Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014269.1 Kokia drynarioides strain JFW-HI SEQ_129302, 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: 222668
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Warning! 171 characters in sequence are not A, C, G, or T
Found at i:7836 original size:3 final size:3
Alignment explanation
Indices: 7828--7871 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
7818 TGCATGTTTT
7828 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
7872 TGAGATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:8381 original size:9 final size:9
Alignment explanation
Indices: 8369--8422 Score: 63
Period size: 9 Copynumber: 6.0 Consensus size: 9
8359 TTAAAAAAAA
8369 TAAAATTAT
1 TAAAATTAT
8378 TAAAATTAT
1 TAAAATTAT
* * *
8387 TACATTTAG
1 TAAAATTAT
*
8396 TAAAAATAT
1 TAAAATTAT
*
8405 AAAAATTAT
1 TAAAATTAT
8414 TAAAATTAT
1 TAAAATTAT
8423 AATTTTTTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (9 bp):
TAAAATTAT
Found at i:8417 original size:18 final size:18
Alignment explanation
Indices: 8353--8424 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 18
8343 AAAACCTATA
* *
8353 AAAAATT-TAAAAAAAAT
1 AAAAATTATTAAAAATAT
*
8370 -AAAATTATTAAAATTAT
1 AAAAATTATTAAAAATAT
* * * *
8387 TACATTTAGTAAAAATAT
1 AAAAATTATTAAAAATAT
*
8405 AAAAATTATTAAAATTAT
1 AAAAATTATTAAAAATAT
8423 AA
1 AA
8425 TTTTTTTTTA
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
16 6 0.15
17 7 0.17
18 28 0.68
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (18 bp):
AAAAATTATTAAAAATAT
Found at i:8490 original size:39 final size:40
Alignment explanation
Indices: 8397--8490 Score: 93
Period size: 42 Copynumber: 2.4 Consensus size: 40
8387 TACATTTAGT
* ** * *
8397 AAAAA-TATAAAAATTATTAAAATTATAATTTTTTTTTAT
1 AAAAATTATAAAAATTATAAAAATTATAATACTTTTATAA
* *
8436 AAAAATCGTAAAAAAATTATAAAAATTGTAA-ACTTTTATAA
1 AAAAAT--TATAAAAATTATAAAAATTATAATACTTTTATAA
8477 AAAAATTATAAAAA
1 AAAAATTATAAAAA
8491 AAATTATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
39 12 0.27
41 12 0.27
42 20 0.45
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (40 bp):
AAAAATTATAAAAATTATAAAAATTATAATACTTTTATAA
Found at i:8492 original size:12 final size:12
Alignment explanation
Indices: 8471--8500 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
8461 TTGTAAACTT
8471 TTAT-AAAAAAA
1 TTATAAAAAAAA
8482 TTATAAAAAAAA
1 TTATAAAAAAAA
8494 TTATAAA
1 TTATAAA
8501 TTGCATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TTATAAAAAAAA
Found at i:14229 original size:30 final size:29
Alignment explanation
Indices: 14193--14259 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 29
14183 TTTTGTATGT
14193 TTTTTTATAATATTTAATAAAATTTAAATA
1 TTTTTTATAATATTTAATAAAATTT-AATA
* * *
14223 TTTTTTATAGTTTTTATTAAAATTTAATA
1 TTTTTTATAATATTTAATAAAATTTAATA
*
14252 ATTTTTAT
1 TTTTTTAT
14260 TTTTATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 11 0.33
30 22 0.67
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTTTTATAATATTTAATAAAATTTAATA
Found at i:14269 original size:30 final size:31
Alignment explanation
Indices: 14194--14270 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 31
14184 TTTGTATGTT
* * *
14194 TTTTTATA-ATATTTAATAAAATTTAAATAT
1 TTTTTATAGTTATTTATTAAAATTTAAATAA
14224 TTTTTATAGTT-TTTATTAAAATTT-AATAA
1 TTTTTATAGTTATTTATTAAAATTTAAATAA
**
14253 TTTTTATTTTTATTTATT
1 TTTTTATAGTTATTTATT
14271 TTTTATCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 13 0.32
30 26 0.65
31 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (31 bp):
TTTTTATAGTTATTTATTAAAATTTAAATAA
Found at i:14567 original size:91 final size:90
Alignment explanation
Indices: 14367--14577 Score: 230
Period size: 90 Copynumber: 2.3 Consensus size: 90
14357 AGTTGAGTTT
* * * * *
14367 AAAAAATCA-AAGG-CTTAATTGTTTTTTTTTTAAAAAGTTTGAGTACCTTTTTGATGCATTTTG
1 AAAAAAT-ATAAGGACTTAATTG-TTTTTTTTGAAAAAATTTGAGGACATTTTTGATCCATTTTG
*
14430 AAAGTTTAAATACCCAATTAAGTGCAA
64 AAAGTTCAAATACCCAATTAAGTGCAA
* * *
14457 AAAAAATGTAAGGACTTAATTGCTTTTTTTGAAAAAATTTGAGGATATTTTTGATCCATTTTGAT
1 AAAAAATATAAGGACTTAATTGTTTTTTTTGAAAAAATTTGAGGACATTTTTGATCCATTTTGA-
* * *
14522 AA-TTCAAATACTCAATTGAGTGTAA
65 AAGTTCAAATACCCAATTAAGTGCAA
** *
14547 AAAAAATTATAAGGGTTTAATTATTTTTTTT
1 AAAAAA-TATAAGGACTTAATTGTTTTTTTT
14578 TTTTTAATTT
Statistics
Matches: 100, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
90 71 0.71
91 29 0.29
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (90 bp):
AAAAAATATAAGGACTTAATTGTTTTTTTTGAAAAAATTTGAGGACATTTTTGATCCATTTTGAA
AGTTCAAATACCCAATTAAGTGCAA
Found at i:30631 original size:23 final size:23
Alignment explanation
Indices: 30605--30651 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
30595 GTTTCTAAAG
30605 ATAACCCTATGGATCCGTTTACT
1 ATAACCCTATGGATCCGTTTACT
* * *
30628 ATAACCTTCTGGATCTGTTTACT
1 ATAACCCTATGGATCCGTTTACT
30651 A
1 A
30652 AGAATCTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (23 bp):
ATAACCCTATGGATCCGTTTACT
Found at i:30860 original size:23 final size:23
Alignment explanation
Indices: 30834--30880 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
30824 GTTTCTAAAG
30834 ATAACCTTGTGGAT-TCGTTTACT
1 ATAACCTTGTGGATAT-GTTTACT
30857 ATAACCTTGTGGATATGTTTACT
1 ATAACCTTGTGGATATGTTTACT
30880 A
1 A
30881 AGAATCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (23 bp):
ATAACCTTGTGGATATGTTTACT
Found at i:30897 original size:229 final size:227
Alignment explanation
Indices: 30489--31085 Score: 962
Period size: 229 Copynumber: 2.6 Consensus size: 227
30479 CTACAATAAC
*
30489 TAATACCAAGGAAATTAGAAGTCACAAGAGGA-AGAAACACATTGATTGAAAGTATCACTTGATA
1 TAATACCAAGGAAATGAGAAGTCACAAGAGGATA-AAACACATTGATTGAAAGTATCACTTGATA
* * *
30553 CGAGAGGTAATTACCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCCTATGGA
65 CGAGAGGCAATT--CGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGA
*
30618 TCCGTTTACTATAACCTTCTGGATCTGTTTACTAAGAATCTTGTAACTAGGAGTTTTAACAAACA
128 TCCGTTTACTATAACCTTCTGGATATGTTTACTAAGAATCTTGTAACTAGGAGTTTTAACAAACA
* ** * *
30683 CGTCTAGGATATGGGAATGCGAAATGTGACACATT
193 CGTCCAGGATATAAGAATGCAAAACGTGACACATT
*
30718 TAATACTAAGGAAATGAGAAGTCACAAGAGGATAAAACACATTGATTGAAAGTATCACTTGATAC
1 TAATACCAAGGAAATGAGAAGTCACAAGAGGATAAAACACATTGATTGAAAGTATCACTTGATAC
30783 GAGAGGCAATCGTCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGAT
66 GAGAGGCAAT--TCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGAT
* *
30848 TCGTTTACTATAACCTTGTGGATATGTTTACTAAGAATCTTGTAACTAGGAGTTTTAACAAACAC
129 CCGTTTACTATAACCTTCTGGATATGTTTACTAAGAATCTTGTAACTAGGAGTTTTAACAAACAC
30913 GTCCAGGATATAAGAATGCAAAACGTGACACATT
194 GTCCAGGATATAAGAATGCAAAACGTGACACATT
* * *
30947 TAATACCAAGGAAAAGAGAAGTCATAAGAGGATGAAACACATTGATTGAAAGTATCACTTGATAC
1 TAATACCAAGGAAATGAGAAGTCACAAGAGGATAAAACACATTGATTGAAAGTATCACTTGATAC
* * *
31012 TAGAGGCAATTACAAAGGAATGGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGATC
66 GAGAGGCAATT-CGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGATC
31077 CGTTTACTA
130 CGTTTACTA
31086 AGAATCTTGT
Statistics
Matches: 343, Mismatches: 21, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
227 1 0.00
228 59 0.17
229 281 0.82
230 1 0.00
231 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (227 bp):
TAATACCAAGGAAATGAGAAGTCACAAGAGGATAAAACACATTGATTGAAAGTATCACTTGATAC
GAGAGGCAATTCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGATCC
GTTTACTATAACCTTCTGGATATGTTTACTAAGAATCTTGTAACTAGGAGTTTTAACAAACACGT
CCAGGATATAAGAATGCAAAACGTGACACATT
Found at i:33548 original size:16 final size:16
Alignment explanation
Indices: 33527--33558 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33517 AGTAATTTTT
*
33527 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
33543 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
33559 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:35295 original size:21 final size:21
Alignment explanation
Indices: 35248--35299 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
35238 TAGAGTTTGC
35248 TGTATCAGTAGAAGTAATAAT
1 TGTATCAGTAGAAGTAATAAT
* ** * *
35269 TATATCAGTATTAGTCATACT
1 TGTATCAGTAGAAGTAATAAT
35290 TGTATCAGTA
1 TGTATCAGTA
35300 AAACCTTCCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCAGTAGAAGTAATAAT
Found at i:38189 original size:21 final size:22
Alignment explanation
Indices: 38146--38198 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
38136 GATATGATAT
*
38146 TTAAGTTAAAATAGTGTATTAA
1 TTAAGTTAAAAAAGTGTATTAA
38168 TTAAGTTAAAGAAAG-G-ATTAA
1 TTAAGTTAAA-AAAGTGTATTAA
38189 TTAAGCTTAA
1 TTAAG-TTAA
38199 TGATGAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 10 0.36
22 15 0.54
23 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.36
Consensus pattern (22 bp):
TTAAGTTAAAAAAGTGTATTAA
Found at i:44711 original size:28 final size:28
Alignment explanation
Indices: 44670--44758 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
44660 ATAGGGGTCG
* * *
44670 AAAATGAAGTTTTGGAGAGTTTAGGGTT
1 AAAACGAAATTTTGGAGAGTTTAGGGTA
* *
44698 AATACGAAATTTTGGAAAGTTTACGGGTA
1 AAAACGAAATTTTGGAGAGTTTA-GGGTA
* *
44727 AAAATGTAATTTTGG-GAAGTTTAGGGTA
1 AAAACGAAATTTTGGAG-AGTTTAGGGTA
44755 AAAA
1 AAAA
44759 TATGATTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
28 28 0.56
29 22 0.44
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (28 bp):
AAAACGAAATTTTGGAGAGTTTAGGGTA
Found at i:44964 original size:87 final size:87
Alignment explanation
Indices: 44707--45095 Score: 317
Period size: 87 Copynumber: 4.4 Consensus size: 87
44697 TAATACGAAA
* * * *
44707 TTTTGGAAAGTTTACGGGTAAAAATGTAATTTTGGGAAGTTT-AGGGTAAAAATATGATTTTTGA
