Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014905.1 Kokia drynarioides strain JFW-HI SEQ_129948, 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: 291145
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 337 characters in sequence are not A, C, G, or T
Found at i:11358 original size:14 final size:14
Alignment explanation
Indices: 11320--11372 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
11310 AATTATGACT
*
11320 TTAATGTATTAAAA
1 TTAATGTTTTAAAA
* * *
11334 TTATTGATTTAAGGA
1 TTAATGTTTTAA-AA
11349 TTAAT-TTTTAAAA
1 TTAATGTTTTAAAA
11362 TTAATGTTTTA
1 TTAATGTTTTA
11373 GTTTTATTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 6 0.20
14 19 0.63
15 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (14 bp):
TTAATGTTTTAAAA
Found at i:15315 original size:27 final size:28
Alignment explanation
Indices: 15249--15315 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
15239 ATACTCTTTG
15249 CTAACTGTTTTAACAACACTAACTGCTA
1 CTAACTGTTTTAACAACACTAACTGCTA
* * * *
15277 CTAACGGCTTTACCAAC-TTAACTGCTA
1 CTAACTGTTTTAACAACACTAACTGCTA
15304 CTAACTGTTTTA
1 CTAACTGTTTTA
15316 TACCTTTACA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 19 0.58
28 14 0.42
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34
Consensus pattern (28 bp):
CTAACTGTTTTAACAACACTAACTGCTA
Found at i:27406 original size:18 final size:18
Alignment explanation
Indices: 27381--27430 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
27371 TTGAAGACGC
*
27381 GAGCTCATCCAAAGTTGT
1 GAGCTCATCCAAAGTTAT
* *
27399 GAGTTCATCGAAAGTTAT
1 GAGCTCATCCAAAGTTAT
*
27417 GAGCTCACCCAAAG
1 GAGCTCATCCAAAG
27431 ACACGAGCTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (18 bp):
GAGCTCATCCAAAGTTAT
Found at i:35535 original size:2 final size:2
Alignment explanation
Indices: 35524--35552 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
35514 GTGGCACCAA
35524 AT AT -T 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
35553 TCATTTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:36194 original size:11 final size:11
Alignment explanation
Indices: 36178--36203 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
36168 ATTTGATTTT
36178 TTAACATTTAC
1 TTAACATTTAC
36189 TTAACATTTAC
1 TTAACATTTAC
36200 TTAA
1 TTAA
36204 TCTTGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAACATTTAC
Found at i:40955 original size:41 final size:41
Alignment explanation
Indices: 40863--40977 Score: 117
Period size: 41 Copynumber: 2.8 Consensus size: 41
40853 TTTGTCTTAG
** *
40863 TCAAGGAAAAACGC-TCCTACGTGGAGGCGATTTTGTCTCAT
1 TCAAGGAAAAGTGCTTCC-ACGTGGAGGCGATTTTATCTCAT
* * * *
40904 TTAAAGAAAAGTGCTTCCACGTGGAGGTGTTTTTATCTCAT
1 TCAAGGAAAAGTGCTTCCACGTGGAGGCGATTTTATCTCAT
* * *
40945 TCAAGGAAAAGTGCTTTCATGTGGAAGC-ATTTT
1 TCAAGGAAAAGTGCTTCCACGTGGAGGCGATTTT
40978 TCTACAATTT
Statistics
Matches: 59, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
40 4 0.07
41 52 0.88
42 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (41 bp):
TCAAGGAAAAGTGCTTCCACGTGGAGGCGATTTTATCTCAT
Found at i:53318 original size:3 final size:3
Alignment explanation
Indices: 53310--53336 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53300 GAGATTATAA
53310 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
53337 CACAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:64093 original size:7 final size:7
Alignment explanation
Indices: 64081--64105 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
64071 AGTAGATAAT
64081 ATTTTAA
1 ATTTTAA
64088 ATTTTAA
1 ATTTTAA
64095 ATTTTAA
1 ATTTTAA
64102 ATTT
1 ATTT
64106 AATTATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTAA
Found at i:64392 original size:16 final size:16
Alignment explanation
Indices: 64373--64413 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
64363 TAATATTAAA
64373 TAAATAATAAATTATT
1 TAAATAATAAATTATT
* *
64389 TAAATAATAATTTTTT
1 TAAATAATAAATTATT
*
64405 TAAAAAATA
1 TAAATAATA
64414 TTGATACGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATAATAAATTATT
Found at i:64814 original size:17 final size:17
Alignment explanation
Indices: 64792--64825 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
64782 AAAAAAATTC
*
64792 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
