Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012035.1 Kokia drynarioides strain JFW-HI SEQ_127033, 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: 69781
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:219 original size:9 final size:10
Alignment explanation
Indices: 204--271 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 10
194 ACAAATTTCT
204 ATAATTTTTA
1 ATAATTTTTA
214 AT-ATTTTT-
1 ATAATTTTTA
*
222 ATATTTTTTTA
1 ATA-ATTTTTA
* *
233 TTAATATTTA
1 ATAATTTTTA
243 ATAATTTTT-
1 ATAATTTTTA
*
252 ATAACTTTTA
1 ATAATTTTTA
* *
262 TTGATTTTTA
1 ATAATTTTTA
272 TTTTTTATAT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
8 2 0.05
9 14 0.32
10 26 0.59
11 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:6383 original size:18 final size:18
Alignment explanation
Indices: 6357--6392 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6347 TTGTCAATTA
6357 GTGAATTTTTTTTTATCC
1 GTGAATTTTTTTTTATCC
*
6375 GTGATTTTTTTTTTATCC
1 GTGAATTTTTTTTTATCC
6393 TTTTCATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.64
Consensus pattern (18 bp):
GTGAATTTTTTTTTATCC
Found at i:7256 original size:2 final size:2
Alignment explanation
Indices: 7249--7285 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7239 AATGTTTTAT
7249 TA TA TA 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 TA TA TA T
7286 TAAAGGACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7857 original size:19 final size:18
Alignment explanation
Indices: 7822--7870 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
7812 AACATAATTT
**
7822 AAAATGAATATTTTAAAGA
1 AAAATGAATATAGTAAA-A
7841 AAAATGAATATAGTAAAA
1 AAAATGAATATAGTAAAA
7859 ATAAATGTAATA
1 A-AAATG-AATA
7871 AAAATATTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.08
19 20 0.77
20 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (18 bp):
AAAATGAATATAGTAAAA
Found at i:9940 original size:23 final size:23
Alignment explanation
Indices: 9914--9957 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
9904 AAAAATGTTA
*
9914 AAATAATAT-AAAAGAAAAAAATT
1 AAATAAT-TCAAAACAAAAAAATT
*
9937 AAATTATTCAAAACAAAAAAA
1 AAATAATTCAAAACAAAAAAA
9958 AATATGGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAATTCAAAACAAAAAAATT
Found at i:19709 original size:19 final size:20
Alignment explanation
Indices: 19682--19725 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
19672 TCATAAAATC
19682 TAAATCTTTAAAGCTTATTT
1 TAAATCTTTAAAGCTTATTT
19702 TAAA-CTTTAAAGCTTATTT
1 TAAATCTTTAAAGCTTATTT
19721 TAAAT
1 TAAAT
19726 ATTACCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.48
Consensus pattern (20 bp):
TAAATCTTTAAAGCTTATTT
Found at i:19939 original size:7 final size:7
Alignment explanation
Indices: 19906--19962 Score: 69
Period size: 7 Copynumber: 8.0 Consensus size: 7
19896 AATCATATAA
19906 CCAATAAC
1 CCAA-AAC
*
19914 CCTAAAC
1 CCAAAAC
* *
19921 CCACAAT
1 CCAAAAC
*
19928 TCAAAAC
1 CCAAAAC
19935 CCAAAAC
1 CCAAAAC
19942 CCAAAAC
1 CCAAAAC
19949 CCAAAAC
1 CCAAAAC
19956 CCAAAAC
1 CCAAAAC
19963 TTATAACCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
7 38 0.93
8 3 0.07
ACGTcount: A:0.53, C:0.40, G:0.00, T:0.07
Consensus pattern (7 bp):
CCAAAAC
Found at i:19970 original size:14 final size:13
Alignment explanation
Indices: 19929--19989 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
19919 ACCCACAATT
*
19929 CAAAACCCAAAACC
1 CAAAA-CCATAACC
*
19943 CAAAACCCAAAACC
1 CAAAA-CCATAACC
*
19957 CAAAACTTATAA-C
1 CAAAAC-CATAACC
*
19970 CATAACCATAACC
1 CAAAACCATAACC
19983 CAAAACC
1 CAAAACC
19990 TATGGCCTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.10
13 14 0.35
14 22 0.55
ACGTcount: A:0.54, C:0.38, G:0.00, T:0.08
Consensus pattern (13 bp):
CAAAACCATAACC
Found at i:20091 original size:21 final size:20
Alignment explanation
Indices: 20062--20146 Score: 73
Period size: 21 Copynumber: 4.1 Consensus size: 20
20052 CTAAGCTCTC
20062 AATCATAAACCTTAAACCCT
1 AATCATAAACCTTAAACCCT
* * **
20082 AATCACTAAATCTAAAACATAT
1 AATCA-TAAACCTTAAAC-CCT
* *
20104 AATCTTAAACCTTAAATCCT
1 AATCATAAACCTTAAACCCT
20124 AAAT-ATATAACCTTAAACCCT
1 -AATCATA-AACCTTAAACCCT
20145 AA
1 AA
20147 AATTTAAACC
