Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009555.1 Kokia drynarioides strain JFW-HI SEQ_124267, 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: 226865
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:9316 original size:27 final size:28
Alignment explanation
Indices: 9259--9316 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
9249 TGTGTCGTTT
** * * *
9259 TTTAAAAATAATTAGGAGTTTGCGTCGG
1 TTTAAAAATAATTAGGAGAATGAGACCG
9287 TTTAAAAATAATTAGGAGAAT-AGACCG
1 TTTAAAAATAATTAGGAGAATGAGACCG
9314 TTT
1 TTT
9317 TTGGGGAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (28 bp):
TTTAAAAATAATTAGGAGAATGAGACCG
Found at i:9683 original size:2 final size:2
Alignment explanation
Indices: 9676--9701 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9666 ATTAATTTTA
9676 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9702 TTGTAAACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13146 original size:4 final size:4
Alignment explanation
Indices: 13137--13209 Score: 74
Period size: 4 Copynumber: 17.8 Consensus size: 4
13127 TTTTACGATG
* * * **
13137 TAAA TAAA TAAA TAAG TAAA TAAC TAAA TTAAC TAAA TAAA TAAA TATT
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA -TAAA TAAA TAAA TAAA TAAA
*
13186 TAAG TAAA TAAA TAAAA TAAA TAA
1 TAAA TAAA TAAA T-AAA TAAA TAA
13210 CTATATATAT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
4 49 0.88
5 7 0.12
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:13193 original size:29 final size:28
Alignment explanation
Indices: 13137--13209 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
13127 TTTTACGATG
*
13137 TAAATAAATAAATAAGTAAATAACTAAA
1 TAAATAAATAAATAAATAAATAACTAAA
* ** *
13165 TTAACTAAATAAATAAATATTTAAGTAAA
1 -TAAATAAATAAATAAATAAATAACTAAA
13194 TAAATAAAATAAATAA
1 TAAAT-AAATAAATAA
13210 CTATATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 4 0.11
29 33 0.89
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAATAAATAAATAAATAAATAACTAAA
Found at i:18226 original size:17 final size:16
Alignment explanation
Indices: 18190--18227 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
18180 ACTTGTATTC
18190 AATATTTAAAATAAAT
1 AATATTTAAAATAAAT
18206 AATAGTTTATAAATAAA-
1 AATA-TTTA-AAATAAAT
18223 AATAT
1 AATAT
18228 CATAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 8 0.40
18 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AATATTTAAAATAAAT
Found at i:18576 original size:3 final size:3
Alignment explanation
Indices: 18568--18613 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
18558 TAAATGCACT
18568 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
18614 TTTAGTCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:18764 original size:21 final size:21
Alignment explanation
Indices: 18725--18764 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18715 AAAAATTATA
* * *
18725 TAAAATTTAAATTAGAAAATC
1 TAAAATATAAAGTAAAAAATC
18746 TAAAATATAAAGTAAAAAA
1 TAAAATATAAAGTAAAAAA
18765 AAAATGAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAATATAAAGTAAAAAATC
Found at i:19528 original size:19 final size:18
Alignment explanation
Indices: 19505--19548 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
19495 ATATAAACTT
19505 ATAAAATATAAAAAATCTA
1 ATAAAATATAAAAAAT-TA
* * *
19524 TTAAAAAATTAAAAATTA
1 ATAAAATATAAAAAATTA
19542 ATAAAAT
1 ATAAAAT
19549 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAAATATAAAAAATTA
Found at i:19538 original size:28 final size:27
Alignment explanation
Indices: 19507--19565 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
19497 ATAAACTTAT
19507 AAAATATAA-AAAATCTATTAAAAAATTA
1 AAAAT-TAATAAAATCTATT-AAAAATTA
* *
19535 AAAATTAATAAAATTTATTTAAAATTA
1 AAAATTAATAAAATCTATTAAAAATTA
19562 AAAA
1 AAAA
19566 AACATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAATTAATAAAATCTATTAAAAATTA
Found at i:19566 original size:28 final size:28
Alignment explanation
Indices: 19479--19566 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
19469 ATTCAATATT
* * * *
19479 AAAATT-ATGAAAATTGATATAAACTTAT
1 AAAATTAAT-AAAATTTATTTAAAATTAA
* *
19507 AAAATATAA-AAAATCTATTAAAAAATTAA
1 AAAAT-TAATAAAATTTATT-TAAAATTAA
19536 AAA-TTAATAAAATTTATTTAAAATTAA
1 AAAATTAATAAAATTTATTTAAAATTAA
19563 AAAA
1 AAAA
19567 ACATATTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
