Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold283
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: 2945114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 15
Found at i:2432747 original size:3 final size:3
Alignment explanation
Indices: 2432739--2432767 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2432729 CTAAATTGCG
2432739 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2432768 TACGATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2434344 original size:16 final size:17
Alignment explanation
Indices: 2434312--2434346 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2434302 TTGCAAGAAC
*
2434312 AAAATAAAGAAATTAAA
1 AAAAAAAAGAAATTAAA
2434329 AAAAAAAAGAAA-TAAA
1 AAAAAAAAGAAATTAAA
2434345 AA
1 AA
2434347 GAAAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAAAAAGAAATTAAA
Found at i:2436022 original size:2 final size:2
Alignment explanation
Indices: 2436015--2436039 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2436005 GATTTTATTC
2436015 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
2436040 TAAGCTGATT
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:2437974 original size:21 final size:21
Alignment explanation
Indices: 2437928--2437980 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2437918 AAACTAATAA
*
2437928 TATAATTATATATAAATATAT
1 TATAATTATATATAAATAAAT
*
2437949 CATAATT-TATATAATATAAAT
1 TATAATTATATATAA-ATAAAT
*
2437970 TATAAATATAT
1 TATAATTATAT
2437981 TAATATCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.27
21 16 0.62
22 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAATTATATATAAATAAAT
Found at i:2438046 original size:26 final size:28
Alignment explanation
Indices: 2437990--2438055 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 28
2437980 TTAATATCTT
*
2437990 TATACTATAAAAATAATAAATAAAATTATAA
1 TATA-TATAAAAATAATAAAT--AATAATAA
2438021 TATATATAAAAAT-ATAAAT-ATAATAA
1 TATATATAAAAATAATAAATAATAATAA
*
2438047 AATATATAA
1 TATATATAA
2438056 GTCATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 14 0.42
29 6 0.18
30 9 0.27
31 4 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
TATATATAAAAATAATAAATAATAATAA
Found at i:2441216 original size:12 final size:12
Alignment explanation
Indices: 2441199--2441237 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2441189 CAACTGGGGG
2441199 TATATACATATA
1 TATATACATATA
*
2441211 TATATATATATA
1 TATATACATATA
* *
2441223 TATGTACGTATA
1 TATATACATATA
2441235 TAT
1 TAT
2441238 GATCAACGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (12 bp):
TATATACATATA
Found at i:2442023 original size:28 final size:28
Alignment explanation
Indices: 2441992--2442057 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
2441982 TAAAAATATT
* * *
2441992 TTAATATTAATATTTA-TTTATTTTATAA
1 TTAA-ATTAATATATATTTTATATAATAA
2442020 TTAAATTTAA-ATATATTTTATATAATAA
1 TTAAA-TTAATATATATTTTATATAATAA
2442048 TTAAATTAAT
1 TTAAATTAAT
2442058 TCAAATCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTAAATTAATATATATTTTATATAATAA
Found at i:2442038 original size:23 final size:24
Alignment explanation
Indices: 2441976--2442043 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 24
2441966 ACTATTATAA
*
2441976 AAATATTAAAAATATTTTA-ATATT
1 AAAT-TTAAATATATTTTATATATT
*
2442000 AATATTT--ATTTATTTTATA-ATT
1 AA-ATTTAAATATATTTTATATATT
2442022 AAATTTAAATATATTTTATATA
1 AAATTTAAATATATTTTATATA
2442044 ATAATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
21 4 0.11
22 13 0.36
23 12 0.33
24 5 0.14
25 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AAATTTAAATATATTTTATATATT
Found at i:2442049 original size:23 final size:23
Alignment explanation
Indices: 2441971--2442053 Score: 59
Period size: 22 Copynumber: 3.7 Consensus size: 23
2441961 ATTTTACTAT
* *
2441971 TATAAAAATATTAAAAATATTTTAA
1 TATAATAAT-TTAAATATATTTT-A
*
2441996 TATTAAT-ATTT--ATTTATTTTA
1 TA-TAATAATTTAAATATATTTTA
*
2442017 TA-ATTAAATTTAAATATATTTTA
1 TATAAT-AATTTAAATATATTTTA
2442040 TATAATAA-TTAAAT
1 TATAATAATTTAAAT
2442054 TAATTCAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
19 2 0.04
21 7 0.15
22 13 0.28
23 13 0.28
24 4 0.09
25 4 0.09
26 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAATAATTTAAATATATTTTA
Found at i:2446961 original size:87 final size:87
Alignment explanation
Indices: 2446847--2447032 Score: 309
Period size: 87 Copynumber: 2.1 Consensus size: 87
2446837 GTGACAGCAA
* *
2446847 AAAGGATGATTCGTCAAGTAGTAAAGAGTGGATTACAGGTTCCTTGAAATTTGATGCAAAGCCTG
1 AAAGGATGATTCATCAAGTAGTAAAGAGTGGATTACAGGTTCCTTGAAATTTGATGCAAAGCCAG
*
2446912 CAGCTCCCTCTAAAGCTTCCTC
66 CAGATCCCTCTAAAGCTTCCTC
* *
2446934 AAAGGATGATTCATCAAGTAGTAAAGAGTGGATTATAGGTTCCTTGGAATTTGATGCAAAGCCAG
1 AAAGGATGATTCATCAAGTAGTAAAGAGTGGATTACAGGTTCCTTGAAATTTGATGCAAAGCCAG
*
2446999 CAGATCCCTCTAAAGCTTCTTC
66 CAGATCCCTCTAAAGCTTCCTC
*
2447021 TAAGGATGATTC
1 AAAGGATGATTC
2447033 CTCATCCTTG
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 92 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (87 bp):
AAAGGATGATTCATCAAGTAGTAAAGAGTGGATTACAGGTTCCTTGAAATTTGATGCAAAGCCAG
CAGATCCCTCTAAAGCTTCCTC
Found at i:2452203 original size:24 final size:25
Alignment explanation
Indices: 2452173--2452252 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 25
2452163 TTATAGCAAG
* *
2452173 ATATAAATATTATATATTTAATATA
1 ATATAAATATTAAATATTTAATAAA
**
2452198 AT-TAAATATTAAATATAAAATAAA
1 ATATAAATATTAAATATTTAATAAA
* * *
2452222 ATAAAAATATTACATATTT-ATTAA
1 ATATAAATATTAAATATTTAATAAA
2452246 ATATAAA
1 ATATAAA
2452253 AATAATATAA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
24 30 0.68
25 14 0.32
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAAATATTAAATATTTAATAAA
Found at i:2452206 original size:17 final size:17
Alignment explanation
Indices: 2452181--2452215 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2452171 AGATATAAAT
* *
2452181 ATTATATATTTAATATA
1 ATTAAATATTAAATATA
2452198 ATTAAATATTAAATATA
1 ATTAAATATTAAATATA
2452215 A
1 A
2452216 AATAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTAAATATTAAATATA
Found at i:2452233 original size:25 final size:26
Alignment explanation
Indices: 2452192--2452256 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
2452182 TTATATATTT
2452192 AATATAATTAAATATTAAATATAAAATA
1 AATATAA--AAATATTAAATATAAAATA
* ** *
2452220 AA-ATAAAAATATTACATATTTATTA
1 AATATAAAAATATTAAATATAAAATA
2452245 AATATAAAAATA
1 AATATAAAAATA
2452257 ATATAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 17 0.53
26 9 0.28
27 4 0.12
28 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
AATATAAAAATATTAAATATAAAATA
Found at i:2452285 original size:37 final size:37
Alignment explanation
Indices: 2452208--2452314 Score: 89
Period size: 35 Copynumber: 2.9 Consensus size: 37
2452198 ATTAAATATT
* * * *
2452208 AAATAT-AAAATAAAATAAAAATATTACA-TATTTATT
1 AAATATAAAAATAATATAATAATTTTA-ATTATTTATC
