Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014080.1 Corchorus capsularis cultivar CVL-1 contig14101, whole genome shotgun sequence
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: 82473
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4547 original size:16 final size:16
Alignment explanation
Indices: 4528--4560 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4518 TTTTTTATAA
4528 AAAATTTGTAATTTTT
1 AAAATTTGTAATTTTT
4544 AAAATTTGTAATTTTT
1 AAAATTTGTAATTTTT
4560 A
1 A
4561 TTTATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
AAAATTTGTAATTTTT
Found at i:5954 original size:17 final size:16
Alignment explanation
Indices: 5899--5950 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
5889 ATCACCCCCC
*
5899 AGATCACTGGTGATCTTA
1 AGATCACCGGTGATC--A
*
5917 AGATCACCAGTGATGCA
1 AGATCACCGGTGAT-CA
5934 AGATCACCGGTGATCA
1 AGATCACCGGTGATCA
5950 A
1 A
5951 AGATTACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 3 0.10
17 14 0.47
18 12 0.40
19 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (16 bp):
AGATCACCGGTGATCA
Found at i:8647 original size:50 final size:50
Alignment explanation
Indices: 8592--8716 Score: 241
Period size: 50 Copynumber: 2.5 Consensus size: 50
8582 GTCTAGTTTT
*
8592 TAATAAAATTTTTCTTTAAAAAAAAGTCTTAACTATTATCCTATCCTAGG
1 TAATAAAATTTGTCTTTAAAAAAAAGTCTTAACTATTATCCTATCCTAGG
8642 TAATAAAATTTGTCTTTAAAAAAAAGTCTTAACTATTATCCTATCCTAGG
1 TAATAAAATTTGTCTTTAAAAAAAAGTCTTAACTATTATCCTATCCTAGG
8692 TAATAAAATTTGTCTTTAAAAAAAA
1 TAATAAAATTTGTCTTTAAAAAAAA
8717 TGAAATCTGA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.38
Consensus pattern (50 bp):
TAATAAAATTTGTCTTTAAAAAAAAGTCTTAACTATTATCCTATCCTAGG
Found at i:14845 original size:21 final size:21
Alignment explanation
Indices: 14819--14859 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
14809 GGAAGGGAAG
* *
14819 CATATTATCTCTAGTATATTC
1 CATATTATCCCTAGGATATTC
14840 CATATTATCCCTAGGATATT
1 CATATTATCCCTAGGATATT
14860 TAATCTTTCT
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:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (21 bp):
CATATTATCCCTAGGATATTC
Found at i:15221 original size:44 final size:43
Alignment explanation
Indices: 15173--15299 Score: 155
Period size: 44 Copynumber: 2.9 Consensus size: 43
15163 TATAAGGAGA
*
15173 TTATCAAAATTTCATATAAAGGTTATCAAATTTTCATGGTGTGG
1 TTATCAAAATTTCATA-AAAGGTTATCAAATTTTCATAGTGTGG
* *
15217 TTATCAAAATTTCATAAGGAGGTTATCAAATTTTCATATTGTGG
1 TTATCAAAATTTCATAA-AAGGTTATCAAATTTTCATAGTGTGG
* * * * *
15261 ATACCAAAATTTCATACCATGGTTATCAAAATTTCATAG
1 TTATCAAAATTTCATA-AAAGGTTATCAAATTTTCATAG
15300 GGTTATCAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
43 1 0.01
44 70 0.99
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (43 bp):
TTATCAAAATTTCATAAAAGGTTATCAAATTTTCATAGTGTGG
Found at i:15251 original size:22 final size:22
Alignment explanation
Indices: 15157--15254 Score: 103
Period size: 22 Copynumber: 4.5 Consensus size: 22
15147 GTGGTTATTT
*
15157 AAATTTT-ATAAGGAGATTATC
1 AAATTTTCATAAGGAGGTTATC
* *
15178 AAAATTTCATATA-AAGGTTATC
1 AAATTTTCATA-AGGAGGTTATC
* *
15200 AAATTTTCAT-GGTGTGGTTATC
1 AAATTTTCATAAG-GAGGTTATC
*
15222 AAAATTTCATAAGGAGGTTATC
1 AAATTTTCATAAGGAGGTTATC
15244 AAATTTTCATA
1 AAATTTTCATA
15255 TTGTGGATAC
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
21 6 0.10
22 53 0.87
23 2 0.03
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (22 bp):
AAATTTTCATAAGGAGGTTATC
Found at i:15274 original size:66 final size:66
Alignment explanation
Indices: 15145--15309 Score: 174
Period size: 66 Copynumber: 2.5 Consensus size: 66
15135 TGTTGTCTCT
** * * * * *
15145 GTGTGGTTATTTAAATTTTATAAGGAGATTATCAAAATTTCATATAAAGGTTATCAAATTTTCAT
1 GTGTGGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATATAAAGGATACCAAAATTTCAT
*
15210 G
66 A
* ***
15211 GTGTGGTTATCAAAATTTCATAAGGAGGTTATCAAATTTTCATATTGTGGATACCAAAATTTCAT
1 GTGTGGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATATAAAGGATACCAAAATTTCAT
15276 A
66 A
***
15277 CCATGGTTATCAAAATTTCAT-A-G-GGTTATCAAA
1 GTGTGGTTATCAAAATTTCATAAGGAGGTTATCAAA
15310 GAGGTTATCG
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
63 10 0.12
64 1 0.01
65 1 0.01
66 72 0.86
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (66 bp):
GTGTGGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATATAAAGGATACCAAAATTTCAT
A
Found at i:15290 original size:22 final size:22
Alignment explanation
Indices: 15173--15299 Score: 114
Period size: 22 Copynumber: 5.8 Consensus size: 22
15163 TATAAGGAGA
*
15173 TTATCAAAATTTCATA-TAAAGG
1 TTATCAAAATTTCATAGT-ATGG
* * *
15195 TTATCAAATTTTCATGGTGTGG
1 TTATCAAAATTTCATAGTATGG
*
15217 TTATCAAAATTTCATAAGGA-GG
1 TTATCAAAATTTCAT-AGTATGG
* * *
15239 TTATCAAATTTTCATATTGTGG
1 TTATCAAAATTTCATAGTATGG
* * **
15261 ATACCAAAATTTCATACCATGG
1 TTATCAAAATTTCATAGTATGG
15283 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
15300 GGTTATCAAA
Statistics
Matches: 81, Mismatches: 21, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.01
22 78 0.96
23 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTATGG
Found at i:15672 original size:41 final size:42
Alignment explanation
Indices: 15602--15747 Score: 100
Period size: 41 Copynumber: 3.4 Consensus size: 42
15592 AAGATCATAT
* * * *
15602 ATTATGAAAATTTCATATGAAGGTAATCAAAATTT-AGTGTA
1 ATTATCAAAATTTTATAGGGAGGTAATCAAAATTTAAGTGTA
* * *
15643 ATTATCAAAATTTTATAGGGAGGTCATCAATATTTCAAAGTGTG
1 ATTATCAAAATTTTATAGGGAGGTAATCAAAATTT--AAGTGTA
* * * * * *
15687 GTTATCAGAAATTCTTATA--GAGGTTATCGAAATTTCATTAGGA
1 ATTATCA-AAATT-TTATAGGGAGGTAATCAAAATTTAAGT-GTA
*
15730 AATATCAAAATTTTATAG
1 ATTATCAAAATTTTATAG
15748 TGTGATTATC
Statistics
Matches: 81, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
41 34 0.42
42 7 0.09
43 6 0.07
44 24 0.30
45 5 0.06
46 5 0.06
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.37
Consensus pattern (42 bp):
ATTATCAAAATTTTATAGGGAGGTAATCAAAATTTAAGTGTA
Found at i:15759 original size:22 final size:22
Alignment explanation
Indices: 15636--15761 Score: 71
Period size: 22 Copynumber: 5.8 Consensus size: 22
