Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 38
Found at i:1329383 original size:28 final size:28
Alignment explanation
Indices: 1329352--1329419 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
1329342 ATATAATTTA
* *
1329352 AATTAATTATATTTTTTATCAAAAAAAT
1 AATTAATTATATTATTTACCAAAAAAAT
* *
1329380 AATTTAAATTA-A-TATTTACCAATAAATT
1 AA-TT-AATTATATTATTTACCAAAAAAAT
1329408 AATTAATTATAT
1 AATTAATTATAT
1329420 AAAAGGAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
26 5 0.16
27 3 0.09
28 16 0.50
29 3 0.09
30 5 0.16
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTAATTATATTATTTACCAAAAAAAT
Found at i:1329670 original size:15 final size:14
Alignment explanation
Indices: 1329602--1329673 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 14
1329592 TTTCGTTTAA
* *
1329602 TTATGTATTTATATT
1 TTAT-TATTAATAAT
1329617 TTATT-TTAATAAT
1 TTATTATTAATAAT
*
1329630 TTAATATTAA-AAT
1 TTATTATTAATAAT
**
1329643 TT-TTAAAAATAAT
1 TTATTATTAATAAT
1329656 TTATTACTTAATAAT
1 TTATTA-TTAATAAT
1329671 TTA
1 TTA
1329674 CTTTAATTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.09
13 20 0.44
14 8 0.18
15 13 0.29
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (14 bp):
TTATTATTAATAAT
Found at i:1329895 original size:21 final size:21
Alignment explanation
Indices: 1329869--1329913 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1329859 AAAAAGATAC
1329869 CTTGGAGACTATCGCAACGAA
1 CTTGGAGACTATCGCAACGAA
*
1329890 CTTGGAGACTATCGCAATGAA
1 CTTGGAGACTATCGCAACGAA
1329911 CTT
1 CTT
1329914 AGAAAATCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (21 bp):
CTTGGAGACTATCGCAACGAA
Found at i:1331307 original size:11 final size:10
Alignment explanation
Indices: 1331283--1331408 Score: 56
Period size: 11 Copynumber: 11.7 Consensus size: 10
1331273 ATAACTATAA
*
1331283 TATATATATA
1 TATATATATT
1331293 TATATATAGTT
1 TATATATA-TT
**
1331304 TATATATAAAG
1 TATATAT-ATT
1331315 TATATATA-T
1 TATATATATT
*
1331324 TATATATATA
1 TATATATATT
*
1331334 AACTATATAGTT
1 TA-TATATA-TT
*
1331346 TATATTTATAT
1 TATATATAT-T
*
1331357 TATTATATAATA
1 TA-TATAT-ATT
* *
1331369 TATATAAACTA
1 TATATATA-TT
1331380 TATATATATT
1 TATATATATT
* *
1331390 ATGTATAAACTT
1 -TATATATA-TT
1331402 TATATAT
1 TATATAT
1331409 CATGTATAAA
Statistics
Matches: 87, Mismatches: 18, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
9 8 0.09
10 13 0.15
11 53 0.61
12 11 0.13
13 2 0.02
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (10 bp):
TATATATATT
Found at i:1331407 original size:2 final size:2
Alignment explanation
Indices: 1331278--1331388 Score: 88
Period size: 2 Copynumber: 55.5 Consensus size: 2
1331268 TTGAAATAAC
* *
1331278 TA TA -A TA TA TA TA TA TA TA TA TA GTT TA TA TA TA AA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * *
1331321 TA T- TA TA TA TA TA AA CTA TA TA GTT TA TA TT TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
1331362 TA TA -A TA TA TA TA AA CTA TA TA TA TA T
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA T
1331389 TATGTATAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
1 5 0.06
2 77 0.89
3 5 0.06
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1331408 original size:22 final size:21
Alignment explanation
Indices: 1331357--1331422 Score: 89
Period size: 20 Copynumber: 3.1 Consensus size: 21
1331347 ATATTTATAT
* *
1331357 TATTATATAATATATATAAAC
1 TATTATATATTATGTATAAAC
1331378 TATATATATATTATGTATAAAC
1 TAT-TATATATTATGTATAAAC
*
1331400 T-TTATATATCATGTATAAAC
1 TATTATATATTATGTATAAAC
1331420 TAT
1 TAT
1331423 AACACTATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 18 0.45
21 5 0.12
22 17 0.43
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (21 bp):
TATTATATATTATGTATAAAC
Found at i:1331515 original size:22 final size:21
Alignment explanation
Indices: 1331283--1331544 Score: 98
Period size: 22 Copynumber: 12.2 Consensus size: 21
1331273 ATAACTATAA
* *
1331283 TATATATATATATATATAGTT
1 TATATATAAATATATATAATT
1331304 TATATATAAAGTATATAT-ATT
1 TATATATAAA-TATATATAATT
* *
1331325 ATATATATAAA-CTATATAGTT
1 -TATATATAAATATATATAATT
* *
1331346 TATATTTATATTATTATATAA--
1 TATATATA-AATA-TATATAATT
1331367 TATATATAAACTATATAT-ATAT
1 TATATATAAA-TATATATAAT-T
* * *
1331389 TATGTATAAACTTTATATATCATG
1 TATATATAAA---TATATATAATT
* * *
1331413 TATAAACTATAACACTATATAGTT
1 TATATA-TA-AATA-TATATAATT
* * *
1331437 TATATATGAACTA-CT-GAA-T
1 TATATAT-AAATATATATAATT
* * *
1331456 TATATATAAA-CTACATAGTT
1 TATATATAAATATATATAATT
1331476 TATTAATATAAAT-TATATAATT
1 TA-T-ATATAAATATATATAATT
1331498 TATATATAAATTATATATGAA-T
1 TATATATAAA-TATATAT-AATT
* * *
1331520 TATTTATAAA-CTATACAATT
1 TATATATAAATATATATAATT
1331540 TATAT
1 TATAT
1331545 TTATATATTA
Statistics
Matches: 177, Mismatches: 37, Indels: 55
0.66 0.14 0.20
Matches are distributed among these distances:
18 2 0.01
19 12 0.07
20 38 0.21
21 27 0.15
22 57 0.32
23 12 0.07
24 23 0.13
25 4 0.02
26 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (21 bp):
TATATATAAATATATATAATT
Found at i:1331521 original size:11 final size:11
Alignment explanation
Indices: 1331453--1331534 Score: 62
Period size: 11 Copynumber: 7.6 Consensus size: 11
1331443 TGAACTACTG
1331453 AATTATATATA
1 AATTATATATA
* * *
1331464 AACTACATAGTT
1 AATTATATA-TA
*
1331476 TATTA-ATATA
1 AATTATATATA
1331486 AA-T-TATATA
1 AATTATATATA
*
1331495 ATTTATATATA
1 AATTATATATA
*
1331506 AATTATATATG
1 AATTATATATA
*
1331517 AATTATTTATA
1 AATTATATATA
*
1331528 AACTATA
1 AATTATA
1331535 CAATTTATAT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
9 7 0.13
10 3 0.06
11 39 0.74
12 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (11 bp):
AATTATATATA
Found at i:1331642 original size:33 final size:33
Alignment explanation
Indices: 1331569--1331642 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
1331559 TAATTATAAA
* * *
1331569 TAATATATACTATGTATAAATTATATAGTTTAT
1 TAATATAAACTATGTATAAACTATAAAGTTTAT
*
1331602 TAATATAAACTATTTATAAACTATAAAGTTTA-
1 TAATATAAACTATGTATAAACTATAAAGTTTAT
1331634 TATATATAA
1 TA-ATATAA
1331643 TATATATGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 2 0.06
33 34 0.94
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (33 bp):
TAATATAAACTATGTATAAACTATAAAGTTTAT
Found at i:1331793 original size:18 final size:19
Alignment explanation
Indices: 1331772--1331821 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
1331762 TGTAAACTGT
1331772 ATAT-ACTATATAGTTTAC
1 ATATGACTATATAGTTTAC
*
1331790 ATATGA-TATACAGTTTAC
1 ATATGACTATATAGTTTAC
1331808 ATATGAACTATATA
1 ATATG-ACTATATA
1331822 TACTAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.74
19 2 0.07
20 5 0.19
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (19 bp):
ATATGACTATATAGTTTAC
Found at i:1331822 original size:29 final size:29
Alignment explanation
Indices: 1331799--1331857 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
1331789 CATATGATAT
1331799 ACAGTTTACATATGAACTATATATACTAA
1 ACAGTTTACATATGAACTATATATACTAA
* * *
1331828 ATAGTTTACATATTAACTATATGTA-TAA
1 ACAGTTTACATATGAACTATATATACTAA
1331856 AC
1 AC
1331858 TATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (29 bp):
ACAGTTTACATATGAACTATATATACTAA
Found at i:1331860 original size:13 final size:13
Alignment explanation
Indices: 1331837--1331876 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1331827 AATAGTTTAC
*
1331837 ATATTAACTATAT
1 ATATAAACTATAT
*
1331850 GTATAAACTATAT
1 ATATAAACTATAT
1331863 ATATAAACTATAT
1 ATATAAACTATAT
1331876 A
1 A
1331877 GTTTACGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (13 bp):
ATATAAACTATAT
Found at i:1331960 original size:2 final size:2
Alignment explanation
Indices: 1331945--1332141 Score: 142
Period size: 2 Copynumber: 98.5 Consensus size: 2
1331935 TATATGCAAC
*
1331945 AT AT AT AA AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1331986 AGT AT AGT TT AC AT AT GA- ACT AT AT AT AA AA ACT AT AT AT AT AT
1 A-T AT A-T AT AT AT AT -AT A-T AT AT AT AT AT A-T AT AT AT AT AT
*
1332030 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1332070 AG CT AT AT AA AT -T AT A- AT TT AT AT AT AA AT -T AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
1332110 AGT -T GAT AT TT AT AT ACT AT AT -T AT AT AT AT A
1 A-T AT -AT AT AT AT AT A-T AT AT AT AT AT AT AT A
1332142 GTTTACTAGT
Statistics
Matches: 157, Mismatches: 20, Indels: 36
0.74 0.09 0.17
Matches are distributed among these distances:
1 9 0.06
2 136 0.87
3 12 0.08
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1331975 original size:27 final size:26
Alignment explanation
Indices: 1331945--1332067 Score: 119
Period size: 25 Copynumber: 4.7 Consensus size: 26
1331935 TATATGCAAC
1331945 ATATATAAAT-TATATATATATATAT
1 ATATATAAATATATATATATATATAT
*
1331970 ATATAT--ATATATATATAGTATAGTTT
1 ATATATAAATATATATATA-TATA-TAT
* * * *
1331996 ACATATGAACTATATATAAAAACTATAT
1 ATATAT-AAATATATATATATA-TATAT
*
1332024 ATATATATATATATATATAT-TATAT
1 ATATATAAATATATATATATATATAT
*
1332049 ATATATATATATATATATA
1 ATATATAAATATATATATA
1332068 AAAGCTATAT
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
23 2 0.03
24 8 0.10
25 34 0.43
26 7 0.09
27 10 0.12
28 8 0.10
29 11 0.14
