Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 23 of 45
Found at i:4200312 original size:17 final size:17
Alignment explanation
Indices: 4200292--4200326 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4200282 AAAGGGCTAG
4200292 ATTTGATATCAATATTT
1 ATTTGATATCAATATTT
*
4200309 ATTTGATATCAATGTTT
1 ATTTGATATCAATATTT
4200326 A
1 A
4200327 AATTATCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (17 bp):
ATTTGATATCAATATTT
Found at i:4202825 original size:2 final size:2
Alignment explanation
Indices: 4202818--4202850 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4202808 GGATGGTTTA
4202818 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
4202851 TTCCGAACTC
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:4211121 original size:18 final size:18
Alignment explanation
Indices: 4211098--4211140 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4211088 GGGGAGAGAG
4211098 AGAAAGAAAAAAAAAAAA
1 AGAAAGAAAAAAAAAAAA
* **
4211116 AGAAAGAAGAAAGGAAAA
1 AGAAAGAAAAAAAAAAAA
4211134 AGAAAGA
1 AGAAAGA
4211141 GATAAAATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAAAAAAAAAA
Found at i:4212001 original size:23 final size:25
Alignment explanation
Indices: 4211952--4212001 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 25
4211942 TTAATAAAAT
* **
4211952 TTAATTAAAATAATTTTTAAATTAA
1 TTAATTAAAATAATTTTAAAACAAA
4211977 TTAATT-AAA-AATTTTAAAACAAA
1 TTAATTAAAATAATTTTAAAACAAA
4212000 TT
1 TT
4212002 TGAAACTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 13 0.59
24 3 0.14
25 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TTAATTAAAATAATTTTAAAACAAA
Found at i:4212218 original size:29 final size:29
Alignment explanation
Indices: 4212184--4212273 Score: 76
Period size: 35 Copynumber: 3.0 Consensus size: 29
4212174 ACAATATTTA
4212184 AAAATATATTAAAATTTTTAATTTTAATT
1 AAAATATATTAAAATTTTTAATTTTAATT
*
4212213 AAAATAACATATATAATATATTTTTAATTTTACTT
1 AAAAT---ATAT-TAA-A-ATTTTTAATTTTAATT
* * *
4212248 ATAA-AT-TTAAAATTTTTTATTATAAT
1 AAAATATATTAAAATTTTTAATTTTAAT
4212274 ATATAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
27 12 0.24
28 1 0.02
29 8 0.16
30 1 0.02
31 2 0.04
32 4 0.08
33 3 0.06
34 1 0.02
35 18 0.36
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
AAAATATATTAAAATTTTTAATTTTAATT
Found at i:4212270 original size:21 final size:23
Alignment explanation
Indices: 4212240--4212281 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4212230 ATATTTTTAA
*
4212240 TTTTACTTATAA-ATTTAAAATT
1 TTTTACTTATAATATATAAAATT
4212262 TTTTA-TTATAATATATAAAA
1 TTTTACTTATAATATATAAAA
4212282 AAACAACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTACTTATAATATATAAAATT
Found at i:4212868 original size:24 final size:23
Alignment explanation
Indices: 4212812--4212869 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
4212802 TCTCATGGTC
4212812 TAATTTTATATTAAATTTATTTAGT
1 TAATTTT-TATT-AATTTATTTAGT
* *
4212837 TATATTTTGATTAATTTATTTATT
1 TA-ATTTTTATTAATTTATTTAGT
4212861 TAATTTTTA
1 TAATTTTTA
4212870 ATTATTAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 6 0.21
24 13 0.45
25 5 0.17
26 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (23 bp):
TAATTTTTATTAATTTATTTAGT
Found at i:4213405 original size:14 final size:16
Alignment explanation
Indices: 4213367--4213406 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
4213357 TATTTTTATT
4213367 ATAATTATAATTTTAGA
1 ATAATTA-AATTTTAGA
4213384 ATAATTAAATTTT-GA
1 ATAATTAAATTTTAGA
4213399 A-AATTAAA
1 ATAATTAAA
4213407 ATTATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 3 0.13
16 6 0.26
17 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
ATAATTAAATTTTAGA
Found at i:4214248 original size:13 final size:13
Alignment explanation
Indices: 4214230--4214265 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
4214220 CGTTGGGCTT
*
4214230 AATGTATTGATAC
1 AATGTATCGATAC
4214243 AATGTATCGATAC
1 AATGTATCGATAC
4214256 AATGTATCGA
1 AATGTATCGA
4214266 CACTGAGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:4214479 original size:20 final size:22
Alignment explanation
Indices: 4214456--4214500 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
4214446 GATACTTTGG
4214456 ATTATTTCT-TGCTTG-AAAAC
1 ATTATTTCTATGCTTGAAAAAC
*
4214476 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTCTATGCTTGAAAAAC
4214498 ATT
1 ATT
4214501 TATACTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 6 0.27
22 8 0.36
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTATTTCTATGCTTGAAAAAC
Found at i:4217093 original size:12 final size:12
Alignment explanation
Indices: 4217076--4217101 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4217066 GGTTTTTTAG
4217076 ATGTATCGATAC
1 ATGTATCGATAC
4217088 ATGTATCGATAC
1 ATGTATCGATAC
4217100 AT
1 AT
4217102 TTTGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:4220223 original size:20 final size:20
Alignment explanation
Indices: 4220200--4220239 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4220190 GCCTAAAATT
4220200 GTTTTATTAATACTAATGTC
1 GTTTTATTAATACTAATGTC
4220220 GTTTTATTAATACTAATGTC
1 GTTTTATTAATACTAATGTC
4220240 AATCACGTGA
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:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
GTTTTATTAATACTAATGTC
Found at i:4223149 original size:33 final size:33
Alignment explanation
Indices: 4223107--4223185 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
4223097 CGTTGGGCTT
4223107 AATGTATCGATACATTTTACCATATATCGATAC
1 AATGTATCGATACATTTTACCATATATCGATAC
*
4223140 AATGTATCGATATATTTTACCATATATCGATAC
1 AATGTATCGATACATTTTACCATATATCGATAC
4223173 AATGTATCGATAC
1 AATGTATCGATAC
4223186 TGAGTGAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (33 bp):
AATGTATCGATACATTTTACCATATATCGATAC
Found at i:4223646 original size:34 final size:34
Alignment explanation
Indices: 4223597--4223661 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
4223587 ATAAAAGATA
*
4223597 TAACTTTTACATATAAATTTATCTCATAAAAACT
1 TAACTTTTACATATAAAATTATCTCATAAAAACT
** * *
4223631 TAACTTTTATGTATAAAATTATTTTATAAAA
1 TAACTTTTACATATAAAATTATCTCATAAAA
4223662 TAATACAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (34 bp):
TAACTTTTACATATAAAATTATCTCATAAAAACT
Found at i:4224557 original size:15 final size:16
Alignment explanation
Indices: 4224527--4224559 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4224517 TAAAATATTA
4224527 TTATATTATTTTATTTT
1 TTATATTA-TTTATTTT
4224544 TTATATTA-TTATTTT
1 TTATATTATTTATTTT
4224559 T
1 T
4224560 AAAAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATATTATTTATTTT
Found at i:4225111 original size:27 final size:28
Alignment explanation
Indices: 4225081--4225134 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
4225071 AGTATTGTAA
4225081 TTATCTTAAATTTG-ATAATAATTTTAT
1 TTATCTTAAATTTGAATAATAATTTTAT
* * *
4225108 TTATTTTTAGTTTGAATAATAATTTTA
1 TTATCTTAAATTTGAATAATAATTTTA
4225135 AATAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (28 bp):
TTATCTTAAATTTGAATAATAATTTTAT
Found at i:4225275 original size:16 final size:16
Alignment explanation
Indices: 4225246--4225287 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4225236 TTAACTATAA
* *
4225246 AATTAATTTTAATTAT
1 AATTAAATTAAATTAT
*
4225262 TATTAAATTAAATTAT
1 AATTAAATTAAATTAT
4225278 AATTAAATTA
1 AATTAAATTA
4225288 TTTTCATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAAATTAAATTAT
Found at i:4225494 original size:24 final size:23
Alignment explanation
Indices: 4225467--4225525 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
4225457 TTAAATTTAT
4225467 TTTTAATTTAAT-TATATATATTAA
1 TTTTAATTTAATATAT-TATATT-A
* *
4225491 TTTTGATAGTAATATATTATATTA
1 TTTTAAT-TTAATATATTATATTA
*
4225515 TTTTTATTTAA
1 TTTTAATTTAA
4225526 AAATAAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 3 0.10
24 13 0.45
25 10 0.34
26 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (23 bp):
TTTTAATTTAATATATTATATTA
Found at i:4225811 original size:24 final size:24
Alignment explanation
Indices: 4225710--4225811 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 24
