233027 TATATATTATGATTTTAGTA
1 TATATATTATGATTTTAGTA
10233047 AATTCATATA
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:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (21 bp):
TATATATTATGATTTTAGTAT
Found at i:10233099 original size:20 final size:21
Alignment explanation
Indices: 10233062--10233111 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
10233052 ATATAATAAT
10233062 AATTATATTAATAATTTTATTA
1 AATTATA-TAATAATTTTATTA
10233084 AATTATATAA-AATTTTATTA
1 AATTATATAATAATTTTATTA
10233104 AATTATAT
1 AATTATAT
10233112 TTAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 18 0.64
21 3 0.11
22 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTATATAATAATTTTATTA
Found at i:10233112 original size:10 final size:10
Alignment explanation
Indices: 10233062--10233112 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
10233052 ATATAATAAT
10233062 AATTATATTAA
1 AATTATATT-A
*
10233073 TAATTTTATTA
1 -AATTATATTA
*
10233084 AATTATATAA
1 AATTATATTA
*
10233094 AATTTTATTA
1 AATTATATTA
10233104 AATTATATT
1 AATTATATT
10233113 TAATAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATTATATTA
Found at i:10233371 original size:45 final size:44
Alignment explanation
Indices: 10233282--10233374 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
10233272 ATTACAACAT
*
10233282 CATTCCATTCAACCAAACACAAGAATACTATTACAACTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAACTCCATTC
* *
10233326 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGCTCCATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAACTCCATTC
10233371 CATT
1 CATT
10233375 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 21 0.48
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.30
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAACTCCATTC
Found at i:10233377 original size:16 final size:16
Alignment explanation
Indices: 10233356--10233394 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
10233346 TTGAATTACT
10233356 ATTACAGCTCCATTCC
1 ATTACAGCTCCATTCC
*
10233372 ATTACAGCTCTATTCC
1 ATTACAGCTCCATTCC
10233388 ATTACAG
1 ATTACAG
10233395 TGAACCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (16 bp):
ATTACAGCTCCATTCC
Found at i:10237206 original size:7 final size:7
Alignment explanation
Indices: 10237194--10237226 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
10237184 AATAAAGTAG
10237194 ATTATAT
1 ATTATAT
10237201 ATTATAT
1 ATTATAT
10237208 A-TATATT
1 ATTATA-T
10237215 ATTATAT
1 ATTATAT
10237222 ATTAT
1 ATTAT
10237227 GATTTTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 4 0.17
7 16 0.67
8 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTATAT
Found at i:10243524 original size:40 final size:40
Alignment explanation
Indices: 10243459--10243559 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 40
10243449 TGACTCAGAA
* *
10243459 CACCGGCATGAAGCCTGCTAGACATTAAGTCT-ATAAAGTT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGA-AAAATT
* *
10243499 CACCAGCATTAAGCCTACTAGACATTAAGTCTGAAAAATT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAATT
10243539 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
10243560 GCACAGAACC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 53 0.98
41 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAAAAATT
