Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 123 of 163
Found at i:33959281 original size:24 final size:24
Alignment explanation
Indices: 33959195--33959269 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
33959185 AGAAATAATC
*
33959195 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
33959219 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
33959243 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
33959267 TTT
1 TTT
33959270 GAGTCAAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:33962029 original size:15 final size:15
Alignment explanation
Indices: 33962009--33962039 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33961999 GCATTTGAGC
33962009 TTGACCACTGCAGGT
1 TTGACCACTGCAGGT
33962024 TTGACCACTGCAGGT
1 TTGACCACTGCAGGT
33962039 T
1 T
33962040 GCTATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (15 bp):
TTGACCACTGCAGGT
Found at i:33964304 original size:45 final size:43
Alignment explanation
Indices: 33964248--33964366 Score: 163
Period size: 45 Copynumber: 2.8 Consensus size: 43
33964238 ATGTAGGGTA
33964248 TTTTTTTGGGTAATGTGTGATGCGTAAAATATACAT-GGGTATTTT
1 TTTTTTTGGGTAATGTGTGATGCGTAAAATAT-CATCGGGTA--TT
*
33964293 TTTTTTTGGGTAATGTGTGATGCGTAAAATATCCTCGGGTATT
1 TTTTTTTGGGTAATGTGTGATGCGTAAAATATCATCGGGTATT
* *
33964336 TCTTTTTGGGTAA--TGTGATGCGTAAGATATC
1 TTTTTTTGGGTAATGTGTGATGCGTAAAATATC
33964367 CACTTTTTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
41 17 0.24
43 14 0.20
44 2 0.03
45 37 0.53
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.45
Consensus pattern (43 bp):
TTTTTTTGGGTAATGTGTGATGCGTAAAATATCATCGGGTATT
Found at i:33973396 original size:19 final size:19
Alignment explanation
Indices: 33973356--33973397 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
33973346 ATCCTAAGTT
*
33973356 TCTTCAATTATATTTTCAA
1 TCTTCAATTATATGTTCAA
*
33973375 TCTT-AATTATTATGTTCTA
1 TCTTCAATTA-TATGTTCAA
33973394 TCTT
1 TCTT
33973398 TCTATTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.57
Consensus pattern (19 bp):
TCTTCAATTATATGTTCAA
Found at i:33976655 original size:16 final size:18
Alignment explanation
Indices: 33976628--33976660 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33976618 TATGATTGGG
33976628 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
33976645 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
33976661 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:33978450 original size:20 final size:19
Alignment explanation
Indices: 33978423--33978460 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
33978413 ATGTTTAAAC
33978423 TTAATAAA-TATTAATTAAT
1 TTAATAAACTA-TAATTAAT
33978442 TTAATTAAACTATAATTAA
1 TTAA-TAAACTATAATTAA
33978461 CAAATACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 11 0.65
21 2 0.12
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAATAAACTATAATTAAT
Found at i:33980457 original size:27 final size:27
Alignment explanation
Indices: 33980419--33980471 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
33980409 GTCGAGAAGC
* *
33980419 ATATAAAAAATATAATAAAGGAAAGAG
1 ATATAAAAAATAGAATAAAGAAAAGAG
*
33980446 ATATAAAGAATAGAATAAAGAAAAGA
1 ATATAAAAAATAGAATAAAGAAAAGA
33980472 CATGCTCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (27 bp):
ATATAAAAAATAGAATAAAGAAAAGAG
Found at i:33981685 original size:21 final size:21
Alignment explanation
Indices: 33981659--33981699 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
33981649 TTACACAAAT
33981659 CAAACATATTGTTAGATTCCC
1 CAAACATATTGTTAGATTCCC
33981680 CAAACATATTGTTAGATTCC
1 CAAACATATTGTTAGATTCC
33981700 TCATGACACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (21 bp):
CAAACATATTGTTAGATTCCC
Found at i:33998684 original size:12 final size:12
Alignment explanation
Indices: 33998659--33998691 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
33998649 CTTATCAAGA
33998659 TAAATATTAAAT
1 TAAATATTAAAT
33998671 TAAAT-TTAATAT
1 TAAATATTAA-AT
33998683 TAAATATTA
1 TAAATATTA
33998692 TTAAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 12 0.63
13 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:33998707 original size:19 final size:18
Alignment explanation
Indices: 33998683--33998749 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 18
33998673 AATTTAATAT
33998683 TAAATATTATTAAATTAA
1 TAAATATTATTAAATTAA
33998701 TAGAATATTTATCTACAA--AA
1 TA-AATA-TTAT-TA-AATTAA
33998721 T-AA-A-TATTAAATTAA
1 TAAATATTATTAAATTAA
33998736 TAAAATATTATTAA
1 T-AAATATTATTAA
33998750 GATCATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 19
0.67 0.00 0.33
Matches are distributed among these distances:
13 2 0.05
14 2 0.05
15 6 0.15
17 3 0.08
18 5 0.13
19 10 0.26
20 7 0.18
21 2 0.05
22 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (18 bp):
TAAATATTATTAAATTAA
Found at i:33998743 original size:54 final size:57
Alignment explanation
Indices: 33998631--33998749 Score: 147
Period size: 59 Copynumber: 2.1 Consensus size: 57
33998621 ATCACTTTAA
* *
33998631 TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATAT
1 TATTAAATTAATAGAATACTTATCAACATAAATA-TAAATTAAATTTAATA-TAAATAT
* *
33998690 TATTAAATTAATAGAATATTTATCTACA-AAATA-AATATTAAA-TTAATA-AAATAT
1 TATTAAATTAATAGAATACTTATCAACATAAATATAA-ATTAAATTTAATATAAATAT
33998744 TATTAA
1 TATTAA
33998750 GATCATTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
54 12 0.22
56 8 0.15
57 6 0.11
58 5 0.09
59 24 0.44
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (57 bp):
TATTAAATTAATAGAATACTTATCAACATAAATATAAATTAAATTTAATATAAATAT
Found at i:34000183 original size:30 final size:31
Alignment explanation
Indices: 34000147--34000204 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
34000137 AATAATATGT
34000147 ATTTTTAT-AATTTTAAAAAATTAAAATCAA
1 ATTTTTATCAATTTTAAAAAATTAAAATCAA
* **
34000177 ATTTTTATCATTTTTAAAGGATTAAAAT
1 ATTTTTATCAATTTTAAAAAATTAAAAT
34000205 GTAGTTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTTTTATCAATTTTAAAAAATTAAAATCAA
Found at i:34002465 original size:29 final size:29
Alignment explanation
Indices: 34002428--34002640 Score: 142
Period size: 29 Copynumber: 7.3 Consensus size: 29
34002418 GACTTTTGGG
34002428 GGGTAAAAAT-GTAATTTTTGGTGAAATCGA
1 GGGT-AAAATGGTAA-TTTTGGTGAAATCGA
* *
34002458 GGTTAAAAAT-G-AGATTTTGG-GAAATTTGA
1 GGGT-AAAATGGTA-ATTTTGGTGAAA-TCGA
34002487 GGGTAAAATGGTAATTTTTGGTGAAATCG-
1 GGGTAAAATGGTAA-TTTTGGTGAAATCGA
* *
34002516 GGGTTAAAAATAG-AATTTT-G-GAAAGTTCGG
1 GGG-T-AAAATGGTAATTTTGGTGAAA--TCGA
*
34002546 GGGTAAAATGGTAATTTTGGTAAAATCGA
1 GGGTAAAATGGTAATTTTGGTGAAATCGA
* * **
34002575 GGGTAAAATGG-AATTTTAG-AAAATTTA
1 GGGTAAAATGGTAATTTTGGTGAAATCGA
*
34002602 GGGGTAAAATGGTGATTTTTGGTGAAATCG-
1 -GGGTAAAATGGT-AATTTTGGTGAAATCGA
34002632 GGGTCAAAA
1 GGGT-AAAA
34002641 ATAGAATTTT
Statistics
Matches: 148, Mismatches: 16, Indels: 38
0.73 0.08 0.19
Matches are distributed among these distances:
27 10 0.07
28 34 0.23
29 50 0.34
30 37 0.25
31 17 0.11
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTGGTGAAATCGA
Found at i:34002501 original size:59 final size:59
Alignment explanation
Indices: 34002428--34002652 Score: 273
Period size: 59 Copynumber: 3.8 Consensus size: 59
34002418 GACTTTTGGG
34002428 GGGTAAAAAT-GTAATTTTTGGTGAAATCGAGGTTAAAAAT-GAGATTTTGGGAAATTTGA
1 GGGT-AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGA-ATTTTGGGAAATTTGA
* * *
34002487 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTT-GGAAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTGGGAAA-TTTGA
* * * * *
34002546 GGGTAAAATGGTAA-TTTTGGTAAAATCGAGGGT-AAAATGGAATTTTAGAAAATTT-A
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTGGGAAATTTGA
* * *
34002602 GGGGTAAAATGGTGATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGG
1 -GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTGG
34002653 AAAGTCTGGG
Statistics
Matches: 142, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
57 27 0.19
58 45 0.32
59 68 0.48
60 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTGGGAAATTTGA
Found at i:34002624 original size:116 final size:118
Alignment explanation
Indices: 34002426--34002678 Score: 356
Period size: 116 Copynumber: 2.2 Consensus size: 118
34002416 TTGACTTTTG
* * * *
34002426 GGGGGTAAAAATGTAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGGAAATTTGAGGGT
1 GGGGGTAAAAATGTAATTTTTGGTAAAATCGAGGGTAAAAATGAGATTTTAGAAAATTTGAGGGT
*
34002491 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGT-T
66 AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAGTCT
34002543 CGGGGGT-AAAATGGTAA-TTTTGGTAAAATCGAGGGT-AAAATG-GAATTTTAGAAAATTT-AG
1 -GGGGGTAAAAAT-GTAATTTTTGGTAAAATCGAGGGTAAAAATGAG-ATTTTAGAAAATTTGA-
*
34002603 GGGTAAAATGGTGATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAGTCT
62 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAGTCT
* *
34002660 GGGGGTCAAAATATAATTT
1 GGGGGTAAAAATGTAATTT
34002679 CTGAACAGTT
Statistics
Matches: 122, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
115 2 0.02
116 80 0.66
117 30 0.25
118 10 0.08
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (118 bp):
GGGGGTAAAAATGTAATTTTTGGTAAAATCGAGGGTAAAAATGAGATTTTAGAAAATTTGAGGGT
AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAGTCT
Found at i:34004347 original size:14 final size:13
Alignment explanation
Indices: 34004328--34004371 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
34004318 CCGGGTCTAT
34004328 TTGGGCTATTGTAA
1 TTGGGCT-TTGTAA
* *
34004342 TTGGGCTTTCTAT
1 TTGGGCTTTGTAA
*
34004355 TTGGCCTTTGTAA
1 TTGGGCTTTGTAA
34004368 TTGG
1 TTGG
34004372 ACTGGATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.14, C:0.11, G:0.27, T:0.48
Consensus pattern (13 bp):
TTGGGCTTTGTAA
Found at i:34004381 original size:26 final size:27
Alignment explanation
Indices: 34004325--34004383 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
