Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007817.1 Corchorus capsularis cultivar CVL-1 contig07838, 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: 36008
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:6546 original size:19 final size:18
Alignment explanation
Indices: 6522--6558 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
6512 TTGAAGATTT
6522 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
6541 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
6559 ATTATTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:8124 original size:28 final size:26
Alignment explanation
Indices: 8071--8124 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
8061 ATGTCTTAGG
* *
8071 TTTAGTTAATTTTAATTAGTTAGTAA
1 TTTAGTTAATTTTAATAAATTAGTAA
*
8097 TTTAGCTTAATTTTTAATAAATTGGTAA
1 TTTAG-TTAA-TTTTAATAAATTAGTAA
8125 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 5 0.22
27 4 0.17
28 14 0.61
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (26 bp):
TTTAGTTAATTTTAATAAATTAGTAA
Found at i:8591 original size:37 final size:37
Alignment explanation
Indices: 8516--8596 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
8506 TACTCCAATA
**
8516 AATTAAGAGTCAAAGTAATGGTAATCAGTAATTAAGT
1 AATTAAGAGTCAAAGTAATGGTAATCAGTAAAGAAGT
*
8553 AATTAAGAGTCAAAGTAATGGTAATCAGTAAAGCAGT
1 AATTAAGAGTCAAAGTAATGGTAATCAGTAAAGAAGT
8590 AATTAAG
1 AATTAAG
8597 TTAAAACAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (37 bp):
AATTAAGAGTCAAAGTAATGGTAATCAGTAAAGAAGT
Found at i:8632 original size:55 final size:55
Alignment explanation
Indices: 8558--8956 Score: 484
Period size: 55 Copynumber: 7.0 Consensus size: 55
8548 TAAGTAATTA
* * * * * *
8558 AGAGTCAAAGTAATGGTAATCAGTAAAGCAGTAATTAAGTTAAAACAGATTAATC
1 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
8613 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATC
1 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
8667 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
1 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
*
8722 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATT
1 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
8777 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
1 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
* * * * *
8832 AGTAAATTGATAGTTAAGAGTCAAGGTAAT-AGTAGTCAGTAAATCGGTAATTAAGTAAAAAGAG
1 AG---AGTCA-AG-GAA-A-T--A-GTAATCAGTA---AAT----CAGTAATTAAGTAAAAAGAG
8896 ATTAATC
49 ATTAATC
*
8903 AGAGTCAA-GATAATAGTAATCAGTAAATCAGTAATAAAGT-AAAA-AGATTAATC
1 AGAGTCAAGGA-AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
8956 A
1 A
8957 AGTGAATTAA
Statistics
Matches: 306, Mismatches: 18, Indels: 42
0.84 0.05 0.11
Matches are distributed among these distances:
53 10 0.03
54 57 0.19
55 170 0.56
58 3 0.01
59 4 0.01
60 2 0.01
61 6 0.02
62 6 0.02
64 6 0.02
65 7 0.02
66 1 0.00
67 3 0.01
68 3 0.01
71 28 0.09
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (55 bp):
AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
Found at i:8686 original size:109 final size:110
Alignment explanation
Indices: 8558--8956 Score: 493
Period size: 109 Copynumber: 3.5 Consensus size: 110
8548 TAAGTAATTA
* * * * * *
8558 AGAGTCAAAGTAATGGTAATCAGTAAAGCAGTAATTAAGTTAAAACAGATTAATCAGAGTCAAGG
1 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGG
8623 AAATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATC
66 AAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
8667 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGG
1 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGG
*
8732 AAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATT
66 AAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
* *
8777 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGA
1 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAG---AGTCA
* *
8842 TAGTTAAGAGTCAAGGTAAT-AGTAGTCAGTAAATCGGTAATTAAGTAAAAAGAGATTAATC
63 -AG-GAA-A-T--A-GTAATCAGTA---A----ATCAGTAATTAAGTAAAAAGAGATTAATC
*
8903 AGAGTCAA-GATAATAGTAATCAGTAAATCAGTAATAAAGT-AAAA-AGATTAATCA
1 AGAGTCAAGGA-AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCA
8957 AGTGAATTAA
Statistics
Matches: 258, Mismatches: 13, Indels: 23
0.88 0.04 0.08
Matches are distributed among these distances:
109 89 0.34
110 70 0.27
113 3 0.01
114 2 0.01
115 2 0.01
116 1 0.00
117 1 0.00
119 5 0.02
120 5 0.02
122 1 0.00
124 10 0.04
125 6 0.02
126 63 0.24
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (110 bp):
AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGG
AAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
Found at i:8832 original size:34 final size:34
Alignment explanation
Indices: 8793--8904 Score: 95
Period size: 34 Copynumber: 3.2 Consensus size: 34
8783 AAGGAAATAG
8793 TAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
1 TAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
* * **
8827 TAATCAGTAAAT-TGATAGTTAAG-AGTCAAG-GTAAT
1 TAATCAGTAAATCAG-TAATTAAGTA-AAAAGAG--AT
* *
8862 AGTAGTCAGTAAATCGGTAATTAAGTAAAAAGAGAT
1 --TAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
8898 TAATCAG
1 TAATCAG
8905 AGTCAAGATA
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
33 3 0.05
34 28 0.47
35 2 0.03
36 2 0.03
37 21 0.36
38 3 0.05
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (34 bp):
TAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
Found at i:8863 original size:126 final size:124
Alignment explanation
Indices: 8722--9028 Score: 417
Period size: 126 Copynumber: 2.5 Consensus size: 124
8712 GAGATTAATC
*
8722 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATTAGAGTCAAGG
1 AGAGTCAAGG-AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA-G
* * *
8787 A-AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATC-AGTAAATTGATAGTTA
64 ATAATAGTAATCAGTAAATCAGTAATAAAGT-AAAA-AGATTAATCAAGTAAATTAATAATTA
* *
8848 AGAGTCAAGGTAATAGTAGTCAGTAAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGA
1 AGAGTCAAGG-AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGA
*
8913 TAATAGTAATCAGTAAATCAGTAATAAAGTAAAAAGATTAATCAAGTGAATTAATAATTA
65 TAATAGTAATCAGTAAATCAGTAATAAAGTAAAAAGATTAATCAAGTAAATTAATAATTA
* * *
8973 AGGGAGT-AA--AAGTAGTAATCAGTAAATCAGCAATTAAGTAAAAAGATAGTAATCAG
1 A--GAGTCAAGGAA-TAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAG
9029 TAAATCGATA
Statistics
Matches: 163, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
123 2 0.01
124 48 0.29
125 20 0.12
126 89 0.55
127 4 0.02
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (124 bp):
AGAGTCAAGGAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGAT
AATAGTAATCAGTAAATCAGTAATAAAGTAAAAAGATTAATCAAGTAAATTAATAATTA
Found at i:8873 original size:181 final size:189
Alignment explanation
Indices: 8667--9084 Score: 566
