Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015381.1 Kokia drynarioides strain JFW-HI SEQ_130428, 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: 2291099
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 587 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:2042941 original size:114 final size:114
Alignment explanation
Indices: 2042783--2043011 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
2042773 TTTAAATAAC
2042783 TAGCATCAGCCACGTAATACTTGAATTCACCGTACAAATAGCCTATAACTTAGATTATAAAAACA
1 TAGCATCAGCCACGTAATACTTGAATTCACCGTACAAATAGCCTATAACTTAGATTATAAAAACA
2042848 TACATAAATTTATTCTATCTTTTCTTTTCTTTTCTTTTACACTTCTTCA
66 TACATAAATTTATTCTATCTTTTCTTTTCTTTTCTTTTACACTTCTTCA
2042897 TAGCATCAGCCACGTAATACTTGAATTCACCGTACAAATAGCCTATAACTTAGATTATAAAAACA
1 TAGCATCAGCCACGTAATACTTGAATTCACCGTACAAATAGCCTATAACTTAGATTATAAAAACA
2042962 TACATAAATTTATTCTATCTTTTCTTTTCTTTTCTTTTACACTTCTTCA
66 TACATAAATTTATTCTATCTTTTCTTTTCTTTTCTTTTACACTTCTTCA
2043011 T
1 T
2043012 CTTCTTTCTT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (114 bp):
TAGCATCAGCCACGTAATACTTGAATTCACCGTACAAATAGCCTATAACTTAGATTATAAAAACA
TACATAAATTTATTCTATCTTTTCTTTTCTTTTCTTTTACACTTCTTCA
Found at i:2044191 original size:18 final size:18
Alignment explanation
Indices: 2044168--2044210 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2044158 GTTTAAGGTG
2044168 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
2044186 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
2044204 TAATTAA
1 TAATTAA
2044211 AAATCTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:2046384 original size:17 final size:18
Alignment explanation
Indices: 2046362--2046395 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2046352 TCTTTTATTT
2046362 GACACAATGCCT-AAAAC
1 GACACAATGCCTCAAAAC
2046379 GACACAATGCCTCAAAA
1 GACACAATGCCTCAAAA
2046396 GATTATAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.29, G:0.12, T:0.12
Consensus pattern (18 bp):
GACACAATGCCTCAAAAC
Found at i:2050222 original size:16 final size:15
Alignment explanation
Indices: 2050203--2050257 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
2050193 TTGAATAGGG
2050203 TTGTAATGAAATATGA
1 TTGTAATGAAATA-GA
*
2050219 TTGTAATAAAATAGA
1 TTGTAATGAAATAGA
* *
2050234 GCTGTAATGAAATAAAA
1 -TTGTAATGAAAT-AGA
2050251 TTGTAAT
1 TTGTAAT
2050258 CAATAATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 28 0.88
17 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.35
Consensus pattern (15 bp):
TTGTAATGAAATAGA
Found at i:2050527 original size:34 final size:33
Alignment explanation
Indices: 2050489--2050564 Score: 125
Period size: 34 Copynumber: 2.3 Consensus size: 33
2050479 ATATAATTAT
2050489 TTTTATATTAAATTATATTAAAATATTTTTTTA
1 TTTTATATTAAATTATATTAAAATATTTTTTTA
*
2050522 GTTTTATATTAAATTATATTCAAATATTTTTTTA
1 -TTTTATATTAAATTATATTAAAATATTTTTTTA
*
2050556 TATTATATT
1 TTTTATATT
2050565 TTTTGAGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 8 0.20
34 32 0.80
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (33 bp):
TTTTATATTAAATTATATTAAAATATTTTTTTA
Found at i:2052876 original size:32 final size:30
Alignment explanation
Indices: 2052838--2052940 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 30
2052828 CATTTGGGTT
2052838 TAATTAAAAGATGAAAATTTTATAATAAAACA
1 TAATTAAAA-ATG-AAATTTTATAATAAAACA
* *
2052870 TAATTAAATTAATTAAA-TTTATTAATAAAATGA
1 TAATTAAA--AATGAAATTTTA-TAATAAAA-CA
*
2052903 TATATAATAAAATGAAATTTTATAATAAAACA
1 TA-ATTA-AAAATGAAATTTTATAATAAAACA
*
2052935 TTATTA
1 TAATTA
2052941 GTGGAAGGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
31 7 0.12
32 21 0.37
33 19 0.33
34 8 0.14
35 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (30 bp):
TAATTAAAAATGAAATTTTATAATAAAACA
Found at i:2054570 original size:2 final size:2
Alignment explanation
Indices: 2054559--2054589 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2054549 TTCCCTCAAT
2054559 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2054590 ACCTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2066980 original size:28 final size:26
Alignment explanation
Indices: 2066928--2066989 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
2066918 AAAGAAGGCG
**
2066928 AATGAGAATTTTTTTTTGGTGAATGA
1 AATGAGAATTTTTTTTTAATGAATGA