1 TTTTGGAAAGTTTA-GGGTAAAAATGTAATTTTTGGAAATTTGAGGGCAAAAATATAATTTTTGA
*
44771 AAAGTTCAGGGTAAAAATGTGAT
65 AAAGTTCAGGGTTAAAATGTGAT
* * * * * *
44794 TTTTGG-AAGTTCGAGGGCAAAAATATAATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTTGA
1 TTTTGGAAAGTT-TAGGGTAAAAATGTAATTTTTGGAAATTTGAGGGCAAAAATATAATTTTTGA
* *
44858 GAAGTTCAAGGTTAAAAATGTGAT
65 AAAGTTCAGGGTT-AAAATGTGAT
* * *
44882 TTTTGG-AAGTTTAGGATAAAAATGTGATTTTTGGAAATTTGATGGCAAAAATATAATTTTAAT-
1 TTTTGGAAAGTTTAGGGTAAAAATGTAATTTTTGGAAATTTGAGGGCAAAAATATAATTTT--TG
* ** * *
44945 AAAATTTTGGGGTTTAAATGTGAG
64 AAAAGTTCAGGGTTAAAATGTGAT
* * * * * *
44969 TTTTGAGTAAGTTT-GAGGTTAAAATGTAATTTTTGGAAAGTTTAAGGGTTAAAAA-GTGATTTT
1 TTTTG-GAAAGTTTAG-GGTAAAAATGTAATTTTTGGAAA-TTTGAGGG-CAAAAATATAATTTT
* * * * *
45032 TG-GAAGTTTAATGGTCAAAATGTGTT
62 TGAAAAG-TTCAGGGTTAAAATGTGAT
*
45058 TTTTGGAAAAGTTT-GAGGTTAAAATGTAATTTTTGGAA
1 TTTTGG-AAAGTTTAG-GGTAAAAATGTAATTTTTGGAA
45096 TGTTTAGGGT
Statistics
Matches: 244, Mismatches: 45, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
86 28 0.11
87 89 0.36
88 36 0.15
89 74 0.30
90 12 0.05
91 5 0.02
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.38
Consensus pattern (87 bp):
TTTTGGAAAGTTTAGGGTAAAAATGTAATTTTTGGAAATTTGAGGGCAAAAATATAATTTTTGAA
AAGTTCAGGGTTAAAATGTGAT
Found at i:44994 original size:30 final size:29
Alignment explanation
Indices: 44707--45124 Score: 232
Period size: 29 Copynumber: 14.3 Consensus size: 29
44697 TAATACGAAA
* *
44707 TTTTGGAAAGTTT-ACGGGTAAAAATGT-AA
1 TTTTGGAAAGTTTGA--GGTTAAAATGTGAT
* * *
44736 TTTTGGGAAGTTT-AGGGTAAAAATATGAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTGAT
* * *
44765 TTTTGAAAAG-TTCAGGGTAAAAATGTGAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTGAT
* ** * *
44794 TTTTGG-AAGTTCGAGGGCAAAAATATAAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTGAT
* ** *
44823 TTTTGG-AAGTTCGAGGGCAAAAATGTAAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTGAT
**
44852 TTTT-GAGAAGTTCAAGGTTAAAAATGTGAT
1 TTTTGGA-AAGTTTGAGGTT-AAAATGTGAT
*
44882 TTTTGG-AAGTTT-AGGATAAAAATGTGAT
1 TTTTGGAAAGTTTGAGG-TTAAAATGTGAT
** * *
44910 TTTTGGAAA-TTTGATGGCAAAAATATAAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTGAT
* * * * *
44939 TTTAAT-AAAATTTTGGGGTTTAAATGTGAG
1 TTT--TGGAAAGTTTGAGGTTAAAATGTGAT
* *
44969 TTTTGAGTAAGTTTGAGGTTAAAATGTAAT
1 TTTTG-GAAAGTTTGAGGTTAAAATGTGAT
* *
44999 TTTTGGAAAGTTTAAGGGTTAAAAAGTGAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTGAT
* * *
45029 TTTTGG-AAGTTTAATGGTCAAAATGTGTT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTGAT
*
45058 TTTTGGAAAAGTTTGAGGTTAAAATGTAAT
1 TTTTGG-AAAGTTTGAGGTTAAAATGTGAT
* * *
45088 TTTTGGAATGTTT-AGGGTTTAAATGTAAT
1 TTTTGGAAAGTTTGA-GGTTAAAATGTGAT
45117 TTTTGGAA
1 TTTTGGAA
45125 GTTCGGGGGC
Statistics
Matches: 318, Mismatches: 51, Indels: 40
0.78 0.12 0.10
Matches are distributed among these distances:
28 41 0.13
29 171 0.54
30 93 0.29
31 13 0.04
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (29 bp):
TTTTGGAAAGTTTGAGGTTAAAATGTGAT
Found at i:45021 original size:59 final size:58
Alignment explanation
Indices: 44707--45124 Score: 301
Period size: 59 Copynumber: 7.1 Consensus size: 58
44697 TAATACGAAA
* * * * *
44707 TTTTGGAAAGTTTACGGGTAAAAATGTAATTTTGGGAAGTTT-AGGGTAAAAATATGAT
1 TTTTGGAAAGTTTAAGGGT-AAAATGTGATTTTTGGAAGTTTGAGGGTAAAAATGTAAT
* * * * *
44765 TTTTGAAAAG-TTCAGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATATAAT
1 TTTTGGAAAGTTTAAGGGT-AAAATGTGATTTTTGGAAGTTTGAGGGTAAAAATGTAAT
** * * ** * *
44823 TTTTGG-AAGTTCGAGGGCAAAAATGTAATTTTTGAGAAGTTCAAGGTTAAAAATGTGAT
1 TTTTGGAAAGTTTAAGGG-TAAAATGTGATTTTTG-GAAGTTTGAGGGTAAAAATGTAAT
* * * * *
44882 TTTTGG-AAGTTT-AGGATAAAAATGTGATTTTTGGAAATTTGATGGCAAAAATATAAT
1 TTTTGGAAAGTTTAAGGGT-AAAATGTGATTTTTGGAAGTTTGAGGGTAAAAATGTAAT
*** * ** * * *
44939 TTTAATAAAATTTTGGGGTTTAAATGTGAGTTTTGAGTAAGTTTGA-GGTTAAAATGTAAT
1 TTTTGGAAAGTTTAAGGG-TAAAATGTGATTTTTG-G-AAGTTTGAGGGTAAAAATGTAAT
* * * * **
44999 TTTTGGAAAGTTTAAGGGTTAAAAAGTGATTTTTGGAAGTTTAATGGTCAAAATGTGTT
1 TTTTGGAAAGTTTAAGGG-TAAAATGTGATTTTTGGAAGTTTGAGGGTAAAAATGTAAT
* * * **
45058 TTTTGGAAAAGTTTGAGGTTAAAATGTAATTTTTGGAATGTTT-AGGGTTTAAATGTAAT
1 TTTTGG-AAAGTTTAAGGGTAAAATGTGATTTTTGGAA-GTTTGAGGGTAAAAATGTAAT
45117 TTTTGGAA
1 TTTTGGAA
45125 GTTCGGGGGC
Statistics
Matches: 283, Mismatches: 64, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
57 48 0.17
58 78 0.28
59 97 0.34
60 53 0.19
61 7 0.02
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (58 bp):
TTTTGGAAAGTTTAAGGGTAAAATGTGATTTTTGGAAGTTTGAGGGTAAAAATGTAAT
Found at i:47435 original size:149 final size:148
Alignment explanation
Indices: 47269--48130 Score: 464
Period size: 149 Copynumber: 5.8 Consensus size: 148
47259 TTCGCCGTTA
* * * * *
47269 CGGCCTCAACCTTTCCCTTTATATCTTCATGGTATC-GGATTCACCATTGCAACTTTAATCC-TT
1 CGGCCTCAACCTTTCCCTTCATATCTCCATGGTACCAGG-TTCACCATTGCAACCTCAA-CCTTT
* *
47332 CCCATCGCATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCGCATCTTCT
64 CCCATCGCATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCGCATCTTCA
* *
47397 TAGGTACCGGGTTCGTCATTG
129 T-GGTAACGGGTTCATCATTG
* * * * ** * **
47418 TGGCCTCAACCTTTCCCTTCGTATCTCCGTGTTACCAGGTTTGCCGTTGCGGCCTCAACCTTTCC
1 CGGCCTCAACCTTTCCCTTCATATCTCCATGGTACCAGGTTCACCATTGCAACCTCAACCTTTCC
* * * * * *
47483 CATTGCATCTTCTTAGGTACCGGGTTTGCCGTTGCGGCCTCAACCTTTCTCTTCGTATCTTCATG
66 CATCGCATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCGCATCTTCATG
*
47548 GTAACGGGTTCATCGTTG
131 GTAACGGGTTCATCATTG
* * * * * * * * ***
47566 CGGTCTCAACCTTTCTCATCACATCTTCTTAGGTACCAGGTTCATCGTTGTGGCCTCAACCTTTC
1 CGGCCTCAACCTTTCCCTTCATATCTCCAT-GGTACCAGGTTCACCATTGCAACCTCAACCTTTC
** * * * * * * * * **
47631 CCATTACATCTTTTAAGGTATCGGATTCGCTGTTGCGGCTTCAATCATTCCCTTCAAATCTTCAT
65 CCATCGCATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCGCATCTTCAT
* *** *
47696 GGTACCGGGTTTGCCGTTG
130 GGTAACGGGTTCATCATTG
** ** ** * ** **
47715 CGGCCTCAACCTTTCCCAACGCATCTTCTTTTAAGTACCAAATTCACCATTGCGGCCTCAATCC-
1 CGGCCTCAACCTTTCCCTTCATATC-TC-CAT-GGTACCAGGTTCACCATTGCAACCTCAA-CCT
* * * * * ** *
47779 TTCCCATCACATCTTCTAAGGTACTGGATTCGTCGTTGCGACCTCAATCC-TTCCTTTCATC-TC
62 TTCCCATCGCATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCGTC-GCATC
* * * * * *
47842 TTTATGGTACCGAGTTTACCGTTG
125 TTCATGGTAACGGGTTCATCATTG
* * * * ** * * **
47866 CGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCAGGTTTGCCGTTACGGCCTCAACCTTTC
1 CGGCCTCAACCTTTCCCTTCATATCTCCAT-GGTACCAGGTTCACCATTGCAACCTCAACCTTTC
* * * * * * * **
47931 CCTTTGTATCTTCGT--GGTACCAGGTTCGCCATTGCGGCCTCAATCTTTCCCATCGCATCTTTT
65 CCATCGCATCTTC-TAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCGCATCTTCA
* **
47994 TAGGTACCGAATTCA-C-TGTCG
129 T-GGTAACGGGTTCATCAT-T-G
* * * * * * * * **
48015 CGGCCTTAATCTTTCCCTTCGTATCTCCGTGGTATCGGGTTTACCGTTGCGGCCTCAACCTTTCC
1 CGGCCTCAACCTTTCCCTTCATATCTCCATGGTACCAGGTTCACCATTGCAACCTCAACCTTTCC
* * * * ***
48080 CATCGCATCTTTTTAGGTATCGGATTCGCCGTCATGGCCTCAATCCTTTCC
66 CATCGCATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCC
48131 TTCATCTCTT
Statistics
Matches: 562, Mismatches: 133, Indels: 35
0.77 0.18 0.05
Matches are distributed among these distances:
147 4 0.01
148 117 0.21
149 310 0.55
150 11 0.02
151 117 0.21
152 3 0.01
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (148 bp):
CGGCCTCAACCTTTCCCTTCATATCTCCATGGTACCAGGTTCACCATTGCAACCTCAACCTTTCC
CATCGCATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCGCATCTTCATG
GTAACGGGTTCATCATTG
Found at i:47464 original size:99 final size:99
Alignment explanation
Indices: 47256--48218 Score: 758
Period size: 99 Copynumber: 9.7 Consensus size: 99
47246 TTGAGGTGCT
* * * * * * * * * *
47256 AGGTTCGCCGTTACGGCCTCAACCTTTCCCTTTATATCTTCAT-GGTATCGGATTCACCATTGCA
1 AGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCG
* * * * * * *
47320 ACTTTAATCC-TTCCCATCGCATCTTCTAAGGTATC
66 GCCTCAA-CCTTTCCCTTCGTATCTTC-ATGGTACC
* * * * * *
47355 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCGCATCTTCTTAGGTACCGGGTTCGTCATTGTG
1 AGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCG
* * *
47420 GCCTCAACCTTTCCCTTCGTATCTCCGTGTTACC
66 GCCTCAACCTTTCCCTTCGTATCTTCATGGTACC
* ** *
47454 AGGTTTGCCGTTGCGGCCTCAACCTTTCCCATTGCATCTTCTTAGGTACCGGGTTTGCCGTTGCG
1 AGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCG
* *
47519 GCCTCAACCTTTCTCTTCGTATCTTCATGGTAAC
66 GCCTCAACCTTTCCCTTCGTATCTTCATGGTACC
* ** * * * ** *
47553 GGGTTCATCGTTGCGGTCTCAACCTTTCTCATCACATCTTCTTAGGTACCAGGTTCATCGTTGTG
1 AGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCG
* * *
47618 GCCTCAACCTTTCCCATTAC--ATCTTTTAAGGTATC
66 GCCTCAACCTTTCCC-TT-CGTATC-TTCATGGTACC
* * * * * * * *
47653 -GGATTCGCTGTTGCGGCTTCAATCATTCCCTTCAAATCTTCAT-GGTACCGGGTTTGCCGTTGC
1 AGG-TTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGC
** * * *
47716 GGCCTCAACCTTTCCCAACGCATCTTCTTTTAAGTACC
65 GGCCTCAACCTTTCCCTTCGTATCTTC--AT-GGTACC
** * * * * * *
47754 AAATTCACCATTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACTGGATTCGTCGTTGC
1 AGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGC
* * * * *
47818 GACCTCAATCC-TTCCTTTCATCTCTTTATGGTACC
65 GGCCTCAA-CCTTTCCCTTCGTATCTTCATGGTACC
** * * *
47853 -GAGTTTACCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCAGGTTTGCCGTTAC
1 AG-GTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGC
* *
47917 GGCCTCAACCTTTCCCTTTGTATCTTCGTGGTACC
65 GGCCTCAACCTTTCCCTTCGTATCTTCATGGTACC
* * * * ** * * *
47952 AGGTTCGCCATTGCGGCCTCAATCTTTCCCATCGCATCTTTTTAGGTACCGAATTCACTGTCGCG
1 AGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCG
* * * * *
