Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 10 of 18
Found at i:1634549 original size:18 final size:19
Alignment explanation
Indices: 1634509--1634555 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1634499 ATATGAGTAT
*
1634509 ATTTA-ATTTTTTAAAATT
1 ATTTATATTTTTTAAAATA
*
1634527 TTTTATATTTTTTAAAA-A
1 ATTTATATTTTTTAAAATA
1634545 ATTTATATTTT
1 ATTTATATTTT
1634556 ATATTCATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTATATTTTTTAAAATA
Found at i:1637096 original size:38 final size:38
Alignment explanation
Indices: 1637050--1637165 Score: 225
Period size: 38 Copynumber: 3.1 Consensus size: 38
1637040 AGTCTGAAGT
1637050 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAAA
1 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAAA
1637088 AAAAAGCTCCCAGGTACTATTAATCTATACGATT-AAA
1 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAAA
1637125 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAAA
1 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAAA
1637163 AAA
1 AAA
1637166 CCTAAGTGGC
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
37 37 0.48
38 40 0.52
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (38 bp):
AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAAA
Found at i:1637126 original size:37 final size:37
Alignment explanation
Indices: 1637050--1637165 Score: 223
Period size: 37 Copynumber: 3.1 Consensus size: 37
1637040 AGTCTGAAGT
1637050 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAAA
1 AAAAAGCTCCCAGGTACTATTAATCTATACGATT-AAA
1637088 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAA
1 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAA
1637125 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAA
1 AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAA
1637162 AAAA
1 AAAA
1637166 CCTAAGTGGC
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
37 44 0.56
38 34 0.44
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (37 bp):
AAAAAGCTCCCAGGTACTATTAATCTATACGATTAAA
Found at i:1639487 original size:3 final size:3
Alignment explanation
Indices: 1639479--1639511 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1639469 GTTTTTCTTT
*
1639479 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1639512 GAGATTCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1642777 original size:30 final size:32
Alignment explanation
Indices: 1642723--1642783 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1642713 TACTATTTGG
1642723 CAAAAAGTAATTTATTCCTTTT-AAATTTTTA
1 CAAAAAGTAATTTATTCCTTTTAAAATTTTTA
*
1642754 CAAAAA-TATATTTATT-TTTTTAAAATTTTT
1 CAAAAAGTA-ATTTATTCCTTTTAAAATTTTT
1642784 TAATAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (32 bp):
CAAAAAGTAATTTATTCCTTTTAAAATTTTTA
Found at i:1642869 original size:19 final size:18
Alignment explanation
Indices: 1642843--1642897 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
1642833 TAAAAAATAA
1642843 ATTTATTTTTATTAATTATT
1 ATTTA-TTTT-TTAATTATT
*
1642863 A-TTATTTTTTAATTGTT
1 ATTTATTTTTTAATTATT
1642880 ATTTAATTTTTTAATTAT
1 ATTT-ATTTTTTAATTAT
1642898 AAAATAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 9 0.29
18 6 0.19
19 15 0.48
20 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTATTTTTTAATTATT
Found at i:1643318 original size:24 final size:24
Alignment explanation
Indices: 1643285--1643346 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
1643275 TGATTTATTT
1643285 TTAAAT-AAAAATAAC-TA-ATACA
1 TTAAATCAAAAATAACATATATA-A
*
1643307 TTAATATCAAAATTAACATATATAA
1 TTAA-ATCAAAAATAACATATATAA
*
1643332 TTAAATTAAAAATAA
1 TTAAATCAAAAATAA
1643347 ATTTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 4 0.12
23 2 0.06
24 17 0.52
25 7 0.21
26 3 0.09
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (24 bp):
TTAAATCAAAAATAACATATATAA
Found at i:1644874 original size:3 final size:3
Alignment explanation
Indices: 1644863--1644896 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1644853 AACTCTTCTT
*
1644863 TCA TAA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1644897 AATAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1644901 original size:3 final size:3
Alignment explanation
Indices: 1644895--1644932 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1644885 CATCATCATC
1644895 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1644933 TTATTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1645130 original size:21 final size:23
Alignment explanation
Indices: 1645093--1645143 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
1645083 AATTATATTT
*
1645093 AAATATGAATCATATATAAAA-A
1 AAATATGAATCAAATATAAAATA
1645115 AAATATGAAT-AAATATAAAATA
1 AAATATGAATCAAATATAAAATA
1645137 AACATAT
1 AA-ATAT
1645144 TTATCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (23 bp):
AAATATGAATCAAATATAAAATA
Found at i:1646530 original size:37 final size:37
Alignment explanation
Indices: 1646484--1646571 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
1646474 TATTTTTTTA
* *
1646484 TATATTTAAAAA-AAATTAAAAATTATATCTTTATATT
1 TATATTTAAAAATAAATTAAAAA-TAGATATTTATATT
* * *
1646521 TATATTTAAAAATATATTTAATATAGATATTTATATT
1 TATATTTAAAAATAAATTAAAAATAGATATTTATATT
*
1646558 CATATTTAAAAATA
1 TATATTTAAAAATA
1646572 TGTTTGATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
37 37 0.84
38 7 0.16
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (37 bp):
TATATTTAAAAATAAATTAAAAATAGATATTTATATT
Found at i:1646550 original size:25 final size:27
Alignment explanation
Indices: 1646499--1646553 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
1646489 TTAAAAAAAA
* **
1646499 TTAAAAATTATATCTTTATATTTATAT
1 TTAAAAATTATATCTTAATATAGATAT
1646526 TTAAAAA-TATAT-TTAATATAGATAT
1 TTAAAAATTATATCTTAATATAGATAT
1646551 TTA
1 TTA
1646554 TATTCATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.52
26 5 0.20
27 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAAAAATTATATCTTAATATAGATAT
Found at i:1646572 original size:37 final size:37
Alignment explanation
Indices: 1646513--1646588 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
1646503 AAATTATATC
* *
1646513 TTTATATTTATATTTAAAAATATATTTAATATAGATA
1 TTTATATTCATATTTAAAAATATATTTAATATAAATA
* *
1646550 TTTATATTCATATTTAAAAATATGTTTGATATAAATA
1 TTTATATTCATATTTAAAAATATATTTAATATAAATA
1646587 TT
1 TT
1646589 AGACGTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (37 bp):
TTTATATTCATATTTAAAAATATATTTAATATAAATA
Found at i:1654001 original size:2 final size:2
Alignment explanation
Indices: 1653994--1654018 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1653984 AAAATCATTT
1653994 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1654019 TGAATGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1654278 original size:2 final size:2
Alignment explanation
Indices: 1654271--1654315 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1654261 TCCCTATTCA
1654271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1654313 AT A
1 AT A
1654316 ATGGTTCAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1655157 original size:19 final size:20
Alignment explanation
Indices: 1655089--1655158 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
1655079 TTAATAATAT
*
1655089 TATATACAATATATAAA-AAA
1 TATATATAATAT-TAAATAAA
1655109 TA-ATATGAATATTAAATAAA
1 TATATAT-AATATTAAATAAA
*
1655129 TATATA-AATATTATA-AAA
1 TATATATAATATTAAATAAA
*
1655147 TTTATATAATAT
1 TATATATAATAT
1655159 AATTTATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
18 8 0.19
19 20 0.47
20 12 0.28
21 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (20 bp):
TATATATAATATTAAATAAA
Found at i:1655406 original size:2 final size:2
Alignment explanation
Indices: 1655399--1655426 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1655389 GATTTCATTC
1655399 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1655427 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1655431 original size:2 final size:2
Alignment explanation
Indices: 1655426--1655454 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1655416 TCTCTCTCTC
1655426 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1655455 CGCTTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1657789 original size:2 final size:2
Alignment explanation
Indices: 1657782--1657815 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1657772 ATCAGGTGTG
1657782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1657816 GTATTATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1658602 original size:42 final size:42
Alignment explanation
Indices: 1658556--1658635 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
1658546 AAAAACATTT
* *
1658556 TTTTACTGCCGCTGAACAAAAGTATTATGAACACATGACTTC
1 TTTTACTGCCACTGAACAAAAATATTATGAACACATGACTTC
* * *
1658598 TTTTACTGCCATTGAACAAAAATATTTTGACCACATGA
1 TTTTACTGCCACTGAACAAAAATATTATGAACACATGA
1658636 TTTCCTATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (42 bp):
TTTTACTGCCACTGAACAAAAATATTATGAACACATGACTTC
Found at i:1666863 original size:20 final size:21
Alignment explanation
Indices: 1666840--1666880 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1666830 AAATTATCCA
1666840 TGCATAAAT-TAAATTAATTT
