Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 64 of 226
Found at i:20724398 original size:3 final size:3
Alignment explanation
Indices: 20724338--20724382 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
20724328 GAGGAGGAAA
* *
20724338 TGG TGG TGG AGG TGG AGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
20724383 AGGAGGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.04, C:0.00, G:0.67, T:0.29
Consensus pattern (3 bp):
TGG
Found at i:20729592 original size:15 final size:15
Alignment explanation
Indices: 20729572--20729601 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20729562 AGCTGGTACT
*
20729572 TCTTCTTCCTCCTCA
1 TCTTCTTCATCCTCA
20729587 TCTTCTTCATCCTCA
1 TCTTCTTCATCCTCA
20729602 CGTTTCTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTTCTTCATCCTCA
Found at i:20734233 original size:130 final size:130
Alignment explanation
Indices: 20734036--20734433 Score: 496
Period size: 131 Copynumber: 3.0 Consensus size: 130
20734026 GATGAGATCG
* *
20734036 TTCATGATGTTAAATCGAATGAACTTAGGCTATAATATTAAATTAACGAGCCTTAACATTATTAG
1 TTCATGATATTAAATCGAATGAACTTAGGCTATGATATTAAATT-ACGAGCCTTAACATTATTAG
* * * *
20734101 CTGCGATCTTATATCAGTGAGCTATTTAGAGTAGCAATATTAAATCAACTAACTCAAATAAAATT
65 CTGCGATCTTAAATCAGTGAGCTATTTAGAGTAGCGATATTAAATCAGCTAACTCAAAGAAAATT
20734166 AT
130 -T
* * * * *
20734168 TT-ATGATATTAAATTGAATAAACTT-GGCTACGATATTAAATTGACGAGCTTTAACATTATCAG
1 TTCATGATATTAAATCGAATGAACTTAGGCTATGATATTAAATT-ACGAGCCTTAACATTATTAG
* * * * * * *
20734231 CTGCAATATTAAATCAGT-AACTTATTTAAAGTAGTGATATTAAATCGGGTAACTCAAAGAAAAT
65 CTGCGATCTTAAATCAGTGAGC-TATTTAGAGTAGCGATATTAAATCAGCTAACTCAAAGAAAAT
20734295 TT
129 TT
* * *
20734297 TTCATGATATTAAATCGAATGAACTTAGGCTGTGATTTTAAATTAGTGAGCCTTAACATTATTAG
1 TTCATGATATTAAATCGAATGAACTTAGGCTATGATATTAAATTA-CGAGCCTTAACATTATTAG
* * * * *
20734362 TTGTGATCTTAAATTAGCGAGCTATTTAGAGTAACGATATTAAATCAGCTAACTCAAAGAAAATT
65 CTGCGATCTTAAATCAGTGAGCTATTTAGAGTAGCGATATTAAATCAGCTAACTCAAAGAAAATT
20734427 T
130 T
20734428 TTCATG
1 TTCATG
20734434 TTAGATAAAC
Statistics
Matches: 222, Mismatches: 39, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
129 5 0.02
130 106 0.48
131 107 0.48
132 4 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (130 bp):
TTCATGATATTAAATCGAATGAACTTAGGCTATGATATTAAATTACGAGCCTTAACATTATTAGC
TGCGATCTTAAATCAGTGAGCTATTTAGAGTAGCGATATTAAATCAGCTAACTCAAAGAAAATTT
Found at i:20742715 original size:6 final size:6
Alignment explanation
Indices: 20742704--20742730 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20742694 TTATTTCCAC
20742704 TACTAG TACTAG TACTAG TACTAG TAC
1 TACTAG TACTAG TACTAG TACTAG TAC
20742731 CGAGTACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (6 bp):
TACTAG
Found at i:20745680 original size:29 final size:31
Alignment explanation
Indices: 20745611--20745683 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
20745601 ATTCAAAAAA
* *
20745611 TACAATGACTAAAATTAATCAATATGTAAAG
1 TACAAGGACTAAAATTAATCAATATGCAAAG
*
20745642 TAC-AGAGACTAAAATTGATCAA-AT-CAAAG
1 TACAAG-GACTAAAATTAATCAATATGCAAAG
20745671 TACAAGGACTAAA
1 TACAAGGACTAAA
20745684 CTCACAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 14 0.38
30 5 0.14
31 18 0.49
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (31 bp):
TACAAGGACTAAAATTAATCAATATGCAAAG
Found at i:20751532 original size:22 final size:21
Alignment explanation
Indices: 20751504--20751547 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
20751494 TCTCTCTATT
*
20751504 TTCTCTCAATCTCTCTTTCAAA
1 TTCTCTCAAACT-TCTTTCAAA
*
20751526 TTCTCTCAAACTTCTTTGAAA
1 TTCTCTCAAACTTCTTTCAAA
20751547 T
1 T
20751548 ATTTGGTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.45
Consensus pattern (21 bp):
TTCTCTCAAACTTCTTTCAAA
Found at i:20755622 original size:15 final size:15
Alignment explanation
Indices: 20755599--20755633 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20755589 ATGTATACTA
*
20755599 TGATACGTGATCGTG
1 TGATGCGTGATCGTG
*
20755614 TGATGCGTGATTGTG
1 TGATGCGTGATCGTG
20755629 TGATG
1 TGATG
20755634 TGTATGAAAT
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:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (15 bp):
TGATGCGTGATCGTG
Found at i:20767881 original size:16 final size:16
Alignment explanation
Indices: 20767856--20767893 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20767846 TTTTAAAAAG
*
20767856 AAAATACTTGTAGA-A
1 AAAATACTTGAAGAGA
20767871 AAAAGTACTTGAAGAGA
1 AAAA-TACTTGAAGAGA
20767888 AAAATA
1 AAAATA
20767894 ATTTGTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 4 0.20
16 11 0.55
17 5 0.25
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (16 bp):
AAAATACTTGAAGAGA
Found at i:20773656 original size:11 final size:11
Alignment explanation
Indices: 20773640--20773700 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
20773630 CGGCCTGAAT
20773640 TATATATTAAA
1 TATATATTAAA
**
20773651 TATATATTATT
1 TATATATTAAA
* *
20773662 TTTA-ATCAAA
1 TATATATTAAA
* *
20773672 TATACTCTTTAA
1 TATA-TATTAAA
20773684 TATATATTAAA
1 TATATATTAAA
20773695 TATATA
1 TATATA
20773701 CTTTTTTGGT
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
10 6 0.17
11 23 0.64
12 7 0.19
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (11 bp):
TATATATTAAA
Found at i:20774415 original size:6 final size:6
Alignment explanation
Indices: 20774404--20774433 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
20774394 GAAATAAATG
20774404 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC
20774434 TATACTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTTC
Found at i:20799191 original size:8 final size:8
Alignment explanation
Indices: 20799178--20799207 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
20799168 CCAGAAAAGC
20799178 TAATATAT
1 TAATATAT
20799186 TAATATAT
1 TAATATAT
20799194 TAATATAT
1 TAATATAT
20799202 TAATAT
1 TAATAT
20799208 TTGGTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TAATATAT
Found at i:20799234 original size:68 final size:68
Alignment explanation
Indices: 20799125--20799259 Score: 261
Period size: 68 Copynumber: 2.0 Consensus size: 68
20799115 TCCAGAAGAG
20799125 TTAATATATCAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
1 TTAATATATCAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
20799190 ATA
66 ATA
*
20799193 TTAATATATTAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
1 TTAATATATCAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
20799258 AT
66 AT
20799260 CTAAAAAGAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (68 bp):
TTAATATATCAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
ATA
Found at i:20799278 original size:68 final size:68
Alignment explanation
Indices: 20799138--20799278 Score: 219
Period size: 68 Copynumber: 2.1 Consensus size: 68
20799128 ATATATCAAT
* * * **
20799138 ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATATTAATATATT
1 ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATATAAAAAGAAC
*
20799203 AAT
66 AAA
*
20799206 ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATCTAAAAAGAAC
1 ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATATAAAAAGAAC
20799271 AAA
66 AAA
20799274 ATTTG
1 ATTTG
20799279 TGATGGTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (68 bp):
ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATATAAAAAGAAC
AAA
Found at i:20808246 original size:17 final size:17
Alignment explanation
Indices: 20808224--20808289 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
20808214 ACATCAAAGG
20808224 ATACAATTAGAACCTGT
1 ATACAATTAGAACCTGT
20808241 ATACAATTAGAACTCTAAG-
1 ATACAATTAGAAC-CT--GT
* **
20808260 ACACAATTAGAAGTTGT
1 ATACAATTAGAACCTGT
20808277 ATACAATTAGAAC
1 ATACAATTAGAAC
20808290 TCTAAGATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
16 1 0.03
17 24 0.60
18 3 0.08
19 11 0.28
20 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (17 bp):
ATACAATTAGAACCTGT
Found at i:20808267 original size:19 final size:19
Alignment explanation
Indices: 20808243--20808296 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
20808233 GAACCTGTAT
20808243 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
20808262 ACAATTAGAAGT-T--GTAT
1 ACAATTAGAACTCTAAG-AC
20808279 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
20808297 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 12 0.43
18 2 0.07
19 12 0.43
20 1 0.04
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:20808278 original size:36 final size:36
