Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018017.1 Corchorus olitorius cultivar O-4 contig18050, 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: 129578
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:93 original size:40 final size:41
Alignment explanation
Indices: 30--107 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
20 ACTTGACCCA
* *
30 CCTAATAATTAAGGAAATAAATTAAATTCAGGTTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCC
*
71 CCTAATAA-TAAGGTAAGAAATTAAATCCAGGTTTAGC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGC
108 TCCTAGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 26 0.76
41 8 0.24
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (41 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCC
Found at i:232 original size:13 final size:13
Alignment explanation
Indices: 210--240 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
200 TGACACGTCA
*
210 GGAGGGACAAATT
1 GGAGGAACAAATT
223 GGAGGAACAAATT
1 GGAGGAACAAATT
236 GGAGG
1 GGAGG
241 GTCATGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.42, T:0.13
Consensus pattern (13 bp):
GGAGGAACAAATT
Found at i:903 original size:64 final size:64
Alignment explanation
Indices: 824--949 Score: 243
Period size: 64 Copynumber: 2.0 Consensus size: 64
814 AAAATACATA
*
824 TCCCAAAGTTGAGCTTTGCGCATTTTGATTATGAAGTAGAAATTAGGCTAAATGTTCAATTTGG
1 TCCCAAAGTTGAGCTTTGCGCATTTTGATTATGAAGTAGAAATTAGGCTAAATGCTCAATTTGG
888 TCCCAAAGTTGAGCTTTGCGCATTTTGATTATGAAGTAGAAATTAGGCTAAATGCTCAATTT
1 TCCCAAAGTTGAGCTTTGCGCATTTTGATTATGAAGTAGAAATTAGGCTAAATGCTCAATTT
950 AATACCAAAG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (64 bp):
TCCCAAAGTTGAGCTTTGCGCATTTTGATTATGAAGTAGAAATTAGGCTAAATGCTCAATTTGG
Found at i:2226 original size:15 final size:15
Alignment explanation
Indices: 2200--2233 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2190 CTTTATTTCT
2200 TTTTTAACTTTTAAAG
1 TTTTTAACTTTT-AAG
2216 TTTTTAA-TTTTAAG
1 TTTTTAACTTTTAAG
2230 TTTT
1 TTTT
2234 ATTTTGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 4 0.22
16 7 0.39
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTTAACTTTTAAG
Found at i:5640 original size:25 final size:24
Alignment explanation
Indices: 5604--5650 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
5594 TCCTTCTATT
5604 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
5627 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
5651 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:21203 original size:9 final size:9
Alignment explanation
Indices: 21189--21238 Score: 79
Period size: 9 Copynumber: 5.9 Consensus size: 9
21179 ATAAGATAAG
21189 TTTTTCTTC
1 TTTTTCTTC
21198 --TTT-TTC
1 TTTTTCTTC
21204 TTTTTCTTC
1 TTTTTCTTC
21213 TTTTTCTTC
1 TTTTTCTTC
21222 TTTTTCTTC
1 TTTTTCTTC
21231 TTTTTCTT
1 TTTTTCTT
21239 AATGCTTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 3 0.08
9 29 0.76
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:21209 original size:15 final size:15
Alignment explanation
Indices: 21189--21238 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
21179 ATAAGATAAG
21189 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTTTTC
21204 TTTTTCTTCTTTTTCTTC
1 TTTTTCTTC--TTT-TTC
21222 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTTTTC
21237 TT
1 TT
21239 AATGCTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 14 0.44
16 3 0.09
17 3 0.09
18 12 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTTCTTTTTC
Found at i:24486 original size:41 final size:43
Alignment explanation
Indices: 24380--24665 Score: 248
Period size: 41 Copynumber: 6.8 Consensus size: 43
24370 CCAATAAATA
* * * *
24380 AAAGTCCCCAAACACA-ATATTAACACAGGGGCAATTCTCTATCT
1 AAAGTCCCCAAACACATTTA-TAACACAGAGGCAA-CCTATATCT
** *
24424 AAAGTCCTTAAACACATTTATAACACAGAGAC-ACCTATATC-
1 AAAGTCCCCAAACACATTTATAACACAGAGGCAACCTATATCT
* * * ** *
24465 AAAGTCCCCAAACACAATTATAGCACAGGGGCGTCTCTAT-TCC
1 AAAGTCCCCAAACACATTTATAACACAGAGGCAAC-CTATATCT
* * *
24508 AAAGTCCTCAAACACATTTATAACACAGAGAC-ATCTATATC-
1 AAAGTCCCCAAACACATTTATAACACAGAGGCAACCTATATCT
* * * *
24549 AAAGTCCCCAAACACATTGATAACACAGGGGCAATTCTCT-TCT
1 AAAGTCCCCAAACACATTTATAACACAGAGGCAA-CCTATATCT
** **
24592 AAAGTCCTTAAACACATTTATAACACAGAGGCTTCC-ATA-CT
1 AAAGTCCCCAAACACATTTATAACACAGAGGCAACCTATATCT
*
24633 AAAGTCCCCAAACACATTTATAACAGAGAGGCA
1 AAAGTCCCCAAACACATTTATAACACAGAGGCA
24666 TTTCTATTTA
Statistics
Matches: 195, Mismatches: 38, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
41 90 0.46
42 15 0.08
43 64 0.33
44 24 0.12
45 2 0.01
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.23
Consensus pattern (43 bp):
AAAGTCCCCAAACACATTTATAACACAGAGGCAACCTATATCT
Found at i:24535 original size:84 final size:85
Alignment explanation
Indices: 24380--24657 Score: 381
Period size: 84 Copynumber: 3.3 Consensus size: 85
24370 CCAATAAATA
24380 AAAGTCCCCAAACACAA-TATTAACACAGGGGCAATTCTCTA-TCTAAAGTCCTTAAACACATTT
1 AAAGTCCCCAAACACAATTA-TAACACAGGGGCAA-TCTCTATTCTAAAGTCCTTAAACACATTT
24443 ATAACACAGAGACACCTATATC
64 ATAACACAGAGACACCTATATC
* * * *
24465 AAAGTCCCCAAACACAATTATAGCACAGGGGC-GTCTCTATTCCAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTATTCTAAAGTCCTTAAACACATTTAT
*
24529 AACACAGAGACATCTATATC
66 AACACAGAGACACCTATATC
*
24549 AAAGTCCCCAAACAC-ATTGATAACACAGGGGCAAT-TCTCTTCTAAAGTCCTTAAACACATTTA
1 AAAGTCCCCAAACACAATT-ATAACACAGGGGCAATCTCTATTCTAAAGTCCTTAAACACATTTA
* *
24612 TAACACAGAGGCTTCC-ATA-C
65 TAACACAGAGAC-ACCTATATC
*
24632 TAAAGTCCCCAAACACATTTATAACA
1 -AAAGTCCCCAAACACAATTATAACA
24658 GAGAGGCATT
Statistics
Matches: 172, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
83 10 0.06
84 128 0.74
85 32 0.19
86 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (85 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTATTCTAAAGTCCTTAAACACATTTAT
AACACAGAGACACCTATATC
Found at i:24735 original size:2 final size:2
Alignment explanation
Indices: 24728--24752 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24718 ATTCCTGTCT
24728 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
