Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 7 of 100
Found at i:1145295 original size:45 final size:43
Alignment explanation
Indices: 1145230--1145401 Score: 151
Period size: 42 Copynumber: 4.0 Consensus size: 43
1145220 AAATTTTGAT
1145230 CAAAGCTCCTCTAAGT-AGAGGCTCAACGACTTTGAGAAACATAAA
1 CAAAGCTCCTCTAA-TCAGAGGCTCAACGACTTTGA-AAA-ATAAA
* *
1145275 CAAAGCTCATCTAATCAGAGGCATC-ACAACTTTGAAAAATAAA
1 CAAAGCTCCTCTAATCAGAGGC-TCAACGACTTTGAAAAATAAA
** * *
1145318 -TTA-CTCCTCTAATCAGAGGCTCAATGACTTTTGAAAAGT-AA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAA
** *
1145359 -ATGGCTCCTCTAATCAGAGGCTCAAAC-ACTTTTGAAAAGTAAA
1 CAAAGCTCCTCTAATCAGAGGCTC-AACGAC-TTTGAAAAATAAA
1145402 TGGCTCTTCT
Statistics
Matches: 109, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
40 2 0.02
41 22 0.20
42 42 0.39
43 9 0.08
44 4 0.04
45 28 0.26
46 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (43 bp):
CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAA
Found at i:1145337 original size:41 final size:42
Alignment explanation
Indices: 1145279--1145432 Score: 181
Period size: 42 Copynumber: 3.7 Consensus size: 42
1145269 CATAAACAAA
* * *
1145279 GCTCATCTAATCAGAGGCATCACA-AC-TTTGAAAAATAAATT
1 GCTCCTCTAATCAGAGGC-TCACACACTTTTGAAAAGTAAATG
* *
1145320 ACTCCTCTAATCAGAGGCTCA-ATGACTTTTGAAAAGTAAATG
1 GCTCCTCTAATCAGAGGCTCACA-CACTTTTGAAAAGTAAATG
*
1145362 GCTCCTCTAATCAGAGGCTCAAACACTTTTGAAAAGTAAATG
1 GCTCCTCTAATCAGAGGCTCACACACTTTTGAAAAGTAAATG
* *
1145404 GCTCTTCTAAACAGAGGCATCACA-ACTTT
1 GCTCCTCTAATCAGAGGC-TCACACACTTT
1145433 GGACAGTAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 18 0.18
42 72 0.73
43 5 0.05
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (42 bp):
GCTCCTCTAATCAGAGGCTCACACACTTTTGAAAAGTAAATG
Found at i:1146459 original size:17 final size:16
Alignment explanation
Indices: 1146428--1146486 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
1146418 TGAGTCCTCA
**
1146428 TTTTTCATTCACTTTT
1 TTTTTCATTTTCTTTT
1146444 TCTTTTCATTTTC-TTT
1 T-TTTTCATTTTCTTTT
1146460 TTTTTCATTTT-TTTT
1 TTTTTCATTTTCTTTT
1146475 CATTTTTCATTT
1 --TTTTTCATTT
1146487 CATTTTTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
15 13 0.35
16 5 0.14
17 19 0.51
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCATTTTCTTTT
Found at i:1146472 original size:10 final size:10
Alignment explanation
Indices: 1146452--1146507 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
1146442 TTTCTTTTCA
1146452 TTTTC-TTTT
1 TTTTCATTTT
1146461 TTTTCATTTT
1 TTTTCATTTT
1146471 TTTTCATTTT
1 TTTTCATTTT
1146481 TCATTTCA-TTT
1 T--TTTCATTTT
*
1146492 TTTCCATTTT
1 TTTTCATTTT
1146502 TTTTCA
1 TTTTCA
1146508 AGCATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 9 0.22
10 23 0.56
11 4 0.10
12 5 0.12
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:1146493 original size:31 final size:32
Alignment explanation
Indices: 1146446--1146507 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
1146436 TCACTTTTTC
* *
1146446 TTTTCATTTTCTTTTTTTTCATTTTTTTTCAT
1 TTTTCATTTTCATTTTTTCCATTTTTTTTCAT
1146478 TTTTCA-TTTCATTTTTTCCATTTTTTTTCA
1 TTTTCATTTTCATTTTTTCCATTTTTTTTCA
1146508 AGCATAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTTCATTTTCATTTTTTCCATTTTTTTTCAT
Found at i:1146503 original size:22 final size:22
Alignment explanation
Indices: 1146462--1146502 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1146452 TTTTCTTTTT
*
1146462 TTTCATTTTTTTTCATTTTTCA
1 TTTCATTTTTTTCCATTTTTCA
1146484 TTTCA-TTTTTTCCATTTTT
1 TTTCATTTTTTTCCATTTTT
1146503 TTTCAAGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTCATTTTTTTCCATTTTTCA
Found at i:1159323 original size:27 final size:27
Alignment explanation
Indices: 1159290--1159345 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1159280 TTCAACCCAA
1159290 CTCAAAATGGCCTACTCCAAACCTAAT
1 CTCAAAATGGCCTACTCCAAACCTAAT
1159317 CTCAAAATGGCCTACTCCAAACCTAAT
1 CTCAAAATGGCCTACTCCAAACCTAAT
1159344 CT
1 CT
1159346 ACTATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.34, G:0.07, T:0.23
Consensus pattern (27 bp):
CTCAAAATGGCCTACTCCAAACCTAAT
Found at i:1161563 original size:27 final size:27
Alignment explanation
Indices: 1161532--1161618 Score: 97
Period size: 27 Copynumber: 3.2 Consensus size: 27
1161522 ATATTAATTT
1161532 AATTTTGATTTTGATATAATGTAAGTA
1 AATTTTGATTTTGATATAATGTAAGTA
* * * *
1161559 AATTTTGATAATTT--TTTAATATTAATTT
1 AATTTTGAT--TTTGATATAAT-GTAAGTA
1161587 AATTTTGATTTTGATATAATGTAAGTA
1 AATTTTGATTTTGATATAATGTAAGTA
1161614 AATTT
1 AATTT
1161619 GATAATTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
26 3 0.06
27 23 0.49
28 18 0.38
29 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (27 bp):
AATTTTGATTTTGATATAATGTAAGTA
Found at i:1161580 original size:55 final size:54
Alignment explanation
Indices: 1161520--1161648 Score: 217
Period size: 55 Copynumber: 2.4 Consensus size: 54
1161510 CAATGATAAA
1161520 TAATATTAATTTAATTTTGATTTTGATATAATGTAAGTAAATTTTGATAATTTTT
1 TAATATTAATTTAATTTTGATTTTGATATAATGTAAGTAAA-TTTGATAATTTTT
1161575 TAATATTAATTTAATTTTGATTTTGATATAATGTAAGTAAATTTGATAATTTTT
1 TAATATTAATTTAATTTTGATTTTGATATAATGTAAGTAAATTTGATAATTTTT
*
1161629 T-ATA-TAATTTTGATTTTGAT
1 TAATATTAA-TTTAATTTTGAT
1161649 AGCTTTTGAT
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
52 3 0.04
53 14 0.19
54 14 0.19
55 41 0.57
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (54 bp):
TAATATTAATTTAATTTTGATTTTGATATAATGTAAGTAAATTTGATAATTTTT
Found at i:1161632 original size:28 final size:28
Alignment explanation
Indices: 1161546--1161632 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
1161536 TTGATTTTGA
1161546 TATAATGTAAGTAAATTTTGATAATTTTT
1 TATAATGTAAGTAAA-TTTGATAATTTTT
* * **
1161575 TA-ATAT-TAATTTAATTTTGAT--TTTGA
1 TATA-ATGTAA-GTAAATTTGATAATTTTT
1161601 TATAATGTAAGTAAATTTGATAATTTTT
1 TATAATGTAAGTAAATTTGATAATTTTT
1161629 TATA
1 TATA
1161633 TAATTTTGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
26 16 0.36
27 4 0.09
28 17 0.39
29 7 0.16
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (28 bp):
TATAATGTAAGTAAATTTGATAATTTTT
Found at i:1161676 original size:21 final size:21
Alignment explanation
Indices: 1161652--1161709 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1161642 TTTTGATAGC
1161652 TTTTGATAAAATTTTAGTAAT
1 TTTTGATAAAATTTTAGTAAT
*
1161673 TTTTGATACAATTTTAGTAAT
1 TTTTGATAAAATTTTAGTAAT
**
1161694 CATTGATAAAATTTTA
1 TTTTGATAAAATTTTA
1161710 ATAACCTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (21 bp):
TTTTGATAAAATTTTAGTAAT
Found at i:1162064 original size:22 final size:22
Alignment explanation
Indices: 1162038--1162372 Score: 174
Period size: 22 Copynumber: 14.9 Consensus size: 22
1162028 TCCAAAAAGT
* * *
1162038 TTATCAATAATTTACAATTAAG
1 TTATCAATGATTTACTATTAAA
* * * *
1162060 TTATCATTAATTTATTATTATA
1 TTATCAATGATTTACTATTAAA
*** * * *
1162082 TTATCAGCAAATTACTACTAAG
1 TTATCAATGATTTACTATTAAA
* * *
1162104 CTATCAATGATATATTATTAAA
1 TTATCAATGATTTACTATTAAA
* *
1162126 TTATCAATAATTTACTACTAAA
1 TTATCAATGATTTACTATTAAA
* *
1162148 TTAGT-ATTGATTTACTATTAAC
1 TTA-TCAATGATTTACTATTAAA
* * *
1162170 TTATGAATGATTTATTATTAAG
1 TTATCAATGATTTACTATTAAA
*
1162192 TTATGAATGATTTACTATTAAA
1 TTATCAATGATTTACTATTAAA
* *
1162214 TTGTTAATGATTTACTATTAAA
1 TTATCAATGATTTACTATTAAA
** * *
1162236 TTATTGATGATTT-GTAATAAAA
1 TTATCAATGATTTACT-ATTAAA
* *
1162258 TTAT-AACTGATTTATTATTAAT
1 TTATCAA-TGATTTACTATTAAA
* * *
1162280 TTATTAATGAGTTACTACAAAGATATTAA
1 TTATCAATGA-TT--TAC---TAT-TAAA
* * * *
1162309 TAATTAATAATTTACTACTAAA
1 TTATCAATGATTTACTATTAAA
*
1162331 TTATCAATAATTTAC-ATATAAA
1 TTATCAATGATTTACTAT-TAAA
*
1162353 TTATCAATGAGTTACTATTA
1 TTATCAATGATTTACTATTA
1162373 TGTTATTATG
Statistics
Matches: 239, Mismatches: 59, Indels: 30
0.73 0.18 0.09
Matches are distributed among these distances:
21 4 0.02
22 207 0.87
23 9 0.04
25 2 0.01
26 3 0.01
28 4 0.02
29 10 0.04
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (22 bp):
TTATCAATGATTTACTATTAAA
Found at i:1162167 original size:44 final size:44
Alignment explanation
Indices: 1162038--1162620 Score: 200
Period size: 44 Copynumber: 13.1 Consensus size: 44
1162028 TCCAAAAAGT
* * * * *
1162038 TTATCAATAATTTACAATTAAGTTATCATTAATTTATTATTATA
1 TTATCAATAATTTACTATTAAGTTATCAATGATTTACTATTAAA
** * * * * *
1162082 TTATCAGCAAATTACTACTAAGCTATCAATGATATATTATTAAA
1 TTATCAATAATTTACTATTAAGTTATCAATGATTTACTATTAAA
* * * *
1162126 TTATCAATAATTTACTACTAAATTAGT-ATTGATTTACTATTAAC
1 TTATCAATAATTTACTATTAAGTTA-TCAATGATTTACTATTAAA
* * * *
1162170 TTATGAATGATTTATTATTAAGTTATGAATGATTTACTATTAAA
1 TTATCAATAATTTACTATTAAGTTATCAATGATTTACTATTAAA
* * * * ** * *
1162214 TTGTTAATGATTTACTATTAAATTATTGATGATTT-GTAATAAAA
1 TTATCAATAATTTACTATTAAGTTATCAATGATTTACT-ATTAAA
* * * *
1162258 TTAT-AACTGATTTATTATTAATTTATTAATGAGTTACTACAAAGATATT-AA
1 TTATCAA-TAATTTACTATTAAGTTATCAATGA-TT--TAC-----TATTAAA
* * * * *
1162309 TAATTAATAATTTACTACTAAATTATCAATAATTTAC-ATATAAA
1 TTATCAATAATTTACTATTAAGTTATCAATGATTTACTAT-TAAA
* * * * * ***
1162353 TTATCAATGAGTTACTATTATGTTAT-TATGCGTTTACTATTTTG
1 TTATCAATAATTTACTATTAAGTTATCAATG-ATTTACTATTAAA
** * * * *** * *
1162397 TTATCTTTAATTTGCTATTTAGTTTTTTGTTATTTACTATAAAA
1 TTATCAATAATTTACTATTAAGTTATCAATGATTTACTATTAAA
* * ** * * * * *
1162441 TAATC-ATAAATTTATTACAAAATTAATC-ATGATTCATTATCAAG
1 TTATCAAT-AATTTACTATTAAGTT-ATCAATGATTTACTATTAAA
* * * * *
1162485 TTATCACTAATTTA-TATTAAATTATCTATAATTTACTATTAAG
1 TTATCAATAATTTACTATTAAGTTATCAATGATTTACTATTAAA
* * * *
1162528 TTATTAATGATTAACTACTACTAAGTTAT--ATCGATTTACTTTTAAA
1 TTATCAATAATT---TACTATTAAGTTATCAAT-GATTTACTATTAAA
** * * * *
1162574 TT-TCAATAATAAACTACTAAATTATCATTGATTTAATATTAAA
1 TTATCAATAATTTACTATTAAGTTATCAATGATTTACTATTAAA
1162617 TTAT
1 TTAT
1162621 TTATAACTTA
Statistics
Matches: 393, Mismatches: 115, Indels: 62
0.69 0.20 0.11
Matches are distributed among these distances:
42 17 0.04
43 50 0.13
44 250 0.64
45 17 0.04
46 15 0.04
47 10 0.03
48 3 0.01
50 2 0.01
51 24 0.06
52 4 0.01
53 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.46
Consensus pattern (44 bp):
TTATCAATAATTTACTATTAAGTTATCAATGATTTACTATTAAA
Found at i:1162246 original size:66 final size:65
Alignment explanation
Indices: 1162109--1162296 Score: 200
Period size: 66 Copynumber: 2.8 Consensus size: 65
1162099 CTAAGCTATC
* * * * *
1162109 AATGATATATTATTAAATTATCAATAATTTACTACTAAATTAG-TATTGATTTACTATTAACTTA
1 AATGATTTATTATTAAATTAT-AATGATTTACTATTAAATT-GTTAATGATTTACTATTAAATTA
1162173 TG
64 TG
*
1162175 AATGATTTATTATTAAGTTATGAATGATTTACTATTAAATTGTTAATGATTTACTATTAAATTAT
1 AATGATTTATTATTAAATTAT-AATGATTTACTATTAAATTGTTAATGATTTACTATTAAATTA-
1162240 TG
64 TG
* * * * * * *
1162242 -ATGATTTGTAATAAAATTATAACTGATTTATTATTAATTTATTAATGAGTTACTA
1 AATGATTTATTATTAAATTATAA-TGATTTACTATTAAATTGTTAATGATTTACTA
1162297 CAAAGATATT
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 3 0.03
66 99 0.95
67 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (65 bp):
AATGATTTATTATTAAATTATAATGATTTACTATTAAATTGTTAATGATTTACTATTAAATTATG
Found at i:1162531 original size:22 final size:22
Alignment explanation
Indices: 1162315--1162663 Score: 83
Period size: 22 Copynumber: 15.8 Consensus size: 22
1162305 TTAATAATTA
* *
1162315 ATAATTTACTACTAAATTATCA
1 ATAATTTACTATTAAATTATCT
*
1162337 ATAATTTAC-ATATAAATTATCA
1 ATAATTTACTAT-TAAATTATCT
* * **
1162359 ATGAGTTACTATTATGTTAT-T
1 ATAATTTACTATTAAATTATCT
** ***
1162380 ATGCGTTTACTATTTTGTTATCT
1 AT-AATTTACTATTAAATTATCT
* * * * * *
1162403 TTAATTTGCTATTTAGTTTTTT
1 ATAATTTACTATTAAATTATCT
* * * *
1162425 GTTATTTACTATAAAATAATC-
1 ATAATTTACTATTAAATTATCT
* **
1162446 ATAAATTTATTACAAAATTAATC-
1 AT-AATTTACTATTAAATT-ATCT
* * * * *
1162469 ATGATTCATTATCAAGTTATC-
1 ATAATTTACTATTAAATTATCT
1162490 ACTAATTTA-TATTAAATTATCT
