Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 7 of 210
Found at i:2674638 original size:29 final size:30
Alignment explanation
Indices: 2674575--2674653 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
2674565 ATTTCAAAAC
*
2674575 TATACATAAACTTTGGTTTAATATGCAATTG
1 TATACATAAACTTTGATTT-ATATGCAATTG
* *
2674606 TATACATGAACTTTGATTT-TATGCAATTT
1 TATACATAAACTTTGATTTATATGCAATTG
* *
2674635 TATATATCAAATTTTGATT
1 TATACAT-AAACTTTGATT
2674654 CAAACCAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.37
30 9 0.22
31 17 0.41
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (30 bp):
TATACATAAACTTTGATTTATATGCAATTG
Found at i:2680326 original size:19 final size:19
Alignment explanation
Indices: 2680281--2680335 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
2680271 TAAAAAAAAT
*
2680281 TATTTTTTAAACATTTTTA
1 TATTTTTTTAACATTTTTA
* *
2680300 TATATTTTTAAGATTTCTTA
1 TATTTTTTTAACATTT-TTA
2680320 -ATTTTTTT--CATTTTTA
1 TATTTTTTTAACATTTTTA
2680336 AAATTTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
19 20 0.67
20 3 0.10
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTTTTTAACATTTTTA
Found at i:2681993 original size:3 final size:3
Alignment explanation
Indices: 2681985--2682017 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2681975 TTCATCAACC
2681985 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2682018 GATTTTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2688828 original size:16 final size:17
Alignment explanation
Indices: 2688787--2688831 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 17
2688777 TAAGCAAGTT
2688787 TAATATTTTTGTCCAAACC
1 TAATATTTTTG--CAAACC
2688806 T-AT-TTTTTG-AAACC
1 TAATATTTTTGCAAACC
2688820 TAATATTTTTGC
1 TAATATTTTTGC
2688832 CCAAGATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 6 0.26
17 6 0.26
18 2 0.09
19 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (17 bp):
TAATATTTTTGCAAACC
Found at i:2689934 original size:32 final size:31
Alignment explanation
Indices: 2689875--2689951 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
2689865 ATCAACAAGT
2689875 TTAATTAA-TTAGTATGAGTTATCAAATTAAA
1 TTAATTAATTTA-TATGAGTTATCAAATTAAA
* *
2689906 TTAATTAATTTATCATGAGTTATTAAATTTAA
1 TTAATTAATTTAT-ATGAGTTATCAAATTAAA
* *
2689938 GTAATTAGTTTATA
1 TTAATTAATTTATA
2689952 AGGTTCTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 10 0.25
32 30 0.75
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.47
Consensus pattern (31 bp):
TTAATTAATTTATATGAGTTATCAAATTAAA
Found at i:2690263 original size:16 final size:16
Alignment explanation
Indices: 2690242--2690281 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
2690232 TCAATTTTAG
2690242 TATTATAA-GAAAATAT
1 TATTATAATGAAAA-AT
2690258 TATTATAATGAAAAAT
1 TATTATAATGAAAAAT
2690274 TATTATAA
1 TATTATAA
2690282 AGAGGTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
TATTATAATGAAAAAT
Found at i:2690706 original size:7 final size:7
Alignment explanation
Indices: 2690690--2690728 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
2690680 TATTTTTTTT
*
2690690 ACCTTAA
1 ACCTTGA
2690697 ACCTTGA
1 ACCTTGA
*
2690704 ACCTTAA
1 ACCTTGA
2690711 ACCTTGA
1 ACCTTGA
*
2690718 ATCTTGA
1 ACCTTGA
2690725 ACCT
1 ACCT
2690729 GGTTCAAGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (7 bp):
ACCTTGA
Found at i:2690709 original size:14 final size:14
Alignment explanation
Indices: 2690690--2690728 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2690680 TATTTTTTTT
2690690 ACCTTAAACCTTGA
1 ACCTTAAACCTTGA
2690704 ACCTTAAACCTTGA
1 ACCTTAAACCTTGA
* *
2690718 ATCTTGAACCT
1 ACCTTAAACCT
2690729 GGTTCAAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (14 bp):
ACCTTAAACCTTGA
Found at i:2691381 original size:8 final size:7
Alignment explanation
Indices: 2691356--2691380 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2691346 ATTAATCATA
2691356 AAAAGAT
1 AAAAGAT
2691363 AAAAGAT
1 AAAAGAT
2691370 AAAAGAT
1 AAAAGAT
2691377 AAAA
1 AAAA
2691381 AATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAGAT
Found at i:2698052 original size:4 final size:4
Alignment explanation
Indices: 2698043--2698072 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2698033 ATCATCGTGA
*
2698043 TATG TATG TATG AATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
2698073 GAGTTACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:2701345 original size:31 final size:30
Alignment explanation
Indices: 2701296--2701355 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
2701286 GAGACAATTG
* * *
2701296 TGACCGATTATAAGGTATGAAAATGCAAATA
1 TGACCAATTACAAAGTATG-AAATGCAAATA
*
2701327 TGACCAATTACAAAGTATGATATGCAAAT
1 TGACCAATTACAAAGTATGAAATGCAAAT
2701356 GTGAATGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (30 bp):
TGACCAATTACAAAGTATGAAATGCAAATA
Found at i:2727471 original size:37 final size:37
Alignment explanation
Indices: 2727421--2727496 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
2727411 AAGCTCATTG
2727421 TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
1 TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
2727458 TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
1 TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
2727495 TC
1 TC
2727497 TTTAAGTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.26, C:0.33, G:0.13, T:0.28
Consensus pattern (37 bp):
TCCCATAGAATATGGACCTCACCATTGGTATCCCCTA
Found at i:2729496 original size:32 final size:34
Alignment explanation
Indices: 2729459--2729530 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 34
2729449 TATTACACAT
*
2729459 TAATTTTAA-TTTAG-TGCATTAAAATATTTTAC
1 TAATTTTAATTTTAGTTACATTAAAATATTTTAC
***
2729491 TAATTTTAATTTTAGTTACATTTTCATATTTTAC
1 TAATTTTAATTTTAGTTACATTAAAATATTTTAC
2729525 TAATTT
1 TAATTT
2729531 CATTGTCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 9 0.26
33 5 0.15
34 20 0.59
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (34 bp):
TAATTTTAATTTTAGTTACATTAAAATATTTTAC
Found at i:2729530 original size:17 final size:16
Alignment explanation
Indices: 2729482--2729530 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
2729472 GTGCATTAAA
2729482 ATATTTTACTAATTTT
1 ATATTTTACTAATTTT
*
2729498 A-ATTTTAGTTACATTTT
1 ATATTTTA-CTA-ATTTT
2729515 CATATTTTACTAATTT
1 -ATATTTTACTAATTT
2729531 CATTGTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 6 0.22
16 3 0.11
17 9 0.33
18 3 0.11
19 6 0.22
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (16 bp):
ATATTTTACTAATTTT
Found at i:2733404 original size:21 final size:21
Alignment explanation
Indices: 2733378--2733432 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
2733368 TCCTCTTTTT
*
2733378 TTTTTATTTTAAAATTTTTAA
1 TTTTTATTTTAAAATTTTAAA
*
2733399 TTTTTATATTTCAAATTTTAAA
1 TTTTTAT-TTTAAAATTTTAAA
* *
2733421 ATTTAATTTTAA
1 TTTTTATTTTAA
2733433 TTATTAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTATTTTAAAATTTTAAA
Found at i:2733409 original size:15 final size:15
Alignment explanation
Indices: 2733377--2733432 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
2733367 CTCCTCTTTT
*
2733377 TTTTTTATTTTAAAA
1 TTTTTAATTTTAAAA
* *
2733392 TTTTTAATTTTTATA
1 TTTTTAATTTTAAAA
**
2733407 TTTCAAATTTTAAAA
1 TTTTTAATTTTAAAA
2733422 --TTTAATTTTAA
1 TTTTTAATTTTAA
2733433 TTATTAGTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 9 0.28
15 23 0.72
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAATTTTAAAA
Found at i:2738980 original size:2 final size:2
Alignment explanation
Indices: 2738975--2739017 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
2738965 TCAAAAAAAC
*
2738975 TA TA TA TA TA TA TA TA TA TA TA TA CTA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
2739018 GTAANNNNNN
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2761656 original size:16 final size:16
Alignment explanation
Indices: 2761635--2761667 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2761625 ATAAAATATT
2761635 TAAAAAA-ATTATAAAA
1 TAAAAAATATTA-AAAA
2761651 TAAAAAATATTAAAAA
1 TAAAAAATATTAAAAA
2761667 T
1 T
2761668 TCAATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAAATATTAAAAA
Found at i:2763495 original size:14 final size:15
Alignment explanation
Indices: 2763473--2763548 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 15
2763463 CAATCAAACA
2763473 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
2763487 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
2763502 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
2763522 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
2763536 ACGGAAAA-CATTT
1 CCAGAAAATCATTT
2763549 CACTGGCTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.43
15 14 0.29
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:2763514 original size:20 final size:20
Alignment explanation
Indices: 2763489--2763528 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2763479 AATATTTTCC
*
2763489 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2763509 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2763529 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2763534 original size:34 final size:35
Alignment explanation
Indices: 2763477--2763543 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2763467 CAAACACCAG
*
2763477 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2763512 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2763544 CATTTCACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2777950 original size:15 final size:15
Alignment explanation
