Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003512.1 Kokia drynarioides strain JFW-HI SEQ_116348, 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: 158074
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1364 original size:23 final size:23
Alignment explanation
Indices: 1291--1372 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
1281 ACATTGTATG
* *
1291 TGAACATGTTCAATTATATGTTTA
1 TGAACATGTTCGATTA-ATGTTAA
* **
1315 TGAACATGTTCGTTTAATGTTCG
1 TGAACATGTTCGATTAATGTTAA
1338 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT-AA
*
1361 TGAATATGTTCG
1 TGAACATGTTCG
1373 TGAACATTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.65
24 14 0.29
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.41
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTAA
Found at i:2914 original size:23 final size:21
Alignment explanation
Indices: 2888--2929 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
2878 CTATATTTAC
2888 AAAATAAATATTTTTGAATATGA
1 AAAAT-AAT-TTTTTGAATATGA
*
2911 AAAATACTTTTTTGAATAT
1 AAAATAATTTTTTGAATAT
2930 ATGTGATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (21 bp):
AAAATAATTTTTTGAATATGA
Found at i:13230 original size:17 final size:16
Alignment explanation
Indices: 13199--13254 Score: 85
Period size: 17 Copynumber: 3.4 Consensus size: 16
13189 TTGGAAATTG
13199 AATTTATTTAAATTTA
1 AATTTATTTAAATTTA
13215 AATTTATTTGAAATTTA
1 AATTTATTT-AAATTTA
*
13232 AATTTATTATAAAATTA
1 AATTTATT-TAAATTTA
13249 AATTTA
1 AATTTA
13255 GAAAGTCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
16 9 0.24
17 27 0.73
18 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATTTATTTAAATTTA
Found at i:13274 original size:13 final size:13
Alignment explanation
Indices: 13256--13307 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 13
13246 TTAAATTTAG
13256 AAAGTCCAATTAA
1 AAAGTCCAATTAA
13269 AAAGTCCAA--AA
1 AAAGTCCAATTAA
13280 CAAAGTCCAATTACA
1 -AAAGTCCAATTA-A
*
13295 AATAGCCCAATTA
1 AA-AGTCCAATTA
13308 CAGATGGCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 2 0.06
12 9 0.27
13 9 0.27
14 3 0.09
15 10 0.30
ACGTcount: A:0.52, C:0.21, G:0.08, T:0.19
Consensus pattern (13 bp):
AAAGTCCAATTAA
Found at i:13306 original size:15 final size:15
Alignment explanation
Indices: 13286--13356 Score: 99
Period size: 15 Copynumber: 4.7 Consensus size: 15
13276 AAAACAAAGT
*
13286 CCAATTACAAATAGC
1 CCAATTACAAATGGC
*
13301 CCAATTACAGATGGC
1 CCAATTACAAATGGC
*
13316 CCAATTACAGATGGC
1 CCAATTACAAATGGC
13331 CCGAA-TACAAATGGC
1 CC-AATTACAAATGGC
13346 CCAATTACAAA
1 CCAATTACAAA
13357 CTACCCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.04
15 47 0.92
16 2 0.04
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.18
Consensus pattern (15 bp):
CCAATTACAAATGGC
Found at i:13320 original size:30 final size:29
Alignment explanation
Indices: 13286--13364 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
13276 AAAACAAAGT
*
13286 CCAATTACAAATAGCCCAATTACAGATGGC
1 CCAATTACAAATAGCCCAA-TACAAATGGC
* *
13316 CCAATTACAGATGGCCCGAATACAAATGGC
1 CCAATTACAAATAGCCC-AATACAAATGGC
13346 CCAATTACAAACTA-CCCAA
1 CCAATTACAAA-TAGCCCAA
13365 AAGCCCAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 2 0.05
30 37 0.88
31 3 0.07
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.18
Consensus pattern (29 bp):
CCAATTACAAATAGCCCAATACAAATGGC
Found at i:13990 original size:7 final size:7
Alignment explanation
Indices: 13978--14007 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
13968 TATTAATAAT
13978 ATTATTA
1 ATTATTA
13985 ATTATTA
1 ATTATTA
13992 ATTATTA
1 ATTATTA
*
13999 ATTAATA
1 ATTATTA
14006 AT
1 AT
14008 AATAAACCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
ATTATTA
Found at i:13997 original size:14 final size:14
Alignment explanation
Indices: 13967--14007 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
13957 ATGTTTTGAT
13967 TTATTAA-TAAT-A
1 TTATTAATTAATAA
*
13979 TTATTAATTATTAA
1 TTATTAATTAATAA
13993 TTATTAATTAATAA
1 TTATTAATTAATAA
14007 T
1 T