1 A-TAATTTACTATTAAATTATCT
*
1162512 ATAATTTACTATTAAGTTAT-T
1 ATAATTTACTATTAAATTATCT
* * *
1162533 AATGATTAACTACTACTAAGTTA--T
1 -ATAATT---TACTATTAAATTATCT
* * *
1162557 ATCGATTTACTTTTAAATT-TCA
1 AT-AATTTACTATTAAATTATCT
** *
1162579 ATAATAAACTACTAAATTATC-
1 ATAATTTACTATTAAATTATCT
* * *
1162600 ATTGATTTAATATTAAATTATTT
1 A-TAATTTACTATTAAATTATCT
* *
1162623 ATAACTTACTACTAAATTTATCT
1 ATAATTTACTATTAAA-TTATCT
*
1162646 ATTAA-TTACTACTAAATT
1 A-TAATTTACTATTAAATT
1162664 GAAATTTACT
Statistics
Matches: 243, Mismatches: 63, Indels: 42
0.70 0.18 0.12
Matches are distributed among these distances:
21 47 0.19
22 147 0.60
23 29 0.12
24 8 0.03
25 12 0.05
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (22 bp):
ATAATTTACTATTAAATTATCT
Found at i:1162709 original size:11 final size:11
Alignment explanation
Indices: 1162677--1162733 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
1162667 ATTTACTTAC
1162677 TATTAAGTTAT
1 TATTAAGTTAT
*
1162688 T-TCTAATTTAT
1 TAT-TAAGTTAT
1162699 TATTAAGTTAT
1 TATTAAGTTAT
* * *
1162710 AATTAATTTTT
1 TATTAAGTTAT
1162721 TATTAAGTTAT
1 TATTAAGTTAT
1162732 TA
1 TA
1162734 ATAATTAACA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 1 0.03
11 34 0.94
12 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (11 bp):
TATTAAGTTAT
Found at i:1162738 original size:22 final size:22
Alignment explanation
Indices: 1162677--1162739 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
1162667 ATTTACTTAC
**
1162677 TATTAAGTTATTTCTAATTTAT
1 TATTAAGTTATTAATAATTTAT
*
1162699 TATTAAGTTA-TAATTAATTTTT
1 TATTAAGTTATTAA-TAATTTAT
1162721 TATTAAGTTATTAATAATT
1 TATTAAGTTATTAATAATT
1162740 AACAACTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.89
23 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (22 bp):
TATTAAGTTATTAATAATTTAT
Found at i:1163260 original size:22 final size:22
Alignment explanation
Indices: 1163247--1163289 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1163237 ATTTACTACT
* *
1163247 AATTTATCGATAATTCACTAAA
1 AATTTATCAATAATTAACTAAA
1163269 AATTTATCAATAATTAACTAA
1 AATTTATCAATAATTAACTAA
1163290 TATACTACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTTATCAATAATTAACTAAA
Found at i:1163572 original size:22 final size:21
Alignment explanation
Indices: 1163528--1163573 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
1163518 GTTGTTATTA
*
1163528 ATTTATATTAAATTATGCATG
1 ATTTATATTAAATTATACATG
1163549 ATTTATTATTAAATTATTAC-TG
1 ATTTA-TATTAAATTA-TACATG
1163571 ATT
1 ATT
1163574 AACTATTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 15 0.68
23 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (21 bp):
ATTTATATTAAATTATACATG
Found at i:1163580 original size:22 final size:22
Alignment explanation
Indices: 1163533--1163581 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1163523 TATTAATTTA
* * *
1163533 TATTAAATTATGCATGATTTAT
1 TATTAAATTATACATGATTAAC
1163555 TATTAAATTATTAC-TGATTAAC
1 TATTAAATTA-TACATGATTAAC
1163577 TATTA
1 TATTA
1163582 TGTTATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (22 bp):
TATTAAATTATACATGATTAAC
Found at i:1163740 original size:22 final size:22
Alignment explanation
Indices: 1163715--1163796 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
1163705 ACTAAAGTTG
* *
1163715 ATTTACTATTAAATTATTACTA
1 ATTTACTACTAAATTATTAATA
* *
1163737 ATTT-CTACTAAATTATTATTG
1 ATTTACTACTAAATTATTAATA
* *
1163758 ATTTATTACTAAATTATCAATA
1 ATTTACTACTAAATTATTAATA
*
1163780 ATTAACTACTAAATTAT
1 ATTTACTACTAAATTAT
1163797 CACTTTTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 18 0.36
22 32 0.64
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (22 bp):
ATTTACTACTAAATTATTAATA
Found at i:1163759 original size:43 final size:44
Alignment explanation
Indices: 1163712--1163796 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 44
1163702 TAAACTAAAG
* * * *
1163712 TTGATTTACTATTAAATTATTACTAATT-TCTACTAAATTATTA
1 TTGATTTACTACTAAATTATCAATAATTAACTACTAAATTATTA
*
1163755 TTGATTTATTACTAAATTATCAATAATTAACTACTAAATTAT
1 TTGATTTACTACTAAATTATCAATAATTAACTACTAAATTAT
1163797 CACTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 24 0.67
44 12 0.33
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.48
Consensus pattern (44 bp):
TTGATTTACTACTAAATTATCAATAATTAACTACTAAATTATTA
Found at i:1163774 original size:11 final size:11
Alignment explanation
Indices: 1163724--1163796 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 11
1163714 GATTTACTAT
1163724 TAAATTATTAC
1 TAAATTATTAC
1163735 T-AATT-TCTAC
1 TAAATTAT-TAC
*
1163745 TAAATTATTAT
1 TAAATTATTAC
* *
1163756 TGATTTATTAC
1 TAAATTATTAC
* *
1163767 TAAATTATCAA
1 TAAATTATTAC
*
1163778 T-AATTAACTAC
1 TAAATT-ATTAC
1163789 TAAATTAT
1 TAAATTAT
1163797 CACTTTTTTT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
9 1 0.02
10 12 0.27
11 27 0.60
12 5 0.11
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (11 bp):
TAAATTATTAC
Found at i:1163961 original size:22 final size:22
Alignment explanation
Indices: 1163936--1164006 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
1163926 TACTAAAAAG
1163936 TTATCAATT-ATTTATTACTAAA
1 TTATC-ATTAATTTATTACTAAA
** * * *
1163958 TTATTGTTCATTTATTATTAAG
1 TTATCATTAATTTATTACTAAA
* *
1163980 TTATCATTAATTTATCAATAAA
1 TTATCATTAATTTATTACTAAA
1164002 TTATC
1 TTATC
1164007 GATGATTATT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 2 0.05
22 36 0.95
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (22 bp):
TTATCATTAATTTATTACTAAA
Found at i:1166448 original size:17 final size:17
Alignment explanation
Indices: 1166421--1166476 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 17
1166411 TTTATTTTAA
1166421 AAATTTT-ATTATACAT
1 AAATTTTAATTATACAT
1166437 AAATTTTAATTATACA-
1 AAATTTTAATTATACAT
* *
1166453 AAATATTAA-AATACAT
1 AAATTTTAATTATACAT
1166469 -AATTTTAA
1 AAATTTTAA
1166477 AAAATAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 12 0.34
16 15 0.43
17 8 0.23
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTTAATTATACAT
Found at i:1166476 original size:15 final size:15
Alignment explanation
Indices: 1166431--1166478 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1166421 AAATTTTATT
*
1166431 ATACATAAATTTTAATT
1 ATACAT-AATTTTAA-A
* *
1166448 ATACAAAATATTAAA
1 ATACATAATTTTAAA
1166463 ATACATAATTTTAAA
1 ATACATAATTTTAAA
1166478 A
1 A
1166479 AATAAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 14 0.54
16 7 0.27
17 5 0.19
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
ATACATAATTTTAAA
Found at i:1172991 original size:34 final size:34
Alignment explanation
Indices: 1172944--1173060 Score: 198
Period size: 34 Copynumber: 3.4 Consensus size: 34
1172934 TCATGTACCC
* *
1172944 ATAAGCTGTTGCTGTCATGTAGTGGAAAAGACAA
1 ATAAGCTGCTGCTGTCATGTAGTGGAAAAGAAAA
1172978 ATAAGCTGCTGCTGTCATGTAGTGGAAAAGAAAA
1 ATAAGCTGCTGCTGTCATGTAGTGGAAAAGAAAA
*
1173012 ATAAGCTGCTTGCTTTCATGTAGTGGAAAAGAAAA
1 ATAAGCTGC-TGCTGTCATGTAGTGGAAAAGAAAA
1173047 ATAAGCTGCTGCTG
1 ATAAGCTGCTGCTG
1173061 CTAGCTGCTG
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
34 45 0.58
35 33 0.42
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (34 bp):
ATAAGCTGCTGCTGTCATGTAGTGGAAAAGAAAA
Found at i:1175749 original size:191 final size:186
Alignment explanation
Indices: 1175436--1176109 Score: 470
Period size: 191 Copynumber: 3.6 Consensus size: 186
1175426 CTTCCAGATG
* * * * * ** *
1175436 GGATTATTCTTACTTTAAATAATACCTTTTAATTATGAAAATACTGGAGTAGCTCAATCGACTAG
1 GGATTATTTTTACGTTAAATAATACCTTTTAATTATAAAAACACTAGAGTAGCTCAATCGGTTAA
* * ** * ** * * * *
1175501 AGTATATAGTTGTTAATCATAAGGTTGTAGGTTTGATCCCTCATTTTAGCGTTTTTTGGGTTTTT
66 AGCATACAACTGTTAATCATAAAGTCATAAGTTTGATCCCTCATTCTAGCATTTTTTGAGTTTTT
* * *
1175566 CAAGAGATTATT-AAGGTGTTAATAATCCCAA-AAAAATGGGA-GGAATAATCCCCTCT-GGAA
131 CAA-AGATTATTCAAAGTGTT--T--T-CCAACAAAAAT-GCATCGAATAATCCCCTCTAGG-A
* *
1175626 TGGATTATTTTTACGTTAAATAATACCTTTTAATTATAAAAACACTAAAGTAGCTCAATTGGTTA
1 -GGATTATTTTTACGTTAAATAATACCTTTTAATTATAAAAACACTAGAGTAGCTCAATCGGTTA
*
1175691 AAGCATACAACTGTTAA-CAATAAAGTCATAAGTTTGATCCCTTC-TTCTAGTATTTTTTGAGTT
65 AAGCATACAACTGTTAATC-ATAAAGTCATAAGTTTGATCCC-TCATTCTAGCATTTTTTGAGTT
* * * *
1175754 TTTCAAAGATTTTTCAAAGTGTTTTCTAACTAAAAATGCATCGAATGATCCCCTCTATGA
128 TTTCAAAGATTATTCAAAGTGTTTTCCAAC-AAAAATGCATCGAATAATCCCCTCTAGGA
* * * *
1175814 GGAAATTATTTTTA-GTTTAAATAATAGCTTTTAATTATAAAAACACTAGATTAGCTTAATCAGT
1 GG--ATTATTTTTACG-TTAAATAATACCTTTTAATTATAAAAACACTAGAGTAGCTCAATCGGT
* ** * * ** * ** * * *
1175878 TAAAGCATACAACTATTAATCATAAAGTTGTAGGCTCAATCTCTTTTTTTAACATGAGTTTTTTA
63 TAAAGCATACAACTGTTAATCATAAAGTCATAAGTTTGATCCCTCATTCTAGCAT---TTTTTGA
* * * ** * * *
1175943 GATTTTTCAAGGATTATTCAAAATATTTTTGATAAAAAAACT-C-TTGAATAATCCCCTCTTGGA
125 G-TTTTTCAAAGATTATTCAAAGTGTTTTCCA-ACAAAAA-TGCATCGAATAATCCCCTCTAGG-
1176006 A
186 A
* * * *
1176007 GAGATTATTCTTA-GTTTAAATAATAGCTTTTAATTATAAAAACACTAGAGTAACTCAAT-GATT
1 G-GATTATTTTTACG-TTAAATAATACCTTTTAATTATAAAAACACTAGAGTAGCTCAATCGGTT
* * * * * * *
1176070 ATAGCACACAACTATTAATTATAATGTCGTAGGTTTGATC
64 AAAGCATACAACTGTTAATCATAAAGTCATAAGTTTGATC
1176110 TTTTCCTTGA
Statistics
Matches: 390, Mismatches: 73, Indels: 40
0.78 0.15 0.08
Matches are distributed among these distances:
186 3 0.01
187 5 0.01
188 22 0.06
189 93 0.24
190 9 0.02
191 147 0.38
192 76 0.19
193 32 0.08
194 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (186 bp):
GGATTATTTTTACGTTAAATAATACCTTTTAATTATAAAAACACTAGAGTAGCTCAATCGGTTAA
AGCATACAACTGTTAATCATAAAGTCATAAGTTTGATCCCTCATTCTAGCATTTTTTGAGTTTTT
CAAAGATTATTCAAAGTGTTTTCCAACAAAAATGCATCGAATAATCCCCTCTAGGA
Found at i:1176050 original size:192 final size:189
Alignment explanation
Indices: 1175608--1176102 Score: 515
Period size: 189 Copynumber: 2.6 Consensus size: 189
1175598 AAAATGGGAG
*
1175608 GAATAATCCCCTC-TGGAATG-GATTATTTTTACG-TTAAATAATACCTTTTAATTATAAAAACA
1 GAATAATCCCCTCTTGGAA-GAGATTATTTTTA-GTTTAAATAATAGCTTTTAATTATAAAAACA
* ** * * * * **
1175670 CTAAAGTAGCTCAATTGGTTAAAGCATACAACTGTTAA-CAATAAAGTCATAAGTTTGATCCCTT
64 CTAGAGTAGCTCAATCAGTTAAAGCATACAACTATTAATC-ATAAAGTCGTAGGCTCAATCCCTT
* * * * **
1175734 CTTCTAGTATTTTTTGAGTTTTTCAAAGATTTTTCAAAGTGTTTTCTAACTAAAAATGCATC
128 CTTCTAATATTTTTTGAGTTTTTCAAAGATTATTCAAAATATTTTCTAACTAAAAAAACATC
* * *
1175796 GAATGATCCCCTCTAT-GAGGAAATTATTTTTAGTTTAAATAATAGCTTTTAATTATAAAAACAC
1 GAATAATCCCCTCT-TGGAAGAGATTATTTTTAGTTTAAATAATAGCTTTTAATTATAAAAACAC
* * * * *
1175860 TAGATTAGCTTAATCAGTTAAAGCATACAACTATTAATCATAAAGTTGTAGGCTCAATCTCTTTT
65 TAGAGTAGCTCAATCAGTTAAAGCATACAACTATTAATCATAAAGTCGTAGGCTCAATCCCTTCT
* * *
1175925 TTTAACATGAGTTTTTT-AGATTTTTCAAGGATTATTCAAAATATTTT-TGA-TAAAAAAAC-TC
130 TCT-A-AT-A-TTTTTTGAG-TTTTTCAAAGATTATTCAAAATATTTTCTAACTAAAAAAACATC
*
1175986 TTGAATAATCCCCTCTTGGAAGAGATTATTCTTAGTTTAAATAATAGCTTTTAATTATAAAAACA
1 --GAATAATCCCCTCTTGGAAGAGATTATTTTTAGTTTAAATAATAGCTTTTAATTATAAAAACA
* * * * * *
1176051 CTAGAGTAACTCAATGA-TTATAGCACACAACTATTAATTATAATGTCGTAGG
64 CTAGAGTAGCTCAATCAGTTAAAGCATACAACTATTAATCATAAAGTCGTAGG
1176103 TTTGATCTTT
Statistics
Matches: 254, Mismatches: 40, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
188 14 0.06
189 92 0.36
190 5 0.02
191 39 0.15
192 75 0.30
193 29 0.11
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (189 bp):
GAATAATCCCCTCTTGGAAGAGATTATTTTTAGTTTAAATAATAGCTTTTAATTATAAAAACACT
AGAGTAGCTCAATCAGTTAAAGCATACAACTATTAATCATAAAGTCGTAGGCTCAATCCCTTCTT
CTAATATTTTTTGAGTTTTTCAAAGATTATTCAAAATATTTTCTAACTAAAAAAACATC
Found at i:1179613 original size:23 final size:20
Alignment explanation
Indices: 1179575--1179618 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 20
1179565 AATTTTGCTG
1179575 ATTTATTCATTAATCTTTTA
1 ATTTATTCATTAATCTTTTA
1179595 ATTTATTACATTATTATCTTTTA
1 ATTTATT-CATTA--ATCTTTTA
1179618 A
1 A
