Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold42.1
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: 2894208
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 43663 characters in sequence are not A, C, G, or T
File 4 of 11
Found at i:731032 original size:37 final size:38
Alignment explanation
Indices: 730991--731062 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
730981 GAACAACAAA
*
730991 TAATAATAATACATTAAT-AA-AAATAATAAGAATGTGT
1 TAATAATAATAAATTAATGAATAAATAATAA-AATGTGT
*
731028 TAATAATAATAAATTAATGAATTAATAATAAAATG
1 TAATAATAATAAATTAATGAATAAATAATAAAATG
731063 AATAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 17 0.55
38 6 0.19
39 8 0.26
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.33
Consensus pattern (38 bp):
TAATAATAATAAATTAATGAATAAATAATAAAATGTGT
Found at i:731055 original size:16 final size:17
Alignment explanation
Indices: 731034--731076 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
731024 GTGTTAATAA
*
731034 TAATAAAT-TAATGAAT
1 TAATAAATAAAATGAAT
731050 TAAT-AATAAAATGAAT
1 TAATAAATAAAATGAAT
*
731066 AAATAAATAAA
1 TAATAAATAAA
731077 CACAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 14 0.61
17 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
TAATAAATAAAATGAAT
Found at i:735548 original size:3 final size:3
Alignment explanation
Indices: 735540--735844 Score: 98
Period size: 3 Copynumber: 99.7 Consensus size: 3
735530 GGGGAAAAAT
* * *
735540 ATA ATA ATA ATA AT- ATA ATA ATA ATA TTA GTA ATA A-A A-A AT- AGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
735584 ACA ACAA ATA ATA ATA ATA CATTA ATA AAA ATA ATA AGA ATGCG TTG
1 ATA A-TA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA AT--A ATA
* * *
735631 ATA ATA GTA A-A TTA AGGA ATTA ATA ATA A-A ATGA ATAA ATAA ATA
1 ATA ATA ATA ATA ATA A-TA A-TA ATA ATA ATA AT-A AT-A AT-A ATA
* * * * * *
735676 A-A CACA AAA ATA A-A AT- ATA ATT ATA ATA GTA ATA TTA ACA A-A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
735718 ATA ATA GTA GTA ATA ATA ATA ATA ATA ATA CATTA ATA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA
* * * *
735765 AGA ATGCG TTA ATA ATA ATA A-A TTA ATGA ATTA ATA ATA A-A ATGA
1 ATA AT--A ATA ATA ATA ATA ATA ATA AT-A A-TA ATA ATA ATA AT-A
735810 ATAA ATAA ATA A-A AT- ATA ATA ATA ATA ATA ATA AT
1 AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
735845 GTGATAAAGC
Statistics
Matches: 229, Mismatches: 45, Indels: 56
0.69 0.14 0.17
Matches are distributed among these distances:
2 24 0.10
3 163 0.71
4 35 0.15
5 7 0.03
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:735790 original size:37 final size:38
Alignment explanation
Indices: 735737--735808 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
735727 GTAATAATAA
*
735737 TAATAATAATACATTAAT-AA-AAATAATAAGAATGCGT
1 TAATAATAATAAATTAATGAATAAATAATAA-AATGCGT
*
735774 TAATAATAATAAATTAATGAATTAATAATAAAATG
1 TAATAATAATAAATTAATGAATAAATAATAAAATG
735809 AATAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 17 0.55
38 6 0.19
39 8 0.26
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (38 bp):
TAATAATAATAAATTAATGAATAAATAATAAAATGCGT
Found at i:735801 original size:16 final size:17
Alignment explanation
Indices: 735780--735824 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
735770 GCGTTAATAA
*
735780 TAATAAAT-TAATGAAT
1 TAATAAATAAAATGAAT
735796 TAAT-AATAAAATGAAT
1 TAATAAATAAAATGAAT
*
735812 AAATAAATAAAAT
1 TAATAAATAAAAT
735825 ATAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 14 0.56
17 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (17 bp):
TAATAAATAAAATGAAT
Found at i:735841 original size:145 final size:141
Alignment explanation
Indices: 735535--735844 Score: 428
Period size: 145 Copynumber: 2.2 Consensus size: 141
735525 GTAATGGGGA
* * *
735535 AAAATATAATAATAATAAT-ATAATAATAATATTAGTAATAAAAAATAGAACAACAAATAATAAT
1 AAAATATAATAATAATAATAATAATAATAATAATAGTAACAAAAAATAGAACAAAAAATAATAAT
* *
735599 AATACATTAATAAAAATAATAAGAATGCGTTGATAATAGTAAATTAAGGAATTAATAATAAAATG
66 AATACATTAATAAAAATAATAAGAATGCGTTAATAATAATAAATTAAGGAATTAATAATAAAATG
735664 AATAAATAAAT
131 AATAAATAAAT
* * * * * **
735675 AAACACA-AA-AATAAAATATAATTATAATAGTAATATTAACAAAATAATAGTAGTAATAATAAT
1 AAA-ATATAATAATAATA-ATAATAATAATAATAATAGTAACAAAA-AATAG-AACAA-AA-AAT
*
735738 AATAATAATACATTAATAAAAATAATAAGAATGCGTTAATAATAATAAATTAATGAATTAATAAT
60 AATAATAATACATTAATAAAAATAATAAGAATGCGTTAATAATAATAAATTAAGGAATTAATAAT
735803 AAAATGAATAAATAAAT
125 AAAATGAATAAATAAAT
735820 AAAATATAATAATAATAATAATAAT
1 AAAATATAATAATAATAATAATAAT
735845 GTGATAAAGC
Statistics
Matches: 145, Mismatches: 16, Indels: 13
0.83 0.09 0.07
Matches are distributed among these distances:
139 6 0.04
140 7 0.05
141 21 0.14
142 5 0.03
143 3 0.02
144 3 0.02
145 94 0.65
146 6 0.04
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (141 bp):
AAAATATAATAATAATAATAATAATAATAATAATAGTAACAAAAAATAGAACAAAAAATAATAAT
AATACATTAATAAAAATAATAAGAATGCGTTAATAATAATAAATTAAGGAATTAATAATAAAATG
AATAAATAAAT
Found at i:735851 original size:20 final size:20
Alignment explanation
Indices: 735731--735851 Score: 82
Period size: 20 Copynumber: 6.3 Consensus size: 20
735721 ATAGTAGTAA
735731 TAATAATAATAATAATACAT-
1 TAATAATAATAATAATA-ATG
* *
735751 TAATAAAAATAATAAGAATGCG
1 TAATAATAATAATAATAAT--G
*
735773 TTAATAATAATAA-ATTAATG
1 -TAATAATAATAATAATAATG
735793 -AAT--TAATAATAA-AATG
1 TAATAATAATAATAATAATG
*
735809 -AAT-A-AATAAATAA-AATA
1 TAATAATAAT-AATAATAATG
735826 TAATAATAATAATAATAATG
1 TAATAATAATAATAATAATG
*
735846 TGATAA
1 TAATAA
735852 AGCAACCAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
16 16 0.20
17 9 0.11
18 6 0.07
19 8 0.10
20 27 0.33
22 4 0.05
23 11 0.14
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (20 bp):
TAATAATAATAATAATAATG
Found at i:738349 original size:15 final size:15
Alignment explanation
Indices: 738331--738369 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
738321 TTAGTCTTAA
738331 TTAATTAATAAAAAC
1 TTAATTAATAAAAAC
* *
738346 TTAATTAATTAAACC
1 TTAATTAATAAAAAC
738361 TTAACTTAA
1 TTAA-TTAA
738370 ATTTAGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAATTAATAAAAAC
Found at i:743434 original size:19 final size:18
Alignment explanation
Indices: 743380--743457 Score: 50
Period size: 22 Copynumber: 4.1 Consensus size: 18
743370 GATTGTCCAT
* *
743380 TTATAAAATTTTAATAAA
1 TTATAAAAATATAATAAA
*
743398 TTAAAAAATATTGAATAATAAA
1 TTATAAAA-A-T--ATAATAAA
*
743420 TTATAAATAATATAAATAAT
1 TTATAAA-AATAT-AATAAA
*
743440 TTTTAAAAATATAA-AAA
1 TTATAAAAATATAATAAA
743457 T
1 T
743458 AATATGAGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
17 3 0.06
18 9 0.19
19 7 0.15
20 12 0.26
21 1 0.02
22 14 0.30
23 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (18 bp):
TTATAAAAATATAATAAA
Found at i:746547 original size:30 final size:31
Alignment explanation
Indices: 746479--746539 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
746469 TTAAAGTAGT
*
746479 AATGAT-AAAATTGTACTTTAACTCCTCTAA
1 AATGATAAAAATTGTAATTTAACTCCTCTAA
*
746509 AATGATAAAAATT-TAATTTAA-TCCTTTAA
1 AATGATAAAAATTGTAATTTAACTCCTCTAA
746538 AA
1 AA
746540 ATTATAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 9 0.32
30 13 0.46
31 6 0.21
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (31 bp):
AATGATAAAAATTGTAATTTAACTCCTCTAA
Found at i:751171 original size:60 final size:60
Alignment explanation
Indices: 751101--751220 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
751091 AAACCGGTGT
751101 ATTTAAACTAAAAGCTTATGTAACCATCGCACATTCTTCCCTTGCTGATGTCCCCACCAA
1 ATTTAAACTAAAAGCTTATGTAACCATCGCACATTCTTCCCTTGCTGATGTCCCCACCAA
*
751161 ATTTAAACTAAAAGCTTATGTAACCATCGCACCTTCTTCCCTTGCTGATGTCCCCACCAA
1 ATTTAAACTAAAAGCTTATGTAACCATCGCACATTCTTCCCTTGCTGATGTCCCCACCAA
751221 CATTCATGCT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.30
Consensus pattern (60 bp):
ATTTAAACTAAAAGCTTATGTAACCATCGCACATTCTTCCCTTGCTGATGTCCCCACCAA
Found at i:760169 original size:42 final size:42
Alignment explanation
Indices: 760122--760207 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
760112 ATCGAGCTAA
* * **
760122 TACTCAATTGGTGATGCGTTTTGTTCTTAAATTTAGTTCTTT
1 TACTCAATTGGTAATGCGTTTTATTCTTAAATTTAAATCTTT
760164 TACTCAATTGGTAATGCGTTTTATTCTTAAATTTAAATCTTT
1 TACTCAATTGGTAATGCGTTTTATTCTTAAATTTAAATCTTT
760206 TA
1 TA
760208 TTTAAAGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.51
Consensus pattern (42 bp):
TACTCAATTGGTAATGCGTTTTATTCTTAAATTTAAATCTTT
Found at i:762743 original size:40 final size:40
Alignment explanation
Indices: 762664--762774 Score: 188
Period size: 40 Copynumber: 2.8 Consensus size: 40
762654 TTGAAGGAAT
*
762664 ATATCCGGGTTAAATTCCGCAGGC-TTGTGCTGGTAATAG
1 ATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATAG
762703 ATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATAG
1 ATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATAG
* *
762743 ATATCTGGGTTAAATCCCACAGGCTTTGTGCT
1 ATATCCGGGTTAAATCCCGCAGGCTTTGTGCT
762775 AGAAATTGGA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
39 23 0.34
40 45 0.66
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (40 bp):
ATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATAG
Found at i:764237 original size:10 final size:10
Alignment explanation
Indices: 764222--764246 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
764212 ATAGAATATA
764222 TTATTTTGTT
1 TTATTTTGTT
764232 TTATTTTGTT
1 TTATTTTGTT
764242 TTATT
1 TTATT
764247 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (10 bp):
TTATTTTGTT
