Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 76 of 279
Found at i:25107889 original size:186 final size:186
Alignment explanation
Indices: 25107575--25107940 Score: 732
Period size: 186 Copynumber: 2.0 Consensus size: 186
25107565 TTGTACCCGA
25107575 CTCCTACTTTTGAGAACTCTGTTGCTCAACCGCAGCTGTTTTAGGTTGACCAACTATGATTGCCT
1 CTCCTACTTTTGAGAACTCTGTTGCTCAACCGCAGCTGTTTTAGGTTGACCAACTATGATTGCCT
25107640 TCGTGTTGAAGGTGCTTGTGTTATTCACTTCACTATCCTTTCTCCTTGGAGCTGATCTTTTAATC
66 TCGTGTTGAAGGTGCTTGTGTTATTCACTTCACTATCCTTTCTCCTTGGAGCTGATCTTTTAATC
25107705 ACTTCCCCCTCGATTTTGCCACCCCTTATGGCATTCTCGATCATCTCTCCCACCAT
131 ACTTCCCCCTCGATTTTGCCACCCCTTATGGCATTCTCGATCATCTCTCCCACCAT
25107761 CTCCTACTTTTGAGAACTCTGTTGCTCAACCGCAGCTGTTTTAGGTTGACCAACTATGATTGCCT
1 CTCCTACTTTTGAGAACTCTGTTGCTCAACCGCAGCTGTTTTAGGTTGACCAACTATGATTGCCT
25107826 TCGTGTTGAAGGTGCTTGTGTTATTCACTTCACTATCCTTTCTCCTTGGAGCTGATCTTTTAATC
66 TCGTGTTGAAGGTGCTTGTGTTATTCACTTCACTATCCTTTCTCCTTGGAGCTGATCTTTTAATC
25107891 ACTTCCCCCTCGATTTTGCCACCCCTTATGGCATTCTCGATCATCTCTCC
131 ACTTCCCCCTCGATTTTGCCACCCCTTATGGCATTCTCGATCATCTCTCC
25107941 TGCCATGACT
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 180 1.00
ACGTcount: A:0.17, C:0.29, G:0.16, T:0.38
Consensus pattern (186 bp):
CTCCTACTTTTGAGAACTCTGTTGCTCAACCGCAGCTGTTTTAGGTTGACCAACTATGATTGCCT
TCGTGTTGAAGGTGCTTGTGTTATTCACTTCACTATCCTTTCTCCTTGGAGCTGATCTTTTAATC
ACTTCCCCCTCGATTTTGCCACCCCTTATGGCATTCTCGATCATCTCTCCCACCAT
Found at i:25113061 original size:12 final size:12
Alignment explanation
Indices: 25113042--25113354 Score: 64
Period size: 12 Copynumber: 25.9 Consensus size: 12
25113032 TAACATAATT
25113042 TATA-AATAAAA
1 TATATAATAAAA
25113053 TATATAAT--AA
1 TATATAATAAAA
*
25113063 TATA-AATAATA
1 TATATAATAAAA
*
25113074 TA-ATAA-ATAA
1 TATATAATAAAA
25113084 TATA-AA-AATATA
1 TATATAATAA-A-A
25113096 TATATAATAAAA
1 TATATAATAAAA
*
25113108 TGTATATAATATAA
1 --TATATAATAAAA
25113122 TATAT-ATAAAA
1 TATATAATAAAA
* *
25113133 GA-A-AGA-AAGA
1 TATATA-ATAAAA
25113143 TATTATAATGAATAA
1 TA-TATAAT-AA-AA
*
25113158 TATATAACAAAATA
1 TATATAA-TAAA-A
25113172 TAATATGTAATAAAA
1 T-ATA--TAATAAAA
*
25113187 TATGTAGAT-AAA
1 TATATA-ATAAAA
25113199 -ATATAATGAAATA
1 TATATAAT-AAA-A
*
25113212 TAATATAATAAGGA
1 T-ATATAATAA-AA
25113226 -ATAT-ATAAAA
1 TATATAATAAAA
25113236 TA-ATAATAAAA
1 TATATAATAAAA
*
25113247 -ATATCAA-AATA
1 TATAT-AATAAAA
*
25113258 TAGTAAAATAAATAA
1 TA-TATAAT-AA-AA
*
25113273 AATATAATAAAA
1 TATATAATAAAA
25113285 -ATAT-AT--AA
1 TATATAATAAAA
*
25113293 CATATAATAAAA
1 TATATAATAAAA
*
25113305 -ATACAAATATAACA
1 TATA-TAATA-AA-A
* *
25113319 GA-ATAAATAATA
1 TATAT-AATAAAA
25113331 TATATAATAAAAA
1 TATATAAT-AAAA
*
25113344 TATATGATAAA
1 TATATAATAAA
25113355 TTTTTTTTAA
Statistics
Matches: 224, Mismatches: 27, Indels: 101
0.64 0.08 0.29
Matches are distributed among these distances:
8 2 0.01
9 7 0.03
10 29 0.13
11 45 0.20
12 48 0.21
13 27 0.12
14 42 0.19
15 18 0.08
16 3 0.01
17 3 0.01
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (12 bp):
TATATAATAAAA
Found at i:25113077 original size:37 final size:39
Alignment explanation
Indices: 25113049--25113355 Score: 128
Period size: 39 Copynumber: 7.8 Consensus size: 39
25113039 ATTTATAAAT
25113049 AAAATATATA-ATAATATAAATAATATAATAAATAATATA
1 AAAATATATATATAATA-AAATAATATAATAAATAATATA
*
25113088 AAAATATATATATAATAAAATGTATATAATATAATATATATA
1 AAAATATATATATAATAAAAT-AATATAATA-AATA-ATATA
* * * * * * * * *
25113130 AAAGAAAGAAAGATATTATAATGA-ATAATATATAACA-A
1 AAA-ATATATATATAATAAAATAATATAATAAATAATATA
* * *
25113168 AATATA-ATATGTAATAAAAT-ATGTAGAT-AA-AATATA
1 AAAATATATATATAATAAAATAATATA-ATAAATAATATA
25113204 ATGAAATATA-ATATAATAAGGAAT-ATAT-A-AAATAATAATA
1 A--AAATATATATATAATAA--AATAATATAATAAATAAT-ATA
* *
25113244 AAAATATCAAAATATAGTAAAATAA-ATAA-AATATAATA-A
1 AAAATAT--ATATATAATAAAATAATATAATAA-ATAATATA
* * * * *
25113283 AAATATATAACATATAAT-AAA-AATACAA-ATATAACAGA
1 AAA-ATAT-ATATATAATAAAATAATATAATAAATAATATA
*
25113321 ATAAATAATATATATAATAAAA-ATATATGATAAAT
1 A-AAAT-ATATATATAATAAAATA-ATATAATAAAT
25113356 TTTTTTTAAA
Statistics
Matches: 205, Mismatches: 33, Indels: 58
0.69 0.11 0.20
Matches are distributed among these distances:
35 4 0.02
36 14 0.07
37 11 0.05
38 43 0.21
39 45 0.22
40 41 0.20
41 26 0.13
42 9 0.04
43 12 0.06
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (39 bp):
AAAATATATATATAATAAAATAATATAATAAATAATATA
Found at i:25113078 original size:14 final size:14
Alignment explanation
Indices: 25113042--25113354 Score: 118
Period size: 15 Copynumber: 21.8 Consensus size: 14
25113032 TAACATAATT
25113042 TATA-AATAAAATA
1 TATATAATAAAATA
25113055 TATAATAATATAAATA
1 TAT-ATAATA-AAATA
25113071 -ATATAAT-AAATA
1 TATATAATAAAATA
25113083 -ATATAA-AAATATA
1 TATATAATAAA-ATA
*
25113096 TATATAATAAAATG
1 TATATAATAAAATA
25113110 TATATAATATAATATA
1 TATATAATA-AA-ATA
* * *
25113126 TATAAAAGAAAGAAA
1 TATATAATAAA-ATA
* *
25113141 GATATTATAATGAATAA
1 TATATAATAA--AAT-A
*
25113158 TATATAACAAAATA
1 TATATAATAAAATA
25113172 TAATATGTAATAAAATA
1 T-ATA--TAATAAAATA
* *
25113189 TGTA-GATAAAATA
1 TATATAATAAAATA
* *
25113202 TA-ATGA-AATATA
1 TATATAATAAAATA
25113214 -ATATAATAAGGAATA
1 TATATAATAA--AATA
*
25113229 TATAAAATAATAATA
1 TATATAATAA-AATA
* *
25113244 AAAAT-ATCAAAATA
1 TATATAAT-AAAATA
*
25113258 TAGTAAAAT-AAATAA
1 TA-TATAATAAAAT-A
*
25113273 AATATAATAAAA-A
1 TATATAATAAAATA
*
25113286 TATATAACATATAATA
1 TATAT-A-ATAAAATA
25113302 -A-A-AATACAAATA
1 TATATAATA-AAATA
* *
25113314 TAACAGAATAAATAATA
1 T-ATATAAT-AA-AATA
25113331 TATATAATAAAA-A
1 TATATAATAAAATA
*
25113344 TATATGATAAA
1 TATATAATAAA
25113355 TTTTTTTTAA
Statistics
Matches: 227, Mismatches: 37, Indels: 72
0.68 0.11 0.21
Matches are distributed among these distances:
11 4 0.02
12 27 0.12
13 35 0.15
14 46 0.20
15 53 0.23
16 37 0.16
17 25 0.11
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (14 bp):
TATATAATAAAATA
Found at i:25113174 original size:17 final size:17
Alignment explanation
Indices: 25113154--25113189 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25113144 ATTATAATGA
25113154 ATAATATATAACAAAAT
1 ATAATATATAACAAAAT
* *
25113171 ATAATATGTAATAAAAT
1 ATAATATATAACAAAAT
25113188 AT
1 AT
25113190 GTAGATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
ATAATATATAACAAAAT
Found at i:25113249 original size:9 final size:9
Alignment explanation
Indices: 25113237--25113307 Score: 56
Period size: 10 Copynumber: 7.4 Consensus size: 9
25113227 TATATAAAAT
25113237 AATAATAAA
1 AATAATAAA
*
25113246 AAT-ATCAA
1 AATAATAAA
25113254 AAT-ATAGTAA
1 AATAATA--AA
25113264 AATAAATAAA
1 AAT-AATAAA
25113274 ATATAATAAA
1 A-ATAATAAA
25113284 AATATATAACA
1 AATA-ATAA-A
*
25113295 TATAATAAA
1 AATAATAAA
25113304 AATA
1 AATA
25113308 CAAATATAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
8 9 0.18
9 10 0.20
10 23 0.45
11 6 0.12
12 3 0.06
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (9 bp):
AATAATAAA
Found at i:25113257 original size:20 final size:18
Alignment explanation
Indices: 25113047--25113347 Score: 124
Period size: 19 Copynumber: 16.2 Consensus size: 18
25113037 TAATTTATAA
*
25113047 ATAAAATAT-ATAATAAT
1 ATAAAATATAATAAAAAT
25113064 ATAAATAATATAATAAATAAT
1 AT-AA-AATATAATAAA-AAT
* *
25113085 ATAAAA-AT-ATATATAT
1 ATAAAATATAATAAAAAT
* *
25113101 AATAAAATGT-AT-ATAAT
1 -ATAAAATATAATAAAAAT
* *
25113118 ATAATATAT-ATAAAAGAA
1 ATAAAATATAATAAAA-AT
* * **
25113136 AGAAAGATATTATAATGA-
1 ATAAA-ATATAATAAAAAT
* *
25113154 ATAATATATAA-CAAAAT
1 ATAAAATATAATAAAAAT
* *
25113171 ATAATATGTAATAAAATATGT
1 ATAAAATATAATAAAA-A--T
*
25113192 AGATAAAATATAAT-GAAAT
1 --ATAAAATATAATAAAAAT
25113211 AT--AATATAATAAGGAATAT
1 ATAAAATATAATAA--AA-AT
25113230 ATAAAATAATAATAAAAAT
1 ATAAAAT-ATAATAAAAAT
* *
25113249 ATCAAAATATAGTAAAATAA
1 AT-AAAATATAATAAAA-AT
25113269 ATAAAATATAATAAAAAT
1 ATAAAATATAATAAAAAT
25113287 ATATAACATATAATAAAAAT
1 ATA-AA-ATATAATAAAAAT
* *
25113307 A-CAAATATAACAGAATAA-
1 ATAAAATATAATA-AA-AAT
25113325 ATAATATATATAATAAAAAT
1 ATAA-A-ATATAATAAAAAT
25113345 ATA
1 ATA
25113348 TGATAAATTT
Statistics
Matches: 215, Mismatches: 35, Indels: 65
0.68 0.11 0.21
Matches are distributed among these distances:
15 8 0.04
16 13 0.06
17 40 0.19
18 28 0.13
19 50 0.23
20 40 0.19
21 17 0.08
22 9 0.04
23 10 0.05
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAAAATATAATAAAAAT
Found at i:25113337 original size:58 final size:61
Alignment explanation
Indices: 25113208--25113348 Score: 184
Period size: 58 Copynumber: 2.4 Consensus size: 61
25113198 AATATAATGA
* **
25113208 AATATAATATAATAAGGAATATATAAAATAATAATAAAAATATCAAAATATAGTAAAATAAAT
1 AATAT-ATATAATAA-AAATATATAAAATAATAATAAAAATATCAAAATATAACAAAATAAAT
* *
25113271 AA-A-ATATAATAAAAATATATAACAT-ATAATAAAAATA-C-AAATATAACAGAATAAAT
1 AATATATATAATAAAAATATATAAAATAATAATAAAAATATCAAAATATAACAAAATAAAT
25113327 AATATATATAATAAAAATATAT
1 AATATATATAATAAAAATATAT
25113349 GATAAATTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
56 17 0.24
57 2 0.03
58 29 0.41
59 11 0.15
60 9 0.13
62 1 0.01
63 2 0.03
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (61 bp):
AATATATATAATAAAAATATATAAAATAATAATAAAAATATCAAAATATAACAAAATAAAT
Found at i:25113659 original size:22 final size:23
Alignment explanation
Indices: 25113634--25113676 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
25113624 GGTTAGGGCT
25113634 AATTT-AAAA-ATAAAATAAAATG
1 AATTTGAAAATATAAAA-AAAATG
25113656 AATTTGAAAATATAAAAAAAA
1 AATTTGAAAATATAAAAAAAA
25113677 CCACAGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 8 0.42
24 6 0.32
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (23 bp):
AATTTGAAAATATAAAAAAAATG
Found at i:25118186 original size:25 final size:25
Alignment explanation
Indices: 25118158--25118207 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
25118148 GTATAAAGAA
25118158 TATAAAAAGAATGAATGAATTTAAG
1 TATAAAAAGAATGAATGAATTTAAG
*
25118183 TATACAAAGAATGAATGAATTTAAG
1 TATAAAAAGAATGAATGAATTTAAG
25118208 AATGATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.54, C:0.02, G:0.16, T:0.28
Consensus pattern (25 bp):
TATAAAAAGAATGAATGAATTTAAG
Found at i:25125424 original size:12 final size:12
Alignment explanation
Indices: 25125417--25125717 Score: 87
Period size: 14 Copynumber: 24.0 Consensus size: 12
25125407 TAAATAAAAT
25125417 ATATAATAATATAA
1 ATAT-ATAATA-AA
25125431 ATCATATAAT-AA
1 AT-ATATAATAAA
25125443 ATAATATAATAAAA
1 AT-ATATAAT-AAA
25125457 TATATATAATAAA
1 -ATATATAATAAA
*
25125470 ATGTATATAATATA
1 A--TATATAATAAA
25125484 ATATAT-ATAAA
1 ATATATAATAAA
* * *
25125495 AGA-A-AGTAAG
1 ATATATAATAAA
25125505 ATATTATAATGAATA
1 ATA-TATAAT-AA-A
*
25125520 ATATATAACAAAA
1 ATATATAA-TAAA
25125533 TATAATATGTAATAAA
