Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 279 of 290
Found at i:89204693 original size:26 final size:29
Alignment explanation
Indices: 89204655--89204714 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
89204645 TATGTAAATA
*
89204655 TTTTAATACTATGTTAT-GA-ATATATAT
1 TTTTTATACTATGTTATAGACATATATAT
*
89204682 TTTTTATA-TATGTTATATACATATATAT
1 TTTTTATACTATGTTATAGACATATATAT
89204710 TTTTT
1 TTTTT
89204715 TAATATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.28
27 8 0.28
28 13 0.45
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTTTATACTATGTTATAGACATATATAT
Found at i:89204720 original size:15 final size:15
Alignment explanation
Indices: 89204673--89204730 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
89204663 CTATGTTATG
89204673 AATATATA-TTTTTT
1 AATATATATTTTTTT
* * *
89204687 -ATATAT-GTTATAT
1 AATATATATTTTTTT
89204700 ACATATATATTTTTTT
1 A-ATATATATTTTTTT
89204716 AATATTATATTTTTT
1 AATA-TATATTTTTT
89204731 ATATATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
13 10 0.29
15 9 0.26
16 15 0.44
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
AATATATATTTTTTT
Found at i:89204723 original size:26 final size:28
Alignment explanation
Indices: 89204674--89204725 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
89204664 TATGTTATGA
*
89204674 ATATATATTTTTTATATATGTTATATAC
1 ATATATATTTTTTATATATATTATATAC
89204702 ATATATATTTTTT-TA-ATATTATAT
1 ATATATATTTTTTATATATATTATAT
89204726 TTTTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
27 2 0.09
28 13 0.57
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
ATATATATTTTTTATATATATTATATAC
Found at i:89204726 original size:16 final size:16
Alignment explanation
Indices: 89204702--89204739 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
89204692 TGTTATATAC
89204702 ATATA-TAT-TTTTTT
1 ATATATTATATTTTTT
89204716 A-ATATTATATTTTTT
1 ATATATTATATTTTTT
89204731 ATATATTAT
1 ATATATTAT
89204740 TATGTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.14
14 4 0.19
15 7 0.33
16 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATATATTATATTTTTT
Found at i:89204763 original size:22 final size:22
Alignment explanation
Indices: 89204721--89204834 Score: 81
Period size: 23 Copynumber: 5.0 Consensus size: 22
89204711 TTTTTAATAT
* *
89204721 TATATTTTTTATATATTATTATG
1 TATATATTTTA-ATATCATTATG
89204744 TATATATTTTAATATCATTA-G
1 TATATATTTTAATATCATTATG
*
89204765 TTATATATTTTTATACTAT-TTTATG
1 -TATATA-TTTTA-A-TATCATTATG
*
89204790 TATATATTTCTAATATTATATAT-
1 TATATATTT-TAATATCAT-TATG
* *
89204813 TAAATATTTCTAATACCATTAT
1 TATATATTT-TAATATCATTAT
89204835 TATTTATATA
Statistics
Matches: 76, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
21 1 0.01
22 20 0.26
23 36 0.47
24 15 0.20
25 4 0.05
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (22 bp):
TATATATTTTAATATCATTATG
Found at i:89204941 original size:11 final size:11
Alignment explanation
Indices: 89204910--89204980 Score: 65
Period size: 11 Copynumber: 6.4 Consensus size: 11
89204900 ATTTCTAATG
*
89204910 TATATATATAT
1 TATATATATTT
*
89204921 CATATATATTT
1 TATATATATTT
*
89204932 TATATATATTA
1 TATATATATTT
*
89204943 TGTATATATTT
1 TATATATATTT
89204954 TA-ATATTATTAGT
1 TATATA-TATT--T
89204967 TATATAT-TTT
1 TATATATATTT
89204977 TATA
1 TATA
89204981 CTATTTCATG
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 8 0.16
11 32 0.65
12 2 0.04
13 4 0.08
14 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (11 bp):
TATATATATTT
Found at i:89204949 original size:24 final size:23
Alignment explanation
Indices: 89204910--89205005 Score: 103
Period size: 22 Copynumber: 4.2 Consensus size: 23
89204900 ATTTCTAATG
*
89204910 TATATATA-TAT-CATATATATTT
1 TATATATATTATGTATATAT-TTT
89204932 TATATATATTATGTATATATTTT
1 TATATATATTATGTATATATTTT
*
89204955 AATAT-TATTA-GTTATATATTTT
1 TATATATATTATG-TATATATTTT
89204977 TATACTAT-TTCATGTATATATTTT
1 TATA-TATATT-ATGTATATATTTT
89205001 TATAT
1 TATAT
89205006 TATCCTTATT
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
21 1 0.02
22 26 0.41
23 14 0.22
24 22 0.34
25 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (23 bp):
TATATATATTATGTATATATTTT
Found at i:89205180 original size:26 final size:25
Alignment explanation
Indices: 89205136--89205255 Score: 81
Period size: 26 Copynumber: 5.0 Consensus size: 25
89205126 CTAATATGTA
* *
89205136 TATACTATGTAAATA-TTTTAATAC
1 TATATTATGTACATATTTTTAATAC
** **
89205160 TATATTATGTATGTATTTTTTAACGC
1 TATATTATGTACATA-TTTTTAATAC
*
89205186 CATATTATGTACATATTTTTAATAC
1 TATATTATGTACATATTTTTAATAC
* *
89205211 TATA-TATATAC---TTTGTAATAC
1 TATATTATGTACATATTTTTAATAC
**
89205232 TATTATTATGTTTATA-TTTTAATA
1 TA-TATTATGTACATATTTTTAATA
89205256 TATGTACGTA
Statistics
Matches: 72, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
21 11 0.15
22 2 0.03
23 4 0.06
24 18 0.25
25 18 0.25
26 19 0.26
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (25 bp):
TATATTATGTACATATTTTTAATAC
Found at i:89207308 original size:16 final size:18
Alignment explanation
Indices: 89207282--89207314 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
89207272 TAAAATTGGG
89207282 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
89207299 TTGA-AAAATTAATTTA
1 TTGAGAAAATTAATTTA
89207315 TCTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:89207320 original size:21 final size:21
Alignment explanation
Indices: 89207291--89207334 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
89207281 GTTGAGAAAA
*
89207291 TTATTTAATTGAAA-AATTAAT
1 TTATCTAATT-AAACAATTAAT
89207312 TTATCTAATTAAATCAATTAAT
1 TTATCTAATTAAA-CAATTAAT
89207334 T
1 T
89207335 AAATAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 9 0.45
22 8 0.40
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
TTATCTAATTAAACAATTAAT
Found at i:89219093 original size:38 final size:38
Alignment explanation
Indices: 89219042--89219119 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
89219032 AAAACTCAAC
89219042 TTTATCAGTTTTCACCCACATTCTTAGTACTTTTATTG
1 TTTATCAGTTTTCACCCACATTCTTAGTACTTTTATTG
*
89219080 TTTATCAGTTTTCACCCACATTCTTAGTATTTTTATTG
1 TTTATCAGTTTTCACCCACATTCTTAGTACTTTTATTG
89219118 TT
1 TT
89219120 AATTGAGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.53
Consensus pattern (38 bp):
TTTATCAGTTTTCACCCACATTCTTAGTACTTTTATTG
Found at i:89227239 original size:14 final size:15
Alignment explanation
Indices: 89227212--89227240 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
89227202 TTGCGTAACC
89227212 TAATTTATATTTTAA
1 TAATTTATATTTTAA
89227227 TAATTTA-ATTTTAA
1 TAATTTATATTTTAA
89227241 AAAAATTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTTATATTTTAA
Found at i:89232565 original size:13 final size:14
Alignment explanation
Indices: 89232549--89232584 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
89232539 CAATCTCATA
89232549 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
89232562 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
89232575 TCTC-ATTTCA
1 TCTCAATTTCA
89232585 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:89232574 original size:18 final size:19
Alignment explanation
Indices: 89232536--89232576 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
89232526 TGGTTCATGT
89232536 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
89232555 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
89232573 TTTC
1 TTTC
89232577 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:89232726 original size:24 final size:24
Alignment explanation
Indices: 89232681--89232747 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
89232671 GTGGATTCCT
*
89232681 CCCAAACACA-CCAGAATATCCAA
1 CCCAAACACACCCGGAATATCCAA
89232704 CCCAAACACACCCGGAATATCCAA
1 CCCAAACACACCCGGAATATCCAA
89232728 CCCAAACACACCCGGAATAT
1 CCCAAACACACCCGGAATAT
89232748 TATAAATCCT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 10 0.24
24 32 0.76
ACGTcount: A:0.43, C:0.40, G:0.07, T:0.09
Consensus pattern (24 bp):
CCCAAACACACCCGGAATATCCAA
Found at i:89233261 original size:15 final size:15
Alignment explanation
Indices: 89233241--89233287 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