34004315 GCACCGGGTC
* * ***
34004325 TATTTGGGCTATTGTAATTGGGCTTTC
1 TATTTGGCCTATTGTAATTGGACTGGA
34004352 TATTTGGCCT-TTGTAATTGGACTGGA
1 TATTTGGCCTATTGTAATTGGACTGGA
34004378 TATTTG
1 TATTTG
34004384 TAAATGAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.17, C:0.10, G:0.25, T:0.47
Consensus pattern (27 bp):
TATTTGGCCTATTGTAATTGGACTGGA
Found at i:34004446 original size:17 final size:17
Alignment explanation
Indices: 34004426--34004470 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
34004416 TTTCAAATGT
34004426 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
34004443 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
*
34004459 ATTTAAAATTAA
1 ATTTAAATTTAA
34004471 TTTCAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:34004467 original size:23 final size:24
Alignment explanation
Indices: 34004441--34004490 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
34004431 AATTTAAAAC
34004441 AAATTTAAATTT-AAA-TAAATTTA
1 AAATTT-AATTTCAAACTAAATTTA
*
34004464 AAA-TTAATTTCAAACTTAATTTA
1 AAATTTAATTTCAAACTAAATTTA
34004487 AAAT
1 AAAT
34004491 CCAAGTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 5 0.22
22 5 0.22
23 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTTAATTTCAAACTAAATTTA
Found at i:34004472 original size:27 final size:28
Alignment explanation
Indices: 34004429--34004482 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
34004419 CAAATGTATT
*
34004429 TAAATTTAAAACAAATTT-AAATTTAAA
1 TAAATTTAAAACAAATTTCAAACTTAAA
**
34004456 TAAATTTAAAATTAATTTCAAACTTAA
1 TAAATTTAAAACAAATTTCAAACTTAA
34004483 TTTAAAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAATTTAAAACAAATTTCAAACTTAAA
Found at i:34004484 original size:12 final size:11
Alignment explanation
Indices: 34004448--34004490 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
34004438 AACAAATTTA
*
34004448 AATTT-AAATA
1 AATTTAAAATT
34004458 AATTTAAAATT
1 AATTTAAAATT
*
34004469 AATTTCAAACTT
1 AATTT-AAAATT
34004481 AATTTAAAAT
1 AATTTAAAAT
34004491 CCAAGTTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 10 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:34006683 original size:23 final size:23
Alignment explanation
Indices: 34006589--34006718 Score: 116
Period size: 23 Copynumber: 5.4 Consensus size: 23
34006579 GTTGGATATG
34006589 AATGAAAAGTGGCACTTCGGTGCAA
1 AATG-AAAGTGGCACTTCGGTGC-A
* **
34006614 TATAGTGAAAGTGACACTTCAATGCA
1 -A-A-TGAAAGTGGCACTTCGGTGCA
34006640 AATGAAAGTGGCACTTCGGTGCA
1 AATGAAAGTGGCACTTCGGTGCA
*
34006663 AATGAAAGTGGCACTTTGGTGCA
1 AATGAAAGTGGCACTTCGGTGCA
* * * * *
34006686 ACTGACAGCGGCACTACGTTGCA
1 AATGAAAGTGGCACTTCGGTGCA
**
34006709 TTTGAAAGTG
1 AATGAAAGTG
34006719 ATTGTTTCAC
Statistics
Matches: 85, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
23 63 0.74
24 1 0.01
25 1 0.01
26 2 0.02
27 16 0.19
28 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (23 bp):
AATGAAAGTGGCACTTCGGTGCA
Found at i:34017464 original size:107 final size:107
Alignment explanation
Indices: 34017272--34017485 Score: 356
Period size: 107 Copynumber: 2.0 Consensus size: 107
34017262 TACAGATCTG
* * *
34017272 AAACTTGTGTTCAATGCATTTGTTTCTCATATCCACATTGCCAAATAAATTGCAATTATTTTGTG
1 AAACTTGTGTTCAATGCATTTGTTTCTCATATCCACATTACCAAATAAATTGCAAATATTTTATG
* *
34017337 TCTAATTTGTTTATAAAATTAATTATGTTAGTTTACTTGCTT
66 TCTAACTTGTTGATAAAATTAATTATGTTAGTTTACTTGCTT
*
34017379 AAACTTGTGTTCAATTCATTTGTTTCTCATATCCACATTACCAAATAAATTGCAAATATTTTATG
1 AAACTTGTGTTCAATGCATTTGTTTCTCATATCCACATTACCAAATAAATTGCAAATATTTTATG
* *
34017444 TCTAACTTGTTGATAGAATTAATTATGTTAGTTTATTTGCTT
66 TCTAACTTGTTGATAAAATTAATTATGTTAGTTTACTTGCTT
34017486 GATATGAATA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 99 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (107 bp):
AAACTTGTGTTCAATGCATTTGTTTCTCATATCCACATTACCAAATAAATTGCAAATATTTTATG
TCTAACTTGTTGATAAAATTAATTATGTTAGTTTACTTGCTT
Found at i:34021782 original size:14 final size:14
Alignment explanation
Indices: 34021759--34021794 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
34021749 TGATAAATTG
*
34021759 AAAAATTAAGTATT
1 AAAAAATAAGTATT
34021773 AAAAAATAAGTATT
1 AAAAAATAAGTATT
*
34021787 GAAAAATA
1 AAAAAATA
34021795 TAAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (14 bp):
AAAAAATAAGTATT
Found at i:34022977 original size:2 final size:2
Alignment explanation
Indices: 34022970--34022994 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34022960 ATGATATAAT
34022970 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
34022995 TTTTGAGAAA
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:34025940 original size:15 final size:15
Alignment explanation
Indices: 34025920--34025949 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34025910 TAGACCAGAT
34025920 GTTCAATGTAAAAGC
1 GTTCAATGTAAAAGC
34025935 GTTCAATGTAAAAGC
1 GTTCAATGTAAAAGC
34025950 TGCAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
GTTCAATGTAAAAGC
Found at i:34046202 original size:18 final size:19
Alignment explanation
Indices: 34046179--34046221 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
34046169 ATATAAGGTG
34046179 TAATTAATTTAAAATT-TT
1 TAATTAATTTAAAATTATT
*
34046197 TAATT-ATTTAAATTTATT
1 TAATTAATTTAAAATTATT
34046215 TAATTAA
1 TAATTAA
34046222 AAACTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 12 0.55
19 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATTAATTTAAAATTATT
Found at i:34058808 original size:23 final size:23
Alignment explanation
Indices: 34058782--34058895 Score: 115
Period size: 23 Copynumber: 5.0 Consensus size: 23
34058772 ATTCTTTGCG
*
34058782 ATGAACAATAAAAATTCTCTAAC
1 ATGAACAATGAAAATTCTCTAAC
* *
34058805 ATGAACAATGAAGATTCTCT-GC
1 ATGAACAATGAAAATTCTCTAAC
* **
34058827 AGTGAAAAAAAAAAATTCTCTAAC
1 A-TGAACAATGAAAATTCTCTAAC
*
34058851 ATGAACAATGAAAATTTTCT-AC
1 ATGAACAATGAAAATTCTCTAAC
* *
34058873 AATGAGCAACGAAAATTCTCTAA
1 -ATGAACAATGAAAATTCTCTAA
34058896 AAAATAACAA
Statistics
Matches: 72, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
22 4 0.06
23 65 0.90
24 3 0.04
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (23 bp):
ATGAACAATGAAAATTCTCTAAC
Found at i:34058817 original size:46 final size:46
Alignment explanation
Indices: 34058762--34058862 Score: 150
Period size: 46 Copynumber: 2.2 Consensus size: 46
34058752 CTCTGGCATA
* * * *
34058762 AACAGTGAAGATTCTTTGC-GATGAACAATAAAAATTCTCTAACATG
1 AACAATGAAGATTCTCTGCAG-TGAAAAAAAAAAATTCTCTAACATG
34058808 AACAATGAAGATTCTCTGCAGTGAAAAAAAAAAATTCTCTAACATG
1 AACAATGAAGATTCTCTGCAGTGAAAAAAAAAAATTCTCTAACATG
34058854 AACAATGAA
1 AACAATGAA
34058863 AATTTTCTAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 49 0.98
47 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.25
Consensus pattern (46 bp):
AACAATGAAGATTCTCTGCAGTGAAAAAAAAAAATTCTCTAACATG
Found at i:34058888 original size:46 final size:46
Alignment explanation
Indices: 34058782--34058895 Score: 138
Period size: 46 Copynumber: 2.5 Consensus size: 46
34058772 ATTCTTTGCG
* * * *
34058782 ATGAACAATAAAAATTCTCTAACATGAACAATGAAGATTCTCTGCA
1 ATGAAAAAAAAAAATTCTCTAACATGAACAATGAAAATTCTCTACA
* *
34058828 GTGAAAAAAAAAAATTCTCTAACATGAACAATGAAAATTTTCTACA
1 ATGAAAAAAAAAAATTCTCTAACATGAACAATGAAAATTCTCTACA
** **
34058874 ATGAGCAACGAAAATTCTCTAA
1 ATGAAAAAAAAAAATTCTCTAA
34058896 AAAATAACAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (46 bp):
ATGAAAAAAAAAAATTCTCTAACATGAACAATGAAAATTCTCTACA
Found at i:34061661 original size:15 final size:15
Alignment explanation
Indices: 34061641--34061670 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34061631 AAAGTAGCAC
34061641 AACTTTTGTAATAGG
1 AACTTTTGTAATAGG
34061656 AACTTTTGTAATAGG
1 AACTTTTGTAATAGG
34061671 CGAATGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (15 bp):
AACTTTTGTAATAGG
Found at i:34063162 original size:30 final size:29
Alignment explanation
Indices: 34063121--34063203 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 29
34063111 ACGTTAACAA
34063121 GACACCCCTCACATTTTCAAGTGGTTCGAG
1 GACA-CCCTCACATTTTCAAGTGGTTCGAG
*
34063151 GACACCTCTCACATTTTCAAGTGGTTCTAG
1 GACACC-CTCACATTTTCAAGTGGTTCGAG
*
34063181 GACACCCTCCACATTTCCAAGTG
1 GACACCCT-CACATTTTCAAGTG
34063204 CTTGTTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
29 4 0.08
30 45 0.92
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (29 bp):
GACACCCTCACATTTTCAAGTGGTTCGAG
Found at i:34064190 original size:22 final size:22
Alignment explanation
Indices: 34064165--34064218 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
34064155 GAAATTTAAA
34064165 ACAAAATATTATGAGGAGAGTT
1 ACAAAATATTATGAGGAGAGTT
* *
34064187 ACAAAACATTATGAGGAGTGTT
1 ACAAAATATTATGAGGAGAGTT
*
34064209 AAAAAATATT
1 ACAAAATATT
34064219 TTGTAGGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.28
Consensus pattern (22 bp):
ACAAAATATTATGAGGAGAGTT
Found at i:34064930 original size:35 final size:34
Alignment explanation
Indices: 34064878--34064958 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 34
34064868 GCTCTCACAT
*
34064878 GTGAGCTCGCATGTTTGTAGAG-TT-CATACTGTTTG
1 GTGAGCTCACATGTTTGTAGAGCTTGCAT--T-TTTG
34064913 GTGAGCTCACA-GTTTTGTAGAGCTTGCATTTTTG
1 GTGAGCTCACATG-TTTGTAGAGCTTGCATTTTTG
34064947 GTGAGCTCACAT
1 GTGAGCTCACAT
34064959 CTTTACATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
34 16 0.39
35 20 0.49
36 2 0.05
37 3 0.07
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.38
Consensus pattern (34 bp):
GTGAGCTCACATGTTTGTAGAGCTTGCATTTTTG
Found at i:34064952 original size:17 final size:17
Alignment explanation
Indices: 34064909--34064957 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
34064899 GTTCATACTG
34064909 TTTGGTGAGCTCACAGT
1 TTTGGTGAGCTCACAGT
** *
34064926 TTT-GTAGAGCTTGCATT
1 TTTGGT-GAGCTCACAGT
34064943 TTTGGTGAGCTCACA
1 TTTGGTGAGCTCACA