2452244 AAATATAAAAATAATATAATAATTTTATATTATTTA-C
1 AAATATAAAAATAATATAATAATTTTA-ATTATTTATC
* * *
2452281 -AA-ATAAAATTAATATATATAAGTTTAATTTTTTA
1 AAATATAAAAATAATATA-ATAATTTTAATTATTTA
2452315 AAAAATTTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
35 20 0.33
36 16 0.27
37 18 0.30
38 6 0.10
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (37 bp):
AAATATAAAAATAATATAATAATTTTAATTATTTATC
Found at i:2452287 original size:35 final size:35
Alignment explanation
Indices: 2452248--2452314 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
2452238 TTTATTAAAT
*
2452248 ATAAAAATAATATA-ATAATTTTATATTATTTACAA
1 ATAAAAATAATATATATAAGTTTA-ATTATTTACAA
* *
2452283 ATAAAATTAATATATATAAGTTTAATTTTTTA
1 ATAAAAATAATATATATAAGTTTAATTATTTA
2452315 AAAAATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 20 0.71
36 8 0.29
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (35 bp):
ATAAAAATAATATATATAAGTTTAATTATTTACAA
Found at i:2471243 original size:2 final size:2
Alignment explanation
Indices: 2471236--2471280 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2471226 TCCACCGGGG
2471236 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
2471278 AT A
1 AT A
2471281 GTATTTTGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2471591 original size:2 final size:2
Alignment explanation
Indices: 2471586--2471619 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2471576 GAGAGACGAC
*
2471586 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2471620 AAAGTAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2471774 original size:2 final size:2
Alignment explanation
Indices: 2471767--2471798 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2471757 AAGATGAGAA
2471767 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
2471799 GTATCCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2472024 original size:21 final size:21
Alignment explanation
Indices: 2472000--2472039 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2471990 AATTTATGTA
* *
2472000 TTATGTCATATTCATATTTTG
1 TTATATCATAATCATATTTTG
*
2472021 TTATATTATAATCATATTT
1 TTATATCATAATCATATTT
2472040 AAAATATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATATCATAATCATATTTTG
Found at i:2472695 original size:37 final size:39
Alignment explanation
Indices: 2472643--2472730 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 39
2472633 TTATATCTGT
* *
2472643 TTAAACTCTTGTAGTA-T-TATATATTTTGTTTAATTCA
1 TTAAACTCTTATAGTATTATATATATTTTGTTTAATTAA
2472680 TTAAACTCTTATAGTATTATATATATTTTGTTTAATTAA
1 TTAAACTCTTATAGTATTATATATATTTTGTTTAATTAA
2472719 TTAAACTCTTAT
1 TTAAACTCTTAT
2472731 TTTACACGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 15 0.32
38 1 0.02
39 31 0.66
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (39 bp):
TTAAACTCTTATAGTATTATATATATTTTGTTTAATTAA
Found at i:2476676 original size:18 final size:18
Alignment explanation
Indices: 2476654--2476742 Score: 54
Period size: 18 Copynumber: 4.7 Consensus size: 18
2476644 TATAATATAA
2476654 ATTATTAATATATAAAAT
1 ATTATTAATATATAAAAT
* *
2476672 TTTATTTAA-ATATAATAT
1 ATTA-TTAATATATAAAAT
* *
2476690 ATTATAAATATGATTATAAT
1 ATTATTAATAT-A-TAAAAT
* *
2476710 ATAATAAAATATATAAATAT
1 ATTAT-TAATATATAAA-AT
* *
2476730 AATATAAATATAT
1 ATTATTAATATAT
2476743 GAATTATTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
17 3 0.05
18 16 0.29
19 16 0.29
20 14 0.25
21 6 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (18 bp):
ATTATTAATATATAAAAT
Found at i:2476688 original size:5 final size:5
Alignment explanation
Indices: 2476680--2476741 Score: 56
Period size: 5 Copynumber: 12.2 Consensus size: 5
2476670 ATTTTATTTA
* * *
2476680 AATAT AATAT ATTAT AAATAT GATTAT AATAT AATAA AATAT -ATA- AATAT
1 AATAT AATAT AATAT -AATAT -AATAT AATAT AATAT AATAT AATAT AATAT
2476730 AATAT AAATAT A
1 AATAT -AATAT A
2476742 TGAATTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
4 6 0.13
5 27 0.59
6 13 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:2476698 original size:27 final size:25
Alignment explanation
Indices: 2476659--2476742 Score: 66
Period size: 27 Copynumber: 3.3 Consensus size: 25
2476649 TATAAATTAT
* *
2476659 TAATATATAAAATTTTATT-TAAATA
1 TAATATATAAAATATGATTAT-AATA
2476684 TAATATATTATAAATATGATTATAATA
1 TAATATA-TA-AAATATGATTATAATA
* * *
2476711 TAATA-A-AATATATAAATATAATA
1 TAATATATAAAATATGATTATAATA
2476734 TAAATATAT
1 T-AATATAT
2476743 GAATTATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
23 14 0.29
24 5 0.10
25 8 0.17
26 3 0.06
27 17 0.35
28 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
TAATATATAAAATATGATTATAATA
Found at i:2476707 original size:12 final size:11
Alignment explanation
Indices: 2476685--2476742 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
2476675 ATTTAAATAT
2476685 AATATATTATA
1 AATATATTATA
2476696 AATATGATTAT-
1 AATAT-ATTATA
2476707 AATATA--ATA
1 AATATATTATA
2476716 AA-ATA-TATA
1 AATATATTATA
*
2476725 AATATAATATA
1 AATATATTATA
2476736 AATATAT
1 AATATAT
2476743 GAATTATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
8 5 0.12
9 7 0.17
10 4 0.10
11 20 0.49
12 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AATATATTATA
Found at i:2479452 original size:2 final size:2
Alignment explanation
Indices: 2479445--2479475 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2479435 TATTGTGCCT
2479445 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 T
2479476 TAAGGCATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2479850 original size:22 final size:23
Alignment explanation
Indices: 2479813--2479861 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
2479803 ATTTATATAT
* *
2479813 TAAAATTATTAATATATTAAAAA
1 TAAAATTATAAATATAATAAAAA
*
2479836 TAAAA-TATAAATATAATATAAA
1 TAAAATTATAAATATAATAAAAA
2479858 TAAA
1 TAAA
2479862 TAAATCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAATTATAAATATAATAAAAA
Found at i:2480188 original size:2 final size:2
Alignment explanation
Indices: 2480172--2480206 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2480162 TTTTTATTTT
2480172 TA TA -A TA TA -A 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 T
2480207 TCGGCAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2485485 original size:24 final size:24
Alignment explanation
Indices: 2485458--2485518 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
2485448 TAGAAGTAAG
* *
2485458 ATATAAATTTATTA-AAATATATTA
1 ATATATATTTAATATAAATA-ATTA
* *
2485482 ATATTTATATAATATAAATAATTA
1 ATATATATTTAATATAAATAATTA
2485506 ATATATATTTAAT
1 ATATATATTTAAT
2485519 TTTTTAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATATTTAATATAAATAATTA
Found at i:2485497 original size:35 final size:34
Alignment explanation
Indices: 2485458--2485539 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
2485448 TAGAAGTAAG
2485458 ATATAAATTTATTAAAATATA-TTAATATTTATATA
1 ATATAAATTTATTAAAATATATTTAAT-TTTATA-A