*
2066954 AATGAGAGTTTTTTTATTAATGCAATG-
1 AATGAGAATTTTTTT-TTAATG-AATGA
*
2066981 AGTGAGAAT
1 AATGAGAAT
2066990 AAGGAATGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 14 0.48
27 11 0.38
28 4 0.14
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.42
Consensus pattern (26 bp):
AATGAGAATTTTTTTTTAATGAATGA
Found at i:2067578 original size:4 final size:4
Alignment explanation
Indices: 2067571--2067601 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2067561 AATAAATATA
2067571 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
2067602 TTGTGTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:2073776 original size:13 final size:13
Alignment explanation
Indices: 2073758--2073785 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2073748 TCAACCATAA
2073758 GAGCATTATTCAT
1 GAGCATTATTCAT
2073771 GAGCATTATTCAT
1 GAGCATTATTCAT
2073784 GA
1 GA
2073786 CTCTATTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (13 bp):
GAGCATTATTCAT
Found at i:2082817 original size:24 final size:24
Alignment explanation
Indices: 2082789--2082836 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2082779 AAAAATCAAA
2082789 ATATTTATAAAATTTTCAAAATTT
1 ATATTTATAAAATTTTCAAAATTT
* *
2082813 ATATTTTTAAAATTTTGAAAATTT
1 ATATTTATAAAATTTTCAAAATTT
2082837 TAAAAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
ATATTTATAAAATTTTCAAAATTT
Found at i:2086490 original size:20 final size:21
Alignment explanation
Indices: 2086465--2086504 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2086455 TTTATTCCAA
*
2086465 AATATT-AATAAAATAATTAG
1 AATATTCAATAAAAAAATTAG
2086485 AATATTCAATAAAAAAATTA
1 AATATTCAATAAAAAAATTA
2086505 TCTCAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
AATATTCAATAAAAAAATTAG
Found at i:2086803 original size:2 final size:2
Alignment explanation
Indices: 2086796--2086822 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2086786 CTGCCTTCTT
2086796 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2086823 GTTTGTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2095120 original size:24 final size:26
Alignment explanation
Indices: 2095093--2095146 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 26
2095083 TTGCGGTTTT
*
2095093 TTTTAATTTATATTTG-AATAC-TAG
1 TTTTAATTTATATGTGCAATACATAG
*
2095117 TTTT-TTTTATATGTGCAATACATAG
1 TTTTAATTTATATGTGCAATACATAG
*
2095142 GTTTA
1 TTTTA
2095147 TTGCGTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 9 0.38
24 9 0.38
25 6 0.25
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.54
Consensus pattern (26 bp):
TTTTAATTTATATGTGCAATACATAG
Found at i:2098414 original size:18 final size:18
Alignment explanation
Indices: 2098391--2098428 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2098381 ATTTGTGATC
2098391 GAAATTGAAAGTGAAAGT
1 GAAATTGAAAGTGAAAGT
* *
2098409 GAAATTGGAATTGAAAGT
1 GAAATTGAAAGTGAAAGT
2098427 GA
1 GA
2098429 TATGAATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (18 bp):
GAAATTGAAAGTGAAAGT
Found at i:2100744 original size:23 final size:22
Alignment explanation
Indices: 2100712--2100756 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2100702 TAAATTTGTG
*
2100712 CCTAAGCCCAAACCCTTTTAAAA
1 CCTAAACCCAAACCC-TTTAAAA
*
2100735 CCTAAACCCAAATCCTTTAAAA
1 CCTAAACCCAAACCCTTTAAAA
2100757 TTAAATCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.42, C:0.33, G:0.02, T:0.22
Consensus pattern (22 bp):
CCTAAACCCAAACCCTTTAAAA
Found at i:2100790 original size:17 final size:18
Alignment explanation
Indices: 2100757--2100791 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2100747 TCCTTTAAAA
*
2100757 TTAAATCCAATAGCCTTT
1 TTAAACCCAATAGCCTTT
2100775 TTAAACCCAA-AGCCTTT
1 TTAAACCCAATAGCCTTT
2100792 AAAAACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (18 bp):
TTAAACCCAATAGCCTTT
Found at i:2106766 original size:31 final size:31
Alignment explanation
Indices: 2106731--2106792 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
2106721 AAGCTGAATA
2106731 CTAAGGAGTTATTATGGTTGCAATTTTTGTT
1 CTAAGGAGTTATTATGGTTGCAATTTTTGTT
2106762 CTAAGGAGTTATTATGGTTGCAATTTTTGTT
1 CTAAGGAGTTATTATGGTTGCAATTTTTGTT
2106793 GTTTCAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (31 bp):
CTAAGGAGTTATTATGGTTGCAATTTTTGTT