34064958 TCTTTACATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 2 0.08
17 21 0.84
18 2 0.08
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (17 bp):
TTTGGTGAGCTCACAGT
Found at i:34070000 original size:10 final size:10
Alignment explanation
Indices: 34069985--34070009 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
34069975 TCTCGAGTTC
34069985 GTGTGCTTGT
1 GTGTGCTTGT
34069995 GTGTGCTTGT
1 GTGTGCTTGT
34070005 GTGTG
1 GTGTG
34070010 TACATTGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.44, T:0.48
Consensus pattern (10 bp):
GTGTGCTTGT
Found at i:34070698 original size:5 final size:5
Alignment explanation
Indices: 34070633--34070679 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
34070623 TATGTTTCTC
34070633 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
34070680 TTTCATTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:34072804 original size:9 final size:9
Alignment explanation
Indices: 34072790--34072819 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
34072780 TAGCTTATTA
34072790 CAGATCATT
1 CAGATCATT
34072799 CAGATCATT
1 CAGATCATT
34072808 CAGATCATT
1 CAGATCATT
34072817 CAG
1 CAG
34072820 GAGGCCTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (9 bp):
CAGATCATT
Found at i:34073120 original size:53 final size:54
Alignment explanation
Indices: 34073060--34073179 Score: 179
Period size: 53 Copynumber: 2.2 Consensus size: 54
34073050 ATTGACACAC
* *
34073060 GCCCGTGTGCCTCAAAATAGTATACACACACCCTGACACATGCTCGTGTGTC-A
1 GCCCGTGTGCCTCAAAATAGTATACACACACCCTGACACACGCCCGTGTGTCTA
* * * *
34073113 GCCCGTGTGCTTCAAAATAGTATACACACACCTTGACACACGCCCTTGTGTCTT
1 GCCCGTGTGCCTCAAAATAGTATACACACACCCTGACACACGCCCGTGTGTCTA
34073167 GCCCGTGTGCCTC
1 GCCCGTGTGCCTC
34073180 CTGCAACTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 47 0.80
54 12 0.20
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (54 bp):
GCCCGTGTGCCTCAAAATAGTATACACACACCCTGACACACGCCCGTGTGTCTA
Found at i:34075275 original size:21 final size:21
Alignment explanation
Indices: 34075249--34075291 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
34075239 GTCTATGGTG
*
34075249 TGAAAAGTTACATTTATACCC
1 TGAAAAGTTACACTTATACCC
34075270 TGAAAAGTTACACTTATACCC
1 TGAAAAGTTACACTTATACCC
34075291 T
1 T
34075292 TTCCATGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (21 bp):
TGAAAAGTTACACTTATACCC
Found at i:34076064 original size:24 final size:24
Alignment explanation
Indices: 34076037--34076109 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
34076027 TTAAACAAAA
34076037 TAAAAGTTATGATAATTATACATT
1 TAAAAGTTATGATAATTATACATT
* * *
34076061 TAAAAATAATTATAATT-TA-A--
1 TAAAAGTTATGATAATTATACATT
* * *
34076081 TAGAAGTTGTGATAATTATGCATT
1 TAAAAGTTATGATAATTATACATT
34076105 TAAAA
1 TAAAA
34076110 ATAATTAGAA
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
20 12 0.34
21 1 0.03
22 2 0.06
23 2 0.06
24 18 0.51
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.40
Consensus pattern (24 bp):
TAAAAGTTATGATAATTATACATT
Found at i:34076094 original size:44 final size:44
Alignment explanation
Indices: 34076035--34076124 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
34076025 TTTTAAACAA
*
34076035 AATAAAAGTTATGATAATTATACATTTAAAAATAATTATAATTT
1 AATAAAAGTTATGATAATTATACATTTAAAAATAATTAGAATTT
* * *
34076079 AATAGAAGTTGTGATAATTATGCATTTAAAAATAATTAGAATTT
1 AATAAAAGTTATGATAATTATACATTTAAAAATAATTAGAATTT
34076123 AA
1 AA
34076125 ATTATAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (44 bp):
AATAAAAGTTATGATAATTATACATTTAAAAATAATTAGAATTT
Found at i:34076133 original size:18 final size:18
Alignment explanation
Indices: 34076092--34076125 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34076082 AGAAGTTGTG
*
34076092 ATAATTATGCATTTAAAA
1 ATAATTATGAATTTAAAA
34076110 ATAATTA-GAATTTAAA
1 ATAATTATGAATTTAAA
34076126 TTATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (18 bp):
ATAATTATGAATTTAAAA
Found at i:34078881 original size:28 final size:30
Alignment explanation
Indices: 34078850--34078912 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
34078840 AAACGGGACC
*
34078850 TTTGGATACC-CGAGGG-TAAAATGGT-AAT
1 TTTGGA-ACCTCGAGGGCAAAAATGGTAAAT
*
34078878 TTTGGACCCTCGAGGGCAAAAATGGTAAAT
1 TTTGGAACCTCGAGGGCAAAAATGGTAAAT
34078908 TTTGG
1 TTTGG
34078913 TGAAATCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 2 0.07
28 12 0.40
29 8 0.27
30 8 0.27
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.29
Consensus pattern (30 bp):
TTTGGAACCTCGAGGGCAAAAATGGTAAAT
Found at i:34079056 original size:58 final size:58
Alignment explanation
Indices: 34078896--34079260 Score: 500
Period size: 58 Copynumber: 6.2 Consensus size: 58
34078886 CTCGAGGGCA
* * *
34078896 AAAATGGTAAATTTTGGTGAAATCATGGTTAAAAATGGAATTTTGGAAAGTTCAGGGAT
1 AAAATGGT-AATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
34078955 AAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCAG-GGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
* * * * *
34079014 GAAATGGTAATTTTGGTAAAATTAGGGTTAAAAATAGAATTTTGGAGAA-TTTGGGGGT
1 AAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGA-AAGTTCGGGGGT
* * * * * *
34079072 GAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTTGGGGTT
1 AAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
* *
34079131 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGT
1 AAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
* * *
34079189 AAAATGGTAATTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAGAGTTCGGGGTT
1 AAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
34079247 AAAATGGTAATTTT
1 AAAATGGTAATTTT
34079261 TGGTAGTTTC
Statistics
Matches: 276, Mismatches: 24, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
58 163 0.59
59 113 0.41
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
Found at i:34079056 original size:117 final size:117
Alignment explanation
Indices: 34078896--34079265 Score: 537
Period size: 117 Copynumber: 3.2 Consensus size: 117
34078886 CTCGAGGGCA
* * *
34078896 AAAATGGTAAATTTTGGTGAAATCATGGTTAAAAATGGAATTTTGGAAAGTTCAGGGATAAAATG
1 AAAATGGT-AATTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATG
*
34078961 GTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
65 GTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTT
* * * ** *
34079014 GAAATGGTAATTTTGGTAAAATTAGGGTTAAAAATAGAATTTTGGAGAA-TTTGGGGGTGAAATG
1 AAAATGGTAATTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGA-AAGTTCAGGGGTAAAATG
* * * *
34079078 GTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAAGTTTGGGGTT
65 GTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTT
* *
34079131 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGG
1 AAAATGGTAATTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGG
* *
34079196 TAA-TTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAGAGTTCGGGGTT
66 TAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTT
34079247 AAAATGGTAATTTTTGGTA
1 AAAATGGTAA-TTTTGGTA
34079266 GTTTCGGGGT
Statistics
Matches: 220, Mismatches: 29, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
116 54 0.25
117 157 0.71
118 9 0.04
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (117 bp):
AAAATGGTAATTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGG
TAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTT
Found at i:34079246 original size:29 final size:29
Alignment explanation
Indices: 34078896--34079289 Score: 258
Period size: 29 Copynumber: 13.5 Consensus size: 29
34078886 CTCGAGGGCA
* * **
34078896 AAAATGGTAAATTTTGGTGAAATCATGGTT
1 AAAATGGT-AATTTTGGAGAATTCGGGGTT
* *
34078926 AAAAATGG-AATTTTGGA-AAGTTCAGGGAT
1 -AAAATGGTAATTTTGGAGAA-TTCGGGGTT
* * *
34078955 AAAATGGTAATTTTTGGTGAAATCGAGGTT
1 AAAATGGTAA-TTTTGGAGAATTCGGGGTT
*
34078985 AAAAATGG-AATTTTGGA-AAGTTCGGGGGT
1 -AAAATGGTAATTTTGGAGAA-TTCGGGGTT
* * *
34079014 GAAATGGTAATTTTGGTAAAATT-AGGGTT
1 AAAATGGTAATTTTGG-AGAATTCGGGGTT
* * *
34079043 AAAAATAG-AATTTTGGAGAATTTGGGGGT
1 -AAAATGGTAATTTTGGAGAATTCGGGGTT
* * *
34079072 GAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAA-TTTTGGAGAATTCGGGGTT
* * *
34079102 AAAAATAG-AATTTTAGA-AAGTTTGGGGTT
1 -AAAATGGTAATTTTGGAGAA-TTCGGGGTT
* *
34079131 AAAATGGTAATTTTGGTGAAATCGGGGTT
1 AAAATGGTAATTTTGGAGAATTCGGGGTT
34079160 AAAAATGG-AATTTTGGA-AAGTTCAGGGG-T
1 -AAAATGGTAATTTTGGAGAA-TTC-GGGGTT
* * **
34079189 AAAATGGTAATTTTGGTGAAATCAAGGTT
1 AAAATGGTAATTTTGGAGAATTCGGGGTT
*
34079218 AAAAATGG-AATTTTGGAGAGTTCGGGGTT
1 -AAAATGGTAATTTTGGAGAATTCGGGGTT
* *
34079247 AAAATGGTAATTTTTGGTAG-TTTCGGGGTC
1 AAAATGGTAA-TTTTGG-AGAATTCGGGGTT
34079277 AAAAT-GTAATTTT
1 AAAATGGTAATTTT
34079290 CTAAAATTTT
Statistics
Matches: 285, Mismatches: 51, Indels: 57
0.73 0.13 0.15
Matches are distributed among these distances:
28 57 0.20
29 124 0.44
30 79 0.28
31 25 0.09
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAGAATTCGGGGTT
Found at i:34080981 original size:7 final size:6
Alignment explanation
Indices: 34080966--34081064 Score: 66
Period size: 6 Copynumber: 17.3 Consensus size: 6
34080956 TTTGGACTTT
* * * * *
34080966 AATTTA AATTTA AA-ATA AATTTA GACTCA AA-TTA AATTCA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
34081012 AAGTTT- AATTTA AATTTA AA--TA AATCTA AATTTA TA-TCA AATTTA
1 AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
34081057 ATTTTA AA
1 AATTTA AA
34081065 ATAAATTAAG
Statistics
Matches: 70, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
4 4 0.06
5 14 0.20
6 49 0.70
7 3 0.04
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:34081036 original size:34 final size:35
Alignment explanation
Indices: 34080966--34081071 Score: 87
Period size: 34 Copynumber: 3.1 Consensus size: 35
34080956 TTTGGACTTT
* * * *
34080966 AATT-TAAATTTAAAAT-AAATTTAGACTCAAATTA
1 AATTCTAAATTT-AAATCAAATTTAAATTTAAAATA
**
34081000 AATTC-AAATTTAAAGTTTAATTTAAATTT-AAATA