* * *
2485493 ATATAAA-TAATTAATATATATTTAATTTTTTAA
1 ATATAAATTTATTAAAATATATTTAATTTTATAA
*
2485526 ATATATAATATATT
1 ATATA-AATTTATT
2485540 TAATATAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 6 0.15
34 18 0.46
35 15 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
ATATAAATTTATTAAAATATATTTAATTTTATAA
Found at i:2485557 original size:54 final size:53
Alignment explanation
Indices: 2485463--2485564 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 53
2485453 GTAAGATATA
* *
2485463 AATTTATTAAAATATATTAATATTTATATAATATAAATAATTAATATATATTT
1 AATTTATTAAAATATAATAATATTTATATAATATAAATAATAAATATATATTT
* *
2485516 AATTTTTTAAATATATAAT-ATATTTAATATAATA-ATGATAATAAATATA
1 AATTTATTAAA-ATATAATAATATTT-ATATAATATA-AATAATAAATATA
2485565 AATATATGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
53 17 0.40
54 25 0.60
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (53 bp):
AATTTATTAAAATATAATAATATTTATATAATATAAATAATAAATATATATTT
Found at i:2485979 original size:3 final size:3
Alignment explanation
Indices: 2485955--2486002 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
2485945 AAATTATAAA
*
2485955 ATT ATT ATGT A-T ATA ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT AT-T ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
2486001 AT
1 AT
2486003 AAATAATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.85
4 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2486509 original size:17 final size:17
Alignment explanation
Indices: 2486466--2486511 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
2486456 GTTAAATTAA
2486466 ATATAAATAAT-TTTAT
1 ATATAAATAATATTTAT
2486482 A-ATAAATTAATATTTAT
1 ATATAAA-TAATATTTAT
*
2486499 ATATTAATAATAT
1 ATATAAATAATAT
2486512 ATATTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.19
16 5 0.19
17 12 0.46
18 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATAAATAATATTTAT
Found at i:2494833 original size:2 final size:2
Alignment explanation
Indices: 2494826--2494855 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2494816 TCTCTTTTGA
2494826 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
2494856 TTGTTAAAAA
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):
AT
Found at i:2505377 original size:17 final size:17
Alignment explanation
Indices: 2505355--2505399 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
2505345 ATAAAATTTG
2505355 AATTTAAAATTTAAATA
1 AATTTAAAATTTAAATA
2505372 AATTTAAAATTTAAATA
1 AATTTAAAATTTAAATA
*
2505389 AATTTTAAATT
1 AATTTAAAATT
2505400 ATTTATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAAATTTAAATA
Found at i:2507589 original size:18 final size:17
Alignment explanation
Indices: 2507556--2507589 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2507546 TTATTAATAG
2507556 ATATATAAAAAATATTA
1 ATATATAAAAAATATTA
*
2507573 ATATATCAAATAATATT
1 ATATAT-AAAAAATATT
2507590 TTATTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATAAAAAATATTA
Found at i:2520430 original size:53 final size:53
Alignment explanation
Indices: 2520350--2520455 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
2520340 GTTCCCTTGG
2520350 CGAATTAGGGAAGCAACTCCTGTGATTAATATCTCATTCAACTTCTTTCTCAA
1 CGAATTAGGGAAGCAACTCCTGTGATTAATATCTCATTCAACTTCTTTCTCAA
2520403 CGAATTAGGGAAGCAACTCCTGTGATTAATATCTCATTCAACTTCTTTCTCAA
1 CGAATTAGGGAAGCAACTCCTGTGATTAATATCTCATTCAACTTCTTTCTCAA
2520456 TCTGTGCTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (53 bp):
CGAATTAGGGAAGCAACTCCTGTGATTAATATCTCATTCAACTTCTTTCTCAA
Found at i:2520937 original size:20 final size:18
Alignment explanation
Indices: 2520899--2520943 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
2520889 AATATCAATT
2520899 AATAATATATAAAAATTTA
1 AATAA-ATATAAAAATTTA
*
2520918 TATAAATATAAAATATTTTA
1 AATAAATATAAAA-A-TTTA
2520938 AATAAA
1 AATAAA
2520944 ATTATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 5 0.23
20 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAAATATAAAAATTTA
Found at i:2520972 original size:18 final size:16
Alignment explanation
Indices: 2520938--2520977 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
2520928 AAATATTTTA
2520938 AATAAAATTATAATAT
1 AATAAAATTATAATAT
2520954 AATAAAATATATAAATAT
1 AATAAAAT-TAT-AATAT
2520972 AATAAA
1 AATAAA
2520978 TAAAAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATTATAATAT
Found at i:2521431 original size:37 final size:37
Alignment explanation
Indices: 2521390--2521487 Score: 110
Period size: 37 Copynumber: 2.6 Consensus size: 37
2521380 TTTAATCCTC
2521390 TTTTCTCTTCAATC-TATAATGAA-TCCCGAGTAGTAAG
1 TTTTCTCTTCAATCGTAT--TGAATTCCCGAGTAGTAAG
* * *
2521427 TTTTCTCTTTATTCGTATTTAATTCCCGAGTAGTAAG
1 TTTTCTCTTCAATCGTATTGAATTCCCGAGTAGTAAG
* * *
2521464 TTTTCTCTTTATTCGTATTTAATT
1 TTTTCTCTTCAATCGTATTGAATT
2521488 ATATTTTTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
36 3 0.05
37 50 0.89
38 3 0.05
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.49
Consensus pattern (37 bp):
TTTTCTCTTCAATCGTATTGAATTCCCGAGTAGTAAG
Found at i:2524612 original size:2 final size:2
Alignment explanation
Indices: 2524605--2524632 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2524595 GGCTTGTACA
2524605 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
2524633 GATTGTTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2527748 original size:3 final size:3
Alignment explanation
Indices: 2527740--2527764 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2527730 TTTTCATGTG
2527740 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2527765 CTTGAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2530624 original size:20 final size:19
Alignment explanation
Indices: 2530589--2530629 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2530579 GAAAAAAAAT
*
2530589 GCTATGCTATGATAAGCTAA
1 GCTATGCTAAGATAAGC-AA
*
2530609 GCTATGCTAAGGTAAGCAA
1 GCTATGCTAAGATAAGCAA
2530628 GC
1 GC
2530630 AACCTTCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (19 bp):
GCTATGCTAAGATAAGCAA
Found at i:2530945 original size:2 final size:2
Alignment explanation
Indices: 2530940--2530978 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2530930 GGAGAAAAAT
* *
2530940 AG AG AG A- AA AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2530979 GACTGTGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2531960 original size:2 final size:2
Alignment explanation
Indices: 2531947--2531982 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2531937 AGTGACAAGA
*
2531947 AT AT AC 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
2531983 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2532893 original size:30 final size:30
Alignment explanation
Indices: 2532859--2532921 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
2532849 AAATAATATA
*
2532859 TTAATGATAAAAGTTTATATTTAAATTTTT
1 TTAATGATAAAAATTTATATTTAAATTTTT
2532889 TTAATGATAAAAATTTATATTTAAATTTTT