1179619 ATATTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
23 9 0.43
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTATTCATTAATCTTTTA
Found at i:1179662 original size:18 final size:19
Alignment explanation
Indices: 1179628--1179663 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1179618 AATATTTTGT
1179628 TATTTTCTAACTAAATATA
1 TATTTTCTAACTAAATATA
*
1179647 TATTTT-TAATTAAATAT
1 TATTTTCTAACTAAATAT
1179664 GTTCAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTTCTAACTAAATATA
Found at i:1180865 original size:19 final size:19
Alignment explanation
Indices: 1180837--1180874 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1180827 ATATATCAAG
* *
1180837 ATAATGATATATTTTTCTT
1 ATAATCATATATCTTTCTT
1180856 ATAATCATATATCTTTCTT
1 ATAATCATATATCTTTCTT
1180875 CATATACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (19 bp):
ATAATCATATATCTTTCTT
Found at i:1194795 original size:21 final size:21
Alignment explanation
Indices: 1194757--1194797 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1194747 ATACAATATA
*
1194757 TTTAAAAATCAAATAAATAAG
1 TTTAAAAATCAAAGAAATAAG
1194778 TTTAAAAAT-ATAAGAAATAA
1 TTTAAAAATCA-AAGAAATAA
1194798 TATCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (21 bp):
TTTAAAAATCAAAGAAATAAG
Found at i:1195011 original size:15 final size:14
Alignment explanation
Indices: 1194991--1195028 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
1194981 AACTTTGGTT
*
1194991 TAAAAAATTAAAATA
1 TAAAAAAATAAAA-A
1195006 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
1195020 TAAAAAAAT
1 TAAAAAAAT
1195029 TCAATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:1195013 original size:16 final size:15
Alignment explanation
Indices: 1194992--1195029 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
1194982 ACTTTGGTTT
1194992 AAAAAATTAAAATATA
1 AAAAAATTAAAA-ATA
1195008 AAAAAA-TAAAAATA
1 AAAAAATTAAAAATA
1195022 AAAAAATT
1 AAAAAATT
1195030 CAATTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 6 0.29
16 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAAATTAAAAATA
Found at i:1195801 original size:29 final size:28
Alignment explanation
Indices: 1195754--1195889 Score: 107
Period size: 32 Copynumber: 4.6 Consensus size: 28
1195744 TGTTAACTCA
*
1195754 TATTAATTA-TATAATAATAAATTTTATT
1 TATTATTTATTAT-ATAATAAATTTTATT
*
1195782 TATTATTGTATTATGTAATAATAAAATTTATT
1 TATTATT-TATTA--T-ATAATAAATTTTATT
*
1195814 TATTAGTTCATAATATAATAATAAATTTTATT
1 TATTA-TT--TATTAT-ATAATAAATTTTATT
* *
1195846 AATTAATTTATTATATAATAAGTTTTATT
1 TATT-ATTTATTATATAATAAATTTTATT
*
1195875 TA-TATTAATTA-ATAA
1 TATTATTTATTATATAA
1195890 AATTATTTTA
Statistics
Matches: 91, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
26 4 0.04
27 7 0.08
28 7 0.08
29 17 0.19
30 7 0.08
32 42 0.46
33 3 0.03
34 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (28 bp):
TATTATTTATTATATAATAAATTTTATT
Found at i:1195801 original size:32 final size:31
Alignment explanation
Indices: 1195754--1195866 Score: 145
Period size: 32 Copynumber: 3.5 Consensus size: 31
1195744 TGTTAACTCA
*
1195754 TATTAATTATATAATAATAAATTTTATTTAT
1 TATTTATTATATAATAATAAATTTTATTTAT
* *
1195785 TATTGTATTATGTAATAATAAAATTTATTTAT
1 TATT-TATTATATAATAATAAATTTTATTTAT
* * *
1195817 TAGTTCATAATATAATAATAAATTTTATTAAT
1 TA-TTTATTATATAATAATAAATTTTATTTAT
1195849 TAATTTATTATATAATAA
1 T-ATTTATTATATAATAA
1195867 GTTTTATTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.06
32 62 0.90
33 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (31 bp):
TATTTATTATATAATAATAAATTTTATTTAT
Found at i:1208471 original size:19 final size:20
Alignment explanation
Indices: 1208444--1208482 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1208434 CTATTTTTCA
1208444 GCTTATTATTT-TGAGCTTT
1 GCTTATTATTTCTGAGCTTT
*
1208463 GCTTTTTATTTCTGAGCTTT
1 GCTTATTATTTCTGAGCTTT
1208483 CTCCTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.59
Consensus pattern (20 bp):
GCTTATTATTTCTGAGCTTT
Found at i:1222553 original size:39 final size:39
Alignment explanation
Indices: 1222504--1222631 Score: 177
Period size: 39 Copynumber: 3.3 Consensus size: 39
1222494 GGAGGGGGGT
*
1222504 GGGA-GGATTGGGTGTGGTGGGGCGTTGGGGGGAAGGTG
1 GGGAGGGATTGGGTGTGGTGGGGTGTTGGGGGGAAGGTG
* *
1222542 GGGAGGGATTGGGTGTGGTAGGGTGTTGGGAGGAAGGTG
1 GGGAGGGATTGGGTGTGGTGGGGTGTTGGGGGGAAGGTG
* * *
1222581 GGGAAGGATCGGGTGTGGTGGGATGTTGGGAGGGAAGGTG
1 GGGAGGGATTGGGTGTGGTGGGGTGTTGGG-GGGAAGGTG
*
1222621 GAGAGGGATTG
1 GGGAGGGATTG
1222632 ATGGGGTGGG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 4 0.05
39 57 0.74
40 16 0.21
ACGTcount: A:0.16, C:0.02, G:0.62, T:0.21
Consensus pattern (39 bp):
GGGAGGGATTGGGTGTGGTGGGGTGTTGGGGGGAAGGTG
Found at i:1222648 original size:44 final size:43
Alignment explanation
Indices: 1222527--1222648 Score: 100
Period size: 39 Copynumber: 3.0 Consensus size: 43
1222517 GTGGTGGGGC
* *
1222527 GTTGGG-GGGAAGGTGGGGAGGGATTG--GGTGT-GGTAGGG-T
1 GTTGGGAGGGAAGGT-GGGAGGGATTGATGGGGTGGGGAGGGAT
** * * *
1222566 GTTGGGA-GGAAGGT--G-GGGAAGGATCGGGTGTGGTGGGAT
1 GTTGGGAGGGAAGGTGGGAGGGATTGATGGGGTGGGGAGGGAT
1222605 GTTGGGAGGGAAGGTGGAGAGGGATTGATGGGGTGGGGAGGGAT
1 GTTGGGAGGGAAGGTGG-GAGGGATTGATGGGGTGGGGAGGGAT
1222649 TGAGTGTGGT
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
35 5 0.08
36 1 0.02
37 3 0.05
38 4 0.07
39 21 0.34
40 7 0.11
43 1 0.02
44 19 0.31
ACGTcount: A:0.17, C:0.01, G:0.61, T:0.20
Consensus pattern (43 bp):
GTTGGGAGGGAAGGTGGGAGGGATTGATGGGGTGGGGAGGGAT
Found at i:1222902 original size:20 final size:20
Alignment explanation
Indices: 1222865--1222901 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1222855 ATTGTGTTAT
*
1222865 ATATTAATTTATAATTTTGC
1 ATATGAATTTATAATTTTGC
1222885 ATATGAATTT-TAATTTT
1 ATATGAATTTATAATTTT
1222902 TTTTGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
ATATGAATTTATAATTTTGC
Found at i:1223153 original size:25 final size:26
Alignment explanation
Indices: 1223125--1223173 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1223115 CTAAAAAATA
*
1223125 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
1223150 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
1223174 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:1226590 original size:6 final size:6
Alignment explanation
Indices: 1226581--1226629 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
1226571 TTTAAGTCCA
* * *
1226581 GATGAT GATGGT GATGGA GATGGT GATGGA GATGGT GATGGT GATGGT
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT
1226629 G
1 G
1226630 CGAATTTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.22, C:0.00, G:0.49, T:0.29
Consensus pattern (6 bp):
GATGGT
Found at i:1226996 original size:18 final size:18
Alignment explanation
Indices: 1226973--1227097 Score: 114
Period size: 18 Copynumber: 6.9 Consensus size: 18
1226963 ATGGTTATTA
1226973 TCCACCTCAAATGTATCC
1 TCCACCTCAAATGTATCC
*
1226991 TCCACCTCCTCAAATATATCC
1 TCCA---CCTCAAATGTATCC
*
1227012 TCCACCTCAAATGTATCAG
1 TCCACCTCAAATGTATC-C
* * *
1227031 T-TACCACAAATGTACCC
1 TCCACCTCAAATGTATCC
* *
1227048 TCCACCACAAATGTATCA
1 TCCACCTCAAATGTATCC
*
1227066 T---CCTCAAATATATCC
1 TCCACCTCAAATGTATCC
1227081 TCCACCTCAAATGTATC
1 TCCACCTCAAATGTATC
1227098 AAGAACAAAG
Statistics
Matches: 85, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
15 12 0.14
17 1 0.01
18 54 0.64
19 1 0.01
21 17 0.20
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.27
Consensus pattern (18 bp):
TCCACCTCAAATGTATCC
Found at i:1227003 original size:21 final size:21
Alignment explanation
Indices: 1226977--1227019 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1226967 TTATTATCCA
*
1226977 CCTCAAATGTATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
1226998 CCTCAAATATATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
1227019 C
1 C
1227020 AAATGTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.44, G:0.02, T:0.28
Consensus pattern (21 bp):
CCTCAAATATATCCTCCACCT
Found at i:1240828 original size:99 final size:99
Alignment explanation
Indices: 1240657--1240859 Score: 406
Period size: 99 Copynumber: 2.1 Consensus size: 99
1240647 TTGATTCATA
1240657 TAGTATGCATGAAAATGATACTTGATCCTATAAAGTATATGAGCCTATAGTTGTTAGGCTATGGT
1 TAGTATGCATGAAAATGATACTTGATCCTATAAAGTATATGAGCCTATAGTTGTTAGGCTATGGT
1240722 TTGCTGATTCTCTTTTTTCTTTCTCTTTACAGAT
66 TTGCTGATTCTCTTTTTTCTTTCTCTTTACAGAT
1240756 TAGTATGCATGAAAATGATACTTGATCCTATAAAGTATATGAGCCTATAGTTGTTAGGCTATGGT
1 TAGTATGCATGAAAATGATACTTGATCCTATAAAGTATATGAGCCTATAGTTGTTAGGCTATGGT
1240821 TTGCTGATTCTCTTTTTTCTTTCTCTTTACAGAT
66 TTGCTGATTCTCTTTTTTCTTTCTCTTTACAGAT
1240855 TAGTA
1 TAGTA
1240860 AGTGATAAGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 104 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (99 bp):
TAGTATGCATGAAAATGATACTTGATCCTATAAAGTATATGAGCCTATAGTTGTTAGGCTATGGT
TTGCTGATTCTCTTTTTTCTTTCTCTTTACAGAT
Found at i:1242430 original size:138 final size:138
Alignment explanation
Indices: 1242196--1242458 Score: 382
Period size: 138 Copynumber: 1.9 Consensus size: 138
1242186 GTTCTGATGG
* * * * *
1242196 TGGTGGATCCCATGTCCCTATTTGCCTTTTAGGTAGCTTAATTGATGGTGCATAGAACCTATTTC
1 TGGTGGATCCCATGCCCCTATTTGCCTTTTAGGTAGCTCAATTGATGGTGCAAAGAAACTAATTC
* * * * * *
1242261 CAGCGTTCAGGTCTCCCCTTCTTCTTGGTCATCTCATCTTAATTTTGTCAACCGGTCAATGGGGT
66 CAACATTCAGGTCTCCCCTTCTTCTTAGTCATCTCATCTCAATTTTCTCAACCAGTCAATGGGGT
1242326 TCTGCAAT
131 TCTGCAAT
* * * *
1242334 TGGTGGATCCCTTGCCCCTGTTTGCTTTTTGGGTAGCTCAATTGATGGTGCAAAGAAACTAATTC
1 TGGTGGATCCCATGCCCCTATTTGCCTTTTAGGTAGCTCAATTGATGGTGCAAAGAAACTAATTC
*
1242399 CAACATTCAGGTCTCCCCTTCTTCTTAGTCATCTCATCTCAATTTTCTGAACCAGTCAAT
66 CAACATTCAGGTCTCCCCTTCTTCTTAGTCATCTCATCTCAATTTTCTCAACCAGTCAAT
1242459 ACTGCATCAA
Statistics
Matches: 109, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 109 1.00
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (138 bp):
TGGTGGATCCCATGCCCCTATTTGCCTTTTAGGTAGCTCAATTGATGGTGCAAAGAAACTAATTC
CAACATTCAGGTCTCCCCTTCTTCTTAGTCATCTCATCTCAATTTTCTCAACCAGTCAATGGGGT
TCTGCAAT
Found at i:1245820 original size:219 final size:218
Alignment explanation
Indices: 1245557--1246585 Score: 1452
Period size: 219 Copynumber: 4.7 Consensus size: 218
1245547 GTTATCTACC
* * ** * * * *
1245557 TGCAACATCAGTGAATTTCCATATTTTGTTGGAACTCTAGAAGGTTTGGAACACCTAGACCTTTC
1 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAACATCTAGATCTCTC
* * ** * *
1245622 TTGCAACAAAATCCGTGTTATAGAGGCAGATATGTTTTCAAAGCTCAAAAATCTCAGTTGGCTTG
66 TTACAACAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTCAG-TGGCTTG
* * * * * * * *
1245687 ATCTTTCACTCAATAGTCAAATATCTCTGAGCACCTCCACCGATGTCAGCCTTTTCTTTCCCAAC
130 ATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTCTTTCCCAAC
*
1245752 CTTCGGTCATTGTCATGTTCTTCT
195 CTTAGGTCATTGTCATGTTCTTCT
1245776 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAACA-CTAGA-CTCT-
1 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAACATCTAGATCTCTC
* * * * * *
1245838 TTGCAACAAAATC--TGTTATAGAGGCAGGTATGTTTTCAAAGCTCAAAAATCTCACGTCGCTTG
66 TTACAACAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTCA-GTGGCTTG
* *
1245901 ATCTTT-CC-C-ATAGTCAACTATCACTGAGTAACACCAACAACGTCAGCC-TTTCTCTTCCCAA
130 ATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTCT-TTCCCAA
*
1245962 CCTTAGGTCATTGTCATTTTCTTCT
194 CCTTAGGTCATTGTCATGTTCTTCT
* *
1245987 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAATATCTAGATCTTTC
1 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAACATCTAGATCTCTC
*
1246052 TTACAACAGAATCAATGTTATTGAGAC-G-TATGTTTTCAAAGCTCAAGAATCTCACGTGGCTTG
66 TTACAACAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTCA-GTGGCTTG
1246115 ATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTC-TTCCCAAC
130 ATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTCTTTCCCAAC
*
1246179 CTTAAGTCATTGTCATGTTCTTCT
195 CTTAGGTCATTGTCATGTTCTTCT
*
1246203 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAAGATCTAGATCTCTC
1 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAACATCTAGATCTCTC
* * *
1246268 TTACAATAGAATCAATGTTATTGAGGCAGATATTGGTTTCAAAGCTCAAGAATCTCCGGTGGCTT
66 TTACAACAGAATCAATGTTATTGAGGCAGATA-TGTTTTCAAAGCTCAAGAATCT-CAGTGGCTT
*
1246333 GATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTCCTTCCCAA
129 GATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTCTTTCCCAA
*
1246398 CCTTGGGTCATTGTCATGTTCTTCT
194 CCTTAGGTCATTGTCATGTTCTTCT
**
1246423 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAAGTTCTAGATCTCTC
1 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAACATCTAGATCTCTC
* * *
1246488 TTACAATAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTCTGGCGGCTTG
66 TTACAACAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTC-AGTGGCTTG
* * * *
1246553 ATCTTTCCTACAACAGTGAACTATCACTCAGCA
130 ATCTTTCCCACAATAGTCAACTATCACTGAGCA
1246586 CCAATCTCAG
Statistics
Matches: 747, Mismatches: 46, Indels: 34
0.90 0.06 0.04
Matches are distributed among these distances:
210 5 0.01
211 113 0.15
212 6 0.01
213 4 0.01
214 102 0.14
215 4 0.01
216 142 0.19
217 41 0.05
218 12 0.02
219 191 0.26
220 127 0.17
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (218 bp):
TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAACATCTAGATCTCTC
TTACAACAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTCAGTGGCTTGA
TCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTCTTTCCCAACC
TTAGGTCATTGTCATGTTCTTCT
Found at i:1246432 original size:436 final size:429
Alignment explanation
Indices: 1245557--1246585 Score: 1467
Period size: 436 Copynumber: 2.4 Consensus size: 429
1245547 GTTATCTACC
* * ** * * * *
1245557 TGCAACATCAGTGAATTTCCATATTTTGTTGGAACTCTAGAAGGTTTGGAACACCTAGACCTTTC
1 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAATATCTAGATCTTTC
* * ** * *
1245622 TTGCAACAAAATCCGTGTTATAGAGGCAGATATGTTTTCAAAGCTCAAAAATCTCAGTTGGCTTG
66 TTACAACAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTCAG-TGGCTTG
* * * * * * * *
1245687 ATCTTTCACTCAATAGTCAAATATCTCTGAGCACCTCCACCGATGTCAGCCTTTTCTTTCCCAAC
130 ATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTCTTTCCCAAC
**
1245752 CTTCGGTCATTGTCATGTTCTTCTTGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGA
195 CTTAAGTCATTGTCATGTTCTTCTTGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGA
* * *
1245817 AGGTTTGGAACACTAGACTCTTTGCAACAAAATCTGTTATAGAGGCAGGTATGTTTTCAAAGCTC
260 AGGTTTGGAACACTAGACTCTTTACAACAAAATCTGTTATAGAGGCAGATATGGTTTCAAAGCTC
*
1245882 AAAAATCTCACGTCGCTTGATCTTTCCCATAGTCAACTATCACTGAGTAACACCAACAACGTCAG
325 AAAAATCTCACGTCGCTTGATCTTTCCCATAGTCAACTATCACTGAGCAACACCAACAACGTCAG
*
1245947 CCTTTCTCTTCCCAACCTTAGGTCATTGTCATTTTCTTCT
390 CCTTTCTCTTCCCAACCTTAGGTCATTGTCATGTTCTTCT
1245987 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAATATCTAGATCTTTC
1 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAATATCTAGATCTTTC
*
1246052 TTACAACAGAATCAATGTTATTGAGAC-G-TATGTTTTCAAAGCTCAAGAATCTCACGTGGCTTG
66 TTACAACAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTCA-GTGGCTTG
1246115 ATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTC-TTCCCAAC
130 ATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTCTTTCCCAAC
1246179 CTTAAGTCATTGTCATGTTCTTCTTGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGA
195 CTTAAGTCATTGTCATGTTCTTCTTGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGA
* * * *
1246244 AGGTTTGGAAGATCTAGATCTCTCTTACAATAGAATCAATGTTATTGAGGCAGATATTGGTTTCA
260 AGGTTTGGAACA-CTAGA-CTCT-TTACAACAAAATC--TGTTATAGAGGCAGATA-TGGTTTCA
* *
1246309 AAGCTCAAGAATCTC-CGGTGGCTTGATCTTTCCCACAATAGTCAACTATCACTGAGCAACACCA
319 AAGCTCAAAAATCTCAC-GTCGCTTGATCTTT-CC-C-ATAGTCAACTATCACTGAGCAACACCA
* *
1246373 ACAATGTCAGCCTTT-TCCTTCCCAACCTTGGGTCATTGTCATGTTCTTCT
380 ACAACGTCAGCCTTTCT-CTTCCCAACCTTAGGTCATTGTCATGTTCTTCT
*
1246423 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAAGT-TCTAGATCTCT
1 TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAA-TATCTAGATCTTT
* * *
1246487 CTTACAATAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTCTGGCGGCTT
65 CTTACAACAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTC-AGTGGCTT
* * * *
1246552 GATCTTTCCTACAACAGTGAACTATCACTCAGCA
129 GATCTTTCCCACAATAGTCAACTATCACTGAGCA
1246586 CCAATCTCAG
Statistics
Matches: 536, Mismatches: 47, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
427 82 0.15
428 85 0.16
429 6 0.01
430 88 0.16
432 16 0.03
433 34 0.06
434 2 0.00
435 2 0.00
436 158 0.29
437 2 0.00
438 61 0.11
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (429 bp):
TGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAAGGTTTGGAATATCTAGATCTTTC
TTACAACAGAATCAATGTTATTGAGGCAGATATGTTTTCAAAGCTCAAGAATCTCAGTGGCTTGA
TCTTTCCCACAATAGTCAACTATCACTGAGCAACACCAACAATGTCAGCCTTTTCTTTCCCAACC
TTAAGTCATTGTCATGTTCTTCTTGCAACATCAGTGAATTTTCAGATTTTGTAAGAAATCTAGAA
GGTTTGGAACACTAGACTCTTTACAACAAAATCTGTTATAGAGGCAGATATGGTTTCAAAGCTCA
AAAATCTCACGTCGCTTGATCTTTCCCATAGTCAACTATCACTGAGCAACACCAACAACGTCAGC
CTTTCTCTTCCCAACCTTAGGTCATTGTCATGTTCTTCT
Found at i:1255998 original size:48 final size:48
Alignment explanation
Indices: 1255916--1256010 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
1255906 AGTAGAGAAA
* *
1255916 GGCAAGAAACTTACATAAGCCGTAAAGAATAACAACATAAATTATGTG
1 GGCAAGAAACTTACATAAGCCATAAAGAACAACAACATAAATTATGTG
* * * *
1255964 GGCAAGCAACTTATATAAGTCATAGAGAACAACAACATAAATTATGT
1 GGCAAGAAACTTACATAAGCCATAAAGAACAACAACATAAATTATGT
1256011 ATCACTTCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (48 bp):
GGCAAGAAACTTACATAAGCCATAAAGAACAACAACATAAATTATGTG
Found at i:1259975 original size:48 final size:48
Alignment explanation
Indices: 1259900--1259994 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
1259890 ACATATGTGG
1259900 ACCTTAATAGCTTGTGAACTTTATTTTCAAGGTTCTGTGGTCTTAAAA
1 ACCTTAATAGCTTGTGAACTTTATTTTCAAGGTTCTGTGGTCTTAAAA
* * *
1259948 ACCTTAATAGCTTGTGAAGTTTGTTTTCAAGGTTTTGTGGTCTTAAA
1 ACCTTAATAGCTTGTGAACTTTATTTTCAAGGTTCTGTGGTCTTAAA
1259995 TACTTTCATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (48 bp):
ACCTTAATAGCTTGTGAACTTTATTTTCAAGGTTCTGTGGTCTTAAAA
Found at i:1267045 original size:58 final size:57
Alignment explanation
Indices: 1266860--1267416 Score: 541
Period size: 58 Copynumber: 9.7 Consensus size: 57
1266850 TTGTGCAGGA
* * ** * *
1266860 AAAATTGACACTTTTAACTTTTTTTC-AAAATATTTTTTAGAAATTTTAATCTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAAATTTAATTTCGAGG
*
1266917 AAAATTGATACTTTCAACTTTTTCC-C-AAAATATCTTTTT-AAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATAT-TTTTTGAAAATTTAATTTCGAGG
* * **
1266973 AAAATTGATACTTTCAATTTTTTCTCAAAAATATTTTTTGGAAACCTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAAATTTAATTTCGAGG
* * * * ** *
1267031 AAAATTGATACTTTCAACTTTTCCTCAAAAACA-ATTTTAAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTAATTTCGAGG
* * *** * * **
1267087 AAAATTAATACTTTCAATTTTTCCTCAAAAA-CCGTTTTAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTAATTTCGAGG
* * **
1267143 AAAATTGATACTTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATAC-TTTCAACTTTTCCTCAAAAA--TATTTTTTGAAAATTTAATTTCGAGG
* * ** *
1267203 AAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTTTGGAAACCTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAAATTTAATTTCGAGG
* * ** *
1267261 AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAAATTTAATTTCGAGG
* ** * *
1267320 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAACCTTAATCTCGAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAAATTTAATTTCGAGG
* *
1267378 AAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1267417 TTGGATTTTA
Statistics
Matches: 430, Mismatches: 55, Indels: 29
0.84 0.11 0.06
Matches are distributed among these distances:
55 5 0.01
56 109 0.25
57 69 0.16
58 145 0.34
59 62 0.14
60 40 0.09
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTAATTTCGAGG
Found at i:1267309 original size:117 final size:116
Alignment explanation
Indices: 1266858--1267419 Score: 667
Period size: 117 Copynumber: 4.9 Consensus size: 116
1266848 TTTTGTGCAG
* * * * ** *
1266858 GAAAAATTGACACTTTTAACTTTTTTTCAAAATATTTTTTAGAAATTTTAATCTCGAGGAAAATT
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTGGAAACCTTAATTTCGAGGAAAATT
* * * * **
1266923 GATACTTTCAACTTTTTCC-C-AAAA-TATCTTTTT-AAACTTTAATTTCGA
66 GATACTTTCAAC-TTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAA
* *
1266971 GGAAAATTGATACTTTCAATTTTTTCTCAAAAATATTTTTTGGAAACCTTAATTTCGAGGAAAAT
1 GAAAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTTGGAAACCTTAATTTCGAGGAAAAT
** *
1267036 TGATACTTTCAACTTTTCCTCAAAAAC---AATTTTAAAAATTTATTTTTAA
65 TGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAA
* ** * ** * **
1267085 GAAAAATTAATACTTTCAA-TTTTTCCTCAAAA-ACCGTTTT-AAAAATTTATTTTTAAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTT-CTCAAAATA-TTTTTTGGAAACCTTAATTTCGAGGAAAA
*
1267147 TTGATACTTTTCAACTTTTCCTCAAAAATTTTTTTTTTGAAAATTTATTTTTAA
64 TTGATAC-TTTCAACTTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAA
* * * *
1267201 GGAAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTTTGGAAACCTTAATTTCGAGAAAAAT
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAA-TATTTTTTGGAAACCTTAATTTCGAGGAAAAT
1267266 TGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAA
65 TGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAA
* *
1267318 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAACCTTAATCTCGAGAAAAAT
1 GAAAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTTGGAAACCTTAATTTCGAGGAAAAT
* *
1267383 TGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTTG
65 TGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTG
1267420 GATTTTATTT
Statistics
Matches: 384, Mismatches: 49, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
112 24 0.06
113 66 0.17
114 77 0.20
115 4 0.01
116 43 0.11
117 144 0.38
118 26 0.07
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (116 bp):
GAAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTGGAAACCTTAATTTCGAGGAAAATT
GATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAA
Found at i:1267442 original size:5 final size:5
Alignment explanation
Indices: 1267434--1267586 Score: 81
Period size: 5 Copynumber: 30.6 Consensus size: 5
1267424 TTATTTAAAG
*
1267434 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT -AAA- AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT
* *
1267482 AAAA- AAAAT AAAGA- AAAGT AAAACA AAAAT AAAAAT AAAAT AAAGAT
1 AAAAT AAAAT AAA-AT AAAAT AAAA-T AAAAT -AAAAT AAAAT AAA-AT
* * * * **
1267529 AAAAG AATAT TAAAT AAACCT AATCT AATAAT -AAAT -AAAT -AAAT AAATAT
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AA-AAT AAAAT AAAAT AAAAT AAA-AT
1267579 AAAAT AAA
1 AAAAT AAA
1267587 TATATAAAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 32
0.71 0.10 0.20
Matches are distributed among these distances:
3 3 0.03
4 21 0.18
5 62 0.53
6 26 0.22
7 4 0.03
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1267473 original size:13 final size:12
Alignment explanation
Indices: 1267434--1267537 Score: 65
Period size: 11 Copynumber: 8.5 Consensus size: 12
1267424 TTATTTAAAG
1267434 AAAATAAAATAA
1 AAAATAAAATAA
*
1267446 TAAAACAAAAT-A
1 -AAAATAAAATAA
*
1267458 AAAGTGAAAATAAA
1 AAAAT-AAAAT-AA
1267472 AAAATAAAATAA
1 AAAATAAAATAA
1267484 AAAA-AATAA-AGA
1 AAAATAA-AATA-A
* *
1267496 AAAGTAAAA-CA
1 AAAATAAAATAA
*
1267507 AAAATAAAA-AT
1 AAAATAAAATAA
1267518 AAAATAAAGATAA
1 AAAATAAA-ATAA
1267531 AAGAATA
1 AA-AATA
1267538 TTAAATAAAC
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
11 23 0.32
12 21 0.29
13 19 0.26
14 9 0.12