Found at i:767906 original size:26 final size:26
Alignment explanation
Indices: 767852--767906 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
767842 ATAATATATT
767852 TATATTATTTTAATTTAATAATTTAA
1 TATATTATTTTAATTTAATAATTTAA
*
767878 TATATT-TTTT-ATATTAA-AATTTTA
1 TATATTATTTTAAT-TTAATAATTTAA
767902 TATAT
1 TATAT
767907 GGTCATCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 13 0.48
25 8 0.30
26 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATATTATTTTAATTTAATAATTTAA
Found at i:770681 original size:11 final size:11
Alignment explanation
Indices: 770665--770694 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
770655 ACAGTGTTGA
770665 AAGGAATACTT
1 AAGGAATACTT
770676 AAGGAATACTT
1 AAGGAATACTT
*
770687 AACGAATA
1 AAGGAATA
770695 AGAACGGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (11 bp):
AAGGAATACTT
Found at i:771040 original size:17 final size:17
Alignment explanation
Indices: 770999--771040 Score: 75
Period size: 18 Copynumber: 2.4 Consensus size: 17
770989 AATGCCATGT
770999 TTTTTGTTACCGAAATC
1 TTTTTGTTACCGAAATC
771016 TATTTTGTTACCGAAATC
1 T-TTTTGTTACCGAAATC
771034 TTTTTGT
1 TTTTTGT
771041 AGAGAGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.52
Consensus pattern (17 bp):
TTTTTGTTACCGAAATC
Found at i:776442 original size:21 final size:21
Alignment explanation
Indices: 776416--776456 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
776406 ATCTGCTCAA
* *
776416 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
776437 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
776457 TTGCTGGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:782406 original size:17 final size:17
Alignment explanation
Indices: 782384--782419 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
782374 AAAAAAATCG
782384 TTTAATACATAAATTTA
1 TTTAATACATAAATTTA
*
782401 TTTAATAGATAAATTTA
1 TTTAATACATAAATTTA
782418 TT
1 TT
782420 AAAGAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAATACATAAATTTA
Found at i:787488 original size:18 final size:18
Alignment explanation
Indices: 787462--787497 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
787452 AAGTGAAATT
787462 TTAAAATATAATTTTATA
1 TTAAAATATAATTTTATA
*
787480 TTAACATATAATTTTATA
1 TTAAAATATAATTTTATA
787498 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAAATATAATTTTATA
Found at i:801233 original size:18 final size:18
Alignment explanation
Indices: 801210--801267 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
801200 TAATGACTTG
801210 TTTTATTAAATTTTAAAA
1 TTTTATTAAATTTTAAAA
* *
801228 TTTTATGT-ACTTTT-TAA
1 TTTTAT-TAAATTTTAAAA
801245 TTTTATTAAGATTTTTAAAA
1 TTTTATTAA-A-TTTTAAAA
801265 TTT
1 TTT
801268 GTAAGATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 1 0.03
17 9 0.29
18 11 0.35
19 5 0.16
20 5 0.16
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTATTAAATTTTAAAA
Found at i:803433 original size:21 final size:22
Alignment explanation
Indices: 803409--803449 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
803399 TAATAATACA
803409 TTAAATTAAA-AAAATAAATTC
1 TTAAATTAAAGAAAATAAATTC
*
803430 TTAATTTAAAGAAAATAAAT
1 TTAAATTAAAGAAAATAAAT
803450 GTAATTATTT
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:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
TTAAATTAAAGAAAATAAATTC
Found at i:818610 original size:12 final size:11
Alignment explanation
Indices: 818595--818635 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
818585 TTGATTTATA
818595 TTTGAATTATTT
1 TTTGAATT-TTT
818607 TTTGAACTTTTT
1 TTTGAA-TTTTT
*
818619 TTTGAACTTTT
1 TTTGAATTTTT
818630 TTTGAA
1 TTTGAA
818636 CTCGTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.37
12 15 0.56
13 2 0.07
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (11 bp):
TTTGAATTTTT
Found at i:818618 original size:11 final size:11
Alignment explanation
Indices: 818604--818637 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
818594 ATTTGAATTA
818604 TTTTTTGAACTT
1 TTTTTTGAAC-T
818616 TTTTTTGAACT
1 TTTTTTGAACT
818627 TTTTTTGAACT
1 TTTTTTGAACT
818638 CGTAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.65
Consensus pattern (11 bp):
TTTTTTGAACT
Found at i:819835 original size:39 final size:41
Alignment explanation
Indices: 819785--819888 Score: 117
Period size: 39 Copynumber: 2.6 Consensus size: 41
819775 TTTTGATATG
* * * *
819785 ACAATATTAAAAACCAATTATG-A-ACAAGAAAATTTTGAA
1 ACAAGATTAAAAACCAATTACGAATAAAAAAAAATTTTGAA
*
819824 ACAGGATTAAAAA--AATTACGAATAAAAAAAAATTTTGAA
1 ACAAGATTAAAAACCAATTACGAATAAAAAAAAATTTTGAA
* *
819863 ACAAGATTAAAAACCAAATACAAATA
1 ACAAGATTAAAAACCAATTACGAATA
819889 GATAAATTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
37 6 0.11
38 1 0.02
39 37 0.70
41 9 0.17
ACGTcount: A:0.61, C:0.10, G:0.08, T:0.22
Consensus pattern (41 bp):
ACAAGATTAAAAACCAATTACGAATAAAAAAAAATTTTGAA
Found at i:831804 original size:55 final size:56
Alignment explanation
Indices: 831668--831790 Score: 187
Period size: 56 Copynumber: 2.2 Consensus size: 56
831658 GGGTGTTGAG
* *
831668 ATATTATCTTTTAGCAATTTGATTCCT-ATGGGATATTATAAGATATTACTATGGA
1 ATATTATCTTTTAGCAATTTGATTCCTAATAGGATATTACAAGATATTACTATGGA
* *
831723 ATATTATCTTTTAGCAATTTGATTCCTAATAGGATATTACAGGATATTATTATGGTA
1 ATATTATCTTTTAGCAATTTGATTCCTAATAGGATATTACAAGATATTACTATGG-A
831780 A-ATTATCTTTT
1 ATATTATCTTTT
831791 GTAATCCGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
55 27 0.44
56 33 0.53
57 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (56 bp):
ATATTATCTTTTAGCAATTTGATTCCTAATAGGATATTACAAGATATTACTATGGA
Found at i:841716 original size:30 final size:30
Alignment explanation
Indices: 841680--841741 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
841670 TTCCCGAGTC
841680 TAGGGGTAAAAGTGTAAATATGTAAAAGTT
1 TAGGGGTAAAAGTGTAAATATGTAAAAGTT
* * * *
841710 TAGGGGTAAAATTGTAATTTTGTTAAAGTT
1 TAGGGGTAAAAGTGTAAATATGTAAAAGTT
841740 TA
1 TA
841742 AGTTAAGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (30 bp):
TAGGGGTAAAAGTGTAAATATGTAAAAGTT
Found at i:845810 original size:15 final size:15
Alignment explanation
Indices: 845790--845822 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
845780 ACTCCATTTT
845790 ATTTATATTAGGATA
1 ATTTATATTAGGATA
845805 ATTTATATTAGGATA
1 ATTTATATTAGGATA
845820 ATT
1 ATT
845823 ATTAGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (15 bp):
ATTTATATTAGGATA
Found at i:848729 original size:25 final size:23
Alignment explanation
Indices: 848687--848738 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
848677 ATTTTTTAAA
* *
848687 AAAATTAAAAATTTAAAAACTCTTT
1 AAAATTAAAAA-TAAAAAAAT-TTT
848712 AAAATTAAAAATAAAAAAATTTT
1 AAAATTAAAAATAAAAAAATTTT
848735 AAAA
1 AAAA
848739 AACATTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 7 0.28
25 11 0.44
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATTAAAAATAAAAAAATTTT
Found at i:850470 original size:25 final size:23
Alignment explanation
Indices: 850428--850479 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
850418 ATTTTTTAAA
* *
850428 AAAATTAAAAATTTAAAAACTCTTT
1 AAAATTAAAAA-TAAAAAAAT-TTT
850453 AAAATTAAAAATAAAAAAATTTT
1 AAAATTAAAAATAAAAAAATTTT
850476 AAAA
1 AAAA
850480 AACATTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 7 0.28
25 11 0.44
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATTAAAAATAAAAAAATTTT
Found at i:854267 original size:28 final size:28
Alignment explanation
Indices: 854206--854273 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
854196 AGTAAATAAC
*
854206 ATTTTTTTAAAATTTTGAAATTAGTTAT
1 ATTTTTTTAAAATTTTGAAATTAGTTAA
*
854234 ATTTTTATAAAATTTTG-AATTA-TTAA
1 ATTTTTTTAAAATTTTGAAATTAGTTAA
854260 ATGATTTTTTAAAA
1 AT--TTTTTTAAAA
854274 ATATTATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.14
27 5 0.14
28 25 0.71
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (28 bp):
ATTTTTTTAAAATTTTGAAATTAGTTAA
Found at i:861960 original size:40 final size:39
Alignment explanation
Indices: 861873--862005 Score: 140
Period size: 35 Copynumber: 3.6 Consensus size: 39
861863 GTTTTCCTCA
*
861873 TTGAAATACCATACCTACATTT-TACAACTCGGTATGG--
1 TTGAAATACCATACCTACATTTCT-CAACTCAGTATGGAT
* *
861910 --GAAATGCCATACCTACATTTCTTAACTCAGTATGGAT
1 TTGAAATACCATACCTACATTTCTCAACTCAGTATGGAT
*
861947 TTGATAATACCATACCTACATTTCACAACTCAGTATGGA-
1 TTGA-AATACCATACCTACATTTCTCAACTCAGTATGGAT
*
861986 -TG--ATACCATACGTACATTTC
1 TTGAAATACCATACCTACATTTC
862006 ACACTTTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
35 47 0.57
36 1 0.01
38 2 0.02
39 2 0.02
40 31 0.37
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (39 bp):
TTGAAATACCATACCTACATTTCTCAACTCAGTATGGAT
Found at i:864545 original size:130 final size:130
Alignment explanation
Indices: 864265--864911 Score: 980
Period size: 130 Copynumber: 5.0 Consensus size: 130
864255 TTTAGAGAAT
* * *
864265 CATGAGTGAAATTCTAAAGGAATATTTGATTATTTTGAAAAAAC-AGAAAATCGCAACCCAGCAC
1 CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAG-AAATCGCAACCCAGCAC
* ** ** *
864329 GATAAGGCACGATTCCCTGAATTGCCAAACATC-GAGTATTACCTTCGTTTCGAAGAGTTTTTAA
65 GATAGGGCACGATTCCC-GAATTGCCAAACATCGGA-TATCGCCTTCGTTTTAAAGAATTTTTAA
864393 AGA
128 AGA
* * *
864396 TATGAGTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGGGAAATCGCAACCCAGCACG
1 CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
* *
864461 ATAGGGCACGATTCCCGAATTGACAAACATCGGGTA-CTGCCTTCGTTTTAAAGAATTTTTAAAG
66 ATAGGGCACGATTCCCGAATTGCCAAACATCGGATATC-GCCTTCGTTTTAAAGAATTTTTAAAG
864525 A
130 A
*
864526 CATGAGCGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
