Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015334.1 Kokia drynarioides strain JFW-HI SEQ_130381, 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: 402212
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 161 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1270 original size:17 final size:16
Alignment explanation
Indices: 1246--1330 Score: 89
Period size: 17 Copynumber: 5.1 Consensus size: 16
1236 TTGGATTTTT
1246 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
* *
1263 TGAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
1280 TAAATTTAATTTTAAAA
1 TAAATTTAATTTT-AAA
* *
1297 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
* *
1313 TAAATTCAATTTTCAA
1 TAAATTTAATTTTAAA
1329 TA
1 TA
1331 GGTCCAGACG
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
16 22 0.39
17 28 0.50
18 6 0.11
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:1284 original size:34 final size:33
Alignment explanation
Indices: 1246--1325 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 33
1236 TTGGATTTTT
* * *
1246 TAAATTTAATTTTATAATGAATTTAAATTTCAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTT-AAA
1280 TAAATTTAATTTTAAAATAAACTTAAATTTAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTTAAA
*
1313 TAAATTCAATTTT
1 TAAATTTAATTTT
1326 CAATAGGTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 15 0.36
34 27 0.64
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (33 bp):
TAAATTTAATTTTAAAATAAACTTAAATTTAAA
Found at i:1330 original size:16 final size:15
Alignment explanation
Indices: 1246--1330 Score: 62
Period size: 16 Copynumber: 5.1 Consensus size: 15
1236 TTGGATTTTT
1246 TAAATTTAATTTTATAA
1 TAAA-TTAATTTTA-AA
* *
1263 TGAATTTAAATTTCAAA
1 T-AAATT-AATTTTAAA
1280 TAAATTTAATTTTAAAA
1 TAAA-TTAATTTT-AAA
*
1297 TAAACTTAAATTTAAA
1 TAAA-TTAATTTTAAA
*
1313 TAAATTCAATTTTCAA
1 TAAATT-AATTTTAAA
1329 TA
1 TA
1331 GGTCCAGACG
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
15 2 0.04
16 23 0.42
17 22 0.40
18 8 0.15
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (15 bp):
TAAATTAATTTTAAA
Found at i:4544 original size:20 final size:20
Alignment explanation
Indices: 4515--4552 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4505 CATTTCTATG
*
4515 TTTTTGTAATTTATAATTTT
1 TTTTTCTAATTTATAATTTT
*
4535 TTTTTCTAATTTGTAATT
1 TTTTTCTAATTTATAATT
4553 ATTTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTCTAATTTATAATTTT
Found at i:4567 original size:16 final size:17
Alignment explanation
Indices: 4543--4576 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4533 TTTTTTTCTA
4543 ATTTGTAATTAT-TTAT
1 ATTTGTAATTATCTTAT
*
4559 ATTTTTAATTATCTTAT
1 ATTTGTAATTATCTTAT
4576 A
1 A
4577 ATTTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTGTAATTATCTTAT
Found at i:5943 original size:105 final size:104
Alignment explanation
Indices: 5636--5923 Score: 400
Period size: 105 Copynumber: 2.8 Consensus size: 104
5626 TAACAACATC
* * * * * *
5636 AGGCTCAATGCCTTGCTTTATCATTGTGTCAACGATATT-TGTAG-TTTCAGAATTCATCCCCTC
1 AGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGAT-TTCTATAGCTTCCA-AAATCATCCCCTC
* * *
5699 CTTGCAACATGCATCGATACATATATTGTACGTAATAACATT
64 CTTGCAATATGCATCGATACATATA-TGTACGTGATAAAATT
* *
5741 AGGCTCAATGTCATGCTTTCTCATTGTGTCAAGGATTTCTATAGCTTCCGAAATCATCCCCTCCT
1 AGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGATTTCTATAGCTTCCAAAATCATCCCCTCCT
*
5806 TGCACTATGCATCGATACATATACTGTACGTGATAAAATT
66 TGCAATATGCATCGATACATATA-TGTACGTGATAAAATT
*
5846 AGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGATTTCTACAGCTTCCAAAATCATCCCCTCCT
1 AGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGATTTCTATAGCTTCCAAAATCATCCCCTCCT
*
5911 TGCAATGTGCATC
66 TGCAATATGCATC
5924 TAACAATGTA
Statistics
Matches: 163, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
104 2 0.01
105 158 0.97
106 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (104 bp):
AGGCTCAATGCCATGCTTTCTCATTGTGTCAAGGATTTCTATAGCTTCCAAAATCATCCCCTCCT
TGCAATATGCATCGATACATATATGTACGTGATAAAATT
Found at i:12682 original size:26 final size:27
Alignment explanation
Indices: 12631--12683 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
12621 TTTGTAAATT
12631 TAATTTTTTATTAATTAAAACATTTATA
1 TAATTTTTTATT-ATTAAAACATTTATA
12659 TAATTTTTATATT-TTAAAAC-TTTAT
1 TAATTTTT-TATTATTAAAACATTTAT
12684 TTACTTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.21
27 7 0.29
28 8 0.33
29 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (27 bp):
TAATTTTTTATTATTAAAACATTTATA
Found at i:13992 original size:47 final size:47
Alignment explanation
Indices: 13938--14037 Score: 191
Period size: 47 Copynumber: 2.1 Consensus size: 47
13928 TAGGTAAAAT
*
13938 AATAAATCGGGTCATTTTAAAAAAATTTATAAAATATAATATAATAA
1 AATAAATCGGGTCATTTTAAAAAAATTTATAAAATATAATACAATAA
13985 AATAAATCGGGTCATTTTAAAAAAATTTATAAAATATAATACAATAA
1 AATAAATCGGGTCATTTTAAAAAAATTTATAAAATATAATACAATAA
14032 AATAAA
1 AATAAA
14038 ATCATATACT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (47 bp):
AATAAATCGGGTCATTTTAAAAAAATTTATAAAATATAATACAATAA
Found at i:15400 original size:3 final size:3
Alignment explanation
Indices: 15392--15430 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
15382 GCTTTTGCTC
*
15392 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
15431 CCTCCTCCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:25157 original size:146 final size:144
Alignment explanation
Indices: 24869--25228 Score: 439
Period size: 146 Copynumber: 2.5 Consensus size: 144
24859 TGTAGAACTT
* * *
24869 AAAGAATGAAAGTGATTTCCTAA-TTATATC-TT-G---ATTAGAATTTCCCTTTAGCCCTAAAA
1 AAAGAATGAAAGTGATTTCCTAATTTA-ATCTTTAGATAATTAGAATTTCCTTTTAGTCCTCAAA
* * * *
24928 ATGTTGGCAACTTTTATTGGTGGCCATATATTTTTCTTTTTCATACACCAGTTGTATATGATGTA
65 ATGTTGGCAACCTTTATTGGTGGCCATATATTTTCCCTTTTCATACACCACTTGTATATGATGTA
24993 AGATCCCAAATCCCA
130 AGATCCCAAATCCCA
*
25008 AAAGAATGAAAGTGATTTCCTAATTCTAATCTTTAGATTAATTATAATTTCCTTTTAGTCCTCAA
1 AAAGAATGAAAGTGATTTCCTAATT-TAATCTTTAGA-TAATTAGAATTTCCTTTTAGTCCTCAA
* *
25073 AATGTTGGCAACCTTTCTTGGTGGCCATAT-TCTTTCCCTTTTCATACACC-CTTTTATATGATG
64 AATGTTGGCAACCTTTATTGGTGGCCATATAT-TTTCCCTTTTCATACACCACTTGTATATGATG
* *
25136 TAAGATCCCACATTCCTA
128 TAAGATCCCA-AATCCCA
* * *
25154 AAAGAATAAAAGTGATTTCCCAATAAGTTTAATCTTTATACTAATTAGAATTTCCTTTTTGTCCT
1 AAAGAATGAAAGTGATTT-CC--TAA-TTTAATCTTTAGA-TAATTAGAATTTCCTTTTAGTCCT
25219 CAAAATGTTG
61 CAAAATGTTG
25229 CGAAGGTTAT
Statistics
Matches: 190, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
139 23 0.12
140 4 0.02
141 4 0.02
142 1 0.01
145 22 0.12
146 87 0.46
147 2 0.01
149 45 0.24
150 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (144 bp):
AAAGAATGAAAGTGATTTCCTAATTTAATCTTTAGATAATTAGAATTTCCTTTTAGTCCTCAAAA
TGTTGGCAACCTTTATTGGTGGCCATATATTTTCCCTTTTCATACACCACTTGTATATGATGTAA
GATCCCAAATCCCA
Found at i:28224 original size:25 final size:25
Alignment explanation
Indices: 28196--28269 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 25
28186 ATTTAACCCT
28196 TTAAAAATGATAAAAATATAAACTA
1 TTAAAAATGATAAAAATATAAACTA
* * *
28221 TT-AAAATAAT-AAAAT-TATA-TT
1 TTAAAAATGATAAAAATATAAACTA
* **
28242 TTTATTATGATAAAAATATAAACTA
1 TTAAAAATGATAAAAATATAAACTA
28267 TTA
1 TTA
28270 GAAGTATTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
21 3 0.08
22 8 0.22
23 10 0.28
24 10 0.28
25 5 0.14
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (25 bp):
TTAAAAATGATAAAAATATAAACTA
Found at i:28232 original size:24 final size:24
Alignment explanation
Indices: 28199--28269 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
28189 TAACCCTTTA
28199 AAAATGATAAAAATATAAACTATT
1 AAAATGATAAAAATATAAACTATT
* * * *
28223 AAAATAAT-AAAAT-TATATTTTT
1 AAAATGATAAAAATATAAACTATT
**
28245 ATTATGATAAAAATATAAACTATT
1 AAAATGATAAAAATATAAACTATT
28269 A
1 A
28270 GAAGTATTTG
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
22 11 0.31
23 10 0.29
24 14 0.40
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (24 bp):
AAAATGATAAAAATATAAACTATT
Found at i:56509 original size:8 final size:8
Alignment explanation
Indices: 56498--56528 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
56488 CCAATACTTT
56498 AAAAAAGA
1 AAAAAAGA
*
56506 AAAAAAAA
1 AAAAAAGA
56514 AAAAAAGA
1 AAAAAAGA
56522 AAAAAAG
1 AAAAAAG
56529 TTTGAGGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:57659 original size:6 final size:6
Alignment explanation
Indices: 57650--57724 Score: 82
Period size: 6 Copynumber: 12.5 Consensus size: 6
57640 CATTTGGTGC
* * * *
57650 CCATGG CCATGG CCATGC CCAT-A TCCATGA CCATGA CCATGC CCAT-A
1 CCATGA CCATGA CCATGA CCATGA -CCATGA CCATGA CCATGA CCATGA
57697 TCCATGA CCATGA CCATGA CCATGA CCA
1 -CCATGA CCATGA CCATGA CCATGA CCA
57725 AATTCCCCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
6 59 0.97
7 2 0.03
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (6 bp):
CCATGA
Found at i:57683 original size:24 final size:24
Alignment explanation
Indices: 57650--57719 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
57640 CATTTGGTGC
* *
57650 CCATGGCCATGGCCATGCCCATAT
1 CCATGACCATGACCATGCCCATAT
57674 CCATGACCATGACCATGCCCATAT
1 CCATGACCATGACCATGCCCATAT
*
57698 CCATGACCATGACCATGACCAT
1 CCATGACCATGACCATGCCCAT
57720 GACCAAATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.27, C:0.37, G:0.16, T:0.20
Consensus pattern (24 bp):
CCATGACCATGACCATGCCCATAT
Found at i:57742 original size:3 final size:3
Alignment explanation
Indices: 57734--57783 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
57724 AAATTCCCCT
* *
57734 TCA TCA TCA TCA TCA TCA TCGA AC- TCA TCA TCA -AA TTCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA TCA -TCA TCA TCA
57779 TCA TC
1 TCA TC
57784 GAACTCATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:57776 original size:30 final size:30
Alignment explanation
Indices: 57740--57805 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