1 AATTCTAAATTTAAA-TCAAATTTAAATTTAAAATA
* *
34081034 AA-TCTAAATTTATATCAAATTTAATTTTAAAATA
1 AATTCTAAATTTAAATCAAATTTAAATTTAAAATA
34081068 AATT
1 AATT
34081072 AAGAAAGGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
33 16 0.28
34 32 0.56
35 9 0.16
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (35 bp):
AATTCTAAATTTAAATCAAATTTAAATTTAAAATA
Found at i:34081043 original size:16 final size:16
Alignment explanation
Indices: 34081022--34081070 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
34081012 AAGTTTAATT
34081022 TAAATTTAAATAAATC
1 TAAATTTAAATAAATC
* *
34081038 TAAATTTATATCAAATT
1 TAAATTTAAAT-AAATC
*
34081055 TAATTTTAAAATAAAT
1 TAAATTT-AAATAAAT
34081071 TAAGAAAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.37
17 14 0.52
18 3 0.11
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATAAATC
Found at i:34090721 original size:26 final size:25
Alignment explanation
Indices: 34090670--34090725 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
34090660 TTTAAATTTC
34090670 AAAAA-TTAAAAAAATTGAAAATAT
1 AAAAATTTAAAAAAATTGAAAATAT
*
34090694 AAAAATTTAAAAAATATTTTAAAA-AT
1 AAAAATTTAAAAAA-A-TTGAAAATAT
34090720 AAAAAT
1 AAAAAT
34090726 AAATTAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 5 0.18
25 8 0.29
26 9 0.32
27 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAATTTAAAAAAATTGAAAATAT
Found at i:34091023 original size:31 final size:32
Alignment explanation
Indices: 34090954--34091033 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
34090944 ATATTTTCAA
34090954 TTTTTTTGTAATTTTTTCTAAAATTTTAACTA-T
1 TTTTTTTG-AA-TTTTTCTAAAATTTTAACTATT
* **
34090987 ATTTTTTGAATTTTTCTAAATATTTT-GTTATT
1 TTTTTTTGAATTTTTCTAAA-ATTTTAACTATT
*
34091019 TTTTTTTGAAATTTT
1 TTTTTTTGAATTTTT
34091034 AACTTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
31 12 0.30
32 21 0.52
33 7 0.17
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.66
Consensus pattern (32 bp):
TTTTTTTGAATTTTTCTAAAATTTTAACTATT
Found at i:34091282 original size:17 final size:16
Alignment explanation
Indices: 34091260--34091318 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 16
34091250 AAGAATATAA
34091260 AAGGTTAAGGAAGAGGG
1 AAGGTTAAGGAAGA-GG
34091277 AAGGTTAAAGGTCAA-AGG
1 AAGGTT-AAGG--AAGAGG
34091295 -AGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGA-GG
34091311 AAGGTTAA
1 AAGGTTAA
34091319 AAGTTAAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
14 2 0.06
15 1 0.03
16 6 0.17
17 18 0.50
18 6 0.17
19 1 0.03
20 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.39, T:0.17
Consensus pattern (16 bp):
AAGGTTAAGGAAGAGG
Found at i:34091299 original size:34 final size:34
Alignment explanation
Indices: 34091261--34091330 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
34091251 AGAATATAAA
*
34091261 AGGTTAAGGAAGAGGGAAGGTTAAAGGTCAAAGG
1 AGGTTAAGGAAGAGGGAAGGTTAAAAGTCAAAGG
* *
34091295 AGGTTAAGGAAGATGGAAGGTTAAAAGTTAAAGG
1 AGGTTAAGGAAGAGGGAAGGTTAAAAGTCAAAGG
34091329 AG
1 AG
34091331 ATGAAAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.01, G:0.39, T:0.17
Consensus pattern (34 bp):
AGGTTAAGGAAGAGGGAAGGTTAAAAGTCAAAGG
Found at i:34096096 original size:2 final size:2
Alignment explanation
Indices: 34096089--34096124 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34096079 GTTATGAAAG
34096089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34096125 TTAAGAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34096504 original size:17 final size:17
Alignment explanation
Indices: 34096482--34096540 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
34096472 AAGAATAAAA
34096482 AAGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATGG
34096499 AAGGTTAAAGGTCAAGA--G
1 AAGGTT-AAGG--AAGATGG
* *
34096517 -AGATTAAGGAAGATGA
1 AAGGTTAAGGAAGATGG
34096533 AAGGTTAA
1 AAGGTTAA
34096541 AAGTCAAGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
14 4 0.12
16 4 0.12
17 16 0.48
18 5 0.15
20 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.34, T:0.19
Consensus pattern (17 bp):
AAGGTTAAGGAAGATGG
Found at i:34096529 original size:34 final size:34
Alignment explanation
Indices: 34096486--34096554 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
34096476 ATAAAAAAGG
* *
34096486 TTAAGGAAGATGGAAGGTTAAAGGTCAAGAGAGA
1 TTAAGGAAGATGAAAGGTTAAAAGTCAAGAGAGA
*
34096520 TTAAGGAAGATGAAAGGTTAAAAGTCAAGGGAGA
1 TTAAGGAAGATGAAAGGTTAAAAGTCAAGAGAGA
34096554 T
1 T
34096555 GAAAAGTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.33, T:0.19
Consensus pattern (34 bp):
TTAAGGAAGATGAAAGGTTAAAAGTCAAGAGAGA
Found at i:34099182 original size:23 final size:22
Alignment explanation
Indices: 34099155--34099205 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
34099145 ACACAAACAG
34099155 AATTTAA-ATTTAAATTTATTGTA
1 AATTTAAGA-TTAAATTTATT-TA
34099178 AATTTAAGATTAAATTTATTTA
1 AATTTAAGATTAAATTTATTTA
34099200 AATTTA
1 AATTTA
34099206 CTAATGTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 8 0.30
23 18 0.67
24 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
AATTTAAGATTAAATTTATTTA
Found at i:34103240 original size:21 final size:20
Alignment explanation
Indices: 34103216--34103256 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34103206 ATGTTGAATA
34103216 TATTAAAAATGTTTTAATTAT
1 TATTAAAAAT-TTTTAATTAT
**
34103237 TATTTGAAATTTTTAATTAT
1 TATTAAAAATTTTTAATTAT
34103257 AATATGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TATTAAAAATTTTTAATTAT
Found at i:34104125 original size:29 final size:28
Alignment explanation
Indices: 34104081--34104162 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 28
34104071 TCAGGGCCCG
34104081 AACTTTTAAAAATTACATTTTTACCTCTA
1 AACTTTTAAAAATTACATTTTTACCTC-A
*
34104110 AATTTTTAAAAATTACA-TTTTATCCTCA
1 AACTTTTAAAAATTACATTTTTA-CCTCA
* * *
34104138 AACTTCTAAAAACTACGTTTTTACC
1 AACTTTTAAAAATTACATTTTTACC
34104163 CCCGAACTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 21 0.46
29 25 0.54
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (28 bp):
AACTTTTAAAAATTACATTTTTACCTCA
Found at i:34104187 original size:29 final size:29
Alignment explanation
Indices: 34104138--34104211 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
34104128 TTTATCCTCA
* * *
34104138 AACTTCTAAAAA-CTACGTTTTTACCCCCG
1 AACTTCCAAAAATC-ACATTTTGACCCCCG
* *
34104167 AACTTCCAAAAATCACATTTTGATCCCTG
1 AACTTCCAAAAATCACATTTTGACCCCCG
34104196 AACTTCTCAAAAATCA
1 AACTTC-CAAAAATCA
34104212 TGTTTTTCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 28 0.74
30 10 0.26
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.30
Consensus pattern (29 bp):
AACTTCCAAAAATCACATTTTGACCCCCG
Found at i:34104426 original size:28 final size:29
Alignment explanation
Indices: 34104375--34104433 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
34104365 TGAATTTCGT
34104375 TTTTTCTCATTTATTTTTTCGTAT-TTTA
1 TTTTTCTCATTTATTTTTTCGTATATTTA
34104403 TTTTTCTCATGTT-TATTTTT-GTATATTTA
1 TTTTTCTCAT-TTAT-TTTTTCGTATATTTA
34104432 TT
1 TT
34104434 CATTCTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.71
Consensus pattern (29 bp):
TTTTTCTCATTTATTTTTTCGTATATTTA
Found at i:34104431 original size:14 final size:14
Alignment explanation
Indices: 34104383--34104433 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
34104373 GTTTTTTCTC
34104383 ATTTATTTTTTCGTAT
1 ATTTA-TTTTT-GTAT
*
34104399 -TTTATTTTTCTCAT
1 ATTTATTTTTGT-AT
*
34104413 GTTTATTTTTGTAT
1 ATTTATTTTTGTAT
34104427 ATTTATT
1 ATTTATT
34104434 CATTCTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 15 0.50
15 14 0.47
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (14 bp):
ATTTATTTTTGTAT
Found at i:34107827 original size:2 final size:2
Alignment explanation
Indices: 34107820--34107863 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
34107810 AGAAATTGCA
34107820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34107862 AT
1 AT
34107864 TAACTGCTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34115518 original size:6 final size:6
Alignment explanation
Indices: 34115507--34115536 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
34115497 TAACATGTAT
*
34115507 ATCTCA ATCTCA GTCTCA ATCTCA ATCTCA
1 ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA
34115537 TGACAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.33
Consensus pattern (6 bp):
ATCTCA
Found at i:34119930 original size:18 final size:20
Alignment explanation
Indices: 34119907--34119950 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
34119897 TAATTCTATA
*
34119907 TATTTTATATTGT-TTTA-T
1 TATTTTATAATGTATTTATT
34119925 TATTTTATAATGTATTTATT
1 TATTTTATAATGTATTTATT
34119945 TATTTT
1 TATTTT
34119951 TGGACCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.52
19 4 0.17
20 7 0.30
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TATTTTATAATGTATTTATT
Found at i:34122292 original size:24 final size:24
Alignment explanation
Indices: 34122241--34122292 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
34122231 TTCATATGTC
* * *
34122241 AAATAAATTATGCTAGTAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
34122265 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
34122289 AAAT
1 AAAT
34122293 CTCCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:34128649 original size:17 final size:18
Alignment explanation
Indices: 34128621--34128657 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
34128611 TTTAGATGGA
34128621 TTATTATGTATTACTCGT
1 TTATTATGTATTACTCGT
34128639 TTATT-TGTATTACTCGT
1 TTATTATGTATTACTCGT
34128656 TT
1 TT
34128658 TGAAGACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (18 bp):
TTATTATGTATTACTCGT
Found at i:34131877 original size:13 final size:13
Alignment explanation
Indices: 34131814--34131877 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
34131804 AAACCATGAA
*
34131814 CCTAAACCTAATAC