89233231 TAATATATAT
89233241 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
89233256 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
89233271 TTCAATCAATATAAA
1 TTCAATCAATATAAA
89233286 TT
1 TT
89233288 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:89235417 original size:15 final size:16
Alignment explanation
Indices: 89235362--89235421 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
89235352 TGGTTGGTAC
89235362 AAAATTTTGATATTTT
1 AAAATTTTGATATTTT
*
89235378 AAAA---T-AGA-TTT
1 AAAATTTTGATATTTT
89235389 AAAATTTTGATATTTT
1 AAAATTTTGATATTTT
*
89235405 AAAATTTT-TTATTTT
1 AAAATTTTGATATTTT
89235420 AA
1 AA
89235422 CCATTTTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
11 7 0.19
12 2 0.06
13 1 0.03
14 1 0.03
15 10 0.28
16 15 0.42
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
AAAATTTTGATATTTT
Found at i:89245216 original size:47 final size:47
Alignment explanation
Indices: 89245106--89245217 Score: 129
Period size: 47 Copynumber: 2.4 Consensus size: 47
89245096 TCCGGGATAA
* * *
89245106 GCACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGT
1 GCACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGT
* * * *
89245153 ACACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-
1 GCACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGT
89245200 GCACATAGTG-TCTCATCG
1 GCACATAGTGCT-TCATCG
89245218 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
46 1 0.02
47 50 0.94
48 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (47 bp):
GCACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGT
Found at i:89253645 original size:3 final size:3
Alignment explanation
Indices: 89253637--89253665 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
89253627 TAGGGTTGCC
89253637 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
89253666 ACGGTGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:89262895 original size:81 final size:81
Alignment explanation
Indices: 89262757--89262905 Score: 262
Period size: 81 Copynumber: 1.8 Consensus size: 81
89262747 TCTACTGGTG
* *
89262757 CCATCTATTTAGAGACAGAGAAGATAGAACCCTTATAGAGTTGTAGAGGCTTGTTTCAAATAGAA
1 CCATCTATTTAGAGACAGAGAAGATAGAACCCTTATAAAGTTGTAGAGGCTTATTTCAAATAGAA
89262822 AAAAAAAACATTCTAC
66 AAAAAAAACATTCTAC
* *
89262838 CCATCTATTTAGAGATAGAGAAGATAGAACCCTTATAAAGTTGTAGAGGTTTATTTCAAATAGAA
1 CCATCTATTTAGAGACAGAGAAGATAGAACCCTTATAAAGTTGTAGAGGCTTATTTCAAATAGAA
89262903 AAA
66 AAA
89262906 GAACATCCTA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (81 bp):
CCATCTATTTAGAGACAGAGAAGATAGAACCCTTATAAAGTTGTAGAGGCTTATTTCAAATAGAA
AAAAAAAACATTCTAC
Found at i:89268312 original size:18 final size:19
Alignment explanation
Indices: 89268289--89268326 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
89268279 AAAACTAAAA
*
89268289 TATATTTTTAAAT-TTATT
1 TATATTATTAAATATTATT
89268307 TATATTATTAAATATTATT
1 TATATTATTAAATATTATT
89268326 T
1 T
89268327 CATCAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTATTAAATATTATT
Found at i:89275234 original size:165 final size:166
Alignment explanation
Indices: 89274975--89275302 Score: 550
Period size: 165 Copynumber: 2.0 Consensus size: 166
89274965 GAGAAATTCT
** * *
89274975 ATTTTTATTATCATAAAAATATATAATTTAATTCCCCCCTAAATCGTATTTCTGGATCTATCACA
1 ATTTTTATTATCATAAAAATATATAATTTAATT-CCCCCTAAATCGTATTTCTCAATCCACCACA
* *
89275040 GAAAAAGGCCATTTCACTATTAACTTTAACGGTCAACCATTAAAGCTATAGAAAAATTATAAAAT
65 AAAAAAGACCATTTCACTATTAACTTTAACGGTCAACCATTAAAGCTATAGAAAAATTATAAAAT
89275105 ACTTCTTTTGGTGCGATAATTTTTATATTTTTTAATA
130 ACTTCTTTTGGTGCGATAATTTTTATATTTTTTAATA
*
89275142 ATTTTTATTATCATAAAAATATATAATTTAATT-CCCCTAAATCGTATTTCTCAATCCGCCACAA
1 ATTTTTATTATCATAAAAATATATAATTTAATTCCCCCTAAATCGTATTTCTCAATCCACCACAA
* * *
89275206 AAAAATACCCTTTCACTATTAACTTTAACGGTCAACCATTAAAGCTATAGAAAAATTATAAAATG
66 AAAAAGACCATTTCACTATTAACTTTAACGGTCAACCATTAAAGCTATAGAAAAATTATAAAATA
89275271 CTTCTTTTGGTGCGATAATTTTTATATTTTTT
131 CTTCTTTTGGTGCGATAATTTTTATATTTTTT
89275303 TTATAAAATT
Statistics
Matches: 151, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
165 118 0.78
167 33 0.22
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.40
Consensus pattern (166 bp):
ATTTTTATTATCATAAAAATATATAATTTAATTCCCCCTAAATCGTATTTCTCAATCCACCACAA
AAAAAGACCATTTCACTATTAACTTTAACGGTCAACCATTAAAGCTATAGAAAAATTATAAAATA
CTTCTTTTGGTGCGATAATTTTTATATTTTTTAATA
Found at i:89275439 original size:18 final size:19
Alignment explanation
Indices: 89275397--89275456 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
89275387 ATTTTATAAA
*
89275397 AAAAATTTACGATTTTTAT
1 AAAATTTTACGATTTTTAT
89275416 AAAATTTTAC-ATTTTTTTAT
1 AAAATTTTACGA--TTTTTAT
** *
89275436 AATTTTTTATGATTTTTAT
1 AAAATTTTACGATTTTTAT
89275455 AA
1 AA
89275457 GTTTTTCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 14 0.41
21 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
AAAATTTTACGATTTTTAT
Found at i:89275441 original size:9 final size:9
Alignment explanation
Indices: 89275429--89275523 Score: 55
Period size: 10 Copynumber: 9.8 Consensus size: 9
89275419 ATTTTACATT
89275429 TTTTTATAA
1 TTTTTATAA
*
89275438 TTTTTTATGA
1 -TTTTTATAA
89275448 TTTTTATAA
1 TTTTTATAA
*
89275457 GTTTTTCTATA
1 -TTTTTATA-A
* *
89275468 TTTTAATATT
1 TTTTTATA-A
89275478 TTTTTATTAAA
1 TTTTTA-T-AA
* *
89275489 ATTTAATAA
1 TTTTTATAA
89275498 TTTTTATAA
1 TTTTTATAA
* *
89275507 CTTTTATGTA
1 TTTTTAT-AA
89275517 TTTTTAT
1 TTTTTAT
89275524 TTTTATCATT
Statistics
Matches: 65, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
9 23 0.35
10 35 0.54
11 6 0.09
12 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:89275445 original size:10 final size:10
Alignment explanation
Indices: 89275409--89275511 Score: 52
Period size: 10 Copynumber: 10.3 Consensus size: 10
89275399 AAATTTACGA
*
89275409 TTTTTATAAA
1 TTTTTATAAT
* * *
89275419 ATTTTACATT
1 TTTTTATAAT
89275429 TTTTTATAAT
1 TTTTTATAAT
*
89275439 TTTTTATGA-
1 TTTTTATAAT
89275448 TTTTTATAAGT
1 TTTTTATAA-T
89275459 TTTTCTAT-A-
1 TTTT-TATAAT
* *
89275468 TTTTAATATT
1 TTTTTATAAT
*
89275478 TTTTTATTAAA
1 TTTTTA-TAAT
* *
89275489 ATTTAATAA-
1 TTTTTATAAT
89275498 TTTTTATAACT
1 TTTTTATAA-T
89275509 TTT
1 TTT
89275512 ATGTATTTTT
Statistics
Matches: 67, Mismatches: 18, Indels: 15
0.67 0.18 0.15
Matches are distributed among these distances:
8 2 0.03
9 19 0.28
10 29 0.43
11 14 0.21
12 3 0.04
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:89275471 original size:19 final size:19
Alignment explanation
Indices: 89275429--89275484 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
89275419 ATTTTACATT
89275429 TTTTTATAATTTTTTATGA
1 TTTTTATAATTTTTTATGA
89275448 TTTTTATAAGTTTTTCTAT-A
1 TTTTTATAA-TTTTT-TATGA
* *
89275468 TTTTAATATTTTTTTAT
1 TTTTTATAATTTTTTAT
89275485 TAAAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 3 0.09
19 14 0.42
20 13 0.39
21 3 0.09
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTTATAATTTTTTATGA
Found at i:89275481 original size:39 final size:39
Alignment explanation
Indices: 89275402--89275484 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
89275392 ATAAAAAAAA
* * *
89275402 TTTACGATTTTTATAAAATTTTACATTTTTTTATAATTT
1 TTTATGATTTTTATAAAATTTTACATATTTTAATAATTT
* * *
89275441 TTTATGATTTTTAT-AAGTTTTTCTATATTTTAATATTTT
1 TTTATGATTTTTATAAAATTTTAC-ATATTTTAATAATTT
89275480 TTTAT
1 TTTAT
89275485 TAAAATTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 7 0.19
39 30 0.81
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (39 bp):
TTTATGATTTTTATAAAATTTTACATATTTTAATAATTT
Found at i:89284452 original size:30 final size:30
Alignment explanation
Indices: 89284370--89284461 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
89284360 AACTATGTTG
* *
89284370 CTCACATAAGCAGAATTTATATCAAGGTTA
1 CTCACAAAAGCAGAATTTATATTAAGGTTA
*
89284400 CTCACAAAAGCAGAATTTATATTAAGGTTT
1 CTCACAAAAGCAGAATTTATATTAAGGTTA
* ** *
89284430 CTCACACAAGCTTAATTTATATT-AGATTA
1 CTCACAAAAGCAGAATTTATATTAAGGTTA
89284459 CTC
1 CTC
89284462 GTCTGGGCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
29 7 0.13
30 47 0.87