Indices: 2777930--2777960 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2777920 CACTTTCAAC
2777930 ATTTTATTCTATTTT
1 ATTTTATTCTATTTT
*
2777945 ATTTTATTGTATTTT
1 ATTTTATTCTATTTT
2777960 A
1 A
2777961 AAATTTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTATTCTATTTT
Found at i:2785139 original size:31 final size:31
Alignment explanation
Indices: 2785104--2785172 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
2785094 CTCAACAATC
*
2785104 CAATGACTTAAATAAAAACTAGTGGATAATT
1 CAATGACTTAAATAAAAACTAGTGAATAATT
* ** *
2785135 CAATGACTTCAATAAAAACTTTTGAATAGTT
1 CAATGACTTAAATAAAAACTAGTGAATAATT
2785166 CAATGAC
1 CAATGAC
2785173 CACTTTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (31 bp):
CAATGACTTAAATAAAAACTAGTGAATAATT
Found at i:2792101 original size:28 final size:28
Alignment explanation
Indices: 2792069--2792160 Score: 98
Period size: 28 Copynumber: 3.2 Consensus size: 28
2792059 GTTCAAACAC
2792069 ACTCATAATAAAAATCAGGGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAA
* *
2792097 ACTCAAGGTCACTAAATAATTA--GTAAACTAA
1 ACTC-A--T-AATAAA-AATCAGGGTAAACTAA
*
2792128 TCTCATAATAAAAATCAGGGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAA
2792156 ACTCA
1 ACTCA
2792161 ATGTCACTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.08
27 5 0.10
28 18 0.35
29 1 0.02
30 1 0.02
31 13 0.25
32 5 0.10
33 4 0.08
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (28 bp):
ACTCATAATAAAAATCAGGGTAAACTAA
Found at i:2792123 original size:31 final size:30
Alignment explanation
Indices: 2792088--2792182 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
2792078 AAAAATCAGG
2792088 GTAAACTAAACTCAAGGTCACTAAATAATTA
1 GTAAACTAAACTCAA-GTCACTAAATAATTA
* * *
2792119 GTAAACTAATCTC-A-T-AATAAA-AATCA
1 GTAAACTAAACTCAAGTCACTAAATAATTA
2792145 GGGTAAACTAAACTCAATGTCACTAAATAATTA
1 --GTAAACTAAACTCAA-GTCACTAAATAATTA
2792178 GTAAA
1 GTAAA
2792183 TTTACATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.08
27 5 0.10
28 13 0.25
29 1 0.02
30 1 0.02
31 18 0.35
32 5 0.10
33 4 0.08
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.26
Consensus pattern (30 bp):
GTAAACTAAACTCAAGTCACTAAATAATTA
Found at i:2792141 original size:59 final size:59
Alignment explanation
Indices: 2792070--2792182 Score: 217
Period size: 59 Copynumber: 1.9 Consensus size: 59
2792060 TTCAAACACA
2792070 CTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAACTAAT
1 CTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAACTAAT
*
2792129 CTCATAATAAAAATCAGGGTAAACTAAACTCAATGTCACTAAATAATTAGTAAA
1 CTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAA
2792183 TTTACATTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.26
Consensus pattern (59 bp):
CTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTCACTAAATAATTAGTAAACTAAT
Found at i:2792266 original size:31 final size:31
Alignment explanation
Indices: 2792225--2792290 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
2792215 CAAATGATCG
*
2792225 TTGAACTATTCAAAAGTTTTCATTTAAGTTA
1 TTGAACTATTCAAAAGTTTTCATTTAAGTCA
* *
2792256 TTGAATTATTCAAAAGTTTTTATTTAAGTCA
1 TTGAACTATTCAAAAGTTTTCATTTAAGTCA
2792287 TTGA
1 TTGA
2792291 GTTGTTAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (31 bp):
TTGAACTATTCAAAAGTTTTCATTTAAGTCA
Found at i:2793035 original size:19 final size:21
Alignment explanation
Indices: 2792997--2793046 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
2792987 TCAAAAGATA
**
2792997 TATAAAAGATATTTTTAAAAA-
1 TATAAAA-ATATTTAAAAAAAG
2793018 T-TAAAAATATTTAAAAAAAG
1 TATAAAAATATTTAAAAAAAG
2793038 TATAAAAAT
1 TATAAAAAT
2793047 TACAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 11 0.44
20 6 0.24
21 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
TATAAAAATATTTAAAAAAAG
Found at i:2802556 original size:9 final size:9
Alignment explanation
Indices: 2802542--2802608 Score: 107
Period size: 9 Copynumber: 7.4 Consensus size: 9
2802532 TTTGGTTAAA
2802542 AATTAACCG
1 AATTAACCG
2802551 AATTAACCG
1 AATTAACCG
*
2802560 AATTACCCG
1 AATTAACCG
2802569 AATTAACCG
1 AATTAACCG
*
2802578 AATTACCCG
1 AATTAACCG
2802587 AATTAACCG
1 AATTAACCG
*
2802596 AATTAACCA
1 AATTAACCG
2802605 AATT
1 AATT
2802609 GAATCACTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:2803225 original size:16 final size:16
Alignment explanation
Indices: 2803204--2803279 Score: 57
Period size: 16 Copynumber: 5.4 Consensus size: 16
2803194 TATCGAGGTT
2803204 ATTAATTTATCGATAA
1 ATTAATTTATCGATAA
2803220 ATTAATATT-T---T--
1 ATTAAT-TTATCGATAA
2803231 ATTAATTTATCGATAA
1 ATTAATTTATCGATAA
*
2803247 ATTAATAT-TC--T--
1 ATTAATTTATCGATAA
2803258 ATTAATTTATCGATAA
1 ATTAATTTATCGATAA
2803274 ATTAAT
1 ATTAAT
2803280 ATTCATTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 24
0.64 0.03 0.33
Matches are distributed among these distances:
10 2 0.04
11 14 0.30
12 2 0.04
13 2 0.04
14 2 0.04
15 2 0.04
16 20 0.43
17 2 0.04
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (16 bp):
ATTAATTTATCGATAA
Found at i:2803232 original size:27 final size:27
Alignment explanation
Indices: 2803202--2803292 Score: 157
Period size: 27 Copynumber: 3.4 Consensus size: 27
2803192 TTTATCGAGG
2803202 TTATTAATTTATCGATAAATTAATATT
1 TTATTAATTTATCGATAAATTAATATT
2803229 TTATTAATTTATCGATAAATTAATATT
1 TTATTAATTTATCGATAAATTAATATT
*
2803256 CTATTAATTTATCGATAAATTAATA-T
1 TTATTAATTTATCGATAAATTAATATT
*
2803282 TCATTAATTTA
1 TTATTAATTTA
2803293 GAGAATATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
26 10 0.16
27 51 0.84
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATTAATATT
Found at i:2803439 original size:36 final size:35
Alignment explanation
Indices: 2803374--2803445 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
2803364 TGAATCAACG
*
2803374 TTAATTGGTTCATGTATAAAAAAAAAAAGAGTTAA
1 TTAATTGATTCATGTATAAAAAAAAAAAGAGTTAA
*
2803409 TTAATTGATTCATGTA-ACCAAAAAGAAAAGAGTTAA
1 TTAATTGATTCATGTATA--AAAAAAAAAAGAGTTAA
2803445 T
1 T
2803446 GATTTCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 1 0.03
35 15 0.45
36 17 0.52
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.31
Consensus pattern (35 bp):
TTAATTGATTCATGTATAAAAAAAAAAAGAGTTAA
Found at i:2813510 original size:7 final size:7
Alignment explanation
Indices: 2813492--2813526 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2813482 AATTAACCAA
*
2813492 AATAAAT
1 AATATAT
2813499 AATATAT
1 AATATAT
*
2813506 TATATAT
1 AATATAT
2813513 AATATAT
1 AATATAT
2813520 AATATAT
1 AATATAT
2813527 TTTTATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATATAT
Found at i:2819668 original size:14 final size:15
Alignment explanation
Indices: 2819648--2819689 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2819638 ATAATGTAAC
2819648 ATATATTTTAATGTT
1 ATATATTTTAATGTT
* *
2819663 -TATATTATAGTGTT
1 ATATATTTTAATGTT
2819677 ATATATTATTAAT
1 ATATATT-TTAAT
2819690 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 12 0.57
15 6 0.29
16 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
ATATATTTTAATGTT
Found at i:2831403 original size:30 final size:31
Alignment explanation
Indices: 2831328--2831414 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
2831318 AAACTTTATG
*
2831328 GGTTTTAGTGAGAATTTTCAAAAATTTTGGTA
1 GGTTTTA-TGAAAATTTTCAAAAATTTTGGTA
* * * * *
2831360 GGTCTAATTAAAATTTTCAAAATTTTTTG-A
1 GGTTTTATGAAAATTTTCAAAAATTTTGGTA
*
2831390 GGTTTTATGAAAATTTATAAAAAAT
1 GGTTTTATGAAAATTT-TCAAAAAT
2831415 GAAGAGTCTA
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
30 14 0.33
31 24 0.56
32 5 0.12
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (31 bp):
GGTTTTATGAAAATTTTCAAAAATTTTGGTA
Found at i:2838368 original size:15 final size:14
Alignment explanation
Indices: 2838341--2838368 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2838331 AATTAGTGTT
2838341 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
2838355 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
2838369 TGGGGGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
GAAAACTAAAAAAA
Found at i:2844827 original size:31 final size:30
Alignment explanation
Indices: 2844791--2844903 Score: 104
Period size: 31 Copynumber: 3.6 Consensus size: 30
2844781 GATTGACTAA
2844791 AATTTTTAAAAATTTTGAAGGTTTTAATGAG
1 AATTTTTAAAAATTTTGAAGG-TTTAATGAG
* * *
2844822 AATTTTTAAACAATTTTGTATGTTTAACT-AA
1 AATTTTTAAA-AATTTTGAAGGTTTAA-TGAG
**
2844853 AACTTTCAAAAAAATTTTTGAATGGTTTAATGAG
1 AA-TTT-TTAAAAA-TTTTGAA-GGTTTAATGAG
2844887 AA-TTTTAAAAATTTTGA
1 AATTTTTAAAAATTTTGA
2844904 GTGGGCTAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
30 6 0.09
31 23 0.35
32 17 0.26
33 10 0.15
34 9 0.14
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.44
Consensus pattern (30 bp):
AATTTTTAAAAATTTTGAAGGTTTAATGAG
Found at i:2844929 original size:65 final size:64
Alignment explanation
Indices: 2844798--2844929 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 64
2844788 TAAAATTTTT
**
2844798 AAAAATTTTGAAGGTTTTAATGAGAATTTTTAAACAATTTTGTATGTTTAACTAAAACTTTCAA
1 AAAAATTTTGAAGGTTTTAATGAGAATTTTTAAACAATTTTGTATGGCTAACTAAAACTTTCAA
* *
2844862 AAAAATTTTTGAATGG-TTTAATGAGAA-TTTTAAA-AATTTTG-AGTGGGCTAATTAAAATTTT
1 AAAAA-TTTTGAA-GGTTTTAATGAGAATTTTTAAACAATTTTGTA-T-GGCTAACTAAAACTTT
2844923 CAA
62 CAA
2844926 AAAA
1 AAAA
2844930 TGTATAATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
62 1 0.02
63 8 0.13
64 31 0.52
65 18 0.30
66 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (64 bp):
AAAAATTTTGAAGGTTTTAATGAGAATTTTTAAACAATTTTGTATGGCTAACTAAAACTTTCAA
Found at i:2854058 original size:100 final size:103
Alignment explanation