4225700 TTTCTTTCAT
** *
4225710 TATATTAAATTTTTAAA-TAATAA
1 TATATTAAATAATTAAATTAAAAA
* * *
4225733 TA-ATTAAGTAATTGAAGTAAAAA
1 TATATTAAATAATTAAATTAAAAA
* ** *
4225756 TAT-TTTAATAAATTTATTTTAAAAC
1 TATATTAAAT-AA-TTAAATTAAAAA
4225781 TA-A-TAAATAATTAAATTAAAAA
1 TATATTAAATAATTAAATTAAAAA
4225803 TATATTAAA
1 TATATTAAA
4225812 AATATTTAAT
Statistics
Matches: 56, Mismatches: 16, Indels: 13
0.66 0.19 0.15
Matches are distributed among these distances:
22 21 0.38
23 16 0.29
24 10 0.18
25 9 0.16
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (24 bp):
TATATTAAATAATTAAATTAAAAA
Found at i:4225840 original size:18 final size:18
Alignment explanation
Indices: 4225791--4225848 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
4225781 TAATAAATAA
4225791 TTAAATTAAAA-ATATAT
1 TTAAATTAAAATATATAT
* **
4225808 TAAAAATATTTAATATATAT
1 T-TAAAT-TAAAATATATAT
4225828 TTAAATTAAAATATA-AT
1 TTAAATTAAAATATATAT
4225845 TTAA
1 TTAA
4225849 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
17 7 0.22
18 11 0.34
19 7 0.22
20 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATTAAAATATATAT
Found at i:4225881 original size:22 final size:22
Alignment explanation
Indices: 4225830--4225881 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
4225820 ATATATATTT
4225830 AAATTAAAATATAATTTAATAAA
1 AAATTAAAATATAATTT-ATAAA
4225853 AAA-TAAAA-ATAATTT-TAAA
1 AAATTAAAATATAATTTATAAA
4225872 ATTAATTAAA
1 A--AATTAAA
4225882 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.19
21 9 0.35
22 9 0.35
23 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATTAAAATATAATTTATAAA
Found at i:4225916 original size:14 final size:15
Alignment explanation
Indices: 4225890--4225918 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4225880 AATTTTTATT
4225890 ATTTTATAATAAAAA
1 ATTTTATAATAAAAA
4225905 ATTTTA-AATAAAAA
1 ATTTTATAATAAAAA
4225919 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTTTATAATAAAAA
Found at i:4228278 original size:79 final size:79
Alignment explanation
Indices: 4228142--4228551 Score: 542
Period size: 79 Copynumber: 5.2 Consensus size: 79
4228132 GAGATAATAA
*** * * *
4228142 CGGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
4228207 TTTAGAAATAAAAT
66 TTTAGAAATAAAAT
* * * *
4228221 CGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTAGAGTATCCTCGACTATGAAAAATTGATGT
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
*
4228286 TTTAGAAATAAAAC
66 TTTAGAAATAAAAT
* * *
4228300 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
*
4228365 TTTAGAAACAAAAT
66 TTTAGAAATAAAAT
*
4228379 CGGGGTTGGAGTATCCCCTC-GAAAGTAACGGGGTTAGAGTATCCCCG---ATGAAAAATTGATG
1 CGGGGTTGGAGTATCCCCTCGGAAA-TAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATG
4228440 TTTTAGAAATAAAA-
65 TTTTAGAAATAAAAT
* * * * * * *
4228454 CTGGGGTTGGAGTGTCCACTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAGTCGGTG
1 C-GGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATG
*
4228519 TTTTGGAAATAAAAT
65 TTTTAGAAATAAAAT
*
4228534 CGGAGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
4228552 GATTATAGAA
Statistics
Matches: 287, Mismatches: 37, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
75 1 0.00
76 62 0.22
77 3 0.01
78 4 0.01
79 216 0.75
80 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
TTTAGAAATAAAAT
Found at i:4228533 original size:155 final size:155
Alignment explanation
Indices: 4228135--4228551 Score: 597
Period size: 155 Copynumber: 2.7 Consensus size: 155
4228125 TATTTTGGAG
**
4228135 ATAATAACGGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAA
1 ATAA-AACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTG-AAAA
* *
4228200 TCGATGATTTAGAAATAAAATCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTAGAGTATCC
64 TCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTAGAGTATCC
*
4228265 TCGACTATGAAAAATTGATGTTTTAGAA
129 TC-ACGATGAAAAATTGATGTTTTAGAA
* *
4228293 ATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAA
1 ATAAAA-CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGA-AAA
** * *
4228358 TTAATATTTTAGAAACAAAATCGGGGTTGGAGTATCCCCTC-GAAAGTAACGGGGTTAGAGTATC
64 TCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAA-TAACGGGGTTAGAGTATC
4228422 C-C-CGATGAAAAATTGATGTTTTAGAA
128 CTCACGATGAAAAATTGATGTTTTAGAA
* *
4228448 ATAAAACTGGGGTTGGAGTGTCCACTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAG
1 ATAAAAC-GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAA-
* * *
4228513 TCGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
64 TCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
4228552 GATTATAGAA
Statistics
Matches: 232, Mismatches: 22, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
154 4 0.02
155 110 0.47
157 8 0.03
158 110 0.47
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (155 bp):
ATAAAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAATC
GATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTAGAGTATCCTC
ACGATGAAAAATTGATGTTTTAGAA
Found at i:4228550 original size:51 final size:50
Alignment explanation
Indices: 4228487--4228653 Score: 210
Period size: 51 Copynumber: 3.3 Consensus size: 50
4228477 AAATAACGGG
*
4228487 GTTGGAGTATCCCCGATTGTGAAAAGTCGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAA-TCGGTGTTTTGGAAATAAAATCGGA
* *
4228538 GTTGGAGTATCCCCGATTATAGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAATCGGTGTTTTGGAAATAAAATCGGA
* * * * *
4228589 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAACCGG-
1 GTTGGAGTATCCCCGATTATG-AAAATCGGTGTTTTGGAAATAAAATCGGA
*
4228639 GATTCGAGTATCCCC
1 G-TTGGAGTATCCCC
4228654 AAGATGAAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
50 2 0.02
51 96 0.93
52 5 0.05
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAATCGGTGTTTTGGAAATAAAATCGGA
Found at i:4231049 original size:13 final size:13
Alignment explanation
Indices: 4231031--4231055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4231021 ACAAAGATCG
4231031 ATGTATCGATACC
1 ATGTATCGATACC
4231044 ATGTATCGATAC
1 ATGTATCGATAC
4231056 ATCTGAATAA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACC
Found at i:4236601 original size:5 final size:5
Alignment explanation
Indices: 4236584--4236615 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
4236574 TATTTCACAA
4236584 ATATT AT-TT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATA
4236616 ATCTTAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:4237140 original size:16 final size:16
Alignment explanation
Indices: 4237067--4237141 Score: 50
Period size: 16 Copynumber: 4.9 Consensus size: 16
4237057 TTTAATATAT
*
4237067 TATTATT-TATAATAA
1 TATTATTATATAAAAA
* ** *
4237082 TAGTATGGTATTAAAA
1 TATTATTATATAAAAA
*
4237098 TATTA--ATTTAAAAA
1 TATTATTATATAAAAA
*
4237112 TTTATATTA-ATAAAAA
1 TAT-TATTATATAAAAA
4237128 TATTATTATATAAA
1 TATTATTATATAAA
4237142 CAAATTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
14 8 0.18
15 12 0.27
16 23 0.52
17 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (16 bp):
TATTATTATATAAAAA
Found at i:4237604 original size:12 final size:12
Alignment explanation
Indices: 4237587--4237642 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
4237577 ATTAAATTAA
4237587 TTTATATAATTT
1 TTTATATAATTT
4237599 TTTATATAATTTAT
1 TTTATATAA-TT-T
4237613 ATTTATATAATTT
1 -TTTATATAATTT
* *
4237626 ATTA-AT-ATAT
1 TTTATATAATTT
4237636 TTTATAT
1 TTTATAT
4237643 TTTATTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.16
11 4 0.11
12 12 0.32
13 3 0.08
14 3 0.08
15 9 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATATAATTT
Found at i:4237621 original size:27 final size:28
Alignment explanation
Indices: 4237586--4237653 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 28
4237576 AATTAAATTA
*
4237586 ATTTATATAATTT-TTTATATAATTTAT
1 ATTTATATAATTTATTAATATAATTTAT
*
4237613 ATTTATATAATTTATTAATATATTTTAT
1 ATTTATATAATTTATTAATATAATTTAT
*
4237641 ATTTTATTTAATT
1 A-TTTATATAATT
4237654 AAATTATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 13 0.36
28 13 0.36
