Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008982.1 Hibiscus syriacus cultivar Beakdansim tig00112344_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: 2253222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1410261 original size:23 final size:22
Alignment explanation
Indices: 1410233--1410283 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 22
1410223 CTTTCTTAAC
1410233 AATTTTAGGATTATATTTTATTT-
1 AATTTTAGGA-TAT-TTTTATTTG
*
1410256 AATTTTTTGGATATTTTTATTTG
1 AA-TTTTAGGATATTTTTATTTG
1410279 AATTT
1 AATTT
1410284 AAAATTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.44
23 7 0.28
24 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (22 bp):
AATTTTAGGATATTTTTATTTG
Found at i:1410410 original size:10 final size:10
Alignment explanation
Indices: 1410397--1410432 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1410387 GACATAAACG
*
1410397 AACGAAAATA
1 AACGAACATA
1410407 AACGAACATA
1 AACGAACATA
*
1410417 AATGAACATA
1 AACGAACATA
1410427 AACGAA
1 AACGAA
1410433 TGAACATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.64, C:0.14, G:0.11, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:1410410 original size:24 final size:24
Alignment explanation
Indices: 1410378--1410446 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
1410368 GCCTAAACAT
*
1410378 AAATAAACGGACATAAACGAACGA
1 AAATAAACGAACATAAACGAACGA
*
1410402 AAATAAACGAACATAAATGAAC-A
1 AAATAAACGAACATAAACGAACGA
** *
1410425 TAAACGAATGAACATAAACGAA
1 -AAATAAACGAACATAAACGAA
1410447 TGTACATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.61, C:0.14, G:0.13, T:0.12
Consensus pattern (24 bp):
AAATAAACGAACATAAACGAACGA
Found at i:1410434 original size:14 final size:14
Alignment explanation
Indices: 1410417--1410468 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
1410407 AACGAACATA
1410417 AATGAACATAAACG
1 AATGAACATAAACG
1410431 AATGAACATAAACG
1 AATGAACATAAACG
* *
1410445 AATGTACATAAATG
1 AATGAACATAAACG
*
1410459 AATAAACATA
1 AATGAACATA
1410469 TTACCGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (14 bp):
AATGAACATAAACG
Found at i:1418954 original size:38 final size:38
Alignment explanation
Indices: 1418890--1418963 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
1418880 TTTAAATTGG
* * * *
1418890 TCCTTAAATTTTTGGATATTTCAATTTTATCCCTAAAC
1 TCCTTAAACTTTTGAACATTTCAATTTCATCCCTAAAC
*
1418928 TCCTTAAACTTTTGAACA-TTCTAATTTCATCTCTAA
1 TCCTTAAACTTTTGAACATTTC-AATTTCATCCCTAA
1418964 CCTACGATCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 3 0.10
38 27 0.90
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (38 bp):
TCCTTAAACTTTTGAACATTTCAATTTCATCCCTAAAC
Found at i:1419278 original size:60 final size:60
Alignment explanation
Indices: 1419154--1419314 Score: 184
Period size: 60 Copynumber: 2.7 Consensus size: 60
1419144 CATATAGTTT
* * * *
1419154 GGGATGAAATTGGAATGTTCAAAAAGTTTGGGGA-TCAATTTAGAATGAAGGTCATAATTTA
1 GGGATGAAATTGAAATATTC-AAAAGTTTGAGGACT-AATTTAGAATGAAGGTCATAATTAA
* * *
1419215 GGGATGAAATTGAAATATTCAAAATTTTGAGGACTAATTTAGTATTATA-GTCATAATTAA
1 GGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAATTTAGAATGA-AGGTCATAATTAA
* * *
1419275 GGGATGAAATTAAAATATTTAAAAGTTT-AGGACCAATTTA
1 GGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAATTTA
1419315 AAATAAAAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
59 11 0.13
60 56 0.64
61 20 0.23
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (60 bp):
GGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAATTTAGAATGAAGGTCATAATTAA