1 TGCATAAATATAAATTAATTT
* *
1666860 TGCATTAATATAACTTAATTT
1 TGCATAAATATAAATTAATTT
1666881 ATCTTCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (21 bp):
TGCATAAATATAAATTAATTT
Found at i:1667605 original size:19 final size:19
Alignment explanation
Indices: 1667581--1667770 Score: 73
Period size: 19 Copynumber: 10.2 Consensus size: 19
1667571 GCAAAAAATT
1667581 TAAAATATAATATAATATA
1 TAAAATATAATATAATATA
1667600 T-AAA-ATAATATAA-ATA
1 TAAAATATAATATAATATA
** *
1667616 TATAAATATTTTAAAAT-TAA
1 TA-AAATATAATATAATAT-A
*
1667636 TATAATATACATTATTAATATA
1 TAAAATATA-A-TA-TAATATA
* *
1667658 -AAAA-ATTATTTAATATA
1 TAAAATATAATATAATATA
* *
1667675 AAATAATTTAA-AT-ATAT-
1 TAA-AATATAATATAATATA
** *
1667692 TATTACATAATCA-AATATA
1 TAAAATATAAT-ATAATATA
1667711 T-AAATATAATATAA-ATA
1 TAAAATATAATATAATATA
* *
1667728 TATAAACATAATAAAATATA
1 TA-AAATATAATATAATATA
* *
1667748 T-AAATAAAACATAAATATA
1 TAAAATATAATAT-AATATA
1667767 TAAA
1 TAAA
1667771 TTATTAATTT
Statistics
Matches: 122, Mismatches: 27, Indels: 43
0.64 0.14 0.22
Matches are distributed among these distances:
16 8 0.07
17 22 0.18
18 33 0.27
19 36 0.30
20 13 0.11
21 5 0.04
22 4 0.03
23 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAATATAATATAATATA
Found at i:1667609 original size:22 final size:24
Alignment explanation
Indices: 1667584--1667644 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
1667574 AAAAATTTAA
1667584 AATATAATATAATA-TATAAAA-T
1 AATATAATATAATATTATAAAATT
*
1667606 AATATAAATATATAAATATTTTAAAATT
1 AATAT--A-ATAT-AATATTATAAAATT
1667634 AATATAATATA
1 AATATAATATA
1667645 CATTATTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
22 5 0.16
24 2 0.06
25 8 0.25
26 5 0.16
27 6 0.19
28 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATATAATATAATATTATAAAATT
Found at i:1667615 original size:28 final size:28
Alignment explanation
Indices: 1667583--1667770 Score: 110
Period size: 28 Copynumber: 6.8 Consensus size: 28
1667573 AAAAAATTTA
1667583 AAATATAATATAATATATAAAATAATAT
1 AAATATAATATAATATATAAAATAATAT
*
1667611 AAATAT-ATA-AATATTTTAAAATTAATAT
1 AAATATAATATAATA-TATAAAA-TAATAT
* *
1667639 -AATATACATTATTAATATAAAAAATTAT-T
1 AAATATA-A-TA-TAATATATAAAATAATAT
* * *
1667668 TAATATAAAATAAT-T-TAAATATATTAT
1 AAATATAATATAATATATAAA-ATAATAT
* *
1667695 -TACATAATCA-AATATATAAATATAATAT
1 AAATATAAT-ATAATATATAAA-ATAATAT
*
1667723 AAATAT-ATA-AACATAATAAAAT-ATAT
1 AAATATAATATAATAT-ATAAAATAATAT
* *
1667749 AAATAAAACATAAATATATAAA
1 AAATATAATAT-AATATATAAA
1667771 TTATTAATTT
Statistics
Matches: 124, Mismatches: 18, Indels: 36
0.70 0.10 0.20
Matches are distributed among these distances:
25 3 0.02
26 25 0.20
27 30 0.24
28 36 0.29
29 10 0.08
30 11 0.09
31 5 0.04
32 4 0.03
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (28 bp):
AAATATAATATAATATATAAAATAATAT
Found at i:1667723 original size:13 final size:13
Alignment explanation
Indices: 1667705--1667766 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
1667695 TACATAATCA
1667705 AATATATAAATAT
1 AATATATAAATAT
1667718 AATATA-AATATAT
1 AATATATAA-ATAT
* *
1667731 AA-ACAT-AATAA
1 AATATATAAATAT
1667742 AATATATAAATA-
1 AATATATAAATAT
*
1667754 AA-ACATAAATAT
1 AATATATAAATAT
1667766 A
1 A
1667767 TAAATTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
11 13 0.32
12 11 0.28
13 16 0.40
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
AATATATAAATAT
Found at i:1667737 original size:37 final size:37
Alignment explanation
Indices: 1667587--1667770 Score: 146
Period size: 37 Copynumber: 5.0 Consensus size: 37
1667577 AATTTAAAAT
* *
1667587 ATAATATAATATATAAA-ATAATATAAATATATAAAT
1 ATAATAAAATATATAAATATAATATAAATATATAAAC
** * *
1667623 ATTTTAAAAT-TAATATAATATACATTATTAATATA-AAAA
1 ATAATAAAATAT-ATA-AATATA-A-TATAAATATATAAAC
* ** * *
1667662 ATTAT-TTA-ATATAAA-ATAATTTAAATATATTATTAC
1 ATAATAAAATATATAAATATAATATAAATATA-TA-AAC
*
1667698 ATAATCAAATATATAAATATAATATAAATATATAAAC
1 ATAATAAAATATATAAATATAATATAAATATATAAAC
* *
1667735 ATAATAAAATATATAAATAAAACATAAATATATAAA
1 ATAATAAAATATATAAATATAATATAAATATATAAA
1667771 TTATTAATTT
Statistics
Matches: 116, Mismatches: 20, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
33 8 0.07
34 1 0.01
35 5 0.04
36 17 0.15
37 41 0.35
38 14 0.12
39 21 0.18
40 9 0.08
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (37 bp):
ATAATAAAATATATAAATATAATATAAATATATAAAC
Found at i:1667764 original size:24 final size:25
Alignment explanation
Indices: 1667710--1667764 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
1667700 AATCAAATAT
*
1667710 ATAAATATAATATAAATATATAAAC
1 ATAAATAAAATATAAATATATAAAC
1667735 AT-AATAAAATATATAA-ATA-AAAC
1 ATAAATAAAATATA-AATATATAAAC
1667758 ATAAATA
1 ATAAATA
1667765 TATAAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.22
24 17 0.63
25 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
ATAAATAAAATATAAATATATAAAC
Found at i:1667771 original size:19 final size:19
Alignment explanation
Indices: 1667583--1667771 Score: 134
Period size: 18 Copynumber: 10.2 Consensus size: 19
1667573 AAAAAATTTA
1667583 AAATATAATAT-AATATAT
1 AAATATAATATAAATATAT
1667601 AAA-ATAATATAAATATAT
1 AAATATAATATAAATATAT
*
1667619 AAATAT--TTTAAA-AT-T
1 AAATATAATATAAATATAT
*
1667634 -AATATAATATACAT-TAT
1 AAATATAATATAAATATAT
*
1667651 TAATATAA-A-AAATTATTTAAT
1 AAATATAATATAAA-TA--T-AT
* *
1667672 ATAAAATAATTTAAATATAT
1 A-AATATAATATAAATATAT
*
1667692 -TAT-TACATAATCAAATATAT
1 AAATATA-AT-AT-AAATATAT
1667712 AAATATAATATAAATATAT
1 AAATATAATATAAATATAT
*
1667731 AAACATAATA-AAATATAT
1 AAATATAATATAAATATAT
* *
1667749 AAATAAAACATAAATATAT
1 AAATATAATATAAATATAT
1667768 AAAT
1 AAAT
1667772 TATTAATTTA
Statistics
Matches: 135, Mismatches: 15, Indels: 41
0.71 0.08 0.21
Matches are distributed among these distances:
14 5 0.04
15 1 0.01
16 9 0.07
17 17 0.13
18 38 0.28
19 32 0.24
20 13 0.10
21 7 0.05
22 8 0.06
23 2 0.01
24 3 0.02
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATAATATAAATATAT
Found at i:1669550 original size:2 final size:2
Alignment explanation
Indices: 1669539--1669574 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1669529 CAAAATTAAA
1669539 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1669575 AAACGGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1673844 original size:15 final size:15
Alignment explanation
Indices: 1673826--1673855 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1673816 GTTTTCCTGC
1673826 TTTTTTCCTTCCTAT
1 TTTTTTCCTTCCTAT
*
1673841 TTTTTTCCTTGCTAT
1 TTTTTTCCTTCCTAT
1673856 ACGAAATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.23, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTTCCTTCCTAT
Found at i:1681947 original size:49 final size:50
Alignment explanation
Indices: 1681855--1681957 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 50
1681845 ATAAAGATTG
* *
1681855 TATTTGATGTAATAAAAATTTATGCATTATTAATAAATAAT-AAAATATAA
1 TATTTGATGTAATAAAAAATTATACATTATTAATAAATAATAAAAATA-AA
* *
1681905 TATTTGAT-TAATAAATAAATTATATATT-TTAA-AAATTTATAAAAATAAA
1 TATTTGATGTAATAAA-AAATTATACATTATTAATAAA-TAATAAAAATAAA
1681954 TATT
1 TATT
1681958 ATAATTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
48 3 0.07
49 20 0.43
50 23 0.50
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (50 bp):
TATTTGATGTAATAAAAAATTATACATTATTAATAAATAATAAAAATAAA
Found at i:1682072 original size:20 final size:23
Alignment explanation
Indices: 1682047--1682088 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
1682037 ATGTAGTAAA
1682047 AATTTT-AT-TTTTAT-ATTAAT
1 AATTTTAATATTTTATAATTAAT
1682067 AATTTTAATATTTTATAATTAA
1 AATTTTAATATTTTATAATTAA
1682089 ATTAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 2 0.11
22 6 0.32
23 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTTTAATATTTTATAATTAAT
Found at i:1682119 original size:33 final size:38
Alignment explanation
Indices: 1682084--1682159 Score: 90
Period size: 40 Copynumber: 2.1 Consensus size: 38
1682074 ATATTTTATA
1682084 ATTAAATTAAA-A-T-AATA-ATTT-AAATTTAATTTA
1 ATTAAATTAAATATTAAATATATTTAAAATTTAATTTA
*
1682117 ATTAATTTAAATTATTAAAATATATTTAAAATTTAATTTA
1 ATTAAATTAAA-TATT-AAATATATTTAAAATTTAATTTA
1682157 ATT
1 ATT
1682160 TAAAACAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
33 10 0.29
35 1 0.03
36 1 0.03
38 4 0.11
39 4 0.11
40 15 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
ATTAAATTAAATATTAAATATATTTAAAATTTAATTTA
Found at i:1682124 original size:20 final size:20
Alignment explanation
Indices: 1682099--1682159 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
1682089 ATTAAAATAA
1682099 TAATTTAAATTTAATTTAAT
1 TAATTTAAATTTAATTTAAT
* *
1682119 TAATTTAAA-TT-ATTAAAA
1 TAATTTAAATTTAATTTAAT
1682137 TATATTTAAAATTTAATTTAAT
1 TA-ATTT-AAATTTAATTTAAT
1682159 T
1 T
1682160 TAAAACAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.21
19 6 0.18
20 12 0.36
21 2 0.06
22 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTTAAATTTAATTTAAT
Found at i:1682129 original size:10 final size:10
Alignment explanation
Indices: 1682099--1682162 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 10
1682089 ATTAAAATAA
1682099 TAATTTAAATT
1 TAATTTAAA-T
1682110 TAATTT-AAT
1 TAATTTAAAT
1682119 TAATTTAAAT
1 TAATTTAAAT
*