Period size: 181 Copynumber: 2.2 Consensus size: 189
8657 GAGATTAATC
*
8667 AGAGTCAAGGAAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGG
1 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA-G
* * *
8732 A-AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGA-GAT-T-AATT-AGAGTCAA-G-G-AA
65 ATAATAGTAATCAGTAAATCAGTAATAAAGTAAAAAGATAATATGAATTAAGAATCAAGGAGAAA
* * * *
8789 A-TAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAGTTA
130 AGTAGTAATCAGTAAATCAGCAATTAAGTAAAAAGAGAGTAATCAGTAAATCGATAATTA
* *
8848 AGAGTCAAGGTAATAGTAGTCAGTAAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGA
1 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGA
* *
8913 TAATAGTAATCAGTAAATCAGTAATAAAGTAAAAAGATTAATCAAGTGAATTAATAATTAAGGGA
66 TAATAGTAATCAGTAAATCAGTAATAAAGTAAAAAGA-TAAT--A-TGAATTAAGAATCAA-GGA
*
8978 GTAAAAGTAGTAATCAGTAAATCAGCAATTAAGTAAAAAGATAGTAATCAGTAAATCGATAATTA
126 G-AAAAGTAGTAATCAGTAAATCAGCAATTAAGTAAAAAGAGAGTAATCAGTAAATCGATAATTA
9043 AGAGTCAAGGTAACAATAGTAATCAGTAAATCAGTAATTAAG
1 AGAGTCAAGGT---AATAGTAATCAGTAAATCAGTAATTAAG
9085 AGTCAATGGA
Statistics
Matches: 204, Mismatches: 15, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
180 2 0.01
181 95 0.47
183 2 0.01
187 1 0.00
188 4 0.02
189 5 0.02
191 1 0.00
192 1 0.00
194 3 0.01
195 64 0.31
198 26 0.13
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (189 bp):
AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGA
TAATAGTAATCAGTAAATCAGTAATAAAGTAAAAAGATAATATGAATTAAGAATCAAGGAGAAAA
GTAGTAATCAGTAAATCAGCAATTAAGTAAAAAGAGAGTAATCAGTAAATCGATAATTA
Found at i:8886 original size:37 final size:36
Alignment explanation
Indices: 8772--8884 Score: 108
Period size: 34 Copynumber: 3.2 Consensus size: 36
8762 AAAAAGAGAT
*
8772 TAATTAGAGTCAAGGAAATAGTAATCAGTAAATCAG
1 TAATTAGAGTCAAGGAAATAGTAATCAGTAAATCGG
* * *
8808 TAATTA-AGT-AA--AAAGAGATTAATCAGTAAATTGA
1 TAATTAGAGTCAAGGAAATAG--TAATCAGTAAATCGG
* * *
8842 TAGTTAAGAGTCAAGGTAATAGTAGTCAGTAAATCGG
1 TAATT-AGAGTCAAGGAAATAGTAATCAGTAAATCGG
8879 TAATTA
1 TAATTA
8885 AGTAAAAAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
32 5 0.08
34 18 0.31
35 4 0.07
36 10 0.17
37 18 0.31
39 4 0.07
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.28
Consensus pattern (36 bp):
TAATTAGAGTCAAGGAAATAGTAATCAGTAAATCGG
Found at i:9042 original size:34 final size:34
Alignment explanation
Indices: 8915--9084 Score: 143
Period size: 34 Copynumber: 4.8 Consensus size: 34
8905 AGTCAAGATA
*
8915 ATAGTAATCAGTAAATCAGTAATAAAGTAAAAAG
1 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAG
* * * *
8949 AT--TAATCAAGTGAATTAATAATTAAGGGAGTAAAAG
1 ATAGTAATC-AGTAAATCAGTAATTAA-GTA--AAAAG
*
8985 -TAGTAATCAGTAAATCAGCAATTAAGTAAAAAG
1 ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAG
9018 ATAGTAATCAGTAAATC-GATAATTAAGAGTCAAGGTAACA-
1 ATAGTAATCAGTAAATCAG-TAATT-A-AGT-AA---AA-AG
9058 ATAGTAATCAGTAAATCAGTAATTAAG
1 ATAGTAATCAGTAAATCAGTAATTAAG
9085 AGTCAATGGA
Statistics
Matches: 109, Mismatches: 11, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
32 5 0.05
33 19 0.17
34 24 0.22
35 4 0.04
36 21 0.19
37 7 0.06
38 2 0.02
39 1 0.01
40 24 0.22
41 2 0.02
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (34 bp):
ATAGTAATCAGTAAATCAGTAATTAAGTAAAAAG
Found at i:9075 original size:74 final size:68
Alignment explanation
Indices: 8914--9146 Score: 209
Period size: 74 Copynumber: 3.2 Consensus size: 68
8904 GAGTCAAGAT
* * * *
8914 AATAGTAATCAGTAAATCAGTAATAAAGTAAAAAGATTAATCAAGTGAATTAATAATTAAGGGAG
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGATTAATCAAGTAAATCAATAATTAAGGAAG
8979 TAA
66 TAA
* *
8982 AAGTAGTAATCAGTAAATCAGCAATTAAGTAAAAAGATAGTAATC-AGTAAATCGATAATTAAGA
1 AA-TAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAT--TAATCAAGTAAATCAATAATTAAG-
9046 GTCAAGGTAA
62 G--AA-GTAA
* ** * *
9056 CAATAGTAATCAGTAAATCAGTAATTAAGAGTCAATGGATTAATC-AGTAAATTAATACTTAAGG
1 -AATAGTAATCAGTAAATCAGTAATT-A-AGTAAAAAGATTAATCAAGTAAATCAATAATTAA--
9120 GAGAAAGTAA
61 G-G-AAGTAA
*
9130 AATTAGTGATCAGTAAA
1 AA-TAGTAATCAGTAAA
9147 GAGAAAAATG
Statistics
Matches: 137, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
68 2 0.01
69 33 0.24
70 15 0.11
71 6 0.04
73 3 0.02
74 62 0.45
75 5 0.04
76 11 0.08
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (68 bp):
AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGATTAATCAAGTAAATCAATAATTAAGGAAG
TAA
Found at i:9248 original size:25 final size:24
Alignment explanation
Indices: 9214--9264 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
9204 GAAGAATGGT
9214 AAAGAGT-AAAGAGTAATCCAGTGAA
1 AAAGAGTAAAAG-GTAAT-CAGTGAA
9239 AAAGAGTAAAATGGTAATCAGTGAA
1 AAAGAGTAAAA-GGTAATCAGTGAA
9264 A
1 A
9265 TGGTAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 15 0.62
26 8 0.33
27 1 0.04
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (24 bp):
AAAGAGTAAAAGGTAATCAGTGAA
Found at i:9267 original size:15 final size:15
Alignment explanation
Indices: 9247--9275 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9237 AAAAAGAGTA
9247 AAATGGTAATCAGTG
1 AAATGGTAATCAGTG
9262 AAATGGTAATCAGT
1 AAATGGTAATCAGT
9276 AAAAAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (15 bp):
AAATGGTAATCAGTG
Found at i:9352 original size:15 final size:15
Alignment explanation
Indices: 9332--9377 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9322 AGCAATCAGT
9332 AAGAGTAAAATGGTA
1 AAGAGTAAAATGGTA
*
9347 AAGAGT--AATCAGTA
1 AAGAGTAAAAT-GGTA
*
9361 AAAAGTAAAATGGTA
1 AAGAGTAAAATGGTA
9376 AA
1 AA
9378 AAAGTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 3 0.12
14 8 0.32
15 11 0.44
16 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.20
Consensus pattern (15 bp):
AAGAGTAAAATGGTA
Found at i:9390 original size:65 final size:64
Alignment explanation
Indices: 9287--9447 Score: 254
Period size: 64 Copynumber: 2.5 Consensus size: 64
9277 AAAAGTAATG
* *
9287 GTAATCAATAAAAAGT-AAATGGTAAAAAAGTAAAAAGCAATCAGTAAGAGTAAAATGGTAAAGA
1 GTAATCAGTAAAAAGTAAAATGGTAAAAAAGTAAAAAGCAATCAATAAGAGT-AAATGGTAAAGA
9351 GTAATCAGTAAAAAGTAAAATGGTAAAAAAGTAAAAAGCAATCAATAAGAGTAAATGGTAAAGA
1 GTAATCAGTAAAAAGTAAAATGGTAAAAAAGTAAAAAGCAATCAATAAGAGTAAATGGTAAAGA
* **
9415 GCAATCAGTAAAGGGTAAAATGGT-AAAAAGTAA
1 GTAATCAGTAAAAAGTAAAATGGTAAAAAAGTAA
9448 TGGTGATTAG
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
63 9 0.10
64 48 0.53
65 34 0.37
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.19
Consensus pattern (64 bp):
GTAATCAGTAAAAAGTAAAATGGTAAAAAAGTAAAAAGCAATCAATAAGAGTAAATGGTAAAGA
Found at i:9412 original size:27 final size:29
Alignment explanation
Indices: 9381--9444 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 29
9371 TGGTAAAAAA
9381 GTAAAAAGCAATCAAT-AAGAGT-AAATG
1 GTAAAAAGCAATCAATAAAGAGTAAAATG
* * *
9408 GTAAAGAGCAATCAGTAAAGGGTAAAATG
1 GTAAAAAGCAATCAATAAAGAGTAAAATG
9437 GTAAAAAG
