Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 12 of 199
Found at i:3720712 original size:6 final size:6
Alignment explanation
Indices: 3720703--3720733 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3720693 TTAAATTTTT
3720703 ATATTA ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA ATATTA A
3720734 ATAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:3720741 original size:18 final size:18
Alignment explanation
Indices: 3720703--3720738 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3720693 TTAAATTTTT
*
3720703 ATATTAATATTAATATTA
1 ATATTAATATTAATATAA
3720721 ATATTAATATTAA-ATAA
1 ATATTAATATTAATATAA
3720738 A
1 A
3720739 ATAAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTAATATTAATATAA
Found at i:3722334 original size:21 final size:21
Alignment explanation
Indices: 3722304--3722343 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3722294 GAGCTTGCCT
* *
3722304 TTATTTTTTTATTTTTAAATC
1 TTATTATTTTAATTTTAAATC
3722325 TTATTATTTTAATTTTAAA
1 TTATTATTTTAATTTTAAA
3722344 AAGATATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTATTTTAATTTTAAATC
Found at i:3727702 original size:16 final size:15
Alignment explanation
Indices: 3727678--3727711 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3727668 AGATTAATTT
3727678 TATTTAAAATTAAAA
1 TATTTAAAATTAAAA
*
3727693 TATTTGAAAATTATAA
1 TATTT-AAAATTAAAA
3727709 TAT
1 TAT
3727712 ACCAAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TATTTAAAATTAAAA
Found at i:3730446 original size:24 final size:27
Alignment explanation
Indices: 3730415--3730473 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
3730405 TATCGGATTA
3730415 ATTATTTA-ATATA-AA-T-ATATAATT
1 ATTATTTACATATATAATTAATATAA-T
3730439 ATTATTTATCATATATAATTAATATAAT
1 ATTATTTA-CATATATAATTAATATAAT
3730467 ATTATTT
1 ATTATTT
3730474 TATAACATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 8 0.27
26 5 0.17
27 2 0.07
28 9 0.30
29 6 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTATTTACATATATAATTAATATAAT
Found at i:3732760 original size:94 final size:95
Alignment explanation
Indices: 3732634--3732856 Score: 252
Period size: 95 Copynumber: 2.4 Consensus size: 95
3732624 TAAATAAGGG
** ** * ** * * *
3732634 ATTAGGGTTTAGGGTTTGTCAATTAAATTAATTAAAAAAATTT-AAAATTGGATTA-GTTTTCGT
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTTAAAAATCAGATTAGGATTTAGA
** * *
3732697 GTTTATTATTTTTTAAGAAAAAATCAATTAA
66 G-TTAAGAGTTTTTAAGAAAAAATCAAATAA
* *
3732728 ATTAGGGTTTAGGGTTACTTGAGTAATTTAATTTAAAAAATTTAAAAATCAGATTAGGATTTAGA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTTAAAAATCAGATTAGGATTTAGA
* *
3732793 GTTAAGGGTTTTTAAGGAAAAATCAAATAA
66 GTTAAGAGTTTTTAAGAAAAAATCAAATAA
*
3732823 ATTAGGGTTCAGGGTTACTTGAGTAAATTAATTA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTA
3732857 TATATTTATA
Statistics
Matches: 106, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
94 36 0.34
95 64 0.60
96 6 0.06
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (95 bp):
ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTTAAAAATCAGATTAGGATTTAGA
GTTAAGAGTTTTTAAGAAAAAATCAAATAA
Found at i:3732962 original size:15 final size:17
Alignment explanation
Indices: 3732925--3732963 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3732915 AAAGAATTTC
3732925 TATTATATTAAAAATTG
1 TATTATATTAAAAATTG
*
3732942 TCTTAT-TTAAAAATT-
1 TATTATATTAAAAATTG
3732957 TATTATA
1 TATTATA
3732964 AAGAATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 5 0.26
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
TATTATATTAAAAATTG
Found at i:3732967 original size:48 final size:48
Alignment explanation
Indices: 3732915--3733034 Score: 154
Period size: 47 Copynumber: 2.5 Consensus size: 48
3732905 GCCTTATTTA
* *
3732915 AAAGAATTTCTATTATATTAAAAATTGTCTTATTTAAAAATTTATTAT
1 AAAGAATTTCTATTATATTAAAAATTGCCTTATTTAAAAAGTTATTAT
* * * *
3732963 AAAGAATTT-TGATTATA-AAAAAACTGCCTTATTTAAAACGTTATTGT
1 AAAGAATTTCT-ATTATATTAAAAATTGCCTTATTTAAAAAGTTATTAT
*
3733010 AAAGAATTTCAATTATATTAAAAAT
1 AAAGAATTTCTATTATATTAAAAAT
3733035 ATTAAAGTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
47 40 0.67
48 20 0.33
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (48 bp):
AAAGAATTTCTATTATATTAAAAATTGCCTTATTTAAAAAGTTATTAT
Found at i:3733325 original size:21 final size:21
Alignment explanation
Indices: 3733301--3733345 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3733291 GTTCAGCTTT
* * *
3733301 CGGCGGGGGTTGTGGTTGCTC
1 CGGCGGGGATTCTGGTTCCTC
*
3733322 CGGCTGGGATTCTGGTTCCTC
1 CGGCGGGGATTCTGGTTCCTC
3733343 CGG
1 CGG
3733346 TAGGGTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.24, G:0.44, T:0.29
Consensus pattern (21 bp):
CGGCGGGGATTCTGGTTCCTC
Found at i:3737177 original size:11 final size:12
Alignment explanation
Indices: 3737158--3737182 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3737148 TTTAACTTTC
3737158 TTTCTTTTTTTT
1 TTTCTTTTTTTT
3737170 TTTCTTTTTTTT
1 TTTCTTTTTTTT
3737182 T
1 T
3737183 CATTCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:3737303 original size:14 final size:14
Alignment explanation
Indices: 3737282--3737314 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3737272 TGGTATGGGT
3737282 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
3737295 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
3737309 TTATAG
1 TTATAG
3737315 ACAAATGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:3742793 original size:3 final size:3
Alignment explanation
Indices: 3742787--3742841 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
3742777 ATGATGATGA
3742787 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
3742835 TGG TGG T
1 TGG TGG T
3742842 ATCATCAAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:3743541 original size:2 final size:2
Alignment explanation
Indices: 3743534--3743566 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3743524 TCCAGCTGAT
3743534 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3743567 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3757396 original size:2 final size:2
Alignment explanation
Indices: 3757389--3757424 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3757379 ACTTTATAGT
3757389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3757425 ATAGAAGAAC
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):
TA
Found at i:3763919 original size:36 final size:36
Alignment explanation
Indices: 3763872--3764098 Score: 310
Period size: 36 Copynumber: 6.0 Consensus size: 36
3763862 GCTAAGCTAC
*
3763872 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
3763908 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
3763944 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
3763980 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
3764022 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
3764062 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
3764098 C
1 C
3764099 TAAAGCTACC
Statistics
Matches: 173, Mismatches: 8, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
36 135 0.78
38 3 0.02
40 3 0.02
42 2 0.01
44 2 0.01
46 28 0.16
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:3764031 original size:46 final size:46
Alignment explanation
Indices: 3763980--3764134 Score: 204
Period size: 46 Copynumber: 3.6 Consensus size: 46
3763970 ATAAGTATAA
3763980 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
3764026 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
3764062 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
3764108 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
3764135 AGTACTCAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
36 28 0.30
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 53 0.57
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:3764038 original size:82 final size:82
Alignment explanation
Indices: 3763944--3764134 Score: 337
Period size: 82 Copynumber: 2.3 Consensus size: 82
3763934 ATAAGTATAG
* *
3763944 CACTTATCACTTTTTCACTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
3764009 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
* * *
3764026 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
3764091 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
3764108 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTATCTCTTGATCAGA
3764135 AGTACTCAAA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 104 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (82 bp):
CACTTATCACTTTATCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
AGTGTAGCTAAAGCTAC
Found at i:3769685 original size:12 final size:12
Alignment explanation
Indices: 3769668--3769692 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3769658 CATGGCTAGG
3769668 GAGACATGTGTT
1 GAGACATGTGTT
3769680 GAGACATGTGTT
1 GAGACATGTGTT
3769692 G
1 G
3769693 GAGGGCAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.36, T:0.32
