Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005524.1 Hibiscus syriacus cultivar Beakdansim tig00012759_pilon, 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: 87097
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3082 original size:19 final size:20
Alignment explanation
Indices: 3035--3083 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
3025 AATCAATTCG
3035 TATCAATACCCAAGGTTCAA
1 TATCAATACCCAAGGTTCAA
** **
3055 TATTGATACTGAAGG-TCAA
1 TATCAATACCCAAGGTTCAA
3074 TATCAATACC
1 TATCAATACC
3084 AACATAATAA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (20 bp):
TATCAATACCCAAGGTTCAA
Found at i:9148 original size:17 final size:17
Alignment explanation
Indices: 9128--9180 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
9118 AATAATTTTT
9128 TTAATAAATTATATTAA
1 TTAATAAATTATATTAA
*
9145 TTAAT-AATAATATT-A
1 TTAATAAATTATATTAA
* *
9160 TTATTATATTATTATTAA
1 TTAATAAATTA-TATTAA
9178 TTA
1 TTA
9181 TATTATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 5 0.17
16 11 0.38
17 9 0.31
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATAAATTATATTAA
Found at i:9170 original size:11 final size:11
Alignment explanation
Indices: 9154--9191 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
9144 ATTAATAATA
9154 ATATTATTATT
1 ATATTATTATT
9165 ATATTATTATT
1 ATATTATTATT
9176 A-ATTA-TATT
1 ATATTATTATT
9185 AT-TTATT
1 ATATTATT
9192 TTTAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.32
10 5 0.20
11 12 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTATTATT
Found at i:9170 original size:23 final size:23
Alignment explanation
Indices: 9129--9191 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
9119 ATAATTTTTT
9129 TAATAA-ATTA-TATTA-ATTAA
1 TAATAATATTATTATTATATTAA
*
9149 TAATAATATTATTATTATATTAT
1 TAATAATATTATTATTATATTAA
*
9172 TATTAAT-TATATTATT-TATT
1 TAATAATAT-TATTATTATATT
9192 TTTAAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 6 0.16
21 4 0.11
22 10 0.27
23 17 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TAATAATATTATTATTATATTAA
Found at i:9191 original size:27 final size:27
Alignment explanation
Indices: 9135--9187 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
9125 TTTTTAATAA
9135 ATTATATTAATTAATAATAATATTATT
1 ATTATATTAATTAATAATAATATTATT
* *
9162 ATTATATT-ATTATTAATTATATTATT
1 ATTATATTAATTAATAATAATATTATT
9188 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATATTAATTAATAATAATATTATT
Found at i:9508 original size:14 final size:15
Alignment explanation
Indices: 9481--9509 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9471 TAAATACATA
9481 AAATATTATTATTTT
1 AAATATTATTATTTT
9496 AAATATT-TTATTTT
1 AAATATTATTATTTT
9510 GAAGTGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATATTATTATTTT
Found at i:10753 original size:31 final size:31
Alignment explanation
Indices: 10712--10770 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
10702 CAAACATCTA
*
10712 CAAAAAATCGAAAACCAAGCGAGAGAGATTG
1 CAAAAAATCGAAAAACAAGCGAGAGAGATTG
* **
10743 CAAAATATCGAAAAACATTCGAGAGAGA
1 CAAAAAATCGAAAAACAAGCGAGAGAGA
10771 AAGTTTTAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.53, C:0.15, G:0.20, T:0.12
Consensus pattern (31 bp):
CAAAAAATCGAAAAACAAGCGAGAGAGATTG
Found at i:11731 original size:52 final size:51
Alignment explanation
Indices: 11666--11785 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 51
11656 AAATTGTTGA
* * *
11666 AATTGAAGCTGTAAATACTATGGACAAT-GGTTTTAAAGAGGAAAAATAATGT
1 AATTGAAGTTGTAAACACTATGGAC-ATGGGTTTTAAAGAGG-AAAATAATGG
* * * *
11718 AATTGAAGTTGTAAACATTGTGGACATGGGTTTTGAAGAGGAAAATAGTGG
1 AATTGAAGTTGTAAACACTATGGACATGGGTTTTAAAGAGGAAAATAATGG
*
11769 AATTGAAATTGTAAACA
1 AATTGAAGTTGTAAACA
11786 ATGTGGAATG
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
51 26 0.44
52 33 0.56
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (51 bp):
AATTGAAGTTGTAAACACTATGGACATGGGTTTTAAAGAGGAAAATAATGG
Found at i:11784 original size:51 final size:52
Alignment explanation
Indices: 11686--11792 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 52
11676 GTAAATACTA
* * *
11686 TGGACAATGGTTTTAAAGAGGAAAAATAATGTAATTGAAGTTGTAAACATTG
1 TGGACAATGGTTTTAAAGAGGAAAAATAATGGAATTGAAATTGTAAACAATG
* *
11738 TGGAC-ATGGGTTTTGAAGAGG-AAAATAGTGGAATTGAAATTGTAAACAATG
1 TGGACAAT-GGTTTTAAAGAGGAAAAATAATGGAATTGAAATTGTAAACAATG
11789 TGGA
1 TGGA
11793 ATGTAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 32 0.65
52 17 0.35
ACGTcount: A:0.40, C:0.04, G:0.27, T:0.29
Consensus pattern (52 bp):
TGGACAATGGTTTTAAAGAGGAAAAATAATGGAATTGAAATTGTAAACAATG
Found at i:13978 original size:22 final size:20
Alignment explanation
Indices: 13953--13995 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
13943 TCATGATGAG
13953 ATATGGAAGATAAAGATGGTTT
1 ATATGGAA-AT-AAGATGGTTT
* *
13975 ATATTGAAATAAGTTGGTTT
1 ATATGGAAATAAGATGGTTT
13995 A
1 A
13996 AGTAATGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (20 bp):
ATATGGAAATAAGATGGTTT
Found at i:14307 original size:19 final size:19
Alignment explanation
Indices: 14283--14329 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
14273 TGATTGGTAT
14283 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGGGTAGTGC
14302 ATCGATGCATGGGTAGTGC
1 ATCGATGCATGGGTAGTGC
14321 ATCGATGCA
1 ATCGATGCA
14330 CATGTTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (19 bp):
ATCGATGCATGGGTAGTGC
Found at i:14363 original size:20 final size:22
Alignment explanation
Indices: 14318--14375 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
14308 GCATGGGTAG
14318 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
14342 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
14362 TGTATCGATGCACT
1 TGCATCGATGCACT
14376 TCAAGAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:15094 original size:25 final size:27
Alignment explanation
Indices: 15053--15104 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
15043 AACTATCACT
*
15053 TATATGAACATGTGAT-A-TGAAAATG
1 TATATGAACATGAGATAAGTGAAAATG
15078 TATAGTGAA-ATGAGATAAGTGAAAATG