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (30 bp):
CTCACAAAAGCAGAATTTATATTAAGGTTA
Found at i:89297140 original size:21 final size:20
Alignment explanation
Indices: 89297114--89297152 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
89297104 TTCACGAATA
89297114 TTTTAAGAATTTAAATTTTTT
1 TTTTAA-AATTTAAATTTTTT
*
89297135 TTTTAAAATTTTAATTTT
1 TTTTAAAATTTAAATTTT
89297153 AATTCTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTAAAATTTAAATTTTTT
Found at i:89304577 original size:16 final size:14
Alignment explanation
Indices: 89304513--89304577 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 14
89304503 ATTTATCATG
89304513 AAATTAACTAAATTAT
1 AAATTAA-TAAA-TAT
*
89304529 ACAATAAATCAAATA-
1 A-AATTAAT-AAATAT
89304544 AAATTAATAAATATT
1 AAATTAATAAATA-T
89304559 AAATTATATAAAATAT
1 AAATTA-AT-AAATAT
89304575 AAA
1 AAA
89304578 CTAAATACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 5 0.12
14 6 0.15
15 7 0.17
16 10 0.24
17 13 0.32
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATTAATAAATAT
Found at i:89306022 original size:9 final size:9
Alignment explanation
Indices: 89306004--89306037 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
89305994 ATTCTATATA
89306004 TTTTAT-AT
1 TTTTATAAT
89306012 TTTTATAAT
1 TTTTATAAT
89306021 TTTTATAAT
1 TTTTATAAT
*
89306030 TTTAATAA
1 TTTTATAA
89306038 AATTCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:89306310 original size:44 final size:42
Alignment explanation
Indices: 89306247--89306574 Score: 369
Period size: 44 Copynumber: 8.0 Consensus size: 42
89306237 CTTTATTAAC
*
89306247 TTTTTTTGTTAGAGGAAAACCCCTCTATTTAAAAAATATATTA
1 TTTTTTTGTTAGAGAAAAACCCCTCTATTT-AAAAATATATTA
*
89306290 TTTCTTTTGTTAGAAAAAAACCCCTCTATTT-AAAA-ATATTA
1 TTT-TTTTGTTAGAGAAAAACCCCTCTATTTAAAAATATATTA
* *
89306331 TTTTTTT-TTAGAGAAAAACCCTTTTATTTAAAAAAATATATTA
1 TTTTTTTGTTAGAGAAAAACCCCTCTATTT--AAAAATATATTA
* *
89306374 -TCTTTTGTTAGAGGAAAACCCCTCTATTTAAAAATA-A-TA
1 TTTTTTTGTTAGAGAAAAACCCCTCTATTTAAAAATATATTA
89306413 TTTTTTTGTTAGAGAAAAA-CCCTCTATTTAAAAATA-A-TA
1 TTTTTTTGTTAGAGAAAAACCCCTCTATTTAAAAATATATTA
* ** *
89306452 --TTATT-TTAGAGAAAAACCATTCTATTT-AAAAGATATTA
1 TTTTTTTGTTAGAGAAAAACCCCTCTATTTAAAAATATATTA
* *
89306490 -TTTTTTGTTAGAGAAAAGCCCCTCTATTTCAAAATATATTTTA
1 TTTTTTTGTTAGAGAAAAACCCCTCTATTT-AAAA-ATATATTA
*
89306533 TTTTTTTATTAGAGAAAAACCCCTCTATTTTAAAAAATATAT
1 TTTTTTTGTTAGAGAAAAACCCCTCTA-TTT-AAAAATATAT
89306575 ATTATTATGA
Statistics
Matches: 243, Mismatches: 25, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
36 16 0.07
37 13 0.05
38 2 0.01
39 45 0.19
40 40 0.16
41 16 0.07
42 16 0.07
43 34 0.14
44 54 0.22
45 7 0.03
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (42 bp):
TTTTTTTGTTAGAGAAAAACCCCTCTATTTAAAAATATATTA
Found at i:89309537 original size:16 final size:15
Alignment explanation
Indices: 89309499--89309540 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
89309489 TAGGCTTCTT
*
89309499 TATAAAAATAA-TAT
1 TATAAAAATAATTAC
*
89309513 TAAAAAAATAATTAAC
1 TATAAAAATAATT-AC
89309529 TATAAAAATAAT
1 TATAAAAATAAT
89309541 GAGAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 10 0.43
15 1 0.04
16 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
TATAAAAATAATTAC
Found at i:89309548 original size:30 final size:30
Alignment explanation
Indices: 89309499--89309556 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
89309489 TAGGCTTCTT
*
89309499 TATAAAAATAATATTAAAAAAATAATTAAC
1 TATAAAAATAATATGAAAAAAATAATTAAC
*
89309529 TATAAAAATAATGA-GAAAAAATTAATTA
1 TATAAAAATAAT-ATGAAAAAAATAATTA
89309557 TGAAAACAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (30 bp):
TATAAAAATAATATGAAAAAAATAATTAAC
Found at i:89310449 original size:3 final size:3
Alignment explanation
Indices: 89310436--89310469 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
89310426 ATTTCATTTA
89310436 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
89310470 ATGGTTTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:89316098 original size:46 final size:46
Alignment explanation
Indices: 89316034--89316261 Score: 296
Period size: 46 Copynumber: 5.0 Consensus size: 46
89316024 TTTGACATGA
* * * * * *
89316034 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* * * *** *
89316080 TGTCATGGTATTTTTCAACCATGTTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
89316126 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
89316172 TGCCACGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
89316218 TGCCATGGTATCTTTCAACCACGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
89316262 AGAGCACACT
Statistics
Matches: 160, Mismatches: 21, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
45 4 0.03
46 156 0.98
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:89319475 original size:19 final size:19
Alignment explanation
Indices: 89319451--89319530 Score: 51
Period size: 19 Copynumber: 4.2 Consensus size: 19
89319441 ACATACATAT
89319451 TATATAGTTATTAAAAATA
1 TATATAGTTATTAAAAATA
89319470 TATATA-TATATATATAAAATA
1 TATATAGT-TAT-TA-AAAATA
* **
89319491 -ATAT-GTAAGAAAAAATA
1 TATATAGTTATTAAAAATA
**
89319508 TAATATAG-TATTCGAAATA
1 T-ATATAGTTATTAAAAATA
89319527 TATA
1 TATA
89319531 CATGATATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 15
0.67 0.12 0.22
Matches are distributed among these distances:
17 6 0.13
18 5 0.11
19 21 0.46
20 8 0.17
21 6 0.13
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (19 bp):
TATATAGTTATTAAAAATA
Found at i:89319609 original size:26 final size:24
Alignment explanation
Indices: 89319580--89319629 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
89319570 TATACGTAAT
89319580 ATATAAAAATGCATATACATAATATA
1 ATATAAAAAT--ATATACATAATATA
* *
89319606 ATATTAAAATATCTACATAATATA
1 ATATAAAAATATATACATAATATA
89319630 TACATATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
26 9 0.41
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (24 bp):
ATATAAAAATATATACATAATATA
Found at i:89319633 original size:11 final size:11
Alignment explanation
Indices: 89319567--89319635 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
89319557 AAAAAGGTAT
*
89319567 ATATATACGTA
1 ATATATACATA
*
89319578 ATATATA-AAA
1 ATATATACATA
89319588 ATGCATATACATA
1 AT--ATATACATA
* *
89319601 ATATAATATTAAA
1 ATAT-ATA-CATA
*
89319614 ATATCTACATA
1 ATATATACATA
89319625 ATATATACATA
1 ATATATACATA
89319636 TTAGAAATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
10 3 0.07
11 21 0.48
12 10 0.23
13 10 0.23
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.35
Consensus pattern (11 bp):
ATATATACATA
Found at i:89320051 original size:12 final size:13
Alignment explanation
Indices: 89320005--89320066 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 13
89319995 TATTAGTACC
* *
89320005 GATAATAATAACA
1 GATATTAATAATA
*
89320018 GAATATTGATAATA
1 G-ATATTAATAATA
89320032 GATA-TAATAAT-
1 GATATTAATAATA
89320043 GATATTAATAA-A
1 GATATTAATAATA
*
89320055 -ATATAAATAATA
1 GATATTAATAATA
89320067 TTAAAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
11 13 0.32
12 13 0.32
13 4 0.10
14 10 0.25
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (13 bp):
GATATTAATAATA
Found at i:89320069 original size:20 final size:20
Alignment explanation
Indices: 89320044--89320084 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
89320034 TATAATAATG
89320044 ATATT-AATAAAATATAAATA
1 ATATTAAATAAAATA-AAATA
89320064 ATATTAAAATAAAATAAAATA
1 ATATT-AAATAAAATAAAATA
89320085 CGTAAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATTAAATAAAATAAAATA
Found at i:89320613 original size:16 final size:16
Alignment explanation
Indices: 89320592--89320628 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
89320582 CGTCCGTAAT
89320592 CGGCGACCGCTGTATA
1 CGGCGACCGCTGTATA
89320608 CGGCGACCGCTGTATA
1 CGGCGACCGCTGTATA
89320624 CGGCG
1 CGGCG
89320629 GCTGGAAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.16
Consensus pattern (16 bp):
CGGCGACCGCTGTATA
Found at i:89322096 original size:24 final size:22
Alignment explanation
Indices: 89322042--89322101 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
89322032 AAAAATGTAT