1 TTAATGATAAAAATTTATATTTAAATTTTT
2532919 TTA
1 TTA
2532922 TTTTAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (30 bp):
TTAATGATAAAAATTTATATTTAAATTTTT
Found at i:2532969 original size:5 final size:5
Alignment explanation
Indices: 2532959--2533012 Score: 53
Period size: 5 Copynumber: 11.6 Consensus size: 5
2532949 TGAAATTAAT
* * *
2532959 TATTA TA-T- TATTA TATTA TATTA TATTT TATTA CA-TA TATTA T-TAA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
2533005 TATTA TAT
1 TATTA TAT
2533013 AAAATTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
3 2 0.05
4 8 0.21
5 29 0.74
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:2533007 original size:28 final size:28
Alignment explanation
Indices: 2532958--2533012 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2532948 TTGAAATTAA
* *
2532958 TTATTATATTATTATATTATATTATATT
1 TTATTACATTATTATATAATATTATATT
2532986 TTATTACATATATTAT-TAATATTATAT
1 TTATTACAT-TATTATATAATATTATAT
2533013 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TTATTACATTATTATATAATATTATATT
Found at i:2535104 original size:2 final size:2
Alignment explanation
Indices: 2535043--2535087 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2535033 TGTGTACAAG
2535043 TA TA TA 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 TA TA TA
2535085 TA T
1 TA T
2535088 TTAATACACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2537688 original size:2 final size:2
Alignment explanation
Indices: 2537681--2537705 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2537671 TTTCGTGAAA
2537681 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 T
2537706 TTTTGGTTTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2567466 original size:16 final size:15
Alignment explanation
Indices: 2567447--2567491 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 15
2567437 TATGATTTTA
2567447 ATTTATTATTATTAAT
1 ATTTATTA-TATTAAT
2567463 ATTT-TTA-ATTAAT
1 ATTTATTATATTAAT
2567476 ATTTATTATAATTAAT
1 ATTTATTAT-ATTAAT
2567492 TATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 10 0.38
14 3 0.12
15 3 0.12
16 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTATATTAAT
Found at i:2571454 original size:23 final size:23
Alignment explanation
Indices: 2571427--2571474 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2571417 GCCATGGGCA
2571427 CAGCAACTAACAAGACTGTAAAC
1 CAGCAACTAACAAGACTGTAAAC
2571450 CAGCAACTAACAAGACTGTAAAC
1 CAGCAACTAACAAGACTGTAAAC
2571473 CA
1 CA
2571475 ACAGAGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.27, G:0.12, T:0.12
Consensus pattern (23 bp):
CAGCAACTAACAAGACTGTAAAC
Found at i:2577014 original size:3 final size:3
Alignment explanation
Indices: 2576999--2577034 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
2576989 ATTTCCAAGA
*
2576999 AAT AAT AAA AAT AAT AAT AAAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
2577035 AACGTGGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2577021 original size:16 final size:16
Alignment explanation
Indices: 2577002--2577035 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2576992 TCCAAGAAAT
2577002 AATAAAAATAATAATA
1 AATAAAAATAATAATA
*
2577018 AATAATAATAATAATA
1 AATAAAAATAATAATA
2577034 AA
1 AA
2577036 ACGTGGCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAAAATAATAATA
Found at i:2577022 original size:19 final size:19
Alignment explanation
Indices: 2576998--2577034 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2576988 TATTTCCAAG
2576998 AAATAATAAAAATAATAAT
1 AAATAATAAAAATAATAAT
*
2577017 AAATAATAATAATAATAA
1 AAATAATAAAAATAATAA
2577035 AACGTGGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATAATAAAAATAATAAT
Found at i:2577729 original size:6 final size:6
Alignment explanation
Indices: 2577720--2577751 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2577710 CAAATCTACG
*
2577720 TGTGCT TGTGCT TGTGCT TGTGCT TGTACT TG
1 TGTGCT TGTGCT TGTGCT TGTGCT TGTGCT TG
2577752 CATAATTGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.16, G:0.31, T:0.50
Consensus pattern (6 bp):
TGTGCT
Found at i:2583710 original size:3 final size:3
Alignment explanation
Indices: 2583702--2583736 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2583692 TTGGAAGATA
2583702 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2583737 AGAGACGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2584229 original size:12 final size:14
Alignment explanation
Indices: 2584202--2584235 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
2584192 TTTTTCCCCT
2584202 GAAAGAAATAGAAA
1 GAAAGAAATAGAAA
2584216 GAAA-AAAT-GAAA
1 GAAAGAAATAGAAA
2584228 GAAAGAAA
1 GAAAGAAA
2584236 AGCCAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.42
13 7 0.37
14 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (14 bp):
GAAAGAAATAGAAA
Found at i:2584301 original size:2 final size:2
Alignment explanation
Indices: 2584294--2584326 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2584284 GTTTAATAGT
2584294 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2584327 TAAATTAACT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2585131 original size:13 final size:14
Alignment explanation
Indices: 2585113--2585141 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2585103 ATATTTAAGC
2585113 TCAACTTCAA-CTT
1 TCAACTTCAAGCTT
2585126 TCAACTTCAAGCTT
1 TCAACTTCAAGCTT
2585140 TC
1 TC
2585142 TTTACTCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.28, C:0.31, G:0.03, T:0.38
Consensus pattern (14 bp):
TCAACTTCAAGCTT
Found at i:2589064 original size:6 final size:6
Alignment explanation
Indices: 2589055--2589097 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
2589045 AACACCGCCG
*
2589055 CTGCCA CTGCCA CTGCCG CTGCCA CTGCCA CTGCCA CTGCCA C
1 CTGCCA CTGCCA CTGCCA CTGCCA CTGCCA CTGCCA CTGCCA C
2589098 CGACACAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.14, C:0.51, G:0.19, T:0.16
Consensus pattern (6 bp):
CTGCCA
Found at i:2589074 original size:18 final size:18
Alignment explanation
Indices: 2589051--2589097 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2589041 CGCCAACACC
2589051 GCCGCTGCCACTGCCACT
1 GCCGCTGCCACTGCCACT
2589069 GCCGCTGCCACTGCCACT
1 GCCGCTGCCACTGCCACT
*
2589087 GCCACTGCCAC
1 GCCGCTGCCAC
2589098 CGACACAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.51, G:0.21, T:0.15
Consensus pattern (18 bp):
GCCGCTGCCACTGCCACT
Found at i:2590330 original size:2 final size:2
Alignment explanation
Indices: 2590323--2590348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2590313 GTTGACTTGG
2590323 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
2590349 GAAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2590886 original size:2 final size:2
Alignment explanation
Indices: 2590831--2590868 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2590821 TAACAACATT
*