Found at i:2112575 original size:10 final size:10
Alignment explanation
Indices: 2112557--2112582 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2112547 TCCATTTTGA
2112557 ATTTTTTTTC
1 ATTTTTTTTC
2112567 ATTTTTTTTC
1 ATTTTTTTTC
2112577 ATTTTT
1 ATTTTT
2112583 GTTGCAGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTTTTC
Found at i:2124605 original size:16 final size:16
Alignment explanation
Indices: 2124584--2124618 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2124574 TTGCTTCTAA
2124584 AAAGCACTTTTGG-GAC
1 AAAGCAC-TTTGGAGAC
2124600 AAAGCACTTTGGAGAC
1 AAAGCACTTTGGAGAC
2124616 AAA
1 AAA
2124619 AGTATTCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (16 bp):
AAAGCACTTTGGAGAC
Found at i:2130096 original size:59 final size:58
Alignment explanation
Indices: 2129990--2130138 Score: 142
Period size: 59 Copynumber: 2.5 Consensus size: 58
2129980 GAAATATCAT
* * * *
2129990 GGACCAACTTGGACCAAAAAACAG-TTCAGCTCCAATATGGGAACAATTACAAAATT-AAG
1 GGACTAACTTGGA-CAAAAAA-AGTTTAAGCCCCAATATGAGAACAATTAC-AAATTCAAG
* * *
2130049 GGACTAACTTGGACAAAAAAATGTTTAAGCCCCAATGTGAGAGCAATTACCAATTCAAG
1 GGACTAACTTGGACAAAAAAA-GTTTAAGCCCCAATATGAGAACAATTACAAATTCAAG
* * *
2130108 GCACTATCTTGGA-AAAAACAAGTTCAAGCCC
1 GGACTAACTTGGACAAAAA-AAGTTTAAGCCC
2130139 GTATGAGGGA
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
57 1 0.01
58 26 0.34
59 49 0.64
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (58 bp):
GGACTAACTTGGACAAAAAAAGTTTAAGCCCCAATATGAGAACAATTACAAATTCAAG
Found at i:2132139 original size:19 final size:19
Alignment explanation
Indices: 2132116--2132151 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2132106 TTTATAAGTT
2132116 TTTTTTATAAAA-ATTATA
1 TTTTTTATAAAACATTATA
2132134 TTTTTTATAAAACATTAT
1 TTTTTTATAAAACATTAT
2132152 GAAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTTATAAAACATTATA
Found at i:2132191 original size:23 final size:25
Alignment explanation
Indices: 2132134--2132197 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 25
2132124 AAAAATTATA
2132134 TTTTTTATAAAACATTATGAAAATT
1 TTTTTTATAAAACATTATGAAAATT
* * *
2132159 ATTTTT-TAAAA-ATT-TTAAATTT
1 TTTTTTATAAAACATTATGAAAATT
*
2132181 TTTTTTATAAATCATTA
1 TTTTTTATAAAACATTA
2132198 CAAAAATACT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 11 0.35
23 7 0.23
24 8 0.26
25 5 0.16
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTTTATAAAACATTATGAAAATT
Found at i:2134011 original size:14 final size:14
Alignment explanation
Indices: 2133992--2134018 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2133982 TTTGAATAGA
2133992 TTAAAAATATATAT
1 TTAAAAATATATAT
2134006 TTAAAAATATATA
1 TTAAAAATATATA
2134019 AAATTATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAAATATATAT
Found at i:2146137 original size:25 final size:23
Alignment explanation
Indices: 2146097--2146142 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2146087 ACAATTAGGG
2146097 AATTATTGTTTAAATTTAATTCA
1 AATTATTGTTTAAATTTAATTCA
*
2146120 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTA-AATTTAATT
2146143 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAAATTTAATTCA
Found at i:2147224 original size:18 final size:19
Alignment explanation
Indices: 2147200--2147242 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2147190 TTCAGTCATT
2147200 ATTTATTATTT-ATTTTTA
1 ATTTATTATTTCATTTTTA
*
2147218 TTTTATTATTTGCATTTTTA
1 ATTTATTATTT-CATTTTTA
2147238 ATTTA
1 ATTTA
2147243 ATTTTTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTATTATTTCATTTTTA
Found at i:2147236 original size:21 final size:18
Alignment explanation
Indices: 2147201--2147261 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 18
2147191 TCAGTCATTA
*
2147201 TTTATTATTTATTTTTAT
1 TTTATTATTTATTTTAAT
2147219 TTTATTATTTGCATTTTTAAT
1 TTTATTATTT--A-TTTTAAT
* * *
2147240 TTAATTTTTCTAATTTAAT
1 TTTATTATT-TATTTTAAT
2147259 TTT
1 TTT
2147262 TTTCCCTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 10 0.29
19 8 0.24
20 2 0.06
21 13 0.38
22 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTATTTATTTTAAT
Found at i:2147253 original size:14 final size:13
Alignment explanation
Indices: 2147232--2147263 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
2147222 ATTATTTGCA
2147232 TTTTTAATTTAAT
1 TTTTTAATTTAAT
