Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015360.1 Kokia drynarioides strain JFW-HI SEQ_130407, 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: 850717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 109 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:661609 original size:58 final size:59
Alignment explanation
Indices: 661519--661758 Score: 200
Period size: 58 Copynumber: 4.2 Consensus size: 59
661509 TAAAAACGTG
* * * * *
661519 ATTTTTGTAAGTTCGA-GGTAATAATGTAATTTTTAATAAG-TT-AGAGGTAATAATGTA
1 ATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTAAGAAGTTTAAG-GGTAAAAATATA
* *
661576 ATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTAAGAAGTTTAAGGGTAAAAATATG
1 ATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTAAGAAGTTTAAGGGTAAAAATATA
* * *
661635 ATTTTTGGAAGTTCGAGGG-CAAAATGTAATTTTTGAGAAGTTT-GGAGGT---AA-A-A
1 ATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTAAGAAGTTTAAG-GGTAAAAATATA
* * * * * * *
661688 A-GTGTGGAAGTTTCGA-GGCAAAAATGTAATTTTT-TGAAGTTTGAGGGCAAAAATGTA
1 ATTTTTGGAAG-TTCGAGGGTAAAAATGTAATTTTTAAGAAGTTTAAGGGTAAAAATATA
661745 ATTTTTGAGAAGTT
1 ATTTTTG-GAAGTT
661759 TGGGGGTTAA
Statistics
Matches: 148, Mismatches: 21, Indels: 27
0.76 0.11 0.14
Matches are distributed among these distances:
52 18 0.12
53 21 0.14
54 1 0.01
55 4 0.03
57 18 0.12
58 50 0.34
59 34 0.23
60 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (59 bp):
ATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTAAGAAGTTTAAGGGTAAAAATATA
Found at i:661611 original size:116 final size:116
Alignment explanation
Indices: 661458--661668 Score: 268
Period size: 116 Copynumber: 1.8 Consensus size: 116
661448 GGTTAAAACA
** * * *
661458 TAATTTTTGGAAAGTTTTAGGGGTAAAATGTCATTTTAGGAAAATTT-GGGGTAAAAACGTGATT
1 TAATTTTTGGAAAGTTCGAGGGGTAAAATGTCATTTTAAG-AAATTTAAGGGTAAAAACATGATT
* *
661522 TTTGTAAGTTCGA-GGTAATAATGTAATTTTTAATAAGTTAGAGGTAATAATG
65 TTTGGAAGTTCGAGGGCAA-AATGTAATTTTTAATAAGTTAGAGGTAATAATG
* * *
661574 TAATTTTTGG-AAGTTCGA-GGGTAAAAATGTGATTTTTAAGAAGTTTAAGGGTAAAAATATGAT
1 TAATTTTTGGAAAGTTCGAGGGGT-AAAATGTCA-TTTTAAGAAATTTAAGGGTAAAAACATGAT
661637 TTTTGGAAGTTCGAGGGCAAAATGTAATTTTT
64 TTTTGGAAGTTCGAGGGCAAAATGTAATTTTT
661669 GAGAAGTTTG
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
114 4 0.05
115 19 0.23
116 54 0.67
117 4 0.05
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (116 bp):
TAATTTTTGGAAAGTTCGAGGGGTAAAATGTCATTTTAAGAAATTTAAGGGTAAAAACATGATTT
TTGGAAGTTCGAGGGCAAAATGTAATTTTTAATAAGTTAGAGGTAATAATG
Found at i:661687 original size:29 final size:28
Alignment explanation
Indices: 661441--661788 Score: 139
Period size: 29 Copynumber: 12.1 Consensus size: 28
661431 AGTTTCAAAG
**
661441 AGTTTGG-GGTTAAAACATAATTTTTGGAA
1 AGTTTGGAGG-TAAAATGTAATTTTTGG-A
* *
661470 AGTTTTAGG-GGTAAAATGTCATTTTAGGAA
1 AG-TTT-GGAGGTAAAATGTAATTTTTGG-A
* * * *
661500 AATTTGG-GGTAAAAACGTGATTTTTGTA
1 AGTTTGGAGGT-AAAATGTAATTTTTGGA
* **
661528 AG-TTCGAGGTAATAATGTAATTTTTAATA
1 AGTTTGGAGGTAA-AATGTAATTTTT-GGA
*
661557 AG-TTAGAGGTAATAATGTAATTTTTGGA
1 AGTTTGGAGGTAA-AATGTAATTTTTGGA
* * *
661585 AG-TTCGAGGGTAAAAATGTGATTTTTAAGA
1 AGTTTGGA-GGT-AAAATGTAATTTTT-GGA
* * *
661615 AGTTT-AAGGGTAAAAATATGATTTTTGGA
1 AGTTTGGA-GGT-AAAATGTAATTTTTGGA
* *
661644 AG-TTCGAGGGCAAAATGTAATTTTTGAGA
1 AGTTTGGA-GGTAAAATGTAATTTTTG-GA
* *
661673 AGTTTGGAGGT-AAA---AA-GTGTGGA
1 AGTTTGGAGGTAAAATGTAATTTTTGGA
* * *
661696 AGTTTCGAGGCAAAAATGTAATTTTTTGA
1 AGTTTGGAGG-TAAAATGTAATTTTTGGA
*
661725 AGTTT-GAGGGCAAAAATGTAATTTTTGAGA
1 AGTTTGGA-GG-TAAAATGTAATTTTTG-GA
* * *
661755 AGTTTGGGGGTTAAAATATGATTTTTGGA
1 AGTTTGGAGG-TAAAATGTAATTTTTGGA
661784 TAGTT
1 -AGTT
661789 CAGAGACCTT
Statistics
Matches: 254, Mismatches: 42, Indels: 45
0.74 0.12 0.13
Matches are distributed among these distances:
23 11 0.04
24 3 0.01
25 5 0.02
27 5 0.02
28 49 0.19
29 100 0.39
30 74 0.29
31 7 0.03
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (28 bp):
AGTTTGGAGGTAAAATGTAATTTTTGGA
Found at i:661740 original size:52 final size:52
Alignment explanation
Indices: 661640--661740 Score: 136
Period size: 52 Copynumber: 1.9 Consensus size: 52
661630 ATATGATTTT
*
661640 TGGAAGTTCGAGGGCAAAATGTAATTTTTGAGAAGTTTGGAGGTAAAAAGTG
1 TGGAAGTTCGAGGGCAAAATGTAATTTTTGAGAAGTTTGGAGGCAAAAAGTG
*
661692 TGGAAGTTTCGA-GGCAAAAATGTAATTTTT-TGAAGTTT-GAGGGCAAAAA
1 TGGAAG-TTCGAGGGC-AAAATGTAATTTTTGAGAAGTTTGGA-GGCAAAAA
661741 TGTAATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
51 2 0.05
52 23 0.52
53 19 0.43
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.30
Consensus pattern (52 bp):
TGGAAGTTCGAGGGCAAAATGTAATTTTTGAGAAGTTTGGAGGCAAAAAGTG
Found at i:661759 original size:30 final size:28
Alignment explanation
Indices: 661510--661760 Score: 140
Period size: 29 Copynumber: 8.9 Consensus size: 28
661500 AATTTGGGGT
* * * *
661510 AAAAACGTGATTTTT-GTAAGTTCGAGGT
1 AAAAATGTAATTTTTAG-AAGTTTGAGGC
* * * *
661538 AATAATGTAATTTTTAATAAGTTAGAGGT
1 AAAAATGTAATTTTT-AGAAGTTTGAGGC
* * * *
661567 AATAATGTAATTTTTGGAAGTTCGAGGGT
1 AAAAATGTAATTTTTAGAAGTTTGA-GGC
* * *
661596 AAAAATGTGATTTTTAAGAAGTTTAAGGGT
1 AAAAATGTAATTTTT-AGAAGTTTGA-GGC
* * * *
661626 AAAAATATGATTTTTGGAAGTTCGAGGGC
1 AAAAATGTAATTTTTAGAAGTTTGA-GGC
*
661655 -AAAATGTAATTTTTGAGAAGTTTGGAGGT
1 AAAAATGTAATTTTT-AGAAGTTT-GAGGC
* *
661684 AAAAA-G-----TGTGGAAGTTTCGAGGC
1 AAAAATGTAATTTTTAGAAGTTT-GAGGC
*
661707 AAAAATGTAATTTTTTGAAGTTTGAGGGC
1 AAAAATGTAATTTTTAGAAGTTTGA-GGC
661736 AAAAATGTAATTTTTGAGAAGTTTG
1 AAAAATGTAATTTTT-AGAAGTTTG
661761 GGGGTTAAAA
Statistics
Matches: 178, Mismatches: 30, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
23 16 0.09
24 3 0.02
28 33 0.19
29 87 0.49
30 39 0.22
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
AAAAATGTAATTTTTAGAAGTTTGAGGC
Found at i:663414 original size:11 final size:11
Alignment explanation
Indices: 663398--663495 Score: 70
Period size: 11 Copynumber: 8.7 Consensus size: 11
663388 TTTGGACTGG
663398 AAATTTAATTT
1 AAATTTAATTT
**
663409 AAATTTAAAAT
1 AAATTTAATTT
663420 AAATTTGAATTT
1 AAATTT-AATTT
* *
663432 AAAATGAATTT
1 AAATTTAATTT
* **
663443 AAACTTAAAAT
1 AAATTTAATTT
*
663454 AAATTTAAATT
1 AAATTTAATTT
*
663465 AAGTTTAAATTT
1 AAATTT-AATTT
* *
663477 AAAATAAATTT
1 AAATTTAATTT
*
663488 AAACTTAA
1 AAATTTAA
663496 AATAGCATCA
Statistics
Matches: 66, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
11 52 0.79
12 14 0.21
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:663430 original size:17 final size:17
Alignment explanation
Indices: 663404--663499 Score: 105
Period size: 17 Copynumber: 6.0 Consensus size: 17
663394 CTGGAAATTT
663404 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
663421 AATTTGAATTTAAAATG
1 AATTTAAATTTAAAATA
*
663438 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
663455 AATTTAAA--T----TA
1 AATTTAAATTTAAAATA
*
663466 AGTTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
663483 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
663500 GCATCAGGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
11 9 0.14
13 1 0.02
15 1 0.02
17 54 0.83
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:663430 original size:28 final size:27
Alignment explanation
Indices: 663399--663489 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 27
663389 TTGGACTGGA
663399 AATTTAATTTAAATTTAAAATAAATTT
1 AATTTAATTTAAATTTAAAATAAATTT
*
663426 GAATTTAAAATGAATTTAAACTTAAAATAAATTT
1 -AA-TT----T-AATTTAAATTTAAAATAAATTT
*
663460 AAATTAAGTTTAAATTTAAAATAAATTT
1 AATTTAA-TTTAAATTTAAAATAAATTT
663488 AA
1 AA
663490 ACTTAAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
27 2 0.04
28 24 0.45
29 2 0.04
32 1 0.02
33 3 0.06
34 21 0.40
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (27 bp):
AATTTAATTTAAATTTAAAATAAATTT
Found at i:663459 original size:45 final size:45
Alignment explanation
Indices: 663408--663499 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
663398 AAATTTAATT
* *
663408 TAAATTTAAAATAAATTTGAATTTAAAATGAATTTAAACTTAAAA
1 TAAATTTAAAATAAATTTAAATTTAAAATAAATTTAAACTTAAAA
* *
663453 TAAATTTAAATTAAGTTTAAATTTAAAATAAATTTAAACTTAAAA
1 TAAATTTAAAATAAATTTAAATTTAAAATAAATTTAAACTTAAAA
663498 TA
1 TA
663500 GCATCAGGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.39
Consensus pattern (45 bp):
TAAATTTAAAATAAATTTAAATTTAAAATAAATTTAAACTTAAAA
Found at i:663977 original size:38 final size:39
Alignment explanation
Indices: 663925--664015 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 39
663915 TGCCCCATGA
* *
663925 TCGGGGTAACAGATTGGTTGATGATGATCTGCCCAAGCT
1 TCGGGGTAAAAGATTGGCTGATGATGATCTGCCCAAGCT
* * * *
663964 T-GGGGTAAAAGATTGGCTGATGGTGATTTGCCCCAGGT
1 TCGGGGTAAAAGATTGGCTGATGATGATCTGCCCAAGCT
664002 TCGGGGTAAAAGAT
1 TCGGGGTAAAAGAT
664016 CAGATGGCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 32 0.71
39 13 0.29
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.27
Consensus pattern (39 bp):
TCGGGGTAAAAGATTGGCTGATGATGATCTGCCCAAGCT
Found at i:664149 original size:39 final size:37