1 GTAAAAAG
9445 TAATGGTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 14 0.45
28 5 0.16
29 12 0.39
ACGTcount: A:0.53, C:0.06, G:0.23, T:0.17
Consensus pattern (29 bp):
GTAAAAAGCAATCAATAAAGAGTAAAATG
Found at i:9586 original size:28 final size:26
Alignment explanation
Indices: 9531--9630 Score: 137
Period size: 28 Copynumber: 3.7 Consensus size: 26
9521 CAGTAAAATG
* * *
9531 AAAATGGTAATCAGTAAAGAAGAATAA
1 AAAATGGTATTCAGTAAAAAAGAGT-A
9558 AAAATGGTATTCAGTTAAAAAAGAGTA
1 AAAATGGTATTCAG-TAAAAAAGAGTA
9585 AAAATGGTATTCAGTAGTAAAAAGAGTA
1 AAAATGGTATTCAGTA--AAAAAGAGTA
9613 AAAATGGTATTCAGTAAA
1 AAAATGGTATTCAGTAAA
9631 GTAAAAAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
26 4 0.06
27 28 0.42
28 35 0.52
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.24
Consensus pattern (26 bp):
AAAATGGTATTCAGTAAAAAAGAGTA
Found at i:9643 original size:28 final size:27
Alignment explanation
Indices: 9531--9643 Score: 97
Period size: 27 Copynumber: 4.1 Consensus size: 27
9521 CAGTAAAATG
* * *
9531 AAAATGGTAATCAGTAAAGAAGAATAA
1 AAAATGGTATTCAGTAAAGAAAAAAAA
* **
9558 AAAATGGTATTCAGTTAAA-AAAGAGTA
1 AAAATGGTATTCAG-TAAAGAAAAAAAA
*
9585 AAAATGGTATTCAGT--AGTAAAAAGAGTA
1 AAAATGGTATTCAGTAAAG-AAAAA-A-AA
*
9613 AAAATGGTATTCAGTAAAGTAAAAAAA
1 AAAATGGTATTCAGTAAAGAAAAAAAA
9640 AAAA
1 AAAA
9644 GAGTAAAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
24 1 0.01
26 5 0.07
27 36 0.51
28 22 0.31
29 4 0.06
30 2 0.03
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.22
Consensus pattern (27 bp):
AAAATGGTATTCAGTAAAGAAAAAAAA
Found at i:9644 original size:36 final size:34
Alignment explanation
Indices: 9574--9700 Score: 149
Period size: 36 Copynumber: 3.8 Consensus size: 34
9564 GTATTCAGTT
9574 AAAAAAGAGTAAAAATGGTATTCAGT--AG----
1 AAAAAAGAGTAAAAATGGTATTCAGTAAAGAAAA
*
9602 TAAAAAGAGTAAAAATGGTATTCAGTAAAGTAAAAA
1 AAAAAAGAGTAAAAATGGTATTCAGTAAAG--AAAA
*
9638 AAAAAAGAGTAAAAATGGTATTCAGCAAAGAAAA
1 AAAAAAGAGTAAAAATGGTATTCAGTAAAGAAAA
* *
9672 GAAAAAGAGTAAAAAATGGCATTCAGTAA
1 AAAAAAGAGT-AAAAATGGTATTCAGTAA
9701 TTTAGTTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
28 25 0.30
30 2 0.02
34 13 0.15
35 16 0.19
36 28 0.33
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (34 bp):
AAAAAAGAGTAAAAATGGTATTCAGTAAAGAAAA
Found at i:10167 original size:41 final size:41
Alignment explanation
Indices: 10066--10900 Score: 644
Period size: 41 Copynumber: 19.6 Consensus size: 41
10056 ACGTTGCGAC
*
10066 AAGGGCAAACTGGGAAATCTAAAACAACACCTTCCGATGAGG
1 AAGGGCAAACTGGGAAAACT-AAACAACACCTTCCGATGAGG
* *
10108 AAGGGCGAACTGGG-AAACTAAACAACACCTTCCGATGGGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
* * * *
10148 AATGGCAAACAGGGAAAACTAAACAACACCTT-CGGTGGGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
* ** *
10188 CAGGGCAAACTGGG-AATTTAAACAACACCTTCCAATGAGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
*
10228 AAGGGCAAGA-TGGGAAATGTAGACTTAAACAATACCTTCCGAT-ATGG
1 AAGGGCAA-ACTGGG-AA---A-AC-TAAACAACACCTTCCGATGA-GG
* * *
10275 AATGGCAAACTGTG-AAACTAAACAACACCTTCCGGTGAGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
** * *
10315 AAGGGCAAACTAAGAAATCTAAACAACACCTTCCGGTGAGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
* * *
10356 AAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
10397 AAGGGCAAGAC-GGGAAATGTAGACTTAAACAACACCTTCCGAT-ATGG
1 AAGGGCAA-ACTGGG-AA---A-AC-TAAACAACACCTTCCGATGA-GG
*
10444 AAGGGCAAACTGGG-AAACTAAACAACACCTTCCGGTGAGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
* * *
10484 AAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
* * * *
10525 AAGGGCAAGACAGGAAATGTAGATTTAAGCAACACCTTCCGAT-ATGG
1 AAGGGCAA-ACTGGGAA---A-A-CTAAACAACACCTTCCGATGA-GG
* * * * *
10572 AAGGGCAAACTAGG-AAACTAAACAACACTTTCTGGTGGGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
* *
10612 AAGGGCAAACTGGGAAAACTAAACAACACCTTCTGATGGGG
1 AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
* * * *
10653 AAGGGCAAATTGGAAATTTGACAACTAGACAACACCTTCCGACT-CGG
1 AAGGGCAAACTGG------GAAAACTAAACAACACCTTCCGA-TGAGG
* *
10700 AAGGGCAAGA-TGGG-AAACTAAACAACACCTTCCGGTGGGG
1 AAGGGCAA-ACTGGGAAAACTAAACAACACCTTCCGATGAGG
* *
10740 AAGGGCAAATTGGGCATTTGACAACTAGACAACACCTTCCGACTG-GG
1 AAGGGCAAACTGGG-A----A-AACTAAACAACACCTTCCGA-TGAGG
* * *
10787 AAGGGCAAGA-TGGGAAAACTAAAGAACACCTTCCGGTGGGG
1 AAGGGCAA-ACTGGGAAAACTAAACAACACCTTCCGATGAGG
* * *
10828 AAGGCCAAATTGGGTATTTGACAACTAGACAACACCTTCCGACTGA-G
1 AAGGGCAAACTGGG-A----A-AACTAAACAACACCTTCCGA-TGAGG
*
10875 AAGGGCAAGA-TGAGAAAACTAAACAA
1 AAGGGCAA-ACTGGGAAAACTAAACAA
10901 AGCTAGGTTT
Statistics
Matches: 654, Mismatches: 76, Indels: 127
0.76 0.09 0.15
Matches are distributed among these distances:
39 17 0.03
40 190 0.29
41 213 0.33
42 29 0.04
45 6 0.01
46 14 0.02
47 177 0.27
48 8 0.01
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (41 bp):
AAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGAGG
Found at i:10436 original size:169 final size:168
Alignment explanation
Indices: 10087--10542 Score: 693
Period size: 169 Copynumber: 2.7 Consensus size: 168
10077 GGGAAATCTA
* * * *
10087 AAACAACACCTTCCGATGA-GGAAGGGCGAACTGGGAAACTAAACAACACCTTCCGATGGGGAAT
1 AAACAACACCTTCCGAT-ATGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAG
* * * * * *
10151 GGCAAAC-AGGGAAAACTAAACAACACCTT-CGGTGGGGCAGGGCAAACTGGGAATTTAAACAAC
65 GGCAAACTA-AGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGAAATCTAAACAAC
*
10214 ACCTTCCAATGAGGAAGGGCAAGATGGGAAATGTAGACTT
129 ACCTTCCAATGAGGAAGGGCAAGACGGGAAATGTAGACTT
* * *
10254 AAACAATACCTTCCGATATGGAATGGCAAACTGTGAAACTAAACAACACCTTCCGGTGAGGAAGG
1 AAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGG
10319 GCAAACTAAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGAGAAATCTAAACAACA
66 GCAAACTAAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTG-GAAATCTAAACAACA
**
10384 CCTTCCGGTGAGGAAGGGCAAGACGGGAAATGTAGACTT
130 CCTTCCAATGAGGAAGGGCAAGACGGGAAATGTAGACTT
10423 AAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGG
1 AAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGG
* *
10488 GCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAGACAGGAAAT
66 GCAAACTAAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAA-ACTGGAAAT
10543 GTAGATTTAA
Statistics
Matches: 263, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
166 1 0.00
167 80 0.30
168 19 0.07
169 160 0.61
170 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (168 bp):
AAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGG
GCAAACTAAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGAAATCTAAACAACAC
CTTCCAATGAGGAAGGGCAAGACGGGAAATGTAGACTT
Found at i:10465 original size:128 final size:126
Alignment explanation
Indices: 10066--10753 Score: 699
Period size: 128 Copynumber: 5.4 Consensus size: 126
10056 ACGTTGCGAC
* *