24753 GTAACAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28967 original size:21 final size:21
Alignment explanation
Indices: 28941--28984 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28931 TTTTTCTGAA
28941 TTGCTAAATACCGCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
** *
28962 TTGCTACTTACTGCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
28983 TT
1 TT
28985 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.41, G:0.09, T:0.36
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCCCTT
Found at i:29247 original size:18 final size:18
Alignment explanation
Indices: 29235--29309 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 18
29225 TTATTTTTTT
29235 TTTAATTATTATTAATTA
1 TTTAATTATTATTAATTA
29253 TTTAATTATTAATTATATTAA
1 TTTAATTATT-ATTA-ATT-A
*
29274 TTTAAATTGTTATT-ATTAA
1 TTT-AATTATTATTAATT-A
*
29293 TTATAATTATAATTAAT
1 TT-TAATTATTATTAAT
29310 AATAATTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
18 10 0.21
19 19 0.40
20 6 0.12
21 7 0.15
22 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (18 bp):
TTTAATTATTATTAATTA
Found at i:29251 original size:10 final size:10
Alignment explanation
Indices: 29236--29309 Score: 50
Period size: 10 Copynumber: 7.5 Consensus size: 10
29226 TATTTTTTTT
29236 TTAATTATTA
1 TTAATTATTA
29246 TTAATTA-T-
1 TTAATTATTA
29254 TTAATTATTAA
1 TTAATTATT-A
29265 TTATATTAATT-
1 TTA-ATT-ATTA
* *
29276 TAAATTGTTA
1 TTAATTATTA
29286 TT-ATTAATTA
1 TTAATT-ATTA
*
29296 -TAATTATAA
1 TTAATTATTA
29305 TTAAT
1 TTAAT
29310 AATAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
8 7 0.14
9 11 0.22
10 21 0.42
11 5 0.10
12 3 0.06
13 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (10 bp):
TTAATTATTA
Found at i:29372 original size:32 final size:32
Alignment explanation
Indices: 29331--29481 Score: 259
Period size: 32 Copynumber: 4.7 Consensus size: 32
29321 AAAAAACTTG
29331 GCCGCCCTCCTAGGGCGGCACTCCATGGTCAT
1 GCCGCCCTCCTAGGGCGGCACTCCATGGTCAT
29363 GCCGCCCTCCTAGGGCGGCACTCCATGGTCAT
1 GCCGCCCTCCTAGGGCGGCACTCCATGGTCAT
*
29395 GCCGCCCTCCTAGGACGGCACTCCATGGTCAT
1 GCCGCCCTCCTAGGGCGGCACTCCATGGTCAT
*
29427 GCCGCCCTCCTTGGGCGGCA-TGCCATGGTCAAT
1 GCCGCCCTCCTAGGGCGGCACT-CCATGGTC-AT
29460 GCCGCCCTCCTAGGGCGGCACT
1 GCCGCCCTCCTAGGGCGGCACT
29482 GGTTATTTTT
Statistics
Matches: 112, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
31 1 0.01
32 89 0.79
33 21 0.19
34 1 0.01
ACGTcount: A:0.13, C:0.40, G:0.28, T:0.19
Consensus pattern (32 bp):
GCCGCCCTCCTAGGGCGGCACTCCATGGTCAT
Found at i:31358 original size:31 final size:31
Alignment explanation
Indices: 31318--31485 Score: 174
Period size: 31 Copynumber: 5.4 Consensus size: 31
31308 TTTGAGCACG
**
31318 TGGCATGCCACGTGTCACTTTTTGAAACATA
1 TGGCATGCCACGTGTCACTTTTTGGTACATA
* * *
31349 TGGTATGCCACGTGTCACTTTTGGGTACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACATA
* ** * *
31380 TGGCGTGATACGTGTCACTTTTTGATACATG
1 TGGCATGCCACGTGTCACTTTTTGGTACATA
* * * *
31411 TGGCGTGCCACATGTCGCTTTTTGGTACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACATA
* * * *
31442 TGGCGTGCCACATGTCGCTTTTTGGTACATG
1 TGGCATGCCACGTGTCACTTTTTGGTACATA
31473 TGGCATGCCACGT
1 TGGCATGCCACGT
31486 CGGACACCGT
Statistics
Matches: 113, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 113 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGGTACATA
Found at i:31402 original size:62 final size:62
Alignment explanation
Indices: 31326--31485 Score: 212
Period size: 62 Copynumber: 2.6 Consensus size: 62
31316 CGTGGCATGC
* * *
31326 CACGTGTCACTTTTTGAAACATATGGTATGCCACGTGTCACTTTTGGGTACACATGGCGTGA
1 CACGTGTCACTTTTTGATACATGTGGCATGCCACGTGTCACTTTTGGGTACACATGGCGTGA
* * * * * *
31388 TACGTGTCACTTTTTGATACATGTGGCGTGCCACATGTCGCTTTTTGGTACACATGGCGTGC
1 CACGTGTCACTTTTTGATACATGTGGCATGCCACGTGTCACTTTTGGGTACACATGGCGTGA
* * *
31450 CACATGTCGCTTTTTGGTACATGTGGCATGCCACGT
1 CACGTGTCACTTTTTGATACATGTGGCATGCCACGT
31486 CGGACACCGT
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 83 1.00
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.34
Consensus pattern (62 bp):
CACGTGTCACTTTTTGATACATGTGGCATGCCACGTGTCACTTTTGGGTACACATGGCGTGA
Found at i:34890 original size:22 final size:22
Alignment explanation
Indices: 34860--35895 Score: 325
Period size: 22 Copynumber: 47.0 Consensus size: 22
34850 AATTACACAA
34860 TTTGGTAACCTCCCTATTAAAT
1 TTTGGTAACCTCCCTATTAAAT
* *
34882 TTTAGTAACCTCTCTATGT-AAT
1 TTTGGTAACCTCCCTAT-TAAAT
* * **
34904 TTTGGTAACCTTCTTAAGAAAT
1 TTTGGTAACCTCCCTATTAAAT
* * * ** *
34926 ATTGGTAACATCGCTAAGATAT
1 TTTGGTAACCTCCCTATTAAAT
*
34948 TTTGGTAACCTTCCTATGT-AAT
1 TTTGGTAACCTCCCTAT-TAAAT
* *
34970 TTTGGTAACATCCCTATAAAAT
1 TTTGGTAACCTCCCTATTAAAT
* *
34992 TTTTGTAACCTCCCTATGTTAA-
1 TTTGGTAACCTCCCTAT-TAAAT
* * *
35014 TTTGATAACCTCCGTATGT-TAT
1 TTTGGTAACCTCCCTAT-TAAAT
* * * *
35036 TTTGGTAACTTTCCTATGAAAC
1 TTTGGTAACCTCCCTATTAAAT
*
35058 TTTGGTAACCTCCCTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
* * *
35080 ATTGGTAACCACCCTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
* *
35102 TTTGGTAACCTCCGTATGT-TAT
1 TTTGGTAACCTCCCTAT-TAAAT
* *
35124 TTTGATAACCTCCCTATGT-TAT
1 TTTGGTAACCTCCCTAT-TAAAT
* * *
35146 TTTGGTAATTCTCCCTATGAAAA
1 TTTGGTAA-CCTCCCTATTAAAT
** *
35169 TTTGGTAACCTCTTTATGT-TAT
1 TTTGGTAACCTCCCTAT-TAAAT
* *
35191 TTTGTTAGCCT-CCT-TTGAAAT
1 TTTGGTAACCTCCCTATT-AAAT
* *
35212 TTTGGTAACCACCCTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
** ** * ** *
35234 GCTCCTTA--TGTC-A-TAGAT
1 TTTGGTAACCTCCCTATTAAAT
* *** *
35252 GTCAT-GTCGAATTCCATTTTGTGTTACTCAAT
1 -T-TTGGT--AA--CC--TCCCTATTA---AAT
* *
35284 TTCGGTAACCTCCCTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
* *
35306 TTTGGTAACCTCACTA-TATTAT
1 TTTGGTAACCTCCCTATTA-AAT
* ** * *
35328 TTTGGAAAATTCACTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
* * *
35350 TTTGGTTACCTCCGTA-TGAAT
1 TTTGGTAACCTCCCTATTAAAT
* *** *
35371 TTTGATAACCTTTATATGT-TAT
1 TTTGGTAACCTCCCTAT-TAAAT
* *
35393 TTTGGTAACCTCCTTATTATAT
1 TTTGGTAACCTCCCTATTAAAT
* * * *
35415 TTTTGTAAACTCCTTATGT-TAT
1 TTTGGTAACCTCCCTAT-TAAAT
* * *
35437 TTTGGTAACTTCCGTATAAAAT