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:1267476 original size:38 final size:37
Alignment explanation
Indices: 1267429--1267531 Score: 111
Period size: 38 Copynumber: 2.7 Consensus size: 37
1267419 GGATTTTATT
* *
1267429 TAAAGAAAATAAAATAATAAAACA-AAATAAAAGTGAAAA
1 TAAA-AAAATAAAATAA-AAAAAATAAAGAAAAGT-AAAA
1267468 TAAAAAAATAAAATAAAAAAAATAAAGAAAAGTAAAA
1 TAAAAAAATAAAATAAAAAAAATAAAGAAAAGTAAAA
* *
1267505 CAAAAATA-AAAATAAAATAAAGATAAA
1 TAAAAAAATAAAATAAAA-AAA-ATAAA
1267532 AGAATATTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
36 9 0.16
37 18 0.32
38 26 0.46
39 4 0.07
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.15
Consensus pattern (37 bp):
TAAAAAAATAAAATAAAAAAAATAAAGAAAAGTAAAA
Found at i:1267587 original size:11 final size:11
Alignment explanation
Indices: 1267434--1267590 Score: 55
Period size: 11 Copynumber: 14.1 Consensus size: 11
1267424 TTATTTAAAG
1267434 AAAATAAAATAAT
1 AAAAT-AAAT-AT
*
1267447 AAAACAAA-AT
1 AAAATAAATAT
1267457 AAAAGTGAAA-AT
1 AAAA-T-AAATAT
1267469 -AAA-AAA-AT
1 AAAATAAATAT
1267477 AAAATAAA-A-
1 AAAATAAATAT
*
1267486 AAAATAAAGA-
1 AAAATAAATAT
* *
1267496 AAAGTAAA-ACA
1 AAAATAAATA-T
*
1267507 AAAATAAAAAT
1 AAAATAAATAT
*
1267518 AAAATAAAGAT
1 AAAATAAATAT
*
1267529 AAAA-GAATAT
1 AAAATAAATAT
*
1267539 TAAATAAACCTAATCT
1 AAAATAAA--T-A--T
*
1267555 AATAATAAATAA
1 AA-AATAAATAT
1267567 ATAAATAAATAT
1 A-AAATAAATAT
1267579 AAAATAAATAT
1 AAAATAAATAT
1267590 A
1 A
1267591 TAAAAAAAAC
Statistics
Matches: 115, Mismatches: 13, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
8 5 0.04
9 12 0.10
10 25 0.22
11 37 0.32
12 19 0.17
13 6 0.05
14 2 0.02
15 1 0.01
16 2 0.02
17 6 0.05
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (11 bp):
AAAATAAATAT
Found at i:1267597 original size:15 final size:14
Alignment explanation
Indices: 1267555--1267597 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1267545 AACCTAATCT
1267555 AATAATAAATAAATA
1 AATAATAAA-AAATA
*
1267570 AATAAATATAAAATA
1 AAT-AATAAAAAATA
1267585 AATATATAAAAAA
1 AATA-ATAAAAAA
1267598 AACTTGGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAATAAAAAATA
Found at i:1268137 original size:13 final size:12
Alignment explanation
Indices: 1268119--1268165 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
1268109 GAAATTTTCC
1268119 AAAAATTTCAGAA
1 AAAAATTTC-GAA
1268132 AAAAATTTCGTAA
1 AAAAATTTCG-AA
* *
1268145 AAAAATCTCCAA
1 AAAAATTTCGAA
1268157 AAAAATTTC
1 AAAAATTTC
1268166 CTCGATTCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (12 bp):
AAAAATTTCGAA
Found at i:1268596 original size:5 final size:5
Alignment explanation
Indices: 1268588--1268652 Score: 53
Period size: 5 Copynumber: 12.8 Consensus size: 5
1268578 ACATAAGATA
* * * *
1268588 AAAAT AAAAGA AAAAT ATACAT AAAA- ACAAT AATA- AAAAT AAAAT AAAAT
1 AAAAT AAAA-T AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1268638 AAAAAT AAAAT AAAA
1 -AAAAT AAAAT AAAA
1268653 ATGTAAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
4 6 0.13
5 28 0.60
6 13 0.28
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1268596 original size:6 final size:6
Alignment explanation
Indices: 1268585--1268675 Score: 73
Period size: 6 Copynumber: 15.2 Consensus size: 6
1268575 AATACATAAG
* * * * *
1268585 ATAAAA AT-AAA AGAAAA ATATAC ATAAAA ACAATA ATAAAA AT-AAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
1268631 AT-AAA ATAAAA AT-AAA ATAAAA ATGTAAAA ATACAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A--TAAAA AT--AAAA ATAAAA A
1268676 AAATAGACTT
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
5 19 0.28
6 37 0.54
8 12 0.18
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:1268654 original size:11 final size:11
Alignment explanation
Indices: 1268580--1268652 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
1268570 TAATAAATAC
*
1268580 ATAAGATAAAA
1 ATAAAATAAAA
*
1268591 ATAAAAGAAAA
1 ATAAAATAAAA
*
1268602 ATATACATAAAA
1 ATA-AAATAAAA
*
1268614 ACAATAATAAAA
1 ATAA-AATAAAA
1268626 ATAAAAT-AAA
1 ATAAAATAAAA
1268636 ATAAAA-ATAAA
1 ATAAAATA-AAA
1268647 ATAAAA
1 ATAAAA
1268653 ATGTAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
10 9 0.18
11 25 0.49
12 17 0.33
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:1268677 original size:51 final size:51
Alignment explanation
Indices: 1268580--1268675 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
1268570 TAATAAATAC
* *
1268580 ATAAGATAAAAATAAAAGAAAAATATACATAAAAACAATAATAAAAATAAA
1 ATAAAATAAAAATAAAAGAAAAATATACATAAAAACAAAAATAAAAATAAA
* * *
1268631 ATAAAATAAAAATAAAATAAAAATGTA-A-AAATACAAAAATAAAAA
1 ATAAAATAAAAATAAAAGAAAAATATACATAAAAACAAAAATAAAAA
1268676 AAATAGACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 15 0.38
50 1 0.03
51 24 0.60
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (51 bp):
ATAAAATAAAAATAAAAGAAAAATATACATAAAAACAAAAATAAAAATAAA
Found at i:1269003 original size:84 final size:84
Alignment explanation
Indices: 1268870--1269154 Score: 271
Period size: 84 Copynumber: 3.3 Consensus size: 84
1268860 AGAGGCTTAA
* * * * * *
1268870 ACGACTTTGGAAGAAATAAAATGGCTCCTCTAATCCAGAGGCTCGACGACTTTGGAAAGTAAATT
1 ACGACTTT-GAA-AAGTAAATTGGCTCCTCTAA-ACAGAGGCACCACGACTTTGAAAAGTAAATT
1268935 GGCTCCTCT-AACAGAGGCACC
63 GGCTCCTCTAAACAGAGGCACC
**
1268956 ACGACTTTGAAAAGTAAATTGGCTCCTCCTAAACAGGAGGC-CCACGACTTAAAAAAGTAAATTG
1 ACGACTTTGAAAAGTAAATTGGCTCCT-CTAAACA-GAGGCACCACGACTTTGAAAAGTAAATTG
1269020 GCTTCCCTCTAAACAGAGGCACC
64 GC-T-CCTCTAAACAGAGGCACC
* * *
1269043 ACGACTTAG-AAAGT-AA--CGC-CCTTTGAAACATGAGGCACCGACGACTTTGAAAAGTAAATT
1 ACGACTTTGAAAAGTAAATTGGCTCCTCT-AAACA-GAGGCACC-ACGACTTTGAAAAGTAAATT
*
1269103 -ACTCCTCTAAACCAGAAGGCCACC
63 GGCTCCTCTAAA-CAG-AGG-CACC
*
1269127 ACGACTTTGAAAAAGTAAATTGCCTCCT
1 ACGACTTTG-AAAAGTAAATTGGCTCCT
1269155 TGACAATCAT
Statistics
Matches: 165, Mismatches: 17, Indels: 30
0.78 0.08 0.14
Matches are distributed among these distances:
81 9 0.05
82 17 0.10
83 8 0.05
84 67 0.41
85 15 0.09
86 23 0.14
87 22 0.13
89 1 0.01
90 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (84 bp):
ACGACTTTGAAAAGTAAATTGGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGGC
TCCTCTAAACAGAGGCACC
Found at i:1269005 original size:43 final size:42
Alignment explanation
Indices: 1268870--1269154 Score: 271
Period size: 43 Copynumber: 6.6 Consensus size: 42
1268860 AGAGGCTTAA
* * * * *
1268870 ACGACTTTGGAAGAAATAAAATGGCTCCTCTAATCCAGAGGCTCG
1 ACGACTTT-GAA-AAGTAAATTGGCTCCTCTAA-ACAGAGGCACC
*
1268915 ACGACTTTGGAAAGTAAATTGGCTCCTCT-AACAGAGGCACC
1 ACGACTTTGAAAAGTAAATTGGCTCCTCTAAACAGAGGCACC
1268956 ACGACTTTGAAAAGTAAATTGGCTCCTCCTAAACAGGAGGC-CC
1 ACGACTTTGAAAAGTAAATTGGCTCCT-CTAAACA-GAGGCACC
**
1268999 ACGACTTAAAAAAGTAAATTGGCTTCCCTCTAAACAGAGGCACC
1 ACGACTTTGAAAAGTAAATTGGC-T-CCTCTAAACAGAGGCACC
* * *
1269043 ACGACTTAG-AAAGT-AA--CGC-CCTTTGAAACATGAGGCACC
1 ACGACTTTGAAAAGTAAATTGGCTCCTCT-AAACA-GAGGCACC
*
1269082 GACGACTTTGAAAAGTAAATT-ACTCCTCTAAACCAGAAGGCCACC
1 -ACGACTTTGAAAAGTAAATTGGCTCCTCTAAA-CAG-AGG-CACC
*
1269127 ACGACTTTGAAAAAGTAAATTGCCTCCT
1 ACGACTTTG-AAAAGTAAATTGGCTCCT
1269155 TGACAATCAT
Statistics
Matches: 205, Mismatches: 16, Indels: 37
0.79 0.06 0.14
Matches are distributed among these distances:
37 4 0.02
38 5 0.02
39 8 0.04
40 10 0.05
41 39 0.19
42 7 0.03
43 58 0.28
44 43 0.21
45 26 0.13
46 5 0.02
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (42 bp):
ACGACTTTGAAAAGTAAATTGGCTCCTCTAAACAGAGGCACC
Found at i:1276606 original size:32 final size:32
Alignment explanation
Indices: 1276570--1276633 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1276560 AATAGTAATG
*
1276570 ATTAAAACTTTTTTTTCTCAGCCGATAATCAA
1 ATTAAAACTTTTTTTTCTCAGCCAATAATCAA
1276602 ATTAAAACTTTTTTTTCTCAGCCAATAATCAA
1 ATTAAAACTTTTTTTTCTCAGCCAATAATCAA
1276634 GTTTATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (32 bp):
ATTAAAACTTTTTTTTCTCAGCCAATAATCAA
Found at i:1282133 original size:51 final size:52
Alignment explanation
Indices: 1282057--1282160 Score: 167
Period size: 51 Copynumber: 2.0 Consensus size: 52
1282047 TGGACAAGAA
*
1282057 GACTTGTAAAAGAAGAATTCTAAAA-GAAA-ATGATTCTTAATAGGCAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAAAGGAAAGA-GATTCTTAATAGGCAAGTTT
*
1282108 GACTTGCAAAAGAAGAATTCTAAAAGGAAAGAGATTCTTATTAGGCAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
1282160 G
1 G
1282161 TATGGTTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
51 24 0.49
52 24 0.49
53 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (52 bp):
GACTTGCAAAAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:1287402 original size:188 final size:187
Alignment explanation
Indices: 1287086--1287459 Score: 498
Period size: 188 Copynumber: 2.0 Consensus size: 187
1287076 AAATTAAATC
* * * * *
1287086 TAAAATTATTAAGGGATATTGTAGAACATTTGAATTTTGTAATGTTAAATCTTATTCTTAGCTTT
1 TAAAATTATTAAGAGATACTGTAGAACATTTGAATTTTATAACGTTAAATCCTATTCTTAGCTTT
* * * *
1287151 TAATTTTTCCAAGTGATCATTTGGCGAATGAAGGTAATATCTAATATTGTAAGAATGGAAGTGTT
66 TAATTTTTCCAAGTGATCATTTGGCAAATAAAGGTAATATCTAATATTGCAAGAATGGAAGTGTC
* *
1287216 CTTAGTTAA-TTGTCATGAATTATGATTATAATTATGCATTTTAATTAAATATTAATA
131 CTTAGTTAAGTT-TCATGAATTATGATTATAATTATACATTCTAATTAAATATTAATA
* * * * *
1287273 TAAAATTATTGAGAGATACTGTAGAACTTTTGAATTTTATAGCGTTAAATCACTGTTCTTAGTTT
1 TAAAATTATTAAGAGATACTGTAGAACATTTGAATTTTATAACGTTAAATC-CTATTCTTAGCTT
* * * * *
1287338 TTATTTTTTCTAAGTGATGATTTGGCAAATAAAGGTAATATCTAATATTGCAGGATTGGAAGTGT
65 TTAATTTTTCCAAGTGATCATTTGGCAAATAAAGGTAATATCTAATATTGCAAGAATGGAAGTGT
* * * *
1287403 CCTTGGTTAAGTTTTATGAATTATGATTATGATTATACATTCTAATTTAATATTAAT
130 CCTTAGTTAAGTTTCATGAATTATGATTATAATTATACATTCTAATTAAATATTAAT
1287460 TAATTTTCAA
Statistics
Matches: 160, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
187 44 0.28
188 114 0.71
189 2 0.01
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.44
Consensus pattern (187 bp):
TAAAATTATTAAGAGATACTGTAGAACATTTGAATTTTATAACGTTAAATCCTATTCTTAGCTTT
TAATTTTTCCAAGTGATCATTTGGCAAATAAAGGTAATATCTAATATTGCAAGAATGGAAGTGTC
CTTAGTTAAGTTTCATGAATTATGATTATAATTATACATTCTAATTAAATATTAATA
Found at i:1289076 original size:70 final size:69
Alignment explanation
Indices: 1288957--1289097 Score: 221
Period size: 70 Copynumber: 2.0 Consensus size: 69
1288947 TAAAGTCTTC
* *
1288957 TGCAATGATTATGACCATCCTTCCATTCTAAAACTGCTTTAGCTATACCAATAAGACTCCATTTG
1 TGCAATGATTATGACCATCCTTCCATTCTAAAACTGCTTGAGCTATACCAATAAGACTCCATTGG
1289022 CTTT
66 CTTT
* *
1289026 TGCAATGATTATGTCCATCCTTTTCCCTT-TAAAACTGCTTGAGCTATACCAATAAGACTCCATT
1 TGCAATGATTATGACCATCC--TTCCATTCTAAAACTGCTTGAGCTATACCAATAAGACTCCATT
1289090 GGCTTT
64 GGCTTT
1289096 TG
1 TG
1289098 GAAAGTAAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
69 19 0.29
70 41 0.62
71 6 0.09
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (69 bp):
TGCAATGATTATGACCATCCTTCCATTCTAAAACTGCTTGAGCTATACCAATAAGACTCCATTGG
CTTT
Found at i:1289533 original size:16 final size:16
Alignment explanation
Indices: 1289501--1289544 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1289491 TATATGTTAG
*
1289501 TAAAAAAATGTATTTTA
1 TAAAAAAAT-TAGTTTA
1289518 TAAAAAAATTAGTTTA
1 TAAAAAAATTAGTTTA
*
1289534 AAATAAAAATT
1 TAA-AAAAATT
1289545 TCTTTATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (16 bp):
TAAAAAAATTAGTTTA
Found at i:1299705 original size:31 final size:31
Alignment explanation
Indices: 1299667--1299730 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
1299657 AGGTAAATGT
*
1299667 ATAATTATAGTGCTGTGGAAGGATAACACAC
1 ATAATTATAGTGCTATGGAAGGATAACACAC
*
1299698 ATAATTATAGTGTTATGGAAGGATAACACAC
1 ATAATTATAGTGCTATGGAAGGATAACACAC
1299729 AT
1 AT
1299731 GCATGGATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (31 bp):
ATAATTATAGTGCTATGGAAGGATAACACAC
Found at i:1300140 original size:27 final size:27
