Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002552.1 Hibiscus syriacus cultivar Beakdansim tig00005179_pilon, 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: 180643
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 1 of 2
Found at i:2596 original size:12 final size:12
Alignment explanation
Indices: 2562--2601 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
2552 TTTTATTTCT
2562 TTTTAAGTTTTCA
1 TTTTAAGTTTT-A
*
2575 TTTTCA-TTTTA
1 TTTTAAGTTTTA
2586 TTTTAAGTTTTA
1 TTTTAAGTTTTA
2598 TTTT
1 TTTT
2602 TAAACATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 13 0.54
13 5 0.21
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTAAGTTTTA
Found at i:3538 original size:23 final size:23
Alignment explanation
Indices: 3508--3555 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
3498 AGCAACTCGC
* *
3508 AGCATCATTGTATCAATTCAGCA
1 AGCATCATTGCATAAATTCAGCA
3531 AGCATCATTGCATAAATTCAGCA
1 AGCATCATTGCATAAATTCAGCA
3554 AG
1 AG
3556 TATCCTGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (23 bp):
AGCATCATTGCATAAATTCAGCA
Found at i:3715 original size:19 final size:20
Alignment explanation
Indices: 3672--3715 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3662 AGAATTAAGA
*
3672 AATATCAAACAGAAGCAAAC
1 AATATAAAACAGAAGCAAAC
* *
3692 AATATAAAACA-AATCAAGC
1 AATATAAAACAGAAGCAAAC
3711 AATAT
1 AATAT
3716 CAAGTAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.61, C:0.16, G:0.07, T:0.16
Consensus pattern (20 bp):
AATATAAAACAGAAGCAAAC
Found at i:6607 original size:22 final size:23
Alignment explanation
Indices: 6579--6635 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
6569 GGGAGTATAA
6579 GATTTGGGGATTTAAG-GTTAGG
1 GATTTGGGGATTTAAGAGTTAGG
* *
6601 GATTTGGGGATTTAAGATTTATG
1 GATTTGGGGATTTAAGAGTTAGG
6624 GATTT-GGGATTT
1 GATTTGGGGATTT
6636 GGGAATTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (23 bp):
GATTTGGGGATTTAAGAGTTAGG
Found at i:7334 original size:18 final size:18
Alignment explanation
Indices: 7311--7368 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
7301 TTTAATGTTT
*
7311 TATTTAATACTTTATACA
1 TATTTAATACTTTATAAA
*
7329 TATTTACATA---TACT-TA
1 TATTTA-ATACTTTA-TAAA
7345 TATTTAATACTTTATAAA
1 TATTTAATACTTTATAAA
7363 TATTTA
1 TATTTA
7369 TTTATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 2 0.06
18 15 0.47
19 3 0.09
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTTAATACTTTATAAA
Found at i:7437 original size:8 final size:8
Alignment explanation
Indices: 7421--7959 Score: 106
Period size: 8 Copynumber: 71.5 Consensus size: 8
7411 TTAATATAAG
7421 TATACTTA
1 TATACTTA
*
7429 TATAGTTATA
1 TATA-CT-TA
7439 TATACTT-
1 TATACTTA
*
7446 TAAACTT-
1 TATACTTA
*
7453 TATATTTA
1 TATACTTA
7461 -ATACTTA
1 TATACTTA
7468 TATACTTA
1 TATACTTA
*
7476 TATA-TTT
1 TATACTTA
*
7483 TATATTTA
1 TATACTTA
*
7491 -ATAATTA
1 TATACTTA
7498 TATACACTT-
1 TAT--ACTTA
7507 TATACTT-
1 TATACTTA
7514 TATTACTTA
1 TA-TACTTA
*
7523 T-TACTTT
1 TATACTTA
7530 TATA--TA
1 TATACTTA
7536 TATA-TATA
1 TATACT-TA
7544 TATA-TATA
1 TATACT-TA
7552 TATAACTTTTA
1 TAT-AC--TTA
7563 TTATACTT-
1 -TATACTTA
7571 TATA-TTA
1 TATACTTA
7578 TATACTTA
1 TATACTTA
*
7586 TAGACTTA
1 TATACTTA
7594 TAGT--TTA
1 TA-TACTTA
*
7601 TACACTTA
1 TATACTTA
*
7609 TACA-TTA
1 TATACTTA
7616 TAGT--TTA
1 TA-TACTTA
*
7623 TATA-TATG
1 TATACT-TA
7631 TATACCTT-
1 TATA-CTTA
7639 TATACTT-
1 TATACTTA
*
7646 TCATACTTC
1 T-ATACTTA
*
7655 TATTC-TA
1 TATACTTA
*
7662 TA-A-TTT
1 TATACTTA
7668 TATACTT-
1 TATACTTA
7675 TAATACTT-
1 T-ATACTTA
7683 TAATACTTA
1 T-ATACTTA
7692 TATACTT-
1 TATACTTA
7699 TAATACTTA
1 T-ATACTTA
*
7708 TATTC-TA
1 TATACTTA
7715 TAGT--TT-
1 TA-TACTTA
7721 TATACTT-
1 TATACTTA
7728 TAATACTTA
1 T-ATACTTA
*
7737 TACACTT-
1 TATACTTA
7744 TAATAC-T-
1 T-ATACTTA
7751 TATA-TTA
1 TATACTTA
* *
7758 TATAGTTT
1 TATACTTA
7766 TATACTT-
1 TATACTTA
7773 TATAC-TA
1 TATACTTA
7780 TATACTT-
1 TATACTTA
*
7787 TAATA-TTT
1 T-ATACTTA
7795 TAATACTTA
1 T-ATACTTA
7804 TAT-C-TA
1 TATACTTA
7810 TAGT--TT-
1 TA-TACTTA
7816 TATACTT-
1 TATACTTA
*
7823 TAATACTTT
1 T-ATACTTA
*
7832 TATACTTT
1 TATACTTA
*
7840 TACACTT-
1 TATACTTA
7847 TAATAC-T-
1 T-ATACTTA
7854 TATA-TTA
1 TATACTTA
* *
7861 TATAGTTT
1 TATACTTA
7869 TATACTT-
1 TATACTTA
*
7876 TATA-GTA
1 TATACTTA
7883 TATACTT-
1 TATACTTA
7890 TAATACTT-
1 T-ATACTTA
*
7898 TAATA-TTT
1 T-ATACTTA
*
7906 TGTA-TTA
1 TATACTTA
7913 TATACTT-
1 TATACTTA
7920 TAATACTT-
1 T-ATACTTA
* *
7928 TTTATTTA
1 TATACTTA
7936 -ATACTT-
1 TATACTTA
7942 TATA-TTA
1 TATACTTA
7949 TATACTT-
1 TATACTTA
7956 TATA
1 TATA
7960 GTTTATAGTT
Statistics
Matches: 419, Mismatches: 40, Indels: 145
0.69 0.07 0.24
Matches are distributed among these distances:
5 2 0.00
6 31 0.07
7 154 0.37
8 196 0.47
9 18 0.04
10 10 0.02
11 4 0.01
12 4 0.01
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (8 bp):
TATACTTA
Found at i:7462 original size:47 final size:44
Alignment explanation
Indices: 7395--7487 Score: 107
Period size: 47 Copynumber: 2.0 Consensus size: 44
7385 TTAATAATTA
*
7395 ATACTTTATATTAATATTAATA-TAAGTATACTTATATAGTTATAT
1 ATACTTTAAATTAATATTAATACTAA-TATACTTATATA-TTATAT
* * *
7440 ATACTTTAAACTTTATATTTAATACTTATATACTTATATATTTTAT
1 ATACTTTAAA-TTAATA-TTAATACTAATATACTTATATATTATAT
7486 AT
1 AT
7488 TTAATAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 9 0.22
46 12 0.29
47 18 0.44
48 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (44 bp):
ATACTTTAAATTAATATTAATACTAATATACTTATATATTATAT
Found at i:7466 original size:21 final size:22
Alignment explanation
Indices: 7343--7501 Score: 73
Period size: 22 Copynumber: 7.2 Consensus size: 22
7333 TACATATACT
*
7343 TATATTTAATACTTTATAA-ATA
1 TATATTTAATACTTTA-AACTTA
* * * *
7365 TTTATTTATATATTTTATATTTA
1 TATATTTA-ATACTTTAAACTTA
* *
7388 -ATAATTAATACTTTATA-TTA
1 TATATTTAATACTTTAAACTTA
* *
7408 -ATA-TTAATA-TAAGTATACTTA
1 TATATTTAATACT--TTAAACTTA
7429 TATAGTTATATATACTTTAAACTT-
1 TATA-TT-TA-ATACTTTAAACTTA
*
7453 TATATTTAATACTTATATACTTA
1 TATATTTAATACTT-TAAACTTA
* *
7476 TATATTTTATA-TTTAATAATTA
1 TATATTTAATACTTTAA-ACTTA
7498 TATA
1 TATA
7502 CACTTTATAC
Statistics
Matches: 109, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
18 1 0.01
19 6 0.06
20 10 0.09
21 20 0.18
22 34 0.31
23 21 0.19
24 5 0.05
25 8 0.07
26 3 0.03
27 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (22 bp):
TATATTTAATACTTTAAACTTA
Found at i:7515 original size:7 final size:7
Alignment explanation
Indices: 7439--7997 Score: 204
Period size: 7 Copynumber: 77.6 Consensus size: 7
7429 TATAGTTATA
7439 TATACTT
1 TATACTT
*
7446 TAAACTT
1 TATACTT
7453 TATA-TT
1 TATACTT
7459 TAATACTT
1 T-ATACTT
7467 ATATACTT
1 -TATACTT
*
7475 ATATATTT
1 -TATACTT
7483 TATA-TT
1 TATACTT
*
7489 TAATAATT
1 T-ATACTT
7497 ATATACACTT
1 -TAT--ACTT
7507 TATACTT
1 TATACTT
7514 TATTAC-T
1 TA-TACTT
7521 TATTACTT
1 TA-TACTT
*
7529 T-TA-TA
1 TATACTT
*
7534 TATA-TA
1 TATACTT
*
7540 TATA-TA
1 TATACTT
*
7546 TATA-TA
1 TATACTT
7552 TATAACTT
1 TAT-ACTT
7560 T-TA--T
1 TATACTT
7564 TATACTT
1 TATACTT
7571 TATA-TT
1 TATACTT
7577 ATATACTT
1 -TATACTT
*
7585 ATAGAC-T
1 -TATACTT
*
7592 TATAGTT
1 TATACTT
*
7599 TATACACT
1 TATAC-TT
*
7607 TATACAT
1 TATACTT
*
7614 TATAGTT
1 TATACTT
*
7621 TATATATAT
1 TATA-CT-T
7630 GTATACCTT
1 -TATA-CTT
7639 TATACTT
1 TATACTT
7646 TCATACTT
1 T-ATACTT
* *
7654 CTATTCTA
1 -TATACTT
*
7662 TA-ATTT
1 TATACTT
7668 TATACTT
1 TATACTT
7675 TAATACTT
1 T-ATACTT
7683 TAATACTT
1 T-ATACTT
7691 ATATACTT
1 -TATACTT
7699 TAATAC-T
1 T-ATACTT
7706 TATA-TT
1 TATACTT
*
7712 CTATAGTTT
1 -TATA-CTT
7721 TATACTT
1 TATACTT
7728 TAATACTT
1 T-ATACTT
*
7736 ATACACTT
1 -TATACTT
7744 TAATAC-T
1 T-ATACTT
7751 TATA-TT
1 TATACTT
*
7757 ATATAGTTT
1 -TATA-CTT
7766 TATACTT
1 TATACTT
*
7773 TATACTA
1 TATACTT
7780 TATACTT
1 TATACTT
*
7787 TAATATTT
1 T-ATACTT
7795 TAATAC-T
1 T-ATACTT
*
7802 TATA-TC
1 TATACTT
*
7808 TATAGTTT
1 TATA-CTT
7816 TATACTT
1 TATACTT
7823 TAATACTTT
1 T-ATAC-TT
7832 TATACTTT
1 TATAC-TT
*
7840 TACACTT
1 TATACTT
7847 TAATAC-T
1 T-ATACTT
7854 TATA-TT
1 TATACTT
*
7860 ATATAGTTT
1 -TATA-CTT
7869 TATACTT
1 TATACTT
* *
7876 TATAGTA
1 TATACTT
7883 TATACTT
1 TATACTT
7890 TAATACTT
1 T-ATACTT
*
7898 TAATATTT
1 T-ATACTT
*
7906 TGTA-TT
1 TATACTT
7912 ATATACTT
1 -TATACTT
7920 TAATACTT
1 T-ATACTT
*
7928 TTTA-TT
1 TATACTT
7934 TAATACTT
1 T-ATACTT
7942 TATA-TT
1 TATACTT
7948 ATATACTT
1 -TATACTT
*
7956 TATAGTT
1 TATACTT
*
7963 TATAGTT
1 TATACTT
*
7970 TATA-TA
1 TATACTT
7976 TATAC--
1 TATACTT
*
7981 -ACACTT
1 TATACTT
7987 TATACTT
1 TATACTT
7994 TATA
1 TATA
7998 TATATAACTA
Statistics
Matches: 439, Mismatches: 50, Indels: 126
0.71 0.08 0.20
Matches are distributed among these distances:
4 5 0.01
5 4 0.01
6 67 0.15
7 171 0.39
8 165 0.38
9 19 0.04
10 8 0.02
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (7 bp):
TATACTT
Found at i:7537 original size:2 final size:2
Alignment explanation
Indices: 7530--7555 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7520 TTATTACTTT
7530 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
7556 ACTTTTATTA
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:7554 original size:54 final size:51
Alignment explanation
Indices: 7397--7587 Score: 143
Period size: 54 Copynumber: 3.7 Consensus size: 51
7387 AATAATTAAT
* *
7397 ACTTTATA-TTAATA-TTA-ATA-TAAGTATACTTATATAGTTATATATACTTTAA
1 ACTTTATATTTAATACTTATATACTTA-TATA-TTATATA-TTATATATA-TAT-A
*
7449 ACTTTATATTTAATACTTATATACTTATATATTTTATATT-TAATAATTATATA
1 ACTTTATATTTAATACTTATATACTTATATATTATATATTAT-AT-A-TATATA
* *
7502 CACTTTATACTTTATTACTTAT-TACTTTTATATATATATATATATATATATATA
1 -ACTTTATA-TTTAATACTTATATACTTATATAT-TATATAT-TATATATATATA
7556 ACTTT-TA-TT-ATACTT-TATA-TTATATACTTATA
1 ACTTTATATTTAATACTTATATACTTATATA-TTATA
7588 GACTTATAGT
Statistics
Matches: 117, Mismatches: 8, Indels: 32
0.75 0.05 0.20
Matches are distributed among these distances:
48 11 0.09
49 8 0.07
50 2 0.02
52 11 0.09
53 16 0.14
54 36 0.31
55 27 0.23
56 5 0.04
57 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (51 bp):
ACTTTATATTTAATACTTATATACTTATATATTATATATTATATATATATA