1 TATA-TGAACATGAGATAAGTGAAAATG
15105 CCCATGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.43
26 5 0.22
27 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.29
Consensus pattern (27 bp):
TATATGAACATGAGATAAGTGAAAATG
Found at i:22201 original size:22 final size:23
Alignment explanation
Indices: 22148--22201 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
22138 TCGATTCCCT
22148 AAAGGAGGGAATCAGTTCCCATTC
1 AAAGG-GGGAATCAGTTCCCATTC
* *
22172 AAAGGGGGAATCGGTTCCCCTTC
1 AAAGGGGGAATCAGTTCCCATTC
22195 -AAGGGGG
1 AAAGGGGG
22202 TATTGATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 7 0.25
23 16 0.57
24 5 0.18
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.19
Consensus pattern (23 bp):
AAAGGGGGAATCAGTTCCCATTC
Found at i:22211 original size:22 final size:23
Alignment explanation
Indices: 22131--22212 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
22121 CAGAACTCGT
*
22131 GGGGGTATCGATTCCC--T-AAA
1 GGGGGAATCGATTCCCATTCAAA
22151 GGAGGGAATC-AGTTCCCATTCAAA
1 GG-GGGAATCGA-TTCCCATTCAAA
* *
22175 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGATTCCCATTCAAA
* *
22197 GGGGGTATTGATTCCC
1 GGGGGAATCGATTCCC
22213 TCTGCACTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.06
21 11 0.22
22 15 0.30
23 16 0.32
24 5 0.10
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.24
Consensus pattern (23 bp):
GGGGGAATCGATTCCCATTCAAA
Found at i:26288 original size:117 final size:117
Alignment explanation
Indices: 26073--26288 Score: 276
Period size: 117 Copynumber: 1.8 Consensus size: 117
26063 TAAATTGAAT
*
26073 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCATTT
1 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTT
* *
26138 TGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTGAAAA
66 TGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTGAAAA
* * * * *
26190 TTTCTTTTTCAA-ATTTTTCAGATTTTATTTTTGAAAGCTCTAACTCATT-TCTCAACATTTCAT
1 TTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACATTTCAT
* * **
26253 TTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAA
64 TTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
26289 TATCATTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 2 0.02
117 78 0.93
118 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (117 bp):
TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTT
TGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTGAAAA
Found at i:33002 original size:38 final size:39
Alignment explanation
Indices: 32949--33026 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
32939 AACTCGTTAT
* *
32949 GCCGGCGTGATGAGTTCCATGAAATAT-TTTTTTAATGG
1 GCCGGCGTGACGAGTTCAATGAAATATATTTTTTAATGG
*
32987 GCCGGCGTGACGAGTTCAATGAGATATATTTTTTAATGG
1 GCCGGCGTGACGAGTTCAATGAAATATATTTTTTAATGG
33026 G
1 G
33027 TTGTGTCACG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 24 0.67
39 12 0.33
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (39 bp):
GCCGGCGTGACGAGTTCAATGAAATATATTTTTTAATGG
Found at i:39285 original size:3 final size:3
Alignment explanation
Indices: 39277--39304 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39267 TAATCCCATT
39277 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
39305 CTTCTTGGTG
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:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:39352 original size:76 final size:76
Alignment explanation
Indices: 39221--39380 Score: 311
Period size: 76 Copynumber: 2.1 Consensus size: 76
39211 AAGGTGATTG
*
39221 AGAAAAAGCTTCTTGGTGATTTGACAATGGTTCCCAGAAGGTCTCCTAATCCCATTGAAGAAGAA
1 AGAAGAAGCTTCTTGGTGATTTGACAATGGTTCCCAGAAGGTCTCCTAATCCCATTGAAGAAGAA
39286 GAAGAAGAAGA
66 GAAGAAGAAGA
39297 AGAAGAAGCTTCTTGGTGATTTGACAATGGTTCCCAGAAGGTCTCCTAATCCCATTGAAGAAGAA
1 AGAAGAAGCTTCTTGGTGATTTGACAATGGTTCCCAGAAGGTCTCCTAATCCCATTGAAGAAGAA
39362 GAAGAAGAAGA
66 GAAGAAGAAGA
39373 AGAAGAAG
1 AGAAGAAG
39381 AAGAAGAAGA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 83 1.00
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (76 bp):
AGAAGAAGCTTCTTGGTGATTTGACAATGGTTCCCAGAAGGTCTCCTAATCCCATTGAAGAAGAA
GAAGAAGAAGA
Found at i:39361 original size:3 final size:3
Alignment explanation
Indices: 39353--39408 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
39343 TAATCCCATT
39353 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
39401 GAA GAA GA
1 GAA GAA GA
39409 TTAACGGAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:39487 original size:129 final size:129
Alignment explanation
Indices: 39353--39612 Score: 502
Period size: 129 Copynumber: 2.0 Consensus size: 129
39343 TAATCCCATT
39353 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATTAACGGAA
1 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATTAACGGAA
39418 GTTAATGATGTAGGGACTTAAACCGTACATACCGATAATGATAGAGACTTAAACAGAACGGACC
66 GTTAATGATGTAGGGACTTAAACCGTACATACCGATAATGATAGAGACTTAAACAGAACGGACC
* *
39482 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGGGTTAACGGAA
1 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATTAACGGAA
39547 GTTAATGATGTAGGGACTTAAACCGTACATACCGATAATGATAGAGACTTAAACAGAACGGACC
66 GTTAATGATGTAGGGACTTAAACCGTACATACCGATAATGATAGAGACTTAAACAGAACGGACC
39611 GA
1 GA
39613 TAACGTGAGG
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.50, C:0.09, G:0.28, T:0.12
Consensus pattern (129 bp):
GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATTAACGGAA
GTTAATGATGTAGGGACTTAAACCGTACATACCGATAATGATAGAGACTTAAACAGAACGGACC
Found at i:39490 original size:3 final size:3
Alignment explanation
Indices: 39482--39534 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
39472 AGAACGGACC
39482 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
39530 GAA GA
1 GAA GA
39535 GGGTTAACGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:40239 original size:4 final size:4
Alignment explanation
Indices: 40232--40260 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
40222 ACTTAATTAA
40232 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
40261 CAGTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:40996 original size:20 final size:21