1 TTTGGTAACCTCCCTATTAAAT
** *
35459 TTTGGTAAGATCGCTATGT-AAT
1 TTTGGTAACCTCCCTAT-TAAAT
* **
35481 TTTGGTAACCTTCCTAAGAAAT
1 TTTGGTAACCTCCCTATTAAAT
* * * * *
35503 ATTGGTAACATCACTATGATAT
1 TTTGGTAACCTCCCTATTAAAT
* **
35525 TTAGGTAACCTTGCTA-TATAAT
1 TTTGGTAACCTCCCTATTA-AAT
*
35547 TTTTGTAA--TGCCCTTATTAAAT
1 TTTGGTAACCT-CCC-TATTAAAT
* *
35569 TTTGTTAACCTCCCTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
* * ** *
35591 TTTTGTACCCTCTTTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
*
35613 TTTGGTAACCTCCATA-TACAAT
1 TTTGGTAACCTCCCTATTA-AAT
* * *
35635 TTTGGTAATCTCCGTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
* *
35657 TTTAGTAACCT-CCTATGTAATT
1 TTTGGTAACCTCCCTAT-TAAAT
** * **
35679 TTTTATAACCTTCCTATGCAAT
1 TTTGGTAACCTCCCTATTAAAT
* * * *
35701 ATTGGTAACGTCCCTATGAAAC
1 TTTGGTAACCTCCCTATTAAAT
*
35723 TTTGGTAACCTCCTCT-TGAAAT
1 TTTGGTAACCTCC-CTATTAAAT
*
35745 TTTGG--ACCTTCCTATGT-AA-
1 TTTGGTAACCTCCCTAT-TAAAT
* * *
35764 TTTGGTAACCACCATAAGT-AAT
1 TTTGGTAACCTCCCT-ATTAAAT
* * * * *
35786 TATGCTAACCACCATATAAAAT
1 TTTGGTAACCTCCCTATTAAAT
* *
35808 TTTGGTAACCTCCTTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
* * * *
35830 TTTTGTAACTTGCCTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
*
35852 TTTGGTAACCTCCCTATGT-TAT
1 TTTGGTAACCTCCCTAT-TAAAT
* *
35874 TTTGGTAACCTCCTTATGAAAT
1 TTTGGTAACCTCCCTATTAAAT
35896 CTCCCTATGA
Statistics
Matches: 732, Mismatches: 222, Indels: 120
0.68 0.21 0.11
Matches are distributed among these distances:
18 3 0.00
19 10 0.01
20 12 0.02
21 45 0.06
22 607 0.83
23 37 0.05
24 1 0.00
25 4 0.01
27 4 0.01
29 4 0.01
31 3 0.00
32 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (22 bp):
TTTGGTAACCTCCCTATTAAAT
Found at i:35888 original size:66 final size:65
Alignment explanation
Indices: 34860--36192 Score: 534
Period size: 66 Copynumber: 20.3 Consensus size: 65
34850 AATTACACAA
* * * *
34860 TTTGGTAACCTCCCTAT-TAAATTTTAGTAACCT-CTCTATGTAATTTTGGTAACCTTCTTAAGA
1 TTTGGTAACCTCCCTATGT-AATTTTGGTAACCTCCT-TATGAAATTTTGGTAA-CTTCCTATGA
34923 AAT
63 AAT
* * * * * * *
34926 ATTGGTAACATCGCTAAG-ATATTTTGGTAACCTTCC-TATGTAATTTTGGTAACATCCCTATAA
1 TTTGGTAACCTCCCTATGTA-ATTTTGGTAACC-TCCTTATGAAATTTTGGTAAC-TTCCTATGA
34989 AAT
63 AAT
* * * **
34992 TTTTGTAACCTCCCTATGTTAA-TTTGATAACCTCCGTATGTTATTTTGGTAACTTTCCTATGAA
1 TTTGGTAACCTCCCTATG-TAATTTTGGTAACCTCCTTATGAAATTTTGGTAAC-TTCCTATGAA
*
35056 AC
64 AT
* * * * * **
35058 TTTGGTAACCTCCCTATGAAATATTGGTAACCACCCTATGAAATTTTGGTAACCTCCGTATGTTA
1 TTTGGTAACCTCCCTATGTAATTTTGGTAACCTCCTTATGAAATTTTGGTAACTTCC-TATGAAA
35123 T
65 T
* * * * * * * **
35124 TTTGATAACCTCCCTATGTTATTTTGGTAATTCTCCCTATGAAAATTTGGTAACCTCTTTATGTT
1 TTTGGTAACCTCCCTATGTAATTTTGGTAA-CCTCCTTATGAAATTTTGGTAACTTC-CTATGAA
35189 AT
64 AT
* * * * * * ** ** * * **
35191 TTTGTTAGCCT-CCTTTGAAATTTTGGTAACCACCCTATGAAATGCTCCTTA-TGTCATA-GATG
1 TTTGGTAACCTCCCTATGTAATTTTGGTAACCTCCTTATGAAATTTTGGTAACT-TCCTATGAAA
35253 T
65 T
** ** * * * *
35254 CAT-GTCGAATTCCAT-TTTGTGTTACTCAATTTCGGTAACCTCCCTATGAAATTTTGGTAACCT
1 TTTGGT--AA--CC-TCCCTATG----T-AATTTTGGTAACCTCCTTATGAAATTTTGGTAACTT
*
35317 CACTAT-ATTAT
56 C-CTATGA-AAT
* ** * * * * * ** **
35328 TTTGGAAAATTCACTATGAAATTTTGGTTACCTCCGTATG-AATTTTGATAACCTTTATATGTTA
1 TTTGGTAACCTCCCTATGTAATTTTGGTAACCTCCTTATGAAATTTTGGTAA-CTTCCTATGAAA
35392 T
65 T
* * * ** *
35393 TTTGGTAACCTCCTTAT-TATATTTTTGTAAACTCCTTATGTTATTTTGGTAACTTCCGTATAAA
1 TTTGGTAACCTCCCTATGTA-ATTTTGGTAACCTCCTTATGAAATTTTGGTAACTTCC-TATGAA
35457 AT
64 AT
** * * * * *
35459 TTTGGTAAGATCGCTATGTAATTTTGGTAACCTTCC-TAAGAAATATTGGTAACATCACTATGAT
1 TTTGGTAACCTCCCTATGTAATTTTGGTAACC-TCCTTATGAAATTTTGGTAACTTC-CTATGAA
35523 AT
64 AT
* ** * * * * * *
35525 TTAGGTAACCTTGCTATATAATTTTTGTAATGC-CCTTATTAAATTTTGTTAACCTCCCTATGAA
1 TTTGGTAACCTCCCTATGTAATTTTGGTAA-CCTCCTTATGAAATTTTGGTAA-CTTCCTATGAA
35589 AT
64 AT
* * ** * *
35591 TTTTGTACCCTCTTTATGAAATTTTGGTAACCTCCATAT-ACAATTTTGGTAA-TCTCCGTATGA
1 TTTGGTAACCTCCCTATGTAATTTTGGTAACCTCCTTATGA-AATTTTGGTAACT-TCC-TATGA
35654 AAT
63 AAT
* ** * * *
35657 TTTAGTAACCT-CCTATGTAATTTTTTATAACCTTCC-TATGCAATATTGGTAACGTCCCTATGA
1 TTTGGTAACCTCCCTATGTAA-TTTTGGTAACC-TCCTTATGAAATTTTGGTAAC-TTCCTATGA
*
35720 AAC
63 AAT
* * ** * *
35723 TTTGGTAACCTCCTCT-TGAAATTTTGG--ACCTTCC-TATGTAA-TTTGGTAACCACCATAAGT
1 TTTGGTAACCTCC-CTATGTAATTTTGGTAACC-TCCTTATGAAATTTTGGTAACTTCC-TATGA
35783 AAT
63 AAT
* * * * ** *
35786 TATGCTAACCACCATATAAAATTTTGGTAACCTCCTTATGAAATTTTTGTAACTTGCCTATGAAA
1 TTTGGTAACCTCCCTATGTAATTTTGGTAACCTCCTTATGAAATTTTGGTAACTT-CCTATGAAA
35851 T
65 T
* *
35852 TTTGGTAACCTCCCTATGTTATTTTGGTAACCTCCTTATGAAA------T--CTCCCTATGAAAT
1 TTTGGTAACCTCCCTATGTAATTTTGGTAACCTCCTTATGAAATTTTGGTAACTTCCTATGAAAT
* * * * ** * *
35909 TTTGATAACCTCCGTATGTTATTTTGATAACCTCCCCATGAAATATGGGTAACCTCCTATCCTTA
1 TTTGGTAACCTCCCTATGTAATTTTGGTAACCTCCTTATGAAATTTTGGTAA----CT-TCC-TA
*
35974 TTAAACT
60 TGAAA-T
* * * *
35981 TTT-GTAACCTCCTTATGT-ATTTTGGTAACGTCGTT-TGAAATTTTGGTAACCTCACTAT-AAA
1 TTTGGTAACCTCCCTATGTAATTTTGGTAACCTCCTTATGAAATTTTGGTAACTTC-CTATGAAA
*
36042 GC
65 -T
** * ** * * * * *
36044 TTTAATAATCGGCCTATGAAATTTTGATAATCTTCC-TATGAAATTTTGGTAACATCGCTATGAT
1 TTTGGTAACCTCCCTATGTAATTTTGGTAA-CCTCCTTATGAAATTTTGGTAACTTC-CTATGAA
36108 AT
64 AT
* * * * *
36110 TTTGGTAACCAT-GCTCTGCAATTTTGGTAACGCTTC-TATG-AATTTTCGGTAACCTTCATATG
1 TTTGGTAACC-TCCCTATGTAATTTTGGTAAC-CTCCTTATGAAATTTT-GGTAA-CTTCCTATG
36172 AAA-
62 AAAT
* *
36175 TTTGGTAACATCACTATG
1 TTTGGTAACCTCCCTATG
36193 ATATTCGCAC
Statistics
Matches: 945, Mismatches: 238, Indels: 169
0.70 0.18 0.12
Matches are distributed among these distances:
57 48 0.05
58 2 0.00
60 1 0.00
62 4 0.00
63 44 0.05
64 36 0.04
65 126 0.13
66 515 0.54
67 72 0.08
68 5 0.01
69 14 0.01
70 15 0.02
71 22 0.02
72 32 0.03
73 5 0.01
74 3 0.00
75 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (65 bp):
TTTGGTAACCTCCCTATGTAATTTTGGTAACCTCCTTATGAAATTTTGGTAACTTCCTATGAAAT
Found at i:35926 original size:22 final size:22
Alignment explanation
Indices: 35896--36119 Score: 105
Period size: 22 Copynumber: 10.0 Consensus size: 22
35886 CTTATGAAAT
35896 CTCCCTATGAAATTTTGATAAC