14008 AATAAACCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 7 0.28
13 3 0.12
14 15 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATTAATTAATAA
Found at i:15218 original size:59 final size:59
Alignment explanation
Indices: 15150--15675 Score: 666
Period size: 59 Copynumber: 8.9 Consensus size: 59
15140 GGAGGTCCTT
*
15150 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTT
1 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* * **
15209 AAACTTTCCAAAAATTACCATTTTACACCCGAACTCCCAAAAATCCCATTTTAAACCTC
1 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* * * * * * *
15268 GAACCTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCC
1 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* * *
15327 GAACTTTCC-AAATTTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTT
1 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* * *
15385 AAACTTTCCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCTC
1 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* * * **
15444 GAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACC-C
1 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
* *
15502 TAAACTTTCCAAAAATTTCCATTTTACCCCCTGAACTTCCACAAATCCCATTTTTGACCCTC
1 -AAACTTTCCAAAAATTACCATTTTACCCCC-GAACTTCCAAAAATCCCATTTTTGA-CCTC
* * * * * *
15564 GAACCTT-CTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCTTTTTTGATCC-G
1 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTC
* * * *
15622 AACCTTT-CGAAAATTACCATTTTACCCTCGAACTTCCAAAACTCCCATTTTTGA
1 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
15676 TTCCGAACCT
Statistics
Matches: 400, Mismatches: 62, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
58 98 0.25
59 251 0.63
60 43 0.11
61 7 0.02
62 1 0.00
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC
Found at i:15458 original size:176 final size:176
Alignment explanation
Indices: 15151--15708 Score: 795
Period size: 176 Copynumber: 3.2 Consensus size: 176
15141 GAGGTCCTTA
15151 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTTAAACTTT
1 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTTAAACTTT
*
15216 CCAAAAATTACCATTTTACACCCGAACTCCCAAAAATCCCATTTTAAACCTCGAACCTTCTAAAA
66 CCAAAAATTACCATTTTAC-CCCGAACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAA
*
15281 ATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCG
130 ATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
*
15328 AACTTTCC-AAATTTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTTAAACTTT
1 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTTAAACTTT
15392 CCAAAAATTACCATTTTACCCTCGAACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAA
66 CCAAAAATTACCATTTTACCC-CGAACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAA
**
15457 ATTACCATTTTACCC-CTAAACTTCCAAAAATCCCATTTTTGACCCTA
130 ATTACCATTTTACCCTC-AAACTTCCAAAAATCCCATTTTTGACCCCG
* * ** *
15504 AACTTTCCAAAAATTTCCATTTTACCCCCTGAACTTCCACAAATCCCATTTTTGACCCTCGAACC
1 AACTTTCCAAAAATTACCATTTTACCCCC-GAACTTCCAAAAATCCCATTTTTGA-CCTTAAACT
* * * * * * *
15569 TT-CTAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCTTTTTTGATC-CGAACCTT-TCG
64 TTCCAAAAATTACCATTTTA-CCCCGAACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCT-A
* * **
15631 AAAATTACCATTTTACCCTCGAACTTCCAAAACTCCCATTTTTGATTCCG
127 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
15681 AACCTTCC-AAAACTACCATTTTGCCCCC
1 AACTTTCCAAAAATTACCATTTTACCCCC
15709 CGTGCATCCA
Statistics
Matches: 345, Mismatches: 28, Indels: 17
0.88 0.07 0.04
Matches are distributed among these distances:
175 3 0.01
176 184 0.53
177 83 0.24
178 64 0.19
179 11 0.03
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.32
Consensus pattern (176 bp):
AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTTAAACTTT
CCAAAAATTACCATTTTACCCCGAACTCCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAAAA
TTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:15690 original size:30 final size:28
Alignment explanation
Indices: 15591--15702 Score: 86
Period size: 30 Copynumber: 3.9 Consensus size: 28
15581 CATTTTACCC
* *