48017 GCCTTAATCTTTCCCTTCGTATCTCCGTGGTATC
66 GCCTCAACCTTTCCCTTCGTATCTTCATGGTACC
* ** * * * * ***
48051 GGGTTTACCGTTGCGGCCTCAACCTTTCCCATCGCATCTTTTTAGGTATCGGATTCGCCGTCATG
1 AGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCG
* * *
48116 GCCTCAATCCTTT-CCTTCATCTCTTCATGGTATC
66 GCCTCAA-CCTTTCCCTTCGTATCTTCATGGTACC
* * * * *
48150 AGGTTCGCTGTTGCGGCCTTAACCTTTCCCATCACATCTTCTTAGGTACCGGATTCTCCGTCGCG
1 AGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCG
48215 GCCT
66 GCCT
48219 TAATCCTTCC
Statistics
Matches: 678, Mismatches: 166, Indels: 40
0.77 0.19 0.05
Matches are distributed among these distances:
97 1 0.00
98 6 0.01
99 525 0.77
100 77 0.11
101 34 0.05
102 33 0.05
103 2 0.00
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (99 bp):
AGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCGTTGCG
GCCTCAACCTTTCCCTTCGTATCTTCATGGTACC
Found at i:48229 original size:50 final size:50
Alignment explanation
Indices: 47330--48218 Score: 562
Period size: 50 Copynumber: 17.9 Consensus size: 50
47320 ACTTTAATCC
* * * *
47330 TTCCCATCGCATCTTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCT
1 TTCCCATCGCATCTTCTTAGGTACCGGATTCTCCGTTGCGGCCTCAACCT
* * * *
47380 TTCCCGTCGCATCTTCTTAGGTACCGGGTTCGT-CATTGTGGCCTCAACCT
1 TTCCCATCGCATCTTCTTAGGTACCGGATTC-TCCGTTGCGGCCTCAACCT
* * * * *
47430 TTCCCTTCGTATCTCCGT-GTTACCAGG-TT-TGCCGTTGCGGCCTCAACCT
1 TTCCCATCGCATCTTCTTAGGTACC-GGATTCT-CCGTTGCGGCCTCAACCT
* *
47479 TTCCCATTGCATCTTCTTAGGTACCGGGTT-TGCCGTTGCGGCCTCAACCT
1 TTCCCATCGCATCTTCTTAGGTACCGGATTCT-CCGTTGCGGCCTCAACCT
* * * * * * *
47529 TTCTCTTCGTATCTTCAT-GGTAACGGGTTCAT-CGTTGCGGTCTCAACCT
1 TTCCCATCGCATCTTCTTAGGTACCGGATTC-TCCGTTGCGGCCTCAACCT
* * *
47578 TTCTCATCACATCTTCTTAGGTACCAGG-TTCAT-CGTTGTGGCCTCAACCT
1 TTCCCATCGCATCTTCTTAGGTACC-GGATTC-TCCGTTGCGGCCTCAACCT
** * * * * * *
47628 TTCCCATTACATCTT-TTAAGGTATCGGATTCGCTGTTGCGGCTTCAATCA
1 TTCCCATCGCATCTTCTT-AGGTACCGGATTCTCCGTTGCGGCCTCAACCT
* ** * *
47678 TTCCCTTCAAATCTTCAT-GGTACCGGGTT-TGCCGTTGCGGCCTCAACCT
1 TTCCCATCGCATCTTCTTAGGTACCGGATTCT-CCGTTGCGGCCTCAACCT
* * ** * *
47727 TTCCCAACGCATCTTCTTTTAAGTACCAAATTCACCATTGCGGCCTCAATCC-
1 TTCCCATCGCATCTTC--TTAGGTACCGGATTCTCCGTTGCGGCCTCAA-CCT
* * * *
47779 TTCCCATCACATCTTCTAAGGTACTGGATTCGT-CGTTGCGACCTCAATCC-
1 TTCCCATCGCATCTTCTTAGGTACCGGATTC-TCCGTTGCGGCCTCAA-CCT
**
47829 TT-CC-TTTCATC-TCTTTATGGTACC-GAGTT-TACCGTTGCGGCCTCAACCT
1 TTCCCATCGCATCTTC-TTA-GGTACCGGA-TTCT-CCGTTGCGGCCTCAACCT
* *
47878 TTCCCATCACATCTTCTTAGGTACCAGG-TT-TGCCGTTACGGCCTCAACCT
1 TTCCCATCGCATCTTCTTAGGTACC-GGATTCT-CCGTTGCGGCCTCAACCT
* * * * * * *
47928 TTCCCTTTGTATCTTCGT-GGTACCAGG-TTCGCCATTGCGGCCTCAATCT
1 TTCCCATCGCATCTTCTTAGGTACC-GGATTCTCCGTTGCGGCCTCAACCT
* * * * * * *
47977 TTCCCATCGCATCTTTTTAGGTACCGAATTCACTGTCGCGGCCTTAATCT
1 TTCCCATCGCATCTTCTTAGGTACCGGATTCTCCGTTGCGGCCTCAACCT
* * * * * *
48027 TTCCCTTCGTATCTCCGT-GGTATCGGGTT-TACCGTTGCGGCCTCAACCT
1 TTCCCATCGCATCTTCTTAGGTACCGGATTCT-CCGTTGCGGCCTCAACCT
* * * ***
48076 TTCCCATCGCATCTTTTTAGGTATCGGATTCGCCGTCATGGCCTCAATCCT
1 TTCCCATCGCATCTTCTTAGGTACCGGATTCTCCGTTGCGGCCTCAA-CCT
* * * * *
48127 TT-CC-T-TCATC-TCTTCATGGTATCAGG-TTCGCTGTTGCGGCCTTAACCT
1 TTCCCATCGCATCTTCTT-A-GGTA-CCGGATTCTCCGTTGCGGCCTCAACCT
* *
48175 TTCCCATCACATCTTCTTAGGTACCGGATTCTCCGTCGCGGCCT
1 TTCCCATCGCATCTTCTTAGGTACCGGATTCTCCGTTGCGGCCT
48219 TAATCCTTCC
Statistics
Matches: 652, Mismatches: 140, Indels: 94
0.74 0.16 0.11
Matches are distributed among these distances:
47 7 0.01
48 21 0.03
49 239 0.37
50 318 0.49
51 23 0.04
52 42 0.06
53 2 0.00
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.35
Consensus pattern (50 bp):
TTCCCATCGCATCTTCTTAGGTACCGGATTCTCCGTTGCGGCCTCAACCT
Found at i:48988 original size:44 final size:43
Alignment explanation
Indices: 48930--49019 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 43
48920 ATTCCTTTGG
*
48930 TTTCAAGACGCCTTTAGCGGGTTTTCATCT-AGATCTCT-TTTTT
1 TTTCAAGACGCCTTTA-CGGGTTTTCAGCTCA-ATCTCTCTTTTT
* * *
48973 TTTCGAGACGTCCTTTATGGGTTTTTAGCTCAATCTCTCTTTTT
1 TTTCAAGACG-CCTTTACGGGTTTTCAGCTCAATCTCTCTTTTT
49017 TTT
1 TTT
49020 AGGCGAAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 25 0.62
44 15 0.38
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.50
Consensus pattern (43 bp):
TTTCAAGACGCCTTTACGGGTTTTCAGCTCAATCTCTCTTTTT
Found at i:48996 original size:43 final size:44
Alignment explanation
Indices: 48894--49019 Score: 109
Period size: 44 Copynumber: 2.9 Consensus size: 44
48884 GAATTTGAGT
* * **
48894 CGCCTTTTGCGGGTTTTCAACTCAAAAT-TC-CTTTGGTTTCAAGA
1 CGCCTTTAGCGGGTTTTCAGCTC--AATCTCTCTTTTTTTTCAAGA
* *
48938 CGCCTTTAGCGGGTTTTCATCT-AGATCTCT-TTTTTTTTCGAGA
1 CGCCTTTAGCGGGTTTTCAGCTCA-ATCTCTCTTTTTTTTCAAGA
* *
48981 CGTCCTTTA-TGGGTTTTTAGCTCAATCTCTCTTTTTTTT
1 CG-CCTTTAGCGGGTTTTCAGCTCAATCTCTCTTTTTTTT
49020 AGGCGAAGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
41 1 0.01
42 2 0.03
43 30 0.44
44 35 0.51
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (44 bp):
CGCCTTTAGCGGGTTTTCAGCTCAATCTCTCTTTTTTTTCAAGA
Found at i:51058 original size:28 final size:29
Alignment explanation
Indices: 51026--51526 Score: 156
Period size: 29 Copynumber: 17.2 Consensus size: 29
51016 AACGAGGTCG
* *
51026 AAAATG-AAGTTTTAGATAG-TTCAGGGTT
1 AAAATGTAA-TTTTAGAAAGTTTAAGGGTT
*
51054 AAAATGTAATTTTGGAAAGTTTAAGGGTT
1 AAAATGTAATTTTAGAAAGTTTAAGGGTT
* * *
51083 AAAATGTAATTTTGGGAAAGTTT-GGGGTA
1 AAAATGTAATTTT-AGAAAGTTTAAGGGTT
* * ** **
51112 AAAATGTGATTTTTGAGAAG-TTCGGGGCA
1 AAAATGTAATTTTAGA-AAGTTTAAGGGTT
* * * * * *
51141 AAAATATGATTTTTGAAAGTTTGACGG-C
1 AAAATGTAATTTTAGAAAGTTTAAGGGTT
*** **
51169 AAAACTGTAAATTTTTAG-AAGTTCGGGGGAA
1 AAAA-TGT-AA-TTTTAGAAAGTTTAAGGGTT
* *
51200 AAAATGTAATTTTAAAGAAGTTT--GGGGT
1 AAAATGTAATTTTAGA-AAGTTTAAGGGTT
* * * * *
51228 ACAAATGTGATTTTTGGAAGTTT-GGGGTAA
1 A-AAATGTAATTTTAGAAAGTTTAAGGGT-T
* * ** *
51258 AAATATGT-TTTTTGGAAA--TTCGGGGGT
1 AAA-ATGTAATTTTAGAAAGTTTAAGGGTT
* *
51285 AAAATATAATTTTTAGAAAATTTTAA-GGTT
1 AAAATGTAA-TTTTAG-AAAGTTTAAGGGTT
* ** *
51315 AAAATATGGTTTTTGAGAAAGTTT-GGGGTT
1 AAAATGT-AATTTT-AGAAAGTTTAAGGGTT
* * *
51345 AAAATGTAATTTTTGGAAAGTTTAGGGGTC
1 AAAATGTAA-TTTTAGAAAGTTTAAGGGTT
* * *
51375 AAAATGTGATTTTTAG-AAGTTTGAA--ATC
1 AAAATGT-AATTTTAGAAAGTTT-AAGGGTT
* * * *
51403 AAAATGTGATTTTTGGAAAGTTTAGGGGTA
1 AAAATGT-AATTTTAGAAAGTTTAAGGGTT
*
51433 AAAATGTAATTTTTGGAAAGTTTAAGGGTT
1 AAAATGTAA-TTTTAGAAAGTTTAAGGGTT
* * * *
51463 AAAATGTATTTTTTGGAAAGTTTAGGGGTC
1 AAAATGTA-ATTTTAGAAAGTTTAAGGGTT
* * *
51493 AAAAT-TGATTTTTGGAAAGTTTAAGGGTC
1 AAAATGT-AATTTTAGAAAGTTTAAGGGTT
51522 AAAAT
1 AAAAT
51527 ATGATTTTTG
Statistics
Matches: 373, Mismatches: 65, Indels: 69
0.74 0.13 0.14
Matches are distributed among these distances:
26 3 0.01
27 5 0.01
28 67 0.18
29 143 0.38
30 141 0.38
31 14 0.04
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAGTTTAAGGGTT
Found at i:51103 original size:30 final size:30
Alignment explanation
Indices: 51049--51543 Score: 348
Period size: 30 Copynumber: 16.9 Consensus size: 30
51039 AGATAGTTCA
* *
51049 GGGTTAAAATGT-AATTTTGGAAAGTTTAA
1 GGGTTAAAATGTGATTTTTGGAAAGTTTAG
* *
51078 GGGTTAAAATGTAATTTTGGGAAAGTTT-G
1 GGGTTAAAATGTGATTTTTGGAAAGTTTAG
* *
51107 GGGTAAAAATGTGATTTTT-GAGAAG-TTCG
1 GGGTTAAAATGTGATTTTTGGA-AAGTTTAG
** *
51136 GGGCAAAAATATGATTTTT-GAAAGTTT-G
1 GGGTTAAAATGTGATTTTTGGAAAGTTTAG
* * * * **
51164 ACGG-CAAAACTGTAAATTTTTAG-AAGTTCGG
1 -GGGTTAAAA-TGT-GATTTTTGGAAAGTTTAG
** * **
51195 GGGAAAAAATGT-AATTTTAAAGAAGTTT-G
1 GGGTTAAAATGTGATTTTTGGA-AAGTTTAG
51224 GGG-TACAAATGTGATTTTTGG-AAGTTT-G
1 GGGTTA-AAATGTGATTTTTGGAAAGTTTAG
* * * *
51252 GGGTAAAAATATGTTTTTTGGAAA--TTCG
1 GGGTTAAAATGTGATTTTTGGAAAGTTTAG
* * * * *
51280 GGGGTAAAATATAATTTTTAGAAAATTTTA-
1 GGGTTAAAATGTGATTTTT-GGAAAGTTTAG
* * *
51310 AGGTTAAAATATGGTTTTTGAGAAAGTTT-G
1 GGGTTAAAATGTGATTTTTG-GAAAGTTTAG
*
51340 GGGTTAAAATGTAATTTTTGGAAAGTTTAG
1 GGGTTAAAATGTGATTTTTGGAAAGTTTAG
* *
51370 GGGTCAAAATGTGATTTTTAG-AAGTTT-G
1 GGGTTAAAATGTGATTTTTGGAAAGTTTAG
*** *
51398 AAATCAAAATGTGATTTTTGGAAAGTTTAG
1 GGGTTAAAATGTGATTTTTGGAAAGTTTAG
* * *
51428 GGGTAAAAATGTAATTTTTGGAAAGTTTAA
1 GGGTTAAAATGTGATTTTTGGAAAGTTTAG
51458 GGGTTAAAATGT-ATTTTTTGGAAAGTTTAG
1 GGGTTAAAATGTGA-TTTTTGGAAAGTTTAG
* *
51488 GGGTCAAAAT-TGATTTTTGGAAAGTTTAA
1 GGGTTAAAATGTGATTTTTGGAAAGTTTAG
* *
51517 GGGTCAAAATATGATTTTTGGAAAGTT
1 GGGTTAAAATGTGATTTTTGGAAAGTT
51544 CGAGGGCCTC
Statistics
Matches: 380, Mismatches: 58, Indels: 55
0.77 0.12 0.11
Matches are distributed among these distances:
27 2 0.01
28 76 0.20
29 122 0.32
30 172 0.45
31 8 0.02
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
GGGTTAAAATGTGATTTTTGGAAAGTTTAG
Found at i:51124 original size:58 final size:59
Alignment explanation
Indices: 51049--51543 Score: 388
Period size: 58 Copynumber: 8.5 Consensus size: 59
51039 AGATAGTTCA
* * * * *
51049 GGGTTAAAATGTAA-TTTTGGAAAGTTTAAGGGTTAAAATGTAATTTTGGGAAAGTTTG
1 GGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTAAAAATGTGATTTTTGGAAAGTTTG
* * * *
51107 GGGTAAAAATGTGATTTTT-GAGAAG-TTCGGGGCAAAAATATGATTTTT-GAAAGTTTG
1 GGGTAAAAATGTAATTTTTGGA-AAGTTTAGGGGTAAAAATGTGATTTTTGGAAAGTTTG
* * * * ** * * **
51164 ACGGCAAAACTGTAAATTTTTAG-AAGTTCGGGGGAAAAAATGT-AATTTTAAAGAAGTTTG
1 -GGGTAAAAATGT-AATTTTTGGAAAGTTTAGGGGTAAAAATGTGATTTTTGGA-AAGTTTG
* * * * *
51224 GGGTACAAATGTGATTTTTGG-AAGTTT-GGGGTAAAAATATGTTTTTTGGAAA-TTCGG
1 GGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTAAAAATGTGATTTTTGGAAAGTT-TG
* * * * *
51281 GGGT-AAAATATAATTTTTAGAAAATTTTAAGGTTAAAATATG-G-TTTTTGAGAAAGTTTG
1 GGGTAAAAATGTAATTTTT-GGAAAGTTTAGGGGTAAAA-ATGTGATTTTTG-GAAAGTTTG
* * *