Found at i:7619 original size:22 final size:22
Alignment explanation
Indices: 7563--7624 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 22
7553 ATAACTTTTA
* *
7563 TTATACTTTATA--TTATATAC
1 TTATACATTATAGTTTATACAC
*
7583 TTATAGACTTATAGTTTATACAC
1 TTATACA-TTATAGTTTATACAC
7606 TTATACATTATAGTTTATA
1 TTATACATTATAGTTTATA
7625 TATATGTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.14
21 5 0.14
22 12 0.34
23 13 0.37
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (22 bp):
TTATACATTATAGTTTATACAC
Found at i:7690 original size:45 final size:45
Alignment explanation
Indices: 7668--7952 Score: 226
Period size: 45 Copynumber: 6.1 Consensus size: 45
7658 TCTATAATTT
* *
7668 TATACTTTAATACTTTAATAC-TTATATACTTTAATACTTATATTC
1 TATAGTTTTATACTTTAATACTTTA-ATACTTTAATACTTATATTC
* *
7713 TATAGTTTTATACTTTAATAC-TTATACACTTTAATACTTATATTA
1 TATAGTTTTATACTTTAATACTTTA-ATACTTTAATACTTATATTC
*
7758 TATAGTTTTATACTTTATACTATATACTTTAATATTTTAATACTTATA-TC
1 TATAGTTTTATAC--T-T--TA-ATACTTTAATACTTTAATACTTATATTC
*
7808 TATAGTTTTATACTTTAATACTTTTATACTTTTACACTTTAATACTTATATTA
1 TATAGTTTTATACTTTAATAC-TTTA-A----T--ACTTTAATACTTATATTC
* * *
7861 TATAGTTTTATACTTT-ATAGTAT-ATACTTTAATACTTTAATATTT
1 TATAGTTTTATACTTTAATACTTTAATACTTTAATAC-TT-ATATTC
* * * *
7906 TGTA-TTATATACTTTAATACTTT-TTA-TTTAATACTTTATATTA
1 TATAGTTTTATACTTTAATACTTTAATACTTTAATAC-TTATATTC
7949 TATA
1 TATA
7953 CTTTATAGTT
Statistics
Matches: 202, Mismatches: 19, Indels: 40
0.77 0.07 0.15
Matches are distributed among these distances:
43 18 0.09
44 27 0.13
45 76 0.38
46 1 0.00
47 2 0.01
48 2 0.01
49 1 0.00
50 17 0.08
51 21 0.10
52 20 0.10
53 17 0.08
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (45 bp):
TATAGTTTTATACTTTAATACTTTAATACTTTAATACTTATATTC
Found at i:7736 original size:29 final size:29
Alignment explanation
Indices: 7637--7877 Score: 157
Period size: 29 Copynumber: 8.4 Consensus size: 29
7627 TATGTATACC
* *
7637 TTTATACTTTCATACTTCTATTCTATAAT
1 TTTATACTTTAATACTTATATTCTATAAT
*
7666 TTTATACTTTAATACTT-TA----ATACT
1 TTTATACTTTAATACTTATATTCTATAAT
* *
7690 TATATACTTTAATACTTATATTCTATAGT
1 TTTATACTTTAATACTTATATTCTATAAT
7719 TTTATACTTTAATACTTATACACTT-TAATACTTAT
1 TTTATACTTTAATACTTAT--A-TTCT-ATA---AT
* * *
7754 ATTATATAGTTTTATACTT-TATACTATATACT
1 -TT-TATACTTTAATACTTATATTCTATA-A-T
* * *
7786 TTAATATTTTAATACTTATA-TCTATAGT
1 TTTATACTTTAATACTTATATTCTATAAT
*
7814 TTTATACTTTAATAC---T-TT-TATACT
1 TTTATACTTTAATACTTATATTCTATAAT
* * *
7838 TTTACACTTTAATACTTATATTATATAGT
1 TTTATACTTTAATACTTATATTCTATAAT
7867 TTTATACTTTA
1 TTTATACTTTA
7878 TAGTATATAC
Statistics
Matches: 169, Mismatches: 20, Indels: 46
0.72 0.09 0.20
Matches are distributed among these distances:
24 39 0.23
25 4 0.02
27 1 0.01
28 18 0.11
29 53 0.31
30 17 0.10
31 8 0.05
32 6 0.04
33 4 0.02
34 2 0.01
35 1 0.01
36 3 0.02
37 13 0.08
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.54
Consensus pattern (29 bp):
TTTATACTTTAATACTTATATTCTATAAT
Found at i:7846 original size:103 final size:93
Alignment explanation
Indices: 7739--7980 Score: 265
Period size: 103 Copynumber: 2.5 Consensus size: 93
7729 AATACTTATA
*
7739 CACTTTAATACTTATAT-TATATAGTTTTATACTTTATACTATATACTTTAATATTTTAATACTT
1 CACTTT-ATA-TTATATATATATAGTTTTATACTTTATA-TATATACTTTAATACTTTAATA--T
* *
7803 ATATCTATAGTTTTATACTTTAATACTTTTATACTTTTA
61 -T-T-TATA-TTATATACTTTAATACTTTT-TA-TTTAA
7842 CACTTTAATACTTATAT-TATATAGTTTTATACTTTATAGTATATACTTTAATACTTTAATATTT
1 CACTTT-ATA-TTATATATATATAGTTTTATACTTTATA-TATATACTTTAATACTTTAATATTT
*
7906 TGTATTATATACTTTAATACTTTTTATTTAA
63 TATATTATATACTTTAATACTTTTTATTTAA
* * *
7937 TACTTTATATTATATACTTTATAG-TTTATAGTTTATATATATAC
1 CACTTTATATTATATA-TATATAGTTTTATACTTTATATATATAC
7981 ACACTTTATA
Statistics
Matches: 129, Mismatches: 8, Indels: 14
0.85 0.05 0.09
Matches are distributed among these distances:
93 13 0.10
94 15 0.12
95 15 0.12
96 2 0.02
97 19 0.15
98 3 0.02
99 1 0.01
100 1 0.01
101 1 0.01
103 59 0.46
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (93 bp):
CACTTTATATTATATATATATAGTTTTATACTTTATATATATACTTTAATACTTTAATATTTTAT
ATTATATACTTTAATACTTTTTATTTAA
Found at i:7957 original size:22 final size:22
Alignment explanation
Indices: 7816--7975 Score: 125
Period size: 22 Copynumber: 7.2 Consensus size: 22
7806 TCTATAGTTT
*
7816 TATACTTTAATACTTTTATACTTT
1 TATACTTTAATAC-TTTATA-TTA
*
7840 TACACTTTAATAC-TTATATTA
1 TATACTTTAATACTTTATATTA
* * *
7861 TATAGTTTTATACTTTATAGTA
1 TATACTTTAATACTTTATATTA
*
7883 TATACTTTAATACTTTAATATTT
1 TATACTTTAATACTTT-ATATTA
*
7906 TGTA--TTATATACTTTAATACTT-
1 TATACTTTA-ATACTTT-ATA-TTA
*
7928 TTTA-TTTAATACTTTATATTA
1 TATACTTTAATACTTTATATTA
*
7949 TATACTTT-ATAGTTTATAGTTTA
1 TATACTTTAATACTTTATA--TTA
7972 TATA
1 TATA
7976 TATACACACT
Statistics
Matches: 113, Mismatches: 14, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.02
21 30 0.27
22 50 0.44
23 19 0.17
24 12 0.11
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (22 bp):
TATACTTTAATACTTTATATTA
Found at i:7963 original size:148 final size:148
Alignment explanation
Indices: 7631--7951 Score: 413
Period size: 148 Copynumber: 2.2 Consensus size: 148
7621 TATATATATG
* * * *
7631 TATACCTTT-ATACTTTCATACTTCTATTCTATAATTTTATACTTTAATACTTTAATACTTATAT
1 TATA-CTTTAATACTTTAATACTTATA-TCTATAGTTTTATACTTTAATACTTTAATACTTATAC
* *
7695 ACTTTAATACTTATATTCTATAGTTTTATACTTTAATACTTATACACTTTAATACTTATATTATA
64 ACTTTAATACTTATATTATATAGTTTTATACTTTAATACGTATACACTTTAATACTTATATTATA
*
7760 TAGTTTTATACTTTATACTA
129 TAGTTATATACTTTATACTA
* * *
7780 TATACTTTAATATTTTAATACTTATATCTATAGTTTTATACTTTAATACTTTTATACTTTTACAC
1 TATACTTTAATACTTTAATACTTATATCTATAGTTTTATACTTTAATACTTTAATACTTATACAC
* * *
7845 TTTAATACTTATATTATATAGTTTTATACTTT-ATA-GTATATACTTTAATACTTTAATATTTTG
66 TTTAATACTTATATTATATAGTTTTATACTTTAATACGTATACACTTTAATAC-TT-ATATTATA
*
7908 TA-TTATATACTTTAATACTT
129 TAGTTATATACTTT-ATACTA
*
7928 TTTA-TTTAATACTTT-ATA-TTATAT
1 TATACTTTAATACTTTAATACTTATAT
7952 ACTTTATAGT
Statistics
Matches: 152, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
145 6 0.04
146 17 0.11
147 25 0.16
148 86 0.57
149 18 0.12
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (148 bp):
TATACTTTAATACTTTAATACTTATATCTATAGTTTTATACTTTAATACTTTAATACTTATACAC
TTTAATACTTATATTATATAGTTTTATACTTTAATACGTATACACTTTAATACTTATATTATATA
GTTATATACTTTATACTA
Found at i:7992 original size:66 final size:66
Alignment explanation
Indices: 7870--7994 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
7860 ATATAGTTTT
* * *
7870 ATACTTTATAGTATATACTTTAATACTTTAATATTTTGTATTATATACTTTAATACTTTTTATTT
1 ATACTTTATAGTATATACTTTAATACTTTAATATTTTATATTACACACTTTAATACTTTTTATTT
7935 A
66 A
* *
7936 ATACTTTATATTATATACTTT-ATAGTTT-ATAGTTTATATATATACACACTTT-ATACTTT
1 ATACTTTATAGTATATACTTTAATACTTTAATA-TTT-TATAT-TACACACTTTAATACTTT
7995 ATATATATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
64 3 0.06
65 9 0.18
66 31 0.61
67 8 0.16
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (66 bp):
ATACTTTATAGTATATACTTTAATACTTTAATATTTTATATTACACACTTTAATACTTTTTATTT
A
Found at i:10975 original size:17 final size:17
Alignment explanation
Indices: 10949--10982 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
10939 TCGGTTATAC
10949 TTCAAACATTT-CATTT
1 TTCAAACATTTCCATTT
10965 TTCATAACATTTCCATTT
1 TTCA-AACATTTCCATTT
10983 GCTACTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (17 bp):
TTCAAACATTTCCATTT
Found at i:12162 original size:11 final size:11
Alignment explanation
Indices: 12141--12171 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
12131 ATAAGGATGT
12141 GGAGAAAATCAG
1 GGAG-AAATCAG
12153 GGAGAAATCAG
1 GGAGAAATCAG
12164 GGAGAAAT
1 GGAGAAAT
12172 GTTAAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.48, C:0.06, G:0.35, T:0.10
Consensus pattern (11 bp):
GGAGAAATCAG
Found at i:19254 original size:43 final size:43
Alignment explanation
Indices: 19152--19259 Score: 153
Period size: 43 Copynumber: 2.5 Consensus size: 43
19142 CTATCATTTG
* *
19152 TTTGGGATCCTCTACAGAGGGTAATATCTCCATCATGTTTCTA
1 TTTGGGATCCTCTACGGAGGGCAATATCTCCATCATGTTTCTA
* * *
19195 TTTAGGATCCTCTACGGAGGGCAATATCTCCATCCTGTTTTTA
1 TTTGGGATCCTCTACGGAGGGCAATATCTCCATCATGTTTCTA
* *
19238 TTTGGGATCCTTTACGGGGGGC
1 TTTGGGATCCTCTACGGAGGGC
19260 TTAATCCCCA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (43 bp):
TTTGGGATCCTCTACGGAGGGCAATATCTCCATCATGTTTCTA
Found at i:19271 original size:43 final size:43
Alignment explanation
Indices: 19156--19280 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
19146 CATTTGTTTG
* * * *
19156 GGATCCTCTACAGAGGGTAATATCTCCATCATGTTTCTATTTA
1 GGATCCTCTACGGAGGGCAATATCCCCATCATGTTTTTATTTA
* * *
19199 GGATCCTCTACGGAGGGCAATATCTCCATCCTGTTTTTATTTG
1 GGATCCTCTACGGAGGGCAATATCCCCATCATGTTTTTATTTA
* * *
19242 GGATCCTTTACGGGGGGC-TTAATCCCCATCATGATTTTT
1 GGATCCTCTACGGAGGGCAAT-ATCCCCATCATG-TTTTT
19281 GTAATTTGAC
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.01
43 64 0.91
44 5 0.07
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (43 bp):
GGATCCTCTACGGAGGGCAATATCCCCATCATGTTTTTATTTA
Found at i:29462 original size:16 final size:16
Alignment explanation
Indices: 29441--29471 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29431 AAAACTAATA
29441 TTTTTAGTAAAATTAT
1 TTTTTAGTAAAATTAT
*
29457 TTTTTATTAAAATTA
1 TTTTTAGTAAAATTA
29472 CCTAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTTTAGTAAAATTAT
Found at i:31070 original size:29 final size:28
Alignment explanation
Indices: 31027--31083 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
31017 GGCATACAAG
*
31027 GAAATAGTTTGAGTCTAAGGCCACACGA
1 GAAATAGTTCGAGTCTAAGGCCACACGA
*
31055 GAAATGAGTTCGAGTCTACGGCCACACGA
1 GAAAT-AGTTCGAGTCTAAGGCCACACGA
31084 TGGCACTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (28 bp):
GAAATAGTTCGAGTCTAAGGCCACACGA
Found at i:33129 original size:5 final size:5
Alignment explanation
Indices: 33119--33143 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
33109 GGTCTGAGGA
33119 AGGGG AGGGG AGGGG AGGGG AGGGG
1 AGGGG AGGGG AGGGG AGGGG AGGGG
33144 CTAAAACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
AGGGG