64809 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
64826 TTATTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:65597 original size:17 final size:17
Alignment explanation
Indices: 65559--65596 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
65549 AATTTAATTC
*
65559 ATTTGATATATTTAAAT
1 ATTTTATATATTTAAAT
65576 ATTTTATATA-TTAAAT
1 ATTTTATATATTTAAAT
65592 ATTTT
1 ATTTT
65597 TTAAAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTATATATTTAAAT
Found at i:68022 original size:6 final size:6
Alignment explanation
Indices: 68011--68051 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
68001 TAGAATTAAA
*
68011 TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
68052 ATGCAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:68146 original size:26 final size:26
Alignment explanation
Indices: 68117--68174 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
68107 TGTCATTTGC
*
68117 TAAACCTTATTAAATAAA-TCCAAATA
1 TAAACATTATTAAATAAACT-CAAATA
* *
68143 TAAAAATTATTAAATAAACTCAAATT
1 TAAACATTATTAAATAAACTCAAATA
68169 TAAACA
1 TAAACA
68175 GAATTAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAACATTATTAAATAAACTCAAATA
Found at i:68180 original size:26 final size:26
Alignment explanation
Indices: 68125--68181 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
68115 GCTAAACCTT
**
68125 ATTAAATAAATCCAAATATAAAAATT
1 ATTAAATAAATCCAAATATAAAAAGA
* *
68151 ATTAAATAAA-CTCAAATTTAAACAGA
1 ATTAAATAAATC-CAAATATAAAAAGA
68177 ATTAA
1 ATTAA
68182 TTCCAAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (26 bp):
ATTAAATAAATCCAAATATAAAAAGA
Found at i:69785 original size:23 final size:23
Alignment explanation
Indices: 69754--69800 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
69744 TAATTCATGC
69754 TTTTCGATATGAAACTCAATAAT
1 TTTTCGATATGAAACTCAATAAT
* *
69777 TTTTTGATATGAAACTCGATAAT
1 TTTTCGATATGAAACTCAATAAT
69800 T
1 T
69801 GAATCGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (23 bp):
TTTTCGATATGAAACTCAATAAT
Found at i:71028 original size:25 final size:25
Alignment explanation
Indices: 70982--71030 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
70972 CTTCTGTTTC
*
70982 CTTTTCTTCTTCAAAACTTTTGCTT
1 CTTTTCTTCTTCAAAACATTTGCTT
71007 CTTTTCCTTCTTCAAAA-ATTTGCT
1 CTTTT-CTTCTTCAAAACATTTGCT
71031 GTTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.18, C:0.24, G:0.04, T:0.53
Consensus pattern (25 bp):
CTTTTCTTCTTCAAAACATTTGCTT
Found at i:79456 original size:59 final size:58
Alignment explanation
Indices: 79380--79763 Score: 269
Period size: 59 Copynumber: 6.4 Consensus size: 58
79370 AAAAAATTTG
* * * *
79380 GTGTTGGTCATGTCATGGTCGGCACCCTCTTTTTGTCTAATAAAAAATCAATTTTTTTT
1 GTGTTGGCCATGCCATGGTCGACACCC-CTTTTTATCTAATAAAAAATCAATTTTTTTT
** * * * **
79439 GTGTTGGCCATTG-CATGGTCGACACCTTTTTTTATCTGAATAGAAATTCAAATTTTTGG
1 GTGTTGGCCA-TGCCATGGTCGACACCCCTTTTTATCT-AATAAAAAATCAATTTTTTTT
* *
79498 GTGTTAGCCATGCCATGAG-CGACACTCCC-TTTTGTC-AGATAAAAAATTCGAATTTTTTTGT
1 GTGTTGGCCATGCCATG-GTCGACAC-CCCTTTTTATCTA-ATAAAAAA-TC-AATTTTTTT-T
* * ** *
79559 GTGTTGGCTATGCCATAGG-CGAAACCTCCTTTTTTATCTGGTAAAAAATCATTTTTTTTTT
1 GTGTTGGCCATGCCAT-GGTCGACACC-CC-TTTTTATCTAATAAAAAATCA-ATTTTTTTT
* * * * * *
79620 GTGTTGACCATGCAATGGTCGACACCCCTTTTTGTC-AGATAAAAAATTTAA-ATTTTTG
1 GTGTTGGCCATGCCATGGTCGACACCCCTTTTTATCTA-ATAAAAAA-TCAATTTTTTTT
* ** * * * *
79678 GTGTAGGCCATTTCATGGCCGACACGCCCTTTTTTATCTAGTAAAAATTTAATTTTTTTT
1 GTGTTGGCCATGCCATGGTCGACAC-CCC-TTTTTATCTAATAAAAAATCAATTTTTTTT
* *
79738 GTGTTGGCCATGCAATGGCCGACACC
1 GTGTTGGCCATGCCATGGTCGACACC
79764 AACTTTCCCT
Statistics
Matches: 251, Mismatches: 52, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
57 1 0.00
58 40 0.16
59 86 0.34
60 57 0.23
61 44 0.18
62 10 0.04
63 13 0.05
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (58 bp):
GTGTTGGCCATGCCATGGTCGACACCCCTTTTTATCTAATAAAAAATCAATTTTTTTT
Found at i:79726 original size:181 final size:178
Alignment explanation
Indices: 79420--79750 Score: 397
Period size: 181 Copynumber: 1.8 Consensus size: 178
79410 TTTTGTCTAA
* ** * *
79420 TAAAAAATCAATTTTTTTTGTGTTGGCCATTGCATGGTCGACACCTTTTTTTATCTGAATAGAAA
1 TAAAAAATCAATTTTTTTTGTGTTGACCATTGCATGGTCGACACCCCTTTTTATCAGAATAAAAA
* *