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATATAAATATATATATATATATAT
Found at i:1332011 original size:62 final size:63
Alignment explanation
Indices: 1331936--1332055 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 63
1331926 TTTTTATAGT
*
1331936 ATATGCAACATATAT-AAATTATATATATATATATATATATATA-TATATATAGTATAGTTTAC
1 ATATGCAACATATATAAAACTATATATATATATATATATATATATTATATATA-TATAGTTTAC
1331998 ATATG-AACTATATATAAAAACTATATATATATATATATATATATATTATATATATATA
1 ATATGCAAC-ATATAT-AAAACTATATATATATATATATATATATATTATATATATATA
1332056 TATATATATA
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
61 3 0.06
62 11 0.21
64 31 0.58
65 8 0.15
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (63 bp):
ATATGCAACATATATAAAACTATATATATATATATATATATATATTATATATATATAGTTTAC
Found at i:1332064 original size:54 final size:55
Alignment explanation
Indices: 1331963--1332110 Score: 174
Period size: 56 Copynumber: 2.6 Consensus size: 55
1331953 ATTATATATA
* * *
1331963 TATATATATATATATATATATATAGTATAGTTTACATATGAACTATATATAAAAAC
1 TATATATATATATATATATATATATTATA-TATATATATGAACTATATATAAAAAC
*
1332019 TATATATATATATATATATATATATTATATATATATAT-ATA-TATATATAAAAGC
1 TATATATATATATATATATATATATTATATATATATATGA-ACTATATATAAAAAC
* * *
1332073 TATATAAATTATAATTTATATATAAATTATATACTATA
1 TATATATA-TAT-ATATATATATATATTATATA-TATA
1332111 GTTGATATTT
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
54 20 0.25
55 11 0.14
56 46 0.57
57 4 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (55 bp):
TATATATATATATATATATATATATTATATATATATATGAACTATATATAAAAAC
Found at i:1332103 original size:27 final size:26
Alignment explanation
Indices: 1331945--1332110 Score: 119
Period size: 29 Copynumber: 6.3 Consensus size: 26
1331935 TATATGCAAC
*
1331945 ATATATA-AAT-TATATATATA-TAT
1 ATATATATAATATATATATAAACTAT
*
1331968 ATATATAT-ATATATATATAGTA-TAGT
1 ATATATATAATATATATATA-AACTA-T
* * *
1331994 TTACATATGAACTATATATAAAAACTAT
1 ATATATAT-AA-TATATATATAAACTAT
* *
1332022 ATATATAT-ATATATATATATATTAT
1 ATATATATAATATATATATAAACTAT
1332047 ATATATATATATATATATATAAAAGCTAT
1 ATATATATA-ATATATATAT-AAA-CTAT
* * *
1332076 ATAAATTATAATTTATATATAAATTAT
1 ATATA-TATAATATATATATAAACTAT
1332103 ATACTATA
1 ATA-TATA
1332111 GTTGATATTT
Statistics
Matches: 114, Mismatches: 15, Indels: 24
0.75 0.10 0.16
Matches are distributed among these distances:
23 9 0.08
24 8 0.07
25 25 0.22
26 8 0.07
27 18 0.16
28 15 0.13
29 27 0.24
30 4 0.04
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (26 bp):
ATATATATAATATATATATAAACTAT
Found at i:1332121 original size:31 final size:31
Alignment explanation
Indices: 1332086--1332144 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1332076 ATAAATTATA
1332086 ATTTATATA-TAAATTATATACTATAGTTGAT
1 ATTTATATACTAAATTATATA-TATAGTTGAT
*
1332117 ATTTATATACTATATTATATATATAGTT
1 ATTTATATACTAAATTATATATATAGTT
1332145 TACTAGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (31 bp):
ATTTATATACTAAATTATATATATAGTTGAT
Found at i:1332226 original size:27 final size:29
Alignment explanation
Indices: 1332196--1332263 Score: 104
Period size: 27 Copynumber: 2.4 Consensus size: 29
1332186 ATATATAAAC
1332196 TATAGTTTATATTTATATACTACAT-A-A
1 TATAGTTTATATTTATATACTACATAACA
* *
1332223 TATAGTTGATATTTATATACTATATAACA
1 TATAGTTTATATTTATATACTACATAACA
1332252 TATAGTTTATAT
1 TATAGTTTATAT
1332264 ATAAACTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.64
28 1 0.03
29 12 0.33
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (29 bp):
TATAGTTTATATTTATATACTACATAACA
Found at i:1332266 original size:20 final size:18
Alignment explanation
Indices: 1332243--1332324 Score: 103
Period size: 18 Copynumber: 4.4 Consensus size: 18
1332233 ATTTATATAC
1332243 TATAT-AACATATAGTTTA
1 TATATGAAC-TATAGTTTA
* *
1332261 TATATAAACTATATAGCTTA
1 TATATGAAC--TATAGTTTA
1332281 TATATGAACTATAGTTTA
1 TATATGAACTATAGTTTA
1332299 TATATGAACTATAGTTTA
1 TATATGAACTATAGTTTA
*
1332317 CATATGAA
1 TATATGAA
1332325 AAGTAAATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
18 38 0.66
19 3 0.05
20 17 0.29
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (18 bp):
TATATGAACTATAGTTTA
Found at i:1332266 original size:27 final size:27
Alignment explanation
Indices: 1332184--1332275 Score: 86
Period size: 27 Copynumber: 3.4 Consensus size: 27
1332174 AGTATATACA
1332184 ATATA-TATA-AAC-TATAGTTTATATTT
1 ATATACTATATAACATATAGTTTATA--T
* *
1332210 ATATACTACAT-A-ATATAGTTGATATTT
1 ATATACTATATAACATATAGTT--TATAT
1332237 ATATACTATATAACATATAGTTTATAT
1 ATATACTATATAACATATAGTTTATAT
*
1332264 ATAAACTATATA
1 ATATACTATATA
1332276 GCTTATATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
26 5 0.09
27 37 0.69
28 1 0.02
29 11 0.20
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (27 bp):
ATATACTATATAACATATAGTTTATAT
Found at i:1332613 original size:13 final size:11
Alignment explanation
Indices: 1332580--1332608 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1332570 TTTACATTTG
1332580 AACTATAGTTA
1 AACTATAGTTA
1332591 AACTATAGTTA
1 AACTATAGTTA
1332602 AACTATA
1 AACTATA
1332609 TAGTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (11 bp):
AACTATAGTTA
Found at i:1333182 original size:54 final size:54
Alignment explanation
Indices: 1333116--1333512 Score: 503
Period size: 54 Copynumber: 7.4 Consensus size: 54
1333106 TTCTTTGAGG
* *
1333116 TGCACA-TGTAGTGCCGATATGGTCGTTCATAAATATATTATGAATTTCGTGGGT
1 TGCACACT-TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGT
* * *
1333170 TGCACACTTAGTGCCGATACGATCGTTCATAAACCTATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGT
* *
1333224 TGCACACTTAGTGTCGATACGGTCGTTCATAAATATATTATGAATTAT-GTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATT-TCGTGGGT
* * * * *
1333278 CGCACACTTAGTGTCGATACGGTCGTTCATAAACACATTATCAATTCCGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGT
* * * *
1333332 TGCACACGTAGTGCCAATACGGTCGTTCATAAACACATTATGGA-TTCTGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTC-GTGGGT
* * * * * *
1333386 TGCACACTTAATGCCGATACGGTCATTCATAAATATATTATGGATTCCTTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGT
* * * * *
1333440 TGCACACTTAGTGTCGATACGGTCGTTCATAAACACAATATGAATTTTGTCGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGT
1333494 TGCACACTTAGTGCCGATA
1 TGCACACTTAGTGCCGATA
1333513 GTACACATAG
Statistics
Matches: 296, Mismatches: 42, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
53 2 0.01
54 291 0.98
55 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (54 bp):
TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGT
Found at i:1333406 original size:162 final size:162
Alignment explanation
Indices: 1333124--1333508 Score: 558
Period size: 162 Copynumber: 2.4 Consensus size: 162
1333114 GGTGCACATG
* * * * *
1333124 TAGTGCCGATATGGTCGTTCATAAATATATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATA
1 TAGTGTCGATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGCCAATA
* * *
1333189 CGATCGTTCATAAACCTATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCAT
66 CGATCGTTCATAAACCTATTATGAATTCCGTGGGTTGCACACTTAATGCCGATACGGTCATTCAT
1333254 AAATATATTATGAATT-ATGTGGGTCGCACACT
131 AAATATATTATGAATTCAT-TGGGTCGCACACT
* * *
1333286 TAGTGTCGATACGGTCGTTCATAAACACATTATCAATTCCGTGGGTTGCACACGTAGTGCCAATA
1 TAGTGTCGATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGCCAATA
* * *
1333351 CGGTCGTTCATAAACAC-ATTATGGATTCTGTGGGTTGCACACTTAATGCCGATACGGTCATTCA
66 CGATCGTTCATAAAC-CTATTATGAATTCCGTGGGTTGCACACTTAATGCCGATACGGTCATTCA
* * *
1333415 TAAATATATTATGGATTCCTTGGGTTGCACACT
130 TAAATATATTATGAATTCATTGGGTCGCACACT
* * *
1333448 TAGTGTCGATACGGTCGTTCATAAACACAATATGAATTTTGTCGGTTGCACACTTAGTGCC
1 TAGTGTCGATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGCC
1333509 GATAGTACAC
Statistics
Matches: 198, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
162 196 0.99
163 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (162 bp):
TAGTGTCGATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGCCAATA
CGATCGTTCATAAACCTATTATGAATTCCGTGGGTTGCACACTTAATGCCGATACGGTCATTCAT
AAATATATTATGAATTCATTGGGTCGCACACT
Found at i:1335465 original size:210 final size:211
Alignment explanation
Indices: 1335102--1335512 Score: 815
Period size: 210 Copynumber: 2.0 Consensus size: 211
1335092 TTTCAAAATC
1335102 TCATAAGGTCCAATGAATCTCGGACTCAGCTTTCCTTTGCGCCCAAACCGCAATGTTTTCTTCTA
1 TCATAAGGTCCAATGAATCTCGGACTCAGCTTTCCTTTGCGCCCAAACCGCAATGTTTTCTTCTA
1335167 GGGCGATACTTTCAGAAATACCTTATCTCCCACTTGAAATTCAATTTCTTTTCTTTTCAAATCAG
66 GGGCGATACTTTCAGAAATACCTTATCTCCCACTTGAAATTCAATTTCTTTTCTTTTCAAATCAG
1335232 TATAAGACTTTTGTCAATCAGAGGCTATCTTTAGATTATCCTGGATAACTTTCACTTTTTCCTCA
131 TATAAGACTTTTGTCAATCAGAGGCTATCTTTAGATTATCCTGGATAACTTTCACTTTTTCCTCA
1335297 ATTTCTCCAAATCTGG
196 ATTTCTCCAAATCTGG
1335313 TCATAAGGTCCAATGAATCTCGGACTCAGC-TTCCTTTGCGCCCAAACCGCAATGTTTTCTTCTA
1 TCATAAGGTCCAATGAATCTCGGACTCAGCTTTCCTTTGCGCCCAAACCGCAATGTTTTCTTCTA
1335377 GGGCGATACTTTCAGAAATACCTTATCTCCCACTTGAAATTCAATTTCTTTTCTTTTCAAATCAG
66 GGGCGATACTTTCAGAAATACCTTATCTCCCACTTGAAATTCAATTTCTTTTCTTTTCAAATCAG
1335442 TATAAGACTTTTGTCAATCAGAGGCTATCTTTAGATTATCCTGGATAACTTTCACTTTTTCCTCA
131 TATAAGACTTTTGTCAATCAGAGGCTATCTTTAGATTATCCTGGATAACTTTCACTTTTTCCTCA