1 CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
* *
864591 ATAGCGCACGATTCCCGAATTGCCAAACATCGGATATCGCCTTCATTTTAAAGAATTTTTAAAGA
66 ATAGGGCACGATTCCCGAATTGCCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAAGA
* *
864656 C--GAGTAAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCTAGCACG
1 CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
* *
864719 ATAGGGCACGATTCCCGAATTGCCAAACATCAGATATGGCCTTCGTTTTAAAGAATTTTTAAAGA
66 ATAGGGCACGATTCCCGAATTGCCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAAGA
* *
864784 CATGAGCGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
1 CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
* * * *
864849 ATAAGGCACGATTCCCGAATTGCCAAACATTGAATATCGCCTTTGTTTTAAAGAATTTTTAAA
66 ATAGGGCACGATTCCCGAATTGCCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAA
864912 TGAATAGGTA
Statistics
Matches: 471, Mismatches: 39, Indels: 13
0.90 0.07 0.02
Matches are distributed among these distances:
128 121 0.26
130 275 0.58
131 74 0.16
132 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (130 bp):
CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
ATAGGGCACGATTCCCGAATTGCCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAAGA
Found at i:864732 original size:258 final size:259
Alignment explanation
Indices: 864265--864911 Score: 1007
Period size: 258 Copynumber: 2.5 Consensus size: 259
864255 TTTAGAGAAT
* * * *
864265 CATGAGTGAAATTCTAAAGGAATATTTGATTATTTTGAAAAAAC-AGAAAATCGCAACCCAGCAC
1 CATGAGCGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAG-AAATCGCAACCCAGCAC
** ** *
864329 GATAAGGCACGATTCCCTGAATTGCCAAACATC-GAGTATTACCTTCGTTTCGAAGAGTTTTTAA
65 GATAAGGCACGATTCCC-GAATTGCCAAACATCGGA-TATCGCCTTCGTTTTAAAGAATTTTTAA
* * *
864393 AGATATGAGTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGGGAAATCGCAACCCAGC
128 AGA-ACGAGTAAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGC
* *
864458 ACGATAGGGCACGATTCCCGAATTGACAAACATCGGGTACT-GCCTTCGTTTTAAAGAATTTTTA
192 ACGATAGGGCACGATTCCCGAATTGACAAACATCAGATA-TGGCCTTCGTTTTAAAGAATTTTTA
864522 AAGA
256 AAGA
864526 CATGAGCGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
1 CATGAGCGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
*
864591 AT-AGCGCACGATTCCCGAATTGCCAAACATCGGATATCGCCTTCATTTTAAAGAATTTTTAAAG
66 ATAAG-GCACGATTCCCGAATTGCCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAAG
* *
864655 -ACGAGTAAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCTAGCACG
130 AACGAGTAAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
*
864719 ATAGGGCACGATTCCCGAATTGCCAAACATCAGATATGGCCTTCGTTTTAAAGAATTTTTAAAGA
195 ATAGGGCACGATTCCCGAATTGACAAACATCAGATATGGCCTTCGTTTTAAAGAATTTTTAAAGA
*
864784 CATGAGCGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
1 CATGAGCGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
* * *
864849 ATAAGGCACGATTCCCGAATTGCCAAACATTGAATATCGCCTTTGTTTTAAAGAATTTTTAAA
66 ATAAGGCACGATTCCCGAATTGCCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAA
864912 TGAATAGGTA
Statistics
Matches: 358, Mismatches: 23, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
257 1 0.00
258 239 0.67
259 2 0.01
260 41 0.11
261 73 0.20
262 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (259 bp):
CATGAGCGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
ATAAGGCACGATTCCCGAATTGCCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAAGA
ACGAGTAAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACGA
TAGGGCACGATTCCCGAATTGACAAACATCAGATATGGCCTTCGTTTTAAAGAATTTTTAAAGA
Found at i:865215 original size:31 final size:31
Alignment explanation
Indices: 865179--865241 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
865169 AATTCAATAC
865179 AACCAAAACAATACACATAATACATAGCATG
1 AACCAAAACAATACACATAATACATAGCATG
*
865210 AACCAAAACAATACACATAGTACATAGCATG
1 AACCAAAACAATACACATAATACATAGCATG
865241 A
1 A
865242 TATAAAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.54, C:0.22, G:0.08, T:0.16
Consensus pattern (31 bp):
AACCAAAACAATACACATAATACATAGCATG
Found at i:866128 original size:29 final size:28
Alignment explanation
Indices: 866067--866128 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
866057 CTAAAAAACC
* *
866067 TAATTGAAATCACATAAAGAAAAGGGCC
1 TAATTGAAATCACATAAAGAAAAAGGCA
*
866095 TAATTGAAATCACATTAAAATAAAAAGG-A
1 TAATTGAAATCACA-T-AAAGAAAAAGGCA
866124 TAATT
1 TAATT
866129 TACAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 14 0.48
29 6 0.21
30 9 0.31
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.24
Consensus pattern (28 bp):
TAATTGAAATCACATAAAGAAAAAGGCA
Found at i:867272 original size:14 final size:14
Alignment explanation
Indices: 867253--867279 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
867243 TAATGGACTG
867253 TTATAATAATTTTA
1 TTATAATAATTTTA
867267 TTATAATAATTTT
1 TTATAATAATTTT
867280 TTTGGTTTTG
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATAATAATTTTA
Found at i:867797 original size:133 final size:133
Alignment explanation
Indices: 867574--867963 Score: 620
Period size: 133 Copynumber: 2.9 Consensus size: 133
867564 CGCAATTTTT
*
867574 AGCCTACTCTACTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCA
867639 AGAATACAAGATTCGCCGTTTTCGATCTGCTCCACTACAGCTTCAGGGGAACAAGATCTACAATC
66 AGAATACAAGATTCGCCGTTTTCGATCTGCTCCACTACAGCTTCAGGGGAACAAGATCTACAATC
867704 TTC
131 TTC
*
867707 AGCCTACTCCATTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCA
867772 AGAATACAAGATTCGCCGTTTTCGATCTGCTCCACTACAGCTTCAGGGGAACAAGATCTACAATC
66 AGAATACAAGATTCGCCGTTTTCGATCTGCTCCACTACAGCTTCAGGGGAACAAGATCTACAATC
867837 TTC
131 TTC
* * * * *
867840 AGCCTACTCCACTACAACTTTAGGGAGCTAGGATTGTGACTTAAATCTACTTCACTGCAGCTTCA
1 AGCCTACTCCACTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCA
* * * ** * * * *
867905 GGAAGACTAGATTCGCTATCTTCGATCTGCTCCGCTGCAACTTCA-GGGAGACAAGATCT
66 AGAATACAAGATTCGCCGTTTTCGATCTGCTCCACTACAGCTTCAGGGGA-ACAAGATCT
867964 GTAGAATCGG
Statistics
Matches: 239, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
132 4 0.02
133 235 0.98
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (133 bp):
AGCCTACTCCACTACAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCA
AGAATACAAGATTCGCCGTTTTCGATCTGCTCCACTACAGCTTCAGGGGAACAAGATCTACAATC
TTC
Found at i:868092 original size:64 final size:64
Alignment explanation
Indices: 867991--868175 Score: 327
Period size: 64 Copynumber: 2.9 Consensus size: 64
867981 GGCCTATGCG
* * *
867991 TATGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAGTG-TTCTTAACTAGATGTGGTGCT
1 TATGTCAAATAATTAGAATGCTATGATCGAAATGAATCAAGTGCTTC-TAACTAAATGTGGTGCT
868055 TATGTCAAATAATTAGAATGCTATGATCGAAATGAATCAAGTGCTTCTAACTAAATGTGGTGCT
1 TATGTCAAATAATTAGAATGCTATGATCGAAATGAATCAAGTGCTTCTAACTAAATGTGGTGCT
868119 TATGTCAAATAATTAGAATGCTATGATCGAAATGAATCAAGTGCTTCTAACTAAATG
1 TATGTCAAATAATTAGAATGCTATGATCGAAATGAATCAAGTGCTTCTAACTAAATG
868176 AATGATCATG
Statistics
Matches: 117, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
64 114 0.97
65 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (64 bp):
TATGTCAAATAATTAGAATGCTATGATCGAAATGAATCAAGTGCTTCTAACTAAATGTGGTGCT
Found at i:876197 original size:19 final size:20
Alignment explanation
Indices: 876160--876200 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
876150 TATGGCCTTT
876160 AATGCATAATGATGTAATGC
1 AATGCATAATGATGTAATGC
876180 AATGCA-AATGCATG-AATGC
1 AATGCATAATG-ATGTAATGC
876199 AA
1 AA
876201 AGGAGGCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (20 bp):
AATGCATAATGATGTAATGC
Found at i:879201 original size:130 final size:130
Alignment explanation
Indices: 878909--879297 Score: 575
Period size: 130 Copynumber: 3.0 Consensus size: 130
878899 TTTAGAGAAT
* * * *
878909 CATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAAAAAATCACAACCCAGCACG
1 CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
* ** * *
878974 ATAGGGCACGATTCCCCGAATT-TCCAAACATC-GAGTATTACCTTCGTTTCAAAGAGTTTTTAA
66 ATAGGGCACGATT-CTCGAATTGT-CAAACATCGGA-TATCGCCTTCGTTTTAAAGAATTTTTAA
879037 AGA
128 AGA
* *
879040 TATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGGGAAATCGCAACCCAGCACG
1 CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
* *
879105 ATAGGGCACGATTCTCAAATTGTCAAACATCGGATATCGCATTCGTTTTAAAGAATTTTTAAAGA
66 ATAGGGCACGATTCTCGAATTGTCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAAGA
* *
879170 CATGAGCGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCATCACG
1 CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
* * *
879235 ATAGGGCACGATTCTCGAATTGCCAAACATCGAATATCGCCTTTGTTTTAAAGAATTTTTAAA
66 ATAGGGCACGATTCTCGAATTGTCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAA
879298 TGAATAGGTA
Statistics
Matches: 234, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
130 159 0.68
131 75 0.32
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (130 bp):
CATGAGTGAAATTCTAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACG
ATAGGGCACGATTCTCGAATTGTCAAACATCGGATATCGCCTTCGTTTTAAAGAATTTTTAAAGA
Found at i:880087 original size:2 final size:2
Alignment explanation
Indices: 880080--880104 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
880070 AAATTTAATA
880080 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
880105 GATCAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:880508 original size:29 final size:28
Alignment explanation
Indices: 880447--880508 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
880437 CTAAAAAACC
* *
880447 TAATTGAAATCACATAAAGAAAAGGGCC
1 TAATTGAAATCACATAAAGAAAAAGGCA
*
880475 TAATTGAAATCACATTAAAATAAAAAGG-A
1 TAATTGAAATCACA-T-AAAGAAAAAGGCA