57730 CCCTTCATCA
* *
57740 TCATCATCATCATCGAACTCATCATCAAAT
1 TCATCATCATCATCGAACTCATCACCAAAC
57770 TCATCATCATCATCGAACTCATCACCAAAC
1 TCATCATCATCATCGAACTCATCACCAAAC
57800 TCATCA
1 TCATCA
57806 AAATTACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.27
Consensus pattern (30 bp):
TCATCATCATCATCGAACTCATCACCAAAC
Found at i:57791 original size:12 final size:11
Alignment explanation
Indices: 57734--57805 Score: 53
Period size: 12 Copynumber: 6.5 Consensus size: 11
57724 AAATTCCCCT
*
57734 TCATCATCATC
1 TCATCATCAAC
57745 ATCATCATCGAAC
1 -TCATCATC-AAC
*
57758 TCATCATCAAA
1 TCATCATCAAC
57769 T--TCATC-A-
1 TCATCATCAAC
57776 TCATCATCGAAC
1 TCATCATC-AAC
*
57788 TCATCACCAAAC
1 TCATCATC-AAC
57800 TCATCA
1 TCATCA
57806 AAATTACAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 10 0.20
11 4 0.08
12 32 0.64
13 2 0.04
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.28
Consensus pattern (11 bp):
TCATCATCAAC
Found at i:57979 original size:3 final size:3
Alignment explanation
Indices: 57971--58003 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
57961 GGTATTCTTT
57971 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
58004 TTACCACCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:58602 original size:12 final size:12
Alignment explanation
Indices: 58585--58615 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
58575 AAGGAAGACA
58585 AGACAGACAAAG
1 AGACAGACAAAG
*
58597 AGACAGACAGAG
1 AGACAGACAAAG
58609 AGACAGA
1 AGACAGA
58616 AGATGAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.29, T:0.00
Consensus pattern (12 bp):
AGACAGACAAAG
Found at i:75236 original size:22 final size:21
Alignment explanation
Indices: 75200--75242 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
75190 AATTAAATTC
*
75200 TTTTAAAATTTTAAAAATTAT
1 TTTTAAAATTCTAAAAATTAT
75221 TTTTAAAAATTCTAAAAATTAT
1 TTTT-AAAATTCTAAAAATTAT
75243 AAACAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAATTCTAAAAATTAT
Found at i:75271 original size:21 final size:21
Alignment explanation
Indices: 75194--75272 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
75184 AAAATCAATT
* *
75194 AAATTCTT-TTAAAATTTTAA
1 AAATTATTATTAAAAATTTAA
*
75214 AAATTATTTTTAAAAATTCTAA
1 AAATTATTATTAAAAATT-TAA
*
75236 AAATTA-TA-AACAAAATTTATA
1 AAATTATTATTA-AAAATTTA-A
75257 AAATT-TTATTAAAAAT
1 AAATTATTATTAAAAAT
75273 AGAAATACCG
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
20 10 0.21
21 28 0.58
22 10 0.21
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTATTATTAAAAATTTAA
Found at i:75852 original size:2 final size:2
Alignment explanation
Indices: 75841--75886 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
75831 GAAATAAATC
*
75841 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75881 AT AT AT
1 AT AT AT
75887 TTTTGAACTA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78167 original size:2 final size:2
Alignment explanation
Indices: 78160--78193 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
78150 CCCATTTCCA
78160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78194 AATTGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81912 original size:18 final size:19
Alignment explanation
Indices: 81889--81924 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
81879 TGATAATTCT
*
81889 TTTTTA-TAAATATTATAA
1 TTTTTATTAAATAATATAA
81907 TTTTTATTAAATAATATA
1 TTTTTATTAAATAATATA
81925 GATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTATTAAATAATATAA
Found at i:81922 original size:22 final size:23
Alignment explanation
Indices: 81871--81930 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
81861 ACTTCATAAT
*
81871 AATAATAATGATAATTCTTTTTTA
1 AATAAT-ATGATAATTCTTTATTA
* *
81895 TA-AATATTATAATT-TTTATTA
1 AATAATATGATAATTCTTTATTA
81916 AATAATATAGATAAT
1 AATAATAT-GATAAT
81931 AAAAAACGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 7 0.24
22 13 0.45
23 8 0.28
24 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (23 bp):
AATAATATGATAATTCTTTATTA
Found at i:86174 original size:6 final size:6
Alignment explanation
Indices: 86163--86189 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
86153 CATCACAAAA
86163 AAAATT AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AAAATT AAAATT AAA
86190 TATCTGTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:93795 original size:26 final size:26
Alignment explanation
Indices: 93766--93823 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
93756 GAGAGACATA
93766 AGTGCTGGGCAATAGAGAGCACACAC
1 AGTGCTGGGCAATAGAGAGCACACAC
93792 AGTGCTGGGCAATAGAGAGCACACAC
1 AGTGCTGGGCAATAGAGAGCACACAC
93818 AGTGCT
1 AGTGCT
93824 AAACAAAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.33, C:0.22, G:0.31, T:0.14
Consensus pattern (26 bp):
AGTGCTGGGCAATAGAGAGCACACAC
Found at i:93872 original size:23 final size:23
Alignment explanation
Indices: 93779--93872 Score: 109
Period size: 23 Copynumber: 4.0 Consensus size: 23
93769 GCTGGGCAAT
93779 AGAGAGCACACACAGTGCTGGGCAAT-
1 AGAGAGCACACACAGTGCT----AATC
*
93805 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACACAGTGCTAATC
* *
93828 AAAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACACAGTGCTAATC
*
93851 AGAGAGCACATACAGTGCTAAT
1 AGAGAGCACACACAGTGCTAAT
93873 AATAGAGAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.03
23 39 0.65
26 19 0.32
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.13
Consensus pattern (23 bp):
AGAGAGCACACACAGTGCTAATC
Found at i:93879 original size:23 final size:23
Alignment explanation
Indices: 93781--93884 Score: 86
Period size: 23 Copynumber: 4.3 Consensus size: 23
93771 TGGGCAATAG
*
93781 AGAGCACACACAGTGCTGGGCAAT-AG
1 AGAGCACACACAGTGCT----AATAAA
93807 AGAGCACACACAGTGCTAA-ACAA
1 AGAGCACACACAGTGCTAATA-AA
* * *
93830 AGAGCACACAAAGTGCTAATCAG
1 AGAGCACACACAGTGCTAATAAA
*
93853 AGAGCACATACAGTGCTAATAATA
1 AGAGCACACACAGTGCTAATAA-A
93877 GAGAGCAC
1 -AGAGCAC
93885 GAGATGTGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
22 2 0.03
23 39 0.60
25 7 0.11
26 17 0.26
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AGAGCACACACAGTGCTAATAAA
Found at i:96236 original size:23 final size:23
Alignment explanation
Indices: 96203--96249 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
96193 TTCCCTTTTG
96203 ACTATTACTATATATTTATAATA
1 ACTATTACTATATATTTATAATA
*
96226 ACTATTGCTATATATTTATAATA
1 ACTATTACTATATATTTATAATA
96249 A
1 A
96250 GTAAAAGTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (23 bp):
ACTATTACTATATATTTATAATA
Found at i:97995 original size:56 final size:57
Alignment explanation
Indices: 97884--97995 Score: 129
Period size: 56 Copynumber: 2.0 Consensus size: 57
97874 ATGGTAGCAT
** * * * * *
97884 AAGAGTTCTTTGAAAATTATTAATTACGTGTATGCTATGTACGTGTTTTCTATTTGA
1 AAGAGTTCTTTGAAAATTAAGAATCACGTGCATGCTATGCACGCGTTTACTATTTGA
*
97941 AAGA-TTCTTTGAAAATTAAGAATCACGTGCATGCTATGCATGCGTTATAC-ATTTG
1 AAGAGTTCTTTGAAAATTAAGAATCACGTGCATGCTATGCACGCGTT-TACTATTTG
97996 CAAATGCCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
56 40 0.87
57 6 0.13
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (57 bp):
AAGAGTTCTTTGAAAATTAAGAATCACGTGCATGCTATGCACGCGTTTACTATTTGA
Found at i:103327 original size:2 final size:2
Alignment explanation
Indices: 103322--103356 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
103312 ATATATATAT
103322 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
103357 AAGACTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:118588 original size:37 final size:37
Alignment explanation
Indices: 118554--118627 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
118544 GTCAAATTAT
118554 AACAAAAT-TAAAGTATGAAGATT-AAATCTTAAATTTG
1 AACAAAATATAAAG-ATGAAGATTGAAA-CTTAAATTTG
* *
118591 AGCAAAATATAAAGATTAAGATTGAAACTTAATATTT
1 AACAAAATATAAAGATGAAGATTGAAACTTAA-ATTT
118628 TTATATAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 20 0.62
38 12 0.38
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (37 bp):
AACAAAATATAAAGATGAAGATTGAAACTTAAATTTG
Found at i:119784 original size:2 final size:2
Alignment explanation
Indices: 119777--119807 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
119767 GAATATCCTT
119777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
119808 TGAAGCTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123531 original size:203 final size:202
Alignment explanation
Indices: 123178--123579 Score: 768
Period size: 203 Copynumber: 2.0 Consensus size: 202
123168 CATGCAGTGA
*
123178 TTTCTTTAAGAGACTAAAATTGATTAGCAGTTCACAGTTTTCAGAATGACATATATTCCAGGATC
1 TTTCTTTAAGAGACTAAAATTGATTAGCAGTTCACAGTTTTCAGAATGACAGATATTCCAGGATC
123243 TGTAACTTGCCTGAATCAAAATATTTGAAAAGTTTTAGCTACTTGAACAAATGTCTATTGGATAG
66 TGTAACTTGCCTGAATCAAAATATTTGAAAAGTTTTAGCTACTTGAACAAATGTCTATTGGATAG
*
123308 AGTAATAAGGAGTTTGATATTGTTTAAGGTTTCAGTTTGAATTTTTTGATATTTTTCATGTCTGG
131 AGTAATAAGGAGCTTGATATTGTTTAAGGTTTCAGTTTGAATTTTTTGATATTTTTCATGTCTGG
123373 TTTACGG
196 TTTACGG
*
123380 TTTCTTTTAAGAGACTAAAATTGATTAGCAGTTCACAGTTTTCAGAATGACAGATATTTCAGGAT
1 TTTC-TTTAAGAGACTAAAATTGATTAGCAGTTCACAGTTTTCAGAATGACAGATATTCCAGGAT
123445 CTGTAACTTGCCTGAATCAAAATATTTGAAAAGTTTTAGCTACTTGAACAAATGTCTATTGGATA
65 CTGTAACTTGCCTGAATCAAAATATTTGAAAAGTTTTAGCTACTTGAACAAATGTCTATTGGATA
123510 GAGTAATAAGGAGCTTGATATTGTTTAAGGTTTCAGTTTGAATTTTTTGATATTTTTCATGTCTG
130 GAGTAATAAGGAGCTTGATATTGTTTAAGGTTTCAGTTTGAATTTTTTGATATTTTTCATGTCTG
123575 GTTTA
195 GTTTA
123580 TAGTTTAGGT
Statistics
Matches: 196, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
202 4 0.02
203 192 0.98
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (202 bp):
TTTCTTTAAGAGACTAAAATTGATTAGCAGTTCACAGTTTTCAGAATGACAGATATTCCAGGATC
TGTAACTTGCCTGAATCAAAATATTTGAAAAGTTTTAGCTACTTGAACAAATGTCTATTGGATAG
AGTAATAAGGAGCTTGATATTGTTTAAGGTTTCAGTTTGAATTTTTTGATATTTTTCATGTCTGG
TTTACGG