51340 GGGTTAAAATGTAATTTTTGGAAAGTTTAGGGGTCAAAATGTGATTTTTAG-AAGTTTG
1 GGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTAAAAATGTGATTTTTGGAAAGTTTG
*** * * * *
51398 AAATCAAAATGTGATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTAAAAATGTGATTTTTGGAAAGTTT-G
* * * *
51458 GGGTTAAAATGTATTTTTTGGAAAGTTTAGGGGTCAAAAT-TGATTTTTGGAAAGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTAAAAATGTGATTTTTGGAAAGTTT-G
* * *
51517 GGGTCAAAATATGATTTTTGGAAAGTT
1 GGGTAAAAATGTAATTTTTGGAAAGTT
51544 CGAGGGCCTC
Statistics
Matches: 346, Mismatches: 70, Indels: 41
0.76 0.15 0.09
Matches are distributed among these distances:
56 13 0.04
57 28 0.08
58 128 0.37
59 114 0.33
60 63 0.18
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (59 bp):
GGGTAAAAATGTAATTTTTGGAAAGTTTAGGGGTAAAAATGTGATTTTTGGAAAGTTTG
Found at i:51358 original size:88 final size:87
Alignment explanation
Indices: 51063--51549 Score: 299
Period size: 88 Copynumber: 5.5 Consensus size: 87
51053 TAAAATGTAA
* * * * * * *
51063 TTTTGGAAAGTTTAAGGGTTAAAATGTAATTTTGGGAAAGTT-TGGGGTAAAAATGTGATTTTTG
1 TTTTGGAAAGTTT-GGGGTAAAAATGTAATTTTTGGAAAGTTCAGGGGTCAAAATATAATTTTT-
* * ***
51127 AGAAGTTCG-GGGCAAAAATATGAT
64 AGAAATTTGAAATC-AAAATATGAT
* * * * * ** *
51151 TTTT-GAAAGTTTGACGGCAAAACTGTAAATTTTTAG-AAGTTCGGGGGAAAAAATGTAATTTTA
1 TTTTGGAAAGTTTG-GGGTAAAAATGT-AATTTTTGGAAAGTTCAGGGGTCAAAATATAATTTT-
* * *** *
51214 AAGAAGTTTGGGGT-ACAAATGTGAT
63 TAGAAATTTGAAATCA-AAATATGAT
* ** *
51239 TTTTGG-AAGTTTGGGGTAAAAATATGTTTTTTGGAAA-TTCGGGGGT-AAAATATAATTTTTAG
1 TTTTGGAAAGTTTGGGGTAAAAATGTAATTTTTGGAAAGTTCAGGGGTCAAAATATAATTTTTAG
* * * *
51301 AAAATTTTAAGGTTAAAATATGGT
66 -AAATTTGAA-ATCAAAATATGAT
* * * *
51325 TTTTGAGAAAGTTTGGGGTTAAAATGTAATTTTTGGAAAGTTTAGGGGTCAAAATGTGATTTTTA
1 TTTTG-GAAAGTTTGGGGTAAAAATGTAATTTTTGGAAAGTTCAGGGGTCAAAATATAATTTTTA
* *
51390 GAAGTTTGAAATCAAAATGTGAT
65 GAAATTTGAAATCAAAATATGAT
* * * * * *
51413 TTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAGTTTAAGGGTTAAAATGTATTTTTTG
1 TTTTGGAAAGTTT-GGGGTAAAAATGTAATTTTTGGAAAGTTCAGGGGTCAAAATATAATTTTTA
***
51478 GAAAGTTTAGGGGTCAAAAT-TGAT
65 GAAA-TTT-GAAATCAAAATATGAT
* * * *
51502 TTTTGGAAAGTTTAAGGGTCAAAATATGATTTTTGGAAAGTTCGAGGG
1 TTTTGGAAAGTTT-GGGGTAAAAATGTAATTTTTGGAAAGTTC-AGGG
51550 CCTCTTAAGC
Statistics
Matches: 320, Mismatches: 60, Indels: 36
0.77 0.14 0.09
Matches are distributed among these distances:
84 2 0.01
85 17 0.05
86 28 0.09
87 42 0.13
88 144 0.45
89 62 0.19
90 25 0.08
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (87 bp):
TTTTGGAAAGTTTGGGGTAAAAATGTAATTTTTGGAAAGTTCAGGGGTCAAAATATAATTTTTAG
AAATTTGAAATCAAAATATGAT
Found at i:55473 original size:17 final size:18
Alignment explanation
Indices: 55453--55486 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55443 AATAATAATG
55453 AATTAAAAATT-TAAAAA
1 AATTAAAAATTATAAAAA
*
55470 AATTAGAAATTATAAAA
1 AATTAAAAATTATAAAA
55487 TTTTTCTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AATTAAAAATTATAAAAA
Found at i:57405 original size:16 final size:15
Alignment explanation
Indices: 57379--57412 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
57369 TTGTTGATTG
57379 ATTTTTGATAAAATT
1 ATTTTTGATAAAATT
*
57394 ATTTTATGATAATATT
1 ATTTT-TGATAAAATT
57410 ATT
1 ATT
57413 AGTTTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (15 bp):
ATTTTTGATAAAATT
Found at i:57510 original size:17 final size:17
Alignment explanation
Indices: 57475--57510 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
57465 TGATATTTGG
* *
57475 ATGATTAAATTTTTTTT
1 ATGATTAAATTATTGTT
57492 ATGATTAAATTATTGTT
1 ATGATTAAATTATTGTT
57509 AT
1 AT
57511 TAAATATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
ATGATTAAATTATTGTT
Found at i:70779 original size:18 final size:18
Alignment explanation
Indices: 70756--70792 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
70746 TTCTTGAGAA
*
70756 ACTTTATATCCTTCAGGG
1 ACTTTAAATCCTTCAGGG
*
70774 ACTTTAAATCCTTCTGGG
1 ACTTTAAATCCTTCAGGG
70792 A
1 A
70793 TTTTCATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (18 bp):
ACTTTAAATCCTTCAGGG
Found at i:74493 original size:32 final size:32
Alignment explanation
Indices: 74432--74495 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
74422 CAAAATATTG
* * *
74432 TTTTTTAATTTTTAAGGGGCCCAACTTTTTTT
1 TTTTTTAATTTTTAAGGGACCAAAATTTTTTT
74464 TTTTTTAATTTTTAA-GGACTCAAAATTTTTTT
1 TTTTTTAATTTTTAAGGGAC-CAAAATTTTTTT
74496 ACTAACTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (32 bp):
TTTTTTAATTTTTAAGGGACCAAAATTTTTTT
Found at i:81097 original size:17 final size:18
Alignment explanation
Indices: 81071--81107 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
81061 GGCCTATAAC
*
81071 AATATGAACATG-AATTA
1 AATATAAACATGAAATTA
81088 AATATAAACATGAAATTA
1 AATATAAACATGAAATTA
81106 AA
1 AA
81108 CACAATCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.27
Consensus pattern (18 bp):
AATATAAACATGAAATTA
Found at i:83997 original size:15 final size:15
Alignment explanation
Indices: 83969--84004 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
83959 TTCCACGAGA
* *
83969 TCTTCCTCAGGATCT
1 TCTTCTTCAAGATCT
83984 TCTTCTTCAAGATCT
1 TCTTCTTCAAGATCT
83999 TCTTCT
1 TCTTCT
84005 ACTTCATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.31, G:0.08, T:0.47
Consensus pattern (15 bp):
TCTTCTTCAAGATCT
Found at i:85651 original size:21 final size:20
Alignment explanation
Indices: 85597--85656 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
85587 TTAGTCCCTA
*
85597 TTATTTTA-TTATTT-GTAT
1 TTATTTTATTTATTTAGTGT
*
85615 TTA-TTTGTTTATTTTAGTGT
1 TTATTTTATTTA-TTTAGTGT
*
85635 TTAATTTTATTTATTTATTGT
1 TT-ATTTTATTTATTTAGTGT
85656 T
1 T
85657 ATCTTGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 3 0.09
18 6 0.18
19 3 0.09
20 5 0.15
21 9 0.27
22 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TTATTTTATTTATTTAGTGT
Found at i:85948 original size:23 final size:22
Alignment explanation
Indices: 85920--85964 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
85910 TATTGTCATG
*
85920 ATCATTATTATATATTACTTATT
1 ATCATTACTATATATTA-TTATT
*
85943 ATCATTACTATTTATTATTATT
1 ATCATTACTATATATTATTATT
85965 TTGTTTGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (22 bp):
ATCATTACTATATATTATTATT
Found at i:88897 original size:12 final size:12
Alignment explanation
Indices: 88882--88925 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
88872 TTTTTATAAA
88882 TATTTTGAATTT
1 TATTTTGAATTT
88894 TATTTTGAA--T
1 TATTTTGAATTT
88904 TATTTTGTAATTTT
1 TATTTTG-AA-TTT
88918 TATTTTGA
1 TATTTTGA
88926 GAAAGACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
12 9 0.32
13 1 0.04
14 8 0.29
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (12 bp):
TATTTTGAATTT
Found at i:88918 original size:24 final size:22
Alignment explanation
Indices: 88882--88925 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
88872 TTTTTATAAA
88882 TATTTTGAATTTTATTTTGAAT
1 TATTTTGAATTTTATTTTGAAT
88904 TATTTTGTAATTTTTATTTTGA
1 TATTTTG-AA-TTTTATTTTGA
88926 GAAAGACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (22 bp):
TATTTTGAATTTTATTTTGAAT
Found at i:101569 original size:18 final size:18
Alignment explanation
Indices: 101548--101596 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
101538 TCATACGAGC
101548 CAGTATGCT-ATAACAAGA
1 CAGTATGCTCA-AACAAGA
* *
101566 CAGTATGCTCAAACGAGT
1 CAGTATGCTCAAACAAGA
101584 CAGTATGCTCAAA
1 CAGTATGCTCAAA
101597 ACGAGCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (18 bp):
CAGTATGCTCAAACAAGA
Found at i:102176 original size:52 final size:52
Alignment explanation
Indices: 102114--102219 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
102104 TAAGCATACC
102114 AATCTATCCATAACTTTCAAGAACAAGCATATTCAACAATGGCAAGTTTTAT
1 AATCTATCCATAACTTTCAAGAACAAGCATATTCAACAATGGCAAGTTTTAT
102166 AATCTATCCATAACTTTCAAGAACAAGCATATTCAACAATGGCAAGTTTTAT
1 AATCTATCCATAACTTTCAAGAACAAGCATATTCAACAATGGCAAGTTTTAT
102218 AA
1 AA
102220 CATTTGAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (52 bp):
AATCTATCCATAACTTTCAAGAACAAGCATATTCAACAATGGCAAGTTTTAT
Found at i:103421 original size:23 final size:23
Alignment explanation
Indices: 103395--103469 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
103385 TCATTCTTTC
*
103395 TTTTCTTTTAGTTGTTT-TTTTAT
1 TTTTCTATTA-TTGTTTATTTTAT
*
103418 TTTTCTATTATTGTTTAGTTTTTT
1 TTTTCTATTATTGTTTA-TTTTAT
* *
103442 TTTTCTAATATTTGATTTATTTAAT
1 TTTTCTATTA-TTG-TTTATTTTAT
103467 TTT
1 TTT
103470 AAGTCATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 6 0.14
23 9 0.21
24 14 0.33
25 10 0.23
26 4 0.09
ACGTcount: A:0.16, C:0.04, G:0.07, T:0.73
Consensus pattern (23 bp):
TTTTCTATTATTGTTTATTTTAT
Found at i:105296 original size:24 final size:24
Alignment explanation
Indices: 105264--105325 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
105254 AATCTTCCAG
*
105264 TTAAACTCTATTTGTTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
* *
105288 TTAAACTCTGTTTATTTGTTTCAG
1 TTAAACTCTATTTATTTGTTTCAA
*
105312 TCAAACTCTTATTT
1 TTAAACTC-TATTT
105326 TAGATTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.24, C:0.15, G:0.08, T:0.53
Consensus pattern (24 bp):
TTAAACTCTATTTATTTGTTTCAA
Found at i:107264 original size:24 final size:24
Alignment explanation
Indices: 107232--107278 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
107222 AATAATCTTC
*
107232 CAATTAAACTTTGTTTATTTGTTA
1 CAATTAAACTCTGTTTATTTGTTA
107256 CAATTAAACTCTGTTTATTTGTT
1 CAATTAAACTCTGTTTATTTGTT
107279 TCAGTCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (24 bp):
CAATTAAACTCTGTTTATTTGTTA
Found at i:107288 original size:24 final size:24