2147245 TTTTCTAATTTAAT
1 TTTT-TAATTTAAT
2147259 TTTTT
1 TTTTT
2147264 TCCCTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:2150119 original size:6 final size:6
Alignment explanation
Indices: 2150095--2150146 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
2150085 CAAAAAAAAA
* *
2150095 ATATTT AT-TTT CATTTTT ATATTT ATATTT ATATTT ATTTTT A-ATTT
1 ATATTT ATATTT -ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
2150142 -TATTT
1 ATATTT
2150147 TAATTATGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
5 10 0.25
6 27 0.68
7 3 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (6 bp):
ATATTT
Found at i:2151055 original size:11 final size:11
Alignment explanation
Indices: 2151039--2151106 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 11
2151029 TTTATTGTTT
2151039 AGAAAAAAAAA
1 AGAAAAAAAAA
2151050 AGAAAAAAAAA
1 AGAAAAAAAAA
*
2151061 GTCGAAAAAAGAAA
1 --AGAAAAAA-AAA
2151075 TTTGAGAAAAAAAAA
1 ----AGAAAAAAAAA
2151090 AGAAAAAAAAAA
1 AG-AAAAAAAAA
2151102 AGAAA
1 AGAAA
2151107 GACAAAAGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
11 16 0.34
12 11 0.23
13 7 0.15
14 3 0.06
15 3 0.06
16 7 0.15
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.06
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:2151100 original size:16 final size:17
Alignment explanation
Indices: 2151081--2151113 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2151071 GAAATTTGAG
2151081 AAAAAAAAAAGA-AAAA
1 AAAAAAAAAAGACAAAA
*
2151097 AAAAAAGAAAGACAAAA
1 AAAAAAAAAAGACAAAA
2151114 GTGTGTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGACAAAA
Found at i:2151113 original size:12 final size:12
Alignment explanation
Indices: 2151041--2151106 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
2151031 TATTGTTTAG
2151041 AAAAAAAAAAGA
1 AAAAAAAAAAGA
**
2151053 AAAAAAAAGTCGA
1 AAAAAAAA-AAGA
**
2151066 AAAAAGAAATTTGA
1 AAAAA-AAA-AAGA
2151080 GAAAAAAAAAAGA
1 -AAAAAAAAAAGA
2151093 AAAAAAAAAAGA
1 AAAAAAAAAAGA
2151105 AA
1 AA
2151107 GACAAAAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
12 22 0.49
13 9 0.20
14 9 0.20
15 5 0.11
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:2152175 original size:25 final size:23
Alignment explanation
Indices: 2152134--2152179 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2152124 TCAATTAGGG
2152134 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
2152157 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
2152180 TGGATCCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Found at i:2152596 original size:15 final size:15
Alignment explanation
Indices: 2152559--2152597 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2152549 TTATGTGCGC
*
2152559 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
2152574 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
2152588 TTAATTCTTG
1 TTAATTCTTG
2152598 TTTGATTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:2159483 original size:14 final size:14
Alignment explanation
Indices: 2159460--2159501 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2159450 ACTTATTACG
*
2159460 AATAATAATTATAA
1 AATAAAAATTATAA
*
2159474 AATAAAAATTATAT
1 AATAAAAATTATAA
*
2159488 AAT-AATATTATAA
1 AATAAAAATTATAA
2159501 A
1 A
2159502 TTCGATGCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAAAAATTATAA
Found at i:2167215 original size:194 final size:194
Alignment explanation
Indices: 2166884--2167273 Score: 672
Period size: 194 Copynumber: 2.0 Consensus size: 194
2166874 AGGTAAACTG
* *
2166884 TGCAACATCACTCTACTCAGAATAATACTTAAACCAAATGAATTATGTTAGTATCGTATACACCC
1 TGCAACATCACTCTACTCAGAATAATACTTAAACCAAATGAAGTATGTTAGAATCGTATACACCC
* * * **
2166949 AGAAACAAGGAGATTTGCCCTTTGGCCTCTGAAGTCTAGGACACATGATCAATTACAAAATGAGT
66 AGAAACAAGGAGACTTGCCCTATGACCTCTGAAGTCTAGGACACAAAATCAATTACAAAATGAGT
* *
2167014 GTGTAAAAGGTCCTACATAGACCAGCCAACCAACCAAAATGTCTAAATTTGCAGTGTCAAGACC
131 CTGTAAAAGGTCCTACATAGACCAACCAACCAACCAAAATGTCTAAATTTGCAGTGTCAAGACC
2167078 TGCAACATCACTCTACTCAGAATAATACTTAAACCAAATGAAGTATGTTAGAATCGTATACACCC
1 TGCAACATCACTCTACTCAGAATAATACTTAAACCAAATGAAGTATGTTAGAATCGTATACACCC
*
2167143 AGAAATAAGGAGACTTGCCCTATGACCTCTGAAGTCTAGGACACAAAATCAATTACAAAATGAGT
66 AGAAACAAGGAGACTTGCCCTATGACCTCTGAAGTCTAGGACACAAAATCAATTACAAAATGAGT
* *