10066 AAGGGCAAACTGGGAAATCTAAAACAACACCTTCCGATGAGGAAGGGCGAACTGGGAAA-CTAAA
1 AAGGGCAAACTGGGAAA-CT-AAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAATCTAAA
* * * **
10130 CAACACCTTCCGATGGGGAATGGCAAACAGGG-AA---A-ACTAAACAACACCTT-CGGTGGGG
64 CAACACCTTCCGATGAGGAAGGGCAAAC-GGGAAATGTAGACTAAACAACACCTTCCGATATGG
* ** **
10188 CAGGGCAAACTGGGAATTTAAACAACACCTTCCAATGAGGAAGGGCAAGA-TGGGAAATGTAGAC
1 AAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGGGCAA-ACTGGGAAA--T---C
* * * * *
10252 TTAAACAATACCTTCCGAT-ATGGAATGGCAAAC-TG---TG-AAACTAAACAACACCTTCCGGT
60 -TAAACAACACCTTCCGATGA-GGAAGGGCAAACGGGAAATGTAGACTAAACAACACCTTCCGAT
10311 GA-GG
123 -ATGG
** *
10315 AAGGGCAAACTAAGAAATCTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGAGAAATCTAAAC
1 AAGGGCAAACTGGGAAA-CTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAATCTAAAC
*
10380 AACACCTTCCGGTGAGGAAGGGCAAGACGGGAAATGTAGACTTAAACAACACCTTCCGATATGG
65 AACACCTTCCGATGAGGAAGGGCAA-ACGGGAAATGTAGAC-TAAACAACACCTTCCGATATGG
*
10444 AAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGAGAAATCTAAACA
1 AAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAATCTAAACA
* * * *
10509 ACACCTTCCGGTGAGGAAGGGCAAGACAGGAAATGTAGATTTAAGCAACACCTTCCGATATGG
66 ACACCTTCCGATGAGGAAGGGCAA-ACGGGAAATGTAGA-CTAAACAACACCTTCCGATATGG
* * * * *
10572 AAGGGCAAACTAGGAAACTAAACAACACTTTCTGGTGGGGAAGGGCAAACTGGGAAAACTAAACA
1 AAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAATCTAAACA
* * ** * * * *
10637 ACACCTTCTGATGGGGAAGGGCAAATTGGAAATTTGACAACTAGACAACACCTTCCGACT-CGG
66 ACACCTTCCGATGAGGAAGGGCAAACGGGAAATGT-A-GACTAAACAACACCTTCCGA-TATGG
* *
10700 AAGGGCAAGA-TGGGAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGG
1 AAGGGCAA-ACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGG
10754 CATTTGACAA
Statistics
Matches: 487, Mismatches: 49, Indels: 54
0.83 0.08 0.09
Matches are distributed among these distances:
120 34 0.07
121 2 0.00
122 40 0.08
123 4 0.01
124 1 0.00
125 2 0.00
126 17 0.03
127 59 0.12
128 291 0.60
129 37 0.08
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (126 bp):
AAGGGCAAACTGGGAAACTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAATCTAAACA
ACACCTTCCGATGAGGAAGGGCAAACGGGAAATGTAGACTAAACAACACCTTCCGATATGG
Found at i:10501 original size:87 final size:82
Alignment explanation
Indices: 10066--10836 Score: 585
Period size: 87 Copynumber: 9.1 Consensus size: 82
10056 ACGTTGCGAC
*
10066 AAGGGCAAACTGGGAAAT---CTAAAACAACACCTTCCGATGAGGAAGGGCGAACTGGGAAACTA
1 AAGGGCAAACT-GGAAATAGACT-AAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGAAACTA
* *
10128 AACAACACCTTCCGATGGGG
63 AACAACACCTTCCGGTGAGG
* * * * * * **
10148 AATGGCAAACAGGGAA-A-ACTAAACAACACCTT-CGGTGGGGCAGGGCAAACTGGGAATTTAAA
1 AAGGGCAAACTGGAAATAGACTAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGAAACTAAA
**
10210 CAACACCTTCCAATGAGG
65 CAACACCTTCCGGTGAGG
* * *
10228 AAGGGCAAGA-TGGGAAATGTAGACTTAAACAATACCTTCCGATATGGAATGGCAAACTGTGAAA
1 AAGGGCAA-ACT-GGAAA--TAGAC-TAAACAACACCTTCCGATA-GGAAGGGCAAACTGGGAAA
10292 CTAAACAACACCTTCCGGTGAGG
60 CTAAACAACACCTTCCGGTGAGG
* * *
10315 AAGGGCAAACTAAGAAAT---CTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGAGAAATCTA
1 AAGGGCAAACT-GGAAATAGACTAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGGAAA-CTA
10377 AACAACACCTTCCGGTGAGG
63 AACAACACCTTCCGGTGAGG
*
10397 AAGGGCAAGACGGGAAATGTAGACTTAAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAAC
1 AAGGGCAA-ACTGGAAA--TAGAC-TAAACAACACCTTCCGATA-GGAAGGGCAAACTGGGAAAC
10462 TAAACAACACCTTCCGGTGAGG
61 TAAACAACACCTTCCGGTGAGG
* * *
10484 AAGGGCAAACTGAGAAAT---CTAAACAACACCTTCCGGTGAGGAAGGGCAAGAC-AGGAAATGT
1 AAGGGCAAACTG-GAAATAGACTAAACAACACCTTCCGAT-AGGAAGGGCAA-ACTGGGAAA-CT
*
10545 AGATTTAAGCAACACCTTCCGAT-ATGG
62 --A---AA-CAACACCTTCCGGTGA-GG
* * * *
10572 AAGGGCAAACTAGG--A-A-ACTAAACAACACTTTCTGGTGGGGAAGGGCAAACTGGGAAAACTA
1 AAGGGCAAACT-GGAAATAGACTAAACAACACCTTCCGAT-AGGAAGGGCAAACTGGG-AAACTA
* * *
10633 AACAACACCTTCTGATGGGG
63 AACAACACCTTCCGGTGAGG
* * * *
10653 AAGGGCAAATTGGAAATTTGACAACTAGACAACACCTTCCGACTCGGAAGGGCAAGA-TGGGAAA
1 AAGGGCAAACTGGAAA--T-A-GACTAAACAACACCTTCCGA-TAGGAAGGGCAA-ACTGGGAAA
*
10717 CTAAACAACACCTTCCGGTGGGG
60 CTAAACAACACCTTCCGGTGAGG
* ** * * *
10740 AAGGGCAAATTGGGCATTTGACAACTAGACAACACCTTCCGACTGGGAAGGGCAAGA-TGGGAAA
1 AAGGGCAAACT-GG-AAAT-A-GACTAAACAACACCTTCCGA-TAGGAAGGGCAA-ACTGGG-AA
* *
10804 ACTAAAGAACACCTTCCGGTGGGG
59 ACTAAACAACACCTTCCGGTGAGG
*
10828 AAGGCCAAA
1 AAGGGCAAA
10837 TTGGGTATTT
Statistics
Matches: 578, Mismatches: 59, Indels: 98
0.79 0.08 0.13
Matches are distributed among these distances:
80 49 0.08
81 111 0.19
82 56 0.10
83 2 0.00
84 3 0.01
85 5 0.01
86 20 0.03
87 199 0.34
88 129 0.22
89 4 0.01
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (82 bp):
AAGGGCAAACTGGAAATAGACTAAACAACACCTTCCGATAGGAAGGGCAAACTGGGAAACTAAAC
AACACCTTCCGGTGAGG
Found at i:10633 original size:169 final size:170
Alignment explanation
Indices: 10066--10669 Score: 660
Period size: 169 Copynumber: 3.6 Consensus size: 170
10056 ACGTTGCGAC
* * *
10066 AAGGGCAA-ACTGGGAA-A-TCTAAAACAACACCTTCCGATGA-GGAAGGGCGAACTGGGAAACT
1 AAGGGCAAGACTGGGAATAGACTTAAACAACACCTTCCGAT-ATGGAAGGGCAAACTGGGAAACT
* * * * * * *
10127 AAACAACACCTTCCGATGGGGAATGGCAAACAGGGAAAACTAAACAACACCTT-CGGTGGGGCAG
65 AAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGAAG
*
10191 GGCAAACTGG----G-AATTTAAACAACACCTTCCAATGAGG
130 GGCAAACTGGAAATGTAATTT-AACAACACCTTCCGATGAGG
* * *
10228 AAGGGCAAGA-TGGGAAATGTAGACTTAAACAATACCTTCCGATATGGAATGGCAAACTGTGAAA
1 AAGGGCAAGACTGGG-AA--TAGACTTAAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAA
* *
10292 CTAAACAACACCTTCCGGTGAGGAAGGGCAAACTAAGAAATCTAAACAACACCTTCCGGTGAGGA
63 CTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGA
* *
10357 AGGGCAAACTGAGAAATCT-A---AACAACACCTTCCGGTGAGG
128 AGGGCAAACTG-GAAATGTAATTTAACAACACCTTCCGATGAGG
10397 AAGGGCAAGAC-GGGAAATGTAGACTTAAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAA
1 AAGGGCAAGACTGGG-AA--TAGACTTAAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAA
*
10461 CTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGA
63 CTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGA
*
10526 AGGGCAAGACAGGAAATGTAGATTTAAGCAACACCTTCCGAT-ATGG
128 AGGGCAA-ACTGGAAATGTA-ATTTAA-CAACACCTTCCGATGA-GG
* * * * **
10572 AAGGGCAA-ACTAGG-A-A-AC-TAAACAACACTTTCTGGTGGGGAAGGGCAAACTGGGAAAACT
1 AAGGGCAAGACTGGGAATAGACTTAAACAACACCTTCCGATATGGAAGGGCAAACTGGG-AAACT
* * *
10632 AAACAACACCTTCTGATGGGGAAGGGCAAATTG-GAAAT
65 AAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAAT
10670 TTGACAACTA
Statistics
Matches: 382, Mismatches: 35, Indels: 44
0.83 0.08 0.10
Matches are distributed among these distances:
162 12 0.03
163 3 0.01
166 2 0.01
167 82 0.21
168 54 0.14
169 192 0.50
170 4 0.01
171 1 0.00
173 2 0.01
174 5 0.01
175 25 0.07