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
20 10 0.20
21 34 0.69
22 5 0.10
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (20 bp):
AATCATAAACCTTAAACCCT
Found at i:20111 original size:35 final size:34
Alignment explanation
Indices: 20026--20127 Score: 91
Period size: 35 Copynumber: 2.9 Consensus size: 34
20016 CAAAAACCAT
* * * *
20026 AAACATATAACATTAAATCCTAAACACTAAGCTCTC
1 AAACATATAAC-TTAAACCCTAATCACTAA-ATCTA
*
20062 AATCATA-AACCTTAAACCCTAATCACTAAATCTA
1 AAACATATAA-CTTAAACCCTAATCACTAAATCTA
*
20096 AAACATATAATCTTAAACCTTAAATC-CTAAAT
1 AAACATATAA-CTTAAACCCT-AATCACTAAAT
20128 ATATAACCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
34 9 0.16
35 35 0.64
36 11 0.20
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.27
Consensus pattern (34 bp):
AAACATATAACTTAAACCCTAATCACTAAATCTA
Found at i:20119 original size:28 final size:28
Alignment explanation
Indices: 20087--20147 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
20077 ACCCTAATCA
*
20087 CTAAAT-CTAAAACATATAATCTTAAACC
1 CTAAATCCT-AAACATATAACCTTAAACC
* *
20115 TTAAATCCTAAATATATAACCTTAAACC
1 CTAAATCCTAAACATATAACCTTAAACC
20143 CTAAA
1 CTAAA
20148 ATTTAAACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (28 bp):
CTAAATCCTAAACATATAACCTTAAACC
Found at i:20147 original size:21 final size:21
Alignment explanation
Indices: 20109--20195 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 21
20099 CATATAATCT
*
20109 TAAACCTTAAATCCT-AAATA
1 TAAACCTTAAACCCTAAAATA
*
20129 TATAACCTTAAACCCTAAAATT
1 TA-AACCTTAAACCCTAAAATA
**
20151 TAAACCTTAAA-TATAAAATCA
1 TAAACCTTAAACCCTAAAAT-A
* *
20172 TAAACCCTAAACTCT-AAATA
1 TAAACCTTAAACCCTAAAATA
20192 TAAA
1 TAAA
20196 ATATTAAACT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
20 13 0.23
21 35 0.62
22 8 0.14
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAACCTTAAACCCTAAAATA
Found at i:20154 original size:35 final size:35
Alignment explanation
Indices: 20115--20217 Score: 97
Period size: 35 Copynumber: 2.9 Consensus size: 35
20105 ATCTTAAACC
*
20115 TTAAATCCTAAATATATAACCTTAAACCCTAAAAT
1 TTAAATCCTAAATATATAAACTTAAACCCTAAAAT
* *
20150 TTAAA-CCTTAAATATA-AAATCATAAACCCTAAACT
1 TTAAATCC-TAAATATATAAA-CTTAAACCCTAAAAT
* *
20185 CTAAAT-ATAAA-ATATTAAACTATAAACCCTAAA
1 TTAAATCCTAAATATA-TAAACT-TAAACCCTAAA
20218 CCATAAACAT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
33 3 0.05
34 9 0.16
35 44 0.79
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.29
Consensus pattern (35 bp):
TTAAATCCTAAATATATAAACTTAAACCCTAAAAT
Found at i:20175 original size:28 final size:28
Alignment explanation
Indices: 20151--20499 Score: 161
Period size: 28 Copynumber: 12.5 Consensus size: 28
20141 CCCTAAAATT
20151 TAAACCTTAAATATAAAATCATAAACCC
1 TAAACCTTAAATATAAAATCATAAACCC
**
20179 TAAA-CTCTAAATATAAAAT-ATTAAACTA
1 TAAACCT-TAAATATAAAATCA-TAAACCC
* *
20207 TAAACCCTAAACCAT-AAA-CATAAACCC
1 TAAACCTTAAA-TATAAAATCATAAACCC
*
20234 TAAACCTT-AA-AT---AT-A-AAACCT
1 TAAACCTTAAATATAAAATCATAAACCC
* * *
20255 TAAACCTTAAATATAAAACCTTAAACCT
1 TAAACCTTAAATATAAAATCATAAACCC
* * *
20283 TAAACTTTAAATATAAAACCTTAAACCC
1 TAAACCTTAAATATAAAATCATAAACCC
* ** * ** * * * *
20311 TACATATAAAACCTTAAACCTTAAATCC
1 TAAACCTTAAATATAAAATCATAAACCC
* *
20339 TAAACCTTAAA-ACAAAACCTTAAATATAAAACCC
1 TAAACCTTAAATATAAAA---T---CAT-AAACCC
*
20373 TAAACCTTAAATATAAAACCCA-AAACCC
1 TAAACCTTAAATATAAAA-TCATAAACCC
** *
20401 TATTTCC-TAAATATAAAATGC-TAAACCT
1 TA-AACCTTAAATATAAAAT-CATAAACCC
* * * *
20429 TCAACCCTAAATATAAAACCATAAAACC
1 TAAACCTTAAATATAAAATCATAAACCC
* * *
20457 TAAACCTTGAATATAAAACCATAAAACCA
1 TAAACCTTAAATATAAAATCAT-AAACCC
20486 TAAACCTTAAATAT
1 TAAACCTTAAATAT
20500 GAAACCTTAA
Statistics
Matches: 243, Mismatches: 51, Indels: 53
0.70 0.15 0.15
Matches are distributed among these distances:
21 13 0.05
22 4 0.02
23 2 0.01
24 2 0.01
26 3 0.01
27 21 0.09
28 153 0.63
29 22 0.09
30 1 0.00
33 1 0.00
34 16 0.07
35 5 0.02
ACGTcount: A:0.52, C:0.22, G:0.01, T:0.25
Consensus pattern (28 bp):
TAAACCTTAAATATAAAATCATAAACCC
Found at i:20176 original size:63 final size:63
Alignment explanation
Indices: 20025--20260 Score: 163
Period size: 63 Copynumber: 3.9 Consensus size: 63