29 10 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTTATATAATTTATTAATATAATTTAT
Found at i:4237628 original size:13 final size:13
Alignment explanation
Indices: 4237581--4237640 Score: 68
Period size: 13 Copynumber: 4.5 Consensus size: 13
4237571 TATAAAATTA
*
4237581 AATTAATTTATAT
1 AATTTATTTATAT
4237594 AATTT-TTTATAT
1 AATTTATTTATAT
4237606 AATTTATATTTATAT
1 AA-TT-TATTTATAT
*
4237621 AATTTATTAATAT
1 AATTTATTTATAT
*
4237634 ATTTTAT
1 AATTTAT
4237641 ATTTTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 9 0.22
13 20 0.49
14 3 0.07
15 9 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATTTATTTATAT
Found at i:4237634 original size:21 final size:22
Alignment explanation
Indices: 4237610--4237700 Score: 64
Period size: 21 Copynumber: 4.2 Consensus size: 22
4237600 TTATATAATT
4237610 TATATTTATATAATTTATT-AA
1 TATATTTATATAATTTATTAAA
* *
4237631 TATATTT-TATATTTTATTTAA
1 TATATTTATATAATTTATTAAA
* *
4237652 T-TAAATTATATATTTTAAATTAAA
1 TAT-ATTTATATAATTT--ATTAAA
* * *
4237676 AATATTTA-ATTATTTATTCAA
1 TATATTTATATAATTTATTAAA
4237697 TATA
1 TATA
4237701 AAAAATTTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
20 11 0.20
21 21 0.38
22 8 0.15
23 5 0.09
24 9 0.16
25 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATTTATATAATTTATTAAA
Found at i:4237662 original size:29 final size:27
Alignment explanation
Indices: 4237586--4237668 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 27
4237576 AATTAAATTA
** *
4237586 ATTTATATAATTTTTTATATAATTTAT
1 ATTTATATAATTAATTATATATTTTAT
*
4237613 ATTTATATAATTTATTAATATATTTTAT
1 ATTTATATAATTAATT-ATATATTTTAT
*
4237641 ATTTTATTTAATTAAATTATATATTTTA
1 A-TTTATATAATT-AATTATATATTTTA
4237669 AATTAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.31
28 11 0.22
29 20 0.41
30 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTATATAATTAATTATATATTTTAT
Found at i:4237663 original size:22 final size:20
Alignment explanation
Indices: 4237615--4237668 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
4237605 TAATTTATAT
* *
4237615 TTATATAATTTATTAATATA
1 TTATATATTTTATTAATAAA
*
4237635 TTTTATATTTTATTTAATTAAA
1 TTATATATTTTA-TTAA-TAAA
4237657 TTATATATTTTA
1 TTATATATTTTA
4237669 AATTAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.36
21 4 0.14
22 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATATTTTATTAATAAA
Found at i:4237674 original size:44 final size:46
Alignment explanation
Indices: 4237560--4237674 Score: 105
Period size: 44 Copynumber: 2.6 Consensus size: 46
4237550 AAAAATATTT
* * *
4237560 ATTTAT-ATTAATATAAAATTAAATTAATTTATATAATTTTTTATATA
1 ATTTATAATT-ATAT-AATTTAAATTAATATATATAATATTTTATATA
* * * *
4237607 ATTTATATTTATATAATTT--ATTAATATATTTTATATTTTATTTA
1 ATTTATAATTATATAATTTAAATTAATATATATAATATTTTATATA
*
4237651 A-TTA-AATTATATATTTTAAATTAA
1 ATTTATAATTATATAATTTAAATTAA
4237675 AAATATTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
42 11 0.20
43 3 0.05
44 26 0.46
46 4 0.07
47 10 0.18
48 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (46 bp):
ATTTATAATTATATAATTTAAATTAATATATATAATATTTTATATA
Found at i:4237726 original size:27 final size:29
Alignment explanation
Indices: 4237673--4237740 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
4237663 ATTTTAAATT
* *
4237673 AAAAATATTTAATTATTTATTCAATA-TA
1 AAAAATATTTAATTATTAAATCAATATTA
4237701 AAAAAT-TTTAATTATTAAAT-ATATATTAA
1 AAAAATATTTAATTATTAAATCA-ATATT-A
4237730 AAAAATATTTA
1 AAAAATATTTA
4237741 TTTAATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 1 0.03
27 15 0.44
28 7 0.21
29 7 0.21
30 4 0.12
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAAATATTTAATTATTAAATCAATATTA
Found at i:4237748 original size:22 final size:22
Alignment explanation
Indices: 4237713--4237774 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
4237703 AAATTTTAAT
4237713 TATTAAA-TATATATTAAAAAAA
1 TATTAAATTA-ATATTAAAAAAA
* *
4237735 TATTTATTTAATA-TAATAAAAA
1 TATTAAATTAATATTAA-AAAAA
4237757 TATTAAATTAAT-TTAAAA
1 TATTAAATTAATATTAAAA
4237775 TTTTATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 5 0.15
22 26 0.79
23 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTAAATTAATATTAAAAAAA
Found at i:4237789 original size:25 final size:24
Alignment explanation
Indices: 4237756--4237813 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
4237746 TATAATAAAA
4237756 ATATTAAATTAATTTAAAATTTTAT
1 ATATTAAATT-ATTTAAAATTTTAT
* * *
4237781 ATATAAAATTTTTTATAATTTTAT
1 ATATTAAATTATTTAAAATTTTAT
4237805 A-ATTAAATT
1 ATATTAAATT
4237814 TAATAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 7 0.24
24 13 0.45
25 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTAAATTATTTAAAATTTTAT
Found at i:4237808 original size:39 final size:38
Alignment explanation
Indices: 4237772--4237844 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 38
4237762 AATTAATTTA
**
4237772 AAATTT-T-ATATATAAAATTTTTTATAATTTTATAATT
1 AAATTTATAATATATAAAATTAATT-TAATTTTATAATT
4237809 AAATTTAATAATATATAAAATTAATTTAATTTTATA
1 AAATTT-ATAATATATAAAATTAATTTAATTTTATA
4237845 TCATCGTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 6 0.19
39 11 0.35
40 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
AAATTTATAATATATAAAATTAATTTAATTTTATAATT
Found at i:4237834 original size:21 final size:21
Alignment explanation
Indices: 4237779--4237838 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
4237769 TTAAAATTTT
*
4237779 ATATATAAAATT--TTTTATA
1 ATATATAAAATTAATTTAATA
* *
4237798 AT-TTTATAATTAAATTTAATA
1 ATATATAAAATT-AATTTAATA
4237819 ATATATAAAATTAATTTAAT
1 ATATATAAAATTAATTTAAT
4237839 TTTATATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 7 0.22
19 2 0.06
21 16 0.50
22 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATAAAATTAATTTAATA
Found at i:4237864 original size:2 final size:2
Alignment explanation
Indices: 4237859--4237886 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4237849 CGTGTGTGTC
4237859 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
4237887 AAAGCAACCT
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):
TA
Found at i:4238985 original size:21 final size:21
Alignment explanation
Indices: 4238950--4239010 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
4238940 TTATATTGAA
*
4238950 TTTATTT-AATTATTTATTAT-
1 TTTATTTAAATAATTTATT-TG
4238970 TATT-TTTAAATAATTTATTTG
1 T-TTATTTAAATAATTTATTTG
*
4238991 TTTATTTAAATAATTAATTT
1 TTTATTTAAATAATTTATTT
4239011 CTTAAATATG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 7 0.20
21 28 0.80
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTATTTAAATAATTTATTTG
Found at i:4240966 original size:19 final size:21
Alignment explanation
Indices: 4240944--4240984 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4240934 TTTATATTTC
4240944 AATTTTA-CAT-TAAAATTAA
1 AATTTTATCATATAAAATTAA
*
4240963 AATTTTATGATATAAAATTAA
1 AATTTTATCATATAAAATTAA
4240984 A
1 A
4240985 CTAATAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 10 0.53
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTTTATCATATAAAATTAA
Found at i:4241549 original size:17 final size:18
Alignment explanation
Indices: 4241517--4241550 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4241507 AAAATAATAA
4241517 TATTAACATGAAATATTT
1 TATTAACATGAAATATTT
*
4241535 TATTAATAT-AAATATT
1 TATTAACATGAAATATT
4241551 AAAAAGAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TATTAACATGAAATATTT
Found at i:4242545 original size:23 final size:22
Alignment explanation
Indices: 4242516--4242559 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
4242506 TTTTAATAAA
4242516 AAAATAATA-AATTATAAAAATTT
1 AAAATAATATAA-TA-AAAAATTT
4242539 AAAATAATATAATAAAAAATT
1 AAAATAATATAATAAAAAATT
4242560 AAATTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 11 0.55
24 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATAATATAATAAAAAATTT
Found at i:4242555 original size:21 final size:21
Alignment explanation
Indices: 4242509--4242571 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
4242499 GTCAATATTT
*
4242509 TAATAAAAAA--ATAATAA-A
1 TAATAAAAAATTAAAATAATA
* *
4242527 TTATAAAAATTTAAAATAATA