Found at i:126426 original size:19 final size:20
Alignment explanation
Indices: 126400--126444 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
126390 GATAGGGAAG
*
126400 GAAAAAAAAAAAGATTAAA-A
1 GAAAAAACAAAA-ATTAAAGA
126420 GAAAAAACAAAAATTAAAGA
1 GAAAAAACAAAAATTAAAGA
126440 GAAAA
1 GAAAA
126445 TATGGTGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (20 bp):
GAAAAAACAAAAATTAAAGA
Found at i:130913 original size:8 final size:9
Alignment explanation
Indices: 130882--130910 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
130872 AAAAAATTTA
130882 TTTAAAATT
1 TTTAAAATT
130891 TTTAAAATT
1 TTTAAAATT
130900 TTTAAAATT
1 TTTAAAATT
130909 TT
1 TT
130911 AAATTAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:142915 original size:29 final size:28
Alignment explanation
Indices: 142857--142922 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
142847 AAGATAAATC
*
142857 AATTTTTTGTTTAATCATTAAATTATTT
1 AATTTTTTGTTTAATCATTAAATTAGTT
*
142885 AATTGTTTTGTTTAAGTCATTCAATT-GTT
1 AATT-TTTTGTTTAA-TCATTAAATTAGTT
142914 AAATTTTTT
1 -AATTTTTT
142923 CAAAATTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 4 0.12
29 16 0.48
30 13 0.39
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.59
Consensus pattern (28 bp):
AATTTTTTGTTTAATCATTAAATTAGTT
Found at i:149381 original size:25 final size:23
Alignment explanation
Indices: 149353--149398 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
149343 ATTAGATCCA
149353 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
149378 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
149399 CCCTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:150987 original size:2 final size:2
Alignment explanation
Indices: 150982--151012 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
150972 AGTGATAGTA
150982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
151013 AATACTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:151822 original size:23 final size:23
Alignment explanation
Indices: 151792--151847 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
151782 AGTGCTGGGT
*
151792 AACAGAGGGCAC-ACACAGTGCTA
1 AACAGAGGGCACGAAAC-GTGCTA
151815 AACAGAGGGCACGAAACGTGCTA
1 AACAGAGGGCACGAAACGTGCTA
151838 AACAGAGGGC
1 AACAGAGGGC
151848 GCGCTAGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 28 0.90
24 3 0.10
ACGTcount: A:0.39, C:0.23, G:0.30, T:0.07
Consensus pattern (23 bp):
AACAGAGGGCACGAAACGTGCTA
Found at i:160305 original size:18 final size:18
Alignment explanation
Indices: 160268--160309 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
160258 ATAATTGATA
**
160268 TGGAGGATACATTTGAGG
1 TGGAGGATACATCGGAGG
*
160286 TGGAGGATACATCGGCGG
1 TGGAGGATACATCGGAGG
160304 TGGAGG
1 TGGAGG
160310 TGGGTGATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.45, T:0.21
Consensus pattern (18 bp):
TGGAGGATACATCGGAGG
Found at i:160309 original size:24 final size:24
Alignment explanation
Indices: 160282--160333 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
160272 GGATACATTT
160282 GAGGTGGAG-GATACATCGGCGGTG
1 GAGGTGG-GTGATACATCGGCGGTG
* *
160306 GAGGTGGGTGATACATTGGGGGTG
1 GAGGTGGGTGATACATCGGCGGTG
160330 GAGG
1 GAGG
160334 ATGCATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.19, C:0.08, G:0.54, T:0.19
Consensus pattern (24 bp):
GAGGTGGGTGATACATCGGCGGTG
Found at i:161265 original size:14 final size:13
Alignment explanation
Indices: 161241--161288 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
161231 CAAAATGTAC
161241 AATATAATTAAAT
1 AATATAATTAAAT
161254 AATATAAATTAAAT
1 AATAT-AATTAAAT
161268 --TA-AATTAAAT
1 AATATAATTAAAT
*
161278 AATTTAATTAA
1 AATATAATTAA
161289 CTATTTACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 8 0.27
12 3 0.10
13 11 0.37
14 8 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATAATTAAAT
Found at i:161279 original size:19 final size:18
Alignment explanation
Indices: 161246--161288 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
161236 TGTACAATAT
161246 AATTAAATAATATAAATTA
1 AATTAAATAATAT-AATTA
*
161265 AATTAAATTAA-ATAATTT
1 AATTAAA-TAATATAATTA
161283 AATTAA
1 AATTAA
161289 CTATTTACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTAAATAATATAATTA
Found at i:166573 original size:32 final size:32
Alignment explanation
Indices: 166535--166601 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
166525 TATAAAATAT
*
166535 TAATAAATAAATTATGAGGTGATGAGAGTTAA
1 TAATAAATAAATTATGAGGTGATGAAAGTTAA
166567 TAATAAATAAATTATGAGGTGATGAAAGTTAA
1 TAATAAATAAATTATGAGGTGATGAAAGTTAA
166599 TAA
1 TAA
166602 CAAAATCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.31
Consensus pattern (32 bp):
TAATAAATAAATTATGAGGTGATGAAAGTTAA
Found at i:176430 original size:19 final size:18
Alignment explanation
Indices: 176406--176441 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
176396 GTTTTGGTAA
176406 AAATATAATAATTGTAAAT
1 AAATATAATAATT-TAAAT
*
176425 AAATATATTAATTTAAA
1 AAATATAATAATTTAAA
176442 ACTCAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AAATATAATAATTTAAAT
Found at i:176993 original size:127 final size:127
Alignment explanation
Indices: 176767--177012 Score: 456
Period size: 127 Copynumber: 1.9 Consensus size: 127
176757 GAAAAGTGTT
*
176767 TTTGAGATGTATATTATTGTCAAAAAGTGTTTTTGAAAAGTTTATGTGATGACTTGATAATTAAA
1 TTTGAGATGTATATTATTGTCAAAAAGTGTTTTTGAAAAGTCTATGTGATGACTTGATAATTAAA
* *
176832 GGTGTTCATCATTCCAAGTGTGATATGAGTTCGAGTTGTACTAATTGCATTTGTGATATGAG
66 GGTGTTCACCACTCCAAGTGTGATATGAGTTCGAGTTGTACTAATTGCATTTGTGATATGAG
*
176894 TTTGAGTTGTATATTATTGTCAAAAAGTGTTTTTGAAAAGTCTATGTGATGACTTGATAATTAAA
1 TTTGAGATGTATATTATTGTCAAAAAGTGTTTTTGAAAAGTCTATGTGATGACTTGATAATTAAA
176959 GGTGTTCACCACTCCAAGTGTGATATGAGTTCGAGTTGTACTAATTGCATTTGT
66 GGTGTTCACCACTCCAAGTGTGATATGAGTTCGAGTTGTACTAATTGCATTTGT
177013 TGTTCGGACT
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 115 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (127 bp):
TTTGAGATGTATATTATTGTCAAAAAGTGTTTTTGAAAAGTCTATGTGATGACTTGATAATTAAA
GGTGTTCACCACTCCAAGTGTGATATGAGTTCGAGTTGTACTAATTGCATTTGTGATATGAG
Found at i:186467 original size:16 final size:16
Alignment explanation
Indices: 186448--186493 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
186438 AGTTAGGGTT
186448 TTTTCAAGTTTAGATC
1 TTTTCAAGTTTAGATC
* *
186464 TTTTCGAGTTTAAATC
1 TTTTCAAGTTTAGATC
* *
186480 TTTTTAAATTTAGA
1 TTTTCAAGTTTAGA
186494 CCAAATAAGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (16 bp):
TTTTCAAGTTTAGATC
Found at i:187792 original size:30 final size:31
Alignment explanation
Indices: 187734--187810 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 31
187724 GTCACTTTCG
* * *
187734 GATTCGGA-TTTTTTAAACTAAAA-TTTTTA
1 GATTCGAATTTTTTTTAACTAAAACTTTTAA
*
187763 GATTCGAATTTTTTTTAACTCAAACTTTTAAA
1 GATTCGAATTTTTTTTAACTAAAACTTTT-AA
* *
187795 GATTAGATTTTTTTTT
1 GATTCGAATTTTTTTT
187811 TAAAAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 7 0.18
30 13 0.33
31 4 0.10
32 15 0.38
ACGTcount: A:0.31, C:0.08, G:0.09, T:0.52
Consensus pattern (31 bp):
GATTCGAATTTTTTTTAACTAAAACTTTTAA
Found at i:187858 original size:18 final size:16
Alignment explanation
Indices: 187821--187858 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
187811 TAAAAAAAAA
187821 AAATTAAACCTTTTTG
1 AAATTAAACCTTTTTG
187837 -AATTCAAATCCTTTTTG
1 AAATT-AAA-CCTTTTTG
187854 AAATT
1 AAATT
187859 TAAGTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.21
16 3 0.16
17 8 0.42
18 4 0.21
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (16 bp):
AAATTAAACCTTTTTG
Found at i:198909 original size:83 final size:85
Alignment explanation
Indices: 198626--198975 Score: 309
Period size: 83 Copynumber: 4.1 Consensus size: 85
198616 CTATTTAGGG
* * ** * *
198626 TTTTTTTTT-TTTTACTATTTATTTGTATATTTGTTACTTAATTAGTAT-AAATAAACTAATTAA
1 TTTTTTTTTGTATTATTATTTATTTGTATGCTTCTTACTTAATTAGTATGAAA-AAATTAATTAA
*
198689 ATACTGAAATGACATATTTGA
65 ATACTGAAATGGCATATTTGA
** * * *
198710 -GATATTAT-TATTATTATTTATTTGTATGCCTCTTACTTAATTAGTATGAAAAAAATTAATTAA
1 TTTTTTTTTGTATTATTATTTATTTGTATGCTTCTTACTTAATTAGTATG-AAAAAATTAATTAA
** * * * *
198773 GCAGTGAAATAGTATGTTTGAGA
65 ATACTGAAATGGCATATTT--GA
* * *
198796 TTTTTTTTTTTTGTATTATTATTTATTTGTATGCTTATCACTTAATTAGTATGAAGAAATTAATT
1 ---TTTTTTTTTGTATTATTATTTATTTGTATGCTTCTTACTTAATTAGTATGAAAAAATTAATT
*
198861 AAATACTGGAATGGCATATTTGA
63 AAATACTGAAATGGCATATTTGA
* * * *
198884 -TTTTTTTTGTA-AATTATTTCTTTGTATGCTTCTTATTTATTTAGTATGAAAAAACTT-ATTAA
1 TTTTTTTTTGTATTATTATTTATTTGTATGCTTCTTACTTAATTAGTATGAAAAAA-TTAATTAA
* * *
198946 ATAGTGAAATGGTATGTTTGA
65 ATACTGAAATGGCATATTTGA
*
198967 GTTTTTTTT
1 TTTTTTTTT
198976 ACGTTTTTTT
Statistics
Matches: 211, Mismatches: 44, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
83 95 0.45
84 43 0.20
85 3 0.01
86 2 0.01
88 2 0.01
90 29 0.14
91 37 0.18
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (85 bp):
TTTTTTTTTGTATTATTATTTATTTGTATGCTTCTTACTTAATTAGTATGAAAAAATTAATTAAA
TACTGAAATGGCATATTTGA
Found at i:198912 original size:174 final size:170
Alignment explanation
Indices: 198626--198975 Score: 441
Period size: 174 Copynumber: 2.0 Consensus size: 170
198616 CTATTTAGGG
* * * *
198626 TTTTTTTTTTTTTACTATTTATTTGTATATTTGTTACTTAATTAGTATAAATAAACTAATTAAAT
1 TTTTTTTTTTTTTACTATTTATTTGTATACTTATCACTTAATTAGTATAAAGAAACTAATTAAAT
*
198691 ACTGAAATGACATATTTGAGATATTATTATTATTATTTATTTGTATGCCTCTTACTTAATTAGTA
66 ACTGAAATGACATATTTGAGATATTATTATAATTATTTATTTGTATGCCTCTTACTTAATTAGTA
*
198756 TGAAAAAAATTAATTAAGCAGTGAAATAGTATGTTTGAGATT
131 TGAAAAAAATT-ATTAAACAGTGAAATAGTATGTTTGAG-TT
* * * *
198798 TTTTTTTTTTGTATTATTATTTATTTGTATGCTTATCACTTAATTAGTATGAAGAAATTAATTAA
1 TTTTTTTTTT-T-TTACTATTTATTTGTATACTTATCACTTAATTAGTATAAAGAAACTAATTAA
* * * * * * * * * *
198863 ATACTGGAATGGCATATTTGA-TTTTTTTTGTAAATTATTTCTTTGTATGCTTCTTATTTATTTA
64 ATACTGAAATGACATATTTGAGATATTATTAT-AATTATTTATTTGTATGCCTCTTACTTAATTA