20015 CCAAAAACCA
* * * * * * * *
20025 TAAACATATAACATTAAATCCTAAACACTAAGCTCTCAATCATA-AACCTTAAACCCTAATCAC
1 TAAACCTAAAACATAAAATCATAAACCCTAAACTCTAAAT-ATATAACCTTAAACCCTAATAAC
* * * * *
20088 TAAATCTAAAACATATAATCTTAAACCTTAAA-TCCTAAATATATAACCTTAAACCCTAA-AATT
1 TAAACCTAAAACATAAAATCATAAACCCTAAACT-CTAAATATATAACCTTAAACCCTAATAA-C
* * * **
20151 TAAACCTTAAATATAAAATCATAAACCCTAAACTCTAAATATAAAATATTAAA--CT-AT-A-
1 TAAACCTAAAACATAAAATCATAAACCCTAAACTCTAAATATATAACCTTAAACCCTAATAAC
* * *
20209 -AACCCTAAACCAT-AAA-CATAAACCCTAAAC-CTTAAATATAAAACCTTAAACC
1 TAAACCTAAAACATAAAATCATAAACCCTAAACTC-TAAATATATAACCTTAAACC
20261 TTAAATATAA
Statistics
Matches: 138, Mismatches: 27, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
54 1 0.01
55 30 0.22
56 3 0.02
57 9 0.07
60 2 0.01
61 2 0.01
62 5 0.04
63 85 0.62
64 1 0.01
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.27
Consensus pattern (63 bp):
TAAACCTAAAACATAAAATCATAAACCCTAAACTCTAAATATATAACCTTAAACCCTAATAAC
Found at i:20224 original size:21 final size:21
Alignment explanation
Indices: 20199--20293 Score: 115
Period size: 21 Copynumber: 4.6 Consensus size: 21
20189 ATATAAAATA
20199 TTAAACTATAAACCCTAAACC
1 TTAAACTATAAACCCTAAACC
*
20220 ATAAAC-ATAAACCCTAAACC
1 TTAAACTATAAACCCTAAACC
*
20240 TTAAA-TATAAAACCTTAAACC
1 TTAAACTAT-AAACCCTAAACC
*
20261 TTAAA-TATAAAACCTTAAACC
1 TTAAACTAT-AAACCCTAAACC
*
20282 TTAAACTTTAAA
1 TTAAACTATAAA
20294 TATAAAACCT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
20 20 0.30
21 45 0.67
22 2 0.03
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (21 bp):
TTAAACTATAAACCCTAAACC
Found at i:20259 original size:7 final size:7
Alignment explanation
Indices: 20207--20383 Score: 99
Period size: 7 Copynumber: 25.6 Consensus size: 7
20197 TATTAAACTA
*
20207 TAAACCC
1 TAAACCT
*
20214 TAAACCA
1 TAAACCT
*
20221 TAAA-CA
1 TAAACCT
*
20227 TAAACCC
1 TAAACCT
20234 TAAACCT
1 TAAACCT
**
20241 TAAATAT
1 TAAACCT
*
20248 AAAACCT
1 TAAACCT
20255 TAAACCT
1 TAAACCT
**
20262 TAAATAT
1 TAAACCT
*
20269 AAAACCT
1 TAAACCT
20276 TAAACCT
1 TAAACCT
*
20283 TAAACTT
1 TAAACCT
**
20290 TAAATAT
1 TAAACCT
*
20297 AAAACCT
1 TAAACCT
*
20304 TAAACCC
1 TAAACCT
* **
20311 TACATAT
1 TAAACCT
*
20318 AAAACCT
1 TAAACCT
20325 TAAACCT
1 TAAACCT
20332 TAAATCC-
1 TAAA-CCT
20339 TAAACCT
1 TAAACCT
*
20346 TAAAAC-
1 TAAACCT
*
20352 AAAACCT
1 TAAACCT
**
20359 TAAATAT
1 TAAACCT
* *
20366 AAAACCC
1 TAAACCT
20373 TAAACCT
1 TAAACCT
20380 TAAA
1 TAAA
20384 TATAAAACCC
Statistics
Matches: 122, Mismatches: 44, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
6 12 0.10
7 108 0.89
8 2 0.02
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACCT
Found at i:20301 original size:21 final size:21
Alignment explanation
Indices: 20277--20392 Score: 117
Period size: 21 Copynumber: 5.2 Consensus size: 21
20267 ATAAAACCTT
*
20277 AAACCTTAAACTTTAAATATA
1 AAACCTTAAACCTTAAATATA
* *
20298 AAACCTTAAACCCTACATATA
1 AAACCTTAAACCTTAAATATA
*
20319 AAACCTTAAACCTTAAATCCT-
1 AAACCTTAAACCTTAAAT-ATA
20340 AAACCTTAAAACAAAACCTTAAATATA
1 AAACCTT------AAACCTTAAATATA
*
20367 AAACCCTAAACCTTAAATATA
1 AAACCTTAAACCTTAAATATA
20388 AAACC
1 AAACC
20393 CAAAACCCTA
Statistics
Matches: 79, Mismatches: 8, Indels: 16
0.77 0.08 0.16
Matches are distributed among these distances:
21 60 0.76
22 1 0.01
26 1 0.01
27 17 0.22
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (21 bp):
AAACCTTAAACCTTAAATATA
Found at i:20426 original size:97 final size:97
Alignment explanation
Indices: 20256--20439 Score: 221
Period size: 97 Copynumber: 1.9 Consensus size: 97
20246 ATAAAACCTT
* * * * *
20256 AAACCTTAAATATAAAACCTTAAACCTTAAACTTTAAATATAAAACCTTAAACCCTACATATAAA
1 AAACCTTAAATATAAAACCCTAAACCTTAAACTATAAATACAAAACCCTAAACCCTAAATATAAA
*
20321 ACCTTAAACCTTAAATCCTAAACCTTAAAACA
66 ACCTTAAACCTTAAACCCTAAACCTTAAAACA
***
20353 AAACCTTAAATATAAAACCCTAAACCTTAAA-TATAAA-ACCCAAAACCCTATTTCCTAAATATA
1 AAACCTTAAATATAAAACCCTAAACCTTAAACTATAAATA--CAAAACCCTAAACCCTAAATATA
* *
20416 AAATGC-TAAACCTTCAACCCTAAA
64 AAA-CCTTAAACCTTAAACCCTAAA
20440 TATAAAACCA
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
95 1 0.01
96 5 0.07
97 66 0.90
98 1 0.01