1335507 ATTTCT
196 ATTTCT
1335513 TTCCTCAAAT
Statistics
Matches: 200, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
210 170 0.85
211 30 0.15
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.38
Consensus pattern (211 bp):
TCATAAGGTCCAATGAATCTCGGACTCAGCTTTCCTTTGCGCCCAAACCGCAATGTTTTCTTCTA
GGGCGATACTTTCAGAAATACCTTATCTCCCACTTGAAATTCAATTTCTTTTCTTTTCAAATCAG
TATAAGACTTTTGTCAATCAGAGGCTATCTTTAGATTATCCTGGATAACTTTCACTTTTTCCTCA
ATTTCTCCAAATCTGG
Found at i:1337854 original size:24 final size:24
Alignment explanation
Indices: 1337844--1337958 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
1337834 CATAATTCAC
* * *
1337844 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
1337868 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* *
1337892 ATCAAGTATTAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
1337916 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1337940 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
1337959 ATCAAATCGA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 2 0.03
24 75 0.95
25 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1337920 original size:12 final size:12
Alignment explanation
Indices: 1337905--1337943 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1337895 AAGTATTAGA
1337905 TCAGAATCCATG
1 TCAGAATCCATG
*
1337917 TCAGATAT-CATA
1 TCAGA-ATCCATG
1337929 TCAGAATCCATG
1 TCAGAATCCATG
1337941 TCA
1 TCA
1337944 AGTATCAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (12 bp):
TCAGAATCCATG
Found at i:1342455 original size:24 final size:23
Alignment explanation
Indices: 1342445--1342569 Score: 108
Period size: 24 Copynumber: 5.2 Consensus size: 23
1342435 CATAATTCAC
*
1342445 ATCAAGTATCATATCAAAATCCA
1 ATCAAGTATCAGATCAAAATCCA
* *
1342468 GGTCAAGTATCAGATCAGAATCCA
1 -ATCAAGTATCAGATCAAAATCCA
*
1342492 AGTCAAGTATCAGATCAGAATCCA
1 A-TCAAGTATCAGATCAAAATCCA
* * *
1342516 TGTC-AGATATCATATCAGAATCCA
1 -ATCAAG-TATCAGATCAAAATCCA
* *
1342540 TGTCAAGTATCAGATCAGAAATCAA
1 -ATCAAGTATCAGATCA-AAATCCA
1342565 ATCAA
1 ATCAA
1342570 AAATCAGGTA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.02
24 77 0.90
25 7 0.08
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (23 bp):
ATCAAGTATCAGATCAAAATCCA
Found at i:1342514 original size:48 final size:48
Alignment explanation
Indices: 1342446--1342559 Score: 167
Period size: 48 Copynumber: 2.4 Consensus size: 48
1342436 ATAATTCACA
* *
1342446 TCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAAG
1 TCAAGTATCAGATCAGAATCCAGGTCAGA-TATCAGATCAGAATCCAAG
* * *
1342494 TCAAGTATCAGATCAGAATCCATGTCAGATATCATATCAGAATCCATG
1 TCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCAAG
1342542 TCAAGTATCAGATCAGAA
1 TCAAGTATCAGATCAGAA
1342560 ATCAAATCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 59 0.98
49 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (48 bp):
TCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCAAG
Found at i:1347156 original size:24 final size:24
Alignment explanation
Indices: 1347141--1347258 Score: 130
Period size: 24 Copynumber: 4.9 Consensus size: 24
1347131 CATAATTCAC
* * *
1347141 GTCAAGTATTATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAA
*
1347165 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
* *
1347189 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAA
* * *
1347213 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
1347237 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
1347259 AAATCGAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
23 2 0.02
24 75 0.90
25 6 0.07
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:1347210 original size:48 final size:48
Alignment explanation
Indices: 1347141--1347255 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 48
1347131 CATAATTCAC
* * *
1347141 GTCAAGTATTATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGGTCAGA-TATCAGATCAGAATCCAA
* * *
1347189 GTCAAGTATCAGATCAGAATCCATGTCAGATATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCAA
1347237 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
1347256 ATCAAATCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 59 0.98
49 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCAA
Found at i:1349587 original size:18 final size:18
Alignment explanation
Indices: 1349564--1349598 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1349554 GGTTGATCGG
1349564 GTCAACGAGTCGGGTCGA
1 GTCAACGAGTCGGGTCGA
*
1349582 GTCAACGGGTCGGGTCG
1 GTCAACGAGTCGGGTCG
1349599 GGTTGTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (18 bp):
GTCAACGAGTCGGGTCGA
Found at i:1353546 original size:54 final size:54
Alignment explanation
Indices: 1353488--1353822 Score: 458
Period size: 54 Copynumber: 6.2 Consensus size: 54
1353478 GGTGCTCACG
* * * *
1353488 TAGTGCCGATAAGGTCATTCATAAACATATTATTAATTAT-GTGGGTTGCACACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAATT-TCGTGGGTTGCACACT
* * * **
1353542 TAGTGCCGATACGGTCGTTCATAAATC-TATTATGAATTTCGTGGGTTTAACACT
1 TAGTGTCGATACGGTCATTCATAAA-CACATTATGAATTTCGTGGGTTGCACACT
* * * * ** *
1353596 TAGTGTCGATACGCTCGTTAACAAACATTTTATGAATTACGTGGGTTGCACACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACT
* *
1353650 TAGTGTCAATACGGTCATTCATAAACACATTATGAATTACGTGGGTTGCACACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACT
*
1353704 TAGTGTCGATACGGTCATTTATAAACACATTATGAATTTCGTGGGTTGCACACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACT
*
1353758 TAGTGTCGATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACT
1353812 TAGTGTCGATA
1 TAGTGTCGATA
1353823 GTACACATAG
Statistics
Matches: 253, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
53 2 0.01
54 250 0.99
55 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
TAGTGTCGATACGGTCATTCATAAACACATTATGAATTTCGTGGGTTGCACACT
Found at i:1355040 original size:24 final size:24
Alignment explanation
Indices: 1355000--1355078 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
1354990 ATATAAACTC
*
1355000 TATAGTTTACATA-TGAACTATATA
1 TATAGTTTA-TTAGTGAACTATATA
*
1355024 TATAGTTTATTAGTGAACTGTATA
1 TATAGTTTATTAGTGAACTATATA
* * *
1355048 AATTGTTTATATAGTATATACTATATA
1 TATAGTTTAT-TAGT-GA-ACTATATA
1355075 TATA
1 TATA
1355079 AACTATAGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
23 2 0.05
24 27 0.63
25 4 0.09
26 1 0.02
27 9 0.21
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (24 bp):
TATAGTTTATTAGTGAACTATATA
Found at i:1355067 original size:7 final size:6
Alignment explanation
Indices: 1355055--1355150 Score: 50
Period size: 7 Copynumber: 14.7 Consensus size: 6
1355045 ATAAATTGTT
* * *
1355055 TATATA GTATATA CTATATA TATAAA CTATAGTT TATATT TATATA CTATATA
1 TATATA -TATATA -TATATA TATATA -TATA-TA TATATA TATATA -TATATA
* * *
1355108 CTATATA TACTATA TAGTATA -ATTTA CATATGA AATATA TATA
1 -TATATA TA-TATA TA-TATA TATATA TATAT-A TATATA TATA
1355151 AAAACTATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
5 3 0.04
6 22 0.30
7 48 0.66
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:1355074 original size:9 final size:8
Alignment explanation
Indices: 1355055--1355150 Score: 50
Period size: 9 Copynumber: 11.0 Consensus size: 8
1355045 ATAAATTGTT
1355055 TATATAGTA
1 TATATA-TA
1355064 TATACTATA
1 TATA-TATA
*
1355073 TATATAAA
1 TATATATA
*
1355081 CTATAGTTTA
1 -TATA-TATA
*
1355091 TATTTATA
1 TATATATA
1355099 TACTATATA
1 TA-TATATA
1355108 CTATATATA
1 -TATATATA
1355117 CTATATAGTA
1 -TATATA-TA
*
1355127 TA-ATTTA
1 TATATATA
* *
1355134 CATATGAAA
1 TATAT-ATA
1355143 TATATATA
1 TATATATA
1355151 AAAACTATAT
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
7 3 0.04
8 14 0.21
9 42 0.63
10 8 0.12
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (8 bp):
TATATATA
Found at i:1355161 original size:2 final size:2
Alignment explanation
Indices: 1355055--1355150 Score: 50
Period size: 2 Copynumber: 44.0 Consensus size: 2
1355045 ATAAATTGTT
* * *
1355055 TA TA TA GTA TA TA CTA TA TA TA TA AA CTA TA GTT TA TA TT TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA
* * *
1355099 TA CTA TA TA CTA TA TA TA CTA TA TA GTA TA -A TT TA CA TA TGA AA
1 TA -TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA T-A TA
1355143 TA TA TA TA
1 TA TA TA TA
1355151 AAAACTATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
1 1 0.01
2 56 0.78
3 15 0.21
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1355201 original size:25 final size:26
Alignment explanation
Indices: 1355146--1355201 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
1355136 TATGAAATAT
*
1355146 ATATAAAAACTATATAAACTATAGTTT
1 ATATAAAAACTATAT-AACTATAGTTG
* *
1355173 ATATAAAAACTATAT-ATTATTGTTG
1 ATATAAAAACTATATAACTATAGTTG
1355198 ATAT
1 ATAT
1355202 TTATATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.42
27 15 0.58
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (26 bp):
ATATAAAAACTATATAACTATAGTTG
Found at i:1355206 original size:29 final size:26
Alignment explanation
Indices: 1355174--1355231 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1355164 CTATAGTTTA
*
1355174 TATAAAAACTATATATTATTGTTGATATT
1 TATAAAAA-TATATA-TATAGTTGAT-TT
*
1355203 TAT-ATAATATATATATAGTTGATTT