15591 CCGAACTTCCAAAAAT-CTCTTTTTTGAT
1 CCGAACTTCCAAAACTAC-CATTTTTGAT
* * *
15619 CCGAACCTTTCGAAAATTACCA-TTTT-ACC
1 CCGAA-C-TTCCAAAACTACCATTTTTGA-T
*
15648 CTCGAACTTCCAAAACTCCCATTTTTGATT
1 C-CGAACTTCCAAAACTACCATTTTTGA-T
15678 CCGAACCTTCCAAAACTACCATTTT
1 CCGAA-CTTCCAAAACTACCATTTT
15703 GCCCCCCGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
28 17 0.26
29 15 0.23
30 33 0.50
31 1 0.02
ACGTcount: A:0.29, C:0.30, G:0.06, T:0.34
Consensus pattern (28 bp):
CCGAACTTCCAAAACTACCATTTTTGAT
Found at i:15703 original size:29 final size:28
Alignment explanation
Indices: 15612--15703 Score: 89
Period size: 30 Copynumber: 3.2 Consensus size: 28
15602 AAAATCTCTT
* *
15612 TTTTGATCCGAACCTTTCGAAAATTACCA
1 TTTTGATCCGAACC-TTCCAAAACTACCA
* *
15641 TTTT-ACCCTCGAA-CTTCCAAAACTCCCA
1 TTTTGA-TC-CGAACCTTCCAAAACTACCA
15669 TTTTTGATTCCGAACCTTCCAAAACTACCA
1 -TTTTGA-TCCGAACCTTCCAAAACTACCA
15699 TTTTG
1 TTTTG
15704 CCCCCCGTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
28 12 0.24
29 19 0.37
30 20 0.39
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.35
Consensus pattern (28 bp):
TTTTGATCCGAACCTTCCAAAACTACCA
Found at i:17800 original size:11 final size:12
Alignment explanation
Indices: 17774--17802 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17764 AACATGGCAT
17774 TCATGTGGATTG
1 TCATGTGGATTG
17786 TCATGTGGA-TG
1 TCATGTGGATTG
17797 TCATGT
1 TCATGT
17803 TAACAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.17, C:0.10, G:0.31, T:0.41
Consensus pattern (12 bp):
TCATGTGGATTG
Found at i:17852 original size:30 final size:31
Alignment explanation
Indices: 17816--17873 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
17806 CAATTAATTA
*
17816 ATTTTTT-TAAAATTTAAAATTAAAAAATAT
1 ATTTTTTAAAAAATTTAAAATTAAAAAATAT
*
17846 ATTTTTTAAAAAATTTAAAATTATAAAA
1 ATTTTTTAAAAAATTTAAAATTAAAAAA
17874 GTTTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
ATTTTTTAAAAAATTTAAAATTAAAAAATAT
Found at i:17879 original size:29 final size:30
Alignment explanation
Indices: 17816--17884 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
17806 CAATTAATTA
17816 ATTTTTTT--AAAATTTAAAATTAAAAAAT
1 ATTTTTTTAAAAAATTTAAAATTAAAAAAT
*
17844 ATATTTTTTAAAAAATTTAAAATTATAAAA-
1 AT-TTTTTTAAAAAATTTAAAATTAAAAAAT
*
17874 GTTTTTTTAAA
1 ATTTTTTTAAA
17885 TTTTTTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 2 0.06
29 15 0.42
30 1 0.03
31 18 0.50
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
ATTTTTTTAAAAAATTTAAAATTAAAAAAT
Found at i:20974 original size:79 final size:79
Alignment explanation
Indices: 20843--21000 Score: 262
Period size: 79 Copynumber: 2.0 Consensus size: 79
20833 GAAGAGGAAG
*
20843 AAATCTCACGGTTCAGGTGAAGGAAATGAAGGGAGTCTTGTACGTGTTGTATGAAGAAAGTTGAT
1 AAATCTCACGATTCAGGTGAAGGAAATGAAGGGAGTCTTGTACGTGTTGTATGAAGAAAGTTGAT
*
20908 GGAGGGTACAGCCC
66 AGAGGGTACAGCCC
* * *
20922 AAATCTCGCGATTCAGGTGAAGGAAATGAGGGGAGTCTTGTACTTGTTGTATGAAGAAAGTTGAT
1 AAATCTCACGATTCAGGTGAAGGAAATGAAGGGAGTCTTGTACGTGTTGTATGAAGAAAGTTGAT
*
20987 AGAGGGTATAGCCC
66 AGAGGGTACAGCCC
21001 CTTCAAAGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.25
Consensus pattern (79 bp):
AAATCTCACGATTCAGGTGAAGGAAATGAAGGGAGTCTTGTACGTGTTGTATGAAGAAAGTTGAT
AGAGGGTACAGCCC
Found at i:25379 original size:18 final size:20
Alignment explanation
Indices: 25358--25396 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
25348 CATTCCAAAC
25358 AACAACACAA-AAAA-TAAA
1 AACAACACAACAAAAGTAAA
25376 AACAACACAACAAAAGTAAA
1 AACAACACAACAAAAGTAAA
25396 A
1 A
25397 TAAACGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.74, C:0.18, G:0.03, T:0.05
Consensus pattern (20 bp):
AACAACACAACAAAAGTAAA
Found at i:46795 original size:9 final size:10
Alignment explanation
Indices: 46781--46833 Score: 60
Period size: 9 Copynumber: 5.5 Consensus size: 10
46771 TTTGCATTGC
46781 CTTCCTT-TT
1 CTTCCTTCTT
46790 CTTCCTTTCTTT
1 CTTCC-TTC-TT
46802 CTT-CTTCTT
1 CTTCCTTCTT
46811 -TTCCTTCTT
1 CTTCCTTCTT
46820 CTT-CTTCTT
1 CTTCCTTCTT
46829 CTTCC
1 CTTCC
46834 ACTTTTTCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
