Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011737.1 Kokia drynarioides strain JFW-HI SEQ_126731, 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: 84214
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:224 original size:16 final size:16
Alignment explanation
Indices: 203--256 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
193 ACGTTATTTA
203 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
*
219 TTATTATT---ATTA-
1 TTATTATTAAAAATAT
* *
231 ATATTATTAAAAACAT
1 TTATTATTAAAAATAT
247 TTATTATTAA
1 TTATTATTAA
257 TAGTCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
15 2 0.07
16 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:238 original size:19 final size:19
Alignment explanation
Indices: 182--238 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
172 TTTCTTTTTT
182 TTATTATTAAAACGTTATTTA
1 TTATTATTAAAA--TTATTTA
*
203 TTATTATTAAAAATATTTA
1 TTATTATTAAAATTATTTA
*
222 TTATTATTAATATTATT
1 TTATTATTAAAATTATT
239 AAAAACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 21 0.64
21 12 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTATTAAAATTATTTA
Found at i:889 original size:15 final size:15
Alignment explanation
Indices: 878--948 Score: 97
Period size: 15 Copynumber: 4.7 Consensus size: 15
868 CATTGGGTCG
878 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
* ***
893 TTTGTACTTGGATAA
1 TTTGTAATTGGGCCA
*
908 TTTGTAATTGGGCCG
1 TTTGTAATTGGGCCA
923 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
938 TTTGTAATTGG
1 TTTGTAATTGG
949 ACTTTGTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.44
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:1002 original size:17 final size:16
Alignment explanation
Indices: 980--1052 Score: 101
Period size: 17 Copynumber: 4.4 Consensus size: 16
970 TTAGACTTTC
*
980 TAAATTTAATTTTATAA
1 TAAATTTAAATTTA-AA
997 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
1014 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
*
1031 TAAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
1047 TAAATT
1 TAAATT
1053 CATTTTCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
16 8 0.16
17 42 0.82
18 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:1031 original size:7 final size:6
Alignment explanation
Indices: 980--1047 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
970 TTAGACTTTC
*
980 TAAATT TAATTT TATAA-- TAAATT TAAATT TCAAA-- TAAATT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT TAAATT
* *
1026 TAAA-A TAAACT TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAAT
1048 AAATTCATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 5 0.10
5 7 0.14
6 34 0.68
7 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:1859 original size:49 final size:49
Alignment explanation
Indices: 1761--1880 Score: 199
Period size: 49 Copynumber: 2.5 Consensus size: 49
1751 ATTTGGTTCA
*
1761 CTTCTCAGTATCTCATCAGGAA--GCTAACCTTTTATCGCTTCGACCTG
1 CTTCTCAGTGTCTCATCAGGAAGCGCTAACCTTTTATCGCTTCGACCTG
*
1808 CTTCTCAGTGTCTCATCAGGAAGCGCTATCCTTTTATCGCTTCGACCTG
1 CTTCTCAGTGTCTCATCAGGAAGCGCTAACCTTTTATCGCTTCGACCTG
*
1857 CTTCTCAGTGTCTTATCAGGAAGC
1 CTTCTCAGTGTCTCATCAGGAAGC
1881 TGGGGTTCGA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
47 21 0.31
49 47 0.69
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.34
Consensus pattern (49 bp):
CTTCTCAGTGTCTCATCAGGAAGCGCTAACCTTTTATCGCTTCGACCTG
Found at i:1974 original size:201 final size:201
Alignment explanation
Indices: 1734--2149 Score: 742
Period size: 201 Copynumber: 2.1 Consensus size: 201
1724 CTCCTCTGTA
* * *
1734 TCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGC
1 TCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTAATCGC
* * *
1799 TTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCGCTATCCTTTTATCGCTTCGACCTGCTTCTCA
66 TTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCGCTAACATTTTATCGCTTCGACCTACTTCTCA
* *
1864 GTGTCTTATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
131 ATGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
1929 TCAGTG
196 TCAGTG
*
1935 TCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATTAGGAAGCTAACCTTTAATCGC
1 TCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTAATCGC
*