1 CTCCCTATGAAATTTTGATAAC
* **
35918 CTCCGTATGTTATTTTGATAAC
1 CTCCCTATGAAATTTTGATAAC
* * * *
35940 CTCCCCATGAAATATGGGTAAC
1 CTCCCTATGAAATTTTGATAAC
*
35962 CTCCTATCCTTATTAAACTTTTG-TAAC
1 CT-C---CC-TATGAAA-TTTTGATAAC
* * *
35989 CTCCTTATG-TATTTTGGTAAC
1 CTCCCTATGAAATTTTGATAAC
* * * *
36010 GT-CGTTTGAAATTTTGGTAAC
1 CTCCCTATGAAATTTTGATAAC
* * * *
36031 CTCACTAT-AAAGCTTTAATAAT
1 CTCCCTATGAAA-TTTTGATAAC
** *
36053 CGGCCTATGAAATTTTGATAAT
1 CTCCCTATGAAATTTTGATAAC
* *
36075 CTTCCTATGAAATTTTGGTAAC
1 CTCCCTATGAAATTTTGATAAC
* * * *
36097 ATCGCTATGATATTTTGGTAAC
1 CTCCCTATGAAATTTTGATAAC
36119 C
1 C
36120 ATGCTCTGCA
Statistics
Matches: 148, Mismatches: 43, Indels: 22
0.69 0.20 0.10
Matches are distributed among these distances:
20 9 0.06
21 21 0.14
22 96 0.65
23 5 0.03
26 3 0.02
27 11 0.07
28 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (22 bp):
CTCCCTATGAAATTTTGATAAC
Found at i:35930 original size:57 final size:57
Alignment explanation
Indices: 35842--35952 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
35832 TTGTAACTTG
* * **
35842 CCTATGAAATTTTGGTAACCTCCCTATGTTATTTTGGTAACCTCCTTATGAAATCTC
1 CCTATGAAATTTTGATAACCTCCCTATGTTATTTTGATAACCTCCCCATGAAATCTC
*
35899 CCTATGAAATTTTGATAACCTCCGTATGTTATTTTGATAACCTCCCCATGAAAT
1 CCTATGAAATTTTGATAACCTCCCTATGTTATTTTGATAACCTCCCCATGAAAT
35953 ATGGGTAACC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.39
Consensus pattern (57 bp):
CCTATGAAATTTTGATAACCTCCCTATGTTATTTTGATAACCTCCCCATGAAATCTC
Found at i:36105 original size:44 final size:44
Alignment explanation
Indices: 36057--36193 Score: 136
Period size: 44 Copynumber: 3.1 Consensus size: 44
36047 AATAATCGGC
* * *
36057 CTATGAAATTTTGATAATCTTCCTATGAAATTTTGGTAACATCG
1 CTATGAAATTTTGGTAACCTTCCTATGAAATTTTGGTAACATCA
* * * * * * *
36101 CTATGATATTTTGGTAACCATGCTCTGCAATTTTGGTAAC-GCTT
1 CTATGAAATTTTGGTAACCTTCCTATGAAATTTTGGTAACATC-A
*
36145 CTATG-AATTTTCGGTAACCTTCATATGAAA-TTTGGTAACATCA
1 CTATGAAATTTT-GGTAACCTTCCTATGAAATTTTGGTAACATCA
36188 CTATGA
1 CTATGA
36194 TATTCGCACA
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
43 20 0.28
44 52 0.72
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (44 bp):
CTATGAAATTTTGGTAACCTTCCTATGAAATTTTGGTAACATCA
Found at i:36133 original size:22 final size:22
Alignment explanation
Indices: 36057--36193 Score: 90
Period size: 22 Copynumber: 6.3 Consensus size: 22
36047 AATAATCGGC
* * *
36057 CTATGAAATTTTGATAATCTTC-
1 CTATG-AATTTTGGTAACCATCG
36079 CTATGAAATTTTGGTAA-CATCG
1 CTATG-AATTTTGGTAACCATCG
36101 CTATGATATTTTGGTAACCAT-G
1 CTATGA-ATTTTGGTAACCATCG
* *
36123 CTCTGCAATTTTGGTAACGC-T-T
1 CTATG-AATTTTGGTAAC-CATCG
*
36145 CTATGAATTTTCGGTAACCTTC-
1 CTATGAATTTT-GGTAACCATCG
* * *
36167 ATATGAAATTTGGTAA-CATCA
1 CTATGAATTTTGGTAACCATCG
36188 CTATGA
1 CTATGA
36194 TATTCGCACA
Statistics
Matches: 97, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
20 3 0.03
21 21 0.22
22 68 0.70
23 5 0.05
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (22 bp):
CTATGAATTTTGGTAACCATCG
Found at i:36791 original size:7 final size:7
Alignment explanation
Indices: 36781--36855 Score: 57
Period size: 7 Copynumber: 10.6 Consensus size: 7
36771 TTTTTTAATT
*
36781 ATTACTA
1 ATTATTA
36788 ATTATTTA
1 ATTA-TTA
36796 ATTATTA
1 ATTATTA
36803 ATTATT-
1 ATTATTA
36809 ATTAATTGAA
1 ATT-ATT--A
*
36819 ATTGTT-
1 ATTATTA
36825 ATTATTA
1 ATTATTA
36832 ATTA-TA
1 ATTATTA
*
36838 ATTAATA
1 ATTATTA
*
36845 ATTAATA
1 ATTATTA
36852 ATTA
1 ATTA
36856 AAAAAGAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
6 14 0.24
7 33 0.57
8 6 0.10
9 2 0.03
10 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (7 bp):
ATTATTA
Found at i:36797 original size:18 final size:18
Alignment explanation
Indices: 36774--36815 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
36764 TTTTTATTTT
*
36774 TTTAATTATTACTAATTA
1 TTTAATTATTAATAATTA
*
36792 TTTAATTATTAATTATTA
1 TTTAATTATTAATAATTA
36810 -TTAATT
1 TTTAATT
36816 GAAATTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAATTATTAATAATTA
Found at i:36954 original size:33 final size:33
Alignment explanation
Indices: 36924--37052 Score: 204
Period size: 33 Copynumber: 3.9 Consensus size: 33
36914 GGAGGCATGA
*
36924 CCATGGTCATGCCACCCAAGGAGGGCGGCATCG
1 CCATGGTCATGCCGCCCAAGGAGGGCGGCATCG
36957 CCATGGTCATGCCGCCCAAGGAGGGCGGCATCG
1 CCATGGTCATGCCGCCCAAGGAGGGCGGCATCG
* **
36990 CCATGGTCATGCTGCCTTAGGAGGGCGGCATCG
1 CCATGGTCATGCCGCCCAAGGAGGGCGGCATCG
* *
37023 CCATGGTCATGCCGTCCTAGGAGGGCGGCA
1 CCATGGTCATGCCGCCCAAGGAGGGCGGCA
37053 CCGATTATTT
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.18, C:0.31, G:0.36, T:0.16
Consensus pattern (33 bp):
CCATGGTCATGCCGCCCAAGGAGGGCGGCATCG
Found at i:50380 original size:13 final size:13
Alignment explanation
Indices: 50362--50394 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
50352 TAGCTTTTCA
*
50362 AGAAAAAAAAAAG
1 AGAAAAAAAAAAC
50375 AGAAAAAAAAAAC
1 AGAAAAAAAAAAC
50388 AGAAAAA
1 AGAAAAA
50395 TTCTCTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAC
Found at i:50523 original size:2 final size:2
Alignment explanation
Indices: 50516--50546 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
50506 TATCTGGATA
50516 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50547 TATTTTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:50550 original size:10 final size:11
Alignment explanation
Indices: 50517--50550 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
50507 ATCTGGATAA
50517 TATATATATAT
1 TATATATATAT
50528 ATATATATATAT
1 -TATATATATAT
50540 TATATAT-TAT
1 TATATATATAT
50550 T
1 T
50551 TTTAGTGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 7 0.32
12 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATATAT
Found at i:55942 original size:12 final size:12
Alignment explanation
Indices: 55912--55945 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
55902 TTAATTGGTT
*
55912 GTTACTAAGTTA
1 GTTACTTAGTTA
55924 GTTACTTAGTTA
1 GTTACTTAGTTA
55936 GTTACTTAGT
1 GTTACTTAGT
55946 CAGCTATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (12 bp):
GTTACTTAGTTA