1 TAATAAAAAATTAAAATAATA
* *
4242548 TAATAAAAAATTAAATTTATA
1 TAATAAAAAATTAAAATAATA
4242569 TAA
1 TAA
4242572 ATTTTTAGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
18 8 0.23
20 6 0.17
21 21 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATAAAAAATTAAAATAATA
Found at i:4242637 original size:2 final size:2
Alignment explanation
Indices: 4242630--4242665 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4242620 ATCTTTCTTT
*
4242630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4242666 ATGCGTGCAA
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4246493 original size:20 final size:20
Alignment explanation
Indices: 4246468--4246542 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
4246458 AAAATTAAAT
4246468 TTAATAATTATATATTTATA
1 TTAATAATTATATATTTATA
* * *
4246488 TTAATATTTATTTATTTTTA
1 TTAATAATTATATATTTATA
4246508 -T-AT-ATTATA-A-TTATA
1 TTAATAATTATATATTTATA
*
4246523 TTTAAAATATTATATATTTA
1 -TTAATA-ATTATATATTTA
4246543 ATAAAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
15 4 0.10
16 1 0.02
17 5 0.12
18 3 0.07
19 1 0.02
20 23 0.56
21 1 0.02
22 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATAATTATATATTTATA
Found at i:4246510 original size:16 final size:17
Alignment explanation
Indices: 4246476--4246545 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
4246466 ATTTAATAAT
4246476 TATA-TATTTATATTAA
1 TATATTATTTATATTAA
* *
4246492 TAT-TTATTTATTTTTA
1 TATATTATTTATATTAA
4246508 TATATTATAATTATATTTAA
1 TATATTAT--TTATA-TTAA
* *
4246528 AATATTATATAT-TTAA
1 TATATTATTTATATTAA
4246544 TA
1 TA
4246546 AAAATTTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
16 21 0.50
17 4 0.10
18 3 0.07
19 4 0.10
20 10 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTATTTATATTAA
Found at i:4246592 original size:88 final size:84
Alignment explanation
Indices: 4246427--4246592 Score: 178
Period size: 89 Copynumber: 1.9 Consensus size: 84
4246417 TATAATTTTT
* * *
4246427 TTATAATATTTTAAAAATATTTAATTATTAAAAAATTAAATTTAATAATTATATATTTATATTAA
1 TTATAATATTTTAAAAATATTTAATTAATAAAAAATTAAATTTAATAAATATATATCTATA-TAA
*
4246492 TATTTATTTATTTTTATATA
65 TATTTATATATTTTTATATA
*
4246512 TTATAATTATATTT-AAAATATTATATATTTAATAAAAATTTAATATATTAATAAAT-TATATCT
1 TTATAA-TAT-TTTAAAAATATT-TA-A-TTAATAAAAAATTAA-AT-TTAATAAATATATATCT
4246575 ATA-AAT-TTTAATATATTT
59 ATATAATATTT-ATATATTT
4246593 ATAATTTATA
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
85 6 0.09
86 11 0.16
87 8 0.12
88 11 0.16
89 13 0.19
90 11 0.16
91 8 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (84 bp):
TTATAATATTTTAAAAATATTTAATTAATAAAAAATTAAATTTAATAAATATATATCTATATAAT
ATTTATATATTTTTATATA
Found at i:4246595 original size:18 final size:18
Alignment explanation
Indices: 4246504--4246630 Score: 58
Period size: 18 Copynumber: 7.3 Consensus size: 18
4246494 TTTATTTATT
* *
4246504 TTTATATATTATAATTATA
1 TTTATAAATTTTAA-TATA
*
4246523 TTTA-AAATATT-ATATA
1 TTTATAAATTTTAATATA
*
4246539 TTTAATAAAAATTTAATATA
1 TTT-AT-AAATTTTAATATA
*
4246559 TTAATAAA---T--TATA
1 TTTATAAATTTTAATATA
*
4246572 TCTATAAATTTTAATATA
1 TTTATAAATTTTAATATA
*
4246590 TTTAT-AATTTATATTA-A
1 TTTATAAATTT-TAATATA
* *
4246607 TTTTTTAATTTTTAAT-TA
1 -TTTATAAATTTTAATATA
4246625 TTTATA
1 TTTATA
4246631 TTATACTTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 28
0.66 0.11 0.23
Matches are distributed among these distances:
13 10 0.12
15 1 0.01
16 8 0.10
17 13 0.16
18 27 0.33
19 15 0.19
20 7 0.09
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTATAAATTTTAATATA
Found at i:4246610 original size:27 final size:28
Alignment explanation
Indices: 4246461--4246610 Score: 98
Period size: 27 Copynumber: 5.3 Consensus size: 28
4246451 TTATTAAAAA
*
4246461 ATTAAATTTAATA-A-TTATATATTTAT
1 ATTAATTTTAATATATTTATATATTTAT
* *
4246487 ATTAATATTT-ATTTATTTTTATATATTAT
1 ATTAAT-TTTAATATATTTATATAT-TTAT
*
4246516 AATT-ATATTTAAAATA-TTATATATTTA-
1 -ATTAAT-TTTAATATATTTATATATTTAT
* * * *
4246543 ATAAAAATTTAATATATTAATAAATTATATCT
1 AT-TAATTTTAATATATTTATATATT-TA--T
*
4246575 ATAAATTTTAATATATTTATA-ATTTAT
1 ATTAATTTTAATATATTTATATATTTAT
4246602 ATTAATTTT
1 ATTAATTTT
4246611 TTAATTTTTA
Statistics
Matches: 97, Mismatches: 14, Indels: 25
0.71 0.10 0.18
Matches are distributed among these distances:
26 9 0.09
27 21 0.22
28 18 0.19
29 21 0.22
30 9 0.09
31 17 0.18
32 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.55
Consensus pattern (28 bp):
ATTAATTTTAATATATTTATATATTTAT
Found at i:4251535 original size:32 final size:37
Alignment explanation
Indices: 4251495--4251581 Score: 121
Period size: 32 Copynumber: 2.5 Consensus size: 37
4251485 AAATAAATAA
*
4251495 ATATTTAAAATTTATAT-AATATA-AATAA-TT-ATT
1 ATATTTAAAATTTATATAAATATATAATAATTTAAAT
4251528 ATA-TTAAAATTTATATAAATATATAATAATTTAAAT
1 ATATTTAAAATTTATATAAATATATAATAATTTAAAT
4251564 ATATTTATAAATTTATAT
1 ATATTTA-AAATTTATAT
4251582 TTTAAAATAG
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
32 13 0.28
33 9 0.19
34 5 0.11
35 2 0.04
36 5 0.11
37 3 0.06
38 10 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (37 bp):
ATATTTAAAATTTATATAAATATATAATAATTTAAAT
Found at i:4251550 original size:20 final size:20
Alignment explanation
Indices: 4251527--4251581 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 20
4251517 AAATAATTAT
4251527 TATATTAAAATTTATATAAA
1 TATATTAAAATTTATATAAA
*
4251547 TATA-TAATAATTTA-A-ATA
1 TATATTAA-AATTTATATAAA
4251565 TAT-TTATAAATTTATAT
1 TATATTA-AAATTTATAT
4251582 TTTAAAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
18 13 0.45
19 6 0.21
20 10 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATTAAAATTTATATAAA
Found at i:4261867 original size:71 final size:71
Alignment explanation
Indices: 4261747--4261890 Score: 216
Period size: 71 Copynumber: 2.0 Consensus size: 71
4261737 TAGGGAAAGA
* * * *
4261747 TTTGTTGGGATCACTTAATCTGGTTTCCATTTCACATCCCAAGAGATTCATTGGTGGCATAGATG
1 TTTGTTAGGATCACTTAATATGGTTTCCATTTCACATCCCAAGACATTCATTGGTGGCACAGATG
4261812 GCCATT
66 GCCATT
** * *
4261818 TTTGTTAGGATCGTTTAATATGGTTTCCATTTCACATCCTAAGACATTCATTGGTGGCACGGATG
1 TTTGTTAGGATCACTTAATATGGTTTCCATTTCACATCCCAAGACATTCATTGGTGGCACAGATG
4261883 GCCATT
66 GCCATT
4261889 TT
1 TT
4261891 GAATAGATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (71 bp):
TTTGTTAGGATCACTTAATATGGTTTCCATTTCACATCCCAAGACATTCATTGGTGGCACAGATG
GCCATT
Found at i:4267853 original size:18 final size:19
Alignment explanation
Indices: 4267819--4267859 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
4267809 AACTTTTTTT
4267819 TTTTAATTTTCACATTTCA
1 TTTTAATTTTCACATTTCA
*
4267838 TTTT-ATTTCTCA-ATTTCC
1 TTTTAATTT-TCACATTTCA
4267856 TTTT
1 TTTT
4267860 GTTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAATTTTCACATTTCA
Found at i:4268501 original size:16 final size:16
Alignment explanation
Indices: 4268480--4268515 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
4268470 AATGAAAAGG
4268480 ATATGTAGATATATAT
1 ATATGTAGATATATAT
4268496 ATATGTAGATATATAT
1 ATATGTAGATATATAT
4268512 ATAT
1 ATAT
4268516 AGGTTCCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (16 bp):
ATATGTAGATATATAT
Found at i:4268578 original size:32 final size:32
Alignment explanation
Indices: 4268517--4268578 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
4268507 TATATATATA
* *
4268517 GGTTCCAAGATTATATCGCCAAGTCGTCGTTT
1 GGTTCCAAGAATATATCGCCAACTCGTCGTTT
*
4268549 GGTTCCAAGAATATATCGCCAACTGGTCGT
1 GGTTCCAAGAATATATCGCCAACTCGTCGT
4268579 CACTCGTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (32 bp):
GGTTCCAAGAATATATCGCCAACTCGTCGTTT
Found at i:4268795 original size:29 final size:29
Alignment explanation
Indices: 4268766--4268829 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
4268756 ATAATTTATA
4268766 AATATAAAATA-AAAAATAATTAAAATAT
1 AATATAAAATATAAAAATAATTAAAATAT
* * *
4268794 AATATATGAATATATAAATATTTAAAAT-T
1 AATATA-AAATATAAAAATAATTAAAATAT
4268823 AATATAA
1 AATATAA
4268830 TAAAAATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 6 0.20
29 11 0.37
30 13 0.43
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (29 bp):