Consensus pattern (12 bp):
GAGACATGTGTT
Found at i:3776488 original size:21 final size:21
Alignment explanation
Indices: 3776462--3776516 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
3776452 AACAGCGGTG
*
3776462 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGCTACTGTA
* *
3776483 GCGGTGATATTTGCTACTGTA
1 GCGGTGAGATTAGCTACTGTA
*
3776504 GCAGTGAGATTAG
1 GCGGTGAGATTAG
3776517 AAACAGCGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.11, G:0.33, T:0.33
Consensus pattern (21 bp):
GCGGTGAGATTAGCTACTGTA
Found at i:3784103 original size:17 final size:18
Alignment explanation
Indices: 3784081--3784119 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3784071 CATTTGCTTC
*
3784081 AAAAAT-AATTTTTATTG
1 AAAAATAAATTCTTATTG
3784098 AAAAATAAAATTCTTATTG
1 AAAAAT-AAATTCTTATTG
3784117 AAA
1 AAA
3784120 TTAGTTCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAAATAAATTCTTATTG
Found at i:3789190 original size:3 final size:3
Alignment explanation
Indices: 3789184--3789250 Score: 79
Period size: 3 Copynumber: 23.7 Consensus size: 3
3789174 TTACACTGTT
* * *
3789184 TTA TTA TT- TTT TTA TTA -TG TTA -TA CTA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3789228 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
3789251 TTAAACATAC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 7 0.12
3 49 0.88
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3793578 original size:29 final size:31
Alignment explanation
Indices: 3793545--3793613 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 31
3793535 AAAAGTTATA
*
3793545 AAAATTATTTTTAAAAA-T-TAAAAATCAT-T
1 AAAATAATTTTTAAAAAGTATAAAAAT-ATCT
*
3793574 AAAATCA--TTTAAAAAGTATAAAAATATCT
1 AAAATAATTTTTAAAAAGTATAAAAATATCT
3793603 AAAATAATTTT
1 AAAATAATTTT
3793614 AATCTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
27 8 0.24
28 3 0.09
29 20 0.61
31 2 0.06
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (31 bp):
AAAATAATTTTTAAAAAGTATAAAAATATCT
Found at i:3802067 original size:17 final size:18
Alignment explanation
Indices: 3802032--3802069 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3802022 TTTTATACTT
3802032 TTTAATAGTTTTAAATGA
1 TTTAATAGTTTTAAATGA
3802050 TTTAATAGTTTT-AATGA
1 TTTAATAGTTTTAAATGA
3802067 TTT
1 TTT
3802070 TTAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (18 bp):
TTTAATAGTTTTAAATGA
Found at i:3802408 original size:16 final size:16
Alignment explanation
Indices: 3802372--3802410 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3802362 GTTTGCTTCG
* *
3802372 CTGTAATGGAATAGAT
1 CTGTAATGGAATAAAA
*
3802388 GTGTAATGGAATAAAA
1 CTGTAATGGAATAAAA
3802404 CTGTAAT
1 CTGTAAT
3802411 AGTAATTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAAAA
Found at i:3802456 original size:45 final size:44
Alignment explanation
Indices: 3802392--3802484 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
3802382 ATAGATGTGT
3802392 AATGGAATAAAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATAGT-ATT-AATGTGTTTGGTTGAATGG
* *
3802437 AATGGAATAGAACTGTAATAGTATTATTGTGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATAGTATTAATGTGTTTGGTTGAATGG
3802481 AATG
1 AATG
3802485 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 2 0.04
44 22 0.49
45 21 0.47
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (44 bp):
AATGGAATAAAACTGTAATAGTATTAATGTGTTTGGTTGAATGG
Found at i:3802706 original size:56 final size:56
Alignment explanation
Indices: 3802598--3802719 Score: 140
Period size: 56 Copynumber: 2.2 Consensus size: 56
3802588 TTATTAATAT
* *
3802598 AAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAATTTAATA
1 AAATAATAAATAATTTAATAAAATTTTAACATAATTATTATT-AATATAATTTAATA
* * * *
3802655 AAA-AATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAATTTACTA
1 AAATAATAAATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AATTTAATA
*
3802711 AAATCATAA
1 AAATAATAA
3802720 TATATAATAC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
55 4 0.07
56 29 0.54
57 21 0.39
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (56 bp):
AAATAATAAATAATTTAATAAAATTTTAACATAATTATTATTAATATAATTTAATA
Found at i:3809447 original size:10 final size:10
Alignment explanation
Indices: 3809428--3809467 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
3809418 CCTAAAGCAT
3809428 AAAAAAAAAC
1 AAAAAAAAAC
*
3809438 AAAAACAAAC
1 AAAAAAAAAC
*
3809448 AAAAAAAAAG
1 AAAAAAAAAC
3809458 AAAGAAAAAA
1 AAA-AAAAAA
3809468 ATAATTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:3820705 original size:4 final size:4
Alignment explanation
Indices: 3820696--3820735 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
3820686 CTTTTTCAGA
3820696 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
3820736 ATCTTTTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3824515 original size:4 final size:4
Alignment explanation
Indices: 3824506--3824565 Score: 120
Period size: 4 Copynumber: 15.0 Consensus size: 4
3824496 CCATGTGATC
3824506 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3824554 ACAT ACAT ACAT
1 ACAT ACAT ACAT
3824566 GAACATATGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:3832359 original size:13 final size:14
Alignment explanation
Indices: 3832329--3832361 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3832319 TTTTACACTG
3832329 ATTTTTTTAATTTA
1 ATTTTTTTAATTTA
*
3832343 ATTTTTTTCATTT-
1 ATTTTTTTAATTTA
3832356 ATTTTT
1 ATTTTT
3832362 CTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTTTTAATTTA
Found at i:3832894 original size:11 final size:12
Alignment explanation
Indices: 3832878--3832909 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
3832868 ATGTGTGATC
3832878 AAATAAAAAT-A
1 AAATAAAAATAA
3832889 AAATAAAAATAA
1 AAATAAAAATAA
3832901 AAATAAAAA
1 AAATAAAAA
3832910 ATCACTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATAAAAATAA
Found at i:3832911 original size:7 final size:6
Alignment explanation
Indices: 3832878--3832909 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3832868 ATGTGTGATC
3832878 AAATAA AAAT-A AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
3832910 ATCACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:3837126 original size:146 final size:149
Alignment explanation
Indices: 3836866--3837252 Score: 443
Period size: 146 Copynumber: 2.6 Consensus size: 149
3836856 CCGCTCTATC
* * * *
3836866 CCCATGATCTAAATGGAAAAATCCAA--CCCATCCCATCTCACCTCAACTCCACATCCACTTTTC
1 CCCACGATATAAAAGGAAAAATCCAACTCCCATCCCATCTCACCTC-ACCCCACATCCACTTTTC
* * * *
3836929 AAACTAAAAAATCACTCCAAATAAAACGGATCGGAATTTAATATAGTGGAGTGAGTCAACACAGA
65 AAAATAAAAAATCACTCCAAATAAAACAGATCGAAATTTAATATAGTGGAGTAAGTCAACACAGA
3836994 GCAG-G-C-AA-T-TAC-TA
130 GCAGAGCCAAACTATACATA
* ** * *
3837008 CCCATGATATAAAAGTTAAAATCCAACCCATCCCATCTCATCTCACCTCACCCCACATTCACTTT
1 CCCACGATATAAAAGGAAAAATCCAA--C-TCCCATCCCATCTCACCTCACCCCACATCCACTTT
* * *
3837073 TCAAAATAAAAAATCACTCCAAATAAAACAGATCGAAATTTGATCTAGTGGAGTAAGTTAACACA
63 TCAAAATAAAAAATCACTCCAAATAAAACAGATCGAAATTTAATATAGTGGAGTAAGTCAACACA
*
3837138 GAGCAGACAATTGCCATAACTATTCTATA
128 GAGCAG---A--GCCA-AACTATAC-ATA
*
3837167 CCCACGATCTAAAAGGAAAAATCCAACT--CATCCCATCTCACCTCACCCCACATCCACTTTTCA
1 CCCACGATATAAAAGGAAAAATCCAACTCCCATCCCATCTCACCTCACCCCACATCCACTTTTCA
3837230 AAATAAAAAATCACTCCAAATAA
66 AAATAAAAAATCACTCCAAATAA
3837253 TTATCATCCC
Statistics
Matches: 206, Mismatches: 21, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
142 22 0.11
146 78 0.38
147 17 0.08
152 1 0.00
153 1 0.00
154 56 0.27
155 2 0.01
156 2 0.01
157 3 0.01
159 24 0.12
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (149 bp):
CCCACGATATAAAAGGAAAAATCCAACTCCCATCCCATCTCACCTCACCCCACATCCACTTTTCA
AAATAAAAAATCACTCCAAATAAAACAGATCGAAATTTAATATAGTGGAGTAAGTCAACACAGAG
CAGAGCCAAACTATACATA
Found at i:3844150 original size:23 final size:23
Alignment explanation
Indices: 3844120--3844168 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
3844110 CATTAGGAGT
3844120 TGAACATAGCAATCTGATTCTCA
1 TGAACATAGCAATCTGATTCTCA
3844143 TGAACATAGCAATCTGATTCTCA
1 TGAACATAGCAATCTGATTCTCA
3844166 TGA
1 TGA
3844169 TAAAATGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (23 bp):
TGAACATAGCAATCTGATTCTCA
Found at i:3846791 original size:24 final size:24
Alignment explanation
Indices: 3846759--3846821 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
3846749 CAATTGTAGT
* * *
3846759 TCAGGTACAGAATCAGATGCATGA
1 TCAGATACAAAATCAGATGCATAA
*
3846783 TCAGATACAAAATTAGATGCATAA
1 TCAGATACAAAATCAGATGCATAA
*
3846807 TCAAATACAAAATCA
1 TCAGATACAAAATCA
3846822 TATCCTACCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
TCAGATACAAAATCAGATGCATAA
Found at i:3850760 original size:18 final size:18
Alignment explanation
Indices: 3850737--3850773 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3850727 TCAACAAATC
3850737 TCCACCTTGACTCATATT
1 TCCACCTTGACTCATATT
3850755 TCCACCTTGACTCATATT
1 TCCACCTTGACTCATATT
3850773 T
1 T