Found at i:10246515 original size:33 final size:33
Alignment explanation
Indices: 10246473--10246539 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
10246463 TTTATGTTCT
10246473 CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
1 CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
10246506 CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
1 CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
10246539 C
1 C
10246540 CTCAAATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (33 bp):
CTTGTAGTTTCGTTTGACACTTAGTCAAATTGG
Found at i:10249752 original size:21 final size:21
Alignment explanation
Indices: 10249728--10249770 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
10249718 AGAAAATAAG
10249728 TAAGATCATAAATTCATTCAT
1 TAAGATCATAAATTCATTCAT
10249749 TAAGATCATAAATTCATTCAT
1 TAAGATCATAAATTCATTCAT
10249770 T
1 T
10249771 CATATATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (21 bp):
TAAGATCATAAATTCATTCAT
Found at i:10249779 original size:16 final size:16
Alignment explanation
Indices: 10249754--10249787 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10249744 TTCATTAAGA
*
10249754 TCATAAATTCATTCAT
1 TCATAAATTCAATCAT
*
10249770 TCATATATTCAATCAT
1 TCATAAATTCAATCAT
10249786 TC
1 TC
10249788 TAATCATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (16 bp):
TCATAAATTCAATCAT
Found at i:10249972 original size:28 final size:29
Alignment explanation
Indices: 10249910--10249993 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
10249900 TTTGAAGAAG
* *
10249910 AGTGGCAAAACTATAAAATTTAGAAAACA
1 AGTGGCAAAACTGTAAAATCTAGAAAACA
10249939 AGTGGCAAAACTGTAAAATCT-GAAAA-A
1 AGTGGCAAAACTGTAAAATCTAGAAAACA
* * *
10249966 TAGTGGCAGAATTGTAAAATCTATAAAA
1 -AGTGGCAAAACTGTAAAATCTAGAAAA
10249994 TGATGGTACA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.02
28 24 0.50
29 23 0.48
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.23
Consensus pattern (29 bp):
AGTGGCAAAACTGTAAAATCTAGAAAACA
Found at i:10250446 original size:33 final size:32
Alignment explanation
Indices: 10250382--10250452 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
10250372 ATAAGAAAGA
*
10250382 TAAATTCTATTAGGATTTGAAAAGGAGTAATT
1 TAAATTCTATTAAGATTTGAAAAGGAGTAATT
* * *
10250414 TAAATTCTAGTTAAGATTTTAATAGGATTAATT
1 TAAATTCTA-TTAAGATTTGAAAAGGAGTAATT
10250447 TGAAAT
1 T-AAAT
10250453 AAATTAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 9 0.27
33 20 0.61
34 4 0.12
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (32 bp):
TAAATTCTATTAAGATTTGAAAAGGAGTAATT
Found at i:10256981 original size:7 final size:7
Alignment explanation
Indices: 10256965--10256997 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
10256955 TTTCAATTTC
*
10256965 ATATTAA
1 ATATTGA
10256972 ATATTGA
1 ATATTGA
10256979 ATATTGA
1 ATATTGA
10256986 ATATTGA
1 ATATTGA
10256993 ATATT
1 ATATT
10256998 TCAATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (7 bp):
ATATTGA
Found at i:10257492 original size:22 final size:20
Alignment explanation
Indices: 10257455--10257498 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
10257445 TTGTATGGCT
*
10257455 TTCTTTTTTTTGTTTTCTTA
1 TTCTTTTTTTTGTTTTATTA
*
10257475 TTCTTTATTTTTATTTTTATTA
1 TTCTTT-TTTTT-GTTTTATTA
10257497 TT
1 TT