1 CCTAAACCCAA-AC
*
34131828 CTTAAA-CCAAAC
1 CCTAAACCCAAAC
*
34131840 CC-AAACCCAAAA
1 CCTAAACCCAAAC
*
34131852 CCAAATCACCCAAAC
1 CCTAA--ACCCAAAC
34131867 CCTAAACCCAA
1 CCTAAACCCAA
34131878 TTTGATTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
11 3 0.08
12 10 0.25
13 11 0.28
14 5 0.12
15 11 0.28
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.11
Consensus pattern (13 bp):
CCTAAACCCAAAC
Found at i:34136699 original size:23 final size:22
Alignment explanation
Indices: 34136651--34136754 Score: 75
Period size: 23 Copynumber: 4.5 Consensus size: 22
34136641 ACACTAGCGC
* *
34136651 GCCCTCTGTTTAGTACGTT-TCAT
1 GCCCTCTGTTTAGCAC-TTGT-GT
*
34136674 GCCCTTTGTTTAGCACTATGTGT
1 GCCCTCTGTTTAGCACT-TGTGT
34136697 GCCCTCTGTTATTAGCACTTCGTGT
1 GCCCTCTG-T-TTAGCACTT-GTGT
* * *
34136722 GTCCTCTGATTAGCACTTTGTTT
1 GCCCTCTGTTTAGCAC-TTGTGT
*
34136745 GCCCTTTGTT
1 GCCCTCTGTT
34136755 ACCCAGCACT
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
22 1 0.02
23 40 0.62
24 5 0.08
25 19 0.29
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (22 bp):
GCCCTCTGTTTAGCACTTGTGT
Found at i:34136721 original size:25 final size:24
Alignment explanation
Indices: 34136683--34136755 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
34136673 TGCCCTTTGT
34136683 TTAGCACTATGTGTGCCCTCTGTTA
1 TTAGCACT-TGTGTGCCCTCTGTTA
*
34136708 TTAGCACTTCGTGTGTCCTCTG--A
1 TTAGCACTT-GTGTGCCCTCTGTTA
* *
34136731 TTAGCACTTTGTTTGCCCTTTGTTA
1 TTAGCAC-TTGTGTGCCCTCTGTTA
34136756 CCCAGCACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 17 0.43
24 3 0.08
25 20 0.50
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (24 bp):
TTAGCACTTGTGTGCCCTCTGTTA
Found at i:34142598 original size:48 final size:47
Alignment explanation
Indices: 34142541--34142649 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 47
34142531 AGCACGTTTC
** *
34142541 GTGCCCTCTGTTCAGCA-TTGTGTGTGCCCTCTATTA-TTAGCACTTCGT
1 GTGCCCTCTGTT-AGCACTT-TGTGTGCCCTCTATTACCCAGCACTT-AT
*
34142589 GTGCCCTCTGATTAGCACTTTGTGTGCCCTCTGTTACCCAGCACTTAT
1 GTGCCCTCTG-TTAGCACTTTGTGTGCCCTCTATTACCCAGCACTTAT
34142637 GTGCCCTCTGTTA
1 GTGCCCTCTGTTA
34142650 AGTATTTCGG
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
47 3 0.06
48 40 0.74
49 11 0.20
ACGTcount: A:0.13, C:0.29, G:0.20, T:0.38
Consensus pattern (47 bp):
GTGCCCTCTGTTAGCACTTTGTGTGCCCTCTATTACCCAGCACTTAT
Found at i:34142606 original size:23 final size:23
Alignment explanation
Indices: 34142519--34142621 Score: 97
Period size: 23 Copynumber: 4.4 Consensus size: 23
34142509 AACACTAGCA
*
34142519 TGCCCTCT-ATTTAGCACGTTT-CG
1 TGCCCTCTGA-TTAGCAC-TTTGTG
34142542 TGCCCTCTG-TTCAGCA-TTGTGTG
1 TGCCCTCTGATT-AGCACTT-TGTG
* *
34142565 TGCCCTCTATTATTAGCACTTCGTG
1 TGCCCTC--TGATTAGCACTTTGTG
34142590 TGCCCTCTGATTAGCACTTTGTG
1 TGCCCTCTGATTAGCACTTTGTG
34142613 TGCCCTCTG
1 TGCCCTCTG
34142622 TTACCCAGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.03
22 3 0.04
23 43 0.64
25 15 0.22
26 4 0.06
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.39
Consensus pattern (23 bp):
TGCCCTCTGATTAGCACTTTGTG
Found at i:34145266 original size:21 final size:20
Alignment explanation
Indices: 34145242--34145282 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34145232 ATGTTGAATA
34145242 TATTAAAAATGTTTTAATTAT
1 TATTAAAAAT-TTTTAATTAT
**
34145263 TATTTGAAATTTTTAATTAT
1 TATTAAAAATTTTTAATTAT
34145283 AATATGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TATTAAAAATTTTTAATTAT
Found at i:34145736 original size:66 final size:66
Alignment explanation
Indices: 34145630--34145765 Score: 263
Period size: 66 Copynumber: 2.1 Consensus size: 66
34145620 AATTGCAACC
34145630 CCAATATCGACCCCAATTGTCACAAATCACTCACTCAAATACCTCACAATACAATCAATAAACTC
1 CCAATATCGACCCCAATTGTCACAAATCACTCACTCAAATACCTCACAATACAATCAATAAACTC
34145695 T
66 T
*
34145696 CCAATATCGACCTCAATTGTCACAAATCACTCACTCAAATACCTCACAATACAATCAATAAACTC
1 CCAATATCGACCCCAATTGTCACAAATCACTCACTCAAATACCTCACAATACAATCAATAAACTC
34145761 T
66 T
34145762 CCAA
1 CCAA
34145766 ATAATACCTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.41, C:0.33, G:0.03, T:0.23
Consensus pattern (66 bp):
CCAATATCGACCCCAATTGTCACAAATCACTCACTCAAATACCTCACAATACAATCAATAAACTC
T
Found at i:34148652 original size:5 final size:6
Alignment explanation
Indices: 34148634--34148660 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34148624 TTACACATGA
34148634 TTCTTT TTCTTT TTCTTT TTCTTT TTC
1 TTCTTT TTCTTT TTCTTT TTCTTT TTC
34148661 CAAATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:34177181 original size:24 final size:24
Alignment explanation
Indices: 34177120--34177182 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
34177110 TAGACTAATA
* *
34177120 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
34177144 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
34177168 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
34177183 GATTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:34177827 original size:51 final size:51
Alignment explanation
Indices: 34177751--34177850 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
34177741 CCTAATTTCT
*
34177751 ACAGTACCACTACCGATTACCTTACTAGATTAATTGTTTCCCATGTGTATA
1 ACAGTACCACTACCGATTACCTTACTAGATGAATTGTTTCCCATGTGTATA
*
34177802 ACAGTACCATTACCGATTACCTTACTAGATGAATTGTTTCCCATGTGTA
1 ACAGTACCACTACCGATTACCTTACTAGATGAATTGTTTCCCATGTGTA
34177851 CAACTCCACC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (51 bp):
ACAGTACCACTACCGATTACCTTACTAGATGAATTGTTTCCCATGTGTATA
Found at i:34183414 original size:3 final size:3
Alignment explanation
Indices: 34183401--34183486 Score: 55
Period size: 3 Copynumber: 27.7 Consensus size: 3
34183391 ATCATCAATG
* * * * * *
34183401 ATA ATA GTA ATA ATA TTA CTA ATA ACA CTA ATA ATGA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
** * *
34183447 ATA ATTA GCA TTA ATGA ATA ATA ATA ATA TTA ATA ATA AT
1 ATA A-TA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT
34183487 GTTTTAATAA
Statistics
Matches: 62, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
3 54 0.87
4 8 0.13
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:34184567 original size:29 final size:30
Alignment explanation
Indices: 34184541--34184678 Score: 117
Period size: 30 Copynumber: 4.6 Consensus size: 30
34184531 AGTCCCTAAC
34184541 CTTTCAAAAATTACATTTTTGACCCTAAAA
1 CTTTCAAAAATTACATTTTTGACCCTAAAA
* * * *
34184571 C-TTCTTAAAATTATATCTTTAACCCTAAAA
1 CTTTC-AAAAATTACATTTTTGACCCTAAAA
* *
34184601 CTTCCAAAAATCACATTTTT-ACCCCT-AAA
1 CTTTCAAAAATTACATTTTTGA-CCCTAAAA
*
34184630 CTTTCAAAAATT-CTATTTTTGA-CCTCGAAA
1 CTTTCAAAAATTAC-ATTTTTGACCCT-AAAA
*
34184660 C-TTGAAAAATTACTATTTT
1 CTTTCAAAAATTAC-ATTTT
34184679 ACCCCCGGAT
Statistics
Matches: 88, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
28 4 0.05
29 32 0.36
30 50 0.57
31 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (30 bp):
CTTTCAAAAATTACATTTTTGACCCTAAAA
Found at i:34184696 original size:59 final size:60
Alignment explanation
Indices: 34184633--34184765 Score: 168
Period size: 59 Copynumber: 2.3 Consensus size: 60
34184623 CCCTAAACTT
*
34184633 TCAAAAATTCTATTTTTG-ACCTCGAAAC-TTGAAAAATTACTATTTTACCCCCGGATGTC
1 TCAAAAATTCTATTTTTGAACCTCGAAACTTTGAAAAATTACCATTTTA-CCCCGGATGTC
* * * * *
34184692 TC-AAAACTCCATTTTTGAATCTCGAAACTTTTAAGAATTACCATTTTACCCCGGATGTC
1 TCAAAAATTCTATTTTTGAACCTCGAAACTTTGAAAAATTACCATTTTACCCCGGATGTC
34184751 -CAAAAATT-TATTTTT
1 TCAAAAATTCTATTTTT
34184766 TGATCCCGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
58 20 0.32
59 27 0.43
60 16 0.25
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (60 bp):
TCAAAAATTCTATTTTTGAACCTCGAAACTTTGAAAAATTACCATTTTACCCCGGATGTC
Found at i:34190118 original size:17 final size:16
Alignment explanation
Indices: 34190096--34190147 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
34190086 CAATGAACAA
34190096 AAAAAAAAAAGAAGAAG
1 AAAAAAAAAAGAA-AAG
34190113 AAAAAAAAAAGAAAAG
1 AAAAAAAAAAGAAAAG
* *
34190129 AAAAGAAAAACAAAA-
1 AAAAAAAAAAGAAAAG
34190144 AAAA
1 AAAA
34190148 GGGAAAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.12
16 16 0.48
17 13 0.39
ACGTcount: A:0.87, C:0.02, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAG
Found at i:34190153 original size:27 final size:28
Alignment explanation
Indices: 34190096--34190159 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
34190086 CAATGAACAA
* * *
34190096 AAAAAAAAAAGAAGAAGAAAAAAAAAAG
1 AAAAAGAAAAGAAAAACAAAAAAAAAAG
**
34190124 -AAAAGAAAAGAAAAACAAAAAAAAGGG
1 AAAAAGAAAAGAAAAACAAAAAAAAAAG
34190151 AAAAAGAAA
1 AAAAAGAAA
34190160 GGAGAGGTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.83, C:0.02, G:0.16, T:0.00
Consensus pattern (28 bp):
AAAAAGAAAAGAAAAACAAAAAAAAAAG
Found at i:34191003 original size:51 final size:49
Alignment explanation
Indices: 34190885--34191407 Score: 195
Period size: 51 Copynumber: 10.4 Consensus size: 49
34190875 AGTATCACGC
* * * * *
34190885 AAAAAGATAAAAGGGAAAGGTCTAAGTCGTAACGGCGGACCGT-GTAACT
1 AAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGGCGGATC-TAGTACCT
* * * * *
34190934 CAGAAGACACGACGGGAAAGATCTAAGATCGCAACGGTGGATCTAGTACCGT
1 AAAAAGACA-AAAGGGAAAGATCTAAG-TCGCAACGGCGGATCTAGTACC-T
* * * * *
34190986 AAAAAGATAAAAGGGAAAGGTATAAGTCACAACGGCGGACCGT-GTACCT
1 AAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGGCGGATC-TAGTACCT
* * * * * * *
34191035 CAGAAGACATGACGGGAAAAATCTAAGATCGTAACGGCGAAT-TCAGTACCAT
1 AAAAAGACA-AAAGGGAAAGATCTAAG-TCGCAACGGCGGATCT-AGTACC-T
* * ** *
34191087 AAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGTAGACCGT-GTACC-
1 AAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGGCGGATC-TAGTACCT
* * * * * *
34191135 ACAAAAGACACGACA-GAAAAGATCTAAGACCACAATGGCGGATCCAGTACAGC-
1 A-AAAAGACA--AAAGGGAAAGATCTAAG-TCGCAACGGCGGATCTAGTAC--CT
* * * * *
34191188 AAAAAGA-TAAAGGGTAAAGGTCTAAGTCGCAACGG-AGAACTGTGTACC-