8 2 0.05
9 22 0.58
10 8 0.21
11 1 0.03
12 5 0.13
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (10 bp):
CTTCCTTCTT
Found at i:46808 original size:3 final size:3
Alignment explanation
Indices: 46800--46832 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
46790 CTTCCTTTCT
46800 TTC TTC TTC TT- TTCC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC
46833 CACTTTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:46824 original size:15 final size:15
Alignment explanation
Indices: 46782--46825 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
46772 TTGCATTGCC
*
46782 TTCCTT-TTCTTCCT
1 TTCCTTCTTCTTCTT
*
46796 TTCTTTCTTCTTCTT
1 TTCCTTCTTCTTCTT
46811 TTCCTTCTTCTTCTT
1 TTCCTTCTTCTTCTT
46826 CTTCTTCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TTCCTTCTTCTTCTT
Found at i:62715 original size:455 final size:455
Alignment explanation
Indices: 61864--62773 Score: 1766
Period size: 455 Copynumber: 2.0 Consensus size: 455
61854 GAAATCATTC
61864 TTAAAAGTGAGACTCAACTGAATGAAGTGGTTACAGATGCTACAGTTAAGGAAGATAATTTAGAT
1 TTAAAAGTGAGACTCAACTGAATGAAGTGGTTACAGATGCTACAGTTAAGGAAGATAATTTAGAT
61929 CTCAACAATGGAAAGATGTCAGAACAATCTAAAAAGCAAACTATAGTTGAAGAGGTTAAACAAAA
66 CTCAACAATGGAAAGATGTCAGAACAATCTAAAAAGCAAACTATAGTTGAAGAGGTTAAACAAAA
61994 TATTGTGGAGACAGAATCAGATCATTTTGTCGCCACAAATGCTACAGCAAAACTGCCTCAGAAAC
131 TATTGTGGAGACAGAATCAGATCATTTTGTCGCCACAAATGCTACAGCAAAACTGCCTCAGAAAC
*
62059 GTGAAGATACATTTTCAAAGAAGAAAAGATTGGGAGAAGTTGAAGCAATCGCACTTACTGAAGGA
196 GTGAAGATACATTGTCAAAGAAGAAAAGATTGGGAGAAGTTGAAGCAATCGCACTTACTGAAGGA
62124 TGCACTATCATGATAATTAAATTGCTCCAAGAATTTAAGGATCCCAAGAGCTTTTCAATACCCTA
261 TGCACTATCATGATAATTAAATTGCTCCAAGAATTTAAGGATCCCAAGAGCTTTTCAATACCCTA
* *
62189 TTCCATTGGTGGTCGGTATATTGGAAAGGCATTATGTGATTTCAATGAAGGTATAATTTTGATGT
326 TTCCATTGGTGATCGGTATATTGGAAAGGCATTATGTGATTTCAATGAAAGTATAATTTTGATGT
62254 CTATATCCGTAATTAAAAAGTTACGGAATTGTAAAAAACACAAGAAAGAGTGGAGATTTTTTGAG
391 CTATATCCGTAATTAAAAAGTTACGGAATTGTAAAAAACACAAGAAAGAGTGGAGATTTTTTGAG
62319 TTAAAAGTGAGACTCAACTGAATGAAGTGGTTACAGATGCTACAGTTAAGGAAGATAATTTAGAT
1 TTAAAAGTGAGACTCAACTGAATGAAGTGGTTACAGATGCTACAGTTAAGGAAGATAATTTAGAT
62384 CTCAACAATGGAAAGATGTCAGAACAATCTAAAAAGCAAACTATAGTTGAAGAGGTTAAACAAAA
66 CTCAACAATGGAAAGATGTCAGAACAATCTAAAAAGCAAACTATAGTTGAAGAGGTTAAACAAAA
62449 TATTGTGGAGACAGAATCAGATCATTTTGTCGCCACAAATGCTACAGCAAAACTGCCTCAGAAAC
131 TATTGTGGAGACAGAATCAGATCATTTTGTCGCCACAAATGCTACAGCAAAACTGCCTCAGAAAC
*
62514 GTGAAGATACATTGTCAAAGAAGATAAGATTGGGAGAAGTTGAAGCAATCGCACTTACTGAAGGA
196 GTGAAGATACATTGTCAAAGAAGAAAAGATTGGGAGAAGTTGAAGCAATCGCACTTACTGAAGGA
*
62579 TGCATTATCATGATAATTAAATTGCTCCAAGAATTTAAGGATCCCAAGAGCTTTTCAATACCCTA
261 TGCACTATCATGATAATTAAATTGCTCCAAGAATTTAAGGATCCCAAGAGCTTTTCAATACCCTA
62644 TTCCATTGGTGATCGGTATATTGGAAAGGCATTATGTGATTTCAATGAAAGTATAATTTTGATGT
326 TTCCATTGGTGATCGGTATATTGGAAAGGCATTATGTGATTTCAATGAAAGTATAATTTTGATGT
*
62709 CTATATCCGTAATTAAGAAGTTACGGAATTGTAAAAAACACAAGAAAGAGTGGAGATTTTTTGAG
391 CTATATCCGTAATTAAAAAGTTACGGAATTGTAAAAAACACAAGAAAGAGTGGAGATTTTTTGAG
62774 ACCATGTGAA
Statistics
Matches: 449, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
455 449 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (455 bp):
TTAAAAGTGAGACTCAACTGAATGAAGTGGTTACAGATGCTACAGTTAAGGAAGATAATTTAGAT
CTCAACAATGGAAAGATGTCAGAACAATCTAAAAAGCAAACTATAGTTGAAGAGGTTAAACAAAA
TATTGTGGAGACAGAATCAGATCATTTTGTCGCCACAAATGCTACAGCAAAACTGCCTCAGAAAC
GTGAAGATACATTGTCAAAGAAGAAAAGATTGGGAGAAGTTGAAGCAATCGCACTTACTGAAGGA
TGCACTATCATGATAATTAAATTGCTCCAAGAATTTAAGGATCCCAAGAGCTTTTCAATACCCTA
TTCCATTGGTGATCGGTATATTGGAAAGGCATTATGTGATTTCAATGAAAGTATAATTTTGATGT
CTATATCCGTAATTAAAAAGTTACGGAATTGTAAAAAACACAAGAAAGAGTGGAGATTTTTTGAG
Found at i:64826 original size:37 final size:37
Alignment explanation
Indices: 64785--64909 Score: 151
Period size: 37 Copynumber: 3.4 Consensus size: 37
64775 TTAATCCAGA
* *
64785 ATTGCACCCAAACATGTCACTGCATGAGCACTTCTAG
1 ATTGCACCCAAACATGTCGCTGCATGAGCACTTATAG
* * *
64822 ATTGCACCCAAACATGTTGCCGCATGAGCACCTATAG
1 ATTGCACCCAAACATGTCGCTGCATGAGCACTTATAG