1682129 T-A-TTAAAA
1 TAATTTAAAT
1682137 TATATTTAAAATT
1 TA-ATTT-AAA-T
*
1682150 TAATTTAATT
1 TAATTTAAAT
1682160 TAA
1 TAA
1682163 AACAAATTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
8 6 0.14
9 8 0.18
10 11 0.25
11 10 0.23
12 7 0.16
13 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:1689747 original size:3 final size:3
Alignment explanation
Indices: 1689739--1689763 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1689729 TAAGAATTAG
1689739 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1689764 GGTAATAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1689984 original size:16 final size:16
Alignment explanation
Indices: 1689965--1690034 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
1689955 AGTATTTTAT
1689965 ATATAATATTATATAA
1 ATATAATATTATATAA
1689981 ATATAAAATATT-T-TAA
1 ATAT--AATATTATATAA
* *
1689997 ATATAATAATA-ATTTA
1 ATATAATATTATA-TAA
1690013 ATA-AA-A-TATATAA
1 ATATAATATTATATAA
1690026 ATATAATAT
1 ATATAATAT
1690035 ATGTACATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
13 7 0.17
14 9 0.21
15 3 0.07
16 16 0.38
17 1 0.02
18 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAATATTATATAA
Found at i:1689984 original size:18 final size:17
Alignment explanation
Indices: 1689963--1690025 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
1689953 AAAGTATTTT
1689963 ATATATAATATTATATAA
1 ATATATAATATT-TATAA
*
1689981 ATATAAAATATTT-TAA
1 ATATATAATATTTATAA
1689997 ATATAATAATAATTTAATAAA
1 ATAT-ATAAT-ATTT-AT-AA
1690018 ATATATAA
1 ATATATAA
1690026 ATATAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 7 0.18
17 5 0.13
18 15 0.39
20 5 0.13
21 6 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATATAATATTTATAA
Found at i:1690053 original size:29 final size:30
Alignment explanation
Indices: 1689983--1690053 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
1689973 TTATATAAAT
* *
1689983 ATAAAATATTTTAAATATAATAATAATTTA
1 ATAAAATATTATAAATATAATAATAATGTA
1690013 ATAAAATA-TATAAATATAAT-AT-ATGTA
1 ATAAAATATTATAAATATAATAATAATGTA
*
1690040 CATAAATTATTATA
1 -ATAAAATATTATA
1690054 TTTAATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.11
28 9 0.25
29 15 0.42
30 8 0.22
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (30 bp):
ATAAAATATTATAAATATAATAATAATGTA
Found at i:1690874 original size:35 final size:35
Alignment explanation
Indices: 1690794--1690898 Score: 97
Period size: 35 Copynumber: 3.0 Consensus size: 35
1690784 TTTTTCATAA
* *
1690794 TTAATTTTTTAATACAAACAT-AATTTAATAATTT
1 TTAATTATTTAATATAAACATAAATTTAATAATTT
** *
1690828 TTAATTATTTAATATAAACATAAATTTGTTTATATT
1 TTAATTATTTAATATAAACATAAATTTAATAAT-TT
* * * *
1690864 TT-ATTGTTTAATATAAATATATATTTTAATTATTT
1 TTAATTATTTAATATAAACATA-AATTTAATAATTT
1690899 ATTATATATA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.33
35 27 0.47
36 12 0.21
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (35 bp):
TTAATTATTTAATATAAACATAAATTTAATAATTT
Found at i:1691818 original size:19 final size:19
Alignment explanation
Indices: 1691794--1691838 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1691784 TGTTTTAAGG
1691794 TTCTTTATCATTATTTTTT
1 TTCTTTATCATTATTTTTT
* * *
1691813 TTCTTTTCTCTTTTTTTTTT
1 TTC-TTTATCATTATTTTTT
1691833 TTCTTT
1 TTCTTT
1691839 TCAAGTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (19 bp):
TTCTTTATCATTATTTTTT
Found at i:1692337 original size:16 final size:17
Alignment explanation
Indices: 1692295--1692389 Score: 50
Period size: 18 Copynumber: 5.2 Consensus size: 17
1692285 TGGATTAGGC
*
1692295 TATAATTTAAATATTTA
1 TATAATTTAAATATTAA
* *
1692312 TTTATTTTTAAAT-TTAA
1 TATA-ATTTAAATATTAA
*
1692329 TATAATTTATATAATTAAA
1 TATAATTTAAAT-ATT-AA
*
1692348 TTATTATTTAAAATATTTTAA
1 -TATAATTT-AAATA--TTAA
1692369 TATTAATATT-AATATTAA
1 TA-TAAT-TTAAATATTAA
1692387 TAT
1 TAT
1692390 TTTTTATAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
16 6 0.10
17 10 0.17
18 15 0.25
19 2 0.03
20 14 0.24
21 8 0.14
22 4 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATAATTTAAATATTAA
Found at i:1692376 original size:6 final size:6
Alignment explanation
Indices: 1692365--1692390 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1692355 TTAAAATATT
1692365 TTAATA TTAATA TTAATA TTAATA TT
1 TTAATA TTAATA TTAATA TTAATA TT
1692391 TTTTATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAATA
Found at i:1692404 original size:29 final size:30
Alignment explanation
Indices: 1692366--1692422 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
1692356 TAAAATATTT
**
1692366 TAATATTAATATT-AATATTAATATTTTTTA
1 TAATATTAAT-TTAAATAAAAATATTTTTTA
1692396 TAATA-TAATTTAAATAAAAATATTTTT
1 TAATATTAATTTAAATAAAAATATTTTT
1692423 ATTAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 17 0.71
30 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TAATATTAATTTAAATAAAAATATTTTTTA
Found at i:1692408 original size:40 final size:40
Alignment explanation
Indices: 1692322--1692412 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 40
1692312 TTTATTTTTA
1692322 AATTTAATATAATTTATATAATTAAATTATTATTTAAAAT
1 AATTTAATATAATTTATATAATTAAATTATTATTTAAAAT
* *
1692362 ATTTTAATATTAATATTA-AT-ATTAATATT-TT-TTATAATAT
1 AATTTAATA-TAAT-TTATATAATTAA-ATTATTATT-TAAAAT
1692402 AATTTAA-ATAA
1 AATTTAATATAA
1692413 AAATATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
38 3 0.07
39 3 0.07
40 26 0.59
41 9 0.20
42 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
AATTTAATATAATTTATATAATTAAATTATTATTTAAAAT
Found at i:1694245 original size:17 final size:17
Alignment explanation
Indices: 1694219--1694251 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1694209 TAATATAAAA
1694219 GTATAAAAATATATTAT
1 GTATAAAAATATATTAT
*
1694236 GTATATAAATATATTA
1 GTATAAAAATATATTA
1694252 ATATATTAAA
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:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
GTATAAAAATATATTAT
Found at i:1694261 original size:17 final size:18
Alignment explanation
Indices: 1694220--1694270 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
1694210 AATATAAAAG
* *
1694220 TATAAAAATATATT-ATG
1 TATATAAATATATTAATA
1694237 TATATAAATATATTAATA
1 TATATAAATATATTAATA
1694255 TAT-TAAA-ATTATTAAT
1 TATATAAATA-TATTAAT
1694271 TTTTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 24 0.80
18 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TATATAAATATATTAATA
Found at i:1694277 original size:17 final size:17
Alignment explanation
Indices: 1694242--1694281 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1694232 TTATGTATAT
1694242 AAATATATTAATATATTA
1 AAAT-TATTAATATATTA
* *
1694260 AAATTATTAATTTTTTA
1 AAATTATTAATATATTA
1694277 AAATT
1 AAATT
1694282 TATTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTATTAATATATTA
Found at i:1696366 original size:17 final size:17
Alignment explanation
Indices: 1696344--1696378 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1696334 CCTGCCTTAT
1696344 TTGGTCATAGCAGCTGA
1 TTGGTCATAGCAGCTGA
1696361 TTGGTCATAGCAGCTGA
1 TTGGTCATAGCAGCTGA
1696378 T
1 T
1696379 CAATTGTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (17 bp):
TTGGTCATAGCAGCTGA
Found at i:1698508 original size:16 final size:16
Alignment explanation
Indices: 1698484--1698517 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1698474 AGTTAGAGAA
1698484 TATTAATAGGAAACAT
1 TATTAATAGGAAACAT
*
1698500 TATTCATAGGAAACAT
1 TATTAATAGGAAACAT
1698516 TA
1 TA
1698518 ATGCATGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (16 bp):
TATTAATAGGAAACAT
Found at i:1700834 original size:17 final size:18
Alignment explanation
Indices: 1700793--1700836 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1700783 AAAGACGATG
*
1700793 AATTATTAA-AATATTTT
1 AATTATTAATAATATTTA
*
1700810 AATCATTAATAAT-TTTA
1 AATTATTAATAATATTTA
1700827 AATTATTAAT
1 AATTATTAAT
1700837 TTTGGTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTATTAATAATATTTA
Found at i:1700950 original size:14 final size:15
Alignment explanation
Indices: 1700909--1700950 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1700899 TATAAAAAAT
1700909 AATAATATTATTAAA
1 AATAATATTATTAAA
*
1700924 AATTAT-TTATTAAA
1 AATAATATTATTAAA
*
1700938 AGTAATATT-TTAA
1 AATAATATTATTAA
1700951 TTTTATCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AATAATATTATTAAA
Found at i:1701756 original size:21 final size:22
Alignment explanation
Indices: 1701729--1701781 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
1701719 GAAATTAAAT
1701729 AATAATATT-TTATTTTT-TAA
1 AATAATATTGTTATTTTTATAA
1701749 AATAAATATTGTTATTTTTAATAA
1 AAT-AATATTGTTATTTTT-ATAA
1701773 AATAATATT
1 AATAATATT
1701782 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.10
21 6 0.21
22 8 0.28
23 6 0.21
24 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATAATATTGTTATTTTTATAA
Found at i:1701775 original size:20 final size:20
Alignment explanation
Indices: 1701726--1701776 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1701716 GATGAAATTA
1701726 AATAATAATATTTTATTTTTT
1 AATAA-AATATTTTATTTTTT
*
1701747 AAAATAAATATTGTTA-TTTTT
1 AATA-AAATATT-TTATTTTTT
1701768 AATAAAATA
1 AATAAAATA
1701777 ATATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 5 0.19