1 -AT-ATA--TAATAAA
*
25125549 ATATGTAGAT-AA
1 ATATATA-ATAAA
25125561 A-ATATAATGAAA
1 ATATATAAT-AAA
*
25125573 TATAATATAATAAGG
1 -AT-ATATAATAA-A
25125588 A-ATAT-ATAAA
1 ATATATAATAAA
25125598 ATA-ATAATAAA
1 ATATATAATAAA
25125609 A-ATATAA-AAA
1 ATATATAATAAA
*
25125619 TATAGTAAAATAAATA
1 -ATA-TATAAT-AA-A
*
25125635 AAATATAATAAA
1 ATATATAATAAA
25125647 A-ATAT-AT--A
1 ATATATAATAAA
*
25125655 ACATATAATAAA
1 ATATATAATAAA
*
25125667 A-ATACAAATATAA
1 ATATA-TAATA-AA
* *
25125680 CAGA-ATAAATAAT
1 -ATATAT-AATAAA
25125693 ATATATAATAAAA
1 ATATATAAT-AAA
*
25125706 ATATATGATAAA
1 ATATATAATAAA
25125718 TTTTTTTTAA
Statistics
Matches: 219, Mismatches: 24, Indels: 90
0.66 0.07 0.27
Matches are distributed among these distances:
8 2 0.01
9 4 0.02
10 19 0.09
11 33 0.15
12 46 0.21
13 30 0.14
14 54 0.25
15 24 0.11
16 4 0.02
17 3 0.01
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (12 bp):
ATATATAATAAA
Found at i:25125441 original size:14 final size:14
Alignment explanation
Indices: 25125393--25125493 Score: 72
Period size: 14 Copynumber: 7.4 Consensus size: 14
25125383 ATATATAGTG
* *
25125393 TATAACATAATTTA
1 TATAATATAAATTA
25125407 TA-AATA-AAATATA
1 TATAATATAAAT-TA
*
25125420 TAATAATATAAATCA
1 T-ATAATATAAATTA
*
25125435 TAT-A-ATAAATAA
1 TATAATATAAATTA
25125447 TATAATA-AAATATA
1 TATAATATAAAT-TA
25125461 TATAATA-AAATGTA
1 TATAATATAAAT-TA
25125475 TATAATAT-AATATA
1 TATAATATAAAT-TA
25125489 TATAA
1 TATAA
25125494 AAGAAAGTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
12 13 0.18
13 12 0.17
14 37 0.51
15 6 0.08
16 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (14 bp):
TATAATATAAATTA
Found at i:25125484 original size:5 final size:5
Alignment explanation
Indices: 25125409--25125644 Score: 66
Period size: 5 Copynumber: 46.8 Consensus size: 5
25125399 ATAATTTATA
* * *
25125409 AATAA AATAT -ATAAT AATAT AA-AT CATAT AATAAAT AATAT AATAA
1 AATAT AATAT AAT-AT AATAT AATAT AATAT AAT--AT AATAT AATAT
* * * *
25125455 AATAT -ATAT AATAA AATGT -ATAT AATAT AATAT -ATAT AAAAG AA-AGT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA-T
* * * * * *
25125502 AAGAT ATTAT AAT-G AATA- ATATAT AACAA AATAT AATATGT AATAA
1 AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT AATA--T AATAT
* * *
25125548 AATATGT AGATAA AATAT AATGA- AATAT AATAT AATAAGG AATAT -ATAA
1 AATA--T A-ATAT AATAT AAT-AT AATAT AATAT AAT-A-T AATAT AATAT
* * * *
25125597 AATAAT AATAAA AATAT AA-A- AATAT AGTAA AATA- AATAA AATAT AATA
1 AAT-AT AAT-AT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA
25125645 AAAATATATA
Statistics
Matches: 170, Mismatches: 34, Indels: 54
0.66 0.13 0.21
Matches are distributed among these distances:
3 2 0.01
4 31 0.18
5 103 0.61
6 17 0.10
7 14 0.08
8 3 0.02
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (5 bp):
AATAT
Found at i:25125491 original size:28 final size:27
Alignment explanation
Indices: 25125393--25125493 Score: 109
Period size: 28 Copynumber: 3.7 Consensus size: 27
25125383 ATATATAGTG
* *
25125393 TATAACATAATTTATA-AATAAAATATA
1 TATAATATAATATATATAATAAAAT-TA
*
25125420 TAATAATATAA-ATCATATAAT-AAATAA
1 T-ATAATATAATAT-ATATAATAAAATTA
*
25125447 TATAATAAAATATATATAATAAAATGTA
1 TATAATATAATATATATAATAAAAT-TA
25125475 TATAATATAATATATATAA
1 TATAATATAATATATATAA
25125494 AAGAAAGTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
26 15 0.24
27 10 0.16
28 34 0.55
29 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (27 bp):
TATAATATAATATATATAATAAAATTA
Found at i:25125537 original size:17 final size:17
Alignment explanation
Indices: 25125517--25125552 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25125507 ATTATAATGA
25125517 ATAATATATAACAAAAT
1 ATAATATATAACAAAAT
* *
25125534 ATAATATGTAATAAAAT
1 ATAATATATAACAAAAT
25125551 AT
1 AT
25125553 GTAGATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
ATAATATATAACAAAAT
Found at i:25125562 original size:13 final size:12
Alignment explanation
Indices: 25125531--25125565 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
25125521 TATATAACAA
*
25125531 AATATAATATGT
1 AATAAAATATGT
25125543 AATAAAATATGT
1 AATAAAATATGT
25125555 AGATAAAATAT
1 A-ATAAAATAT
25125566 AATGAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (12 bp):
AATAAAATATGT
Found at i:25125604 original size:27 final size:26
Alignment explanation
Indices: 25125559--25125711 Score: 87
Period size: 30 Copynumber: 5.3 Consensus size: 26
25125549 ATATGTAGAT
*
25125559 AAAATATAATGAAAT-ATAATATAATA
1 AAAATAT-ATAAAATAATAATATAATA
* *
25125585 AGGAATATATAAAATAATAATAAAAATATA
1 A-AAATATATAAAATAATAAT--ATA-ATA
25125615 AAAATATAGTAAAATAAATAAAATATAATA
1 AAAATATA-TAAAAT-AAT--AATATAATA
25125645 AAAATATATAACATATAATAA-A-AATA
1 AAAATATATAA-A-ATAATAATATAATA
* *
25125671 CAAATATAACAGAATAAATAATATATATAATA
1 -AAA-AT-ATA-TA-AAATAATA-ATATAATA
25125703 AAAATATAT
1 AAAATATAT
25125712 GATAAATTTT
Statistics
Matches: 99, Mismatches: 9, Indels: 36
0.69 0.06 0.25
Matches are distributed among these distances:
26 11 0.11
27 14 0.14
28 4 0.04
29 21 0.21
30 30 0.30
31 12 0.12
32 4 0.04
33 3 0.03
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (26 bp):
AAAATATATAAAATAATAATATAATA
Found at i:25125612 original size:9 final size:9
Alignment explanation
Indices: 25125600--25125670 Score: 65
Period size: 10 Copynumber: 7.4 Consensus size: 9
25125590 TATATAAAAT
25125600 AATAATAAA
1 AATAATAAA
25125609 AAT-ATAAA
1 AATAATAAA
25125617 AAT-ATAGTAA
1 AATAATA--AA
25125627 AATAAATAAA
1 AAT-AATAAA
25125637 ATATAATAAA
1 A-ATAATAAA
25125647 AATATATAACA
1 AATA-ATAA-A
*
25125658 TATAATAAA
1 AATAATAAA
25125667 AATA
1 AATA
25125671 CAAATATAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
8 11 0.21
9 10 0.19
10 23 0.43
11 6 0.11
12 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (9 bp):
AATAATAAA
Found at i:25125630 original size:30 final size:27
Alignment explanation
Indices: 25125588--25125711 Score: 106
Period size: 30 Copynumber: 4.3 Consensus size: 27
25125578 TATAATAAGG
25125588 AATATATAAAATAATAATAAAAATATAAA
1 AATATATAAAAT-A-AATAAAAATATAAA
25125617 AATATAGTAAAATAAATAAAATATAATAAA
1 AATATA-TAAAATAAATAAAA-AT-ATAAA
* *
25125647 AATATATAACATATAATAAAAATACAAA
1 AATATATAAAATA-AATAAAAATATAAA
* * *
25125675 TATA-ACAGAATAAATAATATATATAATAAA
1 AATATATAAAATAAATAA-A-A-AT-ATAAA
25125705 AATATAT
1 AATATAT
25125712 GATAAATTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
26 5 0.06
27 6 0.08
28 15 0.19
29 19 0.25
30 31 0.40
31 1 0.01
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (27 bp):
AATATATAAAATAAATAAAAATATAAA
Found at i:25125639 original size:39 final size:39
Alignment explanation
Indices: 25125576--25125667 Score: 123
Period size: 39 Copynumber: 2.3 Consensus size: 39
25125566 AATGAAATAT
*
25125576 AATATAATAAGGAATATATAAAATAATAATAAAAATATA-AA
1 AATATAATAA--AATAAATAAAAT-ATAATAAAAATATATAA
*
25125617 AATATAGTAAAATAAATAAAATATAATAAAAATATATAA
1 AATATAATAAAATAAATAAAATATAATAAAAATATATAA
*
25125656 CATATAATAAAA
1 AATATAATAAAA
25125668 ATACAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 14 0.30
39 23 0.50
41 9 0.20
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.27
Consensus pattern (39 bp):
AATATAATAAAATAAATAAAATATAATAAAAATATATAA
Found at i:25125660 original size:20 final size:20
Alignment explanation
Indices: 25125576--25125670 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
25125566 AATGAAATAT
*
25125576 AATATAATAAGGAATATATAA
1 AATATAATAA-AAATATATAA
25125597 AATAATAATAAAAATATA-AA
1 AAT-ATAATAAAAATATATAA
* *
25125617 AATATAGT-AAAATAAATAA
1 AATATAATAAAAATATATAA
25125636 AATATAATAAAAATATATAA
1 AATATAATAAAAATATATAA
*
25125656 CATATAATAAAAATA
1 AATATAATAAAAATA
25125671 CAAATATAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
18 7 0.11
19 13 0.20
20 29 0.45
21 9 0.14
22 7 0.11
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.27
Consensus pattern (20 bp):
AATATAATAAAAATATATAA
Found at i:25125700 original size:58 final size:61
Alignment explanation
Indices: 25125571--25125711 Score: 175
Period size: 58 Copynumber: 2.4 Consensus size: 61
25125561 AATATAATGA
* **
25125571 AATATAATATAATAAGGAATATATAAAATAATAATAAAAATATAAAAATATAGTAAAATAAAT
1 AATAT-ATATAATAA-AAATATATAAAATAATAATAAAAATATAAAAATATAACAAAATAAAT
* * *
25125634 AA-A-ATATAATAAAAATATATAACAT-ATAAT-AAAA-ATACAAATATAACAGAATAAAT
1 AATATATATAATAAAAATATATAAAATAATAATAAAAATATAAAAATATAACAAAATAAAT
25125690 AATATATATAATAAAAATATAT
1 AATATATATAATAAAAATATAT
25125712 GATAAATTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
56 20 0.29
57 5 0.07
58 22 0.31
59 11 0.16
60 9 0.13
62 1 0.01
63 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (61 bp):
AATATATATAATAAAAATATATAAAATAATAATAAAAATATAAAAATATAACAAAATAAAT
Found at i:25125716 original size:16 final size:16
Alignment explanation
Indices: 25125406--25125716 Score: 109
Period size: 16 Copynumber: 20.1 Consensus size: 16
25125396 AACATAATTT
*
25125406 ATAAATAAAATATATA
1 ATAAATAATATATATA
25125422 ATAATATAA-ATCATATA
1 ATAA-ATAATAT-ATATA
25125439 AT--A-AATA-ATATA
1 ATAAATAATATATATA
25125451 AT-AA-AATATATATA
1 ATAAATAATATATATA
*
25125465 AT-AA-AATGTATATA
1 ATAAATAATATATATA
*
25125479 ATATAAT-ATATATAAA
1 ATA-AATAATATATATA
* *
25125495 AGAAAGTAAGATATTATA
1 ATAAA-TAATATA-TATA
*
25125513 ATGAATAATATATA-A
1 ATAAATAATATATATA
*
25125528 CA-AAAT-ATAATATGTA
1 -ATAAATAAT-ATATATA
* * *
25125544 ATAAAATATGTAGATAAA
1 AT-AAATA-ATATATATA
25125562 ATATAATGAAATATAATATA
1 ATA-AAT--AATAT-ATATA
** *
25125582 ATAAGGAATATATAAA
1 ATAAATAATATATATA
* *
25125598 AT-AATAATAAAAAT-
1 ATAAATAATATATATA
*
25125612 ATAAA-AATATAGTAAA
1 ATAAATAATATA-TATA
25125628 ATAAATAA-A-ATATA
1 ATAAATAATATATATA
25125642 ATAAA-AATATATA-A
1 ATAAATAATATATATA
25125656 CAT--ATAATA-A-A-A
1 -ATAAATAATATATATA
* * *
25125668 ATACA-AATATAACAGA
1 ATAAATAATAT-ATATA
25125684 ATAAATAATATATATA
1 ATAAATAATATATATA
25125700 ATAAA-AATATATGATA
1 ATAAATAATATAT-ATA
25125716 A
1 A
25125717 ATTTTTTTTA
Statistics
Matches: 224, Mismatches: 33, Indels: 76
0.67 0.10 0.23
Matches are distributed among these distances:
11 2 0.01
12 13 0.06
13 12 0.05
14 46 0.21
15 35 0.16
16 51 0.23
17 38 0.17
18 15 0.07
19 4 0.02
20 8 0.04
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (16 bp):
ATAAATAATATATATA
Found at i:25134114 original size:29 final size:29
Alignment explanation
Indices: 25134051--25134118 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
25134041 TAATCAACCG
*
25134051 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
25134080 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
25134109 CGCACACTTA
1 CGCACACTTA
25134119 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:25134231 original size:174 final size:174