3850774 TCACAATGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (18 bp):
TCCACCTTGACTCATATT
Found at i:3853019 original size:43 final size:43
Alignment explanation
Indices: 3852926--3853037 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 43
3852916 AAAACTTATT
* **
3852926 TTCAAGATCAAGTCTCGGTGACCCTTGAAGCAAACATTATTGA
1 TTCAAGATCAAGTCTCGATGACCCTTGAAGCAAACAGCATTGA
* * *
3852969 TTTAAGATCAAGTCTCGATGACCCTTGAAGCAAACCGCATT-C
1 TTCAAGATCAAGTCTCGATGACCCTTGAAGCAAACAGCATTGA
* * *
3853011 TTCCAAGATGAAGTTTAGATGACCCTT
1 TT-CAAGATCAAGTCTCGATGACCCTT
3853038 AGATCGAAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 2 0.03
43 56 0.97
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (43 bp):
TTCAAGATCAAGTCTCGATGACCCTTGAAGCAAACAGCATTGA
Found at i:3856899 original size:16 final size:16
Alignment explanation
Indices: 3856875--3856943 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
3856865 TTGAATTGCT
*
3856875 ATTATGCCTCTAATCC
1 ATTACGCCTCTAATCC
3856891 ATTACGCCTCTAATCC
1 ATTACGCCTCTAATCC
* *
3856907 ATTACGTCTCTATTCC
1 ATTACGCCTCTAATCC
*
3856923 ATTACGCCTCTATTCC
1 ATTACGCCTCTAATCC
3856939 ATTAC
1 ATTAC
3856944 AGCGAACCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTAATCC
Found at i:3868202 original size:21 final size:22
Alignment explanation
Indices: 3868160--3868202 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
3868150 AAGTGAACAG
3868160 TGCAATAATCGATGAAGAAGAACC
1 TGCAATAATCGAT--AGAAGAACC
3868184 TGCAATAATCGAT-GAAGAA
1 TGCAATAATCGATAGAAGAA
3868203 AAGGAAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
24 13 0.68
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.19
Consensus pattern (22 bp):
TGCAATAATCGATAGAAGAACC
Found at i:3882685 original size:10 final size:10
Alignment explanation
Indices: 3882670--3882695 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3882660 CTTACTGATC
3882670 TGTTAGTATT
1 TGTTAGTATT
3882680 TGTTAGTATT
1 TGTTAGTATT
3882690 TGTTAG
1 TGTTAG
3882696 CACTTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (10 bp):
TGTTAGTATT
Found at i:3885031 original size:35 final size:36
Alignment explanation
Indices: 3884983--3885060 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 36
3884973 ATTTGTTAGA
3884983 TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
** *
3885019 TATT-ATTATGTTTTAAGTTTGTTGGATATTGAAAT
1 TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
*
3885054 GATTGAT
1 TATTGAT
3885061 AATGACAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 31 0.84
36 6 0.16
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.53
Consensus pattern (36 bp):
TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
Found at i:3892247 original size:25 final size:25
Alignment explanation
Indices: 3892213--3892263 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3892203 AACTAGATTC
*
3892213 AAAACATGCTATTAGAAGCAGACTA
1 AAAACATGCTATCAGAAGCAGACTA
* *
3892238 AAAACGTGCTATCAGAAGTAGACTA
1 AAAACATGCTATCAGAAGCAGACTA
3892263 A
1 A
3892264 TACACTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.20
Consensus pattern (25 bp):
AAAACATGCTATCAGAAGCAGACTA
Found at i:3892662 original size:16 final size:15
Alignment explanation
Indices: 3892639--3892672 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3892629 TTTGATAAAT
* *
3892639 TGAAAATTTAAGTGC
1 TGAAAAATTAAGTAC
3892654 TGAAAAATTAAGTAC
1 TGAAAAATTAAGTAC
3892669 TGAA
1 TGAA
3892673 TTTTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (15 bp):
TGAAAAATTAAGTAC
Found at i:3900366 original size:21 final size:23
Alignment explanation
Indices: 3900326--3900374 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 23
3900316 TTCCCTTTAT
*
3900326 TTTTATATATATTTTTTATAAAA
1 TTTTATATATATTTTCTATAAAA
3900349 TTTTAT-TA-ATTTTCTAT--AA
1 TTTTATATATATTTTCTATAAAA
3900368 TTTTATA
1 TTTTATA
3900375 GTTTTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.33
21 8 0.33
22 2 0.08
23 6 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTATATATATTTTCTATAAAA
Found at i:3903280 original size:31 final size:31
Alignment explanation
Indices: 3903242--3903303 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3903232 GGATCTGGGT
3903242 TTTGTTGAAAATAATAAAATGACTAAGTATA
1 TTTGTTGAAAATAATAAAATGACTAAGTATA
3903273 TTTGTTGAAAATAATAAAATGACTAAGTATA
1 TTTGTTGAAAATAATAAAATGACTAAGTATA
3903304 AAATTGGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.35
Consensus pattern (31 bp):
TTTGTTGAAAATAATAAAATGACTAAGTATA
Found at i:3906263 original size:23 final size:24
Alignment explanation
Indices: 3906231--3906276 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3906221 CATAGTAAGA
*
3906231 TTAGAACC-TTGACATGTTTCATT
1 TTAGAACCTTTAACATGTTTCATT
*
3906254 TTAGACCCTTTAACATGTTTCAT
1 TTAGAACCTTTAACATGTTTCAT
3906277 CTTCTTGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (24 bp):
TTAGAACCTTTAACATGTTTCATT
Found at i:3918964 original size:20 final size:20
Alignment explanation
Indices: 3918939--3918978 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3918929 ATGCTGACTT
3918939 GGATGTCCAATTGTGATGAG
1 GGATGTCCAATTGTGATGAG
3918959 GGATGTCCAATTGTGATGAG
1 GGATGTCCAATTGTGATGAG
3918979 AATAGGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.30
Consensus pattern (20 bp):
GGATGTCCAATTGTGATGAG
Found at i:3922136 original size:3 final size:3
Alignment explanation
Indices: 3922121--3922153 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3922111 TATACATAGA
*
3922121 CAT CAT TAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
3922154 TCACAAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (3 bp):
CAT
Found at i:3925284 original size:2 final size:2
Alignment explanation
Indices: 3925277--3925306 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3925267 GCAGCAGATT
3925277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3925307 GTGTATAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3939356 original size:26 final size:24
Alignment explanation
Indices: 3939290--3939362 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 24
3939280 ATGTGAGCAC
* *
3939290 TAACGGGAAGCTCACAAAGAGCCTT
1 TAACGGGAAGCTCA-TAAGAGCCTG
3939315 TAATCGGGAAGCTCATGAAGAGCCATG
1 TAA-CGGGAAGCTCAT-AAGAGCC-TG
*
3939342 TAACGGGACGCTCATAAGAGC
1 TAACGGGAAGCTCATAAGAGC
3939363 TGCGCTGTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.21
26 29 0.69
27 4 0.10
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.16
Consensus pattern (24 bp):
TAACGGGAAGCTCATAAGAGCCTG
Found at i:3939638 original size:18 final size:18
Alignment explanation
Indices: 3939615--3939681 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
3939605 TTTCGTTAAA
3939615 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
3939633 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
* *
3939651 AATTACCCGAATTACCCA
1 AATTAACCGAATTACCCG
*
3939669 AATTAACCTAATT
1 AATTAACCGAATT
3939682 GAATCATACA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.25
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:3939651 original size:27 final size:27
Alignment explanation
Indices: 3939616--3939681 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
3939606 TTCGTTAAAA
*
3939616 ATTAACCGAATTACCCGAATTAACCGA
1 ATTAACCGAATTACCCGAATTAACCAA
* *
3939643 ATTACCCGAATTACCCGAATTACCCAA
1 ATTAACCGAATTACCCGAATTAACCAA
*
3939670 ATTAACCTAATT
1 ATTAACCGAATT
3939682 GAATCATACA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.26
Consensus pattern (27 bp):
ATTAACCGAATTACCCGAATTAACCAA
Found at i:3939681 original size:9 final size:9
Alignment explanation
Indices: 3939615--3939673 Score: 91
Period size: 9 Copynumber: 6.6 Consensus size: 9
3939605 TTTCGTTAAA
*
3939615 AATTAACCG
1 AATTACCCG
3939624 AATTACCCG
1 AATTACCCG
*
3939633 AATTAACCG
1 AATTACCCG
3939642 AATTACCCG
1 AATTACCCG
3939651 AATTACCCG
1 AATTACCCG
*
3939660 AATTACCCA
1 AATTACCCG
3939669 AATTA
1 AATTA
3939674 ACCTAATTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:3953709 original size:6 final size:6
Alignment explanation
Indices: 3953698--3953724 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3953688 TAACCGTCAC
3953698 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
3953725 TTGAATAATT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:3954784 original size:2 final size:2
Alignment explanation
Indices: 3954779--3954827 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3954769 AATAATGTAA
3954779 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
*
3954821 AT TT AT A
1 AT AT AT A
3954828 AAAAAAAGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3955610 original size:29 final size:28
Alignment explanation
Indices: 3955562--3955623 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 28
3955552 CAACTTAACA
3955562 AACAAATACCTAAAATAATAAC-AAATT
1 AACAAATACCTAAAATAATAACAAAATT
3955589 AACAAATACCTCTAAAATAATAACAAAATT
1 AACAAATA-C-CTAAAATAATAACAAAATT
3955619 AACAA
1 AACAA