880504 TAATT
1 TAATT
880509 TACAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 14 0.48
29 6 0.21
30 9 0.31
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.24
Consensus pattern (28 bp):
TAATTGAAATCACATAAAGAAAAAGGCA
Found at i:881596 original size:14 final size:14
Alignment explanation
Indices: 881577--881603 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
881567 TAATGGACTG
881577 TTATAATATTTTTA
1 TTATAATATTTTTA
881591 TTATAATATTTTT
1 TTATAATATTTTT
881604 TTTGGTTTTG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATAATATTTTTA
Found at i:889530 original size:27 final size:27
Alignment explanation
Indices: 889498--889578 Score: 94
Period size: 27 Copynumber: 2.9 Consensus size: 27
889488 CACGGCTTCA
889498 CACACAGCCTATCACATGGTCGTGTGT-
1 CACACAGCCTATCACA-GGTCGTGTGTC
889525 CACACATGGCCTATCACA-GTCGTGTGTC
1 CACACA--GCCTATCACAGGTCGTGTGTC
*
889553 GCACACAGCCTGTCACACGGTCGTGT
1 -CACACAGCCTATCACA-GGTCGTGT
889579 ATCGCACATG
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
27 24 0.51
29 23 0.49
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.23
Consensus pattern (27 bp):
CACACAGCCTATCACAGGTCGTGTGTC
Found at i:889583 original size:29 final size:28
Alignment explanation
Indices: 889498--889586 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 28
889488 CACGGCTTCA
*
889498 CACACAGCCTATCACATGGTCGTGTGTCA
1 CACACAGCCTATCACA-GGTCGTGTGTCG
**
889527 CACATGGCCTATCACA-GTCGTGTGTCG
1 CACACAGCCTATCACAGGTCGTGTGTCG
* *
889554 CACACAGCCTGTCACACGGTCGTGTATCG
1 CACACAGCCTATCACA-GGTCGTGTGTCG
889583 CACA
1 CACA
889587 TGGCCTGGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
27 23 0.45
29 28 0.55
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (28 bp):
CACACAGCCTATCACAGGTCGTGTGTCG
Found at i:889592 original size:29 final size:29
Alignment explanation
Indices: 889504--889608 Score: 106
Period size: 29 Copynumber: 3.7 Consensus size: 29
889494 TTCACACACA
* *
889504 GCCTATCACATGGTCGTGTGTCACACATG
1 GCCTATCACATGGTCGTGTATCGCACATG
* **
889533 GCCTATCACA--GTCGTGTGTCGCACACA
1 GCCTATCACATGGTCGTGTATCGCACATG
* *
889560 GCCTGTCACACGGTCGTGTATCGCACATG
1 GCCTATCACATGGTCGTGTATCGCACATG
** *
889589 GCCTGGCACATGGCCGTGTA
1 GCCTATCACATGGTCGTGTA
889609 GTGTCGACAG
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
27 23 0.36
29 41 0.64
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.24
Consensus pattern (29 bp):
GCCTATCACATGGTCGTGTATCGCACATG
Found at i:891657 original size:15 final size:15
Alignment explanation
Indices: 891633--891664 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
891623 ATAATAGTTT
*
891633 AAATATAAAATAAAA
1 AAATAAAAAATAAAA
891648 AAATAAAAAATAAAA
1 AAATAAAAAATAAAA
891663 AA
1 AA
891665 GGAAATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAATAAAAAATAAAA
Found at i:893516 original size:44 final size:44
Alignment explanation
Indices: 893453--893611 Score: 132
Period size: 45 Copynumber: 3.7 Consensus size: 44
893443 TATTTTTATC
* * * *
893453 CTGCTCTACTGCAACTTCAGTGAGATAAGGATGGTGGCTTC-GAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGGATGCTAGCTTCAG-T
* * * *
893497 TTGCTCCACTGCAACTTCAGGGAGATAAGATATGCTATCTTCAGT
1 CTGCTCCACTGCAACTTCAGAGAGATAAG-GATGCTAGCTTCAGT
* *
893542 CTGCTCCACTGCAACTTTAGAGAGATAAGG-T--TTG-TT-ATGAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGGATGCTAGCTTCA-G-T
* *
893583 CTGCTCTACTGCAACTTCAGAAAGATAAG
1 CTGCTCCACTGCAACTTCAGAGAGATAAG
893612 ATTTATTTAT
Statistics
Matches: 95, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 28 0.29
43 1 0.01
44 26 0.27
45 35 0.37
46 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGGATGCTAGCTTCAGT
Found at i:893794 original size:52 final size:51
Alignment explanation
Indices: 893730--893863 Score: 178
Period size: 52 Copynumber: 2.6 Consensus size: 51
893720 CAATCTGCTT
* *
893730 CACTGCAACTTCAGGAAGATAATATCTGTTTAAACATAGCTTCGATCTATTC
1 CACTGTAACTTCAGG-AGATAAGATCTGTTTAAACATAGCTTCGATCTATTC
*** *
893782 CACTGTAACTTCAGGGAGATAAGATCTGTTTATTTATAGTTTCGATCTATTC
1 CACTGTAACTTCA-GGAGATAAGATCTGTTTAAACATAGCTTCGATCTATTC
*
893834 CACTGTAACTTTAAGGAGATAAGATCTGTT
1 CACTGTAAC-TTCAGGAGATAAGATCTGTT
893864 ATCTTCAGTC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
52 68 0.93
53 5 0.07
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (51 bp):
CACTGTAACTTCAGGAGATAAGATCTGTTTAAACATAGCTTCGATCTATTC
Found at i:893795 original size:141 final size:137
Alignment explanation
Indices: 893501--893806 Score: 343
Period size: 141 Copynumber: 2.2 Consensus size: 137
893491 TTCGATTTGC
*
893501 TCCACTGCAACTTCAGGGAGATAAGATATGCTATCTTCAGTCTGCTCCACTGCAACTTTAGAGAG
1 TCCACTGCAACTTCAGGGAGATAAGATACGCTATCTTCAGTCTGCTCCACTGCAACTTTAGAGAG
* * * *** * *
893566 ATAAGGTTTGTTATGATCTGCTCTACTGCAACTTCAGAAAGATAAGATTTATTTATTTATTGTTT
66 ATAAGGGTGGTTA-GATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTATTTAAACATAGCTT
*
893631 CGATCTGT
130 CGATCTAT
* *
893639 TCCACTGCAACTTCAGGGAAATAAGACT-CGCTATCTTCAGTCTGCTCCACTGTAA-TTTCA-AG
1 TCCACTGCAACTTCAGGGAGATAAGA-TACGCTATCTTCAGTCTGCTCCACTGCAACTTT-AGA-
* * *
893701 GAGATAAGACTGGTGGCTTCA-ATCTGCT-TCACTGCAACTTCAGGAAGATAATATCTGTTTAAA
63 GAGATAAG---GGTGG-TT-AGATCTGCTCT-ACTGCAACTTCAGAAAGATAAGATCTATTTAAA
893764 CATAGCTTCGATCTAT
122 CATAGCTTCGATCTAT
*
893780 TCCACTGTAACTTCAGGGAGATAAGAT
1 TCCACTGCAACTTCAGGGAGATAAGAT
893807 CTGTTTATTT
Statistics
Matches: 142, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
137 4 0.03
138 59 0.42
139 1 0.01
140 2 0.01
141 73 0.51
142 2 0.01
143 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (137 bp):
TCCACTGCAACTTCAGGGAGATAAGATACGCTATCTTCAGTCTGCTCCACTGCAACTTTAGAGAG
ATAAGGGTGGTTAGATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTATTTAAACATAGCTTC
GATCTAT
Found at i:903321 original size:55 final size:55
Alignment explanation
Indices: 903255--903367 Score: 156
Period size: 55 Copynumber: 2.1 Consensus size: 55
903245 CCCGTGTCAA
* * *
903255 TTTAATAGGTTCGA-CCACGGTTCTTCCAAACGGGCATGTCGAATGCCCTTGTTGT
1 TTTAATAGGTTC-ACCCACGGTTCTTCCAAACAGGCATGTCGAACGCCCCTGTTGT
* * *
903310 TTTAATAGGTTCACCCATGGTTCTTCCACACAGGCATGTCGTACGCCCCTGTTGT
1 TTTAATAGGTTCACCCACGGTTCTTCCAAACAGGCATGTCGAACGCCCCTGTTGT
903365 TTT
1 TTT
903368 GGCAGGCTCG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 1 0.02
55 50 0.98
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (55 bp):
TTTAATAGGTTCACCCACGGTTCTTCCAAACAGGCATGTCGAACGCCCCTGTTGT
Found at i:905179 original size:18 final size:18
Alignment explanation
Indices: 905156--905426 Score: 136
Period size: 18 Copynumber: 14.6 Consensus size: 18
905146 GAATAATTAT
905156 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
905174 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
905192 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
905210 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
905236 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
905254 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
905271 ATATTCAGTAACTATTAAG
1 TTATTCAGTAAC-AGTCAG
* * *
905290 GTATTTAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* * *
905307 TTCATTTAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
905326 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
905344 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
905362 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
905380 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
905398 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
905416 TTATTCAGTAA
1 TTATTCAGTAA
905427 TAATTAGTTA
Statistics
Matches: 190, Mismatches: 47, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
17 16 0.08
18 141 0.74
19 17 0.09
21 2 0.01
22 1 0.01
23 2 0.01
26 11 0.06
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:905198 original size:36 final size:36
Alignment explanation
Indices: 905156--905426 Score: 163
Period size: 36 Copynumber: 7.3 Consensus size: 36
905146 GAATAATTAT
*
905156 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
* * ** * *
905192 TTATTCAATAATAACCAGTTATTCAGTATCGATCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
*
905228 TTGATCGGTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA
1 TT-A-----T-T-CAGTAACAGTCAGTTATTCAGTAACAATCA-A
* * * * * *
905272 -TATTCAGTAACTATTAAGGTATTTAGTAGCAGTC-A
1 TTATTCAGTAAC-AGTCAGTTATTCAGTAACAATCAA
* * * **
905307 TTCATTTAGTGACAATCAGTTATTCAGTAATGATCAA
1 TT-ATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
* * *
905344 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATC-AA
* * * * *
905381 -TATCCAGTAACAGTCAATTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
905416 TTATTCAGTAA
1 TTATTCAGTAA
905427 TAATTAGTTA
Statistics
Matches: 174, Mismatches: 45, Indels: 32
0.69 0.18 0.13
Matches are distributed among these distances:
35 10 0.06
36 119 0.68
37 18 0.10
42 2 0.01
43 6 0.03
44 19 0.11
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (36 bp):
TTATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
Found at i:905678 original size:45 final size:45
Alignment explanation
Indices: 905618--905711 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
905608 AATAGTAACA
* * *
905618 GTAATAGTAATAGTAACAGTATTCAACACACAAAGAGCTGAATCG
1 GTAATAGTAACAGTAACAATATTCAACACACAAAGAGCCGAATCG
* * *
905663 GTAATGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
1 GTAATAGTAACAGTAACAATATTCAACACACAAAGAGCCGAATCG
905708 GTAA
1 GTAA
905712 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (45 bp):
GTAATAGTAACAGTAACAATATTCAACACACAAAGAGCCGAATCG
Found at i:906199 original size:27 final size:27