2167208 CTGTAAAAGGTCCTACATAGGCCAACCAACCAACCAAAATGTCTTAATTTGCAGTGTCAAGACC
131 CTGTAAAAGGTCCTACATAGACCAACCAACCAACCAAAATGTCTAAATTTGCAGTGTCAAGACC
2167272 TG
1 TG
2167274 GTCTAGTGTT
Statistics
Matches: 184, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
194 184 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (194 bp):
TGCAACATCACTCTACTCAGAATAATACTTAAACCAAATGAAGTATGTTAGAATCGTATACACCC
AGAAACAAGGAGACTTGCCCTATGACCTCTGAAGTCTAGGACACAAAATCAATTACAAAATGAGT
CTGTAAAAGGTCCTACATAGACCAACCAACCAACCAAAATGTCTAAATTTGCAGTGTCAAGACC
Found at i:2169336 original size:6 final size:6
Alignment explanation
Indices: 2169327--2169352 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2169317 AACTCATTCT
2169327 CACTCA CACTCA CACTCA CACTCA CA
1 CACTCA CACTCA CACTCA CACTCA CA
2169353 TCCTCTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.00, T:0.15
Consensus pattern (6 bp):
CACTCA
Found at i:2171285 original size:42 final size:43
Alignment explanation
Indices: 2171226--2171307 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
2171216 AAATAAAATC
* * *
2171226 AAATTATTACCATACAAA-TAAATTAAAA-TTAATACAATTAAA
1 AAATTATTACAACACAAACTAAATAAAAACTT-ATACAATTAAA
*
2171268 AAATTATTACAACACAAACTAACTAAAAACTTATACAATT
1 AAATTATTACAACACAAACTAAATAAAAACTTATACAATT
2171308 TAAACTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 16 0.47
43 16 0.47
44 2 0.06
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.29
Consensus pattern (43 bp):
AAATTATTACAACACAAACTAAATAAAAACTTATACAATTAAA
Found at i:2172675 original size:17 final size:16
Alignment explanation
Indices: 2172628--2172684 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
2172618 CAAGCCTATT
*
2172628 AAATATAATTATTAAATA
1 AAATATTATT-TT-AATA
*
2172646 AAA-ATTATCTTAATTA
1 AAATATTATTTTAA-TA
2172662 AAATATTATTTTAATA
1 AAATATTATTTTAATA
2172678 AAATATT
1 AAATATT
2172685 TGAGTTTCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.06
16 16 0.47
17 13 0.38
18 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATTATTTTAATA
Found at i:2174888 original size:56 final size:56
Alignment explanation
Indices: 2174802--2174914 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
2174792 GTAAAAATAA
2174802 TGAACATATGAATTGGTTACCATGTTGTAGCCTCACTCCTATGCATTCAACTAGAT
1 TGAACATATGAATTGGTTACCATGTTGTAGCCTCACTCCTATGCATTCAACTAGAT
*
2174858 TGAACATATGAATTGGTTATCATGTTGTAGCCTCACTCCTATGCATTCAACTAGAT
1 TGAACATATGAATTGGTTACCATGTTGTAGCCTCACTCCTATGCATTCAACTAGAT
2174914 T
1 T
2174915 CACTCTCCAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (56 bp):
TGAACATATGAATTGGTTACCATGTTGTAGCCTCACTCCTATGCATTCAACTAGAT
Found at i:2177171 original size:21 final size:21
Alignment explanation
Indices: 2177126--2177178 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2177116 TTACACTAGT
*
2177126 TCTATCGATACAAGTAAGATT
1 TCTATCGATACAAGTAAGATA
* * *
2177147 TCTATCGATATAAGTTATATA
1 TCTATCGATACAAGTAAGATA
*
2177168 TCTACCGATAC
1 TCTATCGATAC
2177179 CAAAAACTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (21 bp):
TCTATCGATACAAGTAAGATA
Found at i:2187809 original size:22 final size:21
Alignment explanation
Indices: 2187779--2187819 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2187769 ACTACACATT
2187779 TTAATAAAATAATAAAATAGC
1 TTAATAAAATAATAAAATAGC
*
2187800 TTAATTAAAATATTAAAATA
1 TTAA-TAAAATAATAAAATA
2187820 TATAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
TTAATAAAATAATAAAATAGC
Found at i:2187827 original size:22 final size:22
Alignment explanation
Indices: 2187783--2187827 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2187773 CACATTTTAA
* *
2187783 TAAAATAATAAAATAGCTTAAT
1 TAAAATAATAAAATAGATAAAT
* *
2187805 TAAAATATTAAAATATATAAAT
1 TAAAATAATAAAATAGATAAAT
2187827 T
1 T
2187828 TAGTTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAATAATAAAATAGATAAAT
Found at i:2194399 original size:62 final size:63
Alignment explanation
Indices: 2194285--2194406 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 63
2194275 TTAACTCTAT
* * * * *
2194285 GTACTATAATAATACAAAGATTGATAGTTTAGGTACCACATTGGATAATTTATGAAAGTATAA
1 GTACTATAATAATACAAAAATTGATAGTTCAAGTACCACATTAGATAATTTATAAAAGTATAA
* * *
2194348 GTACTA-AATAATATAAAAATTGATAGTTCAAGTACCATATTAGATATTTTATAAAAGTA
1 GTACTATAATAATACAAAAATTGATAGTTCAAGTACCACATTAGATAATTTATAAAAGTA