Found at i:60840 original size:12 final size:12
Alignment explanation
Indices: 60798--60840 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
60788 GTTAGTTAGC
*
60798 AGTTAATTGGTT
1 AGTTACTTGGTT
**
60810 -GTTACTAAGTT
1 AGTTACTTGGTT
60821 AGTTACTTGGTT
1 AGTTACTTGGTT
60833 AGTTACTT
1 AGTTACTT
60841 AGTCAACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.23, C:0.07, G:0.21, T:0.49
Consensus pattern (12 bp):
AGTTACTTGGTT
Found at i:65554 original size:21 final size:21
Alignment explanation
Indices: 65516--65583 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
65506 GCGACAAGTC
*
65516 CCCCTTGACGAGAACGGGGAG
1 CCCCTTGACGAGAGCGGGGAG
* *
65537 CCCCTTGACGCGAGCGGGAAGG
1 CCCCTTGACGAGAGCGGGGA-G
* * *
65559 TCACCTTGCCGTGAGCGGGGAG
1 -CCCCTTGACGAGAGCGGGGAG
65581 CCC
1 CCC
65584 TAGATCCTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 19 0.51
22 2 0.05
23 16 0.43
ACGTcount: A:0.18, C:0.32, G:0.38, T:0.12
Consensus pattern (21 bp):
CCCCTTGACGAGAGCGGGGAG
Found at i:66661 original size:25 final size:27
Alignment explanation
Indices: 66608--66662 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
66598 GGAGGATGTG
66608 ATGGGCTAGTAGCCCCAAAAAAAAAATTT
1 ATGGGCTAGTAGCCCC--AAAAAAAATTT
66637 ATGGGCTAGTAG-CCC-AAAAAAATTT
1 ATGGGCTAGTAGCCCCAAAAAAAATTT
66662 A
1 A
66663 AGACTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 11 0.42
28 3 0.12
29 12 0.46
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (27 bp):
ATGGGCTAGTAGCCCCAAAAAAAATTT
Found at i:70729 original size:6 final size:6
Alignment explanation
Indices: 70728--70784 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
70718 TTTTTTCCTT
** *
70728 TTTTCC TTTTCC TTTTCC TTTTTT TTTTCCC TTTTTTC TTTT-C TTTT-C
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTT-CC -TTTTCC TTTTCC TTTTCC
70776 TTTTCC TTT
1 TTTTCC TTT
70785 CCCCCTCATC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 10 0.23
6 28 0.65
7 1 0.02
8 4 0.09
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTCC
Found at i:70745 original size:12 final size:12
Alignment explanation
Indices: 70728--70784 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
70718 TTTTTTCCTT
*
70728 TTTTCCTTTTCC
1 TTTTCCTTTTTC
*
70740 TTTTCCTTTTTT
1 TTTTCCTTTTTC
70752 TTTTCCCTTTTTTC
1 TTTT-CC-TTTTTC
70766 TTTT-C-TTTTC
1 TTTTCCTTTTTC
70776 TTTTCCTTT
1 TTTTCCTTT
70785 CCCCCTCATC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
12 17 0.45
13 2 0.05
14 9 0.24
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTCCTTTTTC
Found at i:70745 original size:20 final size:19
Alignment explanation
Indices: 70720--70784 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
70710 TATTTTCTTT
70720 TTTTCCTTTTTTCCTTTTCC
1 TTTTCCTTTTTT-CTTTTCC
70740 TTTTCCTTTTTT-TTTTCCC
1 TTTTCCTTTTTTCTTTT-CC
70759 TTTT--TTCTTTTCTTTT-C
1 TTTTCCTT-TTTTCTTTTCC
70776 TTTTCCTTT
1 TTTTCCTTT
70785 CCCCCTCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.17
18 9 0.22
19 12 0.30
20 12 0.30
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCCTTTTTTCTTTTCC
Found at i:70763 original size:32 final size:30
Alignment explanation
Indices: 70717--70779 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 30
70707 TTCTATTTTC
*
70717 TTTTTTTCCTTTTTTCCTTTTCCTTTTCCTTT
1 TTTTTTTCCCTTTTTCCTTTT-CTTTT-CTTT
*
70749 TTTTTTTCCCTTTTTTCTTTTCTTTTCTTT
1 TTTTTTTCCCTTTTTCCTTTTCTTTTCTTT
70779 T
1 T
70780 CCTTTCCCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.17
31 5 0.17
32 19 0.66
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (30 bp):
TTTTTTTCCCTTTTTCCTTTTCTTTTCTTT
Found at i:79315 original size:45 final size:45
Alignment explanation
Indices: 79261--79438 Score: 356
Period size: 45 Copynumber: 4.0 Consensus size: 45
79251 GAAGATAAAA
79261 TAAATGTATGGTTAAATTAAATTCAAACGTTTACTATAAATATTC
1 TAAATGTATGGTTAAATTAAATTCAAACGTTTACTATAAATATTC
79306 TAAATGTATGGTTAAATTAAATTCAAACGTTTACTATAAATATTC
1 TAAATGTATGGTTAAATTAAATTCAAACGTTTACTATAAATATTC
79351 TAAATGTATGGTTAAATTAAATTCAAACGTTTACTATAAATATTC
1 TAAATGTATGGTTAAATTAAATTCAAACGTTTACTATAAATATTC
79396 TAAATGTATGGTTAAATTAAATTCAAACGTTTACTATAAATAT
1 TAAATGTATGGTTAAATTAAATTCAAACGTTTACTATAAATAT
79439 CCGTCGTTTT
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (45 bp):
TAAATGTATGGTTAAATTAAATTCAAACGTTTACTATAAATATTC
Found at i:79500 original size:27 final size:28
Alignment explanation
Indices: 79451--79511 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
79441 GTCGTTTTAG
*
79451 TGCATTTTGAACCACTTATTTTTTTAAT
1 TGCATTTTGAACCACTTATTTTTTGAAT
79479 TGCATTTTGAACCACTTA-TTTTTGAAT
1 TGCATTTTGAACCACTTATTTTTTGAAT
*
79506 TTCATT
1 TGCATT
79512 GATCCGTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (28 bp):
TGCATTTTGAACCACTTATTTTTTGAAT
Found at i:79533 original size:12 final size:12
Alignment explanation
Indices: 79513--79548 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
79503 AATTTCATTG
79513 ATCCGTCGATAT
1 ATCCGTCGATAT
*
79525 ATCCATCGATAT
1 ATCCGTCGATAT
79537 ATCCGTCGATAT
1 ATCCGTCGATAT
79549 CTGTATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (12 bp):
ATCCGTCGATAT
Found at i:81082 original size:19 final size:20
Alignment explanation
Indices: 81054--81091 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
81044 ATTAAATATT
*
81054 TTTATGAAA-TTTGATAATC
1 TTTATAAAATTTTGATAATC
81073 TTTATAAAATTTTGATAAT
1 TTTATAAAATTTTGATAAT
81092 TATACTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
TTTATAAAATTTTGATAATC
Found at i:81413 original size:61 final size:61
Alignment explanation
Indices: 81338--81460 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 61
81328 CCTCCATATG
*
81338 AAATTTTGTTAACTTCCCTATCAAATTTTGTTACAC-TCCTTATAAAAATTTTAATAGCCAC
1 AAATTTTGTTAACTTCCCTATAAAATTTTGTTACACTTCC-TATAAAAATTTTAATAGCCAC
81399 AAATTTTGTTAACTTCCCTATAAAATTTTGTTACACTTCCTATAAAAATTTTAATAGCCAC
1 AAATTTTGTTAACTTCCCTATAAAATTTTGTTACACTTCCTATAAAAATTTTAATAGCCAC
81460 A
1 A
81461 TAATGAAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 57 0.95
62 3 0.05
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (61 bp):