Found at i:33453 original size:15 final size:14
Alignment explanation
Indices: 33407--33447 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
33397 GGGTGAGTAT
33407 TTGATTTATTTTAG
1 TTGATTTATTTTAG
33421 TTGATTTATTTTAG
1 TTGATTTATTTTAG
33435 TTGATTTAATTTT
1 TTGATTT-ATTTT
33448 TTTTGAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (14 bp):
TTGATTTATTTTAG
Found at i:40695 original size:19 final size:19
Alignment explanation
Indices: 40671--40709 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
40661 TATACATTGG
40671 GCTATGAATATGAAGTAAA
1 GCTATGAATATGAAGTAAA
* *
40690 GCTATGAATCTTAAGTAAA
1 GCTATGAATATGAAGTAAA
40709 G
1 G
40710 TTACAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (19 bp):
GCTATGAATATGAAGTAAA
Found at i:41476 original size:24 final size:23
Alignment explanation
Indices: 41432--41476 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
41422 CTATTGAAAG
*
41432 AATTAAATTTGATAAGTTTTTAA
1 AATTAAATTTGATAAGGTTTTAA
41455 AATTCAAATTTG-TAATGGTTTT
1 AATT-AAATTTGATAA-GGTTTT
41477 CAACCATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (23 bp):
AATTAAATTTGATAAGGTTTTAA
Found at i:41899 original size:17 final size:16
Alignment explanation
Indices: 41877--41914 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
41867 GCTTTTATTT
41877 TCTTCATCTTC-TCATTC
1 TCTTCAT-TTCTTCA-TC
41894 TCTTCATTTCTTCATC
1 TCTTCATTTCTTCATC
41910 TCTTC
1 TCTTC
41915 TCATTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.11, C:0.34, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTTCATTTCTTCATC
Found at i:45856 original size:13 final size:13
Alignment explanation
Indices: 45823--45861 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
45813 TAGTCTTTGG
*
45823 TTTAGATTTA-AA
1 TTTAGATTTAGAT
*
45835 TTTAAATTTAGAT
1 TTTAGATTTAGAT
45848 TTTAGATTTAGAT
1 TTTAGATTTAGAT
45861 T
1 T
45862 CTTTTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (13 bp):
TTTAGATTTAGAT
Found at i:45857 original size:6 final size:6
Alignment explanation
Indices: 45823--45861 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
45813 TAGTCTTTGG
* *
45823 TTTAGA TTTAAA TTTAAA TTTAGA TTTTAGA TTTAGA TT
1 TTTAGA TTTAGA TTTAGA TTTAGA -TTTAGA TTTAGA TT
45862 CTTTTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (6 bp):
TTTAGA
Found at i:47253 original size:21 final size:22
Alignment explanation
Indices: 47229--47305 Score: 79
Period size: 21 Copynumber: 3.6 Consensus size: 22
47219 TGAAATATAT
47229 GGATCGATC-TTTTAAGGGAAG
1 GGATCGATCATTTTAAGGGAAG
* * **
47250 GGATTGATCATTTTCA-TCAAG
1 GGATCGATCATTTTAAGGGAAG
*
47271 GGATCGATC-CTTTAAGGGAAG
1 GGATCGATCATTTTAAGGGAAG
*
47292 GGATTGATCATTTT
1 GGATCGATCATTTT
47306 CATCGACGGA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
20 4 0.10
21 30 0.71
22 8 0.19
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (22 bp):
GGATCGATCATTTTAAGGGAAG
Found at i:47276 original size:42 final size:42
Alignment explanation
Indices: 47229--47325 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
47219 TGAAATATAT
* *
47229 GGATCGATCTTTTAAGGGAAGGGATTGATCATTTTCATCAAG
1 GGATCGATCCTTTAAGGGAAGGGATTGATCATTTTCATCAAC
*
47271 GGATCGATCCTTTAAGGGAAGGGATTGATCATTTTCATCGAC
1 GGATCGATCCTTTAAGGGAAGGGATTGATCATTTTCATCAAC
47313 GGATCGATCCTTT
1 GGATCGATCCTTT
47326 CAATGAATAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (42 bp):
GGATCGATCCTTTAAGGGAAGGGATTGATCATTTTCATCAAC
Found at i:49100 original size:16 final size:17
Alignment explanation
Indices: 49071--49106 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
49061 TTTTTTTGGC
49071 ATTTTTTTAAAAAAAATG
1 ATTTTTTT-AAAAAAATG
49089 ATTTTTTT-AAAAAATG
1 ATTTTTTTAAAAAAATG
49105 AT
1 AT
49107 GGAAATTGTG
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:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTTTTTTAAAAAAATG
Found at i:49550 original size:133 final size:133
Alignment explanation
Indices: 49312--49577 Score: 496
Period size: 133 Copynumber: 2.0 Consensus size: 133
49302 TAAAGCTTCC
*
49312 TGCAACAAAACAACTGATAAAAAATTATAAATATGTTCTCTAACCACCTAATTCAACCAATTTTT
1 TGCAACAAAACAACTGATAAAAAATTATAAATATGTTCTCTAACCACCTAATTCAACCAATTTTG
*
49377 CTGAATTTGAAAAATTGAAAAGTTTGGGTTTTTGATAAATCTTACCCAAAATTGATGTTTCCGCC
66 CCGAATTTGAAAAATTGAAAAGTTTGGGTTTTTGATAAATCTTACCCAAAATTGATGTTTCCGCC
49442 AAA
131 AAA
*
49445 TGCAACAAAACAACTGATAAACAATTATAAATATGTTCTCTAACCACCTAATTCAACCAATTTTG
1 TGCAACAAAACAACTGATAAAAAATTATAAATATGTTCTCTAACCACCTAATTCAACCAATTTTG
*
49510 CCGAATTTGGAAAATTGAAAAGTTTGGGTTTTTGATAAATCTTACCCAAAATTGATGTTTCCGCC
66 CCGAATTTGAAAAATTGAAAAGTTTGGGTTTTTGATAAATCTTACCCAAAATTGATGTTTCCGCC
49575 AAA
131 AAA
49578 GAAATTTTTC
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 129 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.32
Consensus pattern (133 bp):
TGCAACAAAACAACTGATAAAAAATTATAAATATGTTCTCTAACCACCTAATTCAACCAATTTTG
CCGAATTTGAAAAATTGAAAAGTTTGGGTTTTTGATAAATCTTACCCAAAATTGATGTTTCCGCC
AAA
Found at i:56954 original size:21 final size:19
Alignment explanation
Indices: 56928--56986 Score: 84
Period size: 18 Copynumber: 3.1 Consensus size: 19
56918 ACTGAATATT
*
56928 TGTCCCAAAGGACCACTGATA
1 TGTCCCGAAGGACCACT--TA
56949 TGTCCCGAAGGACCAC-TA
1 TGTCCCGAAGGACCACTTA
56967 TGTCCCGAAGGACCACTTA
1 TGTCCCGAAGGACCACTTA
56986 T
1 T
56987 AATCCCTCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 18 0.50
19 3 0.08
21 15 0.42
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (19 bp):
TGTCCCGAAGGACCACTTA
Found at i:60851 original size:18 final size:18
Alignment explanation
Indices: 60828--60869 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
60818 AAATGGGTAC
60828 CGATACCCTACCCAATAT
1 CGATACCCTACCCAATAT
60846 CGATACCCTACCCAATAT
1 CGATACCCTACCCAATAT
60864 CGATAC
1 CGATAC
60870 AGTTACATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.38, G:0.07, T:0.21
Consensus pattern (18 bp):
CGATACCCTACCCAATAT
Found at i:67060 original size:19 final size:20
Alignment explanation
Indices: 67015--67065 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
67005 CTACTCACAC
*
67015 AGTATCGATACTACTCTTGCT
1 AGTATCGATACTAC-CTAGCT
67036 AGGTATCGATACTA-CTAGCT
1 A-GTATCGATACTACCTAGCT
67056 AGTATCGATA
1 AGTATCGATA
67066 TTGAACTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 9 0.32
20 6 0.21
21 1 0.04
22 12 0.43
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTACCTAGCT
Found at i:69283 original size:13 final size:13
Alignment explanation
Indices: 69265--69289 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69255 TCCCTATTGC
69265 ATATTGAATATGA
1 ATATTGAATATGA
69278 ATATTGAATATG
1 ATATTGAATATG
69290 TTGACTAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
ATATTGAATATGA
Found at i:70213 original size:25 final size:25
Alignment explanation
Indices: 70183--70231 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
70173 AGTCTTGAAT
70183 CCATTGATGAAAAACAAAAAACAAG
1 CCATTGATGAAAAACAAAAAACAAG
*
70208 CCATTGATGAAAAACAAGAAACAA
1 CCATTGATGAAAAACAAAAAACAA
70232 ATATTGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12
Consensus pattern (25 bp):
CCATTGATGAAAAACAAAAAACAAG
Found at i:77880 original size:36 final size:36
Alignment explanation
Indices: 77794--77881 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 36
77784 TTCACCCCAG
* * *
77794 ATTTTATCTCACTTAAGATTATTTTTCTTAAAATAA
1 ATTTTATTTCACTTGAGATTATTTTTCTTAAAACAA
*
77830 ATTTTATTTCACTTGAGATT-GTTTTCTTTAAAACAA
1 ATTTTATTTCACTTGAGATTATTTTTC-TTAAAACAA
* *
77866 TTTTTCTTTCACTTGA
1 ATTTTATTTCACTTGA
77882 AAGTGTTTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 5 0.11
36 40 0.89
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (36 bp):
ATTTTATTTCACTTGAGATTATTTTTCTTAAAACAA
Found at i:77891 original size:35 final size:36
Alignment explanation
Indices: 77816--77902 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
77806 TTAAGATTAT
* * *
77816 TTTTC-TTAAAATAAATTTTATTTCACTTGAGATTG
1 TTTTCTTTAAAACAAATTTTATTTCACTTGAAAGTG
* *
77851 TTTTCTTTAAAACAATTTTTCTTTCACTTGAAAGTG
1 TTTTCTTTAAAACAAATTTTATTTCACTTGAAAGTG
*
77887 -TTTCTCTTGAAACAAA
1 TTTTCT-TTAAAACAAA
77903 CCTTTTTCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 10 0.23
36 33 0.77
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (36 bp):
TTTTCTTTAAAACAAATTTTATTTCACTTGAAAGTG
Found at i:86180 original size:20 final size:20
Alignment explanation
Indices: 86155--86192 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
86145 TTTGGTTCAC
86155 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
86175 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
86193 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:86202 original size:16 final size:18
Alignment explanation
Indices: 86155--86205 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
86145 TTTGGTTCAC
86155 GGAATGTAAGATTACCAGTG
1 GGAA-GTAAGATTACCAG-G
86175 GGAATGTAAGATTACCA-G
1 GGAA-GTAAGATTACCAGG
86193 GGAA-TAAGATTAC
1 GGAAGTAAGATTAC
86206 TGGGAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 5 0.16
20 17 0.55
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGG
Found at i:89590 original size:81 final size:81
Alignment explanation
Indices: 89505--89673 Score: 257
Period size: 81 Copynumber: 2.1 Consensus size: 81
89495 AAGCATATAG
* * *
89505 TCTTTTACCCAAAGACATTTAGCCTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACCCAAAGACATTTAACCTTTCATCTAACTAGCATAATTAACACATTTCTGTCAAATGC
*
89570 ACAGTTAGGAAAATAA
66 ACAGCTAGGAAAATAA
* *
89586 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATAATTAACACATTTCTGTCAAATGC
1 TCTTTTACCCAAAGACATTTAACCTTTCATCTAACTAGCATAATTAACACATTTCTGTCAAATGC
** *
89651 ACAGCTAGGGCATTAA
66 ACAGCTAGGAAAATAA
89667 TCTTTTA
1 TCTTTTA
89674 TTTAGAACAG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACCCAAAGACATTTAACCTTTCATCTAACTAGCATAATTAACACATTTCTGTCAAATGC
ACAGCTAGGAAAATAA
Found at i:92180 original size:81 final size:81
Alignment explanation
Indices: 91972--92299 Score: 419
Period size: 81 Copynumber: 4.1 Consensus size: 81
91962 AAGCATTTAG
* ** * * * * *