Indices: 2853921--2854192 Score: 371
Period size: 104 Copynumber: 2.7 Consensus size: 103
2853911 AAAATTACAT
*
2853921 TAAAAAATCACAAAACAC-TAAACT-AACACTAACAATTTATATAACCTAATCATAAATTACAAA
1 TAAAAAATCACAAAACACAT-AACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAA
**
2853984 CAAAATAACTATAAAA-TTATTT-ATTAAA-TACATTAC
65 CAAAATAACTATAAAATTTATTTAAAAAAAGTACATTAC
2854020 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
1 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
* *
2854085 AAAATAATTATAAAATTTTTTTAAAAAAAGTTACATTAC
66 AAAATAACTATAAAATTTATTTAAAAAAAG-TACATTAC
* * *
2854124 TAAAAGATCACAAAAC-CATATACTAAACACTAACAA-TT-TGTAACCTAATCCCATAAATTATT
1 TAAAAAATCACAAAACACATA-ACTAAACACTAACAATTTATATAACCTAAT--CATAAATTACT
2854186 AACAAAA
63 AACAAAA
2854193 ATAAATAACT
Statistics
Matches: 156, Mismatches: 8, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
99 22 0.14
100 54 0.35
101 5 0.03
102 14 0.09
103 6 0.04
104 55 0.35
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (103 bp):
TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
AAAATAACTATAAAATTTATTTAAAAAAAGTACATTAC
Found at i:2854150 original size:104 final size:99
Alignment explanation
Indices: 2853910--2854192 Score: 355
Period size: 100 Copynumber: 2.8 Consensus size: 99
2853900 TACATTATAT
2853910 AAAAATTACATTA--AAAAATCACAAAA-CACTAAACT-AACACTAACAATTTATATAACCTAAT
1 AAAAATTACATTACTAAAAATCACAAAACCA-T-AACTAAACACTAACAATTTATATAACCTAAT
*
2853971 CATAAATTACAAACAAAATAACTATAAAATTATTTA
64 CATAAATTACTAACAAAATAACTATAAAATTATTTA
**
2854007 TTAAA-TACATTACTAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAAT
1 AAAAATTACATTACT-AAAAATCACAAAAC-CATAACTAAACACTAACAATTTATATAACCTAAT
* *
2854071 CATAAATTACTAACAAAATAATTATAAAATTTTTTTAA
64 CATAAATTACTAACAAAATAACTATAAAA-TTATTT-A
*
2854109 AAAAAGTTACATTACTAAAAGATCACAAAACCATATACTAAACACTAACAA-TT-TGTAACCTAA
1 AAAAA-TTACATTACTAAAA-ATCACAAAACCATA-ACTAAACACTAACAATTTATATAACCTAA
*
2854172 TCCCATAAATTATTAACAAAA
63 T--CATAAATTACTAACAAAA
2854193 ATAAATAACT
Statistics
Matches: 163, Mismatches: 9, Indels: 21
0.84 0.05 0.11
Matches are distributed among these distances:
96 7 0.04
97 3 0.02
99 17 0.10
100 54 0.33
101 7 0.04
102 14 0.09
103 10 0.06
104 51 0.31
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (99 bp):
AAAAATTACATTACTAAAAATCACAAAACCATAACTAAACACTAACAATTTATATAACCTAATCA
TAAATTACTAACAAAATAACTATAAAATTATTTA
Found at i:2854465 original size:60 final size:60
Alignment explanation
Indices: 2854387--2854501 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 60
2854377 TAAACTAAAC
*
2854387 ACAAAAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTACAAAT
1 ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAT
* *
2854447 ACAACAATTTATAGCATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
2854502 TAAAAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (60 bp):
ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAT
Found at i:2854677 original size:17 final size:17
Alignment explanation
Indices: 2854652--2854685 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2854642 AAAATAATAC
*
2854652 ATTACTTTTTTTTTCTT
1 ATTACTTTTATTTTCTT
*
2854669 ATTATTTTTATTTTCTT
1 ATTACTTTTATTTTCTT
2854686 CTCCTTTCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTACTTTTATTTTCTT
Found at i:2854875 original size:28 final size:26
Alignment explanation
Indices: 2854818--2854881 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
2854808 TATCTATGCA
* *
2854818 GCAGAGGGGCGTAGGGGGGCTGTATG
1 GCAGAGGGGCGCAGGGGGGCTGTAGG
*
2854844 GCAGAGGGGCGCAGGGGGGCTGTGCGGG
1 GCAGAGGGGCGCAGGGGGGCTGT--AGG
2854872 GCAGAGGGGC
1 GCAGAGGGGC
2854882 ACAAGGGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 22 0.67
28 11 0.33
ACGTcount: A:0.14, C:0.16, G:0.61, T:0.09
Consensus pattern (26 bp):
GCAGAGGGGCGCAGGGGGGCTGTAGG
Found at i:2861636 original size:26 final size:26
Alignment explanation
Indices: 2861607--2861659 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2861597 TTTCAACCAG
2861607 TTTGTACTAATTTACGAGTCAAAAAA
1 TTTGTACTAATTTACGAGTCAAAAAA
2861633 TTTGTACTAATTTACGAGTCAAAAAA
1 TTTGTACTAATTTACGAGTCAAAAAA
2861659 T
1 T
2861660 CAGCCAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (26 bp):
TTTGTACTAATTTACGAGTCAAAAAA
Found at i:2863763 original size:13 final size:13
Alignment explanation
Indices: 2863745--2863770 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2863735 GCTTCAATAA
2863745 ATGTTTTGACAAT
1 ATGTTTTGACAAT
2863758 ATGTTTTGACAAT
1 ATGTTTTGACAAT
2863771 CAATACAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATGTTTTGACAAT
Found at i:2868730 original size:11 final size:11
Alignment explanation
Indices: 2868714--2868746 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2868704 GGGTGAATTG
2868714 ATCTTTCTCTT
1 ATCTTTCTCTT
*
2868725 ATCTTTTTCTT
1 ATCTTTCTCTT
2868736 ATCTTTCTCTT
1 ATCTTTCTCTT
2868747 TAATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (11 bp):
ATCTTTCTCTT
Found at i:2869986 original size:19 final size:19
Alignment explanation
Indices: 2869962--2869999 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2869952 TTTGATTATT
2869962 TGAAAACCTATTTTAATGA
1 TGAAAACCTATTTTAATGA
2869981 TGAAAACCTATTTTAATGA
1 TGAAAACCTATTTTAATGA
2870000 AAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
TGAAAACCTATTTTAATGA
Found at i:2870005 original size:19 final size:19
Alignment explanation
Indices: 2869964--2870005 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2869954 TGATTATTTG
**
2869964 AAAACCTATTTTAATGATG
1 AAAACCTATTTTAATGAAA
2869983 AAAACCTATTTTAATGAAA
1 AAAACCTATTTTAATGAAA
2870002 AAAA
1 AAAA
2870006 AAATCTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (19 bp):
AAAACCTATTTTAATGAAA
Found at i:2871243 original size:66 final size:65
Alignment explanation
Indices: 2871137--2871267 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 65
2871127 TCGACTAAAC
2871137 CCAAATAATACAAAACCAAAAGGAGAAAGACATGTAAAGCCTCGCGCAAGGGACCAACAACACCC
1 CCAAATAATACAAAACCAAAAGGAGAAAGACATGTAAAGCCTCG-GCAAGGGACCAACAACACCC
2871202 T
65 T
* *
2871203 CCAAATAATACAAAACCAAAAGTAGAAAGAGATGTAAAGCCTCGGCAAGGGACCAACAACACCCT
1 CCAAATAATACAAAACCAAAAGGAGAAAGACATGTAAAGCCTCGGCAAGGGACCAACAACACCCT
2871268 TTATAAGGCT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 21 0.33
66 42 0.67
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.10
Consensus pattern (65 bp):
CCAAATAATACAAAACCAAAAGGAGAAAGACATGTAAAGCCTCGGCAAGGGACCAACAACACCCT
Found at i:2876378 original size:23 final size:24
Alignment explanation
Indices: 2876334--2876378 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
2876324 ATTTTCCCGA
* *
2876334 TAAAAATTTGATTAATTTTATTGT
1 TAAAAATTTAATTAATTCTATTGT
*
2876358 TAAAAA-TTAATTTATTCTATT
1 TAAAAATTTAATTAATTCTATT
2876379 TATGATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAAAAATTTAATTAATTCTATTGT
Found at i:2876679 original size:11 final size:11
Alignment explanation
Indices: 2876663--2876687 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2876653 ACAGCAATGG
2876663 CCAATGTTCAT
1 CCAATGTTCAT
2876674 CCAATGTTCAT
1 CCAATGTTCAT
2876685 CCA
1 CCA
2876688 TCAGAGGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (11 bp):
CCAATGTTCAT
Found at i:2897146 original size:15 final size:16
Alignment explanation
Indices: 2897126--2897159 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2897116 ATCATTCAAA
2897126 AAATTACAAAAAT-AT
1 AAATTACAAAAATAAT
*
2897141 AAATTACTAAAATAAT
1 AAATTACAAAAATAAT
2897157 AAA
1 AAA
2897160 ATTATATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATTACAAAAATAAT
Found at i:2897578 original size:22 final size:21
Alignment explanation
Indices: 2897553--2897609 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
2897543 TTAAAATATT
2897553 AAATTAAATTTTTATTATTT-TA
1 AAATTAAA-TTTTATT-TTTATA
2897575 AAATGT-AATTTTATTTTTATA
1 AAAT-TAAATTTTATTTTTATA
*
2897596 AATTTAAAATTTTA
1 AAATT-AAATTTTA
2897610 AAATACTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
20 4 0.13
21 12 0.40
22 13 0.43
23 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AAATTAAATTTTATTTTTATA
Found at i:2903127 original size:15 final size:15
Alignment explanation
Indices: 2903094--2903127 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2903084 TTACAATAAG
* *
2903094 AAAAATAAAAATTTT
1 AAAAATAAAAATATA
2903109 AAAAATAAAAATATA
1 AAAAATAAAAATATA
2903124 AAAA
1 AAAA
2903128 TTAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAAAATATA
Found at i:2903465 original size:6 final size:6
Alignment explanation
Indices: 2903449--2903483 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2903439 TCATGTATTG
* *
2903449 TGTGTA CGTGTA TGTGTA TGTGTA TGCGTA TGTGT
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGT
2903484 GTGGGTGTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.14, C:0.06, G:0.34, T:0.46
Consensus pattern (6 bp):
TGTGTA
Found at i:2906146 original size:13 final size:13
Alignment explanation
Indices: 2906130--2906159 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2906120 TGGTATGAGT
2906130 TTATGGGTTTTGG
1 TTATGGGTTTTGG
2906143 TTATGGGTTTTGG
1 TTATGGGTTTTGG
2906156 TTAT
1 TTAT
2906160 AGGCAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.33, T:0.57
Consensus pattern (13 bp):
TTATGGGTTTTGG
Found at i:2906318 original size:24 final size:25
Alignment explanation
Indices: 2906291--2906338 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2906281 AGAAGAAAGT
2906291 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
2906315 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