Alignment explanation
Indices: 20808226--20808296 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
20808216 ATCAAAGGAT
20808226 ACAATTAGAACCTGTATACAATTAGAACTCTAAGAC
1 ACAATTAGAACCTGTATACAATTAGAACTCTAAGAC
**
20808262 ACAATTAGAAGTTGTATACAATTAGAACTCTAAGA
1 ACAATTAGAACCTGTATACAATTAGAACTCTAAGA
20808297 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAGAACCTGTATACAATTAGAACTCTAAGAC
Found at i:20813138 original size:48 final size:48
Alignment explanation
Indices: 20813067--20813161 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
20813057 TTCTTTGCTT
*
20813067 AAAAACGCCTAAGTCAACCTAACTCGCAATGATAAAGGATTCAACAGC
1 AAAAACACCTAAGTCAACCTAACTCGCAATGATAAAGGATTCAACAGC
** *
20813115 AAAAACACCTAAGTCGGCCTAACTTGCAATGATAAAGGATTCAACAG
1 AAAAACACCTAAGTCAACCTAACTCGCAATGATAAAGGATTCAACAG
20813162 AATTCCCTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (48 bp):
AAAAACACCTAAGTCAACCTAACTCGCAATGATAAAGGATTCAACAGC
Found at i:20814067 original size:29 final size:29
Alignment explanation
Indices: 20813992--20814058 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
20813982 CTAGTACTCA
* * *
20813992 CCACAAAGGCTTTTCTATCTAGAGTTGTG
1 CCACAAAGGCTTATCTTTCCAGAGTTGTG
* *
20814021 CCACAAAGGCTTATCTTTCCAGAGTTTTT
1 CCACAAAGGCTTATCTTTCCAGAGTTGTG
20814050 CCACAAAGG
1 CCACAAAGG
20814059 TTGTCCTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (29 bp):
CCACAAAGGCTTATCTTTCCAGAGTTGTG
Found at i:20814287 original size:53 final size:53
Alignment explanation
Indices: 20814206--20814364 Score: 237
Period size: 53 Copynumber: 3.0 Consensus size: 53
20814196 TTTTTTAATT
* * * * *
20814206 TTTCCATATGATTCCATAACCCATCAGTTATGATCTTACATGATATGGTCTTC
1 TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
* *
20814259 TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACAATATGGTATTC
1 TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
* *
20814312 TTTCCATATGATGTCATAACTCACCAGTTACGGTCTTACACGATATGGTCTTC
1 TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
20814365 AATGCCATGG
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 95 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (53 bp):
TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
Found at i:20834010 original size:23 final size:22
Alignment explanation
Indices: 20833977--20834033 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
20833967 CAATGATAAT
*
20833977 ATTTTGTTTTTACTTCTCTTTTAC
1 ATTTT-TTTTTACTTCT-TTTTAA
**
20834001 ATTTTTTTTTGTTTCTTTTTAA
1 ATTTTTTTTTACTTCTTTTTAA
*
20834023 ATATTTTTTTA
1 ATTTTTTTTTA
20834034 TGTAAATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 14 0.50
23 9 0.32
24 5 0.18
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.72
Consensus pattern (22 bp):
ATTTTTTTTTACTTCTTTTTAA
Found at i:20834020 original size:22 final size:23
Alignment explanation
Indices: 20833990--20834032 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
20833980 TTGTTTTTAC
* *
20833990 TTCTCTTTTACATTTTTTTTTGT
1 TTCTCTTTTAAATATTTTTTTGT
20834013 TTCT-TTTTAAATATTTTTTT
1 TTCTCTTTTAAATATTTTTTT
20834033 ATGTAAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.74
Consensus pattern (23 bp):
TTCTCTTTTAAATATTTTTTTGT
Found at i:20839082 original size:134 final size:133
Alignment explanation
Indices: 20838916--20839292 Score: 560
Period size: 132 Copynumber: 2.8 Consensus size: 133
20838906 TTAGTGCTTT
* * * *
20838916 TATCCTCGAGTCTTAGGTTCAATTCTTCTCCTACTCACATTTTGTACTTTTTTTATTTCATGTTG
1 TATCCTTGAGTCTTAAGTTTAATTCTTCTCCTACTCACA-TTTGTATTTTTTTTATTTCATGTTG
* * *
20838981 CTTCAAAC-TTTTTAAATTTTTAATTAATTTTTTGAACATATTAGTTTTTTGGTTAGATGGTTGC
65 CTTCAAACTTTTTTTAATTTTTAATTAATTTTTT-AACATATTAGTTCTTTGGTTAGATAGTTGC
20839045 AATTA
129 AATTA
*
20839050 TATCCTTGAGTCTCAAGTTTAATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGC
1 TATCCTTGAGTCTTAAGTTTAATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGC
20839115 TTCAAACTTTTTTTAA-TTTTAATTAATTTTTTAACATATTAGTTCTTTGGTTAGATAGTTGCAA
66 TTCAAACTTTTTTTAATTTTTAATTAATTTTTTAACATATTAGTTCTTTGGTTAGATAGTTGCAA
20839179 TTA
131 TTA
* * * *
20839182 CATCCTTGAGTCTTGAGTTTAATTCCTCTCCTACTCACATTTGCATTTTGTTTTATTTCATGTTG
1 TATCCTTGAGTCTTAAGTTTAATTCTTCTCCTACTCACATTTGTATTTT-TTTTATTTCATGTTG
* * *
20839247 CTTTAAGCTTTTCTTTTATTTTTAATTAATATTTTTAACATATTAG
65 CTTCAAACTTTT-TTTAATTTTTAATTAAT-TTTTTAACATATTAG
20839293 CTTGTTTCCT
Statistics
Matches: 222, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
132 77 0.35
133 73 0.33
134 46 0.21
135 11 0.05
136 15 0.07
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (133 bp):
TATCCTTGAGTCTTAAGTTTAATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGC
TTCAAACTTTTTTTAATTTTTAATTAATTTTTTAACATATTAGTTCTTTGGTTAGATAGTTGCAA
TTA
Found at i:20839469 original size:22 final size:19
Alignment explanation
Indices: 20839399--20839493 Score: 88
Period size: 19 Copynumber: 4.7 Consensus size: 19
20839389 TGTTTCAAGC
20839399 TTTTTTATTTTTAATTAAT
1 TTTTTTATTTTTAATTAAT
20839418 GTTTTGATGATATTTTTAATT-A-
1 -TTTT--T--TATTTTTAATTAAT
*
20839440 -CTTTTATTTTTAATTAATATT
1 TTTTTTATTTTTAATT-A-A-T
20839461 TTTTTTATTTTTAATTAAT
1 TTTTTTATTTTTAATTAAT
20839480 TTTTTTATTTTTAA
1 TTTTTTATTTTTAA
20839494 CTCTTAACCA
Statistics
Matches: 63, Mismatches: 2, Indels: 21
0.73 0.02 0.24
Matches are distributed among these distances:
16 11 0.17
18 1 0.02
19 16 0.25
20 7 0.11
21 1 0.02
22 15 0.24
23 1 0.02
24 11 0.17
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTTATTTTTAATTAAT
Found at i:20839482 original size:16 final size:17
Alignment explanation
Indices: 20839428--20839467 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
20839418 GTTTTGATGA
*
20839428 TATTTTTAATTACT-TT
1 TATTTTTAATTAATATT
20839444 TATTTTTAATTAATATT
1 TATTTTTAATTAATATT
20839461 T-TTTTTA
1 TATTTTTA
20839468 TTTTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTTAATTAATATT
Found at i:20839570 original size:30 final size:31
Alignment explanation
Indices: 20839529--20839596 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
20839519 CATGCTTATA
20839529 AAAATAATTAAAAATA-A-AAAATACATTAATT
1 AAAA-AATTAAAAATACATAAAA-ACATTAATT
*
20839560 AAAAAATTAAAAATATCATCAAAACATTAATT
1 AAAAAATTAAAAATA-CATAAAAACATTAATT
20839592 AAAAA
1 AAAAA
20839597 TAAACTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 11 0.33
31 4 0.12
32 15 0.45
33 3 0.09
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (31 bp):
AAAAAATTAAAAATACATAAAAACATTAATT
Found at i:20840396 original size:20 final size:20
Alignment explanation
Indices: 20840371--20840425 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
20840361 GCAAAAAAAA
* *
20840371 TTATTGTTCTTTTTACTGTT
1 TTATTGTTATTTTTACCGTT
*
20840391 TTATTGCTGTTTTTTTACCGTT
1 TTATTG-T-TATTTTTACCGTT
*
20840413 TTGTTGTTATTTT
1 TTATTGTTATTTT
20840426 CTTGTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 16 0.55
ACGTcount: A:0.09, C:0.09, G:0.13, T:0.69
Consensus pattern (20 bp):
TTATTGTTATTTTTACCGTT
Found at i:20847429 original size:15 final size:15
Alignment explanation
Indices: 20847386--20847429 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20847376 TTTAATTCAT
*
20847386 TTTAAATTATTCAAG
1 TTTAAATTATTTAAG
*
20847401 TTTAGATTATTTTAAG
1 TTTAAATTA-TTTAAG
*
20847417 TTTAAATCATTTA
1 TTTAAATTATTTA
20847430 TACTTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (15 bp):
TTTAAATTATTTAAG
Found at i:20852012 original size:9 final size:9
Alignment explanation
Indices: 20852000--20852039 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
20851990 TTTGAATTTT
20852000 ATAATTCGA
1 ATAATTCGA
* *
20852009 ATAACTCAA
1 ATAATTCGA
*
20852018 ATAATTTGA
1 ATAATTCGA
20852027 ATAATTCGA
1 ATAATTCGA
20852036 ATAA
1 ATAA
20852040 CAGATTGGTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (9 bp):
ATAATTCGA
Found at i:20852216 original size:21 final size:19
Alignment explanation
Indices: 20852171--20852218 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
20852161 TTTATATTTT
*
20852171 TTAAAAAAATATAAAAAAT
1 TTAAAAAAATATAAAAAAG
20852190 TCTAAAAAATATATAAAGAAAG
1 T-TAAAAAA-ATATAAA-AAAG
20852212 TTAAAAA
1 TTAAAAA
20852219 TTTCCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 7 0.28
21 13 0.52
22 4 0.16
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (19 bp):
TTAAAAAAATATAAAAAAG
Found at i:20852449 original size:5 final size:5
Alignment explanation
Indices: 20852434--20852467 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