21 17 0.65
22 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AATAAAATATTTTATTTTTT
Found at i:1701791 original size:23 final size:23
Alignment explanation
Indices: 1701746--1701810 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
1701736 TTTTATTTTT
* **
1701746 TAAAATAAATATTGTTATTTTTAA
1 TAAAAT-AATATTATTAAATTTAA
1701770 TAAAATAATATTATTAAATTT-A
1 TAAAATAATATTATTAAATTTAA
*
1701792 T-TAATAATA-TA-TAAATTTA
1 TAAAATAATATTATTAAATTTA
1701811 GAAACGGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 7 0.19
20 2 0.06
21 7 0.19
22 2 0.06
23 12 0.33
24 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TAAAATAATATTATTAAATTTAA
Found at i:1701798 original size:26 final size:24
Alignment explanation
Indices: 1701732--1701785 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
1701722 ATTAAATAAT
1701732 AATATT-TTATTTTT--TAAAATA
1 AATATTATTATTTTTAATAAAATA
*
1701753 AATATTGTTATTTTTAATAAAAT-
1 AATATTATTATTTTTAATAAAATA
1701776 AATATTATTA
1 AATATTATTA
1701786 AATTTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 6 0.21
22 8 0.28
23 9 0.31
24 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
AATATTATTATTTTTAATAAAATA
Found at i:1709706 original size:2 final size:2
Alignment explanation
Indices: 1709699--1709728 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1709689 CCATGATTTG
1709699 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1709729 GTTTTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1716233 original size:41 final size:41
Alignment explanation
Indices: 1716176--1716254 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
1716166 ATGTGGACTG
*
1716176 TGACATTTGATATAAGAGTTAGCTCTTAGGGTTCTAGCGAT
1 TGACATTTGACATAAGAGTTAGCTCTTAGGGTTCTAGCGAT
*
1716217 TGACATTTGACATAAGAGTTAGCTCTTGGGGTTCTAGC
1 TGACATTTGACATAAGAGTTAGCTCTTAGGGTTCTAGC
1716255 TATGTGCCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (41 bp):
TGACATTTGACATAAGAGTTAGCTCTTAGGGTTCTAGCGAT
Found at i:1717742 original size:14 final size:14
Alignment explanation
Indices: 1717723--1717754 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1717713 AATTTTTTCT
1717723 CATTTCAAAAGGCG
1 CATTTCAAAAGGCG
1717737 CATTTCAAAAGGCG
1 CATTTCAAAAGGCG
1717751 CATT
1 CATT
1717755 GATAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (14 bp):
CATTTCAAAAGGCG
Found at i:1719702 original size:2 final size:2
Alignment explanation
Indices: 1719697--1719739 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1719687 TAACGCAATT
*
1719697 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1719738 TA
1 TA
1719740 AGATCAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1721595 original size:17 final size:16
Alignment explanation
Indices: 1721570--1721603 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1721560 ACGAAATTCT
*
1721570 TAAATATATAATAATCC
1 TAAACATATAAT-ATCC
1721587 TAAACATATAATATCC
1 TAAACATATAATATCC
1721603 T
1 T
1721604 TTAAAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAACATATAATATCC
Found at i:1722088 original size:13 final size:14
Alignment explanation
Indices: 1722061--1722095 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1722051 CAAACGATAA
*
1722061 AAATTATTTTTTTT
1 AAATTATTTTATTT
1722075 AAATT-TTTTATTT
1 AAATTATTTTATTT
1722088 AAATTATT
1 AAATTATT
1722096 AAATCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
AAATTATTTTATTT
Found at i:1722710 original size:2 final size:2
Alignment explanation
Indices: 1722671--1722696 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1722661 TAGTCATTGT
1722671 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1722697 AGTAATTCAT
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):
TA
Found at i:1722829 original size:8 final size:8
Alignment explanation
Indices: 1722816--1722874 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
1722806 AAATTTTAAT
1722816 TTATTTTA
1 TTATTTTA
1722824 TTATTTTA
1 TTATTTTA
*
1722832 TCATTTTA
1 TTATTTTA
1722840 -TATTTTA
1 TTATTTTA
*
1722847 TT-TTATA
1 TTATTTTA
1722854 TTATATTATAA
1 TTAT-TT-T-A
1722865 TTATTTTA
1 TTATTTTA
1722873 TT
1 TT
1722875 TTTATATGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 12 0.29
8 20 0.48
9 2 0.05
10 3 0.07
11 5 0.12
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (8 bp):
TTATTTTA
Found at i:1722845 original size:15 final size:16
Alignment explanation
Indices: 1722818--1722876 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 16
1722808 ATTTTAATTT
1722818 ATTTTATTATTTTATC
1 ATTTTATTATTTTATC
1722834 ATTTTA-TATTTTAT-
1 ATTTTATTATTTTATC
* *
1722848 -TTTATATTATATTATA
1 ATTT-TATTATTTTATC
1722864 ATTATT-TTATTTT
1 ATT-TTATTATTTT
1722877 TATATGTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 3 0.08
14 2 0.06
15 15 0.42
16 12 0.33
17 3 0.08
18 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTATTATTTTATC
Found at i:1722852 original size:33 final size:33
Alignment explanation
Indices: 1722808--1722879 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
1722798 TGTTATAAAA
* * *
1722808 ATTTTAATTTATTTTATTATT-TTATCATTTTAT
1 ATTTTATTTTATATTA-TATTATAATCATTTTAT
*
1722841 ATTTTATTTTATATTATATTATAATTATTTTAT
1 ATTTTATTTTATATTATATTATAATCATTTTAT
1722874 -TTTTAT
1 ATTTTAT
1722880 ATGTTAGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 10 0.29
33 24 0.71
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (33 bp):
ATTTTATTTTATATTATATTATAATCATTTTAT
Found at i:1722855 original size:27 final size:27
Alignment explanation
Indices: 1722808--1722881 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
1722798 TGTTATAAAA
*
1722808 ATTTTA-A-TTTATTTTATTATTTTATC
1 ATTTTATATTTTATTTTA-TATTATATC
*
1722834 ATTTTATATTTTATTTTATATTATATT
1 ATTTTATATTTTATTTTATATTATATC
**
1722861 ATAAT-TATTTTATTTTTATAT
1 ATTTTATATTTTA-TTTTATAT
1722882 GTTAGATGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 13 0.32
27 19 0.46
28 9 0.22
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (27 bp):
ATTTTATATTTTATTTTATATTATATC
Found at i:1723598 original size:18 final size:18
Alignment explanation
Indices: 1723575--1723609 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1723565 AATATTTTAA
* *
1723575 ATATAATTATGATATAAT
1 ATATAAATATAATATAAT
1723593 ATATAAATATAATATAA
1 ATATAAATATAATATAA
1723610 ATGGTTAAAT
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:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
ATATAAATATAATATAAT
Found at i:1723604 original size:13 final size:13
Alignment explanation
Indices: 1723572--1723608 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1723562 AAAAATATTT
1723572 TAAATATAAT-TA
1 TAAATATAATATA
*
1723584 T-GATATAATATA
1 TAAATATAATATA
1723596 TAAATATAATATA
1 TAAATATAATATA
1723609 AATGGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 7 0.33
12 4 0.19
13 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
TAAATATAATATA
Found at i:1732784 original size:21 final size:22
Alignment explanation
Indices: 1732742--1732784 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1732732 AAGTAAAAAC
1732742 GTTTGTCATTTAGATCCAATAA
1 GTTTGTCATTTAGATCCAATAA
*
1732764 GTTTGTCATTTCGAT-CAATAA
1 GTTTGTCATTTAGATCCAATAA
1732785 AATTTCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (22 bp):
GTTTGTCATTTAGATCCAATAA
Found at i:1735696 original size:2 final size:2
Alignment explanation
Indices: 1735689--1735720 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1735679 TGGATTTGCA
1735689 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1735721 TTAAACTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1736309 original size:9 final size:9
Alignment explanation
Indices: 1736297--1736370 Score: 73
Period size: 9 Copynumber: 8.2 Consensus size: 9
1736287 TATATAAATA
1736297 TAAATATAT
1 TAAATATAT
*
1736306 TAAAAATTAT
1 TAAATA-TAT
1736316 TAAATATAT
1 TAAATATAT
*
1736325 TAAA-ATTT
1 TAAATATAT
1736333 TAAATATA-
1 TAAATATAT
*
1736341 -AATATGATAA
1 TAA-AT-ATAT
1736351 TAAATATAT
1 TAAATATAT
1736360 TAAATATAT
1 TAAATATAT
1736369 TA
1 TA
1736371 TTTTTATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
7 2 0.04
8 9 0.17
9 31 0.57
10 10 0.19
11 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
TAAATATAT
Found at i:1736312 original size:17 final size:17
Alignment explanation
Indices: 1736292--1736340 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 17
1736282 TCATTTATAT
1736292 AAATATAAATATATTAA
1 AAATATAAATATATTAA
1736309 AAATTATTAAATATATTAA
1 AAA-TA-TAAATATATTAA
* *
1736328 AATTTTAAATATA
1 AAATATAAATATA
1736341 AATATGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 11 0.39
18 3 0.11
19 14 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATAAATATATTAA
Found at i:1736321 original size:19 final size:17
Alignment explanation
Indices: 1736297--1736340 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 17
1736287 TATATAAATA
1736297 TAAATATATTAAAAATTAT
1 TAAATATATT-AAAATT-T
1736316 TAAATATATTAAAATTT
1 TAAATATATTAAAATTT
1736333 TAAATATA
1 TAAATATA
1736341 AATATGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.36
18 6 0.24
19 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATATTAAAATTT
Found at i:1740370 original size:37 final size:38