91972 TCTTTTACCCAAAGACATTTAGCCTTTCATCTAACTTGCATGATTGACA-CTTTCTGTCAAATGT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGC
* *
92036 ACAGCTAGGCAAATAA
66 ACAACTAGGCAATTAA
* * *
92052 TCTTTTACTC--AGGTATTTAACCTTTCATCTAACCGGCATAATTGACACATTTCTATAAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGC
*
92115 ACAACTAGGCCATTAA
66 ACAACTAGGCAATTAA
* **
92131 TCTTTTACTCAAAGGTATTTAACCTTTCATATAACTTTCATAATTGACACCTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGC
* *
92196 ACAGCTAGGTAATTAA
66 ACAACTAGGCAATTAA
* * *
92212 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGACACCTTTATGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGC
*
92277 ACAACTAGGCCATTAA
66 ACAACTAGGCAATTAA
*
92293 TTTTTTA
1 TCTTTTA
92300 TTTAGAACAG
Statistics
Matches: 212, Mismatches: 33, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
78 31 0.15
79 34 0.16
80 9 0.04
81 138 0.65
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGC
ACAACTAGGCAATTAA
Found at i:92277 original size:162 final size:159
Alignment explanation
Indices: 91972--92299 Score: 467
Period size: 162 Copynumber: 2.0 Consensus size: 159
91962 AAGCATTTAG
* * * * *
91972 TCTTTTACCCAAAGACATTTAGCCTTTCATCTAACTTGCATGATTGACACTTTCTGTCAAATGTA
1 TCTTTTACCCAAAGACATTTAACCTTTCATATAACTTGCATAATTGACACTTTCTATCAAATGCA
92037 CAGCTAGGCAAATAATCTTTTACTCAGGTATTTAACCTTTCATCTAACCGGCATAATTGACACAT
66 CAGCTAGGCAAATAATCTTTTACTCAGGTATTTAACCTTTCATCTAACCGGCATAATTGACACAT
*
92102 TTCTATAAAATGCACAACTAGGCCATTAA
131 TTATATAAAATGCACAACTAGGCCATTAA
* ** *
92131 TCTTTTACTCAAAGGTATTTAACCTTTCATATAACTTTCATAATTGACACCTTTCTATCAAATGC
1 TCTTTTACCCAAAGACATTTAACCTTTCATATAACTTGCATAATTGACA-CTTTCTATCAAATGC
* * * *
92196 ACAGCTAGGTAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGACA
65 ACAGCTAGGCAAATAATCTTTTACTC--AGGTATTTAACCTTTCATCTAACCGGCATAATTGACA
* * *
92261 CCTTTATGTCAAATGCACAACTAGGCCATTAA
128 CATTTATATAAAATGCACAACTAGGCCATTAA
*
92293 TTTTTTA
1 TCTTTTA
92300 TTTAGAACAG
Statistics
Matches: 148, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
159 42 0.28
160 37 0.25
162 69 0.47
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (159 bp):
TCTTTTACCCAAAGACATTTAACCTTTCATATAACTTGCATAATTGACACTTTCTATCAAATGCA
CAGCTAGGCAAATAATCTTTTACTCAGGTATTTAACCTTTCATCTAACCGGCATAATTGACACAT
TTATATAAAATGCACAACTAGGCCATTAA
Found at i:92742 original size:22 final size:19
Alignment explanation
Indices: 92716--92768 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
92706 TACCCCTACC
92716 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACT-CTAT--T
*
92738 ATGGTACCGATACTCTATT
1 ATGGTATCGATACTCTATT
*
92757 ACGGTATCGATA
1 ATGGTATCGATA
92769 TCATTTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.39
21 4 0.14
22 13 0.46
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (19 bp):
ATGGTATCGATACTCTATT
Found at i:97356 original size:46 final size:45
Alignment explanation
Indices: 97274--97397 Score: 135
Period size: 46 Copynumber: 2.7 Consensus size: 45
97264 GATGTGAACT
* * * *
97274 TTTAATGTGGTGTAATATTATTTATGACTTAGACAATATT-TTAGC
1 TTTAATGTGTTGTAGTACTAATTATGACTTAGACAATATTGTT-GC
*
97319 TTTAATGTGTTGTAGTACTAATTATAGACTTCA-ACAATATTGTTGG
1 TTTAATGTGTTGTAGTACTAATTAT-GACTT-AGACAATATTGTTGC
* * *
97365 TTTGATGTGTTGTAGCACTAATTATGAATTAGA
1 TTTAATGTGTTGTAGTACTAATTATGACTTAGA
97398 ATTTGTATTA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
44 1 0.01
45 26 0.39
46 37 0.55
47 3 0.04
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (45 bp):
TTTAATGTGTTGTAGTACTAATTATGACTTAGACAATATTGTTGC
Found at i:97629 original size:13 final size:13
Alignment explanation
Indices: 97616--97684 Score: 111
Period size: 13 Copynumber: 5.3 Consensus size: 13
97606 CTATGGTGCA
*
97616 CATTTATGACGCA
1 CATTTATGACGCG
97629 CATTTATGACGCG
1 CATTTATGACGCG
*
97642 CATTTATGACACG
1 CATTTATGACGCG
*
97655 CATTTATGACGCT
1 CATTTATGACGCG
97668 CATTTATGACGCG
1 CATTTATGACGCG
97681 CATT
1 CATT
97685 GAGCGTCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Consensus pattern (13 bp):
CATTTATGACGCG
Found at i:103862 original size:20 final size:20
Alignment explanation
Indices: 103837--103908 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
103827 CTTACCTTTG
*
103837 GTATCGATACTATATGAATA
1 GTATCGATACTATATCAATA
* * *
103857 GTATCGGTATTGT-TCATATA
1 GTATCGATACTATATCA-ATA
* *
103877 GTATCGATACTGTAACAATA
1 GTATCGATACTATATCAATA
*
103897 GTATCGGTACTA
1 GTATCGATACTA
103909 CATACACATA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 2 0.05
20 37 0.90
21 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (20 bp):
GTATCGATACTATATCAATA
Found at i:104437 original size:19 final size:19
Alignment explanation
Indices: 104413--104453 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
104403 TAGCACAAGA
104413 AATTCAATATATAAAGTCT
1 AATTCAATATATAAAGTCT
104432 AATTCAATATATAAAGTCT
1 AATTCAATATATAAAGTCT
104451 AAT
1 AAT
104454 AAACTTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (19 bp):
AATTCAATATATAAAGTCT
Found at i:105794 original size:24 final size:23
Alignment explanation
Indices: 105737--105844 Score: 85
Period size: 23 Copynumber: 4.7 Consensus size: 23
105727 AGTCAAAAAC
105737 TACCACATAGAATTGCACCGAAG
1 TACCACATAGAATTGCACCGAAG
* * *
105760 TACCTCGTAGAATATGCACGGAAG
1 TACCACATAGAAT-TGCACCGAAG
** *
105784 TGTCACATAGAAATGTC-CCGAAG
1 TACCACATAGAATTG-CACCGAAG
* *
105807 GACCACATAGAAATGTC-CCGAAG
1 TACCACATAGAATTG-CACCGAAG
* *
105830 GACCACGTAGAATTG
1 TACCACATAGAATTG
105845 TCTCAAAGGA
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
23 51 0.74
24 18 0.26
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (23 bp):
TACCACATAGAATTGCACCGAAG
Found at i:105813 original size:23 final size:23
Alignment explanation
Indices: 105787--105857 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
105777 ACGGAAGTGT
105787 CACATAGAAATGTCCCGAAGGAC
1 CACATAGAAATGTCCCGAAGGAC
105810 CACATAGAAATGTCCCGAAGGAC
1 CACATAGAAATGTCCCGAAGGAC
* * * *
105833 CACGTAGAATTGTCTCAAAGGAC
1 CACATAGAAATGTCCCGAAGGAC
105856 CA
1 CA
105858 TGTAGAACCC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.15
Consensus pattern (23 bp):
CACATAGAAATGTCCCGAAGGAC
Found at i:106597 original size:20 final size:20
Alignment explanation
Indices: 106572--106643 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
106562 TCCATCTTAT
106572 AGTATCGATACTGTTCTTCC
1 AGTATCGATACTGTTCTTCC
* *
106592 AATATCGATACTATTCTTCC
1 AGTATCGATACTGTTCTTCC
106612 AGTATCGATACTGTTCTTCC
1 AGTATCGATACTGTTCTTCC
106632 AGTATCGATACT
1 AGTATCGATACT
106644 TAAACCCATA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (20 bp):
AGTATCGATACTGTTCTTCC
Found at i:107235 original size:18 final size:18
Alignment explanation
Indices: 107212--107246 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
107202 AAAATCGGTT
107212 AATTAA-CTGAATTAACCG
1 AATTAACCT-AATTAACCG
107230 AATTAACCTAATTAACC
1 AATTAACCTAATTAACC
107247 TTTAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (18 bp):
AATTAACCTAATTAACCG
Found at i:107380 original size:17 final size:17
Alignment explanation
Indices: 107358--107396 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
107348 TTGAATAAAT
107358 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
107375 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
107392 -AATTA
1 TAATTA
107397 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:111400 original size:13 final size:13
Alignment explanation
Indices: 111378--111407 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
111368 ACTAAACACC
111378 TTTC-ACATACCT
1 TTTCAACATACCT
111390 TTTCAACATACCT
1 TTTCAACATACCT
111403 TTTCA
1 TTTCA
111408 TATTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:114048 original size:24 final size:24
Alignment explanation
Indices: 114000--114050 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
113990 TTTCTTTGCT
* *
114000 TTTCTTCTTTTTGAGTGTTGGAAA
1 TTTCTTCTTTTGGAGTGTTGCAAA
114024 TTTCTTCTTTTGGAGTGCTT-CAAA
1 TTTCTTCTTTTGGAGTG-TTGCAAA
114048 TTT
1 TTT
114051 TTTTATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.55
Consensus pattern (24 bp):
TTTCTTCTTTTGGAGTGTTGCAAA
Found at i:121981 original size:103 final size:103
Alignment explanation
Indices: 121756--121973 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
121746 GTCGAGGGTC
121756 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
121821 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
121859 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
121924 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
121962 TATGTGGTCCTT
1 TATGTGGTCCTT
121974 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:122056 original size:23 final size:23
Alignment explanation
Indices: 121980--122057 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
121970 CCTTATGGAC
* *
121980 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTTCGGTGCA
* * * *
122004 ATTCTACGCGGCACTTTGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
122027 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
122050 ATTATATG
1 ATTATATG
122058 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTTCGGTGCA
Found at i:127898 original size:2 final size:2
Alignment explanation
Indices: 127891--127921 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
127881 CATCAGTTCA
127891 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127922 AAGAACACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128299 original size:16 final size:16
Alignment explanation
Indices: 128278--128316 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
128268 TTGATATGAA
128278 GGTTTTCAAAGTTTTG
1 GGTTTTCAAAGTTTTG
128294 GGTTTTCAAAGTTTTG
1 GGTTTTCAAAGTTTTG
*
128310 TGTTTTC
1 GGTTTTC
128317 TTTATACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (16 bp):
GGTTTTCAAAGTTTTG
Found at i:128773 original size:24 final size:25
Alignment explanation
Indices: 128746--128797 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
128736 TACATTTATT
*
128746 TATTTTTATTA-TAATAATATTACA
1 TATTTTAATTATTAATAATATTACA
* *
128770 TA-TTTAATTATTAATAATTTTATA
1 TATTTTAATTATTAATAATATTACA
128794 TATT
1 TATT