Alignment explanation
Indices: 663925--664365 Score: 252
Period size: 39 Copynumber: 11.4 Consensus size: 37
663915 TGCCCCATGA
* * * *
663925 TCGGGGTAACAGATTGGTTGATGATGATCTGCCCAAGC
1 TCGGGGTAAGAGATT-GATGATGGTGATCTGCCCAGGC
* * * * *
663963 TTGGGGTAAAAGATTGGCTGATGGTGATTTGCCCCAGGT
1 TCGGGGTAAGAGATT-GATGATGGTGATCTG-CCCAGGC
* * ** * *
664002 TCGGGGTAAAAGA-TCA-GATGGCCACAATCCGCCCCAAGC
1 TCGGGGTAAGAGATTGATGATGG---TGATCTG-CCCAGGC
* *
664041 TCGGGGTAAGAGATTGGCTGATGGTGATTTGCCTCAGGC
1 TCGGGGTAAGAGATT-GATGATGGTGATCTGCC-CAGGC
** *
664080 TTAGGGTAAGAGATCGA--ATGGCTGCAATCTGCCTCAGGC
1 TCGGGGTAAGAGATTGATGATGG-TG--ATCTGCC-CAGGC
* *
664119 TCGAGGTAAGAGATTGATTGATGGTGATCTGCCCTAGGT
1 TCGGGGTAAGAGATTGA-TGATGGTGATCTGCCC-AGGC
* *
664158 TCGGGGTGAGAGATTGATTAATGGTGATCTGCTCCAGGC
1 TCGGGGTAAGAGATTGA-TGATGGTGATCTGC-CCAGGC
* * * *
664197 TCGGGGTAAGAGA-TCA-AATGGCTACAATCTACCCCAGGC
1 TCGGGGTAAGAGATTGATGATGG-T--GATCT-GCCCAGGC
* *
664236 TCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCGAGGC
1 TCGGGGTAAGAGATT-GATGATGGTGATCTGCCC-AGGC
*
664275 TCGAGGTAAGAGATTGA--ATGGCTGCAATCTGCCCAGGC
1 TCGGGGTAAGAGATTGATGATGG-TG--ATCTGCCCAGGC
* *
664313 TCGGGATAAGAGATTGGTTGATGGTGATCTGCCCCAAGG-
1 TCGGGGTAAGAGATT-GATGATGGTGATCTG-CCC-AGGC
*
664352 TCGGGGTAAAAGAT
1 TCGGGGTAAGAGAT
664366 CAGATCTTCA
Statistics
Matches: 315, Mismatches: 56, Indels: 63
0.73 0.13 0.15
Matches are distributed among these distances:
36 18 0.06
37 5 0.02
38 59 0.19
39 203 0.64
40 10 0.03
41 7 0.02
42 13 0.04
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (37 bp):
TCGGGGTAAGAGATTGATGATGGTGATCTGCCCAGGC
Found at i:664171 original size:117 final size:117
Alignment explanation
Indices: 664039--664291 Score: 328
Period size: 117 Copynumber: 2.2 Consensus size: 117
664029 TCCGCCCCAA
* * * * *
664039 GCTCGGGGTAAGAGATTGGCTGATGGTGATTTGC-CTCAGGCTTAGGGTAAGAGATCGAATGGCT
1 GCTCGGGGTAAGAGATTGACTAATGGTGATCTGCTC-CAGGCTCAGGGTAAGAGATCAAATGGCT
* * * * *
664103 GCAATCTGCCTCAGGCTCGAGGTAAGAGATTGATTGATGGTGATCTGCCCTAG
65 ACAATCTACCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATCTGCCCGAG
* * * *
664156 GTTCGGGGTGAGAGATTGATTAATGGTGATCTGCTCCAGGCTCGGGGTAAGAGATCAAATGGCTA
1 GCTCGGGGTAAGAGATTGACTAATGGTGATCTGCTCCAGGCTCAGGGTAAGAGATCAAATGGCTA
* * *
664221 CAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCGAG
66 CAATCTACCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATCTGCCCGAG
*
664273 GCTCGAGGTAAGAGATTGA
1 GCTCGGGGTAAGAGATTGA
664292 ATGGCTGCAA
Statistics
Matches: 115, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
117 114 0.99
118 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.25
Consensus pattern (117 bp):
GCTCGGGGTAAGAGATTGACTAATGGTGATCTGCTCCAGGCTCAGGGTAAGAGATCAAATGGCTA
CAATCTACCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATCTGCCCGAG
Found at i:664305 original size:117 final size:114
Alignment explanation
Indices: 664039--664326 Score: 326
Period size: 117 Copynumber: 2.5 Consensus size: 114
664029 TCCGCCCCAA
* * * ** * *
664039 GCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCTCAGGCTTAGGGTAAGAGATCGAATGGCTG
1 GCTCGAGGTAAGAGATT-G-TAATGGTGATCTGCC-CAGGCTCGGGGTAAGAGATCAAATGGCTA
* * * *
664104 CAATCTGCCTCAGGCTCGAGGTAAGAGATTGATTGATGGTGATCTGCCCTAG
63 CAATCTACCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATCTGCCCGAG
* * *
664156 GTTCGGGGTGAGAGATTGATTAATGGTGATCTGCTCCAGGCTCGGGGTAAGAGATCAAATGGCTA
1 GCTCGAGGTAAGAGATTG--TAATGGTGATCTGC-CCAGGCTCGGGGTAAGAGATCAAATGGCTA
* * *
664221 CAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCGAG
63 CAATCTACCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATCTGCCCGAG
*
664273 GCTCGAGGTAAGAGATTG-AATGGCTGCAATCTGCCCAGGCTCGGGATAAGAGAT
1 GCTCGAGGTAAGAGATTGTAATGG-TG--ATCTGCCCAGGCTCGGGGTAAGAGAT
664327 TGGTTGATGG
Statistics
Matches: 146, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
114 5 0.03
115 2 0.01
116 20 0.14
117 118 0.81
118 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.25
Consensus pattern (114 bp):
GCTCGAGGTAAGAGATTGTAATGGTGATCTGCCCAGGCTCGGGGTAAGAGATCAAATGGCTACAA
TCTACCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATCTGCCCGAG
Found at i:666622 original size:3 final size:3
Alignment explanation
Indices: 666614--666640 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
666604 GATCATCCCT
666614 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
666641 AATATCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:675998 original size:58 final size:58
Alignment explanation
Indices: 675908--676024 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
675898 TTGAAAAAAT
675908 ATATTCGATTATCTCGATTTGAAGAAAAATTGTGCCTAGTAAGTTAAGACAAATTTTC
1 ATATTCGATTATCTCGATTTGAAGAAAAATTGTGCCTAGTAAGTTAAGACAAATTTTC
* *
675966 ATATTCGATTATCTTGGTTTGAAGAAAAATTGTGCCTAGTAAGTTAAGACAAATTTTC
1 ATATTCGATTATCTCGATTTGAAGAAAAATTGTGCCTAGTAAGTTAAGACAAATTTTC
676024 A
1 A
676025 AAACCCGAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (58 bp):
ATATTCGATTATCTCGATTTGAAGAAAAATTGTGCCTAGTAAGTTAAGACAAATTTTC
Found at i:676468 original size:29 final size:29
Alignment explanation
Indices: 676346--676671 Score: 197
Period size: 29 Copynumber: 11.1 Consensus size: 29
676336 AAAAAAAAAG
*
676346 AGTTT-GGGGTAAAAATGTAATTTTTGGAA
1 AGTTTAGGGGTAAAAATGTAGTTTTTGG-A
*
676375 AGTTTTAGGGGTAAAAATGTCA-TTTTAGGAA
1 AG-TTTAGGGGTAAAAATGT-AGTTTTTGG-A
* * *
676406 AATTCA-AGGTAAAAATGT-GATTTTTGGA
1 AGTTTAGGGGTAAAAATGTAG-TTTTTGGA
*
676434 AGTTT-GGGGTAATAATGTAGTTTTTGAGA
1 AGTTTAGGGGTAAAAATGTAGTTTTTG-GA
*
676463 AGTTT-GAGGGTAAAAATGTAATTTTTGGA
1 AGTTTAG-GGGTAAAAATGTAGTTTTTGGA
* * *
676492 AGTTTGGGGGTATAAATGTAATTTTTGAGA
1 AGTTTAGGGGTAAAAATGTAGTTTTTG-GA
* * **
676522 AATTTAGGGGTAAAAATGT-GGTTTTAAA
1 AGTTTAGGGGTAAAAATGTAGTTTTTGGA
* * *
676550 ATGTTCAAGGG-AAAAATGTAATTTTTGAGA
1 A-GTTTAGGGGTAAAAATGTAGTTTTTG-GA
* ** *
676580 AG-TTCGAGGGTAAAAATAAAATTTTTGGA
1 AGTTTAG-GGGTAAAAATGTAGTTTTTGGA
* * * * **
676609 AGTATGGGGGCAAAAATGTAATTTTAAGA
1 AGTTTAGGGGTAAAAATGTAGTTTTTGGA
*
676638 AGTTTAAGGGTCAAAATATG-A-TTTTTGGA
1 AGTTTAGGGGT-AAAA-ATGTAGTTTTTGGA
676667 CAGTT
1 -AGTT
676672 CAAGGACCTT
Statistics
Matches: 233, Mismatches: 44, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
28 31 0.13
29 106 0.45
30 70 0.30
31 25 0.11
32 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (29 bp):
AGTTTAGGGGTAAAAATGTAGTTTTTGGA
Found at i:676487 original size:58 final size:57
Alignment explanation
Indices: 676346--676671 Score: 266
Period size: 58 Copynumber: 5.6 Consensus size: 57
676336 AAAAAAAAAG
*
676346 AGTTTG-GGGTAAAAATGTAATTTTTGGAAAGTTTTAGGGGTAAAAATGTCATTTTAG-GA
1 AGTTTGAGGGTAAAAATGTAATTTTTGG-AAG-TTT-GGGGTAAAAATGT-ATTTTTGAGA
** * * * *
676405 AAATTCAAGGTAAAAATGTGATTTTTGGAAGTTTGGGGTAATAATGTAGTTTTTGAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTGGGGTAAAAATGTA-TTTTTGAGA
*
676463 AGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTGGGGGTATAAATGTAATTTTTGAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTT-GGGGTAAAAATGT-ATTTTTGAGA
* ** ** **
676522 AATTT-AGGGGTAAAAATGT-GGTTTTAAAATGTTCAAGGG-AAAAATGTAATTTTTGAGA
1 AGTTTGA-GGGTAAAAATGTAATTTTTGGAA-GTT-TGGGGTAAAAATGT-ATTTTTGAGA
* ** * * * *
676580 AGTTCGAGGGTAAAAATAAAATTTTTGGAAGTATGGGGGCAAAAATGTAATTTTAAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGGAAGT-TTGGGGTAAAAATGTATTTTTGAGA
* * * *
676638 AGTTTAAGGGTCAAAATATGATTTTTGGACAGTT
1 AGTTTGAGGGTAAAAATGTAATTTTTGGA-AGTT
676672 CAAGGACCTT
Statistics
Matches: 215, Mismatches: 39, Indels: 27
0.77 0.14 0.10
Matches are distributed among these distances:
56 1 0.00
57 17 0.08
58 110 0.51
59 67 0.31
60 20 0.09
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (57 bp):
AGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTGGGGTAAAAATGTATTTTTGAGA
Found at i:676673 original size:117 final size:117
Alignment explanation
Indices: 676352--676676 Score: 370
Period size: 117 Copynumber: 2.8 Consensus size: 117
676342 AAAGAGTTTG
* * * *
676352 GGGTAAAAATGTAATTTTTGGAAAGTTTTAGGGGTAAAAATGTCATTTTAGGAAAATTCAA-GGT
1 GGGTAAAAATGTAATTTTTGG-AAG-TTTGGGGGTAAAAATGTAATTTTAAG-AAATTTAAGGGT
** * * *
676416 AAAAATGTGATTTTTGGAAGTT-TGGGGTAATAATGTAGTTTTTGAGAAGTTTGA
63 AAAAATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTCGA
* * *
676470 GGGTAAAAATGTAATTTTTGGAAGTTTGGGGGTATAAATGTAATTTTTGAGAAATTTAGGGGTAA
1 GGGTAAAAATGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAA-TTTTAAGAAATTTAAGGGTAA
* **
676535 AAATGTG-GTTTTAAAATGTTCAAGGG-AAAAATGTAATTTTTGAGAAGTTCGA
65 AAATGTGATTTTTGGAA-GTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTCGA
** * * * *
676587 GGGTAAAAATAAAATTTTTGGAAGTATGGGGGCAAAAATGTAATTTTAAGAAGTTTAAGGGTCAA
1 GGGTAAAAATGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTAAGAAATTTAAGGGTAAA
*
676652 AATATGATTTTTGGACAGTTCAAGG
66 AATGTGATTTTTGGA-AGTTCAAGG
676677 ACCTTCACGG
Statistics
Matches: 173, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
116 51 0.29
117 97 0.56
118 25 0.14
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (117 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTAAGAAATTTAAGGGTAAA
AATGTGATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTCGA
Found at i:678368 original size:11 final size:11
Alignment explanation
Indices: 678352--678415 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
678342 TTTGGATTGG
678352 AAATTTAATTT
1 AAATTTAATTT
**
678363 AAATTTAAAAT
1 AAATTTAATTT
*
678374 AAATTTAAATT
1 AAATTTAATTT
*
678385 AAGTTTAAATTT
1 AAATTT-AATTT
* *
678397 AAAATAAATTT
1 AAATTTAATTT
*
678408 AAACTTAA
1 AAATTTAA
678416 AATAGCATCG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
11 35 0.83
12 7 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:678369 original size:6 final size:6
Alignment explanation
Indices: 678352--678416 Score: 66
Period size: 6 Copynumber: 11.5 Consensus size: 6
678342 TTTGGATTGG
* *
678352 AAATTT -AATTT AAATTT AAA-AT AAATTT AAA-TT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
678397 AAA-AT AAATTT AAACTT AAA
1 AAATTT AAATTT AAATTT AAA
678417 ATAGCATCGG
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
5 17 0.35
6 31 0.65
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
AAATTT
Found at i:678380 original size:17 final size:17
Alignment explanation
Indices: 678352--678419 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
678342 TTTGGATTGG
*
678352 AAATTT-AATTTAAATTT
1 AAATTTAAATTTAAA-AT
* *
678369 AAA-ATAAATTTAAATT
1 AAATTTAAATTTAAAAT
*
678385 AAGTTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
*
678402 AAATTTAAACTTAAAAT
1 AAATTTAAATTTAAAAT
678419 A
1 A
678420 GCATCGGGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
16 5 0.12
17 38 0.88
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:678384 original size:28 final size:28
Alignment explanation
Indices: 678356--678415 Score: 104
Period size: 28 Copynumber: 2.1 Consensus size: 28
678346 GATTGGAAAT
678356 TTAA-TTTAAATTTAAAATAAATTTAAA
1 TTAAGTTTAAATTTAAAATAAATTTAAA
678383 TTAAGTTTAAATTTAAAATAAATTTAAA
1 TTAAGTTTAAATTTAAAATAAATTTAAA
678411 CTTAA
1 -TTAA
678416 AATAGCATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 4 0.13
28 23 0.74
29 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TTAAGTTTAAATTTAAAATAAATTTAAA
Found at i:679599 original size:2 final size:2
Alignment explanation
Indices: 679592--679624 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
679582 AAGTATTTTA
679592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
679625 CAATATTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:690031 original size:4 final size:4
Alignment explanation
Indices: 690022--690057 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
690012 AAATAAACTG
*
690022 GAAA GAAA GAAA GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
690058 GTAATGTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:693050 original size:7 final size:7
Alignment explanation
Indices: 693035--693119 Score: 50
Period size: 7 Copynumber: 12.3 Consensus size: 7
693025 ATTTCATGTA
*
693035 TAGGATT
1 TAGGGTT
693042 TAGGGTT
1 TAGGGTT
*
693049 TAAGGTTT
1 T-AGGGTT
* *
693057 TA-AGTC
1 TAGGGTT
693063 TAGGGTT
1 TAGGGTT
*
693070 TATGGTT
1 TAGGGTT
693077 TAGGGTTT
1 TAGGG-TT
*
693085 TA-AGTT
1 TAGGGTT
*
693091 TAAGGTT
1 TAGGGTT
693098 TA-GGTT
1 TAGGGTT
* *
693104 TAAGTTT
1 TAGGGTT
693111 TAGGGTT
1 TAGGGTT
693118 TA
1 TA
693120 ATGGTATGAA
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
6 13 0.22
7 36 0.61
8 10 0.17
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:693071 original size:28 final size:27
Alignment explanation
Indices: 693035--693112 Score: 95
Period size: 28 Copynumber: 2.9 Consensus size: 27
693025 ATTTCATGTA
*
693035 TAGGATTTAGGGTTTAAGGTTTTAAGTC
1 TAGGGTTTA-GGTTTAAGGTTTTAAGTC
* *
693063 TAGGGTTTATGGTTTAGGGTTTTAAGTT
1 TAGGGTTTA-GGTTTAAGGTTTTAAGTC
*
693091 TAAGGTTTAGGTTTAA-GTTTTA
1 TAGGGTTTAGGTTTAAGGTTTTA
693113 GGGTTTAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.14
27 6 0.14
28 32 0.73
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.47
Consensus pattern (27 bp):
TAGGGTTTAGGTTTAAGGTTTTAAGTC
Found at i:693366 original size:21 final size:22
Alignment explanation
Indices: 693333--693378 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
693323 ATTAGGGTTC
* *
693333 ATTTGCCCTGGAGGAGTAGAGT
1 ATTTGCCCGGGAGGACTAGAGT
693355 ATTT-CCCGGGAGGACTAGAGT
1 ATTTGCCCGGGAGGACTAGAGT
693376 ATT
1 ATT
693379 CGATGGCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (22 bp):
ATTTGCCCGGGAGGACTAGAGT
Found at i:693501 original size:45 final size:44
Alignment explanation
Indices: 693372--693507 Score: 191
Period size: 45 Copynumber: 3.0 Consensus size: 44
693362 GGGAGGACTA
* * * * **
693372 GAGTATTCGATGGCTTGTCAAACTCAGCCTGATATCCTTCCCTT
1 GAGTATTCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
693416 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATT-CGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
*
693461 GAGTATTACGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
1 GAGTATT-CGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
693506 GA
1 GA
693508 TGAGCTATGC
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 7 0.08
45 76 0.92
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.32
Consensus pattern (44 bp):
GAGTATTCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
Found at i:696327 original size:23 final size:22
Alignment explanation
Indices: 696301--696378 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
696291 CTATAACAAC
696301 ATTAAATAACAAATCAATTAAAA
1 ATTAAATAACAAATCAA-TAAAA
*
696324 ATTAAATTAAACAAAACAA-AAAA
1 ATTAAA-T-AACAAATCAATAAAA
* *
696347 CTTAAAATAATCAAATTAAGTAACAA
1 ATT-AAATAA-CAAATCAA-TAA-AA
696373 ATTAAA
1 ATTAAA
696379 ATATTTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
22 2 0.05
23 19 0.44
24 4 0.09
25 14 0.33
26 4 0.09
ACGTcount: A:0.65, C:0.09, G:0.01, T:0.24
Consensus pattern (22 bp):
ATTAAATAACAAATCAATAAAA
Found at i:697491 original size:3 final size:3
Alignment explanation
Indices: 697485--697527 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
697475 TTACAATAAT
697485 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
697528 GAAAAGGGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:699477 original size:228 final size:228
Alignment explanation
Indices: 699080--699538 Score: 767
Period size: 228 Copynumber: 2.0 Consensus size: 228
699070 GATGGGTGTG
*
699080 AATCCACTTGATTTTCATTTACAGTCAAAATCATGGCACTTGGTGTTCTTTATTTTCAGATCGGG
1 AATCCACTTGATTTTCATTTACAGTCAAAATCATGGCACTTGGTGTTCTCTATTTTCAGATCGGG
* * *
699145 TGCTGTCTGTTTTAACCATGATGTTGCTTGTTTGCTTCCTTTCTGTGTTTAAGCTTTTTGATCTG
66 TGCTATCTGTTTTAACCATGATGCTGCTTGTTTGCTTCCTTTCTGTGTTTAAGCTTTTTAATCTG
* * * *
699210 CTCTACTTGGATCCTCTTTGGACATGCTGTTTTGGACTGTGTTTGCTTTCCCTTTGAAATTA-CA
131 CGCTACATAGATCCTCTTTGGACATGCTGTTTTGGACTGTGTTTCCTTTCCCTTTGAAA-TAGCA
*
699274 CTTTACTTTGATACACTTGTAATAAAAAATAAAT
195 CTTTACTTTAATACACTTGTAATAAAAAATAAAT
* *
699308 AATCCACTTGATTTTTATTTACAGTCAAAATCATGGTACTTGGTGTTCTCTATTTTCAGATCGGG
1 AATCCACTTGATTTTCATTTACAGTCAAAATCATGGCACTTGGTGTTCTCTATTTTCAGATCGGG
* * *
699373 TGTTATCTGTTTTAACCATGCTGCTGCTTGTTTGCTTCCTTTCTGTGTTTAAGCTTTTTAATTTG
66 TGCTATCTGTTTTAACCATGATGCTGCTTGTTTGCTTCCTTTCTGTGTTTAAGCTTTTTAATCTG
*
699438 CGCTACATAGATCCTCTTTGGACATGTTGTTTTGGACTGTGTTTCCTTTCCCTTTGAAATAGCAC
131 CGCTACATAGATCCTCTTTGGACATGCTGTTTTGGACTGTGTTTCCTTTCCCTTTGAAATAGCAC
699503 TTTACTTTAATACACTTGTAATAAAAAATAAAT
196 TTTACTTTAATACACTTGTAATAAAAAATAAAT
699536 AAT
1 AAT
699539 ATAATACATG
Statistics
Matches: 215, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
227 2 0.01
228 213 0.99
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (228 bp):
AATCCACTTGATTTTCATTTACAGTCAAAATCATGGCACTTGGTGTTCTCTATTTTCAGATCGGG
TGCTATCTGTTTTAACCATGATGCTGCTTGTTTGCTTCCTTTCTGTGTTTAAGCTTTTTAATCTG
CGCTACATAGATCCTCTTTGGACATGCTGTTTTGGACTGTGTTTCCTTTCCCTTTGAAATAGCAC
TTTACTTTAATACACTTGTAATAAAAAATAAAT
Found at i:699905 original size:17 final size:18
Alignment explanation
Indices: 699878--699914 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
699868 CCTGCATTGT
699878 ATCTCCTTTGTAATAATG
1 ATCTCCTTTGTAATAATG
*
699896 ATCT-CTTTGTTATAATG
1 ATCTCCTTTGTAATAATG
699913 AT
1 AT
699915 TTGTGTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.49
Consensus pattern (18 bp):
ATCTCCTTTGTAATAATG
Found at i:701034 original size:32 final size:32
Alignment explanation
Indices: 700997--701077 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
700987 GAAATCAAGA
* *
700997 TTGTTGGATTTTGAAATTATTATGTTTTAAAC
1 TTGTTGGATATTGAAATTATTATATTTTAAAC
* *
701029 TTGTTGGATATTGAATTTATTATATTTTAAGC
1 TTGTTGGATATTGAAATTATTATATTTTAAAC
701061 TTGTTGGATATTGAAAT
1 TTGTTGGATATTGAAAT
701078 GATTGACAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.52
Consensus pattern (32 bp):
TTGTTGGATATTGAAATTATTATATTTTAAAC
Found at i:703817 original size:35 final size:36
Alignment explanation
Indices: 703724--703826 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