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.26
Consensus pattern (97 bp):
AAACCTTAAATATAAAACCCTAAACCTTAAACTATAAATACAAAACCCTAAACCCTAAATATAAA
ACCTTAAACCTTAAACCCTAAACCTTAAAACA
Found at i:20459 original size:49 final size:48
Alignment explanation
Indices: 20227--20538 Score: 186
Period size: 49 Copynumber: 6.2 Consensus size: 48
20217 ACCATAAACA
* * *
20227 TAAACCCTAAACCTTAAATATAAAACCTTAAACCTTAAATATAAAACCT
1 TAAACCTTAAACCCTAAATATAAAACCTAAAACC-TAAATATAAAACCT
** * *
20276 TAAACCTTAAACTTTAAATATAAAACCTTAAACCCTACATATAAAACCT
1 TAAACCTTAAACCCTAAATATAAAACC-TAAAACCTAAATATAAAACCT
* *
20325 TAAACCTTAAATCCTAAACCT-TAAAA-C-AAAACCTTAAATATAAAACCC
1 TAAACCTTAAACCCTAAA--TATAAAACCTAAAACC-TAAATATAAAACCT
** * *** *
20373 TAAACCTTAAA-TATAAA-ACCCAAAACCCTATTTCCTAAATATAAAATGC-
1 TAAACCTTAAACCCTAAATA--TAAAA-CCTAAAACCTAAATATAAAA-CCT
*
20422 TAAACCTTCAACCCTAAATATAAAACCATAAAACCTAAACCTTGAATATAAAACCAT
1 TAAACCTTAAACCCTAAATATAAAACC-TAAAACCT--A-----AATATAAAACC-T
* * * * * * *
20479 AAAACCATAAACCTTAAATATGAAACCTTAAATCTTAAATATAAAACCA
1 TAAACCTTAAACCCTAAATATAAAACC-TAAAACCTAAATATAAAACCT
*
20528 TAAACCCTAAA
1 TAAACCTTAAA
20539 TATAAAACAA
Statistics
Matches: 203, Mismatches: 37, Indels: 46
0.71 0.13 0.16
Matches are distributed among these distances:
47 13 0.06
48 25 0.12
49 94 0.46
50 29 0.14
51 3 0.01
55 2 0.01
56 9 0.04
57 28 0.14
ACGTcount: A:0.51, C:0.23, G:0.01, T:0.25
Consensus pattern (48 bp):
TAAACCTTAAACCCTAAATATAAAACCTAAAACCTAAATATAAAACCT
Found at i:20561 original size:42 final size:42
Alignment explanation
Indices: 20477--20581 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
20467 ATATAAAACC
* * ** * **
20477 ATAAAACCATAAACCTTAAATATGAAACCTTAAATCTTAAAT
1 ATAAAACCATAAACCCTAAATATAAAACAATAAACCCCAAAT
20519 ATAAAACCATAAACCCTAAATATAAAACAATAAACCCCAAAT
1 ATAAAACCATAAACCCTAAATATAAAACAATAAACCCCAAAT
*
20561 ATAAAATCC-TAAACACTAAAT
1 ATAAAA-CCATAAACCCTAAAT
20582 CCTAAACCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 52 0.96
43 2 0.04
ACGTcount: A:0.56, C:0.20, G:0.01, T:0.23
Consensus pattern (42 bp):
ATAAAACCATAAACCCTAAATATAAAACAATAAACCCCAAAT
Found at i:20581 original size:21 final size:20
Alignment explanation
Indices: 20200--20581 Score: 108
Period size: 21 Copynumber: 18.2 Consensus size: 20
20190 TATAAAATAT
* *
20200 TAAACTATAAACCCTAAACCA
1 TAAA-TATAAAACCTAAACCC
* * *
20221 TAAACATAAACCCTAAACCT
1 TAAATATAAAACCTAAACCC
*
20241 TAAATATAAAACCTTAAACCT
1 TAAATATAAAACC-TAAACCC
20262 TAAATATAAAACCTTAAACCTTAAAC
1 TAAATATAAAACC-TAAACC-----C
20288 TTTAAATATAAAACCTTAAACCC
1 --TAAATATAAAACC-TAAACCC
* *
20311 TACATATAAAACCTTAAACCT
1 TAAATATAAAACC-TAAACCC
*
20332 TAAATCCT-AAACCTTAAAACAAAACC
1 TAAAT-ATAAAACC-T-AAAC----CC
*
20358 TTAAATATAAAACCCTAAACCT
1 -TAAATATAAAA-CCTAAACCC
*
20380 TAAATATAAAACCCAAAACCC
1 TAAATATAAAA-CCTAAACCC
* **
20401 T--AT-T---TCCTAAA-TA
1 TAAATATAAAACCTAAACCC
* *
20414 TAAA-ATGCTAAACCTTCAACCC
1 TAAATAT--AAAACC-TAAACCC
*
20436 TAAATATAAAACCATAAAACC
1 TAAATATAAAACC-TAAACCC
** ** ** *
20457 TAAACCTTGAATATAAAACC
1 TAAATATAAAACCTAAACCC
*
20477 -----ATAAAACCATAAACCT
1 TAAATATAAAACC-TAAACCC
* * *
20493 TAAATATGAAACCTTAAATCT
1 TAAATATAAAACC-TAAACCC
20514 TAAATATAAAACCATAAACCC
1 TAAATATAAAACC-TAAACCC
*
20535 TAAATATAAAACAATAAACCC
1 TAAATATAAAAC-CTAAACCC
* *
20556 CAAATATAAAATCCTAAACAC
1 TAAATATAAAA-CCTAAACCC
20577 TAAAT
1 TAAAT
20582 CCTAAACCTT
Statistics
Matches: 274, Mismatches: 51, Indels: 72
0.69 0.13 0.18
Matches are distributed among these distances:
13 1 0.00
14 5 0.02
15 5 0.02
16 5 0.02
18 1 0.00
19 2 0.01
20 34 0.12
21 170 0.62
22 11 0.04
23 3 0.01
26 6 0.02
27 9 0.03
28 22 0.08
ACGTcount: A:0.52, C:0.23, G:0.01, T:0.24
Consensus pattern (20 bp):
TAAATATAAAACCTAAACCC
Found at i:20595 original size:42 final size:42
Alignment explanation
Indices: 20477--20596 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
20467 ATATAAAACC
* * **
20477 ATAAAACCATAAAC-CTTAAATATGAAACCTTAAATCTTAAAT
1 ATAAAACCATAAACAC-TAAATATAAAACCTTAAACCCCAAAT
* **
20519 ATAAAACCATAAACCCTAAATATAAAACAATAAACCCCAAAT
1 ATAAAACCATAAACACTAAATATAAAACCTTAAACCCCAAAT
*
20561 ATAAAATCC-TAAACACTAAATCCT-AAACCTTAAACC
1 ATAAAA-CCATAAACACTAAAT-ATAAAACCTTAAACC