10257499 TTGTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (20 bp):
TTCTTTTTTTTGTTTTATTA
Found at i:10263303 original size:23 final size:22
Alignment explanation
Indices: 10263260--10263303 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
10263250 TTCTAAGTCG
10263260 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
10263283 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
10263304 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:10263412 original size:45 final size:45
Alignment explanation
Indices: 10263348--10263434 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
10263338 AACAGATACT
* *
10263348 CGGTGGATTCAGCACATAGCAACCACCTAATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTAACTAATCAATGATGTC
* *
10263393 CGGTGGAATCAGCACATAGCAACCACCTTACTAATGAATGAT
1 CGGTGGAATCAGCACATAGCAACCACCTAACTAATCAATGAT
10263435 TTTCGGTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTAACTAATCAATGATGTC
Found at i:10276659 original size:13 final size:13
Alignment explanation
Indices: 10276626--10276663 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
10276616 TTTTGTATGG
10276626 CTTTCTTTCTT-TT
1 CTTTCTTT-TTATT
10276639 CTTT-TTTTTATT
1 CTTTCTTTTTATT
10276651 CTTTCTTTTTATT
1 CTTTCTTTTTATT
10276664 ATACTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 9 0.39
13 12 0.52
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTCTTTTTATT
Found at i:10282194 original size:43 final size:43
Alignment explanation
Indices: 10282133--10282323 Score: 247
Period size: 43 Copynumber: 4.4 Consensus size: 43
10282123 TGTCCTAGAC
** **
10282133 ATGGTCTTACATGGAAATCTCGTATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CAAAATCTCAAATCGATGCCAATAGCCCAGCT
* *
10282177 ATAGTCTTACACAAAATCTCAAATCGATGTCAATAGCCCAGCT
1 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
* * * * * *
10282220 ACGGTCTCACACGAAATCTTAAATCGATGCCAATAACCCAACT
1 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
* *
10282263 ATGGTCTTACACGAAATCTCAAATCGATGCCAATATCCCAGCT
1 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
10282306 ATGGTCTTACACAAAATC
1 ATGGTCTTACACAAAATC
10282324 ACACCTCAGA
Statistics
Matches: 127, Mismatches: 20, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
43 117 0.92
44 10 0.08
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (43 bp):
ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:10282510 original size:31 final size:30
Alignment explanation
Indices: 10282441--10282525 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
10282431 ATCCAATGCT
* * *
10282441 CAAACCAATTCGGCAATATATATATCCATATA
1 CAAATCAATTCGGC-A-ATGTATATCCACATA
* * *
10282473 CGAATCAAATTCGGTAATGTATATCTACATA
1 CAAATC-AATTCGGCAATGTATATCCACATA
10282504 CAAATCAATTCGGCAATGTATA
1 CAAATCAATTCGGCAATGTATA
10282526 AAACATATAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
30 15 0.34
31 17 0.39
32 5 0.11
33 7 0.16
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (30 bp):
CAAATCAATTCGGCAATGTATATCCACATA
Found at i:10282536 original size:31 final size:31
Alignment explanation
Indices: 10282441--10282536 Score: 79
Period size: 30 Copynumber: 3.1 Consensus size: 31
10282431 ATCCAATGCT
* * **
10282441 CAAACCAATTCGGCAATATATATATCCATATA
1 CAAATCAATTCGGCAATGTATA-AAACATATA
* * * *
10282473 CGAATCAAATTCGGTAATGTAT--ATCTACATA