1 AAAAAGACAAAAGGG-AAAGATCTAAGTCGCAACGGCGGATCT-AGTACCT
* * * * * * * *
34191236 ACAGAAGACACGACGAGAAAGATTTAAGACCGCAACGGTGGATCTAGTACCGC
1 A-AAAAGACA-AAAGGGAAAGATCTAAG-TCGCAACGGCGGATCTAGTACC-T
* * *
34191289 AAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGACGGACCGT-GTACCT
1 AAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGGCGGATC-TAGTACCT
* * * * * * * * * * *
34191338 CAGAAGACACGATGAGAAATATCAAAGATCACAACGACGGATCCAGTACCGC
1 AAAAAGACA-AAAGGGAAAGATCTAAG-TCGCAACGGCGGATCTAGTACC-T
34191390 AAAAAGACAAAAGGGAAA
1 AAAAAGACAAAAGGGAAA
34191408 AGTCTTTATC
Statistics
Matches: 335, Mismatches: 105, Indels: 66
0.66 0.21 0.13
Matches are distributed among these distances:
48 3 0.01
49 38 0.11
50 116 0.35
51 136 0.41
52 39 0.12
53 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (49 bp):
AAAAAGACAAAAGGGAAAGATCTAAGTCGCAACGGCGGATCTAGTACCT
Found at i:34191033 original size:50 final size:49
Alignment explanation
Indices: 34190885--34191337 Score: 213
Period size: 51 Copynumber: 9.0 Consensus size: 49
34190875 AGTATCACGC
* *
34190885 AAAAAGATAAAAGGGAAAGGTCTAAGTCGTAACGGCGGACCGTGTAACT
1 AAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCT
* * * * * * * *
34190934 CAGAAGACACGACGGGAAAGATCTAAGATCGCAACGGTGGATC-TAGTACCGT
1 AAAAAGATA-AAAGGGAAAGGTCTAAG-TCGCAACGGCGGACCGT-GTACC-T
* *
34190986 AAAAAGATAAAAGGGAAAGGTATAAGTCACAACGGCGGACCGTGTACCT
1 AAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCT
* * * * * ** * * * *
34191035 CAGAAGACATGACGGGAAAAATCTAAGATCGTAACGGCGAATTC-AGTACCAT
1 AAAAAGATA-AAAGGGAAAGGTCTAAG-TCGCAACGGCGGA-CCGTGTACC-T
**
34191087 AAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGTAGACCGTGTACC-
1 AAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCT
* * * * * * * *
34191135 ACAAAAGACACGACA-GAAAAGATCTAAGACCACAATGGCGGATCC-AGTACAGC-
1 A-AAAAGATA--AAAGGGAAAGGTCTAAG-TCGCAACGGCGGA-CCGTGTAC--CT
* * *
34191188 AAAAAGAT-AAAGGGTAAAGGTCTAAGTCGCAACGGAGAACTGTGTACC-
1 AAAAAGATAAAAGGG-AAAGGTCTAAGTCGCAACGGCGGACCGTGTACCT
* * * * * * * * * * *
34191236 ACAGAAGACACGACGAGAAAGATTTAAGACCGCAACGGTGGATC-TAGTACCGC
1 A-AAAAGATA-AAAGGGAAAGGTCTAAG-TCGCAACGGCGGACCGT-GTACC-T
* *
34191289 AAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGACGGACCGTGTACCT
1 AAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCT
34191338 CAGAAGACAC
Statistics
Matches: 286, Mismatches: 90, Indels: 56
0.66 0.21 0.13
Matches are distributed among these distances:
48 3 0.01
49 29 0.10
50 108 0.38
51 113 0.40
52 30 0.10
53 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (49 bp):
AAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCT
Found at i:34191060 original size:101 final size:101
Alignment explanation
Indices: 34190882--34191412 Score: 645
Period size: 101 Copynumber: 5.3 Consensus size: 101
34190872 CTTAGTATCA
* *
34190882 CGCAAAAAGATAAAAGGGAAAGGTCTAAGTCGTAACGGCGGACCGTGTAACTCAGAAGACACGAC
1 CGCAAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACACGAC
* * *
34190947 GGGAAAGATCTAAGATCGCAACGGTGGATCTAGTAC
66 GAGAAAAATCTAAGATCGCAACGGCGGATCTAGTAC
* * * *
34190983 CGTAAAAAGATAAAAGGGAAAGGTATAAGTCACAACGGCGGACCGTGTACCTCAGAAGACATGAC
1 CGCAAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACACGAC
* * *
34191048 GGGAAAAATCTAAGATCGTAACGGCGAAT-TCAGTAC
66 GAGAAAAATCTAAGATCGCAACGGCGGATCT-AGTAC
** ** * *
34191084 CATAAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGTAGACCGTGTACCACAAAAGACACGAC
1 CGCAAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACACGAC
* * * *
34191149 -AGAAAAGATCTAAGACCACAATGGCGGATCCAGTAC
66 GAGAAAA-ATCTAAGATCGCAACGGCGGATCTAGTAC
* * * * *
34191185 AGCAAAAAGAT-AAAGGGTAAAGGTCTAAGTCGCAACGGAGAACTGTGTACCACAGAAGACACGA
1 CGCAAAAAGATAAAAGGG-AAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACACGA
* * * *
34191249 CGAGAAAGATTTAAGACCGCAACGGTGGATCTAGTAC
65 CGAGAAAAATCTAAGATCGCAACGGCGGATCTAGTAC
* * *
34191286 CGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGACACGAT
1 CGCAAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACACGAC
* * * * *
34191351 GAGAAATATCAAAGATCACAACGACGGATCCAGTAC
66 GAGAAAAATCTAAGATCGCAACGGCGGATCTAGTAC
* *
34191387 CGCAAAAAGACAAAAGGGAAAAGTCT
1 CGCAAAAAGATAAAAGGGAAAGGTCT
34191413 TTATCTCTCT
Statistics
Matches: 368, Mismatches: 56, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
100 12 0.03
101 345 0.94
102 11 0.03
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.14
Consensus pattern (101 bp):
CGCAAAAAGATAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACACGAC
GAGAAAAATCTAAGATCGCAACGGCGGATCTAGTAC
Found at i:34191518 original size:92 final size:92
Alignment explanation
Indices: 34191407--34191652 Score: 440
Period size: 92 Copynumber: 2.7 Consensus size: 92
34191397 CAAAAGGGAA
34191407 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATCCT
34191472 CTTGAAGTTGCAGTAAAGTTGGATAGC
66 CTTGAAGTTGCAGTAAAGTTGGATAGC
*
34191499 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATCCT
34191564 CTTGAAGTTGCAGTAAAGTTGGATAGC
66 CTTGAAGTTGCAGTAAAGTTGGATAGC
* * * *
34191591 AAGTCTTTATCTCTCTAAAGTTGCAGTAAGAGCAAGATGAAGC-TTCAACATCAAATCCTATC
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATC
34191653 TTCATAAAGA
Statistics
Matches: 148, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 16 0.11
92 132 0.89
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (92 bp):
AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATCCT
CTTGAAGTTGCAGTAAAGTTGGATAGC
Found at i:34191864 original size:39 final size:39
Alignment explanation
Indices: 34191736--34191883 Score: 120
Period size: 39 Copynumber: 3.8 Consensus size: 39
34191726 ATAAAGATTC
* * * *
34191736 TGATCTCTTACCCCAAGCCAGAGGCAGATTAAAGCCATT
1 TGATCTCTTACCCCGAGCTAGGGGCAGATTATAGCCATT
* * * * **
34191775 TGATCTTTTACCCCGAGCTTA-GGGCAAATCATCA-TCAAC
1 TGATCTCTTACCCCGAGC-TAGGGGCAGATTAT-AGCCATT
** *
34191814 CAATCTCTTACCCCGAGCTAGGGGCAGATTGTAGCCATT
1 TGATCTCTTACCCCGAGCTAGGGGCAGATTATAGCCATT
* * *
34191853 TGATCTTTTACCCCGAGCTTGGGGTAGATTA
1 TGATCTCTTACCCCGAGCTAGGGGCAGATTA
34191884 CAACCTTCCA
Statistics
Matches: 80, Mismatches: 25, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
38 3 0.04
39 75 0.94
40 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (39 bp):
TGATCTCTTACCCCGAGCTAGGGGCAGATTATAGCCATT
Found at i:34192282 original size:49 final size:49
Alignment explanation
Indices: 34192143--34192260 Score: 236
Period size: 49 Copynumber: 2.4 Consensus size: 49
34192133 TGGACCAAAT
34192143 TCATCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAACGATGCGG
1 TCATCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAACGATGCGG
34192192 TCATCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAACGATGCGG
1 TCATCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAACGATGCGG
34192241 TCATCTTCCTGATGAGATAC
1 TCATCTTCCTGATGAGATAC
34192261 TGAGAAGAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (49 bp):
TCATCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAACGATGCGG
Found at i:34192417 original size:254 final size:255
Alignment explanation
Indices: 34191967--34192472 Score: 798
Period size: 254 Copynumber: 2.0 Consensus size: 255
34191957 GATTGTGATT
* *
34191967 ATTGAAACAAACGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACTCAT
1 ATTGAAACAAACGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
* * * * * * *
34192032 GCTTGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATATTGAGAGGCAGGGCGAAGTA
66 GCTCGATATGAGCAAATCTTCGAACCCCAGATTCCTGATGAGATACTGAGAAGCAGGGCGAAGCA
*
34192097 ATAAAATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATA
131 ATAAAATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATAAGATA
*
34192162 CAAAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACAAAGAAGCGG
196 CAAAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACAAAGAAGCGG
* *
34192222 ATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAATCAAACCCAC
1 ATTGAAACAAACGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
* * *
34192287 GCTCGATATGAGCAAATTTTTGAA-CCCAGATTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
66 GCTCGATATGAGCAAATCTTCGAACCCCAGATTCCTGATGAGATACTGAGAAGCAGGGCGAAGCA
* * *
34192351 ATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATA
131 ATAAAATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATAAGATA
* ** *
34192416 CAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTAAGAAG
196 CAAAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACAAAGAAG
34192473 AAGACCAAAT
Statistics
Matches: 228, Mismatches: 23, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
254 147 0.64
255 81 0.36
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (255 bp):
ATTGAAACAAACGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
GCTCGATATGAGCAAATCTTCGAACCCCAGATTCCTGATGAGATACTGAGAAGCAGGGCGAAGCA
ATAAAATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATAAGATA
CAAAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACAAAGAAGCGG
Found at i:34192464 original size:205 final size:205
Alignment explanation
Indices: 34192195--34192880 Score: 917
Period size: 205 Copynumber: 3.4 Consensus size: 205
34192185 GATGCGGTCA
* * ** *
34192195 TCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATA
1 TCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATA
** * *
34192260 CTGAGAAGAAGATCAAATCAAACCCACGCTCGATATGAGCAAATTTTTGAACCCAGATTCCTGAT
66 CTGAGAAGAAGATCAAATCAAACCCACGCTCGATGCGAGCAAATCTTCGAACCCAGATTCCTGAT
*
34192325 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGG
131 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGG
34192390 ACCAAATTCG
196 ACCAAATTCG
34192400 TCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATA
1 TCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATA
* * * *
34192465 CTAAGAAGAAGACCAAATCAAACCCACGCTTGATGCGAGAAAATCTTCGAACCCCA-ACTTCCTG