20597 ATAAAACCCC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.54, C:0.23, G:0.01, T:0.23
Consensus pattern (42 bp):
ATAAAACCATAAACACTAAATATAAAACCTTAAACCCCAAAT
Found at i:20624 original size:14 final size:14
Alignment explanation
Indices: 20568--20632 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
20558 AATATAAAAT
*
20568 CCTAAACAC-TAAAT
1 CCTAAAC-CTTAAAC
20582 CCTAAACCTTAAAC
1 CCTAAACCTTAAAC
* **
20596 CATAAAACCCCAAAC
1 CCT-AAACCTTAAAC
20611 CCTAAACCTTAAAC
1 CCTAAACCTTAAAC
*
20625 CCCAAACC
1 CCTAAACC
20633 AACACTTGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 1 0.02
14 29 0.71
15 11 0.27
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTAAACCTTAAAC
Found at i:23968 original size:117 final size:117
Alignment explanation
Indices: 23759--23986 Score: 411
Period size: 117 Copynumber: 1.9 Consensus size: 117
23749 CCACCTGGAC
* * *
23759 TCTCTCTGGGGGAAGCAAGGATAGGATAAAACCCTGCTTTTGTAATATTCTTCATCTTAGATGAC
1 TCTCTCAGGGGAAAGCAAGGATAGGATAAAACCCTGCTTTTGTAATATTCGTCATCTTAGATGAC
*
23824 TGTTATGATATTTGTTATTACCTGTCCAAAACACGAATAGGTTCGGATCAAA
66 TGTTATGATATTTGTTATTACCGGTCCAAAACACGAATAGGTTCGGATCAAA
*
23876 TCTCTCAGGGGAAAGCAAGGATAGGATAAAACCTTGCTTTTGTAATATTCGTCATCTTAGATGAC
1 TCTCTCAGGGGAAAGCAAGGATAGGATAAAACCCTGCTTTTGTAATATTCGTCATCTTAGATGAC
23941 TGTTATGATATTTGTTATTACCGGTCCAAAACACGAATAGGTTCGG
66 TGTTATGATATTTGTTATTACCGGTCCAAAACACGAATAGGTTCGG
23987 GTCGAATTCG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 106 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (117 bp):
TCTCTCAGGGGAAAGCAAGGATAGGATAAAACCCTGCTTTTGTAATATTCGTCATCTTAGATGAC
TGTTATGATATTTGTTATTACCGGTCCAAAACACGAATAGGTTCGGATCAAA
Found at i:26025 original size:17 final size:17
Alignment explanation
Indices: 26003--26040 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
25993 ATTCTTTAAA
26003 AAATTAAGTTTTGAAAC
1 AAATTAAGTTTTGAAAC
*
26020 AAATTAAGTTTTGAAAT
1 AAATTAAGTTTTGAAAC
26037 AAAT
1 AAAT
26041 GAACCTGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37
Consensus pattern (17 bp):
AAATTAAGTTTTGAAAC
Found at i:28125 original size:24 final size:26
Alignment explanation
Indices: 28098--28167 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
28088 AATTATACCA
28098 ATTAAG-AA-ATT-ATTGGTAAAAACC
1 ATTAAGCAAGATTAATT-GTAAAAACC
28122 ATTAAGCTAAGATTAATTGTAAAAACC
1 ATTAAGC-AAGATTAATTGTAAAAACC
28149 ATTAAGCTAAGATTAATTG
1 ATTAAGC-AAGATTAATTG
28168 CGACCATAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.14
26 2 0.05
27 31 0.74
28 3 0.07
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (26 bp):
ATTAAGCAAGATTAATTGTAAAAACC
Found at i:28143 original size:27 final size:27
Alignment explanation
Indices: 28113--28167 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
28103 GAAATTATTG
28113 GTAAAAACCATTAAGCTAAGATTAATT
1 GTAAAAACCATTAAGCTAAGATTAATT
28140 GTAAAAACCATTAAGCTAAGATTAATT
1 GTAAAAACCATTAAGCTAAGATTAATT
28167 G
1 G
28168 CGACCATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (27 bp):
GTAAAAACCATTAAGCTAAGATTAATT
Found at i:28742 original size:330 final size:330
Alignment explanation
Indices: 28140--28782 Score: 1097
Period size: 330 Copynumber: 1.9 Consensus size: 330
28130 AAGATTAATT
* *
28140 GTAAAAACCATTAAGCTAAGATTAATTGCGACCATAGAAATTAATCAACTCATGTTTGTCATTCT
1 GTAAAAACCATTAAGCTAAGATTAATTGCGACAATAGAAATTAATCAACTCATGTTTGTCATTCA
* * *
28205 TGCATAATTCATTTGCAACTTTTGTCGTTTTTACAATTTGGTCATTTTTAGTTGATAGTGAGTTT
66 TGCATAATTCATTTGCAACTTTTGTAGTTTTTACAAGTAGGTCATTTTTAGTTGATAGTGAGTTT
* * * * * *
28270 TCACCCTTATTTTTTGAATTGTCGTACTCTAGTGATTAGATAAATATCTATTTATACTTCACATT
131 TCACCCTTATTTTATGAACTGTCGTACTATAGTGAGTAGATAAATAGCTATTGATACTTCACATT
* * *
28335 GCATGTTCTTTTCTCCTGTTTAATTCGAATTTAGATCATACCTTCCTTAGATACGATCCTTGGAA
196 GCATGTTCTTTTCTCCTGTTTAATTCGAATGTAGATCATACCTCCCTTAGATACGATCCTCGGAA
* * *
28400 TACTTTTACATTTCGTTGTAATTTAAAATTGTATTACAATTTGACTTGTATACCAATTAAGAAAT
261 TACTTCTACATTTCGTTGTAATTTAAAACTATATTACAATTTGACTTGTATACCAATTAAGAAAT
28465 TATTG
326 TATTG
28470 GTAAAAACCATTAAGCTAAGATTAATTGCGACAATAGAAATTAATCAACTCATGTTTGTCATTCA
1 GTAAAAACCATTAAGCTAAGATTAATTGCGACAATAGAAATTAATCAACTCATGTTTGTCATTCA
* *
28535 TGCATAGTTTATTTGCAACTTTTGTAGTTTTTACAAGTAGGTCATTTTTAGTTGATAGTGAGTTT