27 14 0.30
28 22 0.47
29 10 0.21
30 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAATTAATAAAATTTATTTAAAATTAA
Found at i:19573 original size:20 final size:20
Alignment explanation
Indices: 19535--19573 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19525 TAAAAAATTA
* **
19535 AAAATTAATAAAATTTATTT
1 AAAATTAAAAAAACATATTT
19555 AAAATTAAAAAAACATATT
1 AAAATTAAAAAAACATATT
19574 ATAATTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTAAAAAAACATATTT
Found at i:19615 original size:29 final size:29
Alignment explanation
Indices: 19573--19646 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
19563 AAAAACATAT
* *
19573 TATAATTTTTTAAAAA-TAATAAAAAGTTG-
1 TATAAATTTATAAAAACT-ATAAAAA-TTGA
*
19602 TA-AAATATTATAAAAACTATTAAAATTGA
1 TATAAAT-TTATAAAAACTATAAAAATTGA
19631 TATAAATTTATAAAAA
1 TATAAATTTATAAAAA
19647 AAACCATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 6 0.16
29 27 0.71
30 5 0.13
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (29 bp):
TATAAATTTATAAAAACTATAAAAATTGA
Found at i:20094 original size:11 final size:10
Alignment explanation
Indices: 20081--20164 Score: 73
Period size: 10 Copynumber: 8.2 Consensus size: 10
20071 AATACTTTTT
20081 TTTTTATAAA
1 TTTTTATAAA
20091 TTTTTATAGAA
1 TTTTTATA-AA
* *
20102 TTTTAATACA
1 TTTTTATAAA
20112 TTTTTATAAA
1 TTTTTATAAA
*
20122 ATTTTA-AATA
1 TTTTTATAA-A
20132 TGTTTTATTAAA
1 T-TTTTA-TAAA
*
20144 TTTAT-TAAA
1 TTTTTATAAA
*
20153 TTTTTATTAA
1 TTTTTATAAA
20163 TT
1 TT
20165 GATTAGAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
9 10 0.17
10 28 0.47
11 17 0.29
12 2 0.03
13 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:20114 original size:21 final size:21
Alignment explanation
Indices: 20081--20159 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
20071 AATACTTTTT
* *
20081 TTTTTATAAATTTTTATAGAA
1 TTTTAATAAATTTTTATAAAA
*
20102 TTTTAATACATTTTTATAAAA
1 TTTTAATAAATTTTTATAAAA
* *
20123 TTTTAA-ATATGTTTTATTAAA
1 TTTTAATAAAT-TTTTATAAAA
*
20144 -TTTATTAAATTTTTAT
1 TTTTAATAAATTTTTAT
20160 TAATTGATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
20 13 0.27
21 36 0.73
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTTAATAAATTTTTATAAAA
Found at i:20164 original size:19 final size:21
Alignment explanation
Indices: 20134--20180 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
20124 TTTAAATATG
*
20134 TTTTATTAAATTTATTA-AAT
1 TTTTATTAAATTGATTAGAAT
20154 TTTTATT-AATTGATTAGAAT
1 TTTTATTAAATTGATTAGAAT
*
20174 TTATATT
1 TTTTATT
20181 TTTATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTATTAAATTGATTAGAAT
Found at i:20188 original size:25 final size:26
Alignment explanation
Indices: 20152--20204 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
20142 AATTTATTAA
20152 ATTTTTATTAAT-TGATTAGAA-TTTAT
1 ATTTTTATTAATATG-TTA-AAGTTTAT
20178 ATTTTTA-TAATATGTTAAAGTTTAT
1 ATTTTTATTAATATGTTAAAGTTTAT
20203 AT
1 AT
20205 CAATTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 2 0.08
25 14 0.56
26 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (26 bp):
ATTTTTATTAATATGTTAAAGTTTAT
Found at i:20241 original size:18 final size:17
Alignment explanation
Indices: 20172--20245 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 17
20162 ATTGATTAGA
20172 ATTTATATTTTTATAAT
1 ATTTATATTTTTATAAT
* *
20189 ATGTTAAAGTTTATATCAAT
1 AT-TTATA-TTTTTAT-AAT
*
20209 -TTTA-ATATTTAATAAT
1 ATTTATAT-TTTTATAAT
20225 ATTTATATCTTTTATAA-
1 ATTTATAT-TTTTATAAT
20242 ATTT
1 ATTT
20246 TTTACTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
16 4 0.09
17 15 0.33
18 16 0.36
19 7 0.16
20 3 0.07
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTATATTTTTATAAT
Found at i:20264 original size:72 final size:71
Alignment explanation
Indices: 20188--20329 Score: 248
Period size: 72 Copynumber: 2.0 Consensus size: 71
20178 ATTTTTATAA
* *
20188 TATGTTAAAGTTTATATCAATTTTAATATTTAATAATATTTATATCTTTTATAAATTTTTTACTT
1 TATGTTAAAGTTTATATCAATTTTAATATTTAATAACATTTATATCTTTTATAAA-TTTTTACTG
20253 ATTTTTT
65 ATTTTTT
*
20260 TATGTTAAAGTTTATATCAGTTTTAATATTTAATAACATTTATATCTTTTATAAATTTTTACTGA
1 TATGTTAAAGTTTATATCAATTTTAATATTTAATAACATTTATATCTTTTATAAATTTTTACTGA
20325 TTTTT
66 TTTTT
20330 GTATTTTTTA
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 14 0.21
72 53 0.79
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (71 bp):