Alignment explanation
Indices: 40971--41063 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
40961 TTTTCCCAAT
*
40971 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
40991 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
41012 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
41032 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
41053 TCGCAATGCGA
1 TCGCAATGCGA
41064 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:41077 original size:20 final size:20
Alignment explanation
Indices: 41052--41146 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
41042 AATTGGGAAA
*
41052 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
41072 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* * *
41093 ATCGTAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
41113 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
41133 TTCGCAACGCGATA
1 ATCGCAACGCGATA
41147 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:41078 original size:41 final size:41
Alignment explanation
Indices: 40971--41063 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
40961 TTTTCCCAAT
40971 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
41012 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
41053 TCGCAATGCGA
1 TCGCAATGCGA
41064 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:41094 original size:41 final size:41
Alignment explanation
Indices: 41049--41126 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
41039 GCGAATTGGG
* * *
41049 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* * *
41090 AAAATCGTAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
41127 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:41359 original size:22 final size:22
Alignment explanation
Indices: 41331--41374 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41321 CACTCTCTCA
*
41331 CCCATCTCCGATGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
41353 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
41375 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:41663 original size:20 final size:20
Alignment explanation
Indices: 41638--41675 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41628 CGATTCTCTC
41638 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
41658 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
41676 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:43014 original size:18 final size:18
Alignment explanation
Indices: 42993--43037 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
42983 TCCACTTCGG
*
42993 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
43011 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
43029 GAGCCATCA
1 GAGCCATCA
43038 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:43573 original size:19 final size:20
Alignment explanation
Indices: 43519--43585 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
43509 TAGTTTACTT
* *
43519 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
43539 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
43559 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
43578 TCGCAACG
1 TCGCAACG
43586 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:43593 original size:14 final size:14
Alignment explanation
Indices: 43574--43631 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
43564 ATGCGAAATG
43574 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
43588 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
43604 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
43620 AAAATCGCAACG
1 AAAATCGCAACG
43632 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:43616 original size:32 final size:33
Alignment explanation
Indices: 43558--43648 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
43548 GGAAATGGCT
43558 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
43591 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
43623 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
43649 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:43687 original size:14 final size:14
Alignment explanation
Indices: 43665--43722 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
43655 TTGTGTTTCG
43665 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
43679 CGTTACGATTTCATTT
1 CGTTGCGATTT--TGT
43695 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
43711 CGTTGCGATTTT
1 CGTTGCGATTTT
43723 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:43697 original size:32 final size:33
Alignment explanation
Indices: 43660--43738 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
43650 GCGATTTGTG
43660 TTTCGCGTTGCGATTTTGTCGTTACGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTACGATTTTCA
*
43692 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTACGATTTTCA
*
43725 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
43739 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTACGATTTTCA
Found at i:43737 original size:19 final size:19
Alignment explanation
Indices: 43711--43776 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
43701 GCGATTTTGT
**
43711 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
43730 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
43750 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
43769 CGTTGCGA
1 CGTTGCGA
43777 ATTTAAGTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:43757 original size:20 final size:19
Alignment explanation
Indices: 43723--43776 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
43713 TTGCGATTTT
*
43723 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
43742 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
43762 CATTTCGCGTTGCGA
1 CATTTCGCGTTGCGA
43777 ATTTAAGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:43874 original size:27 final size:26
Alignment explanation
Indices: 43808--43876 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
43798 AGTAAACTAT
*
43808 TCTT-CTTCTGGAATGTTTATATATG