Alignment explanation
Indices: 107232--107291 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
107222 AATAATCTTC
* *
107232 CAATTAAACTTTGTTTATTTGTTA
1 CAATCAAACTCTGTTTATTTGTTA
* *
107256 CAATTAAACTCTGTTTATTTGTTT
1 CAATCAAACTCTGTTTATTTGTTA
*
107280 CAGTCAAACTCT
1 CAATCAAACTCT
107292 TAGTATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.48
Consensus pattern (24 bp):
CAATCAAACTCTGTTTATTTGTTA
Found at i:111112 original size:41 final size:41
Alignment explanation
Indices: 111036--111325 Score: 303
Period size: 41 Copynumber: 7.1 Consensus size: 41
111026 ATTTTTACTA
* * *
111036 AAAATGCCACTAAAAG-CAGAGCATTAGCGGTGTTTATGAG
1 AAAATGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAG
* * **
111076 AAAATGCCACTAAAGGTCTGAGCATTAGCGGCGTTTATTTG
1 AAAATGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAG
* * * * *
111117 ACAACGCCGCTAAAGGTCTGAGCATTAACGGTGTTTATGAG
1 AAAATGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAG
* * **
111158 AAAACGCCGCTAAAGGTCTGAGCATTAGCGGCGTTTATTTG
1 AAAATGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAG
* * * *
111199 ACAACGCCGCTAAAGGTCAGAGCATTAGTGGCATTTATGAG
1 AAAATGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAG
* * * * *
111240 AAAATGCCGCTAAAGGTCAGAGCAGTAGCGACATTTATTAA
1 AAAATGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAG
** * * *
111281 AAAATATCGCTAAAGGACAGAGTATTAGCGGTGTTTATGAG
1 AAAATGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAG
111322 AAAA
1 AAAA
111326 ACACCGCTAA
Statistics
Matches: 209, Mismatches: 40, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
40 15 0.07
41 194 0.93
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (41 bp):
AAAATGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAG
Found at i:111191 original size:82 final size:82
Alignment explanation
Indices: 111052--111357 Score: 371
Period size: 82 Copynumber: 3.7 Consensus size: 82
111042 CCACTAAAAG
* * *
111052 CAGAGCATTAGCGGTGTTTATGAGAAAATGCCACTAAAGGTCTGAGCATTAGCGGCGTTTATTTG
1 CAGAGCATTAGCGGTGTTTATGAGAAAACGCCGCTAAAGGTCTGAGCATTAGCGACGTTTATTTG
111117 ACAACGCCGCTAAAGGT
66 ACAACGCCGCTAAAGGT
* * *
111134 CTGAGCATTAACGGTGTTTATGAGAAAACGCCGCTAAAGGTCTGAGCATTAGCGGCGTTTATTTG
1 CAGAGCATTAGCGGTGTTTATGAGAAAACGCCGCTAAAGGTCTGAGCATTAGCGACGTTTATTTG
111199 ACAACGCCGCTAAAGGT
66 ACAACGCCGCTAAAGGT
* ** * * * * **
111216 CAGAGCATTAGTGGCATTTATGAGAAAATGCCGCTAAAGGTCAGAGCAGTAGCGACATTTATTAA
1 CAGAGCATTAGCGGTGTTTATGAGAAAACGCCGCTAAAGGTCTGAGCATTAGCGACGTTTATTTG
* *** *
111281 AAAATATCGCTAAAGGA
66 ACAACGCCGCTAAAGGT
* * * * *
111298 CAGAGTATTAGCGGTGTTTATGAGAAAAACACCGCTAAGGGT-TAAGCAATAGCGACGTTT
1 CAGAGCATTAGCGGTGTTTATGAG-AAAACGCCGCTAAAGGTCTGAGCATTAGCGACGTTT
111358 TTTCCATAAA
Statistics
Matches: 191, Mismatches: 32, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
82 177 0.93
83 14 0.07
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (82 bp):
CAGAGCATTAGCGGTGTTTATGAGAAAACGCCGCTAAAGGTCTGAGCATTAGCGACGTTTATTTG
ACAACGCCGCTAAAGGT
Found at i:112503 original size:29 final size:29
Alignment explanation
Indices: 112453--112512 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
112443 ATATGCAATA
* *
112453 TTATATATAAATTTTGATTTTG-TGTAATT
1 TTATATATAAATATTGAATTTGAT-TAATT
112482 TTATATATTAAATATT-AATTTGATTAATT
1 TTATATA-TAAATATTGAATTTGATTAATT
112511 TT
1 TT
112513 CACAAATCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (29 bp):
TTATATATAAATATTGAATTTGATTAATT
Found at i:112722 original size:17 final size:18
Alignment explanation
Indices: 112691--112724 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
112681 AAGATTCATG
112691 TATATAATTACATCAAAT
1 TATATAATTACATCAAAT
*
112709 TATAT-ATTAGATCAAA
1 TATATAATTACATCAAA
112725 GTTCATATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (18 bp):
TATATAATTACATCAAAT
Found at i:113204 original size:41 final size:41
Alignment explanation
Indices: 113153--113307 Score: 132
Period size: 41 Copynumber: 3.7 Consensus size: 41
113143 AAAAAATTAG
* *
113153 AGGTCAAGCAATAGCAGCGTTTATGGAAAAAACGCCGCAAA
1 AGGTAAAGCAATAGCGGCGTTTATGGAAAAAACGCCGCAAA
*** * *
113194 AGGTAAAGCAATAGCGGCGTTT-TTTCATAAACGCTGCAAA
1 AGGTAAAGCAATAGCGGCGTTTATGGAAAAAACGCCGCAAA
* * * ** *
113234 AGGTAAAGTAATAGTGGCATTTATGGGGAAAACGTCGCAAA
1 AGGTAAAGCAATAGCGGCGTTTATGGAAAAAACGCCGCAAA
* * *
113275 AGGTCCAGAGCATTAGCGGCATTTATTGGAAAA
1 AGGT--AAAGCAATAGCGGCGTTTA-TGGAAAA
113308 CGTCGTAAAA
Statistics
Matches: 87, Mismatches: 23, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
40 32 0.37
41 35 0.40
43 15 0.17
44 5 0.06
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.21
Consensus pattern (41 bp):
AGGTAAAGCAATAGCGGCGTTTATGGAAAAAACGCCGCAAA
Found at i:113310 original size:42 final size:42
Alignment explanation
Indices: 113249--113349 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
113239 AAGTAATAGT
113249 GGCATTTATGGGGAAAACGTCGCAAAAGGTCCAGAG-CATTAGC
1 GGCATTTAT-GGGAAAACGTCGCAAAAGGTCCAG-GTCATTAGC
* * *
113292 GGCATTTATTGGAAAACGTCGTAAAATGTCCAGGTCATTAGC
1 GGCATTTATGGGAAAACGTCGCAAAAGGTCCAGGTCATTAGC
*
113334 GGCGTTTATGGGAAAA
1 GGCATTTATGGGAAAA
113350 ACGCTACTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
41 1 0.02
42 42 0.81
43 9 0.17
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (42 bp):
GGCATTTATGGGAAAACGTCGCAAAAGGTCCAGGTCATTAGC
Found at i:113592 original size:17 final size:17
Alignment explanation
Indices: 113550--113594 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
113540 CGCCCTTTTA
* *
113550 TTCTTCACACCAAAATT
1 TTCTTCACGCCAAAATC
*
113567 TTCTTCACGCCAGAATC
1 TTCTTCACGCCAAAATC
113584 TTCTTCACGCC
1 TTCTTCACGCC
113595 GTTCTCTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.24, C:0.36, G:0.07, T:0.33
Consensus pattern (17 bp):
TTCTTCACGCCAAAATC
Found at i:116680 original size:14 final size:14
Alignment explanation
Indices: 116661--116702 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
116651 GACCCTAAAC
*
116661 CCAAATATGTAATT
1 CCAAATATTTAATT
116675 CCAAATATTTAATT
1 CCAAATATTTAATT
*
116689 CAAAATATTTAATT
1 CCAAATATTTAATT
116703 ATTTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (14 bp):
CCAAATATTTAATT
Found at i:116707 original size:8 final size:8
Alignment explanation
Indices: 116694--116722 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
116684 TAATTCAAAA
116694 TATTTAAT
1 TATTTAAT
116702 TATTTAAT
1 TATTTAAT
116710 TATTTAAT
1 TATTTAAT
116718 TATTT
1 TATTT
116723 GTAACTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATTTAAT
Found at i:122019 original size:13 final size:14
Alignment explanation
Indices: 122003--122031 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
121993 TTTTAAATAT
122003 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
122016 TTATAATGGTTTAA
1 TTATAATGGTTTAA
122030 TT
1 TT
122032 CATCGTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:122891 original size:42 final size:43
Alignment explanation
Indices: 122792--122892 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 43
122782 GAGAAAAGCC
* * * *
122792 CGCTAAAGACCATGCTCTTTAGTGGCGTTTGTGGGGAAAGTGT
1 CGCTAAAGACCATGTTCTTTAGCGGCATTTGTGGGCAAAGTGT
* *
122835 CGCTAAAGACCATGTTCTTTAGCGTCATTT-TTGGCAAAGTGT
1 CGCTAAAGACCATGTTCTTTAGCGGCATTTGTGGGCAAAGTGT
*
122877 CGCTAAAGATCATGTT
1 CGCTAAAGACCATGTT
122893 TTATAGTGCG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 25 0.49
43 26 0.51
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (43 bp):
CGCTAAAGACCATGTTCTTTAGCGGCATTTGTGGGCAAAGTGT
Found at i:123912 original size:4 final size:4
Alignment explanation
Indices: 123903--123945 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
123893 ATCATTTACC
*
123903 TTAT TTAT TTAT TTAT CTT-T TTAT TATTT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT -TTAT TTAT T-TAT TTAT TTAT TTAT TT
123946 TCCAGCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 2 0.06
4 27 0.79
5 5 0.15
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:123978 original size:3 final size:3
Alignment explanation
Indices: 123972--124003 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
123962 TATTATTATT
*
123972 ATC ATC ATC ATC ATC ATC ATA ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
124004 TACTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:124017 original size:12 final size:12
Alignment explanation
Indices: 124002--124049 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
123992 AATCATCATC
124002 ATTACTATTATT
1 ATTACTATTATT
*
124014 ATTACTAATATT
1 ATTACTATTATT
* * *
124026 TTTATTATCATT
1 ATTACTATTATT
*
124038 ACTACTATTATT
1 ATTACTATTATT
124050 TTTTATTTAT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTACTATTATT
Found at i:124033 original size:21 final size:22
Alignment explanation
Indices: 124007--124056 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
123997 TCATCATTAC
124007 TATTATTATTACTAATATT-TT
1 TATTATTATTACTAATATTATT
* *
124028 TATTATCATTACTACTATTATT
1 TATTATTATTACTAATATTATT
*
124050 TTTTATT
1 TATTATT
124057 TATTTATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTATTATTACTAATATTATT
Found at i:125230 original size:85 final size:85
Alignment explanation
Indices: 125084--125257 Score: 249
Period size: 85 Copynumber: 2.0 Consensus size: 85
125074 ACCTAAACCT
*
125084 GAGAAGAAAAAGGCAGCAGTAATAACTACTGATGGTAGCCCATCCAAGAGAAGATCCGGATATAA
1 GAGAAGAAAAAGGCAGCAGTAATAACTACTGATGGTAGCCCATCCAAGAGAAGATCAGGATATAA
* *
125149 TGAGGATATTGGAGTAATAG
66 TGAAGATATTGGAGTAATAA
* * * * * * * *
125169 GAGAATAACAAGGCAGCGGTAGTAACTACTGATGGTGGTCCATCCCAGAGAAGATTAGGATATAA