* * * *
64859 ATTGCACCTAAAAACTGTCGCTACATGAGCACTTTTAG
1 ATTGCACCCAAACA-TGTCGCTGCATGAGCACTTATAG
*
64897 ATTGCACCAAAAC
1 ATTGCACCCAAAC
64910 TATCGCTTGA
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
37 44 0.60
38 29 0.40
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (37 bp):
ATTGCACCCAAACATGTCGCTGCATGAGCACTTATAG
Found at i:77022 original size:21 final size:21
Alignment explanation
Indices: 76983--77022 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
76973 AACAAATTAG
*
76983 TAACAAATAAAGATTAAGAAA
1 TAACAAATAAAGATAAAGAAA
77004 TAACAAATAAATG-TAAAGA
1 TAACAAATAAA-GATAAAGA
77023 CAAATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.65, C:0.05, G:0.10, T:0.20
Consensus pattern (21 bp):
TAACAAATAAAGATAAAGAAA
Found at i:77572 original size:37 final size:39
Alignment explanation
Indices: 77530--77637 Score: 152
Period size: 37 Copynumber: 2.8 Consensus size: 39
77520 GAATTGCATC
*
77530 AAAACATGTCGCTACATGAGCACTTCTAGATTGCG-CC-
1 AAAACATGTCGCCACATGAGCACTTCTAGATTGCGTCCA
* *
77567 CAAACATGTCGCCGCATGAGCACCTT-TAGATTGCGTCCA
1 AAAACATGTCGCCACATGAGCA-CTTCTAGATTGCGTCCA
77606 AAAACA-GTCGCCACATGAGCACTTCTAGATTG
1 AAAACATGTCGCCACATGAGCACTTCTAGATTG
77638 TACCAAAACT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
37 31 0.50
38 26 0.42
39 5 0.08
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (39 bp):
AAAACATGTCGCCACATGAGCACTTCTAGATTGCGTCCA
Found at i:82136 original size:37 final size:36
Alignment explanation
Indices: 82078--82188 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 36
82068 TTCAGAATTG
*
82078 CGCCTAAACATGTCGCTGCATGAGCACTTCTAGATTC
1 CGCCCAAACATGTCGC-GCATGAGCACTTCTAGATTC
* * *
82115 CGCCCAAACATGCCGTCGCATGAGCACCTCTAGATTG
1 CGCCCAAACATGTCG-CGCATGAGCACTTCTAGATTC
* * *
82152 CGCCCAAAAACTGTCACCACATGAGCACTTCTAGATT
1 CGCCCAAACA-TGTC-GCGCATGAGCACTTCTAGATT
82189 GTACCAAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
37 40 0.65
38 22 0.35
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (36 bp):
CGCCCAAACATGTCGCGCATGAGCACTTCTAGATTC
Found at i:90264 original size:28 final size:24
Alignment explanation
Indices: 90206--90253 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
90196 ACAATAAGAT
*
90206 AATAAATTAAGTAAATAAATAACCG
1 AATAAATTAA-TAAATAAAAAACCG
90231 AATAAATTAATAAATAAAGAAAC
1 AATAAATTAATAAATAAA-AAAC
90254 AAACGAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (24 bp):
AATAAATTAATAAATAAAAAACCG
Found at i:90451 original size:30 final size:29
Alignment explanation
Indices: 90412--90497 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
90402 TCAATTTTTG
90412 AATTTTTGGAAAGTTCGAGGGTCAAATTCGA
1 AATTTTTGGAAAGTT-GAGGGTCAAATT-GA
* *
90443 AA-TTTTGGAAAGTTTAGGGGTCAAATTTA
1 AATTTTTGGAAAGTTGA-GGGTCAAATTGA
* *
90472 AATTTTTGGATAGTTTGGGGGTCAAA
1 AATTTTTGGAAAG-TTGAGGGTCAAA
90498 ACATAATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.09
30 39 0.83
31 4 0.09
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAAAGTTGAGGGTCAAATTGA
Found at i:90506 original size:30 final size:30
Alignment explanation
Indices: 90412--90507 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 30
90402 TCAATTTTTG
* *
90412 AATTTTTGGAAAG-TTCGAGGGTCAAATTC-GA
1 AATTTTTGGAAAGTTTAG-GGGTCAAA--CATA
**
90443 AA-TTTTGGAAAGTTTAGGGGTCAAATTTA
1 AATTTTTGGAAAGTTTAGGGGTCAAACATA
* *
90472 AATTTTTGGATAGTTTGGGGGTCAAAACAT-
1 AATTTTTGGAAAGTTTAGGGGTC-AAACATA
90502 AATTTT
1 AATTTT
90508 AAAATAAAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
29 3 0.06
30 42 0.78
31 9 0.17
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTAGGGGTCAAACATA
Found at i:91149 original size:9 final size:9
Alignment explanation
Indices: 91137--91167 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
91127 TTTTCCTCTA
91137 ATTTCATGT
1 ATTTCATGT
*
91146 ATTTCATTT
1 ATTTCATGT
91155 ATTTCATGT
1 ATTTCATGT
91164 ATTT
1 ATTT
91168 TTGTGTGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.06, T:0.61
Consensus pattern (9 bp):
ATTTCATGT
Found at i:91533 original size:20 final size:20
Alignment explanation