66 CTGAGAAGAAGATCAAATCAAACCCACGCTCGATGCGAGCAAATCTTCGAA-CCCAGA-TTCCTG
*
34192529 ATGAG-TACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGT
129 ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGT
*
34192593 GGACCAAATTCA
194 GGACCAAATTCG
* * * * *
34192605 TCTTCCTGATGAGATACTGAGAAGCGAATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATA
1 TCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATA
* * * * *
34192670 C--AG-AGAAG-T---ATGCCAACTCGACGCTCGATGCGAGCAAATCTTCAAACCTAGCTTCCTG
66 CTGAGAAGAAGATCAAAT-CAAAC-CCACGCTCGATGCGAGCAAATCTTCGAACCCAGATTCCTG
* * *
34192728 ATGAGATATTGAGAAGCAGGTCGAAGCAATAAAGTGGTTAGCTTCCTGATGAGATACGGAGAAGT
129 ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGT
*
34192793 GAACCAAA-TCAG
194 GGACCAAATTC-G
* * * ** *
34192805 TCTTCCTGATGAA-ACAAAGAGAAGTGGATCAAAACAAGTGATGCAGTCATCTTCCCGATGAGAT
1 TCTTCCTGAT-AAGATACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGAT
34192869 ACTGAGAAGAAG
65 ACTGAGAAGAAG
34192881 GCCAAGTCAA
Statistics
Matches: 424, Mismatches: 46, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
198 2 0.00
199 20 0.05
200 139 0.33
201 1 0.00
202 7 0.02
203 7 0.02
205 233 0.55
206 15 0.04
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (205 bp):
TCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATA
CTGAGAAGAAGATCAAATCAAACCCACGCTCGATGCGAGCAAATCTTCGAACCCAGATTCCTGAT
GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGG
ACCAAATTCG
Found at i:34193249 original size:22 final size:21
Alignment explanation
Indices: 34193223--34193267 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
34193213 GATCAAAAAT
34193223 TTGATTTTAAATTAAGTTTAAA
1 TTGATTTTAAATTAA-TTTAAA
*
34193245 TTGATTTTAAATTTATTTAAA
1 TTGATTTTAAATTAATTTAAA
34193266 TT
1 TT
34193268 TAAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
TTGATTTTAAATTAATTTAAA
Found at i:34193264 original size:27 final size:27
Alignment explanation
Indices: 34193234--34193286 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
34193224 TGATTTTAAA
*
34193234 TTAAGTTTAAATTGATTTTAAATTTAT
1 TTAAATTTAAATTGATTTTAAATTTAT
*
34193261 TTAAATTTAAATTTATTTTAAATTTA
1 TTAAATTTAAATTGATTTTAAATTTA
34193287 AATACAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (27 bp):
TTAAATTTAAATTGATTTTAAATTTAT
Found at i:34193271 original size:16 final size:17
Alignment explanation
Indices: 34193219--34193289 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
34193209 CTTGGATCAA
34193219 AAATTTGATTTTAAA-TT
1 AAATTT-ATTTTAAATTT
* ** * *
34193236 AAGTTTAAATTGATTTT
1 AAATTTATTTTAAATTT
34193253 AAATTTA-TTTAAATTT
1 AAATTTATTTTAAATTT
34193269 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
34193286 AAAT
1 AAAT
34193290 ACAGTTAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
16 17 0.40
17 26 0.60
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:34193286 original size:11 final size:11
Alignment explanation
Indices: 34193219--34193269 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
34193209 CTTGGATCAA
34193219 AAATTTGATTTT
1 AAATTT-ATTTT
* *
34193231 AAATTAAGTTT
1 AAATTTATTTT
*
34193242 AAATTGATTTT
1 AAATTTATTTT
34193253 AAATTTA-TTT
1 AAATTTATTTT
34193263 AAATTTA
1 AAATTTA
34193270 AATTTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 10 0.29
11 19 0.56
12 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (11 bp):
AAATTTATTTT
Found at i:34193297 original size:27 final size:27
Alignment explanation
Indices: 34193228--34193315 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
34193218 AAAATTTGAT
* *
34193228 TTTAAATTAAGTTTAAATTGATTTTAAA
1 TTTAAATAAAG-TTAAATTTATTTTAAA
** *
34193256 TTTATTTAAATTTAAATTTATTTTAAA
1 TTTAAATAAAGTTAAATTTATTTTAAA
* *
34193283 TTTAAATACAGTTAAA-ATAGTTTTAAA
1 TTTAAATAAAGTTAAATTTA-TTTTAAA
*
34193310 CTTAAA
1 TTTAAA
34193316 ATCAAATTTA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
26 2 0.04
27 39 0.81
28 7 0.15
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (27 bp):
TTTAAATAAAGTTAAATTTATTTTAAA
Found at i:34194037 original size:3 final size:3
Alignment explanation
Indices: 34194031--34194119 Score: 61
Period size: 3 Copynumber: 28.7 Consensus size: 3
34194021 ATCATCAATG
* * * * *
34194031 ATA ATA ATA ATA ATA TTA CTA ATA ACA CTA ATA ATGA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
** * * *
34194077 ATA ATTA GCA TTA ATAA ATA ATA ATA ATA ATA TTA ATA TTA AT
1 ATA A-TA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT
34194120 GTTTTAATAA
Statistics
Matches: 65, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
3 57 0.88
4 8 0.12
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:34195202 original size:29 final size:29
Alignment explanation
Indices: 34195151--34195349 Score: 186
Period size: 29 Copynumber: 6.7 Consensus size: 29
34195141 GAAGTCCCTG
*
34195151 AACTTTCAAAAATTACATTTTTTACCCCAA
1 AACTTCCAAAAATTACA-TTTTTACCCCAA
* **
34195181 AATTTCTTAAAATTACATTTTTGACCCCAA
1 AACTTCCAAAAATTACATTTTT-ACCCCAA
* * *
34195211 AACTTCCAAAAATCACATTTTTACCATC-G
1 AACTTCCAAAAATTACATTTTTACC-CCAA
* *
34195240 AACTTCTAAAAATTACATTTTAACCCCAA
1 AACTTCCAAAAATTACATTTTTACCCCAA
* **
34195269 AACTTCCAAAAATTACCTTTTTACCCTTA
1 AACTTCCAAAAATTACATTTTTACCCCAA
*
34195298 AACTTCCAAAAATT-CTATTTTTGACCTCAA
1 AACTTCCAAAAATTAC-ATTTTT-ACCCCAA
* **
34195328 AAGTTGAAAAAATTACTATTTT
1 AACTTCCAAAAATTAC-ATTTT
34195350 GCCCCCGAAT
Statistics
Matches: 136, Mismatches: 27, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
28 2 0.01
29 73 0.54
30 54 0.40
31 7 0.05
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCCAA
Found at i:34197950 original size:17 final size:16
Alignment explanation
Indices: 34197924--34197957 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
34197914 TTTCATTAGC
34197924 AAAAATTAAAAATTTA
1 AAAAATTAAAAATTTA
*
34197940 AAAATATTAAAATTTTA
1 AAAA-ATTAAAAATTTA
34197957 A
1 A
34197958 GTCTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATTAAAAATTTA
Found at i:34199377 original size:24 final size:24
Alignment explanation
Indices: 34199348--34199394 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
34199338 CTATCATAGT
* *
34199348 TTTGTCCACAGTTTTATGGTTTTA
1 TTTGTCCACAGTTTCATAGTTTTA
34199372 TTTGTCCACAGTTTCATAGTTTT
1 TTTGTCCACAGTTTCATAGTTTT
34199395 GTGCATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (24 bp):
TTTGTCCACAGTTTCATAGTTTTA
Found at i:34204720 original size:15 final size:15
Alignment explanation
Indices: 34204700--34204750 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
34204690 TTTCTTCAAG
34204700 TTATATTTTAATCAT
1 TTATATTTTAATCAT
*
34204715 TTATATTTGAA--AT
1 TTATATTTTAATCAT
*
34204728 ATTACATTTTAATCAT
1 -TTATATTTTAATCAT
34204744 TTATATT
1 TTATATT
34204751 ATCACGTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.31
15 16 0.55
16 2 0.07
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (15 bp):
TTATATTTTAATCAT
Found at i:34206542 original size:106 final size:107
Alignment explanation
Indices: 34206276--34206830 Score: 292
Period size: 96 Copynumber: 5.4 Consensus size: 107
34206266 CATACCTTTG
* * * * **
34206276 TTCAAAGATGAATTCTACAAGCTTTACTTGGATATTTAGTTCAATGGTTAATTGTGGAGCTCGTT
1 TTCAAAGATGAATTCTACAAGCTTTAC-TGGACATTTAGTTCAATAGTAAATTATGGAGCAAGTT
* * *
34206341 TTGACCTGAACATTTAGCTCAATAGTATACTCATGTATCTATA
65 TTAACCTGAACATTTAGCTCAATAGTATACTCATATATCCATA
* **
34206384 TCCAAAGATGAATTCTACAAGCTTTACATGGACA-TTATGTTCAATACCAAATTATGGAGCAAG-
1 TTCAAAGATGAATTCTACAAGCTTTAC-TGGACATTTA-GTTCAATAGTAAATTATGGAGCAAGT
* * ** *
34206447 TTTAACCTGAATATTTAGCTCAAT-TTATGTTCATATGTCCCA-A
64 TTTAACCTGAACATTTAGCTCAATAGTATACTCATATAT-CCATA
* * * *
34206490 TTCAAAAATGAATTCTACAAGCTATACTCAGACATTTAGTTCAATAGTAAATTAAGG-G---G--
1 TTCAAAGATGAATTCTACAAGCTTTACT-GGACATTTAGTTCAATAGTAAATTATGGAGCAAGTT
* * * ** **
34206549 ------TGAGCGTTTAGGTCAATAGTATGTTCAT-TCATCTTTA
65 TTAACCTGAACATTTAGCTCAATAGTATACTCATAT-ATCCATA
* * * * * *
34206586 TTTAAAGATGAATTTTACAAGCTTTACTTGAACATTTAATTCAATGGTAAATTATGG-GCAAG-C
1 TTCAAAGATGAATTCTACAAGCTTTAC-TGGACATTTAGTTCAATAGTAAATTATGGAGCAAGTT
** * * * * *
34206649 TTAA-CAAAAGATTAAGCTGAATAGTAAATTCATATATCTC-TA
65 TTAACCTGAACATTTAGCTCAATAGTATACTCATATATC-CATA
* * * * * * *
34206691 TTCAAAGATGAATTCTACAAGC---A-T---TATTTAGCTGAACAATAAATTATTGAGC-AGGTT
1 TTCAAAGATGAATTCTACAAGCTTTACTGGACATTTAGTTCAATAGTAAATTATGGAGCAAGTTT
* *
34206748 TCACCCGAACATTCT-GCTCAATAGTATGA-TCATATATCTC-TA
66 TAACCTGAACATT-TAGCTCAATAGTAT-ACTCATATATC-CATA
* * * *
34206790 TTCAAAGATGGACTCTGCAAGCTTTACTTGAACATTTAGTT
1 TTCAAAGATGAATTCTACAAGCTTTAC-TGGACATTTAGTT
34206831 TAAAAATAAA
Statistics
Matches: 339, Mismatches: 76, Indels: 65
0.71 0.16 0.14
Matches are distributed among these distances:
95 15 0.04
96 58 0.17
97 20 0.06
98 5 0.01
99 49 0.14
100 2 0.01
102 3 0.01
104 1 0.00
105 45 0.13
106 55 0.16
107 37 0.11
108 49 0.14
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (107 bp):
TTCAAAGATGAATTCTACAAGCTTTACTGGACATTTAGTTCAATAGTAAATTATGGAGCAAGTTT
TAACCTGAACATTTAGCTCAATAGTATACTCATATATCCATA
Found at i:34207355 original size:86 final size:87
Alignment explanation
Indices: 34207223--34207382 Score: 211
Period size: 86 Copynumber: 1.9 Consensus size: 87
34207213 AAATAAATTC
* * * *
34207223 AGCAAGTTTCATCCGGAACATTCAGCTCAATATTATGTTCACATAT-CTATTCAAGGAA-AATTT
1 AGCAAGATTCATCCCGAACATTCAGCTCAACATTATGTTCACATATCCTATTCAAAGAAGAA--T
34207286 TCTGCAAGCTTAAATAAAATATTA
64 TCTGCAAGCTTAAATAAAATATTA
* *
34207310 AGCAAGATTCA-CCCGAACATTTAGCTCAACCA-TATGTTCATATATCCTATTCAAAGAAGAATT
1 AGCAAGATTCATCCCGAACATTCAGCTCAA-CATTATGTTCACATATCCTATTCAAAGAAGAATT
34207373 CTGCAAGCTT
65 CTGCAAGCTT
34207383 TTCTCGGACA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
86 40 0.62
87 22 0.34
88 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (87 bp):
AGCAAGATTCATCCCGAACATTCAGCTCAACATTATGTTCACATATCCTATTCAAAGAAGAATTC
TGCAAGCTTAAATAAAATATTA