2194407 CATGAACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
62 45 0.88
63 6 0.12
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.34
Consensus pattern (63 bp):
GTACTATAATAATACAAAAATTGATAGTTCAAGTACCACATTAGATAATTTATAAAAGTATAA
Found at i:2209359 original size:7 final size:7
Alignment explanation
Indices: 2209344--2209375 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2209334 TGGCAAAAGG
*
2209344 AAGGGGA
1 AAGGAGA
2209351 AAGGAGA
1 AAGGAGA
2209358 AAGGAGA
1 AAGGAGA
2209365 AAGGAGA
1 AAGGAGA
2209372 AAGG
1 AAGG
2209376 GGGAAGGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (7 bp):
AAGGAGA
Found at i:2209382 original size:14 final size:14
Alignment explanation
Indices: 2209344--2209382 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2209334 TGGCAAAAGG
2209344 AAGGGGAAAGGAGA
1 AAGGGGAAAGGAGA
*
2209358 AAGGAGAAAGGAGA
1 AAGGGGAAAGGAGA
*
2209372 AAGGGGGAAGG
1 AAGGGGAAAGG
2209383 GGTAAGGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (14 bp):
AAGGGGAAAGGAGA
Found at i:2211944 original size:28 final size:28
Alignment explanation
Indices: 2211884--2211947 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
2211874 TTTTTTTATA
* *
2211884 AAAATAACTCATTTTTTAATTAATTATG
1 AAAATAACTCATTTTTTAATTAAATACG
* * * *
2211912 TAAATAATTTATTTTTTTATTAAATACG
1 AAAATAACTCATTTTTTAATTAAATACG
2211940 AAAATAAC
1 AAAATAAC
2211948 CTAATTACAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (28 bp):
AAAATAACTCATTTTTTAATTAAATACG
Found at i:2212140 original size:13 final size:13
Alignment explanation
Indices: 2212122--2212177 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
2212112 TCTTTTATTT
2212122 TTTTATTATTTAA
1 TTTTATTATTTAA
2212135 TTTTATTA-TTATA
1 TTTTATTATTTA-A
* **
2212148 TTTTATAATAAAA
1 TTTTATTATTTAA
* *
2212161 TATTAGTATTTAA
1 TTTTATTATTTAA
2212174 TTTT
1 TTTT
2212178 TAACCTTTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
12 3 0.09
13 28 0.88
14 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TTTTATTATTTAA
Found at i:2214116 original size:22 final size:22
Alignment explanation
Indices: 2214089--2214135 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2214079 ATTTTATAAT
* *
2214089 TTTCCTT-TCATTTTTATTTTTA
1 TTTCCTTCTAATTTTGA-TTTTA
2214111 TTTCCTTCTAATTTTGATTTTA
1 TTTCCTTCTAATTTTGATTTTA
2214133 TTT
1 TTT
2214136 TTAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCCTTCTAATTTTGATTTTA
Found at i:2216465 original size:22 final size:22
Alignment explanation
Indices: 2216440--2216490 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2216430 TGTTCATTCC
* *
2216440 AATTTTAAGTGTTATGTCATAT
1 AATTTCAAGTGTTATGTAATAT
2216462 AATTTCAAGTGTTATGTAATAT
1 AATTTCAAGTGTTATGTAATAT
2216484 AATTTCA
1 AATTTCA
2216491 CTAAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (22 bp):
AATTTCAAGTGTTATGTAATAT
Found at i:2219922 original size:18 final size:18
Alignment explanation
Indices: 2219896--2219931 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2219886 CCACCAAAAA
2219896 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
2219914 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
2219932 CTTATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:2220058 original size:14 final size:14
Alignment explanation
Indices: 2220039--2220068 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2220029 TAAAATATAA
2220039 AAAAAAAATCATTT
1 AAAAAAAATCATTT
*
2220053 AAAAAAATTCATTT
1 AAAAAAAATCATTT
2220067 AA
1 AA
2220069 TTAAAGTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAAAATCATTT
Found at i:2220170 original size:96 final size:96
Alignment explanation
Indices: 2219940--2220171 Score: 349
Period size: 96 Copynumber: 2.4 Consensus size: 96
2219930 ATCTTATAAA
* *
2219940 ATAAATAAAAAATC-TTTAAAAAAATTTATTTAATTAAACTGGTGGCGCCATTTAATATGGCACC
1 ATAAATAAAAAATCGTTTAAAAAAATTCATTTAATTAAAGTGGTGGCGCCATTTAATATGGCACC
*
2220004 ACCAAAAAAATTTTAAATTTATTTTTAAAAT
66 ACCAAAAAAATTTTAAATTTATTTTAAAAAT
* * * * *
2220035 ATAAAAAAAAAATCATTTAAAAAAATTCATTTAATTAAAGTGGTGGTGCCATTTAATATAGCACA
1 ATAAATAAAAAATCGTTTAAAAAAATTCATTTAATTAAAGTGGTGGCGCCATTTAATATGGCACC
* *
2220100 ATCAAAAAAAATTTAAATTTATTTTAAAAAT
66 ACCAAAAAAATTTTAAATTTATTTTAAAAAT
* *
2220131 ATAAATAATAAATCGTTTAAAAAAATTCATTGAATTAAAGT