1 TATAAAAATATATATATAGTTGATTT
1355228 TATA
1 TATA
1355232 CTATATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 5 0.19
26 9 0.35
27 6 0.23
28 3 0.12
29 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (26 bp):
TATAAAAATATATATATAGTTGATTT
Found at i:1355212 original size:25 final size:27
Alignment explanation
Indices: 1355183--1355240 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
1355173 ATATAAAAAC
*
1355183 TATATAT-TATTGTTGATATTTATA-TA
1 TATATATATATAGTTGAT-TTTATACTA
1355209 -ATATATATATAGTTGATTTTATACTA
1 TATATATATATAGTTGATTTTATACTA
1355235 TATATA
1 TATATA
1355241 ATTTATACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 12 0.43
26 11 0.39
27 5 0.18
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (27 bp):
TATATATATATAGTTGATTTTATACTA
Found at i:1355255 original size:15 final size:16
Alignment explanation
Indices: 1355226--1355267 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
1355216 TATAGTTGAT
1355226 TTTATACTATATATAA
1 TTTATACTATATATAA
1355242 TTTATACT-TATATAA
1 TTTATACTATATATAA
1355257 TTTATACTATA
1 TTTATACTATA
1355268 AATTCAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTATACTATATATAA
Found at i:1355447 original size:18 final size:18
Alignment explanation
Indices: 1355424--1355512 Score: 103
Period size: 18 Copynumber: 5.1 Consensus size: 18
1355414 TATAGTTCAT
1355424 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
*
1355442 TAGTATATATAAACTGTA
1 TAGTATATATAAACTATA
* ***
1355460 TATTATAT-TGTTC-AT-
1 TAGTATATATAAACTATA
1355475 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
*
1355493 TAGTATATATAAACCATA
1 TAGTATATATAAACTATA
1355511 TA
1 TA
1355513 TTATTTAGTT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.12
16 3 0.05
17 4 0.07
18 43 0.75
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:1355486 original size:51 final size:49
Alignment explanation
Indices: 1355381--1355545 Score: 221
Period size: 51 Copynumber: 3.3 Consensus size: 49
1355371 AAAAACTATC
* * *
1355381 TATATATATAGTATATGGTATATATAAACTATA-TATA--GTTCATTAG
1 TATATATAAACTATATAGTATATATAAACTATATTATATTGTTCATTAG
1355427 TATATATAAACTATATAGTATATATAAACTGTATATTATATTGTTCATTAG
1 TATATATAAACTATATAGTATATATAAAC--TATATTATATTGTTCATTAG
1355478 TATATATAAACTATATAGTATATATAAACCATATATTAT-TTAGTTCATTAG
1 TATATATAAACTATATAGTATATATAAA-C-TATATTATATT-GTTCATTAG
*
1355529 TATATATAACCTATATA
1 TATATATAAACTATATA
1355546 TTAATTTATT
Statistics
Matches: 107, Mismatches: 5, Indels: 9
0.88 0.04 0.07
Matches are distributed among these distances:
46 26 0.24
48 4 0.04
49 4 0.04
50 2 0.02
51 70 0.65
52 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (49 bp):
TATATATAAACTATATAGTATATATAAACTATATTATATTGTTCATTAG
Found at i:1355679 original size:61 final size:61
Alignment explanation
Indices: 1355605--1355741 Score: 186
Period size: 61 Copynumber: 2.2 Consensus size: 61
1355595 TATAAGGATC
*
1355605 AAATTGAATAAATTTTAAATATGAAGATTAAATTAATAAATTATAACATTAAATT-TGGACT
1 AAATTGAATAAATTTTAAATATGAAGATTAAATTAATAAATTACAACATTAAATTAT-GACT
* * * * * * *
1355666 AAATTTAAGAAATTTTAAATATGAAGCTTAAATTAGTATATTGCATCATTAAATTATGACT
1 AAATTGAATAAATTTTAAATATGAAGATTAAATTAATAAATTACAACATTAAATTATGACT
1355727 AAATTGAATAAATTT
1 AAATTGAATAAATTT
1355742 AAAACTAGGA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 64 0.98
62 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (61 bp):
AAATTGAATAAATTTTAAATATGAAGATTAAATTAATAAATTACAACATTAAATTATGACT
Found at i:1356246 original size:111 final size:111
Alignment explanation
Indices: 1355983--1356250 Score: 294
Period size: 111 Copynumber: 2.4 Consensus size: 111
1355973 CCAAAAATTG
* ** * *
1355983 TCATTTGATCTTCACAAACACCAAAACCCAAACCATTTCGTATTTTTTTTATATAACACCCATAA
1 TCATTTGATCTTCACAAACACCAAAA-CCAAACCATTTCCT-TTTTTTCGATAAAACACCCAAAA
* * * ** *
1356048 TTTCAACCCTTGTTCATCCTTGTTCATCCGTGTTTATCCCAAAAACCC
64 ATTCAACCCTTATTCATCCATGTTCATCCCAGTTTATCCCAAAAACCA
* * *
1356096 TCATTTGATATTCACAAACACCAAAACCAAACAATTTCCTTTTTTTCGA-ACAAACACCTAAAAA
1 TCATTTGATCTTCACAAACACCAAAACCAAACCATTTCCTTTTTTTCGATA-AAACACCCAAAAA
*
1356160 TTCAA-CCTGTATTCATCCATGTTCATCCCAGTTCT-TCCC-CAAACCA
65 TTCAACCCT-TATTCATCCATGTTCATCCCAGTT-TATCCCAAAAACCA
*
1356206 TTATTTGATCTTCACAAACACCAAAACCTAAACCCA-TTCCTTTTT
1 TCATTTGATCTTCACAAACACCAAAACC-AAA-CCATTTCCTTTTT
1356251 GTATCAAATA
Statistics
Matches: 132, Mismatches: 18, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
110 35 0.27
111 57 0.43
112 15 0.11
113 25 0.19
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (111 bp):
TCATTTGATCTTCACAAACACCAAAACCAAACCATTTCCTTTTTTTCGATAAAACACCCAAAAAT
TCAACCCTTATTCATCCATGTTCATCCCAGTTTATCCCAAAAACCA
Found at i:1356511 original size:6 final size:6
Alignment explanation
Indices: 1356502--1356638 Score: 132
Period size: 6 Copynumber: 22.8 Consensus size: 6
1356492 ACCCTGACCA
* * * * * *
1356502 AAACCC AAACCC AAACCT GAACCC AAACCC GAACCC GAACCT AAACCT
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * * *
1356550 AAACCC AAACCC AGAA-CC AAACCC AAACTC GAACCC AAACCT AAAACC
1 AAACCC AAACCC A-AACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * * *
1356598 AAACCC AAACCC AAACCC GAACCT AAAACC AAACCC GAACC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACC
1356639 TGAATCCAAA
Statistics
Matches: 106, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
5 2 0.02
6 102 0.96
7 2 0.02
ACGTcount: A:0.47, C:0.43, G:0.05, T:0.04
Consensus pattern (6 bp):
AAACCC
Found at i:1356524 original size:18 final size:18
Alignment explanation
Indices: 1356503--1356658 Score: 95
Period size: 18 Copynumber: 8.4 Consensus size: 18
1356493 CCCTGACCAA
1356503 AACCCAAACCCAAACCTG
1 AACCCAAACCCAAACCTG
*
1356521 AACCCAAACCCGAACCCGAACCTA
1 AACCCAAACCC--A----AACCTG
* *
1356545 AACCTAAACCCAAACCCAG
1 AACCCAAACCCAAA-CCTG
1356564 AA-CCAAACCCAAA-CTCG
1 AACCCAAACCCAAACCT-G
* *
1356581 AACCCAAACCTAAAACC-A
1 AACCCAAACC-CAAACCTG
*
1356599 AACCCAAACCCAAACCCG
1 AACCCAAACCCAAACCTG
* * *
1356617 AACCTAAAACCAAACCCG
1 AACCCAAACCCAAACCTG
** *
1356635 AACCTGAATCCAAACC-G
1 AACCCAAACCCAAACCTG
1356652 AACCCAA
1 AACCCAA
1356659 TCTAAACCCG
Statistics
Matches: 110, Mismatches: 16, Indels: 25
0.73 0.11 0.17
Matches are distributed among these distances:
16 1 0.01
17 14 0.13
18 70 0.64
19 7 0.06
20 2 0.02
22 1 0.01
24 15 0.14
ACGTcount: A:0.47, C:0.42, G:0.06, T:0.05
Consensus pattern (18 bp):
AACCCAAACCCAAACCTG
Found at i:1356525 original size:30 final size:29
Alignment explanation
Indices: 1356498--1356650 Score: 146
Period size: 30 Copynumber: 5.1 Consensus size: 29
1356488 CCTAACCCTG
1356498 ACCAAAACCCAAACCCAAACCTGAACCCAA
1 ACCAAAA-CCAAACCCAAACCTGAACCCAA
* * * * *
1356528 ACCCGAACCCGAACCTAAACCTAAACCCAA
1 A-CCAAAACCAAACCCAAACCTGAACCCAA
*
1356558 ACCCAGAACCAAACCCAAA-CTCGAACCCAA
1 A-CCAAAACCAAACCCAAACCT-GAACCCAA
** *
1356588 ACCTAAAACCAAACCCAAACCCAAACCCGA
1 ACC-AAAACCAAACCCAAACCTGAACCCAA
* *
1356618 ACCTAAAACCAAACCCGAACCTGAATCCAA
1 ACC-AAAACCAAACCCAAACCTGAACCCAA
1356648 ACC
1 ACC
1356651 GAACCCAATC
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
29 4 0.04
30 90 0.91
31 5 0.05
ACGTcount: A:0.47, C:0.42, G:0.05, T:0.05
Consensus pattern (29 bp):
ACCAAAACCAAACCCAAACCTGAACCCAA
Found at i:1357260 original size:13 final size:13
Alignment explanation
Indices: 1357228--1357253 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1357218 TACATCTAAC
1357228 GCTAGAAGGCATA
1 GCTAGAAGGCATA
1357241 GCTAGAAGGCATA
1 GCTAGAAGGCATA
1357254 CTGAGAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (13 bp):
GCTAGAAGGCATA
Found at i:1359508 original size:23 final size:23
Alignment explanation
Indices: 1359481--1359533 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1359471 CTTAATGCAG
*
1359481 GATGCTTACTGAATTGATGCAAT
1 GATGCTTACTGAATTGATACAAT
* *
1359504 GATGCTTACTGAATTGGTACAGT
1 GATGCTTACTGAATTGATACAAT
1359527 GATGCTT
1 GATGCTT
1359534 GTCAGTTGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (23 bp):
GATGCTTACTGAATTGATACAAT
Found at i:1360210 original size:18 final size:17
Alignment explanation
Indices: 1360130--1360222 Score: 62
Period size: 18 Copynumber: 5.1 Consensus size: 17
1360120 ATAAAATTTA
*
1360130 TAATATAATAATTATTAA-
1 TAATATAAAAATTA--AAT
*
1360148 TAATATAAAGAATTGGAAT
1 TAATATAAA-AATT-AAAT
**
1360167 TAATATAAAAACCAAATTT
1 TAATATAAAAATTAAA--T
*
1360186 ATAATATACAAATTATAAT
1 -TAATATAAAAATTA-AAT
1360205 TAATATAAAAATTAAAT
1 TAATATAAAAATTAAAT
1360222 T
1 T
1360223 TCAAAAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
17 6 0.10
18 25 0.42
19 15 0.25
20 11 0.19
21 2 0.03
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
TAATATAAAAATTAAAT
Found at i:1360222 original size:38 final size:39
Alignment explanation
Indices: 1360130--1360223 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 39
1360120 ATAAAATTTA
* * *
1360130 TAATATAATAATT--ATTAATAATATAAAGAATTGGAAT
1 TAATATAAAAATTAAATTTATAATATAAAGAATTAGAAT
** * *
1360167 TAATATAAAAACCAAATTTATAATATACA-AATTATAAT
1 TAATATAAAAATTAAATTTATAATATAAAGAATTAGAAT
1360205 TAATATAAAAATTAAATTT
1 TAATATAAAAATTAAATTT
1360224 CAAAAATAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
37 10 0.22
38 24 0.52
39 12 0.26
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (39 bp):