Alignment explanation
Indices: 25133940--25134267 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
25133930 AACTCAAGGT
* * *
25133940 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
*
25134005 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
25134070 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
25134114 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
25134179 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
*
25134244 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
25134268 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:25134259 original size:29 final size:30
Alignment explanation
Indices: 25134220--25134298 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
25134210 CTTAATAATC
25134220 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
25134250 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
25134279 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
25134299 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:25140481 original size:56 final size:56
Alignment explanation
Indices: 25140393--25140679 Score: 400
Period size: 56 Copynumber: 5.2 Consensus size: 56
25140383 GCCACTACAG
* * * * *
25140393 GGTCTTACTCGTAAACACATATCAGAAACACATATCGATGTCAACGTATTAAATGT
1 GGTCTTACTCGCACACACATATCAGAATCACATATCGATGCCAACGTATTAAACGT
* *
25140449 GGTCTTACTTGCACACACATATCAGAATCACATATCGATGCCAACGTATTAAACAT
1 GGTCTTACTCGCACACACATATCAGAATCACATATCGATGCCAACGTATTAAACGT
* *
25140505 GGTCTTACTCGCACACGCATATCAGAATCATATATCGATGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACACATATCAGAATCACATATCGATGCCAACGTATTAAACGT
**
25140561 GGTCTTACTCGCACACACATATTGGAATCACATATCGATGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACACATATCAGAATCACATATCGATGCCAACGTATTAAACGT
* * * *
25140617 GGTCTTACT--CACACATATTTC-GAAATCACATATTGATGCCAACGTATTAAATGT
1 GGTCTTACTCGCACACACATATCAG-AATCACATATCGATGCCAACGTATTAAACGT
*
25140671 GATCTTACT
1 GGTCTTACT
25140680 TGTAATCACA
Statistics
Matches: 209, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.00
54 46 0.22
56 162 0.78
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (56 bp):
GGTCTTACTCGCACACACATATCAGAATCACATATCGATGCCAACGTATTAAACGT
Found at i:25140688 original size:43 final size:43
Alignment explanation
Indices: 25140640--25140822 Score: 192
Period size: 43 Copynumber: 4.3 Consensus size: 43
25140630 CATATTTCGA
* ** **
25140640 AATCACATATTGATGCCAACGTATTAAATGTGATCTTACTTGT
1 AATCACATATCGATGCCAACGTACCAAATGTGATCTTACACGT
* * *
25140683 AATCACATATCGATGCCAACGTCCCAGATGTGGTCTTACACGT
1 AATCACATATCGATGCCAACGTACCAAATGTGATCTTACACGT
* * * * *
25140726 AATCACATATCGATGCCAACGTCCCAGACGTGGTCTTACACTT
1 AATCACATATCGATGCCAACGTACCAAATGTGATCTTACACGT
*
25140769 AATCACATATCGATGCCAATGT-CCTAGACATG-G-TCTTACACGT
1 AATCACATATCGATGCCAACGTACC-A-A-ATGTGATCTTACACGT
25140812 AATCACATATC
1 AATCACATATC
25140823 AAAAATCCTA
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
42 2 0.02
43 118 0.96
44 1 0.01
45 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (43 bp):
AATCACATATCGATGCCAACGTACCAAATGTGATCTTACACGT
Found at i:25145886 original size:34 final size:34
Alignment explanation
Indices: 25145843--25145911 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
25145833 AACGGAGATG
25145843 GTTAGAATTGTTGAAAAATTAAGAGCTAGTGATT
1 GTTAGAATTGTTGAAAAATTAAGAGCTAGTGATT
*
25145877 GTTAGAATTGTTGAAAGATTAAGAGCTAGTGATT
1 GTTAGAATTGTTGAAAAATTAAGAGCTAGTGATT
25145911 G
1 G
25145912 ACTACCATCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (34 bp):
GTTAGAATTGTTGAAAAATTAAGAGCTAGTGATT
Found at i:25152415 original size:39 final size:39
Alignment explanation
Indices: 25152356--25152541 Score: 327
Period size: 39 Copynumber: 4.8 Consensus size: 39
25152346 TTCCAACCCA
25152356 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
**
25152395 AATATCTTCGGGACTTAGCCCGGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
* *
25152434 AATGCCTTCGGGACTTATCCCGGATATAACACTAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
*
25152473 AATGCCTTCGGGACTTAGCCCGGACATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
25152512 AATGCCTTCGGGACTTAGCCCGGATATAAC
1 AATGCCTTCGGGACTTAGCCCGGATATAAC
25152542 TAAGTTCCAT
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 137 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
Found at i:25157885 original size:39 final size:39
Alignment explanation
Indices: 25157827--25157946 Score: 177
Period size: 39 Copynumber: 3.1 Consensus size: 39
25157817 TGTAAATATA
* * *
25157827 TATATGCGAGAATTGTATCCAGACTTCAGGTCCGTAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* *
25157866 TATATGCAAGAATTATATCCGGACTTCATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* *
25157905 TATATGCGAGAATAATATCCGGACTTTAGGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
25157944 TAT
1 TAT
25157947 GTGCTGGACA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (39 bp):
TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
Found at i:25157962 original size:39 final size:37
Alignment explanation
Indices: 25157827--25157962 Score: 137
Period size: 39 Copynumber: 3.5 Consensus size: 37
25157817 TGTAAATATA
* * *
25157827 TATATGCGAGAATTGTATCCAGACTTCAGGTCCGTAGGC
1 TATATGCG-GAA-TATATCCGGACTTCAGGTCCGCAGGC
* *
25157866 TATATGCAAGAATTATATCCGGACTTCATGTCCGCAGGC
1 TATATGC-GGAA-TATATCCGGACTTCAGGTCCGCAGGC
*
25157905 TATATGCGAGAATAATATCCGGACTTTAGGTCCGCAGGC
1 TATATGCG-GAAT-ATATCCGGACTTCAGGTCCGCAGGC
*
25157944 TATGTGCTGGACATATATC
1 TATATGC-GGA-ATATATC
25157963 TGAATTTAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
38 1 0.01
39 79 0.95
40 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (37 bp):
TATATGCGGAATATATCCGGACTTCAGGTCCGCAGGC
Found at i:25165290 original size:39 final size:39
Alignment explanation
Indices: 25165038--25165273 Score: 400
Period size: 39 Copynumber: 6.1 Consensus size: 39
25165028 TGTGAATATA
25165038 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* *
25165077 TATATGCGAGAATTATATCCGGACTTCAGGTCTGCAAGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* * *
25165116 TATAAGCGAGAATTATATCCGGACTTCAGGTCTGCAAGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
*
25165155 TATATGCGAGAATTATATCCGGACTTCAGGTCCACAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
*
25165194 TATATGCGAGAATTATATCCGGACTTCATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
*
25165233 TATATGCGAGAATTATATCCGGACTTTAGGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
25165272 TA
1 TA
25165274 CGTGCTGGAC
Statistics
Matches: 186, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 186 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (39 bp):
TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
Found at i:25170289 original size:16 final size:17
Alignment explanation
Indices: 25170268--25170299 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
25170258 AAATAGGTTG
25170268 AGAAAATT-ATTTAATT
1 AGAAAATTAATTTAATT
25170284 AGAAAATTAATTTAAT
1 AGAAAATTAATTTAAT
25170300 AAATGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
AGAAAATTAATTTAATT
Found at i:25173675 original size:42 final size:42
Alignment explanation
Indices: 25173616--25173779 Score: 179
Period size: 42 Copynumber: 3.9 Consensus size: 42
25173606 TTAAGGTTAC
*
25173616 TGAGACTAT-GTGTAAGACCATATCTGGGATATGGCATCAATA
1 TGAGACT-TCGTGTAAGACCATATCTGGGATATGGCATCAATG
** *
25173658 TGAGACTTCGTGTAAGACCATGCCTGGGATATGACATCAATG
1 TGAGACTTCGTGTAAGACCATATCTGGGATATGGCATCAATG
* * * * * *
25173700 TGATATTTCGTGTAAGACCATAGCTGGGCTATTAGCATCGATG
1 TGAGACTTCGTGTAAGACCATATCTGGGATA-TGGCATCAATG
* *
25173743 CGAGA-TTACATGTAAGACCATATCTGGGATATGGCAT
1 TGAGACTT-CGTGTAAGACCATATCTGGGATATGGCAT
25173780 TGGTATGGTA
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 69 0.68
43 31 0.31
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (42 bp):
TGAGACTTCGTGTAAGACCATATCTGGGATATGGCATCAATG
Found at i:25177714 original size:46 final size:45
Alignment explanation
Indices: 25177614--25177737 Score: 176
Period size: 46 Copynumber: 2.7 Consensus size: 45
25177604 NNNNNNNNAA
* * *
25177614 CTCGTTGAGTTGAGTCCGAGTTCGTGAGATGGATGCGAACGCCTGAG
1 CTCGTTGAGTTGAGTCCGAGTTCCT--TATGGATGCGAACGCCCGAG
25177661 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-CTTATGGATGCGAACGCCCGAG
*
25177707 CTTGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTC-CTTATGG
25177738 GCGGGTTACA
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
46 47 0.66
47 23 0.32
48 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.29
Consensus pattern (45 bp):
CTCGTTGAGTTGAGTCCGAGTTCCTTATGGATGCGAACGCCCGAG
Found at i:25187193 original size:52 final size:51
Alignment explanation
Indices: 25187136--25187238 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 51
25187126 TAGTCATATG
*
25187136 AATTTTGTACAAAGAGAAATTTGGTTCGTAGTAAACAGAGGTCAGACCAGT
1 AATTTTGTACAAAGAGAAATGTGGTTCGTAGTAAACAGAGGTCAGACCAGT
*
25187187 NAATTTTGTACAGAGAGAAATGTGGTTCGTAGTAAACAGAGGTCAGACCAGT
1 -AATTTTGTACAAAGAGAAATGTGGTTCGTAGTAAACAGAGGTCAGACCAGT
25187239 CGAGTCTTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (51 bp):
AATTTTGTACAAAGAGAAATGTGGTTCGTAGTAAACAGAGGTCAGACCAGT
Found at i:25197385 original size:20 final size:20
Alignment explanation
Indices: 25197341--25197385 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
25197331 TCTCAAACTC
*
25197341 CTTTTTCAACTATATCTTTA
1 CTTTTTCAACTATATCTTGA
*
25197361 GTTTTTCAATCTAT-TCTTGA
1 CTTTTTCAA-CTATATCTTGA
25197381 CTTTT
1 CTTTT
25197386 GAAAGCTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.20, C:0.18, G:0.04, T:0.58
Consensus pattern (20 bp):
CTTTTTCAACTATATCTTGA
Found at i:25202365 original size:28 final size:27
Alignment explanation
Indices: 25202333--25202415 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 27
25202323 AACACACCAG
* *
25202333 TATAATCCTCCAAAACACACTAGTATCA
1 TATAATCCTCC-AAACACACTAGAATAA
25202361 TATAATCCTCCGAAACACACTAGAATAA
1 TATAATCCTCC-AAACACACTAGAATAA
25202389 TATAATCCATCCAAACACACTAGAATA
1 TATAATCC-TCCAAACACACTAGAATA
25202416 GCACAGAGTG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
28 48 0.94
29 3 0.06
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.23
Consensus pattern (27 bp):
TATAATCCTCCAAACACACTAGAATAA
Found at i:25202388 original size:23 final size:23
Alignment explanation
Indices: 25202319--25202389 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 23
25202309 AAATGTCCAA
* *
25202319 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACTAGAATAATCCT
25202342 CCAAAACACACTAGTATCATATAATCCT
1 CCAAAACACACTAG----A-ATAATCCT
*
25202370 CCGAAACACACTAGAATAAT