AAATTTTGTTAACTTCCCTATAAAATTTTGTTACACTTCCTATAAAAATTTTAATAGCCAC
Found at i:81446 original size:23 final size:22
Alignment explanation
Indices: 81338--81450 Score: 96
Period size: 22 Copynumber: 5.3 Consensus size: 22
81328 CCTCCATATG
*
81338 AAATTTTGTTAACTTCCCTATC
1 AAATTTTGTTAACTTCCCTATA
*
81360 AAATTTTGTTACAC-TCCTTATA
1 AAATTTTGTTA-ACTTCCCTATA
* ** *
81382 AAA-ATT-TTAA-TAGCC-A-C
1 AAATTTTGTTAACTTCCCTATA
81399 AAATTTTGTTAACTTCCCTATA
1 AAATTTTGTTAACTTCCCTATA
81421 AAATTTTGTTACACTT-CCTATAA
1 AAATTTTGTTA-ACTTCCCTAT-A
81444 AAATTTT
1 AAATTTT
81451 AATAGCCACA
Statistics
Matches: 71, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
17 3 0.04
18 3 0.04
19 6 0.08
20 6 0.08
21 3 0.04
22 36 0.51
23 14 0.20
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (22 bp):
AAATTTTGTTAACTTCCCTATA
Found at i:81472 original size:22 final size:22
Alignment explanation
Indices: 81444--81494 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
81434 CTTCCTATAA
81444 AAATTTTAATAGCCA-CATAATG
1 AAATTTTAATAGCCACCAT-ATG
* *
81466 AAATTTTGATAGCCACCCTATG
1 AAATTTTAATAGCCACCATATG
81488 AAATTTT
1 AAATTTT
81495 GATAACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
AAATTTTAATAGCCACCATATG
Found at i:81495 original size:22 final size:22
Alignment explanation
Indices: 81463--82005 Score: 213
Period size: 22 Copynumber: 24.8 Consensus size: 22
81453 TAGCCACATA
*
81463 ATGAAATTTTGATAGCCACCCT
1 ATGAAATTTTGATAACCACCCT
* *
81485 ATGAAATTTTGATAACCTCCCA
1 ATGAAATTTTGATAACCACCCT
** * **
81507 ATGAAACATTGGTAAACACACATT
1 ATGAAATTTTGAT-AAC-CACCCT
**
81531 ATGAAATTTTGATAACCTTCCT
1 ATGAAATTTTGATAACCACCCT
* * **
81553 AT-AAGATATT-AGTAATCACATT
1 ATGAA-ATTTTGA-TAACCACCCT
* *
81575 ATGAAATTTTGATTACCATACC-
1 ATGAAATTTTGATAACCA-CCCT
* * * *
81597 ATAAAATTGTGAT-ACCTCACT
1 ATGAAATTTTGATAACCACCCT
* *
81618 ATGAAATTTTTATAAACCTCCCT
1 ATGAAATTTTGAT-AACCACCCT
* * *
81641 ATAAAATTTTGATAACCTCCAT
1 ATGAAATTTTGATAACCACCCT
* *
81663 TTGAAATTTTGATAA-C-CTC-
1 ATGAAATTTTGATAACCACCCT
*
81682 ATGAAATTTTGAAAACCA-CCT
1 ATGAAATTTTGATAACCACCCT
* *
81703 CATGAAATTTTGATAACCATCTT
1 -ATGAAATTTTGATAACCACCCT
*
81726 ATAAAATTTTGATAA-CATCCCT
1 ATGAAATTTTGATAACCA-CCCT
* * *
81748 AT-AAATTTT-TTAACCTCCTT
1 ATGAAATTTTGATAACCACCCT
* * *
81768 ATAAAATTTTGTTAACC-TCCT
1 ATGAAATTTTGATAACCACCCT
* ** *
81789 ACGAAATTTTGATAAGAACACT
1 ATGAAATTTTGATAACCACCCT
* * *
81811 ATTAACTTTTGATAACC-CCCA
1 ATGAAATTTTGATAACCACCCT
* *
81832 ATGAAATTTTGATAATTATCTATACC-
1 ATGAAATTTTGAT-A--A-CCA-CCCT
* ** *
81858 ATAAAATTACGATAACTTA-CCT
1 ATGAAATTTTGATAAC-CACCCT
* * *
81880 ATGAAATTTTGTTAATCTCCCT
1 ATGAAATTTTGATAACCACCCT
* * *
81902 ATAAAATTTTGAGAACCACGCT
1 ATGAAATTTTGATAACCACCCT
* * * * *
81924 ATCAAATTTTGTTAATCTCACT
1 ATGAAATTTTGATAACCACCCT
*
81946 AT-AAATTTTGATAA--ACCGATT
1 ATGAAATTTTGATAACCACC--CT
* * * *
81967 ATGAAATTTTAATTACCACACA
1 ATGAAATTTTGATAACCACCCT
*
81989 ATGAAAATTTGATAACC
1 ATGAAATTTTGATAACC
82006 CCTCCCTCTG
Statistics
Matches: 377, Mismatches: 110, Indels: 68
0.68 0.20 0.12
Matches are distributed among these distances:
19 14 0.04
20 12 0.03
21 77 0.20
22 213 0.56
23 32 0.08
24 15 0.04
25 2 0.01
26 10 0.03
27 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACCCT
Found at i:81510 original size:44 final size:44
Alignment explanation
Indices: 81466--82383 Score: 318
Period size: 44 Copynumber: 20.9 Consensus size: 44
81456 CCACATAATG
* * *
81466 AAATTTTGATAGCCACCCTATGAAATTTTGATAACCTCCCAATG
1 AAATTTTGATAACCACCCTATGAAATTTTGATAACCTCCCTATA
** * ** *
81510 AAACATTGGTAAACACACATTATGAAATTTTGATAACCTTCCTATA
1 AAATTTTGAT-AAC-CACCCTATGAAATTTTGATAACCTCCCTATA
* * * ** * *
81556 AGATATT-AGTAATCACATTATGAAATTTTGATTACCATACC-ATA
1 AAATTTTGA-TAACCACCCTATGAAATTTTGATAACC-TCCCTATA
* * * *
81600 AAATTGTGAT-ACCTCACTATGAAATTTTTATAAACCTCCCTATA
1 AAATTTTGATAACCACCCTATGAAATTTTGAT-AACCTCCCTATA
* * * *
81644 AAATTTTGATAACCTCCATTTGAAATTTTGATAACCT--C-ATG
1 AAATTTTGATAACCACCCTATGAAATTTTGATAACCTCCCTATA
* *
81685 AAATTTTGAAAACCA-CCTCATGAAATTTTGATAACCAT-CTTATA
1 AAATTTTGATAACCACCCT-ATGAAATTTTGATAACC-TCCCTATA
* *
81729 AAATTTTGATAA-CATCCCTAT-AAATTTT-TTAACCTCCTTATA
1 AAATTTTGATAACCA-CCCTATGAAATTTTGATAACCTCCCTATA
* * * *** * *
81771 AAATTTTGTTAACC-TCCTACGAAATTTTGATAAGAACACTATT
1 AAATTTTGATAACCACCCTATGAAATTTTGATAACCTCCCTATA
* * * *
81814 AACTTTTGATAACC-CCCAATGAAATTTTGATAATTATCTATACC-ATA
1 AAATTTTGATAACCACCCTATGAAATTTTGAT-A--A-C-CTCCCTATA
** * * *
81861 AAATTACGATAACTTA-CCTATGAAATTTTGTTAATCTCCCTATA
1 AAATTTTGATAAC-CACCCTATGAAATTTTGATAACCTCCCTATA
* * * * * *
81905 AAATTTTGAGAACCACGCTATCAAATTTTGTTAATCTCACTAT-
1 AAATTTTGATAACCACCCTATGAAATTTTGATAACCTCCCTATA
* * * * * *
81948 AAATTTTGATAA--ACCGATTATGAAATTTTAATTACCACACAATGA
1 AAATTTTGATAACCACC--CTATGAAATTTTGATAACCTCCCTAT-A
* * * **
81993 AAA-TTTGATAACCCCTCCCTCTG-AA-----AT-ACCACATTATA
1 AAATTTTGATAA--CCACCCTATGAAATTTTGATAACCTCCCTATA
* * * **
82031 AAATTTTGATAACCACACTATTAAATTTTGATAATCTCCCTCGA
1 AAATTTTGATAACCACCCTATGAAATTTTGATAACCTCCCTATA
* * * * * * * *
82075 AAATTTCGATAACCTCCCCATGAAATTTTGTTTA-C-CCTTGTG
1 AAATTTTGATAACCACCCTATGAAATTTTGATAACCTCCCTATA
* * ** * * * * *
82117 AAATTATGATTATTACACTATGAAATTTTGGT-ACCGACACT-TG
1 AAATTTTGATAACCACCCTATGAAATTTTGATAACC-TCCCTATA
* * * * * *
82160 AAATTTTGATAAGCTCACCCCATCTCACTATGTAATTTTTATAAGCACACTATG
1 AAATTTTGAT-A----A--CCA-C-C-CTATGAAATTTTGATAACCTCCCTATA
* ** * *
82214 AAATTTTGATAATCTTCCTATG-AATTTCTTATAACCTCCATATA
1 AAATTTTGATAACCACCCTATGAAATTT-TGATAACCTCCCTATA
* * **** *
82258 AAATTTTGATAATCGCCCTATGAAATTTTGATAACCAGAGTATG
1 AAATTTTGATAACCACCCTATGAAATTTTGATAACCTCCCTATA
* * * *
82302 AAATTTT-AGTAACCTCCCTGTGAAATTTTGATAACCTTCCAAT-
1 AAATTTTGA-TAACCACCCTATGAAATTTTGATAACCTCCCTATA
* * * * *
82345 GAATTTCGATAACCTCCTTATGAAATTTTGATTACCTCC
1 AAATTTTGATAACCACCCTATGAAATTTTGATAACCTCC
82384 ATATCTAACA
Statistics
Matches: 652, Mismatches: 160, Indels: 125
0.70 0.17 0.13
Matches are distributed among these distances:
37 6 0.01
38 6 0.01
39 16 0.02
40 4 0.01
41 39 0.06
42 58 0.09
43 147 0.23
44 232 0.36
45 40 0.06
46 36 0.06
47 14 0.02
48 19 0.03
49 1 0.00
50 1 0.00
51 1 0.00
53 18 0.03