TATGTTAAAGTTTATATCAATTTTAATATTTAATAACATTTATATCTTTTATAAATTTTTACTGA
TTTTTT
Found at i:22119 original size:20 final size:20
Alignment explanation
Indices: 21999--22121 Score: 99
Period size: 20 Copynumber: 6.2 Consensus size: 20
21989 CACTTCGGTG
* * *
21999 CTGTTTGCAATTCGGTGCCC
1 CTGTATGCACTTCGATGCCC
*
22019 TTGTATGCACTTCGATGCCC
1 CTGTATGCACTTCGATGCCC
** *
22039 CTAAATGCACACTT-G-TGTCC
1 CTGTATG--CACTTCGATGCCC
*
22059 CTGTATGCACTTCGGTGCCC
1 CTGTATGCACTTCGATGCCC
* * *
22079 TTGTCTGCACTTC-AGTACCC
1 CTGTATGCACTTCGA-TGCCC
22099 CTGTATGCACTTCGATGCCC
1 CTGTATGCACTTCGATGCCC
22119 CTG
1 CTG
22122 ATGGTATAGT
Statistics
Matches: 79, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
18 5 0.06
19 1 0.01
20 66 0.84
21 2 0.03
22 5 0.06
ACGTcount: A:0.15, C:0.33, G:0.20, T:0.33
Consensus pattern (20 bp):
CTGTATGCACTTCGATGCCC
Found at i:29191 original size:16 final size:15
Alignment explanation
Indices: 29170--29215 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
29160 ATAATCACTT
29170 AAATATTAAATTAATA
1 AAATATTAAATTAA-A
29186 AAATATT--ATTAAA
1 AAATATTAAATTAAA
29199 ATAAGTATTAAATTAAA
1 A-AA-TATTAAATTAAA
29216 TTTAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.08
14 7 0.27
15 4 0.15
16 7 0.27
17 6 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AAATATTAAATTAAA
Found at i:33145 original size:20 final size:20
Alignment explanation
Indices: 33112--33150 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33102 TGCATTAAGA
33112 TTTATTTCACTTTA-TTTAT
1 TTTATTTCACTTTAGTTTAT
*
33131 TTTATTTTCATTTTAGTTTA
1 TTTA-TTTCACTTTAGTTTA
33151 GTATAGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTATTTCACTTTAGTTTAT
Found at i:36648 original size:47 final size:47
Alignment explanation
Indices: 36596--36691 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
36586 AAAAATTAAA
*
36596 TATATATATATATATACGTATGTAAATTTTGGTACAATTAGCAAGTT
1 TATATATATATATATACGTATGTAAATTTGGGTACAATTAGCAAGTT
*
36643 TATATATATATATATACGTATGTAAATTTGGGTATAATTAGCAAGTT
1 TATATATATATATATACGTATGTAAATTTGGGTACAATTAGCAAGTT
36690 TA
1 TA
36692 ATTAAGCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (47 bp):
TATATATATATATATACGTATGTAAATTTGGGTACAATTAGCAAGTT
Found at i:45603 original size:35 final size:35
Alignment explanation
Indices: 45494--45603 Score: 96
Period size: 41 Copynumber: 2.9 Consensus size: 35
45484 AAATATCACC
*
45494 TCAACAAATTTTTTCTAAAAATAATAACATTAATAAT
1 TCAACAATTTTTTTCTAAAAATAATAACATT-A-AAT
* * * *
45531 TGGAACCGAATTTTAAATT-TAAAAAAAATAAAGATTAAAT
1 T-CAA-C-AATTTT--TTTCTAAAAATAAT-AACATTAAAT
45571 TCAACAATTTTTTTCTAAAAATAATAACATTAA
1 TCAACAATTTTTTTCTAAAAATAATAACATTAA
45604 TAATTGGACC
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
35 9 0.16
36 9 0.16
37 7 0.12
38 3 0.05
39 3 0.05
40 9 0.16
41 10 0.18
42 7 0.12
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (35 bp):
TCAACAATTTTTTTCTAAAAATAATAACATTAAAT
Found at i:45671 original size:20 final size:21
Alignment explanation
Indices: 45634--45672 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
45624 ATTTAAAAAA
*
45634 AAAATTAAAATTAAATTTTTG
1 AAAATTAAAAGTAAATTTTTG
*
45655 AAAA-TAAAAGTATATTTT
1 AAAATTAAAAGTAAATTTT
45673 AACCAACTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
AAAATTAAAAGTAAATTTTTG
Found at i:48347 original size:19 final size:19
Alignment explanation
Indices: 48310--48360 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
48300 TAGGAATTAA
* *
48310 TGTTTTAATAAA-CATTTC
1 TGTTTTAAAAAATAATTTC
48328 TGTTTTAAAAAATAATTTC
1 TGTTTTAAAAAATAATTTC
*
48347 TCTTTTTAAAAAAT
1 T-GTTTTAAAAAAT
48361 TAATAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 11 0.39
19 6 0.21
20 11 0.39
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (19 bp):
TGTTTTAAAAAATAATTTC
Found at i:50621 original size:19 final size:20
Alignment explanation
Indices: 50568--50621 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
50558 ACATTAAATT
*
50568 TAATATTAAGATAATCACAA
1 TAATATTAAGATAATCAAAA
50588 TAATATTAA-ATTAAT-AAAA
1 TAATATTAAGA-TAATCAAAA
*
50607 TACTATTAAGATAAT
1 TAATATTAAGATAAT
50622 TATTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (20 bp):
TAATATTAAGATAATCAAAA
Found at i:50666 original size:17 final size:17
Alignment explanation
Indices: 50629--50667 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