1 ATAAATAAAAAATCGTTTAAAAAAATTCATTTAATTAAAGT
2220172 TAAATGGCAC
Statistics
Matches: 123, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 13 0.11
96 110 0.89
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.34
Consensus pattern (96 bp):
ATAAATAAAAAATCGTTTAAAAAAATTCATTTAATTAAAGTGGTGGCGCCATTTAATATGGCACC
ACCAAAAAAATTTTAAATTTATTTTAAAAAT
Found at i:2220189 original size:83 final size:83
Alignment explanation
Indices: 2220102--2220254 Score: 261
Period size: 83 Copynumber: 1.8 Consensus size: 83
2220092 ATAGCACAAT
*
2220102 CAAAAAAAATTTAAATTTATTTTAAAAATATAAATAATAAATCGTTTAAAAAAATTCATTGAATT
1 CAAAAAAAATTTAAATTTATTTTAAAAATACAAATAATAAATCGTTTAAAAAAATTCATTGAATT
2220167 AAAGTTAAATGGCACCAC
66 AAAGTTAAATGGCACCAC
* * * *
2220185 CAAAAAAATTTTAAATTTATTTTAAAAATACAAATAATAAATCGTTTTAAAAAATTTATTTAATT
1 CAAAAAAAATTTAAATTTATTTTAAAAATACAAATAATAAATCGTTTAAAAAAATTCATTGAATT
2220250 AAAGT
66 AAAGT
2220255 GGTGACACCA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 65 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.36
Consensus pattern (83 bp):
CAAAAAAAATTTAAATTTATTTTAAAAATACAAATAATAAATCGTTTAAAAAAATTCATTGAATT
AAAGTTAAATGGCACCAC
Found at i:2223333 original size:16 final size:17
Alignment explanation
Indices: 2223307--2223342 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2223297 ACTATAACAA
2223307 AGAGAAAAAGAGAAAGG
1 AGAGAAAAAGAGAAAGG
2223324 AGAG-AAAAGAGAAAGG
1 AGAGAAAAAGAGAAAGG
2223340 AGA
1 AGA
2223343 CTCGCTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AGAGAAAAAGAGAAAGG
Found at i:2223478 original size:192 final size:193
Alignment explanation
Indices: 2223131--2223484 Score: 577
Period size: 192 Copynumber: 1.8 Consensus size: 193
2223121 ACTATAACAA
* *
2223131 AGAGAAAAGGAGAAAGGAGATCCGCTTTCTAAGCCCTTTCGCCCCTTTGAAATACCTACCAAACT
1 AGAGAAAAGGAGAAAGGAGATCCGCTTTCTAAGCCCTTTCGCCCCTTTAAAATACCTACCAAACC
* *
2223196 ATCATTAAGAGAGATGGAAAATTGTAAAGAAGTGATGCATGCCTCAATCTAACAATTGAAGATAT
66 ATCATTAAGAGAGATGGAAAATTATAAAGAAGTGATGCATGCCTCAATCCAACAATTGAAGATAT
* *
2223261 CCGAAACTTTCACAATAATAATAATGAACCTCTATAACTATAACAAAGAGAAAAAGAGAAAGG
131 CCGAAACTTTCACAACAACAATAATGAACCTCTATAACTATAACAAAGAGAAAAAGAGAAAGG
* *
2223324 AGAGAAAA-GAGAAAGGAGA-CTCGCTTTCTAAGCCCTTTTGCCCCTTTAAAATATCTACCAAAC
1 AGAGAAAAGGAGAAAGGAGATC-CGCTTTCTAAGCCCTTTCGCCCCTTTAAAATACCTACCAAAC
* **
2223387 CATCATTAAGAGAGATGGAAAATTATAAAGAAGTGATGCATGCCTTAATCCAACTCTTGAAGATA
65 CATCATTAAGAGAGATGGAAAATTATAAAGAAGTGATGCATGCCTCAATCCAACAATTGAAGATA
*
2223452 TCCGAAACTTTCATAACAACAATAATGAACCTC
130 TCCGAAACTTTCACAACAACAATAATGAACCTC
2223485 CAATTGATAG
Statistics
Matches: 148, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
191 1 0.01
192 139 0.94
193 8 0.05
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (193 bp):
AGAGAAAAGGAGAAAGGAGATCCGCTTTCTAAGCCCTTTCGCCCCTTTAAAATACCTACCAAACC
ATCATTAAGAGAGATGGAAAATTATAAAGAAGTGATGCATGCCTCAATCCAACAATTGAAGATAT
CCGAAACTTTCACAACAACAATAATGAACCTCTATAACTATAACAAAGAGAAAAAGAGAAAGG
Found at i:2225650 original size:18 final size:18
Alignment explanation
Indices: 2225614--2225650 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2225604 AAAAATTAAA
*
2225614 TTTTAAAATAATAATATT
1 TTTTAAAATAATAAGATT
*
2225632 TTTTAAAATAATACGATT
1 TTTTAAAATAATAAGATT
2225650 T
1 T
2225651 AAAATTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTTAAAATAATAAGATT
Found at i:2245891 original size:24 final size:24
Alignment explanation
Indices: 2245846--2245891 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2245836 TTCAATATTC
**
2245846 AACAATTACAAAATTATCTTAAAA
1 AACAATTACAAAATTAAATTAAAA
*
2245870 AACAATTATAAAATTAAATTAA
1 AACAATTACAAAATTAAATTAA
2245892 TTGTTTAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (24 bp):
AACAATTACAAAATTAAATTAAAA
Found at i:2247170 original size:3 final size:3
Alignment explanation
Indices: 2247162--2247189 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2247152 TTCCCCTAAA
2247162 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2247190 ATGATTGGTT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2247927 original size:20 final size:20
Alignment explanation
Indices: 2247902--2247977 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 20
2247892 TAAAATTTTA
2247902 AAATTATCATAAATATATTT
1 AAATTATCATAAATATATTT