3955624 TAAAGCAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 8 0.25
28 1 0.03
29 13 0.41
30 10 0.31
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (28 bp):
AACAAATACCTAAAATAATAACAAAATT
Found at i:3964385 original size:10 final size:10
Alignment explanation
Indices: 3964370--3964401 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
3964360 TACTATGAAA
3964370 GTGATTAGAT
1 GTGATTAGAT
3964380 GTGATTAGAT
1 GTGATTAGAT
3964390 GTGATTAGAT
1 GTGATTAGAT
3964400 GT
1 GT
3964402 TTCACTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (10 bp):
GTGATTAGAT
Found at i:3964456 original size:38 final size:38
Alignment explanation
Indices: 3964414--3964520 Score: 146
Period size: 38 Copynumber: 2.8 Consensus size: 38
3964404 CACTATCTTA
3964414 TATGAGTCATAAAAGTAAGTTTGTTTGTTATGTAA-AAG
1 TATGAGTCATAAAAGTAAGTTTGTTTGTTATG-AAGAAG
* * *
3964452 TATGAGTCATAAAAATTAA-TTTGTTTGCTATGAAGATG
1 TATGAGTCAT-AAAAGTAAGTTTGTTTGTTATGAAGAAG
*
3964490 TATGAGTCAAAAAAGTAAGTTTGTTTGTTAT
1 TATGAGTCATAAAAGTAAGTTTGTTTGTTAT
3964521 ACGAGTCATA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
37 9 0.15
38 44 0.73
39 7 0.12
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (38 bp):
TATGAGTCATAAAAGTAAGTTTGTTTGTTATGAAGAAG
Found at i:3970818 original size:14 final size:14
Alignment explanation
Indices: 3970789--3970834 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3970779 ATTTTACAGC
*
3970789 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
3970803 ATTTACAAATATAT
1 ATATACAAATAAAT
3970817 ATATACAAATACAAT
1 ATATACAAATA-AAT
3970832 ATA
1 ATA
3970835 CCAGTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:3983961 original size:16 final size:16
Alignment explanation
Indices: 3983940--3983970 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3983930 ACTGATATAC
3983940 GAAAAAGGAAAAAAAT
1 GAAAAAGGAAAAAAAT
*
3983956 GAAAAATGAAAAAAA
1 GAAAAAGGAAAAAAA
3983971 AAATTTGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
GAAAAAGGAAAAAAAT
Found at i:3984280 original size:215 final size:213
Alignment explanation
Indices: 3983974--3984644 Score: 784
Period size: 215 Copynumber: 3.1 Consensus size: 213
3983964 AAAAAAAAAA
* *
3983974 TTTGGGTGCTGACCTGTCAATGGCCGGCACCCAGTACAAATTTTAAATACAAATTCTTTTTTTTC
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAC-AA-TTTAAATAAAAATTCTTTTTTTTC
*
3984039 GTGTCAGAATCAGATATCAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATG
64 GTGTCAAAATCAGATATCAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATG
*
3984104 GCCGGCACCCAGTACAATTAAAAAGAAAATTCTTTTGTTTTTCGTGTCAAAATCAAATATCAATA
129 GCCGGCACCCAGTA-AATTAAAAA-AAAATTCTTTT-TTTTTCGTGTCAAAATCAGATATCAATA
3984169 TACGAAAAAAATTTAAAATTTTT
191 TACGAAAAAAATTTAAAATTTTT
* *****
3984192 TTTGGGTGCTGGCCTGTCAATGGCAGGCACCCAGTACAA-TTAAATTTTTTTTCTTTTTTTTCGT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAATAAAAATTCTTTTTTTTCGT
* * *
3984256 GTCAAAATTAGATATCAGTATACGAATAAAATTAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGG
66 GTCAAAATCAGATATCAATATACGAA-AAAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGG
* * * * * *
3984320 CTGGCACCCAGTAAAATTTTTTTAAAAAAAATTTACTTTTTTTTCTCTTTTCAGAATTAGATATC
130 CCGGCACCCAGT-AAA-----TTAAAAAAAAATT-CTTTTTTTT-TCGTGTCAAAATCAGATATC
* * *****
3984385 AGTATAC--AAAAAA-GTAAAAAAAAA
187 AATATACGAAAAAAATTTAAAATTTTT
* * *
3984409 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTATAATTTTAAAAAAAAATT-ATTTTTTTCG
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTTAAATAAAAATTCTTTTTTTTCG
* *
3984473 TGTCAAAATCAGATACCAATATACGAAAAAAATTAAAAAAAAATTTTGAGTGCTGGCCTGTCAAT
65 TGTCAAAATCAGATATCAATATACGAAAAAAA-T-AAAAAAAATTTTGGGTGCTGGCCTGTCAAT
* *
3984538 GGCCGGCACCCATTAAA--ATAAAAAAATTC-TTTTTTTTCGTGTCAAAATCAGATATCAATATA
128 GGCCGGCACCCAGTAAATTAAAAAAAAATTCTTTTTTTTTCGTGTCAAAATCAGATATCAATATA
3984600 CGAAAAAAATTTAAAAAAATTTTT
193 CGAAAAAAATTT---AAAATTTTT
* *
3984624 TTTGGGTGCTAGCCTATCAAT
1 TTTGGGTGCTGGCCTGTCAAT
3984645 TTTAATTTTT
Statistics
Matches: 377, Mismatches: 56, Indels: 43
0.79 0.12 0.09
Matches are distributed among these distances:
209 22 0.06
210 7 0.02
211 7 0.02
212 10 0.03
215 102 0.27
216 14 0.04
217 48 0.13
218 75 0.20
219 27 0.07
220 65 0.17
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (213 bp):
TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAATAAAAATTCTTTTTTTTCGT
GTCAAAATCAGATATCAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGC
CGGCACCCAGTAAATTAAAAAAAAATTCTTTTTTTTTCGTGTCAAAATCAGATATCAATATACGA
AAAAAATTTAAAATTTTT
Found at i:3984328 original size:105 final size:106
Alignment explanation
Indices: 3983966--3984621 Score: 763
Period size: 108 Copynumber: 6.1 Consensus size: 106
3983956 GAAAAATGAA
* * *
3983966 AAAAAAAATTTGGGTGCTGACCTGTCAATGGCCGGCACCCAGTACAAATTTTAAATACAAATTCT
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAC-AA-TTTAAAAAAAAATTCT
*
3984031 TTTTTTTCGTGTCAGAATCAGATATCAATATACGAAAAAAA-T
64 TTTTTTTCGTGTCAAAATCAGATATCAATATACGAAAAAAATT
3984073 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTAAAAAGAAAATTCT
1 AAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAA-AAAATTC-
*
3984137 TTTGTTTTTCGTGTCAAAATCAAATATCAATATACGAAAAAAATTT
63 TTT-TTTTTCGTGTCAAAATCAGATATCAATATACGAAAAAAA-TT
**** * ******
3984183 AAAATTTTTTTTGGGTGCTGGCCTGTCAATGGCAGGCACCCAGTACAA-TTAAATTTTTTTTCTT
1 AAAA-AAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTCTT
* * *
3984247 TTTTTTCGTGTCAAAATTAGATATCAGTATACGAATAAAATT
65 TTTTTTCGTGTCAAAATCAGATATCAATATACGAAAAAAATT
* * *
3984289 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCTGGCACCCAGTAAAATTTTTTTAAAAAAAATTT
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA----TTTAAAAAAAAATT
* * * * * * *
3984354 ACTTTTTTTTCTCTTTTCAGAATTAGATATCAGTATAC-AAAAAAGTA
62 -C-TTTTTTT-TCGTGTCAAAATCAGATATCAATATACGAAAAAAATT
* *
3984401 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTATAATTTTAAAAAAAAATT-AT
1 AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTTAAAAAAAAATTCTT
*
3984465 TTTTTTCGTGTCAAAATCAGATACCAATATACGAAAAAAATT
65 TTTTTTCGTGTCAAAATCAGATATCAATATACGAAAAAAATT
* * *
3984507 AAAAAAAAATTTTGAGTGCTGGCCTGTCAATGGCCGGCACCCATTA-AA---ATAAAAAAATTCT
1 -AAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTCT
3984568 TTTTTTTCGTGTCAAAATCAGATATCAATATACGAAAAAAATT
64 TTTTTTTCGTGTCAAAATCAGATATCAATATACGAAAAAAATT
*
3984611 TAAAAAAATTT
1 AAAAAAAATTT
3984622 TTTTTGGGTG
Statistics
Matches: 475, Mismatches: 55, Indels: 43
0.83 0.10 0.08
Matches are distributed among these distances:
102 3 0.01
103 17 0.04
104 42 0.09
105 64 0.13
106 25 0.05
107 58 0.12
108 110 0.23
109 17 0.04
110 56 0.12
111 1 0.00
112 58 0.12
113 24 0.05
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (106 bp):
AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTCTTT
TTTTTCGTGTCAAAATCAGATATCAATATACGAAAAAAATT
Found at i:3985347 original size:211 final size:212
Alignment explanation
Indices: 3984839--3985376 Score: 644
Period size: 211 Copynumber: 2.5 Consensus size: 212
3984829 CGTAATATTA
* *
3984839 TTTTTTCATATACTGATATCTAATTCTGACACGAAAATAAAAAGAATTTTTTTTTTATAAATTGT
1 TTTTTTCGTATACTGATATCTGATTCTGACACG-AAA-AAAAA-AA-TTTTTTTTTA-AAATTGT
* * * ** *
3984904 ACTGGGTGCTGGCTATTGACAAGCCAGCACCCAAAAAAATTTTTTTTTGAATTTTTTCGTATACT
61 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAA-TAATTTTTAAATTTTTTCGTATACT
*** *
3984969 GATATCTGATTCTGACGTTAAAAAAAAGATTTTTTTTTAAATTGTACTGGGTGCCGGCCATTGAC
125 GATATCTGATTCTGACAACAAAAAAAAGATTTTTTTTTAAATTGTA-T-GGTACCGGCCATTGAC
3985034 AGGCCAACACCAAAATTTTTTTTAC
188 AGGCCAACACCAAAATTTTTTTTAC
* ***
3985059 TTTTTTCGTATACCGATATCTGATTCTGACACGAAAAAAAAAGAAAATTTTTT-AAATTGTACTG
1 TTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAA-ATTTTTTTTTAAAATTGTACTG
* * *
3985123 GGTGCCGGCCATTGATAGGTCAGCAACCAAAAAAA-AATTTTTAAATTTTTTTTCGTATACTGAT
65 GGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATAATTTTTAAA--TTTTTTCGTATACTGAT
*
3985187 ATCTGATTTTGA-AACAAAAAAAAGATTTTTTTTT-AA-T-T-T-GTACCGGCCATTGACAGGCC
128 ATCTGATTCTGACAACAAAAAAAAGATTTTTTTTTAAATTGTATGGTACCGGCCATTGACAGGCC
* *
3985246 ATCACTCAAAATTTTTTTTAAAAT
193 AACAC-CAAAATTTTTTTT---AC
3985270 TTTTTTCGTATACTGATATCTGATTCTGACACG-AAAAAAAAATTTTTTTTTAAAATTTGTACTG
1 TTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAATTTTTTTTTAAAA-TTGTACTG
* * *
3985334 GGTGCCAGCCATTGACAGGCCAGCACCCAAAAAATTTATTTTT
65 GGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATAATTTTT
3985377 TTCATTTTTC
Statistics
Matches: 276, Mismatches: 32, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
207 23 0.08
208 13 0.05
209 8 0.03
210 11 0.04
211 72 0.26
212 7 0.03
213 9 0.03
214 19 0.07
215 68 0.25
217 7 0.03
218 6 0.02
219 3 0.01
220 30 0.11
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (212 bp):
TTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAATTTTTTTTTAAAATTGTACTGG
GTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATAATTTTTAAATTTTTTCGTATACTGATATC