50619 AATTATTAAA
*
50629 TTATTTTTTATAAATGT
1 TTATTTTTTATAAATGC
50646 TTATTTTTTA-AATATGC
1 TTATTTTTTATAA-ATGC
50663 TTATT
1 TTATT
50668 ATATTATGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (17 bp):
TTATTTTTTATAAATGC
Found at i:52381 original size:31 final size:30
Alignment explanation
Indices: 52346--52411 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
52336 TTTTTTAGTT
* * *
52346 AAATTTGACCCTCAACTTTTTAAAAAGAATC
1 AAATTTGACCATCAACCTTAT-AAAAGAATC
* *
52377 AAATTTGATCATCAACCTTATAAAAGAGTC
1 AAATTTGACCATCAACCTTATAAAAGAATC
52407 AAATT
1 AAATT
52412 ATTATTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.32
Consensus pattern (30 bp):
AAATTTGACCATCAACCTTATAAAAGAATC
Found at i:59540 original size:26 final size:26
Alignment explanation
Indices: 59483--59540 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
59473 TTGCTTCTTT
*
59483 AATAAATTAATTAACAATGTTCATAA
1 AATAAATTAATTAACAATATTCATAA
** *
59509 TTTAAATTAATTAATAATATT-ATAAA
1 AATAAATTAATTAACAATATTCAT-AA
59535 AATAAA
1 AATAAA
59541 AAGATCATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (26 bp):
AATAAATTAATTAACAATATTCATAA
Found at i:59805 original size:20 final size:20
Alignment explanation
Indices: 59780--59824 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
59770 GGACCCTCCC
*
59780 ACACGGGCTAAGCACATGAT
1 ACACGGCCTAAGCACATGAT
*
59800 ACACGGCCTGAGCACATGAT
1 ACACGGCCTAAGCACATGAT
59820 ACACG
1 ACACG
59825 ACCTGCCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.29, G:0.24, T:0.13
Consensus pattern (20 bp):
ACACGGCCTAAGCACATGAT
Found at i:59829 original size:20 final size:20
Alignment explanation
Indices: 59790--59829 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
59780 ACACGGGCTA
*
59790 AGCACATGATACACGGCCTG
1 AGCACATGATACACGACCTG
59810 AGCACATGATACACGACCTG
1 AGCACATGATACACGACCTG
59830 CCACACAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.15
Consensus pattern (20 bp):
AGCACATGATACACGACCTG
Found at i:64097 original size:19 final size:19
Alignment explanation
Indices: 64073--64109 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
64063 TAAGTATGGC
64073 TCGCGGAAACTAAACTGGG
1 TCGCGGAAACTAAACTGGG
64092 TCGCGGAAACTAAACTGG
1 TCGCGGAAACTAAACTGG
64110 TAATAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.30, T:0.16
Consensus pattern (19 bp):
TCGCGGAAACTAAACTGGG
Found at i:64513 original size:28 final size:29
Alignment explanation
Indices: 64469--64523 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
64459 ATCAAATTTG
64469 TTCATCATAATCAAATTT-GTTATTAACT
1 TTCATCATAATCAAATTTAGTTATTAACT
* *
64497 TTCATCAT-CTCATAATTTATTTATTAA
1 TTCATCATAATCA-AATTTAGTTATTAA
64524 TTTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.13
28 13 0.57
29 7 0.30
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.49
Consensus pattern (29 bp):
TTCATCATAATCAAATTTAGTTATTAACT
Found at i:80938 original size:3 final size:3
Alignment explanation
Indices: 80930--80961 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
80920 ACATTGTTAT
80930 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
80962 TACAATTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:82808 original size:30 final size:29
Alignment explanation
Indices: 82740--82808 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
82730 ACTTTCCAAA
*
82740 ATTTTGACCC-AAACTTTTCAAAAATTAG
1 ATTTTGACCCTAAACTTTCCAAAAATTAG
* * **
82768 AATTTAACCCTAAAACTTTCCAAAAATTTT
1 ATTTTGACCCT-AAACTTTCCAAAAATTAG
82798 ATTTTGACCCT
1 ATTTTGACCCT
82809 TGAATGTCCC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
28 8 0.25
30 24 0.75
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (29 bp):
ATTTTGACCCTAAACTTTCCAAAAATTAG
Found at i:85115 original size:3 final size:3
Alignment explanation
Indices: 85107--85134 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
85097 AAATTGACTC
85107 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
85135 CTACCATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:91501 original size:13 final size:14
Alignment explanation
Indices: 91480--91540 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 14
91470 ATAAAGAGAC
*
91480 AAGAGGAAGCAAA-
1 AAGAAGAAGCAAAG
91493 AAGAAGAAG-AAAG
1 AAGAAGAAGCAAAG
*
91506 CAGAAGAAGCAAGAG
1 AAGAAGAAGCAA-AG
* *
91521 AAGAAAAAAGAAAAG
1 AAG-AAGAAGCAAAG
91536 AAGAA
1 AAGAA