1 CCAAAACACACTAGAATAAT
25202390 ATAATCCATC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 18 0.45
24 1 0.03
28 21 0.52
ACGTcount: A:0.45, C:0.30, G:0.06, T:0.20
Consensus pattern (23 bp):
CCAAAACACACTAGAATAATCCT
Found at i:25202480 original size:13 final size:14
Alignment explanation
Indices: 25202456--25202485 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25202446 GGACATAAAC
25202456 ATCAACATCTCCAA
1 ATCAACATCTCCAA
25202470 ATCAA-ATCTCCAA
1 ATCAACATCTCCAA
25202483 ATC
1 ATC
25202486 CCTTCTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (14 bp):
ATCAACATCTCCAA
Found at i:25202980 original size:36 final size:36
Alignment explanation
Indices: 25202940--25203019 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
25202930 TATCCTATTT
* *
25202940 TCAATTTAATTCTAACTAAACTTACTTATTCTTAAC
1 TCAATTCAATTCTAAATAAACTTACTTATTCTTAAC
25202976 TCAATTCAATTCTAAATAAACTTACTTATTCTTAAC
1 TCAATTCAATTCTAAATAAACTTACTTATTCTTAAC
25203012 TCAATTCA
1 TCAATTCA
25203020 TACTTTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (36 bp):
TCAATTCAATTCTAAATAAACTTACTTATTCTTAAC
Found at i:25203737 original size:47 final size:50
Alignment explanation
Indices: 25203675--25203796 Score: 126
Period size: 47 Copynumber: 2.5 Consensus size: 50
25203665 ATTTTTCTGC
* *
25203675 AAATCAATAGTGGCTTGTCCATAAAGTGTT-CTAGTGGCAGTATAT-T-T
1 AAATCAGTGGTGGCTTGTCCATAAAGTGTTACTAGTGGCAGTATATCTAT
* * * * * *
25203722 ACAT-ATGTGGTGGCTTGTCGACAAAGTGTTATTAGTGGTAGTTTATCTAT
1 AAATCA-GTGGTGGCTTGTCCATAAAGTGTTACTAGTGGCAGTATATCTAT
*
25203772 AAATCAGTGGTGGCTTGTACATAAA
1 AAATCAGTGGTGGCTTGTCCATAAA
25203797 TGGCATTTCA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
46 1 0.02
47 23 0.40
48 12 0.21
49 1 0.02
50 20 0.34
51 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (50 bp):
AAATCAGTGGTGGCTTGTCCATAAAGTGTTACTAGTGGCAGTATATCTAT
Found at i:25213041 original size:43 final size:43
Alignment explanation
Indices: 25212992--25213079 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
25212982 AAGGCTAGGA
* *
25212992 ACAAAAATATTTGAATTTTCCCAAAATCAGATTCGAACCCATG
1 ACAAAAATAATTGAAGTTTCCCAAAATCAGATTCGAACCCATG
*
25213035 ACAAAAATAATTGAAGTTTCCCAAAATCAGATTCGAACCTATG
1 ACAAAAATAATTGAAGTTTCCCAAAATCAGATTCGAACCCATG
25213078 AC
1 AC
25213080 CTCAAACTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.26
Consensus pattern (43 bp):
ACAAAAATAATTGAAGTTTCCCAAAATCAGATTCGAACCCATG
Found at i:25219396 original size:22 final size:20
Alignment explanation
Indices: 25219366--25219411 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
25219356 TGAAATTTTA
25219366 ATTAGTATTATGAGATAAAATT
1 ATTAGTATTATGAGA-AAAA-T
* *
25219388 ATTATTATTATTAGAAAAAT
1 ATTAGTATTATGAGAAAAAT
25219408 ATTA
1 ATTA
25219412 CTGTATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 4 0.18
22 13 0.59
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (20 bp):
ATTAGTATTATGAGAAAAAT
Found at i:25222048 original size:30 final size:31
Alignment explanation
Indices: 25222014--25222075 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 31
25222004 TGGAATGGGC
*
25222014 CTATGGGCCA-TACTGT-TATCTGAAAAGGGG
1 CTATGGCCCATTACTGTAT-TCTGAAAAGGGG
25222044 CTATGGCCCAGTTTACTGTATTCTGAAAAGGG
1 CTATGGCCCA--TTACTGTATTCTGAAAAGGG
25222076 CTTCAGCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 9 0.33
33 17 0.63
34 1 0.04
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (31 bp):
CTATGGCCCATTACTGTATTCTGAAAAGGGG
Found at i:25235921 original size:22 final size:24
Alignment explanation
Indices: 25235893--25235937 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
25235883 TTTTTTTTCA
25235893 ATTTTAA-CTTTTAT-TCAAAAAC
1 ATTTTAATCTTTTATATCAAAAAC
*
25235915 ATTTTAATTTTTTATATCAAAAA
1 ATTTTAATCTTTTATATCAAAAA
25235938 ATATTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 7 0.35
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTTAATCTTTTATATCAAAAAC
Found at i:25236079 original size:18 final size:18
Alignment explanation
Indices: 25236056--25236092 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25236046 ATTTAAGGCC
25236056 TAAATTAAAAAATTGACA
1 TAAATTAAAAAATTGACA
* *
25236074 TAAATTCAAAATTTGACA
1 TAAATTAAAAAATTGACA
25236092 T
1 T
25236093 TCATTTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (18 bp):
TAAATTAAAAAATTGACA
Found at i:25237184 original size:158 final size:158
Alignment explanation
Indices: 25236896--25237214 Score: 593
Period size: 158 Copynumber: 2.0 Consensus size: 158
25236886 TGCCCTCCTG
*
25236896 ATAGTCTTATTAATGTTATTGAACATAATAAGGGCTAGGTCAGACACCTATCAGAATGGATAGAA
1 ATAGTCTTATTAATGTTATTGAACATAATAAGGGCTAGGTCAGAAACCTATCAGAATGGATAGAA
* *
25236961 TCAAGCCACCAATAATCAGTATTGTAAAGCTAGACATGTTTCTTGATAGGACGTCAATTCCAAGT
66 TCAAGCCACCAATAATCAGTATTGTAAAGCTAGACATGTTTCTTGATAGAACGCCAATTCCAAGT
25237026 GATAATCAAATGGAGAACACGATCATGA
131 GATAATCAAATGGAGAACACGATCATGA
25237054 ATAGTCTTATTAATGTTATTGAACATAATAAGGGCTAGGTCAGAAACCTATCAGAATGGATAGAA
1 ATAGTCTTATTAATGTTATTGAACATAATAAGGGCTAGGTCAGAAACCTATCAGAATGGATAGAA
*
25237119 TCAAGCCACCAATAATCAGTGTTGTAAAGCTAGACATGTTTCTTGATAGAACGCCAATTCCAAGT
66 TCAAGCCACCAATAATCAGTATTGTAAAGCTAGACATGTTTCTTGATAGAACGCCAATTCCAAGT
*
25237184 GATAATCAAATGGGGAACACGATCATGA
131 GATAATCAAATGGAGAACACGATCATGA
25237212 ATA
1 ATA
25237215 TTAAGTTTGG
Statistics
Matches: 156, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 156 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (158 bp):
ATAGTCTTATTAATGTTATTGAACATAATAAGGGCTAGGTCAGAAACCTATCAGAATGGATAGAA
TCAAGCCACCAATAATCAGTATTGTAAAGCTAGACATGTTTCTTGATAGAACGCCAATTCCAAGT
GATAATCAAATGGAGAACACGATCATGA
Found at i:25242703 original size:20 final size:20
Alignment explanation
Indices: 25242678--25242725 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
25242668 ATTTTTCAAC
25242678 TTAAAAGAATTCTT-ACTTGA
1 TTAAAAGAATT-TTGACTTGA
**
25242698 TTAAAATTATTTTGACTTGA
1 TTAAAAGAATTTTGACTTGA
25242718 TTATAAAG
1 TTA-AAAG
25242726 TTGATTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (20 bp):
TTAAAAGAATTTTGACTTGA
Found at i:25242844 original size:22 final size:24
Alignment explanation
Indices: 25242818--25242861 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
25242808 ATTTTGTTTA
25242818 ATTTTAACTT-TTAT-TCAAAAAC
1 ATTTTAACTTATTATATCAAAAAC
*
25242840 ATTTTAATTTATTATATCAAAA
1 ATTTTAACTTATTATATCAAAA
25242862 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTTAACTTATTATATCAAAAAC
Found at i:25245787 original size:59 final size:58
Alignment explanation
Indices: 25245686--25245822 Score: 152
Period size: 59 Copynumber: 2.3 Consensus size: 58
25245676 AATATCATGA
* * *
25245686 ACTAACTTGAAT-AAAAAAATTCAAATCCTAATATGAGAACAATTA-CTAAGTTCAAAG
1 ACTAACTTGAATAAAAAAAATTCAAACCCTAAAATAAGAACAATTATC-AAGTTCAAAG
* * *
25245743 ACTAACTTGAATAAAAAAAACTTGAAGCCCTAAAATAAGAACAATTATCAAGTTTAAAG
1 ACTAACTTGAATAAAAAAAA-TTCAAACCCTAAAATAAGAACAATTATCAAGTTCAAAG
* * *
25245802 ATTATCTTGGATAAAGAAAAA
1 ACTAACTTGAATAAA-AAAAA
25245823 ATTTAAAACC
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
57 12 0.18
58 7 0.10
59 42 0.63
60 6 0.09
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (58 bp):
ACTAACTTGAATAAAAAAAATTCAAACCCTAAAATAAGAACAATTATCAAGTTCAAAG
Found at i:25245940 original size:77 final size:78
Alignment explanation
Indices: 25245840--25246016 Score: 234
Period size: 77 Copynumber: 2.3 Consensus size: 78
25245830 ACCAATGTGA
* *
25245840 AAATGTCAATATAAATTTTATCTTCACAAGATAAA-TTGGAAAATATATAAATAAAT-AAAAA-T
1 AAATGTTAATATAAATTTTATCTTCACAAGATAAACTCGG-AAATATATAAAT-AATGAAAAATT
*
25245902 TAAAATATGCAATAT
64 TAAAATATGCAACAT
* **
25245917 AAATGTTAATATAAATTTTATCTTCACAAGTTAAACTCGGAAATATATAAATTTTGAAAAATTTA
1 AAATGTTAATATAAATTTTATCTTCACAAGATAAACTCGGAAATATATAAATAATGAAAAATTTA
25245982 AAATATGCAACAT
66 AAATATGCAACAT
* * *
25245995 ATATGCTAATATAAACTTTATC
1 AAATGTTAATATAAATTTTATC
25246017 ATATATGCTA
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
76 1 0.01
77 50 0.57
78 37 0.42
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.35
Consensus pattern (78 bp):
AAATGTTAATATAAATTTTATCTTCACAAGATAAACTCGGAAATATATAAATAATGAAAAATTTA
AAATATGCAACAT
Found at i:25246019 original size:24 final size:24
Alignment explanation
Indices: 25245992--25246040 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
25245982 AAATATGCAA
25245992 CATATATGCTAATATAAACTTTAT
1 CATATATGCTAATATAAACTTTAT
25246016 CATATATGCTAATATAAACTTTAT
1 CATATATGCTAATATAAACTTTAT
25246040 C
1 C
25246041 TTCATGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (24 bp):
CATATATGCTAATATAAACTTTAT
Found at i:25247671 original size:138 final size:138
Alignment explanation
Indices: 25247423--25247706 Score: 514
Period size: 138 Copynumber: 2.1 Consensus size: 138
25247413 TAGAAAAATG
*
25247423 AATTATATTCTTTCCAAAAGAATATTAACTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAACTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
25247488 TATAATTGTTTATATTAATAAATTCAATAAAATATATACAATTAATATTTTGTATAAATCAAATT
66 TATAATTGTTTATATTAATAAATTCAATAAAATATATACAATTAATATTTTGTATAAATCAAATT
25247553 CATATATT
131 CATATATT
* *
25247561 AATTATATTCTTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAACTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
25247626 TATAATTGTTTATATTAATTAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCAATAAAATATATACAATTAATATTTTGTATAAATCAAATT
25247691 CATATATT
131 CATATATT
25247699 AATTATAT
1 AATTATAT
25247707 CCATGTTCTC
Statistics
Matches: 140, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 140 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAACTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTCAATAAAATATATACAATTAATATTTTGTATAAATCAAATT
CATATATT
Found at i:25252047 original size:18 final size:18
Alignment explanation
Indices: 25252024--25252062 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
25252014 TTTTCCTTTG
25252024 TTGGGCTTGGCCTTACCA
1 TTGGGCTTGGCCTTACCA
*
25252042 TTGGGCTTGGCCTTGCCA
1 TTGGGCTTGGCCTTACCA
25252060 TTG
1 TTG
25252063 TCCTTAGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
TTGGGCTTGGCCTTACCA
Found at i:25255924 original size:28 final size:28
Alignment explanation
Indices: 25255868--25255932 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
25255858 TATACAGTAT
* *
25255868 TAGT-ACAGTCTGGGCCTTAGCCCTGTA
1 TAGTAACAGTCTGGGCCTAAGCCCTATA
*
25255895 TAGTAACAGTGTGGGCCTAAG-CCTAATA
1 TAGTAACAGTCTGGGCCTAAGCCCT-ATA
*
25255923 TAGTATCAGT
1 TAGTAACAGT
25255933 ACAGTGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 7 0.22
28 25 0.78
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (28 bp):
TAGTAACAGTCTGGGCCTAAGCCCTATA
Found at i:25256113 original size:27 final size:27