15626 AATCAAAATT
*
15636 TAGTGTAATTATCAAAATTTTA
1 TAGTGTGATTATCAAAATTTTA
* * * * * *
15658 TAGGGAGGTCATCAATATTTCA
1 TAGTGTGATTATCAAAATTTTA
* *
15680 AAGTGTGGTTATCAGAAATTCTTA
1 TAGTGTGATTATCA-AAATT-TTA
* * *
15704 TAGAG-G-TTATCGAAATTTCA
1 TAGTGTGATTATCAAAATTTTA
* *
15724 TTAG-G-AAATATCAAAATTTTA
1 -TAGTGTGATTATCAAAATTTTA
15745 TAGTGTGATTATCAAAA
1 TAGTGTGATTATCAAAA
15762 GAGTGTGGTA
Statistics
Matches: 75, Mismatches: 23, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
20 6 0.08
21 20 0.27
22 39 0.52
23 5 0.07
24 5 0.07
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (22 bp):
TAGTGTGATTATCAAAATTTTA
Found at i:15914 original size:22 final size:23
Alignment explanation
Indices: 15868--15929 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
15858 TATAAGGAGA
15868 TTATTAAAATTTCATATATAAAGG
1 TTATTAAAATTTCATATAT-AAGG
* *
15892 TTATTAAAATTCCATATGT-AGG
1 TTATTAAAATTTCATATATAAGG
*
15914 TTATTGAAATTTCATA
1 TTATTAAAATTTCATA
15930 GTGTGTGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 17 0.50
24 17 0.50
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (23 bp):
TTATTAAAATTTCATATATAAGG
Found at i:23941 original size:25 final size:25
Alignment explanation
Indices: 23904--23952 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
23894 CTAAATGACA
23904 GAGTTCATATAGTTTATACTCAATT
1 GAGTTCATATAGTTTATACTCAATT
*
23929 GAGTTCATGTAGTTTATACTCAAT
1 GAGTTCATATAGTTTATACTCAAT
23953 CACGGAGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (25 bp):
GAGTTCATATAGTTTATACTCAATT
Found at i:26751 original size:16 final size:16
Alignment explanation
Indices: 26730--26761 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
26720 TCAATGATAG
*
26730 AGATAAGGTTAGAGTT
1 AGATAAGGTTAAAGTT
26746 AGATAAGGTTAAAGTT
1 AGATAAGGTTAAAGTT
26762 TAGTTTGCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (16 bp):
AGATAAGGTTAAAGTT
Found at i:26891 original size:14 final size:15
Alignment explanation
Indices: 26872--26900 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26862 ATTAAATAAA
26872 AGTAAG-TTTGTATT
1 AGTAAGTTTTGTATT
26886 AGTAAGTTTTGTATT
1 AGTAAGTTTTGTATT
26901 GGAAACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
AGTAAGTTTTGTATT
Found at i:27016 original size:32 final size:32
Alignment explanation
Indices: 26975--27036 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
26965 TCCAACCTAA
26975 AACCAATTGGCAAGTGGAAAGGCCCAGCCTCT
1 AACCAATTGGCAAGTGGAAAGGCCCAGCCTCT
*
27007 AACCAATTGGCAAGTGGAGAGGCCCAGCCT
1 AACCAATTGGCAAGTGGAAAGGCCCAGCCT
27037 GTATATAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.15
Consensus pattern (32 bp):
AACCAATTGGCAAGTGGAAAGGCCCAGCCTCT
Found at i:29164 original size:135 final size:134
Alignment explanation
Indices: 29009--29682 Score: 407
Period size: 139 Copynumber: 4.9 Consensus size: 134
28999 AATTACCCTT
* * *
29009 ACTTAATTACACTGAATTAAGTTACTTATTGACT-CTTAACTTCCCTGAATTAAGTTGGTTATTG
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTACTTAA-TTCCCTGAATTAAGTT-GCTATTG
* * * *
29073 ACTTAATTAATTACCTTGAATTAAAGTTGATT-ACTGATTCACTCAATTACTCTGAATTAA-G-C
63 ACTGAATTAATTACCCTGAATT-AAGTT-ATTCACTGACTCACTCAATTACCCTGAATTAATGAC
* *
29135 TACTTACCG
126 TACTGACCC
* * *
29144 ACTTAATTACCCTGAATTAAGTCATTAACTGACTCACTTAATTACCT-AGATTAA---GCTATTT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACT-ACTTAATTCCCTGA-ATTAAGTTGCTATTG
* * *
29205 ACTGACTTAATTACCCTGAATTAAGTTATTCACTGACTCACTTAATTACCCTGAATTAAGTTGAT
63 ACTGAATTAATTACCCTGAATTAAGTTATTCACTGACTCACTCAATTACCCTGAATTAA--TGAC
29270 TACTGACCC
126 TACTGACCC
*
29279 ACTTAATTACCCTGAATTAAGTTGATTACTGACTCACTTAATTGCCCTGAATTAAG-T--TACTG
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACT-ACTTAATT-CCCTGAATTAAGTTGCTATTG
* * * * * * * * * *
29341 TCTTACTTAACTT-TCCTGAACTAAGTTACTAACTGAATTACTTAATTACCCTGAATTAAGGTTG
63 ACTGAATTAA-TTACCCTGAATTAAGTTATTCACTGACTCACTCAATTACCCTGAATTAA---TG
* **
29405 ATTACTGACTT
124 ACTACTGACCC
* * * *
29416 ACTTAATTACCCTGAACTAAGTTGATTACTACTGACTTTCTTAATTACCCTGAATTAAATTGATT
1 ACTTAATTACCCTGAATTAAGTT-A-T--TACTGAC-TACTTAATT-CCCTGAATTAAGTTG-CT
** * * * * *
29481 ACCGACTCACTTAATTACCCTGAATTAAGTTACTT-ATTGAACT-AATTAATTACCCTGAATTAA
59 ATTGACTGAATTAATTACCCTGAATTAAGTTA-TTCACTG-ACTCACTCAATTACCCTGAATTAA
* * *
29544 GTTACTTTTTATCTCACTCT
122 -TGAC----TA-CTGAC-CC
* * *
29564 ACTTAATTACCCTGAATTAA---AGT--TGAACTACTTAATTACCCTGAATTAAGTTACTAACTG
1 ACTTAATTACCCTGAATTAAGTTATTACTG-ACTACTTAATT-CCCTGAATTAAGTTGCT-ATTG
* * * * * *
29624 AATTACTTAAATACCCTGAATTAAGTTGATT-ATTGACTCACTTAATTACCCTGAATTAA
63 ACTGAATTAATTACCCTGAATTAAGTT-ATTCACTGACTCACTCAATTACCCTGAATTAA
29683 GTTACTTATT
Statistics
Matches: 444, Mismatches: 58, Indels: 70
0.78 0.10 0.12
Matches are distributed among these distances:
130 3 0.01
131 30 0.07
132 24 0.05
134 3 0.01
135 74 0.17
136 72 0.16
137 45 0.10
138 5 0.01
139 76 0.17
140 28 0.06
141 3 0.01
142 2 0.00
143 2 0.00
144 48 0.11
145 3 0.01
146 2 0.00
147 4 0.01
148 20 0.05
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (134 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGACTACTTAATTCCCTGAATTAAGTTGCTATTGACT
GAATTAATTACCCTGAATTAAGTTATTCACTGACTCACTCAATTACCCTGAATTAATGACTACTG
ACCC
Found at i:29481 original size:19 final size:19
Alignment explanation
Indices: 29373--29508 Score: 72
Period size: 18 Copynumber: 7.5 Consensus size: 19
29363 AAGTTACTAA
*
29373 CTGAATT-ACTTAATTACC
1 CTGAATTAACTTGATTACC
*
29391 CTGAATTAAGGTTGATTA--
1 CTGAATTAA-CTTGATTACC
* *
29409 CTGACTT-ACTTAATTACC
1 CTGAATTAACTTGATTACC
* * *
29427 CTGAACTAAGTTGATTACTA
1 CTGAATTAACTTGATTAC-C
* * *
29447 CTGACTT-TCTTAATTACC
1 CTGAATTAACTTGATTACC
*
29465 CTGAATTAAATTGATTA-C
1 CTGAATTAACTTGATTACC
* * *
29483 C-G-ACTCACTTAATTACC
1 CTGAATTAACTTGATTACC
29500 CTGAATTAA
1 CTGAATTAA
29509 GTTACTTATT
Statistics
Matches: 82, Mismatches: 26, Indels: 19
0.65 0.20 0.15
Matches are distributed among these distances:
16 15 0.18
17 4 0.05
18 27 0.33
19 25 0.30
20 11 0.13
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (19 bp):
CTGAATTAACTTGATTACC
Found at i:29606 original size:69 final size:65