AATATAAAATATAAAAATAATTAAAATAT
Found at i:4268845 original size:18 final size:17
Alignment explanation
Indices: 4268824--4268869 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
4268814 TTTAAAATTA
4268824 ATATAATAAAAATTATTT
1 ATAT-ATAAAAATTATTT
*
4268842 ATATATCAAAATTTATTT
1 ATATAT-AAAAATTATTT
*
4268860 AAATATAAAA
1 ATATATAAAA
4268870 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATATAAAAATTATTT
Found at i:4268854 original size:17 final size:16
Alignment explanation
Indices: 4268828--4268887 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 16
4268818 AAATTAATAT
4268828 AATA-AAAATTATTTA
1 AATATAAAATTATTTA
*
4268843 TATATCAAAATTTATTTA
1 AATAT-AAAA-TTATTTA
4268861 AATATAAAA-TATTTA
1 AATATAAAATTATTTA
*
4268876 AA-ATATAATTAT
1 AATATAAAATTAT
4268888 AATATAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.13
15 14 0.37
17 8 0.21
18 11 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATAAAATTATTTA
Found at i:4268872 original size:27 final size:27
Alignment explanation
Indices: 4268842--4268894 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
4268832 AAAATTATTT
* *
4268842 ATATATCAAAATTTATTTA-AATATAAA
1 ATAT-TCAAAATATAATTATAATATAAA
*
4268869 ATATTTAAAATATAATTATAATATAA
1 ATATTCAAAATATAATTATAATATAA
4268895 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATTCAAAATATAATTATAATATAAA
Found at i:4268881 original size:16 final size:16
Alignment explanation
Indices: 4268770--4268883 Score: 54
Period size: 15 Copynumber: 7.6 Consensus size: 16
4268760 TTTATAAATA
* *
4268770 TAAAATAAAAAATAAT
1 TAAAATATAAAATATT
*
4268786 TAAAATATAATATA-T
1 TAAAATATAAAATATT
* *
4268801 GAATATAT-AAATATT
1 TAAAATATAAAATATT
4268816 TAAAAT-T--AATA--
1 TAAAATATAAAATATT
4268827 T--AATA-AAAATTATT
1 TAAAATATAAAA-TATT
*
4268841 T-ATATATCAAAATTTATT
1 TAAAATAT-AAAA--TATT
4268859 T-AAATATAAAATATT
1 TAAAATATAAAATATT
4268874 TAAAATATAA
1 TAAAATATAA
4268884 TTATAATATA
Statistics
Matches: 77, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
9 3 0.04
11 3 0.04
12 2 0.03
13 4 0.05
14 6 0.08
15 20 0.26
16 20 0.26
17 8 0.10
18 11 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAAATATAAAATATT
Found at i:4269060 original size:12 final size:12
Alignment explanation
Indices: 4269045--4269069 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4269035 TTAAAATTTT
4269045 TTAAAAATTATA
1 TTAAAAATTATA
4269057 TTAAAAATTATA
1 TTAAAAATTATA
4269069 T
1 T
4269070 CACTAAATTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAAAATTATA
Found at i:4269108 original size:16 final size:16
Alignment explanation
Indices: 4269087--4269119 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4269077 TTAAAATAAA
4269087 TATATTAACTATTTAT
1 TATATTAACTATTTAT
*
4269103 TATATTAATTATTTAT
1 TATATTAACTATTTAT
4269119 T
1 T
4269120 TAATATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTAACTATTTAT
Found at i:4269156 original size:21 final size:20
Alignment explanation
Indices: 4269118--4269167 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4269108 TAATTATTTA
4269118 TTTAATATTAAAAATATTAT
1 TTTAATATTAAAAATATTAT
*
4269138 TTTAATATT-TAAAT-TTATT
1 TTTAATATTAAAAATATTA-T
4269157 TTTAAT-TTAAA
1 TTTAATATTAAA
4269168 TAGCTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 5 0.19
19 12 0.46
20 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATATTAAAAATATTAT
Found at i:4269166 original size:17 final size:19
Alignment explanation
Indices: 4269118--4269169 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
4269108 TAATTATTTA
*
4269118 TTTAATATTAAAAATATTAT
1 TTTAATATT-TAAATATTAT
4269138 TTTAATATTTAAAT-TTAT
1 TTTAATATTTAAATATTAT
*
4269156 TTTTA-ATTTAAATA
1 TTTAATATTTAAATA
4269170 GCTGAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 8 0.28
18 8 0.28
19 4 0.14
20 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATATTTAAATATTAT
Found at i:4269904 original size:4 final size:4
Alignment explanation
Indices: 4269895--4269923 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
4269885 GGATCGCCTG
4269895 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
4269924 CTTGTTTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:4270744 original size:20 final size:20
Alignment explanation
Indices: 4270727--4270762 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
4270717 GATTTAATCC
4270727 AAAA-TAATAT-TTTTTAAT
1 AAAACTAATATATTTTTAAT
4270745 AAAACTAATATATTTTTA
1 AAAACTAATATATTTTTA
4270763 TTTAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAACTAATATATTTTTAAT
Found at i:4270795 original size:22 final size:19
Alignment explanation
Indices: 4270765--4270806 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
4270755 TATTTTTATT
4270765 TAAATTTAAATATAAAATATA
1 TAAATTTAAA-ATAAAA-ATA
4270786 TAAATATTAAAATAAAAATA
1 TAAAT-TTAAAATAAAAATA
4270806 T
1 T
4270807 TTTTTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATTTAAAATAAAAATA
Found at i:4272785 original size:21 final size:20
Alignment explanation
Indices: 4272759--4272797 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4272749 GTCTTTATTT
*
4272759 ATTTTTATTATTAGAAATTGA
1 ATTTTTATAATT-GAAATTGA
4272780 ATTTTTATAATTGAAATT
1 ATTTTTATAATTGAAATT
4272798 AGGTGCAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTTTTATAATTGAAATTGA
Found at i:4273507 original size:39 final size:40
Alignment explanation
Indices: 4273464--4273544 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 40
4273454 TGAAACAATT
* * *
4273464 AATCTCAATTTTAAAATATCTATTTATT-TTTTTCAGAAA
1 AATCTCAATTTTAAAATATCTACTTATTCTTCTTCAAAAA
** *
4273503 AATCTTGATTTTAAAATATTTACTTATTCTTCTTCAAAAA
1 AATCTCAATTTTAAAATATCTACTTATTCTTCTTCAAAAA
4273543 AA
1 AA
4273545 ACTTTAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
39 24 0.69
40 11 0.31
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (40 bp):
AATCTCAATTTTAAAATATCTACTTATTCTTCTTCAAAAA
Found at i:4274117 original size:11 final size:11
Alignment explanation
Indices: 4274073--4274187 Score: 54
Period size: 11 Copynumber: 11.5 Consensus size: 11
4274063 ATTAATATCA
4274073 TATATTTATA-
1 TATATTTATAT
* *
4274083 TAAATTT-TAA
1 TATATTTATAT
4274093 TATA-TTA-A-
1 TATATTTATAT
4274101 TATATTTATAT
1 TATATTTATAT
**
4274112 TATATTCGTAT
1 TATATTTATAT
*
4274123 T-T-TTAATAT
1 TATATTTATAT
*
4274132 TAT-GTTATA-
1 TATATTTATAT
4274141 T-T-TTTATAT
1 TATATTTATAT
* *
4274150 TTTATTTAAAT
1 TATATTTATAT
*
4274161 TATTTTTATAT
1 TATATTTATAT
*
4274172 CATATTTATAT
1 TATATTTATAT
*
4274183 AATAT
1 TATAT
4274188 AATAGTGGTA
Statistics
Matches: 80, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
8 10 0.12
9 16 0.20
10 17 0.21
11 37 0.46
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:4274133 original size:20 final size:18
Alignment explanation
Indices: 4274093--4274155 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
4274083 TAAATTTTAA
*
4274093 TATATTAATATATTTATAT
1 TATATT-ATATTTTTATAT
*
4274112 TATATTCGTATTTTTAATAT
1 TATATT-ATATTTTT-ATAT
*
4274132 TATGTTATATTTTTATAT
1 TATATTATATTTTTATAT
*
4274150 TTTATT
1 TATATT
4274156 TAAATTATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 8 0.22
19 19 0.53
20 9 0.25
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (18 bp):
TATATTATATTTTTATAT
Found at i:4275001 original size:9 final size:9
Alignment explanation
Indices: 4274987--4275012 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4274977 ATTAAATTAT
4274987 TTTTATATA
1 TTTTATATA
4274996 TTTTATATA
1 TTTTATATA
4275005 TTTTATAT
1 TTTTATAT
4275013 TTATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTATATA
Found at i:4275297 original size:48 final size:49
Alignment explanation
Indices: 4275236--4275331 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 49
4275226 TAATAATCAA
* *
4275236 TTTAGTAACATATTAATCGTATATAAAATTA-TGTAAATATGTAAAACG
1 TTTACTAAAATATTAATCGTATATAAAATTATTGTAAATATGTAAAACG
*
4275284 TTTACTAAAATATTAATCGTATATAGAATTATTGTAAATATGTAAAAC
1 TTTACTAAAATATTAATCGTATATAAAATTATTGTAAATATGTAAAAC
4275332 TTATTTAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 28 0.64
49 16 0.36