Found at i:34208846 original size:15 final size:14
Alignment explanation
Indices: 34208821--34208859 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
34208811 TCACATTTTG
34208821 ATTCTCAATTTTATT
1 ATTCTCAA-TTTATT
* *
34208836 GTTCTCGATTTATT
1 ATTCTCAATTTATT
34208850 ATTCTCAATT
1 ATTCTCAATT
34208860 GTCAATTCTC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTCTCAATTTATT
Found at i:34211948 original size:52 final size:52
Alignment explanation
Indices: 34211790--34211973 Score: 228
Period size: 52 Copynumber: 3.5 Consensus size: 52
34211780 TTTCATTTAA
* ** * * *
34211790 TACTCACGATGACA-TATAGTCATCGGACCCCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCCTTTAATCCGTAAAGG-ATTCATT
* * * * *
34211843 TACTCACGATGACACTGAGTCATCGGA-CCTTTAATTCGTCATGAATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATT
34211894 TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATT
*
34211946 TACTCACGATGACACTTAGTCATTGGAC
1 TACTCACGATGACACTTAGTCATCGGAC
34211974 TTTTTCGTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
51 32 0.29
52 55 0.49
53 24 0.21
54 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (52 bp):
TACTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATT
Found at i:34220946 original size:29 final size:29
Alignment explanation
Indices: 34220889--34220946 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
34220879 TGTACATGTG
***
34220889 GAATTTAGTTATTTTACTTTTATTTTTAA
1 GAATTTAGTTATTTTACTTTTAGGATTAA
* *
34220918 GAATTTAGTTATTTTATTTTTCGGATTAA
1 GAATTTAGTTATTTTACTTTTAGGATTAA
34220947 AAAATTCAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (29 bp):
GAATTTAGTTATTTTACTTTTAGGATTAA
Found at i:34231140 original size:17 final size:17
Alignment explanation
Indices: 34231096--34231150 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
34231086 TTAATTAAAC
34231096 TTTTAAATTT-AAAT--
1 TTTTAAATTTAAAATAA
*
34231110 TTTT-AATTCGAAAATAA
1 TTTTAAATT-TAAAATAA
34231127 TTTTAAATTTAAAATAA
1 TTTTAAATTTAAAATAA
*
34231144 ATTTAAA
1 TTTTAAA
34231151 CTCCAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 4 0.12
17 17 0.52
18 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTTAAATTTAAAATAA
Found at i:34231146 original size:18 final size:19
Alignment explanation
Indices: 34231105--34231147 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
34231095 CTTTTAAATT
*
34231105 TAAATTTTTAATTCGAAAA
1 TAAATTTTAAATTCGAAAA
*
34231124 T-AATTTTAAATT-TAAAA
1 TAAATTTTAAATTCGAAAA
34231141 TAAATTT
1 TAAATTT
34231148 AAACTCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 15 0.71
19 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAATTTTAAATTCGAAAA
Found at i:34240115 original size:3 final size:3
Alignment explanation
Indices: 34240109--34240142 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
34240099 TTGAGGAAGA
*
34240109 AGG AGG AGGG TGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG A-GG AGG AGG AGG AGG AGG AGG AGG AGG
34240143 GGTGGAGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.68, T:0.03
Consensus pattern (3 bp):
AGG
Found at i:34263370 original size:40 final size:40
Alignment explanation
Indices: 34263323--34263403 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
34263313 TTTGTGGATA
*
34263323 GCTACCTTTCTTGACATCCAAGTAATTGTTTATATTAATG
1 GCTACCTTTCTTGACATCCAAGTAATTGTTTACATTAATG
34263363 GCTACCTTTCTTGACATCCAAGTAATTGTTTACATTAATG
1 GCTACCTTTCTTGACATCCAAGTAATTGTTTACATTAATG
34263403 G
1 G
34263404 AATTATTTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (40 bp):
GCTACCTTTCTTGACATCCAAGTAATTGTTTACATTAATG
Found at i:34270074 original size:17 final size:17
Alignment explanation
Indices: 34270049--34270092 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
34270039 CTTGTTTAGA
* * *
34270049 AATTATTTTATTATACT
1 AATTTTTTTATAATAAT
34270066 AATTTTTTTATAATAAT
1 AATTTTTTTATAATAAT
34270083 AATTATTTTT
1 AATT-TTTTT
34270093 TAAAAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTTTATAATAAT
Found at i:34270411 original size:20 final size:20
Alignment explanation
Indices: 34270383--34270421 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34270373 AAATTAAATA
*
34270383 TATATTTTTCAAAAAAAAAC
1 TATAATTTTCAAAAAAAAAC
34270403 TATAATTTTCAAAAAAAAA
1 TATAATTTTCAAAAAAAAA
34270422 TTATTCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAATTTTCAAAAAAAAAC
Found at i:34272105 original size:43 final size:44
Alignment explanation
Indices: 34272032--34272127 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 44
34272022 TTATTACAAT
*
34272032 TTAAATTATAATTATTTTAAATGTGAAATTATCACAA-TT-TATA
1 TTAAATTATAATTATTTTAAATAT-AAATTATCACAACTTCTATA
* *
34272075 TTAAATTATAATTATTTTTAAATA-ATAATTATCATAACTTCTATT
1 TTAAATTATAATTA-TTTTAAATATA-AATTATCACAACTTCTATA
34272120 TTAAATTA
1 TTAAATTA
34272128 ATTTTTTAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
42 1 0.02
43 24 0.52
44 10 0.22
45 11 0.24
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (44 bp):
TTAAATTATAATTATTTTAAATATAAATTATCACAACTTCTATA
Found at i:34272130 original size:43 final size:41
Alignment explanation
Indices: 34272032--34272182 Score: 109
Period size: 43 Copynumber: 3.6 Consensus size: 41
34272022 TTATTACAAT
*
34272032 TTAAATTATAATTATTTTAAAT-GTGAAATTATCACAATTTATA
1 TTAAATTATAATT-TTTTAAATAAT--AATTATCACAATTTATA
* *
34272075 TTAAATTATAATTATTTTTAAATAATAATTATCATAACTTCTATT
1 TTAAATTATAA-T-TTTTTAAATAATAATTATCACAA-TT-TATA
* * *
34272120 TTAAA-T-TAATTTTTTAACTAATAATT-TTA-AATTAAATA
1 TTAAATTATAATTTTTTAAATAATAATTATCACAATT-TATA
*
34272158 TTATAATTAT-TTTTTTTAAA-AATAA
1 TTA-AATTATAATTTTTTAAATAATAA
34272183 AAAAAAATAT
Statistics
Matches: 90, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
38 7 0.08
39 9 0.10
40 11 0.12
41 16 0.18
42 1 0.01
43 24 0.27
44 12 0.13
45 10 0.11
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.50
Consensus pattern (41 bp):
TTAAATTATAATTTTTTAAATAATAATTATCACAATTTATA
Found at i:34274328 original size:35 final size:35
Alignment explanation
Indices: 34274287--34274357 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
34274277 GTAAAAATGG
34274287 TTTAAAATCATTCAAACTAAGATAAATTGTAAAGA
1 TTTAAAATCATTCAAACTAAGATAAATTGTAAAGA
34274322 TTTAAAATCATTCAAACTAAGATAAATTGTAAAGA
1 TTTAAAATCATTCAAACTAAGATAAATTGTAAAGA
34274357 T
1 T
34274358 AATGTAAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (35 bp):
TTTAAAATCATTCAAACTAAGATAAATTGTAAAGA
Found at i:34274965 original size:112 final size:112
Alignment explanation
Indices: 34274849--34275067 Score: 341
Period size: 112 Copynumber: 2.0 Consensus size: 112
34274839 AACATGATTA
** * *
34274849 ATAGAATAATCAAAAAATAACATGTGACATGTCATGT-ATACATCATTTTGACATACAAAAGTCA
1 ATAGAATAATCAAAAAATAACATGTGACATACCATGTGA-ACATCATTCTGACATACAAAAATCA
*
34274913 ATTTTTAACAATAAAAATAAATCAAACTTTTAACAGAAAAATGGTTTT
65 ATTTTTAACAATAAAAATAAATCAAACCTTTAACAGAAAAATGGTTTT
* * * *
34274961 ATAGAATAATCAAACAATGACATGTGACATACCATGTGAATATTATTCTGACATACAAAAATCAA
1 ATAGAATAATCAAAAAATAACATGTGACATACCATGTGAACATCATTCTGACATACAAAAATCAA
34275026 TTTTTAACAATAAAAATAAATCAAACCTTTAACAGAAAAATG
66 TTTTTAACAATAAAAATAAATCAAACCTTTAACAGAAAAATG
34275068 AGTCTACTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
112 96 0.99
113 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (112 bp):
ATAGAATAATCAAAAAATAACATGTGACATACCATGTGAACATCATTCTGACATACAAAAATCAA
TTTTTAACAATAAAAATAAATCAAACCTTTAACAGAAAAATGGTTTT
Found at i:34277916 original size:26 final size:25
Alignment explanation
Indices: 34277861--34277918 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
34277851 GGATAGGTTA
34277861 TCATAGGAAATATTATGGTTTTTTT
1 TCATAGGAAATATTATGGTTTTTTT
34277886 TCATAGGAAATATTATGGTTTTTTT
1 TCATAGGAAATATTATGGTTTTTTT
34277911 TCCATAGG
1 T-CATAGG
34277919 GGCTAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 26 0.81
26 6 0.19
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (25 bp):
TCATAGGAAATATTATGGTTTTTTT
Found at i:34284853 original size:21 final size:22
Alignment explanation
Indices: 34284823--34284882 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
34284813 ATTTAAACTT
*
34284823 TTTATTAATTTTAATAATT-TG
1 TTTATAAATTTTAATAATTATG
*
34284844 TTTATAAATTATT-ATAATTATT
1 TTTATAAATT-TTAATAATTATG
34284866 TTTATATTAATTTTAAT
1 TTTATA--AATTTTAAT
34284883 TTGAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 15 0.47
22 9 0.28
23 2 0.06
24 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTATAAATTTTAATAATTATG
Found at i:34285674 original size:19 final size:20
Alignment explanation
Indices: 34285646--34285686 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
34285636 CAAATAATTA
* *
34285646 TTAATTAATATTATT-ATAT
1 TTAATAAATAATATTCATAT
34285665 TTAATAAATAATATTCATAT
1 TTAATAAATAATATTCATAT
34285685 TT
1 TT
34285687 TTGAGAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATAAATAATATTCATAT
Found at i:34291189 original size:60 final size:59
Alignment explanation
Indices: 34291083--34291270 Score: 210
Period size: 60 Copynumber: 3.2 Consensus size: 59
34291073 ACTACACTAG
* * *
34291083 TAGTCACTCAACTATTAGTAAATTTTCTTTTTGGTCATCTAATTATGAAAAGTTACAAAA
1 TAGTCACTCAACCATTAGTAAA-TTTCTTTTTGGTCACCAAATTATGAAAAGTTACAAAA
*
34291143 TATTCAC-CAAACCATTAGTAAATTTCTTTTTGGGTCACCAAATTATGAAAAGTTACAAAA
1 TAGTCACTC-AACCATTAGTAAATTTCTTTTT-GGTCACCAAATTATGAAAAGTTACAAAA
* * *
34291203 TAGTCACTCAACTATTAGT-AA--TATTTTTGGTCACCCAACTTCA--AAAAGTTACAAAA
1 TAGTCACTCAACCATTAGTAAATTTCTTTTTGGTCA-CCAAATT-ATGAAAAGTTACAAAA
34291259 T-GATCACTCAAC
1 TAG-TCACTCAAC
34291271 TATTCATTTT
Statistics
Matches: 114, Mismatches: 8, Indels: 16
0.83 0.06 0.12
Matches are distributed among these distances:
55 1 0.01
56 28 0.25
57 12 0.11
58 1 0.01
59 12 0.11
60 59 0.52
61 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.35
Consensus pattern (59 bp):
TAGTCACTCAACCATTAGTAAATTTCTTTTTGGTCACCAAATTATGAAAAGTTACAAAA
Done.