* * *
198927 GTATGAAAAAACTTATTAAATAGTGAAATGGTATGTTTGAGTT
128 GTATGAAAAAAATTATTAAACAGTGAAATAGTATGTTTGAGTT
198970 TTTTTT
1 TTTTTT
198976 ACGTTTTTTT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
172 18 0.12
173 31 0.20
174 103 0.68
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (170 bp):
TTTTTTTTTTTTTACTATTTATTTGTATACTTATCACTTAATTAGTATAAAGAAACTAATTAAAT
ACTGAAATGACATATTTGAGATATTATTATAATTATTTATTTGTATGCCTCTTACTTAATTAGTA
TGAAAAAAATTATTAAACAGTGAAATAGTATGTTTGAGTT
Found at i:202272 original size:55 final size:57
Alignment explanation
Indices: 202170--202281 Score: 156
Period size: 55 Copynumber: 2.0 Consensus size: 57
202160 TCGACCATTC
* *
202170 CTTTTTTATCTGACTAAAAAAAAATTTTTTGTGTTAGCCATTACATAGCTGACACCCA
1 CTTTTTTATCTGAC-AAAAAAAAATTTTTGGTGTTAGCCATTACATAGCCGACACCCA
* * *
202228 CTTTTTTATCTGAC-AAAAAAAA-TTTTGGTGTTGGTCATTGCATAGCCGACACCC
1 CTTTTTTATCTGACAAAAAAAAATTTTTGGTGTTAGCCATTACATAGCCGACACCC
202282 TCCTTTAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
55 27 0.55
56 8 0.16
58 14 0.29
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (57 bp):
CTTTTTTATCTGACAAAAAAAAATTTTTGGTGTTAGCCATTACATAGCCGACACCCA
Found at i:202301 original size:55 final size:57
Alignment explanation
Indices: 202177--202324 Score: 149
Period size: 55 Copynumber: 2.6 Consensus size: 57
202167 TTCCTTTTTT
* * * * *
202177 ATCTGACTAAAAAAAAATTTTTTGTGTTAGCCATTACATAGCTGACACCCACTTTTTT
1 ATCTGA-TAAAAAAAAATTTTTGGTGTTGGCCATTACATAGCCGACACCCACTCTTTA
* * * *
202235 ATCTGA-CAAAAAAAA-TTTTGGTGTTGGTCATTGCATAGCCGACACCCTC-CTTTA
1 ATCTGATAAAAAAAAATTTTTGGTGTTGGCCATTACATAGCCGACACCCACTCTTTA
*
202289 ATTTGATAAAAAATCAAATTTTTAGGTGTTGGCCAT
1 ATCTGATAAAAAA--AAATTTTT-GGTGTTGGCCAT
202325 GCAATGGCCA
Statistics
Matches: 73, Mismatches: 12, Indels: 9
0.78 0.13 0.10
Matches are distributed among these distances:
54 8 0.11
55 33 0.45
56 8 0.11
57 3 0.04
58 10 0.14
59 11 0.15
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (57 bp):
ATCTGATAAAAAAAAATTTTTGGTGTTGGCCATTACATAGCCGACACCCACTCTTTA
Found at i:202443 original size:120 final size:119
Alignment explanation
Indices: 202250--202552 Score: 348
Period size: 120 Copynumber: 2.5 Consensus size: 119
202240 ACAAAAAAAA
* * *
202250 TTTTGGTGTTGGTCATTGCATAGCCGACACCCTCCTTTAATTTGAT-AAAAAATCAAATTTTTAG
1 TTTTGGTGTTGGCCATTGCATAGCCGACA-CC-CCTTTTATCTGATAAAAAAATCAAATTTTTAG
* *
202314 GTGTTGGCCATGCAATGGCCAACGCCCCCTTTTTGTCA-AGT-AAAAGATTT-AATTT
64 GTGTTGGCCATGCAATGGCCAACACCCCCTTTTT-TCAGA-TAAAAAAATTTAAATTT
* *
202369 TTTTGGTGTTGGCCA-TGCCATAACCGACACCCCTATTTATCTGATAAAAAAAATCAAATTTTTT
1 TTTTGGTGTTGGCCATTG-CATAGCCGACACCCCT-TTTATCTGAT-AAAAAAATCAAATTTTTA
* * *
202433 GGTGTTGGCCATGCAATGGTCGACACCCTCTTTTTTCAGATAAAAAAATTTCAAATTT
63 GGTGTTGGCCATGCAATGGCCAACACCCCCTTTTTTCAGATAAAAAAATTT-AAATTT
* * * *
202491 TTTTGGTGTTGGCCATTGCATGGCCGACACTGCTTTTTATCTGA-ATAAAAAATTAAATTTTT
1 TTTTGGTGTTGGCCATTGCATAGCCGACAC-CCCTTTTATCTGATA-AAAAAATCAAATTTTT
202553 GCATGGTCGA
Statistics
Matches: 158, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
117 3 0.02
118 12 0.08
119 28 0.18
120 57 0.36
121 15 0.09
122 39 0.25
123 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (119 bp):
TTTTGGTGTTGGCCATTGCATAGCCGACACCCCTTTTATCTGATAAAAAAATCAAATTTTTAGGT
GTTGGCCATGCAATGGCCAACACCCCCTTTTTTCAGATAAAAAAATTTAAATTT
Found at i:202506 original size:62 final size:60
Alignment explanation
Indices: 202302--202520 Score: 232
Period size: 60 Copynumber: 3.6 Consensus size: 60
202292 TGATAAAAAA
* * * *
202302 TCAAATTTTTAGGTGTTGGCCATGCAATGGCCAACGCCCCCTTTTTGTCA-AGT-AAAAGATT
1 TCAAATTTTTTGGTGTTGGCCATGCAATGGCCGAC-ACCCCTTTTT-TCAGA-TAAAAAAATT
* * ** * * *
202363 T-AATTTTTTTGGTGTTGGCCATGCCATAACCGACACCCCTATTTATCTGATAAAAAAA-A
1 TCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCT-TTTTTCAGATAAAAAAATT
*
202422 TCAAATTTTTTGGTGTTGGCCATGCAATGGTCGACACCCTCTTTTTTCAGATAAAAAAATT
1 TCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCC-CTTTTTTCAGATAAAAAAATT
202483 TCAAATTTTTTTGGTGTTGGCCATTGC-ATGGCCGACAC
1 TCAAA-TTTTTTGGTGTTGGCCA-TGCAATGGCCGACAC
202521 TGCTTTTTAT
Statistics
Matches: 130, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
59 9 0.07
60 83 0.64
61 8 0.06
62 27 0.21
63 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (60 bp):
TCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTCAGATAAAAAAATT
Found at i:202572 original size:45 final size:44
Alignment explanation
Indices: 202506--202596 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 44
202496 GTGTTGGCCA
**
202506 TTGCATGGCCGACACTGCTTTTTATCT-GAATAAAAAATTAAATTT
1 TTGCATGGCCGACACCCCTTTTTAT-TAG-ATAAAAAATTAAATTT
* * *
202551 TTGCATGGTCGACACCCCTTTTTGTTAGATAAAAAATTTAATTT
1 TTGCATGGCCGACACCCCTTTTTATTAGATAAAAAATTAAATTT
202595 TT
1 TT
202597 TTTTGTGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (44 bp):
TTGCATGGCCGACACCCCTTTTTATTAGATAAAAAATTAAATTT
Found at i:202644 original size:105 final size:108
Alignment explanation
Indices: 202448--202659 Score: 292
Period size: 106 Copynumber: 2.0 Consensus size: 108
202438 TGGCCATGCA
*
202448 ATGGTCGACACCCTCTTTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATTGCATG
1 ATGGTCGACACCCTCTTTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTAGCCATTGCATG
* *
202513 GCCGACACTGCTTTTTATCTGAATAAAAAA-TTAAATTTTTGC
66 GCCGACACCGCTTTTTATCAGAATAAAAAATTTAAATTTTTGC
* * *
202555 ATGGTCGACACCC-CTTTTTGTTAGAT-AAAAAATTT-AATTTTTTTTTGTGTTAGCCA-TGCAA
1 ATGGTCGACACCCTCTTTTT-TCAGATAAAAAAATTTCAAATTTTTTTGGTGTTAGCCATTGC-A
*
202616 TGGCTGACACCCGCTTTTTATCAG-ATAAAAAATTTAAATTTTTG
64 TGGCCGACA-CCGCTTTTTATCAGAATAAAAAATTTAAATTTTTG
202660 GTGTTGGCCA
Statistics
Matches: 94, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
104 3 0.03
105 35 0.37
106 38 0.40
107 18 0.19
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (108 bp):
ATGGTCGACACCCTCTTTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTAGCCATTGCATG
GCCGACACCGCTTTTTATCAGAATAAAAAATTTAAATTTTTGC
Found at i:202704 original size:60 final size:60
Alignment explanation
Indices: 202551--202708 Score: 182
Period size: 60 Copynumber: 2.6 Consensus size: 60
202541 AATTAAATTT
* * * *
202551 TTGCATGGTCGACACCCCTTTTTGT-TAGATAAAAAATTTAATTTTTTTTTGTGTTAGCCA
1 TTGCATGGCCGACACCCCTTTTTATCTAGATAAAAAATTTAA-TATTTTTGGTGTTAGCCA
* *
202611 -TGCAATGGCTGACACCCGCTTTTTATC-AGATAAAAAATTTAA-ATTTTTGGTGTTGGCCA
1 TTGC-ATGGCCGACACCC-CTTTTTATCTAGATAAAAAATTTAATATTTTTGGTGTTAGCCA
202670 TTGCATGGCCGACATCCCCTTTTTTATCTA-ATAAAAAAT
1 TTGCATGGCCGACA-CCCC-TTTTTATCTAGATAAAAAAT
202709 CAATTTTTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
59 27 0.32
60 34 0.40
61 23 0.27
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (60 bp):
TTGCATGGCCGACACCCCTTTTTATCTAGATAAAAAATTTAATATTTTTGGTGTTAGCCA
Found at i:202743 original size:59 final size:59
Alignment explanation
Indices: 202555--202742 Score: 199
Period size: 59 Copynumber: 3.2 Consensus size: 59
202545 AAATTTTTGC
*
202555 ATGGTCGACACCCCTTTTTGT-TAGATAAAAAATTTAATTTTTTTTTGTGTTAGCCATGCA
1 ATGGTCGACACCCCTTTTTATCTAGATAAAAAATTTAA-TTTTTTTT-TGTTAGCCATGCA
* ** *
202615 ATGG-CTGACACCCGCTTTTTATC-AGATAAAAAATTTAAATTTTTGGTGTTGGCCATTGC-
1 ATGGTC-GACACCC-CTTTTTATCTAGATAAAAAATTTAATTTTTTTTTGTTAGCCA-TGCA
* * *
202674 ATGGCCGACATCCCCTTTTTTATCTA-ATAAAAAA-TCAATTTTTTTTTGTTAGTCATGCA
1 ATGGTCGACA-CCCC-TTTTTATCTAGATAAAAAATTTAATTTTTTTTTGTTAGCCATGCA
202733 ATGGTCGACA
1 ATGGTCGACA
202743 TTAACTTTTG
Statistics
Matches: 107, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
58 3 0.03
59 42 0.39
60 39 0.36
61 23 0.21
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (59 bp):
ATGGTCGACACCCCTTTTTATCTAGATAAAAAATTTAATTTTTTTTTGTTAGCCATGCA
Found at i:203656 original size:35 final size:35
Alignment explanation
Indices: 203610--203680 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
203600 TATATATATA
203610 TATATATATATACCGTCAGTACTAGAAATTTGAAT
1 TATATATATATACCGTCAGTACTAGAAATTTGAAT
203645 TATATATATATACCGTCAGTACTAGAAATTTGAAT
1 TATATATATATACCGTCAGTACTAGAAATTTGAAT
203680 T
1 T
203681 TTTTGTTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (35 bp):
TATATATATATACCGTCAGTACTAGAAATTTGAAT
Found at i:206342 original size:23 final size:23
Alignment explanation
Indices: 206312--206366 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
206302 CATTTTTGAA
206312 ATATTTTTTTCAAAAAAAATCTG
1 ATATTTTTTTCAAAAAAAATCTG
206335 ATATTTTTTTCAAAAAAAATCTG
1 ATATTTTTTTCAAAAAAAATCTG
206358 ATATTTTTT
1 ATATTTTTT
206367 ACATTTTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (23 bp):
ATATTTTTTTCAAAAAAAATCTG
Found at i:207540 original size:17 final size:17
Alignment explanation
Indices: 207488--207542 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
207478 TAAATTTAAT
*
207488 TTCTAATTTCCTGTATA
1 TTCTAATTTCTTGTATA
* *
207505 TTTTAA-TT-TT-AAT-
1 TTCTAATTTCTTGTATA
207518 TTCTAATTTCTTGTATA
1 TTCTAATTTCTTGTATA
207535 TTCTAATT
1 TTCTAATT
207543 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
13 5 0.17
14 4 0.14
15 3 0.10
16 4 0.14
17 13 0.45
ACGTcount: A:0.25, C:0.11, G:0.04, T:0.60
Consensus pattern (17 bp):
TTCTAATTTCTTGTATA
Found at i:207542 original size:30 final size:30
Alignment explanation
Indices: 207446--207542 Score: 126
Period size: 30 Copynumber: 3.3 Consensus size: 30
207436 CCGTTTACTT
* *
207446 TTTTAA-TTTAATTTGTAATTTCATT-TTTA
1 TTTTAATTTTAATTTCTAATTTC-TTGTATA
* *
207475 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAATTTTAATTTCTAATTTCTTGTATA
207505 TTTTAATTTTAATTTCTAATTTCTTGTATA
1 TTTTAATTTTAATTTCTAATTTCTTGTATA
*
207535 TTCTAATT
1 TTTTAATT
207543 ATTATTTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
29 7 0.12
30 53 0.88
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAATTTTAATTTCTAATTTCTTGTATA
Found at i:208494 original size:59 final size:59
Alignment explanation
Indices: 208314--208670 Score: 323
Period size: 59 Copynumber: 6.0 Consensus size: 59