1 CAAATC-AATTCGGCAATGTATAAAAC-ATATA
10282504 CAAATCAATTCGGCAATGTATAAAACATATA
1 CAAATCAATTCGGCAATGTATAAAACATATA
10282535 CA
1 CA
10282537 TTTAAATTCA
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
30 15 0.31
31 15 0.31
32 6 0.12
33 13 0.27
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (31 bp):
CAAATCAATTCGGCAATGTATAAAACATATA
Found at i:10284019 original size:31 final size:31
Alignment explanation
Indices: 10283984--10284047 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
10283974 ACAAACATTA
10283984 CAAATTTCAATAATGCCAAGCCATCATATTC
1 CAAATTTCAATAATGCCAAGCCATCATATTC
*
10284015 CAAATTTCAATAATGTCAAGCCATCATATTC
1 CAAATTTCAATAATGCCAAGCCATCATATTC
10284046 CA
1 CA
10284048 CTATCAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.30
Consensus pattern (31 bp):
CAAATTTCAATAATGCCAAGCCATCATATTC
Found at i:10288139 original size:107 final size:107
Alignment explanation
Indices: 10288027--10288230 Score: 345
Period size: 107 Copynumber: 1.9 Consensus size: 107
10288017 GTTGAGGGTT
** *
10288027 AAATTTATTAACTTTTTAAAAATTAATACAAAATTGTAGAATGTATAAACATTGGAATCCATTAT
1 AAATTTATTAACTTTTTAAAAATTAATACAAAATTGTAGAATGTATAAACATTAAAAGCCATTAT
10288092 ACCAATCAAAAAGTAGTATAAATTAATGAAAATGTCGACATC
66 ACCAATCAAAAAGTAGTATAAATTAATGAAAATGTCGACATC
* *
10288134 AAATTTATTAATTTTTTAAAAATTAATACAAAATTTTAGAATGTATAAACATTAAAAGCCATTAT
1 AAATTTATTAACTTTTTAAAAATTAATACAAAATTGTAGAATGTATAAACATTAAAAGCCATTAT
* *
10288199 ATCAATCAAAAATTAGTATAAATTAATGAAAA
66 ACCAATCAAAAAGTAGTATAAATTAATGAAAA
10288231 AAGTGAAGAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 90 1.00
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.34
Consensus pattern (107 bp):
AAATTTATTAACTTTTTAAAAATTAATACAAAATTGTAGAATGTATAAACATTAAAAGCCATTAT
ACCAATCAAAAAGTAGTATAAATTAATGAAAATGTCGACATC
Found at i:10290627 original size:12 final size:12
Alignment explanation
Indices: 10290610--10290634 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10290600 TCTAGGTTGG
10290610 AGGTATAAGGTT
1 AGGTATAAGGTT
10290622 AGGTATAAGGTT
1 AGGTATAAGGTT
10290634 A
1 A
10290635 ATGAAGCACT
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:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (12 bp):
AGGTATAAGGTT
Found at i:10298752 original size:20 final size:19
Alignment explanation
Indices: 10298723--10298764 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
10298713 TTTTCCAATT
10298723 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
10298742 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
10298762 TTT
1 TTT
10298765 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:10304354 original size:15 final size:15
Alignment explanation
Indices: 10304334--10304366 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10304324 TAATTCGAAT
10304334 ATACGATTGGTGTAA
1 ATACGATTGGTGTAA
*
10304349 ATACGATTGTTGTAA
1 ATACGATTGGTGTAA
10304364 ATA
1 ATA
10304367 TCCTTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (15 bp):
ATACGATTGGTGTAA
Found at i:10304509 original size:18 final size:18
Alignment explanation
Indices: 10304448--10304509 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
10304438 TTTATATCTC
10304448 AAAAAATTATAAAAAGCTTCT
1 AAAAAA-TATAAAAA-C-TCT
* *
10304469 AAATAATATATAAAAAATTT
1 AAA-AA-ATATAAAAACTCT
*
10304489 AAAAAGTATAAAAACTCT