* *
89322042 AAAATTATTAAATATTAAAATA
1 AAAATTATAAAATATTAAAAGA
* *
89322064 AAAAATATAAATATATTTTAAAGA
1 AAAATTATAAA-ATA-TTAAAAGA
89322088 AAAATTATAAAATA
1 AAAATTATAAAATA
89322102 ATACGGGCGG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 9 0.29
23 6 0.19
24 16 0.52
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATTATAAAATATTAAAAGA
Found at i:89328536 original size:10 final size:11
Alignment explanation
Indices: 89328511--89328536 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
89328501 TATTTATATG
89328511 TTTTTTAGAAA
1 TTTTTTAGAAA
89328522 TTTTTTAGAAA
1 TTTTTTAGAAA
89328533 TTTT
1 TTTT
89328537 ATAATTTTTC
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (11 bp):
TTTTTTAGAAA
Found at i:89328575 original size:18 final size:19
Alignment explanation
Indices: 89328554--89328590 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
89328544 TTCTTAAAAA
89328554 TATAAA-TTTTGAAATTTT
1 TATAAAGTTTTGAAATTTT
89328572 TATAAATGTTTTGAAATTT
1 TATAAA-GTTTTGAAATTT
89328591 AAATGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TATAAAGTTTTGAAATTTT
Found at i:89337092 original size:10 final size:10
Alignment explanation
Indices: 89337077--89337106 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
89337067 AATCCGTTCC
89337077 TTTATTTTTT
1 TTTATTTTTT
89337087 TTTATTTTTT
1 TTTATTTTTT
89337097 TTTATTTTTT
1 TTTATTTTTT
89337107 GCACTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:89343676 original size:14 final size:14
Alignment explanation
Indices: 89343657--89343683 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89343647 ACTGGATTGA
89343657 TTAAAGATTAAAGG
1 TTAAAGATTAAAGG
89343671 TTAAAGATTAAAG
1 TTAAAGATTAAAG
89343684 CAACTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.30
Consensus pattern (14 bp):
TTAAAGATTAAAGG
Found at i:89346256 original size:15 final size:16
Alignment explanation
Indices: 89346238--89346271 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
89346228 AATAAAAAAT
*
89346238 TATTAAATTAT-TAAA
1 TATTAAATAATATAAA
89346253 TATTAAATAATATAAA
1 TATTAAATAATATAAA
89346269 TAT
1 TAT
89346272 ATGTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATTAAATAATATAAA
Found at i:89346936 original size:16 final size:18
Alignment explanation
Indices: 89346897--89346930 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
89346887 TAAGTTTATA
89346897 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
89346914 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
89346931 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:89349176 original size:38 final size:40
Alignment explanation
Indices: 89349115--89349201 Score: 124
Period size: 38 Copynumber: 2.2 Consensus size: 40
89349105 TAAAAAGTAT
* *
89349115 TTATATTAAAAAAACTATCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAAACTATAATAAATATAATAAATATTTTA
*
89349155 TTATATTAAAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAAACTATAATAAATATAATAAATATTTTA
*
89349193 TTGTATTAA
1 TTATATTAA
89349202 TATAAATGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 28 0.65
39 1 0.02
40 14 0.33
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAAAACTATAATAAATATAATAAATATTTTA
Found at i:89350122 original size:19 final size:20
Alignment explanation
Indices: 89350079--89350115 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
89350069 TTTATTTTAT
89350079 TTATTTTAATATCAATATAA
1 TTATTTTAATATCAATATAA
*
89350099 TTATTTTTAT-TCAATAT
1 TTATTTTAATATCAATAT
89350116 TAATATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTTAATATCAATATAA
Found at i:89352042 original size:15 final size:16
Alignment explanation
Indices: 89352022--89352058 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
89352012 TAATATTTTA
89352022 AAAATTA-TAAAAATT
1 AAAATTATTAAAAATT
89352037 AAAATTATTAAAAATT
1 AAAATTATTAAAAATT
89352053 AAAATT
1 AAAATT
89352059 TAATTTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTATTAAAAATT
Found at i:89354002 original size:10 final size:9
Alignment explanation
Indices: 89353970--89354002 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
89353960 TTTTTCTCAA
89353970 TTTATCTAT
1 TTTATCTAT
89353979 TTTATCTAT
1 TTTATCTAT
89353988 TTTATCTACT
1 TTTATCTA-T
89353998 TTTAT
1 TTTAT
89354003 TTTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTATCTAT
Found at i:89356358 original size:21 final size:21
Alignment explanation
Indices: 89356332--89356372 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
89356322 ACTTTTTTAA
89356332 AAGTTAAAAGT-CAAAACCATT
1 AAGTTAAAA-TACAAAACCATT
89356353 AAGTTAAAATACAAAACCAT
1 AAGTTAAAATACAAAACCAT
89356373 AATATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (21 bp):
AAGTTAAAATACAAAACCATT
Found at i:89366252 original size:3 final size:3
Alignment explanation
Indices: 89366244--89366276 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
89366234 CTTCGAGGCT
89366244 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
89366277 GAACCCCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:89372657 original size:32 final size:32
Alignment explanation
Indices: 89372621--89372684 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
89372611 ACTTTTTCTC
89372621 TTGTTTTTCCACATGTAAATTTTTAATTGGTT
1 TTGTTTTTCCACATGTAAATTTTTAATTGGTT
*
89372653 TTGTTTTTCCACATGTAAGTTTTTAATTGGTT
1 TTGTTTTTCCACATGTAAATTTTTAATTGGTT
89372685 ATATATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.56
Consensus pattern (32 bp):
TTGTTTTTCCACATGTAAATTTTTAATTGGTT
Found at i:89377235 original size:17 final size:17
Alignment explanation
Indices: 89377197--89377237 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
89377187 AAAAAGCAAC
* *
89377197 AGAAGAAAAGAAAAATA
1 AGAAAAAAAGAAAAAAA
*
89377214 GGAAAAAAAGAAAAAAA
1 AGAAAAAAAGAAAAAAA
89377231 AGAAAAA
1 AGAAAAA
89377238 GAACAAGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAGAAAAAAA
Found at i:89380138 original size:20 final size:20
Alignment explanation
Indices: 89380113--89380162 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
89380103 TGGCTTAAAA
89380113 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
89380133 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
89380150 GTGGTAGTGGATT
1 TTGGTAGTGGATT
89380163 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:89384768 original size:20 final size:20
Alignment explanation
Indices: 89384743--89384792 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
89384733 TGGCTTAAAA
89384743 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
89384763 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
89384780 GTGGTAGTGGATT
1 TTGGTAGTGGATT
89384793 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:89388880 original size:49 final size:48
Alignment explanation
Indices: 89388787--89388881 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 48
89388777 ACCACATGCC
* * *
89388787 CGTGTCTATTTAACAGATTGTAACATAGCCTAAGCCACACCACACGAT
1 CGTGTCTATTTAACAGACTCTAACACAGCCTAAGCCACACCACACGAT
* *
89388835 CGTGTCTATTTAGCAGACTCTAAACACGGCCTAAGCCAC-CTCACACG
1 CGTGTCTATTTAACAGACTCT-AACACAGCCTAAGCCACAC-CACACG
89388882 GGCGTGTTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
48 19 0.47
49 21 0.52
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.23
Consensus pattern (48 bp):
CGTGTCTATTTAACAGACTCTAACACAGCCTAAGCCACACCACACGAT
Found at i:89396217 original size:14 final size:14
Alignment explanation
Indices: 89396163--89396220 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
89396153 CCATCTTCTG
89396163 AATATTATTTATAA
1 AATATTATTTATAA
*
89396177 AATACTATGATTCA-AA
1 AATA-T-T-ATTTATAA
*
89396193 AATTTTTATTTATAA
1 AA-TATTATTTATAA
89396208 AATATTATTTATA
1 AATATTATTTATA
89396221 TTATATGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 18 0.51
15 6 0.17
16 6 0.17
17 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (14 bp):
AATATTATTTATAA
Found at i:89404494 original size:12 final size:12
Alignment explanation
Indices: 89404471--89404510 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 12
89404461 TATATATATT
89404471 TAAAAATT-ATA
1 TAAAAATTAATA
89404482 TAAAAATTAATA