2000 TTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCGCTAACATTTTATCGCTTCGACCTACTTCTCA
66 TTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCGCTAACATTTTATCGCTTCGACCTACTTCTCA
2065 ATGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
131 ATGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
2130 TCAGTG
196 TCAGTG
2136 TCTCATCAGGAAGA
1 TCTCATCAGGAAGA
2150 TGACCGCGTT
Statistics
Matches: 205, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
201 205 1.00
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (201 bp):
TCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTAATCGC
TTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCGCTAACATTTTATCGCTTCGACCTACTTCTCA
ATGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
TCAGTG
Found at i:2056 original size:49 final size:49
Alignment explanation
Indices: 1961--2081 Score: 165
Period size: 49 Copynumber: 2.5 Consensus size: 49
1951 AATTTGATTC
* * * *
1961 ACTTCTCAGTATCTCATTAGGAA--GCTAACCTTTAATCGCTTTGACCT
1 ACTTCTCAGTGTCTCATCAGGAAGCGCTAACATTTAATCGCTTCGACCT
* *
2008 GCTTCTCAGTGTCTCATCAGGAAGCGCTAACATTTTATCGCTTCGACCT
1 ACTTCTCAGTGTCTCATCAGGAAGCGCTAACATTTAATCGCTTCGACCT
*
2057 ACTTCTCAATGTCTCATCAGGAAGC
1 ACTTCTCAGTGTCTCATCAGGAAGC
2082 TGGGGTTCGA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 20 0.31
49 44 0.69
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (49 bp):
ACTTCTCAGTGTCTCATCAGGAAGCGCTAACATTTAATCGCTTCGACCT
Found at i:12452 original size:34 final size:34
Alignment explanation
Indices: 12404--12472 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
12394 TTGTTTTAAG
12404 CCGTGCTGATCCTGGTGTAATCCCAAAGCTCAGA
1 CCGTGCTGATCCTGGTGTAATCCCAAAGCTCAGA
*
12438 CCGTTCTGATCCTGGTGTAATCCCAAAGCTCAGA
1 CCGTGCTGATCCTGGTGTAATCCCAAAGCTCAGA
12472 C
1 C
12473 TCATATCCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (34 bp):
CCGTGCTGATCCTGGTGTAATCCCAAAGCTCAGA
Found at i:14265 original size:28 final size:28
Alignment explanation
Indices: 14101--14265 Score: 66
Period size: 28 Copynumber: 5.7 Consensus size: 28
14091 TACCCGTCGG
* *
14101 GGGGGCAAAATGGTAATTTTGGA-TTCTC
1 GGGGGTAAAATGGTAATTTTGGACAT-TC
* ** *
14129 AGGGGCGAAATGGTAATTTTGGGAAAATTC
1 GGGGGTAAAATGGTAATTTT-GG-ACATTC
* * * ** *
14159 GAGGTTAAAAATGGAAATTTTAAACATTT
1 GGGGGT-AAAATGGTAATTTTGGACATTC
* * * **
14188 AGGGGTAAAAGGGTAATTTTAAGAGTTTC
1 GGGGGTAAAATGGTAATTTT-GGACATTC
* *
14217 -GAGGTCGAAAATGG-AGTTTTTGGACATTC
1 GGGGGT--AAAATGGTA-ATTTTGGACATTC
14246 GGGGGTAAAATGGTAATTTT
1 GGGGGTAAAATGGTAATTTT
14266 TGAAAGTTTC
Statistics
Matches: 97, Mismatches: 30, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
28 45 0.46
29 20 0.21
30 19 0.20
31 13 0.13
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.32
Consensus pattern (28 bp):
GGGGGTAAAATGGTAATTTTGGACATTC
Found at i:14296 original size:58 final size:59
Alignment explanation
Indices: 14156--14480 Score: 199
Period size: 59 Copynumber: 5.5 Consensus size: 59
14146 TTTGGGAAAA
* * * * *
14156 TTCGAGGTTAAAAATGGAAATTTT-AAACATTTAGGGGT-AAAAGGGTAA-TTTT-AAGAGT
1 TTCGAGGTCAAAAATGGAAATTTTGGAA-GTTCAGGGGTAAAAATGG-AATTTTTGAA-AGT
* ** *
14214 TTCGAGGTCGAAAATGGAGTTTTTGGACA-TTCGGGGGT-AAAATGGTAATTTTTGAAAGT
1 TTCGAGGTCAAAAATGGAAATTTTGGA-AGTTCAGGGGTAAAAATGG-AATTTTTGAAAGT
* * * * *
14273 TTCAATGTCAAAAAT-GAAATTTTGGAAGTTCAGAGATAAAAATGGAATTTTTGGAAGT
1 TTCGAGGTCAAAAATGGAAATTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGAAAGT
* ** * * *
14331 TTCGGGGTCAAAGTTGTG-ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGAGGTCAAAAATG-GAAATTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGAAAGT
* * * * * *
14390 TTTGGGGTCAAAAATAGG-ATTTTTGGAAGTTTC-GAGGTCAAAAATATG-ATTTTTGGAAG-
1 TTCGAGGTCAAAAAT-GGAAATTTTGGAAG-TTCAGGGGT-AAAAAT-GGAATTTTTGAAAGT
* *
14449 TTC-AGGTGTAAAAATGGAATTTTTGGACAGTT
1 TTCGAGGT-CAAAAATGGAAATTTTGGA-AGTT
14481 TATGGACCTC
Statistics
Matches: 218, Mismatches: 34, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
57 1 0.00
58 78 0.36
59 111 0.51
60 27 0.12
61 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (59 bp):
TTCGAGGTCAAAAATGGAAATTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGAAAGT
Found at i:14355 original size:30 final size:29
Alignment explanation
Indices: 14211--14481 Score: 193
Period size: 30 Copynumber: 9.2 Consensus size: 29
14201 TAATTTTAAG