1 AAAAAATATAAAAACTCT
10304507 AAA
1 AAA
10304510 CTCTTAACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 13 0.38
19 2 0.06
20 5 0.15
21 3 0.09
22 10 0.29
23 1 0.03
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAAAATATAAAAACTCT
Found at i:10306075 original size:17 final size:16
Alignment explanation
Indices: 10306053--10306127 Score: 62
Period size: 17 Copynumber: 4.5 Consensus size: 16
10306043 TTAATATGAC
10306053 TAAAAAATTTTAATAAA
1 TAAAAAATTTTAA-AAA
* *
10306070 TAAAAAATATATAAAAT
1 TAAAAAAT-TTTAAAAA
** *
10306087 TATTAAATATT-AAAA
1 TAAAAAATTTTAAAAA
10306102 TAAAAATATTTTAAAAAA
1 TAAAAA-ATTTT-AAAAA
10306120 TAAAAAAT
1 TAAAAAAT
10306128 AATACCGGTA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
15 7 0.16
16 5 0.11
17 18 0.41
18 14 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAAATTTTAAAAA
Found at i:10315713 original size:53 final size:53
Alignment explanation
Indices: 10315650--10315756 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
10315640 GGAAAGTAAG
* *
10315650 TCATTGTTATCTCTCAATTTTGAAACATTTTTCTTGTGTTTTGACATCATGAC
1 TCATTGTTATCTATCAATTTTGAAACATTTTTCTTATGTTTTGACATCATGAC
*
10315703 TCATTTTTATCTATCAATTTTGAAACATTTTTCTTATGTTTTGACATCATGAC
1 TCATTGTTATCTATCAATTTTGAAACATTTTTCTTATGTTTTGACATCATGAC
10315756 T
1 T
10315757 TCAAATTCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.50
Consensus pattern (53 bp):
TCATTGTTATCTATCAATTTTGAAACATTTTTCTTATGTTTTGACATCATGAC
Found at i:10317706 original size:20 final size:19
Alignment explanation
Indices: 10317676--10317726 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
10317666 TTGGAGCAGG
* *
10317676 AATATCAATACCTTAGGAA
1 AATATCGATACCTTAAGAA
10317695 ATATATCGATACCTTAAGAA
1 A-ATATCGATACCTTAAGAA
10317715 AAGTATCGATAC
1 AA-TATCGATAC
10317727 TGGATTGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (19 bp):
AATATCGATACCTTAAGAA
Found at i:10319961 original size:20 final size:20
Alignment explanation
Indices: 10319936--10319974 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
10319926 ATAATAATAT
10319936 TTTATTAAATAAAAATAATC
1 TTTATTAAATAAAAATAATC
10319956 TTTATTAAATAAAAATAAT
1 TTTATTAAATAAAAATAAT
10319975 ATTATAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTATTAAATAAAAATAATC
Found at i:10325957 original size:20 final size:19
Alignment explanation
Indices: 10325928--10326003 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
10325918 ATTTTAAAAT
*
10325928 CAAGTGAAAATGATTTTAA
1 CAAGTCAAAATGATTTTAA
*
10325947 CCAAGTCAAAATGATTTCAA
1 -CAAGTCAAAATGATTTTAA
* *
10325967 TCAAGTTAAAATCATTTTAA
1 -CAAGTCAAAATGATTTTAA
10325987 CACA-TCAAAATGATTTT
1 CA-AGTCAAAATGATTTT
10326004 CAAATGAGTC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
19 13 0.28
20 34 0.72
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (19 bp):
CAAGTCAAAATGATTTTAA
Found at i:10326006 original size:40 final size:40
Alignment explanation
Indices: 10325925--10326002 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
10325915 ATAATTTTAA
*
10325925 AATCAAGTGAAAATGATTTTAACCAAGTCAAAATGATTTC
1 AATCAAGTGAAAATCATTTTAACCAAGTCAAAATGATTTC
*
10325965 AATCAAGTTAAAATCATTTTAA-CACA-TCAAAATGATTT
1 AATCAAGTGAAAATCATTTTAACCA-AGTCAAAATGATTT
10326003 TCAAATGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 14 0.40