54 14 0.02
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAACCACCCTATGAAATTTTGATAACCTCCCTATA
Found at i:81538 original size:46 final size:44
Alignment explanation
Indices: 81484--81587 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 44
81474 ATAGCCACCC
*
81484 TATGAAATTTTGATAACCTCCCAATGAA-ACATTGGTAAACACACAT
1 TATGAAATTTTGATAACCTCCCAAT-AAGACATTAGT-AA-ACACAT
* * * *
81530 TATGAAATTTTGATAACCTTCCTATAAGATATTAGTAATCACAT
1 TATGAAATTTTGATAACCTCCCAATAAGACATTAGTAAACACAT
81574 TATGAAATTTTGAT
1 TATGAAATTTTGAT
81588 TACCATACCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 19 0.37
45 4 0.08
46 29 0.56
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCAATAAGACATTAGTAAACACAT
Found at i:81624 original size:21 final size:22
Alignment explanation
Indices: 81574--81625 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
81564 GTAATCACAT
*
81574 TATGAAATTTTGATTACCATAC
1 TATGAAATTGTGATTACCATAC
* *
81596 CATAAAATTGTGA-TACC-TCAC
1 TATGAAATTGTGATTACCAT-AC
81617 TATGAAATT
1 TATGAAATT
81626 TTTATAAACC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.04
21 13 0.54
22 10 0.42
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTGTGATTACCATAC
Found at i:81795 original size:85 final size:84
Alignment explanation
Indices: 81530--81959 Score: 259
Period size: 85 Copynumber: 4.9 Consensus size: 84
81520 AAACACACAT
* * * *
81530 TATGAAATTTTGATAACCTTCCTATAAGATATT-AGT-A-ATCACATTATGAAATTTTGATTACC
1 TATGAAATTTTGATAACCTCCCTATAAAATTTTGA-TAACATC-CA-TATGAAATTTTGATAACC
*
81592 ATACCATAAAATTGTGAT-ACCTCAC
63 -T--CATAAAATTTTGATAACCTC-C
* * *
81617 TATGAAATTTTTATAAACCTCCCTATAAAATTTTGATAACCTCCATTTGAAATTTTGATAACCTC
1 TATGAAATTTTGAT-AACCTCCCTATAAAATTTTGATAACATCCATATGAAATTTTGATAACCTC
* * *
81682 ATGAAATTTTGAAAACCACC
65 ATAAAATTTTGATAACCTCC
* * *
81702 TCATGAAATTTTGATAACCAT-CTTATAAAATTTTGATAACATCCCTAT-AAATTTT-TTAACCT
1 T-ATGAAATTTTGATAACC-TCCCTATAAAATTTTGATAACATCCATATGAAATTTTGATAACCT
*
81764 CCTTATAAAATTTTGTTAACCTCC
64 -C--ATAAAATTTTGATAACCTCC
* *** * * * **
81788 TACGAAATTTTGATAAGAACACTATTAACTTTTGATAACCCCCA-ATGAAATTTTGATAATTATC
1 TATGAAATTTTGATAACCTCCCTATAAAATTTTGATAACATCCATATGAAATTTTGAT-A--A-C
* ** *
81852 TATACCATAAAATTACGATAACTTACC
62 -CT--CATAAAATTTTGATAACCT-CC
* * * * * *
81879 TATGAAATTTTGTTAATCTCCCTATAAAATTTTGAGAACCA-CGC-TATCAAATTTTGTTAATCT
1 TATGAAATTTTGATAACCTCCCTATAAAATTTTGATAA-CATC-CATATGAAATTTTGATAACCT
81942 CACTATAAATTTTGATAA
64 CA-TA-AAATTTTGATAA
81960 ACCGATTATG
Statistics
Matches: 264, Mismatches: 54, Indels: 50
0.72 0.15 0.14
Matches are distributed among these distances:
83 6 0.02
84 10 0.04
85 80 0.30
86 37 0.14
87 26 0.10
88 33 0.12
89 6 0.02
90 17 0.06
91 34 0.13
92 15 0.06
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (84 bp):
TATGAAATTTTGATAACCTCCCTATAAAATTTTGATAACATCCATATGAAATTTTGATAACCTCA
TAAAATTTTGATAACCTCC
Found at i:81796 original size:63 final size:62
Alignment explanation
Indices: 81573--81803 Score: 191
Period size: 63 Copynumber: 3.6 Consensus size: 62
81563 AGTAATCACA
* * * *
81573 TTATGAAATTTTGATTACCATACC-ATAAAATTGTGAT-ACCTCACTATGAAATTTTTATAAACC
1 TTATAAAATTTTGATAACC-T-CCTATGAAATTTTGATAACC-C-CTATGAAATTTTT-T-AACC
81636 TCC
60 TCC
* * * ** *
81639 CTATAAAATTTTGATAACCTCCATTTGAAATTTTGATAACCTC-ATGAAATTTTGAAAACCACC
1 TTATAAAATTTTGATAACCTCC-TATGAAATTTTGATAACCCCTATGAAATTTT-TTAACCTCC
* * * *
81702 TCATGAAATTTTGATAACCATCTTATAAAATTTTGATAACATCCCTAT-AAATTTTTTAACCTCC
1 TTATAAAATTTTGATAACC-TCCTATGAAATTTTGATAAC--CCCTATGAAATTTTTTAACCTCC
* *
81766 TTATAAAATTTTGTTAACCTCCTACGAAATTTTGATAA
1 TTATAAAATTTTGATAACCTCCTATGAAATTTTGATAA
81804 GAACACTATT
Statistics
Matches: 131, Mismatches: 26, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
63 53 0.40
64 36 0.27
65 11 0.08
66 28 0.21
67 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.39
Consensus pattern (62 bp):
TTATAAAATTTTGATAACCTCCTATGAAATTTTGATAACCCCTATGAAATTTTTTAACCTCC
Found at i:82056 original size:22 final size:22
Alignment explanation
Indices: 82020--82064 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
82010 CCTCTGAAAT
*
82020 ACCACATTATAAAATTTTGATA
1 ACCACACTATAAAATTTTGATA
*
82042 ACCACACTATTAAATTTTGATA
1 ACCACACTATAAAATTTTGATA
82064 A
1 A
82065 TCTCCCTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (22 bp):
ACCACACTATAAAATTTTGATA
Found at i:82302 original size:66 final size:66
Alignment explanation
Indices: 82209--82335 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
82199 TATAAGCACA
* *** *
82209 CTATGAAATTTTGATAATCTTCCTATGAATTTCTTA-TAACCTCCATATAAAATTTTGATAATCG
1 CTATGAAATTTTGATAACCAGACTATGAAATT-TTAGTAACCTCCATATAAAATTTTGATAATCG
82273 CC
65 CC
* * * *
82275 CTATGAAATTTTGATAACCAGAGTATGAAATTTTAGTAACCTCCCTGTGAAATTTTGATAA
1 CTATGAAATTTTGATAACCAGACTATGAAATTTTAGTAACCTCCATATAAAATTTTGATAA
82336 CCTTCCAATG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 3 0.06
66 48 0.94
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCAGACTATGAAATTTTAGTAACCTCCATATAAAATTTTGATAATCGC
C
Found at i:82382 original size:22 final size:21
Alignment explanation
Indices: 82209--82383 Score: 142
Period size: 22 Copynumber: 8.0 Consensus size: 21
82199 TATAAGCACA
*
82209 CTATGAAATTTTGATAATCTTC
1 CTATGAAATTTTGATAA-CCTC
*
82231 CTATG-AATTTCTTATAACCTC
1 CTATGAAATTT-TGATAACCTC
*
82252 CATATAAAATTTTGATAATCGC-C
1 C-TATGAAATTTTGATAA-C-CTC
**
82275 CTATGAAATTTTGATAACCAGA
1 CTATGAAATTTTGATAACC-TC
*
82297 GTATGAAATTTT-AGTAACCTCC
1 CTATGAAATTTTGA-TAACCT-C
*
82319 CTGTGAAATTTTGATAACCTTC
1 CTATGAAATTTTGATAACC-TC
* *
82341 CAATG-AATTTCGATAACCTC
1 CTATGAAATTTTGATAACCTC
*
82361 CTTATGAAATTTTGATTACCTC
1 C-TATGAAATTTTGATAACCTC
82383 C
1 C
82384 ATATCTAACA
Statistics
Matches: 123, Mismatches: 17, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
20 4 0.03
21 26 0.21
22 82 0.67
23 10 0.08
24 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:82440 original size:22 final size:22
Alignment explanation
Indices: 82409--82538 Score: 117
Period size: 22 Copynumber: 6.0 Consensus size: 22
82399 ATGAAATTTT
* * *
82409 ATTTTAATAACCTCATTATGAA
1 ATTTTGATAACCTCACTATAAA
* *