1 TCTTACTTCTGGAATGTTTATATAAG
* * **
43833 TTTTCCTT-TTAAATGTTTATATAAG
1 TCTTACTTCTGGAATGTTTATATAAG
43858 TGCTTACTTCTGGAATGTT
1 T-CTTACTTCTGGAATGTT
43877 ATCTGAGCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
25 18 0.55
26 8 0.24
27 7 0.21
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (26 bp):
TCTTACTTCTGGAATGTTTATATAAG
Found at i:45664 original size:14 final size:14
Alignment explanation
Indices: 45645--45680 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
45635 ATTGTTTAAT
45645 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
45659 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
45673 TGATTTGT
1 TGATTTGT
45681 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:45806 original size:14 final size:15
Alignment explanation
Indices: 45787--45863 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
45777 CGAAATGGCT
45787 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
45801 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
45819 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
45838 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
45852 ATCGCAATGCGA
1 ATCGCAA-GCGA
45864 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:45819 original size:19 final size:19
Alignment explanation
Indices: 45797--45863 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
45787 ATCGCAACGA
45797 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
45816 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
45834 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
45848 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
45864 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:45939 original size:20 final size:20
Alignment explanation
Indices: 45882--45939 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
45872 TCGCTTTGCG
* *
45882 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
*
45902 ATTTTTGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
45922 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
45940 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:47052 original size:24 final size:24
Alignment explanation
Indices: 46996--47054 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
46986 AGTCAGTATT
* *
46996 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
47020 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
47044 CGAATTTTGAT
1 CGAAATTTGAT
47055 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:49588 original size:33 final size:33
Alignment explanation
Indices: 49546--49671 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
49536 GGAAATTACT
*
49546 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
49579 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
49611 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
49645 ATCGCAATGCGAAATGAAAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCGCAAC
49672 ACGAAATTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:49653 original size:66 final size:66
Alignment explanation
Indices: 49547--49671 Score: 232
Period size: 66 Copynumber: 1.9 Consensus size: 66
49537 GAAATTACTA
*
49547 TCGCAATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
49612 T
66 T
*
49613 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAAC
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAAC
49672 ACGAAATTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
T
Found at i:49705 original size:19 final size:19
Alignment explanation
Indices: 49683--49747 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
49673 CGAAATTAAA
*
49683 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
49702 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
49718 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
49735 TTCGCATTGCGAT
1 TTCGCATTGCGAT
49748 AGTACTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 6 0.17
16 6 0.17
17 6 0.17
19 18 0.50
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:49873 original size:14 final size:14
Alignment explanation
Indices: 49854--49890 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
49844 CATCAATTAA
49854 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
49868 ACAAATCACCTTTT
1 ACAAATCAACTTTT
49882 ACAAATCAA
1 ACAAATCAA
49891 TTAAACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:51296 original size:21 final size:21
Alignment explanation
Indices: 51267--51347 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
51257 GAATGGTGGG
*
51267 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTCAACGATGAT
* * * **
51288 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAT
* * *
51309 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAT
51330 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
51348 AGGAGTGGAC
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.83
22 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAT
Found at i:51329 original size:42 final size:41
Alignment explanation
Indices: 51252--51374 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
51242 GTGAATCGGG
* * * *
51252 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
51294 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * * *
51336 CTCTTCAACGATAGGAGTGGACTATTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
51375 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:53457 original size:33 final size:33
Alignment explanation
Indices: 53400--53497 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
53390 ACGAGATAAT
*
53400 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
53434 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
53467 GACAATCGCAACGCGAAATGAAAATCGCAAC
1 GAGAATCGCAACGCGAAATGACTATCGCAAC
53498 TGCGAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:53492 original size:19 final size:19
Alignment explanation
Indices: 53375--53556 Score: 168
Period size: 19 Copynumber: 9.9 Consensus size: 19
53365 TCTTTTGGTT
*
53375 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