Indices: 91505--91547 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
91495 TATTTATTTG
*
91505 TAATTATAA-AATAAATAAAA
1 TAATAATAATAAT-AATAAAA
91525 TAATAATAATAATAATAAAA
1 TAATAATAATAATAATAAAA
91545 TAA
1 TAA
91548 AAACAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAATAATAATAATAATAAAA
Found at i:92045 original size:101 final size:101
Alignment explanation
Indices: 91866--92075 Score: 242
Period size: 101 Copynumber: 2.1 Consensus size: 101
91856 TCTACTGGAC
* * * * *
91866 ATAGGATTTGATGTTGTAGCTTCAACTTTCTCTGTTGCAACTTCAGGGAGATAAAGATTTACTTT
1 ATAGGATTTGATGTTGTAGCTTCAACTTGCTCTGCTGCAACTTCAGAGAGATAAAGATTCACCTT
* * *
91931 CAAGACTTTAATCTGACCCATTACAACTTCAGGGGT
66 CAAGACTTCAATCTGACCCACTACAACTTCAGGGAT
* * * * * *
91967 ATAGGATTTGGTTTTGTAGCTTCATCTTGCTTTGCTGCAACTTCAGAGAGATTAGGATTCACCTT
1 ATAGGATTTGATGTTGTAGCTTCAACTTGCTCTGCTGCAACTTCAGAGAGATAAAGATTCACCTT
* * * *
92032 CGTAG-CTTCAATCTGATCCACTGCAACTTTAGGGAT
66 C-AAGACTTCAATCTGACCCACTACAACTTCAGGGAT
92068 ATAGGATT
1 ATAGGATT
92076 AGGCTTCACT
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
101 88 0.98
102 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (101 bp):
ATAGGATTTGATGTTGTAGCTTCAACTTGCTCTGCTGCAACTTCAGAGAGATAAAGATTCACCTT
CAAGACTTCAATCTGACCCACTACAACTTCAGGGAT
Found at i:92254 original size:50 final size:50
Alignment explanation
Indices: 92136--92399 Score: 203
Period size: 50 Copynumber: 5.3 Consensus size: 50
92126 TGCGAGTTTT
* * * * *
92136 AATCTACCCCTCTACAACTTTAAGGGTATAAGATTTGCTC-TTGTAGCTTC
1 AATCTGCCCCTCTACAGCTTTAAGAGTATAAGATTCGC-CATTGCAGCTTC
* * * * * * * *
92186 AATTTACCCTTTTCCAGCTTTAGGAGTATAAGATTCGCCCTTACAGCTTC
1 AATCTGCCCCTCTACAGCTTTAAGAGTATAAGATTCGCCATTGCAGCTTC
* * * * * *
92236 AATCTGCCCCTCTACAGCTTTAAGTGTATGAGATTCACCATTGCGGTTTT
1 AATCTGCCCCTCTACAGCTTTAAGAGTATAAGATTCGCCATTGCAGCTTC
* * * *
92286 AA-CTGCCCCTCTTCCAGCTTCAAGAGTATAAGATTCGCAATTGCAGCTTT
1 AATCTGCCCCTC-TACAGCTTTAAGAGTATAAGATTCGCCATTGCAGCTTC
* * * * *
92336 AATCTGCCACTCTTTCAACTTCAAGAGTAT-AGATTCGTCATTGC-GACTTC
1 AATCTGCCCCTC-TACAGCTTTAAGAGTATAAGATTCGCCATTGCAG-CTTC
*
92386 AATCTACCCCTCTA
1 AATCTGCCCCTCTA
92400 TAATTTCGGG
Statistics
Matches: 169, Mismatches: 41, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
49 12 0.07
50 133 0.79
51 24 0.14
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (50 bp):
AATCTGCCCCTCTACAGCTTTAAGAGTATAAGATTCGCCATTGCAGCTTC
Found at i:92370 original size:100 final size:100
Alignment explanation
Indices: 92192--92380 Score: 236
Period size: 100 Copynumber: 1.9 Consensus size: 100
92182 CTTCAATTTA
* * * ** * * *
92192 CCCTTTTCCAGCTTTAGGAGTATAAGATTCGCCCTTACAGCTTCAATCTGCCCCTCTACAGCTTT
1 CCCTCTTCCAGCTTCAAGAGTATAAGATTCGCAATTACAGCTTCAATCTGCCACTCTACAACTTC
*
92257 AAGTGTATGAGATTCACCATTGCGGTTTTAACTGC
66 AAGAGTATGAGATTCACCATTGCGGTTTTAACTGC
* * *
92292 CCCTCTTCCAGCTTCAAGAGTATAAGATTCGCAATTGCAGCTTTAATCTGCCACTCTTTCAACTT
1 CCCTCTTCCAGCTTCAAGAGTATAAGATTCGCAATTACAGCTTCAATCTGCCACTC-TACAACTT
**
92357 CAAGAGTAT-AGATTCGTCATTGCG
65 CAAGAGTATGAGATTCACCATTGCG
92381 ACTTCAATCT
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
100 61 0.82
101 13 0.18
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.33
Consensus pattern (100 bp):
CCCTCTTCCAGCTTCAAGAGTATAAGATTCGCAATTACAGCTTCAATCTGCCACTCTACAACTTC
AAGAGTATGAGATTCACCATTGCGGTTTTAACTGC
Found at i:99776 original size:104 final size:104
Alignment explanation
Indices: 99596--99807 Score: 397
Period size: 104 Copynumber: 2.0 Consensus size: 104
99586 GTCAGCGCAA
99596 TTAAGTCAAATCTGCACACTAAAATTGTTAATATTGTCAATGCAATCAAGATTAATTGTCAAAGT
1 TTAAGTCAAATCTGCACACTAAAATTGTTAATATTGTCAATGCAATCAAGATTAATTGTCAAAGT
*
99661 AATAGAAAGTAAATCAATTGTTGTGGAAGTTCAGAGAAT
66 AACAGAAAGTAAATCAATTGTTGTGGAAGTTCAGAGAAT
99700 TTAAGTCAAATCTGCACACTAAAATTGTTAATATTGTCAATGCAATCAAGATTAATTGTCAAAGT
1 TTAAGTCAAATCTGCACACTAAAATTGTTAATATTGTCAATGCAATCAAGATTAATTGTCAAAGT
* *
99765 AACAGAAAGTAAATCAATTGTTGTGGAAGTTTAGAGATT
66 AACAGAAAGTAAATCAATTGTTGTGGAAGTTCAGAGAAT
99804 TTAA
1 TTAA
99808 ATGCATAAAA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (104 bp):