1 TAAAAATTAATA
89404494 TAAAAAAATTAATA
1 T--AAAAATTAATA
89404508 TAA
1 TAA
89404511 GCGGGCTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 8 0.31
12 6 0.23
14 12 0.46
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAAATTAATA
Found at i:89404500 original size:14 final size:14
Alignment explanation
Indices: 89404478--89404510 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
89404468 ATTTAAAAAT
*
89404478 TATATAAAAATTAA
1 TATAAAAAAATTAA
89404492 TATAAAAAAATTAA
1 TATAAAAAAATTAA
89404506 TATAA
1 TATAA
89404511 GCGGGCTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TATAAAAAAATTAA
Found at i:89411816 original size:43 final size:43
Alignment explanation
Indices: 89411754--89412098 Score: 154
Period size: 43 Copynumber: 7.8 Consensus size: 43
89411744 ATTCACCAAA
* *
89411754 ATTTAATCTGCTCCGCTCCTGCTCAGCGAAGATAAGACCTAGT
1 ATTTAGTCTGCTCCACTCCTGCTCAGCGAAGATAAGACCTAGT
* * *
89411797 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAG-GCT-GAT
1 ATTTAGTCTGCTCCACTCCTGCTCAGCGAAGATAAGACCTAG-T
* * * * * * * **
89411839 GATTGGAATCTGCTCCA-TCGCCGGT-ACGTGGAGATAAGATTCACCAAA
1 -ATT-TAGTCTGCTCCACTC-CTGCTCA-GCGAAGATAAGA--C-CTAGT
* *
89411887 ATTT-GATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTAGT
1 ATTTAG-TCTGCTCCACTCCTGCTCAGCGAAGATAAGACCTAGT
* * * *
89411930 ATTTAGCCTGCTCCACTCCTACTCAGTGAAGATAAG-GCT-GAT
1 ATTTAGTCTGCTCCACTCCTGCTCAGCGAAGATAAGACCTAG-T
* * * * * **
89411972 GATTGGAATCTGCTCCA-TCACCGGT-A-CGTAGAGATAAGATTCACCAAA
1 -ATT-TAGTCTGCTCCACTC-CTGCTCAGCG-A-AGATAAGA--C-CTAGT
* * *
89412020 ATTT-GATCTGCTCCGCTCTTGCTCAGCGAAGATAAGACCTGGT
1 ATTTAG-TCTGCTCCACTCCTGCTCAGCGAAGATAAGACCTAGT
* *
89412063 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAG
1 ATTTAGTCTGCTCCACTCCTGCTCAGCGAAGATAAG
89412099 GCTGATGATT
Statistics
Matches: 215, Mismatches: 57, Indels: 60
0.65 0.17 0.18
Matches are distributed among these distances:
41 2 0.01
42 7 0.03
43 107 0.50
44 44 0.20
46 38 0.18
47 13 0.06
48 4 0.02
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (43 bp):
ATTTAGTCTGCTCCACTCCTGCTCAGCGAAGATAAGACCTAGT
Found at i:89411864 original size:133 final size:133
Alignment explanation
Indices: 89411627--89412240 Score: 1043
Period size: 133 Copynumber: 4.6 Consensus size: 133
89411617 TTGGAACTTT
* * * * *
89411627 ATCTGCTCCGCTCTTGCTCAACGAAGATAAGATCT-GCAATTTAGCCTGCT-CAATCCTGCTCAG
1 ATCTGCTCCGCTCCTGCTCAGCGAAGATAAGACCTAG-TATTTAGCCTGCTCCACTCCTGCTCAG
*
89411690 TGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAA
65 TGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTAGAGATAAGATTCACCAAAA
*
89411755 TTTA
130 TTTG
89411759 ATCTGCTCCGCTCCTGCTCAGCGAAGATAAGACCTAGTATTTAGCCTGCTCCACTCCTGCTCAGT
1 ATCTGCTCCGCTCCTGCTCAGCGAAGATAAGACCTAGTATTTAGCCTGCTCCACTCCTGCTCAGT
*
89411824 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTAGAGATAAGATTCACCAAAAT
89411889 TTG
131 TTG
* *
89411892 ATCTGCTCCGCTCCTGCTCAACGAAGATAAGACCTAGTATTTAGCCTGCTCCACTCCTACTCAGT
1 ATCTGCTCCGCTCCTGCTCAGCGAAGATAAGACCTAGTATTTAGCCTGCTCCACTCCTGCTCAGT
*
89411957 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCACCGGTACGTAGAGATAAGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTAGAGATAAGATTCACCAAAAT
89412022 TTG
131 TTG
* *
89412025 ATCTGCTCCGCTCTTGCTCAGCGAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTGCTCAGT
1 ATCTGCTCCGCTCCTGCTCAGCGAAGATAAGACCTAGTATTTAGCCTGCTCCACTCCTGCTCAGT
*
89412090 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGATACGTAGAGATAAGATTCACCAAAAT
66 GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTAGAGATAAGATTCACCAAAAT
89412155 TTG
131 TTG
* * * *
89412158 ATCTGCTCTGCTCCTGCTCAGCTAAGATAAGACCTGGTATTTAGCCTGCTCCACTCCTACTCAGT
1 ATCTGCTCCGCTCCTGCTCAGCGAAGATAAGACCTAGTATTTAGCCTGCTCCACTCCTGCTCAGT
89412223 GAAGATAAGGCTGATGAT
66 GAAGATAAGGCTGATGAT
89412241 ATCTGTAATC
Statistics
Matches: 460, Mismatches: 20, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
132 44 0.10
133 416 0.90
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (133 bp):
ATCTGCTCCGCTCCTGCTCAGCGAAGATAAGACCTAGTATTTAGCCTGCTCCACTCCTGCTCAGT
GAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTAGAGATAAGATTCACCAAAAT
TTG
Found at i:89417199 original size:23 final size:23
Alignment explanation
Indices: 89417173--89417216 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
89417163 TAGATATGTG
*
89417173 ATGACGTTATCTT-ATAAATATAC
1 ATGAAGTTATCTTGA-AAATATAC
*
89417196 ATGAATTTATCTTGAAAATAT
1 ATGAAGTTATCTTGAAAATAT
89417217 GTTGAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATAC
Found at i:89418983 original size:24 final size:25
Alignment explanation
Indices: 89418930--89418983 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
89418920 TATTATTATT
* *
89418930 AAAAGTAAAGTAAATAAAAAGGAAA
1 AAAAGGAAAGTAAATAAAAAGAAAA
*
89418955 TAAAGGAAAG-AAAT-AAAAGAATAA
1 AAAAGGAAAGTAAATAAAAAGAA-AA
89418979 AAAAG
1 AAAAG
89418984 AAGGAAGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 6 0.25
24 10 0.42
25 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (25 bp):
AAAAGGAAAGTAAATAAAAAGAAAA
Found at i:89420560 original size:21 final size:21
Alignment explanation
Indices: 89420503--89420562 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
89420493 GGCACTTTAT
* *
89420503 GTGTCGTATTTCAAGCACCTCGT
1 GTGTCGT-TTT-AGGCACCTCGA
***
89420526 GTGTCGTACCAGGCACCTCGA
1 GTGTCGTTTTAGGCACCTCGA
89420547 GTGTCGTTTTAGGCAC
1 GTGTCGTTTTAGGCAC
89420563 TTTATGTGTC
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 22 0.76
23 7 0.24
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
GTGTCGTTTTAGGCACCTCGA
Found at i:89428403 original size:23 final size:21
Alignment explanation
Indices: 89428377--89428424 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
89428367 AGGCACTTTA
89428377 TGTGGCCTATTTCAGGCACCTCG
1 TGTGGCCTA--TCAGGCACCTCG
* *
89428400 TGTGTCGTATCAGGCACCTCG
1 TGTGGCCTATCAGGCACCTCG
89428421 TGTG
1 TGTG
89428425 TCGTTTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.70
23 7 0.30
ACGTcount: A:0.12, C:0.27, G:0.29, T:0.31
Consensus pattern (21 bp):
TGTGGCCTATCAGGCACCTCG
Found at i:89428414 original size:21 final size:21
Alignment explanation
Indices: 89428388--89428451 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
89428378 GTGGCCTATT
89428388 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
*
89428409 TCAGGCACCTCGTGTGTCGTT
1 TCAGGCACCTCGTGTGTCGTA
* * **
89428430 TTAGGCACTTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
89428451 T
1 T
89428452 ACTGATCAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTCGTA
Found at i:89433877 original size:21 final size:21
Alignment explanation
Indices: 89433851--89433895 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
89433841 GCTGGCTCAT
*
89433851 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
*
89433872 CATGTTTTTCTGGGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
89433893 CAT
1 CAT
89433896 TTGATCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:89435376 original size:16 final size:15
Alignment explanation
Indices: 89435350--89435383 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
89435340 TTGTTAGGCA
*
89435350 TCCACCAATGTGCTT
1 TCCACCAATGTCCTT
89435365 TCCACTCAATGTCCTT
1 TCCAC-CAATGTCCTT
89435381 TCC
1 TCC
89435384 TTGGAGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.18, C:0.38, G:0.09, T:0.35
Consensus pattern (15 bp):
TCCACCAATGTCCTT
Found at i:89435959 original size:14 final size:14
Alignment explanation
Indices: 89435925--89435951 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89435915 ATCGACTTGT
89435925 ATATTTTATTTATC
1 ATATTTTATTTATC
89435939 ATATTTTATTTAT
1 ATATTTTATTTAT
89435952 TATTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
ATATTTTATTTATC
Found at i:89437529 original size:8 final size:8
Alignment explanation
Indices: 89437516--89437544 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
89437506 TTATGTTTAG
89437516 TATATTAT
1 TATATTAT
89437524 TATATTAT
1 TATATTAT
89437532 TATATTAT
1 TATATTAT
89437540 TATAT
1 TATAT
89437545 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:89437577 original size:5 final size:5