Found at i:1420496 original size:16 final size:17
Alignment explanation
Indices: 1420477--1420510 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
1420467 TTATTTAAAA
1420477 TAAAAAAA-ATTTTTTT
1 TAAAAAAACATTTTTTT
1420493 TAAAAAAACTATTTTTTT
1 TAAAAAAAC-ATTTTTTT
1420511 CAAATCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAAAAACATTTTTTT
Found at i:1421900 original size:6 final size:6
Alignment explanation
Indices: 1421871--1421920 Score: 64
Period size: 6 Copynumber: 8.0 Consensus size: 6
1421861 GGTTAAAGGG
* *
1421871 GGAGAA GGGAGAA GGGGGAG GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA
1 GGAGAA -GGAGAA -GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA
1421921 CACGAGCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
6 28 0.72
7 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (6 bp):
GGAGAA
Found at i:1421906 original size:16 final size:15
Alignment explanation
Indices: 1421866--1421916 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1421856 GAGAAGGTTA
1421866 AAGGGGGAGAAGGGAG
1 AAGGGGGAGAA-GGAG
1421882 AAGGGGGAG--GGAG
1 AAGGGGGAGAAGGAG
1421895 AAGGAGAAGGAGAAGGAG
1 AAGG-G--GGAGAAGGAG
1421913 AAGG
1 AAGG
1421917 AGAACACGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.27
14 1 0.03
16 13 0.43
18 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (15 bp):
AAGGGGGAGAAGGAG
Found at i:1422965 original size:99 final size:99
Alignment explanation
Indices: 1422789--1423184 Score: 639
Period size: 99 Copynumber: 4.0 Consensus size: 99
1422779 CCAAAATCTT
* ** * * *
1422789 CCCAATCTATATGGGAAAGAACAAAATAAGGTACCCTATAAAGTCTAGAGGTGGTGGATCAATTG
1 CCCAATCTATGTGGGAAAGAACAAAATAAGGTACCCTATAAAGTCTAGCCGTAGTAGATCAATGG
*
1422854 AGGAGATGGATTAGAGTCGTCTTCAGACTTTATA
66 AGGAGACGGATTAGAGTCGTCTTCAGACTTTATA
* *
1422888 CCCAATCTATGTGGGAGAGAACAAAATAAGATACCCTATAAAGTCTAGCCGTAGTAGATCAATGG
1 CCCAATCTATGTGGGAAAGAACAAAATAAGGTACCCTATAAAGTCTAGCCGTAGTAGATCAATGG
*
1422953 AGGAGACAGATTAGAGTCGTCTTCAGACTTTATA
66 AGGAGACGGATTAGAGTCGTCTTCAGACTTTATA
* *
1422987 CCCAATCTATGTGGGAAAGAACAAAATAAGGTAACCTGTAAAGTCTAGCCGTAGTAGATCAATGG
1 CCCAATCTATGTGGGAAAGAACAAAATAAGGTACCCTATAAAGTCTAGCCGTAGTAGATCAATGG
1423052 AGGAGACGGATTAGAGTCGTCTTCAGACTTTATA
66 AGGAGACGGATTAGAGTCGTCTTCAGACTTTATA
* * * *
1423086 CCCAATCTATGTGGGAAAGAACAAAATAAGGTAGCCTTTAAAGTCTAGCCGTGGTAGATCAATTG
1 CCCAATCTATGTGGGAAAGAACAAAATAAGGTACCCTATAAAGTCTAGCCGTAGTAGATCAATGG
*
1423151 AGGAGACGGATTAGAGTCGTCTTCAAACTTTATA
66 AGGAGACGGATTAGAGTCGTCTTCAGACTTTATA
1423185 TTGAATCAAT
Statistics
Matches: 277, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 277 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (99 bp):
CCCAATCTATGTGGGAAAGAACAAAATAAGGTACCCTATAAAGTCTAGCCGTAGTAGATCAATGG
AGGAGACGGATTAGAGTCGTCTTCAGACTTTATA
Found at i:1426210 original size:21 final size:21
Alignment explanation
Indices: 1426184--1426223 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1426174 AATTTACGAT
1426184 AAAAAATAATATTTTAAGTAG
1 AAAAAATAATATTTTAAGTAG
*
1426205 AAAAAATATTATTTTAAGT
1 AAAAAATAATATTTTAAGT
1426224 GGCGTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAAAATAATATTTTAAGTAG
Found at i:1430672 original size:20 final size:19
Alignment explanation
Indices: 1430634--1430672 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1430624 GGTGAACACC
*
1430634 AGAACACTCAATACAAAGA
1 AGAACACCCAATACAAAGA
*
1430653 AGAACACCCAGATTCAAAGA
1 AGAACACCCA-ATACAAAGA
1430673 TGCCCAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.54, C:0.23, G:0.13, T:0.10