Alignment explanation
Indices: 25256083--25256139 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
25256073 AGCATAGCTG
25256083 CCAGAAACAGTAAATGTGGCAAAGCCA
1 CCAGAAACAGTAAATGTGGCAAAGCCA
* * * *
25256110 CCAGTATCAGTAATTGTGGCATAGCCA
1 CCAGAAACAGTAAATGTGGCAAAGCCA
25256137 CCA
1 CCA
25256140 ATAATAGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.18
Consensus pattern (27 bp):
CCAGAAACAGTAAATGTGGCAAAGCCA
Found at i:25256154 original size:27 final size:26
Alignment explanation
Indices: 25256090--25256174 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
25256080 CTGCCAGAAA
* *
25256090 CAGTAAATGTGGCAAAGCCACCAGTAT
1 CAGT-AATGTGGCATAGCCACCAATAT
25256117 CAGTAATTGTGGCATAGCCACCAATAAT
1 CAGTAA-TGTGGCATAGCCACCAAT-AT
* * *
25256145 -AGTGAATGTGACATAGTCACCAGTAT
1 CAGT-AATGTGGCATAGCCACCAATAT
25256171 -AGTA
1 CAGTA
25256175 CTTCCTTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 1 0.02
26 7 0.14
27 38 0.76
28 4 0.08
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (26 bp):
CAGTAATGTGGCATAGCCACCAATAT
Found at i:25256341 original size:27 final size:27
Alignment explanation
Indices: 25256310--25256452 Score: 187
Period size: 27 Copynumber: 5.3 Consensus size: 27
25256300 GCCATAATCA
* * * *
25256310 TCATTTTACCATATAGGGGTATTAAGG
1 TCATTTTACCCTACAGGGGCATTACGG
*
25256337 TCATTTTACCATACAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* *
25256364 TTATTTTACCCTACAAGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
*
25256391 TCATTTTACCCTACAGGGACATTACGG
1 TCATTTTACCCTACAGGGGCATTACGG
* * *
25256418 TCATTTTACCCTATAGGGGTATTAGGG
1 TCATTTTACCCTACAGGGGCATTACGG
25256445 TCATTTTA
1 TCATTTTA
25256453 TCTATATTGG
Statistics
Matches: 103, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 103 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCATTACGG
Found at i:25259270 original size:18 final size:18
Alignment explanation
Indices: 25259247--25259289 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
25259237 CAACTAATGG
25259247 CACTCACTAGAATTCCTA
1 CACTCACTAGAATTCCTA
**
25259265 CACTCACTAGAATTTTTA
1 CACTCACTAGAATTCCTA
25259283 CACTCAC
1 CACTCAC
25259290 AATGCACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.30
Consensus pattern (18 bp):
CACTCACTAGAATTCCTA
Found at i:25262815 original size:98 final size:98
Alignment explanation
Indices: 25262646--25262941 Score: 574
Period size: 98 Copynumber: 3.0 Consensus size: 98
25262636 AGGGCTGTTA
*
25262646 CATCCATATAGTGCTCGCCCATAAACTTTCTCTTAAAAACCTCAAGAAAATATCCCCAAGTCAAA
1 CATCCATATGGTGCTCGCCCATAAACTTTCTCTTAAAAACCTCAAGAAAATATCCCCAAGTCAAA
25262711 TGATCAGTAGTAGTACCTCTCTTAATAGTATTC
66 TGATCAGTAGTAGTACCTCTCTTAATAGTATTC
25262744 CATCCATATGGTGCTCGCCCATAAACTTTCTCTTAAAAACCTCAAGAAAATATCCCCAAGTCAAA
1 CATCCATATGGTGCTCGCCCATAAACTTTCTCTTAAAAACCTCAAGAAAATATCCCCAAGTCAAA
25262809 TGATCAGTAGTAGTACCTCTCTTAATAGTATTC
66 TGATCAGTAGTAGTACCTCTCTTAATAGTATTC
25262842 CATCCATATGGTGCTCGCCCATAAACTTTCTCTTAAAAACCTCAAGAAAATATCCCCAAGTCAAA
1 CATCCATATGGTGCTCGCCCATAAACTTTCTCTTAAAAACCTCAAGAAAATATCCCCAAGTCAAA
*
25262907 TGATCAGTAGTAGTACCTTTCTTAATAGTATTC
66 TGATCAGTAGTAGTACCTCTCTTAATAGTATTC
25262940 CA
1 CA
25262942 CCAACGATAA
Statistics
Matches: 196, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 196 1.00
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (98 bp):
CATCCATATGGTGCTCGCCCATAAACTTTCTCTTAAAAACCTCAAGAAAATATCCCCAAGTCAAA
TGATCAGTAGTAGTACCTCTCTTAATAGTATTC
Found at i:25269821 original size:20 final size:20
Alignment explanation
Indices: 25269798--25270094 Score: 224
Period size: 20 Copynumber: 15.1 Consensus size: 20
25269788 GCACGAATGG
**
25269798 ACAAACAGGGGTACTGAAGT
1 ACAAACAGGGGTACCAAAGT
*
25269818 ACAAACAGGAGTACCAAAGT
1 ACAAACAGGGGTACCAAAGT
25269838 ACAAACAGGGGTACCAAAGT
1 ACAAACAGGGGTACCAAAGT
* * *
25269858 ACATACAGGAGTACCAAAAT
1 ACAAACAGGGGTACCAAAGT
*
25269878 ATAAACAGGGGTACCAAAGT
1 ACAAACAGGGGTACCAAAGT
* * * * * *
25269898 GCATACAAGAGTATCGAAGT
1 ACAAACAGGGGTACCAAAGT
*
25269918 ACAAGCAGGGGTACCAAAGT
1 ACAAACAGGGGTACCAAAGT
* * * *
25269938 ACATACAAGAGTACCGAAGT
1 ACAAACAGGGGTACCAAAGT
* *
25269958 ACAAAC-GGCGTACCAAAGA
1 ACAAACAGGGGTACCAAAGT
25269977 ACAAACAGGGGTACCAAAGT
1 ACAAACAGGGGTACCAAAGT
* * *
25269997 ACATACA--TG-ACCGAAGT
1 ACAAACAGGGGTACCAAAGT
* * **
25270014 ACAAACAAGGCTACTGAAGT
1 ACAAACAGGGGTACCAAAGT
* ** * *
25270034 ACAAATAAAGGTATCGAAGT
1 ACAAACAGGGGTACCAAAGT
* *
25270054 ACAAATAGGGGTACCGAAGT
1 ACAAACAGGGGTACCAAAGT
** **
25270074 ACGTACAGGCATACCAAAGT
1 ACAAACAGGGGTACCAAAGT
25270094 A
1 A
25270095 AATTCACATA
Statistics
Matches: 215, Mismatches: 58, Indels: 8
0.77 0.21 0.03
Matches are distributed among these distances:
17 13 0.06
18 1 0.00
19 15 0.07
20 186 0.87
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (20 bp):
ACAAACAGGGGTACCAAAGT
Found at i:25269842 original size:40 final size:40
Alignment explanation
Indices: 25269798--25269999 Score: 253
Period size: 40 Copynumber: 5.1 Consensus size: 40
25269788 GCACGAATGG
** *
25269798 ACAAACAGGGGTACTGAAGTACAAACAGGAGTACCAAAGT
1 ACAAACAGGGGTACCAAAGTACATACAGGAGTACCAAAGT
*
25269838 ACAAACAGGGGTACCAAAGTACATACAGGAGTACCAAAAT
1 ACAAACAGGGGTACCAAAGTACATACAGGAGTACCAAAGT
* * * * *
25269878 ATAAACAGGGGTACCAAAGTGCATACAAGAGTATCGAAGT
1 ACAAACAGGGGTACCAAAGTACATACAGGAGTACCAAAGT
* * *
25269918 ACAAGCAGGGGTACCAAAGTACATACAAGAGTACCGAAGT
1 ACAAACAGGGGTACCAAAGTACATACAGGAGTACCAAAGT
* * * *
25269958 ACAAAC-GGCGTACCAAAGAACAAACAGGGGTACCAAAGT
1 ACAAACAGGGGTACCAAAGTACATACAGGAGTACCAAAGT
25269997 ACA
1 ACA
25270000 TACATGACCG
Statistics
Matches: 141, Mismatches: 21, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
39 30 0.21
40 111 0.79
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (40 bp):
ACAAACAGGGGTACCAAAGTACATACAGGAGTACCAAAGT
Found at i:25272056 original size:174 final size:174
Alignment explanation
Indices: 25271766--25272112 Score: 676
Period size: 174 Copynumber: 2.0 Consensus size: 174
25271756 TTTTACAGAA
*
25271766 TTCAAAATGTGTTGTATTTGATCTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATATAAAT
1 TTCAAAATGTGTTGTATTTGATCTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATAGAAAT
*
25271831 TTTATCTTATAATCATTTTTGTACAATTTATAATGATTTTCTAAAAACAGAACAGGGAATCTAGT
66 TTTATCTTATAATCATTTTTGTACAATTTATAATGATTTCCTAAAAACAGAACAGGGAATCTAGT
25271896 AGTCATTTTGACTCAGCCCCACAATACTTCAAATATCTCAAGAC
131 AGTCATTTTGACTCAGCCCCACAATACTTCAAATATCTCAAGAC
25271940 TTCAAAATGTGTTGTATTTGATCTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATAGAAAT
1 TTCAAAATGTGTTGTATTTGATCTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATAGAAAT
25272005 TTTATCTTATAATCATTTTTGTACAATTTATAATGATTTCCTAAAAACAGAACAGGGAATCTAGT
66 TTTATCTTATAATCATTTTTGTACAATTTATAATGATTTCCTAAAAACAGAACAGGGAATCTAGT
25272070 AGTCATTTTGACTCAGCCCCACAATACTTCAAATATCTCAAGA
131 AGTCATTTTGACTCAGCCCCACAATACTTCAAATATCTCAAGA
25272113 TCGGTAACTC
Statistics
Matches: 171, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 171 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (174 bp):
TTCAAAATGTGTTGTATTTGATCTCATTTGAAACTAGACTCATTAAGGAGTCTAAGCATAGAAAT
TTTATCTTATAATCATTTTTGTACAATTTATAATGATTTCCTAAAAACAGAACAGGGAATCTAGT
AGTCATTTTGACTCAGCCCCACAATACTTCAAATATCTCAAGAC
Found at i:25279242 original size:27 final size:27
Alignment explanation
Indices: 25279212--25279389 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
25279202 ATATTGAGTC
* * * *
25279212 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
25279239 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
25279266 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
25279294 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
25279321 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
25279348 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
25279375 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25279390 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:25279351 original size:82 final size:81
Alignment explanation
Indices: 25279233--25279388 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
25279223 TGCTATATAA
* *
25279233 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
25279298 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
25279315 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
25279379 CACTTAGTGC
65 CACTTAGTGC
25279389 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:25284227 original size:19 final size:19
Alignment explanation
Indices: 25284203--25284241 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
25284193 CGGCTCGGGC
25284203 GTGGTTCAACTATGGGGGT
1 GTGGTTCAACTATGGGGGT
* *
25284222 GTGGTTCTACTATGGTGGT
1 GTGGTTCAACTATGGGGGT
25284241 G
1 G
25284242 AGGAAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.41, T:0.36
Consensus pattern (19 bp):
GTGGTTCAACTATGGGGGT
Found at i:25294327 original size:12 final size:12
Alignment explanation
Indices: 25294310--25294351 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
25294300 GAGAAGAAAA
25294310 AAGTAAATAAGT
1 AAGTAAATAAGT
* **
25294322 AAGTAAAGAAAA
1 AAGTAAATAAGT
25294334 AAGTAAATAAGT
1 AAGTAAATAAGT
25294346 AAGTAA
1 AAGTAA
25294352 TAATAATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (12 bp):
AAGTAAATAAGT
Found at i:25294330 original size:24 final size:24
Alignment explanation
Indices: 25294303--25294351 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
25294293 TTCCTAAGAG
25294303 AAGAAAAAAGTAAATAAGTAAGTA
1 AAGAAAAAAGTAAATAAGTAAGTA
25294327 AAGAAAAAAGTAAATAAGTAAGTA
1 AAGAAAAAAGTAAATAAGTAAGTA
25294351 A
1 A
25294352 TAATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.16
Consensus pattern (24 bp):
AAGAAAAAAGTAAATAAGTAAGTA
Found at i:25297988 original size:17 final size:19
Alignment explanation
Indices: 25297966--25298004 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
25297956 AATCAACCGA
*
25297966 CTCATAC-ACTTGAT-AAT
1 CTCATACGACCTGATGAAT
25297983 CTCATACGACCTGATGAAT
1 CTCATACGACCTGATGAAT
25298002 CTC
1 CTC
25298005 GGACTTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (19 bp):
CTCATACGACCTGATGAAT
Found at i:25333564 original size:22 final size:23
Alignment explanation
Indices: 25333517--25333564 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
25333507 TGAATTGTGT
*
25333517 TTAT-TTATATGATTGTATTGAA
1 TTATGTTATATGATTGTATCGAA
*
25333539 -TATGTTATGTGATTGTA-CGAA
1 TTATGTTATATGATTGTATCGAA
25333560 TTATG
1 TTATG
25333565 AATGTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (23 bp):
TTATGTTATATGATTGTATCGAA
Found at i:25335697 original size:25 final size:24
Alignment explanation
Indices: 25335656--25335734 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