53394 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
53414 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
53432 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
53448 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
53466 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
53481 GAAATGAAAATCGCAACTGC
1 GAAATGAAAATCGCAAC-GC
* *
53501 GAAATAAAAATCGCAACGT
1 GAAATGAAAATCGCAACGC
53520 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
53539 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
53557 TTGCGATTAT
Statistics
Matches: 134, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 58 0.43
20 45 0.34
21 2 0.01
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:53524 original size:39 final size:38
Alignment explanation
Indices: 53470--53557 Score: 149
Period size: 39 Copynumber: 2.3 Consensus size: 38
53460 GCGACCAGAC
*
53470 AATCGCAACGCGAAATGAAAATCGCAACTGCGAAATAAA
1 AATCGCAACGTGAAATGAAAATCGCAAC-GCGAAATAAA
*
53509 AATCGCAACGTGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGTGAAATGAAAATCGCAACGCGAAATAAA
53547 AATCGCAACGT
1 AATCGCAACGT
53558 TGCGATTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 20 0.43
39 27 0.57
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (38 bp):
AATCGCAACGTGAAATGAAAATCGCAACGCGAAATAAA
Found at i:54143 original size:20 final size:20
Alignment explanation
Indices: 54118--54170 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
54108 GCGCTATGTA
54118 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
54138 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
54158 TATCTCGTTGCGA
1 AATCGCGTTGCGA
54171 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:54204 original size:20 final size:20
Alignment explanation
Indices: 54179--54232 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
54169 GATTTTGTAT
54179 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
54199 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
54219 TATCGCATTGCGAT
1 TATCGCATTGCGAT
54233 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:54217 original size:61 final size:61
Alignment explanation
Indices: 54119--54235 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
54109 CGCTATGTAA
* * * * *
54119 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
54180 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
54236 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:54251 original size:61 final size:61
Alignment explanation
Indices: 54119--54253 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
54109 CGCTATGTAA
* * * * * ** *
54119 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
54180 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
54242 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
54254 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:54385 original size:28 final size:28
Alignment explanation
Indices: 54345--54413 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
54335 AAAATGCAAC
*
54345 GCGAATTTGCGATAATGGAGATCGCGTT
1 GCGAATTAGCGATAATGGAGATCGCGTT
54373 GCGAATTAGCGATAATGGAGATCGCGTT
1 GCGAATTAGCGATAATGGAGATCGCGTT
54401 GCGAATTAGCGAT
1 GCGAATTAGCGAT
54414 CGCATTGCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (28 bp):
GCGAATTAGCGATAATGGAGATCGCGTT
Found at i:54847 original size:40 final size:44
Alignment explanation
Indices: 54760--54847 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 44
54750 GTATAAGTTC
* * *
54760 TAATTAATTTTAATTAAGGCTTACTACTGTCTCATATTTTTGTT
1 TAATTAATTTTAATTAAGGATTACTACTGTCTCATATTTATGCT
54804 TAATTAA-TTTAATTAAGGATTACTACTGTCTCA-A-TTAT-CT
1 TAATTAATTTTAATTAAGGATTACTACTGTCTCATATTTATGCT
54844 TAAT
1 TAAT
54848 ACTATAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 5 0.12
41 3 0.07
42 1 0.02
43 25 0.61
44 7 0.17
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (44 bp):
TAATTAATTTTAATTAAGGATTACTACTGTCTCATATTTATGCT
Found at i:56377 original size:81 final size:81
Alignment explanation
Indices: 56290--56438 Score: 192
Period size: 81 Copynumber: 1.8 Consensus size: 81
56280 TAGATCCTCA
** * * * * **
56290 TTACTTACACAT-TTAATTAATTTGATCCTGATTTTAATTTAATTTAATAAATTTAATATTCAAA
1 TTACTTACA-ATCTTAACCAATTTGATCCTAATTTCAATTTAAATTAATAAATCTAATACCCAAA
56354 TCAGGTGGTGACACTCG
65 TCAGGTGGTGACACTCG
* *
56371 TTACTTACATTCTTAACCAATTTGATCTTAATTTCAATTTAAATTAATAAATCTAATACCCAAAT
1 TTACTTACAATCTTAACCAATTTGATCCTAATTTCAATTTAAATTAATAAATCTAATACCCAAAT
56436 CAG
66 CAG
56439 ACAATGACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.02
81 56 0.98
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (81 bp):
TTACTTACAATCTTAACCAATTTGATCCTAATTTCAATTTAAATTAATAAATCTAATACCCAAAT
CAGGTGGTGACACTCG
Found at i:56838 original size:20 final size:20
Alignment explanation
Indices: 56808--57004 Score: 112
Period size: 20 Copynumber: 9.7 Consensus size: 20
56798 GTTTCCAAAT
*
56808 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
56828 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
** *
56848 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
56871 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* * *
56891 TCGCAATGCGAGTATGACAA
1 TCGCAATGCGATTCTGACTA
* *
56911 TCGAAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
56931 TCGCAACGAGATTTTTGACTA
1 TCGCAATGCGA-TTCTGACTA
* *
56952 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
*
56972 TCGCAACGCGATGT-TGACTA
1 TCGCAATGCGAT-TCTGACTA
56992 TCGCAATGCGATT
1 TCGCAATGCGATT
57005 TTCAAAGCGC
Statistics
Matches: 138, Mismatches: 30, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
19 4 0.03
20 91 0.66
21 30 0.22
22 9 0.07
23 3 0.02
24 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:56860 original size:41 final size:42
Alignment explanation
Indices: 56765--56881 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 42
56755 TGCGATCGAT
* * *
56765 AATTCGCAACGCGATCTCCG-GTATCGCAAAT-C-AGTTTCCA
1 AATTCGCAACGCGATTTCCGACTATCGC-AATGCGATTTTCCA
* *
56805 AATTCGCAACGCGA-TTCTGACTATCGCATTGCGATTTTCCA
1 AATTCGCAACGCGATTTCCGACTATCGCAATGCGATTTTCCA