TGATTCTGACAACAAAAAAAAGATTTTTTTTTAAATTGTATGGTACCGGCCATTGACAGGCCAAC
ACCAAAATTTTTTTTAC
Found at i:3985392 original size:16 final size:16
Alignment explanation
Indices: 3985371--3985402 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3985361 CAAAAAATTT
3985371 ATTTTTTTCATTTTTC
1 ATTTTTTTCATTTTTC
*
3985387 ATTTTTTTCCTTTTTC
1 ATTTTTTTCATTTTTC
3985403 GTATATCTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTTTCATTTTTC
Found at i:3991308 original size:27 final size:27
Alignment explanation
Indices: 3991270--3991345 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
3991260 TAGTATTGGC
* *
3991270 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTACCTGGGAGGCGCCAATGATGGT
3991297 GCCTACCTGGGAGGCGCCAATGATGGT
1 GCCTACCTGGGAGGCGCCAATGATGGT
**
3991324 GCCT-CTCTAAGAGGCGCCAATG
1 GCCTAC-CTGGGAGGCGCCAATG
3991346 CTGTTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.02
27 43 0.98
ACGTcount: A:0.18, C:0.26, G:0.36, T:0.20
Consensus pattern (27 bp):
GCCTACCTGGGAGGCGCCAATGATGGT
Found at i:3991451 original size:22 final size:23
Alignment explanation
Indices: 3991399--3991451 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
3991389 TTACTCCAGA
*
3991399 AAGAAATAAGAAGGAAGGAAGCAG
1 AAGAAA-AAGAAGGAAGGAAGAAG
*
3991423 AAG-AAAAGAATGAAGGAA-AAG
1 AAGAAAAAGAAGGAAGGAAGAAG
3991444 AAGAAAAA
1 AAGAAAAA
3991452 AATTAGGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 5 0.19
22 16 0.62
23 2 0.08
24 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.28, T:0.04
Consensus pattern (23 bp):
AAGAAAAAGAAGGAAGGAAGAAG
Found at i:3994459 original size:7 final size:7
Alignment explanation
Indices: 3994447--3994481 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
3994437 AAGTAATCCT
3994447 TACAGGA
1 TACAGGA
3994454 TACAGGA
1 TACAGGA
3994461 TACAGGA
1 TACAGGA
3994468 TACAGGA
1 TACAGGA
3994475 TACAGGA
1 TACAGGA
3994482 GCCTGGAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (7 bp):
TACAGGA
Found at i:3996955 original size:37 final size:37
Alignment explanation
Indices: 3996905--3996983 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
3996895 CAAGGTTTGC
3996905 ACTTCCACATCTTCCACACCCACATCCCTTATGAGTT
1 ACTTCCACATCTTCCACACCCACATCCCTTATGAGTT
*
3996942 ACTTCCACATCTTCCACACCCACATGCCTTATGAGTT
1 ACTTCCACATCTTCCACACCCACATCCCTTATGAGTT
3996979 ACTTC
1 ACTTC
3996984 ATCACAAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.24, C:0.39, G:0.06, T:0.30
Consensus pattern (37 bp):
ACTTCCACATCTTCCACACCCACATCCCTTATGAGTT
Found at i:4000856 original size:23 final size:23
Alignment explanation
Indices: 4000786--4000871 Score: 110
Period size: 21 Copynumber: 4.0 Consensus size: 23
4000776 CCTGATCAAT
4000786 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
4000807 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
4000827 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
4000850 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
4000872 TCGGCAAAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.16
21 23 0.42
23 23 0.42
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:4000868 original size:44 final size:41
Alignment explanation
Indices: 4000786--4000872 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 41
4000776 CCTGATCAAT
* *
4000786 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
4000827 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
4000871 AT
1 AT
4000873 CGGCAAAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 11 0.28
42 10 0.25
43 1 0.03
44 18 0.45
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:4001912 original size:19 final size:22
Alignment explanation
Indices: 4001885--4001929 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 22
4001875 TTACTTACTT
*
4001885 TATTTTAATAAT-A-ATAAT-A
1 TATTATAATAATCATATAATAA
4001904 TATTATAATAATCATATAATAA
1 TATTATAATAATCATATAATAA
4001926 TATT
1 TATT
4001930 TTATTCACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 5 0.23
22 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTATAATAATCATATAATAA
Found at i:4002107 original size:25 final size:26
Alignment explanation
Indices: 4002072--4002124 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
4002062 TATTATCTTA
4002072 ATTTTAATTAAT-ATAA-TTTATAAT
1 ATTTTAATTAATAATAATTTTATAAT
4002096 ATTTTAATTTAATAATAATTTTATAAT
1 ATTTTAA-TTAATAATAATTTTATAAT
4002123 AT
1 AT
4002125 AAATCAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 7 0.27
25 5 0.19
26 4 0.15
27 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTAATTAATAATAATTTTATAAT
Found at i:4002110 original size:16 final size:16
Alignment explanation
Indices: 4002085--4002118 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
4002075 TTAATTAATA
4002085 TAATTTATAAT-ATTT
1 TAATTTATAATAATTT
4002100 TAATTTAATAATAATTT
1 TAATTT-ATAATAATTT
4002117 TA
1 TA
4002119 TAATATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 5 0.29
17 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTTATAATAATTT
Found at i:4031269 original size:15 final size:17
Alignment explanation
Indices: 4031249--4031280 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4031239 CTATGCTTTC
4031249 GTCA-TTGGA-AGCTAT
1 GTCATTTGGACAGCTAT
4031264 GTCATTTGGACAGCTAT
1 GTCATTTGGACAGCTAT
4031281 TGCCGGGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 5 0.33
17 6 0.40
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (17 bp):
GTCATTTGGACAGCTAT
Found at i:4043401 original size:110 final size:107
Alignment explanation
Indices: 4043211--4043414 Score: 293
Period size: 110 Copynumber: 1.9 Consensus size: 107
4043201 GATTAAGATA
* * * *
4043211 TAAGAGGATATTTGGCTATTTGGTCCAACGAGAAATCGAAGCCCAGCACATTAAGGCACGTTTTC
1 TAAGAGGATATTTGGCTATTTGGTCCAACGAAAAATCGAAACCCAACACATTAAGGCACGCTTTC
*
4043276 TCGAATTTCCAAATGCAAAACATTGCCTTATTTTGAAACTTT
66 TCGAATTCCCAAATGCAAAACATTGCCTTATTTTGAAACTTT
* *
4043318 TAAGAGGATATTTGGCTATTTTGTCGAACGAAAAAAAATCGAAACCCAACACATTAAGGCACGCT
1 TAAGAGGATATTTGGCTATTTGGTCCAACG---AAAAATCGAAACCCAACACATTAAGGCACGCT
*
4043383 TTCTCGAA-TCCACAAATGCAAAATATTGCCTT
63 TTCTCGAATTCC-CAAATGCAAAACATTGCCTT
4043415 TATTATTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 28 0.33
109 2 0.02
110 55 0.65
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (107 bp):
TAAGAGGATATTTGGCTATTTGGTCCAACGAAAAATCGAAACCCAACACATTAAGGCACGCTTTC
TCGAATTCCCAAATGCAAAACATTGCCTTATTTTGAAACTTT
Found at i:4043970 original size:8 final size:8
Alignment explanation
Indices: 4043959--4043988 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
4043949 AATAAAATAA
4043959 ATAAAATT
1 ATAAAATT
4043967 ATAAAATT
1 ATAAAATT
4043975 ATAAAATT
1 ATAAAATT
4043983 ATAAAA
1 ATAAAA
4043989 ATGTACAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
ATAAAATT
Found at i:4044223 original size:2 final size:2
Alignment explanation
Indices: 4044218--4044276 Score: 77
Period size: 2 Copynumber: 30.0 Consensus size: 2
4044208 AATATGCACG
* *
4044218 TA TA TA TA TA T- TA TA -A AA AA GTA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
4044259 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
4044277 ACAAAACTTG
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.04
2 50 0.94
3 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4044367 original size:3 final size:3
Alignment explanation
Indices: 4044316--4044347 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4044306 GATACATAGC
4044316 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4044348 TTATTACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:4045928 original size:44 final size:44
Alignment explanation
Indices: 4045880--4046337 Score: 145
Period size: 44 Copynumber: 10.4 Consensus size: 44
4045870 CTTCGATCTG
4045880 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
* * * * * * *
4045924 CTCCACTACTGCTTAGAGAGATAGGA-CT--AATGGATTAAATCTGCTT
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAAT--CTTCAA-C--CTA
* * * * * *
4045970 CTCCACTA-T-CTTGAGAAGAT-A-AGATTC-ACCATCTTCAATCTG
1 CTCCACTACTGCTT-AG--GGTGACAGAATCTGCAATCTTCAACCTA
*
4046012 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
* * * * *
4046056 CTCCACTACTGCTTAGGGAGATAGGA-CT--AATGGCTTAAATCTACTT
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAAT--CTTCAA-C--CTA
* * * * * *
4046102 CTCCACTA-T-CTTGAGAAGAT-A-AGATTC-ACCATCTTCGATCTA
1 CTCCACTACTGCTT-AG--GGTGACAGAATCTGCAATCTTCAACCTA
* *
4046144 CTCCACTACTACTTAGGGTGACAGAATCTGCAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
* * * * * * *
4046188 CTTCACTACTGCTTAGGGAGATAGGA-CT--AATGGCTTAAATTTGCTT
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAAT--CTTCAA---CCTA
* * * * * * * *
4046234 CTTCACTA-T-CTTGAGAAGAT-A-AGATTC-ACCATCTTCGATCTG
1 CTCCACTACTGCTT-AG--GGTGACAGAATCTGCAATCTTCAACCTA
4046276 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
*
4046320 CTCCACTACTACTTAGGG
1 CTCCACTACTGCTTAGGG
4046338 AGATAAGACT
Statistics
Matches: 293, Mismatches: 73, Indels: 96
0.63 0.16 0.21