TAATATAAAAATTAAATTTATAATATAAAGAATTAGAAT
Found at i:1361512 original size:3 final size:3
Alignment explanation
Indices: 1361499--1361531 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1361489 ATTTAATTAT
1361499 ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1361532 ATGTGACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1362385 original size:30 final size:29
Alignment explanation
Indices: 1362329--1362388 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
1362319 AAATAATACT
* *
1362329 CTCAAAAGTCAATAAAAAGTTCAATTATA
1 CTCAAAACTCAATAAAAAATTCAATTATA
1362358 CTCACAAACTCAATTAAAAAATT-AATTATA
1 CTCA-AAACTCAA-TAAAAAATTCAATTATA
1362388 C
1 C
1362389 CTTCAAAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 4 0.15
30 15 0.56
31 8 0.30
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (29 bp):
CTCAAAACTCAATAAAAAATTCAATTATA
Found at i:1362507 original size:21 final size:21
Alignment explanation
Indices: 1362478--1362522 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1362468 GGAATGCTAT
*
1362478 TCAATACAATAG-ATTGTTATA
1 TCAACACAATAGAATT-TTATA
1362499 TCAACACAATAGAATTTTATA
1 TCAACACAATAGAATTTTATA
1362520 TCA
1 TCA
1362523 GTACTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (21 bp):
TCAACACAATAGAATTTTATA
Found at i:1363313 original size:28 final size:28
Alignment explanation
Indices: 1363254--1363313 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
1363244 CTTCATACAA
* *
1363254 TTTTTAAATTTGACTCCCTAAAATATAT
1 TTTTTAAATTTGACACCCTAAAATATAG
1363282 TTTTTAAAATTTGACACTCC-AAAATA-AG
1 TTTTT-AAATTTGACAC-CCTAAAATATAG
1363310 TTTT
1 TTTT
1363314 GGAAAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 10 0.36
29 16 0.57
30 2 0.07
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (28 bp):
TTTTTAAATTTGACACCCTAAAATATAG
Found at i:1364461 original size:2 final size:2
Alignment explanation
Indices: 1364454--1364483 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1364444 TTTAAAACAT
1364454 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1364484 CCCCCATCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1364794 original size:12 final size:12
Alignment explanation
Indices: 1364779--1364838 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
1364769 CAGACATCAA
1364779 AACAGAATTCAG
1 AACAGAATTCAG
*
1364791 AACA-TATATCAG
1 AACAGAAT-TCAG
*
1364803 AACAGAATCCA-
1 AACAGAATTCAG
*
1364814 AATCAGAAATCAG
1 AA-CAGAATTCAG
*
1364827 AAAAGAATTCAG
1 AACAGAATTCAG
1364839 GTAATGTATC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
11 4 0.11
12 29 0.78
13 4 0.11
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:1364801 original size:24 final size:24
Alignment explanation
Indices: 1364774--1364861 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 24
1364764 GATATCAGAC
1364774 ATCAAAACAGAATTCAGAACATAT
1 ATCAAAACAGAATTCAGAACATAT
* * * *
1364798 ATCAGAACAGAATCCA-AATCAGAA
1 ATCAAAACAGAATTCAGAA-CATAT
* *
1364822 ATCAGAAA-AGAATTCAGGTA-ATGT
1 ATCA-AAACAGAATTCA-GAACATAT
*
1364846 ATCATAACAGAATTCA
1 ATCAAAACAGAATTCA
1364862 AGTCGAAAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
23 4 0.08
24 41 0.85
25 2 0.04
26 1 0.02
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.20
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGAACATAT
Found at i:1369640 original size:24 final size:24
Alignment explanation
Indices: 1369534--1369642 Score: 89
Period size: 24 Copynumber: 4.5 Consensus size: 24
1369524 AAACGGAGAT
*
1369534 GTCAGAAATCAAAACAAAATTC-A
1 GTCAGAAATCAGAACAAAATTCAA
* * * * *
1369557 GAACATATATCAGAACATAATCCATA
1 G-TCAGAAATCAGAACAAAATTCA-A
*
1369583 -TCAGAAATCAGAACAAAATTCAG
1 GTCAGAAATCAGAACAAAATTCAA
* *
1369606 GTCATG-TATCAGAACAGAATTCAA
1 GTCA-GAAATCAGAACAAAATTCAA
1369630 GTCAGAAATCAGA
1 GTCAGAAATCAGA
1369643 TAAAATATTT
Statistics
Matches: 64, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
23 2 0.03
24 60 0.94
25 1 0.02
26 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (24 bp):
GTCAGAAATCAGAACAAAATTCAA
Found at i:1369641 original size:48 final size:49
Alignment explanation
Indices: 1369534--1369642 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 49
1369524 AAACGGAGAT
* *
1369534 GTCAGAAATCAAAACAAAATTCAGAACATATATCAGAACATAATCCATA
1 GTCAGAAATCAGAACAAAATTCAGAACATATATCAGAACAGAATCCATA
** * *
1369583 -TCAGAAATCAGAACAAAATTCAGGTCATGTATCAGAACAGAATTCA-A
1 GTCAGAAATCAGAACAAAATTCAGAACATATATCAGAACAGAATCCATA
1369630 GTCAGAAATCAGA
1 GTCAGAAATCAGA
1369643 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (49 bp):
GTCAGAAATCAGAACAAAATTCAGAACATATATCAGAACAGAATCCATA
Found at i:1374187 original size:24 final size:23
Alignment explanation
Indices: 1374130--1374237 Score: 92
Period size: 24 Copynumber: 4.5 Consensus size: 23
1374120 AATGGAGCTG
* *
1374130 TCAGAAATCAAAACAAAATTCAGA
1 TCAGAAATCAGAACAGAATTCA-A
* * * *
1374154 ACATATATCAGAACAGAATCCATA
1 TCAGAAATCAGAACAGAATTCA-A
*
1374178 TCAGAAATCAGAACAGAATTCAGG
1 TCAGAAATCAGAACAGAATTCA-A
*
1374202 TCATG-TATCAGAACAGAATTCAA
1 TCA-GAAATCAGAACAGAATTCAA
1374225 GTCAGAAATCAGA
1 -TCAGAAATCAGA
1374238 TAAAATATTT
Statistics
Matches: 65, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (23 bp):
TCAGAAATCAGAACAGAATTCAA
Found at i:1374194 original size:12 final size:12
Alignment explanation
Indices: 1374131--1374200 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1374121 ATGGAGCTGT
*
1374131 CAGAAATCAAAA
1 CAGAAATCAGAA
1374143 CA-AAATTCAGAA
1 CAGAAA-TCAGAA
* *
1374155 CATATATCAGAA
1 CAGAAATCAGAA
* *
1374167 CAG-AATCCATAT
1 CAGAAAT-CAGAA
1374179 CAGAAATCAGAA
1 CAGAAATCAGAA
*
1374191 CAGAATTCAG
1 CAGAAATCAG
1374201 GTCATGTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 5 0.11
12 35 0.78
13 5 0.11
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:1374236 original size:48 final size:49
Alignment explanation
Indices: 1374129--1374237 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 49
1374119 AAATGGAGCT
*
1374129 GTCAGAAATCAAAACAAAATTCAGAACATATATCAGAACAGAATCCATA
1 GTCAGAAATCAGAACAAAATTCAGAACATATATCAGAACAGAATCCATA
* ** * *
1374178 -TCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAACAGAATTCA-A
1 GTCAGAAATCAGAACAAAATTCAGAACATATATCAGAACAGAATCCATA
1374225 GTCAGAAATCAGA
1 GTCAGAAATCAGA
1374238 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (49 bp):
GTCAGAAATCAGAACAAAATTCAGAACATATATCAGAACAGAATCCATA
Found at i:1378641 original size:17 final size:17
Alignment explanation
Indices: 1378619--1378654 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1378609 GCCATTTTTA
*
1378619 TACTGATACTCATAGGG
1 TACTGATACTAATAGGG
1378636 TACTGATACTAATAGGG
1 TACTGATACTAATAGGG
1378653 TA
1 TA
1378655 TCAATACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (17 bp):
TACTGATACTAATAGGG
Found at i:1379801 original size:32 final size:32
Alignment explanation
Indices: 1379751--1379836 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 32
1379741 AGATACTAGT
* * * *
1379751 AGTGTTACATTCAAATAATGCAAAATAGGGTC
1 AGTGTTGCATTTAGATAATGCAAAAGAGGGTC
* * *
1379783 AGTGTTGCATTTAGATAATGCACAAGAGTGTT
1 AGTGTTGCATTTAGATAATGCAAAAGAGGGTC
* * *
1379815 AGTATCGTATTTAGATAATGCA
1 AGTGTTGCATTTAGATAATGCA
1379837 TAACAGTTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (32 bp):
AGTGTTGCATTTAGATAATGCAAAAGAGGGTC
Found at i:1385001 original size:21 final size:22
Alignment explanation
Indices: 1384977--1385037 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
1384967 TGCCAGCTTT
1384977 GTCAAACCAATCAAGTTAGT-G
1 GTCAAACCAATCAAGTTAGTAG
*
1384998 GTCAAA-C-AT-AAGGTCTTGTAG
1 GTCAAACCAATCAA-GT-TAGTAG
1385019 GTCAAACCAATCAAGTTAG
1 GTCAAACCAATCAAGTTAG
1385038 ACGTAGGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 4 0.12
21 13 0.41
22 3 0.09
23 4 0.12
24 2 0.06
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (22 bp):
GTCAAACCAATCAAGTTAGTAG
Found at i:1387338 original size:20 final size:20
Alignment explanation
Indices: 1387313--1387365 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1387303 TTCAAGCAGG
1387313 GAGTATCGATACTTCTGGAA
1 GAGTATCGATACTTCTGGAA
1387333 GAGTATCGATACTTCTGGAA
1 GAGTATCGATACTTCTGGAA
1387353 GAGTATCGATACT
1 GAGTATCGATACT
1387366 GCCCCTACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
GAGTATCGATACTTCTGGAA
Found at i:1392756 original size:21 final size:21
Alignment explanation
Indices: 1392717--1392829 Score: 122
Period size: 21 Copynumber: 5.5 Consensus size: 21
1392707 AACTCCAGTT
* *
1392717 TCGCAACACAGTT-TCCAAAA
1 TCGCAACGCGGTTCTCCAAAA
*
1392737 TCGCAACGCGATTCTCCAAAA
1 TCGCAACGCGGTTCTCCAAAA
* * *
1392758 GCGCAACGTGGTT-TTCAAAA
1 TCGCAACGCGGTTCTCCAAAA
1392778 TCGCAACGCGGTTCTCCAAAA
1 TCGCAACGCGGTTCTCCAAAA
* * * *
1392799 TAGCAACGCGGTTTTTCAAAT
1 TCGCAACGCGGTTCTCCAAAA
1392820 TCGCAACGCG
1 TCGCAACGCG
1392830 TTGCGAAAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
20 27 0.36
21 49 0.64
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (21 bp):
TCGCAACGCGGTTCTCCAAAA
Found at i:1392763 original size:41 final size:41
Alignment explanation
Indices: 1392718--1392798 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
1392708 ACTCCAGTTT