128798 AACTTAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 7 0.30
24 15 0.65
25 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTTTAATTATTAATAATATTACA
Found at i:129599 original size:53 final size:53
Alignment explanation
Indices: 129515--129621 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
129505 AAATATTGTT
* * *
129515 CTAAGCAGAACCATAGAAGCTCCAAGGAGCCAACCTTAGTTACTGTTACAATA
1 CTAAGCAGAACCATAGAAGCTCCAAGAAGCCAACCTTAATTACTGCTACAATA
* *
129568 CTAAGCAGAACCTTAGAAGCTCCAAGAAGCCAACCTTAATTACTGCTACTATA
1 CTAAGCAGAACCATAGAAGCTCCAAGAAGCCAACCTTAATTACTGCTACAATA
129621 C
1 C
129622 ATCATGCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.21
Consensus pattern (53 bp):
CTAAGCAGAACCATAGAAGCTCCAAGAAGCCAACCTTAATTACTGCTACAATA
Found at i:133042 original size:33 final size:32
Alignment explanation
Indices: 133005--133102 Score: 160
Period size: 33 Copynumber: 3.0 Consensus size: 32
132995 GTACAATGAA
133005 ATTTATATTTAAATATTAAAATAAAAATTAAAG
1 ATTTA-ATTTAAATATTAAAATAAAAATTAAAG
133038 ATTTAATTTAAATATTAAAATATAAAATTAAAG
1 ATTTAATTTAAATATTAAAATA-AAAATTAAAG
*
133071 ATTTCATTTAAATATTAAAATAAAATATTAAA
1 ATTTAATTTAAATATTAAAATAAAA-ATTAAA
133103 TATAAAAATA
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
32 20 0.32
33 42 0.68
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (32 bp):
ATTTAATTTAAATATTAAAATAAAAATTAAAG
Found at i:133055 original size:7 final size:7
Alignment explanation
Indices: 133013--133122 Score: 81
Period size: 7 Copynumber: 16.4 Consensus size: 7
133003 AAATTTATAT
133013 TTAAATA
1 TTAAATA
133020 TTAAA-A
1 TTAAATA
*
133026 -TAAAAA
1 TTAAATA
*
133032 TTAAAGA
1 TTAAATA
*
133039 TTTAAT-
1 TTAAATA
133045 TTAAATA
1 TTAAATA
133052 TTAAA-A
1 TTAAATA
133058 TATAAA-A
1 T-TAAATA
*
133065 TTAAAGA
1 TTAAATA
**
133072 TTTCAT-
1 TTAAATA
133078 TTAAATA
1 TTAAATA
133085 TTAAA-A
1 TTAAATA
*
133091 TAAAATA
1 TTAAATA
133098 TTAAATA
1 TTAAATA
*
133105 TAAAAATA
1 T-TAAATA
133113 TTAAATA
1 TTAAATA
133120 TTA
1 TTA
133123 TTCATGGGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
5 4 0.05
6 22 0.27
7 50 0.61
8 6 0.07
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (7 bp):
TTAAATA
Found at i:133112 original size:15 final size:14
Alignment explanation
Indices: 133015--133120 Score: 75
Period size: 13 Copynumber: 7.9 Consensus size: 14
133005 ATTTATATTT
133015 AAATATTAAA-ATA
1 AAATATTAAATATA
* *
133028 AAA-ATTAAAGATT
1 AAATATTAAATATA
*
133041 TAAT-TTAAATATTA
1 AAATATTAAATA-TA
*
133055 AAATATAAAAT-TA
1 AAATATTAAATATA
* *
133068 AAGAT-TT-CAT-TT
1 AA-ATATTAAATATA
133080 AAATATTAAA-ATA
1 AAATATTAAATATA
133093 AAATATTAAATATAA
1 AAATATTAAATAT-A
133108 AAATATTAAATAT
1 AAATATTAAATAT
133121 TATTCATGGG
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
11 2 0.03
12 13 0.18
13 30 0.42
14 8 0.11
15 19 0.26
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATATTAAATATA
Found at i:133112 original size:20 final size:20
Alignment explanation
Indices: 133013--133122 Score: 80
Period size: 20 Copynumber: 5.2 Consensus size: 20
133003 AAATTTATAT
133013 TTAAATATTAAAATAAAA-A
1 TTAAATATTAAAATAAAATA
* * * *
133032 TTAAAGATTTAATTTAAATA
1 TTAAATATTAAAATAAAATA
133052 TTAAA-ATATAAAATTAAAGATTTCA
1 TTAAATAT-TAAAA-TAAA-A--T-A
133077 TTTAAATATTAAAATAAAATA
1 -TTAAATATTAAAATAAAATA
*
133098 TTAAATATAAAAATATTAAATA
1 TTAAATATTAAAATA--AAATA
133120 TTA
1 TTA
133123 TTCATGGGAA
Statistics
Matches: 72, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
19 16 0.22
20 23 0.32
21 4 0.06
22 10 0.14
24 2 0.03
25 5 0.07
26 10 0.14
27 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (20 bp):
TTAAATATTAAAATAAAATA
Found at i:133193 original size:38 final size:38
Alignment explanation
Indices: 133150--133323 Score: 196
Period size: 38 Copynumber: 4.6 Consensus size: 38
133140 AATCGTTGTC
* * *
133150 TTAAATAATAAATATTAAATCATTATTAGTAATCATTA
1 TTAAATAATTAGTATTAAATCATTATTAGTAATTATTA
* *
133188 TTAAATCATTAGTATTAAATCATTAAATTA-TTATTATTA
1 TTAAATAATTAGTATTAAATCATT--ATTAGTAATTATTA
*
133227 TTAAATAATTAGTATTAAATCATTA--AAT-ATTATTA
1 TTAAATAATTAGTATTAAATCATTATTAGTAATTATTA
* *
133262 TTAAATCATTAGTATTCAATCATTATTAGTAATTATTA
1 TTAAATAATTAGTATTAAATCATTATTAGTAATTATTA
**
133300 TTAAATCAA-TAACATTAAATCATT
1 TTAAAT-AATTAGTATTAAATCATT
133324 TCATTATTGT
Statistics
Matches: 116, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
35 31 0.27
36 1 0.01
37 3 0.03
38 46 0.40
39 31 0.27
40 4 0.03
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (38 bp):
TTAAATAATTAGTATTAAATCATTATTAGTAATTATTA
Found at i:133205 original size:14 final size:13
Alignment explanation
Indices: 133161--133287 Score: 78
Period size: 14 Copynumber: 10.2 Consensus size: 13
133151 TAAATAATAA
133161 ATATTAAATCATT
1 ATATTAAATCATT
*
133174 ATTAGT-AATCA-T
1 A-TATTAAATCATT
133186 -TATTAAATCATT
1 ATATTAAATCATT
133198 AGTATTAAATCATT
1 A-TATTAAATCATT
* *
133212 AAATT--ATTATT
1 ATATTAAATCATT
*
133223 ATTATTAAATAATT
1 A-TATTAAATCATT
133237 AGTATTAAATC---
1 A-TATTAAATCATT
133248 --ATTAAAT-ATT
1 ATATTAAATCATT
133258 ATTATTAAATCATT
1 A-TATTAAATCATT
*
133272 AGTATTCAATCATT
1 A-TATTAAATCATT
133286 AT
1 AT
133288 TAGTAATTAT
Statistics
Matches: 89, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
8 7 0.08
10 3 0.03
11 11 0.12
12 5 0.06
13 17 0.19
14 46 0.52
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (13 bp):
ATATTAAATCATT
Found at i:133231 original size:17 final size:17
Alignment explanation
Indices: 133209--133277 Score: 57
Period size: 17 Copynumber: 4.0 Consensus size: 17
133199 GTATTAAATC
* *
133209 ATTAAATTATTATTATT
1 ATTAAATAATTAGTATT
133226 ATTAAATAATTAGTATT
1 ATTAAATAATTAGTATT
* * * * *
133243 AAATCATTAAATATTATT
1 -ATTAAATAATTAGTATT
*
133261 ATTAAATCATTAGTATT
1 ATTAAATAATTAGTATT
133278 CAATCATTAT
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
17 26 0.68
18 12 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
ATTAAATAATTAGTATT
Found at i:136443 original size:38 final size:38
Alignment explanation
Indices: 136392--136478 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 38
136382 TGCAACCACC
* ** *
136392 AACCATCAACCTACCCGGGATATTAATGGATAATTAAT
1 AACCACCAACCTACCCAAGATATTAAAGGATAATTAAT
* *
136430 AACCACCAACCTACCCAAGTTATTAAAGGATAATTATT
1 AACCACCAACCTACCCAAGATATTAAAGGATAATTAAT
*
136468 AACCGCCAACC
1 AACCACCAACC
136479 ACCAACCTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.23
Consensus pattern (38 bp):
AACCACCAACCTACCCAAGATATTAAAGGATAATTAAT
Found at i:136724 original size:45 final size:45
Alignment explanation
Indices: 136649--136738 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 45
136639 TTTCCCATTC
*** * * *
136649 AACCACCAACCTGGAACCTACTCGGATTATTCATGAATGATTAAT
1 AACCACCAACCACCAACCTACCCGGATTATTAATGAATAATTAAT
*
136694 AACCACCAACCACCAACCTACCC-GAGTTATTAATGTATAATTAAT
1 AACCACCAACCACCAACCTACCCGGA-TTATTAATGAATAATTAAT
136739 TAATGGTGTC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.26
Consensus pattern (45 bp):
AACCACCAACCACCAACCTACCCGGATTATTAATGAATAATTAAT
Found at i:139282 original size:40 final size:40
Alignment explanation
Indices: 139235--139464 Score: 259
Period size: 40 Copynumber: 6.0 Consensus size: 40
139225 TGCAGGTTTA
*
139235 TAATACACTTCGGTGTATATGGTGGGCACGACTTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* **
139275 TAATACACTTCGGTGTATATAGTGGGCACTCCCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * * *
139315 TAATA-ACTTTGGTGTATATAGTGGGCATGCCCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
139354 TAATACACTTTGGTGTATATGGTGAGCACGACC-------
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
139387 T--T--ACTTCGATGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
139423 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
139463 TA
1 TA
139465 GCCCTACAGT
Statistics
Matches: 162, Mismatches: 16, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
29 23 0.14
31 1 0.01
33 1 0.01
36 1 0.01
38 1 0.01
39 36 0.22
40 99 0.61
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:139389 original size:79 final size:80
Alignment explanation
Indices: 139235--139464 Score: 232
Period size: 69 Copynumber: 3.0 Consensus size: 80
139225 TGCAGGTTTA
* * *
139235 TAATACACTTCGGTGTATATGGTGGGCACGACTTTATGTGTAATACACTTCGGTGTATATAGTGG
1 TAATACACTTCGGTGTATATAGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATAGTGA
**
139300 GCACTCCCTTATGTG
66 GCACGACCTTATGTG
* * * * *
139315 TAATA-ACTTTGGTGTATATAGTGGGCATGCCCTTATGTGTAATACACTTTGGTGTATATGGTGA
1 TAATACACTTCGGTGTATATAGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATAGTGA
139379 GCACGACC-------
66 GCACGACCTTATGTG
* * * * *
139387 T--T--ACTTCGATGTATATGGTGGGAACGACCTTATGTGTAATACACTTCGGTGTATATGGTGG
1 TAATACACTTCGGTGTATATAGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATAGTGA
*
139448 GAACGACCTTATGTG
66 GCACGACCTTATGTG
139463 TA
1 TA
139465 GCCCTACAGT
Statistics
Matches: 123, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
69 58 0.47
70 1 0.01
72 1 0.01
76 1 0.01
79 57 0.46
80 5 0.04
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (80 bp):
TAATACACTTCGGTGTATATAGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATAGTGA
GCACGACCTTATGTG
Found at i:146887 original size:40 final size:40
Alignment explanation
Indices: 146839--147041 Score: 325
Period size: 40 Copynumber: 5.1 Consensus size: 40
146829 TGCAGGTTTA
*
146839 TAATACACTTCGGTGTATATGGTGGGCACGACTTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * *
146879 TAAAACACTTCAGTGTATATGGTGGGCACGCCCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
146919 TAATACACTTCGGTGTATATGGTTGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
146959 TAATACACTTCGATGTATATGGTGGGCACGACCTTCTGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
**
146999 TAATACACTTCGGTGTATATGGTACGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
147039 TAA
1 TAA
147042 CACTACGGGG
Statistics
Matches: 148, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 148 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:149631 original size:2 final size:2
Alignment explanation