2906339 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:2906856 original size:43 final size:43
Alignment explanation
Indices: 2906796--2906890 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
2906786 AATGATGATA
*
2906796 TAAAATT-ATACAAATATAAATTATTTTATTTTATATGTCTTT
1 TAAAATTAAAACAAATATAAATTATTTTATTTTATATGTCTTT
*
2906838 TAAAATTAAAACAAATATAAATTATTTTATTTTGTATGTCTTT
1 TAAAATTAAAACAAATATAAATTATTTTATTTTATATGTCTTT
2906881 TAAAATTAAA
1 TAAAATTAAA
2906891 GGAAACAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 7 0.14
43 43 0.86
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (43 bp):
TAAAATTAAAACAAATATAAATTATTTTATTTTATATGTCTTT
Found at i:2910321 original size:27 final size:27
Alignment explanation
Indices: 2910283--2910347 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
2910273 ATTGATAAGG
*
2910283 ACGTAAAATTTTAGTGGGTTACACTAC
1 ACGTAAAATTTTAGTGGGTTAAACTAC
2910310 ACGTAAAATTTTAGTGGGTTAAACTAC
1 ACGTAAAATTTTAGTGGGTTAAACTAC
*
2910337 ACATAAGAATT
1 ACGTAA-AATT
2910348 GATAAGAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 31 0.89
28 4 0.11
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (27 bp):
ACGTAAAATTTTAGTGGGTTAAACTAC
Found at i:2911819 original size:230 final size:229
Alignment explanation
Indices: 2911546--2912035 Score: 647
Period size: 230 Copynumber: 2.1 Consensus size: 229
2911536 TATAATACAA
*
2911546 CGCCGCTAAAT-ATCAGTATTAGCGGCGCTTCTAGTTAAGCGCCGCAAGATAT-GCACACCAAAA
1 CGCCGCTAAATCAT-ATTATTAGCGGCGCTTCTAG-TAAGCGCCGCAAGATATAGCA-ACCAAAA
* * *
2911609 CGCAGAGCTT-GGTATTGAGGTATATTAG-ATGTAGTGGCGCTTT-CTG-GAAA-CGCCGCAAAA
63 CGCAGAGCTTAGATATTGACGTATACTAGAAT-TAGTGGCG-TTTAC-GAGAAATCGCCGCAAAA
* *
2911669 GT-ATACTATTAGCGGCGCTTTCTTAGAAGCGCCGCAATATATATATTAACGGAAACGCTGCGTT
125 -TCATACTATTAGCGGCGCTTTCTTAGAAGCGCCGC-A-AGATATATTAACCGAAACGCTGCGTT
*
2911733 TAAATCTTGATGTATACTGGATTTAGTGGCGTTCACGAGAAAT
187 TAAATCTTGATGTATACTGGAATTAGTGGCGTTCACGAGAAAT
** *
2911776 CGCCGCTAAATCATATTATTAGCGGCGCTTGCTAAG-AAGCGCCGCAAGATATATTAACCTAAAC
1 CGCCGCTAAATCATATTATTAGCGGCGCTT-CT-AGTAAGCGCCGCAAGATATAGCAACCAAAAC
* * * * * *
2911840 GCTGCGTTTAGATCTTGACGTATACTGGAATTAGTGGCGTTTACGAGAAATCGCCGCTAAATCAT
64 GCAGAGCTTAGATATTGACGTATACTAGAATTAGTGGCGTTTACGAGAAATCGCCGCAAAATCAT
* *
2911905 ATTATTAGCGGCGCTTTCTTAGAAGCGCTGCAAGATATATTAACCGAAACGCTGCGTTTAAATCT
129 ACTATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCT
2911970 TGATGTATACTGGAATTAGTGGCGTTCACGAGAAAT
194 TGATGTATACTGGAATTAGTGGCGTTCACGAGAAAT
*
2912006 CGCCGCTAAATCATATTATTAGCAGCGCTT
1 CGCCGCTAAATCATATTATTAGCGGCGCTT
2912036 ATTTGTTATT
Statistics
Matches: 231, Mismatches: 19, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
230 154 0.67
231 33 0.14
232 44 0.19
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (229 bp):
CGCCGCTAAATCATATTATTAGCGGCGCTTCTAGTAAGCGCCGCAAGATATAGCAACCAAAACGC
AGAGCTTAGATATTGACGTATACTAGAATTAGTGGCGTTTACGAGAAATCGCCGCAAAATCATAC
TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
ATGTATACTGGAATTAGTGGCGTTCACGAGAAAT
Found at i:2911866 original size:115 final size:115
Alignment explanation
Indices: 2911675--2912035 Score: 605
Period size: 115 Copynumber: 3.1 Consensus size: 115
2911665 AAAAGTATAC
* *
2911675 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAATATATATATTAACGGAAACGCTGCGTTTAAATCT
1 TATTAGCGGCGCTTTCTTAGAAGCGCCGC-A-AGATATATTAACCGAAACGCTGCGTTTAAATCT
*
2911740 TGATGTATACTGGATTTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
64 TGATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
* * * *
2911792 TATTAGCGGCGCTTGCTAAGAAGCGCCGCAAGATATATTAACCTAAACGCTGCGTTTAGATCTTG
1 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
* *
2911857 ACGTATACTGGAATTAGTGGCGTTTACGAGAAATCGCCGCTAAATCATAT
66 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
*
2911907 TATTAGCGGCGCTTTCTTAGAAGCGCTGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
1 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
2911972 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
66 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
*
2912022 TATTAGCAGCGCTT
1 TATTAGCGGCGCTT
2912036 ATTTGTTATT
Statistics
Matches: 227, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
115 199 0.88
116 1 0.00
117 27 0.12
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (115 bp):
TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
Found at i:2912346 original size:7 final size:7
Alignment explanation
Indices: 2912333--2912383 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 7
2912323 ATGGTATTTT
2912333 GGGTTTA
1 GGGTTTA
*
2912340 AGGTTTA
1 GGGTTTA
2912347 GGAGTTTA
1 GG-GTTTA
*
2912355 GGGTGTA
1 GGGTTTA
*
2912362 AGGTTTA
1 GGGTTTA
*
2912369 GGGTTTG
1 GGGTTTA
2912376 GGGTTTA
1 GGGTTTA
2912383 G
1 G
2912384 ACTGCTTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
7 28 0.80
8 7 0.20
ACGTcount: A:0.18, C:0.00, G:0.43, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:2912363 original size:22 final size:21
Alignment explanation
Indices: 2912333--2912379 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
2912323 ATGGTATTTT
*
2912333 GGGTTTAAGGTTTAGGAGTTTA
1 GGGTGTAAGGTTTAGG-GTTTA
*
2912355 GGGTGTAAGGTTTAGGGTTTG
1 GGGTGTAAGGTTTAGGGTTTA
2912376 GGGT
1 GGGT
2912380 TTAGACTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (21 bp):
GGGTGTAAGGTTTAGGGTTTA
Found at i:2913620 original size:45 final size:45
Alignment explanation
Indices: 2913570--2913660 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
2913560 TGTTGCGTCC
* * *
2913570 TTCTTGCCCAATTTCTTGAATTCCCAAATCCGTAAATCGCCTCCT
1 TTCTTGCCCAATTTCTTAAAATCCCAAATCCCTAAATCGCCTCCT
* *
2913615 TTCTTGCCTAATTTCTTAAAATCCGAAATCCCTAAATCGCCTCCT
1 TTCTTGCCCAATTTCTTAAAATCCCAAATCCCTAAATCGCCTCCT
2913660 T
1 T
2913661 CCTCCTTCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (45 bp):
TTCTTGCCCAATTTCTTAAAATCCCAAATCCCTAAATCGCCTCCT
Found at i:2914872 original size:21 final size:21
Alignment explanation
Indices: 2914846--2914893 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2914836 CAACAACTTA
* *
2914846 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
2914867 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
2914888 AAGCAG
1 AAGCAG
2914894 CGATAGAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:2914895 original size:12 final size:12
Alignment explanation
Indices: 2914857--2914905 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
2914847 AGCAGATGCG
2914857 GCAGCGAGAGAA
1 GCAGCGAGAGAA
**
2914869 GCA--GAG-GCC
1 GCAGCGAGAGAA
2914878 GCAGCGAGAGAA
1 GCAGCGAGAGAA
*
2914890 GCAGCGATAGAA
1 GCAGCGAGAGAA
2914902 GCAG
1 GCAG
2914906 AGGTTCAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
9 4 0.14
10 3 0.10
11 3 0.10
12 19 0.66
ACGTcount: A:0.37, C:0.20, G:0.41, T:0.02
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:2915418 original size:85 final size:86
Alignment explanation
Indices: 2915327--2915703 Score: 283
Period size: 85 Copynumber: 4.5 Consensus size: 86
2915317 TTTGTGAAAT
*
2915327 AAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCATTTTTGAAC-AAGCGCCGCTATAGAACATC
1 AAGCGCCGCTAAAGAACACTGATC-TTTAGCGGCATTTTT-AACTAAGCGCCGCTAAAGAACATC
2915389 A-CTTTTAGAGACGTTT-TCTTCCA
64 ATC-TTTAGAGACGTTTAT-TTCCA
* * ** *
2915412 AAGCGCCGCTAAAGAAC-TTGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACACTGATCTTTAGCGGCATTTTTAACTAAGCGCCGCTAAAGAACATCAT
* * *
2915476 CTTTAGCGGCGTTTATTTCCT
66 CTTTAGAGACGTTTATTTCCA
* * * * * **
2915497 TAGCGCCGCTAAAGAACA-TGATTTTTAGCGACGTTTATT-TCTAAGCGCCGCTAAAGAACATGG
1 AAGCGCCGCTAAAGAACACTGATCTTTAGCGGCATTT-TTAACTAAGCGCCGCTAAAGAACATCA
* * * *
2915560 TCTTTAGTGGCTTTTATTT-CT
65 TCTTTAGAGACGTTTATTTCCA
* * * * *** * * *
2915581 AAGCGCCGCTAAAGAACA-TGGTCTTTAGTGACGTTTATTTTTTTAGCGCCACTAAAGAACATGA
1 AAGCGCCGCTAAAGAACACTGATCTTTAGCGGCATTT-TTAACTAAGCGCCGCTAAAGAACATCA
* * * * *
2915645 TCTTTAGCGGCATTT-TTTTCT
65 TCTTTAGAGACGTTTATTTCCA
* *
2915666 AAGCGCCGCTAAAGAACA-TGATCTTTAGGGGCGTTTTT
1 AAGCGCCGCTAAAGAACACTGATCTTTAGCGGCATTTTT
2915704 TTCTGTAAGC
Statistics
Matches: 255, Mismatches: 28, Indels: 19
0.84 0.09 0.06
Matches are distributed among these distances:
84 44 0.17
85 206 0.81
86 5 0.02
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (86 bp):
AAGCGCCGCTAAAGAACACTGATCTTTAGCGGCATTTTTAACTAAGCGCCGCTAAAGAACATCAT
CTTTAGAGACGTTTATTTCCA
Found at i:2915469 original size:42 final size:42
Alignment explanation
Indices: 2915326--2915723 Score: 437
Period size: 42 Copynumber: 9.4 Consensus size: 42
2915316 GTTTGTGAAA
* **
2915326 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCATTTTTGAAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TTC
* * * * *
2915369 -AAGCGCCGCTATAGAACATCA-CTTTTAGAGACGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTTC
* *
2915411 AAAGCGCCGCTAAAGAACTTGATCTTTAGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
*
2915453 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTC
* * * *
2915496 TTAGCGCCGCTAAAGAACATGATTTTTAGCGACGTTTATTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
2915538 TAAGCGCCGCTAAAGAACATGGTCTTTAGTGGC-TTTTATTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TTTC
* * * *
2915580 TAAGCGCCGCTAAAGAACATGGTCTTTAGTGACGTTTATTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTC
* * *
2915623 TTAGCGCCACTAAAGAACATGATCTTTAGCGGCATTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
*
2915665 TAAGCGCCGCTAAAGAACATGATCTTTAGGGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
*
2915707 TGTAAGCGCCGCAAAAG
1 --TAAGCGCCGCTAAAG
2915724 TTTGCGACGT