TTAAGTCAAATCTGCACACTAAAATTGTTAATATTGTCAATGCAATCAAGATTAATTGTCAAAGT
AACAGAAAGTAAATCAATTGTTGTGGAAGTTCAGAGAAT
Found at i:102135 original size:6 final size:6
Alignment explanation
Indices: 102124--102179 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
102114 TACATAATTT
**
102124 TTTTTC TTTTTC -TTTTC TCTTTTC TTTTTC --TTTC TTTTTC TCATT-
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
102169 TTTTTC TTTTT
1 TTTTTC TTTTT
102180 AAGTGACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.10
5 8 0.20
6 23 0.56
7 6 0.15
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:102148 original size:18 final size:16
Alignment explanation
Indices: 102124--102179 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 16
102114 TACATAATTT
102124 TTTTTCTTTTTCTTTTC
1 TTTTTCTTTTTC-TTTC
102141 TCTTTTCTTTTTCTTTC
1 T-TTTTCTTTTTCTTTC
102158 TTTTTCTCATTTT-TTTC
1 TTTTTCT--TTTTCTTTC
102175 TTTTT
1 TTTTT
102180 AAGTGACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.17
17 15 0.42
18 15 0.42
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTTTCTTTC
Found at i:104978 original size:15 final size:14
Alignment explanation
Indices: 104960--104991 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
104950 AATTAAAACG
104960 AAACAAATAAAAGTA
1 AAACAAATAAAAG-A
104975 AAACAAATAAAAGA
1 AAACAAATAAAAGA
104989 AAA
1 AAA
104992 GGTGAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.09
Consensus pattern (14 bp):
AAACAAATAAAAGA
Found at i:108416 original size:18 final size:18
Alignment explanation
Indices: 108393--108428 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
108383 AGTAGATAAA
108393 GGCATAAGGTTAATACTT
1 GGCATAAGGTTAATACTT
108411 GGCATAAGGTTAATACTT
1 GGCATAAGGTTAATACTT
108429 ACTTCCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (18 bp):
GGCATAAGGTTAATACTT
Found at i:116638 original size:30 final size:31
Alignment explanation
Indices: 116590--116647 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
116580 CATTAAAATC
* *
116590 AGGTCAAATTTTGAATTTTTGGAAAGTTCAA
1 AGGTCAAATTTGGAATTTTTAGAAAGTTCAA
116621 AGGTCAAA-TTGGAATTTTTAGAAAGTT
1 AGGTCAAATTTGGAATTTTTAGAAAGTT
116648 TGGGGGCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (31 bp):
AGGTCAAATTTGGAATTTTTAGAAAGTTCAA
Found at i:116659 original size:30 final size:31
Alignment explanation
Indices: 116625--116683 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
116615 GTTCAAAGGT
*
116625 CAAATTGGAATTTTTAGA-AAGTTTGGGGGC
1 CAAATTGAAATTTTTAGACAAGTTTGGGGGC
* * *
116655 CAAATTTAAATTTTTGGACAATTTTGGGG
1 CAAATTGAAATTTTTAGACAAGTTTGGGG
116684 TCAAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.37
Consensus pattern (31 bp):
CAAATTGAAATTTTTAGACAAGTTTGGGGGC
Found at i:117709 original size:20 final size:20
Alignment explanation
Indices: 117684--117724 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
117674 ATTTGTATTT
*
117684 ATAAAAT-AATAATAAAAATA
1 ATAAAATGAA-AACAAAAATA
117704 ATAAAATGAAAACAAAAATA
1 ATAAAATGAAAACAAAAATA
117724 A
1 A
117725 GAAATGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (20 bp):
ATAAAATGAAAACAAAAATA
Found at i:121879 original size:26 final size:27
Alignment explanation
Indices: 121832--121886 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
121822 ACTTTAATTT
121832 AATTTAAATAATAAAAATAATTTT-TA
1 AATTTAAATAATAAAAATAATTTTATA
* *
121858 AATTTAAATTAATTATAA-AATTTTATA
1 AATTTAAA-TAATAAAAATAATTTTATA
121885 AA
1 AA
121887 ATATCAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTTAAATAATAAAAATAATTTTATA
Found at i:122515 original size:14 final size:14
Alignment explanation
Indices: 122496--122553 Score: 73
Period size: 14 Copynumber: 4.2 Consensus size: 14
122486 ATTATTTTAT
*
122496 CTTGAATCTCGAAC
1 CTTGAATCTCAAAC
122510 CTTGAA-CTCAAAC
1 CTTGAATCTCAAAC
*
122523 CTTGAATCTTAAAC
1 CTTGAATCTCAAAC
* *
122537 CATGAATCTCGAAC
1 CTTGAATCTCAAAC
122551 CTT
1 CTT
122554 AAGGTTCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
13 12 0.32
14 25 0.68
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.29