20852424 ATAATTTCTC
* *
20852434 TCGAT TTGAT TCGAT TCGAT TCGAT TCGAC TCGA
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
20852468 CTTGACTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (5 bp):
TCGAT
Found at i:20852454 original size:15 final size:15
Alignment explanation
Indices: 20852433--20852472 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
20852423 AATAATTTCT
20852433 CTCGATTTGATTCGA
1 CTCGATTTGATTCGA
* *
20852448 TTCGATTCGATTCGA
1 CTCGATTTGATTCGA
*
20852463 CTCGACTTGA
1 CTCGATTTGA
20852473 CTTGAATTTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (15 bp):
CTCGATTTGATTCGA
Found at i:20856496 original size:25 final size:24
Alignment explanation
Indices: 20856468--20856595 Score: 73
Period size: 24 Copynumber: 5.2 Consensus size: 24
20856458 GTATAACAGA
20856468 AAGCTCATATGAGCCATGTAACGGG
1 AAGCTCATATGAGCCAT-TAACGGG
* * * ** *
20856493 AAGCTGATCTGGGCTGTATAACAGG
1 AAGCTCATATGAGCCAT-TAACGGG
* *
20856518 AAGATCATAAGAGCCA-TAACCGGG
1 AAGCTCATATGAGCCATTAA-CGGG
** *
20856542 AAGCTCATGCGAGCCAATAACGGG
1 AAGCTCATATGAGCCATTAACGGG
* *
20856566 TAGCTTCGA-A-GAGCTATTAACGGG
1 AAGC-TC-ATATGAGCCATTAACGGG
20856590 AAGCTC
1 AAGCTC
20856596 CAGATAGCCA
Statistics
Matches: 76, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
23 5 0.07
24 38 0.50
25 32 0.42
26 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (24 bp):
AAGCTCATATGAGCCATTAACGGG
Found at i:20856726 original size:25 final size:25
Alignment explanation
Indices: 20856698--20856746 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
20856688 GAAGCTAACG
* *
20856698 AAGAGCCATATAATGGAAAGCTCGC
1 AAGAACCATATAAAGGAAAGCTCGC
* *
20856723 AAGAACTATATAAAGGGAAGCTCG
1 AAGAACCATATAAAGGAAAGCTCG
20856747 AGATGGCCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.16
Consensus pattern (25 bp):
AAGAACCATATAAAGGAAAGCTCGC
Found at i:20864042 original size:14 final size:14
Alignment explanation
Indices: 20864005--20864039 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
20863995 ATCTTATATA
20864005 TTTTTTTTGTTTTC
1 TTTTTTTTGTTTTC
*
20864019 TTTGTTTTG-TTTC
1 TTTTTTTTGTTTTC
20864032 TTTTTTTT
1 TTTTTTTT
20864040 TGTGTTGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.86
Consensus pattern (14 bp):
TTTTTTTTGTTTTC
Found at i:20865468 original size:12 final size:13
Alignment explanation
Indices: 20865445--20865473 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20865435 ATCTAAAAAA
20865445 AGAAGTGAAATGT
1 AGAAGTGAAATGT
20865458 AGAAG-GAAATGT
1 AGAAGTGAAATGT
20865470 AGAA
1 AGAA
20865474 ACCTATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (13 bp):
AGAAGTGAAATGT
Found at i:20880058 original size:23 final size:23
Alignment explanation
Indices: 20879984--20880058 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
20879974 TTGAGAACGT
* ** *
20879984 TAAACAAACATATTCACAAATGT
1 TAAACAAACATGTTTGCAAATGC
* ** *
20880007 TAAAAAGAACATGTTTGTGAATAC
1 TAAACA-AACATGTTTGCAAATGC
*
20880031 CAAACAAACATGTTTGCAAATGC
1 TAAACAAACATGTTTGCAAATGC
20880054 TAAAC
1 TAAAC
20880059 GAATTGATCC
Statistics
Matches: 37, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
23 23 0.62
24 14 0.38
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (23 bp):
TAAACAAACATGTTTGCAAATGC
Found at i:20886719 original size:15 final size:15
Alignment explanation
Indices: 20886699--20886728 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20886689 CTTATCAAAT
*
20886699 GGAACCTTTTACAAC
1 GGAACCTCTTACAAC
20886714 GGAACCTCTTACAAC
1 GGAACCTCTTACAAC
20886729 CTTAGCTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.23
Consensus pattern (15 bp):
GGAACCTCTTACAAC
Found at i:20894399 original size:40 final size:40
Alignment explanation
Indices: 20894355--20894475 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 40
20894345 GAAAGTGTGT
* *
20894355 TCAGGGGTACAAAAGTACAAATAGGGGCACGTATG-GTCAA
1 TCAGGGGTACAGAAGTACAAACAGGGGCACGTATGTG-CAA
*
20894395 TCAGGGGTACTGAAGTACAAACAGGGGCACGTATGTGCAA
1 TCAGGGGTACAGAAGTACAAACAGGGGCACGTATGTGCAA
* * **
20894435 TCAGGGGTACGGAAGTACAAACAGGGGAAATTATGTGCAA
1 TCAGGGGTACAGAAGTACAAACAGGGGCACGTATGTGCAA
20894475 T
1 T
20894476 AATTTAATTA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 72 0.99
41 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.31, T:0.18
Consensus pattern (40 bp):
TCAGGGGTACAGAAGTACAAACAGGGGCACGTATGTGCAA
Found at i:20894400 original size:20 final size:20
Alignment explanation
Indices: 20894377--20894461 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
20894367 AAGTACAAAT
20894377 AGGGGCACGTATGGT-CAATC
1 AGGGGCACGTAT-GTACAATC
* * *
20894397 AGGGGTAC-TGAAGTACAAAC
1 AGGGGCACGT-ATGTACAATC
*
20894417 AGGGGCACGTATGTGCAATC
1 AGGGGCACGTATGTACAATC
* * * *
20894437 AGGGGTACGGAAGTACAAAC
1 AGGGGCACGTATGTACAATC
20894457 AGGGG
1 AGGGG
20894462 AAATTATGTG
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
19 3 0.06
20 46 0.92
21 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.15
Consensus pattern (20 bp):
AGGGGCACGTATGTACAATC
Found at i:20894500 original size:21 final size:22
Alignment explanation
Indices: 20894476--20894516 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20894466 TATGTGCAAT
*
20894476 AATTTAATT-ATTAACTATAGA
1 AATTTAATTAAATAACTATAGA
20894497 AATTTAATTAAATAACTATA
1 AATTTAATTAAATAACTATA
20894517 ATTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTTAATTAAATAACTATAGA
Found at i:20900411 original size:17 final size:17
Alignment explanation
Indices: 20900389--20900423 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20900379 GTTTTTAATG
20900389 TAAACCAAGACCAAAAT
1 TAAACCAAGACCAAAAT
20900406 TAAACCAAGACCAAAAT
1 TAAACCAAGACCAAAAT
20900423 T
1 T
20900424 CTCTATCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.23, G:0.06, T:0.14
Consensus pattern (17 bp):
TAAACCAAGACCAAAAT
Found at i:20904765 original size:42 final size:43
Alignment explanation
Indices: 20904718--20904799 Score: 157
Period size: 42 Copynumber: 1.9 Consensus size: 43
20904708 AGTTACACGG
20904718 CGTGTGTCCCTGTTTCGAATACTCACACGGCC-GAGACATGAC
1 CGTGTGTCCCTGTTTCGAATACTCACACGGCCTGAGACATGAC
20904760 CGTGTGTCCCTGTTTCGAATACTCACACGGCCTGAGACAT
1 CGTGTGTCCCTGTTTCGAATACTCACACGGCCTGAGACAT
20904800 AGGCGTGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
42 32 0.82
43 7 0.18
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (43 bp):
CGTGTGTCCCTGTTTCGAATACTCACACGGCCTGAGACATGAC
Found at i:20909832 original size:42 final size:42
Alignment explanation
Indices: 20909753--20909835 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
20909743 TCAAAAAAAA
*
20909753 TCAAAAATCCCAAAAATATTTTCCATCTTTGTCTTTAATTTT
1 TCAAAAATCCCAAAAATATTTTCCATCATTGTCTTTAATTTT
* * *
20909795 TCAAAAAT-CCAAAAATATTTTTCTTCATTGTTTTTTAATTT
1 TCAAAAATCCCAAAAATATTTTCCATCATTG-TCTTTAATTT
20909836 GTGTTATTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 19 0.53
42 17 0.47
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (42 bp):
TCAAAAATCCCAAAAATATTTTCCATCATTGTCTTTAATTTT
Found at i:20918435 original size:26 final size:26
Alignment explanation
Indices: 20918400--20918459 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
20918390 ATTTTTCTTG
*
20918400 AAATTTTACCGGGGGTAAAATCATCA
1 AAATTTTACCGAGGGTAAAATCATCA
* *
20918426 AATTTTTACCGAGGGTAAAATTATCA
1 AAATTTTACCGAGGGTAAAATCATCA
20918452 AAATTTTA
1 AAATTTTA
20918460 TTGAGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (26 bp):
AAATTTTACCGAGGGTAAAATCATCA
Found at i:20927320 original size:7 final size:6
Alignment explanation
Indices: 20927304--20927360 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
20927294 TGTTTCCTGC
* *
20927304 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
*
20927354 AATAAT A
1 AAAAAT A
20927361 GGAAAATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
5 5 0.11
6 28 0.62
7 7 0.16
8 5 0.11
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:20929733 original size:31 final size:29
Alignment explanation
Indices: 20929665--20929736 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
20929655 CTCAAGTTAT
* *
20929665 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTATGTTTCAAATGTAAC
* **
20929694 GTTTTAGTCACTTATGTTATCATGTTGTAAC
1 ATTTTAGTCACTTATGTT-TCA-AATGTAAC
20929725 ATTTTAGTCACT
1 ATTTTAGTCACT
20929737 GAGCCGTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.49
30 2 0.06
31 16 0.46
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