25335646 CCTGTAAATT
25335656 GGTAAGCTT-ATACGAGCTGAGAATC
1 GGTAAGCTTCAT--GAGCTGAGAATC
*
25335681 GGTAAGCTCTCATGAGCTG-CAATC
1 GGTAAGCT-TCATGAGCTGAGAATC
* * *
25335705 AGTAAGCTTATATGAGCTGAGAATT
1 GGTAAGCTT-CATGAGCTGAGAATC
25335730 GGTAA
1 GGTAA
25335735 TCCCTAATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.02
24 19 0.43
25 21 0.48
26 1 0.02
27 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (24 bp):
GGTAAGCTTCATGAGCTGAGAATC
Found at i:25335719 original size:24 final size:25
Alignment explanation
Indices: 25335657--25335724 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
25335647 CTGTAAATTG
* * *
25335657 GTAAGCTTATACGAGCTGAGAATCG
1 GTAAGCTTATATGAGCTGACAATCA
*
25335682 GTAAGCTCT-CATGAGCTG-CAATCA
1 GTAAGCT-TATATGAGCTGACAATCA
25335706 GTAAGCTTATATGAGCTGA
1 GTAAGCTTATATGAGCTGA
25335725 GAATTGGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.03
24 19 0.54
25 14 0.40
26 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (25 bp):
GTAAGCTTATATGAGCTGACAATCA
Found at i:25337423 original size:30 final size:30
Alignment explanation
Indices: 25337380--25337484 Score: 131
Period size: 30 Copynumber: 3.5 Consensus size: 30
25337370 GGATATTGAT
*
25337380 TATGTAAAGGGATGGTGACGACCATCAAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
* * * *
25337410 TATGAAAAAGGATGGTGACAACCACCGAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
* *
25337440 TATGAAAAGGGATGGCT-TCGACTATCAAAC
1 TATGAAAAGGGATGG-TGACGACCATCAAAC
25337470 TATGAAAAGGGATGG
1 TATGAAAAGGGATGG
25337485 CTTCGGCTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 62 0.98
31 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (30 bp):
TATGAAAAGGGATGGTGACGACCATCAAAC
Found at i:25337485 original size:30 final size:30
Alignment explanation
Indices: 25337437--25337602 Score: 179
Period size: 30 Copynumber: 5.5 Consensus size: 30
25337427 ACAACCACCG
*
25337437 AACTATGAAAAGGGATGGCTTCGACTATCA
1 AACTATGAAAAGGGATGGCTTCGGCTATCA
25337467 AACTATGAAAAGGGATGGCTTCGGCTATCA
1 AACTATGAAAAGGGATGGCTTCGGCTATCA
* * * *
25337497 ATCTATGAAAAGGAATGACTTAGGCTATCA
1 AACTATGAAAAGGGATGGCTTCGGCTATCA
** * ***
25337527 ATTTATGAAAAGAGATATTTTCGGCTATCA
1 AACTATGAAAAGGGATGGCTTCGGCTATCA
* * * * * *
25337557 GATTATGAAAAGGGATAGCTTTGGCTGTCG
1 AACTATGAAAAGGGATGGCTTCGGCTATCA
25337587 AACTATGAAAAGGGAT
1 AACTATGAAAAGGGAT
25337603 AACTTTGGTT
Statistics
Matches: 114, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 114 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (30 bp):
AACTATGAAAAGGGATGGCTTCGGCTATCA
Found at i:25337503 original size:60 final size:59
Alignment explanation
Indices: 25337440--25337633 Score: 199
Period size: 60 Copynumber: 3.2 Consensus size: 59
25337430 ACCACCGAAC
* * **
25337440 TATGAAAAGGGATGGCTTCGACTATCAAACTATGAAAAGGGATGGCTTCGGCTATCAAT
1 TATGAAAAGGGATGGCTTAGGCTATCAAACTATGAAAAGGGATAACTTCGGCTATCAAT
* * ** * **
25337499 CTATGAAAAGGAATGACTTAGGCTATCAATTTATGAAAAGAGATATTTTCGGCTATCAGAT
1 -TATGAAAAGGGATGGCTTAGGCTATCAAACTATGAAAAGGGATAACTTCGGCTATCA-AT
* * * * * *
25337560 TATGAAAAGGGATAGCTTTGGCTGTCGAACTATGAAAAGGGATAACTTTGGTTATCGAAT
1 TATGAAAAGGGATGGCTTAGGCTATCAAACTATGAAAAGGGATAACTTCGGCTATC-AAT
*
25337620 TAAGAAAAGGGATG
1 TATGAAAAGGGATG
25337634 TGTCAACCAT
Statistics
Matches: 107, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
60 104 0.97
61 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (59 bp):
TATGAAAAGGGATGGCTTAGGCTATCAAACTATGAAAAGGGATAACTTCGGCTATCAAT
Found at i:25337534 original size:90 final size:90
Alignment explanation
Indices: 25337435--25337633 Score: 222
Period size: 90 Copynumber: 2.2 Consensus size: 90
25337425 TGACAACCAC
* *
25337435 CGAACTATGAAAAGGGATGGCTTCGACTATCAAACTATGAAAAGGGATGGCTTCGGCTATC-AAT
1 CGAATTATGAAAAGGGATGGCTTCGACTATCAAACTATGAAAAGGGATAGCTTCGGCTATCGAA-
*
25337499 CTATGAAAAGGAATGACTTAGGCTAT
65 CTATGAAAAGGAATAACTTAGGCTAT
* *** * * * * *
25337525 C-AATTTATGAAAAGAGATATTTTCGGCTATCAGATTATGAAAAGGGATAGCTTTGGCTGTCGAA
1 CGAA-TTATGAAAAGGGATGGCTTCGACTATCAAACTATGAAAAGGGATAGCTTCGGCTATCGAA
* * *
25337589 CTATGAAAAGGGATAACTTTGGTTAT
65 CTATGAAAAGGAATAACTTAGGCTAT
*
25337615 CGAATTAAGAAAAGGGATG
1 CGAATTATGAAAAGGGATG
25337634 TGTCAACCAT
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
89 2 0.02
90 82 0.93
91 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (90 bp):
CGAATTATGAAAAGGGATGGCTTCGACTATCAAACTATGAAAAGGGATAGCTTCGGCTATCGAAC
TATGAAAAGGAATAACTTAGGCTAT
Found at i:25337603 original size:30 final size:29
Alignment explanation
Indices: 25337437--25337632 Score: 162
Period size: 30 Copynumber: 6.6 Consensus size: 29
25337427 ACAACCACCG
* * *
25337437 AACTATGAAAAGGGATGGCTTCGACTATC
1 AACTATGAAAAGGGATAGCTTTGGCTATC
* *
25337466 AAACTATGAAAAGGGATGGCTTCGGCTATC
1 -AACTATGAAAAGGGATAGCTTTGGCTATC
* *
25337496 AATCTATGAAAAGGAAT-GACTTAGGCTATC
1 AA-CTATGAAAAGGGATAG-CTTTGGCTATC
* * *
25337526 AATTTATGAAAAGAGATA-TTTTCGGCTATC
1 AA-CTATGAAAAGGGATAGCTTT-GGCTATC
* *
25337556 AGATTATGAAAAGGGATAGCTTTGGCTGTC
1 A-ACTATGAAAAGGGATAGCTTTGGCTATC
* *
25337586 GAACTATGAAAAGGGATAACTTTGGTTATC
1 -AACTATGAAAAGGGATAGCTTTGGCTATC
* *
25337616 GAATTAAGAAAAGGGAT
1 -AACTATGAAAAGGGAT
25337633 GTGTCAACCA
Statistics
Matches: 142, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.04
30 132 0.93
31 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (29 bp):
AACTATGAAAAGGGATAGCTTTGGCTATC
Found at i:25338783 original size:31 final size:31
Alignment explanation
Indices: 25338741--25338819 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
25338731 TTTAACGATT
*
25338741 ACTGGGTCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
25338772 ACTGGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
25338803 ATTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
25338820 ACTATAAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:25338911 original size:101 final size:101
Alignment explanation
Indices: 25338793--25338989 Score: 394
Period size: 101 Copynumber: 2.0 Consensus size: 101
25338783 GCCTTATCAT
25338793 AAATCATATCATTGGGCCGAAGCCTTTACTATAAACGGTATGGCCCTTAGGCCCATTTCAATATC
1 AAATCATATCATTGGGCCGAAGCCTTTACTATAAACGGTATGGCCCTTAGGCCCATTTCAATATC
25338858 ACATGTAATGTCAATGGATGTATGCAAGCCCTTCAC
66 ACATGTAATGTCAATGGATGTATGCAAGCCCTTCAC
25338894 AAATCATATCATTGGGCCGAAGCCTTTACTATAAACGGTATGGCCCTTAGGCCCATTTCAATATC
1 AAATCATATCATTGGGCCGAAGCCTTTACTATAAACGGTATGGCCCTTAGGCCCATTTCAATATC
25338959 ACATGTAATGTCAATGGATGTATGCAAGCCC
66 ACATGTAATGTCAATGGATGTATGCAAGCCC
25338990 ATTTGGGGAG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (101 bp):
AAATCATATCATTGGGCCGAAGCCTTTACTATAAACGGTATGGCCCTTAGGCCCATTTCAATATC
ACATGTAATGTCAATGGATGTATGCAAGCCCTTCAC
Found at i:25339153 original size:24 final size:23
Alignment explanation
Indices: 25339126--25339233 Score: 126
Period size: 25 Copynumber: 4.4 Consensus size: 23
25339116 CTGGAGGCCT
*
25339126 AGCCTCTTTTATTAACTGGGGCAA
1 AGCC-CTTTTATAAACTGGGGCAA
25339150 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTT-ATAAACTGGGGCAA
25339174 AGCCCTTTTAGGTAAACTGGGGCAA
1 AGCCCTTTTA--TAAACTGGGGCAA
* *
25339199 AGCCCTTTTGGGTAAACTGGGGCAT
1 AGCCCTTTT--ATAAACTGGGGCAA
*
25339224 ACCCCTTTTA
1 AGCCCTTTTA
25339234 GCACTTCCTC
Statistics
Matches: 74, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.08
24 26 0.35
25 42 0.57
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (23 bp):
AGCCCTTTTATAAACTGGGGCAA
Found at i:25339195 original size:25 final size:25
Alignment explanation
Indices: 25339139--25339234 Score: 149
Period size: 25 Copynumber: 3.9 Consensus size: 25
25339129 CTCTTTTATT
*
25339139 AACTGGGGCAAAGCCCTTTT-GATA
1 AACTGGGGCAAAGCCCTTTTAGGTA
25339163 AACTGGGGCAAAGCCCTTTTAGGTA
1 AACTGGGGCAAAGCCCTTTTAGGTA
*
25339188 AACTGGGGCAAAGCCCTTTTGGGTA
1 AACTGGGGCAAAGCCCTTTTAGGTA
* *
25339213 AACTGGGGCATACCCCTTTTAG
1 AACTGGGGCAAAGCCCTTTTAG
25339235 CACTTCCTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
24 20 0.30
25 46 0.70
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTAGGTA
Found at i:25340188 original size:27 final size:27
Alignment explanation
Indices: 25340135--25340494 Score: 242
Period size: 27 Copynumber: 13.3 Consensus size: 27
25340125 TTTCACCCTA
* * * * *
25340135 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
** * *
25340162 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
* ** *
25340189 CAATGGTATTTTTATAATTTTTAGAAAGT
1 CAAGGGTATTTTGGTAA-TTTTATAAA-T
25340218 CAAGGGTATTTCT-GTAATTTTATAAAT
1 CAAGGGTATTT-TGGTAATTTTATAAAT
* *
25340245 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
** * * *
25340272 TGAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
25340298 CTAGCGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTGGTAATTTTATAAAT
* * *
25340325 CTAGGGGTATTTTGGTAATTTTACAAAC
1 C-AAGGGTATTTTGGTAATTTTATAAAT
* * * *
25340353 CAGGGGTATTTTAGCAATTTTATAGA-
1 CAAGGGTATTTTGGTAATTTTATAAAT
* * **
25340379 CTAGGGTTTTTTGGTAATTTTATTGAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* * *
25340406 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
25340433 CAAGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* ***** *
25340460 CGAGGGTAAAACAGTAATTCTATAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
25340487 CAAGGGTA
1 CAAGGGTA
25340495 AAACAGTAAT
Statistics
Matches: 268, Mismatches: 57, Indels: 16
0.79 0.17 0.05
Matches are distributed among these distances:
26 23 0.09
27 214 0.80
28 17 0.06
29 13 0.05
30 1 0.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTATAAAT
Found at i:25340495 original size:27 final size:27
Alignment explanation
Indices: 25340445--25340575 Score: 183
Period size: 27 Copynumber: 4.9 Consensus size: 27
25340435 AGGGTATTTT
* *
25340445 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
25340472 AGTAATTCTATAAATCAAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
25340499 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
* *
25340526 -GACAATTCTGTAAATCGAGGGTAAAAC
1 AG-TAATTCTATAAATCGAGGGTAAAAC
* *
25340553 GGTAATTCTATAAATCGATGGTA
1 AGTAATTCTATAAATCGAGGGTA
25340576 CTTTGGTAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.01
27 91 0.98
28 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (27 bp):
AGTAATTCTATAAATCGAGGGTAAAAC
Found at i:25361972 original size:81 final size:81
Alignment explanation
Indices: 25361837--25361987 Score: 302
Period size: 81 Copynumber: 1.9 Consensus size: 81
25361827 TGGAATGTAG
25361837 TGCGCAAAAAGGTGTGTAACCACACCCTTCCTTACTGTAGATCGGCAAAAGCCGAAAACTCGAAG
1 TGCGCAAAAAGGTGTGTAACCACACCCTTCCTTACTGTAGATCGGCAAAAGCCGAAAACTCGAAG
25361902 TGCTGGTTCACTTGAT
66 TGCTGGTTCACTTGAT
25361918 TGCGCAAAAAGGTGTGTAACCACACCCTTCCTTACTGTAGATCGGCAAAAGCCGAAAACTCGAAG