2590831 TA TA TA TT TA T- TA T- 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 TA TA
2590869 ATCTACCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2591498 original size:20 final size:20
Alignment explanation
Indices: 2591475--2591515 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2591465 ATTGAGCAAG
2591475 TACATATTGAAATGGTAATT
1 TACATATTGAAATGGTAATT
2591495 TACATATTGAAATGGTAATT
1 TACATATTGAAATGGTAATT
2591515 T
1 T
2591516 TATAGTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (20 bp):
TACATATTGAAATGGTAATT
Found at i:2596540 original size:2 final size:2
Alignment explanation
Indices: 2596533--2596572 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2596523 CCCACTGATA
2596533 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
2596573 TTTAATGAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2598443 original size:2 final size:2
Alignment explanation
Indices: 2598438--2598474 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2598428 TTTTTTTTTA
2598438 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2598475 AGCACTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 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):
AT
Found at i:2601969 original size:18 final size:18
Alignment explanation
Indices: 2601948--2601984 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2601938 TTGCATCCAT
2601948 GTTCAAGATTGCCTCAAC
1 GTTCAAGATTGCCTCAAC
*
2601966 GTTCAAGATTGCTTCAAC
1 GTTCAAGATTGCCTCAAC
2601984 G
1 G
2601985 CTGACGCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (18 bp):
GTTCAAGATTGCCTCAAC
Found at i:2606285 original size:44 final size:43
Alignment explanation
Indices: 2606235--2606331 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 43
2606225 AATATATATT
* *
2606235 TTAATTAGT-TTATTATAATTATAAATATAA-TAAATATTATAAAA
1 TTAATTA-TATTAATATAA-TATAAAAATAATTAAA-ATTATAAAA
*
2606279 TTAATTATAATTAATATAATATAAAAATAATTAAAATTTTAAAA
1 TTAATTAT-ATTAATATAATATAAAAATAATTAAAATTATAAAA
2606323 -TAATTATAT
1 TTAATTATAT
2606332 AATTAAATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
42 2 0.04
43 8 0.17
44 25 0.53
45 12 0.26
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (43 bp):
TTAATTATATTAATATAATATAAAAATAATTAAAATTATAAAA
Found at i:2606286 original size:30 final size:29
Alignment explanation
Indices: 2606250--2606342 Score: 81
Period size: 26 Copynumber: 3.2 Consensus size: 29
2606240 TAGTTTATTA
2606250 TAATTATAAATATAATAAATATTATAAAAT
1 TAATTATAAAT-TAATAAATATTATAAAAT
2606280 TAATTAT-AATTAATATAATA-TA-AAAA-
1 TAATTATAAATTAATA-AATATTATAAAAT
* *
2606306 TAATTA-AAATT-TTAAAATAATTATATAAT
1 TAATTATAAATTAAT-AAAT-ATTATAAAAT
2606335 TAAATTAT
1 T-AATTAT
2606343 GATCATTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
25 4 0.08
26 12 0.23
27 6 0.12
28 10 0.19
29 8 0.15
30 12 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TAATTATAAATTAATAAATATTATAAAAT
Found at i:2606288 original size:36 final size:36
Alignment explanation
Indices: 2606246--2606316 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
2606236 TAATTAGTTT
*
2606246 ATTATAATT-ATA-AATATAATAAATATTATAAAATTA
1 ATTATAATTAATATAATATAA-AAATAAT-TAAAATTA
2606282 ATTATAATTAATATAATATAAAAATAATTAAAATT
1 ATTATAATTAATATAATATAAAAATAATTAAAATT
2606317 TTAAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 16 0.50
37 9 0.28
38 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
ATTATAATTAATATAATATAAAAATAATTAAAATTA
Found at i:2606291 original size:18 final size:18
Alignment explanation
Indices: 2606246--2606315 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 18
2606236 TAATTAGTTT
2606246 ATTATAATTATAAATATA
1 ATTATAATTATAAATATA
*
2606264 A-TAAATATTATAAA-ATTA
1 ATTATA-ATTATAAATA-TA
2606282 ATTATAATTAATATAATATA
1 ATTATAATT-ATA-AATATA
**
2606302 AAAATAATTA-AAAT
1 ATTATAATTATAAAT
2606316 TTTAAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
17 7 0.17
18 16 0.38
19 7 0.17
20 11 0.26
21 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATAATTATAAATATA
Found at i:2606332 original size:36 final size:36
Alignment explanation
Indices: 2606249--2606338 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 36
2606239 TTAGTTTATT
*
2606249 ATAATTATA-AATATAATAAATATTATAAAATTAATT
1 ATAATTATATAATATAA-AAATATTATAAAATTAATA
*
2606285 ATAATTAATATAATATAAAAATAATTA-AAATTTTAA-A
1 ATAATT-ATATAATATAAAAAT-ATTATAAA-ATTAATA
2606322 ATAATTATATAAT-TAAA
1 ATAATTATATAATATAAA
2606339 TTATGATCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
35 4 0.08
36 13 0.27
37 16 0.33
38 15 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (36 bp):
ATAATTATATAATATAAAAATATTATAAAATTAATA
Found at i:2608928 original size:20 final size:21
Alignment explanation
Indices: 2608899--2608939 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2608889 ATTTTAAATA
2608899 TTTAAATATTTATAT-TATTT
1 TTTAAATATTTATATATATTT
* *
2608919 TTTAATTATTTTTATATATTT
1 TTTAAATATTTATATATATTT
2608940 ATAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTAAATATTTATATATATTT
Found at i:2608954 original size:22 final size:22
Alignment explanation
Indices: 2608903--2608954 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
2608893 TAAATATTTA
**
2608903 AATATTTATATTATTTTTTAAT
1 AATATTTATATTATTTTAAAAT
* *
2608925 TATTTTTATA-TATTTATAAAAT
1 AATATTTATATTATTT-TAAAAT
2608947 AATATTTA
1 AATATTTA
2608955 ATAATATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AATATTTATATTATTTTAAAAT
Found at i:2609110 original size:11 final size:10
Alignment explanation
Indices: 2609082--2609130 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
2609072 TTATAAATCT
*
2609082 TATAAATAAT
1 TATAAATAAA
*
2609092 TTTAAATAAGA
1 TATAAATAA-A
2609103 TATAAATATAA
1 TATAAATA-AA
2609114 TAATAAATAAA
1 T-ATAAATAAA
2609125 TATAAA
1 TATAAA
2609131 AATAATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 13 0.39
11 12 0.36
12 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
TATAAATAAA
Found at i:2609141 original size:24 final size:24
Alignment explanation
Indices: 2609085--2609150 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
2609075 TAAATCTTAT
2609085 AAATAATTT--TAAATAAGATATAA
1 AAATAATTTAATAAATAA-ATATAA
*
2609108 ATATAA--TAATAAATAAATATAA
1 AAATAATTTAATAAATAAATATAA
*
2609130 AAATAATTTAATAAACAAATA
1 AAATAATTTAATAAATAAATA
2609151 ACATCATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.03
22 11 0.31
23 12 0.33
24 12 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATAATTTAATAAATAAATATAA
Found at i:2609142 original size:16 final size:16
Alignment explanation
Indices: 2609104--2609135 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2609094 TAAATAAGAT
*
2609104 ATAAATATAATAATAA
1 ATAAATATAAAAATAA
2609120 ATAAATATAAAAATAA
1 ATAAATATAAAAATAA
2609136 TTTAATAAAC
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAATATAAAAATAA
Found at i:2610744 original size:20 final size:20
Alignment explanation