703714 AATATAATCA
* *
703724 GTCACATGGCATTAAGAACATACGCACATATTTTCT
1 GTCACATGGCATAAAGAACATACCCACATATTTTCT
*
703760 GTCACATGGCATGAAGAACATACCCACATATTTT-T
1 GTCACATGGCATAAAGAACATACCCACATATTTTCT
* *
703795 GTCACATGACATAAAGATCATACCCACATATT
1 GTCACATGGCATAAAGAACATACCCACATATT
703827 CACTTTCACA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 30 0.48
36 32 0.52
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (36 bp):
GTCACATGGCATAAAGAACATACCCACATATTTTCT
Found at i:703942 original size:23 final size:23
Alignment explanation
Indices: 703907--704324 Score: 538
Period size: 23 Copynumber: 18.3 Consensus size: 23
703897 ATCTTAATTC
703907 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
703930 TTTAACCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
703953 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
703976 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
703999 TTTGAGCAAAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
704022 TTTAAGCTCAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
704045 TTTGAGCACAAATCACATCAATA
1 TTTAAGCACAAATCACATTAATA
* * *
704068 TTTAAGCATAAATTACATTAACA
1 TTTAAGCACAAATCACATTAATA
*
704091 TTTGAGCACAAAT--CA-T-ATA
1 TTTAAGCACAAATCACATTAATA
*
704110 TTTAAGCACAACTCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
704133 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
704156 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
704179 TTTGAGGACAAATGACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
704202 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
704225 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
704248 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
704271 TTTAAGCAGAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
704294 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
704317 TTTAAGCA
1 TTTAAGCA
704325 TGGATATAAG
Statistics
Matches: 342, Mismatches: 49, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
19 13 0.04
20 1 0.00
21 4 0.01
22 1 0.00
23 323 0.94
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:709098 original size:17 final size:18
Alignment explanation
Indices: 709067--709104 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
709057 TAGCATTTAG
*
709067 TGTCATTGCATTTTTATT
1 TGTCACTGCATTTTTATT
709085 TGTCACTGCA-TTTTATT
1 TGTCACTGCATTTTTATT
709102 TGT
1 TGT
709105 TAGTACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (18 bp):
TGTCACTGCATTTTTATT
Found at i:712869 original size:18 final size:18
Alignment explanation
Indices: 712846--712986 Score: 142
Period size: 18 Copynumber: 7.8 Consensus size: 18
712836 CGAAAGGAAT
*
712846 AGCATACTGGCTCATTTA
1 AGCATACTGGCTCGTTTA
* *
712864 AGCATATTGGTTCG-TTA
1 AGCATACTGGCTCGTTTA
* *
712881 GAGCATACTAGCTCGTTTG
1 -AGCATACTGGCTCGTTTA
** *
712900 AGCATACTGGCTTATTTG
1 AGCATACTGGCTCGTTTA
712918 AGCATACTGGCTCG-TTA
1 AGCATACTGGCTCGTTTA
* *
712935 GAGCATACTAGCTCGTTTG
1 -AGCATACTGGCTCGTTTA
*
712954 AGCATACTGGCTCGTTAA
1 AGCATACTGGCTCGTTTA
*
712972 AGCATACTGACTCGT
1 AGCATACTGGCTCGT
712987 AAGAGCATTA
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
17 5 0.05
18 91 0.91
19 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (18 bp):
AGCATACTGGCTCGTTTA
Found at i:712933 original size:54 final size:54
Alignment explanation
Indices: 712846--713000 Score: 229
Period size: 54 Copynumber: 2.9 Consensus size: 54
712836 CGAAAGGAAT
* *
712846 AGCATACTGGCTCATTTAAGCATATTGGTTCGTTAGAGCATACTAGCTCGTTTG
1 AGCATACTGGCTCATTTAAGCATACTGGCTCGTTAGAGCATACTAGCTCGTTTG
* *
712900 AGCATACTGGCTTATTTGAGCATACTGGCTCGTTAGAGCATACTAGCTCGTTTG
1 AGCATACTGGCTCATTTAAGCATACTGGCTCGTTAGAGCATACTAGCTCGTTTG
* * * *
712954 AGCATACTGGCTCGTTAAAGCATACTGACTCGTAAGAGCATTACTAG
1 AGCATACTGGCTCATTTAAGCATACTGGCTCGTTAGAGCA-TACTAG
713001 ATCGCAAGAG
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
54 84 0.93
55 6 0.07
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (54 bp):
AGCATACTGGCTCATTTAAGCATACTGGCTCGTTAGAGCATACTAGCTCGTTTG
Found at i:712993 original size:18 final size:18
Alignment explanation
Indices: 712917--712994 Score: 79
Period size: 18 Copynumber: 4.3 Consensus size: 18
712907 TGGCTTATTT
* *
712917 GAGCATACTGGCTCGTTA
1 GAGCATACTGACTCGTAA
**
712935 GAGCATACT-AGCTCGTTT
1 GAGCATACTGA-CTCGTAA
*
712953 GAGCATACTGGCTCGTTAA
1 GAGCATACTGACTCG-TAA
712972 -AGCATACTGACTCGTAA
1 GAGCATACTGACTCGTAA
712989 GAGCAT
1 GAGCAT
712995 TACTAGATCG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
17 3 0.06
18 46 0.92
19 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (18 bp):
GAGCATACTGACTCGTAA
Found at i:716357 original size:21 final size:24
Alignment explanation
Indices: 716316--716361 Score: 71
Period size: 21 Copynumber: 2.0 Consensus size: 24
716306 ACCCTACCCA
716316 ACCCATTGACTCGAGTTGACTTTG
1 ACCCATTGACTCGAGTTGACTTTG
716340 ACCCATTGAC-C-A-TTGACTTTG
1 ACCCATTGACTCGAGTTGACTTTG
716361 A
1 A
716362 TAGTTGACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 1 0.05
23 1 0.05
24 10 0.45
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (24 bp):
ACCCATTGACTCGAGTTGACTTTG
Found at i:724270 original size:43 final size:43
Alignment explanation
Indices: 724222--724308 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
724212 AAGAACCTCA
724222 TGGTATGCAGACTATGTGAACTATTTAACAAAATGGATGTTCC
1 TGGTATGCAGACTATGTGAACTATTTAACAAAATGGATGTTCC
*
724265 TGGTATGCAGACTATGTGAACTATTTAACAAAATGGGTGTTCC
1 TGGTATGCAGACTATGTGAACTATTTAACAAAATGGATGTTCC
724308 T
1 T
724309 AGCAAAAGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (43 bp):
TGGTATGCAGACTATGTGAACTATTTAACAAAATGGATGTTCC
Found at i:734606 original size:52 final size:52
Alignment explanation
Indices: 734528--734766 Score: 370
Period size: 52 Copynumber: 4.6 Consensus size: 52
734518 TAAATGCAAA
*
734528 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGTATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
734580 AGGTCCGATGACTATGTGTCATCGTGATTATACGAATCTTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
734632 AGGACCGATGACTATGTGTCATGGTGAGTATATGAATCTTTTACGGAGTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
** *
734684 AGGTCCGATGACTATGTGTCATTATGAGTATATGAATCCTTTTCGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
734736 AGGTCCAATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
734767 TAAATGAGAA
Statistics
Matches: 169, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 169 1.00
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:737588 original size:22 final size:21
Alignment explanation
Indices: 737549--737589 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
737539 TTTTTAAAAG
**
737549 ATAAAGACTAAGTTAAAATCT
1 ATAAAGACTAAGGGAAAATCT
737570 ATAAAGACATAAGGGAAAAT
1 ATAAAGAC-TAAGGGAAAAT
737590 ACTTGATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (21 bp):
ATAAAGACTAAGGGAAAATCT
Found at i:738770 original size:123 final size:123
Alignment explanation
Indices: 738546--738798 Score: 488
Period size: 123 Copynumber: 2.0 Consensus size: 123
738536 CAAAGATGTG
738546 TACTAATTGAAAAGTCCAAATAGGGGTTGGCTTTTTAGCTCTAGATGTATCCAAACAATGCATTA
1 TACT-ATTGAAAAGTCCAAATAGGGGTTGGCTTTTTAGCTCTAGATGTATCCAAACAATGCATTA
*
738611 GGTCATCCCTAAACACTTGAATATGCATAAATATCAATTTAATCACCCAATCTCAAAAT
65 GGTCATCCCTAAACACCTGAATATGCATAAATATCAATTTAATCACCCAATCTCAAAAT
738670 TACTATTGAAAAGTCCAAATAGGGGTTGGCTTTTTAGCTCTAGATGTATCCAAACAATGCATTAG
1 TACTATTGAAAAGTCCAAATAGGGGTTGGCTTTTTAGCTCTAGATGTATCCAAACAATGCATTAG
738735 GTCATCCCTAAACACCTGAATATGCATAAATATCAATTTAATCACCCAATCTCAAAAT
66 GTCATCCCTAAACACCTGAATATGCATAAATATCAATTTAATCACCCAATCTCAAAAT
738793 TACTAT
1 TACTAT
738799 CTATAATGTA
Statistics
Matches: 128, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
123 124 0.97
124 4 0.03
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (123 bp):
TACTATTGAAAAGTCCAAATAGGGGTTGGCTTTTTAGCTCTAGATGTATCCAAACAATGCATTAG
GTCATCCCTAAACACCTGAATATGCATAAATATCAATTTAATCACCCAATCTCAAAAT
Found at i:741448 original size:32 final size:32
Alignment explanation
Indices: 741403--741463 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
741393 AGTGTTAGTG
* * *
741403 TGCACTTCGGCACTCGTGAATAGTCTGTTCTA
1 TGCACTTCAGCACTCGAGAACAGTCTGTTCTA
741435 TGCACTTCAGCACTCGAGAACAGTCTGTT
1 TGCACTTCAGCACTCGAGAACAGTCTGTT
741464 AAATCACTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (32 bp):
TGCACTTCAGCACTCGAGAACAGTCTGTTCTA
Found at i:746512 original size:17 final size:17
Alignment explanation
Indices: 746474--746509 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
746464 ACTACAATGC
*
746474 AAATGCATTGACAAATA
1 AAATGCAGTGACAAATA
746491 AAATGCAGTGAC-AATA
1 AAATGCAGTGACAAATA
746507 AAA
1 AAA
746510 ATGTGATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.19
Consensus pattern (17 bp):
AAATGCAGTGACAAATA
Found at i:754064 original size:21 final size:22
Alignment explanation
Indices: 754018--754070 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
754008 TTGTAAGTAC
* *