Alignment explanation
Indices: 29517--29689 Score: 188
Period size: 69 Copynumber: 2.5 Consensus size: 65
29507 AAGTTACTTA
* * * *
29517 TTGAACTAATTAATTACCCTGAATTAAGTTACTTTTTATCTCACTCTACTTAATTACCCTGAATT
1 TTGAACTACTTAATTACCCTGAATTAAGTTAC--TTTAACTCAAT-TACTTAAATACCCTGAATT
29582 AAAG
63 -AAG
*
29586 TTGAACTACTTAATTACCCTGAATTAAGTTAC--TAACTGAATTACTTAAATACCCTGAATTAAG
1 TTGAACTACTTAATTACCCTGAATTAAGTTACTTTAACTCAATTACTTAAATACCCTGAATTAAG
29649 TTGATTATTGACTCACTTAATTACCCTGAATTAAGTTACTT
1 TTG---A---ACT-ACTTAATTACCCTGAATTAAGTTACTT
29690 ATTACTGATT
Statistics
Matches: 90, Mismatches: 5, Indels: 15
0.82 0.05 0.14
Matches are distributed among these distances:
63 6 0.07
64 18 0.20
65 6 0.07
66 1 0.01
69 34 0.38
70 25 0.28
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (65 bp):
TTGAACTACTTAATTACCCTGAATTAAGTTACTTTAACTCAATTACTTAAATACCCTGAATTAAG
Found at i:29685 original size:35 final size:35
Alignment explanation
Indices: 29009--29685 Score: 567
Period size: 35 Copynumber: 19.7 Consensus size: 35
28999 AATTACCCTT
* *
29009 ACTTAATTACACTGAATTAAGTT-ACTTATTGACT-
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
* * *
29043 -CTTAACTT-CCCTGAATTAAGTTGGTTATTGACTT
1 ACTTAA-TTACCCTGAATTAAGTTGATTACTGACTC
* * *
29077 AATTAATTACCTTGAATTAAAGTTGATTACTGATTC
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTC
* * * *
29113 ACTCAATTACTCTGAATTAAGCT-ACTTAC---C-G
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
*
29144 ACTTAATTACCCTGAATTAAG-TCATTAACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATT-ACTGACTC
* *
29179 ACTTAATTA-CCT-AGATTAAGCT-ATT--T-ACTG
1 ACTTAATTACCCTGA-ATTAAGTTGATTACTGACTC
29209 ACTTAATTACCCTGAATTAAGTT-ATTCACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATT-ACTGACTC
*
29244 ACTTAATTACCCTGAATTAAGTTGATTACTGACCC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
29279 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * *
29314 ACTTAATTGCCCTGAATTAA---G-TTACTGTCTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
* * * * *
29345 ACTTAACTT-TCCTGAACTAAGTT-ACTAACTGAATT
1 ACTTAA-TTACCCTGAATTAAGTTGA-TTACTGACTC
*
29380 ACTTAATTACCCTGAATTAAGGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAA-GTTGATTACTGACTC
* *
29416 ACTTAATTACCCTGAACTAAGTTGATTACTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGA-T--TACTGACTC
* * *
29454 TCTTAATTACCCTGAATTAAATTGATTACCGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
*
29489 ACTTAATTACCCTGAATTAAGTT-ACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTG-ACTC
* *
29524 AATTAATTACCCTGAATTAAGTT-ACTTTTTATCTCACTC
1 ACTTAATTACCCTGAATTAAGTTGA----TTA-CTGACTC
29563 TACTTAATTACCCTGAATTAAAGTTG---A---ACT-
1 -ACTTAATTACCCTGAATT-AAGTTGATTACTGACTC
* * *
29593 ACTTAATTACCCTGAATTAAGTT-ACTAACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTC
* *
29628 ACTTAAATACCCTGAATTAAGTTGATTATTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
29663 ACTTAATTACCCTGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
29686 ACTTATTACT
Statistics
Matches: 533, Mismatches: 57, Indels: 105
0.77 0.08 0.15
Matches are distributed among these distances:
28 5 0.01
29 18 0.03
30 15 0.03
31 63 0.12
32 4 0.01
33 28 0.05
34 24 0.05
35 249 0.47
36 65 0.12
37 2 0.00
38 37 0.07
39 1 0.00
40 17 0.03
41 5 0.01
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.38
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
Found at i:32106 original size:22 final size:22
Alignment explanation
Indices: 32078--32121 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
32068 TGTTATATTA
32078 TACTAAATG-CAAGAAGTGAATT
1 TACTAAATGCCAA-AAGTGAATT
32100 TACTAAATGCCAAAAGTGAATT
1 TACTAAATGCCAAAAGTGAATT
32122 AGAAAATGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (22 bp):
TACTAAATGCCAAAAGTGAATT
Found at i:40711 original size:416 final size:399
Alignment explanation
Indices: 39904--40736 Score: 1008
Period size: 416 Copynumber: 2.0 Consensus size: 399
39894 AATTGACTCG
* *
39904 ATTAAGAGAATGATCGATCTTTGTTTTCTTTTTAGATGTGCTTTGCTTTGTACAATTAAGGATAC
1 ATTAAAAGAATGATCGATCTTTGTTTTCTTTTTAGATGTGCTTTGCTTTGTACAATGAAGGATAC
39969 TATATTTTTGCTCTACTATGTTTGTGTTTAAATTGAAGGTTTTTTTATATACATTCTTTTTTCAA
66 TATATTTTTGCTCTACTATGTTTGTGTTTAAATTGAAGGTTTTTTTATATACATTCTTTTTTCAA
*
40034 AGTAAATATAAGATGATCTCTCATGGCAGCTTGAAATGATGAAAAATCTGCCAATTGCCAAAGCT
131 AGTAAATATAAGATGATCTCTCATGGCAGCTTGAAATGATGAAAAATCTGCCAATTGACAAAGCT
*
40099 CTTTCAAATATTTACCTAATTCACAAAAAAAAAAAAAAAAAAAAAAAATAGGATGAAATCACAAA
196 CTTTCAAATACTTACCTAATTCAC--------------AAAAAAAAAATAGGATGAAATCACAAA
* * *
40164 GGGCCGGTTGGTGTTTAATGAATTTTACAATGAACATATTAAGTAATTACAACAAACCTTGTAAC
247 ---------GGTGTTTAATAAATTTTACAATGAACAAATTAAGTAATAACAACAAACCTTGTAAC
* *
40229 AATTTCCAATCGGTTTAAATGCCTAAATGCACCCTAAAGTTTATATGGACTGCCACTTTACAACC
303 AATTTCCAATCGGTTTAAATGCCTAAATGCAACCTAAAGTTTATAAGGACTGCCACTTTACAACC
*
40294 TACTTCTTTTTTATTTTGATCATATCGCATTCTCA
368 TA--T-TTTTTTATTTTGATCATAACGCATTCTCA
40329 ATTAAAAGAATGATCGGATCTTTGTTTTCTTTTTAGATGTGCTTTGCTTTGTACAATGAAGGATA
1 ATTAAAAGAATGATC-GATCTTTGTTTTCTTTTTAGATGTGCTTTGCTTTGTACAATGAAGGATA
*
40394 CTATATATATATTTTTGCTCTACTATGTTTGTGTTTAAATTGAAAGTTTTTTATATATATATAAT
65 C------TATATTTTTGCTCTACTATGTTTGTGTTTAAATTG-AAG-GTTTT-T-T-TATAT-A-
* * * *
40459 TATTTGTTTTTTCAAAGT-AA-ATAAGATGATCTCTCATGGCAGCTTGAAGGTGATGAAAATTCT
117 CA-TTCTTTTTTCAAAGTAAATATAAGATGATCTCTCATGGCAGCTTGAA-ATGATGAAAAATCT
* * ** *
40522 GCCTATTGACAAAGCTCTTTCAATTACTTACCTAATTCAC-AAAAAAATTTTGGATGAAATCACA
180 GCCAATTGACAAAGCTCTTTCAAATACTTACCTAATTCACAAAAAAAAAATAGGATGAAATCACA
* *
40586 AA-GTGTTTAATAAATTTTACAATGGACAAATTAAGTAATCGAATAACAAACCTTGTAACAATTT
245 AAGGTGTTTAATAAATTTTACAATGAACAAATTAAGTAAT--AACAACAAACCTTGTAACAATTT
* * * *
40650 CCAATCGGTTTAAATGCCTAAATGCAACCTAAAGTTTATAAGGATTGCTATTTTGCAACCTATTT
308 CCAATCGGTTTAAATGCCTAAATGCAACCTAAAGTTTATAAGGACTGCCACTTTACAACCTATTT
40715 TTTTATTTTGATCATAACGCAT
373 TTTTATTTTGATCATAACGCAT
40737 CCTAATGTTT
Statistics
Matches: 364, Mismatches: 26, Indels: 48
0.83 0.06 0.11
Matches are distributed among these distances:
413 23 0.06
414 35 0.10
416 77 0.21