Alignment explanation
Indices: 906166--906334 Score: 187
Period size: 27 Copynumber: 6.3 Consensus size: 27
906156 CAAATTATTG
* *
906166 AAATACCCTCGACTTGTAAAATTACCA
1 AAATACCCTCGATTTATAAAATTACCA
* * * *
906193 AAGTACCCCCAATTTATAAAATTACCC
1 AAATACCCTCGATTTATAAAATTACCA
* * *
906220 AAATATCCTTGATTTGTAAAATTACCA
1 AAATACCCTCGATTTATAAAATTACCA
* * *
906247 AAATACCCTTGGTTTACAAAATTACCA
1 AAATACCCTCGATTTATAAAATTACCA
**
906274 AAATACCCTCGATCAATAAAATTACCA
1 AAATACCCTCGATTTATAAAATTACCA
*
906301 AAATACCC-CTAGTTTATAAAATTACCA
1 AAATACCCTCGA-TTTATAAAATTACCA
906328 AAATACC
1 AAATACC
906335 TCTAATTTGT
Statistics
Matches: 116, Mismatches: 25, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
26 2 0.02
27 114 0.98
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.28
Consensus pattern (27 bp):
AAATACCCTCGATTTATAAAATTACCA
Found at i:906239 original size:54 final size:53
Alignment explanation
Indices: 906179--906361 Score: 206
Period size: 54 Copynumber: 3.4 Consensus size: 53
906169 TACCCTCGAC
* * * *
906179 TTGTAAAATTACCAAAGTACCCCCAATTTATAAAATTACCCAAATATCCTTGAT
1 TTGTAAAATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATA-CCTTGAT
* * * *
906233 TTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGAT
1 TTGTAAAATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATA-CCTTGAT
*** *
906287 CAATAAAATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCTCTAAT
1 TTGTAAAATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCT-TGAT
*
906341 TTGTGAAATTA-CAGAAATACC
1 TTGTAAAATTACCA-AAATACC
906362 TCTGTAGGGT
Statistics
Matches: 106, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
53 5 0.05
54 101 0.95
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (53 bp):
TTGTAAAATTACCAAAATACCCCTAGTTTATAAAATTACCAAAATACCTTGAT
Found at i:906293 original size:81 final size:81
Alignment explanation
Indices: 906183--906334 Score: 207
Period size: 81 Copynumber: 1.9 Consensus size: 81
906173 CTCGACTTGT
* ** * * * *
906183 AAAATTACCAAAGTACCCCCAATTTATAAAATTACCCAAATA-TCCTTGATTTGTAAAATTACCA
1 AAAATTACCAAAATACCCCCAATCAATAAAATTACCAAAATACCCCTAG-TTTATAAAATTACCA
906247 AAATACCCTTGGTTTAC
65 AAATACCCTTGGTTTAC
* *
906264 AAAATTACCAAAATACCCTCGATCAATAAAATTACCAAAATACCCCTAGTTTATAAAATTACCAA
1 AAAATTACCAAAATACCCCCAATCAATAAAATTACCAAAATACCCCTAGTTTATAAAATTACCAA
906329 AATACC
66 AATACC
906335 TCTAATTTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
81 57 0.93
82 4 0.07
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.28
Consensus pattern (81 bp):
AAAATTACCAAAATACCCCCAATCAATAAAATTACCAAAATACCCCTAGTTTATAAAATTACCAA
AATACCCTTGGTTTAC
Found at i:906349 original size:27 final size:27
Alignment explanation
Indices: 906182--906364 Score: 158
Period size: 27 Copynumber: 6.8 Consensus size: 27
906172 CCTCGACTTG
* * *
906182 TAAAATTACCAAAGTACCCCCAATTTA
1 TAAAATTACCAAAATACCTCTAATTTA
* * *
906209 TAAAATTACCCAAATATCCT-TGATTTG
1 TAAAATTACCAAAATA-CCTCTAATTTA
**
906236 TAAAATTACCAAAATACC-CTTGGTTTA
1 TAAAATTACCAAAATACCTC-TAATTTA
* * **
906263 CAAAATTACCAAAATACC-CTCGATCAA
1 TAAAATTACCAAAATACCTCT-AATTTA
* *
906290 TAAAATTACCAAAATACCCCTAGTTTA
1 TAAAATTACCAAAATACCTCTAATTTA
*
906317 TAAAATTACCAAAATACCTCTAATTTG
1 TAAAATTACCAAAATACCTCTAATTTA
*
906344 TGAAATTA-CAGAAATACCTCT
1 TAAAATTACCA-AAATACCTCT
906365 GTAGGGTAGA
Statistics
Matches: 128, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
26 5 0.04
27 119 0.93
28 4 0.03
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (27 bp):
TAAAATTACCAAAATACCTCTAATTTA
Found at i:906350 original size:81 final size:81
Alignment explanation
Indices: 906179--906361 Score: 192
Period size: 81 Copynumber: 2.3 Consensus size: 81
906169 TACCCTCGAC
* ** * * * *
906179 TTGTAAAATTACCAAAGTACCCCCAATTTATAAAATTACCCAAATATCCTTGATTTGTAAAATTA
1 TTGTAAAATTACCAAAATACCCCCAATCAATAAAATTACCAAAATACCCTAGATTTATAAAATTA
**
906244 CCAAAATACCCTTGGT
66 CCAAAATACCCTTAAT
** * *
906260 TTACAAAATTACCAAAATACCCTCGATCAATAAAATTACCAAAATACCCCTAG-TTTATAAAATT
1 TTGTAAAATTACCAAAATACCCCCAATCAATAAAATTACCAAAATA-CCCTAGATTTATAAAATT
906324 ACCAAAATA-CCTCTAAT
65 ACCAAAATACCCT-TAAT
*
906341 TTGTGAAATTA-CAGAAATACC
1 TTGTAAAATTACCA-AAATACC
906362 TCTGTAGGGT
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
80 5 0.06
81 74 0.89
82 4 0.05
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (81 bp):
TTGTAAAATTACCAAAATACCCCCAATCAATAAAATTACCAAAATACCCTAGATTTATAAAATTA
CCAAAATACCCTTAAT
Found at i:906377 original size:27 final size:26
Alignment explanation
Indices: 906347--906433 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 26
906337 TAATTTGTGA
906347 AATTACAGAAATACCTCTGTAGGGTAG
1 AATTACAGAAATACC-CTGTAGGGTAG
906374 AATTACCA-AAATACCCCTGTAGGGTAG
1 AATTA-CAGAAATA-CCCTGTAGGGTAG
* *
906401 AATTACAGAAATACCCTTGTGGGGTAA
1 AATTACAGAAATACCC-TGTAGGGTAG
906428 AATTAC
1 AATTAC
906434 CATTTTGCCC
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
26 5 0.09
27 45 0.83
28 4 0.07
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (26 bp):
AATTACAGAAATACCCTGTAGGGTAG
Found at i:906860 original size:6 final size:6
Alignment explanation
Indices: 906829--906928 Score: 89
Period size: 6 Copynumber: 16.3 Consensus size: 6
906819 TTGCATTCAC
* * *
906829 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
906878 ATTCTG -TCACTTG ATTCTG ATTCTG ATTCTG ATTCTA ATTCT- AGTTCTG
1 ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG
906927 AT
1 AT
906929 AATGTTTCTT
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
5 4 0.05
6 64 0.83
7 7 0.09
8 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:906882 original size:37 final size:37
Alignment explanation
Indices: 906829--906944 Score: 137
Period size: 37 Copynumber: 3.2 Consensus size: 37
906819 TTGCATTCAC
* *
906829 ATTCTGATTTTGATTCTGTTACCTGATACTGATTCTG
1 ATTCTGATTCTAATTCTGTTACCTGATACTGATTCTG
* * *
906866 ATTCTGATTCTAATTCTGTCACTTGATTCTGATTCTG
1 ATTCTGATTCTAATTCTGTTACCTGATACTGATTCTG
* * *
906903 ATTCTGATTCTAATTCTAGTT--CTGATAATGTTTCTT
1 ATTCTGATTCTAATTCT-GTTACCTGATACTGATTCTG
906939 ATTCTG
1 ATTCTG
906945 TAATGGGTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
36 16 0.24
37 49 0.73
38 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (37 bp):
ATTCTGATTCTAATTCTGTTACCTGATACTGATTCTG
Found at i:907636 original size:45 final size:44
Alignment explanation
Indices: 907569--907703 Score: 225
Period size: 45 Copynumber: 3.0 Consensus size: 44
907559 TTGGGGTGTT
* *
907569 ACAATATTCGACACACACAGTGCCGAATCGATAATAGTAGCAGTA
1 ACAATATTCGACACACAAAGTGCCGAATCG-TAACAGTAGCAGTA
907614 ACAATATTCGACACACAAAGTGCCGAATCTGTAACAGTAGCAGTA
1 ACAATATTCGACACACAAAGTGCCGAATC-GTAACAGTAGCAGTA
907659 ACAATATTCGACACACAAAGTGCCGAATCGGTAACAGTAGCAGTA
1 ACAATATTCGACACACAAAGTGCCGAATC-GTAACAGTAGCAGTA
907704 GCGGTAACAA
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
45 85 0.99
46 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (44 bp):
ACAATATTCGACACACAAAGTGCCGAATCGTAACAGTAGCAGTA
Found at i:908136 original size:15 final size:16
Alignment explanation
Indices: 908099--908148 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
908089 CAATACACAT
908099 TTCAATT-AA-TCATAA
1 TTCAATTCAATTCA-AA
* *
908114 TTCCATTCCATTC-AA
1 TTCAATTCAATTCAAA
908129 TTCAATTCAATTCAAA
1 TTCAATTCAATTCAAA
908145 TTCA
1 TTCA
908149 CTTTTCCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 19 0.68
16 7 0.25
17 2 0.07
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (16 bp):
TTCAATTCAATTCAAA
Found at i:908336 original size:26 final size:26
Alignment explanation
Indices: 908280--908337 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
908270 ACATATTCAT
*
908280 AATTTATTTTATTTTTATTCAACTCA
1 AATTTATTTTATTTTTATCCAACTCA
* * *
908306 TATTTTTTTTATTTATTGTCCAA-TCA
1 AATTTATTTTATTT-TTATCCAACTCA
908332 AATTTA
1 AATTTA
908338 AAATCACTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (26 bp):
AATTTATTTTATTTTTATCCAACTCA
Found at i:908532 original size:21 final size:21
Alignment explanation
Indices: 908507--908567 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
908497 TTCAATTTCC
908507 ATTCAATAA-CAATTCACATAT
1 ATTCAATAATCAATTCA-ATAT
908528 ATTC-ATAAATCAATTCAATAT
1 ATTCAAT-AATCAATTCAATAT
* * *
908549 AATCAATATTCAATCCAAT
1 ATTCAATAATCAATTCAAT
908568 TCATATAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 23 0.68
22 9 0.26
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTCAATAATCAATTCAATAT
Found at i:928332 original size:29 final size:29
Alignment explanation
Indices: 928295--928397 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 29
928285 GGTTGAAGAA
928295 CTCGCACACACAGTGCCTCAATTACCGAT
1 CTCGCACACACAGTGCCTCAATTACCGAT
* ** **
928324 CTCGCACACATAGTG-CTCGGTTAAAGGAAT
1 CTCGCACACACAGTGCCTCAATT-ACCG-AT
*
928354 -TTGCACACACAGTGCCTCAATTACCGAT
1 CTCGCACACACAGTGCCTCAATTACCGAT
*
928382 CTCGCACACATAGTGC
1 CTCGCACACACAGTGC
928398 TCGGTTAAAG
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
28 7 0.12
29 43 0.75
30 7 0.12
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (29 bp):
CTCGCACACACAGTGCCTCAATTACCGAT
Found at i:928376 original size:58 final size:58
Alignment explanation
Indices: 928263--928429 Score: 291
Period size: 58 Copynumber: 2.9 Consensus size: 58
928253 GCCCACTGAT
* * * *
928263 CGATCTCGCACACATAGTGCTTGGTTGAA-GAACTCGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTCAATTAC
928320 CGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTCAATTAC
928378 CGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTC
1 CGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTC
928430 TAATCATTCG
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
57 27 0.26
58 78 0.74
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (58 bp):
CGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTCAATTAC
Found at i:928417 original size:29 final size:29
Alignment explanation
Indices: 928327--928426 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
928317 TACCGATCTC
*
928327 GCACACATAGTGCTCGGTTAAAGGAATTT
1 GCACACACAGTGCTCGGTTAAAGGAATTT
** ** *
928356 GCACACACAGTGCCTCAATT-ACCG-ATCTC
1 GCACACACAGTG-CTCGGTTAAAGGAAT-TT
*
928385 GCACACATAGTGCTCGGTTAAAGGAATTT
1 GCACACACAGTGCTCGGTTAAAGGAATTT
928414 GCACACACAGTGC
1 GCACACACAGTGC
928427 CTCTAATCAT
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
28 7 0.13
29 40 0.74
30 7 0.13
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (29 bp):
GCACACACAGTGCTCGGTTAAAGGAATTT
Found at i:928645 original size:43 final size:43
Alignment explanation
Indices: 928595--928716 Score: 199
Period size: 43 Copynumber: 2.8 Consensus size: 43
928585 CACCAGCATT
*
928595 AAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACG
* * * *
928638 AATCCTGCTAGGCACGAAGGCCCAAATACACATCATCGGTACG
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACG
928681 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCAC
1 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCAC
928717 TGAGTTTCAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.12
Consensus pattern (43 bp):
AAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACG
Found at i:931133 original size:27 final size:26
Alignment explanation
Indices: 931028--931151 Score: 180
Period size: 26 Copynumber: 4.8 Consensus size: 26
931018 CCTCTTTAAT
**
931028 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
931053 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
931078 AATTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
* *
931104 AACTGGAGCATAAGCCATTTTTCAATA
1 AACTGGGGCATAAGCC-CTTTTCAATA
931131 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
931152 GGACTTCATC
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
25 32 0.36
26 33 0.37
27 24 0.27
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:931226 original size:20 final size:21
Alignment explanation
Indices: 931201--931267 Score: 88
Period size: 20 Copynumber: 3.3 Consensus size: 21
931191 TTATGAGTAC
931201 ATCATGTGCATATTC-TACAT
1 ATCATGTGCATATTCATACAT
931221 ATCATGTGCATA-TCATACAT
1 ATCATGTGCATATTCATACAT
*
931241 ATCATGAGCATA-TCATATCA-
1 ATCATGTGCATATTCATA-CAT
931261 ATCATGT
1 ATCATGT
931268 ATATCAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.05
20 39 0.91
21 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (21 bp):
ATCATGTGCATATTCATACAT
Found at i:931350 original size:25 final size:25
Alignment explanation
Indices: 931303--931350 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
931293 ATAAGTAAAC
* * * *
931303 CCTAGGGGTATAACGGTCGTTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
931328 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
931351 CATAATACAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:931431 original size:65 final size:65
Alignment explanation
Indices: 931327--931454 Score: 247
Period size: 65 Copynumber: 2.0 Consensus size: 65
931317 GGTCGTTTTT
*
931327 ACCTAGGGGCAAAACAGTCATTTTCATAATACAAGGGTAATTTTATAATTTTACCAAATATTAAG
1 ACCTAGGGGCAAAACAGTCATTTTCATAATACAAGGGTAATTTCATAATTTTACCAAATATTAAG
931392 ACCTAGGGGCAAAACAGTCATTTTCATAATACAAGGGTAATTTCATAATTTTACCAAATATTA
1 ACCTAGGGGCAAAACAGTCATTTTCATAATACAAGGGTAATTTCATAATTTTACCAAATATTA
931455 GGGTTTTTCG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (65 bp):
ACCTAGGGGCAAAACAGTCATTTTCATAATACAAGGGTAATTTCATAATTTTACCAAATATTAAG
Found at i:931877 original size:8 final size:8
Alignment explanation
Indices: 931864--931891 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
931854 AAATGCCAGA
931864 ATTTCGGC
1 ATTTCGGC
931872 ATTTCGGC
1 ATTTCGGC
931880 ATTTCGGC
1 ATTTCGGC
931888 ATTT
1 ATTT
931892 ATCGTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (8 bp):
ATTTCGGC
Found at i:932762 original size:14 final size:15
Alignment explanation
Indices: 932739--932773 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
932729 CGGTCCAAGT
*
932739 GAAAAGAAAG-AAAA
1 GAAAAAAAAGAAAAA
932753 GAAAAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
932768 GAAAAA
1 GAAAAA
932774 TGCCACCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:939342 original size:8 final size:8
Alignment explanation
Indices: 939329--939356 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
939319 AAATGCCAGA
939329 ATTTCGGC
1 ATTTCGGC
939337 ATTTCGGC
1 ATTTCGGC
939345 ATTTCGGC
1 ATTTCGGC
939353 ATTT
1 ATTT
939357 ATCGTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (8 bp):
ATTTCGGC
Found at i:940226 original size:14 final size:15
Alignment explanation
Indices: 940203--940237 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
940193 CGGTCCAAGT
*
940203 GAAAAGAAAGAAAAA
1 GAAAAAAAAGAAAAA
940218 -AAAAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
940232 GAAAAA
1 GAAAAA
940238 TGCCACCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:961142 original size:35 final size:34
Alignment explanation
Indices: 961087--961174 Score: 126
Period size: 35 Copynumber: 2.6 Consensus size: 34
961077 CATATTATTT
*
961087 TATATAAATTTTTTCTTTTAAATCTATTTATGTA
1 TATATATATTTTTTCTTTTAAATCTATTTATGTA
*
961121 TATATATATATTTTTCTTTTAAATTTATTTATGTA
1 TATATATAT-TTTTTCTTTTAAATCTATTTATGTA
*
961156 TATA-AT-TTGTTTCTTTTAA
1 TATATATATTTTTTCTTTTAA
961175 GGACCCTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
32 11 0.22
33 1 0.02
34 10 0.20
35 28 0.56
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (34 bp):
TATATATATTTTTTCTTTTAAATCTATTTATGTA
Found at i:961296 original size:22 final size:20
Alignment explanation
Indices: 961271--961310 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
961261 TTCATTTCAT
961271 ATATATCATTATTTTTAAATCA
1 ATATAT-ATTA-TTTTAAATCA
*
961293 ATATATTTTATTTTAAAT
1 ATATATATTATTTTAAAT
961311 TATTTTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATATTATTTTAAATCA
Found at i:963359 original size:29 final size:29
Alignment explanation
Indices: 963325--963390 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
963315 ATAGAGGTTA
* * * *
963325 GATCAAATTAATCTTTCTATTATTAAATG
1 GATCAAATTAATCTATATACTATTAAAAG
*
963354 GATCAAATTAGTCTATATACTATTAAAAG
1 GATCAAATTAATCTATATACTATTAAAAG
963383 GAATCAAA
1 G-ATCAAA
963391 CAATAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (29 bp):
GATCAAATTAATCTATATACTATTAAAAG
Found at i:965099 original size:36 final size:36
Alignment explanation
Indices: 965052--965126 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
965042 GAACATTTGT
*
965052 TAAAGCATGATTGTGAATGAATTAAACCAAGAATTG
1 TAAAGCATGATTGTGAACGAATTAAACCAAGAATTG
* *
965088 TAAAGCATGATTGTGAACGAATTAAATCAAGAGTTG
1 TAAAGCATGATTGTGAACGAATTAAACCAAGAATTG
965124 TAA
1 TAA
965127 TTGTTCTAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (36 bp):
TAAAGCATGATTGTGAACGAATTAAACCAAGAATTG
Found at i:979383 original size:24 final size:25
Alignment explanation
Indices: 979351--979399 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
979341 AAGTACGACG
*
979351 CCATTGTTGAATTTTCAG-AACAAT
1 CCATTGTTGAATTTTAAGAAACAAT
979375 CCATTGTTGAATTTTAAGAAACAAT
1 CCATTGTTGAATTTTAAGAAACAAT
979400 GTCACACTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (25 bp):
CCATTGTTGAATTTTAAGAAACAAT
Found at i:981690 original size:18 final size:20
Alignment explanation
Indices: 981667--981704 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
981657 ACGTGGCAGT
981667 CCAAC-TAGATTT-TAAATG
1 CCAACTTAGATTTCTAAATG
*
981685 CCAACTTGGATTTCTAAATG
1 CCAACTTAGATTTCTAAATG
981705 AGAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (20 bp):
CCAACTTAGATTTCTAAATG
Found at i:983016 original size:18 final size:18
Alignment explanation
Indices: 982980--983018 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
982970 ACCAGTTTAA
*
982980 TTAAAAATTATTAAGATT
1 TTAAAAATTATTAAAATT
*
982998 TTAAAAATT-TTAAAAAT
1 TTAAAAATTATTAAAATT
983015 TTAA
1 TTAA
983019 TCATCTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TTAAAAATTATTAAAATT
Found at i:988779 original size:30 final size:30
Alignment explanation
Indices: 988727--988784 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
988717 CATGGCCATG
* *
988727 ACACACGGGTGTGTGGTCTACCCGTGTGTC
1 ACACACGGGCGTGTGGTCTACCCATGTGTC
*
988757 ACACATGGGCGTGTGGAT-TACCCATGTG
1 ACACACGGGCGTGTGG-TCTACCCATGTG
988785 GAACTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26
Consensus pattern (30 bp):
ACACACGGGCGTGTGGTCTACCCATGTGTC
Found at i:991605 original size:30 final size:30
Alignment explanation
Indices: 991571--991631 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
991561 AAGCACAAAT
*
991571 ATAATAACCATATATAAATAATA-ATGTAAA
1 ATAATAACAATATA-AAATAATATATGTAAA
* *
991601 ATAATAATAATATAAAATAATATATTTAAA
1 ATAATAACAATATAAAATAATATATGTAAA
991631 A
1 A
991632 CGTAAGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (30 bp):
ATAATAACAATATAAAATAATATATGTAAA
Found at i:991608 original size:16 final size:16
Alignment explanation
Indices: 991587--991622 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
991577 ACCATATATA
*
991587 AATAATAATGTAAAAT
1 AATAATAATATAAAAT
991603 AATAATAATATAAAAT
1 AATAATAATATAAAAT
991619 AATA
1 AATA
991623 TATTTAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATAATATAAAAT
Found at i:991747 original size:25 final size:25
Alignment explanation
Indices: 991713--991766 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
991703 ATAATATATG
991713 ATAAAAATATAAGTAGTA-TTTTTTA
1 ATAAAAATATAAGTA-TAGTTTTTTA
* *
991738 ATAATAATATATGTATAGTTTTTT-
1 ATAAAAATATAAGTATAGTTTTTTA
991762 ATAAA
1 ATAAA
991767 TAGATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (25 bp):
ATAAAAATATAAGTATAGTTTTTTA
Found at i:994945 original size:18 final size:18
Alignment explanation
Indices: 994924--994966 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
994914 ATAATTTAAA
994924 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
994942 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
994960 ATGTAAA
1 ATATAAA
994967 AACAGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:995069 original size:19 final size:20
Alignment explanation
Indices: 995045--995087 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
995035 CCAAACACTG
995045 GAAAAGTAAATCATTTTC-A
1 GAAAAGTAAATCATTTTCTA
995064 GAAAAGTAAATCATTTTCTA
1 GAAAAGTAAATCATTTTCTA
995084 GAAA
1 GAAA
995088 TTATTTTCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (20 bp):
GAAAAGTAAATCATTTTCTA
Found at i:1011537 original size:9 final size:9
Alignment explanation
Indices: 1011525--1011550 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1011515 TTTGTGAGAT
1011525 TTTTGAGCC
1 TTTTGAGCC
1011534 TTTTGAGCC
1 TTTTGAGCC
1011543 TTTTGAGC
1 TTTTGAGC
1011551 ATCTATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (9 bp):
TTTTGAGCC
Found at i:1012204 original size:126 final size:126
Alignment explanation
Indices: 1011979--1012231 Score: 497
Period size: 126 Copynumber: 2.0 Consensus size: 126
1011969 CTAGTTAGAC
1011979 AATTTTTCAATTCAATCTCGATTCTAACCCTTTCTTTCAGCTTGTGACCACACCTATAACCAAGC
1 AATTTTTCAATTCAATCTCGATTCTAACCCTTTCTTTCAGCTTGTGACCACACCTATAACCAAGC
1012044 CTCATTAAAACCCTTTAAAGACCTTTTGATTAATGTATCATCTTAAATTATAGTGGTGTAG
66 CTCATTAAAACCCTTTAAAGACCTTTTGATTAATGTATCATCTTAAATTATAGTGGTGTAG
1012105 AATTTTTCAATTCAATCTCGATTCTAACCCTTTCTTTCAGCTTGTGACCACACCTATAACCAAGC
1 AATTTTTCAATTCAATCTCGATTCTAACCCTTTCTTTCAGCTTGTGACCACACCTATAACCAAGC
*
1012170 CTTATTAAAACCCTTTAAAGACCTTTTGATTAATGTATCATCTTAAATTATAGTGGTGTAG
66 CTCATTAAAACCCTTTAAAGACCTTTTGATTAATGTATCATCTTAAATTATAGTGGTGTAG
1012231 A
1 A
1012232 TTTAATTTTC
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (126 bp):
AATTTTTCAATTCAATCTCGATTCTAACCCTTTCTTTCAGCTTGTGACCACACCTATAACCAAGC
CTCATTAAAACCCTTTAAAGACCTTTTGATTAATGTATCATCTTAAATTATAGTGGTGTAG
Found at i:1015261 original size:26 final size:26
Alignment explanation
Indices: 1015225--1015277 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1015215 GAACGCTTGG
*
1015225 AATCAAATTCATAGAATGAAAATGTA
1 AATCAAATTCATAGAATAAAAATGTA
1015251 AATCAAATTCATAGAATAAAAATGTA
1 AATCAAATTCATAGAATAAAAATGTA
1015277 A
1 A
1015278 CACCCCTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.26
Consensus pattern (26 bp):
AATCAAATTCATAGAATAAAAATGTA
Found at i:1015527 original size:20 final size:20
Alignment explanation
Indices: 1015502--1015554 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1015492 AGATAGGGGC
* *
1015502 ACACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCCTGGA
1015522 ACACGCCCGTGTGGCCTGGA
1 ACACGCCCGTGTGGCCTGGA
*
1015542 ACATGCCCGTGTG
1 ACACGCCCGTGTG
1015555 CTACAGCCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.32, G:0.36, T:0.19
Consensus pattern (20 bp):
ACACGCCCGTGTGGCCTGGA
Found at i:1017400 original size:17 final size:16
Alignment explanation
Indices: 1017378--1017414 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1017368 AAACTCTAAA
*
1017378 TTTCCCTTTTCTTTTTC
1 TTTCCCTTTT-TCTTTC
1017395 TTTCCCTTTTTCTTTC
1 TTTCCCTTTTTCTTTC
1017411 TTTC
1 TTTC
1017415 TTTCTCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTCCCTTTTTCTTTC
Found at i:1031062 original size:20 final size:20
Alignment explanation
Indices: 1031037--1031085 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1031027 AGGGGCACAC
* *
1031037 GCCCGTGTGGCTTGGGACAA
1 GCCCGTGTGGCCTGGAACAA
*
1031057 GCCCGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAA
1031077 GCCCGTGTG
1 GCCCGTGTG
1031086 CTGCAGCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.12, C:0.29, G:0.39, T:0.20
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAA
Found at i:1049205 original size:27 final size:27
Alignment explanation
Indices: 1049170--1049281 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
1049160 AGCATGGCTG
* *
1049170 CCAGAACAGATAA-AGTGACAGAGTCA
1 CCAGAACAGATAATAGTGGCAGAGCCA
* *
1049196 CCAGATACAGATAATCGTGGTAGAGCCA
1 CCAGA-ACAGATAATAGTGGCAGAGCCA
1049224 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAATA-GTGGCAGAGCCA
* * *
1049251 CCAGATCAGATAATCGTGGCATAGCCA
1 CCAGAACAGATAATAGTGGCAGAGCCA
1049278 CCAG
1 CCAG
1049282 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.11
27 48 0.66
28 17 0.23
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.14
Consensus pattern (27 bp):
CCAGAACAGATAATAGTGGCAGAGCCA
Found at i:1049261 original size:54 final size:54
Alignment explanation
Indices: 1049170--1049281 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
1049160 AGCATGGCTG
* *
1049170 CCAGAACAGATAAAGTGACAGAGTCACCAGATACAGATAATCGTGGTAGAGCCA
1 CCAGAACAGATAAAGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* *
1049224 CCAGAACAGA-AATATGTGGCAGAGCCACCAGAT-CAGATAATCGTGGCATAGCCA
1 CCAGAACAGATAA-A-GTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
1049278 CCAG
1 CCAG
1049282 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
53 2 0.04
54 34 0.65
55 16 0.31
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.14
Consensus pattern (54 bp):
CCAGAACAGATAAAGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:1050677 original size:24 final size:24
Alignment explanation
Indices: 1050650--1050720 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
1050640 CTAGATTTCC
** *
1050650 TCCCTTATCTGCTCCTAACTCCTA
1 TCCCTTATCAACTCCTAAATCCTA
1050674 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
*
1050698 TCCCTTATCAACCCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
1050721 CTCATGACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.24, C:0.41, G:0.01, T:0.34
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:1054558 original size:13 final size:13
Alignment explanation
Indices: 1054540--1054570 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1054530 ATTTTTGGCA
*
1054540 CCCCTGCTAGGCG
1 CCCCTGCCAGGCG
1054553 CCCCTGCCAGGCG
1 CCCCTGCCAGGCG
1054566 CCCCT
1 CCCCT
1054571 CGACCTCGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.55, G:0.26, T:0.13
Consensus pattern (13 bp):
CCCCTGCCAGGCG
Found at i:1057023 original size:28 final size:27
Alignment explanation
Indices: 1056978--1057084 Score: 119
Period size: 27 Copynumber: 3.9 Consensus size: 27
1056968 GGCTGCCAAA
* * *
1056978 ACAGATAATGTGACAGAGTCACCAGAT
1 ACAGAAAATGTGGCAGAGCCACCAGAT
1057005 ACAGAAAATCGTGGCAGAGCCACCAGA-
1 ACAGAAAAT-GTGGCAGAGCCACCAGAT
1057032 ACAGAAATATGTGGCAGAGCCACCAGAT
1 ACAGAAA-ATGTGGCAGAGCCACCAGAT
* * *
1057060 -CAGCTAATTGTGGCATAGCCACCAG
1 ACAG-AAAATGTGGCAGAGCCACCAG
1057085 GACGCTTCCT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
27 51 0.73
28 19 0.27
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.15
Consensus pattern (27 bp):
ACAGAAAATGTGGCAGAGCCACCAGAT
Found at i:1057080 original size:54 final size:54
Alignment explanation
Indices: 1056977--1057084 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
1056967 TGGCTGCCAA
* *
1056977 AACAGATAATGTGACAGAGTCACCAGATACAGAAAATCGTGGCAGAGCCACCAG
1 AACAGAAAATGTGACAGAGCCACCAGATACAGAAAATCGTGGCAGAGCCACCAG
* ** * *
1057031 AACAGAAATATGTGGCAGAGCCACCAGAT-CAGCTAATTGTGGCATAGCCACCAG
1 AACAGAAA-ATGTGACAGAGCCACCAGATACAGAAAATCGTGGCAGAGCCACCAG
1057085 GACGCTTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
54 28 0.61
55 18 0.39
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
AACAGAAAATGTGACAGAGCCACCAGATACAGAAAATCGTGGCAGAGCCACCAG
Found at i:1058538 original size:24 final size:24
Alignment explanation
Indices: 1058511--1058581 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
1058501 CTAGATTTCC
**
1058511 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
1058535 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
*
1058559 TCCCTTATCAACCCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
1058582 CTCCTGACAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.25, C:0.39, G:0.01, T:0.34
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:1059937 original size:14 final size:14
Alignment explanation
Indices: 1059918--1059948 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1059908 AGTAAAATAG
1059918 ATTCTTAAATATTT
1 ATTCTTAAATATTT
1059932 ATTCTTAAATATTT
1 ATTCTTAAATATTT
1059946 ATT
1 ATT
1059949 AAAAATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTCTTAAATATTT
Found at i:1060725 original size:43 final size:40
Alignment explanation
Indices: 1060639--1060737 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 40
1060629 CGACCTCGAG
*
1060639 TCGATGAGGCACTATATGTGCCGTAATATTGCTTCGGATAAT
1 TCGATGAGGCAC--TATGTGCCGTAATATTGCTTCGAATAAT
* * *
1060681 TCTGATGAGGCACTATGTGTCGTATTATTGCTTTGAATTAAAT
1 TC-GATGAGGCACTATGTGCCGTAATATTGCTTCGAA-T-AAT
*
1060724 TCGATGAGGTACTA
1 TCGATGAGGCACTA
1060738 GGTACCGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
41 20 0.41
42 14 0.29
43 15 0.31
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (40 bp):