Matches are distributed among these distances:
41 15 0.05
42 32 0.11
43 42 0.14
44 133 0.45
45 27 0.09
46 36 0.12
47 8 0.03
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
Found at i:4046462 original size:44 final size:44
Alignment explanation
Indices: 4046408--4046607 Score: 135
Period size: 44 Copynumber: 4.5 Consensus size: 44
4046398 CTTCGATCTG
* *
4046408 CTCCAGTACTGCTTAGGGTGATAGAATTTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAGAATTTGCAATCTTCAACCTA
* * * *
4046452 CTCCACTACTGCTTAGGGAGATAGGA-CT--AATGGCTTAAATTCGCTT
1 CTCCACTACTGCTTAGGGAGATAGAATTTGCAAT--CTTCAA--C-CTA
* ** * * * *
4046498 CTCCGCTA-T-CTT-GGGAAGATA-AGATTCACCATCTTCGATCTG
1 CTCCACTACTGCTTAGGG-AGATAGA-ATTTGCAATCTTCAACCTA
* *
4046540 CTCCACTACTACTTAGGGTGATAGAATTTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAGAATTTGCAATCTTCAACCTA
* *
4046584 TTCGACTACTGCTTAGGGAGATAG
1 CTCCACTACTGCTTAGGGAGATAG
4046608 GACTAATGGC
Statistics
Matches: 115, Mismatches: 27, Indels: 28
0.68 0.16 0.16
Matches are distributed among these distances:
41 3 0.03
42 9 0.08
43 10 0.09
44 72 0.63
45 10 0.09
46 9 0.08
47 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAGAATTTGCAATCTTCAACCTA
Found at i:4046894 original size:132 final size:132
Alignment explanation
Indices: 4045715--4046875 Score: 1813
Period size: 132 Copynumber: 8.8 Consensus size: 132
4045705 TCCCTATTAC
* * * * *
4045715 CTTGGGAATATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAAGGAGACAGAATCTGCA
1 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
4045780 GTCTTCAACCTACTCGACTACTGCTTGGGGAGATTGGACTAATGGCTTAAATCTGCTTC-CTCAC
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTC-CAC
4045844 TAT
130 TAT
4045847 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* *
4045912 ATCTTCAACCTACTCCACTACTGCTTAGAGAGATAGGACTAATGGATTAAATCTGCTTCTCCACT
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
4045977 AT
131 AT
*
4045979 CTTGAGAAGATAAGATTCACCATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* *
4046044 ATTTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACT
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
4046109 AT
131 AT
* *
4046111 CTTGAGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTACTTAGGGTGACAGAATCTGCA
1 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
4046176 ATTTTCAACCTACTTCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATTTGCTTCTTCACT
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
4046241 AT
131 AT
4046243 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
4046308 ATCTTCAACCTACTCCACTACTACTTAGGGAGATAAGACTAATGGCTTAAATATGCTTCTCCGCT
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
4046373 AT
131 AT
* * *
4046375 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCAGTACTGCTTAGGGTGATAGAATTTGCA
1 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
*
4046440 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAAT-TCGCTTCTCCGC
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCT-GCTTCTCCAC
4046504 TAT
130 TAT
* * * *
4046507 CTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGATAGAATTTGCA
1 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
4046572 ATCTTCAACCTATTCGACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCGCT
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
4046637 AT
131 AT
* * * * * *
4046639 CTTGGGAAGATAAGATTCACCATATTCGATCTGTTCCACTACTGCTTAGTGTGATAGAATCTACA
1 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* ** **
4046704 AGCTTCAACCTACTCCACTACTGCTTAGGGAGATAAAACTAATGGCTTAAATCTGCTTCTCTGCT
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
4046769 AT
131 AT
* * * *
4046771 CTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGTA
1 CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* *
4046836 ATTTTCAACCTACTCCACTACTGTTTAGGGAGATAGGACT
66 ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACT
4046876 GGTGGTTTCG
Statistics
Matches: 957, Mismatches: 69, Indels: 6
0.93 0.07 0.01
Matches are distributed among these distances:
131 1 0.00
132 954 1.00
133 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (132 bp):
CTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
ATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
AT
Found at i:4047237 original size:24 final size:24
Alignment explanation
Indices: 4047183--4047239 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
4047173 TGGATTGCCC
* *
4047183 CCACTGAAATCTTCAAAGTTCAAT
1 CCACTGTAACCTTCAAAGTTCAAT
* *
4047207 CCGCTGTAACCTTCAAGGTT-AAGT
1 CCACTGTAACCTTCAAAGTTCAA-T
4047231 CCACTGTAA
1 CCACTGTAA
4047240 TTTTGGGACA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (24 bp):
CCACTGTAACCTTCAAAGTTCAAT
Found at i:4048066 original size:42 final size:42
Alignment explanation
Indices: 4048019--4048099 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
4048009 GGTATAGCAA
4048019 GATCACCACATACCCCAATCTGATCAAAATTTGAGCTGCTCT
1 GATCACCACATACCCCAATCTGATCAAAATTTGAGCTGCTCT
*** ** *
4048061 GATCACTTTATGTCCCATTCTGATCAAAATTTGAGCTGC
1 GATCACCACATACCCCAATCTGATCAAAATTTGAGCTGC
4048100 CATTTTCGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (42 bp):
GATCACCACATACCCCAATCTGATCAAAATTTGAGCTGCTCT
Found at i:4051488 original size:9 final size:8
Alignment explanation
Indices: 4051465--4051489 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4051455 TTCAATTTTC
4051465 GACAAAAA
1 GACAAAAA
4051473 GACAAAAA
1 GACAAAAA
4051481 GACAAAAA
1 GACAAAAA
4051489 G
1 G
4051490 TCATCAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (8 bp):
GACAAAAA
Found at i:4052065 original size:111 final size:107
Alignment explanation
Indices: 4051889--4052093 Score: 259
Period size: 111 Copynumber: 1.9 Consensus size: 107
4051879 GATTAAGATA
* * * * * * *
4051889 TAAGAGGATATTTGGCTATTTGGTCTAACGAGAAATCGAAGCCTAGCACATTAGGGCACGTTTTC
1 TAAGAGGATATTTGGCTATTTAGTCGAACGAAAAATCGAAACCCAACACATTAGGGCACGCTTTC
*
4051954 TCGAATTTC-CAAACGTAAAACATTGCCTTATTTTGAAACTTT
66 TCGAA-TTCACAAACGCAAAACATTGCCTTATTTTGAAACTTT
*
4051996 TAAGAGGATATTTTGGCTATTTAGTCGAACGAAAAAAAATCGAAACCCAACACATTAGGGCATGC
1 TAAGAGGATA-TTTGGCTATTTAGTCGAACG---AAAAATCGAAACCCAACACATTAGGGCACGC
* *
4052061 TTTCTCGAATTCACAAATGCAAAATATTGCCTT
62 TTTCTCGAATTCACAAACGCAAAACATTGCCTT
4052094 TATTATTTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 10 0.12
108 18 0.22
110 3 0.04
111 51 0.62
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (107 bp):
TAAGAGGATATTTGGCTATTTAGTCGAACGAAAAATCGAAACCCAACACATTAGGGCACGCTTTC
TCGAATTCACAAACGCAAAACATTGCCTTATTTTGAAACTTT
Found at i:4052649 original size:8 final size:8
Alignment explanation
Indices: 4052638--4052675 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
4052628 AAATAAATAA
4052638 ATAAAATT
1 ATAAAATT
4052646 ATAAAATT
1 ATAAAATT
4052654 ATAAAATT
1 ATAAAATT
4052662 ATAAAATT
1 ATAAAATT
4052670 ATAAAA
1 ATAAAA
4052676 ATGTACAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
ATAAAATT
Found at i:4052649 original size:16 final size:16
Alignment explanation
Indices: 4052632--4052675 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
4052622 GTAAATAAAT
4052632 AAATAAATAAAATTATA
1 AAAT-AATAAAATTATA
*
4052649 AAATTATAAAATTATA
1 AAATAATAAAATTATA
*
4052665 AAATTATAAAA
1 AAATAATAAAA
4052676 ATGTACAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAATAAAATTATA
Found at i:4052873 original size:2 final size:2
Alignment explanation
Indices: 4052866--4052959 Score: 68
Period size: 2 Copynumber: 48.5 Consensus size: 2
4052856 ATGAATCATA
* *
4052866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A- AC AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * ** * * * *
4052906 AA AA AT AT GC AC GT AT AT AT AT AT AT AT AT AT AT -T AT AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4052947 AT GT AT AT AT AT A
1 AT AT AT AT AT AT A
4052960 ACAAAACTTG
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
1 3 0.04
2 72 0.96
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:4054095 original size:30 final size:29
Alignment explanation
Indices: 4054054--4054113 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
4054044 GGTTAGGTAG
* * *
4054054 ATTGTGCCTATTGGGTTTGGGTAGTTGGTT
1 ATTGGGCCTATTGGGTTCGGG-AGTCGGTT
4054084 ATTGGGCCTATTGGGTTCGGGAGTCGGTT
1 ATTGGGCCTATTGGGTTCGGGAGTCGGTT
4054113 A
1 A
4054114 CGTATGAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.40
Consensus pattern (29 bp):
ATTGGGCCTATTGGGTTCGGGAGTCGGTT
Found at i:4054447 original size:110 final size:107
Alignment explanation
Indices: 4054257--4054460 Score: 293
Period size: 110 Copynumber: 1.9 Consensus size: 107
4054247 GATTAAGATA
* * * *
4054257 TAAGAGGATATTTGGCTATTTGGTCCAACGAGAAATCGAAGCCCAGCACATTAAGGCACGTTTTC
1 TAAGAGGATATTTGGCTATTTGGTCCAACGAAAAATCGAAACCCAACACATTAAGGCACGCTTTC
*
4054322 TCGAATTTCCAAATGCAAAACATTGCCTTATTTTGAAACTTT
66 TCGAATTCCCAAATGCAAAACATTGCCTTATTTTGAAACTTT
* *
4054364 TAAGAGGATATTTGGCTATTTTGTCGAACGAAAAAAAATCGAAACCCAACACATTAAGGCACGCT