79485 TTCAAATTTTTGGGTGTTAGCCATGCCATGAGCGACACTCCCTTTTGTCAGATAAAAAATTCGAA
66 TTCAAATTTTTGGGTGTTAGCCATGCCATGAGCGACACGCCCTTTTATCAGATAAAAAATT-GAA
*
79550 TTTTTTTGTGTGTTGGCTATGCCATAGGCGAAACCTCCTTTTTTATCTGG
130 TTTTTTT-TGTGTTGGCCATGCCATAGGCGAAACCTCCTTTTTTATCTGG
* *
79600 TAAAAAATCATTTTTTTTTTGTGTTGACCA-TGCAATGGTCGACACCCCTTTTTGTCAG-ATAAA
1 TAAAAAATCA-ATTTTTTTTGTGTTGACCATTGC-ATGGTCGACACCCCTTTTTATCAGAAT-AA
* **
79663 AAATTTAAATTTTT-GGTG-TAGGCCATTTCATG-GCCGACACGCCCTTTTTTATCTAG-T-AAA
63 AAATTCAAATTTTTGGGTGTTA-GCCATGCCATGAG-CGACACGCCC--TTTTATC-AGATAAAA
*
79723 AATTTAATTTTTTTTGTGTTGGCCATGC
123 AATTGAATTTTTTTTGTGTTGGCCATGC
79751 AATGGCCGAC
Statistics
Matches: 129, Mismatches: 14, Indels: 17
0.81 0.09 0.11
Matches are distributed among these distances:
179 16 0.12
180 46 0.36
181 58 0.45
182 7 0.05
183 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (178 bp):
TAAAAAATCAATTTTTTTTGTGTTGACCATTGCATGGTCGACACCCCTTTTTATCAGAATAAAAA
TTCAAATTTTTGGGTGTTAGCCATGCCATGAGCGACACGCCCTTTTATCAGATAAAAAATTGAAT
TTTTTTTGTGTTGGCCATGCCATAGGCGAAACCTCCTTTTTTATCTGG
Found at i:79761 original size:118 final size:117
Alignment explanation
Indices: 79380--79763 Score: 368
Period size: 118 Copynumber: 3.2 Consensus size: 117
79370 AAAAAATTTG
* * *
79380 GTGTTGGTCATGTC-ATGGTCGGCACCCTCTTTTTGTCTA-ATAAAAAA-TCAATTTTTTTTGTG
1 GTGTTGGCCATG-CAATGGTCGACACCC-CTTTTTGTC-AGATAAAAAATTCAATTTTTTTGGTG
* * * * * **
79442 TTGGCCATTGCATGGTCGACA-CCTTTTTTTATCTGAATAGAAATTCAAATTTTTGG
63 TTGGCCATTCCATGG-CGACACCCCTTTTTTATCT-AGTAAAAATTCAATTTTTTTT
* *
79498 GTGTTAGCCATGCCATGAG-CGACACTCCC-TTTTGTCAGATAAAAAATTCGAATTTTTTTGTGT
1 GTGTTGGCCATGCAATG-GTCGACAC-CCCTTTTTGTCAGATAAAAAATTC-AATTTTTTTG-GT
* * * * * *
79561 GTTGGCTATGCCATAGGCGAAACCTCCTTTTTTATCTGGTAAAAAATCATTTTTTTTTT
62 GTTGGCCATTCCAT-GGCGACACC-CCTTTTTTATCTAGTAAAAATTCA-ATTTTTTTT
* * * *
79620 GTGTTGACCATGCAATGGTCGACACCCCTTTTTGTCAGATAAAAAATTTAA-ATTTTTGGTGTAG
1 GTGTTGGCCATGCAATGGTCGACACCCCTTTTTGTCAGATAAAAAATTCAATTTTTTTGGTGTTG
* *
79684 GCCATTTCATGGCCGACACGCCCTTTTTTATCTAGTAAAAATTTAATTTTTTTT
66 GCCATTCCATGG-CGACAC-CCCTTTTTTATCTAGTAAAAATTCAATTTTTTTT
*
79738 GTGTTGGCCATGCAATGGCCGACACC
1 GTGTTGGCCATGCAATGGTCGACACC
79764 AACTTTCCCT
Statistics
Matches: 218, Mismatches: 33, Indels: 30
0.78 0.12 0.11
Matches are distributed among these distances:
116 1 0.00
117 16 0.07
118 55 0.25
119 50 0.23
120 24 0.11
121 17 0.08
122 55 0.25
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (117 bp):
GTGTTGGCCATGCAATGGTCGACACCCCTTTTTGTCAGATAAAAAATTCAATTTTTTTGGTGTTG
GCCATTCCATGGCGACACCCCTTTTTTATCTAGTAAAAATTCAATTTTTTTT
Found at i:83458 original size:12 final size:12
Alignment explanation
Indices: 83441--83488 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
83431 TATTTGTGTA
83441 AAAATTAATTTG
1 AAAATTAATTTG
83453 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
83467 TTGAAATTAATTTG
1 --AAAATTAATTTG
83481 AAAATTAA
1 AAAATTAA
83489 GGTACATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 18 0.60
14 2 0.07
16 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:83709 original size:88 final size:86
Alignment explanation
Indices: 83603--83820 Score: 359
Period size: 88 Copynumber: 2.5 Consensus size: 86
83593 AATTTAACAT
*
83603 TATTTAAATAAAAAAGATTATTATTATATTTCAATTTATATCAAATAATGTATTGATTTGACAAT
1 TATTTAAATAAAAAAGATTATTATTATATTTCAATTTTTATCAAATAATGTATTGATTTGACAAT
83668 ACATTATTTATCAAATTTTAA
66 ACATTATTTATCAAATTTTAA
* * *
83689 TATTTAAATAAAAAAAAGATTATTATTATATTACAATTTTTATTAAATAATGTGTTGATTTGACA
1 TATTTAAAT--AAAAAAGATTATTATTATATTTCAATTTTTATCAAATAATGTATTGATTTGACA
83754 ATACATTATTTATCAAATTTTAA
64 ATACATTATTTATCAAATTTTAA
*
83777 TATTTAAAT-TAAAA-ATTATTATTATATTTCAATTTTTATCAAAT
1 TATTTAAATAAAAAAGATTATTATTATATTTCAATTTTTATCAAAT
83821 TTTAAATTTA
Statistics
Matches: 123, Mismatches: 7, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
84 28 0.23
85 4 0.03
86 9 0.07
88 82 0.67
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (86 bp):
TATTTAAATAAAAAAGATTATTATTATATTTCAATTTTTATCAAATAATGTATTGATTTGACAAT
ACATTATTTATCAAATTTTAA
Found at i:83960 original size:22 final size:23
Alignment explanation
Indices: 83913--83973 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
83903 TGGACCACCC
* *
83913 AAATTTCACCTCACC-TAAACGT