Alignment explanation
Indices: 1300104--1300157 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1300094 AATATAAGTA
*
1300104 AATTTCGAT-AACTTTTGATATAATTTT
1 AATTTCGATAAAC-TTTGATAAAATTTT
*
1300131 AATTTTGATAAACTTTGATAAAATTTT
1 AATTTCGATAAACTTTGATAAAATTTT
1300158 GGTAACTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (27 bp):
AATTTCGATAAACTTTGATAAAATTTT
Found at i:1300157 original size:21 final size:21
Alignment explanation
Indices: 1300131--1300221 Score: 78
Period size: 21 Copynumber: 4.3 Consensus size: 21
1300121 ATATAATTTT
*
1300131 AATTTTGATAAACTTTGATAA
1 AATTTTGGTAAACTTTGATAA
* *
1300152 AATTTTGGT-AACTTTCAATAT
1 AATTTTGGTAAACTTT-GATAA
*
1300173 AATTTTGGT-AACTTATGATAT
1 AATTTTGGTAAACTT-TGATAA
* * * *
1300194 AATCTCGGTAACCATTGATAA
1 AATTTTGGTAAACTTTGATAA
1300215 AATTTTG
1 AATTTTG
1300222 ATAATTTTCT
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
20 6 0.11
21 46 0.82
22 4 0.07
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (21 bp):
AATTTTGGTAAACTTTGATAA
Found at i:1300287 original size:21 final size:21
Alignment explanation
Indices: 1300261--1300300 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1300251 TTGATGTAAT
1300261 CTTTTGATAACTTA-TGATATA
1 CTTTTGATAA-TTATTGATATA
*
1300282 CTTTTGGTAATTATTGATA
1 CTTTTGATAATTATTGATA
1300301 AAATTTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.50
Consensus pattern (21 bp):
CTTTTGATAATTATTGATATA
Found at i:1300630 original size:22 final size:21
Alignment explanation
Indices: 1300603--1300666 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 21
1300593 TTAGCGATTC
1300603 ACTATTAAGTTATCAATAATAT
1 ACTATTAA-TTATCAATAATAT
* *
1300625 ATTATTAATATATCAATGATAT
1 ACTATTAAT-TATCAATAATAT
*
1300647 ACTGTTAAATTATCAATAAT
1 ACTATT-AATTATCAATAAT
1300667 TTAGTGCTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.89
23 3 0.09
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (21 bp):
ACTATTAATTATCAATAATAT
Found at i:1300698 original size:22 final size:22
Alignment explanation
Indices: 1300652--1300777 Score: 112
Period size: 22 Copynumber: 5.7 Consensus size: 22
1300642 GATATACTGT
* * * *
1300652 TAAATTATCAATAATTTAGTGC
1 TAAATTATGAATGATTTACTAC
* *
1300674 TAAATTA-GCATTTATTTACTAC
1 TAAATTATG-AATGATTTACTAC
* *
1300696 TAATTTATGAATTATTTACTAC
1 TAAATTATGAATGATTTACTAC
* *
1300718 TAAGTTATGACTGATTTACTAC
1 TAAATTATGAATGATTTACTAC
*
1300740 TAAATTATTAATGATTTACTAC
1 TAAATTATGAATGATTTACTAC
*
1300762 TAAGTTACT-AATGATT
1 TAAATTA-TGAATGATT
1300778 GTTATAAAGT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
22 85 0.98
23 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (22 bp):
TAAATTATGAATGATTTACTAC
Found at i:1300777 original size:44 final size:44
Alignment explanation
Indices: 1300687--1300777 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
1300677 ATTAGCATTT
* * *
1300687 ATTTACTACTAATTTATGAATTATTTACTACTAAGTTATGACTG
1 ATTTACTACTAAATTATGAATGATTTACTACTAAGTTATGAATG
*
1300731 ATTTACTACTAAATTATTAATGATTTACTACTAAGTTACT-AATG
1 ATTTACTACTAAATTATGAATGATTTACTACTAAGTTA-TGAATG
1300775 ATT
1 ATT
1300778 GTTATAAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (44 bp):
ATTTACTACTAAATTATGAATGATTTACTACTAAGTTATGAATG
Found at i:1300850 original size:30 final size:29
Alignment explanation
Indices: 1300815--1300881 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
1300805 TAATTTATTG
*
1300815 ATAATTAACTAC-AAAGTTATTAATAATTA
1 ATAATTAACTACTAAA-TTATCAATAATTA
* * *
1300844 ACTAATTTACTACTAAATTATCACTAATTT
1 A-TAATTAACTACTAAATTATCAATAATTA
1300874 ATAATTAA
1 ATAATTAA
1300882 ATTATTTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
29 7 0.23
30 21 0.68
31 3 0.10
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.40
Consensus pattern (29 bp):
ATAATTAACTACTAAATTATCAATAATTA
Found at i:1300870 original size:22 final size:22
Alignment explanation
Indices: 1300846--1300952 Score: 110
Period size: 22 Copynumber: 4.9 Consensus size: 22
1300836 AATAATTAAC
*
1300846 TAATTTACTACTAAATTATCAC
1 TAATTTACTACTAAATTATCAA
* ***
1300868 TAATTTA-TAATTAAATTATTTG
1 TAATTTACT-ACTAAATTATCAA
*
1300890 TAATTTACTACTAAGTTATCAA
1 TAATTTACTACTAAATTATCAA
1300912 TAATTTA-TATCTAAATTATCAA
1 TAATTTACTA-CTAAATTATCAA
* *
1300934 TAATTTACTATTATATTAT
1 TAATTTACTACTAAATTAT
1300953 TATGCATTTA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
21 3 0.04
22 63 0.91
23 3 0.04
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATTTACTACTAAATTATCAA
Found at i:1300894 original size:44 final size:44
Alignment explanation
Indices: 1300846--1300930 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
1300836 AATAATTAAC
*
1300846 TAATTTACTACTAAATTATCACTAATTTATAAT-TAAATTATTTG
1 TAATTTACTACTAAATTATCAATAATTTAT-ATCTAAATTATTTG
*
1300890 TAATTTACTACTAAGTTATCAATAATTTATATCTAAATTAT
1 TAATTTACTACTAAATTATCAATAATTTATATCTAAATTAT
1300931 CAATAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 2 0.05
44 36 0.95
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.47
Consensus pattern (44 bp):
TAATTTACTACTAAATTATCAATAATTTATATCTAAATTATTTG
Found at i:1300938 original size:44 final size:44
Alignment explanation
Indices: 1300846--1300952 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
1300836 AATAATTAAC
* ***
1300846 TAATTTACTACTAAATTATCACTAATTTATAATTAAATTATTTG
1 TAATTTACTACTAAATTATCAATAATTTATAATTAAATTATCAA
*
1300890 TAATTTACTACTAAGTTATCAATAATTTAT-ATCTAAATTATCAA
1 TAATTTACTACTAAATTATCAATAATTTATAAT-TAAATTATCAA
* *
1300934 TAATTTACTATTATATTAT
1 TAATTTACTACTAAATTAT
1300953 TATGCATTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
43 2 0.04
44 52 0.96
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (44 bp):
TAATTTACTACTAAATTATCAATAATTTATAATTAAATTATCAA
Found at i:1301076 original size:21 final size:23
Alignment explanation
Indices: 1301052--1301107 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 23
1301042 CATGACTCAT
1301052 TATTAAGTTATCAC-TAATTTA-
1 TATTAAGTTATCACATAATTTAC
* *
1301073 TATTAAATTAAC-CATAATTTAC
1 TATTAAGTTATCACATAATTTAC
1301095 TATTAAGTTATCA
1 TATTAAGTTATCA
1301108 TTGATTAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
22 10 0.36
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (23 bp):
TATTAAGTTATCACATAATTTAC
Found at i:1301086 original size:43 final size:44
Alignment explanation
Indices: 1301024--1301107 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
1301014 ATCATCATAG
* *
1301024 ATTTATTATAAAATTAACCATGACTCATTATTAAGTTATCACTA
1 ATTTATTATAAAATTAACCATAACTCACTATTAAGTTATCACTA
* * *
1301068 ATTTA-TATTAAATTAACCATAATTTACTATTAAGTTATCA
1 ATTTATTATAAAATTAACCATAACTCACTATTAAGTTATCA
1301108 TTGATTAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 30 0.86
44 5 0.14
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.43
Consensus pattern (44 bp):
ATTTATTATAAAATTAACCATAACTCACTATTAAGTTATCACTA
Found at i:1304889 original size:18 final size:18
Alignment explanation
Indices: 1304868--1304935 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 18
1304858 ATACTATGCT
1304868 TGAAAAAAAAAGAAAAAA
1 TGAAAAAAAAAGAAAAAA
1304886 TGAAATGAAAAAA-ATGAAAAA
1 TGAAA--AAAAAAGA--AAAAA
*
1304907 TGAAAAAAAAATGAAAAGA
1 TGAAAAAAAAA-GAAAAAA
1304926 --AAAAAAAAAG
1 TGAAAAAAAAAG
1304936 TGAATGAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
16 1 0.02
17 9 0.21
18 5 0.12
19 11 0.26
20 6 0.14
21 11 0.26
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (18 bp):
TGAAAAAAAAAGAAAAAA
Found at i:1304896 original size:21 final size:19
Alignment explanation
Indices: 1304870--1304935 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 19
1304860 ACTATGCTTG
1304870 AAAAAAAAAGAAAAAATGA
1 AAAAAAAAAGAAAAAATGA
1304889 AATGAAAAAAATG-AAAAATGA
1 AA--AAAAAAA-GAAAAAATGA
*
1304910 AAAAAAAATG--AAAA-GA
1 AAAAAAAAAGAAAAAATGA
1304926 AAAAAAAAAG
1 AAAAAAAAAG
1304936 TGAATGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 11 0.26
17 4 0.10
18 1 0.02
19 8 0.19
21 17 0.40
22 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAATGA
Found at i:1304907 original size:16 final size:14
Alignment explanation
Indices: 1304880--1304931 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
1304870 AAAAAAAAAG
1304880 AAAAAATGAAATGA
1 AAAAAATGAAATGA
1304894 AAAAAATGAAAAATGAAA
1 AAAAAATG--AAATG--A
*
1304912 AAAAAATGAAAAGA
1 AAAAAATGAAATGA
1304926 AAAAAA
1 AAAAAA
1304932 AAAGTGAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 15 0.45
16 9 0.27
18 9 0.27
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (14 bp):
AAAAAATGAAATGA
Found at i:1304932 original size:16 final size:16
Alignment explanation
Indices: 1304880--1304933 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
1304870 AAAAAAAAAG
*
1304880 AAAAAATGAAATG--A
1 AAAAAATGAAAAGAAA
1304894 AAAAAATGAAAAATGAAA
1 AAAAAATG-AAAA-GAAA
1304912 AAAAAATGAAAAGAAA
1 AAAAAATGAAAAGAAA
1304928 AAAAAA
1 AAAAAA
1304934 AGTGAATGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
14 8 0.23
15 3 0.09
16 11 0.31
17 4 0.11
18 9 0.26
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (16 bp):
AAAAAATGAAAAGAAA
Found at i:1304939 original size:18 final size:17
Alignment explanation
Indices: 1304868--1304939 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 17
1304858 ATACTATGCT
*
1304868 TGAAAAAAAAAGAAAAAA
1 TGAAAAGAAAA-AAAAAA
*
1304886 TGAAATG---AAAAAAA
1 TGAAAAGAAAAAAAAAA
1304900 TGAAAA-ATGAAAAAAAAA
1 TGAAAAGA--AAAAAAAAA
1304918 TGAAAAGAAAAAAAAAA
1 TGAAAAGAAAAAAAAAA
1304935 GTGAA
1 -TGAA
1304940 TGAAAAAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
17 9 0.20
18 22 0.50
19 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (17 bp):
TGAAAAGAAAAAAAAAA
Found at i:1304944 original size:17 final size:17
Alignment explanation
Indices: 1304875--1304946 Score: 71
Period size: 17 Copynumber: 4.3 Consensus size: 17
1304865 GCTTGAAAAA
1304875 AAAAGAAAAAATGAAATG
1 AAAA-AAAAAATGAAATG
*
1304893 AAAAAAATGAA--AAATG
1 AAAAAAA-AAATGAAATG
*
1304909 -AAAAAAAAATGAAAAG
1 AAAAAAAAAATGAAATG
1304925 AAAAAAAAAAGTG-AATG
1 AAAAAAAAAA-TGAAATG
1304942 AAAAA
1 AAAAA
1304947 GGAGGACTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
14 2 0.04
15 6 0.13
16 9 0.20
17 20 0.44
18 8 0.18
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (17 bp):
AAAAAAAAAATGAAATG
Found at i:1305992 original size:41 final size:41
Alignment explanation
Indices: 1305942--1306370 Score: 245
Period size: 41 Copynumber: 10.1 Consensus size: 41
1305932 ATGATTTTTA
* *
1305942 AGGATCAATTTATTTTTCAAAGTTG-TGATGCCTCTGATTAG
1 AGGAGCAATTTATTTTTAAAAGTTGTTGA-GCCTCTGATTAG
* * *
1305983 AGGAGCAATTTACTTTTCAAAAGCTGTTGAACCTCTGATTAG
1 AGGAGCAATTTA-TTTTTAAAAGTTGTTGAGCCTCTGATTAG
** *
1306025 AGGAGCCTTTTATTTTTAAAAGTCGTTGAGCCTCTGATTAG
1 AGGAGCAATTTATTTTTAAAAGTTGTTGAGCCTCTGATTAG
* ** * * * *
1306066 AAGAGCCTTTTATTTTTAAAAGTCGTTAAGCCTTTGTTTAG
1 AGGAGCAATTTATTTTTAAAAGTTGTTGAGCCTCTGATTAG
* ** ** **
1306107 AAGAGCTTTGTTTACTTTCCAAAAGTCATTGAGCCTCTGATTAG
1 AGGAGC--AATTTA-TTTTTAAAAGTTGTTGAGCCTCTGATTAG
* ** * *
1306151 AAGAGCCTTTTATTTTTAAAAGTCGTTAAGCCTCT-ATTTAG
1 AGGAGCAATTTATTTTTAAAAGTTGTTGAGCCTCTGA-TTAG
** * *
1306192 AGGAGCTTTGTTTATCTTTTTAAAAGTCGTTGAGCCTCTGTTTAG
1 AGGAGC--AATTTA--TTTTTAAAAGTTGTTGAGCCTCTGATTAG
* * * ** *
1306237 AGAAGCTTTATTTATTTTTTCAAAGTCCTTGAGCCTCTGTTTAG
1 AGGAGC--AATTTA-TTTTTAAAAGTTGTTGAGCCTCTGATTAG
* ** *
1306281 AGAAGCTTTGTTTATTTTTTTGAAA-TTGTTGAGCCTCT-ATTTAG
1 AGGAGC--AATTTA--TTTTTAAAAGTTGTTGAGCCTCTGA-TTAG
* * ** *
1306325 AAGAGCAATTTATTTTTCCAAAGTCATTGAGCCTCTGCTTAG
1 AGGAGCAATTTATTTTT-AAAAGTTGTTGAGCCTCTGATTAG
1306367 AGGA
1 AGGA
1306371 ATCTTCGTTT
Statistics
Matches: 319, Mismatches: 53, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
40 6 0.02
41 110 0.34
42 57 0.18
43 11 0.03
44 88 0.28
45 47 0.15