Alignment explanation
Indices: 89437567--89437607 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
89437557 TTATGTTTTA
89437567 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
89437608 AAACTAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:89437643 original size:20 final size:20
Alignment explanation
Indices: 89437615--89437653 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
89437605 TATAAACTAA
* *
89437615 AGAAGCAAATGAAAGGAAAT
1 AGAAACAAATGAAACGAAAT
89437635 AGAAACAAATGAAACGAAA
1 AGAAACAAATGAAACGAAA
89437654 CAGAGAGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.08, G:0.21, T:0.08
Consensus pattern (20 bp):
AGAAACAAATGAAACGAAAT
Found at i:89439083 original size:31 final size:30
Alignment explanation
Indices: 89438997--89439084 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 30
89438987 TGATTTAATG
* * *
89438997 TGCAATTGTATACAT-TAACTTTAATTTGG
1 TGCAATTATATACATGAAACTTTAATTTGC
* *
89439026 TGCAATTATATACATGATACTCTAATTGTGC
1 TGCAATTATATACATGAAACTTTAATT-TGC
* **
89439057 TTCAATTATATATTTGAAACTTTAATTT
1 TGCAATTATATACATGAAACTTTAATTT
89439085 TGATTTAATC
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 14 0.30
30 9 0.19
31 24 0.51
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.45
Consensus pattern (30 bp):
TGCAATTATATACATGAAACTTTAATTTGC
Found at i:89443822 original size:16 final size:17
Alignment explanation
Indices: 89443798--89443840 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
89443788 ATTACATGTG
89443798 AAAATAATAAAATAAA-T
1 AAAA-AATAAAATAAATT
* *
89443815 AAACAATAAATTAAATT
1 AAAAAATAAAATAAATT
89443832 AAAAAATAA
1 AAAAAATAA
89443841 CTCTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAATAAAATAAATT
Found at i:89444447 original size:19 final size:20
Alignment explanation
Indices: 89444420--89444457 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
89444410 ATGAATAGTC
89444420 ACATAATAATTTAA-CATAT
1 ACATAATAATTTAATCATAT
*
89444439 ACATCATAATTTAATCATA
1 ACATAATAATTTAATCATA
89444458 ATATCCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (20 bp):
ACATAATAATTTAATCATAT
Found at i:89450096 original size:11 final size:11
Alignment explanation
Indices: 89450080--89450121 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
89450070 AAAAATTTGA
89450080 AATAAAATAAT
1 AATAAAATAAT
89450091 AATAAAATAAT
1 AATAAAATAAT
* *
89450102 AA-AAACTGAT
1 AATAAAATAAT
89450112 AAATAAAATA
1 -AATAAAATA
89450122 TTGAGCTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 6 0.24
11 15 0.60
12 4 0.16
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:89454903 original size:16 final size:16
Alignment explanation
Indices: 89454882--89454935 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
89454872 TTTGGTTCGT
89454882 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
* * **
89454898 TGTAATAGTATAGAAT
1 TGTAATGGAATAGAGC
89454914 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
89454930 TGTAAT
1 TGTAAT
89454936 CAGTAATTCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:89454969 original size:46 final size:43
Alignment explanation
Indices: 89454917--89455010 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 43
89454907 ATAGAATTGT
*
89454917 AATGGAATAGAGCTGTAATCAGTAATTCAATTG-TTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTC--TTGATTTGGTTGAATGG
*
89454963 AATGGAATAGAACTGTAATGGTATTCTTGTATTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCTTG-ATTTGGTTGAATGG
89455007 AATG
1 AATG
89455011 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
42 3 0.07
44 21 0.48
45 2 0.05
46 18 0.41
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (43 bp):
AATGGAATAGAACTGTAATAGTATTCTTGATTTGGTTGAATGG
Found at i:89457525 original size:9 final size:9
Alignment explanation
Indices: 89457481--89457602 Score: 59
Period size: 9 Copynumber: 12.8 Consensus size: 9
89457471 ATTATTATTA
89457481 TTATAAA-T
1 TTATAAATT
*
89457489 TTATAAGTT
1 TTATAAATT
*
89457498 TATATCAATT
1 T-TATAAATT
*
89457508 ATA-ATAATT
1 TTATA-AATT
89457517 TTATAAATT
1 TTATAAATT
* *
89457526 TTATGATTT
1 TTATAAATT
89457535 TTATAGAATT
1 TTATA-AATT
*
89457545 TTAATATATTT
1 TT-ATA-AATT
89457556 TTATAAAATT
1 TTAT-AAATT
*
89457566 TTAAAATATT
1 TTATAA-ATT
**
89457576 TTAGATATGTT
1 TT--ATAAATT
*
89457587 TTATAACTT
1 TTATAAATT
89457596 TTATAAA
1 TTATAAA
89457603 AAGAATTATA
Statistics
Matches: 84, Mismatches: 20, Indels: 19
0.68 0.16 0.15
Matches are distributed among these distances:
8 6 0.07
9 38 0.45
10 25 0.30
11 13 0.15
12 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (9 bp):
TTATAAATT
Found at i:89457557 original size:21 final size:20
Alignment explanation
Indices: 89457515--89457577 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
89457505 ATTATAATAA
*
89457515 TTTTATAAATTTT-AT-GAT
1 TTTTATAAATTTTAATATAT
89457533 TTTTATAGAATTTTAATATAT
1 TTTTATA-AATTTTAATATAT
*
89457554 TTTTATAAAATTTTAAAATAT
1 TTTTAT-AAATTTTAATATAT
89457575 TTT
1 TTT
89457578 AGATATGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.18
19 6 0.15
20 2 0.05
21 23 0.59
22 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTATAAATTTTAATATAT
Found at i:89465644 original size:37 final size:37
Alignment explanation
Indices: 89465594--89465669 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
89465584 ATCTCATCCA
*
89465594 TCTTCTCATATCATCTATTTTATGCAAATTGCCCCAC
1 TCTTCTCATATCATATATTTTATGCAAATTGCCCCAC
*
89465631 TCTTCTCATATCATATATTTTATGCAAATTGCTCCAC
1 TCTTCTCATATCATATATTTTATGCAAATTGCCCCAC
89465668 TC
1 TC
89465670 AGGACAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.28, G:0.05, T:0.42
Consensus pattern (37 bp):
TCTTCTCATATCATATATTTTATGCAAATTGCCCCAC
Found at i:89467385 original size:3 final size:3
Alignment explanation
Indices: 89467377--89467420 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
89467367 TTATGCTGTG
89467377 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT A
89467421 AGGAATGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:89469577 original size:21 final size:22
Alignment explanation
Indices: 89469551--89469597 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
89469541 CTCTGCTCAA
*
89469551 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
89469572 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
89469594 ACTC
1 ACTC
89469598 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:89477744 original size:4 final size:4
Alignment explanation
Indices: 89477737--89477799 Score: 99
Period size: 4 Copynumber: 15.8 Consensus size: 4
89477727 GGCATATATA
* *
89477737 TATG TATG TATG TGTG TGTG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
89477785 TATG TATG TCTG TAT
1 TATG TATG TATG TAT
89477800 ATTGTGTGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.21, C:0.02, G:0.27, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:89479024 original size:18 final size:18
Alignment explanation
Indices: 89479001--89479055 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
89478991 TTCTTTTATC
*
89479001 AAATATATAAAAAATAAA
1 AAATATATATAAAATAAA
* *
89479019 AAATATGTATAAAATGAA
1 AAATATATATAAAATAAA
* *
89479037 AAATAAATATATAATAAA
1 AAATATATATAAAATAAA
89479055 A
1 A
89479056 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (18 bp):
AAATATATATAAAATAAA
Found at i:89479066 original size:22 final size:21
Alignment explanation
Indices: 89479001--89479115 Score: 69
Period size: 23 Copynumber: 5.3 Consensus size: 21
89478991 TTCTTTTATC
89479001 AAATATATAA-AAAA-T-AAA
1 AAATATATAATAAAATTAAAA
* *
89479019 AAATATGT-ATAAAATGAAAAA
1 AAATATATAATAAAAT-TAAAA
89479040 TAAATATATAATAAAATTCAAAA
1 -AAATATATAATAAAATT-AAAA
*
89479063 AAATAT-TATCTCAAAATTATAAA
1 AAATATATA-AT-AAAATTA-AAA
* *
89479086 AATTACTAAAATAAAATTTAGAAA
1 AAATA-TATAATAAAA-TTA-AAA
89479110 AAATAT
1 AAATAT
89479116 GGTAAATGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
17 1 0.01
18 11 0.15
21 5 0.07
22 15 0.20
23 29 0.39
24 12 0.16
25 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (21 bp):
AAATATATAATAAAATTAAAA
Found at i:89479299 original size:19 final size:21
Alignment explanation