Indices: 2610719--2610756 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2610709 ATAGAATATA
2610719 GATATATAAGTATAAAAACT
1 GATATATAAGTATAAAAACT
2610739 GATATATAAGTATAAAAA
1 GATATATAAGTATAAAAA
2610757 TTATGTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.29
Consensus pattern (20 bp):
GATATATAAGTATAAAAACT
Found at i:2610898 original size:3 final size:3
Alignment explanation
Indices: 2610890--2610917 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2610880 GCTTGGTGGC
2610890 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2610918 ACAGTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2618680 original size:6 final size:6
Alignment explanation
Indices: 2618671--2618698 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2618661 TTTTTTTTTG
2618671 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
2618699 TCTGGGTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:2618972 original size:2 final size:2
Alignment explanation
Indices: 2618965--2619004 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2618955 TGAAAATAGA
2618965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2619005 GAAGACACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2629772 original size:12 final size:12
Alignment explanation
Indices: 2629755--2629781 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2629745 CAAAAACTGG
2629755 TCACAACCAATT
1 TCACAACCAATT
2629767 TCACAACCAATT
1 TCACAACCAATT
2629779 TCA
1 TCA
2629782 GACAGCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (12 bp):
TCACAACCAATT
Found at i:2633031 original size:2 final size:2
Alignment explanation
Indices: 2633026--2633084 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
2633016 ATATATATAT
* * * ** *
2633026 AC AC AC AC AC AC AC AC AC AC AC AC AT GC AC AC AC AC GC GT GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
2633068 GC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
2633085 TATACGTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.42, C:0.46, G:0.08, T:0.03
Consensus pattern (2 bp):
AC
Found at i:2638029 original size:23 final size:25
Alignment explanation
Indices: 2637998--2638043 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
2637988 ATAAATTAAT
2637998 TTTAATTTAATAA-AATA-ATATCA
1 TTTAATTTAATAATAATATATATCA
* *
2638021 TTTATTTTATTAATAATATATAT
1 TTTAATTTAATAATAATATATAT
2638044 TAAATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 4 0.21
25 4 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTAATTTAATAATAATATATATCA
Found at i:2638069 original size:24 final size:24
Alignment explanation
Indices: 2638042--2638101 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 24
2638032 AATAATATAT
2638042 ATTAAATATAAATTAAAAAAATTA
1 ATTAAATATAAATTAAAAAAATTA
* *
2638066 ATTAAAAAT-AA-TAATAAAATTA
1 ATTAAATATAAATTAAAAAAATTA
*
2638088 AGT-AATA-AAATTAA
1 ATTAAATATAAATTAA
2638102 CGATCAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 5 0.17
22 15 0.50
23 2 0.07
24 8 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
ATTAAATATAAATTAAAAAAATTA
Found at i:2638270 original size:33 final size:33
Alignment explanation
Indices: 2638202--2638292 Score: 87
Period size: 33 Copynumber: 2.7 Consensus size: 33
2638192 ATAATATAAA
* *
2638202 TTATTAAATAT-TTTAAATAATATATTAAAAAAT
1 TTATTAATTATATTTAAAT-ATATTTTAAAAAAT
** *
2638235 TTATTAATTATATTTAAATATATTTTATCATAT
1 TTATTAATTATATTTAAATATATTTTAAAAAAT
*
2638268 TTATT-ATTATTATTTTAAATTTATT
1 TTATTAATTA-TA-TTTAAATATATT
2638293 AAACATAAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
32 4 0.08
33 27 0.55
34 18 0.37
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (33 bp):
TTATTAATTATATTTAAATATATTTTAAAAAAT
Found at i:2652209 original size:3 final size:3
Alignment explanation
Indices: 2652203--2652240 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2652193 TGTTGTATCA
2652203 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2652241 AGCCATTTTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2652375 original size:11 final size:11
Alignment explanation
Indices: 2652336--2652377 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2652326 TTTCTAAAGT
2652336 ATTATTTATAA
1 ATTATTTATAA
2652347 ATTAATTT-TAA
1 ATT-ATTTATAA
* *
2652358 ATCATTTATCA
1 ATTATTTATAA
2652369 ATTATTTAT
1 ATTATTTAT
2652378 TTTTATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.15
11 18 0.69
12 4 0.15
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTATTTATAA
Found at i:2653091 original size:18 final size:18
Alignment explanation
Indices: 2653057--2653099 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
2653047 TTTTTCATTC
*
2653057 TTTTAAGGCATACTTTTTT
1 TTTTAAGGCATA-TTTTCT
2653076 TTTTAAGTGCAT-TTTTCT
1 TTTTAAG-GCATATTTTCT
2653094 TTTTAA
1 TTTTAA
2653100 AAAAATTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 7 0.32
20 4 0.18
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.60
Consensus pattern (18 bp):
TTTTAAGGCATATTTTCT
Found at i:2653096 original size:20 final size:19
Alignment explanation
Indices: 2653047--2653097 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
2653037 ATCTTATAAG
*
2653047 TTTTTCATTCTTTTAAGGCA
1 TTTTTC-TTTTTTTAAGGCA
*
2653067 TACTTT-TTTTTTTAAGTGCA
1 T-TTTTCTTTTTTTAAG-GCA
2653087 TTTTTCTTTTT
1 TTTTTCTTTTT
2653098 AAAAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 12 0.48
20 10 0.40
21 3 0.12
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTTTCTTTTTTTAAGGCA
Found at i:2663074 original size:19 final size:21
Alignment explanation
Indices: 2663044--2663097 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2663034 CAAAATAAAT
2663044 ATAAATAA-TTATATTT-T-TA
1 ATAAA-AATTTATATTTATGTA
2663063 ATAAAAATTTATATTTAATGTA
1 ATAAAAATTTATATTT-ATGTA
*
2663085 TTAAAAATTTATA
1 ATAAAAATTTATA
2663098 AATTTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.07
19 13 0.43
21 1 0.03
22 14 0.47
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAAAAATTTATATTTATGTA
Found at i:2663081 original size:17 final size:19
Alignment explanation
Indices: 2663044--2663081 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
2663034 CAAAATAAAT
*
2663044 ATAAATAATTATATTTTTA
1 ATAAATAATTATATATTTA
2663063 ATAAA-AATT-TATATTTA
1 ATAAATAATTATATATTTA
2663080 AT
1 AT
2663082 GTATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 4 0.22
19 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAAATAATTATATATTTA
Found at i:2667681 original size:14 final size:14
Alignment explanation
Indices: 2667662--2667690 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2667652 TTTAGACTAA
2667662 ATATGTATATATAT
1 ATATGTATATATAT
2667676 ATATGTATATATAT
1 ATATGTATATATAT
2667690 A
1 A
2667691 GAATAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:2670253 original size:44 final size:44
Alignment explanation
Indices: 2670190--2670280 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
2670180 TTATCCACGA