* *
14211 AGTTTCGAGGTCGAAAATGGAGTTTTTGGA
1 AGTTTCGGGGTCAAAAATGGA-TTTTTGGA
*
14241 CA--TTCGGGGGT--AAAATGGTAATTTTTGAA
1 -AGTTTC-GGGGTCAAAAATGG--ATTTTTGGA
*** * *
14270 AGTTTCAATGTCAAAAATGAAATTTTGGA
1 AGTTTCGGGGTCAAAAATGGATTTTTGGA
* *
14299 AG-TTCAGAGAT-AAAAATGGAATTTTTGGA
1 AGTTTC-GGGGTCAAAAATGG-ATTTTTGGA
**
14328 AGTTTCGGGGTCAAAGTTGTGATTTTTGGA
1 AGTTTCGGGGTCAAAAATG-GATTTTTGGA
14358 AG-TTCGGGGGT-AAAAATGGAATTTTTGGA
1 AGTTTC-GGGGTCAAAAATGG-ATTTTTGGA
*
14387 AGTTTTGGGGTCAAAAATAGGATTTTTGGA
1 AGTTTCGGGGTCAAAAAT-GGATTTTTGGA
* *
14417 AGTTTCGAGGTCAAAAATATGATTTTTGGA
1 AGTTTCGGGGTCAAAAAT-GGATTTTTGGA
*
14447 AG-TTCAGGTGT-AAAAATGGAATTTTTGGA
1 AGTTTC-GGGGTCAAAAATGG-ATTTTTGGA
14476 CAGTTT
1 -AGTTT
14482 ATGGACCTCG
Statistics
Matches: 193, Mismatches: 26, Indels: 42
0.74 0.10 0.16
Matches are distributed among these distances:
28 20 0.10
29 78 0.40
30 83 0.43
31 12 0.06
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.35
Consensus pattern (29 bp):
AGTTTCGGGGTCAAAAATGGATTTTTGGA
Found at i:14397 original size:59 final size:58
Alignment explanation
Indices: 14211--14480 Score: 216
Period size: 59 Copynumber: 4.6 Consensus size: 58
14201 TAATTTTAAG
* * * *
14211 AGTTTCGAGGTCGAAAAT-GGAGTTTTTGGACA-TTCGGGGGT-AAAATGGTAATTTTTGAA
1 AGTTTCGGGGTCAAAAATAGGA-TTTTTGGA-AGTTC-GAGGTAAAAATGG-AATTTTTGGA
*** * * *
14270 AGTTTCAATGTCAAAAAT-GAAATTTTGGAAGTTCAGAGATAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTC-GAGGTAAAAATGGAATTTTTGGA
* * *
14328 AGTTTCGGGGTC-AAAGTTGTGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTCAAAAATAG-GATTTTTGGAAGTTC-GAGGTAAAAATGGAATTTTTGGA
* *
14387 AGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTTCGAGGTCAAAAATATG-ATTTTTGGA
1 AGTTTCGGGGTCAAAAATAGGATTTTTGGAAG-TTCGAGGT-AAAAAT-GGAATTTTTGGA
*
14447 AG-TTCAGGTGT-AAAAAT-GGAATTTTTGGACAGTT
1 AGTTTC-GGGGTCAAAAATAGG-ATTTTTGGA-AGTT
14481 TATGGACCTC
Statistics
Matches: 175, Mismatches: 25, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
57 5 0.03
58 34 0.19
59 104 0.59
60 31 0.18
61 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.35
Consensus pattern (58 bp):
AGTTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGAGGTAAAAATGGAATTTTTGGA
Found at i:14429 original size:89 final size:90
Alignment explanation
Indices: 14310--14481 Score: 267
Period size: 89 Copynumber: 1.9 Consensus size: 90
14300 GTTCAGAGAT
* ** * *
14310 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAGTTGTGATTTTTGGAAGTTCGGGGGTAAAAAT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATATGATTTTTGGAAGTTCAGGGGTAAAAAT
14375 GGAATTTTTGGA-AGTTTTGGGGTC
66 GGAATTTTTGGACAGTTTTGGGGTC
*
14399 AAAAATAGG-ATTTTTGGAAGTTTCGAGGTCAAAAATATGATTTTTGGAAGTTCAGGTGTAAAAA
1 AAAAAT-GGAATTTTTGGAAGTTTCGAGGTCAAAAATATGATTTTTGGAAGTTCAGGGGTAAAAA
14463 TGGAATTTTTGGACAGTTT
65 TGGAATTTTTGGACAGTTT
14482 ATGGACCTCG
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
89 68 0.91
90 7 0.09
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (90 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATATGATTTTTGGAAGTTCAGGGGTAAAAAT
GGAATTTTTGGACAGTTTTGGGGTC
Found at i:15553 original size:16 final size:16
Alignment explanation
Indices: 15532--15585 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
15522 AAGTTATTTA
15532 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
**
15548 TTATTATTATTAATA-
1 TTATTATTAAAAATAT
15563 TTATTA--AAAAA-AT
1 TTATTATTAAAAATAT
15576 TTATTATTAA
1 TTATTATTAA
15586 TAGTCATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
12 1 0.03
13 9 0.29
15 8 0.26
16 13 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:15554 original size:22 final size:21
Alignment explanation
Indices: 15511--15560 Score: 86
Period size: 19 Copynumber: 2.5 Consensus size: 21
15501 TTTCCTTTTT
15511 TTATTATTAAAAAGTTATTTA
1 TTATTATTAAAAAGTTATTTA
15532 TTATTATTAAAAA--TATTTA
1 TTATTATTAAAAAGTTATTTA
15551 TTATTATTAA
1 TTATTATTAA
15561 TATTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTATTATTAAAAAGTTATTTA
Found at i:15567 original size:19 final size:19
Alignment explanation
Indices: 15511--15567 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
15501 TTTCCTTTTT
15511 TTATTATTAAAAAGTTATTTA
1 TTATTATT-AAAA-TTATTTA
*
15532 TTATTATTAAAAATATTTA
1 TTATTATTAAAATTATTTA
*
15551 TTATTATTAATATTATT