Alignment explanation
Indices: 1740305--1740504 Score: 219
Period size: 37 Copynumber: 5.2 Consensus size: 38
1740295 AGAAAAAAAT
* **
1740305 ATTCGAATCTTGTTTTTTGAATAAGAGATTATATACTGAG
1 ATTCGAATCTT-TTTTTT-AGTAAGAGATTATATACCAAG
* **
1740345 ATTCGAAT-TTTTGTTTAGTAAGAGATTATATGTCAAG
1 ATTCGAATCTTTTTTTTAGTAAGAGATTATATACCAAG
* *
1740382 ATTCGAATCTTATTTTTT--TAAGGGATTATATAACAAG
1 ATTCGAATCTT-TTTTTTAGTAAGAGATTATATACCAAG
**
1740419 ATTCGAATCTTTTTTTTAGTAAG-GATTATGCACCAAG
1 ATTCGAATCTTTTTTTTAGTAAGAGATTATATACCAAG
*
1740456 ATTCGAATCTTGTTTTTTTGAGTAAGAGGTTATATACCAAG
1 ATTCGAATC-T-TTTTTTT-AGTAAGAGATTATATACCAAG
1740497 ATTCGAAT
1 ATTCGAAT
1740505 AATTAAGATT
Statistics
Matches: 136, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
36 6 0.04
37 71 0.52
38 12 0.09
39 14 0.10
40 14 0.10
41 19 0.14
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (38 bp):
ATTCGAATCTTTTTTTTAGTAAGAGATTATATACCAAG
Found at i:1740569 original size:41 final size:40
Alignment explanation
Indices: 1740524--1740836 Score: 129
Period size: 40 Copynumber: 8.0 Consensus size: 40
1740514 TCGAATCTTG
* * *
1740524 TTTTTTTGAGTAAGGAATTATGCATCAAGATTCTCAT-TTTA
1 TTTTTTT-AGTAAGGAATTATACACCAAGATTC-AATATTTA
*
1740565 TTTTTTTAGTAAGGGATTATACACCAAGATTCAATATTTA
1 TTTTTTTAGTAAGGAATTATACACCAAGATTCAATATTTA
* * * *
1740605 --TTTTTAGCAA-GAGATTATGCACTAAGATTC--GA-TT-
1 TTTTTTTAGTAAGGA-ATTATACACCAAGATTCAATATTTA
* * * * * * *
1740639 TTTTTTAAGTAA-AAGATTATGCACTAAAATTTAAATCTTTA
1 TTTTTTTAGTAAGGA-ATTATACACCAAGA-TTCAATATTTA
* * * *
1740680 TTTTTTTACTAA-AATATTATGCACCAAGATTCGAAT-CTTA
1 TTTTTTTAGTAAGGA-ATTATACACCAAGATTC-AATATTTA
* * * *
1740720 TTTTTTTTGAATAAGGGATTAGACACCAAGATTCAA-A--AA
1 -TTTTTTT-AGTAAGGAATTATACACCAAGATTCAATATTTA
** * * *
1740759 AATTTTGAGTAA-GAGATTATGCACCAAGATTCGAAT-TTTT
1 TTTTTTTAGTAAGGA-ATTATACACCAAGATTC-AATATTTA
** *
1740799 TTTTTTTTTTAAGAAATTATACACCAAGATTCAA-ATTT
1 TTTTTTTAGTAAGGAATTATACACCAAGATTCAATATTT
1740837 TTTAAAAAAA
Statistics
Matches: 206, Mismatches: 45, Indels: 44
0.70 0.15 0.15
Matches are distributed among these distances:
35 2 0.01
36 25 0.12
37 22 0.11
38 30 0.15
39 8 0.04
40 56 0.27
41 44 0.21
42 19 0.09
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (40 bp):
TTTTTTTAGTAAGGAATTATACACCAAGATTCAATATTTA
Found at i:1740585 original size:96 final size:92
Alignment explanation
Indices: 1740416--1740600 Score: 248
Period size: 96 Copynumber: 2.0 Consensus size: 92
1740406 ATTATATAAC
*
1740416 AAGATTCGAATCTTTTTTTTAGTAAGGATTATGCACCAAGATTCGAATCTTGTTTTTTTGAGTAA
1 AAGATTCGAATCTTTTTTTTAGTAAGGATTATGCACCAAGATTCGAATCTTATTTTTTTGAGTAA
*
1740481 GAGGTTATATACCAAGATTCGAATAATT
66 GAGGTTATACACCAAGATTC-AATAATT
* ** *
1740509 AAGATTCGAATCTTGTTTTTTTGAGTAAGGAATTATGCATCAAGATTCTCATTTTATTTTTTT-A
1 AAGATTCGAATC-T-TTTTTTT-AGTAAGG-ATTATGCACCAAGATTCGAATCTTATTTTTTTGA
1740573 GTAAG-GGATTATACACCAAGATTCAATA
62 GTAAGAGG-TTATACACCAAGATTCAATA
1740601 TTTATTTTTA
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
93 12 0.15
94 1 0.01
95 13 0.16
96 28 0.35
97 27 0.33
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (92 bp):
AAGATTCGAATCTTTTTTTTAGTAAGGATTATGCACCAAGATTCGAATCTTATTTTTTTGAGTAA
GAGGTTATACACCAAGATTCAATAATT
Found at i:1740660 original size:36 final size:36
Alignment explanation
Indices: 1740563--1740802 Score: 124
Period size: 38 Copynumber: 6.2 Consensus size: 36
1740553 ATTCTCATTT
* * *
1740563 TATTTTTTTAGTAAGGGATTATACACCAAGATTCAA
1 TATTTTTTTAGTAAGAGATTATGCACTAAGATTCAA
* *
1740599 TATTTATTTTTAGCAAGAGATTATGCACTAAGATTCGA
1 TA-TT-TTTTTAGTAAGAGATTATGCACTAAGATTCAA
* * *
1740637 T-TTTTTTTAAGTAAAAGATTATGCACTAAAATTTAAA
1 TATTTTTTT-AGTAAGAGATTATGCACTAAGA-TTCAA
* * * *
1740674 TCTTTATTTTTTTACTAAAATATTATGCACCAAGATTCGAA
1 ----TATTTTTTTAGTAAGAGATTATGCACTAAGATTC-AA
* * *
1740715 TCTTATTTTTTTTGAATAAGGGATTA-GACACCAAGATTCAAA
1 ---TA-TTTTTTT-AGTAAGAGATTATG-CACTAAGATTC-AA
* ** * *
1740757 AAAATTTTGAGTAAGAGATTATGCACCAAGATTCGAA
1 TATTTTTTTAGTAAGAGATTATGCACTAAGATTC-AA
*
1740794 TTTTTTTTT
1 TATTTTTTT
1740803 TTTTTTAAGA
Statistics
Matches: 156, Mismatches: 34, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
35 5 0.03
36 23 0.15
37 32 0.21
38 33 0.21
39 1 0.01
40 5 0.03
41 29 0.19
42 28 0.18
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (36 bp):
TATTTTTTTAGTAAGAGATTATGCACTAAGATTCAA
Found at i:1741975 original size:1 final size:1
Alignment explanation
Indices: 1741969--1741998 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
1741959 AAACTACCTC
*
1741969 TTTTTTTTTTTCTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1741999 GAGGAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:1741984 original size:12 final size:12
Alignment explanation
Indices: 1741967--1741998 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1741957 CCAAACTACC
1741967 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1741979 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1741991 T-TTTTTTT
1 TCTTTTTTT
1741999 GAGGAAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:1752088 original size:21 final size:21
Alignment explanation
Indices: 1752055--1752096 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1752045 CATTCAAAGC
1752055 TTTTAATAATTTA-TGATAAAA
1 TTTTAATAATTTAGT-ATAAAA
**
1752076 TTTTAATTTTTTAGTATAAAA
1 TTTTAATAATTTAGTATAAAA
1752097 AAGATCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
TTTTAATAATTTAGTATAAAA
Found at i:1752179 original size:26 final size:26
Alignment explanation
Indices: 1752123--1752180 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
1752113 ATAAAAAATT
1752123 ATAAAAATTAATTAAATTTAAATTTA
1 ATAAAAATTAATTAAATTTAAATTTA
* *
1752149 TTAAATATTAACTT-AA-TTAAATTTAA
1 ATAAAAATTAA-TTAAATTTAAATTT-A
1752175 ATAAAA
1 ATAAAA
1752181 TTTTAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
25 8 0.31
26 16 0.62
27 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAAAAATTAATTAAATTTAAATTTA
Found at i:1752182 original size:16 final size:15
Alignment explanation
Indices: 1752127--1752176 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1752117 AAAATTATAA
1752127 AAATTAATTAAATTT
1 AAATTAATTAAATTT
*
1752142 AAATTTATTAAATATT
1 AAATTAATTAAAT-TT
*
1752158 AACTTAATTAAATTT
1 AAATTAATTAAATTT
1752173 AAAT
1 AAAT
1752177 AAAATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATTAATTAAATTT
Found at i:1752193 original size:26 final size:28
Alignment explanation
Indices: 1752128--1752193 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
1752118 AAATTATAAA
1752128 AATTAATTAAATTTAAATTTATTAAATATT
1 AATTAATTAAATTTAAA-TTA-TAAATATT
*
1752158 AACTTAATTAAATTTAAA-TA-AAATTTT
1 AA-TTAATTAAATTTAAATTATAAATATT
*
1752185 AATTTATTA
1 AATTAATTA
1752194 TAAAATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 6 0.18
27 8 0.24
29 2 0.06
30 2 0.06
31 15 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTAATTAAATTTAAATTATAAATATT
Found at i:1754186 original size:12 final size:12
Alignment explanation
Indices: 1754169--1754234 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
1754159 GTATGAAAAT
1754169 ATATAAATATTA
1 ATATAAATATTA
1754181 ATATAAA-ATTA
1 ATATAAATATTA
*
1754192 ATTTTAAAT-TTA
1 A-TATAAATATTA
*
1754204 ATTATAAA-AAT-
1 A-TATAAATATTA
*
1754215 ATATAAATATAA
1 ATATAAATATTA
1754227 ATA-AAATA
1 ATATAAATA
1754235 AAATAACTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
10 6 0.14
11 12 0.27
12 26 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATAAATATTA
Found at i:1754819 original size:10 final size:10
Alignment explanation
Indices: 1754804--1754829 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1754794 CTTTGTACGG
1754804 TAAATTTTTT
1 TAAATTTTTT
1754814 TAAATTTTTT
1 TAAATTTTTT
1754824 TAAATT
1 TAAATT
1754830 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TAAATTTTTT
Found at i:1754842 original size:16 final size:15
Alignment explanation
Indices: 1754813--1754854 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1754803 GTAAATTTTT
1754813 TTAAATTTTT-TTAAA
1 TTAAATTTTTATT-AA
*
1754828 TTATATTTTTATTAA
1 TTAAATTTTTATTAA
1754843 TTAAATTTTTAT
1 TTAAATTTTTAT
1754855 GTTGGGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 22 0.92
16 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTAAATTTTTATTAA
Found at i:1755812 original size:19 final size:19
Alignment explanation
Indices: 1755788--1755830 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1755778 AGACCTTAAC
*
1755788 TTAAAACAGTAT-TTTTAT
1 TTAAAACAATATATTTTAT
*
1755806 ATTAAAATAATATATTTTAT
1 -TTAAAACAATATATTTTAT
1755826 TTAAA
1 TTAAA
1755831 TTTAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAAAACAATATATTTTAT
Found at i:1757728 original size:39 final size:39
Alignment explanation
Indices: 1757685--1757762 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
1757675 TAATACGCCA
1757685 TATTTAATCA-ATAATTAAA-AGATAAATATATAATATATT
1 TATTTAATCAGAT-ATTAAACA-ATAAATATATAATATATT
* * * *
1757724 TATTTGATGAGCTATTAAACAATAAATGTATAATATATT
1 TATTTAATCAGATATTAAACAATAAATATATAATATATT
1757763 AAAAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (39 bp):
TATTTAATCAGATATTAAACAATAAATATATAATATATT
Found at i:1758855 original size:2 final size:2
Alignment explanation