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (41 bp):
AGGAGCAATTTATTTTTAAAAGTTGTTGAGCCTCTGATTAG
Found at i:1306140 original size:85 final size:86
Alignment explanation
Indices: 1305971--1306400 Score: 362
Period size: 85 Copynumber: 5.0 Consensus size: 86
1305961 AAGTTGTGAT
* ** * * * *
1305971 GCCTCTGATTAGAGGAGCAATTTACTTTTCAAAAG-CTGTTGAA-CCTCTGATTAGAGGAGC-CT
1 GCCTCTGATTAGAAGAGCCTTTTA-TTTTTAAAAGTC-GTT-AAGCCTCTGTTTAGAAGAGCTTT
*
1306033 -TTTAT-TTT-TAAAAGTCGTTGA
63 GTTTATCTTTCCAAAAGTCGTTGA
*
1306054 GCCTCTGATTAGAAGAGCCTTTTATTTTTAAAAGTCGTTAAGCCTTTGTTTAGAAGAGCTTTGTT
1 GCCTCTGATTAGAAGAGCCTTTTATTTTTAAAAGTCGTTAAGCCTCTGTTTAGAAGAGCTTTGTT
*
1306119 TA-CTTTCCAAAAGTCATTGA
66 TATCTTTCCAAAAGTCGTTGA
* *
1306139 GCCTCTGATTAGAAGAGCCTTTTATTTTTAAAAGTCGTTAAGCCTCTATTTAGAGGAGCTTTGTT
1 GCCTCTGATTAGAAGAGCCTTTTATTTTTAAAAGTCGTTAAGCCTCTGTTTAGAAGAGCTTTGTT
**
1306204 TATCTTTTTAAAAGTCGTTGA
66 TATCTTTCCAAAAGTCGTTGA
* * * * *
1306225 GCCTCTGTTTAG-AGAAGCTTTATTTATTTTTTCAAAGTCCTTGAGCCTCTGTTTAG-AGAAGCT
1 GCCTCTGATTAGAAG-AGC-CT-TTTA-TTTTTAAAAGTCGTTAAGCCTCTGTTTAGAAG-AGCT
* *** *
1306288 TTGTTTATTTTTTTGAAA-TTGTTGA
61 TTGTTTATCTTTCCAAAAGTCGTTGA
** * * * * * * *
1306313 GCCTCT-ATTTAGAAGAGCAATTTATTTTTCCAAAGTCATTGAGCCTCTGCTTAGAGGAATCTTC
1 GCCTCTGA-TTAGAAGAGCCTTTTATTTTT-AAAAGTCGTTAAGCCTCTGTTTAGAAG-AGCTTT
* *
1306377 GTTTATTTTTCCAAAACT-GTTGA
63 GTTTATCTTTCCAAAAGTCGTTGA
1306400 G
1 G
1306401 TATCTGTCAT
Statistics
Matches: 293, Mismatches: 37, Indels: 30
0.81 0.10 0.08
Matches are distributed among these distances:
81 2 0.01
82 26 0.09
83 23 0.08
84 7 0.02
85 82 0.28
86 55 0.19
87 26 0.09
88 25 0.09
89 47 0.16
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (86 bp):
GCCTCTGATTAGAAGAGCCTTTTATTTTTAAAAGTCGTTAAGCCTCTGTTTAGAAGAGCTTTGTT
TATCTTTCCAAAAGTCGTTGA
Found at i:1306142 original size:44 final size:43
Alignment explanation
Indices: 1305991--1306386 Score: 321
Period size: 41 Copynumber: 9.2 Consensus size: 43
1305981 AGAGGAGCAA
* * * * *
1305991 TTTACTTTTCAAAAG-CTGTTGAACCTCTGATTAGAGGAGC-CT-
1 TTTA-TTTTTAAAAGTC-GTTGAGCCTCTGTTTAGAAGAGCTTTG
* *
1306033 TTTATTTTTAAAAGTCGTTGAGCCTCTGATTAGAAGAGC-CT-
1 TTTATTTTTAAAAGTCGTTGAGCCTCTGTTTAGAAGAGCTTTG
* *
1306074 TTTATTTTTAAAAGTCGTTAAGCCTTTGTTTAGAAGAGCTTTG
1 TTTATTTTTAAAAGTCGTTGAGCCTCTGTTTAGAAGAGCTTTG
** * * *
1306117 TTTACTTTCCAAAAGTCATTGAGCCTCTGATTAGAAGAGC-CT-
1 TTTA-TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAAGAGCTTTG
* * *
1306159 TTTATTTTTAAAAGTCGTTAAGCCTCTATTTAGAGGAGCTTTG
1 TTTATTTTTAAAAGTCGTTGAGCCTCTGTTTAGAAGAGCTTTG
*
1306202 TTTATCTTTTTAAAAGTCGTTGAGCCTCTGTTTAG-AGAAGCTTTA
1 TTTA--TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAAG-AGCTTTG
* *
1306247 TTTATTTTTTCAAAGTCCTTGAGCCTCTGTTTAG-AGAAGCTTTG
1 TTTA-TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAAG-AGCTTTG
* * * **
1306291 TTTATTTTTTTGAAA-TTGTTGAGCCTCTATTTAGAAGAGC--AA
1 TTTA--TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAAGAGCTTTG
* * * * * *
1306333 TTTATTTTTCCAAAGTCATTGAGCCTCTGCTTAGAGGAATCTTCG
1 TTTATTTTT-AAAAGTCGTTGAGCCTCTGTTTAGAAG-AGCTTTG
1306378 TTTATTTTT
1 TTTATTTTT
1306387 CCAAAACTGT
Statistics
Matches: 293, Mismatches: 45, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
40 5 0.02
41 99 0.34
42 32 0.11
43 11 0.04
44 89 0.30
45 57 0.19
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (43 bp):
TTTATTTTTAAAAGTCGTTGAGCCTCTGTTTAGAAGAGCTTTG
Found at i:1306348 original size:130 final size:126
Alignment explanation
Indices: 1306009--1306391 Score: 398
Period size: 130 Copynumber: 3.0 Consensus size: 126
1305999 TCAAAAGCTG
* * *
1306009 TTGAACCTCTGATTAGAGGAGCCTTTTATTTTTAAAAGTCGTTGAGCCTCTGA-TTAGAAGAGCC
1 TTGAGCCTCTGATTAGAAGAGCCTTTTATTTTTAAAAGTCGTTGAGCCTCT-ATTTAGAAGAGCA
* * * *
1306073 TTTTATTTTTAAAAGTCGTTAAGCCTTTGTTTAGA-AGAGCTTTGTTTA-CTTTCCAAAAGTCA
65 ATTTATTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGA-AGCTTTGTTTATTTTTCC-AAAGTCA
* *
1306135 TTGAGCCTCTGATTAGAAGAGCCTTTTATTTTTAAAAGTCGTTAAGCCTCTATTTAGAGGAGCTT
1 TTGAGCCTCTGATTAGAAGAGCCTTTTATTTTTAAAAGTCGTTGAGCCTCTATTTAGAAGAGC--
** * * *
1306200 TGTTTATCTTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGAAGCTTTATTTATTTTTTCAAAGTCC
64 AATTTA--TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGAAGCTTTGTTTATTTTTCCAAAGTCA
* * * *
1306265 TTGAGCCTCTGTTTAG-AGAAGCTTTGTTTATTTTTTTGAAA-TTGTTGAGCCTCTATTTAGAAG
1 TTGAGCCTCTGATTAGAAG-AGC-CT-TTTA--TTTTTAAAAGTCGTTGAGCCTCTATTTAGAAG
* * * * *
1306328 AGCAATTTATTTTTCCAAAGTCATTGAGCCTCTGCTTAGAGGAATCTTCGTTTATTTTTCCAAA
61 AGCAATTTATTTTT-AAAAGTCGTTGAGCCTCTGTTTAGA-GAAGCTTTGTTTATTTTTCCAAA
1306392 ACTGTTGAGT
Statistics
Matches: 216, Mismatches: 27, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
125 1 0.00
126 57 0.26
128 4 0.02
129 7 0.03
130 84 0.39
131 29 0.13
132 4 0.02
133 22 0.10
134 8 0.04
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (126 bp):
TTGAGCCTCTGATTAGAAGAGCCTTTTATTTTTAAAAGTCGTTGAGCCTCTATTTAGAAGAGCAA
TTTATTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGAAGCTTTGTTTATTTTTCCAAAGTCA
Found at i:1306658 original size:7 final size:7
Alignment explanation
Indices: 1306640--1306672 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1306630 TATTTTATTT
1306640 TATTTT-
1 TATTTTG
1306646 TATTTTG
1 TATTTTG
1306653 TATTTTG
1 TATTTTG
1306660 TATTTTG
1 TATTTTG
1306667 TATTTT
1 TATTTT
1306673 TTGTATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (7 bp):
TATTTTG
Found at i:1306665 original size:14 final size:13
Alignment explanation
Indices: 1306632--1306673 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
1306622 TTTCATTTTA
1306632 TTTTA-TTT-TAT
1 TTTTATTTTGTAT
1306643 TTTTATTTTGTAT
1 TTTTATTTTGTAT
1306656 TTTGTATTTTGTAT
1 TTT-TATTTTGTAT
1306670 TTTT
1 TTTT
1306674 TGTATCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.18
12 3 0.11
13 7 0.25
14 13 0.46
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTATTTTGTAT
Found at i:1306689 original size:4 final size:4
Alignment explanation
Indices: 1306680--1306749 Score: 51
Period size: 4 Copynumber: 18.0 Consensus size: 4
1306670 TTTTTGTATC
* *
1306680 TTAT TTAT TTAT TTA- TTAT TTAT GTAT TTA- TTAT TACTAT TTAT TAAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T--TAT TTAT TTAT
*
1306728 ATAT ATTA- TTA- TTA- TTAT TTAT
1 TTAT -TTAT TTAT TTAT TTAT TTAT
1306750 CTGTTAATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
3 15 0.28
4 33 0.61
5 2 0.04
6 4 0.07
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (4 bp):
TTAT
Found at i:1306708 original size:23 final size:22
Alignment explanation
Indices: 1306680--1306854 Score: 72
Period size: 20 Copynumber: 8.2 Consensus size: 22
1306670 TTTTTGTATC
1306680 TTATTTATTTATTTATTATTTA
1 TTATTTATTTATTTATTATTTA
*
1306702 TGTATTTA-TTA-TTACTATTTA
1 T-TATTTATTTATTTATTATTTA
* *
1306723 TTA-ATATATA-TTATTA-TTA
1 TTATTTATTTATTTATTATTTA
* * * *
1306742 TTATTTATCT-GTTAATATATA
1 TTATTTATTTATTTATTATTTA
*
1306763 TATACTTTA-TTA-TTATTTATCTA
1 T-TA-TTTATTTATTTA-TTATTTA
1306786 TTA-TTA-TTA-TTATTATTTA
1 TTATTTATTTATTTATTATTTA
1306805 TCTATTAATATTT-TTTAATTATTT-
1 T-TATT--TATTTATTT-ATTATTTA
* * *
1306829 TT-TTTAGTTATCTATTAATATA
1 TTATTTATTTATTTATT-ATTTA
1306851 TTAT
1 TTAT
1306855 CTTTATTTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 39
0.69 0.09 0.23
Matches are distributed among these distances:
19 15 0.13
20 36 0.31
21 19 0.16
22 16 0.14
23 20 0.17
24 5 0.04
25 7 0.06
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTTATTTATTTATTATTTA
Found at i:1306713 original size:3 final size:3
Alignment explanation
Indices: 1306692--1306854 Score: 73
Period size: 3 Copynumber: 50.3 Consensus size: 3
1306682 ATTTATTTAT
* *
1306692 TTA TTA TTTA TGTA TTTA TTA TTA CTA TTTA TTA ATA TATA TTA TTA
1 TTA TTA -TTA T-TA -TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA
* * *
1306739 TTA TTA TTTA TCTG TTA ATA TATA TATA CT- TTA TTA TTA TTTA TCTA
1 TTA TTA -TTA T-TA TTA TTA T-TA T-TA TTA TTA TTA TTA -TTA T-TA
* * *
1306786 TTA TTA TTA TTA TTA TTTA TCTA TTA ATA TT- TT- TTAA TTA TTT TTT
1 TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TT-A TTA TTA TTA
*
1306832 TTA GTTA TCTA TTA ATA -TA TTA T
1 TTA -TTA T-TA TTA TTA TTA TTA T
1306855 CTTTATTTTT
Statistics
Matches: 127, Mismatches: 15, Indels: 36
0.71 0.08 0.20
Matches are distributed among these distances:
2 7 0.06
3 76 0.60
4 43 0.34
5 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1306743 original size:59 final size:59
Alignment explanation
Indices: 1306680--1306810 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 59
1306670 TTTTTGTATC
* * *
1306680 TTATTTATTTATTTATTATTTATGTATTTA-TTATTACTATTTAT-TAATATATATTATTA
1 TTATTTATTTATTTATTA-ATATATATATACTTATTACTATTTATCTAATAT-TATTATTA
* * * *
1306739 TTA-TTATTTATCTGTTAATATATATATACTTTATTATTATTTATCTATTATTATTATTA
1 TTATTTATTTATTTATTAATATATATATAC-TTATTACTATTTATCTAATATTATTATTA
*
1306798 TTATTTATCTATT
1 TTATTTATTTATT
1306811 AATATTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
57 8 0.14
58 12 0.20
59 27 0.46
60 12 0.20
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (59 bp):
TTATTTATTTATTTATTAATATATATATACTTATTACTATTTATCTAATATTATTATTA
Found at i:1306778 original size:33 final size:31
Alignment explanation
Indices: 1306680--1306811 Score: 124
Period size: 33 Copynumber: 4.1 Consensus size: 31
1306670 TTTTTGTATC
* * *
1306680 TTATTTATTTATTTATTATTTATGTATTTATTA
1 TTATTTATCTA-TTAATATATAT-TATTTATTA
* *
1306713 TTA-CTATTTATTAATATATATTA-TTATTA
1 TTATTTATCTATTAATATATATTATTTATTA
*
1306742 TTATTTATCTGTTAATATATATATACTTTATTA
1 TTATTTATCTATTAATATATAT-TA-TTTATTA
*
1306775 TTATTTATCTATTATTATTATTATTATTTATCTA
1 TTATTTATCTATTAATA-TA-TATTATTTAT-TA
1306809 TTA
1 TTA
1306812 ATATTTTTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
29 9 0.11
30 17 0.20
31 11 0.13
32 6 0.07
33 29 0.35
34 9 0.11
35 3 0.04
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (31 bp):
TTATTTATCTATTAATATATATTATTTATTA
Found at i:1306816 original size:26 final size:26
Alignment explanation
Indices: 1306688--1306828 Score: 105
Period size: 26 Copynumber: 5.2 Consensus size: 26
1306678 TCTTATTTAT
*
1306688 TTATTTATTATTTATGTATTTATTATTA
1 TTATTTATTA-TTATATA-TTATTATTA
* *
1306716 CTATTTATTAATATATATTATTATTA
1 TTATTTATTATTATATATTATTATTA
*
1306742 TTATTTATCTGTTA-ATATATATATACTTTA
1 TTATTTAT-TATTATATAT-TAT-TA--TTA
1306772 TTA-TTATTTATCTAT-TATTATTATTA
1 TTATTTA-TTAT-TATATATTATTATTA
1306798 TTATTTATCTATTA-ATATT-TT-TTAA
1 TTATTTAT-TATTATATATTATTATT-A
1306823 TTATTT
1 TTATTT
1306829 TTTTTAGTTA
Statistics
Matches: 94, Mismatches: 7, Indels: 27
0.73 0.05 0.21
Matches are distributed among these distances:
24 2 0.02
25 9 0.10
26 33 0.35
27 17 0.18
28 13 0.14
29 8 0.09
30 12 0.13
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (26 bp):
TTATTTATTATTATATATTATTATTA
Found at i:1306821 original size:17 final size:16
Alignment explanation
Indices: 1306684--1306827 Score: 66
Period size: 17 Copynumber: 8.8 Consensus size: 16
1306674 TGTATCTTAT
1306684 TTATTTATTTATT-AT-
1 TTATTTA-TTATTAATA
* *
1306699 TTATGTATTTATTATTA
1 TTATTTA-TTATTAATA
* *
1306716 CTATTTATTAATATATA
1 TTATTTATTATTA-ATA
1306733 TTA-TTATTATT-AT-
1 TTATTTATTATTAATA
* * *
1306746 TTATCTGTTAATATATA
1 TTATTTATTATTA-ATA
*
1306763 TATACTTTATTATTATTTA
1 T-TA-TTTATTATTA-ATA
*
1306782 TCTA-TTATTATTATTA
1 T-TATTTATTATTAATA
1306798 TTATTTATCTATTAATA
1 TTATTTAT-TATTAATA
*
1306815 TTTTTTAATTATT
1 TTATTT-ATTATT
1306828 TTTTTTAGTT
Statistics
Matches: 99, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
13 3 0.03
14 7 0.07
15 14 0.14
16 23 0.23
17 35 0.35
18 4 0.04
19 13 0.13
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (16 bp):
TTATTTATTATTAATA
Found at i:1306840 original size:34 final size:34