1 TTATTATTAAAATTATT
15568 AAAAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 21 0.64
20 4 0.12
21 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTATTAAAATTATTTA
Found at i:16215 original size:15 final size:15
Alignment explanation
Indices: 16195--16288 Score: 143
Period size: 15 Copynumber: 6.3 Consensus size: 15
16185 TGGGTTGACT
* *
16195 TTGGGCCATTGGTAC
1 TTGGGCCATTTGTAA
16210 TTGGGCCATTTGTAA
1 TTGGGCCATTTGTAA
*
16225 TTGGGCCGTTTGTAA
1 TTGGGCCATTTGTAA
*
16240 TTGGGCCATTTGTAC
1 TTGGGCCATTTGTAA
16255 TTGGGCCATTTGTAA
1 TTGGGCCATTTGTAA
*
16270 TTGGGCCGTTTGTAA
1 TTGGGCCATTTGTAA
16285 TTGG
1 TTGG
16289 ACTTTGTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 72 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.39
Consensus pattern (15 bp):
TTGGGCCATTTGTAA
Found at i:16246 original size:45 final size:45
Alignment explanation
Indices: 16195--16288 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
16185 TGGGTTGACT
16195 TTGGGCCATTGGTACTTGGGCCATTTGTAATTGGGCCGTTTGTAA
1 TTGGGCCATTGGTACTTGGGCCATTTGTAATTGGGCCGTTTGTAA
*
16240 TTGGGCCATTTGTACTTGGGCCATTTGTAATTGGGCCGTTTGTAA
1 TTGGGCCATTGGTACTTGGGCCATTTGTAATTGGGCCGTTTGTAA
16285 TTGG
1 TTGG
16289 ACTTTGTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.39
Consensus pattern (45 bp):
TTGGGCCATTGGTACTTGGGCCATTTGTAATTGGGCCGTTTGTAA
Found at i:16342 original size:17 final size:16
Alignment explanation
Indices: 16320--16387 Score: 73
Period size: 16 Copynumber: 4.1 Consensus size: 16
16310 TTGGATTTTC
16320 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
16337 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
* *
16354 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
* *
16370 TAAATTCAATTTTCAA
1 TAAATTTAATTTTAAA
16386 TA
1 TA
16388 GGTCCAGACA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 21 0.50
17 15 0.36
18 6 0.14
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:16387 original size:16 final size:16
Alignment explanation
Indices: 16320--16387 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
16310 TTGGATTTTC
* *
16320 TAAATTTAATTTTATAA
1 TAAATTTAAATTT-CAA
16337 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTC-AA
* *
16354 TAAACTTAAATTTAAA
1 TAAATTTAAATTTCAA
* *
16370 TAAATTCAATTTTCAA
1 TAAATTTAAATTTCAA
16386 TA
1 TA
16388 GGTCCAGACA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 16 0.38
17 26 0.62
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAAATTTCAA
Found at i:20749 original size:24 final size:25
Alignment explanation
Indices: 20703--20753 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
20693 GAAAAATAGT
**
20703 AATATTAAAAGTGTTAATCCCAAAAA
1 AATATTAAAAG-GTTAAAACCAAAAA
20729 AATATTAAAA-GTTAAAACCAAAAA
1 AATATTAAAAGGTTAAAACCAAAAA
20753 A
1 A
20754 CCCATAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.57
26 10 0.43
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.24
Consensus pattern (25 bp):
AATATTAAAAGGTTAAAACCAAAAA
Found at i:23658 original size:14 final size:14
Alignment explanation
Indices: 23636--23708 Score: 67
Period size: 14 Copynumber: 5.2 Consensus size: 14
23626 CACAAATCTA
*
23636 GAATTTGCATGTAT
1 GAATCTGCATGTAT
*
23650 GAATCTGCATCTAT
1 GAATCTGCATGTAT
*
23664 GAAT-TCACATGTAT
1 GAATCT-GCATGTAT
* *
23678 GAATCTGTATCTAT
1 GAATCTGCATGTAT
* *
23692 GAACCCGCATGTAT
1 GAATCTGCATGTAT
23706 GAA
1 GAA
23709 ATCAATACAT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
13 1 0.02
14 44 0.96
15 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (14 bp):
GAATCTGCATGTAT
Found at i:23674 original size:28 final size:28
Alignment explanation
Indices: 23643--23708 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
23633 CTAGAATTTG
**
23643 CATGTATGAATCTGCATCTATGAATTCA
1 CATGTATGAATCTGCATCTATGAACCCA
* *
23671 CATGTATGAATCTGTATCTATGAACCCG
1 CATGTATGAATCTGCATCTATGAACCCA
23699 CATGTATGAA
1 CATGTATGAA
23709 ATCAATACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (28 bp):
CATGTATGAATCTGCATCTATGAACCCA
Found at i:27690 original size:21 final size:21
Alignment explanation
Indices: 27651--27690 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27641 ATATGTCACA
*
27651 TCAGTAATTTCATTTTGAATT
1 TCAGTAATTTCATTCTGAATT
* *
27672 TCAGTATTTTTATTCTGAA
1 TCAGTAATTTCATTCTGAA