66 TGCATAATTCATTTGCAACTTTTGTAGTTTTTACAAGTAGGTCATTTTTAGTTGATAGTGAGTTT
28600 TCACCCTTATTTTATGAACTGTCGTACTATAGTGAGTAGATAAATAGCTATTGATACTTCACATT
131 TCACCCTTATTTTATGAACTGTCGTACTATAGTGAGTAGATAAATAGCTATTGATACTTCACATT
* *
28665 GCATGTTCTTTTCTCCTGTTTAATTCGAGTGTAGATCATACCTCCCTTGGATACGATCCTCGGAA
196 GCATGTTCTTTTCTCCTGTTTAATTCGAATGTAGATCATACCTCCCTTAGATACGATCCTCGGAA
28730 TACTTCTACATTTCGTTGTAATTTAAAACTATATTACAATTTGACTTGTATAC
261 TACTTCTACATTTCGTTGTAATTTAAAACTATATTACAATTTGACTTGTATAC
28783 TTACCATACA
Statistics
Matches: 292, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
330 292 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.42
Consensus pattern (330 bp):
GTAAAAACCATTAAGCTAAGATTAATTGCGACAATAGAAATTAATCAACTCATGTTTGTCATTCA
TGCATAATTCATTTGCAACTTTTGTAGTTTTTACAAGTAGGTCATTTTTAGTTGATAGTGAGTTT
TCACCCTTATTTTATGAACTGTCGTACTATAGTGAGTAGATAAATAGCTATTGATACTTCACATT
GCATGTTCTTTTCTCCTGTTTAATTCGAATGTAGATCATACCTCCCTTAGATACGATCCTCGGAA
TACTTCTACATTTCGTTGTAATTTAAAACTATATTACAATTTGACTTGTATACCAATTAAGAAAT
TATTG
Found at i:29879 original size:12 final size:12
Alignment explanation
Indices: 29862--29909 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
29852 TATATGATAT
* *
29862 AAAAGAATAAAG
1 AAAAGAAAAAAA
29874 AAAAGAAAAAAA
1 AAAAGAAAAAAA
*
29886 AAAAGAAACAAA
1 AAAAGAAAAAAA
*
29898 AGAAGAACAAAA
1 AAAAGAA-AAAA
29910 CAGAAGCTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 27 0.90
13 3 0.10
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:29909 original size:21 final size:22
Alignment explanation
Indices: 29874--29914 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
29864 AAGAATAAAG
29874 AAAAGAAAAAAAAAA-AGAAAC
1 AAAAGAAAAAAAAAACAGAAAC
* *
29895 AAAAGAAGAACAAAACAGAA
1 AAAAGAAAAAAAAAACAGAA
29915 GCTCAAACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAAAAACAGAAAC
Found at i:34199 original size:12 final size:12
Alignment explanation
Indices: 34182--34229 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
34172 TATATGATAT
* *
34182 AAAAGAATAAAG
1 AAAAGAAAAAAA
34194 AAAAGAAAAAAA
1 AAAAGAAAAAAA
*
34206 AAAAGAAACAAA
1 AAAAGAAAAAAA
*
34218 AGAAGAACAAAA
1 AAAAGAA-AAAA
34230 CAGAAGCTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 27 0.90
13 3 0.10
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:34229 original size:21 final size:22
Alignment explanation
Indices: 34194--34234 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
34184 AAGAATAAAG
34194 AAAAGAAAAAAAAAA-AGAAAC
1 AAAAGAAAAAAAAAACAGAAAC
* *
34215 AAAAGAAGAACAAAACAGAA
1 AAAAGAAAAAAAAAACAGAA
34235 GCTCAAACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAAAAACAGAAAC
Found at i:37914 original size:19 final size:18
Alignment explanation
Indices: 37890--37925 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
37880 TTTTTTTTTA
*
37890 ATTTTTAATTTTATTTAAT
1 ATTTTTAAATTT-TTTAAT
37909 ATTTTTAAATTTTTTAA
1 ATTTTTAAATTTTTTAA
37926 CAATGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTAAATTTTTTAAT
Found at i:43051 original size:26 final size:26
Alignment explanation
Indices: 42982--43052 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 26
42972 ATTCCCATCT
*
42982 ATATT-ATTTTTTA-AT-TTTTTAAA
1 ATATTAATATTTTATATATTTTTAAA
* *
43005 ATATTAATATTATAT-TA-TTTTAAC
1 ATATTAATATTTTATATATTTTTAAA
43029 AT-TTAATAATTTTATATATTTTTA
1 ATATTAAT-ATTTTATATATTTTTA
43053 TTTATTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
23 10 0.26
24 21 0.55
25 2 0.05
26 5 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
ATATTAATATTTTATATATTTTTAAA
Found at i:44188 original size:27 final size:26
Alignment explanation
Indices: 44151--44213 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
44141 AAATATCGAG
*
44151 ATTTAAGGTTT-GAGTTCGAAATTCAAA
1 ATTTAA-GTTTGGA-TTCAAAATTCAAA
44178 ATTTAGAGTTTGGATTCAAAATTCAAA
1 ATTTA-AGTTTGGATTCAAAATTCAAA
*
44205 GTTTAAGTT
1 ATTTAAGTT
44214 CAGCGTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.12
27 25 0.78
28 3 0.09
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (26 bp):
ATTTAAGTTTGGATTCAAAATTCAAA
Found at i:44207 original size:20 final size:20
Alignment explanation