1 GAGAAGAAAAAGGCAGCAGTAATAACTACTGATGGTAGCCCATCCAAGAGAAGATCAGGATATAA
125234 TGAAGATATTGGAGTAATAA
66 TGAAGATATTGGAGTAATAA
125254 GAGA
1 GAGA
125258 TGAGTTGCGA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (85 bp):
GAGAAGAAAAAGGCAGCAGTAATAACTACTGATGGTAGCCCATCCAAGAGAAGATCAGGATATAA
TGAAGATATTGGAGTAATAA
Found at i:125554 original size:21 final size:21
Alignment explanation
Indices: 125530--125581 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
125520 ATAATACCAT
125530 AATCCAAATACAAAGTTTAGA
1 AATCCAAATACAAAGTTTAGA
* * *
125551 AATCCAAACATAAAGTTTATA
1 AATCCAAATACAAAGTTTAGA
*
125572 GATCCAAATA
1 AATCCAAATA
125582 ACATAATCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (21 bp):
AATCCAAATACAAAGTTTAGA
Found at i:130211 original size:23 final size:23
Alignment explanation
Indices: 130179--130665 Score: 561
Period size: 23 Copynumber: 21.3 Consensus size: 23
130169 TTAATTCTTG
*
130179 AAGCATAAATCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
* * *
130202 AATCATAAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
* *
130225 AAGCATACATCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
* * *
130248 AAGCATACATCACATTAATATAT
1 AAGCACAAATCACATTAATATTT
* *
130271 GAGCACAAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
* *
130294 AAGTACAAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
* * *
130317 GAGGACAAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
*
130340 ATGCACAAATCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
* *
130363 AAGCATAAATCACATTAATAATT
1 AAGCACAAATCACATTAATATTT
* *
130386 GAGCACAAATCATATT-ATATTT
1 AAGCACAAATCACATTAATATTT
130408 AAGCACAAATCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
* * *
130431 GAGAACAAATTGA-ATTAATATTT
1 AAGCACAAA-TCACATTAATATTT
*
130454 AAGCATAAATCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
130477 AAGCACAAATCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
* * * *
130500 GAGAACCAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
*
130523 AAGCACAAATCACACTAAT-TTT
1 AAGCACAAATCACATTAATATTT
* *
130545 CAGCACAAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
*
130568 AAGCATAAATCACATTAAT-TCTT
1 AAGCACAAATCACATTAATAT-TT
130591 AAGC-CTAAATCACATTAATATTT
1 AAGCAC-AAATCACATTAATATTT
* * *
130614 AATCATAAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
* * *
130637 AATCATAAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
130660 AAGCAC
1 AAGCAC
130666 GGATATAAGA
Statistics
Matches: 399, Mismatches: 57, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
22 41 0.10
23 355 0.89
24 3 0.01
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (23 bp):
AAGCACAAATCACATTAATATTT
Found at i:132184 original size:7 final size:7
Alignment explanation
Indices: 132172--132200 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
132162 GAAAATTCAT
132172 TTTCTTC
1 TTTCTTC
132179 TTTCTTC
1 TTTCTTC
132186 TTTCTTC
1 TTTCTTC
132193 -TTCTTC
1 TTTCTTC
132199 TT
1 TT
132201 CTTTTGCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCTTC
Found at i:133268 original size:24 final size:24
Alignment explanation
Indices: 133241--133304 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
133231 ACTCTATTCG
* *
133241 GGCTTGAATGAGCTAACTTATTTA
1 GGCTCGAATGAGCTAACCTATTTA
*
133265 GGCTCGTAA-GAGCTAACCTATTTG
1 GGCTCG-AATGAGCTAACCTATTTA
*
133289 GGCTCGTATGAGCTAA
1 GGCTCGAATGAGCTAA
133305 ATTTATGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 31 0.91
25 2 0.06
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (24 bp):
GGCTCGAATGAGCTAACCTATTTA
Found at i:142725 original size:124 final size:124
Alignment explanation
Indices: 142505--142871 Score: 644
Period size: 124 Copynumber: 3.0 Consensus size: 124
142495 TGAATGCAGC
* * *
142505 CACAAGATCAGCTGATAATTACGACCAAGAGATGTCATCGCATTGCAACTAAACCTTGAATGAAT
1 CACAAGATCAGCTGGTAATTGCGACCAAGAGATGTCATCGCATTGCAACTAAACCTTGAATGAGT
142570 AGAATCAAACTGAATCCATAGTTGGAAGCACCAACGCAGGAATTTCACAGATGTCGTTG
66 AGAATCAAACTGAATCCATAGTTGGAAGCACCAACGCAGGAATTTCACAGATGTCGTTG
142629 CACAAGATCAGCTGGTAATTGCGACCAAGAGATGTCATCGCATTGCAACTAAACCTTGAATGAGT
1 CACAAGATCAGCTGGTAATTGCGACCAAGAGATGTCATCGCATTGCAACTAAACCTTGAATGAGT
* **
142694 TGAATCAAGTTGAATCCATAGTTGGAAGCACCAACGCAGGAATTTCACAGATGTCGTTG
66 AGAATCAAACTGAATCCATAGTTGGAAGCACCAACGCAGGAATTTCACAGATGTCGTTG
*
142753 CACAAGATTAGCTGGTAATTGCGACCAAGAGATGTCATCGCATTGCAACTAAACCTTGAATGAGT
1 CACAAGATCAGCTGGTAATTGCGACCAAGAGATGTCATCGCATTGCAACTAAACCTTGAATGAGT
* **
142818 AGAATCAACCTGAATCCATAGTTGGAAGCACCAAAACAGGAATTTCACAGATGT
66 AGAATCAAACTGAATCCATAGTTGGAAGCACCAACGCAGGAATTTCACAGATGT
142872 TGCTGCAATT
Statistics
Matches: 231, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
124 231 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (124 bp):
CACAAGATCAGCTGGTAATTGCGACCAAGAGATGTCATCGCATTGCAACTAAACCTTGAATGAGT
AGAATCAAACTGAATCCATAGTTGGAAGCACCAACGCAGGAATTTCACAGATGTCGTTG
Found at i:176244 original size:21 final size:21
Alignment explanation
Indices: 176218--176290 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 21
176208 GGAGTTTTTG
176218 GTATCGGTAGATACATGACTT
1 GTATCGGTAGATACATGACTT
176239 GTATCGGTAGATACATGACTT
1 GTATCGGTAGATACATGACTT
176260 GTATCGGTAGA-A-ATTGCACTT
1 GTATCGGTAGATACA-TG-ACTT
176281 GTATCGGTAG
1 GTATCGGTAG
176291 GACTAGCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.02
20 3 0.06
21 46 0.92
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGATACATGACTT
Found at i:177414 original size:23 final size:23
Alignment explanation
Indices: 177372--177724 Score: 429
Period size: 23 Copynumber: 15.4 Consensus size: 23
177362 ATCCTAATTC
* *
177372 TTTAAGTACAAAGCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
177395 TTTAATCATAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
177418 TTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
177441 TTTAAGCATACATCACATTATTA
1 TTTAAGCACAAATCACATTAATA
* *
177464 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
177487 TTTAAGCACAAATCACATTAATC
1 TTTAAGCACAAATCACATTAATA
* * * *
177510 TTTGAGTACAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
177533 TTTAAGCTCAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
177556 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
177579 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
177602 TTTAAGCACAAATCACACTAAT-
1 TTTAAGCACAAATCACATTAATA
* *
177624 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
177647 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
177670 CTTCAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
177693 TTTAATCATAAATCATATCAATA
1 TTTAAGCACAAATCACATTAATA
177716 TTTAAGCAC
1 TTTAAGCAC
177725 GGATATAAGA
Statistics
Matches: 275, Mismatches: 54, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
22 19 0.07
23 256 0.93
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:178046 original size:16 final size:17
Alignment explanation
Indices: 178022--178055 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
178012 TCTTAAATCG
178022 AAACCTTAAAC-CTAAT
1 AAACCTTAAACTCTAAT
*
178038 AAACTTTAAACTCTAAT
1 AAACCTTAAACTCTAAT
178055 A
1 A
178056 TCTCAGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (17 bp):
AAACCTTAAACTCTAAT
Found at i:181253 original size:32 final size:32
Alignment explanation
Indices: 181191--181254 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
181181 TCTCTCATAA
*
181191 AAAAATAAGATTATTATTAAATATAATTTTAT
1 AAAAATAAGATTATAATTAAATATAATTTTAT
* * *
181223 AAAAATAATA-TATAATTTAATAATATTTTTAT
1 AAAAATAAGATTATAATTAAAT-ATAATTTTAT
181255 TATAATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (32 bp):
AAAAATAAGATTATAATTAAATATAATTTTAT
Found at i:181317 original size:62 final size:59
Alignment explanation
Indices: 181200--181317 Score: 130
Period size: 62 Copynumber: 1.9 Consensus size: 59
181190 AAAAAATAAG
* * * * **
181200 ATTATTATTAAATATAATTTTATAAAAATAATATATAATTTAATAATATTTTTATTATA
1 ATTATTATTAAATATAATTATAAAAAAATAATACATAATTTAATAAAATAATTATTATA
*
181259 ATTATTATTAAAATATGAATTAATAAAAAAATAATACATGATATTAA-AAAATAATTATT
1 ATTATTATT-AAATAT-AATT-ATAAAAAAATAATACATAAT-TTAATAAAATAATTATT
181318 TATTTTATCC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
59 9 0.19
60 6 0.12
61 4 0.08
62 25 0.52
63 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATATAATTATAAAAAAATAATACATAATTTAATAAAATAATTATTATA
Found at i:181480 original size:14 final size:14
Alignment explanation
Indices: 181438--181480 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
181428 GTAAAAAAAA
*
181438 AAAAAAAAGATGTTC
1 AAAAAAAA-ATATTC
*
181453 AAAAAAATATTATTC
1 AAAAAAA-AATATTC
181468 AAAAAAAAATATT
1 AAAAAAAAATATT
181481 TATATAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.21
15 18 0.75
16 1 0.04
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (14 bp):
AAAAAAAAATATTC
Found at i:184352 original size:17 final size:18
Alignment explanation
Indices: 184326--184363 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
184316 CCCTTTTAAA
184326 TTTTATGCA-TATATTTAT
1 TTTTATGCATTAT-TTTAT
184344 TTTTA-GCATTATTTTAT
1 TTTTATGCATTATTTTAT
184361 TTT
1 TTT
184364 ATTTACTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTATGCATTATTTTAT
Found at i:192395 original size:99 final size:99
Alignment explanation
Indices: 192254--192661 Score: 433
Period size: 99 Copynumber: 4.1 Consensus size: 99
192244 GATACCTTAG
* ** * ** * *
192254 AGATACGAAGGGAACTGTTGAGGCCACAACAGCGAACTTGGTACCTTAGAAGACATGATGGGAAG
1 AGATATGAAGGGAAAAGTTGAGGCTACAATGGCGAACCTGGTACCTTAGAAGACATGATGGGAAA
192319 GATCGAGGCTGCAACGGCGGATCTGGTACCATGA
66 GATCGAGGCTGCAACGGCGGATCTGGTACCATGA