40 21 0.60
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (40 bp):
AATCAAGTGAAAATCATTTTAACCAAGTCAAAATGATTTC
Found at i:10326880 original size:17 final size:18
Alignment explanation
Indices: 10326858--10326892 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10326848 CTCTAAATTC
10326858 TTTTTGTCATTG-TTTCA
1 TTTTTGTCATTGCTTTCA
*
10326875 TTTTTGTCTTTGCTTTCA
1 TTTTTGTCATTGCTTTCA
10326893 CCAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.09, C:0.14, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTTGTCATTGCTTTCA
Found at i:10333906 original size:23 final size:23
Alignment explanation
Indices: 10333874--10333923 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
10333864 GTTCATACGG
* *
10333874 CTACTGTAATATCCCAAAAATTA
1 CTACTATAATACCCCAAAAATTA
10333897 CTACTATAATACCCCAAAAATTA
1 CTACTATAATACCCCAAAAATTA
10333920 CTAC
1 CTAC
10333924 AGTAAGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (23 bp):
CTACTATAATACCCCAAAAATTA
Found at i:10345580 original size:13 final size:13
Alignment explanation
Indices: 10345542--10345580 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
10345532 CTATAGACTA
10345542 TTTAA-ATTTGGT
1 TTTAATATTTGGT
10345554 TTTAATATTT-GT
1 TTTAATATTTGGT
10345566 TTTAATATTTGGT
1 TTTAATATTTGGT
10345579 TT
1 TT
10345581 GGGCCCTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (13 bp):
TTTAATATTTGGT
Found at i:10346859 original size:43 final size:44
Alignment explanation
Indices: 10346768--10346868 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 44
10346758 ATGTGATTTC
* *
10346768 ATGTAAGACCATATCTAGGACATTGGCATCGAAGTGAGAGAACG
1 ATGTAAGACCATATCTAGGACAGTGGCATCGAAATGAGAGAACG
* * * **
10346812 -TGTAAGACCATGTCTGGGACAGTGGCATCGAAATGTGTTAA-G
1 ATGTAAGACCATATCTAGGACAGTGGCATCGAAATGAGAGAACG
10346854 ATGTAAGACCATATC
1 ATGTAAGACCATATC
10346869 CGGAATATGG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 47 0.98
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.24
Consensus pattern (44 bp):
ATGTAAGACCATATCTAGGACAGTGGCATCGAAATGAGAGAACG
Found at i:10350286 original size:52 final size:52
Alignment explanation
Indices: 10350208--10350311 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
10350198 TCATGCTCAA
*
10350208 TTAATCTCCGGTTTAGCTCAGTTATCATTCCCATCGAGAATCTTGAGAAATG
1 TTAATCTCCAGTTTAGCTCAGTTATCATTCCCATCGAGAATCTTGAGAAATG
* *
10350260 TTAATCTCCATTTTAGCTC-GATTATCATTCCGATCGAGAATCTTGAGAAATG
1 TTAATCTCCAGTTTAGCTCAG-TTATCATTCCCATCGAGAATCTTGAGAAATG
10350312 AACCCGTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 1 0.02
52 47 0.98
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (52 bp):
TTAATCTCCAGTTTAGCTCAGTTATCATTCCCATCGAGAATCTTGAGAAATG
Found at i:10351838 original size:22 final size:22
Alignment explanation
Indices: 10351813--10351952 Score: 84
Period size: 22 Copynumber: 6.3 Consensus size: 22
10351803 AAAAATGAAT
* *
10351813 AGCATTTAACCAACATTCGGAC
1 AGCATTTAAACAACATTCAGAC
*
10351835 AGCATTTAAATAACATTCAGAC
1 AGCATTTAAACAACATTCAGAC
* ** * ** * *
10351857 AACATTAGTATGCTAAAAAACAAAA
1 AGCATT--TAAAC-AACATTCAGAC
* * *
10351882 AACATTTAACCAACATTCGGAC
1 AGCATTTAAACAACATTCAGAC
* *
10351904 AGCATTTAACCAACATTCGGAC
1 AGCATTTAAACAACATTCAGAC
*
10351926 AGCATTT-AACAACATTCGGAC
1 AGCATTTAAACAACATTCAGAC
*
10351947 AACATT
1 AGCATT