2670190 TCTATAATTAGCCAAGTTGACGGATTACAGAACGTGGATGTATT
1 TCTATAATTAGCCAAGTTGACGGATTACAGAACGTGGATGTATT
2670234 TCTATAATTAGCCAAGTTGACGGATTACAGAACGTGGATGTATT
1 TCTATAATTAGCCAAGTTGACGGATTACAGAACGTGGATGTATT
2670278 TCT
1 TCT
2670281 TTGCAAATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (44 bp):
TCTATAATTAGCCAAGTTGACGGATTACAGAACGTGGATGTATT
Found at i:2671015 original size:2 final size:2
Alignment explanation
Indices: 2671010--2671036 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2671000 AGACTAAATG
2671010 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 T
2671037 CTAGCATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2672096 original size:27 final size:27
Alignment explanation
Indices: 2672059--2672113 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
2672049 CAAAAAGGAA
*
2672059 AAAAAGCAAAACAGCATCTTGAAAACC
1 AAAAAGCAAAACAACATCTTGAAAACC
*
2672086 AAAAAGGAAAACAACATCTTGAAAACC
1 AAAAAGCAAAACAACATCTTGAAAACC
2672113 A
1 A
2672114 TGGAGGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.11
Consensus pattern (27 bp):
AAAAAGCAAAACAACATCTTGAAAACC
Found at i:2674110 original size:23 final size:23
Alignment explanation
Indices: 2674084--2674135 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2674074 TATATTTTTA
2674084 AAATTTTTATAAATTAAT-AAATT
1 AAATTTTT-TAAATTAATAAAATT
* *
2674107 AAATTATTTGAATTAATAAAATT
1 AAATTTTTTAAATTAATAAAATT
*
2674130 TAATTT
1 AAATTT
2674136 AATTTAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATTTTTTAAATTAATAAAATT
Found at i:2677464 original size:3 final size:3
Alignment explanation
Indices: 2677456--2677493 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2677446 GTTGATAGGT
*
2677456 GAA GAA GAA GAA GAA GAA GAT GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2677494 GCTGCCCTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:2686458 original size:23 final size:23
Alignment explanation
Indices: 2686421--2686528 Score: 92
Period size: 23 Copynumber: 4.4 Consensus size: 23
2686411 ATATAATAAT
*
2686421 TTATGTATTTATATTATATTTATA
1 TTATTTATTT-TATTATATTTATA
* *
2686445 TTATTTATTTTATTATAATTAAA
1 TTATTTATTTTATTATATTTATA
*
2686468 TTTAAAATATTATTTTATATAAATTTATA
1 -TT---AT-TTATTTTAT-TATATTTATA
* *
2686497 TTATATATTTTAATATATTTAT-
1 TTATTTATTTTATTATATTTATA
2686519 TTATTTATTT
1 TTATTTATTT
2686529 ATTTTCACCA
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
22 9 0.13
23 19 0.28
24 18 0.26
25 2 0.03
27 2 0.03
28 11 0.16
29 7 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (23 bp):
TTATTTATTTTATTATATTTATA
Found at i:2686869 original size:2 final size:2
Alignment explanation
Indices: 2686856--2686896 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2686846 CAATATTTAT
*
2686856 TA TA TG TA 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 TA T
2686897 CCTTGGATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2687166 original size:9 final size:9
Alignment explanation
Indices: 2687128--2687166 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2687118 TTAAATTAAT
*
2687128 AAATATTAA
1 AAATATTTA
2687137 AAATATTTA
1 AAATATTTA
*
2687146 AAATAATATA
1 AAAT-ATTTA
2687156 AAATATTTA
1 AAATATTTA
2687165 AA
1 AA
2687167 TAACATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATATTTA
Found at i:2687167 original size:18 final size:18
Alignment explanation
Indices: 2687127--2687183 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
2687117 TTTAAATTAA
*
2687127 TAAATATTA-AAAATATT
1 TAAATAATATAAAATATT
2687144 TAAAATAATATAAAATATT
1 T-AAATAATATAAAATATT
* *
2687163 TAAATAACATATAAT-TT
1 TAAATAATATAAAATATT
2687180 TAAA
1 TAAA
2687184 ATTTTCTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.20
18 19 0.54
19 9 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATAATATAAAATATT
Found at i:2687185 original size:18 final size:19
Alignment explanation
Indices: 2687136--2687185 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
2687126 ATAAATATTA
*
2687136 AAAATATTTAAAATAATAT
1 AAAATATTTAAAATAACAT
2687155 AAAATATTT-AAATAACAT
1 AAAATATTTAAAATAACAT
*
2687173 ATAAT-TTTAAAAT
1 AAAATATTTAAAAT
2687186 TTTCTTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 16 0.57
19 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATTTAAAATAACAT
Found at i:2689105 original size:2 final size:2
Alignment explanation
Indices: 2689098--2689124 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2689088 ATTGTATTTA
2689098 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2689125 CAGTAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2689351 original size:13 final size:13
Alignment explanation
Indices: 2689333--2689359 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2689323 TTAAATCCCA
2689333 GCATATTATTGAT
1 GCATATTATTGAT
2689346 GCATATTATTGAT
1 GCATATTATTGAT
2689359 G
1 G
2689360 ACTTGATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (13 bp):
GCATATTATTGAT
Found at i:2691347 original size:14 final size:14
Alignment explanation
Indices: 2691328--2691357 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2691318 AATAATACTC
2691328 TTTGATACAGGTAT
1 TTTGATACAGGTAT
2691342 TTTGATACAGGTAT
1 TTTGATACAGGTAT
2691356 TT
1 TT
2691358 AGCACATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (14 bp):
TTTGATACAGGTAT
Found at i:2691415 original size:13 final size:14
Alignment explanation
Indices: 2691394--2691482 Score: 65
Period size: 14 Copynumber: 6.3 Consensus size: 14
2691384 TAGCATAGGC
2691394 ACTTTGACACAGGT
1 ACTTTGACACAGGT
* *
2691408 AC-TTGACACGGGC
1 ACTTTGACACAGGT
*
2691421 ACTTTGACATAGGT
1 ACTTTGACACAGGT
*
2691435 ATCTTT-AGCACAGAT
1 A-CTTTGA-CACAGGT
* *
2691450 ACTTTTGATACGGGT
1 AC-TTTGACACAGGT
* *
2691465 ATTTTGACACAAGT
1 ACTTTGACACAGGT
2691479 ACTT
1 ACTT
2691483 GGCATAGTAA
Statistics
Matches: 55, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
13 11 0.20
14 25 0.45
15 18 0.33
16 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (14 bp):
ACTTTGACACAGGT
Found at i:2691427 original size:14 final size:14
Alignment explanation
Indices: 2691390--2691429 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
2691380 TATCTAGCAT
2691390 AGGCACTTTGACAC
1 AGGCACTTTGACAC
*
2691404 AGGTAC-TTGACAC
1 AGGCACTTTGACAC
*
2691417 GGGCACTTTGACA
1 AGGCACTTTGACA
2691430 TAGGTATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (14 bp):
AGGCACTTTGACAC
Found at i:2696698 original size:2 final size:2
Alignment explanation
Indices: 2696691--2696761 Score: 52
Period size: 2 Copynumber: 34.0 Consensus size: 2
2696681 CTGATCCAAG
* * * * *
2696691 AT AT AT AT AT AT AT AT AT GT AT AT GT AT AA AGT AT TT AT GAT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT -AT AT
* *
2696735 AGT AT CT AT AT AT AT AT AT AT GT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT
2696762 TATTTCTTTC
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
2 48 0.92