Indices: 1758850--1758882 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1758840 AAAAAATTAT
*
1758850 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1758883 CGATGAGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1759177 original size:2 final size:2
Alignment explanation
Indices: 1759170--1759216 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1759160 TAGTAGCAGG
*
1759170 GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1759212 GA GA G
1 GA GA G
1759217 TAAATAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1759232 original size:5 final size:5
Alignment explanation
Indices: 1759218--1759259 Score: 68
Period size: 5 Copynumber: 8.4 Consensus size: 5
1759208 GAGAGAGAGT
1759218 AAAT- AAATA AAATA AAATA AAATA AAATA AAATA AAACTA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA-TA AA
1759260 GAATAGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 28 0.78
6 4 0.11
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1759311 original size:7 final size:7
Alignment explanation
Indices: 1759295--1759326 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1759285 ATATTGCAGC
*
1759295 AAAAGGA
1 AAAAGAA
1759302 AAAAGAA
1 AAAAGAA
1759309 AAAAGAA
1 AAAAGAA
1759316 AAAAGAA
1 AAAAGAA
1759323 AAAA
1 AAAA
1759327 ACAGAGCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:1759917 original size:17 final size:17
Alignment explanation
Indices: 1759894--1759932 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1759884 AAAGAAGCTC
* *
1759894 TTTTTTTTTTTTTTTCAA
1 TTTTTTTATCTTTTT-AA
1759912 TTTTTTTATCTTTTTAA
1 TTTTTTTATCTTTTTAA
1759929 TTTT
1 TTTT
1759933 GGGATTATTT
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:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTATCTTTTTAA
Found at i:1762789 original size:21 final size:22
Alignment explanation
Indices: 1762763--1762804 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1762753 ACTAAAATAA
1762763 CATA-GTTATTTATTTTCTTGC
1 CATAGGTTATTTATTTTCTTGC
*
1762784 CATAGTGTTATTTCTTTTCTT
1 CATAG-GTTATTTATTTTCTT
1762805 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.60
Consensus pattern (22 bp):
CATAGGTTATTTATTTTCTTGC
Found at i:1772773 original size:39 final size:38
Alignment explanation
Indices: 1772695--1772827 Score: 101
Period size: 40 Copynumber: 3.3 Consensus size: 38
1772685 AGATAAAACT
* ** *
1772695 AATTATTAATATTTT-TTTTAATTTTATAAATAAATTAAA
1 AATTATTAATATTTTATTTTTATTAAATATAT-AA-TAAA
1772734 AATTATTACATATTTTATTTTTATTAAATATATAATAAA
1 AATTATTA-ATATTTTATTTTTATTAAATATATAATAAA
* *
1772773 AATATATGATAAT-TTTTAATTTTATATTAATATATATGATAAT
1 AAT-TAT--TAATATTTT-ATTTT-TATTAA-ATATATAATAAA
1772816 AATTCA-TAATAT
1 AATT-ATTAATAT
1772828 AATATATATA
Statistics
Matches: 78, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
39 15 0.19
40 20 0.26
41 20 0.26
42 9 0.12
43 14 0.18
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (38 bp):
AATTATTAATATTTTATTTTTATTAAATATATAATAAA
Found at i:1773315 original size:2 final size:2
Alignment explanation
Indices: 1773308--1773335 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1773298 TTGGAGCAAA
1773308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1773336 TTTTGGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1791696 original size:29 final size:29
Alignment explanation
Indices: 1791635--1791711 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 29
1791625 TTTTATTATT
* * *
1791635 TTTTATTTTTTTTATA-AAAAATTTTAAA
1 TTTTATATTTTTTATATTAAAATCTTAAA
*
1791663 TTTTA-ATTTTTTATATTAAAATCTTACA
1 TTTTATATTTTTTATATTAAAATCTTAAA
1791691 TATTTATATTTATTTAATATT
1 T-TTTATATTT-TTT-ATATT
1791712 TAATTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 9 0.22
28 15 0.38
29 4 0.10
30 4 0.10
31 3 0.08
32 5 0.12
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTATATTTTTTATATTAAAATCTTAAA
Found at i:1791751 original size:30 final size:30
Alignment explanation
Indices: 1791691--1791751 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
1791681 AAATCTTACA
* *
1791691 TATTTATATTTATTTAATATTTAATTTTTT
1 TATTTATATTTAATTAATATTTAATATTTT
1791721 TATTTA-ATTTAATTAA-ATTTAAATCATTTT
1 TATTTATATTTAATTAATATTT-AAT-ATTTT
1791751 T
1 T
1791752 CAATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 12 0.44
30 11 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
TATTTATATTTAATTAATATTTAATATTTT
Found at i:1791984 original size:75 final size:76
Alignment explanation
Indices: 1791842--1791988 Score: 219
Period size: 76 Copynumber: 1.9 Consensus size: 76
1791832 CAAATTAAAT
** * *
1791842 TTATTTTATTTTTTTAATTTTTTTGTTAAAAATGAAATTTAATTTTTATTTTTATATTAAATCTT
1 TTATTTTATTTTTTTAATTTTTTTGAAAAAAATAAAATTTAATTTATATTTTTATATTAAATCTT
1791907 TCATATTAGAA
66 TCATATTAGAA
1791918 TTATTTTATTATTTTTAATTTTTTT-AAAAAAATAAAATTTAA-TTATA-TTTTATATTAAAATC
1 TTATTTTATT-TTTTTAATTTTTTTGAAAAAAATAAAATTTAATTTATATTTTTATATT-AAATC
1791980 TTTCATATT
64 TTTCATATT
1791989 TTTAATTCTT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
74 9 0.14
75 18 0.28
76 24 0.37
77 14 0.22
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (76 bp):
TTATTTTATTTTTTTAATTTTTTTGAAAAAAATAAAATTTAATTTATATTTTTATATTAAATCTT
TCATATTAGAA
Found at i:1792015 original size:135 final size:135
Alignment explanation
Indices: 1791852--1792096 Score: 347
Period size: 135 Copynumber: 1.8 Consensus size: 135
1791842 TTATTTTATT
*
1791852 TTTTTAATTTTTTTGTTAAAAATGAAATTTAA-TTTTTAT-TTTTATATT-AAATCTTTCATATT
1 TTTTTAATTTTTTTGTTAAAAATAAAATTTAATTTTTTATATTTTATATTAAAATCTTTCATA-T
* *
1791914 AGAATTATTT-TATTATTTTTAATTTTTTTAAAAAAATAAAATTTAATTATATTTTATATTAAAA
65 A-AA-TATTTATATAATATTTAA-TTTTTTAAAAAAATAAAATTTAATTATATTTTATATTAAAA
1791978 TCTTTCATA
127 TCTTTCATA
1791987 TTTTTAATTCTTTTTGTT-AAAATAAAATTTAATTTTTTATATTTTATATTAAAATCTTTCATAT
1 TTTTTAATT-TTTTTGTTAAAAATAAAATTTAATTTTTTATATTTTATATTAAAATCTTTCATAT
* ** *
1792051 ATATATTTATATAATATTTAATTTTTTAATTAAATAATATTTAATT
65 AAATATTTATATAATATTTAATTTTTTAAAAAAATAAAATTTAATT
1792097 TTTTTAATTG
Statistics
Matches: 98, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
135 49 0.50
136 26 0.27
137 11 0.11
138 12 0.12
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (135 bp):
TTTTTAATTTTTTTGTTAAAAATAAAATTTAATTTTTTATATTTTATATTAAAATCTTTCATATA
AATATTTATATAATATTTAATTTTTTAAAAAAATAAAATTTAATTATATTTTATATTAAAATCTT
TCATA
Found at i:1792043 original size:63 final size:58
Alignment explanation
Indices: 1791927--1792050 Score: 176
Period size: 63 Copynumber: 2.1 Consensus size: 58
1791917 ATTATTTTAT
1791927 TATTTTTAATTTTTTTAAAAAAATAAAATTTAATTATATTTTATATTAAAATCTTTCA
1 TATTTTTAATTTTTTTAAAAAAATAAAATTTAATTATATTTTATATTAAAATCTTTCA
***
1791985 TATTTTTAATTCTTTTTGTTAAAATAAAATTTAATTTTTTATATTTTATATTAAAATCTTTCA
1 TATTTTTAATT-TTTTTAAAAAAATAAAATTTAA----TTATATTTTATATTAAAATCTTTCA
1792048 TAT
1 TAT
1792051 ATATATTTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
58 11 0.19
59 19 0.33
63 28 0.48
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (58 bp):
TATTTTTAATTTTTTTAAAAAAATAAAATTTAATTATATTTTATATTAAAATCTTTCA
Found at i:1792090 original size:23 final size:24
Alignment explanation
Indices: 1792061--1792105 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
1792051 ATATATTTAT
1792061 ATAATATTTAA-TTTTTTAATTAA
1 ATAATATTTAATTTTTTTAATTAA
1792084 ATAATATTTAATTTTTTTAATT
1 ATAATATTTAATTTTTTTAATT
1792106 GAATCAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATAATATTTAATTTTTTTAATTAA
Found at i:1792117 original size:23 final size:23
Alignment explanation
Indices: 1792061--1792115 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1792051 ATATATTTAT
*
1792061 ATAATATTTAATTTTTTAATTAA
1 ATAAGATTTAATTTTTTAATTAA
* *
1792084 ATAATATTTAATTTTTTTAATTGA
1 ATAAGATTTAA-TTTTTTAATTAA
*
1792108 ATCAGATT
1 ATAAGATT
1792116 AAACTTGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (23 bp):
ATAAGATTTAATTTTTTAATTAA
Found at i:1793636 original size:13 final size:13
Alignment explanation
Indices: 1793606--1793652 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
1793596 AAAGTTTTAT
1793606 TTAAATTT-AAAA
1 TTAAATTTAAAAA
*
1793618 TGAAATTTAAAAA
1 TTAAATTTAAAAA
1793631 TTAAATTTAAATAA
1 TTAAATTTAAA-AA
*
1793645 TAAAATTT
1 TTAAATTT
1793653 TTACTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 7 0.23
13 14 0.47
14 9 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
TTAAATTTAAAAA
Found at i:1793762 original size:26 final size:26
Alignment explanation
Indices: 1793732--1793784 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1793722 TCCAACTTTT
*
1793732 CGCTTAAACTCGACTTTATCCAATTA
1 CGCTTAAACTCGACTTCATCCAATTA
*
1793758 CGCTTAAACTCGACTTCATCCGATTA
1 CGCTTAAACTCGACTTCATCCAATTA
1793784 C
1 C
1793785 ACCTGAGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (26 bp):
CGCTTAAACTCGACTTCATCCAATTA
Found at i:1797197 original size:1 final size:1
Alignment explanation
Indices: 1797191--1797215 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1797181 GCAGGAACTG
1797191 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1797216 GCTGAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1799758 original size:20 final size:18
Alignment explanation
Indices: 1799729--1799768 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1799719 GTAAAAATAA