754018 ATTTGATTTTGCAGATTTTGAT
1 ATTTTATTTTGCAGATTTTAAT
*
754040 ATTTTATTTTGGAGA-TTTAAT
1 ATTTTATTTTGCAGATTTTAAT
754061 ATTTTATTTT
1 ATTTTATTTT
754071 AATTAGAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.25, C:0.02, G:0.13, T:0.60
Consensus pattern (22 bp):
ATTTTATTTTGCAGATTTTAAT
Found at i:780994 original size:68 final size:68
Alignment explanation
Indices: 780885--781089 Score: 365
Period size: 68 Copynumber: 3.0 Consensus size: 68
780875 CCTGAGCTCA
* *
780885 AATCCCTACCAGAGTTCCCTGTCTTCCCTCCTATTATTAAGGAATTTACCTTATCCTCTGACCAG
1 AATCCCTACCAGAGTTCCCTGTCTTCCCACCTATTATTAAGGAATCTACCTTATCCTCTGACCAG
780950 CCT
66 CCT
*
780953 AATCCCTACCAGAGTTCCCTGTCTTCCCACCTATTATTAAGGAATCTACCTTATCCTCTGACAAG
1 AATCCCTACCAGAGTTCCCTGTCTTCCCACCTATTATTAAGGAATCTACCTTATCCTCTGACCAG
781018 CCT
66 CCT
* *
781021 AATCCCTACAAAAGTTCCCTGTCTTCCCACCTATTATTAAGGAATCTACCTTATCCTCTGACCAG
1 AATCCCTACCAGAGTTCCCTGTCTTCCCACCTATTATTAAGGAATCTACCTTATCCTCTGACCAG
781086 CCT
66 CCT
781089 A
1 A
781090 CTCTTGATGG
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 131 1.00
ACGTcount: A:0.25, C:0.34, G:0.10, T:0.32
Consensus pattern (68 bp):
AATCCCTACCAGAGTTCCCTGTCTTCCCACCTATTATTAAGGAATCTACCTTATCCTCTGACCAG
CCT
Found at i:782074 original size:64 final size:64
Alignment explanation
Indices: 781973--782102 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
781963 TTGGGGCACA
*
781973 TTTACGTTCGGGGGAATTTGTGTGAAATGGAAATGTAATTGCTCCCACATTTTTGAGAATTTAC
1 TTTACGTTCGGGGGAATTTGTGTGAAATGGAAATGTAATTGCTCCCACATTTTCGAGAATTTAC
782037 TTTACGTTCGGGGGAATTTGTGTGAAATGGAAATGTAATTGCTCCCACATTTTCGAGAATTTAC
1 TTTACGTTCGGGGGAATTTGTGTGAAATGGAAATGTAATTGCTCCCACATTTTCGAGAATTTAC
782101 TT
1 TT
782103 GTGTCTTTAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (64 bp):
TTTACGTTCGGGGGAATTTGTGTGAAATGGAAATGTAATTGCTCCCACATTTTCGAGAATTTAC
Found at i:782575 original size:17 final size:17
Alignment explanation
Indices: 782537--782596 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 17
782527 CAGTCACTTG
782537 AAAAAAGAAAATGAGAAA
1 AAAAAAGAAAA-GAGAAA
*
782555 AAGAAATA-AAAAAAGAAA
1 AA-AAA-AGAAAAGAGAAA
782573 AGAGAAAAGAAAAGAAGAAA
1 A-A-AAAAGAAAAG-AGAAA
782593 AAAA
1 AAAA
782597 TGTTCGCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
18 11 0.31
19 17 0.49
20 7 0.20
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAAAGAGAAA
Found at i:782580 original size:12 final size:12
Alignment explanation
Indices: 782539--782593 Score: 58
Period size: 12 Copynumber: 4.3 Consensus size: 12
782529 GTCACTTGAA
782539 AAAAGAAAATGAG
1 AAAAGAAAA-GAG
*
782552 AAAAAGAAATA-AA
1 -AAAAGAAA-AGAG
782565 AAAAGAAAAGAG
1 AAAAGAAAAGAG
782577 AAAAGAAAAGAAG
1 AAAAGAAAAG-AG
782590 AAAA
1 AAAA
782594 AAATGTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 1 0.03
12 19 0.53
13 7 0.19
14 8 0.22
15 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:782593 original size:25 final size:26
Alignment explanation
Indices: 782537--782584 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
782527 CAGTCACTTG
782537 AAAAAAGAAAATGAGAAAAAGAAATA
1 AAAAAAGAAAATGAGAAAAAGAAATA
782563 AAAAAAGAAAA-GAG-AAAAGAAA
1 AAAAAAGAAAATGAGAAAAAGAAA
782585 AGAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.36
25 3 0.14
26 11 0.50
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (26 bp):
AAAAAAGAAAATGAGAAAAAGAAATA
Found at i:787807 original size:14 final size:13
Alignment explanation
Indices: 787785--787815 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
787775 AGTAAATCAT
787785 TTTTCAAAAAATA
1 TTTTCAAAAAATA
787798 TTTTCTAAAAAATA
1 TTTTC-AAAAAATA
787812 TTTT
1 TTTT
787816 ACTGTCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTCAAAAAATA
Found at i:798710 original size:2 final size:2
Alignment explanation
Indices: 798703--798734 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
798693 TCTTAATTTG
*
798703 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
798735 GTATGTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:805169 original size:6 final size:6
Alignment explanation
Indices: 805149--805227 Score: 50
Period size: 6 Copynumber: 12.3 Consensus size: 6
805139 GTTGGTAAAA
* * * * *
805149 AAAGTC AAGAGTC AAAGTC AAAGTT AACGATT AAAGGTC AAAGTT AATACTC
1 AAAGTC AA-AGTC AAAGTC AAAGTC AAAG-TC AAA-GTC AAAGTC AA-AGTC
* *
805201 AAAGTC AACAGTT AAAGTC AAACTC AA
1 AAAGTC AA-AGTC AAAGTC AAAGTC AA
805228 TGGGTCAAAG
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
6 33 0.58
7 23 0.40
8 1 0.02
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (6 bp):
AAAGTC
Found at i:805189 original size:33 final size:33
Alignment explanation
Indices: 805149--805246 Score: 103
Period size: 33 Copynumber: 3.0 Consensus size: 33
805139 GTTGGTAAAA
805149 AAAGTCAAGAGTCAA-AGTCAAAGTTAACGA-TT
1 AAAGTCAA-AGTCAATAGTCAAAGTTAACGAGTT
* * *
805181 AAAGGTCAAAGTTAATACTCAAAGTCAAC-AGTT
1 AAA-GTCAAAGTCAATAGTCAAAGTTAACGAGTT
* *
805214 AAAGTCAAACTCAATGGGTCAAAGTTAACGAGT
1 AAAGTCAAAGTCAAT-AGTCAAAGTTAACGAGT
805247 CAAATCGATA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
32 19 0.36
33 31 0.58
34 3 0.06
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.22
Consensus pattern (33 bp):
AAAGTCAAAGTCAATAGTCAAAGTTAACGAGTT
Found at i:805204 original size:20 final size:19
Alignment explanation
Indices: 805160--805215 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
805150 AAGTCAAGAG
805160 TCAAAGTCAAAGTTAACGA
1 TCAAAGTCAAAGTTAACGA
* *
805179 TTAAAGGTCAAAGTTAA-TA
1 TCAAA-GTCAAAGTTAACGA
805198 CTCAAAGTCAACAGTTAA
1 -TCAAAGTCAA-AGTTAA
805216 AGTCAAACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (19 bp):
TCAAAGTCAAAGTTAACGA
Found at i:806689 original size:57 final size:59
Alignment explanation
Indices: 806623--806749 Score: 179
Period size: 57 Copynumber: 2.2 Consensus size: 59
806613 CAAATGATTT
* * * *
806623 TAAAATTATTAAAATTATTATTTTTAAATAT-AATTTTTTTAA-TTATTTTTTAAAAT-A
1 TAAAATTATTAAAATTATT-TTTTAAAATATAAAATTATTAAATTTATTTTTTAAAATAA
*
806680 TAAAATTATTAAAATTATTTTTTAAAATATAAAATTATTAAATTTATTTTTTTAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAATATAAAATTATTAAATTTATTTTTTAAAATAA
806739 TAAAATTATTA
1 TAAAATTATTA
806750 TATAATTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
56 10 0.16
57 27 0.44
58 13 0.21
59 12 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (59 bp):
TAAAATTATTAAAATTATTTTTTAAAATATAAAATTATTAAATTTATTTTTTAAAATAA
Found at i:806693 original size:16 final size:16
Alignment explanation
Indices: 806672--806721 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
806662 TAATTATTTT
806672 TTAAAATATAAAATTA
1 TTAAAATATAAAATTA
* *
806688 TTAAAAT-T--ATTTT
1 TTAAAATATAAAATTA
806701 TTAAAATATAAAATTA
1 TTAAAATATAAAATTA
806717 TTAAA
1 TTAAA
806722 TTTATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 10 0.37
14 1 0.04
15 1 0.04
16 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATAAAATTA
Found at i:806696 original size:29 final size:29
Alignment explanation
Indices: 806623--806749 Score: 168
Period size: 29 Copynumber: 4.4 Consensus size: 29
806613 CAAATGATTT
*
806623 TAAAATTATTAAAATTATTATTTTTAAATA
1 TAAAATTATTAAAATTATT-TTTTAAAATA
* **
806653 T--AATTTTTTTAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
806680 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
* *
806709 TAAAATTATTAAATTTATTTTTTTAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAAT-A
806739 TAAAATTATTA
1 TAAAATTATTA
806750 TATAATTTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.12
28 13 0.15
29 49 0.58
30 13 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:806706 original size:13 final size:13
Alignment explanation
Indices: 806631--806707 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 13
806621 TTTAAAATTA
806631 TTAAAATTATTATTT
1 TTAAAATTA-T-TTT
*
806646 TTAAATATAATTTT
1 TTAAA-ATTATTTT
*
806660 TT-TAATTATTTT
1 TTAAAATTATTTT
* *
806672 TTAAAATATAAAATTA
1 TTAAAAT-T--ATTTT
806688 TTAAAATTATTTT
1 TTAAAATTATTTT
806701 TTAAAAT
1 TTAAAAT
806708 ATAAAATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
12 9 0.18
13 14 0.29
14 6 0.12
15 7 0.14
16 13 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAAATTATTTT
Found at i:807950 original size:11 final size:12
Alignment explanation
Indices: 807932--807962 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
807922 GGAAATTAAA
807932 ATGATGAAGAAG
1 ATGATGAAGAAG
807944 A-GATGAAGAAG
1 ATGATGAAGAAG
807955 ATGATGAA
1 ATGATGAA
807963 ATTGGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
ATGATGAAGAAG
Found at i:808007 original size:30 final size:30
Alignment explanation
Indices: 807973--808039 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
807963 ATTGGAAATT
807973 AAAATTA-TTTAATAATTTTATTATTTCAAA
1 AAAATTATTTTAATAATTTTA-TATTTCAAA
* *
808003 AAAATAATTTTAATAATTTTATATTTTAAA
1 AAAATTATTTTAATAATTTTATATTTCAAA
808033 AATAATT
1 AA-AATT
808040 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
AAAATTATTTTAATAATTTTATATTTCAAA
Found at i:808033 original size:28 final size:28