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (170 bp):
AAGGGCAAGACTGGGAATAGACTTAAACAACACCTTCCGATATGGAAGGGCAAACTGGGAAACTA
AACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAATCTAAACAACACCTTCCGGTGAGGAAGG
GCAAACTGGAAATGTAATTTAACAACACCTTCCGATGAGG
Found at i:10702 original size:47 final size:48
Alignment explanation
Indices: 10628--10882 Score: 212
Period size: 47 Copynumber: 5.7 Consensus size: 48
10618 AAACTGGGAA
* *
10628 AACTAAACAACACCTTCTGA-TGGGGAAGGGCAAATTGGAAATTTGAC
1 AACTAGACAACACCTTCCGACTGGGGAAGGGCAAATTGGAAATTTGAC
*
10675 AACTAGACAACACCTTCCGACT-CGGAAGGGCAAGA-TGG------GA-
1 AACTAGACAACACCTTCCGACTGGGGAAGGGCAA-ATTGGAAATTTGAC
* * **
10715 AACTAAACAACACCTTCCG-GTGGGGAAGGGCAAATTGGGCATTTGAC
1 AACTAGACAACACCTTCCGACTGGGGAAGGGCAAATTGGAAATTTGAC
*
10762 AACTAGACAACACCTTCCGACT-GGGAAGGGCAAGATGGGAAA----AC
1 AACTAGACAACACCTTCCGACTGGGGAAGGGCAA-ATTGGAAATTTGAC
* * **
10806 TAA--AG--AACACCTTCCG-GTGGGGAAGGCCAAATTGGGTATTTGAC
1 -AACTAGACAACACCTTCCGACTGGGGAAGGGCAAATTGGAAATTTGAC
*
10850 AACTAGACAACACCTTCCGACT-GAGAAGGGCAA
1 AACTAGACAACACCTTCCGACTGGGGAAGGGCAA
10883 GATGAGAAAA
Statistics
Matches: 165, Mismatches: 19, Indels: 48
0.71 0.08 0.21
Matches are distributed among these distances:
39 2 0.01
40 37 0.22
41 23 0.14
43 4 0.02
44 4 0.02
45 4 0.02
46 2 0.01
47 80 0.48
48 9 0.05
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (48 bp):
AACTAGACAACACCTTCCGACTGGGGAAGGGCAAATTGGAAATTTGAC
Found at i:10703 original size:88 final size:87
Alignment explanation
Indices: 10610--10900 Score: 460
Period size: 88 Copynumber: 3.3 Consensus size: 87
10600 TTTCTGGTGG
* * *
10610 GGAAGGGCAA-ACTGGGAAAACTAAACAACACCTTCTGATGGGGAAGGGCAAATTGGAAATTTGA
1 GGAAGGGCAAGA-TGGGAAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTGA
10674 CAACTAGACAACACCTTCCGACT
65 CAACTAGACAACACCTTCCGACT
*
10697 CGGAAGGGCAAGATGGG-AAACTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGCATTTGA
1 -GGAAGGGCAAGATGGGAAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTGA
10761 CAACTAGACAACACCTTCCGACT
65 CAACTAGACAACACCTTCCGACT
* * *
10784 GGGAAGGGCAAGATGGGAAAACTAAAGAACACCTTCCGGTGGGGAAGGCCAAATTGGGTATTTGA
1 -GGAAGGGCAAGATGGGAAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTGA
10849 CAACTAGACAACACCTTCCGACT
65 CAACTAGACAACACCTTCCGACT
*
10872 GAGAAGGGCAAGATGAGAAAACTAAACAA
1 G-GAAGGGCAAGATGGGAAAACTAAACAA
10901 AGCTAGGTTT
Statistics
Matches: 190, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
87 83 0.44
88 106 0.56
89 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (87 bp):
GGAAGGGCAAGATGGGAAAACTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTGAC
AACTAGACAACACCTTCCGACT
Found at i:10704 original size:175 final size:168
Alignment explanation
Indices: 10087--10900 Score: 481
Period size: 169 Copynumber: 4.8 Consensus size: 168
10077 GGGAAATCTA
* *
10087 AAACAACACCTTCCGA-TGAGGAAGGGCGAACTGGG-AAACTAAACAACACCTTCCGATGGGGAA
1 AAACAACACCTTCCGACTG-GGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGGTGGGGAA
* ** * * * *** * * **
10150 TGGCAAACAGG----GAAAACTAAACAACACCTTCGGTGGGGCAGGGCAA-ACTGGGAATTTAAA
65 GGGCAAATTGGATTTGACAACTAGACAACACCTTCCGACTGGAAGGGCAAGAC-AGGAAACTAAA
* * *
10210 CAACACCTTCCAAT-GAGGAAGGGC-AAG-ATGGGAAATGTAGACTT
129 CAACACCTTCCGATAG-GGAAGGGCAAAGCATAGG--A--CA-AC-T
* * * * *
10254 AAACAATACCTTCCGA-TATGGAATGGCAAACTGTG-AAACTAAACAACACCTTCCGGTGAGGAA
1 AAACAACACCTTCCGACT-GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGGTGGGGAA
* * * * *
10317 GGGCAAACT--A--AGA-AATCTAAACAACACCTTCCG-GTGAGGAAGGGCAA-ACTGAGAAATC
65 GGGCAAATTGGATTTGACAA-CTAGACAACACCTTCCGACT--GGAAGGGCAAGACAG-GAAA-C
* * * * *
10375 TAAACAACACCTTCCGGT-GAGGAAGGGCAAGACGGGAAATGTA-GACTT
125 TAAACAACACCTTCCGATAG-GGAAGGGCAA-A--GCATA-GGACAAC-T
* *
10423 AAACAACACCTTCCGA-TATGGAAGGGCAAACTGGG-AAACTAAACAACACCTTCCGGTGAGGAA
1 AAACAACACCTTCCGACT-GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGGTGGGGAA
* * * *
10486 GGGCAAACT-GA---GA-AATCTAAACAACACCTTCCG-GTGAGGAAGGGCAAGACAGGAAATGT
65 GGGCAAATTGGATTTGACAA-CTAGACAACACCTTCCGACT--GGAAGGGCAAGACAGGAAA-CT
*
10545 AGATTTAAGCAACACCTTCCGATATGGAAGGGCAAA-C-TAGGA-AACT
126 --A---AA-CAACACCTTCCGATAGGGAAGGGCAAAGCATAGGACAACT
* * * * *
10591 AAACAACACTTTCTG-GTGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCTGATGGGGAA
1 AAACAACACCTTCCGACT-GGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGGTGGGGAA
**
10655 GGGCAAATTGGAAATTTGACAACTAGACAACACCTTCCGACTCGGAAGGGCAAGATGGGAAACTA
65 GGGCAAATTGG--ATTTGACAACTAGACAACACCTTCCGACT-GGAAGGGCAAGACAGGAAACTA
* * **
10720 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGCATTTGACAACT
127 AACAACACCTTCCGATAGGGAAGGGCAAA----GCATAGGACAACT
* *
10766 AGACAACACCTTCCGACTGGGAAGGGCAAGA-TGGGAAAACTAAAGAACACCTTCCGGTGGGGAA
1 AAACAACACCTTCCGACTGGGAAGGGCAA-ACTGGGAAAACTAAACAACACCTTCCGGTGGGGAA
* * *
10830 GGCCAAATTGGGTATTTGACAACTAGACAACACCTTCCGACTGAGAAGGGCAAGATGAGAAAACT
65 GGGCAAATT-GG-ATTTGACAACTAGACAACACCTTCCGACTG-GAAGGGCAAGA-CAGGAAACT
10895 AAACAA
126 AAACAA
10901 AGCTAGGTTT
Statistics
Matches: 539, Mismatches: 63, Indels: 81
0.79 0.09 0.12
Matches are distributed among these distances:
166 3 0.01
167 81 0.15
168 69 0.13
169 180 0.33
170 7 0.01
171 2 0.00
172 2 0.00
173 3 0.01
174 9 0.02
175 164 0.30
176 19 0.04
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.16
Consensus pattern (168 bp):
AAACAACACCTTCCGACTGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGGTGGGGAAG
GGCAAATTGGATTTGACAACTAGACAACACCTTCCGACTGGAAGGGCAAGACAGGAAACTAAACA
ACACCTTCCGATAGGGAAGGGCAAAGCATAGGACAACT
Found at i:10971 original size:16 final size:15
Alignment explanation
Indices: 10944--10973 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10934 TAACCTAATC
10944 ATGATAGATGCATGA
1 ATGATAGATGCATGA
10959 ATGATATGATGCATG
1 ATGATA-GATGCATG
10974 CAAAGTCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (15 bp):
ATGATAGATGCATGA
Found at i:11194 original size:37 final size:36
Alignment explanation
Indices: 11121--12203 Score: 886
Period size: 37 Copynumber: 29.3 Consensus size: 36
11111 CACCTTTACC
* * * *
11121 CAAGGATTTGATAATAAACCTGAACAAGAATCTTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* *
11158 CAA-GATTTTGATGAAACACCTAAACAGGGACATTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* * *
11195 CAAGGATTTCATAAGAAACCTAAACAGGAATCTTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* * *
11232 CAA-GATTTTGATGAGACACCTAAACAGGGACCTTTAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* * **
11269 CAAGGATTTAATAAGAAACCTAAACAGGAATATTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* *
11306 C-ATGATTTTGATGAGACACCTAAACATGG-ACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACA-GGAACCTTAAA
* * *
11343 CAAGGATTTGATAAGAAACCTAAACAGAAATCTTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* *