208304 AGGGAAAGTT
*
208314 GGTGTCGGCCATTG-CATGGCCAACA--AAAAAATTTG-ATTTTTTACCAGATAAAAAAAG
1 GGTGTCGGCCA-TGACATGGCCAACACCAAAAAATTTGAATTTTTTATCAGAT-AAAAAAG
* * ** *
208371 GCGTGTCAGCCATGACATAGCCAACACCAAAAAAAAATGAATTTTTTATCTGA-AAAAAAGG
1 G-GTGTCGGCCATGACATGGCCAACACC-AAAAAATTTGAATTTTTTATCAGATAAAAAA-G
* * * * * *
208432 GGTGTCAGTCATGGCATGGCCAACACCCAAAAATTTGATTTTTTTTTCAGATAAAAAAG
1 GGTGTCGGCCATGACATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAAG
* * * * *
208491 GGTGTCGGCCAT-ACAATGACCAACACCAAAAAATTTTAAAATTTTTATCTGA-AAAAATGG
1 GGTGTCGGCCATGAC-ATGGCCAACACCAAAAAA-TTTGAATTTTTTATCAGATAAAAA-AG
* * * * * * * *
208551 GGTATCGGTCATTACATGGTCAACACAAAAAAATTTGATTTTTTTATCAGATAAATAGG
1 GGTGTCGGCCATGACATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAAG
* * * * *
208610 GGTGTCGGCCATGGCATGACCAACACCAAAAAAATTGAATTTTTTATCTGACAAAAAAG
1 GGTGTCGGCCATGACATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAAG
208669 GG
1 GG
208671 GGTCCCAAAA
Statistics
Matches: 238, Mismatches: 49, Indels: 24
0.77 0.16 0.08
Matches are distributed among these distances:
57 3 0.01
58 20 0.08
59 114 0.48
60 78 0.33
61 12 0.05
62 11 0.05
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (59 bp):
GGTGTCGGCCATGACATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAAG
Found at i:208536 original size:119 final size:117
Alignment explanation
Indices: 208327--208671 Score: 428
Period size: 119 Copynumber: 2.9 Consensus size: 117
208317 GTCGGCCATT
* *
208327 GCATGGCCAACA-AAAAAATTTGA-TTTTTTACCAGATAAAAAAAGGCGTGTCAGCCATGACAT-
1 GCATGGCCAACACAAAAAATTTGATTTTTTTATCAGAT-AAAAAAGG-GTGTCGGCCATGACATG
* *
208389 AGCCAACACCAAAAAAAAATGAATTTTTTATCTGAAAAAAAGGGGTGTCAGTCATG
64 A-CCAACACC-AAAAAAATTGAATTTTTTATCTGAAAAAAAGGGGTATCAGTCATG
* *
208445 GCATGGCCAACACCCAAAAATTTGATTTTTTTTTCAGATAAAAAAGGGTGTCGGCCAT-ACAATG
1 GCATGGCCAACA-CAAAAAATTTGATTTTTTTATCAGATAAAAAAGGGTGTCGGCCATGAC-ATG
* * * * * *
208509 ACCAACACCAAAAAATTTTAAAATTTTTATCTGAAAAAATGGGGTATCGGTCATT
64 ACCAACACCAAAAAA-ATTGAATTTTTTATCTGAAAAAAAGGGGTATCAGTCATG
* * * * *
208564 ACATGGTCAACACAAAAAAATTTGATTTTTTTATCAGATAAATAGGGGTGTCGGCCATGGCATGA
1 GCATGGCCAACAC-AAAAAATTTGATTTTTTTATCAGATAAAAAAGGGTGTCGGCCATGACATGA
208629 CCAACACCAAAAAAATTGAATTTTTTATCTGACAAAAAAGGGG
65 CCAACACCAAAAAAATTGAATTTTTTATCTGA-AAAAAAGGGG
208672 GTCCCAAAAA
Statistics
Matches: 195, Mismatches: 23, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
118 36 0.18
119 128 0.66
120 20 0.10
121 11 0.06
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (117 bp):
GCATGGCCAACACAAAAAATTTGATTTTTTTATCAGATAAAAAAGGGTGTCGGCCATGACATGAC
CAACACCAAAAAAATTGAATTTTTTATCTGAAAAAAAGGGGTATCAGTCATG
Found at i:208829 original size:58 final size:57
Alignment explanation
Indices: 208688--208968 Score: 266
Period size: 58 Copynumber: 4.9 Consensus size: 57
208678 AAAATTTGAT
* * * * *
208688 TTTTTTTATCAGAT-TAAAAGGGGGTGTCGATCATGCAATGACCAATACC--AAAAT
1 TTTTTTTGTCAGATAAAAAAGGGGGTGTCGACCATGCAATGACCAACACCAAAAAAA
* * * * *
208742 TTTTTTTGTCAAATAAAAAAGGAGATGTCGACCATGCAATAACCAACATCAAAATAAA
1 TTTTTTTGTCAGATAAAAAAGGGGGTGTCGACCATGCAATGACCAACACCAAAA-AAA
*** * *
208800 TTTTTTTGTCAGATAAAAAAGGGGGTGTCGGTAATACAATGATCAACACCAAAAAATTTGA
1 TTTTTTTGTCAGATAAAAAAGGGGGTGTCGACCATGCAATGACCAACACCAAAAAA----A
* * * * * *
208861 TTTTTTTATCAGAT-TAAAAGGGGGTGTTGGCCATGCAATGACGAACATCAAAAAAA
1 TTTTTTTGTCAGATAAAAAAGGGGGTGTCGACCATGCAATGACCAACACCAAAAAAA
* *
208917 TTTTTCCTGTCAGATAAAAAA-GGGGTGTCGACCATGCAATGGCCAACACCAA
1 TTTTT-TTGTCAGATAAAAAAGGGGGTGTCGACCATGCAATGACCAACACCAA
208969 TTTTTTTTTA
Statistics
Matches: 180, Mismatches: 37, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
54 12 0.07
55 28 0.16
56 6 0.03
57 37 0.21
58 50 0.28
60 33 0.18
61 14 0.08
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (57 bp):
TTTTTTTGTCAGATAAAAAAGGGGGTGTCGACCATGCAATGACCAACACCAAAAAAA
Found at i:208916 original size:61 final size:61
Alignment explanation
Indices: 208799--208919 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 61
208789 ATCAAAATAA
* * *
208799 ATTTTTTTGTCAGATAAAAAAGGGGGTGTCGGTAATACAATGATCAACACCAAAAAATTTG
1 ATTTTTTTATCAGATAAAAAAGGGGGTGTCGGCAATACAATGATCAACACAAAAAAATTTG
* * * *
208860 ATTTTTTTATCAGAT-TAAAAGGGGGTGTTGGCCATGCAATGA-CGAACATCAAAAAAATTT
1 ATTTTTTTATCAGATAAAAAAGGGGGTGTCGGCAATACAATGATC-AACA-CAAAAAAATTT
208920 TTCCTGTCAG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
59 1 0.02
60 26 0.51
61 24 0.47
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (61 bp):
ATTTTTTTATCAGATAAAAAAGGGGGTGTCGGCAATACAATGATCAACACAAAAAAATTTG
Found at i:212511 original size:21 final size:21
Alignment explanation
Indices: 212470--212513 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
212460 ATGACAAATA
*
212470 TTTCAACTTTCTTTTCTCCAT
1 TTTCAACTTTCTTTTCGCCAT
*
212491 TTTCATCTTTCCTTTT-GCCAT
1 TTTCAACTTT-CTTTTCGCCAT
212512 TT
1 TT
212514 CCTTGTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.11, C:0.27, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTCAACTTTCTTTTCGCCAT
Found at i:220722 original size:4 final size:4
Alignment explanation
Indices: 220713--220739 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
220703 CGACAACCAA
220713 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
220740 AGAGTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:227132 original size:60 final size:61
Alignment explanation
Indices: 226911--227366 Score: 346
Period size: 60 Copynumber: 7.5 Consensus size: 61
226901 GGAAAAAAAA
* * *
226911 TTTTGATGTTGGTCATTG-TATGGCCGACATCCCTTTTTAATTC-GATAAAAAAAA-TCAAATTT
1 TTTTG-TGTTGGTCA-TGCAATGGCCGACACCCCCTTTT--TTCAGATAAAAAAAATTCAAATTT
* ** * * * **
226973 TTTGGTGTTGACCATGCAATGGTCGACA-CCCCTTTTTTCAGATAAAAAAATTTAAAAAAAT
1 TTTTGTGTTGGTCATGCAATGGCCGACACCCCCTTTTTTCAGATAAAAAAAATT-CAAATTT
227034 TTTTGTGTTGGTCATGCAATGGCCGACACCCCCTTTTTTCAGATAAAAAAAATTCAAAATTT
1 TTTTGTGTTGGTCATGCAATGGCCGACACCCCCTTTTTTCAGATAAAAAAAATTC-AAATTT
* * * * * * *
227096 TTTTGTGTTAGCCATGCCATGGCCGACACACCTTTTTTGTCA-A-ATAAAAAATTCGAATTT
1 TTTTGTGTTGGTCATGCAATGGCCGACACCCCCTTTTT-TCAGATAAAAAAAATTCAAATTT
* * * * * **
227156 TTTTGTGTTGGTCATGCCATGGTCGACAGCCCCTTTTTCATCTGGT-AAAAAAA-TCATTTTT
1 TTTTGTGTTGGTCATGCAATGGCCGACACCCCCTTTTT--TCAGATAAAAAAAATTCAAATTT
* * * *
227217 TTTTGTGTCGGTCATGCAATGGCCGACACCCTCTTTTTGT--GA-ATAAAAAATTCAATTTTT
1 TTTTGTGTTGGTCATGCAATGGCCGACACCCCCTTTTT-TCAGATAAAAAAAATTCAA-ATTT
* * * ** * *
227277 TTTTGTGTTGATCATGCCATGGTCGACACCCCCTTTTTATTTGGT--AAAACATT-AAATTT
1 TTTTGTGTTGGTCATGCAATGGCCGACACCCCCTTTTT-TCAGATAAAAAAAATTCAAATTT
* * *
227336 TTTTGGTGTTGGCCATGGAATGGTCGACACC
1 TTTT-GTGTTGGTCATGCAATGGCCGACACC
227367 AACTTCTCCT
Statistics
Matches: 317, Mismatches: 60, Indels: 36
0.77 0.15 0.09
Matches are distributed among these distances:
58 10 0.03
59 20 0.06
60 110 0.35
61 101 0.32
62 73 0.23
63 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (61 bp):
TTTTGTGTTGGTCATGCAATGGCCGACACCCCCTTTTTTCAGATAAAAAAAATTCAAATTT
Found at i:227254 original size:121 final size:119
Alignment explanation
Indices: 226958--227366 Score: 425
Period size: 121 Copynumber: 3.4 Consensus size: 119
226948 TAATTCGATA
* * *
226958 AAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGGTCGACACCC-CTTTTT-TCAGATAAAAA
1 AAAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCTCTTTTTGTCAAAT-AAAA
* ** * * * *
227021 AATTTAAAAAAATTTTTGTGTTGGTCATGCAATGGCCGACACCCCCTTTTT-TCAGAT
65 AA-TT--CAATTTTTTTGTGTTGGTCATGCCATGGTCGACACCCCCTTTTTATCTGGT
* * *
227078 AAAAAAAATTCAAAATTTTTTTGTGTTAGCCATGCCATGGCCGACACACCT-TTTTTGTCAAATA
1 -AAAAAAA-TC-AAATTTTTTGGTGTTGGCCATGCAATGGCCGACAC-CCTCTTTTTGTCAAATA
*
227142 AAAAATTCGAATTTTTTTGTGTTGGTCATGCCATGGTCGACAGCCCCTTTTTCATCTGGT
62 AAAAATTC-AATTTTTTTGTGTTGGTCATGCCATGGTCGACACCCCCTTTTT-ATCTGGT
** * * * *
227202 AAAAAAATCATTTTTTTTTGTGTCGGTCATGCAATGGCCGACACCCTCTTTTTGT-GAATAAAAA
1 AAAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCTCTTTTTGTCAAATAAAAA
* *
227266 ATTCAATTTTTTTTTGTGTTGATCATGCCATGGTCGACACCCCCTTTTTATTTGGT
66 ATTCAA--TTTTTTTGTGTTGGTCATGCCATGGTCGACACCCCCTTTTTATCTGGT
* * * *
227322 -AAAACATTAAATTTTTTTGGTGTTGGCCATGGAATGGTCGACACC
1 AAAAAAATCAAA-TTTTTTGGTGTTGGCCATGCAATGGCCGACACC
227367 AACTTCTCCT
Statistics
Matches: 243, Mismatches: 33, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
119 9 0.04
120 49 0.20
121 82 0.34
122 42 0.17
123 39 0.16
124 17 0.07
125 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (119 bp):
AAAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCTCTTTTTGTCAAATAAAAA
ATTCAATTTTTTTGTGTTGGTCATGCCATGGTCGACACCCCCTTTTTATCTGGT
Found at i:228176 original size:30 final size:30
Alignment explanation
Indices: 228158--228239 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
228148 AATATATAGA
228158 AAATTAGAAATTAAAATTAAAATATACATG
1 AAATTAGAAATTAAAATTAAAATATACATG
* * * *
228188 AAATTAGAAATTAAATTTAAAATAAAAACG
1 AAATTAGAAATTAAAATTAAAATATACATG
* *
228218 AAATTACAAATTAAATTTAAAA
1 AAATTAGAAATTAAAATTAAAA
228240 AGTAAACAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATTAGAAATTAAAATTAAAATATACATG
Found at i:229943 original size:30 final size:30
Alignment explanation
Indices: 229909--229969 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
229899 CATTAAGATC
229909 AATATCTATTCCAGAACGCTGGCTTACTGG
1 AATATCTATTCCAGAACGCTGGCTTACTGG
*
229939 AATATCTATTCCAGAACGTTGGCTTACTGG
1 AATATCTATTCCAGAACGCTGGCTTACTGG
229969 A
1 A
229970 TTTAAGACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (30 bp):
AATATCTATTCCAGAACGCTGGCTTACTGG
Found at i:230022 original size:23 final size:23
Alignment explanation
Indices: 229992--230037 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
229982 ATTGGTTTGG
229992 GGTGTGATATCTTCACGAACAAC
1 GGTGTGATATCTTCACGAACAAC
230015 GGTGTGATATCTTCACGAACAAC
1 GGTGTGATATCTTCACGAACAAC
230038 TCAATCGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (23 bp):
GGTGTGATATCTTCACGAACAAC