1 TGCGCAAAAAGGTGTGTAACCACACCCTTCCTTACTGTAGATCGGCAAAAGCCGAAAACTCGAAG
25361983 TGCTG
66 TGCTG
25361988 AAGCTTCAGC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (81 bp):
TGCGCAAAAAGGTGTGTAACCACACCCTTCCTTACTGTAGATCGGCAAAAGCCGAAAACTCGAAG
TGCTGGTTCACTTGAT
Found at i:25362450 original size:27 final size:27
Alignment explanation
Indices: 25362387--25362453 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
25362377 ACCCCAAAAT
*
25362387 GGGTAAAATAACCATAATACCCCTATA
1 GGGTAAAATGACCATAATACCCCTATA
*
25362414 GGGTAAAATGACCATAATGCCCCTATA
1 GGGTAAAATGACCATAATACCCCTATA
25362441 GGGTAAAATGACC
1 GGGTAAAATGACC
25362454 GTGATACCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (27 bp):
GGGTAAAATGACCATAATACCCCTATA
Found at i:25362660 original size:27 final size:26
Alignment explanation
Indices: 25362630--25362723 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 26
25362620 GTACTAATGA
*
25362630 CTATGTCACATTCACTGTTACTGGTGG
1 CTATGCCACATT-ACTGTTACTGGTGG
*
25362657 CTATGCCACAATTACTGATACTGGTGG
1 CTATGCCAC-ATTACTGTTACTGGTGG
* * **
25362684 CTTTGCCACATTTACTGTTTCTGGCAG
1 CTATGCCACA-TTACTGTTACTGGTGG
*
25362711 CTATGCTACATTA
1 CTATGCCACATTA
25362724 TTATTGCTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
26 4 0.07
27 49 0.88
28 3 0.05
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (26 bp):
CTATGCCACATTACTGTTACTGGTGG
Found at i:25362917 original size:28 final size:28
Alignment explanation
Indices: 25362866--25362956 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
25362856 GCACTGATAT
* * * *
25362866 TGTATTGGGCTTAGGCTCACACTGTTAC
1 TGTATAGGGCTAAGGCCCAGACTGTTAC
25362894 TGTATAGGGCTAAGGCCCAGACTGTACTGATAC
1 TGTATAGGGCTAAGGCCCAGACTG---T--TAC
* * *
25362927 TGAATAGGGCTCAGGCCCAGACTGCTAC
1 TGTATAGGGCTAAGGCCCAGACTGTTAC
25362955 TG
1 TG
25362957 CATGCACTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
28 25 0.49
31 1 0.02
33 25 0.49
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (28 bp):
TGTATAGGGCTAAGGCCCAGACTGTTAC
Found at i:25362934 original size:33 final size:34
Alignment explanation
Indices: 25362886--25362956 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
25362876 TTAGGCTCAC
* *
25362886 ACTGTTACTGTATAGGGCTAAGGCCCAGACTG-T
1 ACTGATACTGAATAGGGCTAAGGCCCAGACTGCT
*
25362919 ACTGATACTGAATAGGGCTCAGGCCCAGACTGCT
1 ACTGATACTGAATAGGGCTAAGGCCCAGACTGCT
25362953 ACTG
1 ACTG
25362957 CATGCACTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 29 0.85
34 5 0.15
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (34 bp):
ACTGATACTGAATAGGGCTAAGGCCCAGACTGCT
Found at i:25366340 original size:125 final size:125
Alignment explanation
Indices: 25366118--25366601 Score: 846
Period size: 125 Copynumber: 3.9 Consensus size: 125
25366108 AGCAAATGTG
* *
25366118 AGTTTTGGCTCTGAGAAGTTGGTTTTCTAGGACATATAGTATCGGCTGATGGCATTAGAGTTGAT
1 AGTTTTGGCTCTGAGAAGTTGGTTTTCTAGGACATATAGTATCGGCTGATGGCATCAAAGTTGAT
25366183 CCAAGTAAAATTTCAACAGTT-TGTGACTGGAAACCACTGAGAAATGTATCTGAAGTTAGA
66 CCAAGTAAAATTTCAACAGTTGT-TGACTGGAAACCACTGAGAAATGTATCTGAAGTTAGA
* *
25366243 AGTTTTGGCTCTGAGAAGTTGGTTTTCTAGGACATATAGTATCGGCTGATGGCATTAGAGTTGAT
1 AGTTTTGGCTCTGAGAAGTTGGTTTTCTAGGACATATAGTATCGGCTGATGGCATCAAAGTTGAT
25366308 CCAAGTAAAATTTCAACAGTT-TGTGACTGGAAACCACTGAGAAATGTATCTGAAGTTAGA
66 CCAAGTAAAATTTCAACAGTTGT-TGACTGGAAACCACTGAGAAATGTATCTGAAGTTAGA
* **
25366368 AGTTTTGGCTCTGAGAAGTTGGTTTTCTGGGACATATAGTATCGGCTGATGTTATCAAAGTTGAT
1 AGTTTTGGCTCTGAGAAGTTGGTTTTCTAGGACATATAGTATCGGCTGATGGCATCAAAGTTGAT
25366433 CCAAGTAAAATTTCAACAGTTGTTGACTGGAAACCACTGAGAAATGTATCTGAAGTTAGA
66 CCAAGTAAAATTTCAACAGTTGTTGACTGGAAACCACTGAGAAATGTATCTGAAGTTAGA
* **
25366493 AGTTTTGGCTCTGAGAAGTTGGTTTTCTGGGACATATAGTATCGGCTGATGTTATCAAAGTTGAT
1 AGTTTTGGCTCTGAGAAGTTGGTTTTCTAGGACATATAGTATCGGCTGATGGCATCAAAGTTGAT
25366558 CCAAGTAAAATTTCAACAGTTGTTGACTGGAAACCACTGAGAAA
66 CCAAGTAAAATTTCAACAGTTGTTGACTGGAAACCACTGAGAAA
25366602 GATGTGATAT
Statistics
Matches: 353, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
125 352 1.00
126 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.32
Consensus pattern (125 bp):
AGTTTTGGCTCTGAGAAGTTGGTTTTCTAGGACATATAGTATCGGCTGATGGCATCAAAGTTGAT
CCAAGTAAAATTTCAACAGTTGTTGACTGGAAACCACTGAGAAATGTATCTGAAGTTAGA
Found at i:25367779 original size:13 final size:13
Alignment explanation
Indices: 25367761--25367790 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25367751 GCTCAGCAGG
25367761 GACACGACCGTGT
1 GACACGACCGTGT
*
25367774 GACACGGCCGTGT
1 GACACGACCGTGT
25367787 GACA
1 GACA
25367791 TGATTGCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.33, T:0.13
Consensus pattern (13 bp):
GACACGACCGTGT
Found at i:25368801 original size:24 final size:24
Alignment explanation
Indices: 25368769--25368815 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
25368759 ATGTACAATG
**
25368769 ATTAGAATTTGAAGGCAGTTGGGT
1 ATTAGAATTCAAAGGCAGTTGGGT
25368793 ATTAGAATTCAAAGGCAGTTGGG
1 ATTAGAATTCAAAGGCAGTTGGG
25368816 AGAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.30
Consensus pattern (24 bp):
ATTAGAATTCAAAGGCAGTTGGGT
Found at i:25375049 original size:56 final size:56
Alignment explanation
Indices: 25374958--25375080 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
25374948 GAGATTGGCG
* * *
25374958 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
25375015 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
25375070 CTGAGTGTGCG
1 CTAAGTGTGCG
25375081 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:25375067 original size:27 final size:28
Alignment explanation
Indices: 25374958--25375080 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
25374948 GAGATTGGCG
* * * *
25374958 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
25374987 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
25375015 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
25375043 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
25375070 CTGAGTGTGCG
1 CTAAGTGTGCG
25375081 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:25375091 original size:27 final size:27
Alignment explanation
Indices: 25374983--25375093 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
25374973 TAAATTGTAC
* * *
25374983 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
25375011 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
25375039 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
25375066 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
25375093 A
1 A
25375094 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:25383233 original size:16 final size:16
Alignment explanation
Indices: 25383212--25383245 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
25383202 ACCAATGACT
25383212 ATTGAAAGCTGCTAAC
1 ATTGAAAGCTGCTAAC
25383228 ATTGAAAGCTGCTAAC
1 ATTGAAAGCTGCTAAC
25383244 AT
1 AT
25383246 ATATGAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (16 bp):
ATTGAAAGCTGCTAAC
Found at i:25383476 original size:8 final size:7
Alignment explanation
Indices: 25383438--25383474 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
25383428 CTGAGTATAG
25383438 TAGGGTT
1 TAGGGTT
25383445 TAGGGTT
1 TAGGGTT
*
25383452 TAAGGTT
1 TAGGGTT
25383459 TAGGGTTT
1 TAGGG-TT
25383467 TAGGGTT
1 TAGGGTT
25383474 T
1 T
25383475 TAAGGTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
TAGGGTT
Found at i:25384972 original size:33 final size:33
Alignment explanation
Indices: 25384926--25384993 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
25384916 AAACCCTTAG
25384926 AGAGAGAAAAAACTTTCATGGCCAAATTGGGTA
1 AGAGAGAAAAAACTTTCATGGCCAAATTGGGTA
* *
25384959 AGAGAGAAGAAACTTTCATGGCCAATTTGGGTA
1 AGAGAGAAAAAACTTTCATGGCCAAATTGGGTA
25384992 AG
1 AG
25384994 TTTCCTTGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (33 bp):
AGAGAGAAAAAACTTTCATGGCCAAATTGGGTA
Found at i:25388310 original size:35 final size:35
Alignment explanation
Indices: 25388241--25388310 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
25388231 AGACCAAGGA
* * *
25388241 AGAACCAATACTATAGATAGTATTGACTTGAACCT
1 AGAACCAATACTATAGAAAGTATTGACCTAAACCT
*
25388276 AGAACCAATACTATTGAAAGTATTGACCTAAACCT
1 AGAACCAATACTATAGAAAGTATTGACCTAAACCT
25388311 TATACGACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (35 bp):
AGAACCAATACTATAGAAAGTATTGACCTAAACCT
Found at i:25390047 original size:44 final size:42
Alignment explanation
Indices: 25389968--25390071 Score: 104
Period size: 43 Copynumber: 2.4 Consensus size: 42
25389958 TGGCTGTGTA
* * *
25389968 AATGGCACTATGTGTGCGATACCAATATAAGTTCGGTTTAATGC
1 AATGGCACTAAGTGTGCAATACCAATATAAGTTCGG-CTAAT-C
* *
25390012 AATGGCACTAAGTGTGCAATA-TAAT-TATAGCTTCGGCTAATT
1 AATGGCACTAAGTGTGCAATACCAATATA-AG-TTCGGCTAATC
25390054 AATTGGCACTAAGTGTGC
1 AA-TGGCACTAAGTGTGC
25390072 TAGTTCGTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 4 0.08
43 24 0.46
44 24 0.46
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (42 bp):
AATGGCACTAAGTGTGCAATACCAATATAAGTTCGGCTAATC
Found at i:25394780 original size:54 final size:54
Alignment explanation
Indices: 25394722--25394886 Score: 206
Period size: 54 Copynumber: 3.2 Consensus size: 54
25394712 CAACACTTGA
25394722 TTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
1 TTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
** **
25394776 TTCTTGCTCAC-ATGCTCTTTCAATC-TCAA----TCTCT-TTTT-C-ATTTT-GA
1 TTCTTGCTCACTAT-CT-TTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
25394822 TTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
1 TTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
25394876 TTCTTGCTCAC
1 TTCTTGCTCAC
25394887 ATGCTCTTTC
Statistics
Matches: 91, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
45 6 0.07
46 17 0.19
47 7 0.08
48 1 0.01
49 4 0.04
50 10 0.11
51 4 0.04
52 1 0.01
53 7 0.08
54 28 0.31
55 6 0.07
ACGTcount: A:0.13, C:0.28, G:0.04, T:0.56
Consensus pattern (54 bp):
TTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
Found at i:25394831 original size:100 final size:100
Alignment explanation
Indices: 25394718--25394918 Score: 402
Period size: 100 Copynumber: 2.0 Consensus size: 100
25394708 TTAACAACAC
25394718 TTGATTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTTTTCTTGC
1 TTGATTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTTTTCTTGC
25394783 TCACATGCTCTTTCAATCTCAATCTCTTTTTCATT
66 TCACATGCTCTTTCAATCTCAATCTCTTTTTCATT
25394818 TTGATTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTTTTCTTGC
1 TTGATTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTTTTCTTGC
25394883 TCACATGCTCTTTCAATCTCAATCTCTTTTTCATT
66 TCACATGCTCTTTCAATCTCAATCTCTTTTTCATT
25394918 T
1 T