11380 CAA-GATTTTGATGAAATACCTAAACAGGGACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* * *
11417 CAAGGATTTCATAAGAAACCTAAACAGGAATCTTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* * *
11454 CAA-GATTTTGATACGATACCTAAACAGGGACCTTAAA
1 CAAGGA-TTTGATA-AACACCTAAACAGGAACCTTAAA
* * **
11491 CAAGGATTTAATAAGAAACCTAAACAGGATTCTTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* *
11528 CAA-GATTTTGATGAGACACCTAAACAGGGACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* * *
11565 CAAGGATTTCATAGAA-ACCTAAATAGGAATCTTAAA
1 CAAGGATTTGATA-AACACCTAAACAGGAACCTTAAA
* *
11601 CAA-GATTTTGATGAGACACCTAAACAGGGACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* * *
11638 CAAGGATTTCATAAGAAACCTAAACAGGAATCTTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* * *
11675 CAA-GATTTTGATGAGACACCTAAAAAGGGACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* **
11712 CAAGGATTTGATAAGAAACCTAAACAGGAATATTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* * *
11749 C-ATGATTTTGGTGAGACACCTAAACAGGAACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* * *
11786 CAAGGATTTGATAAGAAACCTAAACAGAAATCTTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
*
11823 CAA-GATTTTGATGAAACACCTAAACAGGGACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* * * * **
11860 CAAGGATTTCATAAGAAATCTAAACATGAATATTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
*
11897 CAA-GATTTTGATGAGACACCTAAACAGGAACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* * * *
11934 CAAGGATTTGATAAGAAATCTAAATAGGAATCTTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* * *
11971 CAA-GATTTTGATGAGACACCTAAATAGGGACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
* *
12008 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
* * *
12045 CAA-GATTTTGATGAAACACCTAAACAGGGACATTGAA
1 CAAGGA-TTTGAT-AAACACCTAAACAGGAACCTTAAA
** *
12082 CAAGGATTTGATAAGACACCTAAACAGGAATTTTGAA
1 CAAGGATTTGATAA-ACACCTAAACAGGAACCTTAAA
*
12119 CTA-GATTTTGATGAAACACCTAAACATGG-ACCTTAAA
1 CAAGGA-TTTGAT-AAACACCTAAACA-GGAACCTTAAA
* ** *
12156 CAAGGATTTGATTAGACACCTAAACAGGAATTTTGAA
1 CAAGGATTTGA-TAAACACCTAAACAGGAACCTTAAA
*
12193 CAAGGTTTTGA
1 CAAGGATTTGA
12204 CGTTACTGAA
Statistics
Matches: 835, Mismatches: 150, Indels: 122
0.75 0.14 0.11
Matches are distributed among these distances:
35 2 0.00
36 73 0.09
37 708 0.85
38 52 0.06
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (36 bp):
CAAGGATTTGATAAACACCTAAACAGGAACCTTAAA
Found at i:11242 original size:74 final size:74
Alignment explanation
Indices: 11121--12203 Score: 1693
Period size: 74 Copynumber: 14.6 Consensus size: 74
11111 CACCTTTACC
* * * *
11121 CAAGGATTTGATAATAAACCTGAACAAGAATCTTAAACAAGATTTTGATGAAACACCTAAACAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
*
11186 GACATTAAA
66 GACCTTAAA
*
11195 CAAGGATTTCATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
*
11260 GACCTTTAA
66 GACCTTAAA
* * * *
11269 CAAGGATTTAATAAGAAACCTAAACAGGAATATTAAACATGATTTTGATGAGACACCTAAACATG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
11334 GACCTTAAA
66 GACCTTAAA
* * *
11343 CAAGGATTTGATAAGAAACCTAAACAGAAATCTTAAACAAGATTTTGATGAAATACCTAAACAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
11408 GACCTTAAA
66 GACCTTAAA
* *
11417 CAAGGATTTCATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGAT-ACGATACCTAAACAG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGA-GACACCTAAACAG
11481 GGACCTTAAA
65 GGACCTTAAA
* *
11491 CAAGGATTTAATAAGAAACCTAAACAGGATTCTTAAACAAGATTTTGATGAGACACCTAAACAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
11556 GACCTTAAA
66 GACCTTAAA
* *
11565 CAAGGATTTCAT-AGAAACCTAAATAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
11629 GACCTTAAA
66 GACCTTAAA
* *
11638 CAAGGATTTCATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAAAAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
11703 GACCTTAAA
66 GACCTTAAA
* * *
11712 CAAGGATTTGATAAGAAACCTAAACAGGAATATTAAACATGATTTTGGTGAGACACCTAAACAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
*
11777 AACCTTAAA
66 GACCTTAAA
* *
11786 CAAGGATTTGATAAGAAACCTAAACAGAAATCTTAAACAAGATTTTGATGAAACACCTAAACAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
11851 GACCTTAAA
66 GACCTTAAA
* * * *
11860 CAAGGATTTCATAAGAAATCTAAACATGAATATTAAACAAGATTTTGATGAGACACCTAAACAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
*
11925 AACCTTAAA
66 GACCTTAAA
* * *
11934 CAAGGATTTGATAAGAAATCTAAATAGGAATCTTAAACAAGATTTTGATGAGACACCTAAATAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
11999 GACCTTAAA
66 GACCTTAAA
*
12008 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAAACACCTAAACAGG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
* *
12073 GACATTGAA
66 GACCTTAAA
* * * * * *
12082 CAAGGATTTGATAAGACACCTAAACAGGAATTTTGAACTAGATTTTGATGAAACACCTAAACATG
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
12147 GACCTTAAA
66 GACCTTAAA
* * * * *
12156 CAAGGATTTGATTAGACACCTAAACAGGAATTTTGAACAAGGTTTTGA
1 CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGA
12204 CGTTACTGAA
Statistics
Matches: 935, Mismatches: 71, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
73 72 0.08
74 862 0.92
75 1 0.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (74 bp):
CAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACCTAAACAGG
GACCTTAAA
Found at i:13116 original size:87 final size:87
Alignment explanation
Indices: 12956--13116 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
12946 TGCCCTAAAC
* * * * *
12956 CTTCTTCCAATTTGGTCATGCATTGATATTCCCAACTGAATTGATGGTTCTAGATCAGCTTCTCA
1 CTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGGTTCTAGATCAACTTCCCA
13021 CCTCAAGAATTATTTCCGAAAT
66 CCTCAAGAATTATTTCCGAAAT
*
13043 CTTCCTCCAATTTGATCATGCATTGATATTTCCAACTCAATTGAT-GTT-TACGGATCAACTTCC
1 CTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGGTTCTA--GATCAACTTCC
* *
13106 CATCTTAAGAA
64 CACCTCAAGAA
13117 ATGTTCAAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 2 0.03
86 3 0.05
87 59 0.92
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (87 bp):
CTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGGTTCTAGATCAACTTCCCA
CCTCAAGAATTATTTCCGAAAT
Found at i:13254 original size:5 final size:5
Alignment explanation
Indices: 13244--13290 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
13234 AACCTTTTGA
** *
13244 TTTCT TTTCT TTTCT TTTCT TTT-T TTGAT TTCTCT TTTTT TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT-TCT TTTCT TTTCT TT
13291 AGATTGTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
4 3 0.09
5 29 0.83
6 3 0.09
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:13279 original size:15 final size:15
Alignment explanation
Indices: 13238--13284 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
13228 AATTTGAACC
13238 TTTTGATTTCT-TTT
1 TTTTGATTTCTCTTT
*
13252 CTTTT-CTTT-TCTTT
1 -TTTTGATTTCTCTTT