1799729 TTTTACAATTTTCTTTCTTT
1 TTTTACAATTTT-TTT-TTT
*
1799749 TTTTATAATTTTTTTTTT
1 TTTTACAATTTTTTTTTT
1799767 TT
1 TT
1799769 ACAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTACAATTTTTTTTTT
Found at i:1800503 original size:2 final size:2
Alignment explanation
Indices: 1800496--1800521 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1800486 ATTTTAGGTA
1800496 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
1800522 GATGAAGCAG
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:1806336 original size:2 final size:2
Alignment explanation
Indices: 1806329--1806354 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1806319 TCGATCATTA
1806329 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
1806355 TCCCAAACTT
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:1808420 original size:53 final size:52
Alignment explanation
Indices: 1808320--1809087 Score: 669
Period size: 53 Copynumber: 15.2 Consensus size: 52
1808310 TTTATTTAAA
*
1808320 ATTTTCATATTAAATCTTAAATTATTATTTAAAAATAATAAAAATTAAAAAAT
1 ATTTT-ATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATTAAAAAAT
* * * * *
1808373 ATTATATAATAAATTTTGAATTACTTTTTAAAAAATAATAAAAATT-AAAAA-
1 ATTTTATATTAAATCTTAAATTACTATTT-AAAAATAATAAAAATTAAAAAAT
* *
1808424 ATTATATATTAAATCTTGAATTACTATTT--AAA-AAT---AA-T-AAAAAT
1 ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATTAAAAAAT
* * * *
1808468 ATTTTACATTAAGATCTCAAGTT-CTATTT-AAATTAATAAAAATTAAAAAAATAT
1 ATTTTATATTAA-ATCTTAAATTACTATTTAAAAATAATAAAAATT--AAAAA-AT
* * *
1808522 ATTTTATATTAAATATTATATTACTATTTGAAAAATAATAAAAATT-AAATAT
1 ATTTTATATTAAATCTTAAATTACTATTT-AAAAATAATAAAAATTAAAAAAT
* * *
1808574 ATTTT-TATTGAATCTCAAATTACTTTTTAAAAAATAATAAAAAATT-AAAAAT
1 ATTTTATATTAAATCTTAAATTACTATTT-AAAAATAAT-AAAAATTAAAAAAT
* ***
1808626 ATTTTATATTAAATCTTGAATTACTAATTTAAAAAT-A-AAAAATTTTGAAA-
1 ATTTTATATTAAATCTTAAATTACT-ATTTAAAAATAATAAAAATTAAAAAAT
* *
1808676 A-TTT-TATTAAATCTCAAATTACTATTTAAAAATAATAAAAATT--AAATT
1 ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATTAAAAAAT
1808724 ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAA-T-AAAAAT
1 ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATTAAAAAAT
* * * * * *
1808774 AATTCATATTAAATTTTGAATTACTGTTTAAAAATAA-AAAAA--AGAAAAT
1 ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATTAAAAAAT
* * * *
1808823 A--TGATATTAAATCTTGAATTAC-AATTAAAAATAATATAAATTAAAAAAT
1 ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATTAAAAAAT
* * * *
1808872 ATTTTATATTAAATCTTGAATTATTATTTACAAATAATAAAAAATTTAAAAAT
1 ATTTTATATTAAATCTTAAATTACTATTTAAAAATAAT-AAAAATTAAAAAAT
* * *
1808925 ATTTTATATTAAATCTCAAATTACTTTTTTAAAAATAAGAAAAATTTTAAAAATAT
1 ATTTTATATTAAATCTTAAATTAC-TATTTAAAAATAATAAAAA--TTAAAAA-AT
* * *
1808981 ATTTTATATTAAAT-TCCAAAATACTA--T-----TAATAAAAATTAAAAAAAC
1 ATTTTATATTAAATCT-TAAATTACTATTTAAAAATAATAAAAATT-AAAAAAT
* *
1809027 ATTTTATATTAAATCTTAAATTA-TTTTTAAAAAATAATAAAAAATAAAAAAT
1 ATTTTATATTAAATCTTAAATTACTATTT-AAAAATAATAAAAATTAAAAAAT
* *
1809079 GTTCTATAT
1 ATTTTATAT
1809088 ATGTATTGGG
Statistics
Matches: 589, Mismatches: 77, Indels: 99
0.77 0.10 0.13
Matches are distributed among these distances:
43 6 0.01
44 18 0.03
45 10 0.02
46 35 0.06
47 45 0.08
48 30 0.05
49 34 0.06
50 81 0.14
51 75 0.13
52 73 0.12
53 104 0.18
54 33 0.06
55 8 0.01
56 37 0.06
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (52 bp):
ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATTAAAAAAT
Found at i:1808515 original size:50 final size:51
Alignment explanation
Indices: 1808452--1809076 Score: 531
Period size: 50 Copynumber: 12.3 Consensus size: 51
1808442 AATTACTATT
* * *
1808452 TAAAAATAATAAAAATATTTTACATTAAGATCTCAAGTT-CTATTT-AAATTAA
1 TAAAAAT--TAAAAATATTTTATATTAA-ATCTCAAATTACTATTTAAAAATAA
* * *
1808504 TAAAAATTAAAAAAATATATTTTATATTAAATATTATATTACTATTTGAAAAATAA
1 TAAAAATT---AAAA-ATATTTTATATTAAATCTCAAATTACTATTT-AAAAATAA
* * *
1808560 TAAAAATTAAATATATTTT-TATTGAATCTCAAATTACTTTTTAAAAAATAA
1 TAAAAATTAAAAATATTTTATATTAAATCTCAAATTACTATTT-AAAAATAA
**
1808611 TAAAAAATTAAAAATATTTTATATTAAATCTTGAATTACTAATTTAAAAATAA
1 T-AAAAATTAAAAATATTTTATATTAAATCTCAAATTACT-ATTTAAAAATAA
* **
1808664 -AAAATTTTGAAA-A-TTT-TATTAAATCTCAAATTACTATTTAAAAATAA
1 TAAAAATTAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
* *
1808711 TAAAAATT-AAATTATTTTATATTAAATCTTAAATTACTATTTAAAAATAA
1 TAAAAATTAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
* * * ** *
1808761 TAAAAA-TAAAAATAATTCATATTAAATTTTGAATTACTGTTTAAAAATAA
1 TAAAAATTAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
* ** *
1808811 -AAAAA--AGAAAATA--TGATATTAAATCTTGAATTAC-AATTAAAAATAA
1 TAAAAATTA-AAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
* ** * *
1808857 TATAAATTAAAAAATATTTTATATTAAATCTTGAATTATTATTTACAAATAA
1 TAAAAATT-AAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
*
1808909 TAAAAAATTTAAAAATATTTTATATTAAATCTCAAATTACTTTTTTAAAAATAA
1 T-AAAAA-TTAAAAATATTTTATATTAAATCTCAAATTAC-TATTTAAAAATAA
* *
1808963 GAAAAATTTTAAAAATATATTTTATATTAAAT-TCCAAAATACTA-TTAATAAA-AA
1 TAAAAA--TT-AAAA-ATATTTTATATTAAATCT-CAAATTACTATTTAA-AAATAA
* * * *
1809017 T--TAA--AAAAACATTTTATATTAAATCTTAAATTA-TTTTTAAAAAATAA
1 TAAAAATTAAAAATATTTTATATTAAATCTCAAATTACTATTT-AAAAATAA
*
1809064 TAAAAAATAAAAA
1 TAAAAATTAAAAA
1809077 ATGTTCTATA
Statistics
Matches: 476, Mismatches: 58, Indels: 79
0.78 0.09 0.13
Matches are distributed among these distances:
45 1 0.00
46 35 0.07
47 47 0.10
48 25 0.05
49 26 0.05
50 75 0.16
51 60 0.13
52 44 0.09
53 73 0.15
54 44 0.09
55 9 0.02
56 37 0.08
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (51 bp):
TAAAAATTAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
Found at i:1808588 original size:149 final size:143
Alignment explanation
Indices: 1808328--1809069 Score: 464
Period size: 148 Copynumber: 4.9 Consensus size: 143
1808318 AAATTTTCAT
* * * * *
1808328 ATTAAATCTTAAATTATTATTTAAAAATAATAAAAATTAAAAAATATTATATAATAAATTTTGAA
1 ATTAAATCTTCAATTACTATTT--AAATAATAAAAATTAAAAAATATTTTATATTAAATATT-AA
* * * *
1808393 TTACTTTTTAAAAAATAATAAAAATTAAA-AAATTATATATTAAATCTTGAATTACTATTTAAAA
63 TTACTATTT-AAAAATAATAAAAATTAAATATATT-TTTATTAAATCTTAAATTACTATTTAAAA
1808457 ATAATAAAAATATTTTAC
126 ATAATAAAAATATTTTAC
1808475 ATTAAGATC-TCAAGTT-CTATTTAAATTAATAAAAATTAAAAAAATATATTTTATATTAAATAT
1 ATTAA-ATCTTCAA-TTACTATTTAAA-TAATAAAAATT--AAAAA-ATATTTTATATTAAATAT
* * *
1808538 TATATTACTATTTGAAAAATAATAAAAATTAAATATATTTTTATTGAATCTCAAATTACTTTTTA
60 TA-ATTACTATTT-AAAAATAATAAAAATTAAATATATTTTTATTAAATCTTAAATTACTATTT-
*
1808603 AAAAATAATAAAAAATTAAAAATATTTTAT
122 --AAA-AAT----AA-TAAAAATATTTTAC
* *** * *
1808633 ATTAAATCTTGAATTACTAATTTAAA-AATAAAAAATTTTGAAA-A-TTT-TATTAAATCTCAAA
1 ATTAAATCTTCAATTACT-ATTTAAATAAT-AAAAATTAAAAAATATTTTATATTAAATAT-TAA
1808694 TTACTATTTAAAAATAATAAAAATTAAAT-TATTTTATATTAAATCTTAAATTACTATTTAAAAA
63 TTACTATTTAAAAATAATAAAAATTAAATATATTTT-TATTAAATCTTAAATTACTATTTAAAAA
* *
1808758 TAATAAAAATAAAAATAATTCAT
127 TAATAAAAAT----AT--TTTAC
* * * * * *
1808781 ATTAAATTTTGAATTACTGTTTAAA-AATAAAAA--AAAGAAA-ATATGATATTAAATCTTGAAT
1 ATTAAATCTTCAATTACTATTTAAATAATAAAAATTAAA-AAATATTTTATATTAAATATT-AAT
* * * * *
1808842 TAC-AATTAAAAATAATATAAATTAAAAAATATTTTATATTAAATCTTGAATTATTATTTACAAA
64 TACTATTTAAAAATAATAAAAATT-AAATATATTTT-TATTAAATCTTAAATTACTATTT--AAA
*
1808906 TAATAAAAAATTTAAAAATATTTTAT
125 -AAT----AA--TAAAAATATTTTAC
* *
1808932 ATTAAATC-TCAAATTACTTTTTTAAAAATAAGAAAAATTTTAAAAATATATTTTATATTAAAT-
1 ATTAAATCTTC-AATTAC-TATTT--AAATAATAAAAA--TTAAAAA-ATATTTTATATTAAATA
* * * * * *
1808995 TCCAAAATACTA-TTAATAAA-AATTAAAA--AAACAT-TTTATATTAAATCTTAAATTA-TTTT
59 T--TAATTACTATTTAA-AAATAATAAAAATTAAATATATTTTTATTAAATCTTAAATTACTATT
1809054 TAAAAAATAATAAAAA
121 T-AAAAATAATAAAAA
1809070 ATAAAAAATG
Statistics
Matches: 483, Mismatches: 53, Indels: 119
0.74 0.08 0.18
Matches are distributed among these distances:
142 7 0.01
143 2 0.00
145 7 0.01
146 43 0.09
147 44 0.09
148 65 0.13
149 64 0.13
150 14 0.03
151 60 0.12
152 29 0.06
153 12 0.02
154 8 0.02
155 26 0.05
156 5 0.01
157 22 0.05
158 32 0.07
159 12 0.02
160 27 0.06
161 4 0.01
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (143 bp):
ATTAAATCTTCAATTACTATTTAAATAATAAAAATTAAAAAATATTTTATATTAAATATTAATTA
CTATTTAAAAATAATAAAAATTAAATATATTTTTATTAAATCTTAAATTACTATTTAAAAATAAT
AAAAATATTTTAC
Found at i:1808643 original size:202 final size:195
Alignment explanation
Indices: 1808320--1808995 Score: 681
Period size: 201 Copynumber: 3.3 Consensus size: 195
1808310 TTTATTTAAA
* *
1808320 ATTTTCATATTAAATCTTAAATTATTATTTAAAAATAATAAAAATTAAAAAATATTATATAATAA
1 ATTTT-ATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATT-AAAAATATT-TATATTAA
*
1808385 ATTTTGAATTACTTTTTAAAAAATAAT-AAAAATTAAAAA-ATTATATATTAAATCTTGAATTAC
63 ATTTTGAATTACTTTTTAAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCTTGAATTAC
* *
1808448 TATTTAAAAATAATAAAAATATTTTACATTAAGATCTCAAGTT-CTATTT-AAATTAATAAAAAT
128 TATTTAAAAATAATAAAAATATTTT--ATTAA-ATCTCAAATTACTATTTAAAAATAATAAAAAT
1808511 TAAAAAAATAT
190 T----AAAT-T
* * * * *
1808522 ATTTTATATTAAATATTATATTACTATTTGAAAAATAATAAAAATTAAATATATTTTTATTGAAT
1 ATTTTATATTAAATCTTAAATTACTATTT-AAAAATAATAAAAATTAAAAATATTTATATTAAAT