424 23 0.06
425 14 0.04
426 49 0.13
432 35 0.10
433 3 0.01
434 4 0.01
435 1 0.00
436 1 0.00
437 5 0.01
438 29 0.08
439 51 0.14
440 14 0.04
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (399 bp):
ATTAAAAGAATGATCGATCTTTGTTTTCTTTTTAGATGTGCTTTGCTTTGTACAATGAAGGATAC
TATATTTTTGCTCTACTATGTTTGTGTTTAAATTGAAGGTTTTTTTATATACATTCTTTTTTCAA
AGTAAATATAAGATGATCTCTCATGGCAGCTTGAAATGATGAAAAATCTGCCAATTGACAAAGCT
CTTTCAAATACTTACCTAATTCACAAAAAAAAAATAGGATGAAATCACAAAGGTGTTTAATAAAT
TTTACAATGAACAAATTAAGTAATAACAACAAACCTTGTAACAATTTCCAATCGGTTTAAATGCC
TAAATGCAACCTAAAGTTTATAAGGACTGCCACTTTACAACCTATTTTTTTATTTTGATCATAAC
GCATTCTCA
Found at i:41760 original size:13 final size:13
Alignment explanation
Indices: 41742--41768 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41732 TCTATAAATT
41742 TATAAATTTTATC
1 TATAAATTTTATC
41755 TATAAATTTTATC
1 TATAAATTTTATC
41768 T
1 T
41769 TAGTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (13 bp):
TATAAATTTTATC
Found at i:45521 original size:24 final size:25
Alignment explanation
Indices: 45466--45552 Score: 74
Period size: 24 Copynumber: 3.6 Consensus size: 25
45456 CCATTTGACC
*
45466 AAAAAACAGTAAGTTAAGAGC-C-TA-
1 AAAAAACAGAAAGTT-AGA-CACTTAT
*
45490 AAAAAACAGAAAGTTAGACATTTAT
1 AAAAAACAGAAAGTTAGACACTTAT
* * **
45515 -AAGAACAGACAGTTTTACACTTAT
1 AAAAAACAGAAAGTTAGACACTTAT
45539 AAAAAACAGAAAGT
1 AAAAAACAGAAAGT
45553 ACCTTGTGCT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
22 1 0.02
23 3 0.06
24 35 0.70
25 11 0.22
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (25 bp):
AAAAAACAGAAAGTTAGACACTTAT
Found at i:46579 original size:15 final size:15
Alignment explanation
Indices: 46559--46601 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
46549 GGCCGAGATG
*
46559 CAGTAGAAGGCCCTA
1 CAGTAGATGGCCCTA
* *
46574 CAGTAGATGGCTCTG
1 CAGTAGATGGCCCTA
46589 CAGTAGATGGCCC
1 CAGTAGATGGCCC
46602 AACCCCAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.19
Consensus pattern (15 bp):
CAGTAGATGGCCCTA
Found at i:46887 original size:30 final size:30
Alignment explanation
Indices: 46851--46926 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
46841 CCTCTCCAAT
46851 ATTGTTATCTTCCACTTGCTGCTCGTTTCC
1 ATTGTTATCTTCCACTTGCTGCTCGTTTCC
* *
46881 ATTGTTATCTTCCATTTGCTGCTGGTTTCC
1 ATTGTTATCTTCCACTTGCTGCTCGTTTCC
*
46911 ATTGTTGTCTTCCACT
1 ATTGTTATCTTCCACT
46927 ACTACTTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.11, C:0.26, G:0.14, T:0.49
Consensus pattern (30 bp):
ATTGTTATCTTCCACTTGCTGCTCGTTTCC
Found at i:47385 original size:33 final size:35
Alignment explanation
Indices: 47338--47409 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
47328 AAAAATTGAA
*
47338 AAAAAAAACATTAG-ATATGCTCAAACATAGTCAC
1 AAAAAAAACATTAGAACATGCTCAAACATAGTCAC
*
47372 AAAACAAA-ATTAGAAACATGCTCAAACATAGTCAC
1 AAAAAAAACATTAG-AACATGCTCAAACATAGTCAC
47407 AAA
1 AAA
47410 GCCAAATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 5 0.15
34 7 0.21
35 22 0.65
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (35 bp):
AAAAAAAACATTAGAACATGCTCAAACATAGTCAC
Found at i:49959 original size:174 final size:174
Alignment explanation
Indices: 49669--50019 Score: 675
Period size: 174 Copynumber: 2.0 Consensus size: 174
49659 TACAGTCACA
49669 GAACATTCTTAACGTAGCAAGGGCTTTAAGGTTTCAAGTTCAGTTACCTATTAGCTTTTGGGGTG
1 GAACATTCTTAACGTAGCAAGGGCTTTAAGGTTTCAAGTTCAGTTACCTATTAGCTTTTGGGGTG
*
49734 AGTGTGTTCTTCATGTTGTTTTTTTAATAAATAGAATACCAACTCCAATTCTTAATAATGTCTCA
66 AGTGTGTTCTTCATGCTGTTTTTTTAATAAATAGAATACCAACTCCAATTCTTAATAATGTCTCA
*
49799 CCATTTGAAGTTTTGTATTTTTAACCACCTGAGCTTGACCAATT
131 CCATTTGAAGTTTTGTATTCTTAACCACCTGAGCTTGACCAATT
*
49843 GAACATTCTTAATGTAGCAAGGGCTTTAAGGTTTCAAGTTCAGTTACCTATTAGCTTTTGGGGTG
1 GAACATTCTTAACGTAGCAAGGGCTTTAAGGTTTCAAGTTCAGTTACCTATTAGCTTTTGGGGTG
49908 AGTGTGTTCTTCATGCTGTTTTTTTAATAAATAGAATACCAACTCCAATTCTTAATAATGTCTCA
66 AGTGTGTTCTTCATGCTGTTTTTTTAATAAATAGAATACCAACTCCAATTCTTAATAATGTCTCA
49973 CCATTTGAAGTTTTGTATTCTTAACCACCTGAGCTTGACCAATT
131 CCATTTGAAGTTTTGTATTCTTAACCACCTGAGCTTGACCAATT
50017 GAA
1 GAA
50020 AGTTTTTTGA
Statistics
Matches: 174, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (174 bp):
GAACATTCTTAACGTAGCAAGGGCTTTAAGGTTTCAAGTTCAGTTACCTATTAGCTTTTGGGGTG
AGTGTGTTCTTCATGCTGTTTTTTTAATAAATAGAATACCAACTCCAATTCTTAATAATGTCTCA
CCATTTGAAGTTTTGTATTCTTAACCACCTGAGCTTGACCAATT
Found at i:54610 original size:36 final size:36
Alignment explanation
Indices: 54553--54622 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
54543 CCTTTAGGAC
* *
54553 ATATTGATAATTATTTTGTATAACATGCCAGCTATA
1 ATATCGATAATTATTTTGTATAACAGGCCAGCTATA
*
54589 ATATCGATAATT-TTTTAGTATAGCAGGCCAGCTA
1 ATATCGATAATTATTTT-GTATAACAGGCCAGCTA
54623 ATATAATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (36 bp):
ATATCGATAATTATTTTGTATAACAGGCCAGCTATA
Found at i:59141 original size:17 final size:17
Alignment explanation
Indices: 59116--59168 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
59106 GTAAACGCAC
* * *
59116 TATATTATATATTATTA
1 TATAATATATAATATAA
*
59133 TATAGTATATAATATAA
1 TATAATATATAATATAA
59150 TATAATATATAATAATAA
1 TATAATATATAAT-ATAA
59168 T
1 T
59169 TATCAAATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 26 0.84
18 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TATAATATATAATATAA
Found at i:60570 original size:2 final size:2
Alignment explanation
Indices: 60563--60591 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60553 AACATCTAAT
60563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60592 TCATACATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66762 original size:6 final size:6
Alignment explanation
Indices: 66751--66779 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
66741 AAAAGAACAG
66751 AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
66780 TAAAGTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:69953 original size:31 final size:31
Alignment explanation
Indices: 69916--70047 Score: 147
Period size: 31 Copynumber: 4.5 Consensus size: 31
69906 ACGGTGTCCG
69916 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