Found at i:230954 original size:28 final size:28
Alignment explanation
Indices: 230914--230979 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
230904 CAGGCGATCG
*
230914 TTCGATGGCAGAGTTCCATTAACCGACC
1 TTCGATAGCAGAGTTCCATTAACCGACC
*
230942 TTCGATAGCAGAGTTCCGTTAACCGACC
1 TTCGATAGCAGAGTTCCATTAACCGACC
230970 TTCGATAGCA
1 TTCGATAGCA
230980 TAACCTTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (28 bp):
TTCGATAGCAGAGTTCCATTAACCGACC
Found at i:231504 original size:59 final size:61
Alignment explanation
Indices: 231337--231607 Score: 308
Period size: 59 Copynumber: 4.6 Consensus size: 61
231327 TCAGCCATTA
* * * *
231337 CATGGTCAACACCAAAAAAATTT-AATTTTTTACCAAATAAAAAA-GGGGTGTCGACCATTG
1 CATGGCCAACACC-AAAAAATTTGAATTTTTTATCAGATAAAAAAGGGGGTGTCGACCATGG
* *
231397 CATGGCCAACA-C-AAAAA-TTGATTTTTTTACCAGATAAAAAAGGGGGTGTCGACCATGG
1 CATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAAGGGGGTGTCGACCATGG
* * * * *
231455 CATGGTCAACA-CAAAAAATTTGAATTTTTTATCTGA-CAAAAAGGAGGTGTCGGCCATGG
1 CATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAAGGGGGTGTCGACCATGG
* * * *
231514 AATGGCCAACACCAAAAAA-TTGAATTTTTTATCTGA-CAAAAAGGGGGTGTCGACCATTG
1 CATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAAGGGGGTGTCGACCATGG
** *
231573 CATGGCCAACATTAAAAAATTTGATTTTTTTATCA
1 CATGGCCAACACCAAAAAATTTGAATTTTTTATCA
231608 AACAATGGCC
Statistics
Matches: 184, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
56 2 0.01
57 24 0.13
58 26 0.14
59 88 0.48
60 44 0.24
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (61 bp):
CATGGCCAACACCAAAAAATTTGAATTTTTTATCAGATAAAAAAGGGGGTGTCGACCATGG
Found at i:232534 original size:20 final size:19
Alignment explanation
Indices: 232509--232553 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
232499 TGTCAAGCAC
*
232509 TTTTTTTT-TTTTAAATGAA
1 TTTTTTTTATTTTTAAT-AA
*
232528 TTTTTTTTATTTTTCATAA
1 TTTTTTTTATTTTTAATAA
232547 TTTTTTT
1 TTTTTTT
232554 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTTTTATTTTTAATAA
Found at i:234403 original size:3 final size:3
Alignment explanation
Indices: 234395--234431 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
234385 AAACACCCTT
234395 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
234432 ATAAATATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:237039 original size:56 final size:56
Alignment explanation
Indices: 236974--237086 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
236964 AAGAAAAAGT
*
236974 AAACTTCTTTTCCAGTAATTTGAACAAGTTCAACTCTTAAAATCCACCTAAATAGG
1 AAACTTCTTTTCAAGTAATTTGAACAAGTTCAACTCTTAAAATCCACCTAAATAGG
237030 AAACTTCTTTTCAAGTAATTTGAACAAGTTCAACTCTTAAAATCCACCTAAATAGG
1 AAACTTCTTTTCAAGTAATTTGAACAAGTTCAACTCTTAAAATCCACCTAAATAGG
237086 A
1 A
237087 CTATGTTCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (56 bp):
AAACTTCTTTTCAAGTAATTTGAACAAGTTCAACTCTTAAAATCCACCTAAATAGG
Found at i:244874 original size:20 final size:20
Alignment explanation
Indices: 244849--244888 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
244839 TCCATTCATT
244849 GGCCTCCAATTGGAAGAACC
1 GGCCTCCAATTGGAAGAACC
244869 GGCCTCCAATTGGAAGAACC
1 GGCCTCCAATTGGAAGAACC
244889 TTGTAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (20 bp):
GGCCTCCAATTGGAAGAACC
Found at i:250682 original size:4 final size:4
Alignment explanation
Indices: 250675--250700 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
250665 ACTATATATA
250675 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
250701 CACCTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:266986 original size:12 final size:12
Alignment explanation
Indices: 266969--267005 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
266959 AGTTTTGAGT
266969 TTCGAGTTCAAG
1 TTCGAGTTCAAG
266981 TTCGAGTTCAAG
1 TTCGAGTTCAAG
266993 TTCGAGTTCAAG
1 TTCGAGTTCAAG
267005 T
1 T
267006 AGAGTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (12 bp):
TTCGAGTTCAAG
Found at i:267156 original size:18 final size:19
Alignment explanation
Indices: 267133--267176 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
267123 ATTAAAAAAA
*
267133 TAAAATTCAATATAATT-T
1 TAAAATTCAAAATAATTAT
* *
267151 TAAAATTTAAAATATTTAT
1 TAAAATTCAAAATAATTAT
267170 TAAAATT
1 TAAAATT
267177 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAATTCAAAATAATTAT
Found at i:267190 original size:20 final size:19
Alignment explanation
Indices: 267150--267187 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
267140 CAATATAATT
267150 TTAAAATTTAAAATATTTA
1 TTAAAATTTAAAATATTTA
*
267169 TTAAAATTTTAAA-ATTTA
1 TTAAAATTTAAAATATTTA
267187 T
1 T
267188 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAAATTTAAAATATTTA
Found at i:268086 original size:20 final size:19
Alignment explanation
Indices: 268048--268104 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
268038 AATACAAAAT
268048 AATTCAAAATAACTTTA-AAA
1 AATTCAAAAT-A-TTTATAAA
*
268068 CATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
268087 AACTTCAAAATTTTTATA
1 AA-TTCAAAATATTTATA
268105 TTTCTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 4 0.12
19 5 0.16
20 23 0.72
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:268927 original size:23 final size:23
Alignment explanation
Indices: 268901--268948 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
268891 CGCTCTCATC
268901 CCCTTCAAAATTTACTCCTCACT
1 CCCTTCAAAATTTACTCCTCACT
268924 CCCTTCAAAATTTACTCCTCACT
1 CCCTTCAAAATTTACTCCTCACT
268947 CC
1 CC
268949 TTCCTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.42, G:0.00, T:0.33
Consensus pattern (23 bp):
CCCTTCAAAATTTACTCCTCACT
Found at i:282154 original size:151 final size:151
Alignment explanation
Indices: 281867--282237 Score: 541
Period size: 151 Copynumber: 2.4 Consensus size: 151
281857 TATTTAAAAT
* * * ***
281867 ATATTTATAA-TTT-TATATATATTATTCAAGCTCATTAATCCAATTTAATAATTAAAATTGGTT
1 ATATTT-TAATTTTATATATATATTACTCAAGCTTATTAAACCAACCCAATAATTAAAATTGGTT
* *
281930 AAGTTAATTAAATAATCAAATCGATAGATCGAAAGTTATTGCAGTCAATTGAGTAAGATCAATTT
65 AACTTAATTAAATAATCAAATCGATAGACCGAAAGTTATTGCAGTCAATTGAGTAAGATCAATTT
*
281995 AATAAAAAATTCATTGATTTTA
130 AATAAAAAACTCATTGATTTTA
282017 ATATTTTAATTTTATATATATATTACTCAAGCTTATTAAACCAACCCAATAATTAAAATTGGTTA
1 ATATTTTAATTTTATATATATATTACTCAAGCTTATTAAACCAACCCAATAATTAAAATTGGTTA
* * * *
282082 ACTTAATTAACTAATCGAATCGATAGACCTAAAGTTACTT-TAGTCAATTGAGTAAGATCAATTT
66 ACTTAATTAAATAATCAAATCGATAGACCGAAAGTTA-TTGCAGTCAATTGAGTAAGATCAATTT
282146 AATAAAAAACTCATTGATTTTA
130 AATAAAAAACTCATTGATTTTA
*
282168 ATATTTTAATTATATATATATATATATTACTCTAGCTTATTAAACCAACCCAATAATTAAAATTG
1 ATATTTTAA-T-T-T-TATATATATATTACTCAAGCTTATTAAACCAACCCAATAATTAAAATTG
282233 GTTAA
62 GTTAA
282238 AGGCTTAATA
Statistics
Matches: 200, Mismatches: 14, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
149 3 0.01
150 9 0.05
151 130 0.65
152 3 0.01
153 1 0.00
154 1 0.00
155 53 0.26
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (151 bp):
ATATTTTAATTTTATATATATATTACTCAAGCTTATTAAACCAACCCAATAATTAAAATTGGTTA
ACTTAATTAAATAATCAAATCGATAGACCGAAAGTTATTGCAGTCAATTGAGTAAGATCAATTTA
ATAAAAAACTCATTGATTTTA
Found at i:286036 original size:31 final size:31
Alignment explanation
Indices: 286001--286064 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
285991 AAAATAAAAA
286001 TAAAATATAAATAAATGAT-ATTTTTTAAATG
1 TAAAATATAAATAAATGATAATTTTTT-AATG
*
286032 TAAAATATAAATAAATGGTAATTTTTTAATG
1 TAAAATATAAATAAATGATAATTTTTTAATG
286063 TA
1 TA
286065 TTTATAAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 24 0.77
32 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (31 bp):
TAAAATATAAATAAATGATAATTTTTTAATG
Found at i:286404 original size:28 final size:29
Alignment explanation
Indices: 286342--286416 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
286332 TCATATTCTA
286342 AATTAATATAT-T-ATTAATACATAAAAT
1 AATTAATATATATAATTAATACATAAAAT
*
286369 AATATAATATATATAATTATTAC-TAAAAGT
1 AAT-TAATATATATAATTAATACATAAAA-T
286399 -ATTAATACATATATAATT
1 AATTAAT--ATATATAATT
286417 CAAAAAATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
27 3 0.07
28 12 0.29
29 8 0.20
30 18 0.44
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (29 bp):
AATTAATATATATAATTAATACATAAAAT
Found at i:286499 original size:29 final size:30
Alignment explanation
Indices: 286467--286526 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
286457 ATATTTAATG
*
286467 TCAACA-AATAATTTAAAA-ATATAAAAAAA
1 TCAACATAA-AATTAAAAATATATAAAAAAA
*
286496 TCAATATTAAAATTAAAAATATATAAAAAAA
1 TCAACA-TAAAATTAAAAATATATAAAAAAA
286527 AAGTTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 5 0.19
30 8 0.31
31 13 0.50
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (30 bp):
TCAACATAAAATTAAAAATATATAAAAAAA
Found at i:286514 original size:22 final size:21
Alignment explanation
Indices: 286472--286514 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
286462 TAATGTCAAC
286472 AAATAATTTAAAAATATAAAA
1 AAATAATTTAAAAATATAAAA
286493 AAATCAATATT-AAAAT-TAAAA
1 AAAT-AAT-TTAAAAATATAAAA
286514 A
1 A
286515 TATATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 10 0.50
22 8 0.40
23 2 0.10
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAATTTAAAAATATAAAA
Found at i:290891 original size:39 final size:40
Alignment explanation
Indices: 290829--290905 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
290819 TTTTTATGTT
* *
290829 ATTACAACATCTATTACATTCAACCAAACATAAGAATAAC
1 ATTACAACATCAATTACATTCAACCAAACATAAAAATAAC
290869 ATTACAA-ATCAATT-CTATTCAACCAAACATAAAAATA
1 ATTACAACATCAATTAC-ATTCAACCAAACATAAAAATA
290906 TTATTATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 1 0.03
39 26 0.76
40 7 0.21
ACGTcount: A:0.52, C:0.21, G:0.01, T:0.26
Consensus pattern (40 bp):
ATTACAACATCAATTACATTCAACCAAACATAAAAATAAC
Found at i:293708 original size:2 final size:2
Alignment explanation