Indices: 44171--44208 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44161 TGAGTTCGAA
* *
44171 ATTCAAAATTTAGAGTTTGG
1 ATTCAAAATTCAAAGTTTGG
44191 ATTCAAAATTCAAAGTTT
1 ATTCAAAATTCAAAGTTT
44209 AAGTTCAGCG
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:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (20 bp):
ATTCAAAATTCAAAGTTTGG
Found at i:44299 original size:14 final size:14
Alignment explanation
Indices: 44282--44326 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
44272 TGGGATTATT
44282 GTTTTGGATTTAAG
1 GTTTTGGATTTAAG
* * *
44296 GTTTGGGATTTTAT
1 GTTTTGGATTTAAG
44310 GTTTTGGATTTAAG
1 GTTTTGGATTTAAG
44324 GTT
1 GTT
44327 CAAGGTTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (14 bp):
GTTTTGGATTTAAG
Found at i:44301 original size:27 final size:28
Alignment explanation
Indices: 44266--44326 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
44256 TCAAGGTTTA
*
44266 AAGGGTTGGGATTAT-TGTTTTGGATTT
1 AAGGTTTGGGATTATATGTTTTGGATTT
*
44293 AAGGTTTGGGATTTTATGTTTTGGATTT
1 AAGGTTTGGGATTATATGTTTTGGATTT
44321 AAGGTT
1 AAGGTT
44327 CAAGGTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (28 bp):
AAGGTTTGGGATTATATGTTTTGGATTT
Found at i:44678 original size:6 final size:6
Alignment explanation
Indices: 44654--44761 Score: 91
Period size: 6 Copynumber: 18.7 Consensus size: 6
44644 GATTTATTTC
* * * **
44654 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * *
44701 TAAATT T-ATTT TAAATT TAAATT T-AGTT TAAATT TGAAA-- TAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT
*
44746 TAAACT TAAATT TAAA
1 TAAATT TAAATT TAAA
44762 ATCAATTACA
Statistics
Matches: 79, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
4 2 0.03
5 13 0.16
6 61 0.77
7 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:44698 original size:18 final size:17
Alignment explanation
Indices: 44675--44759 Score: 109
Period size: 17 Copynumber: 4.9 Consensus size: 17
44665 TTACTTTAAA
*
44675 TTTAAATTTAAATTCATT
1 TTTAAATTTAAATTTA-T
44693 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
44710 TTTAAATTTAAATTTAG
1 TTTAAATTTAAATTTAT
*
44727 TTTAAATTTGAAA-TAAT
1 TTTAAATTT-AAATTTAT
*
44744 TTTAAACTTAAATTTA
1 TTTAAATTTAAATTTA
44760 AAATCAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
16 3 0.05
17 38 0.64
18 18 0.31
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:44714 original size:41 final size:41
Alignment explanation
Indices: 44640--44725 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
44630 TTAAATGTGT
* *
44640 TTTAGATTTATTTCTAAAATTAAATTTACTTTAAATTTAAA
1 TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
* * *
44681 TTTAAATTCATTTTTAAATTTAAATTTATTTTAAATTTAAA
1 TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
44722 TTTA
1 TTTA
44726 GTTTAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (41 bp):
TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
Found at i:44746 original size:34 final size:35
Alignment explanation
Indices: 44659--44759 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 35
44649 ATTTCTAAAA
** * * *
44659 TTAAATTTACTTTAAATTTAAATTTAAATTCATTT
1 TTAAATTTAAATTAATTTTAAATTTAAATTTATGT
*
44694 TTAAATTTAAATTTATTTTAAATTTAAATTTA-GT
1 TTAAATTTAAATTAATTTTAAATTTAAATTTATGT
*
44728 TTAAATTTGAAA-TAATTTTAAACTTAAATTTA
1 TTAAATTT-AAATTAATTTTAAATTTAAATTTA
44760 AAATCAATTA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
34 27 0.47
35 30 0.53
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (35 bp):
TTAAATTTAAATTAATTTTAAATTTAAATTTATGT
Found at i:45480 original size:18 final size:18
Alignment explanation
Indices: 45459--45498 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
45449 TCAGTATTAA
* *
45459 TAATAGTCATAATGACAT
1 TAATAGTAATAATAACAT
*
45477 TAATGGTAATAATAACAT
1 TAATAGTAATAATAACAT
45495 TAAT
1 TAAT
45499 TAATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (18 bp):
TAATAGTAATAATAACAT
Found at i:46769 original size:29 final size:29
Alignment explanation
Indices: 46735--47030 Score: 164
Period size: 29 Copynumber: 10.2 Consensus size: 29
46725 TAAAAATTAT
46735 ATTTTTACCCTCGAACTTTCCAAAATTCC
1 ATTTTTACCCTCGAACTTTCCAAAATTCC
* * ** **
46764 ATTTTTGACCCT-AAATTTTTTGAAAATTAT