1 AAATTTCAACTCACCAAAAACGT
*
83935 AAATTTCAACTCACCAAAAATG-
1 AAATTTCAACTCACCAAAAACGT
**
83957 AAATTTCTGCTCACCAA
1 AAATTTCAACTCACCAA
83974 CACCCCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.41, C:0.28, G:0.05, T:0.26
Consensus pattern (23 bp):
AAATTTCAACTCACCAAAAACGT
Found at i:86285 original size:30 final size:30
Alignment explanation
Indices: 86251--86342 Score: 130
Period size: 30 Copynumber: 3.1 Consensus size: 30
86241 TCCGTTTACT
* * * *
86251 TTTTAAATTTAATTTATAATTTCGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
86281 TTTTAAATTTAATTTCTAATTTCCTATATA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
* *
86311 TTTTAATTTTAATTTCTAATTTCCTCTATA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
86341 TT
1 TT
86343 CTAATTATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.29, C:0.09, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTATATA
Found at i:86319 original size:17 final size:17
Alignment explanation
Indices: 86294--86348 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
86284 TAAATTTAAT
86294 TTCTAATTTCCTATATA
1 TTCTAATTTCCTATATA
*
86311 TTTTAATTT--TA-AT-
1 TTCTAATTTCCTATATA
*
86324 TTCTAATTTCCTCTATA
1 TTCTAATTTCCTATATA
86341 TTCTAATT
1 TTCTAATT
86349 ATTATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 8 0.26
14 2 0.06
15 3 0.10
16 2 0.06
17 16 0.52
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCTAATTTCCTATATA
Found at i:87220 original size:60 final size:60
Alignment explanation
Indices: 87148--87447 Score: 272
Period size: 61 Copynumber: 5.0 Consensus size: 60
87138 AGGAAAAGTT
** *
87148 GGTGTCGGTCATTGCATGACCAACAC-AAAAAAATTTGATTTTTTACCAAATAAAAAAGG
1 GGTGTCGACCATTGCATGACCAACACAAAAAAAATTTAATTTTTTACCAAATAAAAAAGG
* * * * * *
87207 GGATGTTGATCATTGCATGGCCAACACAAAAAAAAAATTAATTTTTTACCATATAAAAAAAG
1 GG-TGTCGACCATTGCATGACCAACAC-AAAAAAAATTTAATTTTTTACCAAATAAAAAAGG
* ** *
87269 GGTGTCGACCATTGCATGACCAACACAAAAAAAATTTAAATTTTTTATCTGACAAAAAAGG
1 GGTGTCGACCATTGCATGACCAACACAAAAAAAATTT-AATTTTTTACCAAATAAAAAAGG
* * * *
87330 GGTGTCGACCATGGCATGACCAACATC--CAAAAATTTGA-TTTTTATTCAAAT-AAAAAGG
1 GGTGTCGACCATTGCATGACCAACA-CAAAAAAAATTTAATTTTTTA-CCAAATAAAAAAGG
* * * * * *
87388 AGTGTCGGCCA-TGCAATGATCAACAC-CAAAAAATTTAAATTTTTTTATCAAACAAAAAAG
1 GGTGTCGACCATTGC-ATGACCAACACAAAAAAAATTT-AA-TTTTTTACCAAATAAAAAAG
87448 AAGTGTCAGT
Statistics
Matches: 200, Mismatches: 29, Indels: 22
0.80 0.12 0.09
Matches are distributed among these distances:
57 3 0.01
58 39 0.19
59 7 0.04
60 44 0.22
61 75 0.38
62 32 0.16
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (60 bp):
GGTGTCGACCATTGCATGACCAACACAAAAAAAATTTAATTTTTTACCAAATAAAAAAGG
Found at i:87400 original size:58 final size:57
Alignment explanation
Indices: 87261--87445 Score: 180
Period size: 58 Copynumber: 3.1 Consensus size: 57
87251 TTTACCATAT
* *
87261 AAAAAAAGGGTGTCGACCATTGCATGACCAACACAAAAAAAATTTAAATTTTTTATCTGA
1 AAAAAAAGGGTGTCGACCA-TGCATGACCAACAC--CAAAAATTTAAATTTTTTATCTCA
* *
87321 CAAAAAAGGGGTGTCGACCATGGCATGACCAACATCCAAAAATTT-GA-TTTTTAT-TCA
1 -AAAAAAAGGGTGTCGACCAT-GCATGACCAACA-CCAAAAATTTAAATTTTTTATCTCA
* * *
87378 AATAAAAAGGAGTGTCGGCCATGCAATGATCAACACCAAAAAATTTAAATTTTTT-TATCA
1 AA-AAAAAGG-GTGTCGACCATGC-ATGACCAACACC-AAAAATTTAAATTTTTTATCTCA
87438 AACAAAAA
1 AA-AAAAA
87446 AGAAGTGTCA
Statistics
Matches: 106, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
56 2 0.02
57 12 0.11
58 34 0.32
59 3 0.03
60 24 0.23
61 30 0.28
62 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (57 bp):
AAAAAAAGGGTGTCGACCATGCATGACCAACACCAAAAATTTAAATTTTTTATCTCA
Found at i:87509 original size:55 final size:55
Alignment explanation
Indices: 87322--87594 Score: 154
Period size: 55 Copynumber: 4.9 Consensus size: 55
87312 TTTATCTGAC
* * * *
87322 AAAAAAGGGGTGTC-GACCATGGCATGACCAACATCCAAAAATTTGATTTTTAT-TCAAAT
1 AAAAAAGGGGTGTCAG-CCATGACATGATCAATA-CC-AAAATTT--TTTTT-TGTCAGAT
* * * * * *
87381 -AAAAAGGAGTGTCGGCCATG-CAATGATCAACACCAAAAAATTTAAATTTTTTTATCAAAC
1 AAAAAAGGGGTGTCAGCCATGAC-ATGATCAATACC--AAAA-TT---TTTTTTTGTCAGAT
** *
87441 AAAAAAGAAGTGTCAGTCATGACATGATCAATACCAAAATTTTTTTTTGTCAGAT
1 AAAAAAGGGGTGTCAGCCATGACATGATCAATACCAAAATTTTTTTTTGTCAGAT
*
87496 AAAAAAGGGGTGTCACCCATGACATGA-CTAACT-CCAAAA--TTTTTTTGTCAGAT
1 AAAAAAGGGGTGTCAGCCATGACATGATC-AA-TACCAAAATTTTTTTTTGTCAGAT