13266 TTTTGATTTCTCTTT
1 TTTTGATTTCTCTTT
13281 TTTT
1 TTTT
13285 TTCTTTAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 5 0.19
14 9 0.33
15 13 0.48
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTGATTTCTCTTT
Found at i:14031 original size:1 final size:1
Alignment explanation
Indices: 14025--14081 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
14015 GATGTCACAA
* * * ** * *
14025 TTTTTTTTCTTTTTCTTTTCTTTTTTTTTTACTTCTTTTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14082 GGCAACTTCT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.88
Consensus pattern (1 bp):
T
Found at i:14045 original size:11 final size:10
Alignment explanation
Indices: 14025--14081 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 10
14015 GATGTCACAA
14025 TTTTTTTTCT
1 TTTTTTTTCT
14035 TTTTCTTTTCTT
1 TTTT-TTTTC-T
14047 TTTTTTTTACT
1 TTTTTTTT-CT
*
14058 TCTTTTTTTGT
1 T-TTTTTTTCT
14069 TTTTTTTT-T
1 TTTTTTTTCT
14078 TTTT
1 TTTT
14082 GGCAACTTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 5 0.12
10 11 0.26
11 13 0.31
12 13 0.31
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.88
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:14060 original size:26 final size:27
Alignment explanation
Indices: 14031--14081 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
14021 ACAATTTTTT
14031 TTCTTTTTCT-TTTCTTTTTTTTTTAC
1 TTCTTTTTCTGTTTCTTTTTTTTTTAC
* *
14057 TTCTTTTTTTGTTTTTTTTTTTTTT
1 TTCTTTTTCTGTTTCTTTTTTTTTT
14082 GGCAACTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (27 bp):
TTCTTTTTCTGTTTCTTTTTTTTTTAC
Found at i:14066 original size:23 final size:22
Alignment explanation
Indices: 14025--14081 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
14015 GATGTCACAA
14025 TTTTTTTTCTTTTTCTTTTCTT
1 TTTTTTTTCTTTTTCTTTTCTT
*
14047 TTTTTTTTACTTCTTT-TTTTGTT
1 TTTTTTTT-CTT-TTTCTTTTCTT
14070 TTTTTTTT-TTTT
1 TTTTTTTTCTTTT
14082 GGCAACTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 8 0.25
23 17 0.53
24 3 0.09
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.88
Consensus pattern (22 bp):
TTTTTTTTCTTTTTCTTTTCTT
Found at i:14081 original size:15 final size:16
Alignment explanation
Indices: 14025--14082 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
14015 GATGTCACAA
*
14025 TTTTTTTTCTTTTTCT
1 TTTTTTTTGTTTTTCT
14041 TTTCTTTTT-TTTTTACT
1 TTT-TTTTTGTTTTT-CT
14058 TCTTTTTTTGTTTTT-T
1 T-TTTTTTTGTTTTTCT
14074 TTTTTTTTG
1 TTTTTTTTG
14083 GCAACTTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.21
16 10 0.26
17 13 0.34
18 7 0.18
ACGTcount: A:0.02, C:0.09, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTTTTGTTTTTCT
Found at i:14692 original size:47 final size:47
Alignment explanation
Indices: 14638--15011 Score: 302
Period size: 47 Copynumber: 7.6 Consensus size: 47
14628 TTTTTGCTTA
* * ** *
14638 TTTACTGATTTACTGATTGCTATTACCTTGTTTCTGATTAATCTCTT
1 TTTACTGAATTACTGATTTCTATTACCTTGACTCTGATTAATCCCTT
* * *
14685 TTTACTGATTTACTGACTTCTATTACCTTGACTCTGATTAATCTC-T
1 TTTACTGAATTACTGATTTCTATTACCTTGACTCTGATTAATCCCTT
* *
14731 TTTACTTAATTATTGATTTACTAATTACTATTACCTTGACTCTGATTAATCCCTT
1 TTTACTGAATTACTG----A-T--TT-CTATTACCTTGACTCTGATTAATCCCTT
* * *
14786 TTTACTTAATTACTGATTTCTATTGCCTTGACTCTGGTTAAT-CCTT
1 TTTACTGAATTACTGATTTCTATTACCTTGACTCTGATTAATCCCTT
* * *
14832 TTTACTTAATTACTGATTTCTATTGCCTTGACTCTGGTTAATCCCTT
1 TTTACTGAATTACTGATTTCTATTACCTTGACTCTGATTAATCCCTT
* *
14879 TTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTTTGATTAATCCCTT
1 TTTACTGAATTACTG----A-T--TT-CTATTACCTTGACTCTGATTAATCCCTT
* * * * * * * *
14934 TTTACTTAATTACTGACTTACTGATCACTATTAACTTTGACTAATCTCTT
1 TTTACTGAATTACTGA-TTTCT-ATTAC-CTTGACTCTGATTAATCCCTT
*
14984 TTTACTCAATTACTGATTTACTGATTAC
1 TTTACTGAATTACTGATTT-CT-ATTAC
15012 TATTACTTTA
Statistics
Matches: 282, Mismatches: 24, Indels: 39
0.82 0.07 0.11
Matches are distributed among these distances:
46 59 0.21
47 81 0.29
48 4 0.01
49 7 0.02
50 41 0.15
51 5 0.02
52 1 0.00
53 2 0.01
54 27 0.10
55 55 0.20
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (47 bp):
TTTACTGAATTACTGATTTCTATTACCTTGACTCTGATTAATCCCTT
Found at i:14696 original size:55 final size:55
Alignment explanation
Indices: 14608--15056 Score: 413
Period size: 55 Copynumber: 8.7 Consensus size: 55
14598 AACTTTGACT
* * * * * *
14608 CTTGATCTCTTATTACTATCTTTTTGCTTATTTACTGATTTACTGATTGCTATTAC
1 CTTGA-CTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
**
14664 CTTGTTTCTGATTAATCTC----T--TT--TTACTGATTTACTGACTT-CTATTAC
1 CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGA-TTACTATTAC
* *
14711 CTTGACTCTGATTAATCTC-TTTTACTTAATTATTGATTTACTAATTACTATTAC
1 CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
* *
14765 CTTGACTCTGATTAATCCCTTTTTACTTAATTACTG----A-T--TT-CTATTGC
1 CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
* *
14812 CTTGACTCTGGTTAATC-CTTTTTACTTAATTACTG----A-T--TT-CTATTGC
1 CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
* *
14858 CTTGACTCTGGTTAATCCCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
1 CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
* * * *
14913 CTTGACTTTGATTAATCCCTTTTTACTTAATTACTGACTTACTGATCACTATTA-
1 CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
* * *
14967 ----ACTTTGACTAATCTCTTTTTACTCAATTACTGATTTACTGATTACTATTAC
1 CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
* * * *
15018 TTTAACTCTGATTAATCTCCTTTTACTTAATTATTGATT
1 CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATT
15057 GCCCTCTTTT
Statistics
Matches: 341, Mismatches: 28, Indels: 49
0.82 0.07 0.12
Matches are distributed among these distances:
46 46 0.13
47 79 0.23
48 4 0.01
49 2 0.01
50 47 0.14
51 3 0.01
52 3 0.01
53 2 0.01
54 40 0.12
55 111 0.33
56 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (55 bp):
CTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTAC
Found at i:14768 original size:101 final size:100
Alignment explanation
Indices: 14625--15056 Score: 337
Period size: 101 Copynumber: 4.2 Consensus size: 100
14615 TCTTATTACT
* * * **
14625 ATCT-TTTTGCTTATTTACTGATTTACTGATTGCTATTACCTTGTT-TCTGATTAATCTCTTTTT
1 ATCTCTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTTATCT-ATTAA-CTCTAATT
14688 ACTGATTTACTGACTT-CTATTACCTTGACTCTGATTA
64 ACTGATTTACTGA-TTACTATTACCTTGACTCTGATTA
* * * **
14725 ATCTCTTTTACTTAATTATTGATTTACTAATTACTATTACCTTG--ACTCTGATTAATCCCTTTT
1 ATCTCTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTTA-TCT-ATTAA-CTCTAAT
* * * * *
14788 TACTTAATTACTGATTTCTATTGCCTTGACTCTGGTTA
63 TACTGATTTACTGATTACTATTACCTTGACTCTGATTA
* * * * *
14826 ATC-CTTTTTACTTAATTACTGATTT-CT-ATTGCCT-TGACTCTGGTTAATCCCTTTTTACT-T
1 ATCTC-TTTTACTTAATTACTGATTTACTGATT-ACTATTAC-CTTGTT-AT--CTATTAACTCT
*
14886 AATTACTGATTTACTGATTACTATTACCTTGACTTTGATTA
60 AATTACTGATTTACTGATTACTATTACCTTGACTCTGATTA
* * * * * * *