** *
2247922 AAATTAAAATAAATAAAATTTT
1 AAATTATCATAAAT-ATA-TTT
2247944 AAAATTATCATAAATATATTT
1 -AAATTATCATAAATATATTT
2247965 AAATTATCATAAA
1 AAATTATCATAAA
2247978 ATTATATATT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 25 0.53
21 5 0.11
22 5 0.11
23 12 0.26
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATTATCATAAATATATTT
Found at i:2247977 original size:43 final size:43
Alignment explanation
Indices: 2247882--2247970 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
2247872 CTGAAAAAAT
*
2247882 TTAAAAGAAATAAAATTTTAAAATTATCATAAATATATTTAAA
1 TTAAAATAAATAAAATTTTAAAATTATCATAAATATATTTAAA
2247925 TTAAAATAAATAAAATTTTAAAATTATCATAAATATATTTAAA
1 TTAAAATAAATAAAATTTTAAAATTATCATAAATATATTTAAA
2247968 TTA
1 TTA
2247971 TCATAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (43 bp):
TTAAAATAAATAAAATTTTAAAATTATCATAAATATATTTAAA
Found at i:2251873 original size:11 final size:11
Alignment explanation
Indices: 2251857--2251884 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2251847 GTTACTAAGG
2251857 TTTTTTTCTTT
1 TTTTTTTCTTT
2251868 TTTTTTTCTTT
1 TTTTTTTCTTT
2251879 TTTTTT
1 TTTTTT
2251885 ACCTTTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:2274614 original size:20 final size:20
Alignment explanation
Indices: 2274591--2274650 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 20
2274581 TATTTTTGGA
2274591 ATTTTTAATGTATTTTATAT
1 ATTTTTAATGTATTTTATAT
* ** ** *
2274611 ATTTTAAATAAATTCGATGT
1 ATTTTTAATGTATTTTATAT
2274631 A-TTTTAATGT-TTTTATAT
1 ATTTTTAATGTATTTTATAT
2274649 AT
1 AT
2274651 AATAAATATT
Statistics
Matches: 27, Mismatches: 12, Indels: 3
0.64 0.29 0.07
Matches are distributed among these distances:
18 6 0.22
19 6 0.22
20 15 0.56
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (20 bp):
ATTTTTAATGTATTTTATAT
Found at i:2277594 original size:73 final size:73
Alignment explanation
Indices: 2277469--2277614 Score: 193
Period size: 73 Copynumber: 2.0 Consensus size: 73
2277459 AAGTCATTTG
* ** * * * **
2277469 CTTATAGTATACACACGAAATTTGTATAAATCATCACTAATGATCAGTTCAATGCCCAATAAATA
1 CTTATAGTAAACACAAAAAATTTGAATAAATCATCACTAATAACCACCTCAATGCCCAATAAATA
2277534 CTGAAGTT
66 CTGAAGTT
* *
2277542 CTTATAGTAAACACAAAAAATTTGAATAAATCATCACTAATAACCACCTCAATGCCCAGTAGATA
1 CTTATAGTAAACACAAAAAATTTGAATAAATCATCACTAATAACCACCTCAATGCCCAATAAATA
*
2277607 TTGAAGTT
66 CTGAAGTT
2277615 ATCAAGATGG
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (73 bp):
CTTATAGTAAACACAAAAAATTTGAATAAATCATCACTAATAACCACCTCAATGCCCAATAAATA
CTGAAGTT
Found at i:2279675 original size:45 final size:45
Alignment explanation
Indices: 2279611--2279702 Score: 141
Period size: 45 Copynumber: 2.0 Consensus size: 45
2279601 GTGCAGAATA
*
2279611 AAGCTTCTCACTTGCTAGCTGAC-AGTTAACCTCCTCATTGACATT
1 AAGCTTCTCACTTGCTAGCTGACTA-TCAACCTCCTCATTGACATT
* *
2279656 AAGCTTCTTACTTGCTAGCTGGCTATCAACCTCCTCATTGACATT
1 AAGCTTCTCACTTGCTAGCTGACTATCAACCTCCTCATTGACATT
2279701 AA
1 AA
2279703 TTTTCTCTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (45 bp):
AAGCTTCTCACTTGCTAGCTGACTATCAACCTCCTCATTGACATT
Found at i:2281920 original size:12 final size:12
Alignment explanation
Indices: 2281903--2281932 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2281893 TAAACAAAAC
2281903 CAATAATAATAA
1 CAATAATAATAA
2281915 CAATAATAATAA
1 CAATAATAATAA
*
2281927 TAATAA
1 CAATAA
2281933 CAATCCATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (12 bp):
CAATAATAATAA
Found at i:2281921 original size:9 final size:9
Alignment explanation
Indices: 2281907--2281936 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2281897 CAAAACCAAT
2281907 AATAATAAC
1 AATAATAAC
*
2281916 AATAATAAT
1 AATAATAAC
2281925 AATAATAAC
1 AATAATAAC
2281934 AAT
1 AAT
2281937 CCATCTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (9 bp):
AATAATAAC
Found at i:2285287 original size:20 final size:20
Alignment explanation
Indices: 2285221--2285270 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2285211 GCCAACTGCA
2285221 TCAGCAAGCATCGAGCAGCG
1 TCAGCAAGCATCGAGCAGCG
2285241 TCAGCAAGCATCGAGCAGCG
1 TCAGCAAGCATCGAGCAGCG
2285261 TCAGCAAGCA
1 TCAGCAAGCA
2285271 GTAGGCAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.30, G:0.28, T:0.10
Consensus pattern (20 bp):
TCAGCAAGCATCGAGCAGCG
Done.