Statistics
Matches: 305, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
41 4 0.01
42 179 0.59
43 106 0.35
44 16 0.05
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:2915552 original size:127 final size:126
Alignment explanation
Indices: 2915370--2915723 Score: 467
Period size: 127 Copynumber: 2.8 Consensus size: 126
2915360 TTTTTGAACA
* * * * * *
2915370 AGCGCCGCTATAGAACATCACTTTTAGAGACGTTTTCTTCCAAAGCGCCGCTAAAGAACTTGATC
1 AGCGCCGCTAAAGAACATGATTTTTAGCGACGTTTT-TT-CTAAGCGCCGCTAAAGAACATGATC
*
2915435 TTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTCCTT
64 TTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTATTTCCTT
*
2915498 AGCGCCGCTAAAGAACATGATTTTTAGCGACGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCT
1 AGCGCCGCTAAAGAACATGATTTTTAGCGACGTTT-TTTCTAAGCGCCGCTAAAGAACATGATCT
* * * **
2915563 TTAGTGGC-TTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGACGTTTATTTTTTT
65 TTAGCGGCGTTTT-TTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTATTTCCTT
* * * *
2915625 AGCGCCACTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
1 AGCGCCGCTAAAGAACATGATTTTTAGCGAC-GTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
* *
2915690 TTAGGGGCGTTTTTTTCTGTAAGCGCCGCAAAAG
65 TTAGCGGCGTTTTTTTC--TAAGCGCCGCTAAAG
2915724 TTTGCGACGT
Statistics
Matches: 200, Mismatches: 20, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
126 4 0.02
127 141 0.70
128 40 0.20
129 15 0.08
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (126 bp):
AGCGCCGCTAAAGAACATGATTTTTAGCGACGTTTTTTCTAAGCGCCGCTAAAGAACATGATCTT
TAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTATTTCCTT
Found at i:2927832 original size:42 final size:42
Alignment explanation
Indices: 2927705--2927816 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
2927695 GATTGAACGT
* * *
2927705 CAGTATTCGGTTTGTCCCTCGAGAGCCTGGGTGATTGAAATG
1 CAGTATCCGGTTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
* *
2927747 CAGTATCTGGTTTGTCCTTGGAGAGCTTGGGTGATTGAAATG
1 CAGTATCCGGTTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
2927789 CAGTA-CCGGATTTGTCCTTGGAGAGCCT
1 CAGTATCCGG-TTTGTCCTTGGAGAGCCT
2927817 AGGTCGTTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 3 0.05
42 59 0.95
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (42 bp):
CAGTATCCGGTTTGTCCTTGGAGAGCCTGGGTGATTGAAATG
Found at i:2927841 original size:42 final size:42
Alignment explanation
Indices: 2927715--2927845 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 42
2927705 CAGTATTCGG
* * * * ** *
2927715 TTTGTCCCTCGAGAGCCTGGGTGATTGAAATGCAGTATCTGG-
1 TTTGTCCTTGGAGAGCCTAGGTGATTCAAATGCACCA-CCGGA
* * * **
2927757 TTTGTCCTTGGAGAGCTTGGGTGATTGAAATGCAGTACCGGA
1 TTTGTCCTTGGAGAGCCTAGGTGATTCAAATGCACCACCGGA
*
2927799 TTTGTCCTTGGAGAGCCTAGGTCG-TTCAAATGCACCATCGGA
1 TTTGTCCTTGGAGAGCCTAGGT-GATTCAAATGCACCACCGGA
2927841 TTTGT
1 TTTGT
2927846 TCATGGGGAG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 3 0.04
42 73 0.95
43 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (42 bp):
TTTGTCCTTGGAGAGCCTAGGTGATTCAAATGCACCACCGGA
Found at i:2932706 original size:21 final size:20
Alignment explanation
Indices: 2932678--2932719 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2932668 ATCATATATT
2932678 GATTGATAAAAAATAAAGTA
1 GATTGATAAAAAATAAAGTA
**
2932698 GATTAGATATCAAATAAAGTA
1 GATT-GATAAAAAATAAAGTA
2932719 G
1 G
2932720 GCAGACCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.55, C:0.02, G:0.17, T:0.26
Consensus pattern (20 bp):
GATTGATAAAAAATAAAGTA
Found at i:2937001 original size:22 final size:24
Alignment explanation
Indices: 2936957--2937001 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
2936947 GCTTCATGTT
*
2936957 ATTTTTTATAAACTTTATATATAG
1 ATTTTTTATAAACTATATATATAG
*
2936981 ATTTTTTA-AAA-TATATTTATA
1 ATTTTTTATAAACTATATATATA
2937002 AGTTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTTTTATAAACTATATATATAG
Found at i:2940915 original size:33 final size:33
Alignment explanation
Indices: 2940878--2940989 Score: 197
Period size: 33 Copynumber: 3.4 Consensus size: 33
2940868 GCCTGTAGAT
*
2940878 AAAAGGAATATATTTATAGTAGTACTACAAGCC
1 AAAAGGAATATATTTATAGTAGTAGTACAAGCC
2940911 AAAAGGAATATATTTATAGTAGTAGTACAAGCC
1 AAAAGGAATATATTTATAGTAGTAGTACAAGCC
*
2940944 AAAAAGAATATATTTATAGTAGTAGTACAAGCC
1 AAAAGGAATATATTTATAGTAGTAGTACAAGCC
*
2940977 AAAACGAATATAT
1 AAAAGGAATATAT
2940990 CATATCTAGG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (33 bp):
AAAAGGAATATATTTATAGTAGTAGTACAAGCC
Found at i:2947241 original size:29 final size:29
Alignment explanation
Indices: 2947153--2947242 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 29
2947143 AATTGGTAAT
* * *
2947153 TAAATTATATTGTTTTTCACATCTTGATACT
1 TAAACTATATT-TTTTTCACA-ATTGATACC
* *
2947184 TAAACT-TTTTTTTTATCACAATTGGTACC
1 TAAACTATATTTTTT-TCACAATTGATACC
2947213 TAAACTATATTTTTTTC-CAAGTTGATACC
1 TAAACTATATTTTTTTCACAA-TTGATACC
2947242 T
1 T
2947243 TTATTAGTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 3 0.06
29 26 0.53
30 15 0.31
31 5 0.10
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (29 bp):
TAAACTATATTTTTTTCACAATTGATACC
Found at i:2960053 original size:3 final size:3
Alignment explanation
Indices: 2960038--2960071 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2960028 AGGAACTATT
* *
2960038 CTG CTG TTG CTG CTG CTG CGG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
2960072 GGAAAGTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.32, G:0.35, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:2960072 original size:15 final size:15
Alignment explanation
Indices: 2960045--2960073 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2960035 ATTCTGCTGT
2960045 TGCTGCTGCTGCGGC
1 TGCTGCTGCTGCGGC
2960060 TGCTGCTGCTGCGG
1 TGCTGCTGCTGCGG
2960074 AAAGTGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.31, G:0.41, T:0.28
Consensus pattern (15 bp):
TGCTGCTGCTGCGGC
Found at i:2960106 original size:15 final size:15
Alignment explanation
Indices: 2960088--2960127 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2960078 TGATGAGGAG
*
2960088 GAGGGTGAGGAAAGC
1 GAGGGAGAGGAAAGC
*
2960103 GAGGGAGAGGAAAGT
1 GAGGGAGAGGAAAGC
*
2960118 GAAGGAGAGG
1 GAGGGAGAGG
2960128 GAGAGGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.55, T:0.05
Consensus pattern (15 bp):
GAGGGAGAGGAAAGC
Found at i:2960127 original size:21 final size:21
Alignment explanation
Indices: 2960103--2960143 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2960093 TGAGGAAAGC
*
2960103 GAGGGAGAGGAAAGTGAAGGA
1 GAGGGAGAGGAAAGGGAAGGA
*
2960124 GAGGGAGAGGAGAGGGAAGG
1 GAGGGAGAGGAAAGGGAAGG
2960144 GATGAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.59, T:0.02
Consensus pattern (21 bp):
GAGGGAGAGGAAAGGGAAGGA
Found at i:2977137 original size:96 final size:96
Alignment explanation
Indices: 2977025--2977215 Score: 373
Period size: 96 Copynumber: 2.0 Consensus size: 96
2977015 TTTAATAATA
*
2977025 ATTTGAATTGTTTGGAACTTGGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
1 ATTTGAATTGTTTGGAACTTAGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
2977090 TTGAATATGATGAATAGTAATTTGAGATATG
66 TTGAATATGATGAATAGTAATTTGAGATATG
2977121 ATTTGAATTGTTTGGAACTTAGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
1 ATTTGAATTGTTTGGAACTTAGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
2977186 TTGAATATGATGAATAGTAATTTGAGATAT
66 TTGAATATGATGAATAGTAATTTGAGATAT
2977216 TTAATGAATT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.32
Consensus pattern (96 bp):
ATTTGAATTGTTTGGAACTTAGTACAAAAGGTGAGATATGGACTAAATCGTAAAGAAATGATAAA
TTGAATATGATGAATAGTAATTTGAGATATG
Found at i:2986123 original size:210 final size:210
Alignment explanation
Indices: 2985759--2986808 Score: 1665
Period size: 210 Copynumber: 5.0 Consensus size: 210
2985749 CAATCTATAA
* *
2985759 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCATGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* *
2985824 GTTCCCTCAGC-GAATTTTGCCAGTGAGCAGATGTTGCAAATCTTAGGGAAATCTTCTGATCCTG
66 GTTTCCTCA-CAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG
* * *
2985888 ACAATTTATCCC-ATTCTGGTTTATACATGAGTGATGAAATTCATGAAAATTCACAAGTGGAATC
130 ACAATTTA-CCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATC
*
2985952 TGTCATCAGTAATCCAT
194 TGTCATCAGTGATCCAT
* * *
2985969 TTGAATCCTCTGCCTCATCCAATATCATTTTAAGCGATGAGATCTCCACGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* * * *
2986034 GTTTCCTCGCAGAATTTTGCCAGTGAACATATGTTGCAAATCTCAGGGAAATCTTCTGATACTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* * *
2986099 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCAAAAAAATTCACAAGGGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
2986164 TCATCAATGATCCAT
196 TCATCAGTGATCCAT
* *
2986179 TTGAATCCTCTGCCTCATCCAATATCATTACAAGCAATGGGATCTCCACAAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* *
2986244 ATTTCCTCACAGAATTTTGCCAGTGAGCAGATGCTGCAAATCTCAGGGAAATCTTCTGATCCTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* *
2986309 CAATTTTCCCTATACTGATTTATACATGAGTGGTGAAATTCATAAAAATTCACAAGTGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
2986374 TCATTAGTGATCCAT
196 TCATCAGTGATCCAT
2986389 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* * * *
2986454 GTTGCCTCACAGAATTTTGCCAGTGAACATATGTTGCAAATCTCAGGGAAATCTTCTGATACTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* *
2986519 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCAAAAAAATTCACAAGTGGAATCTG
131 CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
2986584 TCATCAATGATCCAT