69947 ATGTGGCACGCCACATGTACCAAAAAGT--C
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
69976 A--T-----GCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
70000 ACATGCCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
70031 ACGTGGCATGCCACGTG
1 ACGTGGCACGCCACGTG
70048 CACAAAAGGA
Statistics
Matches: 86, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
22 19 0.22
24 2 0.02
26 1 0.01
27 1 0.01
29 2 0.02
31 61 0.71
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.15
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:70004 original size:19 final size:20
Alignment explanation
Indices: 69958--70004 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
69948 TGTGGCACGC
*
69958 CACATGTACCAAAAAGTCATGC
1 CACATGTACCAAAAAG--ATGA
69980 CACATGTACCAAAAAG-TGA
1 CACATGTACCAAAAAGATGA
69999 CACATG
1 CACATG
70005 CCACGCCACG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
22 16 0.67
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.17
Consensus pattern (20 bp):
CACATGTACCAAAAAGATGA
Found at i:70010 original size:53 final size:53
Alignment explanation
Indices: 69925--70027 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
69915 GACGTGGCAC
* ** *
69925 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCAT
1 GCCACATGTACCAAAAAGTGACACATGCCACGCCACATGTACCAAAAAGTCAT
*
69978 GCCACATGTACCAAAAAGTGACACATGCCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGCCACGCCACATGTACCAAAAAGT
70028 GACACGTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGCCACGCCACATGTACCAAAAAGTCAT
Found at i:70477 original size:2 final size:2
Alignment explanation
Indices: 70464--70494 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
70454 GTTAAAAATA
70464 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
70495 GTTCTATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70976 original size:62 final size:62
Alignment explanation
Indices: 70908--71036 Score: 197
Period size: 62 Copynumber: 2.1 Consensus size: 62
70898 ATTAAATTAA
* *
70908 AAATTATTATAATTACACTATTTTTGT-TGACATCCTTATGAAATTTTGATAACATTCCTATG
1 AAATTATGATAATTACACCATTTTT-TATGACATCCTTATGAAATTTTGATAACATTCCTATG
* * *
70970 AAATTATGATTATTACACCATTTTTTATGACTTCCTTATGAAATTTTGATAACCTTCCTATG
1 AAATTATGATAATTACACCATTTTTTATGACATCCTTATGAAATTTTGATAACATTCCTATG
71032 AAATT
1 AAATT
71037 TCAATAACGA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 1 0.02
62 60 0.98
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (62 bp):
AAATTATGATAATTACACCATTTTTTATGACATCCTTATGAAATTTTGATAACATTCCTATG
Found at i:71031 original size:22 final size:22
Alignment explanation
Indices: 71000--71175 Score: 92
Period size: 22 Copynumber: 8.0 Consensus size: 22
70990 TTTTTTATGA
71000 CTTCCTTATGAAATTTTGATAAC
1 CTTCC-TATGAAATTTTGATAAC
**
71023 CTTCCTATGAAATTTCAATAAC
1 CTTCCTATGAAATTTTGATAAC
** * * * **
71045 GATGCTATGGAATTTCGGGAAC
1 CTTCCTATGAAATTTTGATAAC
** * **
71067 CTTTTTAT--ATTTTTTTTAAC
1 CTTCCTATGAAATTTTGATAAC
* * *
71087 CTTCTTATGAAATTTTGTTAAT
1 CTTCCTATGAAATTTTGATAAC
* *
71109 CTCCCTAAGAAATTTTGA-AGAC
1 CTTCCTATGAAATTTTGATA-AC
*
71131 C-TCACTATGAAATTTCGATAA-
1 CTTC-CTATGAAATTTTGATAAC
*
71152 CTTCCAAATGAAATTTTGATAAC
1 CTTCC-TATGAAATTTTGATAAC
71175 C
1 C
71176 AACACCATAA
Statistics
Matches: 113, Mismatches: 32, Indels: 16
0.70 0.20 0.10
Matches are distributed among these distances:
20 14 0.12
21 4 0.04
22 88 0.78
23 7 0.06
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTCCTATGAAATTTTGATAAC
Found at i:71244 original size:22 final size:22
Alignment explanation
Indices: 71219--71261 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
71209 ATATTGATAA
*
71219 CCACGTTATGAAAATTTAAAAG
1 CCACGTTATAAAAATTTAAAAG
71241 CCACGTTATAAAAATTTAAAA
1 CCACGTTATAAAAATTTAAAA
71262 ACCTGCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (22 bp):
CCACGTTATAAAAATTTAAAAG
Found at i:71374 original size:23 final size:22
Alignment explanation
Indices: 71340--71590 Score: 171
Period size: 22 Copynumber: 11.6 Consensus size: 22
71330 CCTCATTAAT
71340 TATGAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCC
* * *
71363 TATAAAATTTTGATAAATCTCCT
1 TATGAAATTTTGAT-AACCTCCC
* *
71386 TATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCTCCC
*
71408 TATGAAAATCTTGATAA-----C
1 TATG-AAATTTTGATAACCTCCC
*
71426 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
** **
71447 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCC
* **
71469 TATGAAATTTTGTTAATATCCC
1 TATGAAATTTTGATAACCTCCC
* **
71491 AATGAAATTTTGATAACC-CTTT
1 TATGAAATTTTGATAACCTC-CC
* **
71513 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CCC
* * *
71535 TATAAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTCCC
*
71557 TATGAAATTTTGATATCCTCCC
1 TATGAAATTTTGATAACCTCCC
71579 --TGAAATTTTGAT
1 TATGAAATTTTGAT
71591 TACTCCATAA
Statistics
Matches: 176, Mismatches: 41, Indels: 25
0.73 0.17 0.10
Matches are distributed among these distances:
16 11 0.06
18 2 0.01
20 12 0.07
21 7 0.04
22 95 0.54
23 49 0.28
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:71920 original size:37 final size:37
Alignment explanation
Indices: 71879--71974 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 37
71869 ATCTAAGCCC
* *
71879 AAATAGGACGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
** *
71916 AAATACAACGATTGGAAACAAAGACAAAAGGCAAAATT
1 AAATAGGACG-TTGGAAACAAAGACAAAAAGCAAAATT
*
71954 AAATAGGATGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
71975 AAGTCAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
37 19 0.38
38 31 0.62
ACGTcount: A:0.54, C:0.10, G:0.21, T:0.15
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:72276 original size:23 final size:22
Alignment explanation
Indices: 72250--72304 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
72240 CAATGAACTT
*
72250 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACA-TATGAGATA
* ** *
72273 TTGATATCCTCCATATGATATA
1 TTGATAACCAACATATGAGATA
72295 TTGATAACCA
1 TTGATAACCA
72305 CGTTATGAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (22 bp):
TTGATAACCAACATATGAGATA