TCGATGAGGCACTATGTGCCGTAATATTGCTTCGAATAAT
Found at i:1064241 original size:25 final size:25
Alignment explanation
Indices: 1064212--1064261 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1064202 CCTTATAATA
* * *
1064212 TAAAAATGACCGTTTTGCCCCTAGG
1 TAAAAATGACCATTATACCCCTAGG
1064237 TAAAAATGACCATTATACCCCTAGG
1 TAAAAATGACCATTATACCCCTAGG
1064262 GTTTATGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (25 bp):
TAAAAATGACCATTATACCCCTAGG
Found at i:1064333 original size:19 final size:20
Alignment explanation
Indices: 1064305--1064362 Score: 100
Period size: 19 Copynumber: 3.0 Consensus size: 20
1064295 TAAACATGGT
1064305 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
1064325 ATG-ATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
1064344 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
1064363 TGTATTCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:1064342 original size:11 final size:11
Alignment explanation
Indices: 1064309--1064363 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
1064299 CATGGTATGT
1064309 ATGATATGCAC
1 ATGATATGCAC
*
1064320 ATGACATG---
1 ATGATATGCAC
1064328 ATGATATGCAC
1 ATGATATGCAC
*
1064339 ATGATATG--T
1 ATGATATGCAC
1064348 ATGATATGCAC
1 ATGATATGCAC
1064359 ATGAT
1 ATGAT
1064364 GTATTCATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
8 7 0.20
9 8 0.23
11 20 0.57
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:1064353 original size:20 final size:20
Alignment explanation
Indices: 1064298--1064363 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
1064288 ATTTTGATAA
*
1064298 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
1064318 ACATGACATG-ATGATATGC
1 ACATGATATGTATGATATGC
1064337 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
1064357 ACATGAT
1 ACATGAT
1064364 GTATTCATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
19 18 0.43
20 24 0.57
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:1064492 original size:23 final size:23
Alignment explanation
Indices: 1064414--1064672 Score: 455
Period size: 23 Copynumber: 11.1 Consensus size: 23
1064404 AGGAAGTGAA
*
1064414 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
1064438 AAAGGGCTTATGCCCCAGTTGTT
1 AAAGGGCTTATGCCCCAGTTATT
1064461 AAAAGGGCTTATGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
1064485 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
1064508 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
1064531 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
1064554 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
1064577 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
1064600 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
1064623 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
1064646 AAAAAGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
1064670 AAA
1 AAA
1064673 AGAGGCTAGG
Statistics
Matches: 228, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
23 164 0.72
24 64 0.28
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:1064921 original size:31 final size:31
Alignment explanation
Indices: 1064886--1064949 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1064876 CATTTACAGT
*
1064886 AAAGGCTTCGGCCCATTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
1064917 AAAGGCTTCGGCCCAGTGTTATGATATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1064948 AA
1 AA
1064950 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:1072510 original size:25 final size:25
Alignment explanation
Indices: 1072481--1072528 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1072471 TTATAATATG
* * *
1072481 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
1072506 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
1072529 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:1072600 original size:19 final size:20
Alignment explanation
Indices: 1072572--1072629 Score: 91
Period size: 19 Copynumber: 3.0 Consensus size: 20
1072562 GAAACATGTT
1072572 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
* *
1072592 ATG-ATGATATGCACATAAT
1 ATGTATGATATGCACATGAC
1072611 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
1072630 TGTATTCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:1072707 original size:24 final size:24
Alignment explanation
Indices: 1072680--1072808 Score: 197
Period size: 24 Copynumber: 5.4 Consensus size: 24
1072670 GAGGAAGTGA
* *
1072680 AAAAGGGCTTATGCCCCACTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
1072704 AAAAGGGCTTATGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT
1072728 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
1072752 -AAAGGGTTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
1072775 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
1072799 AAAAGAGGCT
1 AAAAG-GGCT
1072809 AGGCCTCCAG
Statistics
Matches: 96, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
23 22 0.23
24 70 0.73
25 4 0.04
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:1072770 original size:47 final size:47
Alignment explanation
Indices: 1072680--1072801 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
1072670 GAGGAAGTGA
* * *
1072680 AAAAGGGCTTATGCCCCACTTATCAAAAGGGCTTATGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTATT
*
1072728 AAAAGGGCTTATGCCCCAGTTATTAAAGGGTTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
*
1072775 AAAAGGGCTTTTGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
1072802 AGAGGCTAGG
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 47 0.68
48 22 0.32
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
Found at i:1073069 original size:31 final size:31
Alignment explanation
Indices: 1073015--1073078 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1073005 CATTTATAGT
*
1073015 AAAGGCTTCGGCCCATTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* ** *
1073046 AAAGGCTTCGGCCCGGTGTTATGATATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1073077 AA
1 AA
1073079 TATGAAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:1075197 original size:44 final size:44
Alignment explanation
Indices: 1075134--1075606 Score: 368
Period size: 44 Copynumber: 10.6 Consensus size: 44
1075124 GTTATTGTGG
* * * * *
1075134 CAAATCTTATCTCTTTGAAGTTGCAATAGAGCTA-ATTAAAACCA
1 CAAATCTTATCTCCTTGAAGTTGCAGTAGAAC-AGATTAAAGCTA
* * *
1075178 CAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAAATTAAAGCCA
1 CAAATCTTATCTCCTTGAAGTTGCAGTAGAACAGATTAAAGCTA
* * * * *
1075222 TAAATCTTATCTCCCTGAAGTTGCAATACAACAGATTGAAA-ATA
1 CAAATCTTATCTCCTTGAAGTTGCAGTAGAACAGATT-AAAGCTA
* *
1075266 GCAAATCTTATCT-CTCTGAAGTTGCAGTAGAATAGATTAAAGCCA
1 -CAAATCTTATCTCCT-TGAAGTTGCAGTAGAACAGATTAAAGCTA
* * * ** *
1075311 TAAATCTTATCTCCCTGAAGTTGCAAT-GCAGTAGATTGAAA-ATA
1 CAAATCTTATCTCCTTGAAGTTGCAGTAG-AACAGATT-AAAGCTA
**
1075355 GCAAATCTTATCTTTTTGAAGTTGCAGTAGAACAGATTAAAGCTA
1 -CAAATCTTATCTCCTTGAAGTTGCAGTAGAACAGATTAAAGCTA
1075400 CAAATCTTATCT-CTCTGAAGTTGCAGTAGAACAGATTAAAG-TAA
1 CAAATCTTATCTCCT-TGAAGTTGCAGTAGAACAGATTAAAGCT-A
* * * * * *
1075444 CAATTCTTATCTCATTGAAGCTGCAATAGAACAGATTGAAGTTA
1 CAAATCTTATCTCCTTGAAGTTGCAGTAGAACAGATTAAAGCTA
* * * * * *
1075488 CAAATCTCATCTCCCTGAAGTTTCAGTAGAGCAAATTAAAGCGA
1 CAAATCTTATCTCCTTGAAGTTGCAGTAGAACAGATTAAAGCTA
* * * * ** * *
1075532 GAAATCCTAT-GCCTCTGAAGTTGCAGTGGGTCGGATTAAATCAAGTCA
1 CAAATCTTATCTCCT-TGAAGTTGCAGTAGAACAGATTAAAGC---T-A
*
1075580 CAAATCTTATCTCCCTGAAGTTGCAGT
1 CAAATCTTATCTCCTTGAAGTTGCAGT
1075607 GGAGTAGATT
Statistics
Matches: 341, Mismatches: 67, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
43 6 0.02
44 241 0.71
45 70 0.21
46 1 0.00
48 21 0.06
49 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (44 bp):
CAAATCTTATCTCCTTGAAGTTGCAGTAGAACAGATTAAAGCTA
Found at i:1075293 original size:89 final size:88
Alignment explanation
Indices: 1075134--1075604 Score: 423
Period size: 89 Copynumber: 5.3 Consensus size: 88
1075124 GTTATTGTGG
** * * *
1075134 CAAATCTTATCTCTTTGAAGTTGCAATAGAGCTA-ATTAAAACCA-CAAATCTTATCTC-CTTGA
1 CAAATCTTATCTCCCTGAAGTTGCAATACAAC-AGATTAAAA-TAGCAAATCTTATCTCTC-TGA
* *
1075196 AGTTGCAGTAGAGCAAATTAAAGCCA
63 AGTTGCAGTAGAACAGATTAAAGCCA
*
1075222 TAAATCTTATCTCCCTGAAGTTGCAATACAACAGATTGAAAATAGCAAATCTTATCTCTCTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAATACAACAGATT-AAAATAGCAAATCTTATCTCTCTGAAG
*
1075287 TTGCAGTAGAATAGATTAAAGCCA
65 TTGCAGTAGAACAGATTAAAGCCA
* * ** * *
1075311 TAAATCTTATCTCCCTGAAGTTGCAATGCAGTAGATTGAAAATAGCAAATCTTATCTTTTTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAATACAACAGATT-AAAATAGCAAATCTTATCTCTCTGAAG
*
1075376 TTGCAGTAGAACAGATTAAAGCTA
65 TTGCAGTAGAACAGATTAAAGCCA
* * * * * *
1075400 CAAATCTTATCTCTCTGAAGTTGCAGTAGAACAGATTAAAGTAACAATTCTTATCTCAT-TGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAATACAACAGATTAAAATAGCAAATCTTATCTC-TCTGAAG
* * * **
1075464 CTGCAATAGAACAGATTGAAGTTA
65 TTGCAGTAGAACAGATTAAAGCCA
* * * * * * ** *
1075488 CAAATCTCATCTCCCTGAAGTTTCAGTAGAGCAAATTAAAGCGAG-AAATCCTATGC-CTCTGAA
1 CAAATCTTATCTCCCTGAAGTTGCAATACAACAGATTAAA-ATAGCAAATCTTAT-CTCTCTGAA
* ** * *
1075551 GTTGCAGTGGGTCGGATTAAATCAAGTCA
64 GTTGCAGTAGAACAGATT--A--AAGCCA
1075580 CAAATCTTATCTCCCTGAAGTTGCA
1 CAAATCTTATCTCCCTGAAGTTGCA
1075605 GTGGAGTAGA
Statistics
Matches: 320, Mismatches: 51, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
87 2 0.01
88 131 0.41
89 158 0.49
90 1 0.00
92 28 0.09
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (88 bp):
CAAATCTTATCTCCCTGAAGTTGCAATACAACAGATTAAAATAGCAAATCTTATCTCTCTGAAGT
TGCAGTAGAACAGATTAAAGCCA
Done.