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (49 bp):
TTTACTAAAATATTAATCGTATATAAAATTATTGTAAATATGTAAAACG
Found at i:4275623 original size:29 final size:28
Alignment explanation
Indices: 4275574--4275637 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
4275564 TTAGGTATTT
*
4275574 ATTAATTAAAATAATTTTATTATTTAAA
1 ATTAATTAAAATAATTTTATTAATTAAA
* *
4275602 TTTAATTATAA-AATTATATATTAATTAAA
1 ATTAATTAAAATAATT-T-TATTAATTAAA
4275631 ATTAATT
1 ATTAATT
4275638 TTTATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 10 0.33
29 16 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTAATTAAAATAATTTTATTAATTAAA
Found at i:4284276 original size:18 final size:20
Alignment explanation
Indices: 4284248--4284291 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
4284238 ACATAAAGAG
4284248 AAAAATATATAAAAA-TAAA
1 AAAAATATATAAAAATTAAA
*
4284267 AAAAAT-TATAAAAATTACA
1 AAAAATATATAAAAATTAAA
4284286 AAAAAT
1 AAAAAT
4284292 CAAAATCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATATATAAAAATTAAA
Found at i:4285313 original size:13 final size:13
Alignment explanation
Indices: 4285295--4285320 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4285285 TTAAATTGAT
4285295 ATTATTTTTTATA
1 ATTATTTTTTATA
4285308 ATTATTTTTTATA
1 ATTATTTTTTATA
4285321 TTTTATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTATTTTTTATA
Found at i:4286768 original size:2 final size:2
Alignment explanation
Indices: 4286761--4286791 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4286751 TTTCTTAAGG
4286761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4286792 GGAAACATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4290593 original size:2 final size:2
Alignment explanation
Indices: 4290586--4290611 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4290576 ATAACACCAA
4290586 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
4290612 TAATATGTAA
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:4291703 original size:35 final size:37
Alignment explanation
Indices: 4291664--4291748 Score: 88
Period size: 39 Copynumber: 2.3 Consensus size: 37
4291654 TATGTTTTTG
*
4291664 ATATTAAATATACTTAATATTTTA-A-AATATTT-TAT
1 ATATTAAATATAATT-ATATTTTATATAATATTTATAT
*
4291699 ATATTTAATA-AATTATATTTTATATTAATATTTAAATAT
1 ATATTAAATATAATTATATTTTATA-TAATATTT--ATAT
4291738 ATATTAAATAT
1 ATATTAAATAT
4291749 TAACATCAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
33 8 0.20
34 4 0.10
35 9 0.22
36 7 0.17
39 12 0.30
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (37 bp):
ATATTAAATATAATTATATTTTATATAATATTTATAT
Found at i:4291738 original size:23 final size:23
Alignment explanation
Indices: 4291672--4291739 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
4291662 TGATATTAAA
4291672 TATACTTAATATTTTAAA-ATATTT
1 TATA-TTAATA-TTTAAATATATTT
4291696 TATA-T-AT-TTAATAAATTATATTT
1 TATATTAATATT--TAAA-TATATTT
4291719 TATATTAATATTTAAATATAT
1 TATATTAATATTTAAATATAT
4291740 ATTAAATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
19 2 0.05
21 6 0.16
22 1 0.03
23 15 0.41
24 9 0.24
25 2 0.05
26 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATTAATATTTAAATATATTT
Found at i:4294405 original size:2 final size:2
Alignment explanation
Indices: 4294400--4294428 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4294390 TTAAAAAATT
4294400 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 T
4294429 TTCTAGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4294756 original size:19 final size:22
Alignment explanation
Indices: 4294706--4294746 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4294696 ATAGTTTATT
4294706 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAATTATAAAATATA
*
4294727 TAAATTTTAATTAAAAAATA
1 TAAATTTTAATTATAAAATA
4294747 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATTTTAATTATAAAATATA
Found at i:4296546 original size:20 final size:21
Alignment explanation
Indices: 4296518--4296556 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4296508 TATACCACAT
*
4296518 TAAATATT-ATTTTTTATATA
1 TAAAAATTAATTTTTTATATA
4296538 TAAAAATTAATTTTTTATA
1 TAAAAATTAATTTTTTATA
4296557 AATTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAAAATTAATTTTTTATATA
Found at i:4296851 original size:30 final size:32
Alignment explanation
Indices: 4296817--4296887 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 32
4296807 AATAAATAAT
* *
4296817 TTTATTTAATTTTAATA-ATTAATAATATT-A
1 TTTATTTAATTTTAATATATCAAAAATATTAA
* *
4296847 TTTA-TGATTTTTAATATATCAAAAATATTAA
1 TTTATTTAATTTTAATATATCAAAAATATTAA
*
4296878 TTTATATAAT
1 TTTATTTAAT
4296888 AATTTTAAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
29 10 0.32
30 14 0.45
31 5 0.16
32 2 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
TTTATTTAATTTTAATATATCAAAAATATTAA
Found at i:4297579 original size:2 final size:2
Alignment explanation
Indices: 4297572--4297616 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4297562 CAGCTACCGA
4297572 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
4297614 AT A
1 AT A
4297617 ACTCTTCTAA
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:4302045 original size:26 final size:25
Alignment explanation
Indices: 4302016--4302064 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
4302006 CTCAATTTTA
*
4302016 AAAATTATAAAAATAAATTTAAATAT
1 AAAATTATAAAAACAAA-TTAAATAT
*
4302042 AAAATTATAATAACAAATTAAAT
1 AAAATTATAAAAACAAATTAAAT
4302065 TTATTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATTATAAAAACAAATTAAATAT
Found at i:4302121 original size:15 final size:15
Alignment explanation
Indices: 4302087--4302134 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
4302077 ATTTTTGATC
* *
4302087 AAAATATAAATTTTAT
1 AAAATTTAAA-TTTAA
4302103 AAAATTTAAATTTAA
1 AAAATTTAAATTTAA
4302118 AAAATTTAAATTTAA
1 AAAATTTAAATTTAA
4302133 AA
1 AA
4302135 TTGATCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 21 0.70
16 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTAAATTTAA
Found at i:4302177 original size:15 final size:15
Alignment explanation
Indices: 4302154--4302188 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4302144 ACTCAAATTT
*
4302154 AATATTAAAAATAAA
1 AATAATAAAAATAAA
*
4302169 AATAATAAAATTAAA
1 AATAATAAAAATAAA
4302184 AATAA
1 AATAA
4302189 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAATAAAAATAAA
Found at i:4302489 original size:17 final size:17
Alignment explanation
Indices: 4302469--4302501 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4302459 AATATTTAAA
4302469 ATATTTTAATTTTTATC
1 ATATTTTAATTTTTATC
*
4302486 ATATTTTATTTTTTAT
1 ATATTTTAATTTTTAT
4302502 AATAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATATTTTAATTTTTATC
Found at i:4304621 original size:15 final size:15
Alignment explanation
Indices: 4304575--4304624 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
4304565 TTCATGTATA
*
4304575 ATTTTTAATTTAAAA
1 ATTTTTAATTTAAAT
* *
4304590 ATATTTAAATT--AT
1 ATTTTTAATTTAAAT
4304603 ATTTTTAATTTAAAT
1 ATTTTTAATTTAAAT
4304618 ATTTTTA
1 ATTTTTA
4304625 GAAAGCTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 10 0.36
15 18 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTAATTTAAAT
Found at i:4304964 original size:2 final size:2
Alignment explanation
Indices: 4304957--4304988 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4304947 AGATAAGATA
4304957 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
4304989 GCTGAATTGA
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:4305150 original size:17 final size:17
Alignment explanation
Indices: 4305117--4305150 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4305107 CGAGGTTAAT
* *
4305117 ATTATTAAAGTATTTGA
1 ATTATTAAAATAATTGA
4305134 ATTATTAAAATAATTGA
1 ATTATTAAAATAATTGA
4305151 TACAGATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
ATTATTAAAATAATTGA
Found at i:4309156 original size:21 final size:20
Alignment explanation
Indices: 4309131--4309176 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
4309121 ATATCATCTT
4309131 AATAAAAAAATTTTAAATAA