Found at i:72368 original size:22 final size:22
Alignment explanation
Indices: 72330--72389 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
72320 AAAACCTCCA
*
72330 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* * **
72352 TCTGAAATTTTGATAATTGCAC
1 TATGAAATTGTGATAATCACAC
72374 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
72390 CTTCGCTATA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:72398 original size:22 final size:22
Alignment explanation
Indices: 72349--72411 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
72339 TTAGTAATCA
*
72349 CACTCTGAAATTTTGATAATTG
1 CACTATGAAATTTTGATAATTG
*
72371 CACTATGAAATTGTGATAACTT-
1 CACTATGAAATTTTGATAA-TTG
* *
72393 CGCTATAAAATTTTGATAA
1 CACTATGAAATTTTGATAA
72412 ATCTTCTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 33 0.94
23 2 0.06
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
CACTATGAAATTTTGATAATTG
Found at i:72426 original size:23 final size:23
Alignment explanation
Indices: 72396--72477 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
72386 ATAACTTCGC
72396 TATAAAATTTTGATAAATCTTCT
1 TATAAAATTTTGATAAATCTTCT
* **
72419 TATAAAATTTTGATAAACCCCCT
1 TATAAAATTTTGATAAATCTTCT
* *
72442 TATAAAATTTTGACAACT-TTCT
1 TATAAAATTTTGATAAATCTTCT
* *
72464 TATGAAATCTTGAT
1 TATAAAATTTTGAT
72478 GACTACAAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 13 0.27
23 35 0.73
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (23 bp):
TATAAAATTTTGATAAATCTTCT
Found at i:72534 original size:22 final size:21
Alignment explanation
Indices: 72509--72750 Score: 114
Period size: 22 Copynumber: 11.6 Consensus size: 21
72499 CCCTATAATT
72509 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
72531 TTTTGTTAATCTCCATATGAAA
1 TTTTGATAACCT-CATATGAAA
*
72553 TTTTGATATACAT-ACTATGAAA
1 TTTTGATA-ACCTCA-TATGAAA
* * *
72575 TTTTGAAAACCCTCTTGTGAAA
1 TTTTGATAA-CCTCATATGAAA
* *
72597 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-CA-TATGAAA
* *
72619 TTTTCATAACCTTCACATGAAA
1 TTTTGATAACC-TCATATGAAA
* **
72641 TTTTGATATCCTC-CCT-AAA
1 TTTTGATAACCTCATATGAAA
* *
72660 TTTTGATATCCTCCT-TGAAA
1 TTTTGATAACCTCATATGAAA
* *
72680 TTTTGATTA-CTCAATAATAAAA
1 TTTTGATAACCTC-AT-ATGAAA
* *
72702 GTTTAATAACCT--TCAT--AA
1 TTTTGATAACCTCAT-ATGAAA
*
72720 -TTTGGTAA-C-CATATGAAA
1 TTTTGATAACCTCATATGAAA
72738 TTTTGATAACCTC
1 TTTTGATAACCTC
72751 GCCAGAAATA
Statistics
Matches: 166, Mismatches: 32, Indels: 45
0.68 0.13 0.19
Matches are distributed among these distances:
16 3 0.02
17 7 0.04
18 4 0.02
19 27 0.16
20 19 0.11
21 7 0.04
22 88 0.53
23 10 0.06
24 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:72682 original size:20 final size:20
Alignment explanation
Indices: 72636--72686 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
72626 AACCTTCACA
72636 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
72656 T-AAATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
72675 TGAAATTTTGAT
1 TGAAATTTTGAT
72687 TACTCAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:72822 original size:22 final size:22
Alignment explanation
Indices: 72795--73028 Score: 109
Period size: 22 Copynumber: 11.0 Consensus size: 22
72785 ATTTTCAAAA
72795 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
72817 TTTGATAACCTC----T---AT
1 TTTGATAACCTCTTTATGAAAT
* * *
72832 TTTGTTGACCCCTTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * * **
72854 TTTGATAATCACATTAAGTTAT
1 TTTGATAACCTCTTTATGAAAT
*
72876 TTTGATAACCTCGCTT-TGAAAT
1 TTTGATAACCTC-TTTATGAAAT
* ** **
72898 TTTAATAACAACACTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
*
72920 TTTGATAATCT-TTCTAT-AAAT
1 TTTGATAACCTCTT-TATGAAAT
72941 TTTGATAATCCGATCTTTATGAAAT
1 TTTGATAA-CC--TCTTTATGAAAT
* * * *
72966 TTCGATAATCACTTTATGAGA-
1 TTTGATAACCTCTTTATGAAAT
* *
72987 TTTGATAACCT-TCTATCAAAT
1 TTTGATAACCTCTTTATGAAAT
* *
73008 TTTGGT-A-CTCCTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
73028 T
1 T
73029 GAGACTTTTA
Statistics
Matches: 152, Mismatches: 43, Indels: 36
0.66 0.19 0.16
Matches are distributed among these distances:
15 11 0.07
18 1 0.01
19 3 0.02
20 15 0.10
21 26 0.17
22 76 0.50
23 2 0.01
24 5 0.03
25 13 0.09
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (22 bp):
TTTGATAACCTCTTTATGAAAT
Found at i:73011 original size:21 final size:22
Alignment explanation
Indices: 72911--73099 Score: 97
Period size: 22 Copynumber: 8.4 Consensus size: 22
72901 AATAACAACA
*
72911 CTATGAAATTTTGATAATCTTT
1 CTATGAAATTTTGATAATCCTT
72933 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAATCC--T-T
* *
72957 TTATGAAATTTCGATAATCACTT
1 CTATGAAATTTTGATAATC-CTT
*
72980 -TATGAGA-TTTGATAA-CCTT
1 CTATGAAATTTTGATAATCCTT
* * *
72999 CTATCAAATTTTGGTACTCCTT
1 CTATGAAATTTTGATAATCCTT
* *
73021 ATGAAATTGAGACTTTT-ATAA-CCTT
1 CT---A-TGA-AATTTTGATAATCCTT
**
73046 CATATGAAATTTTGATAA-CCACA
1 C-TATGAAATTTTGATAATCC-TT
*
73069 CTATAAAATTTTGATAA-CCTCT
1 CTATGAAATTTTGATAATCCT-T
*
73091 CCATGAAAT
1 CTATGAAAT
73100 ATTTAATGAA
Statistics
Matches: 127, Mismatches: 23, Indels: 34
0.69 0.12 0.18
Matches are distributed among these distances:
19 3 0.02
20 6 0.05
21 32 0.25
22 48 0.38
23 4 0.03
24 5 0.04
25 18 0.14
26 6 0.05
27 5 0.04
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCCTT
Found at i:73133 original size:22 final size:22
Alignment explanation
Indices: 73105--73163 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
73095 GAAATATTTA
*
73105 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCACACT
*
73127 ATGAAATTCTT-ATAACCTCACT
1 ATGAAATT-TTGATAACCACACT
*
73149 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
73164 TCTCTTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:73231 original size:22 final size:22
Alignment explanation
Indices: 73199--73339 Score: 124
Period size: 22 Copynumber: 6.3 Consensus size: 22
73189 TTGTGATAAT
* *
73199 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTAA
* * **
73221 TAACCAACCTAAGAGGTTTTAA
1 TAACCATCCTATGAAATTTTAA
**
73243 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTAA
*
73267 TAACCA-CACTATGAAATTTTGA