1 TAAGAGGATATTTGGCTATTTGGTCCAACG---AAAAATCGAAACCCAACACATTAAGGCACGCT
*
4054429 TTCTCGAA-TCCACAAATGCAAAATATTGCCTT
63 TTCTCGAATTCC-CAAATGCAAAACATTGCCTT
4054461 TATTATTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 28 0.33
109 2 0.02
110 55 0.65
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (107 bp):
TAAGAGGATATTTGGCTATTTGGTCCAACGAAAAATCGAAACCCAACACATTAAGGCACGCTTTC
TCGAATTCCCAAATGCAAAACATTGCCTTATTTTGAAACTTT
Found at i:4055020 original size:8 final size:8
Alignment explanation
Indices: 4055009--4055038 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
4054999 AAATAAATAA
4055009 ATAAAATT
1 ATAAAATT
4055017 ATAAAATT
1 ATAAAATT
4055025 ATAAAATT
1 ATAAAATT
4055033 ATAAAA
1 ATAAAA
4055039 ATGTACAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
ATAAAATT
Found at i:4055020 original size:16 final size:16
Alignment explanation
Indices: 4055003--4055038 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4054993 ATAAATAAAT
4055003 AAATAAATAAAATTATA
1 AAAT-AATAAAATTATA
*
4055020 AAATTATAAAATTATA
1 AAATAATAAAATTATA
4055036 AAA
1 AAA
4055039 ATGTACAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAATAAAATTATA
Found at i:4055236 original size:2 final size:2
Alignment explanation
Indices: 4055229--4055322 Score: 68
Period size: 2 Copynumber: 48.5 Consensus size: 2
4055219 ATGAATCATA
* *
4055229 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A- AC AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * ** * * * *
4055269 AA AA AT AT GC AC GT AT AT AT AT AT AT AT AT AT AT -T AT AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4055310 AT GT AT AT AT AT A
1 AT AT AT AT AT AT A
4055323 ACAAAACTTG
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
1 3 0.04
2 72 0.96
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:4056853 original size:26 final size:24
Alignment explanation
Indices: 4056823--4056879 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
4056813 GAAGCTTCGG
4056823 AGAGCTATTAATCAGAAAGCTCACAA
1 AGAGCTATT-ATCAGAAAGCTCA-AA
* *
4056849 AGAGCAATTATCAGGAAGCTCAAA
1 AGAGCTATTATCAGAAAGCTCAAA
4056873 AGAGCTA
1 AGAGCTA
4056880 AGGTGTGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 8 0.29
25 12 0.43
26 8 0.29
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (24 bp):
AGAGCTATTATCAGAAAGCTCAAA
Found at i:4058746 original size:2 final size:2
Alignment explanation
Indices: 4058739--4058763 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4058729 CATAAGCAAA
4058739 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 A
4058764 GTAAGTCTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4059392 original size:17 final size:17
Alignment explanation
Indices: 4059367--4059406 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
4059357 TTCAAGAAAT
*
4059367 TTAAACCAAAACTCACC
1 TTAATCCAAAACTCACC
4059384 TTAATCCAAAACTCACC
1 TTAATCCAAAACTCACC
4059401 TTAATC
1 TTAATC
4059407 GCTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (17 bp):
TTAATCCAAAACTCACC
Found at i:4067264 original size:29 final size:27
Alignment explanation
Indices: 4067232--4067302 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
4067222 AAAAATAAAA
**
4067232 ATTTACCAAAATACTACAAGTTTTTTTTT
1 ATTTACCAAAATA-TACAA-ACTTTTTTT
*
4067261 ATTTACCAAAATATATAAACTTTTTTT
1 ATTTACCAAAATATACAAACTTTTTTT
4067288 ATTTACCAAAATATA
1 ATTTACCAAAATATA
4067303 TAAAAAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 22 0.56
28 4 0.10
29 13 0.33
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.45
Consensus pattern (27 bp):
ATTTACCAAAATATACAAACTTTTTTT
Found at i:4067292 original size:27 final size:27
Alignment explanation
Indices: 4067254--4067306 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
4067244 ACTACAAGTT
4067254 TTTTTTTATTTACCAAAATATATAAAC
1 TTTTTTTATTTACCAAAATATATAAAC
4067281 TTTTTTTATTTACCAAAATATATAAA
1 TTTTTTTATTTACCAAAATATATAAA
4067307 AAAAACCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTTTTTATTTACCAAAATATATAAAC
Found at i:4067327 original size:18 final size:19
Alignment explanation
Indices: 4067292--4067331 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
4067282 TTTTTTATTT
*
4067292 ACCAAAATATATAAAAAAA
1 ACCAAAATATAAAAAAAAA
4067311 ACCAAAAT-TAAAAAAAAA
1 ACCAAAATATAAAAAAAAA
4067329 ACC
1 ACC
4067332 TGACAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.72, C:0.15, G:0.00, T:0.12
Consensus pattern (19 bp):
ACCAAAATATAAAAAAAAA
Found at i:4067631 original size:3 final size:3
Alignment explanation
Indices: 4067613--4067668 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
4067603 AAAATAAAAG
*
4067613 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4067659 TAT TAT TAT T
1 TAT TAT TAT T
4067669 GTTGTTGTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:4067673 original size:3 final size:3
Alignment explanation
Indices: 4067667--4067704 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4067657 ATTATTATTA
4067667 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
4067705 AGTATGAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:4074026 original size:13 final size:13
Alignment explanation
Indices: 4074010--4074034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4074000 TTCATGTACA
4074010 TTTTTCGCATTTC
1 TTTTTCGCATTTC
4074023 TTTTTCGCATTT
1 TTTTTCGCATTT
4074035 ATTTATTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTTTCGCATTTC
Found at i:4074396 original size:21 final size:20
Alignment explanation
Indices: 4074344--4074540 Score: 113
Period size: 21 Copynumber: 9.5 Consensus size: 20
4074334 AAAATTACCT
* *
4074344 TTTTTTCCCTT-TTTTTTCC
1 TTTTTTCTCTTCTTCTTTCC
* *
4074363 TTTCTTCCCTCTTCTTCTTCTTC
1 TTT-TT-TCTCTTCTTCTT-TCC
*
4074386 TTTTTTCTCTTCTCCTTTCCC
1 TTTTTTCTCTTCTTCTTT-CC
4074407 TTTCTTTC-CTTCCTTCTTT-C
1 TTT-TTTCTCTT-CTTCTTTCC
4074427 TTTTTTCTTCTTCTTTCTTTCC
1 TTTTTTC-TCTTC-TTCTTTCC
*
4074449 TTTTTTCTCTTCTCCTTTCC
1 TTTTTTCTCTTCTTCTTTCC
* **
4074469 TTTTCTT-TCTT-TCCTCCCC
1 TTTT-TTCTCTTCTTCTTTCC
4074488 TTTCTTTCT-TTCTTTCTTT-C
1 TTT-TTTCTCTTC-TTCTTTCC
*
4074508 TTTCTTTCCTCTCCTTTCTTT-C
1 TTT-TTT-CTCTTC-TTCTTTCC
4074530 TTTCTTTCTCT
1 TTT-TTTCTCT
4074541 CTTTCTGCCC
Statistics
Matches: 145, Mismatches: 15, Indels: 34
0.75 0.08 0.18
Matches are distributed among these distances:
19 20 0.14
20 33 0.23
21 46 0.32
22 41 0.28
23 5 0.03
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTTCTCTTCTTCTTTCC
Found at i:4074425 original size:22 final size:21
Alignment explanation
Indices: 4074358--4074537 Score: 103
Period size: 22 Copynumber: 8.6 Consensus size: 21
4074348 TTCCCTTTTT
* *
4074358 TTTCCTTTCTTCCCTCTTCTTC
1 TTTCCTTTCTTTCCT-TCCTTC
* *
4074380 TTCTTCTTT-TTTCTCTT-CTCC
1 TT-TCCTTTCTTTC-CTTCCTTC
4074401 TTTCCCTTTCTTTCCTTCCTTC
1 TTT-CCTTTCTTTCCTTCCTTC
*
4074423 TTT-CTTT-TTTCTTCTTCTTTC
1 TTTCCTTTCTTTC--CTTCCTTC
*
4074444 TTTCCTTT-TTTCTCTT-CTCC
1 TTTCCTTTCTTTC-CTTCCTTC
*
4074464 TTTCCTTTTCTTTCTTTCC-TC
1 TTTCC-TTTCTTTCCTTCCTTC
* * *
4074485 --CCCTTTCTTTCTTTCTTTC
1 TTTCCTTTCTTTCCTTCCTTC
4074504 TTT-CTTTCTTTCCTCTCCTTTC
1 TTTCCTTTCTTTCCT-TCC-TTC
4074526 TTT-CTTTCTTTC
1 TTTCCTTTCTTTC
4074538 TCTCTTTCTG
Statistics
Matches: 127, Mismatches: 15, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
18 12 0.09
19 8 0.06
20 22 0.17
21 34 0.27
22 44 0.35
23 7 0.06
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTCCTTTCTTTCCTTCCTTC
Found at i:4074427 original size:4 final size:4
Alignment explanation
Indices: 4074406--4074546 Score: 112
Period size: 4 Copynumber: 34.5 Consensus size: 4
4074396 TCTCCTTTCC
* *
4074406 CTTT CTTT CCTT CCTT CTTT CTTT -TTT C-TT C-TT CTTT CTTT CCTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT
* **
4074452 -TTT CTCTT C-TC CTTT CCTTTT CTTT CTTT CCTCCC CTTT CTTT CTTT
1 CTTT CT-TT CTTT CTTT -C-TTT CTTT CTTT -CT-TT CTTT CTTT CTTT
* *
4074499 CTTT CTTT CTTT CTTT CCTCTC CTTT CTTT CTTT CTTT CTCT CTTT CT
1 CTTT CTTT CTTT CTTT -CT-TT CTTT CTTT CTTT CTTT CTTT CTTT CT
4074547 GCCCCAACCA
Statistics
Matches: 113, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
3 14 0.12
4 78 0.69
5 17 0.15
6 4 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:4074427 original size:34 final size:34
Alignment explanation
Indices: 4074367--4074483 Score: 111
Period size: 34 Copynumber: 3.6 Consensus size: 34
4074357 TTTTCCTTTC
*
4074367 TTCCCTCTTCTTCTTCTT-CTTTTTTCTCTTCTCCT
1 TTCCCT-TTCTT-TCCTTCCTTTTTTCTCTTCTCCT
* * *
4074402 TTCCCTTTCTTTCCTTCCTTCTTTCT-TTTTTC-
1 TTCCCTTTCTTTCCTTCCTTTTTTCTCTTCTCCT
*
4074434 TT--C-TTCTTTCTTTCCTTTTTTCTCTTCTCCT
1 TTCCCTTTCTTTCCTTCCTTTTTTCTCTTCTCCT
* *
4074465 TTCCTTTTCTTTCTTTCCT
1 TTCCCTTTCTTTCCTTCCT
4074484 CCCCTTTCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
29 18 0.27
30 5 0.07
31 2 0.03
32 2 0.03
33 8 0.12
34 26 0.39
35 6 0.09
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (34 bp):
TTCCCTTTCTTTCCTTCCTTTTTTCTCTTCTCCT