ATTTTAGTCACTTATGTTTCAAATGTAAC
Found at i:20932400 original size:44 final size:44
Alignment explanation
Indices: 20932342--20932430 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
20932332 ATGGCCAAAT
20932342 CTTAAATAGGTGGCACTTTGGAATAAACACAGGTTTTGTTCTTA
1 CTTAAATAGGTGGCACTTTGGAATAAACACAGGTTTTGTTCTTA
*
20932386 CTTAAATAGGTGGCACTTTGGAATGAACACAGGTTTTGTTCTTA
1 CTTAAATAGGTGGCACTTTGGAATAAACACAGGTTTTGTTCTTA
20932430 C
1 C
20932431 ATATGCATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (44 bp):
CTTAAATAGGTGGCACTTTGGAATAAACACAGGTTTTGTTCTTA
Found at i:20943605 original size:11 final size:11
Alignment explanation
Indices: 20943542--20943603 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
20943532 ATAAATCCTT
20943542 TCTCTAATTTCC
1 TCTC-AATTTCC
20943554 TCTCAATTTCC
1 TCTCAATTTCC
* *
20943565 ACTCAATTTGC
1 TCTCAATTTCC
20943576 TCTCAATTTCC
1 TCTCAATTTCC
20943587 TCTCAAATTT-C
1 TCTC-AATTTCC
20943598 TCTCAA
1 TCTCAA
20943604 ATCCCTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
10 2 0.04
11 34 0.76
12 9 0.20
ACGTcount: A:0.23, C:0.32, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:20945485 original size:18 final size:18
Alignment explanation
Indices: 20945454--20945496 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
20945444 TGCCAGGTGC
** *
20945454 GTATCCTAGTCCTTTTAT
1 GTATCCTAACCCTTATAT
20945472 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
20945490 GTTTCCT
1 GTATCCT
20945497 TTTTCTAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:20946259 original size:29 final size:27
Alignment explanation
Indices: 20946200--20946263 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 27
20946190 TTCTTGATTT
*
20946200 ATATTATAAAAATATTATTTAATTAAA
1 ATATTATAAAAATATTATTAAATTAAA
* *
20946227 ATATTATAAATTATATTAATTAAATTAAG
1 ATATTATAAA-AATATT-ATTAAATTAAA
20946256 ATATTATA
1 ATATTATA
20946264 TTATTAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 10 0.31
28 5 0.16
29 17 0.53
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
ATATTATAAAAATATTATTAAATTAAA
Found at i:20947255 original size:3 final size:3
Alignment explanation
Indices: 20947247--20947290 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
20947237 ATTAGGTAAG
20947247 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20947291 AGATGAGTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20956944 original size:23 final size:19
Alignment explanation
Indices: 20956918--20956968 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
20956908 CCGGCCCATT
20956918 TTTTAATAAACACAAAAAATTTA
1 TTTTAA-AAACA-AAAAAA--TA
*
20956941 TTTTAAAAATAAAAAAATA
1 TTTTAAAAACAAAAAAATA
20956960 TTTTAAAAA
1 TTTTAAAAA
20956969 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 11 0.41
21 6 0.22
22 4 0.15
23 6 0.22
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTTAAAAACAAAAAAATA
Found at i:20956980 original size:10 final size:11
Alignment explanation
Indices: 20956953--20956978 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20956943 TTAAAAATAA
20956953 AAAAATATTTT
1 AAAAATATTTT
20956964 AAAAATATTTT
1 AAAAATATTTT
20956975 AAAA
1 AAAA
20956979 TAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:20957323 original size:27 final size:27
Alignment explanation
Indices: 20957293--20957347 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
20957283 TTAAGACGGG
20957293 AATCCCCTAAGCCCCTATTTATTTATT
1 AATCCCCTAAGCCCCTATTTATTTATT
20957320 AATCCCCTAAGCCCCTATTTATTTATT
1 AATCCCCTAAGCCCCTATTTATTTATT
20957347 A
1 A
20957348 TATGTGTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.40
Consensus pattern (27 bp):
AATCCCCTAAGCCCCTATTTATTTATT
Found at i:20960189 original size:18 final size:18
Alignment explanation
Indices: 20960162--20960198 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20960152 AAGTGACAAG
*
20960162 TGGTAGCTTTAGCTACAC
1 TGGTAACTTTAGCTACAC
20960180 TGGTAACTTTAGCTACAC
1 TGGTAACTTTAGCTACAC
20960198 T
1 T
20960199 TATTTGATCA
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:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (18 bp):
TGGTAACTTTAGCTACAC
Found at i:20960332 original size:45 final size:45
Alignment explanation
Indices: 20960189--20960362 Score: 271
Period size: 46 Copynumber: 3.9 Consensus size: 45
20960179 CTGGTAACTT
* *
20960189 TAGCTACACTTATTTGATCAAGTGACAAAGTGATAAGTGGTAGCC
1 TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCC
20960234 TCAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCC
1 T-AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCC
*
20960280 TTAGCTACACTTATCTGATCAAGTAAAAAAGTGATAAGTGGTAGCC
1 -TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCC
* *
20960326 TAGCTACACTTATCTGATTAAG-G-ACAAGTGATAAGTG
1 TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTG
20960363 ATCATACGTA
Statistics
Matches: 121, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
43 13 0.11
45 22 0.18
46 85 0.70
47 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (45 bp):
TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCC
Found at i:20962960 original size:21 final size:22
Alignment explanation
Indices: 20962934--20962988 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
20962924 AAATAGGGTG
20962934 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
20962955 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
*
20962976 GCAGTGAGATTAG
1 GCGGTGAGATTAG
20962989 AAACAGCAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:20967198 original size:18 final size:18
Alignment explanation
Indices: 20967175--20967209 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20967165 TTTGCAACCC
20967175 AAGGGGAAGGGGAAAGGA
1 AAGGGGAAGGGGAAAGGA
20967193 AAGGGGAAGGGGAAAGG
1 AAGGGGAAGGGGAAAGG
20967210 GGAGAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGGA
Found at i:20968923 original size:11 final size:11
Alignment explanation
Indices: 20968899--20968964 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 11
20968889 TTTCTCATAT
20968899 TTCCTCTC-AA
1 TTCCTCTCAAA
20968909 TTCCTCTCAAA
1 TTCCTCTCAAA
20968920 TTCCT-TCCAAAA
1 TTCCTCT-C-AAA
*
20968932 TT-CTCTCAAT
1 TTCCTCTCAAA
20968942 TTCCT-TCCAAAA
1 TTCCTCT-C-AAA
20968954 TT-CTCTCAAA
1 TTCCTCTCAAA
20968964 T
1 T
20968965 CTATATTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
10 18 0.39
11 17 0.37
12 11 0.24
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (11 bp):
TTCCTCTCAAA
Found at i:20968937 original size:22 final size:22
Alignment explanation
Indices: 20968907--20968964 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
20968897 ATTTCCTCTC
20968907 AATTCCTCTCAAATTCCTTCCAA
1 AATT-CTCTCAAATTCCTTCCAA
*
20968930 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAAATTCCTTCCAA
20968952 AATTCTCTCAAAT
1 AATTCTCTCAAAT
20968965 CTATATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTCTCTCAAATTCCTTCCAA
Found at i:20969013 original size:50 final size:51
Alignment explanation
Indices: 20968934--20969048 Score: 187
Period size: 50 Copynumber: 2.3 Consensus size: 51
20968924 TTCCAAAATT
* * *
20968934 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCTATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
20968985 CTCTCAATTTCCTT-AAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
*
20969035 TTCTCAATTTCCTT
1 CTCTCAATTTCCTT
20969049 TTTTAAAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 46 0.77
51 14 0.23
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTAAATTTC
Found at i:20970204 original size:7 final size:7
Alignment explanation
Indices: 20970194--20970218 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20970184 ATTCGACTGA
20970194 TATTTAG
1 TATTTAG
20970201 TATTTAG
1 TATTTAG
20970208 TATTTAG
1 TATTTAG
20970215 TATT
1 TATT
20970219 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:20971505 original size:50 final size:50
Alignment explanation
Indices: 20971415--20971986 Score: 633
Period size: 50 Copynumber: 11.3 Consensus size: 50
20971405 TATGACATTT
* * * *
20971415 AATAAAAACCCT-AGCCTAACCTAATTCATTTAAAAACCCTAAACCCTTA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
* * *
20971464 ATTAAAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCATTA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
*
20971514 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
* * * *
20971564 AATAAAAACCCTAATCGTAGCCTAATTTAATTAAAAGCCCTAATCCCTTA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
* * * *