91541 AAAAACCTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 3 0.08
13 16 0.41
14 4 0.10
15 9 0.23
16 7 0.18
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGCAAAG
Found at i:91532 original size:22 final size:20
Alignment explanation
Indices: 91497--91539 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
91487 AGCAAAAAGA
**
91497 AGAAGAAAGCAGAAGAAGCAAG
1 AGAAGAAAAAAGAA-AAG-AAG
91519 AGAAGAAAAAAGAAAAGAAG
1 AGAAGAAAAAAGAAAAGAAG
91539 A
1 A
91540 AAAAAACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 3 0.16
22 12 0.63
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (20 bp):
AGAAGAAAAAAGAAAAGAAG
Found at i:92895 original size:48 final size:48
Alignment explanation
Indices: 92824--92918 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
92814 AAAAACGCCT
* *
92824 CTAAAGAACATGTTCTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAG
1 CTAAAGAACATGGTCTTTAGCGGCACTTTTCCCACAAGCGCCGCTAAG
92872 CTAAAGAACATGGTCTTTAGCGGCACTTTTCCCACAAGCGCCGCTAA
1 CTAAAGAACATGGTCTTTAGCGGCACTTTTCCCACAAGCGCCGCTAA
92919 TATTAACAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (48 bp):
CTAAAGAACATGGTCTTTAGCGGCACTTTTCCCACAAGCGCCGCTAAG
Found at i:97572 original size:41 final size:41
Alignment explanation
Indices: 97527--97607 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
97517 TGTTATTGAA
* **
97527 CTTTAGCGGCGCTTCCTCATAAGCGTCGCTAATGCTCTGAC
1 CTTTAGCGGCGCTTCCTAATAAGCACCGCTAATGCTCTGAC
* *
97568 CTTTAGCGGCGCTTTCTAATAAGCACCGCTATTGCTCTGA
1 CTTTAGCGGCGCTTCCTAATAAGCACCGCTAATGCTCTGA
97608 TTTCTCTGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGCTTCCTAATAAGCACCGCTAATGCTCTGAC
Found at i:119840 original size:64 final size:64
Alignment explanation
Indices: 119739--119871 Score: 266
Period size: 64 Copynumber: 2.1 Consensus size: 64
119729 TGATGTTTAT
119739 TTTTTGTAGTTGCATTTATTATTCTTTTTCTAACTTTTATTGATTAACTAATCTTTTAAAATTC
1 TTTTTGTAGTTGCATTTATTATTCTTTTTCTAACTTTTATTGATTAACTAATCTTTTAAAATTC
119803 TTTTTGTAGTTGCATTTATTATTCTTTTTCTAACTTTTATTGATTAACTAATCTTTTAAAATTC
1 TTTTTGTAGTTGCATTTATTATTCTTTTTCTAACTTTTATTGATTAACTAATCTTTTAAAATTC
119867 TTTTT
1 TTTTT
119872 AGGTGTTTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.59
Consensus pattern (64 bp):
TTTTTGTAGTTGCATTTATTATTCTTTTTCTAACTTTTATTGATTAACTAATCTTTTAAAATTC
Found at i:127247 original size:3 final size:3
Alignment explanation
Indices: 127239--127295 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
127229 GTATTGAGGT
* *
127239 AGA AGA AGA AGAA AGA A-A ATA AGA AGA AAA AGA AG- AGA AGGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA
*
127284 AAA AGA AGA AGA
1 AGA AGA AGA AGA
127296 CATTGCCTCG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
2 4 0.09
3 35 0.78
4 6 0.13
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:127264 original size:18 final size:17
Alignment explanation
Indices: 127239--127295 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
127229 GTATTGAGGT
127239 AGAAGAAGAAGAAAGAAA
1 AGAAGAAGAA-AAAGAAA
* *
127257 ATAAGAAGAAAAAGAAG
1 AGAAGAAGAAAAAGAAA
127274 AGAAGGAAGAAAAAGAAGA
1 AGAA-GAAGAAAAAGAA-A
127293 AGA
1 AGA
127296 CATTGCCTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 9 0.27
18 21 0.64
19 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (17 bp):
AGAAGAAGAAAAAGAAA
Found at i:127265 original size:21 final size:23
Alignment explanation
Indices: 127239--127295 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
127229 GTATTGAGGT
*
127239 AGAAGAAGAAGAA-AGAA-AATA
1 AGAAGAAGAAGAAGAGAAGAAGA
*
127260 AGAAGAAAAAGAAGAGAAGGAAGA
1 AGAAGAAGAAGAAGAGAA-GAAGA
*
127284 AAAAGAAGAAGA
1 AGAAGAAGAAGA
127296 CATTGCCTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 12 0.41
22 4 0.14
24 13 0.45
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (23 bp):
AGAAGAAGAAGAAGAGAAGAAGA
Found at i:132663 original size:26 final size:26
Alignment explanation
Indices: 132634--132686 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
132624 TTCTAGGCGT
132634 AATTCTGGACACATTCATGCAGCGAC
1 AATTCTGGACACATTCATGCAGCGAC
* ** *
132660 AATTTTGGACATGTTCATGCAGTGAC
1 AATTCTGGACACATTCATGCAGCGAC
132686 A
1 A
132687 TAACTAGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (26 bp):
AATTCTGGACACATTCATGCAGCGAC
Found at i:132717 original size:37 final size:37
Alignment explanation