196 TCATCAGTGATCCAT
* * *
2986599 TTGAATCCTTTGCCTCATCCAATATCATTGCAAGCAATGGGATCTCCACAAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
* *
2986664 ATTTCCTCACAGAATTTTGCCAGTGAGCAGATGCTGCAAATCTCAGGGAAATCTTCTGATCCTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* ** *
2986729 CAATATT-CCCTATACTGATTTATGCACAAGTGATGAAATTCATAAAATTTCACAAGTGGAATCT
131 CAAT-TTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCT
*
2986793 GTCATCAGTCATCCAT
195 GTCATCAGTGATCCAT
2986809 CATCATCCTC
Statistics
Matches: 771, Mismatches: 66, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
209 4 0.01
210 765 0.99
211 2 0.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (210 bp):
TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGGGATCTCCACGAGTTTACCTGATCCA
GTTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
CAATTTACCCTATACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
TCATCAGTGATCCAT
Found at i:3000136 original size:32 final size:32
Alignment explanation
Indices: 3000070--3000139 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
3000060 AAAAACATTG
**
3000070 ATAG-TTCAGTGACTTAAATAAAAACTTTTGA
1 ATAGTTTCAGTGACTTAAATAAAAACTTTCAA
*
3000101 ATAGTTTC-GTGACTTAGAATGAAAACTTTCAA
1 ATAGTTTCAGTGACTTA-AATAAAAACTTTCAA
3000133 ATAGTTT
1 ATAGTTT
3000140 AGTAATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (32 bp):
ATAGTTTCAGTGACTTAAATAAAAACTTTCAA
Found at i:3005437 original size:48 final size:48
Alignment explanation
Indices: 3005366--3005500 Score: 225
Period size: 48 Copynumber: 2.8 Consensus size: 48
3005356 TAACAGAAGT
* * * * *
3005366 GATAAAATGAACATAAATTTCATTTCCATAACATAATTTGTGGTAATC
1 GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
3005414 GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
1 GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
3005462 GATAAGATGAACATAAATTTCATTTTCATAACATAACTT
1 GATAAGATGAACATAAATTTCATTTTCATAACATAACTT
3005501 ATTACAATAG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (48 bp):
GATAAGATGAACATAAATTTCATTTTCATAACATAACTTGTAGTAATA
Found at i:3009890 original size:741 final size:743
Alignment explanation
Indices: 3008456--3009907 Score: 2211
Period size: 745 Copynumber: 2.0 Consensus size: 743
3008446 TGAACTTTTT
* * * *
3008456 ACCTATATCAGTAACTTCAAGACTAAGCTACAGTATAATTTTTTAATAAAGATCAGCAATCTCAG
1 ACCTATATCAGTAACTTCAAGACTAAGCTACAATAAAATGTTTGAATAAAGATCAGCAATCTCAG
* *
3008521 CCAAAAGATGGTGAATATTTATATAATCATCATAAGACACATCAGGTTTGATGATTCATTTTCAT
66 CCAAAAGATGGTGAATATTTATATAATCATCATAACACAAATCAGGTTTGATGATTCATTTTCAT
*
3008586 AATAGATTGCAGCAACTGACAAAAAAAAGGAGGAAAAAAAAGTTATATCAATTAAAATTTGACCC
131 AATAGATTGCAGCAACTGACAAAAAAAAGGAGGAAAAAAAAGTTAAATCAATTAAAATTTGACCC
3008651 CAAATTCCCAGAAAATTAAACAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCA
196 CAAATTCCCAGAAAATTAAACAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCA
3008716 TCATTCAAATGCAGAAATGATGGATAAGCATCATCACACCTCCTTGCATATCTTAAGAAAATCAA
261 TCATTCAAATGCAGAAATGATGGATAAGCATCATCACACCTCCTTGCATATCTTAAGAAAATCAA
*
3008781 ATCCTATGAAGCATAAAAAAGTAGAACCATTAACTTATAGCAATTTCTGTTTGGCAAATTAACAA
326 ATCCTATGAAGCATAAAAAACTAGAACCATTAAC-TATAG-AATTTCTGTTTGGCAAATTAACAA
* *
3008846 ATTGAAAATAATCATAAAAAGAGAATATTTTACAGTTTACATCCCATTGGAGTAATGGTAAATGA
389 AATGAAAATAATCATAAAAAGAGAATATTTTACAGTTTACACCCCATTGGAGTAATGGTAAATGA
*
3008911 ATCAGATAGACGATCGCTAATGTCTCAGCATATTGCAACTCAGACTAGGTGTCAAATGTCTATCT
454 ATCAGATAGACGATCGCTAATGTCTCAGCATATTGCAACTCAGACTAGGTGTCAAATATCTATCT
3008976 TCATATCCACATTCAATCAAATTTTAAAAAAATAAGATTTTTAGAAAAAATGTTGCAAACAAGTG
519 TCATATCCACATTCAATCAAATTTTAAAAAAATAAGATTTTTAGAAAAAATGTTGCAAACAAGTG
*
3009041 AAGCTGCAGACAATAATTACAAGTGGAAATCAGATAAAAATGTCAATCACCAATTTTGCATATGA
584 AAGCTGCAGACAATAATTACAAGTGGAAATCAGATAAAAATGTCAATCACCAATTTTGCATACGA
*
3009106 AGACATTATTATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATGTTCCCTTTTTCCCT
649 AGACATTAATATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATGTTCCCTTTTTCCCT
3009171 TGAAAACCATAGCTCAAACAAAAACATTTG
714 TGAAAACCATAGCTCAAACAAAAACATTTG
* * * *
3009201 ACCTATATCATTAATTTCAGGACTGAGCTACAATAAAATGTTTGAATAAAGATCAGCAATCTCAG
1 ACCTATATCAGTAACTTCAAGACTAAGCTACAATAAAATGTTTGAATAAAGATCAGCAATCTCAG
* * * *
3009266 CCGAAAGATGGTGATTATTTATATAATCATCATAACATAAATCAGGTTTGATTATTCATTTTCAT
66 CCAAAAGATGGTGAATATTTATATAATCATCATAACACAAATCAGGTTTGATGATTCATTTTCAT
* ** * *
3009331 CATAGATTGCAGCAACTGAC-GGAAAAATGAGGCAAAAAACAA-TTAAATCAATTAAAATTTGCC
131 AATAGATTGCAGCAACTGACAAAAAAAAGGAGG-AAAAAA-AAGTTAAATCAATTAAAATTTGAC
* *
3009394 CCCCAATTCCCA-AAAATGGTAAAGAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTA
194 CCCAAATTCCCAGAAAAT--TAAACAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTA
** **
3009458 TTCATCATTCAAATGCAGAAATGATGGATAAGTTTCATCACACCTCCTTGCATATCTTTTGAAGA
257 TTCATCATTCAAATGCAGAAATGATGGATAAGCATCATCACACCTCCTTGCATATCTTAAGAA-A
* * * *
3009523 ATCAAATCTTATTAAGCAATAAAAAACTAG-AGC-TT-A-T-T-G-ATTT-T-TTT-TCAAA-TA
321 ATCAAATCCTATGAAGC-ATAAAAAACTAGAACCATTAACTATAGAATTTCTGTTTGGCAAATTA
*
3009577 A-AAGAAT-AAAATATAGTCA-ATAAAAGTGAATATTTTACAGTTTACACCCCTCATTGGAGTAA
385 ACAA-AATGAAAATA-A-TCATA-AAAAGAGAATATTTTACAGTTTACA-CCC-CATTGGAGTAA
* * * *
3009639 TGGTAGATGGATCAGATAGTCGATCGCTAATGTCTCAGCATATTGCAACTCAGACTGGGTGTCAA
444 TGGTAAATGAATCAGATAGACGATCGCTAATGTCTCAGCATATTGCAACTCAGACTAGGTGTCAA
*
3009704 ATATCTATCTTCATATCCACATTCAATCAATTTTTTTAAAAAAAATAAGATTTTTA-AACAAAAT
509 ATATCTATCTTCATATCCACATTCAATCAA--ATTTT-AAAAAAATAAGATTTTTAGAA-AAAAT
* *
3009768 TTTGCAAACAAGTGAAGCTGCAGACAATAATTACATGTGGAAATCAGATAAAAATGTCAATCACC
570 GTTGCAAACAAGTGAAGCTGCAGACAATAATTACAAGTGGAAATCAGATAAAAATGTCAATCACC
*
3009833 AATTTTGCATACGAAGACATTAATATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATT
635 AATTTTGCATACGAAGACATTAATATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATG
3009898 TTCCCTTTTT
700 TTCCCTTTTT
3009908 TTCTCAAAAA
Statistics
Matches: 646, Mismatches: 45, Indels: 36
0.89 0.06 0.05
Matches are distributed among these distances:
734 8 0.01
735 7 0.01
736 31 0.05
737 5 0.01
738 102 0.16
739 4 0.01
740 6 0.01
741 159 0.25
742 1 0.00
743 1 0.00
744 14 0.02
745 172 0.27
746 107 0.17
747 18 0.03
748 11 0.02
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (743 bp):
ACCTATATCAGTAACTTCAAGACTAAGCTACAATAAAATGTTTGAATAAAGATCAGCAATCTCAG
CCAAAAGATGGTGAATATTTATATAATCATCATAACACAAATCAGGTTTGATGATTCATTTTCAT
AATAGATTGCAGCAACTGACAAAAAAAAGGAGGAAAAAAAAGTTAAATCAATTAAAATTTGACCC
CAAATTCCCAGAAAATTAAACAAAATATGCAAAAGAGATCAGATGGTAGTGCATGTTTGTATTCA
TCATTCAAATGCAGAAATGATGGATAAGCATCATCACACCTCCTTGCATATCTTAAGAAAATCAA
ATCCTATGAAGCATAAAAAACTAGAACCATTAACTATAGAATTTCTGTTTGGCAAATTAACAAAA
TGAAAATAATCATAAAAAGAGAATATTTTACAGTTTACACCCCATTGGAGTAATGGTAAATGAAT
CAGATAGACGATCGCTAATGTCTCAGCATATTGCAACTCAGACTAGGTGTCAAATATCTATCTTC
ATATCCACATTCAATCAAATTTTAAAAAAATAAGATTTTTAGAAAAAATGTTGCAAACAAGTGAA
GCTGCAGACAATAATTACAAGTGGAAATCAGATAAAAATGTCAATCACCAATTTTGCATACGAAG
ACATTAATATATGCAAAGTAAGACTGGGGCGACAATAACTATCATCATGTTCCCTTTTTCCCTTG
AAAACCATAGCTCAAACAAAAACATTTG
Found at i:3010487 original size:30 final size:31
Alignment explanation
Indices: 3010451--3010518 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 31
3010441 TTTTTTTACA
3010451 TTCATTTTAGTCACTCAACTTTAAT-AAATT
1 TTCATTTTAGTCACTCAACTTTAATAAAATT
3010481 TTCATTTTAGTCACTCAACTTTAATAAAATT
1 TTCATTTTAGTCACTCAACTTTAATAAAATT
3010512 TT-ATTTT
1 TTCATTTT
3010519 GATCACTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 30 0.81
31 7 0.19
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (31 bp):
TTCATTTTAGTCACTCAACTTTAATAAAATT
Found at i:3010957 original size:21 final size:21
Alignment explanation
Indices: 3010933--3011006 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
3010923 ATAAGGGAAA
3010933 ACTTGGGTTTTCCGGTGAACT
1 ACTTGGGTTTTCCGGTGAACT
** *
3010954 ACTTGGGTTTTAAAAGG-GAA-A
1 ACTTGGGTTTT--CCGGTGAACT
3010975 ACTTGGGTTTTCCGGTGAACT
1 ACTTGGGTTTTCCGGTGAACT
*
3010996 ACTTGGATTTT
1 ACTTGGGTTTT
3011007 AAAAGTTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 3 0.07
21 32 0.76
22 3 0.07
23 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.38
Consensus pattern (21 bp):
ACTTGGGTTTTCCGGTGAACT
Found at i:3010984 original size:42 final size:42
Alignment explanation
Indices: 3010925--3011011 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
3010915 TCTTGATAAT
*
3010925 AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGGTTTTAA
1 AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGATTTTAA
3010967 AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGATTTTAA
1 AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGATTTTAA
3011009 AAG
1 AAG
3011012 TTTCATCACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.11, G:0.28, T:0.32
Consensus pattern (42 bp):
AAGGGAAAACTTGGGTTTTCCGGTGAACTACTTGGATTTTAA
Found at i:3011657 original size:8 final size:8
Alignment explanation
Indices: 3011644--3011681 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
3011634 TTTAAAATAC
3011644 TTTTTTAA
1 TTTTTTAA
3011652 TTTTTTAA
1 TTTTTTAA
*
3011660 -TTTTAAA
1 TTTTTTAA
3011667 TTTTTTAA
1 TTTTTTAA
3011675 TTTTTTA
1 TTTTTTA
3011682 CAAATACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTAA
Found at i:3011664 original size:27 final size:23
Alignment explanation
Indices: 3011626--3011681 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
3011616 TTTATTTTTA
3011626 TTTTTAACTTTAAAATACTTTTTTAAT
1 TTTTTAACTTT--AA-A-TTTTTTAAT
*
3011653 TTTTTAATTTTAAATTTTTTAAT
1 TTTTTAACTTTAAATTTTTTAAT
3011676 TTTTTA
1 TTTTTA
3011682 CAAATACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 15 0.54