***
56846 AATTCGCGTTGCGATTTTCCGACTATCGCAATGCGA
1 AATTCGCAACGCGA-TTTCCGACTATCGCAATGCGA
56882 ATATGTAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
39 5 0.08
40 21 0.34
41 18 0.29
43 18 0.29
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (42 bp):
AATTCGCAACGCGATTTCCGACTATCGCAATGCGATTTTCCA
Found at i:56962 original size:41 final size:40
Alignment explanation
Indices: 56905--57004 Score: 137
Period size: 41 Copynumber: 2.5 Consensus size: 40
56895 AATGCGAGTA
* * *
56905 TGACAATCGAAACGCGATTCTGACTATCGCAACGAGATTTT
1 TGACTATCGCAACGCGATTCTGACTATCGCAACGAGA-TGT
* *
56946 TGACTATCGCAACGCGATTCTGACTGTCGCAACGCGATGT
1 TGACTATCGCAACGCGATTCTGACTATCGCAACGAGATGT
*
56986 TGACTATCGCAATGCGATT
1 TGACTATCGCAACGCGATT
57005 TTCAAAGCGC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 20 0.38
41 33 0.62
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (40 bp):
TGACTATCGCAACGCGATTCTGACTATCGCAACGAGATGT
Found at i:57205 original size:22 final size:22
Alignment explanation
Indices: 57180--57222 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
57170 GGCGACATCC
57180 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
57202 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
57223 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:57634 original size:19 final size:20
Alignment explanation
Indices: 57612--57703 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
57602 AATCGCAATA
57612 CGATTTT-AGTTTCGCGTTG
1 CGATTTTCAGTTTCGCGTTG
57631 CGATTTTCA-TTTCGCGTTG
1 CGATTTTCAGTTTCGCGTTG
** **
57650 CGATAGTCAAATTCGCGTTG
1 CGATTTTCAGTTTCGCGTTG
* *
57670 CGATTTTCATTTTCGTGTTG
1 CGATTTTCAGTTTCGCGTTG
*
57690 CGATTTTAAGTTTC
1 CGATTTTCAGTTTC
57704 AGAAACTATT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
19 24 0.39
20 37 0.61
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
CGATTTTCAGTTTCGCGTTG
Found at i:57666 original size:20 final size:19
Alignment explanation
Indices: 57622--57673 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
57612 CGATTTTAGT
** *
57622 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTCAA
57641 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTC-AA
57661 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
57674 TTTCATTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.38
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTCAA
Found at i:59633 original size:20 final size:20
Alignment explanation
Indices: 59604--59669 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
59594 TAGTTTACTT
*
59604 TCGCATCGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
59624 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
59644 CCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
59664 TCGCAA
1 TCGCAA
59670 TGAAAGAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:60147 original size:18 final size:20
Alignment explanation
Indices: 60107--60148 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
60097 CTCACTTGTC
60107 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-CTCCCCT
60128 ATCGTTCAAGAGG-T-CCCT
1 ATCGTTCAAGAGGCTCCCCT
60146 ATC
1 ATC
60149 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
21 13 0.62
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGTTCAAGAGGCTCCCCT
Found at i:61641 original size:14 final size:14
Alignment explanation
Indices: 61605--61666 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
61595 TTGCTTGTTT
*
61605 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
61619 AATTAATTTGTAAA
1 AATTGATTTGTAAA
* *
61633 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
61648 TATTGATGTGTAAA
1 AATTGATTTGTAAA
61662 TAATT
1 -AATT
61667 TTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:61790 original size:20 final size:20
Alignment explanation
Indices: 61765--61817 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
61755 AGGTACACTT
* *
61765 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACACAAAA
* *
61785 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAACACAAAA
*
61805 TCACAACGCGAAA
1 TCGCAACGCGAAA
61818 GTCAATTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACACAAAA
Found at i:61916 original size:20 final size:20
Alignment explanation
Indices: 61861--62011 Score: 86
Period size: 20 Copynumber: 7.8 Consensus size: 20
61851 GCGATTTACT
* *
61861 CGTTGCGATAGTCAAATAC-
1 CGTTGCGATACTCAAATTCG
61880 CAGTTGCGATAAC-CAAATTCG
1 C-GTTGCGAT-ACTCAAATTCG
* *
61901 CGTTACGATACTCAAATTTG
1 CGTTGCGATACTCAAATTCG
* * *
61921 CATTGTGATAGTCAAATTCG
1 CGTTGCGATACTCAAATTCG
*
61941 CGTTGCGAT--T----TTCT
1 CGTTGCGATACTCAAATTCG
* * *
61955 CGTTGCTATAGTCAAA-TAG
1 CGTTGCGATACTCAAATTCG
*
61974 CCGTTGCGATAGTCAAATTCG
1 -CGTTGCGATACTCAAATTCG
* *
61995 CGTTGCAATATTCAAAT
1 CGTTGCGATACTCAAAT
62012 GAATGTGTAA
Statistics
Matches: 101, Mismatches: 19, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
14 11 0.11
16 1 0.01
18 1 0.01
19 4 0.04
20 80 0.79
21 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (20 bp):
CGTTGCGATACTCAAATTCG
Found at i:62010 original size:94 final size:94
Alignment explanation
Indices: 61833--62011 Score: 252
Period size: 94 Copynumber: 1.9 Consensus size: 94
61823 TTCGCGTTGC
* *
61833 GATAGTCTAATACGCTTTGCGATTTACTCGTTGCGATAGTCAAATACCAGTTGCGATAACCAAAT
1 GATAGTCAAATACGCGTTGCGATTTACTCGTTGCGATAGTCAAATACCAGTTGCGATAACCAAAT
*
61898 TCGCGTTACGATACTCAAATTTGCATTGT
66 TCGCGTTACAATACTCAAATTTGCATTGT
* * * **
61927 GATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCTATAGTCAAATAGCC-GTTGCGATAGTCAAA
1 GATAGTCAAATACGCGTTGCGATTTACTCGTTGCGATAGTCAAATA-CCAGTTGCGATAACCAAA
* *
61991 TTCGCGTTGCAATATTCAAAT
65 TTCGCGTTACAATACTCAAAT
62012 GAATGTGTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 72 0.97
95 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (94 bp):
GATAGTCAAATACGCGTTGCGATTTACTCGTTGCGATAGTCAAATACCAGTTGCGATAACCAAAT
TCGCGTTACAATACTCAAATTTGCATTGT
Found at i:62194 original size:18 final size:18
Alignment explanation
Indices: 62171--62205 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