27691 AAAAATCAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (21 bp):
TCAGTAATTTCATTCTGAATT
Found at i:29032 original size:107 final size:107
Alignment explanation
Indices: 28846--29062 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 107
28836 AGCAACTTCC
28846 TAACAATTAAAAGGAAAATCTATTTCAGCATGATTATTTGGAAAGTTTTATTTTAAAAAAATTTA
1 TAACAATTAAAAGGAAAATCTATTTCAGCATGATTATTTGGAAAGTTTTATTTTAAAAAAATTTA
* *
28911 ATATCATCATTTTAATCGAAATAATTAAGGGTTTCAATTATA
66 ATATCATAATTTTAATCGAAATAATTAAAGGTTTCAATTATA
*
28953 TAACAATTAAAAGGAAAATCTATTTTAGCATGATTATTTGGAAAGTTTTATTTTAAAAAAATTTA
1 TAACAATTAAAAGGAAAATCTATTTCAGCATGATTATTTGGAAAGTTTTATTTTAAAAAAATTTA
29018 ATATCATAATTTTAATCGAAATAATTAAAGGTTTCAATTATA
66 ATATCATAATTTTAATCGAAATAATTAAAGGTTTCAATTATA
29060 TAA
1 TAA
29063 ACTAAATTAA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (107 bp):
TAACAATTAAAAGGAAAATCTATTTCAGCATGATTATTTGGAAAGTTTTATTTTAAAAAAATTTA
ATATCATAATTTTAATCGAAATAATTAAAGGTTTCAATTATA
Found at i:29973 original size:21 final size:21
Alignment explanation
Indices: 29926--29974 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
29916 TTTCAAAAAT
* * *
29926 TATTTTTAGAAAATGTAATGA
1 TATTTTTAGAAAAAGAAATAA
* *
29947 TTTTTTTATAAAAAGAAATAA
1 TATTTTTAGAAAAAGAAATAA
29968 TATTTTT
1 TATTTTT
29975 GGTGTTTGGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (21 bp):
TATTTTTAGAAAAAGAAATAA
Found at i:30480 original size:22 final size:24
Alignment explanation
Indices: 30443--30495 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
30433 ATAATATTTT
30443 ATATTTTAGTGATAAAATAAT-TAG
1 ATATTTTA-TGATAAAATAATGTAG
*
30467 ATATTTT-TGATAAAATTATGTAG
1 ATATTTTATGATAAAATAATGTAG
30490 A-ATTTT
1 ATATTTT
30496 CATAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 16 0.59
23 4 0.15
24 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (24 bp):
ATATTTTATGATAAAATAATGTAG
Found at i:30500 original size:21 final size:22
Alignment explanation
Indices: 30454--30500 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
30444 TATTTTAGTG
*
30454 ATAAAATAATTAGATATTTTTG
1 ATAAAATAATTAGATATTTTTC
*
30476 ATAAAATTATGTAGA-A-TTTTC
1 ATAAAATAAT-TAGATATTTTTC
30497 ATAA
1 ATAA
30501 TTTATCCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 8 0.36
22 10 0.45
23 4 0.18
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (22 bp):
ATAAAATAATTAGATATTTTTC
Found at i:30755 original size:62 final size:62
Alignment explanation
Indices: 30658--30783 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
30648 TATAGCAAAC
30658 TTAGTTTGTTGTAGAGACAACTAGTGCACATATTGGAGGAGAGTGAAAGATGAAATTAAGGT
1 TTAGTTTGTTGTAGAGACAACTAGTGCACATATTGGAGGAGAGTGAAAGATGAAATTAAGGT
30720 TTAGTTTGTTGTAGAGACAACTAGTGCACATATTGGAGGAGAGTGAAAGATGAAATTAAGGT
1 TTAGTTTGTTGTAGAGACAACTAGTGCACATATTGGAGGAGAGTGAAAGATGAAATTAAGGT
30782 TT
1 TT
30784 GGTATAGAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (62 bp):
TTAGTTTGTTGTAGAGACAACTAGTGCACATATTGGAGGAGAGTGAAAGATGAAATTAAGGT
Found at i:38475 original size:28 final size:28
Alignment explanation
Indices: 38435--38489 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
38425 GATATTCGAT
38435 TTACTCCTTGTTGACCCAAAGGTCATGC
1 TTACTCCTTGTTGACCCAAAGGTCATGC
38463 TTACTCCTTGTTGACCCAAAGGTCATG
1 TTACTCCTTGTTGACCCAAAGGTCATG
38490 ATGCTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (28 bp):
TTACTCCTTGTTGACCCAAAGGTCATGC
Found at i:48269 original size:32 final size:36
Alignment explanation
Indices: 48227--48297 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 36
48217 TTGGTCCTTG
*
48227 TAATTTTTATTT-TG-TTTTAATTT-AA-TTTAATT
1 TAATTCTTATTTCTGTTTTTAATTTCAATTTTAATT
48259 TAATTCTTATTTCTGTTTTTAATTTGCAATTTTAATT
1 TAATTCTTATTTCTGTTTTTAATTT-CAATTTTAATT
48296 TA
1 TA
48298 GTCCATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
32 11 0.33
33 2 0.06
34 9 0.27
36 2 0.06
37 9 0.27
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (36 bp):
TAATTCTTATTTCTGTTTTTAATTTCAATTTTAATT
Found at i:49508 original size:14 final size:14
Alignment explanation
Indices: 49481--49517 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
49471 ACTTAATTAA
49481 AATTTATATTAAAT
1 AATTTATATTAAAT
49495 AATTT-TATTAAA-
1 AATTTATATTAAAT
49507 ATATTTATATT
1 A-ATTTATATT
49518 TTATACTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.05