24 1 0.04
25 2 0.07
27 10 0.36
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTAACTTTAAATTTTTTAAT
Found at i:3011674 original size:36 final size:39
Alignment explanation
Indices: 3011634--3011719 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 39
3011624 TATTTTTAAC
*
3011634 TTTAAAATACTTTTT-TAAT-TTTTTAATTTTAAAT-TT
1 TTTAAAATACTTTTTAAAATATTTTTAATTTTAAATATT
3011670 TTT--AAT--TTTTTACAAATACTTTTTAATTTTAAATATT
1 TTTAAAATACTTTTTA-AAATA-TTTTTAATTTTAAATATT
3011707 TTTAAAATACTTT
1 TTTAAAATACTTT
3011720 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
32 5 0.12
34 6 0.15
36 18 0.45
37 5 0.12
39 3 0.08
41 3 0.08
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (39 bp):
TTTAAAATACTTTTTAAAATATTTTTAATTTTAAATATT
Found at i:3011692 original size:29 final size:28
Alignment explanation
Indices: 3011660--3011719 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
3011650 AATTTTTTAA
*
3011660 TTTTAAATTTTTTAAT-TTTTTACAAATAC
1 TTTTAAA-TTTTAAATATTTTTA-AAATAC
*
3011689 TTTTTAATTTTAAATATTTTTAAAATAC
1 TTTTAAATTTTAAATATTTTTAAAATAC
3011717 TTT
1 TTT
3011720 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTAAATTTTAAATATTTTTAAAATAC
Found at i:3017634 original size:38 final size:38
Alignment explanation
Indices: 3017583--3017661 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
3017573 TGTTATAAAC
3017583 ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
1 ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
*
3017621 ACATAGGCATGCATACAAAAGAACTGTAGCAAAGCATG
1 ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
3017659 ACA
1 ACA
3017662 ATGCCCAGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (38 bp):
ACATAGGCATGCATACAAAAGAACTGTAACAAAGCATG
Found at i:3023992 original size:23 final size:23
Alignment explanation
Indices: 3023966--3024741 Score: 226
Period size: 23 Copynumber: 34.1 Consensus size: 23
3023956 GGCCATTACA
*
3023966 TTACATCATTTAAACACCTCAAC
1 TTACATCATTTAAACACCTCAAT
*
3023989 TTACAACACTTT-AACATCC-CAAT
1 TTACATCA-TTTAAACA-CCTCAAT
* * *
3024012 TAACAACATTTATACACCTCAA-
1 TTACATCATTTAAACACCTCAAT
* *
3024034 TTACAGCGA--TAAACATCTCAAT
1 TTACATC-ATTTAAACACCTCAAT
* * * *
3024056 TT-CTAGCAACTAAAACACTTCAAT
1 TTAC-ATC-ATTTAAACACCTCAAT
* *
3024080 TTACAACATTTAAACACTTCAAT
1 TTACATCATTTAAACACCTCAAT
* *
3024103 TTGCAGTGC-TTT-AACACTTCAAT
1 TTACA-T-CATTTAAACACCTCAAT
* *
3024126 TTACATCATTTGAGCACCTCAAT
1 TTACATCATTTAAACACCTCAAT
* * *
3024149 TTACAGCAATTAAACACTTCAAT
1 TTACATCATTTAAACACCTCAAT
* * * **
3024172 TT--A-CATGTAACACCCCTTACC
1 TTACATCATTTAA-ACACCTCAAT
** * * * *
3024193 CGAGACCATTT-AACGCCTCAAC
1 TTACATCATTTAAACACCTCAAT
*
3024215 TTACAACACTTT-AACATCCT-AAT
1 TTACATCA-TTTAAACA-CCTCAAT
* * *
3024238 TAACACCATTTATACACCTCAA-
1 TTACATCATTTAAACACCTCAAT
* *
3024260 TTACAGCGA--TAAACATCTCAAT
1 TTACATC-ATTTAAACACCTCAAT
* * ** * *
3024282 TTCCAGCAACTAAAGGA-TTCAAT
1 TTACATCATTTAAA-CACCTCAAT
* * *
3024305 TTGCAGT-ACTTAAAACACTTCAAT
1 TTACA-TCA-TTTAAACACCTCAAT
* * *
3024329 TTACAACATTTAAATACTTCAAT
1 TTACATCATTTAAACACCTCAAT
* * ** *
3024352 TTGCAGCACCTAAACACTTCAAT
1 TTACATCATTTAAACACCTCAAT
* *
3024375 TTACATCATTTGAGCACCTCAAT
1 TTACATCATTTAAACACCTCAAT
* * * *
3024398 TTATAGCAATTAAACACTTCAAT
1 TTACATCATTTAAACACCTCAAT
* *
3024421 TTACAGCATTTAAACACCTCAAC
1 TTACATCATTTAAACACCTCAAT
*
3024444 TTACAACACTTT-AACATCCT-AAT
1 TTACATCA-TTTAAACA-CCTCAAT
* * *
3024467 TAACACCATTTATACACCTCAA-
1 TTACATCATTTAAACACCTCAAT
* * *
3024489 TTACAGCGA--TAAACATCTCAGT
1 TTACATC-ATTTAAACACCTCAAT
* ** **
3024511 TT-CAGCAACTAAACAATTCAAT
1 TTACATCATTTAAACACCTCAAT
* * *
3024533 TTGCAGT-ACTTAAAACACTTCAAT
1 TTACA-TCA-TTTAAACACCTCAAT
* *
3024557 TTACAACATTTAAACACTTCAAT
1 TTACATCATTTAAACACCTCAAT
* * *
3024580 TTGCAGCACTTT-AACACTTCAAT
1 TTACATCA-TTTAAACACCTCAAT
* * *
3024603 TCACAACATTTAAATACCTCAAT
1 TTACATCATTTAAACACCTCAAT
* * *
3024626 TTGCAGCACTTT-AACACTTCAAT
1 TTACATCA-TTTAAACACCTCAAT
* *
3024649 TTACAACATTTAAACACTTCAAT
1 TTACATCATTTAAACACCTCAAT
* * * *
3024672 TTGCAGCACTTT-AACATCTCTAT
1 TTACATCA-TTTAAACACCTCAAT
* * * *
3024695 TAACAACATTTATACACCTTAA-
1 TTACATCATTTAAACACCTCAAT
* * * *
3024717 TTACAACAATAAAACATCTCAAT
1 TTACATCATTTAAACACCTCAAT
3024740 TT
1 TT
3024742 TCAGCAACTA
Statistics
Matches: 564, Mismatches: 139, Indels: 100
0.70 0.17 0.12
Matches are distributed among these distances:
20 6 0.01
21 42 0.07
22 98 0.17
23 341 0.60
24 75 0.13
25 2 0.00
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (23 bp):
TTACATCATTTAAACACCTCAAT
Found at i:3024598 original size:228 final size:227
Alignment explanation
Indices: 3023966--3024776 Score: 978
Period size: 228 Copynumber: 3.6 Consensus size: 227
3023956 GGCCATTACA
* *
3023966 TTACATCATTTAAACACCTCAACTTACAACACTTTAACATCCCAATTAACAACATTTATACACCT
1 TTACAACATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTTATACACCT
* * *
3024031 CAATTACAGCGATAAACATCTCAATTTCTAGCAACTAAAACACTTCAATTTACA--ACATTTAAA
66 CAATTACAGCGATAAACATCTCAATTTC-AGCAACT-AAACAATTCAATTTGCAGTAC-TTAAAA
* * * * * * *
3024094 CACTTCAATTTGCAGTGC-TTT-AACACTTCAATTTACATCA-TTTGAGCACCTCAATTTACAGC
128 CACTTCAATTTACA--ACATTTAAACACTTCAATTTGCAGCACTTT-AACACTTCAATTTACAAC
* * * **
3024156 AATTAAACACTTCAA-TTTA-C-ATGTAACACCCCTT-ACC
190 ATTTAAACACCTCAATTTTAGCAAT-TAA-A-CACTTCAAT
** * * * *
3024193 CGAGACCATTT-AACGCCTCAACTTACAACACTTTAACATCCTAATTAACACCATTTATACACCT
1 TTACAACATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTTATACACCT
**
3024257 CAATTACAGCGATAAACATCTCAATTTCCAGCAACTAAAGGATTCAATTTGCAGTACTTAAAACA
66 CAATTACAGCGATAAACATCTCAATTT-CAGCAACTAAACAATTCAATTTGCAGTACTTAAAACA
* * * * *
3024322 CTTCAATTTACAACATTTAAATACTTCAATTTGCAGCACCTAAACACTTCAATTTACATCATTTG
130 CTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACATTTA
*
3024387 AGCACCTCAATTTATAGCAATTAAACACTTCAAT
195 AACACCTCAATTT-TAGCAATTAAACACTTCAAT
* *
3024421 TTACAGCATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACACCATTTATACACCT
1 TTACAACATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTTATACACCT
*
3024486 CAATTACAGCGATAAACATCTCAGTTTCAGCAACTAAACAATTCAATTTGCAGTACTTAAAACAC
66 CAATTACAGCGATAAACATCTCAATTTCAGCAACTAAACAATTCAATTTGCAGTACTTAAAACAC
*
3024551 TTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAACATTTAA
131 TTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACATTTAA
* * * *
3024616 ATACCTCAATTTGCAGCACTTTAACACTTCAAT
196 ACACCTCAATTT-TAGCAATTAAACACTTCAAT
* * * *
3024649 TTACAACATTTAAACACTTCAATTTGCAGCACTTTAACATCTCT-ATTAACAACATTTATACACC
1 TTACAACATTTAAACACCTCAACTTACAACACTTTAACATC-CTAATTAACAACATTTATACACC
* * * * *
3024713 TTAATTACAACAATAAAACATCTCAATTTTCAGCAACTAAACACTTCAAATTGCAGTACTTAAA
65 TCAATTACAGCGAT-AAACATCTCAA-TTTCAGCAACTAAACAATTCAATTTGCAGTACTTAAA
3024777 CAGGGCTTTA
Statistics
Matches: 508, Mismatches: 61, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
224 1 0.00
225 16 0.03
226 144 0.28
227 17 0.03
228 199 0.39
229 94 0.19
230 37 0.07
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (227 bp):
TTACAACATTTAAACACCTCAACTTACAACACTTTAACATCCTAATTAACAACATTTATACACCT
CAATTACAGCGATAAACATCTCAATTTCAGCAACTAAACAATTCAATTTGCAGTACTTAAAACAC
TTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAACATTTAA
ACACCTCAATTTTAGCAATTAAACACTTCAAT
Found at i:3042353 original size:23 final size:23
Alignment explanation
Indices: 3042303--3042365 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
3042293 ATTGACAAGT
*
3042303 ATTTTATAAATATATA--ATAAG
1 ATTTTAAAAATATATATGATAAG
*
3042324 ATATTAAAAATATATATGATGAA-
1 ATTTTAAAAATATATATGAT-AAG
* *
3042347 ATTTTAAAATTATTTATGA
1 ATTTTAAAAATATATATGA
3042366 AATAAAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.41
23 18 0.53
24 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
ATTTTAAAAATATATATGATAAG
Found at i:3042456 original size:20 final size:21
Alignment explanation
Indices: 3042422--3042470 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
3042412 ATAGATGCGA
*
3042422 ATATATGTATATACT-AATGTT
1 ATATAT-TGTATACTAAATGTT
*
3042443 ATATATTGTATACTGAAATTTT
1 ATATATTGTATACT-AAATGTT
3042465 ATATAT
1 ATATAT
3042471 ACAGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (21 bp):
ATATATTGTATACTAAATGTT
Found at i:3049325 original size:38 final size:38
Alignment explanation
Indices: 3049282--3049357 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
3049272 TTTAAGTATG
*
3049282 TCAAGAAA-ACTGGTGAGCATATAGGTATTTAAGGCAAT
1 TCAAGAAACA-TGATGAGCATATAGGTATTTAAGGCAAT
* *
3049320 TCAAGAAACATTATGAGCATATAGGTATTTGAGGCAAT
1 TCAAGAAACATGATGAGCATATAGGTATTTAAGGCAAT
3049358 CCAGATGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (38 bp):
TCAAGAAACATGATGAGCATATAGGTATTTAAGGCAAT
Found at i:3063120 original size:17 final size:18
Alignment explanation
Indices: 3063094--3063128 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3063084 CATGTTTTTA
*
3063094 TTTAATAATTTGATTAAT
1 TTTAATAATTAGATTAAT
3063112 TTTAA-AATTAGATTAAT
1 TTTAATAATTAGATTAAT
3063129 ATAATATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTAATAATTAGATTAAT
Found at i:3063191 original size:24 final size:24
Alignment explanation
Indices: 3063144--3063191 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3063134 ATTCTGTACC
* *
3063144 TATATTTAATTTTAGTGTTTAATT
1 TATATTTAATTTTAGTCTTAAATT
**
3063168 TATATTTAATTTTTTTCTTAAATT
1 TATATTTAATTTTAGTCTTAAATT
3063192 CGCCGATGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (24 bp):
TATATTTAATTTTAGTCTTAAATT
Found at i:3064076 original size:29 final size:28
Alignment explanation
Indices: 3064022--3064076 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
3064012 ATTTTAAGTT