3 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2700595 original size:3 final size:3
Alignment explanation
Indices: 2700589--2700631 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
2700579 CTCTTCCTCC
*
2700589 TCT TCT TCT TCT TGT TCT TCT TCT T-T TCCT TCT TCTT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TC-T TCT TCT
2700632 CACTATTCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.80
4 5 0.14
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2703262 original size:34 final size:34
Alignment explanation
Indices: 2703207--2703423 Score: 258
Period size: 34 Copynumber: 6.4 Consensus size: 34
2703197 TGAAAAAAGA
* *
2703207 TGTTGATTAAAT-GGTGATTTGGTAGTTTATCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
2703240 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * * *
2703274 TGTTGACTAAATAGGAGATTTGATAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* **
2703308 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
2703342 TATTGATTAAATGGGTGATTTGGTGGCTTACTAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
2703376 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
2703410 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2703424 TGGTTTTTAC
Statistics
Matches: 155, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
33 15 0.10
34 139 0.90
35 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:2703410 original size:102 final size:101
Alignment explanation
Indices: 2703207--2703423 Score: 319
Period size: 102 Copynumber: 2.1 Consensus size: 101
2703197 TGAAAAAAGA
** * * * *
2703207 TGTTGATTAAATGGTGATTTGGTAGTTTATCATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
2703272 ATTGTTGACTAAATAGGAGATTTGATAGCTTACCAT
66 ATTGTTGACTAAATAGGAGATTTGATAGCTTACCAT
2703308 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
* * * *
2703373 TATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATAGG-AGATTTGATAGCTTACCAT
2703410 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2703424 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
101 16 0.15
102 88 0.85
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATAGGAGATTTGATAGCTTACCAT
Found at i:2707889 original size:34 final size:34
Alignment explanation
Indices: 2707832--2708084 Score: 321
Period size: 34 Copynumber: 7.5 Consensus size: 34
2707822 AAGTGGGAGA
*
2707832 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
*
2707865 ATTGTTGATTAAATGGGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * **
2707899 ATTGTTGATTAAATGGGTGATTTGATGGTTTGTC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2707933 ATTGTTGACTAAATAGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2707967 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2708001 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2708035 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2708069 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2708085 TGGTTTTTAC
Statistics
Matches: 190, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 17 0.09
34 172 0.91
35 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2708038 original size:102 final size:101
Alignment explanation
Indices: 2707832--2708083 Score: 360
Period size: 102 Copynumber: 2.5 Consensus size: 101
2707822 AAGTGGGAGA
* * * * ** *
2707832 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTAGTTTA
1 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTTA
* * **
2707897 CCATTGTTGATTAAATGGGTGATTTGATGGTTTGTC
66 CCATTATTGATTAAATGGGTGATTTGATGGCTTACC
2707933 ATTGTTGACTAAATAGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTT
1 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTT
*
2707998 ACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
65 ACCATTATTGATTAAATGGGTGATTTGATGGCTTACC
* *
2708035 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCATTGTTGATTAAATG
1 ATTGTTGACTAAATGG-AGATTTGGTAGCTTACCATTGTTGATTAAATG
2708084 GTGGTTTTTA
Statistics
Matches: 135, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
101 15 0.11
102 120 0.89
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (101 bp):
ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTTA
CCATTATTGATTAAATGGGTGATTTGATGGCTTACC
Found at i:2713388 original size:18 final size:18
Alignment explanation
Indices: 2713361--2713396 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2713351 CACCTCCACT
2713361 ACCAGCACCGCCATTTCC
1 ACCAGCACCGCCATTTCC
*
2713379 ACCAGTACCGCCATTTCC
1 ACCAGCACCGCCATTTCC
2713397 TGAGGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.47, G:0.11, T:0.19
Consensus pattern (18 bp):
ACCAGCACCGCCATTTCC
Found at i:2713966 original size:20 final size:20
Alignment explanation
Indices: 2713943--2713981 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2713933 TTTAAAATTA
2713943 ATTTTTATAATTTTTTATAT
1 ATTTTTATAATTTTTTATAT
2713963 ATTTTTATAATTTTTTATA
1 ATTTTTATAATTTTTTATA
2713982 AAATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTATAATTTTTTATAT
Found at i:2713968 original size:12 final size:10
Alignment explanation
Indices: 2713944--2713982 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
2713934 TTAAAATTAA
2713944 TTTTTATAAT
1 TTTTTATAAT
2713954 TTTTTAT-AT
1 TTTTTATAAT
2713963 ATTTTTATAAT
1 -TTTTTATAAT
2713974 TTTTTATAA
1 TTTTTATAA
2713983 AATTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.07
10 23 0.85
11 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:2714405 original size:21 final size:21
Alignment explanation
Indices: 2714362--2714406 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2714352 TAATTTTATT
*
2714362 TATTTTTTTAAAATTTAAATAA
1 TATTTTTTTAAAA-TAAAATAA
2714384 TATTTTTTTAAAA-AAAATTAA
1 TATTTTTTTAAAATAAAA-TAA
2714405 TA
1 TA
2714407 CAAAATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 5 0.24
22 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTTTTTTAAAATAAAATAA
Found at i:2714784 original size:13 final size:11
Alignment explanation
Indices: 2714753--2714795 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
2714743 ATTTATTAAA
2714753 TATATTAATTT
1 TATATTAATTT
2714764 TGATATTAATATGT
1 T-ATATTAAT-T-T
2714778 TATATTAATTT
1 TATATTAATTT
2714789 TAT-TTAA
1 TATATTAA
2714796 GAAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.14
11 5 0.17
12 9 0.31
13 9 0.31
14 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (11 bp):
TATATTAATTT
Found at i:2714838 original size:16 final size:14
Alignment explanation
Indices: 2714800--2714859 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
2714790 ATTTAAGAAA
2714800 TAAA-AAATTAATT
1 TAAATAAATTAATT
2714813 TAAATAAATTAATT
1 TAAATAAATTAATT
*
2714827 T-CA-AAATTAA-T
1 TAAATAAATTAATT
2714838 T-AAT-AATTAAATT
1 TAAATAAATT-AATT
*
2714851 AAAATAAAT
1 TAAATAAAT
2714860 CTAAAACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
11 7 0.18
12 9 0.24
13 6 0.16
14 13 0.34
15 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATAAATTAATT
Done.