Indices: 149626--149659 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
149616 AAACACATCG
149626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149660 CTAAATTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152114 original size:278 final size:278
Alignment explanation
Indices: 151617--152122 Score: 710
Period size: 278 Copynumber: 1.8 Consensus size: 278
151607 TCAATCTGGA
* * *
151617 GATAATTTGGTGACAACACAGTTCCTACATGATGAGAAAGTCTAATTGTATGAGGTTGACACTAC
1 GATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTCTAATTATATGAGGATGACACTAC
* * * * *
151682 TCATTCGCATTGAGGAGATTTGTTAGGTGGACGACATTGTTCCTACATGGTGAGGATGTCTAGCT
66 TCATACGCATTGAGGAGATTTGTCAGGTCGACGACATTGTTCCTACATGATGAGGACGTCTAGCT
* * * *
151747 ATCTTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTATGGTTATCTAAGGA
131 ATCTTTAGGGATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTATGATTACCTAAGGA
* * *
151812 TGACGTGGCTCTTACGCGTTGAGGAGATCTGGTTGGTGGAAGACATTGTTCCTACGTGATGGGTA
196 TGACGTGACTCCTACGCGTTGAGGAGATATGGTTGGTGGAAGACATTGTTCCTACGTGATGGGTA
151877 AGTCTAGCCGTCTTTGGG
261 AGTCTAGCCGTCTTTGGG
* * * * *
151895 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTAATTATCTGAGGATGACACTGC
1 GATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTCTAATTATATGAGGATGACACTAC
* * * *
151960 TCCTACGCATTGAGGAGATTTGGTCA-GTCGATGACATTGTTCCTACGTGATGAGGACGTCTAGT
66 TCATACGCATTGAGGAGATTT-GTCAGGTCGACGACATTGTTCCTACATGATGAGGACGTCTAGC
* * * * *
152024 TATCTTTAGGGATACTTTGGAGACAACACAGTTCCTACATGATGAGGAAGTCTGATTGCCTGAGG
130 TATCTTTAGGGATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTATGATTACCTAAGG
*
152089 ATGACGCT-ACTCCTACTCGTTGAGGAGATATGGT
195 ATGACG-TGACTCCTACGCGTTGAGGAGATATGGT
152123 CAGTTGCCAG
Statistics
Matches: 196, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
278 192 0.98
279 4 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (278 bp):
GATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTCTAATTATATGAGGATGACACTAC
TCATACGCATTGAGGAGATTTGTCAGGTCGACGACATTGTTCCTACATGATGAGGACGTCTAGCT
ATCTTTAGGGATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTATGATTACCTAAGGA
TGACGTGACTCCTACGCGTTGAGGAGATATGGTTGGTGGAAGACATTGTTCCTACGTGATGGGTA
AGTCTAGCCGTCTTTGGG
Found at i:152123 original size:139 final size:138
Alignment explanation
Indices: 151617--152126 Score: 565
Period size: 139 Copynumber: 3.7 Consensus size: 138
151607 TCAATCTGGA
* * * *
151617 GATAATTTGGTGACAACACAGTTCCTACATGATGAGAAAGTCTAATTGTATGAGGTTGACACTAC
1 GATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTCTAATTATCTGAGGATGACACTAC
* * * * * * * *
151682 TCATTCGCATTGAGGAGATTTGTTAGGTGGACGACATTGTTCCTACATGGTGAGGATGTCTAGCT
66 TCCTACGCATTGAGGAGATTGGTCA-GTGGAAGACATTGTTCCTACGTGATGAGGAAGTCTAGCT
151747 ATCTTTAGG
130 ATCTTTAGG
* * * ** * * *
151756 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGAAAGTATGGTTATCTAAGGATGAC-GTGG
1 GATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTCTAATTATCTGAGGATGACACT-A
* * **
151820 CTCTTACGCGTTGAGGAGATCTGGTTGGTGGAAGACATTGTTCCTACGTGATG-GGTAAGTCTAG
65 CTCCTACGCATTGAGGAGAT-TGGTCAGTGGAAGACATTGTTCCTACGTGATGAGG-AAGTCTAG
** *
151884 CCGTCTTTGGG
128 CTATCTTTAGG
* * * *
151895 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTAATTATCTGAGGATGACACTGC
1 GATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTCTAATTATCTGAGGATGACACTAC
* * * *
151960 TCCTACGCATTGAGGAGATTTGGTCAGTCGATGACATTGTTCCTACGTGATGAGGACGTCTAGTT
66 TCCTACGCATTGAGGAGA-TTGGTCAGTGGAAGACATTGTTCCTACGTGATGAGGAAGTCTAGCT
152025 ATCTTTAGG
130 ATCTTTAGG
* * * ** *
152034 GATACTTTGGAGACAACACAGTTCCTACATGATGAGGAAGTCTGATTGCCTGAGGATGACGCTAC
1 GATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTCTAATTATCTGAGGATGACACTAC
* *
152099 TCCTACTCGTTGAGGAGATATGGTCAGT
66 TCCTACGCATTGAGGAGAT-TGGTCAGT
152127 TGCCAGTGAT
Statistics
Matches: 313, Mismatches: 51, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
138 4 0.01
139 301 0.96
140 8 0.03
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (138 bp):
GATAATTTGGAGACAACACAGTTCCTACATGATGAGAAAGTCTAATTATCTGAGGATGACACTAC
TCCTACGCATTGAGGAGATTGGTCAGTGGAAGACATTGTTCCTACGTGATGAGGAAGTCTAGCTA
TCTTTAGG
Found at i:152405 original size:67 final size:67
Alignment explanation
Indices: 152247--152487 Score: 272
Period size: 66 Copynumber: 3.6 Consensus size: 67
152237 GAAGCAAATT
* * * * ** * * * * *
152247 TGTTTCAATAGAAGCTATCTTAGGCGAGATAAAATTTTATTTCGATTGAAAC-ATTTCAAA-ATT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACGAAACTTTGTTTCGATAGAAACAATCTCAAAGGTT
152310 TA
66 TA
* * *
152312 TGTTTCAAGGAAAAACTATCTAAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGT
1 TGTTTCAA-GAGAAACTATCTCAAGCGAGACGAAACTTTGTTTCGATAGAAACAATCTCAAAGGT
152377 TTA
65 TTA
*
152380 TGTTTCAAGAGAAACTATCTCAAGCGAGAC-AAACTTTGTTTCGATAGAAACAAACTCAAAGGTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACGAAACTTTGTTTCGATAGAAACAATCTCAAAGGTT
152444 TA
66 TA
* * * * *
152446 TGTTTCAAAAGAAATTGTCTCAAGCGAGATGAAATTTTGTTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACGAAACTTTGTTT
152488 TTAGGAAAAT
Statistics
Matches: 150, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
65 8 0.05
66 93 0.62
67 37 0.25
68 12 0.08
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACGAAACTTTGTTTCGATAGAAACAATCTCAAAGGTT
TA
Found at i:152505 original size:133 final size:132
Alignment explanation
Indices: 152247--152487 Score: 288
Period size: 133 Copynumber: 1.8 Consensus size: 132
152237 GAAGCAAATT
* * * * * * **
152247 TGTTTCAATAGAAGCTATCTTAGGCGAGATAAAATTTTATTTCGATTGAAACATTTCAAAATTTA
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAACTTTATTTCGATAGAAACAACTCAAAATTTA
152312 TGTTTCAAGGAAAAACTATCTAAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGT
66 TGTTTCAA-GAAAAACTATCTAAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGT
152377 TTA
130 TTA
* * *
152380 TGTTTCAAGAGAAACTATCTCAAGCGAGA-CAAACTTTGTTTCGATAGAAACAAACTCAAAGGTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAACTTTATTTCGATAGAAAC-AACTCAAA-ATT
* * * * *
152444 TATGTTTCAA-AAGAAATTGTCTCAAGCGAGATGAAATTTTGTTT
64 TATGTTTCAAGAA-AAACTATCTAAAGCGAGACGAAACTTTGTTT
152488 TTAGGAAAAT
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
132 20 0.22
133 57 0.64
134 12 0.13
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (132 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAACTTTATTTCGATAGAAACAACTCAAAATTTA
TGTTTCAAGAAAAACTATCTAAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTT
TA
Found at i:152692 original size:36 final size:36
Alignment explanation
Indices: 152608--152676 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
152598 AAGGATTTGT
* *
152608 GTTTCAAGAGAAATTGTCTCAAGTGAGACAAAATTA
1 GTTTCAAGAGAAATTGTCTCAAGGGAGAAAAAATTA
152644 GTTTCAAGAGAAATTGTCTCAAGGGAGAAAAAA
1 GTTTCAAGAGAAATTGTCTCAAGGGAGAAAAAA
152677 ATTGTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (36 bp):
GTTTCAAGAGAAATTGTCTCAAGGGAGAAAAAATTA
Found at i:155390 original size:13 final size:14
Alignment explanation
Indices: 155372--155437 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
155362 TTGCGTGTTC
155372 TTCTTTTCTTT-CT
1 TTCTTTTCTTTGCT
*
155385 TTCTTTTCCTTTGAT
1 TTCTTTT-CTTTGCT
155400 TT-TTTCTCTTTGCT
1 TTCTTT-TCTTTGCT
155414 CTT-TTTTCTTTG-T
1 -TTCTTTTCTTTGCT
*
155427 TTCTTATCTTT
1 TTCTTTTCTTT
155438 TTCCTATCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 2 0.04
13 15 0.33
14 19 0.42
15 9 0.20
ACGTcount: A:0.03, C:0.20, G:0.05, T:0.73
Consensus pattern (14 bp):
TTCTTTTCTTTGCT
Found at i:160517 original size:24 final size:23
Alignment explanation
Indices: 160477--160525 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
160467 GAGCTAAGTC
160477 CTTTTCTCTTTACATTTTTGCTCT
1 CTTTTCTCTTTACATTTTT-CTCT
*
160501 CTTTTCCTCTTT-TATTTTTCTCT
1 CTTTT-CTCTTTACATTTTTCTCT
160524 CT
1 CT
160526 CCGTTCAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 11 0.48
25 6 0.26
ACGTcount: A:0.06, C:0.27, G:0.02, T:0.65
Consensus pattern (23 bp):
CTTTTCTCTTTACATTTTTCTCT
Found at i:161257 original size:3 final size:3
Alignment explanation
Indices: 161249--161294 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
161239 AAATATATGG
161249 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
161295 TTATATTAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:162290 original size:20 final size:20
Alignment explanation
Indices: 162265--162374 Score: 105
Period size: 20 Copynumber: 5.5 Consensus size: 20
162255 TTTTCCGACT
*
162265 ATCGCAATGCGAGTATGACA
1 ATCGCAATGCGATTATGACA
* *
162285 ATCGCAACGCGAATATGTA-A
1 ATCGCAATGCGATTATG-ACA
* *
162305 ATCGCCATGCGATTATGACT
1 ATCGCAATGCGATTATGACA
* *
162325 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATTATGACA
* * *
162345 ATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATTATGACA
*
162365 GTCGCAATGC
1 ATCGCAATGC
162375 AATTTTCAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 75 0.97
21 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATTATGACA
Found at i:162349 original size:40 final size:40
Alignment explanation
Indices: 162261--162374 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 40
162251 GCGATTTTCC
* * *
162261 GACTATCGCAATGCGAGTATGACAATCGCAACGCGAATAT
1 GACTATCGCAATGCGATTATGACTATCGCAATGCGAATAT
* * * *
162301 GTA-AATCGCCATGCGATTATGACTATCGCAATGCGATTCT
1 G-ACTATCGCAATGCGATTATGACTATCGCAATGCGAATAT
* * *
162341 GACTATCGCAACGCGATTCTGACTGTCGCAATGC
1 GACTATCGCAATGCGATTATGACTATCGCAATGC
162375 AATTTTCAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.02
40 58 0.97
41 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (40 bp):
GACTATCGCAATGCGATTATGACTATCGCAATGCGAATAT
Found at i:162594 original size:22 final size:22
Alignment explanation
Indices: 162543--162600 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
162533 CACTCTCTAA
* *
162543 GGCGACATCCGTCCCCATCTCC
1 GGCGAAATCCGTCTCCATCTCC
* * *
162565 GACAAAATCAGTCTCCATCTCC
1 GGCGAAATCCGTCTCCATCTCC
162587 GGCGAAATCCGTCT
1 GGCGAAATCCGTCT
162601 ATCTCCATCT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.40, G:0.17, T:0.21
Consensus pattern (22 bp):
GGCGAAATCCGTCTCCATCTCC