13 11 0.52
14 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTTATATTAAAT
Found at i:58438 original size:824 final size:828
Alignment explanation
Indices: 56827--58451 Score: 2295
Period size: 824 Copynumber: 2.0 Consensus size: 828
56817 CAATCTTTGG
* * * *
56827 TATTTCACCACCGTAGGTGGCCGAGGCCACCATCCCCAATGAAGGGTGGTTCACTAGTCGGATGA
1 TATTCCACCACCGTAGGTGGCCGAGGCCACCATCCCCAATGAAAGGTGGTTCACTACTCGAATGA
* *
56892 CGACTCCATGAACGTCCCATGTTCGTGCGTGGCCCTTTCGAAGAGGAGAAAATAAAAAGGGAACA
66 CGACTCCATGAACATCCCATGTTCGTGCGTGGCCCTTTCGAAGAGGAGAAAATAAAAAGGGAAAA
* *
56957 AAGCCCTTTCGAAATAAACCCTAGGAATCGAAATTTTATGGATTTCTTAGGGTTTTGAAACTAGA
131 AAGCCCTTTCGAAACAAACCCTAGGAATCGAAATTTTATGGATTTCTTAGGGTTTTGAAACCAGA
57022 TCTAAAAGTTCAACCCTAGATTTGGAATAGAAAAAAACAAAGGAAAAGGGTGTCTTTTTGACTTC
196 TCTAAAAGTTCAACCCTAGATTTGGAATAGAAAAAAACAAAGGAAAAGGGTGTCTTTTTGACTTC
* *
57087 CCAACCATTGTAGGCGGCGGTCTCCATTGTCGATGATCGGTGGCCACGGCGATTAGAAACCAAAT
261 CCAACCATCGTAGGCGGCGGTCTCCATCGTCGATGATCGGTGGCCACGGCG--TAG-AACCAAAT
* * *
57152 CCTAGGTGGTCGGATATGAGGGCTTTAGAGAGAAAAAGGGAAGGGTGAGAAGTTTTTTTTTTTTT
323 CCTAGGTGGTCAGACATGAGGGCTTTAGAGAGAAAAAGGGAAGGGTGAGAAG----TTTTGTTTT
*
57217 TTTAAATGGTTGACAAATGAAGTTTTTTCTCAAAAAATTGATATTTATTGACACCCTATACGACA
384 TTAAAATGGTTGACAAATGAAGTTTTTTCTCAAAAAATTGATATTTATTGACACCCTATACGACA
* * * * * *
57282 TCCTTTTGAAGTGAGCATTTTGTGCTCTATACGACATCATTTGCCTCTACCCGAANTGACCTTGA
449 TCCGTTTGAAGCGAGCATTTTGTGCTCCAAACGACATCATTTGCCTCTACCCGAAATGACCTAGA
* * * * ** *
57347 TCCGCCCCACCAAGGTCCGCTCGTCTTTGTTAAAAGGGTAAATTATTTCTGTAGTCCCTTCACAT
514 TCCGCCCCACCAAAGTCCGCACGTCTTTATTAAAAGGGAAAATTATTTCCATAGTCCCTCCACAT
* * *
57412 TTTAGGGCATTCCGATTTGGTCCCTTTTCACATAATTTATGCTCCATACGGCGTCGTTTCAGGCC
579 TTTAGGGCATTCCGATTTGGTCCCTTTTCACATAATCTATGCTCCATACGACATCGTTTCAGGCC
* * * * * * *
57477 TGATTCTAGTGGCCTTGGAACGGCGTCGTTTTACGTGACCTGAAGACTCGATCCGAATCCTTTTT
644 TGATTCTAGTGGCCTTGGAACGACGTCATTTCACATGACCCGAAGACCCGATCCGAACCCTTTTT
** * * *
57542 AGGGTCCGTGTGTTTTTTAAAAAAGGGAAATTGTTCCCCAGGTCCTTTCGCATTTTCATTTTATT
709 AGGGTCCGCATGTTTTTTAAAAAAGGGAAATTATTCCCCAGGTCCTTCCACATTTTCATTTTATT
*
57607 TTAAATTTGTCCTTTT-TTTTAAAAAAAAACTTTTTAAATTCGGCCACATGATTT
774 ATAAATTTGTCCTTTTGTTTTAAAAAAAAACTTTTTAAATTCGGCCACATGATTT
* * * * *
57661 TATTCCACCATCGTAGGTGGTCGAGGCCACCATCCCCGATGAAAGGTGGTTCACTCCTTGAATGA
1 TATTCCACCACCGTAGGTGGCCGAGGCCACCATCCCCAATGAAAGGTGGTTCACTACTCGAATGA
* * ** *
57726 CGGCTCTATGAACATTTCATGTTCGTGCGTGGCCCTTTCGAAGAGGATAAAATAAAAAGGGAAAA
66 CGACTCCATGAACATCCCATGTTCGTGCGTGGCCCTTTCGAAGAGGAGAAAATAAAAAGGGAAAA
*
57791 AAGCCCTTTCGAAACAAACCCTAGGAATCGAAATTTTATGGATTTCTTGGGGGTTTTGAAACCAG
131 AAGCCCTTTCGAAACAAACCCTAGGAATCGAAATTTTATGGATTTCTT-AGGGTTTTGAAACCAG
* * * * *
57856 ATCTAAAGGATTTAACCTTAGATTTGGAATCGAAAAAAA-AAAGGAAAAGGGTGTCTTTTTTACT
195 ATCTAAAAG-TTCAACCCTAGATTTGGAATAGAAAAAAACAAAGGAAAAGGGTGTCTTTTTGACT
**
57920 TCCTGACCATCGTAGGCGGCGGTCTCCATCGTCGATGA-CTGGTGGCCAC-G-G-AG-ACCAAAT
259 TCCCAACCATCGTAGGCGGCGGTCTCCATCGTCGATGATC-GGTGGCCACGGCGTAGAACCAAAT
* *
57980 CCTAGGTGGTCAGACGTGGGGGCTTTAGAGAGAAAAAGGGAAGGGTGAGAAG-TTTGTTTTTTAA
323 CCTAGGTGGTCAGACATGAGGGCTTTAGAGAGAAAAAGGGAAGGGTGAGAAGTTTTGTTTTTTAA
* * * *
58044 AATGGGTTGACAAATGAAGTTTTTTCTCAAAAAATTGATATTTATTGACACCTTATACGGCGTCG
388 AAT-GGTTGACAAATGAAGTTTTTTCTCAAAAAATTGATATTTATTGACACCCTATACGACATCC
* * *
58109 GTTTGAAGCGAGCATTTTGTGCTCCAAAC-AGCGTCGTTTGTCTCTACCC-AAATCGATCC-AGA
452 GTTTGAAGCGAGCATTTTGTGCTCCAAACGA-CATCATTTGCCTCTACCCGAAAT-GA-CCTAGA
* *
58171 TTCGCCCCACCAAAGTCTGCACGT-TTCTATTAAAAGGGAAAATTATTTCCATAGTCCCTCCACA
514 TCCGCCCCACCAAAGTCCGCACGTCTT-TATTAAAAGGGAAAATTATTTCCATAGTCCCTCCACA
*
58235 TTTTAGGGCATTCCGATTTGGTCCCTTTTCACATAATCTATGCTCCATACGACATTGTTTCAGGC
578 TTTTAGGGCATTCCGATTTGGTCCCTTTTCACATAATCTATGCTCCATACGACATCGTTTCAGGC
* * * **
58300 CTGATTCTAGTGGCCTTGGAACGATGTCATTTCGCATGACCCGAGGACCCGATCCGGGCCCTTTT
643 CTGATTCTAGTGGCCTTGGAACGACGTCATTTCACATGACCCGAAGACCCGATCCGAACCCTTTT
*
58365 TAGGGTCCGCATG-TTTTTAAAAAAGGGGAAATTATTGCCCAGGTCCTTCCACATTTTCATTTTA
708 TAGGGTCCGCATGTTTTTTAAAAAA-GGGAAATTATTCCCCAGGTCCTTCCACATTTTCATTTTA
*
58429 TTATAAATTTTTCCTTTTGTTTT
772 TTATAAATTTGTCCTTTTGTTTT
58452 TTTTTTAACT
Statistics
Matches: 701, Mismatches: 80, Indels: 29
0.87 0.10 0.04
Matches are distributed among these distances:
823 30 0.04