Indices: 89479270--89479312 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
89479260 TTAATTTTTT
*
89479270 AAAATTGATTAAAATTTGT-A
1 AAAATTGATTAAAAATTGTGA
89479290 AAAATT-ATTAAAAATTGTGA
1 AAAATTGATTAAAAATTGTGA
89479310 AAA
1 AAA
89479313 CTATAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (21 bp):
AAAATTGATTAAAAATTGTGA
Found at i:89480519 original size:24 final size:24
Alignment explanation
Indices: 89480491--89480542 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
89480481 TTTCTAAAAG
* *
89480491 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
89480515 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
89480539 ATTT
1 ATTT
89480543 GACCTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:89485470 original size:95 final size:95
Alignment explanation
Indices: 89485344--89485530 Score: 347
Period size: 95 Copynumber: 2.0 Consensus size: 95
89485334 CCCCTGTCTC
89485344 GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAAAGTAATTTAT
1 GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAAAGTAATTTAT
*
89485409 CATAACCTTGTAATTACATGAAATAGACAG
66 CATAACCCTGTAATTACATGAAATAGACAG
*
89485439 GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAGAGTAATTTAT
1 GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAAAGTAATTTAT
*
89485504 CATAACCCTGTAATTAGATGAAATAGA
66 CATAACCCTGTAATTACATGAAATAGA
89485531 TTATTATGTA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (95 bp):
GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAAAGTAATTTAT
CATAACCCTGTAATTACATGAAATAGACAG
Found at i:89490244 original size:21 final size:20
Alignment explanation
Indices: 89490219--89490267 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
89490209 AAATAAATAC
*
89490219 CATAAAAATTTTAAAACTTTT
1 CATAAAAATTCTAAAA-TTTT
89490240 CAT-AAAATTCTAAAATTTT
1 CATAAAAATTCTAAAATTTT
89490259 CTATAAAAA
1 C-ATAAAAA
89490268 AAAACCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 5 0.20
20 13 0.52
21 7 0.28
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (20 bp):
CATAAAAATTCTAAAATTTT
Found at i:89493606 original size:63 final size:63
Alignment explanation
Indices: 89493531--89493666 Score: 254
Period size: 63 Copynumber: 2.2 Consensus size: 63
89493521 GAAAATTATT
*
89493531 GGGGCTAAAGTAAGGAAATTTTGGTAAGGAAATGATTAAATTGAATTAAGAAAAGAGGAGAAA
1 GGGGCTAGAGTAAGGAAATTTTGGTAAGGAAATGATTAAATTGAATTAAGAAAAGAGGAGAAA
89493594 GGGGCTAGAGTAAGGAAATTTTGGTAAGGAAATGATTAAATTGAATTAAGAAAAGAGGAGAAA
1 GGGGCTAGAGTAAGGAAATTTTGGTAAGGAAATGATTAAATTGAATTAAGAAAAGAGGAGAAA
*
89493657 GGGACTAGAG
1 GGGGCTAGAG
89493667 GTGGAAATTA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.46, C:0.02, G:0.31, T:0.21
Consensus pattern (63 bp):
GGGGCTAGAGTAAGGAAATTTTGGTAAGGAAATGATTAAATTGAATTAAGAAAAGAGGAGAAA
Found at i:89494340 original size:25 final size:23
Alignment explanation
Indices: 89494311--89494374 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 23
89494301 CTATTTGGCA
*
89494311 TTTGTGGCGTATTCTGTATGCTGCC
1 TTTGTGGCGTATTCTGTAT--AGCC
* *
89494336 TTTGTGGCATACTCTG-ATAGCC
1 TTTGTGGCGTATTCTGTATAGCC
89494358 TTTGTGGCGTATTCTGT
1 TTTGTGGCGTATTCTGT
89494375 CTGGCCCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 17 0.52
24 2 0.06
25 14 0.42
ACGTcount: A:0.11, C:0.19, G:0.27, T:0.44
Consensus pattern (23 bp):
TTTGTGGCGTATTCTGTATAGCC
Found at i:89494361 original size:22 final size:22
Alignment explanation
Indices: 89494333--89494398 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
89494323 TCTGTATGCT
89494333 GCCTTTGTGGCATACTCTGATA
1 GCCTTTGTGGCATACTCTGATA
* * * *
89494355 GCCTTTGTGGCGTATTCTGTCTG
1 GCCTTTGTGGCATACTCTG-ATA
* *
89494378 GCCCTTGTGGTATACTCTGAT
1 GCCTTTGTGGCATACTCTGAT
89494399 GAGTTTATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.12, C:0.23, G:0.26, T:0.39
Consensus pattern (22 bp):
GCCTTTGTGGCATACTCTGATA
Found at i:89494364 original size:47 final size:45
Alignment explanation
Indices: 89494311--89494398 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
89494301 CTATTTGGCA
*
89494311 TTTGTGGCGTATTCTGTATGCTGCCTTTGTGGCATACTCTGATAGCC
1 TTTGTGGCGTATTCTGTATG--GCCCTTGTGGCATACTCTGATAGCC
* *
89494358 TTTGTGGCGTATTCTGTCTGGCCCTTGTGGTATACTCTGAT
1 TTTGTGGCGTATTCTGTATGGCCCTTGTGGCATACTCTGAT
89494399 GAGTTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 19 0.50
47 19 0.50
ACGTcount: A:0.11, C:0.20, G:0.26, T:0.42
Consensus pattern (45 bp):
TTTGTGGCGTATTCTGTATGGCCCTTGTGGCATACTCTGATAGCC
Found at i:89496534 original size:6 final size:6
Alignment explanation
Indices: 89496523--89496547 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
89496513 AATTGCATAG
89496523 ATAATT ATAATT ATAATT ATAATT A
1 ATAATT ATAATT ATAATT ATAATT A
89496548 AAAAATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:89496740 original size:29 final size:29
Alignment explanation
Indices: 89496706--89496770 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
89496696 TAAATGAACT
89496706 TTAAATTT-TAAATTAAAAAAATAAAAAGA
1 TTAAATTTCTAAA-TAAAAAAATAAAAAGA
* * * *
89496735 TTAAATTTCTGAATATAAAAATATAAATA
1 TTAAATTTCTAAATAAAAAAATAAAAAGA
89496764 TTAAATT
1 TTAAATT
89496771 CCATACGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (29 bp):
TTAAATTTCTAAATAAAAAAATAAAAAGA
Found at i:89505204 original size:20 final size:20
Alignment explanation
Indices: 89505164--89505207 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
89505154 AATAGTTGAA
**
89505164 AAAAATTAAAATTTTGTTTT
1 AAAAATTAAAATTTTCCTTT
*
89505184 AAAAATTTAAATTTTCCTTT
1 AAAAATTAAAATTTTCCTTT
89505204 AAAA
1 AAAA
89505208 TAACAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAAATTAAAATTTTCCTTT
Found at i:89505261 original size:145 final size:142
Alignment explanation
Indices: 89504856--89505262 Score: 480
Period size: 144 Copynumber: 2.8 Consensus size: 142
89504846 AAAACCTTAT
* * *
89504856 TTCGAAATAGTT-AAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTT
1 TTCGAAATAGTTGAAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATAAC--
* *
89504920 AAAAAACATATTTTTTATTTTTCAAAATTTAAATTTTCTC-CTTTTTAAAAAAAAATTATTTTTC
64 -AAAAA-A-A---TTTATTTTTCAAAATCTAAATTTTCTCTTTTTTTAAAAAAAAATTATTTTTC
* *
89504984 TTAAAGATTAACGATTTTAT
123 TTAAAGATTAAAGATTTTAC
* **
89505004 TTTGATGTAGTTGAAAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGACA
1 TTCGAAATAGTTG-AAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAAT-A-A
* * * ***
89505069 AAAAAAAATTTATTTTTCAAAATCTAATTTTTTTCCTTTTTTT-AAAAAATGCTATTTTTCTTAA
63 CAAAAAAATTTATTTTTCAAAATCTAAATTTTCT-CTTTTTTTAAAAAAAAATTATTTTTCTTAA
*
89505133 AGATTAAAGCTTTTAC
127 AGATTAAAGATTTTAC
* * *
89505149 TTCGAAATAGTTGAAAAAAATTAAAATTTTGTTTTAAAAATTTAAATTTTCCTTTAAAATAACAA
1 TTCGAAATAGTTGAAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATAACAA
*
89505214 AAAAATTTATTTGTT-AAAATCTAAACTTTCTCTTTTTTTAAAAAAAAAT
66 AAAAATTTATTT-TTCAAAATCTAAATTTTCTCTTTTTTTAAAAAAAAAT
89505263 CAAAACTTTT
Statistics
Matches: 221, Mismatches: 30, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
141 8 0.04
142 34 0.15
143 3 0.01
144 67 0.30
145 42 0.19
146 5 0.02
147 1 0.00
148 10 0.05
149 5 0.02
150 45 0.20
152 1 0.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (142 bp):
TTCGAAATAGTTGAAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATAACAA
AAAAATTTATTTTTCAAAATCTAAATTTTCTCTTTTTTTAAAAAAAAATTATTTTTCTTAAAGAT
TAAAGATTTTAC
Found at i:89519745 original size:10 final size:9
Alignment explanation
Indices: 89519732--89519765 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
89519722 ATTAATTTTG
89519732 ATTAAATTAA
1 ATTAAATT-A
89519742 ATTAAATTA
1 ATTAAATTA
*
89519751 ATCAAATTA
1 ATTAAATTA
89519760 ATTAAA
1 ATTAAA
89519766 ATAAATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
ATTAAATTA
Found at i:89526510 original size:9 final size:9
Alignment explanation
Indices: 89526481--89526510 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
89526471 TAAATTTTAC
89526481 AATTCGAAT
1 AATTCGAAT
*
89526490 AACTCGAAT
1 AATTCGAAT
89526499 AATTCGAAT
1 AATTCGAAT
89526508 AAT
1 AAT
89526511 AAATTGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:89533057 original size:4 final size:4