Found at i:164810 original size:20 final size:20
Alignment explanation
Indices: 164785--164852 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
164775 TAGTTTACTT
164785 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
164805 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
164825 TCGCAACACGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
164845 TCGCAACG
1 TCGCAACG
164853 AAAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:164926 original size:20 final size:20
Alignment explanation
Indices: 164901--164948 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
164891 CTCTCGTTGA
164901 GATAGTCAAATTCGCATTGC
1 GATAGTCAAATTCGCATTGC
** * *
164921 GATAGTCATTTTTGCGTTGC
1 GATAGTCAAATTCGCATTGC
164941 GATAGTCA
1 GATAGTCA
164949 TTTTTGCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (20 bp):
GATAGTCAAATTCGCATTGC
Found at i:164949 original size:20 final size:20
Alignment explanation
Indices: 164920--164990 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
164910 ATTCGCATTG
*
164920 CGATAGTCATTTTTGCGTTG
1 CGATAGTCATTTTTGCGTTA
164940 CGATAGTCATTTTTGCGTTA
1 CGATAGTCATTTTTGCGTTA
*
164960 CGATAGTCATTTTCGCGTTA
1 CGATAGTCATTTTTGCGTTA
164980 CGATAGTCATT
1 CGATAGTCATT
164991 CATGTTGCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (20 bp):
CGATAGTCATTTTTGCGTTA
Found at i:165566 original size:42 final size:42
Alignment explanation
Indices: 165496--165587 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
165486 CCTGTCATCG
* *
165496 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAACA
* ** *
165538 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
*
165580 TTCTAGAG
1 TTCAAGAG
165588 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
Found at i:166995 original size:30 final size:30
Alignment explanation
Indices: 166961--167050 Score: 138
Period size: 30 Copynumber: 3.2 Consensus size: 30
166951 ATAAGAGTTG
166961 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
166991 ATTTGTTTAATTGATGTGTAAATAATTC--
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
167019 A----TTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
167045 ATTTGT
1 ATTTGT
167051 GCTTGTTTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
24 23 0.43
26 1 0.02
28 1 0.02
30 29 0.54
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.52
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:167028 original size:24 final size:26
Alignment explanation
Indices: 166966--167048 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 26
166956 AGTTGATTTG
166966 TTTAATTGATGTGTAAATAATTCTTATTT
1 TTTAATTGATGTGTAAATAATTC-TA--T
166995 GTTTAATTGATGTGTAAATAATTC-A-
1 -TTTAATTGATGTGTAAATAATTCTAT
167020 TTTAATTGATGTGTAAATAATTCTTAT
1 TTTAATTGATGTGTAAATAATTC-TAT
167047 TT
1 TT
167049 GTGCTTGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
24 23 0.46
26 1 0.02
27 2 0.04
28 1 0.02
30 23 0.46
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.52
Consensus pattern (26 bp):
TTTAATTGATGTGTAAATAATTCTAT
Found at i:167030 original size:54 final size:53
Alignment explanation
Indices: 166966--167105 Score: 169
Period size: 54 Copynumber: 2.6 Consensus size: 53
166956 AGTTGATTTG
*
166966 TTTAATTGATGTGTAAATAATTCTTATTTGTTTAATTGATGTG-TAAATAATTCA
1 TTTAATTGATGTGTAAATAATTCTTATTTGTTTAATTAAT-TGATAAA-AATTCA
** * *
167020 TTTAATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTTGA
1 TTTAATTGATGTGTAAATAATTCTTATTTGT--TTAATTAATTGA-TAAAAATTCA
167076 -TT-ATTGATGTGTAAATAATTCTTATTTGTT
1 TTTAATTGATGTGTAAATAATTCTTATTTGTT
167106 CTTGTTTAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
52 1 0.01
54 58 0.75
55 4 0.05
56 10 0.13
57 4 0.05
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (53 bp):
TTTAATTGATGTGTAAATAATTCTTATTTGTTTAATTAATTGATAAAAATTCA
Found at i:167247 original size:20 final size:20
Alignment explanation
Indices: 167199--167516 Score: 255
Period size: 20 Copynumber: 16.9 Consensus size: 20
167189 TGCGATTTCT
167199 CGTTGCGATAGTCAAATTC-
1 CGTTGCGATAGTCAAATTCG
* *
167218 CTGTTACGATAATCAAATTCG
1 C-GTTGCGATAGTCAAATTCG
*
167239 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
167258 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
167272 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
167292 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
167312 CGTTGTGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* ** *
167332 CTTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCAAATTCG
* **
167352 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
167372 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
167386 CGTTGCGATTA-TCAAATTCG
1 CGTTGCGA-TAGTCAAATTCG
**
167406 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
167426 CTTTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
167440 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
167460 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
167480 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
167500 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
167517 GAATGTGTAA
Statistics
Matches: 245, Mismatches: 33, Indels: 41
0.77 0.10 0.13
Matches are distributed among these distances:
14 30 0.12
15 1 0.00
16 3 0.01
17 1 0.00
18 2 0.01
19 20 0.08
20 187 0.76
21 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:167285 original size:73 final size:72
Alignment explanation
Indices: 167156--167340 Score: 237
Period size: 73 Copynumber: 2.5 Consensus size: 72
167146 TTCAATCTGC
* * * * *
167156 ATCATATTCACGTTGCGATAGTCTAATACACTTTGCGATTTCTCGTTGCGATAGTCAAATTC-CT
1 ATCAAATTCGCGTTGCGATAGTC-ATTTCGCTTTGCGATTTCTCGTTGCGATAGTCAAATTCGC-
167220 GTTACGATA
64 GTTACGATA
*
167229 ATCAAATTCGCGTTGCGATAGTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAATTCGCG
1 ATCAAATTCGCGTTGCGATAGTCATTTCGCTTTGCGATT-TCTCGTTGCGATAGTCAAATTCGCG
*
167294 TTGCGATA
65 TTACGATA
* * *
167302 GTTAAATTCGCGTTGTGATAGTCATATTCGCTTTGCGAT
1 ATCAAATTCGCGTTGCGATAGTCAT-TTCGCTTTGCGAT
167341 AGTCATTTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
72 12 0.12
73 73 0.74
74 13 0.13
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (72 bp):
ATCAAATTCGCGTTGCGATAGTCATTTCGCTTTGCGATTTCTCGTTGCGATAGTCAAATTCGCGT
TACGATA
Found at i:167416 original size:54 final size:54
Alignment explanation
Indices: 167224--167488 Score: 300
Period size: 54 Copynumber: 4.8 Consensus size: 54
167214 ATTCCTGTTA
* *
167224 CGATAATCAAATTCGCGTTGCGATAGTCA-TTTCGCGTTGCGATTATCTCGTTG
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTATCCCGTTG
* ** * * *
167277 CGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGTGATAGTCATATTCGCTTTG
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCG--A-T--TA-TCCCGTTG
** * * *
167337 CGATAGTCATTTTTGCATTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTG
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTATCCCGTTG
*
167391 CGATTA-TCAAATTCGCGTTGCGATAGTCATTTTCGCTTTGCGATTATCCCGTTG
1 CGA-TAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTATCCCGTTG
* * *
167445 CGATATTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGAT
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGAT
167489 AGTCATATTC
Statistics
Matches: 178, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
53 29 0.16
54 100 0.56
55 4 0.02
56 1 0.01
57 2 0.01
58 1 0.01
59 2 0.01
60 39 0.22
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (54 bp):
CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTATCCCGTTG
Found at i:167712 original size:18 final size:18
Alignment explanation
Indices: 167689--167723 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
167679 GAACCGGTTG
*
167689 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
167707 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
167724 GTCTTTTCCT
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:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:169766 original size:14 final size:14
Alignment explanation
Indices: 169747--169783 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
169737 TCCCGTGGCA
169747 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
169761 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
169775 TTCTTCTTC
1 TT-TTCTTC
169784 TTCCTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:170007 original size:24 final size:24
Alignment explanation
Indices: 169973--170026 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
169963 CTGAAACATC
169973 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
169997 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
170021 ATCAAA
1 ATCAAA
170027 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:170871 original size:20 final size:20
Alignment explanation
Indices: 170843--170976 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
170833 TTGAAATTCA
* *
170843 GCATTGCGACAGTTAGAATC
1 GCATTGCGATAGTCAGAATC
*
170863 GCGTTGCGATAGTCAGAATC
1 GCATTGCGATAGTCAGAATC
*
170883 GCATTGCGATAGTCATAATC
1 GCATTGCGATAGTCAGAATC
* * *
170903 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CAGAATC
* *
170923 GCATTGCGATAGTCATACTC
1 GCATTGCGATAGTCAGAATC
* * *
170943 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CAGAATC
170963 GCATTGCGATAGTC
1 GCATTGCGATAGTC
170977 GGAAAATCAC
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.96
21 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (20 bp):
GCATTGCGATAGTCAGAATC
Found at i:170925 original size:40 final size:40
Alignment explanation
Indices: 170881--170976 Score: 183
Period size: 40 Copynumber: 2.4 Consensus size: 40
170871 ATAGTCAGAA
170881 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
*
170921 TCGCATTGCGATAGTCATACTCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
170961 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
170977 GGAAAATCAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
Found at i:171001 original size:21 final size:21
Alignment explanation
Indices: 170977--171035 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
170967 TGCGATAGTC
170977 GGAAAATCACAACGCGAATTT
1 GGAAAATCACAACGCGAATTT