25394919 CTTTCATTCT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.14, C:0.27, G:0.04, T:0.55
Consensus pattern (100 bp):
TTGATTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTTTTCTTGC
TCACATGCTCTTTCAATCTCAATCTCTTTTTCATT
Found at i:25394905 original size:54 final size:54
Alignment explanation
Indices: 25394722--25394907 Score: 198
Period size: 54 Copynumber: 3.6 Consensus size: 54
25394712 CAACACTTGA
**
25394722 TTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
1 TTCTTGCTCACTATCTTTTCAATCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
**
25394776 TTCTTGCTCAC-ATGCTCTTTCAATC-TCAA----TCTCT-TTTT-C-ATTTT-GA
1 TTCTTGCTCACTAT-CT-TTTCAATCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
**
25394822 TTCTTGCTCACTATCTTTTCTTTCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
1 TTCTTGCTCACTATCTTTTCAATCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
25394876 TTCTTGCTCAC-ATGCTCTTTCAATC-TCAATCT
1 TTCTTGCTCACTAT-CT-TTTCAATCTTCAATCT
25394908 CTTTTTCATT
Statistics
Matches: 108, Mismatches: 10, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
45 6 0.06
46 17 0.16
47 7 0.06
48 1 0.01
49 4 0.04
50 10 0.09
51 4 0.04
52 1 0.01
53 9 0.08
54 37 0.34
55 12 0.11
ACGTcount: A:0.14, C:0.28, G:0.04, T:0.54
Consensus pattern (54 bp):
TTCTTGCTCACTATCTTTTCAATCTTCAATCTTTCTCTCTTTTCCAATTTTCTT
Found at i:25394929 original size:27 final size:28
Alignment explanation
Indices: 25394891--25394949 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
25394881 GCTCACATGC
25394891 TCTTTCAATCTCAATCTCTTTTTC-ATT
1 TCTTTCAATCTCAATCTCTTTTTCGATT
* ** *
25394918 TCTTTCATTCTCTTTTTCTTTTTCGATT
1 TCTTTCAATCTCAATCTCTTTTTCGATT
25394946 TCTT
1 TCTT
25394950 CTAGTATTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.12, C:0.24, G:0.02, T:0.63
Consensus pattern (28 bp):
TCTTTCAATCTCAATCTCTTTTTCGATT
Found at i:25396366 original size:40 final size:40
Alignment explanation
Indices: 25396322--25396583 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
25396312 GCTCCTCGTT
* *
25396322 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
25396362 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
25396402 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
25396441 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
25396480 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
25396519 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
25396560 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
25396584 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:25407473 original size:20 final size:21
Alignment explanation
Indices: 25407448--25407487 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25407438 TAGACTGAAA
25407448 AAACTA-ATTGTTGTTAATTT
1 AAACTACATTGTTGTTAATTT
* *
25407468 AAACTACTTTTTTGTTAATT
1 AAACTACATTGTTGTTAATT
25407488 ACTTGGATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
AAACTACATTGTTGTTAATTT
Found at i:25409739 original size:30 final size:31
Alignment explanation
Indices: 25409689--25409757 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 31
25409679 AATCATTTGG
*
25409689 AAATGAATGTAGGTTTCCAAAAAAGAAAATGA
1 AAATGAA-GTAGGATTCCAAAAAAGAAAATGA
*
25409721 AAATGAA-TAGGATTCCAAAAATGAAAATGA
1 AAATGAAGTAGGATTCCAAAAAAGAAAATGA
25409751 AAATGAA
1 AAATGAA
25409758 AATTAAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 28 0.80
32 7 0.20
ACGTcount: A:0.57, C:0.06, G:0.17, T:0.20
Consensus pattern (31 bp):
AAATGAAGTAGGATTCCAAAAAAGAAAATGA
Found at i:25412224 original size:13 final size:15
Alignment explanation
Indices: 25412198--25412230 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
25412188 TCTAGTTATG
25412198 ATTTTTTGTCTTTTC
1 ATTTTTTGTCTTTTC
25412213 ATTTTTT-T-TTTTC
1 ATTTTTTGTCTTTTC
25412226 ATTTT
1 ATTTT
25412231 AGATTGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 1 0.06
15 7 0.39
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (15 bp):
ATTTTTTGTCTTTTC
Found at i:25414421 original size:38 final size:38
Alignment explanation
Indices: 25414379--25414454 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
25414369 TATGGTTTGT
*
25414379 AAATAAGAACTGTGCTAATCAATTGTAGGACATCGGAA
1 AAATAAGAACTATGCTAATCAATTGTAGGACATCGGAA
25414417 AAATAAGAACTATGCTAATCAATTGTAGGACATCGGAA
1 AAATAAGAACTATGCTAATCAATTGTAGGACATCGGAA
25414455 GAGATCTCAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (38 bp):
AAATAAGAACTATGCTAATCAATTGTAGGACATCGGAA
Found at i:25419654 original size:39 final size:39
Alignment explanation
Indices: 25419606--25419682 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
25419596 ACGTATAATT
25419606 CTTAAACAATATCATAACATATAAAAATAGGTATGTACC
1 CTTAAACAATATCATAACATATAAAAATAGGTATGTACC
*
25419645 CTTAAACAATATTATAACATATAAAAATAGGTATGTAC
1 CTTAAACAATATCATAACATATAAAAATAGGTATGTAC
25419683 ACATTAATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (39 bp):
CTTAAACAATATCATAACATATAAAAATAGGTATGTACC
Found at i:25430325 original size:35 final size:34
Alignment explanation
Indices: 25430274--25430342 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 34
25430264 CGTATCATCA
25430274 TTCCCAACCTTCCTGGGTTCATCCAACACTCTTT
1 TTCCCAACCTTCCTGGGTTCATCCAACACTCTTT
* *
25430308 NTTCCCAACCTTTCTGGGTTCATCCAACTCTCTTT
1 -TTCCCAACCTTCCTGGGTTCATCCAACACTCTTT
25430343 CCATCAAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.16, C:0.36, G:0.09, T:0.38
Consensus pattern (34 bp):
TTCCCAACCTTCCTGGGTTCATCCAACACTCTTT
Found at i:25434244 original size:12 final size:13
Alignment explanation
Indices: 25434215--25434247 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
25434205 CAATATTCAA
25434215 TAAAATATCATCTT
1 TAAAATATCA-CTT
25434229 TAAAATATCA-TT
1 TAAAATATCACTT
25434241 TAAAATA
1 TAAAATA
25434248 ATACCCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
14 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAAATATCACTT
Found at i:25437780 original size:137 final size:137
Alignment explanation
Indices: 25437534--25437820 Score: 502
Period size: 137 Copynumber: 2.1 Consensus size: 137
25437524 TATTGGGCCT
** * *
25437534 AAGCCCATTCAGGTAACAGTGATACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCATT
1 AAGCCCATTTGGGTAACAGTGATACTGGACCAGAGCCCTTTTCAGATTACAATAAACAGGGCATT
25437599 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
25437664 CATATGC
131 CATATGC
* * *
25437671 AAGCCCATTTGGGTAACGGTGGTACTGGACCAGAGCCCTTTTCAGATTACAATAAACAGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGACCAGAGCCCTTTTCAGATTACAATAAACAGGGCATT
25437736 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
*
25437801 TATATGC
131 CATATGC
25437808 AAGCCCATTTGGG
1 AAGCCCATTTGGG
25437821 GATACTACTC
Statistics
Matches: 142, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
137 142 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGATACTGGACCAGAGCCCTTTTCAGATTACAATAAACAGGGCATT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:25438105 original size:25 final size:27
Alignment explanation
Indices: 25438068--25438121 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
25438058 TCAAACATGC
25438068 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
25438094 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
25438120 AT
1 AT
25438122 AATAGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:25438129 original size:26 final size:27
Alignment explanation
Indices: 25438100--25438160 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
25438090 GGGTATTTCG
* * *
25438100 GTAATTTTGC-ACCTAGGGGTATAATA
1 GTAATTTTCCAACATAGGGCTATAATA
*
25438126 GTAATTTTCCATACATAGGGCTATTATA
1 GTAATTTTCCA-ACATAGGGCTATAATA
25438154 GTAATTT
1 GTAATTT
25438161 AGCTGCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 9 0.31
28 20 0.69
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.39
Consensus pattern (27 bp):
GTAATTTTCCAACATAGGGCTATAATA
Found at i:25439642 original size:26 final size:26
Alignment explanation
Indices: 25439606--25439689 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
25439596 CATGAAATTC
*
25439606 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
25439632 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
25439658 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
25439684 TTATCA
1 TTATCA
25439690 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:25441972 original size:5 final size:5
Alignment explanation
Indices: 25441962--25441989 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
25441952 CCAATTTGTA
25441962 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
25441990 GAACACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:25444440 original size:31 final size:29
Alignment explanation
Indices: 25444386--25444456 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 29
25444376 CGATTTTTGC
*
25444386 TTCTTATTTTATTGCTATATTCATATTCA
1 TTCTTATTTTATTGATATATTCATATTCA
*
25444415 TTCTTATTTTGTTGATAGATATTCATATTCA
1 TTCTTATTTTATTGAT--ATATTCATATTCA
25444446 TT-TTACTTTTA
1 TTCTTA-TTTTA
25444457 AGTTTTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 14 0.39
30 3 0.08
31 19 0.53
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.59
Consensus pattern (29 bp):
TTCTTATTTTATTGATATATTCATATTCA
Found at i:25448392 original size:138 final size:138
Alignment explanation
Indices: 25448140--25448508 Score: 513
Period size: 138 Copynumber: 2.6 Consensus size: 138
25448130 TTTGACATGA
* * * * *
25448140 TGCCATAGTTTCTTTCAACTATGGTCTTACTCATTCATTTTCTGTCATGTTGCCATGGTATCTTT
1 TGCCATGGTATCTTTCAACCATGGTC-T--T-ATTCATTTTATGTCACGTTGCCATGGTATCTTT
* * * **
25448205 CAACCATGGTCTTATTCTTTTCATGTCACGTTGCTATGGTATCTTTCAACCATGGTCTTATTCAT
62 CAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
25448270 TTCATATCAGGT
127 TTCATATCAGGT
*
25448282 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTTATGTCACGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTATGTCACGTTGCCATGGTATCTTTCAAC
25448347 CATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
66 CATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
25448412 TATCAGGT
131 TATCAGGT
* * ** * * * *
25448420 TGCCATGATATCTTTCAACCATGATCTTACACATTTCATATCAGGTTGCCGTGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTATGTCACGTTGCCATGGTATCTTTCAAC
**
25448485 CATGGTCTTACACATTTCATATCA
66 CATGGTCTTATTCATTTCATATCA
25448509 GAGAGCACAC
Statistics
Matches: 205, Mismatches: 22, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
138 180 0.88
139 1 0.00
141 1 0.00
142 23 0.11
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (138 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTATGTCACGTTGCCATGGTATCTTTCAAC
CATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
TATCAGGT
Done.