Found at i:4074460 original size:63 final size:65
Alignment explanation
Indices: 4074372--4074517 Score: 203
Period size: 63 Copynumber: 2.3 Consensus size: 65
4074362 CTTTCTTCCC
*
4074372 TCTTCTTC-TTC-TT-CTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCCT-TCTTTCTTT-TT
1 TCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCCTCCCTTTCTTTCTT
* *
4074432 TCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCTTTTCTTTCTTTCCTCCCCTTTCTTTCT
1 TCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCCT-CCCTTTCTTTCT
4074497 T
65 T
4074498 TCTTTCTTTCTTTCTTTCCT
1 TC-TTC-TTCTTTCTTTCCT
4074518 CTCCTTTCTT
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
60 8 0.11
61 3 0.04
62 2 0.03
63 34 0.45
65 8 0.11
66 4 0.05
67 3 0.04
68 13 0.17
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (65 bp):
TCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCCTCCCTTTCTTTCTT
Found at i:4074508 original size:34 final size:34
Alignment explanation
Indices: 4074406--4074546 Score: 159
Period size: 34 Copynumber: 4.2 Consensus size: 34
4074396 TCTCCTTTCC
4074406 CTTTCTTTCCTTCC-TTCTTTCTTT-TTTCTTCTT
1 CTTTCTTTCCTTCCTTTCTTTCTTTCTTTCTT-TT
* *
4074439 CTTTCTTTCCTT-TTTTCTCTTC-TCCTTTCCTTTT
1 CTTTCTTTCCTTCCTTTCT-TTCTTTCTTT-CTTTT
*
4074473 CTTTCTTTCCTCCCCTTTCTTTCTTTCTTTC-TTT
1 CTTTCTTTCCT-TCCTTTCTTTCTTTCTTTCTTTT
*
4074507 CTTTCTTTCCTCTCCTTTCTTTCTTTCTTTC-TCT
1 CTTTCTTTCCT-TCCTTTCTTTCTTTCTTTCTTTT
4074541 CTTTCT
1 CTTTCT
4074547 GCCCCAACCA
Statistics
Matches: 94, Mismatches: 7, Indels: 13
0.82 0.06 0.11
Matches are distributed among these distances:
33 17 0.18
34 60 0.64
35 7 0.07
36 10 0.11
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (34 bp):
CTTTCTTTCCTTCCTTTCTTTCTTTCTTTCTTTT
Found at i:4074609 original size:27 final size:27
Alignment explanation
Indices: 4074577--4074652 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
4074567 TAACACCAAC
4074577 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
4074604 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
4074631 TGGTGCCGCCAATACCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
4074653 GTGACCAGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:4074785 original size:27 final size:28
Alignment explanation
Indices: 4074724--4074794 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 28
4074714 GTTTTTTTTG
*
4074724 ATATATTTTGGTAAATAAAAAAAAGTTT
1 ATATATTTTGGTAAATAAAAAAAACTTT
4074752 ATATATTTTGGTAAAT-AAAAAAACTTGT
1 ATATATTTTGGTAAATAAAAAAAACTT-T
*
4074780 A-GTATTTTGGTAAAT
1 ATATATTTTGGTAAAT
4074795 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAACTTT
Found at i:4078173 original size:2 final size:2
Alignment explanation
Indices: 4078116--4078154 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4078106 AGCATAGTTT
*
4078116 TA TA AA TA TA TA TA 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 TA TA TA TA TA TA TA T
4078155 TATCACAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4086867 original size:29 final size:29
Alignment explanation
Indices: 4086841--4086902 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
4086831 ACGTTTTACC
4086841 AAAATCAACCCA-TTCTCATAAATTTTAAA
1 AAAATCAACCCATTTCT-ATAAATTTTAAA
* * **
4086870 AAAATCGACCTATTTCTATAAATTAAAAA
1 AAAATCAACCCATTTCTATAAATTTTAAA
4086899 AAAA
1 AAAA
4086903 AGACATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (29 bp):
AAAATCAACCCATTTCTATAAATTTTAAA
Found at i:4089987 original size:3 final size:3
Alignment explanation
Indices: 4089979--4090004 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4089969 TTTACTGTAT
4089979 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
4090005 TCATTATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:4098432 original size:10 final size:10
Alignment explanation
Indices: 4098419--4098448 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
4098409 GATTTAGATC
*
4098419 ATTTTACGTT
1 ATTTTAAGTT
4098429 ATTTTAAGTT
1 ATTTTAAGTT
4098439 ATTTTAAGTT
1 ATTTTAAGTT
4098449 GGGATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (10 bp):
ATTTTAAGTT
Found at i:4101558 original size:5 final size:5
Alignment explanation
Indices: 4101548--4101573 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4101538 TGAGCATTCG
4101548 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
4101574 AATTTTCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:4104823 original size:18 final size:18
Alignment explanation
Indices: 4104755--4104815 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
4104745 GGCCTAATAA
*
4104755 GAGCAATCGGTCCAAGGG
1 GAGCATTCGGTCCAAGGG
4104773 GAGCATTCGGTCCAAGGG
1 GAGCATTCGGTCCAAGGG
4104791 GAGCATTCGGTCCAAGGG
1 GAGCATTCGGTCCAAGGG
4104809 GAGCATT
1 GAGCATT
4104816 TGGCCCAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.25, C:0.21, G:0.38, T:0.16
Consensus pattern (18 bp):
GAGCATTCGGTCCAAGGG
Found at i:4105136 original size:105 final size:105
Alignment explanation
Indices: 4104954--4105142 Score: 333
Period size: 105 Copynumber: 1.8 Consensus size: 105
4104944 GTCCTGCACA
* *
4104954 ATTATAGCCATCAACACACACATTTTGACCAGAAACACAATTAGTTTGACCACCCCCAAAATAAT
1 ATTATAGCCATCAACACACACATTTTGACCAGAAACACAATTAGTTTGACCAACCCCAAAACAAT
4105019 TTTGACCAAAATTATTTCCTGCACGTTGTTCCAAAAAACC
66 TTTGACCAAAATTATTTCCTGCACGTTGTTCCAAAAAACC
* * *
4105059 ATTATAGCCATCAGCACACACATTTTGACCAGAAACACCATTATTTTGACCAACCCCAAAACAAT
1 ATTATAGCCATCAACACACACATTTTGACCAGAAACACAATTAGTTTGACCAACCCCAAAACAAT
4105124 TTTGACCAAAATTATTTCC
66 TTTGACCAAAATTATTTCC
4105143 ATAATAATTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 79 1.00
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (105 bp):
ATTATAGCCATCAACACACACATTTTGACCAGAAACACAATTAGTTTGACCAACCCCAAAACAAT
TTTGACCAAAATTATTTCCTGCACGTTGTTCCAAAAAACC
Found at i:4114492 original size:24 final size:24
Alignment explanation
Indices: 4114430--4114481 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4114420 TTTTTAGAAG
* * *
4114430 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAATATAATAT
4114454 ATTTAGCATTTATTAATATAATAT
1 ATTTAGCATTTATTAATATAATAT
4114478 ATTT
1 ATTT
4114482 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAATATAATAT
Found at i:4116217 original size:31 final size:31
Alignment explanation
Indices: 4116179--4116524 Score: 268
Period size: 31 Copynumber: 11.2 Consensus size: 31
4116169 CTTGTGGGAT
*
4116179 GCCTCACCATCTCGCGAAGTGATTCTATCAC
1 GCCTCACCATCTCGCGAAGTGATCCTATCAC
**
4116210 GCCTCACCATCTCGCGAAGTGATTTTATCAC
1 GCCTCACCATCTCGCGAAGTGATCCTATCAC
* * * *
4116241 ACCTCACCATCTCGCAAAGTGATCATGTCAC
1 GCCTCACCATCTCGCGAAGTGATCCTATCAC
* * * * *
4116272 GCCTCATCATTTCACGAGGTGATCCCATCAC
1 GCCTCACCATCTCGCGAAGTGATCCTATCAC
* * * * *
4116303 GCCTCACTATCTCACTAACTGATCTTATCAC
1 GCCTCACCATCTCGCGAAGTGATCCTATCAC
* * * * *
4116334 GTCTCACTATCTCGCTAAGTGATCCCATCAT
1 GCCTCACCATCTCGCGAAGTGATCCTATCAC
* * *
4116365 ACCTCACCAACTCGCGAAGTGA-CC-GTCAC
1 GCCTCACCATCTCGCGAAGTGATCCTATCAC
* * * *
4116394 GCCTCACCATCTCACTAAGTGATCCCATTAC
1 GCCTCACCATCTCGCGAAGTGATCCTATCAC
* * ** * *
4116425 ACCTCACCACCTCATGAAGTTAT-CTCGTCAC
1 GCCTCACCATCTCGCGAAGTGATCCT-ATCAC
* * * *
4116456 GCCTCACCATCTTGTGAAGTGATCCCATCAT
1 GCCTCACCATCTCGCGAAGTGATCCTATCAC
* *
4116487 GCCTCACCATCTAC-CTAAGTGATCCTGTCAC
1 GCCTCACCATCT-CGCGAAGTGATCCTATCAC
*
4116518 ACCTCAC
1 GCCTCAC
4116525 AACCTCACAA
Statistics
Matches: 245, Mismatches: 65, Indels: 10
0.77 0.20 0.03
Matches are distributed among these distances:
29 21 0.09
30 5 0.02
31 218 0.89
32 1 0.00
ACGTcount: A:0.25, C:0.36, G:0.13, T:0.26
Consensus pattern (31 bp):
GCCTCACCATCTCGCGAAGTGATCCTATCAC
Found at i:4116277 original size:62 final size:61
Alignment explanation
Indices: 4116180--4116524 Score: 316
Period size: 62 Copynumber: 5.6 Consensus size: 61
4116170 TTGTGGGATG
* ***
4116180 CCTCACCATCTCGCGAAGTGATTCTATCACGCCTCACCATCTCGCGAAGTGATTTTATCACA
1 CCTCACCATCTCGCGAAGTGA-TCTGTCACGCCTCACCATCTCGCGAAGTGATCCCATCACA
* * * * * *
4116242 CCTCACCATCTCGCAAAGTGATCATGTCACGCCTCATCATTTCACGAGGTGATCCCATCACG
1 CCTCACCATCTCGCGAAGTGATC-TGTCACGCCTCACCATCTCGCGAAGTGATCCCATCACA
* * * * * * * * *
4116304 CCTCACTATCTCACTAACTGATCTTATCACGTCTCACTATCTCGCTAAGTGATCCCATCATA
1 CCTCACCATCTCGCGAAGTGATC-TGTCACGCCTCACCATCTCGCGAAGTGATCCCATCACA
* * * * *
4116366 CCTCACCAACTCGCGAAGTGA-CCGTCACGCCTCACCATCTCACTAAGTGATCCCATTACA
1 CCTCACCATCTCGCGAAGTGATCTGTCACGCCTCACCATCTCGCGAAGTGATCCCATCACA
* ** * * * **
4116426 CCTCACCACCTCATGAAGTTATCTCGTCACGCCTCACCATCTTGTGAAGTGATCCCATCATG
1 CCTCACCATCTCGCGAAGTGATCT-GTCACGCCTCACCATCTCGCGAAGTGATCCCATCACA
* *
4116488 CCTCACCATCTAC-CTAAGTGATCCTGTCACACCTCAC
1 CCTCACCATCT-CGCGAAGTGAT-CTGTCACGCCTCAC
4116525 AACCTCACAA
Statistics
Matches: 224, Mismatches: 54, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
60 48 0.21
61 4 0.02
62 169 0.75
63 3 0.01
ACGTcount: A:0.25, C:0.37, G:0.13, T:0.26
Consensus pattern (61 bp):
CCTCACCATCTCGCGAAGTGATCTGTCACGCCTCACCATCTCGCGAAGTGATCCCATCACA
Done.