170998 GGAAAATCACAACGCGAATTT
1 GGAAAATCACAACGCGAATTT
* *
171019 GGAAAATCGCAATGCGA
1 GGAAAATCACAACGCGA
171036 TAGTCAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (21 bp):
GGAAAATCACAACGCGAATTT
Found at i:172524 original size:37 final size:37
Alignment explanation
Indices: 172398--172534 Score: 149
Period size: 37 Copynumber: 3.8 Consensus size: 37
172388 ATTTTTCGTC
*
172398 CTACTAGGATTCAAACTCCTAAAAAT--GATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
172433 -T--TAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* ** * *
172467 TTGTTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
172504 CTACTAGTATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
172535 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
32 22 0.25
34 9 0.10
35 1 0.01
37 55 0.63
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:172941 original size:2 final size:2
Alignment explanation
Indices: 172936--172960 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
172926 TTATTAGTGT
172936 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
172961 TCCTATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:173090 original size:16 final size:18
Alignment explanation
Indices: 173069--173103 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
173059 TTTACTCATT
173069 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
173085 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
173103 T
1 T
173104 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:173182 original size:28 final size:27
Alignment explanation
Indices: 173125--173182 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
173115 CTTTTACTTG
*
173125 TTTTATTTATTATTTGCATTATCATTTA
1 TTTTATTTATTATTTGCA-TATCATATA
*
173153 TTTTATTTAGTTGTTTGC-TATGCATATA
1 TTTTATTTA-TTATTTGCATAT-CATATA
173181 TT
1 TT
173183 AGTGTTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 3 0.12
28 16 0.62
29 7 0.27
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62
Consensus pattern (27 bp):
TTTTATTTATTATTTGCATATCATATA
Found at i:176290 original size:15 final size:15
Alignment explanation
Indices: 176270--176346 Score: 70
Period size: 16 Copynumber: 5.0 Consensus size: 15
176260 CAATCAAGAA
176270 CAAAAAAGAAAAGAAG
1 CAAAAAAGAAAA-AAG
*
176286 CAAAAAAGCAAAAAG
1 CAAAAAAGAAAAAAG
176301 CAAAAAA-AAACAAAG
1 CAAAAAAGAAA-AAAG
*
176316 -AAAAAGAGAAACAAG
1 CAAAAA-AGAAAAAAG
176331 -AACAAAAGGAAAAAAG
1 CAA-AAAA-GAAAAAAG
176347 AGCAAAAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.13
15 21 0.40
16 24 0.46
ACGTcount: A:0.75, C:0.09, G:0.16, T:0.00
Consensus pattern (15 bp):
CAAAAAAGAAAAAAG
Found at i:176296 original size:8 final size:8
Alignment explanation
Indices: 176270--176307 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
176260 CAATCAAGAA
176270 CAAAAAAG
1 CAAAAAAG
176278 -AAAAGAAG
1 CAAAA-AAG
176286 CAAAAAAG
1 CAAAAAAG
176294 C-AAAAAG
1 CAAAAAAG
176301 CAAAAAA
1 CAAAAAA
176308 AAACAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 11 0.41
8 12 0.44
9 4 0.15
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (8 bp):
CAAAAAAG
Found at i:176299 original size:18 final size:15
Alignment explanation
Indices: 176265--176337 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 15
176255 AGACCCAATC
176265 AAGAACAAAAAAGAA
1 AAGAACAAAAAAGAA
176280 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAG-AA
*
176297 AA-AGCAAAAAA-AA
1 AAGAACAAAAAAGAA
*
176310 ACA-AAGAAAAAGAGAAA
1 A-AGAACAAAAA-AG-AA
176327 CAAGAACAAAA
1 -AAGAACAAAA
176338 GGAAAAAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
13 3 0.07
14 7 0.15
15 13 0.28
16 9 0.20
17 7 0.15
18 7 0.15
ACGTcount: A:0.77, C:0.10, G:0.14, T:0.00
Consensus pattern (15 bp):
AAGAACAAAAAAGAA
Found at i:176308 original size:16 final size:16
Alignment explanation
Indices: 176265--176307 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
176255 AGACCCAATC
176265 AAGAA-CAAAAAAGAA
1 AAGAAGCAAAAAAGAA
*
176280 AAGAAGCAAAAAAGCA
1 AAGAAGCAAAAAAGAA
176296 AA-AAGCAAAAAA
1 AAGAAGCAAAAAA
176308 AAACAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.77, C:0.09, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAAGCAAAAAAGAA
Found at i:176342 original size:16 final size:17
Alignment explanation
Indices: 176265--176353 Score: 50
Period size: 16 Copynumber: 5.6 Consensus size: 17
176255 AGACCCAATC
*
176265 AAGAACAAAA-A-AGAA
1 AAGAACAAAAGAGAAAA
* *
176280 AAGAAGCAAAAAAGCAAA
1 AAGAA-CAAAAGAGAAAA
*
176298 AAGCAA-AAAA-A-AACA
1 AAG-AACAAAAGAGAAAA
*
176313 AAG-A-AAAAGAGAAAC
1 AAGAACAAAAGAGAAAA
176328 AAGAACAAAAG-GAAAA
1 AAGAACAAAAGAGAAAA
*
176344 AAGAGCAAAA
1 AAGAACAAAA
176354 ATCAAAAAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
13 5 0.09
14 1 0.02
15 15 0.26
16 20 0.34
17 10 0.17
18 5 0.09
19 2 0.03
ACGTcount: A:0.75, C:0.09, G:0.16, T:0.00
Consensus pattern (17 bp):
AAGAACAAAAGAGAAAA
Found at i:176367 original size:7 final size:7
Alignment explanation
Indices: 176271--176367 Score: 70
Period size: 7 Copynumber: 12.7 Consensus size: 7
176261 AATCAAGAAC
176271 AAAAAAG
1 AAAAAAG
176278 AAAAGAAG
1 AAAA-AAG
176286 CAAAAAAG
1 -AAAAAAG
*
176294 CAAAAAG
1 AAAAAAG
176301 CAAAAAA-
1 -AAAAAAG
176308 AAACAAAG
1 AAA-AAAG
176316 AAAAAGAG
1 AAAAA-AG
*
176324 AAACAAG
1 AAAAAAG
176331 AACAAAAGG
1 AA-AAAA-G
176340 AAAAAAG
1 AAAAAAG
*
176347 AGCAAAAAT
1 A--AAAAAG
*
176356 CAAAAAG
1 AAAAAAG
176363 AAAAA
1 AAAAA
176368 GGGACAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
6 3 0.04
7 30 0.42
8 27 0.38
9 12 0.17
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:177022 original size:22 final size:22
Alignment explanation
Indices: 176997--177045 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
176987 CCATCAATCT
* *
176997 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
177019 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
177041 TTTGA
1 TTTGA
177046 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:178040 original size:15 final size:15
Alignment explanation
Indices: 177975--178040 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
177965 GAGTTTTGTC
* *
177975 TCTCTTGAGACAGTT
1 TCTCTTGAAACAATT
*
177990 TCCCTTGAAACAAATTTT
1 TCTCTTGAAAC-AA--TT
* *
178008 CTCTCTTGAGACAGTT
1 -TCTCTTGAAACAATT
178024 TCTCTTGAAACAATT
1 TCTCTTGAAACAATT
178039 TC
1 TC
178041 GTCTATCTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
15 24 0.62
16 3 0.08
18 3 0.08
19 9 0.23
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (15 bp):
TCTCTTGAAACAATT
Found at i:178086 original size:36 final size:36
Alignment explanation
Indices: 177968--178244 Score: 274
Period size: 36 Copynumber: 8.0 Consensus size: 36
177958 ACTAGAAGAG
177968 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
178004 -TTT-TCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
178037 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
178073 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
178109 --------ATATTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * * *
178137 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
178173 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
178208 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
178245 ACCTTTGAAT
Statistics
Matches: 196, Mismatches: 30, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
27 2 0.01
28 20 0.10
33 2 0.01
34 29 0.15
35 33 0.17
36 106 0.54
37 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:178184 original size:100 final size:100
Alignment explanation
Indices: 177966--178207 Score: 276
Period size: 100 Copynumber: 2.4 Consensus size: 100
177956 TCACTAGAAG
* *
177966 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTCTCTCTTGAGACAGTTTCTCTTG
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-----TATATTGAGACAGTTTCTCTTG
* *
178031 AAACAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATA
61 AAACAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATA
* *
178071 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-ATATTGA-ATATGTTT-TCTTTGAAA
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATATTGAGACA-GTTTCTC-TTGAAA
* ** *
178133 CAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACT-
64 C-AATTCCGTCTACCTTGAGACAGTTTCCCTT-GAAATA
*
178171 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
178208 TTTTCGTCTA
Statistics
Matches: 121, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
98 4 0.03
99 16 0.13
100 60 0.50
101 4 0.03
105 37 0.31
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (100 bp):
AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATATTGAGACAGTTTCTCTTGAAACA
ATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATA
Found at i:178202 original size:136 final size:133
Alignment explanation
Indices: 177994--178306 Score: 380
Period size: 136 Copynumber: 2.3 Consensus size: 133
177984 ACAGTTTCCC
* *
177994 TTGAAACAAATTTTCTCTCTTGAGACAGTTTCTCTTGAAACAATTTCGTCTATCTTGAGACAGTT
1 TTGAAACAAATTGTCTCCCTTGAGACAGTTTCTCTTGAAACAATTTCGTCTATCTTGAGACAGTT
*
178059 TCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTGAATATGTT
66 TCCCTTGAAA-AAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTGAATATGTT
178123 TTCT
130 TTCT
* * * * *
178127 TTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAGTTTTGTCTCTCTTGAGACA
1 TTGAAACAAATT--GTCTCCCTTGAGACAGTTTCTCTTGAAAC-AATTTCGTCTATCTTGAGACA
* * *
178192 GTTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCT-TTGAATT
63 GTTTCCCTTGAAAAAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAA--TATTGAATA
* * *
178256 TATTTCCC
126 TGTTTTCT
* * *
178264 CTAAAACAAATTTTATCTCCCTTGAGACAG-TTCTCTTGAAACA
1 TTGAAACAAA--TTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
178307 CAAAATCTTC
Statistics
Matches: 153, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
133 12 0.08
135 32 0.21
136 72 0.47
137 34 0.22
138 1 0.01
139 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (133 bp):
TTGAAACAAATTGTCTCCCTTGAGACAGTTTCTCTTGAAACAATTTCGTCTATCTTGAGACAGTT
TCCCTTGAAAAAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTGAATATGTTT
TCT
Done.