Alignment explanation
Indices: 807980--808069 Score: 117
Period size: 28 Copynumber: 3.1 Consensus size: 28
807970 ATTAAAATTA
*
807980 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT--TAAAAATAAT
808011 TTTAATAATTTTATATTTTAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAATAAT
* * *
808039 TTAAAAAAATTTATATTTTAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAATAAT
808067 TTT
1 TTT
808070 GCTGACGTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 36 0.67
30 5 0.09
31 13 0.24
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTAATAATTTTATATTTTAAAAATAAT
Found at i:808061 original size:16 final size:16
Alignment explanation
Indices: 808009--808062 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
807999 CAAAAAAATA
* *
808009 ATTTTAATAATTTTAT
1 ATTTTAAAAAATTTAT
808025 ATTTT-AAAAA--TA-
1 ATTTTAAAAAATTTAT
*
808037 ATTTAAAAAAATTTAT
1 ATTTTAAAAAATTTAT
808053 ATTTTAAAAA
1 ATTTTAAAAA
808063 TAATTTTGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
12 4 0.13
13 7 0.23
15 5 0.17
16 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTTAAAAAATTTAT
Found at i:812887 original size:17 final size:17
Alignment explanation
Indices: 812864--812903 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
812854 ATAATCGTTT
812864 CTGCATTATTAATGTCA
1 CTGCATTATTAATGTCA
* * *
812881 TTGCATTTTTATTGTCA
1 CTGCATTATTAATGTCA
812898 CTGCAT
1 CTGCAT
812904 CTACATTGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (17 bp):
CTGCATTATTAATGTCA
Found at i:813971 original size:20 final size:20
Alignment explanation
Indices: 813946--813984 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
813936 ATCGTGTATC
813946 AAAAATTCCAGATCAAAAAT
1 AAAAATTCCAGATCAAAAAT
* *
813966 AAAAATTTCAGTTCAAAAA
1 AAAAATTCCAGATCAAAAA
813985 GTTTCAGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAATTCCAGATCAAAAAT
Found at i:827244 original size:78 final size:78
Alignment explanation
Indices: 827152--827341 Score: 231
Period size: 78 Copynumber: 2.4 Consensus size: 78
827142 CGATCAGAGG
* *
827152 GCAGATCT-CAGCCATCCGATCTTTTACCTCGAGCCTAGGGCAAATCACCATCAGCCAATCGCTT
1 GCAGAT-TGCAGCCATCCGATCTTTTACCCCGAGCCTAGGGCAAATCACCATCAACCAATCGCTT
827216 ACCCCAAGCATGG-
65 ACCCCAAGCATGGA
* * * *
827229 GACAGATTGCAGCCATCTGATCTTTTACCCCGAGCTTAGGGCAAATCACCATCAACTAATCTCTT
1 G-CAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGGGCAAATCACCATCAACCAATCGCTT
* *
827294 ACCCCGAGCCTGGA
65 ACCCCAAGCATGGA
* * ** *
827308 GTAGATTGCAGCCGTCTAAACTTTTACCCCGAGC
1 GCAGATTGCAGCCATCCGATCTTTTACCCCGAGC
827342 ATGGGGCTGA
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
77 2 0.02
78 95 0.97
79 1 0.01
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (78 bp):
GCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGGGCAAATCACCATCAACCAATCGCTTA
CCCCAAGCATGGA
Found at i:827296 original size:39 final size:38
Alignment explanation
Indices: 827170--827302 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
827160 CAGCCATCCG
* * * *
827170 ATCTTTTACCTCGAGCCTAGGGCAAATCACCATCAGCCA
1 ATCTCTTACCCCGAGCATAGGGCAAATCACCATCA-CTA
* * * *
827209 ATCGCTTACCCCAAGCAT-GGGACAGATTGCAGCCAT--CTG
1 ATCTCTTACCCCGAGCATAGGG-CA-AAT-CA-CCATCACTA
* *
827248 ATCTTTTACCCCGAGCTTAGGGCAAATCACCATCAACTA
1 ATCTCTTACCCCGAGCATAGGGCAAATCACCATC-ACTA
827287 ATCTCTTACCCCGAGC
1 ATCTCTTACCCCGAGC
827303 CTGGAGTAGA
Statistics
Matches: 71, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
36 4 0.06
37 2 0.03
38 5 0.07
39 49 0.69
40 5 0.07
41 2 0.03
42 4 0.06
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCATAGGGCAAATCACCATCACTA
Found at i:827549 original size:39 final size:38
Alignment explanation
Indices: 827506--827729 Score: 116
Period size: 39 Copynumber: 5.8 Consensus size: 38
827496 TGTAGTCATC
* *
827506 CAATCTTTTACCCCGAGCCTAAGGCAGATCACCTTTAG
1 CAATCTCTTACCCCGAGCCTAAGGCAGATCACCATTAG
* * ** *
827544 ACAATCTCTTACCCGGAGCTTGGGGCAGATAGTAACCATT--
1 -CAATCTCTTACCCCGAGCCTAAGGCAG--A-TCACCATTAG
* *
827584 CAATCGT-TTACCCCGAGCCTAAGGCAAATCACCATCAG
1 CAATC-TCTTACCCCGAGCCTAAGGCAGATCACCATTAG
* * * *
827622 CCAATCTCTTACCCCAAGCTTGATGCAGATTGCATCCATT--
1 -CAATCTCTTACCCCGAGCCTAAGGCAGA-T-CA-CCATTAG
* * * * ** * *
827662 CGATCTTTTATCCCGAGCTTGGGGCAGATCACTATCAG
1 CAATCTCTTACCCCGAGCCTAAGGCAGATCACCATTAG
**
827700 TCAATCTCTTACCCCGAGCCTGGGGCAGAT
1 -CAATCTCTTACCCCGAGCCTAAGGCAGAT
827730 TTCAACCATT
Statistics
Matches: 139, Mismatches: 32, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
36 9 0.06
37 3 0.02
38 2 0.01
39 110 0.79
40 2 0.01
41 3 0.02
42 10 0.07
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (38 bp):
CAATCTCTTACCCCGAGCCTAAGGCAGATCACCATTAG
Found at i:827728 original size:78 final size:78
Alignment explanation
Indices: 827411--827827 Score: 368
Period size: 78 Copynumber: 5.4 Consensus size: 78
827401 ATGAGCCTGA
** * * * * ** *
827411 GGCAGATTGCAACCATTTGATCTTTTATCCCAAGCCTGGGGCAGATCACCACCAGTTACTCTCTT
1 GGCAGATTGCAACCATTCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTT
* *
827476 ACCTCGATCTTGG
66 ACCCCGAGCTTGG
* * * ** * * * * *
827489 GGTAAATTGTAGTCATCCAATCTTTTACCCCGAGCCTAAGGCAGATCACCTTTAGACAATCTCTT
1 GGCAGATTGCAACCATTCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTT
*
827554 ACCCGGAGCTTGG
66 ACCCCGAGCTTGG
* * * * *
827567 GGCAGATAGTAACCATTCAATCGTTTACCCCGAGCCTAAGGCAAATCACCATCAGCCAATCTCTT
1 GGCAGATTGCAACCATTCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTT
* *
827632 ACCCCAAGCTTGA
66 ACCCCGAGCTTGG
* * * * * * * *
827645 TGCAGATTGCATCCATTCGATCTTTTATCCCGAGCTTGGGGCAGATCACTATCAGTCAATCTCTT
1 GGCAGATTGCAACCATTCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTT
*
827710 ACCCCGAGCCTGG
66 ACCCCGAGCTTGG
* * * * * * * * *
827723 GGCAGATTTCAACCATTCGATATTTTACCTCGATCAT-GGGTAGATCACCGTCAGCCAATCTTTT
1 GGCAGATTGCAACCATTCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTT
* * *
827787 ACCCCGTGATAGG
66 ACCCCGAGCTTGG
*
827800 GGCAGATTGCAACCATTCAATCTCTTAC
1 GGCAGATTGCAACCATTCAATCTTTTAC
827828 AAAAAAAATC
Statistics
Matches: 267, Mismatches: 72, Indels: 1
0.79 0.21 0.00
Matches are distributed among these distances:
77 55 0.21
78 212 0.79
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (78 bp):
GGCAGATTGCAACCATTCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTT
ACCCCGAGCTTGG
Found at i:827751 original size:39 final size:39
Alignment explanation
Indices: 827403--827751 Score: 107
Period size: 39 Copynumber: 8.9 Consensus size: 39
827393 GCCATTCGAT
* * * *
827403 GAGCCTGAGGCAGATTGCAACCATTTGATCTTTTATCCC
1 GAGCCTGGGGCAGATTACAACCATTCGATCTTTTACCCC
* * * * *
827442 AAGCCTGGGGCAGATCACCACCAGTT--ACTCTCTTACCTC
1 GAGCCTGGGGCAGATTACAACCA-TTCGA-TCTTTTACCCC
* * * * ** ** * *
827481 GATCTTGGGGTAAATTGTAGTCATCCAATCTTTTACCCC
1 GAGCCTGGGGCAGATTACAACCATTCGATCTTTTACCCC
** * * * *
827520 GAGCCTAAGGCAGA-T-C-ACCTTTAGACAATCTCTTACCCG
1 GAGCCTGGGGCAGATTACAACCATT---CGATCTTTTACCCC
* * * *
827559 GAGCTTGGGGCAGA-TAGTAACCATTCAATCGTTTACCCC
1 GAGCCTGGGGCAGATTA-CAACCATTCGATCTTTTACCCC
** * * * * ** * *
827598 GAGCCTAAGGCAAATCACCATCAGCCAATCTCTTACCCC
1 GAGCCTGGGGCAGATTACAACCATTCGATCTTTTACCCC
* * ** * * *
827637 AAGCTTGATGCAGATTGCATCCATTCGATCTTTTATCCC
1 GAGCCTGGGGCAGATTACAACCATTCGATCTTTTACCCC
* * * * * * *
827676 GAGCTTGGGGCAGATCACTATCAGTCAATCTCTTACCCC
1 GAGCCTGGGGCAGATTACAACCATTCGATCTTTTACCCC
* *
827715 GAGCCTGGGGCAGATTTCAACCATTCGATATTTTACC
1 GAGCCTGGGGCAGATTACAACCATTCGATCTTTTACC
827752 TCGATCATGG
Statistics
Matches: 208, Mismatches: 91, Indels: 22
0.65 0.28 0.07
Matches are distributed among these distances:
36 2 0.01
38 3 0.01
39 194 0.93
40 4 0.02
42 5 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (39 bp):
GAGCCTGGGGCAGATTACAACCATTCGATCTTTTACCCC
Found at i:833361 original size:57 final size:56
Alignment explanation
Indices: 833240--833371 Score: 147
Period size: 57 Copynumber: 2.2 Consensus size: 56
833230 GAGAAAAATT
* * *
833240 AAAAAAAAAAAGGGTCGAGATGAAAACCCGCAAAAGGTATCTTAAAACAAAAAAAA
1 AAAAAAAAAAAGAGTCAAGATGAAAACCCGCAAAAGGGATCTTAAAACAAAAAAAA
* * *
833296 AAAGAAAAAACAGAGTCAAGATGAAAACTCGCAAAGTGGGATCTTAAAACCCAAAGAAAGAA
1 AAA-AAAAAAAAGAGTCAAGATGAAAACCCGCAAA-AGGGATCTTAAAA--CAAA-AAA-AA
833358 AAAAAAGAAAAAGA
1 AAAAAA-AAAAAGA
833372 TGGAAAAAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
56 3 0.05
57 27 0.44
58 11 0.18
60 4 0.06
61 6 0.10
62 11 0.18
ACGTcount: A:0.61, C:0.12, G:0.17, T:0.10
Consensus pattern (56 bp):
AAAAAAAAAAAGAGTCAAGATGAAAACCCGCAAAAGGGATCTTAAAACAAAAAAAA
Found at i:835379 original size:99 final size:99
Alignment explanation
Indices: 835116--835621 Score: 386
Period size: 99 Copynumber: 5.1 Consensus size: 99
835106 ACACCAGCTA
* * * * * *
835116 AACACCAAATCCTATACCCTTAAAGTTGCAGTGGATCAGATTAAAACAAGTAGCAGATCTTAATA
1 AACACCAAATCCTATACCCTTAAAGTTGTAATGGGTCAGATTAAAACAAGAAGAAGATCTCAATA
* *
835181 TCCCTGAGGTTACAATGGAATGGAGTGAAGATAC
66 TCCCTGAGGTTACAGTGGAATGGAGTGAAGTTAC
* * * * ** * * * * *
835215 TACACCAACTTCTATACCCTTAAAATTACAAAAGGG-CGGAGTAAACCAAGTAATG--GATCTTA