Indices: 132676--132760 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
132666 GGACATGTTC
*
132676 ATGCAGTGACA-TAACTAGG-TGCAATTGAAGAATATTT
1 ATGCAGTGACAGT-ACT-GGATGCAATTAAAGAATATTT
* * *
132713 ATGCAGTGATAGTCCTGGATTCAATTAAAGAATATTT
1 ATGCAGTGACAGTACTGGATGCAATTAAAGAATATTT
*
132750 ATGCAGCGACA
1 ATGCAGTGACA
132761 ATCTTGGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 2 0.05
37 37 0.93
38 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (37 bp):
ATGCAGTGACAGTACTGGATGCAATTAAAGAATATTT
Found at i:135924 original size:14 final size:14
Alignment explanation
Indices: 135905--135947 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
135895 AATAACACAT
*
135905 AAATAAATAAATAA
1 AAATAAACAAATAA
135919 AAATAAACAAATAA
1 AAATAAACAAATAA
**
135933 TTATAAAC-AATAA
1 AAATAAACAAATAA
135946 AA
1 AA
135948 TAATAGGGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAACAAATAA
Found at i:135930 original size:18 final size:20
Alignment explanation
Indices: 135898--135946 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
135888 ATCATAAAAT
*
135898 AACACATAAATAAATAA-ATA
1 AACA-ATAAACAAATAATATA
135918 AA-AATAAACAAATAATTATA
1 AACAATAAACAAATAA-TATA
135938 AACAATAAA
1 AACAATAAA
135947 ATAATAGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 7 0.28
21 6 0.24
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.20
Consensus pattern (20 bp):
AACAATAAACAAATAATATA
Found at i:136023 original size:16 final size:17
Alignment explanation
Indices: 135968--136024 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
135958 TACGCATGAA
*
135968 AATAGATAACAAATAAAT
1 AATAAATAA-AAATAAAT
*
135986 AA-AATACAAAAATAAAT
1 AATAA-ATAAAAATAAAT
*
136003 AATAAATAAAATTAAAT
1 AATAAATAAAAATAAAT
136020 -ATAAA
1 AATAAA
136025 AGCAAGAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 5 0.15
17 21 0.64
18 7 0.21
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (17 bp):
AATAAATAAAAATAAAT
Found at i:137343 original size:13 final size:12
Alignment explanation
Indices: 137316--137349 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
137306 TCAAAGTGCG
137316 TTTATTGTATTA
1 TTTATTGTATTA
*
137328 TTTATTTTATTTA
1 TTTATTGTA-TTA
137341 TTTATTGTA
1 TTTATTGTA
137350 AATAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTTATTGTATTA
Found at i:138694 original size:13 final size:14
Alignment explanation
Indices: 138676--138708 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
138666 ACAGAAAAAA
138676 AGATGATTAAAT-T
1 AGATGATTAAATAT
138689 AGATGATTAAATAT
1 AGATGATTAAATAT
138703 AGATGA
1 AGATGA
138709 AATAAGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (14 bp):
AGATGATTAAATAT
Found at i:141921 original size:13 final size:15
Alignment explanation
Indices: 141899--141938 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
141889 ATTTCTTTTA
141899 TTTTATTTA-TTTCT
1 TTTTATTTATTTTCT
141913 TTTTA-TTATTTTCT
1 TTTTATTTATTTTCT
*
141927 TTTTCTTTATTT
1 TTTTATTTATTT
141939 GTTTAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 14 0.61
15 6 0.26
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTATTTTCT
Found at i:150525 original size:24 final size:25
Alignment explanation
Indices: 150493--150550 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 25
150483 TAAAAAAAAA
150493 TTCTTCCTTTTTTTTTTCTTT-ATT
1 TTCTTCCTTTTTTTTTTCTTTCATT
*
150517 TTCTTCCTTTTTTTTTTCTTTCTTT
1 TTCTTCCTTTTTTTTTTCTTTCATT
150542 TTCTTCCTT
1 TTCTTCCTT
150551 CCTTCTTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (25 bp):
TTCTTCCTTTTTTTTTTCTTTCATT
Found at i:150551 original size:4 final size:4
Alignment explanation
Indices: 150493--150596 Score: 77
Period size: 4 Copynumber: 26.0 Consensus size: 4
150483 TAAAAAAAAA
* * * * *
150493 TTCT TCCT TT-T TTTT TTCT TTATT TTCT TCCT TT-T TTTT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT
* * * * *
150540 TTTT CTTCC TTCC TTCT TTCC TTCT TTCT TTCT TTCT TTCT TTCC TTCT
1 TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
*
150589 TTCC TTCT
1 TTCT TTCT
150597 CTCTACTTCT
Statistics
Matches: 78, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
3 6 0.08
4 67 0.86
5 5 0.06
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:150551 original size:29 final size:28
Alignment explanation
Indices: 150499--150570 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