20971614 AATAAAAACCCTAACCCTAACCTAATTCAGTTAAAAACCTTAAACCCTTA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
* *** * *
20971664 ATTAAAAACCCTAA-CCTAATTTAA-TTCATTTAAAACCCTAAACCCTTA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
* *
20971712 ATTAAAAA---T---CCTAACCTAATTTAATTAAAAACCCT-AACCCTAACCTAA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCT----T-A
* * *
20971760 TTCAATTAAAACCCTAAACCTTAAACCCTAGCCTAATTTAATTAAAAGCTCTAAACCCTTA
1 ---AA-TAAAA-AC----CC-T-AACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
*
20971821 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAATCCTAAACCCTTA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
* * *
20971871 AATAAAAACCCTAACCCTAACCTAATTCAACTAAAAACCCTAAACCCTTA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
* *
20971921 ATTAAAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTA
1 AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
20971971 AATAAAAACCCTAACC
1 AATAAAAACCCTAACC
20971987 TAATTTAATT
Statistics
Matches: 447, Mismatches: 51, Indels: 49
0.82 0.09 0.09
Matches are distributed among these distances:
43 14 0.03
44 13 0.03
45 1 0.00
47 1 0.00
48 28 0.06
49 19 0.04
50 322 0.72
51 2 0.00
52 7 0.02
56 1 0.00
57 5 0.01
58 2 0.00
61 2 0.00
62 1 0.00
65 23 0.05
66 6 0.01
ACGTcount: A:0.45, C:0.27, G:0.02, T:0.26
Consensus pattern (50 bp):
AATAAAAACCCTAACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTA
Found at i:20971619 original size:21 final size:20
Alignment explanation
Indices: 20971590--20971631 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
20971580 GTAGCCTAAT
* *
20971590 TTAATTAAAAGCCCTAATCCC
1 TTAAATAAAAACCCTAA-CCC
20971611 TTAAATAAAAACCCTAACCC
1 TTAAATAAAAACCCTAACCC
20971631 T
1 T
20971632 AACCTAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.43, C:0.29, G:0.02, T:0.26
Consensus pattern (20 bp):
TTAAATAAAAACCCTAACCC
Found at i:20971701 original size:71 final size:69
Alignment explanation
Indices: 20971656--20971936 Score: 156
Period size: 71 Copynumber: 4.1 Consensus size: 69
20971646 AAAAACCTTA
** * *
20971656 AACC-CTTAATTAAAAACCCTAA-CCTAATTTAATTCATTTAAAACCCTAAACCCTTAATTAAAA
1 AACCACTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCT-AACCATTAATTAAAA
20971719 ATCCT
65 ATCCT
*
20971724 AACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTAAACC-----TT--
1 AACC--ACTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCT-AACCATTAATTAA
*
20971782 AAACCCT
63 AAATCCT
* * * * * * **** *
20971789 AGCCTAATTTAATTAAAAGCTCTAAACCCTTAA-ATAA--AAACCCTAACCCTAGCCTAATTTAA
1 AACC--ACTTAATTAAAAACCCT-AACCC-TAACCTAATTCAATTAAAACCCTAACC--A-TTAA
20971851 TTAAAAATCCT
59 TTAAAAATCCT
* * *
20971862 AAACC-CTTAAATAAAAACCCTAACCCTAACCTAATTCAACTAAAAACCCTAAACCCTTAATTAA
1 -AACCACTTAATTAAAAACCCTAACCCTAACCTAATTCAA-TTAAAACCCT-AACCATTAATTAA
*
20971926 AAACCCT
63 AAATCCT
20971933 AACC
1 AACC
20971937 CTAGCCTAAT
Statistics
Matches: 161, Mismatches: 30, Indels: 42
0.69 0.13 0.18
Matches are distributed among these distances:
63 3 0.02
64 8 0.05
65 26 0.16
66 8 0.05
67 5 0.03
68 4 0.02
69 3 0.02
70 12 0.07
71 45 0.28
72 29 0.18
73 12 0.07
74 6 0.04
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.26
Consensus pattern (69 bp):
AACCACTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTAACCATTAATTAAAAA
TCCT
Found at i:20971739 original size:23 final size:23
Alignment explanation
Indices: 20971626--20971750 Score: 100
Period size: 23 Copynumber: 5.4 Consensus size: 23
20971616 TAAAAACCCT
* *
20971626 AACCCTAACCTAATTCAGTTAAA
1 AACCCTAACCTAATTTAATTAAA
* *
20971649 AACCTTAAACC---CTTAATTAAA
1 AACCCT-AACCTAATTTAATTAAA
20971670 AACCCTAACCTAATTTAATTCATTTAA
1 AACCCTAACCTAATTTAATT-A---AA
*
20971697 AACCCTAAACC---CTTAATTAAA
1 AACCCT-AACCTAATTTAATTAAA
*
20971718 AATCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
20971741 AACCCTAACC
1 AACCCTAACC
20971751 CTAACCTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
20 8 0.10
21 19 0.24
23 29 0.36
24 6 0.08
25 6 0.08
27 8 0.10
28 4 0.05
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.29
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:20971787 original size:36 final size:38
Alignment explanation
Indices: 20971740--20971822 Score: 111
Period size: 36 Copynumber: 2.3 Consensus size: 38
20971730 ATTTAATTAA
20971740 AAACCC-T-AACCCTAACCTAATTCAATTAAAA-CCCT
1 AAACCCTTAAACCCTAACCTAATTCAATTAAAAGCCCT
* * *
20971775 AAA-CCTTAAACCCTAGCCTAATTTAATTAAAAGCTCT
1 AAACCCTTAAACCCTAACCTAATTCAATTAAAAGCCCT
20971812 AAACCCTTAAA
1 AAACCCTTAAA
20971823 TAAAAACCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 2 0.05
35 4 0.10
36 22 0.54
37 6 0.15
38 7 0.17
ACGTcount: A:0.43, C:0.29, G:0.02, T:0.25
Consensus pattern (38 bp):
AAACCCTTAAACCCTAACCTAATTCAATTAAAAGCCCT
Found at i:20971871 original size:257 final size:259
Alignment explanation
Indices: 20971526--20971996 Score: 784
Period size: 257 Copynumber: 1.8 Consensus size: 259
20971516 TAAAAACCCT
* *
20971526 AACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAATCGTAGCCTAATT
1 AACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAACCCTAGCCTAATT
* * ** *
20971591 TAATTAAAAGCCCTAATCCCTTAAATAAAAACCCTAACCCTAACCTAATTCAGTTAAAAACCTTA
66 TAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAACTAAAAACCCTA
** * *
20971656 AACCCTTAATTAAAAACCCTAA-CCTAATTTAATTCATTTAAAA-CCCTAAACCCTTAATTAAAA
131 AACCCTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAAGCCCTAAACCCTTAAATAAAA
*
20971719 ATCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTAAACCTTA
196 ACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTAAACCTTA
*
20971783 AACCCTAGCCTAATTTAATTAAAAGCTCTAAACCCTTAAATAAAAACCCTAACCCTAGCCTAATT
1 AACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAACCCTAGCCTAATT
*
20971848 TAATTAAAAATCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAACTAAAAACCCTA
66 TAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAACTAAAAACCCTA
* *
20971913 AACCCTTAATTAAAAACCCTAACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAA
131 AACCCTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAAGCCCTAAACCCTTAAATAAAA
20971978 ACCCTAACCTAATTTAATT
196 ACCCTAACCTAATTTAATT
20971997 CATTTAAAAA
Statistics
Matches: 196, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
257 143 0.73
258 16 0.08
259 37 0.19
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.27
Consensus pattern (259 bp):
AACCCTAGCCTAATTTAATTAAAAGCCCTAAACCCTTAAATAAAAACCCTAACCCTAGCCTAATT
TAATTAAAAACCCTAAACCCTTAAATAAAAACCCTAACCCTAACCTAATTCAACTAAAAACCCTA
AACCCTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAAGCCCTAAACCCTTAAATAAAA
ACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTAAACCTTA
Found at i:20971876 original size:21 final size:20
Alignment explanation
Indices: 20971847--20971938 Score: 58
Period size: 21 Copynumber: 4.0 Consensus size: 20
20971837 CTAGCCTAAT
* *
20971847 TTAATTAAAAATCCTAAACCC
1 TTAAATAAAAACCCT-AACCC
20971868 TTAAATAAAAACCCTAACCC
1 TTAAATAAAAACCCTAACCC
20971888 TAACCTAATTCAACTAAAAACCCTAAACCC
1 T----T-A---AA-TAAAAACCCT-AACCC
*
20971918 TTAATTAAAAACCCTAACCC
1 TTAAATAAAAACCCTAACCC
20971938 T
1 T
20971939 AGCCTAATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 21
0.71 0.04 0.26
Matches are distributed among these distances:
20 12 0.21
21 23 0.40
22 1 0.02
24 1 0.02
25 2 0.03
26 1 0.02
28 2 0.03
29 10 0.17
30 6 0.10
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (20 bp):
TTAAATAAAAACCCTAACCC
Found at i:20972251 original size:20 final size:21
Alignment explanation
Indices: 20972228--20972277 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
20972218 ATTTTAAAAT
*
20972228 ATTTTTTACATAC-TTTTTTA
1 ATTTTTTAAATACTTTTTTTA
*
20972248 A-TTTTAAAATACTTTTTTTA
1 ATTTTTTAAATACTTTTTTTA
20972268 ATTTTTTAAA
1 ATTTTTTAAA
20972278 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.36
20 9 0.36
21 7 0.28
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTTAAATACTTTTTTTA
Found at i:20972252 original size:19 final size:20
Alignment explanation
Indices: 20972230--20972273 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20972220 TTTAAAATAT
*
20972230 TTTTTACATAC-TTTTTTAA
1 TTTTTAAATACTTTTTTTAA
*
20972249 TTTTAAAATACTTTTTTTAA
1 TTTTTAAATACTTTTTTTAA
20972269 TTTTT
1 TTTTT
20972274 TAAAATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTAAATACTTTTTTTAA
Found at i:20972281 original size:30 final size:29
Alignment explanation