1 TAACCATC-CTATGAAATTTTAA
*
73289 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTAA
* *
73311 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTAA
73333 TAACCAT
1 TAACCAT
73340 ATAGAGACAA
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
21 3 0.03
22 74 0.77
23 3 0.03
24 16 0.17
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTAA
Found at i:73770 original size:209 final size:209
Alignment explanation
Indices: 73403--73784 Score: 719
Period size: 209 Copynumber: 1.8 Consensus size: 209
73393 TTTCCAATTG
*
73403 AACAAAATGAATGCGGCAAAACATTATATAACGAAGAGATGGAGCTTCACTAACAATAATATTGT
1 AACAAAATGAATGCAGCAAAACATTATATAACGAAGAGATGGAGCTTCACTAACAATAATATTGT
73468 ACGTGTTAGTGTTAATTTAATCTTTTTATTGAAATTTAAAAATTAAAAGTAAAAGTAAAATATTA
66 ACGTGTTAGTGTTAATTTAATCTTTTTATTGAAATTTAAAAATTAAAAGTAAAAGTAAAATATTA
73533 AATTCAAAAAATAATAGTAAAGGAAATTTGCATGTTCATCAACCCTAAAATTATACTAAATTTTA
131 AATTCAAAAAATAATAGTAAAGGAAATTTGCATGTTCATCAACCCTAAAATTATACTAAATTTTA
73598 ATTAATTTTGAAAT
196 ATTAATTTTGAAAT
* *
73612 AACAAAGTGAATGCAGCAAAACATTATATAACGAAGAGATGGAGCTTCACTAACAATAGTATTGT
1 AACAAAATGAATGCAGCAAAACATTATATAACGAAGAGATGGAGCTTCACTAACAATAATATTGT
**
73677 ACGTGTTAGTGTTAATTTAATCTTTTTATTGCCATTTAAAAATTAAAAGTAAAAGTAAAATATTA
66 ACGTGTTAGTGTTAATTTAATCTTTTTATTGAAATTTAAAAATTAAAAGTAAAAGTAAAATATTA
73742 AATTCAAAAAATAATAGTAAAGGAAATTTGCATGTTCATCAAC
131 AATTCAAAAAATAATAGTAAAGGAAATTTGCATGTTCATCAAC
73785 TAAAATCAAT
Statistics
Matches: 168, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
209 168 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (209 bp):
AACAAAATGAATGCAGCAAAACATTATATAACGAAGAGATGGAGCTTCACTAACAATAATATTGT
ACGTGTTAGTGTTAATTTAATCTTTTTATTGAAATTTAAAAATTAAAAGTAAAAGTAAAATATTA
AATTCAAAAAATAATAGTAAAGGAAATTTGCATGTTCATCAACCCTAAAATTATACTAAATTTTA
ATTAATTTTGAAAT
Found at i:74082 original size:32 final size:32
Alignment explanation
Indices: 74046--74112 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
74036 TTAGTAATGG
*
74046 CAATTTAGAAATATGTTTTAAAGAA-AATGGTA
1 CAATTTAGAAATATGTTTTAAA-AATAAGGGTA
*
74078 CAA-TTGGAAATATGTTTTAAAAATAAGGGTA
1 CAATTTAGAAATATGTTTTAAAAATAAGGGTA
74109 CAAT
1 CAAT
74113 CGGAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.06
31 26 0.84
32 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.33
Consensus pattern (32 bp):
CAATTTAGAAATATGTTTTAAAAATAAGGGTA
Found at i:74088 original size:31 final size:31
Alignment explanation
Indices: 74053--74118 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
74043 TGGCAATTTA
* *
74053 GAAATATGTTTTAAAGAA-AATGGTACAATTG
1 GAAATATGTTTTAAA-AATAAGGGTACAATCG
74084 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
74115 GAAA
1 GAAA
74119 ATATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:74524 original size:31 final size:31
Alignment explanation
Indices: 74468--74533 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
74458 GACAATTTAA
* *
74468 AAATATGTTTTTTTAAAAAAGGGTACAATTGG
1 AAATATG-TTTTTAAAAAAAGGGTACAATCGG
74500 AAATATG-TTTTAAAAATAAGGGTACAATCGG
1 AAATATGTTTTTAAAAA-AAGGGTACAATCGG
74531 AAA
1 AAA
74534 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 8 0.26
31 16 0.52
32 7 0.23
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (31 bp):
AAATATGTTTTTAAAAAAAGGGTACAATCGG
Found at i:74569 original size:2 final size:2
Alignment explanation
Indices: 74562--74595 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
74552 TTCGTACTTT
*
74562 TA TA TA TA GTA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
74596 TCCACAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:78150 original size:32 final size:31
Alignment explanation
Indices: 78109--78198 Score: 146
Period size: 32 Copynumber: 2.9 Consensus size: 31
78099 GAACCTGAAT
78109 CCGAAAAAACTCAAACCCGGAAAAAAACGAAC
1 CCGAAAAAACTCAAACCC-GAAAAAAACGAAC
*
78141 CCGAAAAAACTCAAACCCGAAAAAACTCGAAC
1 CCGAAAAAACTCAAACCCGAAAAAA-ACGAAC
78173 CCGAAAAAACTCAAACCC-AAAAAAAC
1 CCGAAAAAACTCAAACCCGAAAAAAAC
78199 CTAAATCCGA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
30 1 0.02
31 13 0.24
32 41 0.75
ACGTcount: A:0.57, C:0.30, G:0.09, T:0.04
Consensus pattern (31 bp):
CCGAAAAAACTCAAACCCGAAAAAAACGAAC
Found at i:78211 original size:16 final size:16
Alignment explanation
Indices: 78109--78211 Score: 129
Period size: 16 Copynumber: 6.4 Consensus size: 16
78099 GAACCTGAAT
78109 CCGAAAAAACTCAAAC
1 CCGAAAAAACTCAAAC
* *
78125 CCGGAAAAAA-ACGAAC
1 CC-GAAAAAACTCAAAC
78141 CCGAAAAAACTCAAAC
1 CCGAAAAAACTCAAAC
*
78157 CCGAAAAAACTCGAAC
1 CCGAAAAAACTCAAAC
78173 CCGAAAAAACTCAAAC
1 CCGAAAAAACTCAAAC
* *
78189 CCAAAAAAAC-CTAAAT
1 CCGAAAAAACTC-AAAC
78205 CCGAAAA
1 CCGAAAA
78212 TTTATGAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
15 8 0.11
16 60 0.80
17 7 0.09
ACGTcount: A:0.56, C:0.29, G:0.09, T:0.06
Consensus pattern (16 bp):
CCGAAAAAACTCAAAC
Found at i:78385 original size:32 final size:31
Alignment explanation
Indices: 78359--78466 Score: 135
Period size: 32 Copynumber: 3.4 Consensus size: 31
78349 ACCCAAACAG
* *
78359 AACCTGAATCTGAATTAACCTGACCCAAATTC
1 AACCCGAACCTGAATTAACCTGACCCAAA-TC
* *
78391 AACCCGAACCTGAATTAATCTGACCCAAATT
1 AACCCGAACCTGAATTAACCTGACCCAAATC
* *
78422 AACCCGAACCCGAATTAACCTGATCCAAATCC
1 AACCCGAACCTGAATTAACCTGACCCAAAT-C
*
78454 AACCCAAACCTGA
1 AACCCGAACCTGA
78467 CTCAAGTCCG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 28 0.43
32 37 0.57
ACGTcount: A:0.39, C:0.32, G:0.09, T:0.19
Consensus pattern (31 bp):
AACCCGAACCTGAATTAACCTGACCCAAATC
Found at i:82056 original size:327 final size:328
Alignment explanation
Indices: 81366--82244 Score: 920
Period size: 327 Copynumber: 2.7 Consensus size: 328
81356 AATTAGCCTT
* * * * * *
81366 AAAAATTTGTTTTTACGAGTATGTA-AATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAA
1 AAAAATTTGATTTTACGAATATCTAGAATCATGTTTCGATTTAATTAAAAATTAATTTAAAAAAA
* * * **
81430 TATGAAAAACGATATTAAAACCGTGAAAAGTCC-TCCAATCTTTTCGGTGTTAAATTATATATAT
66 TATGAAAAATGATATTAAAAGCGTGAAAAGACCTTCCAATCTTTTCGGCATTAAATTATATATAT
* * * * * * * * * *
81494 TTATGAGTATTTTAGCCCAAAAAAATGACGAAAAAATTTTTCAAGTCATTTTTTACAAAATTTTA