Consensus pattern (14 bp):
CTTGAATCTCAAAC
Found at i:123979 original size:23 final size:25
Alignment explanation
Indices: 123934--123982 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
123924 TTTATAAGAT
123934 TAAAACTATTAAGTGATAATTAATA
1 TAAAACTATTAAGTGATAATTAATA
123959 TAAAA-TA-TAAGTG-TAATTTAATA
1 TAAAACTATTAAGTGATAA-TTAATA
123982 T
1 T
123983 GCATCAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 3 0.13
23 13 0.57
24 2 0.09
25 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (25 bp):
TAAAACTATTAAGTGATAATTAATA
Found at i:125439 original size:87 final size:86
Alignment explanation
Indices: 125288--125448 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 86
125278 CATAAGGATG
* * * *
125288 AGTTTTTACTCTTAATGAATTCATAACCCATACTTTTGGTTGTTCTATTGAGATGGACTTGATGA
1 AGTTTTTACTCTTAATGAATTCATAACCCAGACTTTTGGTGGTCCTATTGAGACGGACTTGATGA
125353 ATTCACCGACTTGAGAGGTTA
66 ATTCACCGACTTGAGAGGTTA
* *
125374 AGTTTATTACTCTTAATGAGTTCATATCCCAGA-TTTTGAGTGGTCCTATTGAGACGGACTTGAT
1 AGTTT-TTACTCTTAATGAATTCATAACCCAGACTTTTG-GTGGTCCTATTGAGACGGACTTGAT
125438 GAATTCACCGA
64 GAATTCACCGA
125449 ACTTAAGTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
86 10 0.15
87 57 0.85
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (86 bp):
AGTTTTTACTCTTAATGAATTCATAACCCAGACTTTTGGTGGTCCTATTGAGACGGACTTGATGA
ATTCACCGACTTGAGAGGTTA
Found at i:126590 original size:3 final size:3
Alignment explanation
Indices: 126582--126634 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
126572 TTAAAATGGA
126582 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
126630 ATT AT
1 ATT AT
126635 ACTCTACACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:129034 original size:18 final size:18
Alignment explanation
Indices: 129011--129074 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
129001 AAAGATGGTA
*
129011 ATGAAGATTGTTTAGGTG
1 ATGAAGATTGTTCAGGTG
*
129029 ATGAAGATTGTTCAAGT-
1 ATGAAGATTGTTCAGGTG
* *
129046 AAGAAAGATTATTCAGGTG
1 ATG-AAGATTGTTCAGGTG
129065 ATGAAGATTG
1 ATGAAGATTG
129075 GTTTGGTAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 2 0.05
18 33 0.89
19 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (18 bp):
ATGAAGATTGTTCAGGTG
Found at i:129084 original size:36 final size:36
Alignment explanation
Indices: 129006--129085 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
128996 GTGGAAAAGA
* *
129006 TGGTAATG-AAGATTGTTTAGGTGATGAAGATTGTTC
1 TGGTAA-GAAAGATTATTCAGGTGATGAAGATTGTTC
**
129042 AAGTAAGAAAGATTATTCAGGTGATGAAGATTGGTT-
1 TGGTAAGAAAGATTATTCAGGTGATGAAGATT-GTTC
129078 TGGTAAGA
1 TGGTAAGA
129086 TTGCTGAGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
35 1 0.03
36 32 0.89
37 3 0.08
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (36 bp):
TGGTAAGAAAGATTATTCAGGTGATGAAGATTGTTC
Found at i:151796 original size:16 final size:15
Alignment explanation
Indices: 151771--151800 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
151761 AAAAAGTGTT
151771 TTAATTATTATTTAA
1 TTAATTATTATTTAA
151786 TTAAGTTATTATTTA
1 TTAA-TTATTATTTA
151801 GTCGACTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTAATTATTATTTAA
Found at i:156121 original size:97 final size:97
Alignment explanation
Indices: 155955--156154 Score: 391
Period size: 97 Copynumber: 2.1 Consensus size: 97
155945 AGCCTTGACA
*
155955 AGGTTGCATGATATTAAGAAATTTTTTCTTAATTAATTACCCATTCGCATTTAATTTAATAAATT
1 AGGTTGCATGATATTAAGAAATTTTTTCTTAATTAATTACCCATTCGCATTTAATTTAATAAATA
156020 ATAATAAAATCAAAAGAAAAAAACTGAAAATC
66 ATAATAAAATCAAAAGAAAAAAACTGAAAATC
156052 AGGTTGCATGATATTAAGAAATTTTTTCTTAATTAATTACCCATTCGCATTTAATTTAATAAATA
1 AGGTTGCATGATATTAAGAAATTTTTTCTTAATTAATTACCCATTCGCATTTAATTTAATAAATA
156117 ATAATAAAATCAAAAGAAAAAAACTGAAAATC
66 ATAATAAAATCAAAAGAAAAAAACTGAAAATC
156149 AGGTTG
1 AGGTTG
156155 AAAATTTTGA
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 102 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (97 bp):
AGGTTGCATGATATTAAGAAATTTTTTCTTAATTAATTACCCATTCGCATTTAATTTAATAAATA
ATAATAAAATCAAAAGAAAAAAACTGAAAATC
Done.