14927 ATCCCTTTTTACTTAATTACTGACTTACTGATCACTATTAACTTTGACTAATCTCTTTTTACTC-
1 ATCTC-TTTTACTTAATTACTGATTTACTGATTACTATT-ACCTTG--T--TATCTATTAACTCT
* *
14991 AATTACTGATTTACTGATTACTATTACTTTAACTCTGATTA
60 AATTACTGATTTACTGATTACTATTACCTTGACTCTGATTA
*
15032 ATCTCCTTTTACTTAATTATTGATT
1 ATCT-CTTTTACTTAATTACTGATT
15057 GCCCTCTTTT
Statistics
Matches: 271, Mismatches: 38, Indels: 41
0.77 0.11 0.12
Matches are distributed among these distances:
99 6 0.02
100 14 0.05
101 140 0.52
102 23 0.08
103 8 0.03
104 7 0.03
105 69 0.25
106 2 0.01
107 1 0.00
108 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.50
Consensus pattern (100 bp):
ATCTCTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTTATCTATTAACTCTAATTAC
TGATTTACTGATTACTATTACCTTGACTCTGATTA
Found at i:14815 original size:148 final size:148
Alignment explanation
Indices: 14638--14999 Score: 465
Period size: 148 Copynumber: 2.4 Consensus size: 148
14628 TTTTTGCTTA
* * ** *
14638 TTTACTGATTTACTGATTGCTATTACCTTGTTTCTGATTAATCTCTTTTTACTGATTTACTGACT
1 TTTACTTAATTACTGATTGCTATTACCTTGACTCTGATTAATC-CTTTTTACTGAATTACTGACT
* *
14703 TCTATTACCTTGACTCTGATTAATCTC-TTTTACTTAATTATTGATTTACTAATTACTATTACCT
65 TCTATTACCTTGACTCTGATTAATCCCTTTTTACTTAATTACTGATTTACTAATTACTATTACCT
14767 TGACTCTGATTAATCCCTT
130 TGACTCTGATTAATCCCTT
* * * * *
14786 TTTACTTAATTACTGATTTCTATTGCCTTGACTCTGGTTAATCCTTTTTACTTAATTACTGATTT
1 TTTACTTAATTACTGATTGCTATTACCTTGACTCTGATTAATCCTTTTTACTGAATTACTGACTT
* * *
14851 CTATTGCCTTGACTCTGGTTAATCCCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTT
66 CTATTACCTTGACTCTGATTAATCCCTTTTTACTTAATTACTGATTTACTAATTACTATTACCTT
*
14916 GACTTTGATTAATCCCTT
131 GACTCTGATTAATCCCTT
* * * * * * *
14934 TTTACTTAATTACTGACTTACTGATCACTATTAACTTTGACTAATCTCTTTTTACTCAATTACTG
1 TTTACTTAATTACTGA-TTGCT-ATTAC-CTTGACTCTGATTAATC-CTTTTTACTGAATTACTG
14999 A
62 A
15000 TTTACTGATT
Statistics
Matches: 184, Mismatches: 25, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
147 42 0.23
148 105 0.57
149 4 0.02
150 3 0.02
151 12 0.07
152 18 0.10
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.49
Consensus pattern (148 bp):
TTTACTTAATTACTGATTGCTATTACCTTGACTCTGATTAATCCTTTTTACTGAATTACTGACTT
CTATTACCTTGACTCTGATTAATCCCTTTTTACTTAATTACTGATTTACTAATTACTATTACCTT
GACTCTGATTAATCCCTT
Found at i:14995 original size:50 final size:49
Alignment explanation
Indices: 14917--15020 Score: 154
Period size: 50 Copynumber: 2.1 Consensus size: 49
14907 TATTACCTTG
* *
14917 ACTTTGATTAATCCCTTTTTACTTAATTACTGACTTACTGATCACTATT
1 ACTTTGACTAATCCCTTTTTACTCAATTACTGACTTACTGATCACTATT
* * *
14966 AACTTTGACTAATCTCTTTTTACTCAATTACTGATTTACTGATTACTATT
1 -ACTTTGACTAATCCCTTTTTACTCAATTACTGACTTACTGATCACTATT
15016 ACTTT
1 ACTTT
15021 AACTCTGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 5 0.10
50 44 0.90
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (49 bp):
ACTTTGACTAATCCCTTTTTACTCAATTACTGACTTACTGATCACTATT
Found at i:17396 original size:32 final size:32
Alignment explanation
Indices: 17359--17420 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
17349 ATCTGCACCA
17359 AATTAATTAGT-ATTTGTACAAATTAATACAAT
1 AATTAA-TAGTAATTTGTACAAATTAATACAAT
*
17391 AATTAATATTAATTTGTACAAATTAATACA
1 AATTAATAGTAATTTGTACAAATTAATACA
17421 GTTTGTACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.40
Consensus pattern (32 bp):
AATTAATAGTAATTTGTACAAATTAATACAAT
Found at i:17416 original size:20 final size:19
Alignment explanation
Indices: 17391--17432 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17381 TTAATACAAT
*
17391 AATTAATATTAATTTGTACA
1 AATTAATA-CAATTTGTACA
*
17411 AATTAATACAGTTTGTACA
1 AATTAATACAATTTGTACA
17430 AAT
1 AAT
17433 ATATTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (19 bp):
AATTAATACAATTTGTACA
Found at i:19699 original size:51 final size:50
Alignment explanation
Indices: 19545--19699 Score: 156
Period size: 51 Copynumber: 3.1 Consensus size: 50
19535 AAATGTGACA
* *
19545 TTTTATTTACTAA--ACTTAAAAATTCAATCTTTTATTCAAACGTTAAATC
1 TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAA-GATAAATC
* * ** *
19594 -TTTATTTACTAGTTACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT-
1 TTTTATTTACCAATTACT-TAAAAATTCAATCTTTTATTCAAAGAT-AAATC
* * *
19644 TTTTATTTTCCAATTACTTAAAAATTCAATCTTTCATTTAAATGATAAATC
1 TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAA-GATAAATC
19695 TTTTA
1 TTTTA
19700 GCCATATACC
Statistics
Matches: 86, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
48 11 0.13
50 28 0.33
51 47 0.55
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.45
Consensus pattern (50 bp):
TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGATAAATC
Found at i:22099 original size:27 final size:27
Alignment explanation
Indices: 22039--22145 Score: 151
Period size: 27 Copynumber: 3.9 Consensus size: 27
22029 GTGATCTTAA
* *
22039 AAAAATGACTAAAATGCCCCCCTGAGTGC
1 AAAAATGACCAAAATG--CCCCTGGGTGC
22068 AAAAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
*
22095 GAAAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
* *
22122 AAAAATGACCAAAATACCCTTGGG
1 AAAAATGACCAAAATGCCCCTGGG
22146 CGACTCTAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
27 57 0.79
29 15 0.21
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGGGTGC
Found at i:31065 original size:63 final size:64
Alignment explanation
Indices: 30992--31155 Score: 165
Period size: 62 Copynumber: 2.6 Consensus size: 64
30982 CACATCATAC
* * * * *
30992 ACTGCTGAATAATATCATAAATTCCGAGTACAGAATTAA-ACACATAGTCTGAAAATAGCAT-CT
1 ACTGCCGAATAATACCATAAACTCCGAGTACAGAATTAATA-ACATAGTCTGAAAACACCATCCT
* * * * ** * *
31055 ACTGCCGAATAATACCATGAACTACAAGCATTGAA-TAATAACATAGTCTGGAAACACCGTCCT
1 ACTGCCGAATAATACCATAAACTCCGAGTACAGAATTAATAACATAGTCTGAAAACACCATCCT
*
31118 -CTGCCGAATAATACCATAAACTCCGAGTACATAATTAA
1 ACTGCCGAATAATACCATAAACTCCGAGTACAGAATTAA
31156 CTACTTTATT
Statistics
Matches: 78, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
62 46 0.59
63 32 0.41
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.24
Consensus pattern (64 bp):
ACTGCCGAATAATACCATAAACTCCGAGTACAGAATTAATAACATAGTCTGAAAACACCATCCT
Found at i:32270 original size:33 final size:33
Alignment explanation
Indices: 32233--32339 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
32223 CGCCAAGCGA
* *
32233 TGGCCGGTTG-TGGCCGGACATGT-CTATGTCACG
1 TGGCCGG-TGATGGCCGGACATCTCCGA-GTCACG
*
32266 TGGCCGGTGATGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGATGGCCGGACATCTCCGAGTCACG
* * * * * * *
32299 TGGCCGGAGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGATGGCCGGACATCTCCGAGTCACG
32332 TGGCCGGT
1 TGGCCGGT
32340 CACTCGCGCC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 2 0.03
33 58 0.94
34 2 0.03
ACGTcount: A:0.11, C:0.28, G:0.38, T:0.22
Consensus pattern (33 bp):
TGGCCGGTGATGGCCGGACATCTCCGAGTCACG
Done.