* * * * *
87549 -AAAATGGGATATCAGCCATG-CAATGATCGATACC-AATTTTTTTTTT
1 AAAAAAGGGGTGTCAGCCATGAC-ATGATCAATACCAAAATTTTTTTTT
87595 CAAATTCTCG
Statistics
Matches: 177, Mismatches: 20, Indels: 40
0.75 0.08 0.17
Matches are distributed among these distances:
51 4 0.02
52 23 0.13
53 22 0.12
54 1 0.01
55 42 0.24
56 1 0.01
57 3 0.02
58 33 0.19
59 8 0.05
60 10 0.06
61 28 0.16
62 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (55 bp):
AAAAAAGGGGTGTCAGCCATGACATGATCAATACCAAAATTTTTTTTTGTCAGAT
Found at i:93235 original size:20 final size:20
Alignment explanation
Indices: 93210--93270 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
93200 AATAAAAAAG
93210 AATCGATTCAAAAAGCAATA
1 AATCGATTCAAAAAGCAATA
* * *
93230 AATCGATTTAAAATAACAAAA
1 AATCGATTCAAAA-AGCAATA
*
93251 AATCGATTCTAAACAGCAAT
1 AATCGATTC-AAAAAGCAAT
93271 GAAACCAAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 12 0.38
21 17 0.53
22 3 0.09
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (20 bp):
AATCGATTCAAAAAGCAATA
Found at i:93255 original size:21 final size:21
Alignment explanation
Indices: 93199--93263 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
93189 GAATAAAATT
*
93199 AAATAA-AAAAGAATCGATTCA
1 AAATAACAAAA-AATCGATTTA
* *
93220 AAA-AGCAATAAATCGATTTA
1 AAATAACAAAAAATCGATTTA
93240 AAATAACAAAAAATCGATTCTA
1 AAATAACAAAAAATCGATT-TA
93262 AA
1 AA
93264 CAGCAATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 13 0.36
21 19 0.53
22 4 0.11
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAACAAAAAATCGATTTA
Found at i:99207 original size:2 final size:2
Alignment explanation
Indices: 99200--99241 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
99190 TAGTTTACCC
*
99200 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
99242 CATAATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115202 original size:3 final size:3
Alignment explanation
Indices: 115156--115182 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
115146 CTGCTGTCCC
115156 CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA
115183 AATGGGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:120565 original size:3 final size:3
Alignment explanation
Indices: 120557--120586 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
120547 CACCCATCCT
120557 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
120587 AAAGAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:121642 original size:3 final size:3
Alignment explanation
Indices: 121595--121623 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
121585 CCCCTACATT
121595 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
121624 TAAATCGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:122944 original size:2 final size:2
Alignment explanation
Indices: 122937--122967 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
122927 ATTAGTCACA
*
122937 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
122968 GATGAGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:146112 original size:228 final size:227
Alignment explanation
Indices: 145706--146368 Score: 740
Period size: 228 Copynumber: 2.9 Consensus size: 227
145696 CTCTGAAGAA
* * * * *
145706 GATGCAGATCTTTGTGAAAACCCTCACCGGCAAGACCATAACACTCGAGGTCGAAAGCTCCGACA
1 GATGCAGATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
* * * *
145771 CCATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCCGACCAGCAGCGTCTC
66 CCATCGACAACGTTAAGGCCAAGATTCAAGATAAGG-AGGGATCCCACCTGACCAGCAGCGTCTC
* ** * * ** *
145836 ATTTTCGCTGGCAAACAGCTCGAAGACGGTCGGACCCTT-GCCGATTATAACATCCAGAAAGAAT
130 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGA-CCTTGGCTGATTATAACATCCAGAAAGAAT
*
145900 CCACCCTCCACCTCGTCTT-ACGCCTTAGAGG-GG
194 CCACCCTTCACCTCGTCTTGA-GCCTTAGAGGAGG
* * * *
145933 GCATGCAAATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGTTCCGAC
1 G-ATGCAGATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGAC
* *
145998 ACCATCGACAACGTTAAGGCCAAGATTCAAGATAAGGAGGGCATCCCACCTGACCAACAGCGTTT
65 ACCATCGACAACGTTAAGGCCAAGATTCAAGATAAGGAGGG-ATCCCACCTGACCAGCAGCGTCT
*
146063 GATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCA-AAAGGAA
129 CATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAA-GAA
* * * * *