1 AACACCAAATCCTATACCCTTAAAGTT-GTAATGGGTCAGATTAAAACAAG-AA-GAAGATCTCA
* *
835277 ATGTCCCTAAGGTTACAGTGGAATGGAGTGAAGTTAC
63 ATATCCCTGAGGTTACAGTGGAATGGAGTGAAGTTAC
* * * * * * *
835314 AACACTAAATCCTATACCCTTGAAGTTGTAGTGGGTCAGATTAAAGCCAGAAGAAGTTCTCAATG
1 AACACCAAATCCTATACCCTTAAAGTTGTAATGGGTCAGATTAAAACAAGAAGAAGATCTCAATA
*
835379 TCCCTGAGGTTACAGTGGAATTGAGTGAAGCTT-C
66 TCCCTGAGGTTACAGTGGAATGGAGTGAAG-TTAC
* * * * * *
835413 AACAACAAATCCTAT-CTTCC-TGAAGCTGTAATGAAGT-AGATTAAAACAAGTAGCAGATCTCA
1 AACACCAAATCCTATAC--CCTTAAAGTTGTAATG-GGTCAGATTAAAACAAGAAGAAGATCTCA
* * * *
835475 ATATCCTTGAGGTTACAGTGGAATGGAGAGAAGCTAT
63 ATATCCCTGAGGTTACAGTGGAATGGAGTGAAGTTAC
* * * * * ** *
835512 TACACCAACTCTTATACCCTTAAAATTATAA-AAGTGC-GAAGTAAAACAAGTAACG--GATCTC
1 AACACCAAATCCTATACCCTTAAAGTTGTAATGGGT-CAG-ATTAAAACAAG-AA-GAAGATCTC
* * *
835573 AATGTCCCTGAGATTACAGTGGAATAGAGTGAAGTTAC
62 AATATCCCTGAGGTTACAGTGGAATGGAGTGAAGTTAC
835611 AACACCAAATC
1 AACACCAAATC
835622 TATTACACCT
Statistics
Matches: 318, Mismatches: 71, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
97 4 0.01
98 11 0.03
99 289 0.91
100 12 0.04
101 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (99 bp):
AACACCAAATCCTATACCCTTAAAGTTGTAATGGGTCAGATTAAAACAAGAAGAAGATCTCAATA
TCCCTGAGGTTACAGTGGAATGGAGTGAAGTTAC
Found at i:835817 original size:49 final size:49
Alignment explanation
Indices: 835648--836169 Score: 390
Period size: 49 Copynumber: 10.6 Consensus size: 49
835638 ATAGAGGGGC
* ** * **
835648 AGATTGAAGCTGCAAGGGCGAATCTTATACCCTTA-AAGCTGT-AAAAGAA
1 AGATTGAAGCCGCAACAGCGAATCTTATA-CCTTAGAA-ATGTGAAGGGAA
* ** * * *
835697 CAAATTGAAGCCGCAAGGGTGAATCTAATATACC-TAGAGATGTGAAGAGAA
1 -AGATTGAAGCCGCAACAGCGAATCT--TATACCTTAGAAATGTGAAGGGAA
* * *
835748 AGATTGAAGCCACAATAGCGAATCTTATACCTTAGAAATGTGGAGGGAA
1 AGATTGAAGCCGCAACAGCGAATCTTATACCTTAGAAATGTGAAGGGAA
* * *
835797 ATATTGAAACCGCAACAGCGAATCTTATACCTTA-AAGGTGTGAAGGGAA
1 AGATTGAAGCCGCAACAGCGAATCTTATACCTTAGAA-ATGTGAAGGGAA
* ** * *
835846 AGATTAAAGCCGCAACAATGAATCTTATA-CTCTAGAGATGTGGAGGGAA
1 AGATTGAAGCCGCAACAGCGAATCTTATACCT-TAGAAATGTGAAGGGAA
* * * *
835895 AGATTGAAACCGCAA-TGACGAATAC-TATACCCTAGAGATGTGAAGGGAA
1 AGATTGAAGCCGCAACAG-CGAAT-CTTATACCTTAGAAATGTGAAGGGAA
* * * * *
835944 AGATTGAAGCTGGAACGGTGAATCTTATACCCTA-AATATGTGAAGGGAA
1 AGATTGAAGCCGCAACAGCGAATCTTATACCTTAGAA-ATGTGAAGGGAA
* * *
835993 AGATTGAAGTCGCAAC-GACGAATCTTATAACC-TAGAGATGTGGAGGGAA
1 AGATTGAAGCCGCAACAG-CGAATCTTAT-ACCTTAGAAATGTGAAGGGAA
* * *
836042 AGATTGAAGCCGTAAC-GATGAATCTTATACCTCA-AAGATGTGAAGGGAA
1 AGATTGAAGCCGCAACAG-CGAATCTTATACCTTAGAA-ATGTGAAGGGAA
* ** * **
836091 AGATTGAAGCCACAATGGCGAATCTTATATCC-TAAAAATAAGAAGGGAA
1 AGATTGAAGCCGCAACAGCGAATCTTATA-CCTTAGAAATGTGAAGGGAA
836140 AGATTGAAGCCGC-ACTTA-CGAATCTTATAC
1 AGATTGAAGCCGCAAC--AGCGAATCTTATAC
836170 ACTGAAGATG
Statistics
Matches: 385, Mismatches: 63, Indels: 50
0.77 0.13 0.10
Matches are distributed among these distances:
48 19 0.05
49 293 0.76
50 60 0.16
51 9 0.02
52 4 0.01
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (49 bp):
AGATTGAAGCCGCAACAGCGAATCTTATACCTTAGAAATGTGAAGGGAA
Found at i:835869 original size:98 final size:97
Alignment explanation
Indices: 835667--836153 Score: 453
Period size: 98 Copynumber: 4.9 Consensus size: 97
835657 CTGCAAGGGC
* ** * * * **
835667 GAATCTTATACCCTTAAAGCTGT-AAAAGAACAAATTGAAGCCGCAAGGGTGAATCTAATATACC
1 GAATCTTATA-CCTTAAAGATGTGAAGGGAA-AGATTGAAACCGCAACGACGAATCT--TATACC
* * * * **
835731 TAGAGATGTGAAGAGAAAGATTGAAGCCACAATAGC
62 TAAAGATGTGAAGGGAAAGATTGAAGCCGCAACAAT
* *
835767 GAATCTTATACCTTAGAA-ATGTGGAGGGAAATATTGAAACCGCAAC-AGCGAATCTTATACCTT
1 GAATCTTATACCTTA-AAGATGTGAAGGGAAAGATTGAAACCGCAACGA-CGAATCTTATACC-T
* *
835830 AAAGGTGTGAAGGGAAAGATTAAAGCCGCAACAAT
63 AAAGATGTGAAGGGAAAGATTGAAGCCGCAACAAT
* * *
835865 GAATCTTATA-CTCTAGAGATGTGGAGGGAAAGATTGAAACCGCAATGACGAATAC-TATACCCT
1 GAATCTTATACCT-TAAAGATGTGAAGGGAAAGATTGAAACCGCAACGACGAAT-CTTATA-CCT
* * * **
835928 AGAGATGTGAAGGGAAAGATTGAAGCTGGAACGGT
63 AAAGATGTGAAGGGAAAGATTGAAGCCGCAACAAT
* * ** *
835963 GAATCTTATACCCTAAATATGTGAAGGGAAAGATTGAAGTCGCAACGACGAATCTTATAACCTAG
1 GAATCTTATACCTTAAAGATGTGAAGGGAAAGATTGAAACCGCAACGACGAATCTTAT-ACCTAA
* * *
836028 AGATGTGGAGGGAAAGATTGAAGCCGTAACGAT
65 AGATGTGAAGGGAAAGATTGAAGCCGCAACAAT
* * * * *
836061 GAATCTTATACCTCAAAGATGTGAAGGGAAAGATTGAAGCCACAATGGCGAATCTTATATCCTAA
1 GAATCTTATACCTTAAAGATGTGAAGGGAAAGATTGAAACCGCAACGACGAATCTTATA-CCTAA
* **
836126 AAATAAGAAGGGAAAGATTGAAGCCGCA
65 AGATGTGAAGGGAAAGATTGAAGCCGCA
836154 CTTACGAATC
Statistics
Matches: 323, Mismatches: 51, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
97 11 0.03
98 263 0.81
99 33 0.10
100 16 0.05
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (97 bp):
GAATCTTATACCTTAAAGATGTGAAGGGAAAGATTGAAACCGCAACGACGAATCTTATACCTAAA
GATGTGAAGGGAAAGATTGAAGCCGCAACAAT
Found at i:835917 original size:147 final size:147
Alignment explanation
Indices: 835648--836299 Score: 558
Period size: 147 Copynumber: 4.4 Consensus size: 147
835638 ATAGAGGGGC
* * * ** *
835648 AGATTGAAGCTGCAAGGGCGAATCTTATACCCTTAAAGCTGT-AAAAGAACAAATTGAAGCCGCA
1 AGATTGAAGCCGCAACGGCGAATCTTATACCCTTAAAGATGTGAAGGGAA-AGATTGAAGCCGCA
* * * * *
835712 AGGGTGAATCTAATATACCTAGAGATGTGAAGAGAAAGATTGAAGCCACAAT-AGCGAATCTTAT
65 ACGATGAATCT--TATACCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGA-CGAATCTTAT
*
835776 ACCTTAGAAATGTGGAGGGAA
127 ACCTTAGAAATGTGAAGGGAA
* * * * *
835797 ATATTGAAACCGCAACAGCGAATCTTATA-CCTTAAAGGTGTGAAGGGAAAGATTAAAGCCGCAA
1 AGATTGAAGCCGCAACGGCGAATCTTATACCCTTAAAGATGTGAAGGGAAAGATTGAAGCCGCAA
* *
835861 CAATGAATCTTATACTCTAGAGATGTGGAGGGAAAGATTGAAACCGCAATGACGAATAC-TATAC
66 CGATGAATCTTATAC-CTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGACGAAT-CTTATAC
* *
835925 CCTAGAGATGTGAAGGGAA
129 CTTAGAAATGTGAAGGGAA
* * * * *
835944 AGATTGAAGCTGGAACGGTGAATCTTATACCC-TAAATATGTGAAGGGAAAGATTGAAGTCGCAA
1 AGATTGAAGCCGCAACGGCGAATCTTATACCCTTAAAGATGTGAAGGGAAAGATTGAAGCCGCAA
* * * *
836008 CGACGAATCTTATAACCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAACGATGAATCTTATACC
66 CGATGAATCTTAT-ACCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGACGAATCTTATACC
*
836073 TCA-AAGATGTGAAGGGAA
130 TTAGAA-ATGTGAAGGGAA
* * * * **
836091 AGATTGAAGCCACAATGGCGAATCTTATATCC-TAAAAATAAGAAGGGAAAGATTGAAGCCGC-A
1 AGATTGAAGCCGCAACGGCGAATCTTATACCCTTAAAGATGTGAAGGGAAAGATTGAAGCCGCAA
* * * * * *** * **
836154 CTTACGAATCTTATACACT-GAAGATGAGGAGATGCAA-ATTGAAGTTACAAAGGTGAATCTTAT
66 C-GATGAATCTTATAC-CTAG-AGATGTGGAG-GGAAAGATTGAAGCCGCAATGACGAATCTTAT
* ** *
836217 A-CTCTAAAAGATGAAAAAGGG-C
127 ACCT-TAGAA-ATG-TGAAGGGAA
** *
836239 AGATTGAAGCTACAACGGCAAATCTTATACCC-TAAGAGATGT-AGAGGGAAAGATTGAAGCC
1 AGATTGAAGCCGCAACGGCGAATCTTATACCCTTAA-AGATGTGA-AGGGAAAGATTGAAGCC
836300 ATAACGGCAA
Statistics
Matches: 416, Mismatches: 70, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
146 14 0.03
147 270 0.65
148 78 0.19
149 54 0.13
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (147 bp):
AGATTGAAGCCGCAACGGCGAATCTTATACCCTTAAAGATGTGAAGGGAAAGATTGAAGCCGCAA
CGATGAATCTTATACCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGACGAATCTTATACCT
TAGAAATGTGAAGGGAA
Found at i:837717 original size:2 final size:2
Alignment explanation
Indices: 837712--837740 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
837702 TTTATAATCA
837712 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 A
837741 ATTATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:837788 original size:13 final size:14
Alignment explanation
Indices: 837770--837798 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
837760 ATCCTTTCAT
837770 ATTTTTTAAA-TTA
1 ATTTTTTAAACTTA
837783 ATTTTTTAAACTTA
1 ATTTTTTAAACTTA
837797 AT
1 AT
837799 CCCATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTTTAAACTTA
Found at i:838850 original size:3 final size:3
Alignment explanation
Indices: 838844--838874 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
838834 GTATGTGTTG
*
838844 TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
838875 AGTTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:840159 original size:17 final size:17
Alignment explanation
Indices: 840123--840187 Score: 76
Period size: 18 Copynumber: 3.7 Consensus size: 17
840113 CGAACTCCCT
840123 TTAAATTTATTTTAAAAA
1 TTAAATTTA-TTTAAAAA
* *
840141 TTAAATTTGTTTGAAAAT
1 TTAAATTTATTT-AAAAA
* *
840159 TTAAATTTATTTTAAAT
1 TTAAATTTATTTAAAAA
840176 TTAAATTTATTT
1 TTAAATTTATTT
840188 TGAATTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
17 19 0.45
18 23 0.55
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTAAAAA
Found at i:840166 original size:6 final size:6
Alignment explanation
Indices: 840155--840250 Score: 67
Period size: 6 Copynumber: 16.7 Consensus size: 6
840145 ATTTGTTTGA
* * * *
840155 AAATTT AAATTT -ATTTT AAATTT AAATTT -ATTTT GAATTC AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * * *
840201 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAAATT -ACTAT AAATTT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT
840247 AAAT
1 AAAT
840251 AAAGCTAAAA
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
5 19 0.28
6 44 0.66
7 4 0.06
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:840188 original size:17 final size:17
Alignment explanation
Indices: 840122--840250 Score: 141
Period size: 17 Copynumber: 7.4 Consensus size: 17
840112 CCGAACTCCC
840122 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
840140 ATTAAATTTGTTTGAAAA
1 TTTAAATTTATTT-TAAA
840158 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
840175 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
* * *
840192 TTCAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
840209 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* * *
840227 TTTAAAATTACTATAAA
1 TTTAAATTTATTTTAAA
840244 TTTAAAT
1 TTTAAAT
840251 AAAGCTAAAA
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
17 53 0.58
18 38 0.42
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:840640 original size:29 final size:29
Alignment explanation
Indices: 840605--840666 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
840595 AAACAAAAAA
*
840605 GAATGATAACTATATAGGCTATAAAAGTC
1 GAATGATAACTATATAGGCTATAAAAGCC
*
840634 GAATGATGACTATATAGGCTATAAAAGCC
1 GAATGATAACTATATAGGCTATAAAAGCC
840663 GAAT
1 GAAT
840667 TCATTTCGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (29 bp):
GAATGATAACTATATAGGCTATAAAAGCC
Found at i:842135 original size:30 final size:30
Alignment explanation
Indices: 842082--842451 Score: 204
Period size: 30 Copynumber: 12.5 Consensus size: 30
842072 AAAATCTCAT
*
842082 TTTTGACCTCGAACC-TT-CTAAAATTACCA
1 TTTTGACCCCGAACCTTTAC-AAAATTACCA
842111 TTTT-ACCCCGAACCTTATACAAAATTACCA
1 TTTTGACCCCGAACCTT-TACAAAATTACCA
*
842141 TTTTGACCCCAAACCTTCTA-AAAATTACCA
1 TTTTGACCCCGAACCTT-TACAAAATTACCA
* * * * *
842171 TTTT-ACCCCCAAAC-TTCCAAAAATCCCA
1 TTTTGACCCCGAACCTTTACAAAATTACCA
* * *
842199 TTTTCAACCCCAAACC-TTCCAAAATTACCA
1 TTTT-GACCCCGAACCTTTACAAAATTACCA
* * * *
842229 TTTT-ACCCTTGAACC--TCCAAAAATCCCA
1 TTTTGACCC-CGAACCTTTACAAAATTACCA
* ** *
842257 TTTTTAACCCTAAACCTTCTAAAAAATTACCA
1 -TTTTGACCCCGAACCTT-TACAAAATTACCA
* * *
842289 TTTT-ACCCCCGAA-C-TTCCAAAAATCCCA
1 TTTTGA-CCCCGAACCTTTACAAAATTACCA
842317 TTTTTGACCCCGAACCTTTTA-AAAATTACCA
1 -TTTTGACCCCGAACC-TTTACAAAATTACCA
*** *
842348 TTTTTGACCTTAAAACTTCTA-AAAATTACCA
1 -TTTTGACCCCGAACCTT-TACAAAATTACCA
* * *
842379 TTTT-ACCCTCGAA-C-TTCCAAAAATCCCA
1 TTTTGACCC-CGAACCTTTACAAAATTACCA
842407 TTTTTGACCCCGAACCTTT-CAAAAATTACCA
1 -TTTTGACCCCGAACCTTTAC-AAAATTACCA
842438 TTTT-ACCCTCGAAC
1 TTTTGACCC-CGAAC
842452 TTCCAAAAAT
Statistics
Matches: 271, Mismatches: 42, Indels: 55
0.74 0.11 0.15
Matches are distributed among these distances:
27 2 0.01
28 55 0.20
29 54 0.20
30 84 0.31
31 65 0.24
32 11 0.04
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (30 bp):
TTTTGACCCCGAACCTTTACAAAATTACCA
Found at i:842163 original size:59 final size:58
Alignment explanation
Indices: 842066--842505 Score: 328
Period size: 59 Copynumber: 7.4 Consensus size: 58
842056 AGTCCCTGAA
* *
842066 CTTCCAAAAAT-CTCATTTTTGACCTCGAACCTTCT-AAAATTACCATTTTACCCCGAAC
1 CTTCCAAAAATAC-CA-TTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCCCGAAC
* * * *
842124 CTTATACAAAATTACCATTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCCCCAAA
1 C-T-TCCAAAAATACCATTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCCCGAAC
* * * *
842184 CTTCCAAAAATCCCATTTTCAACCCCAAACCTTC-CAAAATTACCATTTTACCCTTGAAC
1 CTTCCAAAAATACCATTTT-GACCCCAAACCTTCTAAAAATTACCATTTTACCC-CGAAC
* * *
842243 C-TCCAAAAATCCCATTTTTAACCCTAAACCTTCTAAAAAATTACCATTTTACCCCCGAA-
1 CTTCCAAAAATACCA-TTTTGACCCCAAACCTTCT-AAAAATTACCATTTTA-CCCCGAAC
* * * *** *
842302 CTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTTTGACCTTAAAA
1 CTTCCAAAAATACCA-TTTTGACCCCAAACCTTCTAAAAATTACCA-TTTT-ACCCCGAAC
* * * *
842363 CTTCTAAAAATTACCATTTT-ACCCTCGAA-CTTCCAAAAA-TCCCATTTTTGACCCCGAAC
1 CTTCCAAAAA-TACCATTTTGACCC-CAAACCTTCTAAAAATTACCA-TTTT-ACCCCGAAC
* * * *
842422 CTTTCAAAAATTACCATTTT-ACCCTCGAA-CTTCCAAAAA-T-CTCATTTTTTACTCCGAAC
1 CTTCCAAAAA-TACCATTTTGACCC-CAAACCTTCTAAAAATTAC-CA--TTTTACCCCGAAC
* * *
842481 CATCCAAAACTACCATTTTGCCCCC
1 CTTCCAAAAATACCATTTTGACCCC
842506 GTGCATCCGA
Statistics
Matches: 323, Mismatches: 40, Indels: 38
0.81 0.10 0.09
Matches are distributed among these distances:
58 70 0.22
59 124 0.38
60 103 0.32
61 22 0.07
62 4 0.01
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (58 bp):
CTTCCAAAAATACCATTTTGACCCCAAACCTTCTAAAAATTACCATTTTACCCCGAAC
Found at i:842234 original size:118 final size:118
Alignment explanation
Indices: 842064--842351 Score: 384
Period size: 118 Copynumber: 2.4 Consensus size: 118
842054 GAAGTCCCTG
* * *
842064 AACTTCCAAAAATCTCATTTTTGACCTCGAACCTTCTAAAATTACCATTTTACCC-CGAACCTTA
1 AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAATTACCATTTTACCCTCGAACC---
* *
842128 TACAAAATTACCA-TTTTGACCCCAAACCTTCT-AAAAATTACCATTTTACCCCCA
63 TACAAAAATACCATTTTTAACCCCAAACCTTCTAAAAAATTACCATTTTACCCCCA
** * * * *
842182 AACTTCCAAAAATCCCATTTTCAACCCCAAACCTTCCAAAATTACCATTTTACCCTTGAACCTCC
1 AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAATTACCATTTTACCCTCGAACCTAC
* * *
842247 AAAAATCCCATTTTTAACCCTAAACCTTCTAAAAAATTACCATTTTACCCCCG
66 AAAAATACCATTTTTAACCCCAAACCTTCTAAAAAATTACCATTTTACCCCCA
*
842300 AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTTAAAAATTACCATTTT
1 AACTTCCAAAAATCCCATTTTTGACCCCGAACC-TTCAAAAATTACCATTTT
842352 TGACCTTAAA
Statistics
Matches: 148, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
116 10 0.07
117 17 0.11
118 100 0.68
119 21 0.14
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (118 bp):
AACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAATTACCATTTTACCCTCGAACCTAC
AAAAATACCATTTTTAACCCCAAACCTTCTAAAAAATTACCATTTTACCCCCA
Found at i:842375 original size:90 final size:90
Alignment explanation
Indices: 842066--842441 Score: 362
Period size: 90 Copynumber: 4.2 Consensus size: 90
842056 AGTCCCTGAA
* * *
842066 CTTCCAAAAA-T-CTCATTTTTGACCTCGAACCTTCT-AAAATTACCATTTTA-CCCCGAACCTT
1 CTTCCAAAAATTAC-CATTTTTGACCCCAAAACTTCTAAAAATTACCATTTTACCCCCGAACC-T
* * *
842127 ATACAAAATTACCATTTTGACCCCAAAC
64 -TCCAAAAATACCATTTTGACCCCGAAC
* * * * * *
842155 CTTCTAAAAATTACCA-TTTT-ACCCCCAAACTTCCAAAAA-TCCCATTTTCAACCCCAAACCTT
1 CTTCCAAAAATTACCATTTTTGACCCCAAAACTTCTAAAAATTACCATTTT-ACCCCCGAACCTT
* *
842217 CCAAAATTACCATTTT-ACCCTTGAAC
65 CCAAAAATACCATTTTGACCC-CGAAC
* * * *
842243 C-TCCAAAAA-TCCCATTTTTAACCCTAAACCTTCTAAAAAATTACCATTTTACCCCCGAA-CTT
1 CTTCCAAAAATTACCATTTTTGACCCCAAAACTTCT-AAAAATTACCATTTTACCCCCGAACCTT
*
842305 CCAAAAATCCCATTTTTGACCCCGAAC
65 CCAAAAATACCA-TTTTGACCCCGAAC
** ** *
842332 CTTTTAAAAATTACCATTTTTGACCTTAAAACTTCTAAAAATTACCATTTTACCCTCGAA-CTTC
1 CTTCCAAAAATTACCATTTTTGACCCCAAAACTTCTAAAAATTACCATTTTACCCCCGAACCTTC
*
842396 CAAAAATCCCATTTTTGACCCCGAAC
66 CAAAAATACCA-TTTTGACCCCGAAC
*
842422 CTTTCAAAAATTACCATTTT
1 CTTCCAAAAATTACCATTTT
842442 ACCCTCGAAC
Statistics
Matches: 243, Mismatches: 30, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
86 4 0.02
87 15 0.06
88 61 0.25
89 40 0.16
90 101 0.42
91 22 0.09
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.32
Consensus pattern (90 bp):
CTTCCAAAAATTACCATTTTTGACCCCAAAACTTCTAAAAATTACCATTTTACCCCCGAACCTTC
CAAAAATACCATTTTGACCCCGAAC
Found at i:842487 original size:30 final size:30
Alignment explanation
Indices: 842066--842489 Score: 160
Period size: 30 Copynumber: 14.3 Consensus size: 30
842056 AGTCCCTGAA
* *
842066 CTTCCAAAAATCTCATTTTTGACCTCGAAC
1 CTTCCAAAAATCTCATTTTTTACCCCGAAC
* *
842096 CTTCTAAAATTAC-CA--TTTTACCCCGAAC
1 CTTCCAAAAAT-CTCATTTTTTACCCCGAAC
** * *
842124 CTTATACAAAAT-TACCA-TTTTGACCCCAAAC
1 CTTCCA-AAAATCT--CATTTTTTACCCCGAAC
* * *
842155 CTTCTAAAAAT-TACCA--TTTTACCCCCAAA
1 CTTCCAAAAATCT--CATTTTTTACCCCGAAC
* ** *
842184 CTTCCAAAAATCCCATTTTCAACCCCAAAC
1 CTTCCAAAAATCTCATTTTTTACCCCGAAC
* *
842214 CTTCCAAAATTAC-CA--TTTTACCCTTGAAC
1 CTTCCAAAAAT-CTCATTTTTTACCC-CGAAC
* * **
842243 C-TCCAAAAATCCCATTTTTAACCCTAAAC
1 CTTCCAAAAATCTCATTTTTTACCCCGAAC
*
842272 CTTCTAAAAAAT-TACCA--TTTTACCCCCGAA-
1 CTTC-CAAAAATCT--CATTTTTTA-CCCCGAAC
* *
842302 CTTCCAAAAATCCCATTTTTGACCCCGAAC
1 CTTCCAAAAATCTCATTTTTTACCCCGAAC
** * *** *
842332 CTTTTAAAAAT-TACCATTTTTGACCTTAAAA
1 CTTCCAAAAATCT--CATTTTTTACCCCGAAC
*
842363 CTTCTAAAAAT-TACCA--TTTTACCCTCGAA-
1 CTTCCAAAAATCT--CATTTTTTACCC-CGAAC
* *
842392 CTTCCAAAAATCCCATTTTTGACCCCGAAC
1 CTTCCAAAAATCTCATTTTTTACCCCGAAC
*
842422 CTTTCAAAAAT-TACCA--TTTTACCCTCGAA-
1 CTTCCAAAAATCT--CATTTTTTACCC-CGAAC
*
842451 CTTCCAAAAATCTCATTTTTTACTCCGAAC
1 CTTCCAAAAATCTCATTTTTTACCCCGAAC
*
842481 CATCCAAAA
1 CTTCCAAAA
842490 CTACCATTTT
Statistics
Matches: 302, Mismatches: 55, Indels: 74
0.70 0.13 0.17
Matches are distributed among these distances:
27 1 0.00
28 40 0.13
29 87 0.29
30 113 0.37
31 59 0.20
32 2 0.01
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (30 bp):
CTTCCAAAAATCTCATTTTTTACCCCGAAC
Done.