1 AATAAAAAAATTTTAAATAA
* * *
4309151 ATATAAATAATTTTTTAATAA
1 A-ATAAAAAAATTTTAAATAA
4309172 AATAA
1 AATAA
4309177 TACCATTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATAAAAAAATTTTAAATAA
Found at i:4310234 original size:31 final size:31
Alignment explanation
Indices: 4310179--4310237 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
4310169 TTCGGTGCTA
4310179 ATTTTTTTATATTATATATATTTATGTTTAT
1 ATTTTTTTATATTATATATATTTATGTTTAT
* *
4310210 ATTTTCTTTTTATTAT-TATGTTTATGTT
1 ATTTT-TTTATATTATATATATTTATGTT
4310238 AAATCTACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (31 bp):
ATTTTTTTATATTATATATATTTATGTTTAT
Found at i:4310809 original size:15 final size:16
Alignment explanation
Indices: 4310791--4310826 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
4310781 TTTTTAAAAA
4310791 ATTTATC-TTTAAGAG
1 ATTTATCTTTTAAGAG
4310806 ATTTATCTTTTTAAGAG
1 ATTTATC-TTTTAAGAG
4310823 ATTT
1 ATTT
4310827 TAAGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
17 12 0.63
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (16 bp):
ATTTATCTTTTAAGAG
Found at i:4310820 original size:17 final size:17
Alignment explanation
Indices: 4310781--4310826 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
4310771 AAATTGTAAG
* *
4310781 TTTTTAAAAAATTTATC
1 TTTTTAAGAGATTTATC
4310798 --TTTAAGAGATTTATC
1 TTTTTAAGAGATTTATC
4310813 TTTTTAAGAGATTT
1 TTTTTAAGAGATTT
4310827 TAAGAGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 13 0.52
17 12 0.48
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (17 bp):
TTTTTAAGAGATTTATC
Found at i:4312496 original size:23 final size:23
Alignment explanation
Indices: 4312470--4312513 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
4312460 ATTATTTATC
4312470 ATATTATTT-ATTTAATATCAAAA
1 ATATTATTTAATTTAA-ATCAAAA
*
4312493 ATATTTTTTAATTTAAATCAA
1 ATATTATTTAATTTAAATCAA
4312514 TTTAACCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTATTTAATTTAAATCAAAA
Found at i:4312853 original size:22 final size:22
Alignment explanation
Indices: 4312811--4312853 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4312801 AATATAATTA
**
4312811 AATATATTAAAAATTTTGATAT
1 AATATATTAAAAATTACGATAT
*
4312833 AATATATTTAAAATTACGATA
1 AATATATTAAAAATTACGATA
4312854 CGATATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (22 bp):
AATATATTAAAAATTACGATAT
Found at i:4313126 original size:3 final size:3
Alignment explanation
Indices: 4313120--4313158 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
4313110 ATAATAATAT
*
4313120 TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA GTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4313159 GTAACAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4313142 original size:20 final size:20
Alignment explanation
Indices: 4313119--4313158 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4313109 TATAATAATA
*
4313119 TTTATTATTATTATTATTAT
1 TTTATTATTATTAGTATTAT
4313139 TTTATTATTATTAGTATTAT
1 TTTATTATTATTAGTATTAT
4313159 GTAACAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTATTATTATTAGTATTAT
Found at i:4313143 original size:17 final size:17
Alignment explanation
Indices: 4313123--4313156 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4313113 ATAATATTTA
*
4313123 TTATTATTATTATTATT
1 TTATTATTATTAGTATT
4313140 TTATTATTATTAGTATT
1 TTATTATTATTAGTATT
4313157 ATGTAACAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTATTATTAGTATT
Found at i:4314740 original size:17 final size:16
Alignment explanation
Indices: 4314710--4314748 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
4314700 CTAATTTTTA
*
4314710 AATT-TAAATTAATCT
1 AATTATAAATAAATCT
4314725 AATCTATAAATAAATCT
1 AAT-TATAAATAAATCT
4314742 AATTATA
1 AATTATA
4314749 GATACTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 5 0.24
17 13 0.62
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTATAAATAAATCT
Found at i:4315445 original size:3 final size:3
Alignment explanation
Indices: 4315432--4315469 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
4315422 GGGGGAAATA
4315432 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4315470 TAGATAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4316512 original size:21 final size:20
Alignment explanation
Indices: 4316486--4316525 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
4316476 TTTTATTAAT
4316486 TTAAAATAAATTAAATTAAAA
1 TTAAAATAAATT-AATTAAAA
*
4316507 TTAAAATTAATTAATTAAA
1 TTAAAATAAATTAATTAAA
4316526 TTTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAATAAATTAATTAAAA
Found at i:4316899 original size:13 final size:13
Alignment explanation
Indices: 4316881--4316910 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4316871 TATGTTTTTC
4316881 ATATTAAAGATAA
1 ATATTAAAGATAA
*
4316894 ATATTAAATATAA
1 ATATTAAAGATAA
4316907 ATAT
1 ATAT
4316911 ATATTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATATTAAAGATAA
Found at i:4316920 original size:17 final size:17
Alignment explanation
Indices: 4316894--4316985 Score: 67
Period size: 17 Copynumber: 5.0 Consensus size: 17
4316884 TTAAAGATAA
*
4316894 ATATTAAATATAAATAT
1 ATATTTAATATAAATAT
*
4316911 ATATTTAATATAATTTATT
1 ATATTTAATATAA-ATA-T
* *
4316930 ATATTTAAAAAATTATATAT
1 ATATTT--AATA-TAAATAT
*
4316950 CATATTTATATCTAAATAT
1 -ATATTTA-ATATAAATAT
*
4316969 ATATTAAATATAAATAT
1 ATATTTAATATAAATAT
4316986 CATACATAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
17 21 0.36
18 8 0.14
19 14 0.24
20 2 0.03
21 11 0.19
22 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTTAATATAAATAT
Found at i:4316956 original size:21 final size:20
Alignment explanation
Indices: 4316907--4316957 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
4316897 TTAAATATAA
*
4316907 ATATATATTTAATATAATTT
1 ATATATATTTAATAAAATTT
4316927 AT-TATATTTAA-AAAATTAT
1 ATATATATTTAATAAAATT-T
4316946 ATATCATATTTA
1 ATAT-ATATTTA
4316958 TATCTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 3 0.11
21 7 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATATTTAATAAAATTT
Found at i:4329319 original size:20 final size:20
Alignment explanation
Indices: 4329294--4329338 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4329284 TAGGAAGCTT
*
4329294 TGAAATATTCTAGAAGGATC
1 TGAAATAATCTAGAAGGATC
* *
4329314 TGAAATAATGTAGAAGGTTC
1 TGAAATAATCTAGAAGGATC
4329334 TGAAA
1 TGAAA
4329339 CATTGTGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (20 bp):
TGAAATAATCTAGAAGGATC
Found at i:4331089 original size:20 final size:20
Alignment explanation
Indices: 4331061--4331109 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
4331051 TTGTGGAAGC
*
4331061 TCTGAAATATTCTAGAAGGA
1 TCTGAAATAATCTAGAAGGA
* * *
4331081 TCTGGAATAATGTAGAAGGT
1 TCTGAAATAATCTAGAAGGA
4331101 TCTAGAAAT
1 TCT-GAAAT
4331110 TGTAAAAGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (20 bp):
TCTGAAATAATCTAGAAGGA
Found at i:4333229 original size:24 final size:25
Alignment explanation
Indices: 4333162--4333232 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 25
4333152 TTAATTATTA
4333162 TTAAA-AATTTATTT-TTATTAATAT
1 TTAAATAATTT-TTTATTATTAATAT
* * **
4333186 TTATAT-ATTTTTAAAAATTAA-AT
1 TTAAATAATTTTTTATTATTAATAT
4333209 TTAAATAATTTTTTATTATTAATA
1 TTAAATAATTTTTTATTATTAATA
4333233 GTGATACATA
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
23 9 0.26
24 25 0.71
25 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAAATAATTTTTTATTATTAATAT
Found at i:4334008 original size:16 final size:17
Alignment explanation
Indices: 4333987--4334019 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4333977 AATTTATTTT
4333987 ATTTAAATT-AAATTAA
1 ATTTAAATTAAAATTAA
*
4334003 ATTTAATTTAAAATTAA
1 ATTTAAATTAAAATTAA
4334020 TAAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTAAATTAAAATTAA
Found at i:4334097 original size:19 final size:19
Alignment explanation
Indices: 4334073--4334121 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
4334063 TATTAAATAA
*
4334073 TAATTTACAT-TGAATAAGT
1 TAATTTAAATATGAA-AAGT
4334092 TAATTTGAAATATGAAAAGT
1 TAATTT-AAATATGAAAAGT
4334112 TATATTTAAA