146127 TCCACCCTTCACCTTGTTTTGAGGCTTCGTGGAGG
193 TCCACCCTTCACCTCGTCTTGAGCCTTAGAGGAGG
* * * * * * * * * *
146162 GATGCAGATTTTTGTCAAGACTTTGACCGGCAAAACAATCACCTTGGAGGTTGAAAGCTCCGATA
1 GATGCAGATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
* * * * * * ** *
146227 CCATTGACAATGTTAAGGCAAAGATTCAGGATAAGGAAGGAATCCCACCTGATCAGCAAAGGCTC
66 CCATCGACAACGTTAAGGCCAAGATTCAAGATAAGG-AGGGATCCCACCTGACCAGCAGCGTCTC
* * * * *
146292 ATCTTTGCCGGCAAACAATTGGAAGATGGGAGGACTTTGGCTGATTATAACATTCAGAAAGAGTC
130 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGAATC
*
146357 TACCCTTCACCT
195 CACCCTTCACCT
146369 TGTTCTTCGT
Statistics
Matches: 366, Mismatches: 62, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
227 12 0.03
228 344 0.94
229 10 0.03
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.21
Consensus pattern (227 bp):
GATGCAGATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
CCATCGACAACGTTAAGGCCAAGATTCAAGATAAGGAGGGATCCCACCTGACCAGCAGCGTCTCA
TCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGAATCC
ACCCTTCACCTCGTCTTGAGCCTTAGAGGAGG
Found at i:154143 original size:5 final size:5
Alignment explanation
Indices: 154133--154171 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
154123 AATTTGGGAA
154133 GGAGT GGAGT GGAGT GGAGT GGAGT GGAGT GGAGT GGAG
1 GGAGT GGAGT GGAGT GGAGT GGAGT GGAGT GGAGT GGAG
154172 CAATTGGGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.21, C:0.00, G:0.62, T:0.18
Consensus pattern (5 bp):
GGAGT
Found at i:154344 original size:7 final size:7
Alignment explanation
Indices: 154332--154359 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
154322 TTAACGGAAT
154332 AACATCA
1 AACATCA
154339 AACATCA
1 AACATCA
154346 AACATCA
1 AACATCA
154353 AACATCA
1 AACATCA
154360 TAATTCACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (7 bp):
AACATCA
Found at i:155487 original size:20 final size:20
Alignment explanation
Indices: 155449--155487 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
155439 GTTAAATCAA
*
155449 GTTAATTAAAACTTGATTAC
1 GTTAATTAAAACTTAATTAC
155469 GTTAATT-AAACTTTAATTA
1 GTTAATTAAAAC-TTAATTA
155488 AACTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (20 bp):
GTTAATTAAAACTTAATTAC
Found at i:167327 original size:13 final size:13
Alignment explanation
Indices: 167310--167373 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
167300 TTTTAAACTA
167310 AATTTTTCAAAAG
1 AATTTTTCAAAAG
* * *
167323 CATTTCTCAAGAAT
1 AATTTTTCAA-AAG
167337 AATTTTTCACAAA-
1 AATTTTTCA-AAAG
167350 AATTTTT-AAAAG
1 AATTTTTCAAAAG
167362 CAATTTTT-AAAA
1 -AATTTTTCAAAA
167374 AATAATGCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 3 0.07
12 1 0.02
13 26 0.62
14 11 0.26
15 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (13 bp):
AATTTTTCAAAAG
Found at i:174378 original size:18 final size:18
Alignment explanation
Indices: 174355--174391 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
174345 AAAGCTGCCT
174355 TGCGATTGAGTTCAGCTG
1 TGCGATTGAGTTCAGCTG
174373 TGCGATTGAGTTCAGCTG
1 TGCGATTGAGTTCAGCTG
174391 T
1 T
174392 CAAGAACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35
Consensus pattern (18 bp):
TGCGATTGAGTTCAGCTG
Found at i:180465 original size:21 final size:20
Alignment explanation
Indices: 180429--180470 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
180419 AAATTTTTAT
*
180429 TAAAAATCATTTATATGTTA
1 TAAAAATCATTTATATATTA
180449 TAAAAAT-ATTATAATATATTA
1 TAAAAATCATT-T-ATATATTA
180470 T
1 T
180471 TTATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 3 0.16
20 8 0.42
21 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAAAATCATTTATATATTA
Found at i:189690 original size:16 final size:18
Alignment explanation
Indices: 189664--189706 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
189654 TTTTTTAGTT
*
189664 TGTAATATTT-TATATTA
1 TGTAATTTTTGTATATTA
*
189681 TGTTATTTTTGTATATTA
1 TGTAATTTTTGTATATTA
189699 TGTAATTT
1 TGTAATTT
189707 ATAACATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (18 bp):
TGTAATTTTTGTATATTA
Found at i:194401 original size:6 final size:6
Alignment explanation
Indices: 194384--194418 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
194374 TTAGACTTTG
*
194384 CCGGAA CTGGAA CCGGAA CCGGAA CCGGAA CCGGA