150489 AAAATTCTTC
150499 CTTTTTTT-TTTCTTTATTTTCTTCCTT
1 CTTTTTTTCTTTCTTTATTTTCTTCCTT
*
150526 TTTTTTTTCTTTCTTT-TTCTTCCTTCCTT
1 CTTTTTTTCTTTCTTTATT-TT-CTTCCTT
**
150555 CTTTCCTTCTTTCTTT
1 CTTTTTTTCTTTCTTT
150571 CTTTCTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 9 0.24
28 9 0.24
29 20 0.53
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (28 bp):
CTTTTTTTCTTTCTTTATTTTCTTCCTT
Found at i:163077 original size:18 final size:16
Alignment explanation
Indices: 163052--163117 Score: 78
Period size: 16 Copynumber: 3.9 Consensus size: 16
163042 AAAAAATTAA
*
163052 ATTTTTTTTATTTCTCT
1 ATTTTTTTT-TTCCTCT
163069 CATTATTTTTTTTCCTCT
1 -ATT-TTTTTTTTCCTCT
*
163087 ATTTTTTTCTTCCTCT
1 ATTTTTTTTTTCCTCT
163103 ATTTTTTTTCTTCCT
1 ATTTTTTTT-TTCCT
163118 TTATAATGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 20 0.47
17 8 0.19
18 9 0.21
19 6 0.14
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTTTTTCCTCT
Found at i:163093 original size:13 final size:14
Alignment explanation
Indices: 163072--163112 Score: 64
Period size: 15 Copynumber: 2.8 Consensus size: 14
163062 TTTCTCTCAT
163072 TATTTTTTTTCCTC
1 TATTTTTTTTCCTC
163086 TATTTTTTTCTTCCTC
1 TA-TTTTTT-TTCCTC
163102 TATTTTTTTTC
1 TATTTTTTTTC
163113 TTCCTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.20
15 12 0.48
16 8 0.32
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTTTTCCTC
Found at i:163114 original size:17 final size:17
Alignment explanation
Indices: 163052--163117 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
163042 AAAAAATTAA
* *
163052 ATTTTTTTTATTTCTCT
1 ATTTTTTTTCTTCCTCT
163069 CATTATTTTTT-TTCCTCT
1 -ATT-TTTTTTCTTCCTCT
163087 A-TTTTTTTCTTCCTCT
1 ATTTTTTTTCTTCCTCT
163103 ATTTTTTTTCTTCCT
1 ATTTTTTTTCTTCCT
163118 TTATAATGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
15 6 0.14
16 9 0.20
17 14 0.32
18 9 0.20
19 6 0.14
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTTCTTCCTCT
Found at i:163695 original size:31 final size:30
Alignment explanation
Indices: 163644--163716 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
163634 CGAAAAAATG
**
163644 TAGTTTAGGTACTATTTGTGACTAAAAAA-AA
1 TAGTTTAGGTACTAAATGTGA--AAAAAAGAA
*
163675 TA-TTTAGGTACTAAAATGTGAAAAAAAGTA
1 TAGTTTAGGTACT-AAATGTGAAAAAAAGAA
163705 TAGTTTAGGTAC
1 TAGTTTAGGTAC
163717 CAAGTTGTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 6 0.17
30 13 0.36
31 17 0.47
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.34
Consensus pattern (30 bp):
TAGTTTAGGTACTAAATGTGAAAAAAAGAA
Found at i:169836 original size:24 final size:23
Alignment explanation
Indices: 169800--169846 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
169790 AACTATTCAT
169800 TTTATCTTAATTTGC-TCTGACAA
1 TTTATCTTAATTTGCGT-TGACAA
*
169823 TTTATTTTATATTTGCGTTGACAA
1 TTTATCTTA-ATTTGCGTTGACAA
169847 ATTAACTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.51
Consensus pattern (23 bp):
TTTATCTTAATTTGCGTTGACAA
Found at i:173251 original size:2 final size:2
Alignment explanation
Indices: 173244--173270 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
173234 TTTATTATTC
173244 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 T
173271 TCTTTTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:188270 original size:34 final size:34
Alignment explanation
Indices: 188232--188297 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
188222 CTATAGTATA
*
188232 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* *
188266 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
188298 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:188271 original size:17 final size:17
Alignment explanation
Indices: 188240--188297 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
188230 TAATTGTCCC
* *
188240 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
188257 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
188274 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
188291 TGCATTT
1 TGCATTT
188298 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:189201 original size:17 final size:17
Alignment explanation
Indices: 189174--189217 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
189164 AAAATAAAAT
*
189174 AAAATGAAAATTA-AGAG
1 AAAA-GAAAATGAGAGAG
189191 AAAGAGAAAATGAGAGAG
1 AAA-AGAAAATGAGAGAG
189209 AAAAGAAAA