824 329 0.47
825 6 0.01
828 55 0.08
830 2 0.00
833 1 0.00
834 163 0.23
835 89 0.13
836 26 0.04
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (828 bp):
TATTCCACCACCGTAGGTGGCCGAGGCCACCATCCCCAATGAAAGGTGGTTCACTACTCGAATGA
CGACTCCATGAACATCCCATGTTCGTGCGTGGCCCTTTCGAAGAGGAGAAAATAAAAAGGGAAAA
AAGCCCTTTCGAAACAAACCCTAGGAATCGAAATTTTATGGATTTCTTAGGGTTTTGAAACCAGA
TCTAAAAGTTCAACCCTAGATTTGGAATAGAAAAAAACAAAGGAAAAGGGTGTCTTTTTGACTTC
CCAACCATCGTAGGCGGCGGTCTCCATCGTCGATGATCGGTGGCCACGGCGTAGAACCAAATCCT
AGGTGGTCAGACATGAGGGCTTTAGAGAGAAAAAGGGAAGGGTGAGAAGTTTTGTTTTTTAAAAT
GGTTGACAAATGAAGTTTTTTCTCAAAAAATTGATATTTATTGACACCCTATACGACATCCGTTT
GAAGCGAGCATTTTGTGCTCCAAACGACATCATTTGCCTCTACCCGAAATGACCTAGATCCGCCC
CACCAAAGTCCGCACGTCTTTATTAAAAGGGAAAATTATTTCCATAGTCCCTCCACATTTTAGGG
CATTCCGATTTGGTCCCTTTTCACATAATCTATGCTCCATACGACATCGTTTCAGGCCTGATTCT
AGTGGCCTTGGAACGACGTCATTTCACATGACCCGAAGACCCGATCCGAACCCTTTTTAGGGTCC
GCATGTTTTTTAAAAAAGGGAAATTATTCCCCAGGTCCTTCCACATTTTCATTTTATTATAAATT
TGTCCTTTTGTTTTAAAAAAAAACTTTTTAAATTCGGCCACATGATTT
Found at i:59850 original size:14 final size:15
Alignment explanation
Indices: 59820--59872 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 15
59810 AGAACATTAT
*
59820 TTAAAATTTAAAATTA
1 TTAAAA-TTAAATTTA
59836 TTAAAA-TAAATTTA
1 TTAAAATTAAATTTA
59850 TTATATGAATTAAATTTA
1 TTA-A--AATTAAATTTA
59868 TTAAA
1 TTAAA
59873 TAATAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
14 10 0.31
15 2 0.06
16 6 0.19
17 3 0.09
18 11 0.34
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TTAAAATTAAATTTA
Found at i:59910 original size:18 final size:19
Alignment explanation
Indices: 59845--59916 Score: 62
Period size: 18 Copynumber: 3.9 Consensus size: 19
59835 ATTAAAATAA
59845 ATTTATTATATGAATTAA--
1 ATTTATTATAT-AATTAATT
* *
59863 ATTTATTAAATAATAAATT
1 ATTTATTATATAATTAATT
*
59882 A-TT-TTAAATATATTAATT
1 ATTTATTATATA-ATTAATT
*
59900 ATTTATTATATCATTAA
1 ATTTATTATATAATTAA
59917 ATTAATATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
17 12 0.27
18 19 0.43
19 8 0.18
20 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
ATTTATTATATAATTAATT
Found at i:65555 original size:7 final size:7
Alignment explanation
Indices: 65536--65570 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
65526 TAAACCTTCC
65536 TTAAAATA
1 TTAAAA-A
65544 TTAAAAA
1 TTAAAAA
65551 TTAAAAA
1 TTAAAAA
*
65558 TTTAAAA
1 TTAAAAA
65565 TTAAAA
1 TTAAAA
65571 TAAATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
TTAAAAA
Found at i:65566 original size:14 final size:15
Alignment explanation
Indices: 65536--65572 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
65526 TAAACCTTCC
65536 TTAAAATATTAAAAA
1 TTAAAATATTAAAAA
*
65551 TTAAAA-ATTTAAAA
1 TTAAAATATTAAAAA
65565 TTAAAATA
1 TTAAAATA
65573 AATATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAATATTAAAAA
Found at i:69814 original size:28 final size:27
Alignment explanation
Indices: 69761--69814 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
69751 GTTTTAATGG
* **
69761 CTAAAATAATAAATAACTAATTATAAT
1 CTAAAATAATAAATAACAAAAAATAAT
*
69788 CTAAAGTAATGAAATAACAAAAAATAA
1 CTAAAATAAT-AAATAACAAAAAATAA
69815 ATAAATGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (27 bp):
CTAAAATAATAAATAACAAAAAATAAT
Found at i:73121 original size:49 final size:49
Alignment explanation
Indices: 73011--73145 Score: 148
Period size: 49 Copynumber: 2.8 Consensus size: 49
73001 CAGAAAAGTG
*
73011 AGATGGGCCACTGGTAGGGCATGTTAGTTGATAACCAAATTGGTAGATA
1 AGATGGGCCACTGGTAGGGCATGTTAGTTGATAACCAAATTGGTAAATA
* * **
73060 AGATAGGCCACTGGTAGGGCATGTTAGTTGCTAATTAGAA-TGGTAAATA
1 AGATGGGCCACTGGTAGGGCATGTTAGTTGATAACCA-AATTGGTAAATA
* * * * *
73109 TGTTGGGTCACTGGTTA-GGCATGTTATTTGTTAACCA
1 AGATGGGCCACTGG-TAGGGCATGTTAGTTGATAACCA
73146 GCCTGGCGAT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
49 67 0.94
50 4 0.06
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (49 bp):
AGATGGGCCACTGGTAGGGCATGTTAGTTGATAACCAAATTGGTAAATA
Found at i:75000 original size:26 final size:26
Alignment explanation
Indices: 74964--75032 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 26
74954 TAACCATATA
* *
74964 TGCTCACACGAGCTGTGAAATGGGTC
1 TGCTCACACGAGATGTGAAATGGGCC
74990 TGCTCACACGAGATGTGAAATGGGCC
1 TGCTCACACGAGATGTGAAATGGGCC
*
75016 TGCTCACACGAGTTGTG