* * * * *
192353 CGATATGAAGGGAAAAGCTGAGGCTACAATGGCGAACCTGGTATCTTAAAAGACATGATGGGAAG
1 AGATATGAAGGGAAAAGTTGAGGCTACAATGGCGAACCTGGTACCTTAGAAGACATGATGGGAAA
* ** * *
192418 GATCGAGG-TCGTAATAGTGTATCTGGTACCATGA
66 GATCGAGGCT-GCAACGGCGGATCTGGTACCATGA
* * * * * * *
192452 AGATATGAA-CGAAAAGGTTGAGGCTGCAATGACAAACCCGATACCTTAGAAGACATGATGAGAA
1 AGATATGAAGGGAAAA-GTTGAGGCTACAATGGCGAACCTGGTACCTTAGAAGACATGATGGGAA
* *
192516 AGATCGAGGCTGCAACGGCTGATCTGATACCATGA
65 AGATCGAGGCTGCAACGGCGGATCTGGTACCATGA
* * ** *
192551 AGATATGAAGGGAAAGGTTGAGGCTACAACGGCGAACCTGGTACCTTAGAAGATGTGATGGAAAA
1 AGATATGAAGGGAAAAGTTGAGGCTACAATGGCGAACCTGGTACCTTAGAAGACATGATGGGAAA
* * * * *
192616 GATCGAGGCCGCAACGACAGATCTAGTAACATGA
66 GATCGAGGCTGCAACGGCGGATCTGGTACCATGA
* *
192650 AAATATAAAGGG
1 AGATATGAAGGG
192662 GATAGGTTGA
Statistics
Matches: 250, Mismatches: 55, Indels: 8
0.80 0.18 0.03
Matches are distributed among these distances:
98 6 0.02
99 239 0.96
100 5 0.02
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (99 bp):
AGATATGAAGGGAAAAGTTGAGGCTACAATGGCGAACCTGGTACCTTAGAAGACATGATGGGAAA
GATCGAGGCTGCAACGGCGGATCTGGTACCATGA
Found at i:192614 original size:49 final size:49
Alignment explanation
Indices: 192270--192614 Score: 182
Period size: 49 Copynumber: 7.0 Consensus size: 49
192260 GAAGGGAACT
* * * * *
192270 GTTGAGGCCACAACAGCGAACTTGGTACCTTAGAAGACATGATGGGAAG
1 GTTGAGGCTACAACGGCGAACCTGGTACCTTAGAAGATATGATGGAAAG
* * * * * * * *
192319 GATCGAGGCTGCAACGGCGGATCTGGTACCAT-GACGATATGAAGGGAAAA
1 G-TTGAGGCTACAACGGCGAACCTGGTACCTTAGAAGATATG-ATGGAAAG
* * * * * *
192369 GCTGAGGCTACAATGGCGAACCTGGTATCTTAAAAGACATGATGGGAAG
1 GTTGAGGCTACAACGGCGAACCTGGTACCTTAGAAGATATGATGGAAAG
* * * * * * *
192418 GATCGAGGTCGTA-ATA--GTGTATCTGGTACCAT-GAAGATATGAACGAAAAG
1 G-TTGAGG-C-TACA-ACGGCGAACCTGGTACCTTAGAAGATATG-ATGGAAAG
* * * * * * *
192468 GTTGAGGCTGCAATGACAAACCCGATACCTTAGAAGACATGATGAGAAAG
1 GTTGAGGCTACAACGGCGAACCTGGTACCTTAGAAGATATGATG-GAAAG
* * * * * * *
192518 ATCGAGGCTGCAACGGCTG-ATCTGATACCAT-GAAGATATGAAGGGAAAG
1 GTTGAGGCTACAACGGC-GAACCTGGTACCTTAGAAGATATG-ATGGAAAG
*
192567 GTTGAGGCTACAACGGCGAACCTGGTACCTTAGAAGATGTGATGGAAA
1 GTTGAGGCTACAACGGCGAACCTGGTACCTTAGAAGATATGATGGAAA
192615 AGATCGAGGC
Statistics
Matches: 209, Mismatches: 70, Indels: 34
0.67 0.22 0.11
Matches are distributed among these distances:
47 2 0.01
48 3 0.01
49 100 0.48
50 99 0.47
51 2 0.01
52 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (49 bp):
GTTGAGGCTACAACGGCGAACCTGGTACCTTAGAAGATATGATGGAAAG
Found at i:192631 original size:50 final size:50
Alignment explanation
Indices: 192280--192631 Score: 214
Period size: 50 Copynumber: 7.1 Consensus size: 50
192270 GTTGAGGCCA
* * * * *
192280 CAACAGCGAACTTGGTACCTTAGAAGACATGATGGGAAGGATCGAGGCTG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGAAAAGATCGAGGCTG
* * * * * * *
192330 CAACGGCGGATCTGGTACCAT-GACGATATGAAGGGAAAAGCT-GAGGCTA
1 CAACGGCGAACCTGGTACCTTAGAAGATATG-ATGGAAAAGATCGAGGCTG
* * * * * *
192379 CAATGGCGAACCTGGTATCTTAAAAGACATGATGGGAAGGATCGAGG-TCG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGAAAAGATCGAGGCT-G
* ** * * * * ** * *
192429 TAATAGTGTATCTGGTACCAT-GAAGATATGAACGAAAAGGTTGAGGCTG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGAAAAGATCGAGGCTG
* * * * * *
192478 CAATGACAAACCCGATACCTTAGAAGACATGAT-GAGAAAGATCGAGGCTG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGA-AAAGATCGAGGCTG
* * * * * * * *
192528 CAACGGCTG-ATCTGATACCAT-GAAGATATGAAGGGAAAGGTTGAGGCTA
1 CAACGGC-GAACCTGGTACCTTAGAAGATATGATGGAAAAGATCGAGGCTG
* *
192577 CAACGGCGAACCTGGTACCTTAGAAGATGTGATGGAAAAGATCGAGGCCG
1 CAACGGCGAACCTGGTACCTTAGAAGATATGATGGAAAAGATCGAGGCTG
192627 CAACG
1 CAACG
192632 ACAGATCTAG
Statistics
Matches: 215, Mismatches: 76, Indels: 22
0.69 0.24 0.07
Matches are distributed among these distances:
48 1 0.00
49 104 0.48
50 110 0.51
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (50 bp):
CAACGGCGAACCTGGTACCTTAGAAGATATGATGGAAAAGATCGAGGCTG
Found at i:192708 original size:198 final size:198
Alignment explanation
Indices: 192295--192709 Score: 492
Period size: 198 Copynumber: 2.1 Consensus size: 198
192285 GCGAACTTGG
* * * *
192295 TACCTTAGAAGACATGATGGGAAGGATCGAGGCTGCAACGGCGGATCTGGTACCATGACGATATG
1 TACCTTAGAAGACATGATGAGAAAGATCGAGGCTGCAACGGCGGATCTGATACCATGAAGATATG
* * * *
192360 AAGGGAAAAGCTGAGGCTACAATGGCGAACCTGGTATCTTAAAAGACATGATGGGAAGGATCGAG
66 AAGGGAAAAGCTGAGGCTACAACGGCGAACCTGGTACCTTAAAAGACATGATGGAAAAGATCGAG
* * * ** * * * * * ** *
192425 GTCGTAATAGTGTATCTGGTACCATGAAGATATGAACGAAAAGGTTGAGGCTGCAATGACAAACC
131 GCCGCAAGACAGTATCTAGTAACATGAAAATATAAACGAAAAGGTTGAAGCCACAACGACAAACC
192490 CGA
196 CGA
*
192493 TACCTTAGAAGACATGATGAGAAAGATCGAGGCTGCAACGGCTGATCTGATACCATGAAGATATG
1 TACCTTAGAAGACATGATGAGAAAGATCGAGGCTGCAACGGCGGATCTGATACCATGAAGATATG
* * * **
192558 AAGGGAAAGGTTGAGGCTACAACGGCGAACCTGGTACCTTAGAAGATGTGATGGAAAAGATCGAG
66 AAGGGAAAAGCTGAGGCTACAACGGCGAACCTGGTACCTTAAAAGACATGATGGAAAAGATCGAG
* * * *
192623 GCCGCAACGACAG-ATCTAGTAACATGAAAATATAAAGGGGATAGGTTGAATCCACAACGACAAA
131 GCCGCAA-GACAGTATCTAGTAACATGAAAATATAAA-CGAAAAGGTTGAAGCCACAACGACAAA
**
192687 CCTTA
194 CCCGA
*
192692 TACCCTAGAA-ACATGATG
1 TACCTTAGAAGACATGATG
192710 GGAATGATTG
Statistics
Matches: 181, Mismatches: 34, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
198 148 0.82
199 33 0.18
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (198 bp):
TACCTTAGAAGACATGATGAGAAAGATCGAGGCTGCAACGGCGGATCTGATACCATGAAGATATG
AAGGGAAAAGCTGAGGCTACAACGGCGAACCTGGTACCTTAAAAGACATGATGGAAAAGATCGAG
GCCGCAAGACAGTATCTAGTAACATGAAAATATAAACGAAAAGGTTGAAGCCACAACGACAAACC
CGA
Found at i:192709 original size:99 final size:100
Alignment explanation
Indices: 192295--192710 Score: 279
Period size: 99 Copynumber: 4.2 Consensus size: 100
192285 GCGAACTTGG
* * * * * * **
192295 TACCTTAGAAGACATGATGG-GAAGGATCGAGGCTGCAACGGCGGATCTGGTACCATGACGATAT
1 TACCTTAGAAGACATGATGGAGAAAGATCGAGGCCGCAACGACAGATCTGATAACATGAAAATAT
* * * * * * * * *
192359 GAAGGGAAAAGCTGAGGCTACAATGGCGAACCTGG
66 AAAGGGAAAGGTTGAAGCCACAACGACAAACCTGA
* * * * * * ** * * *
192394 TATCTTAAAAGACATGATGG-GAAGGATCGAGGTCGTAA-TAGTGTATCTGGTACCATGAAGATA
1 TACCTTAGAAGACATGATGGAGAAAGATCGAGGCCGCAACGACAG-ATCTGATAACATGAAAATA
* * * * ** * *
192457 TGAACGAAAAGGTTGAGGCTGCAATGACAAACCCGA
65 TAAAGGGAAAGGTTGAAGCCACAACGACAAACCTGA
* * * * *
192493 TACCTTAGAAGACATGAT-GAGAAAGATCGAGGCTGCAACGGCTGATCTGATACCATGAAGATAT
1 TACCTTAGAAGACATGATGGAGAAAGATCGAGGCCGCAACGACAGATCTGATAACATGAAAATAT
* * * * * *
192557 GAAGGGAAAGGTTGAGGCTACAACGGCGAACCTGG
66 AAAGGGAAAGGTTGAAGCCACAACGACAAACCTGA
**
192592 TACCTTAGAAGATGTGATGGA-AAAGATCGAGGCCGCAACGACAGATCT-AGTAACATGAAAATA
1 TACCTTAGAAGACATGATGGAGAAAGATCGAGGCCGCAACGACAGATCTGA-TAACATGAAAATA
* * *
192655 TAAAGGGGATAGGTTGAATCCACAACGACAAACCTTA
65 TAAA-GGGAAAGGTTGAAGCCACAACGACAAACCTGA
*
192692 TACCCTAGAA-ACATGATGG
1 TACCTTAGAAGACATGATGG
192711 GAATGATTGA
Statistics
Matches: 255, Mismatches: 56, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
98 3 0.01
99 215 0.84
100 37 0.15
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (100 bp):
TACCTTAGAAGACATGATGGAGAAAGATCGAGGCCGCAACGACAGATCTGATAACATGAAAATAT
AAAGGGAAAGGTTGAAGCCACAACGACAAACCTGA
Found at i:195290 original size:15 final size:15
Alignment explanation
Indices: 195233--195290 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
195223 ATACGCCGCA
*
195233 TCATTTTTGT-ACTT
1 TCATTTTGGTCACTT
*
195247 TCATTTTGGTCAC-C
1 TCATTTTGGTCACTT
*
195261 TAATTTTTAGGTCACTT
1 TCA-TTTT-GGTCACTT
195278 TCATTTTGGTCAC
1 TCATTTTGGTCAC
195291 CCAAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
14 11 0.31
15 12 0.34
16 10 0.29
17 2 0.06
ACGTcount: A:0.17, C:0.19, G:0.12, T:0.52
Consensus pattern (15 bp):
TCATTTTGGTCACTT
Found at i:198644 original size:17 final size:17
Alignment explanation
Indices: 198612--198645 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
198602 GTAGGTTTTA
* *
198612 TAATTAAATAATATATT
1 TAATTAAAAAAAATATT
198629 TAATTAAAAAAAATATT
1 TAATTAAAAAAAATATT
198646 GTATGCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTAAAAAAAATATT
Found at i:201840 original size:59 final size:59
Alignment explanation
Indices: 201744--202000 Score: 383
Period size: 59 Copynumber: 4.3 Consensus size: 59
201734 ACATCCGGGA
* *
201744 GTAAAATGGTAATTTTTTGGAA-GTATCGGGGTCAAAAATGAGA-TTTTGGAAGTTTGGGG
1 GTAAAATGGTAA-TTTTTGGAAGGT-TCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
* *
201803 GTAAAATGGTAGTTTTTGGAAGGTTCGAGGTAAAAAAATGGGATTTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGT-CAAAAATGGGATTTTTGGAAGTTTGGGG
* * *
201863 GTAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGGCTTTTTGGAAGTTTGAGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
* **
201922 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGTGATTTTTGGAAGTTCAGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
201981 GTAAAATGGTAATTTTTGGA
1 GTAAAATGGTAATTTTTGGA
202001 TAGTTTAGGG
Statistics
Matches: 180, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
58 15 0.08
59 120 0.67
60 45 0.25
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.34
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
Found at i:201995 original size:29 final size:28
Alignment explanation
Indices: 201739--202005 Score: 195
Period size: 29 Copynumber: 9.0 Consensus size: 28
201729 TTCGGACATC
201739 CGGGAGTAAAATGGTAATTTTTTGGAAGTAT
1 CGGG-GTAAAATGGTAA-TTTTTGGAAGT-T
201770 CGGGGTCAAAAAT-G-AGA-TTTTGGAAGTTT
1 CGGGGT--AAAATGGTA-ATTTTTGGAAG-TT
* *
201799 GGGGGTAAAATGGTAGTTTTTGGAAGGTT
1 CGGGGTAAAATGGTAATTTTTGGAA-GTT
* *