1392718 CGCAACACAGTTTCCAAAATCGCAACGCGATTCTCCAAAAG
1 CGCAACACAGTTTCCAAAATCGCAACGCGATTCTCCAAAAG
*** * *
1392759 CGCAACGTGGTTTTCAAAATCGCAACGCGGTTCTCCAAAA
1 CGCAACACAGTTTCCAAAATCGCAACGCGATTCTCCAAAA
1392799 TAGCAACGCG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (41 bp):
CGCAACACAGTTTCCAAAATCGCAACGCGATTCTCCAAAAG
Found at i:1392805 original size:41 final size:41
Alignment explanation
Indices: 1392727--1392829 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
1392717 TCGCAACACA
* * *
1392727 GTTTCCAAAATCGCAACGCGATTCTCCAAAAGCGCAACGTG
1 GTTTTCAAAATCGCAACGCGATTCTCCAAAAGAGCAACGCG
* *
1392768 GTTTTCAAAATCGCAACGCGGTTCTCCAAAATAGCAACGCG
1 GTTTTCAAAATCGCAACGCGATTCTCCAAAAGAGCAACGCG
*
1392809 GTTTTTCAAATTCGCAACGCG
1 G-TTTTCAAAATCGCAACGCG
1392830 TTGCGAAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
41 37 0.67
42 18 0.33
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (41 bp):
GTTTTCAAAATCGCAACGCGATTCTCCAAAAGAGCAACGCG
Found at i:1392889 original size:20 final size:20
Alignment explanation
Indices: 1392866--1392926 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1392856 TTTGACTTCT
*
1392866 GTGTTGCGAATTACAAATTC
1 GTGTTGCGATTTACAAATTC
1392886 GTGTTGCGATTTACAAATTC
1 GTGTTGCGATTTACAAATTC
** *
1392906 GCATTGCGATTTACATATTC
1 GTGTTGCGATTTACAAATTC
1392926 G
1 G
1392927 CGTGTTGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (20 bp):
GTGTTGCGATTTACAAATTC
Found at i:1396853 original size:18 final size:18
Alignment explanation
Indices: 1396832--1396872 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1396822 CGACCCGTTT
1396832 ACCCGACCAATTGACCCG
1 ACCCGACCAATTGACCCG
**
1396850 ACCCGACCTGTTGACCCG
1 ACCCGACCAATTGACCCG
1396868 ACCCG
1 ACCCG
1396873 TTGACTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.46, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCAATTGACCCG
Found at i:1398240 original size:18 final size:18
Alignment explanation
Indices: 1398214--1398249 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1398204 TCGAAAGGAC
*
1398214 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1398232 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1398250 CAGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1399433 original size:23 final size:24
Alignment explanation
Indices: 1399386--1399476 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
1399376 TCAAATTTGA
* * *
1399386 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
* *
1399410 ATTCTAATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGACCTGG
*
1399433 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
1399457 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
1399477 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:1399455 original size:47 final size:48
Alignment explanation
Indices: 1399386--1399476 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
1399376 TCAAATTTGA
* * *
1399386 ATTCTGTTATGATACCTGACCTGGATTCTAATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTAATATGATACTTGACATGG
* *
1399433 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTAATATGATACTTGAC
1399477 TTGAATTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTAATATGATACTTGACATGG
Found at i:1399602 original size:35 final size:35
Alignment explanation
Indices: 1399563--1399663 Score: 202
Period size: 35 Copynumber: 2.9 Consensus size: 35
1399553 ATTACTTGGA
1399563 GGTTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
1 GGTTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
1399598 GGTTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
1 GGTTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
1399633 GGTTCCTCGGCTGTGTGCTCAGGGCCTTACT
1 GGTTCCTCGGCTGTGTGCTCAGGGCCTTACT
1399664 GGATGTGACG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.08, C:0.31, G:0.30, T:0.32
Consensus pattern (35 bp):
GGTTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
Found at i:1401678 original size:13 final size:13
Alignment explanation
Indices: 1401619--1401665 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
1401609 ACCGGTCATA
1401619 ACCCGACCAGTTT
1 ACCCGACCAGTTT
*
1401632 ACCCGACCCGTTT
1 ACCCGACCAGTTT
*
1401645 ACCCGACCAGTTG
1 ACCCGACCAGTTT
1401658 ACCCGACC
1 ACCCGACC
1401666 CGACCCGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.21, C:0.45, G:0.17, T:0.17
Consensus pattern (13 bp):
ACCCGACCAGTTT
Found at i:1403039 original size:18 final size:18
Alignment explanation
Indices: 1403013--1403048 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1403003 TCGAAATGAC
*
1403013 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1403031 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1403049 CGGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1404222 original size:24 final size:24
Alignment explanation
Indices: 1404186--1404276 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
1404176 TCAAATTTGA
* * *
1404186 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
1404210 ATGT-TGATCTGATA-TTGACATGG
1 AT-TCTGATCTGATACTTGACCTGG
*
1404233 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
1404257 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
1404277 TTGAATTATG
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.02
23 19 0.34
24 35 0.62
25 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:1404255 original size:47 final size:48
Alignment explanation
Indices: 1404186--1404276 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 48
1404176 TCAAATTTGA
* * *
1404186 ATTCTGTTATGATACCTGACCTGGATGT-TGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGAT-TCTGATATGATACTTGACATGG
*
1404233 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
1404277 TTGAATTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 1 0.03
47 32 0.84
48 5 0.13
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:1405253 original size:8 final size:8
Alignment explanation
Indices: 1405240--1405266 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1405230 ATATACTTAA
1405240 AATAATTT
1 AATAATTT
1405248 AATAATTT
1 AATAATTT
1405256 AATAATTT
1 AATAATTT
1405264 AAT
1 AAT
1405267 TTTATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATAATTT
Found at i:1411456 original size:51 final size:51
Alignment explanation
Indices: 1411359--1411466 Score: 141
Period size: 51 Copynumber: 2.1 Consensus size: 51
1411349 ATATTTACAC
1411359 TTATATATGAATCATATCAATTTAAACTATAATAAATTCAAAAAAAAAT-T-A
1 TTATATATGAATCATATCAATTTAAACTATAATAAA-T-AAAAAAAAATATAA
* *
1411410 TTATATATGAATTATATCAATTTTAACTATAATAAA-AAATATAAAAATATAA
1 TTATATATGAATCATATCAATTTAAACTATAATAAATAAA-A-AAAAATATAA
1411462 TTATA
1 TTATA
1411467 ATAAAAATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
48 3 0.06
49 1 0.02
50 6 0.12
51 35 0.69
52 6 0.12
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (51 bp):
TTATATATGAATCATATCAATTTAAACTATAATAAATAAAAAAAAATATAA
Found at i:1411487 original size:17 final size:16
Alignment explanation
Indices: 1411448--1411487 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1411438 ATAATAAAAA
1411448 ATATAAAAATATAATT
1 ATATAAAAATATAATT
*
1411464 ATAATAAAAATATATTTT
1 AT-ATAAAAATATA-ATT
1411482 ATATAA
1 ATATAA
1411488 CTCATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 15 0.71
18 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAAAATATAATT
Found at i:1411566 original size:13 final size:13
Alignment explanation
Indices: 1411535--1411560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1411525 TATTTATTTT
1411535 TAAATAATTAAAA
1 TAAATAATTAAAA
1411548 TAAATAATTAAAA
1 TAAATAATTAAAA
1411561 GTAATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATAATTAAAA
Found at i:1412456 original size:29 final size:29
Alignment explanation
Indices: 1412411--1412468 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1412401 TAAAATTATT
1412411 TTCGCTTAAAAGGACTATTGTCTCTTAAA
1 TTCGCTTAAAAGGACTATTGTCTCTTAAA
*
1412440 TTCGCTTAAAAGTACTATTGTCTCTTAAA
1 TTCGCTTAAAAGGACTATTGTCTCTTAAA
1412469 GTATATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (29 bp):
TTCGCTTAAAAGGACTATTGTCTCTTAAA
Found at i:1412744 original size:18 final size:18
Alignment explanation
Indices: 1412700--1412744 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1412690 TTCCCCCTTC
*
1412700 TCCTTCCCCTCCCCATCA
1 TCCTCCCCCTCCCCATCA
1412718 TCCTCCCCCTCCCCATCA
1 TCCTCCCCCTCCCCATCA
1412736 TCCTCCCCC
1 TCCTCCCCC
1412745 CACCTCTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.67, G:0.00, T:0.24
Consensus pattern (18 bp):
TCCTCCCCCTCCCCATCA
Found at i:1432348 original size:17 final size:17
Alignment explanation
Indices: 1432308--1432341 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1432298 ATGCACGAGC
1432308 AAGCAATTTATAAAGTT
1 AAGCAATTTATAAAGTT
1432325 AAGCAATTTATAAAGTT
1 AAGCAATTTATAAAGTT
1432342 TGTCAATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
AAGCAATTTATAAAGTT
Found at i:1438637 original size:30 final size:28
Alignment explanation
Indices: 1438591--1438648 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
1438581 CTTTTCCAAA
* * *
1438591 AAAAATTAATTAGGTCCCCTAACTTTTC
1 AAAAATTAATAAGGTCCCCAAAATTTTC
1438619 AAAAATTACATAATGGTCCCCAAAATTTTC