Indices: 293701--293732 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
293691 ATCTAAAATA
293701 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
293733 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:293737 original size:2 final size:2
Alignment explanation
Indices: 293732--293756 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
293722 TCTCTCTCTC
293732 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
293757 TAATGTATAT
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:296910 original size:29 final size:30
Alignment explanation
Indices: 296845--296921 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
296835 TTAAAATTAT
* *
296845 ACATGAATTATGATTTAATGTGTAATTGTAT
1 ACATGAATTTTGATTT-ATGTGTAATTGTAC
** *
296876 GTATGAATTTTGATTT-TGTGTAATTTTAC
1 ACATGAATTTTGATTTATGTGTAATTGTAC
296905 ACATGAAATTTTGATTT
1 ACATG-AATTTTGATTT
296922 GGTTCAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 14 0.37
30 11 0.29
31 13 0.34
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (30 bp):
ACATGAATTTTGATTTATGTGTAATTGTAC
Found at i:300791 original size:13 final size:13
Alignment explanation
Indices: 300751--300779 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
300741 AAAGTTATGA
300751 ATTAATTATTGTT
1 ATTAATTATTGTT
300764 ATTAATTATTGTT
1 ATTAATTATTGTT
300777 ATT
1 ATT
300780 GATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (13 bp):
ATTAATTATTGTT
Found at i:313823 original size:27 final size:27
Alignment explanation
Indices: 313773--313843 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
313763 CGAACTTTGA
* *
313773 AAGAATAACTTTTGTGACGAACTCCAG
1 AAGAATAACCTTTGTGGCGAACTCCAG
**
313800 AAGAATAACCTTTGTGGCGAACTCTGG
1 AAGAATAACCTTTGTGGCGAACTCCAG
* *
313827 GAGAATAGCCTTTGTGG
1 AAGAATAACCTTTGTGG
313844 TGAATTATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (27 bp):
AAGAATAACCTTTGTGGCGAACTCCAG
Found at i:319676 original size:33 final size:33
Alignment explanation
Indices: 319629--319717 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
319619 TGTTTTTCAT
*
319629 AACGG-TCCCTCACCCCCAACGGTCATAAACCC
1 AACGGCTCCCCCACCCCCAACGGTCATAAACCC
* *
319661 AACGGCTCCCCCACCCCCAACAGTCATAAACCT
1 AACGGCTCCCCCACCCCCAACGGTCATAAACCC
*
319694 AATGGCTCCCCCACCCCCAACGGT
1 AACGGCTCCCCCACCCCCAACGGT
319718 TATTTCATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 5 0.10
33 46 0.90
ACGTcount: A:0.27, C:0.48, G:0.12, T:0.12
Consensus pattern (33 bp):
AACGGCTCCCCCACCCCCAACGGTCATAAACCC
Found at i:322663 original size:19 final size:19
Alignment explanation
Indices: 322639--322686 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
322629 TTGACCGACC
* *
322639 AAAAACCCAAACAAAATAG
1 AAAAACCCAAACAAAAAAA
*
322658 AAAAA-CCAAANAAAAAAA
1 AAAAACCCAAACAAAAAAA
*
322676 AAAAACACAAA
1 AAAAACCCAAA
322687 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.77, C:0.17, G:0.02, T:0.02
Consensus pattern (19 bp):
AAAAACCCAAACAAAAAAA
Found at i:324324 original size:30 final size:27
Alignment explanation
Indices: 324288--324353 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 27
324278 TATTTTTATC
***
324288 AATCCTTTTATTTTGTTTTCTTAAAAATT
1 AATCCTTTTATTCCCTTTT-TT-AAAATT
324317 AAATCCTTTTATTCCCTTTTTTAAAATT
1 -AATCCTTTTATTCCCTTTTTTAAAATT
324345 AATCCTTTT
1 AATCCTTTT
324354 GTTATATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.27
28 6 0.18
29 2 0.06
30 16 0.48
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.56
Consensus pattern (27 bp):
AATCCTTTTATTCCCTTTTTTAAAATT
Found at i:336430 original size:21 final size:20
Alignment explanation
Indices: 336403--336450 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
336393 ATTAAAACCC
336403 AAAAAAGGAACAAAAAGAAAA
1 AAAAAAGGAA-AAAAAGAAAA
* *
336424 GAAAAAGGAAAGAAAGAAAA
1 AAAAAAGGAAAAAAAGAAAA
336444 AAAAAAG
1 AAAAAAG
336451 TCGAGATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAAAGGAAAAAAAGAAAA
Found at i:336955 original size:24 final size:24
Alignment explanation
Indices: 336923--336973 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
336913 AAGAAAATTT
*
336923 GAGGCAAAAAGCGTGAATGTGAAA
1 GAGGCAAAAAGCATGAATGTGAAA
*
336947 GAGGCAAAAAGCATGAATGTGGAA
1 GAGGCAAAAAGCATGAATGTGAAA
336971 GAG
1 GAG
336974 TTAGGAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.35, T:0.12
Consensus pattern (24 bp):
GAGGCAAAAAGCATGAATGTGAAA
Found at i:337153 original size:23 final size:25
Alignment explanation
Indices: 337127--337172 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
337117 CCAATTAGGG
337127 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
337150 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
337173 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:338278 original size:12 final size:13
Alignment explanation
Indices: 338261--338290 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
338251 ATATTTTTTG
338261 TTTTTA-ATTTAA
1 TTTTTACATTTAA
338273 TTTTTACATTTAA
1 TTTTTACATTTAA
338286 TTTTT
1 TTTTT
338291 TTATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTACATTTAA
Found at i:338296 original size:13 final size:13
Alignment explanation
Indices: 338261--338302 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
338251 ATATTTTTTG
338261 TTTTTAATTTAA-
1 TTTTTAATTTAAT
338273 TTTTTACATTTAAT
1 TTTTTA-ATTTAAT
* *
338287 TTTTTTATTTTAT
1 TTTTTAATTTAAT
338300 TTT
1 TTT
338303 ATAGGTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 6 0.23
13 15 0.58
14 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:339798 original size:42 final size:41
Alignment explanation
Indices: 339700--340152 Score: 394
Period size: 42 Copynumber: 11.2 Consensus size: 41
339690 GTTACATCAT
* * *
339700 CCATCTAATATCTTACCCCGATCATGGGGTAGATTGAAG--
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAA
*
339739 CCATCCAATCTCTTACCCCGATCATAGGGCAGATTGAAGATA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-A
* *
339781 CCATCCAATCTCTTACCCCGATAATGGGGCAGATTG-A-AC
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAA
* *
339820 CCATCCAATCTCTTACCCCGATCATGGGGCAAACTGAAGACA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-A
** * ** *
339862 CCATTTAATCTCTTACCTCGATCATAAGGTAGATTGAAG--
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAA
* * ** *
339901 TCATCTAATCTCTTACCTTGATCATGGGGCAAATTGAAGATA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-A
*
339943 CCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-A
*
339985 TCA-CTCAATCTCTTACCCCGATCATGGGGCAGATTGAAG--
1 CCATC-CAATCTCTTACCCCGATCATGGGGCAGATTGAAGAA
** * *** *
340024 CCATCCAATCT-TTACCCTAACCAAAAGACAGATTGAAGACA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-A
* * * * *
340065 CTATCCAATCTCTAACCCCGACCATGGGACAGATAGAAG--
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAA
* * *** *
340104 CCATCAAATCTTTTACCATAACCA-GAGGGCAGATTGAAG-A
1 CCATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAGAA
340144 CCATCCAAT
1 CCATCCAAT
340153 ATTTTATCCC
Statistics
Matches: 338, Mismatches: 59, Indels: 33
0.79 0.14 0.08
Matches are distributed among these distances:
38 21 0.06
39 136 0.40
40 11 0.03
41 13 0.04
42 157 0.46
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (41 bp):
CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAA
Found at i:339835 original size:81 final size:81
Alignment explanation
Indices: 339700--340040 Score: 429
Period size: 81 Copynumber: 4.2 Consensus size: 81
339690 GTTACATCAT
* * * *
339700 CCATCTAATATCTTACCCCGATCATGGGGTAGATTGAAGCCATCCAATCTCTTACCCCGATCATA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATG
*
339765 GGGCAGATTGAAGATA
66 GGGCAAATTGAAGATA
* *
339781 CCATCCAATCTCTTACCCCGATAATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCATG
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATG
* *
339846 GGGCAAACTGAAGACA
66 GGGCAAATTGAAGATA
** * ** * * * **
339862 CCATTTAATCTCTTACCTCGATCATAAGGTAGATTGAAGTCATCTAATCTCTTACCTTGATCATG
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATG
339927 GGGCAAATTGAAGATA
66 GGGCAAATTGAAGATA
* *
339943 CCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACATCACTCAATCTCTTACCCCGATC
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCCAT--C-CAATCTCTTACCCCGATC
*
340008 ATGGGGCAGATTGAAG---
63 ATGGGGCAAATTGAAGATA
340024 CCATCCAATCT-TTACCC
1 CCATCCAATCTCTTACCC
340041 TAACCAAAAG
Statistics
Matches: 222, Mismatches: 35, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
80 6 0.03
81 185 0.83
83 1 0.00
84 30 0.14
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (81 bp):
CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATG
GGGCAAATTGAAGATA
Found at i:339966 original size:123 final size:120
Alignment explanation
Indices: 339700--340040 Score: 386
Period size: 123 Copynumber: 2.8 Consensus size: 120
339690 GTTACATCAT
* * * * *
339700 CCATCTAATATCTTACCCCGATCATGGGGTAGATTGAAG---CCA-TCCAATCTCTTACCCCGAT
1 CCATCCAATCTCTTACCCCGATCATGGGGCAAACTGAAGACACCACT-CAATCTCTTACCCCGAT
* *
339761 CATAGGGCAGATTGAAGATACCATCCAATCTCTTACCCCGATAATGGGGCAGATTGAAC
65 CATAGGGCAGATTGAAG-T--CATCCAATCTCTTACCCCGATAATGGGGCAAATTGAAA
* * *
339820 CCATCCAATCTCTTACCCCGATCATGGGGCAAACTGAAGACACCATTTAATCTCTTACCTCGATC
1 CCATCCAATCTCTTACCCCGATCATGGGGCAAACTGAAGACACCACTCAATCTCTTACCCCGATC
* * * ** *
339885 ATAAGGTAGATTGAAGTCATCTAATCTCTTACCTTGATCATGGGGCAAATTGAAGATA
66 ATAGGGCAGATTGAAGTCATCCAATCTCTTACCCCGATAATGGGGCAAATTG-A-A-A
* * * *
339943 CCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACATCACTCAATCTCTTACCCCGATC
1 CCATCCAATCTCTTACCCCGATCATGGGGCAAACTGAAGACACCACTCAATCTCTTACCCCGATC
* *
340008 ATGGGGCAGATTGAAGCCATCCAATCT-TTACCC
66 ATAGGGCAGATTGAAGTCATCCAATCTCTTACCC
340041 TAACCAAAAG
Statistics
Matches: 186, Mismatches: 28, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
120 64 0.34
121 1 0.01
122 7 0.04
123 113 0.61
124 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (120 bp):