Alignment explanation
Indices: 1306788--1306868 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
1306778 TTTATCTATT
* * * * *
1306788 ATTATTATTATTATTTATCTATTAATATTTTTTA
1 ATTATTTTTTTTAGTTATCTATTAATATATTATA
*
1306822 ATTATTTTTTTTAGTTATCTATTAATATATTATC
1 ATTATTTTTTTTAGTTATCTATTAATATATTATA
*
1306856 TTTATTTTTTTTA
1 ATTATTTTTTTTA
1306869 ATTTTTTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (34 bp):
ATTATTTTTTTTAGTTATCTATTAATATATTATA
Found at i:1306890 original size:57 final size:57
Alignment explanation
Indices: 1306731--1306854 Score: 148
Period size: 56 Copynumber: 2.2 Consensus size: 57
1306721 TATTAATATA
* * * * *
1306731 TATTATTATTATTATTTATCTGTTAATA-TATAT-A-TACTTTATTATTATTTATCTAT
1 TATTATTATTATTATTTATCTATTAATATTTTTTAATTA-TTT-TTTTTAGTTATCTAT
1306787 TATTATTATTATTATTTATCTATTAATATTTTTTAATTATTTTTTTTAGTTATCTAT
1 TATTATTATTATTATTTATCTATTAATATTTTTTAATTATTTTTTTTAGTTATCTAT
*
1306844 TAATA-TATTAT
1 TATTATTATTAT
1306855 CTTTATTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
56 33 0.56
57 20 0.34
58 4 0.07
59 2 0.03
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (57 bp):
TATTATTATTATTATTTATCTATTAATATTTTTTAATTATTTTTTTTAGTTATCTAT
Found at i:1307442 original size:15 final size:15
Alignment explanation
Indices: 1307403--1307445 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1307393 TGGTTCGGGT
*
1307403 AGAGAGAGGGAGGAG
1 AGAGAGAGGGAAGAG
*
1307418 A-AAAGAAGGGAAGAG
1 AGAGAG-AGGGAAGAG
1307433 AGAGAGAGGGAAG
1 AGAGAGAGGGAAG
1307446 GGGAGATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.13
15 17 0.74
16 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (15 bp):
AGAGAGAGGGAAGAG
Found at i:1307725 original size:10 final size:10
Alignment explanation
Indices: 1307712--1307801 Score: 51
Period size: 10 Copynumber: 8.6 Consensus size: 10
1307702 TTTTTTCTTT
1307712 TTATTTATTA
1 TTATTTATTA
1307722 TTATTATTATTA
1 TTA-T-TTATTA
1307734 TTATTTATTGA
1 TTATTTATT-A
* **
1307745 TTAGATTAGAA
1 TTA-TTTATTA
*
1307756 TTATTTAGTA
1 TTATTTATTA
1307766 TT-TCTTATT-
1 TTAT-TTATTA
*
1307775 TTATTTTATTT
1 TTA-TTTATTA
1307786 TTATTTTATT-
1 TTA-TTTATTA
1307796 TTATTT
1 TTATTT
1307802 TTTTTTGATT
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
9 6 0.09
10 27 0.41
11 21 0.32
12 12 0.18
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (10 bp):
TTATTTATTA
Found at i:1307780 original size:5 final size:5
Alignment explanation
Indices: 1307770--1307813 Score: 61
Period size: 5 Copynumber: 8.4 Consensus size: 5
1307760 TTAGTATTTC
*
1307770 TTATT TTATT TTATTT TTATT TTATT TTATT TTTTT TTGATT TT
1 TTATT TTATT TTA-TT TTATT TTATT TTATT TTATT TT-ATT TT
1307814 CTTTAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
5 26 0.74
6 9 0.26
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:1307789 original size:11 final size:11
Alignment explanation
Indices: 1307773--1307813 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1307763 GTATTTCTTA
1307773 TTTTATTTTAT
1 TTTTATTTTAT
1307784 TTTTATTTTA-
1 TTTTATTTTAT
1307794 TTTTATTTT-T
1 TTTTATTTTAT
1307804 TTTTGATTTT
1 TTTT-ATTTT
1307814 CTTTAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 13 0.46
11 15 0.54
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:1307791 original size:16 final size:16
Alignment explanation
Indices: 1307764--1307813 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
1307754 AATTATTTAG
1307764 TATTTCTTATTTTATTT
1 TATTT-TTATTTTATTT
1307781 TATTTTTATTTTATTT
1 TATTTTTATTTTATTT
1307797 TATTTTT-TTTTGATTT
1 TATTTTTATTTT-ATTT
1307813 T
1 T
1307814 CTTTAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.12
16 23 0.72
17 5 0.16
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (16 bp):
TATTTTTATTTTATTT
Found at i:1307796 original size:21 final size:21
Alignment explanation
Indices: 1307770--1307813 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1307760 TTAGTATTTC
1307770 TTATTTTATTTTATTTTT-ATT
1 TTATTTTATTTT-TTTTTGATT
1307791 TTATTTTATTTTTTTTTGATT
1 TTATTTTATTTTTTTTTGATT
1307812 TT
1 TT
1307814 CTTTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (21 bp):
TTATTTTATTTTTTTTTGATT
Found at i:1307950 original size:58 final size:58
Alignment explanation
Indices: 1307827--1308225 Score: 549
Period size: 57 Copynumber: 6.8 Consensus size: 58
1307817 TAAATAAAAA
*
1307827 TTCTAAAAATATATTTTTGAGGAGAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTT
1 TTCTAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTT
*
1307886 TTCTAAAAAATATTTTTG-GAAAAAGTTGAAAGTATCAA-TTTCCTTGAAAATAAGTTTT
1 TTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG--TT
* *
1307944 TTCT-AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTT
1 TTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTT
* *
1308001 TTCTGAAAAATATTTTTGA-GAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTT
1 TTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTT
* *
1308058 TTCTAAAAAATATTTTCGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAA-TT
1 TTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTT
* *
1308115 TTCTAAAAAAGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAG-T
1 TTCTAAAAAA---TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTT
* * * *
1308176 TTCAGAAAAAAATATTTTTGGGGAAAGGTTGAAAGTATCAATTTTTCTTG
1 TTC--TAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
1308226 TACAAAAGCA
Statistics
Matches: 308, Mismatches: 19, Indels: 25
0.88 0.05 0.07
Matches are distributed among these distances:
56 16 0.05
57 101 0.33
58 82 0.27
59 24 0.08
60 73 0.24
61 6 0.02
63 6 0.02
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (58 bp):
TTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTT
Found at i:1307983 original size:115 final size:117
Alignment explanation
Indices: 1307827--1308225 Score: 533
Period size: 115 Copynumber: 3.4 Consensus size: 117
1307817 TAAATAAAAA
*
1307827 TTCTAAAAATATATTTTTGAGGAGAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCTAA
1 TTCTAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCTAA
1307892 AAAATATTTTTGGAAAAAGTTGAAAGTATCAA-TTTCCTTGAAAATAAGTTTT
65 AAAATATTTTTGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTT
* * *
1307944 TTCT-AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCTGAA
1 TTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCTAAA
*
1308008 AAATATTTTT-GAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG--TT
66 AAATATTTTTGGA-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTT
* *
1308058 TTCTAAAAAATATTTTCGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAA-TTTTCTAAA
1 TTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCTAAA
* * *
1308122 AAAGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAG-TTT
66 AAA---TATTTTTG-GAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTT
**** * * *
1308178 CAGAAAAAAATATTTTTGGGGAAAGGTTGAAAGTATCAATTTTTCTTG
1 TTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
1308226 TACAAAAGCA
Statistics
Matches: 249, Mismatches: 23, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
114 19 0.08
115 126 0.51
116 19 0.08
117 10 0.04
118 30 0.12
119 4 0.02
120 41 0.16
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (117 bp):
TTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCTAAA
AAATATTTTTGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTT
Found at i:1308318 original size:21 final size:20
Alignment explanation
Indices: 1308277--1308318 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1308267 TAAAGCTGAA
**
1308277 TCATTTTTTTCTTTTTTTTT
1 TCATTTTTTTCTTTTCCTTT
1308297 TCATTTTATTTCTTTTCCTTT
1 TCATTTT-TTTCTTTTCCTTT
1308318 T
1 T
1308319 TGTTCTCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (20 bp):
TCATTTTTTTCTTTTCCTTT
Found at i:1308817 original size:22 final size:22
Alignment explanation
Indices: 1308757--1308809 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1308747 ACGTTATGAC
*
1308757 ATTTACTATTAAGTTATCATTG
1 ATTTACTATTAAGTTATCAATG
* *
1308779 ATTAACTATTATGTTATCAATG
1 ATTTACTATTAAGTTATCAATG
1308801 ATTTACTAT
1 ATTTACTAT
1308810 AAACTTATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (22 bp):
ATTTACTATTAAGTTATCAATG
Found at i:1308878 original size:22 final size:21
Alignment explanation
Indices: 1308835--1308996 Score: 82
Period size: 22 Copynumber: 7.6 Consensus size: 21
1308825 TACTTTAATA
* *
1308835 ACTACTAGATTATCAAATATTT
1 ACTACTAAATTAT-AATTATTT
*
1308857 ACTACTAATTTATAATTGATTT
1 ACTACTAAATTATAATT-ATTT
** * *
1308879 AAAACTAAGTTATTTATTATTT
1 ACTACTAAATTA-TAATTATTT
1308901 ACTACT--A-T-TAATTATTT
1 ACTACTAAATTATAATTATTT
* * *
1308918 ACTATTAAACTGA-AACTGATTT
1 ACTACTAAA-TTATAA-TTATTT
* *
1308940 ACTATTAAATTATCATTAATTT
1 ACTACTAAATTATAATT-ATTT
* * *
1308962 ACTATTAAGTTATAATAAATTT
1 ACTACTAAATTATAAT-TATTT
*
1308984 ATTACTAAATTAT
1 ACTACTAAATTAT
1308997 CAATAATTAA
Statistics
Matches: 106, Mismatches: 23, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
17 13 0.12
19 2 0.02
21 8 0.08
22 79 0.75
23 4 0.04
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (21 bp):
ACTACTAAATTATAATTATTT
Found at i:1308914 original size:17 final size:17
Alignment explanation
Indices: 1308889--1308921 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1308879 AAAACTAAGT
*
1308889 TATTTATTATTTACTAC
1 TATTAATTATTTACTAC
1308906 TATTAATTATTTACTA
1 TATTAATTATTTACTA
1308922 TTAAACTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTAATTATTTACTAC
Found at i:1309004 original size:22 final size:22
Alignment explanation
Indices: 1308936--1309020 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 22
1308926 ACTGAAACTG
*
1308936 ATTTACTATTAAATTATCATTA
1 ATTTACTATTAAATTATCAATA
*
1308958 ATTTACTATTAAGTTAT-AATAA
1 ATTTACTATTAAATTATCAAT-A
* *
1308980 ATTTATTACTAAATTATCAATA
1 ATTTACTATTAAATTATCAATA
* *
1309002 ATTAACTATTAAGTTATCA
1 ATTTACTATTAAATTATCA
1309021 CTTTTTTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
21 2 0.04
22 47 0.90
23 3 0.06
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTACTATTAAATTATCAATA
Found at i:1309247 original size:22 final size:22
Alignment explanation
Indices: 1309222--1309264 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1309212 TTTAAAATTG
1309222 ATTTACTATTAAATTATTACTA
1 ATTTACTATTAAATTATTACTA
*
1309244 ATTTACTATTAAGTTATTACT
1 ATTTACTATTAAATTATTACT
1309265 TTTTTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTACTATTAAATTATTACTA
Found at i:1311766 original size:32 final size:31
Alignment explanation
Indices: 1311692--1311773 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 31
1311682 ACATTCTATC
*
1311692 AATTAAAA-ACATTAATTTTTTTATTTAAAAA
1 AATTAAAATACA-TAATTTTTTTATATAAAAA
**
1311723 AATTATTATACATAATTTTTATTATATAAAAA
1 AATTAAAATACATAATTTTT-TTATATAAAAA
*
1311755 TATTAAAATACATAATTTT
1 AATTAAAATACATAATTTT
1311774 CAAAAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
31 14 0.33
32 29 0.67
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (31 bp):
AATTAAAATACATAATTTTTTTATATAAAAA
Found at i:1313868 original size:69 final size:69
Alignment explanation
Indices: 1313757--1313885 Score: 206
Period size: 69 Copynumber: 1.9 Consensus size: 69
1313747 TTTGAAGTCT
*
1313757 TGTCCATCCTTTTCTACTAAAACTGCTTTAGCTATACCAATAAGACTCCATTTGCCTTTGCAATG
1 TGTCCATCCTTTCCTACTAAAACTGCTTTAGCTATACCAATAAGACTCCATTTGCCTTTGCAATG
1313822 ATTA
66 ATTA
* * *
1313826 TGTCCATCCTTTCCCT-TTAAAATTGCTTTAGCTATACCAATAAGACTCCATTTGCTTTTG
1 TGTCCATCCTTT-CCTACTAAAACTGCTTTAGCTATACCAATAAGACTCCATTTGCCTTTG
1313886 GAAAATAAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 53 0.96
70 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.40
Consensus pattern (69 bp):
TGTCCATCCTTTCCTACTAAAACTGCTTTAGCTATACCAATAAGACTCCATTTGCCTTTGCAATG
ATTA
Done.