62161 AAGCCGGTTG
*
62171 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
62189 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
62206 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:63365 original size:20 final size:20
Alignment explanation
Indices: 63340--63379 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
63330 TGAATTAGAG
63340 GTTTCAGATTTGCCAACCCC
1 GTTTCAGATTTGCCAACCCC
63360 GTTTCAGATTTGCCAACCCC
1 GTTTCAGATTTGCCAACCCC
63380 ATAAGCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.35, G:0.15, T:0.30
Consensus pattern (20 bp):
GTTTCAGATTTGCCAACCCC
Found at i:64281 original size:14 final size:15
Alignment explanation
Indices: 64262--64298 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
64252 TCCCGTGGTA
64262 TTTTCTTCGGGGA-C
1 TTTTCTTCGGGGATC
*
64276 TTTTCTTCGGGGATT
1 TTTTCTTCGGGGATC
64291 TTTTCTTC
1 TTTTCTTC
64299 TTATTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.05, C:0.19, G:0.22, T:0.54
Consensus pattern (15 bp):
TTTTCTTCGGGGATC
Found at i:64522 original size:24 final size:24
Alignment explanation
Indices: 64488--64541 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
64478 CTGAAACATC
64488 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
64512 ATCAAAGTCCGTGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
64536 ATCAAA
1 ATCAAA
64542 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:65449 original size:20 final size:20
Alignment explanation
Indices: 65363--65449 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
65353 AAATTCAGTG
* *
65363 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* *
65383 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* *
65403 TTGCGATAGTTAGAATCACA
1 TTGCGATAGTCAGAATCGCA
*
65423 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
65443 TTGCGAT
1 TTGCGAT
65450 TTACATATTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:65449 original size:40 final size:40
Alignment explanation
Indices: 65363--65493 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 40
65353 AAATTCAGTG
* * * * * *
65363 TTGCGACAGTCAGAATCGCGTTGCGACAGTCAGAATCGCG
1 TTGCGATAGTTAGAATCGCATTGCGATAGTCATAATCGCA
*
65403 TTGCGATAGTTAGAATCACATTGCGATAGTCATAATCGCA
1 TTGCGATAGTTAGAATCGCATTGCGATAGTCATAATCGCA
* * *
65443 TTGCGAT--TTACATATTCGCATTGCGAT-TTACATATTCGCA
1 TTGCGATAGTTAGA-A-TCGCATTGCGATAGT-CATAATCGCA
65483 TTGCGATAGTT
1 TTGCGATAGTT
65494 GAAAAATCGC
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
38 4 0.05
39 2 0.03
40 67 0.89
42 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (40 bp):
TTGCGATAGTTAGAATCGCATTGCGATAGTCATAATCGCA
Found at i:65456 original size:20 final size:20
Alignment explanation
Indices: 65433--65489 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
65423 TTGCGATAGT
*
65433 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
65453 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
65473 CATATTCGCATTGCGAT
1 CATATTCGCATTGCGAT
65490 AGTTGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:65510 original size:22 final size:22
Alignment explanation
Indices: 65485--65535 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
65475 TATTCGCATT
65485 GCGATAGTTGAAAAATCGCAAC
1 GCGATAGTTGAAAAATCGCAAC
* * *
65507 GCGA-ATTTGGAAAATCGCAAT
1 GCGATAGTTGAAAAATCGCAAC
65528 GCGATAGT
1 GCGATAGT
65536 AAGAGTCGCG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (22 bp):
GCGATAGTTGAAAAATCGCAAC
Found at i:72634 original size:23 final size:23
Alignment explanation
Indices: 72604--72647 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
72594 ATATAAAATT
* *
72604 TGTCCCAAAGGACCGCATAGAAA
1 TGTCCCAAAAGACCACATAGAAA
72627 TGTCCCAAAAGACCACATAGA
1 TGTCCCAAAAGACCACATAGA
72648 TGTTTCGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14
Consensus pattern (23 bp):
TGTCCCAAAAGACCACATAGAAA
Found at i:73515 original size:19 final size:22
Alignment explanation
Indices: 73462--73517 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
73452 GGTACTCTTA
*
73462 CTATAGTACCGATACTACCCAC
1 CTATGGTACCGATACTACCCAC
* *
73484 CTATGGTATCGATGCT-CCC-C
1 CTATGGTACCGATACTACCCAC
73504 CTA-GGTACCGATAC
1 CTATGGTACCGATAC
73518 AATTTTTACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 9 0.31
20 4 0.14
21 3 0.10
22 13 0.45
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (22 bp):
CTATGGTACCGATACTACCCAC
Found at i:78292 original size:16 final size:19
Alignment explanation
Indices: 78244--78294 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
78234 AAAATGCTAA
78244 AGTGTACCGATACACTCTG
1 AGTGTACCGATACACTCTG
78263 TAGTGTATCC-ATACA-T-TG
1 -AGTGTA-CCGATACACTCTG
78281 -GTGTACCGATACAC
1 AGTGTACCGATACAC
78295 CCTACAGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.07
16 10 0.36
18 2 0.07
19 1 0.04
20 11 0.39
21 2 0.07
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (19 bp):
AGTGTACCGATACACTCTG
Found at i:78412 original size:20 final size:18
Alignment explanation
Indices: 78363--78413 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 18
78353 ATACACACGA
78363 TAGTGTATCCATACATTG
1 TAGTGTATCCATACATTG
78381 --GTGTA-CCGATACATTTTG
1 TAGTGTATCC-ATACA--TTG
78399 TAGTGTATCCATACA
1 TAGTGTATCCATACA
78414 CCCTGGCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
15 2 0.07
16 10 0.37
18 3 0.11
20 10 0.37
21 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (18 bp):
TAGTGTATCCATACATTG
Found at i:79950 original size:17 final size:18
Alignment explanation
Indices: 79915--79950 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
79905 TGAGGTGGAT
79915 GAAGATGATGATGAACAA
1 GAAGATGATGATGAACAA
*
79933 GAAGATGA-GATGATCAA
1 GAAGATGATGATGAACAA
79950 G
1 G
79951 CTTTTAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.06, G:0.31, T:0.17
Consensus pattern (18 bp):
GAAGATGATGATGAACAA
Found at i:80375 original size:19 final size:19
Alignment explanation
Indices: 80336--80376 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
80326 ATTAAAGATG
* *
80336 AATTGATTTTGAAAGTTAA
1 AATTGATTTTGAAAATCAA
80355 AATTGATTTTGAAAATCAA