10351953 AGTATGCTAA
Statistics
Matches: 92, Mismatches: 23, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
21 18 0.20
22 57 0.62
23 3 0.03
24 2 0.02
25 12 0.13
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.24
Consensus pattern (22 bp):
AGCATTTAAACAACATTCAGAC
Found at i:10351876 original size:69 final size:69
Alignment explanation
Indices: 10351785--10351931 Score: 204
Period size: 69 Copynumber: 2.1 Consensus size: 69
10351775 CACCAATTTG
** * * *
10351785 GACAACATTAAAATGCTAAAAAATGAATAGCATTTAACCAACATTCGGACAGCATTTAAATAACA
1 GACAACATTAAAATGCTAAAAAACAAAAAACATTTAACCAACATTCGGACAGCATTTAAACAACA
10351850 TTCA
66 TTCA
** *
10351854 GACAACATTAGTATGCTAAAAAACAAAAAACATTTAACCAACATTCGGACAGCATTTAACCAACA
1 GACAACATTAAAATGCTAAAAAACAAAAAACATTTAACCAACATTCGGACAGCATTTAAACAACA
*
10351919 TTCG
66 TTCA
*
10351923 GACAGCATT
1 GACAACATT
10351932 TAACAACATT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (69 bp):
GACAACATTAAAATGCTAAAAAACAAAAAACATTTAACCAACATTCGGACAGCATTTAAACAACA
TTCA
Found at i:10352005 original size:11 final size:11
Alignment explanation
Indices: 10351991--10352028 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
10351981 AGCATTTAAC
10351991 CAACATTCAGA
1 CAACATTCAGA
* *
10352002 CAACATTTAAA
1 CAACATTCAGA
10352013 CAACATTCAGA
1 CAACATTCAGA
10352024 CAACA
1 CAACA
10352029 CCTTGTCATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.50, C:0.26, G:0.05, T:0.18
Consensus pattern (11 bp):
CAACATTCAGA
Found at i:10352008 original size:22 final size:22
Alignment explanation
Indices: 10351978--10352028 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
10351968 GAAATACTCG
* *
10351978 GACAGCATTTAACCAACATTCA
1 GACAACATTTAAACAACATTCA
10352000 GACAACATTTAAACAACATTCA
1 GACAACATTTAAACAACATTCA
10352022 GACAACA
1 GACAACA
10352029 CCTTGTCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.25, G:0.08, T:0.20
Consensus pattern (22 bp):
GACAACATTTAAACAACATTCA
Found at i:10359593 original size:22 final size:22
Alignment explanation
Indices: 10359568--10359870 Score: 216
Period size: 22 Copynumber: 13.4 Consensus size: 22
10359558 GTTAAAACAT
10359568 GAACAGCATTTAACCAACATTC
1 GAACAGCATTTAACCAACATTC
10359590 GAACAGCATTTAACCAACATTC
1 GAACAGCATTTAACCAACATTC
* **
10359612 GGACAGCATTTAAAAAACATTC
1 GAACAGCATTTAACCAACATTC
* * * * **
10359634 GAACAACATTAGTATGCTAAAAAAC
1 GAACAGCATT--TA-ACCAACATTC
*
10359659 GAATAGCATTTAACCAACATTC
1 GAACAGCATTTAACCAACATTC
* * * *
10359681 GGACAACATTTAAACAAAATTC
1 GAACAGCATTTAACCAACATTC
* * * **
10359703 -AGACAGCATTAGTATGCTAAAAAAC
1 GA-ACAGCATT--TA-ACCAACATTC
10359728 GAACAGCATTTAACCAACATTC
1 GAACAGCATTTAACCAACATTC
*
10359750 GAACAACATTTAACCAACATTC
1 GAACAGCATTTAACCAACATTC
* * * *
10359772 GGACAACATTAGTATGATACAA-AAT-
1 GAACAGCATT--TA--A-CCAACATTC
10359797 GAACAGCATTTAACCAACATTC
1 GAACAGCATTTAACCAACATTC
*
10359819 GAACAGCATTTAACCAACATTT
1 GAACAGCATTTAACCAACATTC
* * *
10359841 GGATAGCATTTAAACAACATTC
1 GAACAGCATTTAACCAACATTC
*
10359863 GAATAGCA
1 GAACAGCA
10359871 CCCTGTCATC
Statistics
Matches: 217, Mismatches: 49, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
20 3 0.01
21 3 0.01
22 159 0.73
23 6 0.03
24 6 0.03
25 33 0.15
26 4 0.02
27 3 0.01
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (22 bp):
GAACAGCATTTAACCAACATTC
Done.