1 TA-ATTTAAA
4334122 GCCTAAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 12 0.46
21 8 0.31
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (19 bp):
TAATTTAAATATGAAAAGT
Found at i:4335359 original size:246 final size:248
Alignment explanation
Indices: 4334853--4335796 Score: 1393
Period size: 246 Copynumber: 3.9 Consensus size: 248
4334843 TTTGACTTGA
* * * * * *
4334853 GTCTTTTATGTTAGTATTAATGTTTGACCTATTTTTTAGATAAGTTTAATTTTTTTGTCTTAAAA
1 GTCTTTTATGTTGGTATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTATCTTAATA
* * *
4334918 TTTTTATTTAGATCTTCA-AAGATATATATCATATCAATTTTAGAAGTTGAGTAAGTAACCCGAC
66 TTTTTATTTAAATCTTCATAA-ATATATATCATATCAATTTCAGAAGTTAAGTAAGTAACCCGAC
** * * *
4334982 TTTTAAACAGATCCAAAAATGAA-CAAAGTTAAGCTTCTAAAAAAGAGCAACATAAATGAAAAAA
130 TCATAAACAGGTCCAAAAAT-AAGCAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAA
* *
4335046 AAGGAGAAAGAAAATTTCTCCAGGTTCTAGGTTAGGATCATGGCAGTTGATATTA
194 AAGGAGAAAGAAAATTTCTCTAGGTTCTAGGTTAGGATCATGGCAGTTGATATTG
*
4335101 GTCTTTTATGTTGGTATTAATGTTTGACCTATTTTTTAAATAAATTTAA-TTTTTTATCTTAATA
1 GTCTTTTATGTTGGTATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTATCTTAATA
* *
4335165 TTTTTATTTAAATCTTCATAAATATATATCATATCAATTTCAAAAGTTAAGTAAGTAGCCCGACT
66 TTTTTATTTAAATCTTCATAAATATATATCATATCAATTTCAGAAGTTAAGTAAGTAACCCGACT
* *
4335230 CATCAACAGGTCCAAAAATAAGCAAAGTGAAGCATCTAAAAAAAA-CAACATAAATGAAAAAAAA
131 CATAAACAGGTCCAAAAATAAGCAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAA
*
4335294 GGAGAAAGAAAATTTCTCTAGGTTGTAGGTTAGGATCATGGCAGTTGATATTG
196 GGAGAAAGAAAATTTCTCTAGGTTCTAGGTTAGGATCATGGCAGTTGATATTG
* *
4335347 GTCTTTTATGTTGGTATCAATGTTTAACCTATTTTTTAAATAAGTTTAA-TTTTTTATCTTAATA
1 GTCTTTTATGTTGGTATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTATCTTAATA
*
4335411 TTTTTATTTAAATCTTCATAGATATATATCATATCAATTTCAGAAG-T---TAAGTAACCCGACT
66 TTTTTATTTAAATCTTCATAAATATATATCATATCAATTTCAGAAGTTAAGTAAGTAACCCGACT
4335472 CATAAACAGGTCCAAAAATAAGCAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAA
131 CATAAACAGGTCCAAAAATAAGCAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAA
*
4335537 GGAGAAAGAAAATTTCTCTAGGTTCTAGGTTAGGATCATGGTAGTTGATATTG
196 GGAGAAAGAAAATTTCTCTAGGTTCTAGGTTAGGATCATGGCAGTTGATATTG
* *
4335590 ATCTTTTATGTTGGTATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTACCTTAATA
1 GTCTTTTATGTTGGTATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTATCTTAATA
* * * * **
4335655 CTTTTATTTAAATCTTCATAGATATATATCATATCAATTTCAGAGGTTGAA-TAAATAATTCGA-
66 TTTTTATTTAAATCTTCATAAATATATATCATATCAATTTCAGAAGTT-AAGTAAGTAACCCGAC
*
4335718 T--T---C--GTACCAAAAATAAGCAAAGTTAAGTATCTAAAAAAAAGCAACATAAATGAAAAAA
130 TCATAAACAGGT-CCAAAAATAAGCAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAA
* *
4335776 AAGAAGAAAGAAATTTTCTCT
194 AAGGAGAAAGAAAATTTCTCT
4335797 TTAGGATCAT
Statistics
Matches: 645, Mismatches: 42, Indels: 25
0.91 0.06 0.04
Matches are distributed among these distances:
240 2 0.00
241 70 0.11
242 57 0.09
243 116 0.18
244 58 0.09
245 3 0.00
246 176 0.27
247 106 0.16
248 57 0.09
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (248 bp):
GTCTTTTATGTTGGTATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTATCTTAATA
TTTTTATTTAAATCTTCATAAATATATATCATATCAATTTCAGAAGTTAAGTAAGTAACCCGACT
CATAAACAGGTCCAAAAATAAGCAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAA
GGAGAAAGAAAATTTCTCTAGGTTCTAGGTTAGGATCATGGCAGTTGATATTG
Found at i:4335544 original size:489 final size:487
Alignment explanation
Indices: 4334853--4335796 Score: 1438
Period size: 489 Copynumber: 1.9 Consensus size: 487
4334843 TTTGACTTGA
* * * *
4334853 GTCTTTTATGTTAGTATTAATGTTTGACCTATTTTTTAGATAAGTTTAATTTTTTTGTCTTAAAA
1 GTCTTTTATGTTAGTATCAATGTTTAACCTATTTTTTAAATAAGTTTAATTTTTTTATCTTAAAA
* *
4334918 TTTTTATTTAGATCTTCAAAGATATATATCATATCAATTTTAGAAGTTGAGTAAGTAACCCGACT
66 TTTTTATTTAAATCTTCAAAGATATATATCATATCAATTTCAGAAGTT--GTAAGTAACCCGACT
** * *
4334983 TTTAAACAGATCCAAAAATGAACAAAGTTAAGCTTCTAAAAAAGAGCAACATAAATGAAAAAAAA
129 CATAAACAGATCCAAAAATGAACAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAA
4335048 GGAGAAAGAAAATTTCTCCAGGTTCTAGGTTAGGATCATGGCAGTTGATATT-AGTCTTTTATGT
194 GGAGAAAGAAAATTTCTCCAGGTTCTAGGTTAGGATCATGGCAGTTGATATTGA-TCTTTTATGT
* * *
4335112 TGGTATTAATGTTTGACCTATTTTTTAAATAAATTTAA-TTTTTTATCTTAATATTTTTATTTAA
258 TGGTATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTACCTTAATACTTTTATTTAA
* *
4335176 ATCTTCATAAATATATATCATATCAATTTCAAAAGTT-AAGTAAGTAGCCCGACTCATCAACAGG
323 ATCTTCATAAATATATATCATATCAATTTCAAAAGTTGAA-TAAATAACCCGA-T--T---C--G
*
4335240 T-CCAAAAATAAGCAAAGTGAAGCATCTAAAAAAAA-CAACATAAATGAAAAAAAAGGAGAAAGA
379 TACCAAAAATAAGCAAAGTGAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAAGAAGAAAGA
4335303 AAATTTCTCTAGGTTGTAGGTTAGGATCATGGCAGTTGATATTG
444 AAATTTCTCTAGGTTGTAGGTTAGGATCATGGCAGTTGATATTG
* *
4335347 GTCTTTTATGTTGGTATCAATGTTTAACCTATTTTTTAAATAAGTTTAA-TTTTTTATCTTAATA
1 GTCTTTTATGTTAGTATCAATGTTTAACCTATTTTTTAAATAAGTTTAATTTTTTTATCTTAAAA
*
4335411 TTTTTATTTAAATCTTCATAGATATATATCATATCAATTTCAGAAG-T-TAAGTAACCCGACTCA
66 TTTTTATTTAAATCTTCAAAGATATATATCATATCAATTTCAGAAGTTGTAAGTAACCCGACTCA
*
4335474 TAAACAGGTCCAAAAAT-AAGCAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAAG
131 TAAACAGATCCAAAAATGAA-CAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAAG
* *
4335538 GAGAAAGAAAATTTCTCTAGGTTCTAGGTTAGGATCATGGTAGTTGATATTGATCTTTTATGTTG
195 GAGAAAGAAAATTTCTCCAGGTTCTAGGTTAGGATCATGGCAGTTGATATTGATCTTTTATGTTG
4335603 GTATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTACCTTAATACTTTTATTTAAAT
260 GTATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTACCTTAATACTTTTATTTAAAT
* * * **
4335668 CTTCATAGATATATATCATATCAATTTCAGAGGTTGAATAAATAATTCGATTCGTACCAAAAATA
325 CTTCATAAATATATATCATATCAATTTCAAAAGTTGAATAAATAACCCGATTCGTACCAAAAATA
* * *
4335733 AGCAAAGTTAAGTATCTAAAAAAAAGCAACATAAATGAAAAAAAAGAAGAAAGAAATTTTCTCT
390 AGCAAAGTGAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAAGAAGAAAGAAAATTTCTCT
4335797 TTAGGATCAT
Statistics
Matches: 414, Mismatches: 30, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
482 2 0.00
483 32 0.08
484 37 0.09
487 1 0.00
488 2 0.00
489 169 0.41
490 67 0.16
491 2 0.00
492 1 0.00
493 56 0.14
494 45 0.11
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (487 bp):
GTCTTTTATGTTAGTATCAATGTTTAACCTATTTTTTAAATAAGTTTAATTTTTTTATCTTAAAA
TTTTTATTTAAATCTTCAAAGATATATATCATATCAATTTCAGAAGTTGTAAGTAACCCGACTCA
TAAACAGATCCAAAAATGAACAAAGTTAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAAGG
AGAAAGAAAATTTCTCCAGGTTCTAGGTTAGGATCATGGCAGTTGATATTGATCTTTTATGTTGG
TATCAATGTTTGACCTATTTTTTAAATAAATTTAATTTTTTTACCTTAATACTTTTATTTAAATC
TTCATAAATATATATCATATCAATTTCAAAAGTTGAATAAATAACCCGATTCGTACCAAAAATAA
GCAAAGTGAAGCATCTAAAAAAAAGCAACATAAATGAAAAAAAAGAAGAAAGAAAATTTCTCTAG
GTTGTAGGTTAGGATCATGGCAGTTGATATTG
Found at i:4336292 original size:17 final size:16
Alignment explanation
Indices: 4336255--4336299 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
4336245 TTTTAATAGT
*
4336255 AAATAAATATTAAATA
1 AAATAAATATTTAATA
*
4336271 TAATAAATATTTAATAA
1 AAATAAATATTTAAT-A
*
4336288 AAATATATATTT
1 AAATAAATATTT
4336300 GATTAAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATAAATATTTAATA
Found at i:4337117 original size:19 final size:17
Alignment explanation
Indices: 4337083--4337135 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
4337073 AAATTAAAAA
4337083 TATAATATT-TTAATATAT
1 TATAATATTATT-ATAT-T
4337101 TAATAATATTATTATATT
1 T-ATAATATTATTATATT
4337119 TA-AATATTATTATATT
1 TATAATATTATTATATT
4337135 T
1 T
4337136 GAAAGTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 15 0.45
17 1 0.03
18 3 0.09
19 12 0.36
20 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATAATATTATTATATT
Found at i:4337562 original size:12 final size:11
Alignment explanation
Indices: 4337539--4337568 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
4337529 GATGTTAAAT
4337539 TAAATAAATAA
1 TAAATAAATAA
4337550 TAAATATAATAA
1 TAAATA-AATAA
4337562 TAAATAA
1 TAAATAA
4337569 TTGATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATAAATAA
Done.