201828 CGAGGTAAAAAAATGG-GATTTTTGGAAGTTT
1 CGGGGT---AAAATGGTAATTTTTGGAAG-TT
*
201859 GGGGGTAAAATGGTAATTTTTGGAAGGTT
1 CGGGGTAAAATGGTAATTTTTGGAA-GTT
** **
201888 CAAGGTCAAAAATGG-GCTTTTTGGAAGTT
1 CGGGGT--AAAATGGTAATTTTTGGAAGTT
*
201917 TGAGGGTAAAATGGTAATTTTTGGAAGGTT
1 CG-GGGTAAAATGGTAATTTTTGGAA-GTT
* *
201947 CGAGGTCAAAAAT-GTGATTTTTGGAAGTT
1 CGGGGT--AAAATGGTAATTTTTGGAAGTT
201976 CAGGGGTAAAATGGTAATTTTTGGATAGTT
1 C-GGGGTAAAATGGTAATTTTTGGA-AGTT
202006 TAGGGACCTC
Statistics
Matches: 188, Mismatches: 24, Indels: 49
0.72 0.09 0.19
Matches are distributed among these distances:
27 5 0.03
28 20 0.11
29 75 0.40
30 43 0.23
31 33 0.18
32 12 0.06
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (28 bp):
CGGGGTAAAATGGTAATTTTTGGAAGTT
Found at i:203073 original size:12 final size:12
Alignment explanation
Indices: 203058--203142 Score: 59
Period size: 12 Copynumber: 7.3 Consensus size: 12
203048 TTATTTTTTA
*
203058 ATTAATGCTATT
1 ATTAATGTTATT
*
203070 ATTAATATTATT
1 ATTAATGTTATT
* *
203082 ATTGATGTCATT
1 ATTAATGTTATT
* *
203094 ATTATTGTTATC
1 ATTAATGTTATT
203106 ATTAA---TATT
1 ATTAATGTTATT
* *
203115 GTTAATGATATT
1 ATTAATGTTATT
* *
203127 AGTAATATTATT
1 ATTAATGTTATT
203139 ATTA
1 ATTA
203143 TTATTGCCAA
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
9 7 0.13
12 46 0.87
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (12 bp):
ATTAATGTTATT
Found at i:203094 original size:15 final size:15
Alignment explanation
Indices: 203076--203115 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
203066 TATTATTAAT
*
203076 ATTATTATTGATGTC
1 ATTATTATTGATATC
*
203091 ATTATTATTGTTATC
1 ATTATTATTGATATC
*
203106 ATTAATATTG
1 ATTATTATTG
203116 TTAATGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (15 bp):
ATTATTATTGATATC
Found at i:204535 original size:15 final size:15
Alignment explanation
Indices: 204478--204535 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
204468 ATACGCCGCA
*
204478 TCATTTTTGT-ACTT
1 TCATTTTGGTCACTT
*
204492 TCATTTTGGTCAC-C
1 TCATTTTGGTCACTT
*
204506 TAATTTTTAGGTCACTT
1 TCA-TTTT-GGTCACTT
204523 TCATTTTGGTCAC
1 TCATTTTGGTCAC
204536 CCAAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
14 11 0.31
15 12 0.34
16 10 0.29
17 2 0.06
ACGTcount: A:0.17, C:0.19, G:0.12, T:0.52
Consensus pattern (15 bp):
TCATTTTGGTCACTT
Found at i:207889 original size:17 final size:17
Alignment explanation
Indices: 207857--207890 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
207847 GTAGGTTTTA
* *
207857 TAATTAAATAATATATT
1 TAATTAAAAAAAATATT
207874 TAATTAAAAAAAATATT
1 TAATTAAAAAAAATATT
207891 GTATGCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTAAAAAAAATATT
Found at i:211085 original size:59 final size:59
Alignment explanation
Indices: 210989--211245 Score: 383
Period size: 59 Copynumber: 4.3 Consensus size: 59
210979 ACATCCGGGA
* *
210989 GTAAAATGGTAATTTTTTGGAA-GTATCGGGGTCAAAAATGAGA-TTTTGGAAGTTTGGGG
1 GTAAAATGGTAA-TTTTTGGAAGGT-TCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
* *
211048 GTAAAATGGTAGTTTTTGGAAGGTTCGAGGTAAAAAAATGGGATTTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGT-CAAAAATGGGATTTTTGGAAGTTTGGGG
* * *
211108 GTAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGGCTTTTTGGAAGTTTGAGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
* **
211167 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGTGATTTTTGGAAGTTCAGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
211226 GTAAAATGGTAATTTTTGGA
1 GTAAAATGGTAATTTTTGGA
211246 TAGTTTAGGG
Statistics
Matches: 180, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
58 15 0.08
59 120 0.67
60 45 0.25
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.34
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
Found at i:211240 original size:29 final size:28
Alignment explanation
Indices: 210984--211250 Score: 195
Period size: 29 Copynumber: 9.0 Consensus size: 28
210974 TTCGGACATC
210984 CGGGAGTAAAATGGTAATTTTTTGGAAGTAT
1 CGGG-GTAAAATGGTAA-TTTTTGGAAGT-T
211015 CGGGGTCAAAAAT-G-AGA-TTTTGGAAGTTT
1 CGGGGT--AAAATGGTA-ATTTTTGGAAG-TT
* *
211044 GGGGGTAAAATGGTAGTTTTTGGAAGGTT
1 CGGGGTAAAATGGTAATTTTTGGAA-GTT
* *
211073 CGAGGTAAAAAAATGG-GATTTTTGGAAGTTT
1 CGGGGT---AAAATGGTAATTTTTGGAAG-TT
*
211104 GGGGGTAAAATGGTAATTTTTGGAAGGTT
1 CGGGGTAAAATGGTAATTTTTGGAA-GTT
** **
211133 CAAGGTCAAAAATGG-GCTTTTTGGAAGTT
1 CGGGGT--AAAATGGTAATTTTTGGAAGTT
*
211162 TGAGGGTAAAATGGTAATTTTTGGAAGGTT
1 CG-GGGTAAAATGGTAATTTTTGGAA-GTT
* *
211192 CGAGGTCAAAAAT-GTGATTTTTGGAAGTT
1 CGGGGT--AAAATGGTAATTTTTGGAAGTT
211221 CAGGGGTAAAATGGTAATTTTTGGATAGTT
1 C-GGGGTAAAATGGTAATTTTTGGA-AGTT
211251 TAGGGACCTC
Statistics
Matches: 188, Mismatches: 24, Indels: 49
0.72 0.09 0.19
Matches are distributed among these distances:
27 5 0.03
28 20 0.11
29 75 0.40
30 43 0.23
31 33 0.18
32 12 0.06
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (28 bp):
CGGGGTAAAATGGTAATTTTTGGAAGTT
Found at i:212318 original size:12 final size:12
Alignment explanation
Indices: 212303--212387 Score: 59
Period size: 12 Copynumber: 7.3 Consensus size: 12
212293 TTATTTTTTA
*
212303 ATTAATGCTATT
1 ATTAATGTTATT
*
212315 ATTAATATTATT
1 ATTAATGTTATT
* *
212327 ATTGATGTCATT
1 ATTAATGTTATT
* *
212339 ATTATTGTTATC
1 ATTAATGTTATT
212351 ATTAA---TATT
1 ATTAATGTTATT
* *
212360 GTTAATGATATT
1 ATTAATGTTATT
* *
212372 AGTAATATTATT
1 ATTAATGTTATT
212384 ATTA
1 ATTA
212388 TTATTGCCAA
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
9 7 0.13
12 46 0.87
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (12 bp):
ATTAATGTTATT
Found at i:212339 original size:15 final size:15
Alignment explanation
Indices: 212321--212360 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
212311 TATTATTAAT
*
212321 ATTATTATTGATGTC
1 ATTATTATTGATATC
*
212336 ATTATTATTGTTATC
1 ATTATTATTGATATC
*
212351 ATTAATATTG
1 ATTATTATTG
212361 TTAATGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (15 bp):
ATTATTATTGATATC
Found at i:213040 original size:13 final size:13
Alignment explanation
Indices: 213022--213053 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
213012 TCCAAGAATG
213022 TAATTTGGACTTT
1 TAATTTGGACTTT
*
213035 TAATTTGGGCTTT
1 TAATTTGGACTTT
213048 TAATTT
1 TAATTT
213054 TAAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (13 bp):
TAATTTGGACTTT
Found at i:213102 original size:6 final size:6
Alignment explanation
Indices: 213091--213154 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
213081 AATTTAAAGC
**
213091 AAATTT AAATTT AAAAAGAT AAATTT AAATTT AACA--T AAATTT AAATTT
1 AAATTT AAATTT --AAATTT AAATTT AAATTT AA-ATTT AAATTT AAATTT
**
213140 AAAAAT AAATTT AAA
1 AAATTT AAATTT AAA
213155 CCAATTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 36 0.80
7 1 0.02
8 4 0.09
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (6 bp):
AAATTT
Found at i:213102 original size:17 final size:17
Alignment explanation
Indices: 213080--213154 Score: 80
Period size: 17 Copynumber: 4.2 Consensus size: 17
213070 AAATCCATTC
*
213080 AAATTTAAAGCAAATTT
1 AAATTTAAAGTAAATTT
213097 AAATTTAAAAAGATAAATTT
1 AAATTT--AAAG-TAAATTT
213117 AAATTTAACA-TAAATTT
1 AAATTTAA-AGTAAATTT
*
213134 AAATTTAAAAATAAATTT
1 AAATTT-AAAGTAAATTT
213152 AAA
1 AAA
213155 CCAATTTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
17 20 0.39
18 14 0.27
19 5 0.10
20 12 0.24
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATTTAAAGTAAATTT
Found at i:213121 original size:37 final size:35
Alignment explanation
Indices: 213080--213154 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 35
213070 AAATCCATTC
213080 AAATTTAA-AGCAAATTTAAATTTAAAAAGATAAATTT
1 AAATTTAACA-CAAATTTAAATTT-AAAA-ATAAATTT
*
213117 AAATTTAACATAAATTTAAATTTAAAAATAAATTT
1 AAATTTAACACAAATTTAAATTTAAAAATAAATTT
213152 AAA
1 AAA
213155 CCAATTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
35 11 0.31
36 4 0.11
37 20 0.56
38 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (35 bp):
AAATTTAACACAAATTTAAATTTAAAAATAAATTT
Found at i:214025 original size:37 final size:37
Alignment explanation
Indices: 213972--214117 Score: 103
Period size: 37 Copynumber: 3.6 Consensus size: 37
213962 TTTCAATCCG
*
213972 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCA
1 CTTCTCAGTATCTCATCAGGAAGACGAATTTGGTCCA
* * * *
214009 CTTCTCAGTATTTCATCAGGAAGCTAACTGCATCGTTTGTTTCAATCCG
1 CTTCTCAGTATCTCATCAGGAAG---AC-G-A--ATTTG-----GTCCA
** *
214058 CTTCTCTATATCTCATTAGGAAGACGAATTTGGTCCA
1 CTTCTCAGTATCTCATCAGGAAGACGAATTTGGTCCA
*
214095 CTTCTCAGTATTTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
214118 CTAACCTTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
37 43 0.53
40 2 0.02
41 1 0.01
42 5 0.06
44 5 0.06
45 1 0.01
46 2 0.02
49 22 0.27
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (37 bp):
CTTCTCAGTATCTCATCAGGAAGACGAATTTGGTCCA
Found at i:214058 original size:86 final size:86
Alignment explanation
Indices: 213949--214122 Score: 321
Period size: 86 Copynumber: 2.0 Consensus size: 86
213939 CGGGAAGATG
* *
213949 ACTGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT
1 ACTGCATCGTTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCT
214014 CAGTATTTCATCAGGAAGCTA
66 CAGTATTTCATCAGGAAGCTA
*
214035 ACTGCATCGTTTGTTTCAATCCGCTTCTCTATATCTCATTAGGAAGACGAATTTGGTCCACTTCT
1 ACTGCATCGTTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCT
214100 CAGTATTTCATCAGGAAGCTA
66 CAGTATTTCATCAGGAAGCTA
214121 AC
1 AC
214123 CTTTTTATCA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (86 bp):
ACTGCATCGTTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCT
CAGTATTTCATCAGGAAGCTA
Done.