131 TTAAGAGTATTGT-G-ACTAAAAATTGA-GGAAAAATATTTCAGGTCAATTTTTGCAAAATTTTA
* * * * * *
81559 GCCAAAATCATATATTAATCATGACGGTTTTTTTGCTAAAAACGCGTCTCAGGGCCCCGACTTAG
193 GCCGAAATC--GT-GTAA-CATCACGGTTTTTTGGCTAAAAACGCGTCTCAGGGCCCCGACTCAG
* * * * *
81624 TTTTGCATGAATTTGGTGCCGAGACTCCTTTAATAATCTATATTCATCTAATCAAATCCTAGACA
254 TTTTGCATGAATTTGGTGCCAAAACTCCTTAAATAATCTATATTCATCTAACCAAATCCTACACA
*
81689 TATTGAATTT
319 TATTGAATTA
** *
81699 AAGGATTTGATTTTACGAATATCT-GAATCATGTTTCGATTTAATTAAAAATTAATTCAAAAAAA
1 AAAAATTTGATTTTACGAATATCTAGAATCATGTTTCGATTTAATTAAAAATTAATTTAAAAAAA
* * * * *
81763 TATGAAAAAATGATATTATAAGCTTGAAAAG-CCTTCCAATATTTTTGGCATTTAATTATATATA
66 TATG-AAAAATGATATTAAAAGCGTGAAAAGACCTTCCAATCTTTTCGGCATTAAATTATATATA
* * *
81827 TTCTAAGAGTATTGTGGCTAAAAATTGAGGAAAAATATTACGGGTCAATTTTTGCAAAATTTTAG
130 TT-TAAGAGTATTGTGACTAAAAATTGAGGAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAG
* * * **
81892 ACGAAATCGTGTAACATCACGGTTTTTTGGCTAAAAACGCATTCTTA-GGCCCCGGGTCAGTTTT
194 CCGAAATCGTGTAACATCACGGTTTTTTGGCTAAAAACGC-GTCTCAGGGCCCCGACTCAGTTTT
* * **
81956 GCATGATTTTGTTG-CAAAACTCCTTGAAAT-ATCTATATTCATCTAACCAAATTTTAACCACAT
258 GCATGAATTTGGTGCCAAAACTCCTT-AAATAATCTATATTCATCTAACCAAATCCT-A-CACAT
82019 -TTG-ATTA
320 ATTGAATTA
* ** * *
82026 AAAAATTTGCTTTTACGACCAT-TAGAATCATGTTTCTATTTAATTAAAAATTAATTTGAAAAAA
1 AAAAATTTGATTTTACGAATATCTAGAATCATGTTTCGATTTAATTAAAAATTAATTTAAAAAAA
* * * * *
82090 TA-GAAAAATGATATTAGAAGCGTGAGAAGACCTT-CAATCTTTTCAGCATTGAATTATATATTT
66 TATGAAAAATGATATTAAAAGCGTGAAAAGACCTTCCAATCTTTTCGGCATTAAATTATATATAT
* *
82153 TTAATGAGTAATGTGACTAAAAATTGA-GAAAAATATTTCAGATCAATTTTTGCAAAATTTTAGC
131 TTAA-GAGTATTGTGACTAAAAATTGAGGAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAGC
* * *
82217 CGAAATTGTGTACCATCATGGTTCTTTT
195 CGAAATCGTGTAACATCACGGTT-TTTT
82245 TTTTTTTTTT
Statistics
Matches: 458, Mismatches: 76, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
324 56 0.12
325 72 0.16
326 6 0.01
327 90 0.20
328 57 0.12
329 11 0.02
330 1 0.00
332 36 0.08
333 69 0.15
334 50 0.11
335 10 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (328 bp):
AAAAATTTGATTTTACGAATATCTAGAATCATGTTTCGATTTAATTAAAAATTAATTTAAAAAAA
TATGAAAAATGATATTAAAAGCGTGAAAAGACCTTCCAATCTTTTCGGCATTAAATTATATATAT
TTAAGAGTATTGTGACTAAAAATTGAGGAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAGCC
GAAATCGTGTAACATCACGGTTTTTTGGCTAAAAACGCGTCTCAGGGCCCCGACTCAGTTTTGCA
TGAATTTGGTGCCAAAACTCCTTAAATAATCTATATTCATCTAACCAAATCCTACACATATTGAA
TTA
Found at i:82416 original size:335 final size:325
Alignment explanation
Indices: 81364--82455 Score: 807
Period size: 335 Copynumber: 3.3 Consensus size: 325
81354 GCAATTAGCC
* * * * * *
81364 TTAAAAATTTGTTTTTACGAGTATGTAAATCTTGTTTCGATTTAATTAGAAATTAATTT-AGAAA
1 TTAAGAATTTGATTTTACGAATATCTAAATCATGTTTCGATTTAATTAAAAATTAATTTGA-AAA
* * * * * ** *
81428 AATATGAAAAACGATATTAAAACCGTGAAAAGTCC-TCCAATCTTTTCGGTGTTAAATTATATAT
65 AATA-GAAAAATGATATTAGAAGCGTGAAAAG-CCTTCCAATATTTTCAGCATTGAATTATATAT
* * * * * * * * * * *
81492 ATT-TATGAGTATTTTAGCCCAAAAAAATGACGAAAAAATTTTTCA-AGTCATTTTTTACAAAAT
128 ATTCTAAGAGTAATGT-G-ACTAAAAATTGA-GGAAAAATATTACAGA-TCAATTTTTGCAAAAT
* * * * * * * *
81555 TTTAGCCAAAATCATATATTAATCATGACGGTTTTTTTGCTAAAAACGC-GTCTCAGGGCCCCGA
189 TTTAGACGAAATC--GT-GTAA-CATCACGGTTTTTTGGCTAAAAACGCATTCTCA-GGCCCCGG
* * * * * * * * * * *
81619 CTTAGTTTTGCATGAATTTGGTGCCGAGACTCCTT-TAATAATCTATATTCATCTAATCAAATCC
249 GTCAATTTTGCATGATTTTGTTG-CAAAACTCCTTGAAAT-ATATATATTCATCTAACCAAATTC
* *
81683 TAGA-CATATTGAAT
312 TA-ACCACATTGTAT
* * **
81697 TTAAGGATTTGATTTTACGAATATCTGAATCATGTTTCGATTTAATTAAAAATTAATTCAAAAAA
1 TTAAGAATTTGATTTTACGAATATCTAAATCATGTTTCGATTTAATTAAAAATTAATTTGAAAAA
* * ** *
81762 ATATGAAAAAATGATATTATAAGCTTGAAAAGCCTTCCAATATTTTTGGCATTTAATTATATATA
66 ATA-G-AAAAATGATATTAGAAGCGTGAAAAGCCTTCCAATATTTTCAGCATTGAATTATATATA
* * * *
81827 TTCTAAGAGTATTGTGGCTAAAAATTGAGGAAAAATATTACGGGTCAATTTTTGCAAAATTTTAG
129 TTCTAAGAGTAATGTGACTAAAAATTGAGGAAAAATATTACAGATCAATTTTTGCAAAATTTTAG
* *
81892 ACGAAATCGTGTAACATCACGGTTTTTTGGCTAAAAACGCATTCTTAGGCCCCGGGTCAGTTTTG
194 ACGAAATCGTGTAACATCACGGTTTTTTGGCTAAAAACGCATTCTCAGGCCCCGGGTCAATTTTG
* *
81957 CATGATTTTGTTGCAAAACTCCTTGAAATATCTATATTCATCTAACCAAATTTTAACCACATT-T
259 CATGATTTTGTTGCAAAACTCCTTGAAATATATATATTCATCTAACCAAATTCTAACCACATTGT
82021 GAT
324 -AT
* * * ** *
82024 TAAAAAATTTGCTTTTACGACCAT-TAGAATCATGTTTCTATTTAATTAAAAATTAATTTGAAAA
1 TTAAGAATTTGATTTTACGAATATCTA-AATCATGTTTCGATTTAATTAAAAATTAATTTGAAAA
* *
82088 AATAGAAAAATGATATTAGAAGCGTGAGAAGACCTT-CAATCTTTTCAGCATTGAATTATATAT-
65 AATAGAAAAATGATATTAGAAGCGTGAAAAG-CCTTCCAATATTTTCAGCATTGAATTATATATA
* *
82151 TTTTAATGAGTAATGTGACTAAAAATTGA-GAAAAATATTTCAGATCAATTTTTGCAAAATTTTA
129 TTCTAA-GAGTAATGTGACTAAAAATTGAGGAAAAATATTACAGATCAATTTTTGCAAAATTTTA
* * * * * * * *
82215 GCCGAAATTGTGTACCATCATGGTTCTTTTTTTTTTTTTTTTGCTAAAAACGCGTT-TCGGGCCT
193 GACGAAATCGTGTAACATCACGG------------TTTTTTGGCTAAAAACGCATTCTCAGGCCC
** * * * * **
82279 TTGGTTAATTTTGCATGATTTT-TTACGGCAAGACT-CTTTAAA-ATATATCTTCATCTAACTGA
246 CGGGTCAATTTTGCATGATTTTGTT---GCAAAACTCCTTGAAATATATATATTCATCTAACCAA
*
82341 A-TCTCACCTACATTGTAT
308 ATTCTAACC-ACATTGTAT
* * * * * * *
82359 TTAAGAATTTGTTTTTACGAGTTTCTAAATCTTGTTTCGATTTAACTAGATATTAATTTGGAAAT
1 TTAAGAATTTGATTTTACGAATATCTAAATCATGTTTCGATTTAATTAAAAATTAATTT-GAAA-
*
82424 TAAATAGGAAAAT-AGTATTAGAAGCGTGAAAA
64 -AAATAGAAAAATGA-TATTAGAAGCGTGAAAA
82456 AAGGGCTTTC
Statistics
Matches: 617, Mismatches: 108, Indels: 63
0.78 0.14 0.08
Matches are distributed among these distances:
324 56 0.09
325 66 0.11
326 7 0.01
327 95 0.15
328 53 0.09
329 7 0.01
330 1 0.00
332 35 0.06
333 70 0.11
334 58 0.09
335 102 0.17
336 32 0.05
337 8 0.01
338 27 0.04
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (325 bp):
TTAAGAATTTGATTTTACGAATATCTAAATCATGTTTCGATTTAATTAAAAATTAATTTGAAAAA
ATAGAAAAATGATATTAGAAGCGTGAAAAGCCTTCCAATATTTTCAGCATTGAATTATATATATT
CTAAGAGTAATGTGACTAAAAATTGAGGAAAAATATTACAGATCAATTTTTGCAAAATTTTAGAC
GAAATCGTGTAACATCACGGTTTTTTGGCTAAAAACGCATTCTCAGGCCCCGGGTCAATTTTGCA
TGATTTTGTTGCAAAACTCCTTGAAATATATATATTCATCTAACCAAATTCTAACCACATTGTAT
Done.