1 AATTGATTTTGAAAATCAA
80374 AAT
1 AAT
80377 AAAATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (19 bp):
AATTGATTTTGAAAATCAA
Found at i:81245 original size:22 final size:22
Alignment explanation
Indices: 81217--81261 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
81207 TCATTGAATT
*
81217 TCATGTATTACTAACATGTTTG
1 TCATGTACTACTAACATGTTTG
81239 TCATGTACTACTAACATGTTTG
1 TCATGTACTACTAACATGTTTG
81261 T
1 T
81262 TATTCTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (22 bp):
TCATGTACTACTAACATGTTTG
Found at i:81808 original size:16 final size:17
Alignment explanation
Indices: 81760--81810 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
81750 AAAATGTTGA
81760 AGTGTACCGATACACTCTG
1 AGTGTACCGATACA--CTG
81779 CAGTGTATCC-ATACACTG
1 -AGTGTA-CCGATACACTG
81797 -GTGTACCGATACAC
1 AGTGTACCGATACAC
81811 CCTGCAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 11 0.38
18 3 0.10
20 11 0.38
21 2 0.07
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (17 bp):
AGTGTACCGATACACTG
Found at i:81828 original size:20 final size:20
Alignment explanation
Indices: 81760--81821 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
81750 AAAATGTTGA
*
81760 AGTGTACCGATACACTCTGC
1 AGTGTACCGATACACCCTGC
81780 AGTGTATCC-ATACA--CTG-
1 AGTGTA-CCGATACACCCTGC
81797 -GTGTACCGATACACCCTGC
1 AGTGTACCGATACACCCTGC
81816 AGTGTA
1 AGTGTA
81822 TCCATACCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.06
16 10 0.28
18 6 0.17
20 16 0.44
21 2 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (20 bp):
AGTGTACCGATACACCCTGC
Found at i:81885 original size:20 final size:19
Alignment explanation
Indices: 81860--81921 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
81850 AAATGTAATT
81860 AGTGTACCGATACACCCTGC
1 AGTGTACCGATACA-CCTGC
81880 AGTGTATCC-ATACA-CTG-
1 AGTGTA-CCGATACACCTGC
*
81897 -GTATACCGATACACTCTGC
1 AGTGTACCGATACAC-CTGC
81916 AGTGTA
1 AGTGTA
81922 TCTATACACT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 2 0.06
16 9 0.26
18 6 0.18
20 15 0.44
21 2 0.06
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (19 bp):
AGTGTACCGATACACCTGC
Found at i:82000 original size:21 final size:21
Alignment explanation
Indices: 81974--82014 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
81964 TTTGAATTTA
* *
81974 ATGAAGGTGTATCGATACCCT
1 ATGAAGGGGTACCGATACCCT
81995 ATGAAGGGGTACCGATACCC
1 ATGAAGGGGTACCGATACCC
82015 CATGTTATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (21 bp):
ATGAAGGGGTACCGATACCCT
Found at i:83911 original size:19 final size:19
Alignment explanation
Indices: 83872--83925 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
83862 ATTAAAGATG
*
83872 AATTGATTTTGAAAGTAAA
1 AATTGATTTTGAAAATAAA
*
83891 AATTGATTTTGAAAATCAA
1 AATTGATTTTGAAAATAAA
83910 AA-TGAAATTTTGAAAA
1 AATTG--ATTTTGAAAA
83926 ATGATTTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 2 0.06
19 19 0.61
20 10 0.32
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (19 bp):
AATTGATTTTGAAAATAAA
Found at i:85292 original size:16 final size:16
Alignment explanation
Indices: 85251--85301 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 16
85241 AAAATGCTAA
85251 AGTGTACCGATACACTCT
1 AGTGTACCGATACA--CT
85269 GCAGTGTATCC-ATACACT
1 --AGTGTA-CCGATACACT
85287 AGTGTACCGATACAC
1 AGTGTACCGATACAC
85302 CCTACAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
18 2 0.07
20 11 0.38
21 2 0.07
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (16 bp):
AGTGTACCGATACACT
Found at i:85298 original size:36 final size:36
Alignment explanation
Indices: 85251--85421 Score: 139
Period size: 36 Copynumber: 5.0 Consensus size: 36
85241 AAAATGCTAA
*
85251 AGTGTACCGATACACTCTGCAGTGTATCCATACACT
1 AGTGTACCGATACACCCTGCAGTGTATCCATACACT
* *
85287 AGTGTACCGATACACCCTACAGTGTATCCATACCCCT
1 AGTGTACCGATACACCCTGCAGTGTATCCATA-CACT
* * * *
85324 A-TG-ACTGCTCAAACACC-G-A----AT-C-TA-ATT
1 AGTGTACCGAT-ACAC-CCTGCAGTGTATCCATACACT
85351 AGTGTACCGATACACCCTGCAGTGTATCCATACACT
1 AGTGTACCGATACACCCTGCAGTGTATCCATACACT
* * * *
85387 GGTGTACTGATACACTCTGTAGTGTATCCATACAC
1 AGTGTACCGATACACCCTGCAGTGTATCCATACAC
85422 CCTGGCTGCA
Statistics
Matches: 104, Mismatches: 17, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
27 4 0.04
28 6 0.06
29 7 0.07
30 1 0.01
31 2 0.02
33 2 0.02
34 1 0.01
35 7 0.07
36 68 0.65
37 6 0.06
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (36 bp):
AGTGTACCGATACACCCTGCAGTGTATCCATACACT
Found at i:85319 original size:20 final size:20
Alignment explanation
Indices: 85251--85324 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
85241 AAAATGCTAA
* *
85251 AGTGTACCGATACACTCTGC
1 AGTGTACCGATACACCCTAC
85271 AGTGTATCC-ATACA--CT--
1 AGTGTA-CCGATACACCCTAC
85287 AGTGTACCGATACACCCTAC
1 AGTGTACCGATACACCCTAC
85307 AGTGTATCC-ATAC-CCCTA
1 AGTGTA-CCGATACACCCTA
85325 TGACTGCTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.04
16 11 0.23
18 4 0.09
19 5 0.11
20 21 0.45
21 4 0.09
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
AGTGTACCGATACACCCTAC
Found at i:85376 original size:20 final size:19
Alignment explanation
Indices: 85351--85425 Score: 61
Period size: 20 Copynumber: 4.0 Consensus size: 19
85341 GAATCTAATT
85351 AGTGTA-CCGATACACCCTG
1 AGTGTATCC-ATACACCCTG
85370 CAGTGTATCCATACA--CTG
1 -AGTGTATCCATACACCCTG
* *
85388 -GTGTA-CTGATACACTCTG
1 AGTGTATC-CATACACCCTG
85406 TAGTGTATCCATACACCCTG
1 -AGTGTATCCATACACCCTG
85426 GCTGCAATGG
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
15 1 0.02
16 10 0.22
18 6 0.13
20 25 0.56
21 3 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (19 bp):
AGTGTATCCATACACCCTG
Found at i:86395 original size:24 final size:24
Alignment explanation
Indices: 86366--86422 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
86356 GCAAGAGTGT
*
86366 ACTAATACAAGAGTGCGCAAAGGC
1 ACTAATACAAGAGTACGCAAAGGC
* * *
86390 ATTAATACAGGTGTACGCAAAGGC
1 ACTAATACAAGAGTACGCAAAGGC
86414 ACTAATACA
1 ACTAATACA
86423 TGATTAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (24 bp):
ACTAATACAAGAGTACGCAAAGGC
Done.