1 ATTTTT-ACCCTCGAA-CTTTCCAAAATTCC
*
46794 ATTTTTACCCTCGAACTTCCCAAAATTCC
1 ATTTTTACCCTCGAACTTTCCAAAATTCC
* * *
46823 ATTTTTAACCCT-AAACTTTCTAAAAATTAC
1 ATTTTT-ACCCTCGAACTTTC-CAAAATTCC
* *
46853 ATTTTTACTCTCGAACTTCCCAAAATTCC
1 ATTTTTACCCTCGAACTTTCCAAAATTCC
* * *
46882 ATTTTTGA-CATCG-ATTTTCCCAAAAATTAC
1 ATTTTT-ACCCTCGAACTTT-CC-AAAATTCC
* * *
46912 ATTTTTACCC-CTAAATTTTCAAAAATTCC
1 ATTTTTACCCTC-GAACTTTCCAAAATTCC
* * *
46941 ATTTTAACCC-CAAAAC-TTCCAAAAATTAC
1 ATTTTTACCCTC-GAACTTTCC-AAAATTCC
* ** *
46970 A-TTTTACAC-CGAACTTTAAAAAAATCC
1 ATTTTTACCCTCGAACTTTCCAAAATTCC
**
46997 ATTTTTGA-CCTCGAA-AGTCCAAAATTACC
1 ATTTTT-ACCCTCGAACTTTCCAAAATT-CC
47026 ATTTT
1 ATTTT
47031 GCCCCCGGGT
Statistics
Matches: 200, Mismatches: 49, Indels: 36
0.70 0.17 0.13
Matches are distributed among these distances:
27 10 0.05
28 26 0.13
29 97 0.49
30 62 0.31
31 5 0.03
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTTCCAAAATTCC
Found at i:46793 original size:59 final size:59
Alignment explanation
Indices: 46632--47006 Score: 304
Period size: 59 Copynumber: 6.4 Consensus size: 59
46622 TCCTTAAACT
* * * *
46632 TTTCCAAAATT--ATATTTTAACCCCTAAACTTT-TACAAAATTATATTTTAACCCCCAAAC
1 TTTCCAAAATTCCAT-TTTTGA-CCCTAAACTTTCTA-AAAATTATATTTTTACCCTCGAAC
* * *
46691 TTCTCAAAAATT--ATATTTTGATCCCCAAACTCTCTAAAAATTATATTTTTACCCTCGAAC
1 TT-TCCAAAATTCCAT-TTTTGA-CCCTAAACTTTCTAAAAATTATATTTTTACCCTCGAAC
* * *
46751 TTTCCAAAATTCCATTTTTGACCCTAAATTTTTTGAAAATTATATTTTTACCCTCGAAC
1 TTTCCAAAATTCCATTTTTGACCCTAAACTTTCTAAAAATTATATTTTTACCCTCGAAC
* * * *
46810 TTCCCAAAATTCCATTTTTAACCCTAAACTTTCTAAAAATTACATTTTTACTCTCGAAC
1 TTTCCAAAATTCCATTTTTGACCCTAAACTTTCTAAAAATTATATTTTTACCCTCGAAC
* * ** * * * * *
46869 TTCCCAAAATTCCATTTTTGA-CATCGATTTTCCCAAAAATTACATTTTTACCC-CTAAAT
1 TTTCCAAAATTCCATTTTTGACCCTAAACTTT-CTAAAAATTATATTTTTACCCTC-GAAC
* * * * * *
46928 TTTCAAAAATTCCA-TTTTAACCCCAAAAC-TTCCAAAAATTACA-TTTTACAC-CGAAC
1 TTTCCAAAATTCCATTTTTGA-CCCTAAACTTTCTAAAAATTATATTTTTACCCTCGAAC
** *
46984 TTTAAAAAAATCCATTTTTGACC
1 TTTCCAAAATTCCATTTTTGACC
47007 TCGAAAGTCC
Statistics
Matches: 263, Mismatches: 44, Indels: 21
0.80 0.13 0.06
Matches are distributed among these distances:
56 16 0.06
57 13 0.05
58 24 0.09
59 150 0.57
60 56 0.21
61 4 0.02
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (59 bp):
TTTCCAAAATTCCATTTTTGACCCTAAACTTTCTAAAAATTATATTTTTACCCTCGAAC
Found at i:46849 original size:30 final size:30
Alignment explanation
Indices: 46637--46974 Score: 164
Period size: 30 Copynumber: 11.4 Consensus size: 30
46627 AAACTTTTCC
*
46637 AAAATTATA-TTTTAACCCCTAAACTTT-TA
1 AAAATTACATTTTTAA-CCCTAAACTTTCTA
* *
46666 CAAAATTATA-TTTTAACCCCCAAAC-TTCTCA
1 -AAAATTACATTTTTAA-CCCTAAACTTTCT-A
* * * * *
46697 AAAATTATATTTTGATCCCCAAACTCTCTA
1 AAAATTACATTTTTAACCCTAAACTTTCTA
* * *
46727 AAAATTATATTTTT-ACCCTCGAACTTTC-C
1 AAAATTACATTTTTAACCCT-AAACTTTCTA
* * * * *
46756 AAAATTCCATTTTTGACCCTAAATTTTTTG
1 AAAATTACATTTTTAACCCTAAACTTTCTA
* * **
46786 AAAATTATATTTTT-ACCCTCGAAC-TTCCC
1 AAAATTACATTTTTAACCCT-AAACTTTCTA
*
46815 AAAATTCCATTTTTAACCCTAAACTTTCTA
1 AAAATTACATTTTTAACCCTAAACTTTCTA
* * **
46845 AAAATTACATTTTT-ACTCTCGAAC-TTCCC
1 AAAATTACATTTTTAACCCT-AAACTTTCTA
* * * ** * *
46874 AAAATTCCATTTTTGA-CATCGATTTTCCCA
1 AAAATTACATTTTTAACCCTAAACTTT-CTA
* *
46904 AAAATTACATTTTTACCCCTAAATTTTC-A
1 AAAATTACATTTTTAACCCTAAACTTTCTA
* * *
46933 AAAATTCCA-TTTTAACCCCAAAAC-TTCCA
1 AAAATTACATTTTTAA-CCCTAAACTTTCTA
46962 AAAATTACATTTT
1 AAAATTACATTTT
46975 ACACCGAACT
Statistics
Matches: 239, Mismatches: 51, Indels: 36
0.73 0.16 0.11
Matches are distributed among these distances:
28 9 0.04
29 91 0.38
30 124 0.52
31 15 0.06
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTTAACCCTAAACTTTCTA
Found at i:67569 original size:21 final size:20
Alignment explanation
Indices: 67538--67586 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
67528 AATAATAAAT
*
67538 AAAATT-AAAAAAGT-TTTAA
1 AAAATTAAAAAAACTATTT-A
67557 AAAATTAATAAAAACTATTTA
1 AAAATTAA-AAAAACTATTTA
67578 AAAATTAAA
1 AAAATTAAA
67587 GTCCAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 15 0.58
22 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATTAAAAAAACTATTTA
Done.