Indices: 20972218--20972289 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
20972208 TATTTTTTTT
*
20972218 ATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTTTAAAATATTTTTTACATA-TTTTTAA
20972248 ATTTTAAAATACTTTTTTTA-AT-TTTTTAAA
1 ATTTTAAAATA--TTTTTTACATATTTTT-AA
20972278 ATTTTTAAAATA
1 A-TTTTAAAATA
20972290 AAAATGGGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 5 0.14
30 13 0.35
31 12 0.32
32 7 0.19
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTTAAAATATTTTTTACATATTTTTAA
Found at i:20972687 original size:116 final size:116
Alignment explanation
Indices: 20972483--20972700 Score: 400
Period size: 116 Copynumber: 1.9 Consensus size: 116
20972473 AACCTTAACG
*
20972483 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
*
20972548 ATTTTACTAACCATTAGTACAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
* *
20972599 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTATATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
20972664 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
20972701 CAATTTATCA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 98 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
Found at i:20972717 original size:17 final size:18
Alignment explanation
Indices: 20972676--20972717 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
20972666 TTTACTAACC
* *
20972676 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
20972694 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
20972711 ATTAATA
1 ATTAATA
20972718 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:20977253 original size:21 final size:21
Alignment explanation
Indices: 20977228--20977270 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
20977218 ATTTAAGAAT
20977228 TTTTTATTA-AATTATATATTA
1 TTTTTA-TAGAATTATATATTA
*
20977249 TTTTTATAGTATTATATATTA
1 TTTTTATAGAATTATATATTA
20977270 T
1 T
20977271 GATTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTATAGAATTATATATTA
Found at i:20977329 original size:20 final size:20
Alignment explanation
Indices: 20977229--20977340 Score: 78
Period size: 20 Copynumber: 5.8 Consensus size: 20
20977219 TTTAAGAATT
20977229 TTTTATTAAATTATATATTA
1 TTTTATTAAATTATATATTA
*
20977249 TTTT-TATAGTATTATATATTA
1 TTTTAT-TA-AATTATATATTA
*
20977270 TGATTT-TTTAATTA-ATA-TA
1 T--TTTATTAAATTATATATTA
* * * *
20977289 -ATAATTATATTA-AGA--A
1 TTTTATTAAATTATATATTA
20977305 TTTTATTAAATTATATATTA
1 TTTTATTAAATTATATATTA
20977325 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
20977341 TTAATAATAA
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
16 2 0.03
17 17 0.24
18 2 0.03
19 3 0.04
20 26 0.37
21 16 0.23
22 1 0.01
23 4 0.06
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATTAAATTATATATTA
Found at i:20977346 original size:55 final size:54
Alignment explanation
Indices: 20977259--20977406 Score: 147
Period size: 58 Copynumber: 2.6 Consensus size: 54
20977249 TTTTTATAGT
* * * *
20977259 ATTATATATTATGATTT-TTTAATTA-ATATAATAATTATATTAAGAATTTTATTAA
1 ATTATATATTAT--TTTATTAAATTATATTTAATAATTATATTAA-AATATGATTAA
* *
20977314 ATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGGTTAA
1 ATTATATATTATTTTATTAAATTATA-TT--TAATAATTATATTAAAATATGATTAA
* *
20977371 ATTATTTATTATTTTTATTAAATTATTTTTAATAAT
1 ATTATATATTA-TTTTATTAAATTATATTTAATAAT
20977407 AATTTTATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
53 3 0.04
54 7 0.09
55 20 0.25
56 1 0.01
57 20 0.25
58 28 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (54 bp):
ATTATATATTATTTTATTAAATTATATTTAATAATTATATTAAAATATGATTAA
Found at i:20977389 original size:58 final size:57
Alignment explanation
Indices: 20977286--20977420 Score: 189
Period size: 58 Copynumber: 2.3 Consensus size: 57
20977276 TTTAATTAAT
* *
20977286 ATAATAATTATATTAAGAATTTTATTAAATTATATATTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAATTATATTTA
* * * *
20977344 ATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTTATTAAATTATTTTTA
1 ATAATAATTATATTAAAATATGATTAAATTATATATTA-TTTTATTAAATTATATTTA
*
20977402 ATAATAATTTTATTAAAAT
1 ATAATAATTATATTAAAAT
20977421 TTAATAACAA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 18 0.26
58 50 0.74
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAATTATATTTA
Found at i:20977397 original size:14 final size:14
Alignment explanation
Indices: 20977378--20977418 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
20977368 TAAATTATTT
20977378 ATTATTTTTATTAA
1 ATTATTTTTATTAA
*
20977392 ATTATTTTTAAT-A
1 ATTATTTTTATTAA
*
20977405 A-TAATTTTATTAA
1 ATTATTTTTATTAA
20977418 A
1 A
20977419 ATTTAATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTTTTATTAA
Found at i:20977608 original size:16 final size:16
Alignment explanation
Indices: 20977587--20977657 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
20977577 TGAATTACTG
*
20977587 ATTACAGCT-TCATTCC
1 ATTACAGCTCT-ATTCA
*
20977603 ATTACAACTCTATTCA
1 ATTACAGCTCTATTCA
*
20977619 ATTACAAC-CTTATTCA
1 ATTACAGCTC-TATTCA
* *
20977635 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCA
20977651 ATTACAG
1 ATTACAG
20977658 TTAACCAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.02
16 45 0.94
17 2 0.04
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:20977623 original size:32 final size:31
Alignment explanation
Indices: 20977587--20977657 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
20977577 TGAATTACTG
* *
20977587 ATTACAGCTTCATTCCATTACAACTCTATTCA
1 ATTACAGCTT-ATTCAATTACAACCCTATTCA
* * *
20977619 ATTACAACCTTATTCAATTACAGCCCTATTCC
1 ATTAC-AGCTTATTCAATTACAACCCTATTCA
20977651 ATTACAG
1 ATTACAG
20977658 TTAACCAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
31 1 0.03
32 27 0.84
33 4 0.12
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.35
Consensus pattern (31 bp):
ATTACAGCTTATTCAATTACAACCCTATTCA
Found at i:20979046 original size:3 final size:3
Alignment explanation
Indices: 20978940--20979035 Score: 165
Period size: 3 Copynumber: 32.0 Consensus size: 3
20978930 CGACGACGAC
*
20978940 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
20978988 GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
20979036 ACCTAAGAAG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20980065 original size:22 final size:22
Alignment explanation
Indices: 20979980--20980065 Score: 63
Period size: 22 Copynumber: 3.9 Consensus size: 22
20979970 AAAAAATATA
*
20979980 AAATACATATAATAATAAA-TTT
1 AAATA-ATATAAAAATAAATTTT
*
20980002 AAA-AATAT-AAAA-AAATTTG
1 AAATAATATAAAAATAAATTTT
* *
20980021 ACAAAAATAATAATATATAAAATTTT
1 A-AATAAT-ATAA-AAAT-AAATTTT
20980047 AAATAATATAAAAATAAAT
1 AAATAATATAAAAATAAAT
20980066 AATATTTAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
18 3 0.06
19 6 0.12
20 6 0.12
21 4 0.08
22 9 0.18
23 4 0.08
24 6 0.12
25 5 0.10
26 7 0.14
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (22 bp):
AAATAATATAAAAATAAATTTT
Found at i:20980066 original size:15 final size:15
Alignment explanation
Indices: 20980023--20980070 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
20980013 AAAATTTGAC
20980023 AAAAAT-AATAATAT
1 AAAAATAAATAATAT
20980037 ATAAAATTTTAAATAATAT
1 A-AAAA---TAAATAATAT
20980056 AAAAATAAATAATAT
1 AAAAATAAATAATAT
20980071 TTAGTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.03
15 14 0.48
18 5 0.17
19 9 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATAAATAATAT
Found at i:20980313 original size:30 final size:29
Alignment explanation
Indices: 20980274--20980335 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
20980264 AAAAATATAA
20980274 AATAATAAATTTAAAAT-TTATATTAAAATT
1 AATAATAAA--TAAAATATTATATTAAAATT
* *
20980304 AATATTAAATAAAATAATTATATTAATATT
1 AATAATAAATAAAAT-ATTATATTAAAATT
20980334 AA
1 AA
20980336 AAAAAGCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.21
30 22 0.79
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATAATAAATAAAATATTATATTAAAATT
Found at i:20980501 original size:29 final size:29
Alignment explanation
Indices: 20980469--20980546 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
20980459 ATATTAATAT
*
20980469 AAAATTTAAATTTATTATTATACT-TTTTG
1 AAAATTTATATTTATTATTATA-TATTTTG
* *
20980498 AAAATGTT-TATTTATTTTTATATATTTTT
1 AAAAT-TTATATTTATTATTATATATTTTG
*
20980527 AAATTTTATATATTATTATT
1 AAAATTTATAT-TTATTATT
20980547 TATTGTGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
28 3 0.08
29 28 0.70
30 9 0.22
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (29 bp):
AAAATTTATATTTATTATTATATATTTTG