CCATCCAATCTCTTACCCCGATCATGGGGCAAACTGAAGACACCACTCAATCTCTTACCCCGATC
ATAGGGCAGATTGAAGTCATCCAATCTCTTACCCCGATAATGGGGCAAATTGAAA
Found at i:339977 original size:162 final size:164
Alignment explanation
Indices: 339700--340015 Score: 474
Period size: 162 Copynumber: 1.9 Consensus size: 164
339690 GTTACATCAT
**
339700 CCATCTAATATCTTACCCCGATCATGGGGTAGATTGAAGCCATCCAATCTCTTACCCCGATCATA
1 CCATCTAATATCTTACCCCGATCATAAGGTAGATTGAAGCCATCCAATCTCTTACCCCGATCATA
* *
339765 GGGCAGATTGAAGATACCATCCAATCTCTTACCCCGATAATGGGGCAGATTGAACCCAT-C-CAA
66 GGGCAAATTGAAGATACCATCCAATCTCTTACCCCGATAATGGGGCAGATTGAACACATACTCAA
339828 TCTCTTACCCCGATCATGGGGCAAACTGAAGACA
131 TCTCTTACCCCGATCATGGGGCAAACTGAAGACA
* * * * * ** *
339862 CCATTTAATCTCTTACCTCGATCATAAGGTAGATTGAAGTCATCTAATCTCTTACCTTGATCATG
1 CCATCTAATATCTTACCCCGATCATAAGGTAGATTGAAGCCATCCAATCTCTTACCCCGATCATA
* * *
339927 GGGCAAATTGAAGATACCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACATCACTCA
66 GGGCAAATTGAAGATACCATCCAATCTCTTACCCCGATAATGGGGCAGATTGAACACAT-ACTCA
339992 ATCTCTTACCCCGATCATGGGGCA
130 ATCTCTTACCCCGATCATGGGGCA
340016 GATTGAAGCC
Statistics
Matches: 136, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 109 0.80
164 1 0.01
165 26 0.19
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (164 bp):
CCATCTAATATCTTACCCCGATCATAAGGTAGATTGAAGCCATCCAATCTCTTACCCCGATCATA
GGGCAAATTGAAGATACCATCCAATCTCTTACCCCGATAATGGGGCAGATTGAACACATACTCAA
TCTCTTACCCCGATCATGGGGCAAACTGAAGACA
Found at i:340083 original size:80 final size:80
Alignment explanation
Indices: 339730--340152 Score: 266
Period size: 81 Copynumber: 5.3 Consensus size: 80
339720 ATCATGGGGT
* *
339730 AGATTGAAG-C-C-ATCCAATCTCTTACCCCGATCATAGGGCAGATTGAAGATACCATCCAATCT
1 AGATTGAAGACACTATCCAATCTCTAACCCCGATCATGGGGCAGATTGAAG---CCATCCAATCT
** * *
339792 CTTACCCCGA-TAATGGGGC
63 -TTACCCTAACCAA-AGGGC
* * * * **
339811 AGATTG-A-AC-CCATCCAATCTCTTACCCCGATCATGGGGCAAACTGAAGACACCATTTAATCT
1 AGATTGAAGACACTATCCAATCTCTAACCCCGATCATGGGGCAGATTGAAG---CCATCCAATCT
* * *
339873 CTTA-CCTCGATCATAA-GGT
63 -TTACCCT-AACCA-AAGGGC
* * * ** *
339892 AGATTGAAG--TC-ATCTAATCTCTTACCTTGATCATGGGGCAAATTGAAGATACCATCCAATCT
1 AGATTGAAGACACTATCCAATCTCTAACCCCGATCATGGGGCAGATTGAAG---CCATCCAATCT
* * **
339954 CTTACCCTGATCATGGGGC
63 -TTACCCTAACCAAAGGGC
*
339973 AGATTGAAGACA-TCA-CTCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCCATCCAATCTT
1 AGATTGAAGACACT-ATC-CAATCTCTAACCCCGATCATGGGGCAGATTGAAGCCATCCAATCTT
* *
340036 TACCCTAACCAAAAGAC
64 TACCCTAACCAAAGGGC
* * * *
340053 AGATTGAAGACACTATCCAATCTCTAACCCCGACCATGGGACAGATAGAAGCCATCAAATCTTTT
1 AGATTGAAGACACTATCCAATCTCTAACCCCGATCATGGGGCAGATTGAAGCCATCCAATC-TTT
* *
340118 ACCATAACCAGAGGGC
65 ACCCTAACCAAAGGGC
340134 AGATTGAAGAC-C-ATCCAAT
1 AGATTGAAGACACTATCCAAT
340153 ATTTTATCCC
Statistics
Matches: 284, Mismatches: 40, Indels: 38
0.78 0.11 0.10
Matches are distributed among these distances:
79 7 0.02
80 70 0.25
81 168 0.59
82 6 0.02
83 2 0.01
84 31 0.11
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (80 bp):
AGATTGAAGACACTATCCAATCTCTAACCCCGATCATGGGGCAGATTGAAGCCATCCAATCTTTA
CCCTAACCAAAGGGC
Found at i:340237 original size:45 final size:42
Alignment explanation
Indices: 339730--340238 Score: 160
Period size: 42 Copynumber: 12.4 Consensus size: 42
339720 ATCATGGGGT
* ** *
339730 AGATTGAAG--CCATCCAATCTCTTACCCCGAT-CATAGGGC
1 AGATTGAAGCACCATCCAATCTTTTACCCTAATCCAGAGGGC
* * ** *
339769 AGATTGAAGATACCATCCAATCTCTTACCCCGAT-AATG-GGGC
1 AGATTGAAG-CACCATCCAATCTTTTACCCTAATCCA-GAGGGC
* **
339811 AGATTGAA-C-CCATCCAATCTCTTACCCCGAT-CATG-GGGC
1 AGATTGAAGCACCATCCAATCTTTTACCCTAATCCA-GAGGGC
* * ** * * * * *
339850 AAACTGAAGACACCATTTAATCTCTTA-CCTCGAT-CATAAGGT
1 AGATTGAAG-CACCATCCAATCTTTTACCCT-AATCCAGAGGGC
* * * * *
339892 AGATTGAAG--TCATCTAATCTCTTACCTTGAT-CATG-GGGC
1 AGATTGAAGCACCATCCAATCTTTTACCCTAATCCA-GAGGGC
* * * *
339931 AAATTGAAGATACCATCCAATCTCTTACCCTGAT-CATG-GGGC
1 AGATTGAAG-CACCATCCAATCTTTTACCCTAATCCA-GAGGGC
* * **
339973 AGATTGAAGACATCA-CTCAATCTCTTACCCCGAT-CATG-GGGC
1 AGATTGAAG-CACCATC-CAATCTTTTACCCTAATCCA-GAGGGC
* * *
340015 AGATTGAAG--CCATCCAATC-TTTACCCTAA-CCAAAAGAC
1 AGATTGAAGCACCATCCAATCTTTTACCCTAATCCAGAGGGC
* * * ** *
340053 AGATTGAAGACACTATCCAATCTCTAACCCCGA-CCATG-GGAC
1 AGATTGAAG-CACCATCCAATCTTTTACCCTAATCCA-GAGGGC
* * *
340095 AGATAGAAG--CCATCAAATCTTTTACCATAA-CCAGAGGGC
1 AGATTGAAGCACCATCCAATCTTTTACCCTAATCCAGAGGGC
* ** *
340134 AGATTGAAG-ACCATCCAATATTTTATCCCTAATTAAGAAGGGT
1 AGATTGAAGCACCATCCAATCTTTTA-CCCTAATCCAG-AGGGC
* * *
340177 AGATTAAAACCACCATCCAATCTTTTACCCCCAATCCAGAGGGGC
1 AGATT-GAAGCACCATCCAATCTTTTA-CCCTAATCCAGA-GGGC
340222 AGATTGAAGCTACCATC
1 AGATTGAAGC-ACCATC
340239 TCATAAAATC
Statistics
Matches: 370, Mismatches: 68, Indels: 58
0.75 0.14 0.12
Matches are distributed among these distances:
38 21 0.06
39 107 0.29
40 16 0.04
41 18 0.05
42 156 0.42
43 9 0.02
44 6 0.02
45 37 0.10
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (42 bp):
AGATTGAAGCACCATCCAATCTTTTACCCTAATCCAGAGGGC
Found at i:342329 original size:29 final size:28
Alignment explanation
Indices: 342273--342341 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 28
342263 ATTTTTTATT
*
342273 ATTAATCCTTTTATTCTATTTTCTTAAA
1 ATTAATCCTTTTATTCCATTTTCTTAAA
*
342301 ATTTAAATCCTTTTATTCCCTTTT-TTAAA
1 A-TT-AATCCTTTTATTCCATTTTCTTAAA
342330 ATTAATCCTTTT
1 ATTAATCCTTTT
342342 GTTATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.24
28 3 0.08
29 8 0.22
30 17 0.46
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTAATCCTTTTATTCCATTTTCTTAAA
Found at i:342340 original size:57 final size:58
Alignment explanation
Indices: 342264--342375 Score: 145
Period size: 57 Copynumber: 1.9 Consensus size: 58
342254 ATTTTATTTA
** * *
342264 TTTTTTATTATTAATCCTTTTATTCTATTTTCTTAAA-ATTTAAATCCTTTTATTCCC
1 TTTTTTAAAATTAATCCTTTTATTATATTTTCTTAAACATTTAAATCATTTTATTCCC
* * *
342321 TTTTTTAAAATTAATCCTTTTGTTATATTTTTTTAAATCCTTTAAATCATTTTAT
1 TTTTTTAAAATTAATCCTTTTATTATATTTTCTTAAA-CATTTAAATCATTTTAT
342376 CATTTCTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
57 32 0.70
59 14 0.30
ACGTcount: A:0.27, C:0.12, G:0.01, T:0.60
Consensus pattern (58 bp):
TTTTTTAAAATTAATCCTTTTATTATATTTTCTTAAACATTTAAATCATTTTATTCCC
Found at i:342351 original size:27 final size:27
Alignment explanation
Indices: 342255--342358 Score: 111
Period size: 27 Copynumber: 3.8 Consensus size: 27
342245 ATCCTTTTTA
**
342255 TTTTATT-TATTTTTTATTATTAATCC
1 TTTTATTCTATTTTTTAAAATTAATCC
342281 TTTTATTCTATTTTCTTAAAATTTAAATCC
1 TTTTATTCTATTTT-TTAAAA-TT-AATCC
**
342311 TTTTATTCCCTTTTTTAAAATTAATCC
1 TTTTATTCTATTTTTTAAAATTAATCC
* * *
342338 TTTTGTTATATTTTTTTAAAT
1 TTTTATTCTATTTTTTAAAAT
342359 CCTTTAAATC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.11
27 27 0.42
28 6 0.09
29 8 0.12
30 17 0.26
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTTATTCTATTTTTTAAAATTAATCC
Found at i:342743 original size:105 final size:104
Alignment explanation
Indices: 342581--342794 Score: 320
Period size: 105 Copynumber: 2.0 Consensus size: 104
342571 TGTTTTTTTA
* * *
342581 TTTTAGGGAATTCAAGAAATTGTGCCTAACATGTTAGGTATGATTTTTCCTTTGAACCTAAATAA
1 TTTTAGGGAATTCAAAAAATTGTGCCTAACATGATAGGTATGATTTTTCCTTCGAACCTAAATAA
* * *
342646 TCGAGTATCTTTTTTAAAATCAATAAATGTTCCATGTTC
66 TCAAATATCCTTTTTAAAATCAATAAATGTTCCATGTTC
* * *
342685 TTTTAGGGAATTCAAAAAATTGTGCCCTAACGTGATGGGTATGGTTTTTCCTTCGAACCTAAATA
1 TTTTAGGGAATTCAAAAAATTGTG-CCTAACATGATAGGTATGATTTTTCCTTCGAACCTAAATA
* *
342750 ATCAAATATCCTTTTTAAAATCAATAAATGTTCGATGTTT
65 ATCAAATATCCTTTTTAAAATCAATAAATGTTCCATGTTC
342790 TTTTA
1 TTTTA
342795 TTTAGGGAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
104 23 0.23
105 75 0.77
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (104 bp):
TTTTAGGGAATTCAAAAAATTGTGCCTAACATGATAGGTATGATTTTTCCTTCGAACCTAAATAA
TCAAATATCCTTTTTAAAATCAATAAATGTTCCATGTTC
Found at i:343521 original size:27 final size:27
Alignment explanation
Indices: 343489--343542 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
343479 TATCTCGATT
*
343489 TGAAGAAAAGTCTCACCTAGTAAGTTA
1 TGAAGAAAAGTCGCACCTAGTAAGTTA
343516 TGAAGAAAAGTCGCACCTAGTAAGTTA
1 TGAAGAAAAGTCGCACCTAGTAAGTTA
343543 AGGCACAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (27 bp):
TGAAGAAAAGTCGCACCTAGTAAGTTA
Found at i:344035 original size:29 final size:29
Alignment explanation
Indices: 344003--344399 Score: 87
Period size: 29 Copynumber: 13.8 Consensus size: 29
343993 TAGACATCTA
344003 GGGGT-AAAATGGTACTTTTTGGAAGAATC
1 GGGGTAAAAATGG-ACTTTTTGGAAGAATC
* * * * *
344032 GGGGTCAAAATAGA-ATTTTGCAAG-TTC
1 GGGGTAAAAATGGACTTTTTGGAAGAATC
* *
344059 GAGGGT-AATATGGTCATTTTTGGAA-AATC
1 G-GGGTAAAAATGGAC-TTTTTGGAAGAATC
* ** *
344088 GGGGTCAAAAAATGGAATTTTTGGAAGTTTA
1 GGGGT--AAAAATGGACTTTTTGGAAGAATC
* * * *
344119 GAGGT-AAGAT-GATATTTTTGGAA-AAAC
1 GGGGTAAAAATGGA-CTTTTTGGAAGAATC
* ** * ** ** *
344146 TAGACTCAAAAATGGAATTTTTAAAAGTCTG
1 -GGGGT-AAAAATGGACTTTTTGGAAGAATC
* *
344177 GGGGT-AAAATGGTAATTTTTGGAAAAATC
1 GGGGTAAAAATGG-ACTTTTTGGAAGAATC
* * *
344206 GAGGTAAAAAATGGA-ATTTTGGAA-AGTTC
1 GGGGT-AAAAATGGACTTTTTGGAAGA-ATC
* * *
344235 GGGGTAAAAATGTAATTTTT-G--G--TT
1 GGGGTAAAAATGGACTTTTTGGAAGAATC
* * *
344259 AGGGTAAAAAATGGAATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGACTTTTTGGAAGAATC
* *
344288 GGGGGTAAAAATGTATTTTTTGGGAA-AATC
1 -GGGGTAAAAATGGACTTTTT-GGAAGAATC
* * *
344318 GGGGTCAAAAGTGGAATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGACTTTTTGGAAGAATC
* * * * *
344347 GGGGT-AAATTGTAATTTTTTGAAAAATC
1 GGGGTAAAAATGGACTTTTTGGAAGAATC
* *
344375 GAGGTCAAAAATGGAATTTTTGGAA
1 GGGGT-AAAAATGGACTTTTTGGAA
344400 TTTAGAGGTA
Statistics
Matches: 265, Mismatches: 69, Indels: 67
0.66 0.17 0.17
Matches are distributed among these distances:
24 5 0.02
25 14 0.05
26 1 0.00
27 25 0.09
28 55 0.21
29 78 0.29
30 67 0.25
31 20 0.08
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (29 bp):
GGGGTAAAAATGGACTTTTTGGAAGAATC
Done.