Alignment explanation
Indices: 89533048--89533072 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
89533038 AATGAGGCGA
89533048 GGAT GGAT GGAT GGAT GGAT GGAT G
1 GGAT GGAT GGAT GGAT GGAT GGAT G
89533073 TATTGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.52, T:0.24
Consensus pattern (4 bp):
GGAT
Found at i:89538266 original size:47 final size:48
Alignment explanation
Indices: 89538214--89538319 Score: 117
Period size: 54 Copynumber: 2.1 Consensus size: 48
89538204 TGGTTGGACC
89538214 ATGGC-AACAAGTGATAAGC-GATATCCGTATAAGACCATAGCTAGGCT
1 ATGGCAAACAAGTGATAA-CTGATATCCGTATAAGACCATAGCTAGGCT
* *
89538261 ATGGCATCGAAAAACAAGTGATAACTGATTTCCGTATAAGACCATAGCTGGGCT
1 ATGG---C---AAACAAGTGATAACTGATATCCGTATAAGACCATAGCTAGGCT
89538315 ATGGC
1 ATGGC
89538320 TTTGGATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
47 4 0.08
50 1 0.02
51 1 0.02
53 1 0.02
54 42 0.86
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (48 bp):
ATGGCAAACAAGTGATAACTGATATCCGTATAAGACCATAGCTAGGCT
Found at i:89541340 original size:25 final size:25
Alignment explanation
Indices: 89541312--89541413 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 25
89541302 TTACCTAAAT
89541312 AGCCTATGTGGCGTA-TTATTTGGAA
1 AGCCTATGTGGCG-AGTTATTTGGAA
*
89541337 AGCCT-TAGTGGAGAGGTTATTTGGGAA
1 AGCCTAT-GTGGCGA-GTTATTT-GGAA
* * *
89541364 A-CCTTTGTGGCGAGTTATCTGAAA
1 AGCCTATGTGGCGAGTTATTTGGAA
*
89541388 AGCTTATGTGGCGTA-TTATTTGGAA
1 AGCCTATGTGGCG-AGTTATTTGGAA
89541413 A
1 A
89541414 ACCTTAGTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
24 6 0.10
25 34 0.55
26 16 0.26
27 6 0.10
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.34
Consensus pattern (25 bp):
AGCCTATGTGGCGAGTTATTTGGAA
Found at i:89541368 original size:26 final size:25
Alignment explanation
Indices: 89541327--89541443 Score: 89
Period size: 26 Copynumber: 4.6 Consensus size: 25
89541317 ATGTGGCGTA
89541327 TTATTTGGAAAGCCTTAGTGGAGAGG
1 TTATTTGGAAAGCCTTAGTGGAGA-G
* *
89541353 TTATTTGGGAAA-CCTTTGTGGCGAG
1 TTATTT-GGAAAGCCTTAGTGGAGAG
* * *
89541378 TTATCTGAAAAG-CTTATGTGGCGTA-
1 TTATTTGGAAAGCCTTA-GTGGAG-AG
*
89541403 TTATTTGGAAAACCTTAGTAGTGAG-G
1 TTATTTGGAAAGCCTTAGT-G-GAGAG
*
89541429 TCATTTGGAAAGCCT
1 TTATTTGGAAAGCCT
89541444 GTAAAATGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
24 7 0.10
25 23 0.32
26 35 0.49
27 7 0.10
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.34
Consensus pattern (25 bp):
TTATTTGGAAAGCCTTAGTGGAGAG
Found at i:89541402 original size:76 final size:77
Alignment explanation
Indices: 89541276--89541443 Score: 218
Period size: 76 Copynumber: 2.2 Consensus size: 77
89541266 TTTATGACAA
* *
89541276 GTTATTT-GTAAAGCCTTTGTAGCAAGTTACCTAAATAGCCTATGTGGCGTATTATTTGGAAAGC
1 GTTATTTGGGAAAGCCTTTGTAGCAAGTTACCTAAATAGCCTATGTGGCGTATTATTTGGAAAAC
*
89541340 CTTAGTGGAGAG
66 CTTAGTAGAGAG
* * * *
89541352 GTTATTTGGGAAA-CCTTTGTGGCGAGTTATCTGAAA-AGCTTATGTGGCGTATTATTTGGAAAA
1 GTTATTTGGGAAAGCCTTTGTAGCAAGTTACCT-AAATAGCCTATGTGGCGTATTATTTGGAAAA
*
89541415 CCTTAGTAGTGAG
65 CCTTAGTAGAGAG
*
89541428 GTCATTT-GGAAAGCCT
1 GTTATTTGGGAAAGCCT
89541444 GTAAAATGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
75 5 0.06
76 68 0.85
77 7 0.09
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (77 bp):
GTTATTTGGGAAAGCCTTTGTAGCAAGTTACCTAAATAGCCTATGTGGCGTATTATTTGGAAAAC
CTTAGTAGAGAG
Found at i:89542541 original size:34 final size:34
Alignment explanation
Indices: 89542498--89542563 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
89542488 AATGCATAAT
*
89542498 TAAGTCTTTATTGTATTTTATTCCATATCACAAC
1 TAAGTCTTTATTGTATTTTATTCCACATCACAAC
89542532 TAAGTCTTTATTGTATTTTATTCCACATCACA
1 TAAGTCTTTATTGTATTTTATTCCACATCACA
89542564 TTATATGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (34 bp):
TAAGTCTTTATTGTATTTTATTCCACATCACAAC
Found at i:89553397 original size:30 final size:30
Alignment explanation
Indices: 89553363--89553425 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
89553353 ACTTAACAAG
*
89553363 CAAATGGCTCTAAAATAGA-AACAAAATTAA
1 CAAATGCCTCTAAAATA-ATAACAAAATTAA
*
89553393 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
89553423 CAA
1 CAA
89553426 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.57, C:0.14, G:0.06, T:0.22
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:89561923 original size:26 final size:26
Alignment explanation
Indices: 89561894--89561943 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
89561884 CTCAGAAAAA
89561894 TTTTGATGATTTTACCCTTGGTAATT
1 TTTTGATGATTTTACCCTTGGTAATT
*
89561920 TTTTGATGATTTTGCCCTTGGTAA
1 TTTTGATGATTTTACCCTTGGTAA
89561944 AATTTCGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (26 bp):
TTTTGATGATTTTACCCTTGGTAATT
Found at i:89562049 original size:6 final size:6
Alignment explanation
Indices: 89562038--89562074 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
89562028 TGCAAACGGA
* *
89562038 TCATTT TCATTT TCATTT TCATTT CCATTT CCATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT T
89562075 TGAAAACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (6 bp):
TCATTT
Found at i:89565968 original size:12 final size:12
Alignment explanation
Indices: 89565951--89565975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89565941 GAGTAGCAAA
89565951 ACTGCCCTGAAT
1 ACTGCCCTGAAT
89565963 ACTGCCCTGAAT
1 ACTGCCCTGAAT
89565975 A
1 A
89565976 TTTGGATGAG
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:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGCCCTGAAT
Found at i:89566182 original size:11 final size:11
Alignment explanation
Indices: 89566165--89566207 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
89566155 TAAATAAGAG
89566165 AAAATAAAATT
1 AAAATAAAATT
* *
89566176 TAAATAAAAATA
1 AAAAT-AAAATT
*
89566188 AAAATAAAAAT
1 AAAATAAAATT
89566199 AAAATAAAA
1 AAAATAAAA
89566208 GGACTCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATAAAATT
Found at i:89566186 original size:6 final size:6
Alignment explanation
Indices: 89566150--89566207 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
89566140 ATAAGTCTTC
* **
89566150 AAAAAT AAATAAG AGAAAAT -AAAAT TTAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAA-AAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
89566199 -AAAAT AAAA
1 AAAAAT AAAA
89566208 GGACTCAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 10 0.23
6 26 0.60
7 5 0.12
8 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:89572200 original size:30 final size:30
Alignment explanation
Indices: 89572159--89572215 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
89572149 ACGGCCATGA
*
89572159 CACACGGGCGTGTGGCCTACCCGTGTGTCT
1 CACACGAGCGTGTGGCCTACCCGTGTGTCT
*
89572189 CACACGAGCGTGTGGTCTACCCGTGTG
1 CACACGAGCGTGTGGCCTACCCGTGTG
89572216 GAAGTGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.32, G:0.33, T:0.23
Consensus pattern (30 bp):
CACACGAGCGTGTGGCCTACCCGTGTGTCT
Found at i:89578757 original size:24 final size:24
Alignment explanation
Indices: 89578730--89578781 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
89578720 TTAGTAAGTC
*
89578730 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
89578754 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
89578778 AAAT
1 AAAT
89578782 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:89580727 original size:24 final size:24
Alignment explanation
Indices: 89580700--89580751 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
89580690 TTAGTAAGTC
*
89580700 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
89580724 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
89580748 AAAT
1 AAAT
89580752 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:89582208 original size:7 final size:7
Alignment explanation
Indices: 89582200--89582230 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
89582190 AAGAGGGTCT
*
89582200 CTAGTCT
1 CTAGTCC
89582207 CTAGTCC
1 CTAGTCC
89582214 CTAGTCC
1 CTAGTCC
89582221 CTAGTCC
1 CTAGTCC
89582228 CTA
1 CTA
89582231 CCCTATTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.39, G:0.13, T:0.32
Consensus pattern (7 bp):
CTAGTCC
Done.