1 AAAAGAAAA
189218 GATAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (17 bp):
AAAAGAAAATGAGAGAG
Found at i:189971 original size:37 final size:38
Alignment explanation
Indices: 189875--189972 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
189865 ATTTTCGGAA
* * *
189875 TGCACCCAAGACTGTCACTGAATAAATATTCTTCAAAT
1 TGCACCTAAGAATGTCACTGCATAAATATTCTTCAAAT
* * *
189913 TGCATCT-AGAACTATCACTGCATAAGTATTCTTC-AAT
1 TGCACCTAAGAA-TGTCACTGCATAAATATTCTTCAAAT
*
189950 TGCACCTAAGAATGTCGCTGCAT
1 TGCACCTAAGAATGTCACTGCAT
189973 GAACATGTCC
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
37 21 0.43
38 28 0.57
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (38 bp):
TGCACCTAAGAATGTCACTGCATAAATATTCTTCAAAT
Found at i:189994 original size:26 final size:26
Alignment explanation
Indices: 189964--190014 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
189954 CCTAAGAATG
*
189964 TCGCTGCATGAACATGTCCAGAATTA
1 TCGCTGCATGAACATGTCCAAAATTA
*
189990 TCGCTGCATGAACGTGTCCAAAATT
1 TCGCTGCATGAACATGTCCAAAATT
190015 GTGCCTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (26 bp):
TCGCTGCATGAACATGTCCAAAATTA
Found at i:199135 original size:18 final size:18
Alignment explanation
Indices: 199114--199161 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
199104 AAGTGAAACC
199114 TGAGGAGAAGAAGGAAAA
1 TGAGGAGAAGAAGGAAAA
199132 TGAGGA-AGAGAAGGAAAA
1 TGAGGAGA-AGAAGGAAAA
* *
199150 AGAAGAGAAGAA
1 TGAGGAGAAGAA
199162 TAAAGAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.38, T:0.04
Consensus pattern (18 bp):
TGAGGAGAAGAAGGAAAA
Found at i:205075 original size:12 final size:12
Alignment explanation
Indices: 205058--205085 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
205048 GGGTATTGGG
205058 GAAGAAAAAGAA
1 GAAGAAAAAGAA
205070 GAAGAAAAAGAA
1 GAAGAAAAAGAA
205082 GAAG
1 GAAG
205086 GAGAGAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAGAA
Found at i:206725 original size:36 final size:38
Alignment explanation
Indices: 206685--206781 Score: 137
Period size: 36 Copynumber: 2.6 Consensus size: 38
206675 CAAAATAACA
* *
206685 TCCAAATTTGCGCCCAAAACTATCGCTG-A-GAGCACT
1 TCCAAATTTGCACCCAAAACTATCGCCGCATGAGCACT
*
206721 TCCAAATTTGCACCCAAAACTGTCGCCGCATGAGCACT
1 TCCAAATTTGCACCCAAAACTATCGCCGCATGAGCACT
*
206759 TCCAGA-TTGCACCCAAAACTATC
1 TCCAAATTTGCACCCAAAACTATC
206782 ACCGTAGGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
36 25 0.46
37 17 0.31
38 12 0.22
ACGTcount: A:0.31, C:0.33, G:0.14, T:0.22
Consensus pattern (38 bp):
TCCAAATTTGCACCCAAAACTATCGCCGCATGAGCACT
Found at i:206924 original size:26 final size:26
Alignment explanation
Indices: 206890--206943 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
206880 CACCCAGGAA
206890 TGTCACTGCATAAACATGTCTAGAAT
1 TGTCACTGCATAAACATGTCTAGAAT
* * **
206916 TGTCGCTGCATGAATGTGTCTAGAAT
1 TGTCACTGCATAAACATGTCTAGAAT
206942 TG
1 TG
206944 CATTTAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (26 bp):
TGTCACTGCATAAACATGTCTAGAAT
Found at i:210951 original size:38 final size:38
Alignment explanation
Indices: 210898--210973 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
210888 TTTGGAGATC
*
210898 ATCTTCAAACTTTTTCTTACCAAGTTTTCTTTCTTGGA
1 ATCTTCAAACGTTTTCTTACCAAGTTTTCTTTCTTGGA
*
210936 ATCTTCAAGCGTTTTCTTACCAAGTTTTCTTTCTTGGA
1 ATCTTCAAACGTTTTCTTACCAAGTTTTCTTTCTTGGA
210974 GGGAAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.49
Consensus pattern (38 bp):
ATCTTCAAACGTTTTCTTACCAAGTTTTCTTTCTTGGA
Found at i:216043 original size:12 final size:12
Alignment explanation
Indices: 216026--216064 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
216016 CAGGTTCTGT
216026 TTCTTCTTTTTC
1 TTCTTCTTTTTC
* *
216038 TTCTTCCTTTCC
1 TTCTTCTTTTTC
216050 TTCTTCTTTTTC
1 TTCTTCTTTTTC
216062 TTC
1 TTC
216065 ATCCTTCTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTCTTTTTC
Found at i:222542 original size:34 final size:34
Alignment explanation
Indices: 222499--222567 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
222489 TTGTTAACAT
*
222499 AGTATGCATTTTCTGCGTGTTGTGGACAGTCTTC
1 AGTATGCATTTTCTACGTGTTGTGGACAGTCTTC
222533 AGTATGCATTTTCTACGTGTTGTGGACAGTCTTC
1 AGTATGCATTTTCTACGTGTTGTGGACAGTCTTC
222567 A
1 A
222568 TAGTTGTGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (34 bp):
AGTATGCATTTTCTACGTGTTGTGGACAGTCTTC
Done.