1 AAAAATTA-ATAA-GGTCCCCAAAATTTTC
1438649 TAAGGCTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.32
29 3 0.12
30 14 0.56
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (28 bp):
AAAAATTAATAAGGTCCCCAAAATTTTC
Found at i:1445209 original size:170 final size:170
Alignment explanation
Indices: 1444927--1445267 Score: 682
Period size: 170 Copynumber: 2.0 Consensus size: 170
1444917 GTCCCCCAAC
1444927 TTTTCAAAAAATTACATAATGGTCTCCAAATTTTTCTAAGCCTTGTAGAATACTTCCTACATCAT
1 TTTTCAAAAAATTACATAATGGTCTCCAAATTTTTCTAAGCCTTGTAGAATACTTCCTACATCAT
1444992 TTCCAGCCCTTTCTTAATTTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGTCGAATGGTTC
66 TTCCAGCCCTTTCTTAATTTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGTCGAATGGTTC
1445057 AAAGTTCCAAAACTAGGTTTTTCATGATTTTGTTCGATTT
131 AAAGTTCCAAAACTAGGTTTTTCATGATTTTGTTCGATTT
1445097 TTTTCAAAAAATTACATAATGGTCTCCAAATTTTTCTAAGCCTTGTAGAATACTTCCTACATCAT
1 TTTTCAAAAAATTACATAATGGTCTCCAAATTTTTCTAAGCCTTGTAGAATACTTCCTACATCAT
1445162 TTCCAGCCCTTTCTTAATTTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGTCGAATGGTTC
66 TTCCAGCCCTTTCTTAATTTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGTCGAATGGTTC
1445227 AAAGTTCCAAAACTAGGTTTTTCATGATTTTGTTCGATTT
131 AAAGTTCCAAAACTAGGTTTTTCATGATTTTGTTCGATTT
1445267 T
1 T
1445268 GATTCGATTC
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 171 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (170 bp):
TTTTCAAAAAATTACATAATGGTCTCCAAATTTTTCTAAGCCTTGTAGAATACTTCCTACATCAT
TTCCAGCCCTTTCTTAATTTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGTCGAATGGTTC
AAAGTTCCAAAACTAGGTTTTTCATGATTTTGTTCGATTT
Found at i:1445846 original size:31 final size:31
Alignment explanation
Indices: 1445811--1445873 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1445801 TAATTACCAT
1445811 CAAACCAAGACACCTCAACCTTATCATCTTC
1 CAAACCAAGACACCTCAACCTTATCATCTTC
1445842 CAAACCAAGACACCTCAACCTTATCATCTTC
1 CAAACCAAGACACCTCAACCTTATCATCTTC
1445873 C
1 C
1445874 TTAAGTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.40, G:0.03, T:0.22
Consensus pattern (31 bp):
CAAACCAAGACACCTCAACCTTATCATCTTC
Found at i:1448233 original size:19 final size:19
Alignment explanation
Indices: 1448209--1448250 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1448199 TGGCAGAATG
1448209 GAGTGAAGAAGAGAAGAAA
1 GAGTGAAGAAGAGAAGAAA
1448228 GAGTGAAGAAGAGAAGAAA
1 GAGTGAAGAAGAGAAGAAA
1448247 GAGT
1 GAGT
1448251 TCCAACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (19 bp):
GAGTGAAGAAGAGAAGAAA
Found at i:1449360 original size:17 final size:18
Alignment explanation
Indices: 1449321--1449362 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
1449311 AGGAGCGTCG
1449321 GTGTATCGGTACACTTTTAA
1 GTGTATCGGTACAC--TTAA
1449341 GTGTATCGGTACAC-TAA
1 GTGTATCGGTACACTTAA
1449358 GTGTA
1 GTGTA
1449363 AAATTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
20 14 0.64
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (18 bp):
GTGTATCGGTACACTTAA
Found at i:1449656 original size:55 final size:55
Alignment explanation
Indices: 1449457--1449655 Score: 290
Period size: 55 Copynumber: 3.6 Consensus size: 55
1449447 CCTAAGCCAG
* * * * ** * *
1449457 GGGTGTATCGGTAGATCAGACAGTGTATCAATACACAAAATGCATTCAATGTTGG
1 GGGTGTATCGATACATCAAAGAGTGTATCGGTACACAAAATGCATTCGATGTTGT
* *
1449512 GGGTGTATCGATACATCAAAGAGTGTATTGGTACACAAAATGTATTCGATGTTGT
1 GGGTGTATCGATACATCAAAGAGTGTATCGGTACACAAAATGCATTCGATGTTGT
* *
1449567 GGGTGTATCGATACATCAAAGAGTGTATCGGTACCCAAAAGGCATTCGATGTTGT
1 GGGTGTATCGATACATCAAAGAGTGTATCGGTACACAAAATGCATTCGATGTTGT
1449622 GGGTGTATCGATACATCAAAGAGTGTATCGGTAC
1 GGGTGTATCGATACATCAAAGAGTGTATCGGTAC
1449656 CTCCCTTTGT
Statistics
Matches: 130, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 130 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (55 bp):
GGGTGTATCGATACATCAAAGAGTGTATCGGTACACAAAATGCATTCGATGTTGT
Found at i:1452353 original size:21 final size:21
Alignment explanation
Indices: 1452297--1452353 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1452287 ACTATCATAG
* *
1452297 TGTATCAATACATAATGACGA
1 TGTATCGATACATAGTGACGA
*
1452318 TGTATCGATACATAGTGAGGA
1 TGTATCGATACATAGTGACGA
1452339 TGTATCGATACATAG
1 TGTATCGATACATAG
1452354 GTATCGATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATAGTGACGA
Found at i:1453991 original size:19 final size:19
Alignment explanation
Indices: 1453945--1453994 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1453935 TTCTTGAGTA
**
1453945 TAGCCTTGAGCAACAAGTC
1 TAGCCTTGTTCAACAAGTC
1453964 TAGCCTTGTTCAACAAGTC
1 TAGCCTTGTTCAACAAGTC
1453983 TAGCCTTGTTCA
1 TAGCCTTGTTCA
1453995 TCTCTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (19 bp):
TAGCCTTGTTCAACAAGTC
Found at i:1455962 original size:82 final size:82
Alignment explanation
Indices: 1455859--1456022 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
1455849 ATTTGTGTAG
1455859 GATATCCTTTCTTTAGTAGTAATGAGTTCTTTAGGAACCCATATACTTCTAACGATTTTACCATT
1 GATATCCTTTCTTTAGTAGTAATGAGTTCTTTAGGAACCCATATACTTCTAACGATTTTACCATT
1455924 AGAGGTTCTTTGGGGAC
66 AGAGGTTCTTTGGGGAC
1455941 GATATCCTTTCTTTAGTAGTAATGAGTTCTTTAGGAACCCATATACTTCTAACGATTTTACCATT
1 GATATCCTTTCTTTAGTAGTAATGAGTTCTTTAGGAACCCATATACTTCTAACGATTTTACCATT
1456006 AGAGGTTCTTTGGGGAC
66 AGAGGTTCTTTGGGGAC
1456023 CTCTATGATT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (82 bp):
GATATCCTTTCTTTAGTAGTAATGAGTTCTTTAGGAACCCATATACTTCTAACGATTTTACCATT
AGAGGTTCTTTGGGGAC
Found at i:1456134 original size:18 final size:18
Alignment explanation
Indices: 1456111--1456147 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1456101 AAACTTTATT
1456111 AAAAGAA-ACTTTAAGATC
1 AAAAGAAGA-TTTAAGATC
1456129 AAAAGAAGATTTAAGATC
1 AAAAGAAGATTTAAGATC
1456147 A
1 A
1456148 TCAATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.22
Consensus pattern (18 bp):
AAAAGAAGATTTAAGATC
Found at i:1466619 original size:7 final size:7
Alignment explanation
Indices: 1466609--1466668 Score: 61
Period size: 7 Copynumber: 8.7 Consensus size: 7
1466599 TATATATATA
1466609 ATATTTT
1 ATATTTT
1466616 ATATTTT
1 ATATTTT
*
1466623 -TATATT
1 ATATTTT
*
1466629 A-ATTAT
1 ATATTTT
* *
1466635 ATATATA
1 ATATTTT
1466642 ATATTTT
1 ATATTTT
1466649 ATATTTT
1 ATATTTT
1466656 ATATTTTT
1 ATA-TTTT
1466664 ATATT
1 ATATT
1466669 AATTATATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 9 0.21
7 26 0.62
8 7 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
ATATTTT
Found at i:1466641 original size:33 final size:32
Alignment explanation
Indices: 1466599--1466660 Score: 115
Period size: 33 Copynumber: 1.9 Consensus size: 32
1466589 GCCCCGATTA
1466599 TATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATA-TTTTATATTAAT
1466632 TATATATATAATATTTTATATTTTATATT
1 TATATATATAATATTTTATATTTTATATT
1466661 TTTATATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
TATATATATAATATTTTATATTTTATATTAAT
Found at i:1467380 original size:17 final size:18
Alignment explanation
Indices: 1467350--1467390 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1467340 TTAGGGATAC
* *
1467350 TATTCATTTTATTTTATT
1 TATTTATTTAATTTTATT
1467368 T-TTTATTTAATTTTATT
1 TATTTATTTAATTTTATT
1467385 TATTTA
1 TATTTA
1467391 GATAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTTATTTAATTTTATT
Found at i:1473142 original size:35 final size:36
Alignment explanation
Indices: 1473101--1473181 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
1473091 AAAACAATCA
*
1473101 TCAATTACATTCTAAACCCCAAATTTC-AAAACACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAACACT
* *
1473136 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAACACT
*
1473172 TAAATTACAT
1 TCAATTACAT
1473182 GACCAACTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 25 0.61
36 16 0.39
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAAACACT
Found at i:1473850 original size:147 final size:149
Alignment explanation
Indices: 1473613--1473905 Score: 484
Period size: 147 Copynumber: 2.0 Consensus size: 149
1473603 AAACTATTTA
* * *
1473613 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAAAAGAAACTCAAA
* *
1473678 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAATTCAAATCGAAAATATTTC-AGTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAATATTTCGAGCCAACT
*
1473742 A-TTTTATAAATTGAACTG
131 ATTTTTATAAACTGAACTG
*
1473760 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTCAATTTAAAAAGAAACT-AGA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAAAAGAAACTCA-A
*
1473824 AAATTCAATTCAATTCGACTTTATTTAAATTTTATAAACTCAAATCGAAAATATTTCGAGCCAAC
65 AAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAATATTTCGAGCCAAC
1473889 TATTTTTATAAACTGAA
130 TATTTTTATAAACTGAA
1473906 TTGAGTATTT
Statistics
Matches: 135, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
146 1 0.01
147 113 0.84
148 8 0.06
149 13 0.10
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (149 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAAAAGAAACTCAAA
AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAATATTTCGAGCCAACT
ATTTTTATAAACTGAACTG
Found at i:1474125 original size:35 final size:36
Alignment explanation
Indices: 1474086--1474161 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 36