Found at i:20980532 original size:51 final size:51
Alignment explanation
Indices: 20980473--20980628 Score: 190
Period size: 53 Copynumber: 2.9 Consensus size: 51
20980463 TAATATAAAA
*
20980473 TTTAAATTTATTATTATACTTTTTGAAAATGTTTATTTATTTTTATAT-ATT
1 TTTAAATTTATTATTATATTTTTTGAAAAT-TTTATTTATTTTTATATAATT
*
20980524 TTTAAATTTTATATATTATTATTTATTGTGAACAATATT-TTTATTTTTATATAATT
1 TTTAAA-TTTAT-TATTA-TATTT-TT-TGAA-AATTTTATTTATTTTTATATAATT
*
20980580 TTTAAATTTATTATTATATTTTTTAGAAAATATTTATCTATTTTTATAT
1 TTTAAATTTATTATTATATTTTTT-GAAAAT-TTTATTTATTTTTATAT
20980629 GTATTTTTTG
Statistics
Matches: 91, Mismatches: 4, Indels: 18
0.81 0.04 0.16
Matches are distributed among these distances:
51 10 0.11
52 12 0.13
53 22 0.24
54 9 0.10
55 20 0.22
56 15 0.16
57 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (51 bp):
TTTAAATTTATTATTATATTTTTTGAAAATTTTATTTATTTTTATATAATT
Found at i:20980602 original size:21 final size:22
Alignment explanation
Indices: 20980563--20980604 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
20980553 GAACAATATT
*
20980563 TTTATTTTTATATAATTTTTAAA
1 TTTATTATTATAT-ATTTTTAAA
20980586 TTTATTATTATAT-TTTTTA
1 TTTATTATTATATATTTTTA
20980605 GAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATTATTATATATTTTTAAA
Found at i:20981808 original size:53 final size:53
Alignment explanation
Indices: 20981732--20981836 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
20981722 TCTTTTTCAA
*
20981732 TTTGTAAGACACAATGTTGTCGGTATTGAACAAAATTGTTTAACTATTTTTTG
1 TTTGTAAGACACAATGTTGTCGGTATTGAACAAAATCGTTTAACTATTTTTTG
* * * * *
20981785 TTTGTAATATACAATGTTTTCGGTTTTGAACAAAATCGTTTAACTTTTTTTT
1 TTTGTAAGACACAATGTTGTCGGTATTGAACAAAATCGTTTAACTATTTTTT
20981837 TAGTATTGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (53 bp):
TTTGTAAGACACAATGTTGTCGGTATTGAACAAAATCGTTTAACTATTTTTTG
Found at i:20986459 original size:3 final size:3
Alignment explanation
Indices: 20986451--20986480 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20986441 GGTTTGAAAC
20986451 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20986481 AGCTTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20992891 original size:21 final size:19
Alignment explanation
Indices: 20992867--20992905 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
20992857 TAGACTATCG
*
20992867 AGAAAATATAAGTTACAACAA
1 AGAAAACAT-AGTTA-AACAA
20992888 AGAAAACATAGTTAAACA
1 AGAAAACATAGTTAAACA
20992906 GAGATTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (19 bp):
AGAAAACATAGTTAAACAA
Found at i:20994376 original size:19 final size:19
Alignment explanation
Indices: 20994354--20994412 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
20994344 ACATTTAATT
*
20994354 AATTTTTTTAAATTTTAAA
1 AATTATTTTAAATTTTAAA
**
20994373 AATTATTTTAAAAATTAAA
1 AATTATTTTAAATTTTAAA
*
20994392 AA-TAATTTAAATTATTAAA
1 AATTATTTTAAATT-TTAAA
20994411 AA
1 AA
20994413 GTATAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 8 0.24
19 25 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTATTTTAAATTTTAAA
Found at i:20994382 original size:12 final size:12
Alignment explanation
Indices: 20994365--20994389 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20994355 ATTTTTTTAA
20994365 ATTTTAAAAATT
1 ATTTTAAAAATT
20994377 ATTTTAAAAATT
1 ATTTTAAAAATT
20994389 A
1 A
20994390 AAAATAATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAAATT
Found at i:20994889 original size:11 final size:11
Alignment explanation
Indices: 20994873--20994898 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20994863 TTATTTTTAA
20994873 TTTTAAAATAC
1 TTTTAAAATAC
20994884 TTTTAAAATAC
1 TTTTAAAATAC
20994895 TTTT
1 TTTT
20994899 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:20994933 original size:40 final size:40
Alignment explanation
Indices: 20994866--20995006 Score: 203
Period size: 41 Copynumber: 3.4 Consensus size: 40
20994856 TATTTTTTTA
*
20994866 TTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAATTT
1 TTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAATTT
* *
20994907 TTTTTAATTTTAAAA-ATTTTTTAAATACTTTTTTACTTTT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA-ATTT
20994947 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAATTTT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA-TTT
20994988 TGTTTTAATTTTTAAAATA
1 T-TTTTAA-TTTTAAAATA
20995007 AATTTTTGGT
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
39 7 0.08
40 29 0.32
41 38 0.42
42 6 0.07
43 10 0.11
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (40 bp):
TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAATTT
Found at i:20997441 original size:20 final size:20
Alignment explanation
Indices: 20997413--20997450 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20997403 TATTTTCCAA
*
20997413 TAAATCATTTTACAGAAAAG
1 TAAAACATTTTACAGAAAAG
*
20997433 TAAAACATTTTCCAGAAA
1 TAAAACATTTTACAGAAA
20997451 TCATTTTACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (20 bp):
TAAAACATTTTACAGAAAAG
Found at i:20997455 original size:34 final size:35
Alignment explanation
Indices: 20997399--20997465 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
20997389 CAAACACCAG
* *
20997399 AAAATATTTTCCAATAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAAGAAATCATTTTACAGAAAAGT
*
20997434 AAAACATTTTCC-AGAAATCATTTTACGGAAAA
1 AAAACATTTTCCAAGAAATCATTTTACAGAAAA
20997466 TATTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAAGAAATCATTTTACAGAAAAGT
Found at i:21002503 original size:23 final size:23
Alignment explanation
Indices: 21002477--21002526 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
21002467 ACCTTTATCT
21002477 ATGTAAACCAACGAATATTTAAC
1 ATGTAAACCAACGAATATTTAAC
*** * *
21002500 ATGTGGTCCAATGAATATTTAAG
1 ATGTAAACCAACGAATATTTAAC
21002523 ATGT
1 ATGT
21002527 GATGCCATCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (23 bp):
ATGTAAACCAACGAATATTTAAC
Found at i:21002527 original size:23 final size:23
Alignment explanation
Indices: 21002484--21002527 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21002474 TCTATGTAAA
21002484 CCAACGAATATTTAACATGTGGT
1 CCAACGAATATTTAACATGTGGT
* *
21002507 CCAATGAATATTTAAGATGTG
1 CCAACGAATATTTAACATGTG
21002528 ATGCCATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (23 bp):
CCAACGAATATTTAACATGTGGT
Found at i:21003026 original size:24 final size:24
Alignment explanation
Indices: 21002999--21003047 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
21002989 AATTTAATTG
*
21002999 ATTTTGATTTTTATA-ATTTTTAAT
1 ATTTTAATTTTT-TAGATTTTTAAT
21003023 ATTTTAATTTTTTAGATTTTTAAT
1 ATTTTAATTTTTTAGATTTTTAAT
21003047 A
1 A
21003048 AATTTTAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
ATTTTAATTTTTTAGATTTTTAAT
Found at i:21003030 original size:34 final size:32
Alignment explanation
Indices: 21002984--21003054 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 32
21002974 AACAAAAACC
*
21002984 TTTTAAATTTAATTGATTTT-GATTTTT-ATAAT
1 TTTTAAATTTAATT--TTTTAGATTTTTAATAAA
21003016 TTTTAATATTTTAATTTTTTAGATTTTTAATAAA
1 TTTTAA-A-TTTAATTTTTTAGATTTTTAATAAA
21003050 TTTTA
1 TTTTA
21003055 GATAGTGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
32 10 0.29
33 8 0.24
34 16 0.47
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.63
Consensus pattern (32 bp):
TTTTAAATTTAATTTTTTAGATTTTTAATAAA
Found at i:21003045 original size:16 final size:16
Alignment explanation
Indices: 21003000--21003046 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
21002990 ATTTAATTGA
*
21003000 TTTT-GATTTTTATAAT
1 TTTTAGATTTTTA-ATT
21003016 TTTTA-ATATTTTAATT
1 TTTTAGAT-TTTTAATT
21003032 TTTTAGATTTTTAAT
1 TTTTAGATTTTTAAT
21003047 AAATTTTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (16 bp):
TTTTAGATTTTTAATT
Found at i:21012624 original size:21 final size:21
Alignment explanation
Indices: 21012598--21012648 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
21012588 CAACGGTGGA
21012598 GGTGAGATTGGATACTGTAGC
1 GGTGAGATTGGATACTGTAGC
21012619 GGTGAGATTGGATACTGTAGC
1 GGTGAGATTGGATACTGTAGC
*
21012640 AGTGAGATT
1 GGTGAGATT
21012649 AGAAACAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.37, T:0.29
Consensus pattern (21 bp):
GGTGAGATTGGATACTGTAGC
Found at i:21017842 original size:16 final size:17
Alignment explanation
Indices: 21017816--21017852 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
21017806 GTTTTTTCCG
21017816 GGAGAAGTGGGAAAGAA
1 GGAGAAGTGGGAAAGAA
*
21017833 GGAG-AGTGGGAAAGCA