1 CCGGAA CCGGAA CCGGAA CCGGAA CCGGAA CCGGA
194419 GTTTCGGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.34, T:0.03
Consensus pattern (6 bp):
CCGGAA
Found at i:201192 original size:18 final size:18
Alignment explanation
Indices: 201141--201192 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
201131 CTACGTATAG
*
201141 ATATTTAATATTTTATTTT
1 ATATTTAATA-TTTATTAT
**
201160 ATATAAAAT-TATTATTAT
1 ATATTTAATAT-TTATTAT
201178 ATATTTAATATTTAT
1 ATATTTAATATTTAT
201193 CCTAATTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 1 0.04
18 17 0.65
19 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTAATATTTATTAT
Found at i:201812 original size:15 final size:15
Alignment explanation
Indices: 201792--201821 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
201782 AATTTAACTA
201792 AAAAATAATAAAATT
1 AAAAATAATAAAATT
*
201807 AAAAATATTAAAATT
1 AAAAATAATAAAATT
201822 TAAATTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATAATAAAATT
Found at i:202934 original size:2 final size:2
Alignment explanation
Indices: 202927--202955 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
202917 AGGAAAGCTG
202927 TA TA TA TA T- 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
202956 ATGAATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:203628 original size:3 final size:3
Alignment explanation
Indices: 203620--203645 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
203610 TACAATGGTT
203620 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
203646 TTGAGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:209362 original size:5 final size:5
Alignment explanation
Indices: 209354--209378 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
209344 TGCAATGCAT
209354 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
209379 TATTTCTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:231321 original size:17 final size:17
Alignment explanation
Indices: 231295--231330 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
231285 ATCTCTATTT
*
231295 TTCTCTTCTTATTCTTC
1 TTCTCCTCTTATTCTTC
*
231312 TTCTCCTCTTCTTCTTC
1 TTCTCCTCTTATTCTTC
231329 TT
1 TT
231331 TTTCTCATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (17 bp):
TTCTCCTCTTATTCTTC
Found at i:231322 original size:20 final size:20
Alignment explanation
Indices: 231297--231341 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
231287 CTCTATTTTT
231297 CTCTTCTTATTCTTCTTCTC
1 CTCTTCTTATTCTTCTTCTC
* *
231317 CTCTTCTTCTTCTTTTTCTC
1 CTCTTCTTATTCTTCTTCTC
*
231337 ATCTT
1 CTCTT
231342 AAACCCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTCTTATTCTTCTTCTC
Found at i:231341 original size:17 final size:17
Alignment explanation
Indices: 231292--231342 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
231282 AGCATCTCTA
231292 TTTTTCTCTTCTTATTC
1 TTTTTCTCTTCTTATTC
*
231309 TTCTTCTCCTCTTCTTCTTC
1 TT-TT-T-CTCTTCTTATTC
*
231329 TTTTTCTCATCTTA
1 TTTTTCTCTTCTTA
231343 AACCCTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
19 3 0.11
20 13 0.46
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTCTCTTCTTATTC
Found at i:234368 original size:19 final size:19
Alignment explanation
Indices: 234344--234392 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
234334 TTGGTGAGGC
234344 TTATTTTAAT-TTTGATTAT
1 TTATTTTAATATTT-ATTAT
* *
234363 TTATTTAAATATTTTTTAT
1 TTATTTTAATATTTATTAT
*
234382 TAATTTTAATA
1 TTATTTTAATA
234393 AATTAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTTTAATATTTATTAT
Found at i:235462 original size:6 final size:6
Alignment explanation
Indices: 235451--235483 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
235441 GCAATCCAAC
235451 GCTATT GCTATT GCTATT GCTATT GCTATT GCT
1 GCTATT GCTATT GCTATT GCTATT GCTATT GCT
235484 GTTTGCTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.48
Consensus pattern (6 bp):
GCTATT
Found at i:237881 original size:19 final size:19
Alignment explanation
Indices: 237845--237879 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
237835 TTTTACATGA
237845 TTTTCTATCTTTATTTTTC
1 TTTTCTATCTTTATTTTTC
237864 TTTTCTAT-TTT-TTTTT
1 TTTTCTATCTTTATTTTT
237880 TTTACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTATCTTTATTTTTC
Found at i:241238 original size:21 final size:21