1474076 GTTGGGCATA
*
1474086 TAATTGAAGTATTTTGGAATTTAAGG-TTTAGAATG
1 TAATTGAAGCATTTTGGAATTTAAGGTTTTAGAATG
* *
1474121 TAATTGAAGCATTTTGGATTTTATGGTTTTAGAATG
1 TAATTGAAGCATTTTGGAATTTAAGGTTTTAGAATG
1474157 TAATT
1 TAATT
1474162 AATGATTGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 23 0.62
36 14 0.38
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (36 bp):
TAATTGAAGCATTTTGGAATTTAAGGTTTTAGAATG
Found at i:1475261 original size:26 final size:27
Alignment explanation
Indices: 1475231--1475293 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 27
1475221 ATGCCGGGCC
1475231 AATTTTTTAATTGAATCG-AATAA-AAA
1 AATTTTTTAATTGAAT-GAAATAAGAAA
*
1475257 AA---TTTAATAGAATGAAATAAGAAA
1 AATTTTTTAATTGAATGAAATAAGAAA
1475281 AATATTTTTAATT
1 AAT-TTTTTAATT
1475294 TAAGTACACG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
22 1 0.03
23 15 0.52
24 5 0.17
26 2 0.07
28 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (27 bp):
AATTTTTTAATTGAATGAAATAAGAAA
Found at i:1476187 original size:20 final size:20
Alignment explanation
Indices: 1476143--1476190 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1476133 GTCATATCTT
1476143 TTCACCAAGAGTAGTACCTC
1 TTCACCAAGAGTAGTACCTC
* * **
1476163 CTCACCAAGAGTTGTGTCTC
1 TTCACCAAGAGTAGTACCTC
1476183 TTCACCAA
1 TTCACCAA
1476191 AGATCACCTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (20 bp):
TTCACCAAGAGTAGTACCTC
Found at i:1477632 original size:50 final size:50
Alignment explanation
Indices: 1477574--1477669 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
1477564 TTACCTGAAT
** *
1477574 GACAAAACTGAATATATGACCACAAGTATTTATACTCGATTTTGATGCAC
1 GACAAAACTGAATATATGACCACAAACATTTATAATCGATTTTGATGCAC
1477624 GACAAAACTGAATATATGACCACAAACATTTATAATCGATTTTGAT
1 GACAAAACTGAATATATGACCACAAACATTTATAATCGATTTTGAT
1477670 TATACTCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (50 bp):
GACAAAACTGAATATATGACCACAAACATTTATAATCGATTTTGATGCAC
Found at i:1478801 original size:17 final size:17
Alignment explanation
Indices: 1478779--1478811 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1478769 AACATGTTTA
*
1478779 AAAATAAAACTTAAAAT
1 AAAATAAAAATTAAAAT
1478796 AAAATAAAAATTAAAA
1 AAAATAAAAATTAAAA
1478812 CTTGAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAAAAATTAAAAT
Found at i:1478810 original size:24 final size:24
Alignment explanation
Indices: 1478777--1478829 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
1478767 TTAACATGTT
*
1478777 TAAAAATAAAACTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAAGAAAA
1478800 TAAAAATTAAAACTTGAAAAGAAAA
1 TAAAAA-TAAAACTTGAAAAGAAAA
*
1478825 GAAAA
1 TAAAA
1478830 GAAAGAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 6 0.23
24 8 0.31
25 12 0.46
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAAGAAAA
Found at i:1479922 original size:12 final size:12
Alignment explanation
Indices: 1479905--1479945 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1479895 TCTCATGTTT
*
1479905 TTTTCTATTTTC
1 TTTTCTTTTTTC
1479917 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
1479929 TGTTTTTTTTTTC
1 T-TTTCTTTTTTC
1479942 TTTT
1 TTTT
1479946 TAAAATGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:1479925 original size:19 final size:20
Alignment explanation
Indices: 1479903--1479946 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1479893 TTTCTCATGT
1479903 TTTTTTCT-ATTTTCTTTTC
1 TTTTTTCTGATTTTCTTTTC
* *
1479922 TTTTTTCTGTTTTTTTTTTC
1 TTTTTTCTGATTTTCTTTTC
1479942 TTTTT
1 TTTTT
1479947 AAAATGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTTTTCTGATTTTCTTTTC
Found at i:1479946 original size:12 final size:12
Alignment explanation
Indices: 1479912--1479946 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1479902 TTTTTTTCTA
*
1479912 TTTTCTTTTCTT
1 TTTTCTTTTTTT
1479924 TTTTCTGTTTTTT
1 TTTTCT-TTTTTT
1479937 TTTTCTTTTT
1 TTTTCTTTTT
1479947 AAAATGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:1485157 original size:17 final size:17
Alignment explanation
Indices: 1485135--1485167 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1485125 TAACTGTTTA
*
1485135 AAAATAAAACTTAAAAT
1 AAAATAAAAATTAAAAT
1485152 AAAATAAAAATTAAAA
1 AAAATAAAAATTAAAA
1485168 CTTGAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAAAAATTAAAAT
Found at i:1485166 original size:24 final size:25
Alignment explanation
Indices: 1485133--1485189 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1485123 CTTAACTGTT
*
1485133 TAAAAA-TAAAACTT-AAAATAAAA
1 TAAAAATTAAAACTTGAAAAGAAAA
1485156 TAAAAATTAAAACTTGAAAAGAAAA
1 TAAAAATTAAAACTTGAAAAGAAAA
*
1485181 GAAACAATT
1 TAAA-AATT
1485190 TTATAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 8 0.28
25 11 0.38
26 4 0.14
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (25 bp):
TAAAAATTAAAACTTGAAAAGAAAA
Found at i:1490429 original size:150 final size:149
Alignment explanation
Indices: 1490142--1490448 Score: 533
Period size: 154 Copynumber: 2.0 Consensus size: 149
1490132 AGAACGAAGC
1490142 ATATACAATTGAGATATCATTTTATTCGGTCTCTTCTGAAGATGGGATTTTGAAACTTGAAAATT
1 ATATACAATTGAGATATCATTTTATTCGGTCTCTTCTGAAGATGGGATTTTGAAACTTGAAAATT
1490207 AGGGAGCTCAAAATCCGGCAGACATGTTGACAAAGACGGTGACAAAGACAACTGAAGTTGTGTTC
66 AGGGAGCTCAAAATCCGGCAGACATGTTGACAAAGACGGTGACAAAGACAACTGAAGTTGTGTT-
1490272 AGCTTCAGTTGGCATACTAG
130 AGCTTCAGTTGGCATACTAG
1490292 ATATACAATTGAGATATCATTTTATTCGGTCTCTTCTGGAAGATGGGATTTTGAAACTTGAAAAG
1 ATATACAATTGAGATATCATTTTATTCGGTCTCTTCT-GAAGATGGGATTTTGAAACTTG-AAA-
*
1490357 ATTAGTGGAGCTCAAAATCCGGCAGACATGTTGACAAAGACGGTGACCACAGACAAACTGAAGTT
63 ATTAG-GGAGCTCAAAATCCGGCAGACATGTTGACAAAGACGGTGA-CAAAGAC-AACTGAAGTT
1490422 GTGTTCAGCTTCAGTTGGCATACTAG
125 GTGTT-AGCTTCAGTTGGCATACTAG
1490448 A
1 A
1490449 ATAACAAGAC
Statistics
Matches: 150, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
150 37 0.25
151 22 0.15
152 3 0.02
153 5 0.03
154 40 0.27
155 6 0.04
156 37 0.25
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (149 bp):
ATATACAATTGAGATATCATTTTATTCGGTCTCTTCTGAAGATGGGATTTTGAAACTTGAAAATT
AGGGAGCTCAAAATCCGGCAGACATGTTGACAAAGACGGTGACAAAGACAACTGAAGTTGTGTTA
GCTTCAGTTGGCATACTAG
Found at i:1497051 original size:5 final size:5
Alignment explanation
Indices: 1497041--1497119 Score: 90
Period size: 5 Copynumber: 16.0 Consensus size: 5
1497031 CAAAAAAAAG
* * *
1497041 AATAA AAT-A AATAA CATAA AGTAA AGTAA AATAA AATAA AAT-A AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
* *
1497089 AACAA GATAA AATAA AATAGA AATAA AATAA
1 AATAA AATAA AATAA AATA-A AATAA AATAA
1497120 GAAAAAGATG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
4 8 0.13
5 50 0.79
6 5 0.08
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:1497073 original size:29 final size:28
Alignment explanation
Indices: 1497041--1497107 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 28
1497031 CAAAAAAAAG
1497041 AATAAAATAAATAACATAAAGTA-AAG-TAA
1 AATAAAATAAATAA-ATAAA--ACAAGATAA
1497070 AATAAAATAAAATAAATAAAACAAGATAA
1 AATAAAAT-AAATAAATAAAACAAGATAA
1497099 AATAAAATA
1 AATAAAATA
1497108 GAAATAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
27 1 0.03
28 4 0.11
29 24 0.69
30 6 0.17
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.19
Consensus pattern (28 bp):
AATAAAATAAATAAATAAAACAAGATAA
Found at i:1497098 original size:24 final size:25
Alignment explanation
Indices: 1497071--1497125 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
1497061 GTAAAGTAAA
1497071 ATAAAATAAAAT-AAATAAAACAAG
1 ATAAAATAAAATAAAATAAAACAAG
*
1497095 ATAAAATAAAATAGAAATAAAATAAG
1 ATAAAATAAAATA-AAATAAAACAAG
1497121 A-AAAA
1 ATAAAA
1497126 GATGATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 12 0.43
25 4 0.14
26 12 0.43
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.16
Consensus pattern (25 bp):
ATAAAATAAAATAAAATAAAACAAG
Found at i:1497142 original size:35 final size:34
Alignment explanation
Indices: 1497041--1497224 Score: 111
Period size: 34 Copynumber: 5.5 Consensus size: 34
1497031 CAAAAAAAAG
*
1497041 AATAAAATAAATAACATA-AAG-TAAAGTAAAATAA
1 AATAAAATAAATAA-A-ACAAGATAAAATAAAATAA
1497075 AATAAAATAAATAAAACAAGATAAAATAAAATAGA
1 AATAAAATAAATAAAACAAGATAAAATAAAATA-A
* * * *
1497110 AATAAAATAAGA-AAAAGATGATTAAATCAAATAA
1 AATAAAATAA-ATAAAACAAGATAAAATAAAATAA
* *
1497144 AA-AGAAA-CAA-AAAAC-A-A-AAATTAAAATTAA
1 AATA-AAATAAATAAAACAAGATAAAATAAAA-TAA
* * * *
1497174 AATTAAAAAAAATAAAACCATGAT-ATATATAATAA
1 AA-TAAAATAAATAAAA-CAAGATAAAATAAAATAA
1497209 AA-AGAAATAAATAAAA
1 AATA-AAATAAATAAAA
1497225 AGGATGAAAA
Statistics
Matches: 118, Mismatches: 17, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
29 6 0.05
30 6 0.05
31 3 0.03
32 9 0.08
33 11 0.09
34 43 0.36
35 33 0.28
36 7 0.06
ACGTcount: A:0.72, C:0.04, G:0.05, T:0.19
Consensus pattern (34 bp):
AATAAAATAAATAAAACAAGATAAAATAAAATAA
Found at i:1497306 original size:14 final size:14
Alignment explanation
Indices: 1497271--1497297 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1497261 TTATGTGAAG
1497271 AAAAATAAAAATAA
1 AAAAATAAAAATAA
1497285 AAAAATAAAAATA
1 AAAAATAAAAATA
1497298 TATAGATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAATAA
Done.