1 GGAGAAGTGGGAAAGAA
21017849 GGAG
1 GGAG
21017853 TTGACAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.41, C:0.03, G:0.51, T:0.05
Consensus pattern (17 bp):
GGAGAAGTGGGAAAGAA
Found at i:21021184 original size:42 final size:42
Alignment explanation
Indices: 21021133--21021293 Score: 186
Period size: 42 Copynumber: 3.8 Consensus size: 42
21021123 TAATAAATAT
* *
21021133 ATTTATTTTTTAAATTTTAAAATATTTTTTACATAC-TTTTTTA
1 ATTT-TTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTA
21021176 ATTTTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 A-TTTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
**
21021219 A-TTTTTTTTAATTTTAAAATATTTTTAAAAATA-TTTTTAAA
1 ATTTTTTTTTAATTTTAAAATATTTTT-AAAATACTTTTTTTA
* *
21021260 ATACTTTTTTTAATTTTTTAAA-ATTTTTAAAATA
1 AT-TTTTTTTTAA-TTTTAAAATATTTTTAAAATA
21021294 AAAATGGGCC
Statistics
Matches: 106, Mismatches: 6, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
41 32 0.30
42 34 0.32
43 30 0.28
44 10 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (42 bp):
ATTTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:21021215 original size:53 final size:51
Alignment explanation
Indices: 21021147--21021294 Score: 129
Period size: 53 Copynumber: 2.8 Consensus size: 51
21021137 ATTTTTTAAA
* ****
21021147 TTTTAAAATATTTTTTACATACTTTTTTAATTTTTTTTTTAATTTT-AAAATAT
1 TTTTAAAATACTTTTTA-AT-CTTTTTTAA-TTTTAAAATAATTTTAAAAATAT
* *
21021200 TTTTAAAATACTTTTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAAATAT
1 TTTTAAAATAC--TTTTTAATCTTTTTTAATTTTAAAATAATTTTAAAAATAT
*
21021253 TTTTAAAATACTTTTTTTAAT-TTTTTAAAATTTTTAAAATAA
1 TTTTAAAATAC--TTTTTAATCTTTTT-TAA-TTTTAAAATAA
21021295 AAATGGGCCG
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
52 15 0.19
53 48 0.59
54 12 0.15
55 6 0.07
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (51 bp):
TTTTAAAATACTTTTTAATCTTTTTTAATTTTAAAATAATTTTAAAAATAT
Found at i:21021256 original size:30 final size:30
Alignment explanation
Indices: 21021200--21021256 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
21021190 TTTAAAATAT
** *
21021200 TTTTAAAATACTTTTTTTAATTTTTTTTAA
1 TTTTAAAATACTTTTTAAAATATTTTTTAA
21021230 TTTTAAAATA-TTTTTAAAAATATTTTT
1 TTTTAAAATACTTTTT-AAAATATTTTT
21021257 AAAATACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTAAAATACTTTTTAAAATATTTTTTAA
Found at i:21021267 original size:12 final size:11
Alignment explanation
Indices: 21021189--21021293 Score: 80
Period size: 12 Copynumber: 9.9 Consensus size: 11
21021179 TTTTTTTTAA
21021189 TTTTAAAATAT
1 TTTTAAAATAT
21021200 TTTTAAAATACT
1 TTTTAAAATA-T
**
21021212 TTTTTTAAT-T
1 TTTTAAAATAT
* *
21021222 TTTT---TTAA
1 TTTTAAAATAT
21021230 TTTTAAAATAT
1 TTTTAAAATAT
21021241 TTTTAAAAATAT
1 TTTT-AAAATAT
21021253 TTTTAAAATACT
1 TTTTAAAATA-T
**
21021265 TTTTTTAAT-T
1 TTTTAAAATAT
21021275 TTTT-AAA-AT
1 TTTTAAAATAT
21021284 TTTTAAAATA
1 TTTTAAAATA
21021294 AAAATGGGCC
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
7 1 0.01
8 4 0.05
9 7 0.09
10 13 0.17
11 23 0.31
12 27 0.36
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:21021278 original size:23 final size:22
Alignment explanation
Indices: 21021189--21021268 Score: 60
Period size: 23 Copynumber: 3.7 Consensus size: 22
21021179 TTTTTTTTAA
*
21021189 TTTTAAAATATTTTTAAAATACT
1 TTTTAAAATATTTTTAAAA-AAT
** **
21021212 TTTTTTAAT-TTTTT--TTAA-
1 TTTTAAAATATTTTTAAAAAAT
21021230 TTTTAAAATATTTTTAAAAATAT
1 TTTTAAAATATTTTTAAAAA-AT
21021253 TTTTAAAATACTTTTT
1 TTTTAAAATA-TTTTT
21021269 TTAATTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 11
0.68 0.15 0.18
Matches are distributed among these distances:
18 7 0.17
19 6 0.14
21 1 0.02
22 6 0.14
23 17 0.40
24 5 0.12
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAAATATTTTTAAAAAAT
Found at i:21024176 original size:26 final size:25
Alignment explanation
Indices: 21024129--21024180 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
21024119 CAAACAGGAC
*
21024129 ATAAGAAATTAACATCAGAATATAAA
1 ATAAGAAATTAACATCAAAATA-AAA
* *
21024155 ATAAGAACTTAACATTAAAATAAAA
1 ATAAGAAATTAACATCAAAATAAAA
21024180 A
1 A
21024181 CAAATCACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.23
Consensus pattern (25 bp):
ATAAGAAATTAACATCAAAATAAAA
Found at i:21026803 original size:21 final size:22
Alignment explanation
Indices: 21026777--21026823 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
21026767 CTCTGCTCAA
*
21026777 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
21026798 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
21026820 ACTC
1 ACTC
21026824 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:21030180 original size:25 final size:25
Alignment explanation
Indices: 21030152--21030202 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
21030142 TGCAAAATCA
*
21030152 ACATCGAGTCTAGTGGAATTAAAGT
1 ACATCGAGTCGAGTGGAATTAAAGT
21030177 ACATCGAGTCGAGTGGAATTAAAGT
1 ACATCGAGTCGAGTGGAATTAAAGT
21030202 A
1 A
21030203 TCTCGTGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (25 bp):
ACATCGAGTCGAGTGGAATTAAAGT
Found at i:21034917 original size:24 final size:26
Alignment explanation
Indices: 21034857--21034917 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
21034847 CGATACTCAA
*
21034857 CTCGTATGAGCTTACCGATTTTTCAG
1 CTCGTATGAGCTTACCGATTTTACAG
* *
21034883 CTCGGAGGAGCTTACC-A-TTTACAG
1 CTCGTATGAGCTTACCGATTTTACAG
21034907 CTCGTATGAGC
1 CTCGTATGAGC
21034918 ATACATGTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 15 0.50
25 1 0.03
26 14 0.47
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (26 bp):
CTCGTATGAGCTTACCGATTTTACAG
Found at i:21056185 original size:15 final size:15
Alignment explanation
Indices: 21056165--21056195 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21056155 CCAACCTTCA
21056165 AATTTTACCTCAATT
1 AATTTTACCTCAATT
21056180 AATTTTACCTCAATT
1 AATTTTACCTCAATT
21056195 A
1 A
21056196 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:21058455 original size:11 final size:11
Alignment explanation
Indices: 21058439--21058465 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21058429 TAGAAATTAG
21058439 TTTGTGAAACT
1 TTTGTGAAACT
21058450 TTTGTGAAACT
1 TTTGTGAAACT
21058461 TTTGT
1 TTTGT
21058466 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:21059998 original size:93 final size:92
Alignment explanation
Indices: 21059866--21060060 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
21059856 TTGATTTTAG
* *
21059866 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
21059930 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
21059958 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
21060023 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
21060051 CAAATTCATA
1 TAAATTCATA
21060061 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:21060118 original size:17 final size:17
Alignment explanation
Indices: 21060093--21060126 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21060083 ATAATTTTAA
*
21060093 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
21060110 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
21060127 TTAATATTAA
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:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:21060128 original size:15 final size:16
Alignment explanation
Indices: 21060093--21060131 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
21060083 ATAATTTTAA
*
21060093 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
21060110 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
21060125 ATTTAAT
1 ATTTAAT
21060132 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:21060135 original size:17 final size:18
Alignment explanation
Indices: 21060097--21060136 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
21060087 TTTTAAATTT
*
21060097 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
21060115 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
21060131 TATTAA
1 TATTAA
21060137 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:21060251 original size:15 final size:15
Alignment explanation
Indices: 21060216--21060267 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
21060206 TTAAGAATTT
*
21060216 TATTAAATTAT-ATA
1 TATTTAATTATAATA
21060230 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
21060244 TATTTAATAATAAT-
1 TATTTAATTATAATA
21060258 TATGTTAATT
1 TAT-TTAATT
21060268 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Done.