* **
1808587 CTCAAATTACTTTTTAAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCTTGAATTACTA
65 TTTGAATTACTTTTTAAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCTTGAATTACT-
* *
1808652 ATTTAAAAATAAAAAATTTTGAAAATTTTATTAAATCTCAAATTACTATTTAAAAATAATAAAAA
129 ATTTAAAAATAATAAA-----AATATTTTATTAAATCTCAAATTACTATTTAAAAATAATAAAAA
1808717 TTAAATT
189 TTAAATT
*
1808724 ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAA-TAAAAATAATTCATATTAAAT
1 ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATTAAAAAT-ATTTATATTAAAT
* * * *
1808788 TTTGAATTACTGTTT-AAAAATAA-AAAAAA--GAAAATA--TGATATTAAATCTTGAATTACAA
65 TTTGAATTACTTTTTAAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCTTGAATTACTA
* ** * *
1808847 TTAAAAATAATATAAATTAAAAAATATTTTATATTAAATCTTGAATTATTATTTACAAATAATAA
130 TT--TAA-AA-AT-AA-T-AAAAATA-TTT-TATTAAATCTCAAATTACTATTTAAAAATAAT-A
*
1808912 AAAATTTAAAAAT
185 AAAA-TT-AAATT
* * *
1808925 ATTTTATATTAAATCTCAAATTACTTTTTTAAAAATAAGAAAAATTTTAAAAATATATTTTATAT
1 ATTTTATATTAAATCTTAAATTAC-TATTTAAAAATAATAAAAA--TT-AAAA-ATA-TTTATAT
1808990 TAAATT
60 TAAATT
1808996 CCAAAATACT
Statistics
Matches: 403, Mismatches: 40, Indels: 57
0.81 0.08 0.11
Matches are distributed among these distances:
194 3 0.01
195 20 0.05
196 5 0.01
197 11 0.03
198 30 0.07
199 13 0.03
200 45 0.11
201 106 0.26
202 90 0.22
203 19 0.05
205 10 0.02
206 16 0.04
207 28 0.07
208 7 0.02
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (195 bp):
ATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAATTAAAAATATTTATATTAAATT
TTGAATTACTTTTTAAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCTTGAATTACTAT
TTAAAAATAATAAAAATATTTTATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTAAATT
Found at i:1808722 original size:28 final size:28
Alignment explanation
Indices: 1808691--1808767 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 28
1808681 ATTAAATCTC
1808691 AAATTACTATTTAAAAATAATAAAAATT
1 AAATTACTATTTAAAAATAATAAAAATT
* **
1808719 AAATTA-T-TTT----ATATTAAATCTT
1 AAATTACTATTTAAAAATAATAAAAATT
1808741 AAATTACTATTTAAAAATAATAAAAAT
1 AAATTACTATTTAAAAATAATAAAAAT
1808768 AAAAATAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
22 15 0.41
23 1 0.03
24 3 0.08
26 3 0.08
27 1 0.03
28 14 0.38
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
AAATTACTATTTAAAAATAATAAAAATT
Found at i:1809014 original size:300 final size:301
Alignment explanation
Indices: 1808403--1809076 Score: 729
Period size: 300 Copynumber: 2.2 Consensus size: 301
1808393 TTACTTTTTA
* *
1808403 AAAAATAATAAAAATTAAAAAATTATATATTAAATCTTGAATTACTATTTAAAAATAATAAAAAT
1 AAAAATAATAAAAATTAAAAAATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAAT
* *
1808468 ----ATTTTACATTAAGATCTCAAGTTCTATTTAAATTAATAAAAATTAAAAAAATATATTTTAT
66 AAAAATTTCACATTAAGATCTCAAGTTCTATTTAAA-TAATAAAAA-TAAAAAAATATA-TTGAT
* * *
1808529 ATTAAATATTATATTACTATTTGAAAAATAATAAAAATTAAATATATTTTTATTGAATCTCAAAT
128 ATTAAATATTATATTACTAATTGAAAAATAATAAAAATTAAAAATATTTTTATTAAATCTCAAAT
**
1808594 TACTTTTTAAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCTTGAATTACTAATTTAAA
193 TACTTTTTAAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCTCAAATTACTAATTTAAA
* * **
1808659 AATAAAAAATTTTGAAAATTTTATTAAATCTCAAATTACTATTT
258 AATAAAAAATTTTAAAAATTTTATTAAATCTCAAATTACAAAAT
**
1808703 AAAAATAATAAAAATTAAATTATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAAT
1 AAAAATAATAAAAATTAAAAAATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAAT
* * * * *
1808768 AAAAATAATTCATATTAA-ATTTTGAA-TTACTGTTTAAA-AATAAAAA-AAAGAAA-ATA-TGA
66 AAAAAT--TTCACATTAAGA-TCTCAAGTT-CTATTTAAATAATAAAAATAAAAAAATATATTGA
* * *
1808827 TATTAAATCTTGA-ATTAC-AATT-AAAAATAATATAAATTAAAAAATATTTTATATTAAATCTT
127 TATTAAATATT-ATATTACTAATTGAAAAATAATAAAAATT-AAAAATATTTT-TATTAAATCTC
* * **
1808889 GAATTA-TTATTT-ACAAATAATAAAAAATTTAAAAATATTTTATATTAAATCTCAAATTACTTT
189 AAATTACTT-TTTAAAAAATAATAAAAAA-TTAAAAATATTTTATATTAAATCTCAAATTACTAA
* *
1808952 TTTAAAAATAAGAAAAATTTTAAAAATATATT-TTATAT-T-AAATTCCAAAAT
252 TTTAAAAAT-A-AAAAATTTTAAAAAT-T-TTATTAAATCTCAAATTACAAAAT
** * *
1809003 ACTATTAATAAAAATTAAAAAAACATTTTATATTAAATCTTAAATTA-TTTTTAAAAAATAATAA
1 AAAAATAATAAAAATT--AAAAA-ATTTTATATTAAATCTTAAATTACTATTT-AAAAATAAT-A
1809067 AAAATAAAAA
61 AAAATAAAAA
1809077 ATGTTCTATA
Statistics
Matches: 317, Mismatches: 35, Indels: 40
0.81 0.09 0.10
Matches are distributed among these distances:
297 15 0.05
298 29 0.09
299 74 0.23
300 84 0.26
301 18 0.06
302 19 0.06
303 34 0.11
304 21 0.07
305 3 0.01
306 20 0.06
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (301 bp):
AAAAATAATAAAAATTAAAAAATTTTATATTAAATCTTAAATTACTATTTAAAAATAATAAAAAT
AAAAATTTCACATTAAGATCTCAAGTTCTATTTAAATAATAAAAATAAAAAAATATATTGATATT
AAATATTATATTACTAATTGAAAAATAATAAAAATTAAAAATATTTTTATTAAATCTCAAATTAC
TTTTTAAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCTCAAATTACTAATTTAAAAAT
AAAAAATTTTAAAAATTTTATTAAATCTCAAATTACAAAAT
Found at i:1809040 original size:23 final size:23
Alignment explanation
Indices: 1808971--1809040 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
1808961 AAGAAAAATT
*
1808971 TTAAAAATATATTTTATATTAAA
1 TTAAAAATACATTTTATATTAAA
* * *
1808994 TTCCAAAATAC-TATTA-ATAAAAA
1 TT-AAAAATACATTTTATAT-TAAA
*
1809017 TTAAAAAAACATTTTATATTAAA
1 TTAAAAATACATTTTATATTAAA
1809040 T
1 T
1809041 CTTAAATTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
22 8 0.23
23 19 0.54
24 8 0.23
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAAAATACATTTTATATTAAA
Found at i:1809066 original size:353 final size:346
Alignment explanation
Indices: 1808318--1809075 Score: 856
Period size: 353 Copynumber: 2.1 Consensus size: 346
1808308 AGTTTATTTA
1808318 AAATTTTCATATTAAATCTTAAATTATTATTTAAAAATAATAAAAATTAAAAAATATTATATAAT
1 AAATTTT-ATATTAAATCTTAAATTATT-TTTAAAAATAATAAAAATT--AAAATATTATATAAT
* * * * *
1808383 AAATTTTGAATTACTTTTTAAAAAATAATAAAAATTAAAAAATTATATATTAAATCTTGAATTAC
62 AAATCTTAAATTACTATTTAAAAAATAATAAAAATAAAAAAATTACATATTAAATCTTGAATTAC
* * * * * * *
1808448 TATTTAAAAATAATAAAAATATTTTACATTAAGATCTCAAGTTCTATTTAAATTAATAAAAATTA
127 TATTTAAAAATAAAAAAAAAATATGACATTAAGATCTCAAGTTCAATTAAAAATAATAAAAATT-
*
1808513 AAAAAATATATTTTATATTAAATATTATATTACTATTTGAAAAATAATAAAAATTAAATATATTT
191 AAAAAATATATTTTATATTAAATATTATATTACTATTTGAAAAATAATAAAAATTAAAAATATTT
* * *
1808578 TTATTGAATCTCAAATTACTTTTTAAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCTT
256 TTATTAAATCTCAAATTACTTTTTAAAAAATAAGAAAAAATTAAAAATATTTTATATTAAATCTC
* *
1808643 GAATTACTAATTTAAAAATAAAAAATTTT
321 AAAATACTAATTTAAAAATAAAAAA---T
* * * * * *
1808672 GAAAATTT-TATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTAAATTATTTTATATTAA
1 -AAATTTTATATTAAATCTTAAATTA-TTTTTAAAAATAATAAAAATTAAAATATTATATAATAA
*
1808736 ATCTTAAATTACTATTT-AAAAATAATAAAAATAAAAATAATT-CATATTAAATTTTGAATTACT
64 ATCTTAAATTACTATTTAAAAAATAATAAAAATAAAAA-AATTACATATTAAATCTTGAATTACT
* * * *
1808799 GTTTAAAAATAAAAAAAAGAAAATATGATATTAA-ATCTTGAA-TTACAATTAAAAATAATATAA
128 ATTTAAAAAT--AAAAAA-AAAATATGACATTAAGATC-TCAAGTT-CAATTAAAAATAATAAAA
* * *
1808862 ATT-AAAAA-ATATTTTATATTAAATCTTGA-ATTATTATTT-ACAAATAATAAAAAATTTAAAA
188 ATTAAAAAATATATTTTATATTAAATATT-ATATTACTATTTGAAAAATAAT-AAAAA-TTAAAA
* *
1808923 ATATTTTATATTAAATCTCAAATTACTTTTTTAAAAATAAGAAAAATTTTAAAAATATATTTTAT
250 ATATTTT-TATTAAATCTCAAATTACTTTTTAAAAAATAAGAAAAA-ATT-AAAA-ATATTTTAT
1808988 ATTAAAT-TCCAAAATACT-ATTAATAAAAATTAAAAAA-
311 ATTAAATCT-CAAAATACTAATT--TAAAAA-TAAAAAAT
* *
1809025 ACATTTTATATTAAATCTTAAATTATTTTTAAAAAATAATAAAAAATAAAA
1 AAATTTTATATTAAATCTTAAATTATTTTT-AAAAATAATAAAAATTAAAA
1809076 AATGTTCTAT
Statistics
Matches: 343, Mismatches: 40, Indels: 42
0.81 0.09 0.10
Matches are distributed among these distances:
349 8 0.02
350 79 0.23
351 50 0.15
352 54 0.16
353 102 0.30
354 9 0.03
355 28 0.08
356 6 0.02
357 7 0.02
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (346 bp):
AAATTTTATATTAAATCTTAAATTATTTTTAAAAATAATAAAAATTAAAATATTATATAATAAAT
CTTAAATTACTATTTAAAAAATAATAAAAATAAAAAAATTACATATTAAATCTTGAATTACTATT
TAAAAATAAAAAAAAAATATGACATTAAGATCTCAAGTTCAATTAAAAATAATAAAAATTAAAAA
ATATATTTTATATTAAATATTATATTACTATTTGAAAAATAATAAAAATTAAAAATATTTTTATT
AAATCTCAAATTACTTTTTAAAAAATAAGAAAAAATTAAAAATATTTTATATTAAATCTCAAAAT
ACTAATTTAAAAATAAAAAAT
Found at i:1809348 original size:22 final size:23
Alignment explanation
Indices: 1809302--1809349 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1809292 TCATTTTTAA
1809302 TCATATACACATTCTAGTTAAAG
1 TCATATACACATTCTAGTTAAAG
* *
1809325 TCATATATACATT-TAGTTACAG
1 TCATATACACATTCTAGTTAAAG
1809347 TCA
1 TCA
1809350 AATCTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
TCATATACACATTCTAGTTAAAG
Found at i:1809388 original size:24 final size:24
Alignment explanation
Indices: 1809326--1809388 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
1809316 TAGTTAAAGT
* *
1809326 CATATATACATTTAGTTACAGTCA
1 CATATATATATTTAATTACAGTCA
* * *
1809350 -A-ATCTATATTCAATTATAGTCA
1 CATATATATATTTAATTACAGTCA
1809372 CATATATATATTTAATT
1 CATATATATATTTAATT
1809389 TTGTTCGAGT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
22 16 0.53
23 2 0.07
24 12 0.40
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.43
Consensus pattern (24 bp):
CATATATATATTTAATTACAGTCA
Done.