*
3064022 AATAATGATAAAATTATATTTTACCTAA
1 AATAATGATAAAATTATATTTAACCTAA
3064050 AATAATGATAAAAATT-TAATTTAACCT
1 AATAATGAT-AAAATTAT-ATTTAACCT
3064077 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (28 bp):
AATAATGATAAAATTATATTTAACCTAA
Found at i:3068364 original size:29 final size:29
Alignment explanation
Indices: 3068304--3068365 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
3068294 TTTGTAAATT
* *
3068304 TTTCATTTTTCATTTTAATTTTTAAAGCC
1 TTTCATTTTTCATATTAATTTTTAAAGAC
*
3068333 TTTCATTTTTCATATT-ATTTATTATAGAC
1 TTTCATTTTTCATATTAATTT-TTAAAGAC
3068362 TTTC
1 TTTC
3068366 CAGATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTCATTTTTCATATTAATTTTTAAAGAC
Found at i:3076663 original size:13 final size:14
Alignment explanation
Indices: 3076645--3076677 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3076635 TTTTTTTCTT
3076645 AATAATT-AATATC
1 AATAATTAAATATC
*
3076658 AATAATTAAATATG
1 AATAATTAAATATC
3076672 AATAAT
1 AATAAT
3076678 CACTTATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
AATAATTAAATATC
Found at i:3103212 original size:23 final size:21
Alignment explanation
Indices: 3103186--3103237 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 21
3103176 AAAAAGCTTT
3103186 TAAACTATTATATTTT-GTTTAAA
1 TAAACTATT-T-TTTTAG-TTAAA
3103209 TAAATCCTATTTTTTTAGTTAAA
1 TAAA--CTATTTTTTTAGTTAAA
3103232 TAAACT
1 TAAACT
3103238 CTTAACTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 2 0.08
23 17 0.65
24 2 0.08
25 5 0.19
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (21 bp):
TAAACTATTTTTTTAGTTAAA
Found at i:3109912 original size:20 final size:20
Alignment explanation
Indices: 3109878--3109925 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
3109868 AATGACAGCA
*
3109878 AAAAAACAACAATAATGATAG-
1 AAAAAATAACAATAAT-A-AGT
3109899 AAAAAATAAC-ATAATAAGT
1 AAAAAATAACAATAATAAGT
3109918 AAAAAATA
1 AAAAAATA
3109926 TGAGCACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
20 5 0.20
21 9 0.36
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (20 bp):
AAAAAATAACAATAATAAGT
Found at i:3109923 original size:21 final size:21
Alignment explanation
Indices: 3109877--3109923 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3109867 TAATGACAGC
*
3109877 AAAAAAACAACAATAATGATA
1 AAAAAAACAACAATAATAATA
* *
3109898 GAAAAAATAAC-ATAATAAGTA
1 AAAAAAACAACAATAATAA-TA
3109919 AAAAA
1 AAAAA
3109924 TATGAGCACT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.15
Consensus pattern (21 bp):
AAAAAAACAACAATAATAATA
Found at i:3112467 original size:15 final size:17
Alignment explanation
Indices: 3112447--3112483 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
3112437 ATAAATTCAA
3112447 TAATTTA-ATTTAAAT-
1 TAATTTACATTTAAATG
*
3112462 TAATTTACTTTTAAATG
1 TAATTTACATTTAAATG
3112479 TAATT
1 TAATT
3112484 ATAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TAATTTACATTTAAATG
Found at i:3118490 original size:34 final size:34
Alignment explanation
Indices: 3118447--3118511 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
3118437 CATGGATTGT
* *
3118447 AAAACGTAAATTGTTAAGTGTATGAGCATGTTGA
1 AAAACGTAAATTGTCAAGCGTATGAGCATGTTGA
*
3118481 AAAACGTAAATTGTCATGCGTATGAGCATGT
1 AAAACGTAAATTGTCAAGCGTATGAGCATGT
3118512 ATGGTGTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (34 bp):
AAAACGTAAATTGTCAAGCGTATGAGCATGTTGA
Found at i:3131984 original size:49 final size:50
Alignment explanation
Indices: 3131895--3131993 Score: 148
Period size: 49 Copynumber: 2.0 Consensus size: 50
3131885 TTATTTTTTT
* *
3131895 AATTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAATATTTTTAAAAA
1 AATTTAAAAATAC-TTTTTTAAATTTTTTTAATTTTAAATACTTTTAAAAA
3131946 AATTTAAAAATAC-TTTTTAAA-TTTTTTAATTTTAAAATACTTTTAAAA
1 AATTTAAAAATACTTTTTTAAATTTTTTTAATTTT-AAATACTTTTAAAA
3131994 TACTTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 12 0.27
49 21 0.47
51 12 0.27
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (50 bp):
AATTTAAAAATACTTTTTTAAATTTTTTTAATTTTAAATACTTTTAAAAA
Found at i:3132002 original size:39 final size:38
Alignment explanation
Indices: 3131882--3132010 Score: 127
Period size: 38 Copynumber: 3.3 Consensus size: 38
3131872 ATAATAAATA
* *
3131882 TTTTTATTTTTTTAATTTTAAAATACTTTTTTTAAAT--T
1 TTTTTAATTTTTTAATTTTAAAATAC--TTTTAAAATACT
* * * * *
3131920 TTTTTAATTTTAAATATTTTTAAAAAAATTTAAAAATACT
1 TTTTTAATTTT--TTAATTTTAAAATACTTTTAAAATACT
*
3131960 TTTTAAATTTTTTAATTTTAAAATACTTTTAAAATACTT
1 TTTTTAATTTTTTAATTTTAAAATACTTTTAAAATAC-T
3131999 TTTTTAATTTTT
1 TTTTTAATTTTT
3132011 GTTTTAATTT
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
38 38 0.53
39 12 0.17
40 22 0.31
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (38 bp):
TTTTTAATTTTTTAATTTTAAAATACTTTTAAAATACT
Found at i:3136938 original size:33 final size:33
Alignment explanation
Indices: 3136875--3136938 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
3136865 TTTTATTAAA
* *
3136875 ATAATATTTTAATTACCTATTATTTTATTTTAGG
1 ATAATATTTTAATTA-CTAGTAGTTTATTTTAGG
3136909 ATAATACTTTTAATT-CTAGTAGTTTATTTT
1 ATAATA-TTTTAATTACTAGTAGTTTATTTT
3136939 TTATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 13 0.48
34 6 0.22
35 8 0.30
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (33 bp):
ATAATATTTTAATTACTAGTAGTTTATTTTAGG
Found at i:3143005 original size:2 final size:2
Alignment explanation
Indices: 3142998--3143023 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3142988 CCTCTTCATT
3142998 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3143024 ACTGCCTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3153815 original size:35 final size:35
Alignment explanation
Indices: 3153776--3153846 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
3153766 CTATGAGTAT
3153776 GGCAACCTCATACTATCTCAACAATAGGAATATTA
1 GGCAACCTCATACTATCTCAACAATAGGAATATTA
3153811 GGCAACCTCATACTATCTCAACAATAGGAATATTA
1 GGCAACCTCATACTATCTCAACAATAGGAATATTA
3153846 G
1 G
3153847 AGAAAGTACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (35 bp):
GGCAACCTCATACTATCTCAACAATAGGAATATTA
Found at i:3162951 original size:18 final size:18
Alignment explanation
Indices: 3162930--3162964 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3162920 GGTGGGGGTG
3162930 ATGGTCATGGCCATGGTC
1 ATGGTCATGGCCATGGTC
*
3162948 ATGGTGATGGCCATGGT
1 ATGGTCATGGCCATGGT
3162965 GATTATTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.17, G:0.37, T:0.29
Consensus pattern (18 bp):
ATGGTCATGGCCATGGTC
Found at i:3162957 original size:12 final size:12
Alignment explanation
Indices: 3162926--3162967 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3162916 TGGTGGTGGG
3162926 GGTGATGGTCAT
1 GGTGATGGTCAT
**
3162938 GGCCATGGTCAT
1 GGTGATGGTCAT
*
3162950 GGTGATGGCCAT
1 GGTGATGGTCAT
3162962 GGTGAT
1 GGTGAT
3162968 TATTGGAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29
Consensus pattern (12 bp):
GGTGATGGTCAT
Found at i:3168067 original size:23 final size:23
Alignment explanation
Indices: 3168041--3168085 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3168031 TAAACATTAA
3168041 AAAATGTTAA-AAAAACTATATAC
1 AAAATGTTAATAAAAA-TATATAC
*
3168064 AAAATTTTAATAAAAATATATA
1 AAAATGTTAATAAAAATATATA
3168086 TAATTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATGTTAATAAAAATATATAC
Found at i:3169274 original size:36 final size:36
Alignment explanation
Indices: 3169227--3169298 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3169217 CCGAATCATG
3169227 TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
1 TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
3169263 TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
1 TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
3169299 CTAACTACGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (36 bp):
TTCCCTTCGGTGTATTGGAAACCAAGATGCACCGCA
Found at i:3178703 original size:16 final size:17
Alignment explanation
Indices: 3178682--3178717 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
3178672 CTTCGCGTGG
3178682 GGACATTTGA-ATCTAT
1 GGACATTTGATATCTAT
3178698 GGACATTTGATTATCTAT
1 GGACATTTGA-TATCTAT
3178716 GG
1 GG
3178718 GTTGCTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
18 8 0.44
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (17 bp):
GGACATTTGATATCTAT
Found at i:3181098 original size:25 final size:25
Alignment explanation
Indices: 3181067--3181116 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3181057 TAGAAAGCAA
3181067 ATAAATATTTAAAAACACAGACAAT
1 ATAAATATTTAAAAACACAGACAAT
*
3181092 ATAAATATTTAAAAACCCAGACAAT
1 ATAAATATTTAAAAACACAGACAAT
3181117 CTTTTACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.58, C:0.14, G:0.04, T:0.24
Consensus pattern (25 bp):
ATAAATATTTAAAAACACAGACAAT
Found at i:3181135 original size:18 final size:18
Alignment explanation
Indices: 3181112--3181149 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3181102 AAAAACCCAG
*
3181112 ACAATCTTTTACTTATCT
1 ACAATCTTTTACTTACCT
3181130 ACAATCTTTTACTTACCT
1 ACAATCTTTTACTTACCT
3181148 AC
1 AC
3181150 GAGAATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (18 bp):
ACAATCTTTTACTTACCT
Found at i:3191258 original size:21 final size:21
Alignment explanation
Indices: 3191208--3191260 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
3191198 TTTTTTAACC
*
3191208 TAAAAT-TTAGACCCTAAATT
1 TAAAATCTTAAACCCTAAATT
* * * *
3191228 CAAGACCTTAAACCTTAAATT
1 TAAAATCTTAAACCCTAAATT
3191249 TAAAATCTTAAA
1 TAAAATCTTAAA
3191261 TTACAGTCCT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (21 bp):
TAAAATCTTAAACCCTAAATT
Done.