82431 ATTTTGATAACATC-CCATAAA
1 ATTTTGATAACCTCACTATAAA
82452 A--TTGATAA-CTACACTATAAA
1 ATTTTGATAACCT-CACTATAAA
* * *
82472 ATTTTAATATCCT-ATCTATGAA
1 ATTTTGATAACCTCA-CTATAAA
*
82494 ATTTTGGTAACCTCACTATAAA
1 ATTTTGATAACCTCACTATAAA
*
82516 ATTTTGATAACCACACTATAAA
1 ATTTTGATAACCTCACTATAAA
82538 A
1 A
82539 GTTTAGTAAC
Statistics
Matches: 85, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.01
19 8 0.09
20 7 0.08
21 6 0.07
22 60 0.71
23 3 0.04
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.36
Consensus pattern (22 bp):
ATTTTGATAACCTCACTATAAA
Found at i:82548 original size:22 final size:21
Alignment explanation
Indices: 82447--82552 Score: 72
Period size: 22 Copynumber: 4.9 Consensus size: 21
82437 ATAACATCCC
* *
82447 ATAAAATTGA-TAACTACACT
1 ATAAAATTTAGTAACCACACT
* * *
82467 ATAAAATTTTAATATCCTA-TCT
1 ATAAAA-TTTAGTAACC-ACACT
* * *
82489 ATGAAATTTTGGTAACCTCACT
1 AT-AAAATTTAGTAACCACACT
*
82511 ATAAAATTTTGATAACCACACT
1 ATAAAATTTAG-TAACCACACT
82533 ATAAAAGTTTAGTAACCACA
1 ATAAAA-TTTAGTAACCACA
82553 ATGAATTTTG
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
20 6 0.09
21 10 0.15
22 41 0.63
23 8 0.12
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (21 bp):
ATAAAATTTAGTAACCACACT
Found at i:83074 original size:21 final size:21
Alignment explanation
Indices: 83050--83093 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
83040 GAGATCGTTC
83050 TTTTTAATATAGTATAGATTA
1 TTTTTAATATAGTATAGATTA
83071 TTTTTAATATAGTATAGATTA
1 TTTTTAATATAGTATAGATTA
83092 TT
1 TT
83094 CAGTATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
TTTTTAATATAGTATAGATTA
Found at i:83101 original size:21 final size:21
Alignment explanation
Indices: 83054--83098 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
83044 TCGTTCTTTT
**
83054 TAATATAGTATAGATTATTTT
1 TAATATAGTATAGATTATTAG
83075 TAATATAGTATAGATTATTCAG
1 TAATATAGTATAGATTATT-AG
83097 TA
1 TA
83099 TATCACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (21 bp):
TAATATAGTATAGATTATTAG
Found at i:89046 original size:16 final size:16
Alignment explanation
Indices: 89027--89062 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
89017 CATATCTTTT
89027 CATTTGGCAAAAGTAC
1 CATTTGGCAAAAGTAC
89043 CATTTGGCAAAAGTAC
1 CATTTGGCAAAAGTAC
89059 CATT
1 CATT
89063 GTCCCCCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (16 bp):
CATTTGGCAAAAGTAC
Found at i:89145 original size:29 final size:27
Alignment explanation
Indices: 89084--89146 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 27
89074 ACTTGTAGCG
*
89084 TTTGGACGTTTTCCCCCTAAACTTCAA
1 TTTGGACATTTTCCCCCTAAACTTCAA
*
89111 TCTTGGACATTTTGCCCCCTGAACTCTCAA
1 T-TTGGACATTTT-CCCCCTAAACT-TCAA
89141 TTTGGA
1 TTTGGA
89147 GCCCCGTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.03
28 10 0.32
29 15 0.48
30 5 0.16
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.37
Consensus pattern (27 bp):
TTTGGACATTTTCCCCCTAAACTTCAA
Found at i:93158 original size:15 final size:15
Alignment explanation
Indices: 93138--93172 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
93128 AGAGAATCTC
93138 TTCTTGTTTCACATG
1 TTCTTGTTTCACATG
93153 TTCTTGTTTCACATG
1 TTCTTGTTTCACATG
93168 TTCTT
1 TTCTT
93173 TCTTTGCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.11, T:0.57
Consensus pattern (15 bp):
TTCTTGTTTCACATG
Found at i:107798 original size:30 final size:30
Alignment explanation
Indices: 107762--107833 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 30
107752 AATTTGACAA
107762 TTTTTGTATAGTTTTTTTTTGGC-ACTACAC
1 TTTTTGTATAGTTTTTTTTTGGCGA-TACAC
107792 TTTTTGTATAG-TTTTTTTTGGCGATACAC
1 TTTTTGTATAGTTTTTTTTTGGCGATACAC
107821 TTTTT-TATAGTTT
1 TTTTTGTATAGTTT
107834 AGGGGCCTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
28 5 0.12
29 23 0.57
30 12 0.30
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.60
Consensus pattern (30 bp):
TTTTTGTATAGTTTTTTTTTGGCGATACAC
Found at i:112447 original size:18 final size:16
Alignment explanation
Indices: 112412--112445 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
112402 AATATGAACT
112412 TAAATTTTGAGGTATA
1 TAAATTTTGAGGTATA
112428 TAAATTTTGAGGTATA
1 TAAATTTTGAGGTATA
112444 TA
1 TA
112446 TATTAAACCT
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:0.00, G:0.18, T:0.44
Consensus pattern (16 bp):
TAAATTTTGAGGTATA
Found at i:119463 original size:19 final size:19
Alignment explanation
Indices: 119441--119491 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
119431 GGGCTGAAAT
119441 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
119460 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
119479 TAATT-ATTATTAA
1 TAATTAATTATTAA
119492 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:126027 original size:21 final size:21
Alignment explanation
Indices: 126001--126114 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
125991 TGCTAGAAGT
126001 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
126022 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
126043 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
126064 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
* *
126085 TCATTGGAGAATGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
126106 TCATCGGAG
1 TCATTGGAG
126115 TTGCCTAAGA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 2 0.02
21 84 0.98
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:126044 original size:42 final size:42
Alignment explanation
Indices: 125997--126114 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
125987 AAGATGCTAG
125997 AAGTTCATTGGAGCAA-GTTCCAAGCTCATTGGAGAAGGTTCC
1 AAGTTCATTGGAG-AAGGTTCCAAGCTCATTGGAGAAGGTTCC
*
126039 AAGTTCATTGGAGAAGGTTCCAAGTTCATTGGAGAAGGTTCC
1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC
* * * *
126081 AAGATCATTGGAGAATGTTTCAAGCTCATCGGAG
1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAG
126115 TTGCCTAAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
41 2 0.03
42 67 0.97
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (42 bp):
AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC
Done.