1 TGCTCACACGAGATGTG
75033 GGTCGATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (26 bp):
TGCTCACACGAGATGTGAAATGGGCC
Found at i:75278 original size:158 final size:158
Alignment explanation
Indices: 74990--75317 Score: 453
Period size: 158 Copynumber: 2.1 Consensus size: 158
74980 GAAATGGGTC
** * * *
74990 TGCTCACACGAGATGTGAAATGGGCCTGCTCACACGAGTTGTGGGTCGATATGTGGAGCTACACG
1 TGCTCACACGAGATGTGAAATGGGCCTGCTCACACGAACTGTGGGTCAAGATGTAGAGCTACACG
* * ** * * *
75055 ATATTGCTCACACGAGCTATGGAGAATCCGCAATAAATGTTGGACCTCAGTCATTGGTAGGACAT
66 ATATTGCTCACACGAGCTAAGGAGAATCCGCAACAAATGCAGGACCTCAGCCATCGGTAGAACAT
*
75120 CTAAGACCAACACCCATATAACTTGTAA
131 CCAAGACCAACACCCATATAACTTGTAA
* *
75148 TGCTCACACGAGTTGTGAAATGGGCCTGCTCACATC-AACTGTGGGTCAAGATGTTAG-GTTACA
1 TGCTCACACGAGATGTGAAATGGGCCTGCTCACA-CGAACTGTGGGTCAAGATG-TAGAGCTACA
* * * *
75211 TGATGTTGCTCACACGAGCTAAGGAGAATTCGCAACCAATGCAGGACCTCAGCCATCGGTAGAAC
64 CGATATTGCTCACACGAGCTAAGGAGAATCCGCAACAAATGCAGGACCTCAGCCATCGGTAGAAC
75276 ATCCAAGACCAACACCCATATAACTTGTAA
129 ATCCAAGACCAACACCCATATAACTTGTAA
75306 TGCTCACACGAG
1 TGCTCACACGAG
75318 CTGTAACTGT
Statistics
Matches: 149, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
158 146 0.98
159 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (158 bp):
TGCTCACACGAGATGTGAAATGGGCCTGCTCACACGAACTGTGGGTCAAGATGTAGAGCTACACG
ATATTGCTCACACGAGCTAAGGAGAATCCGCAACAAATGCAGGACCTCAGCCATCGGTAGAACAT
CCAAGACCAACACCCATATAACTTGTAA
Found at i:75481 original size:196 final size:196
Alignment explanation
Indices: 75147--75503 Score: 491
Period size: 196 Copynumber: 1.8 Consensus size: 196
75137 ATAACTTGTA
* * *
75147 ATGCTCACACGAGTTGTGAAATGGGCCTGCTCACATCAACTGTGGGTCAAGATGTTAGGTTACAT
1 ATGCTCACACGAGCTGTGAAATGGGCCTGCTCACATCAACTGTGGGTCAAGATGTTAGGCTACAC
* * * * * **
75212 GATGTTGCTCACACGAGCTAAGGAGAATTCGCAACCAATGCAGGACCTCAGCCATCGGTAGAACA
66 GATGTTGCTCACACGAGCTAAGGAGAATCCACAACAAATGCAAGACATCAGCCATCAATAGAACA
*
75277 TCCAAGACCAACACCCATATAACTTGTAATGCTCACACGAGCTGTAACTGTGACATGCAACCATA
131 TCCAAGACCAACACCCATATAACCTGTAATGCTCACACGAGCTGTAACTGTGACATGCAACCATA
75342 T
196 T
* * **
75343 ATGCTCACACGAGCTGTGAAATGGGTCTGCTCACA-CGAGCTGTGGGTCGGGATGTTAGGCTACA
1 ATGCTCACACGAGCTGTGAAATGGGCCTGCTCACATC-AACTGTGGGTCAAGATGTTAGGCTACA
* * ** * * *
75407 CGATGTTGCTCACATGAGTTGTGGAGAATCCACAGCAAATGCAATACATCAGCCATCAATAGGAC
65 CGATGTTGCTCACACGAGCTAAGGAGAATCCACAACAAATGCAAGACATCAGCCATCAATAGAAC
*
75472 ATCCAAGACCAGCACCCATATAACCTGTAATG
130 ATCCAAGACCAACACCCATATAACCTGTAATG
75504 ACATGTCATT
Statistics
Matches: 137, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
195 1 0.01
196 136 0.99
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (196 bp):
ATGCTCACACGAGCTGTGAAATGGGCCTGCTCACATCAACTGTGGGTCAAGATGTTAGGCTACAC
GATGTTGCTCACACGAGCTAAGGAGAATCCACAACAAATGCAAGACATCAGCCATCAATAGAACA
TCCAAGACCAACACCCATATAACCTGTAATGCTCACACGAGCTGTAACTGTGACATGCAACCATA
T
Found at i:76357 original size:21 final size:20
Alignment explanation
Indices: 76329--76367 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
76319 GTTTCTCTCG
76329 TTTCTTT-ATCTAAATAATAA
1 TTTCTTTAAT-TAAATAATAA
76349 TTTCATTTAATTAAATAAT
1 TTTC-TTTAATTAAATAAT
76368 TCAAATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTCTTTAATTAAATAATAA
Found at i:76698 original size:21 final size:20
Alignment explanation
Indices: 76660--76698 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
76650 TTTCATAGCT
* *
76660 TCAAAATCTAACACTTTCTA
1 TCAAAATCAAACAATTTCTA
76680 TCAAAACTCAAACAATTTC
1 TCAAAA-TCAAACAATTTC
76699 ACTCTAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.31
Consensus pattern (20 bp):
TCAAAATCAAACAATTTCTA
Found at i:79277 original size:17 final size:17
Alignment explanation
Indices: 79257--79290 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
79247 ATCACTCGCT
79257 ATTTCAATAACATTTTC
1 ATTTCAATAACATTTTC
79274 ATTTCAATAACATTTTC
1 ATTTCAATAACATTTTC
79291 CATATAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTCAATAACATTTTC
Found at i:80488 original size:2 final size:2
Alignment explanation
Indices: 80476--80516 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
80466 ACACTAATAA
*
80476 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
80517 AATTTATCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.