Alignment explanation
Indices: 241205--241262 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
241195 AAACCTAGGA
*
241205 TTTTATAGAGAAATACTCAG-GT
1 TTTTATAG-GAAAAACT-AGAGT
*
241227 TTTTATAGGAAAAACTTGAGT
1 TTTTATAGGAAAAACTAGAGT
241248 TTTTATAGGAAAAAC
1 TTTTATAGGAAAAAC
241263 CAATTTATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 1 0.03
21 24 0.73
22 8 0.24
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (21 bp):
TTTTATAGGAAAAACTAGAGT
Found at i:241319 original size:22 final size:22
Alignment explanation
Indices: 241272--241320 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
241262 CCAATTTATC
** *
241272 TTTTTTTTATTATTATTATTAT
1 TTTTTTTTAGAATTATTATTAG
241294 TTTTTTTTAGAATTGATT-TTAG
1 TTTTTTTTAGAATT-ATTATTAG
241316 TTTTT
1 TTTTT
241321 CTATAATCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.73
Consensus pattern (22 bp):
TTTTTTTTAGAATTATTATTAG
Found at i:245489 original size:22 final size:25
Alignment explanation
Indices: 245446--245498 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 25
245436 TAAAATAATT
245446 TATTTATCACTAATTTTATAAA-TA
1 TATTTATCACTAATTTTATAAACTA
*
245470 -ATTTAT-ATTAATTGTT-TAAACTA
1 TATTTATCACTAATT-TTATAAACTA
245493 TATTTA
1 TATTTA
245499 AATATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 10 0.40
23 10 0.40
24 5 0.20
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.53
Consensus pattern (25 bp):
TATTTATCACTAATTTTATAAACTA
Found at i:247717 original size:6 final size:6
Alignment explanation
Indices: 247681--247714 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
247671 GGTTCAACTC
* *
247681 CCAGTT CCAGTT CCAGTT CCAGTT TCAGGT CCAG
1 CCAGTT CCAGTT CCAGTT CCAGTT CCAGTT CCAG
247715 GTCTACTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.32, G:0.21, T:0.29
Consensus pattern (6 bp):
CCAGTT
Found at i:251775 original size:33 final size:34
Alignment explanation
Indices: 251725--251799 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 34
251715 AAGTAATTTG
251725 AAGTCTGA-AGTTCATGATAAAAGAAG-GACCTTC
1 AAGTCTGAGAGTTCATGATAAAAGAAGTGA-CTTC
* *
251758 AAGTCTGAGA-TTTATGATAAAAGAAGTGATTTC
1 AAGTCTGAGAGTTCATGATAAAAGAAGTGACTTC
251791 AAGTCTGAG
1 AAGTCTGAG
251800 GTTTTTGGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 35 0.92
34 3 0.08
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Consensus pattern (34 bp):
AAGTCTGAGAGTTCATGATAAAAGAAGTGACTTC
Found at i:269874 original size:17 final size:18
Alignment explanation
Indices: 269827--269877 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
269817 AAAAGATATG
*
269827 AATATATAT-TATTATAT
1 AATATATATATATTATAA
269844 AATCATATTAATATATTA-AA
1 AAT-ATA-T-ATATATTATAA
269864 AATATATATATATT
1 AATATATATATATT
269878 CTAATTGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 10 0.34
18 4 0.14
19 4 0.14
20 6 0.21
21 5 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AATATATATATATTATAA
Found at i:275760 original size:17 final size:18
Alignment explanation
Indices: 275729--275763 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
275719 CATACAAGTA
*
275729 ATTTTTATAATAATAAAT
1 ATTTTTATAAAAATAAAT
275747 ATTTTTA-AAAAATAAAT
1 ATTTTTATAAAAATAAAT
275764 TATATGACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTTATAAAAATAAAT
Found at i:281696 original size:21 final size:21
Alignment explanation
Indices: 281668--281711 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
281658 TATTTTTTTT
*
281668 ATTTTTATAT-ATTTTTTAAA
1 ATTTTTATATCATTTTTAAAA
*
281688 ATTTATTATTTCATTTTTAAAA
1 ATTT-TTATATCATTTTTAAAA
281710 AT
1 AT
281712 ATTTGTGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
22 11 0.55
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTATATCATTTTTAAAA
Found at i:287189 original size:15 final size:15
Alignment explanation
Indices: 287131--287183 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
287121 TATTATAATT
* *
287131 TTTTATATATTTTAA
1 TTTTATAAATTTAAA
*
287146 TTATATATAACTTTAAA
1 TT-T-TATAAATTTAAA
*
287163 TTTTATAAATTTATA
1 TTTTATAAATTTAAA
287178 TTTTAT
1 TTTTAT
287184 TTATTTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 18 0.58
16 2 0.06
17 11 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTATAAATTTAAA
Done.