Consensus pattern (19 bp):
AGAACACCCAATACAAAGA
Found at i:1437903 original size:6 final size:6
Alignment explanation
Indices: 1437889--1437926 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
1437879 TAAATTAAAT
*
1437889 TATTTA TATTCA TATTTA TATTTA TATTTA TATTTA TA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TA
1437927 AATATCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:1438272 original size:16 final size:16
Alignment explanation
Indices: 1438238--1438269 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1438228 TCATTTATAT
1438238 TTAATTTATTAACTAA
1 TTAATTTATTAACTAA
1438254 TTAATTTGATTAACTA
1 TTAATTT-ATTAACTA
1438270 TTATGAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAATTTATTAACTAA
Found at i:1438695 original size:31 final size:31
Alignment explanation
Indices: 1438660--1438736 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
1438650 TCAAAATACA
*
1438660 TAAGATATTGTCACCTTTGTTTTTATTTATT
1 TAAGATATGGTCACCTTTGTTTTTATTTATT
*
1438691 TAAGATATGGTCACTTTTGTTTTTATTTATT
1 TAAGATATGGTCACCTTTGTTTTTATTTATT
*
1438722 TAAGATGTGGTCACC
1 TAAGATATGGTCACC
1438737 ACATGTTAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.52
Consensus pattern (31 bp):
TAAGATATGGTCACCTTTGTTTTTATTTATT
Found at i:1441980 original size:15 final size:14
Alignment explanation
Indices: 1441954--1441998 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1441944 TATTAGAATA
1441954 ATTTATTTAATATT
1 ATTTATTTAATATT
1441968 ATTTATGTTAATATT
1 ATTTAT-TTAATATT
*
1441983 A-TTATTAAAATATT
1 ATTTATT-TAATATT
1441997 AT
1 AT
1441999 ATCTACAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 17 0.63
15 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:1442125 original size:23 final size:23
Alignment explanation
Indices: 1442099--1442142 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1442089 AAATAATATA
*
1442099 TAAAAATAATATTATTAAAATGT
1 TAAAAATAATAATATTAAAATGT
*
1442122 TAAAAATTATAATATTAAAAT
1 TAAAAATAATAATATTAAAAT
1442143 AAAAATATTA
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:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAAAATAATAATATTAAAATGT
Found at i:1442157 original size:42 final size:43
Alignment explanation
Indices: 1442098--1442182 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 43
1442088 AAAATAATAT
1442098 ATAAAAATAATATTATTAAAATGTTAAA-AAT-TATAATATTAAA
1 ATAAAAATAATATTATT-AAATGTTAAACAATATAT-ATATTAAA
* * *
1442141 ATAAAAATATTA-TATTATATTTTAAACAATATATATATTAAA
1 ATAAAAATAATATTATTAAATGTTAAACAATATATATATTAAA
1442183 TATTCAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 8 0.22
42 15 0.41
43 14 0.38
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (43 bp):
ATAAAAATAATATTATTAAATGTTAAACAATATATATATTAAA
Found at i:1442191 original size:23 final size:22
Alignment explanation
Indices: 1442106--1442193 Score: 69
Period size: 23 Copynumber: 4.1 Consensus size: 22
1442096 ATATAAAAAT
* *
1442106 AATATTAT-TAAAATGTTAAA-
1 AATATTATATTAAATATTAAAC
*
1442126 AATTATAATATTAAA-A-TAAA-
1 AA-TATTATATTAAATATTAAAC
* *
1442146 AATATTATATTATATTTTAAAC
1 AATATTATATTAAATATTAAAC
*
1442168 AATATATATATTAAATATTCAAC
1 AATAT-TATATTAAATATTAAAC
1442191 AAT
1 AAT
1442194 TTAATAATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
19 10 0.19
20 8 0.15
21 9 0.17
22 9 0.17
23 17 0.32
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (22 bp):
AATATTATATTAAATATTAAAC
Found at i:1442325 original size:21 final size:22
Alignment explanation
Indices: 1442284--1442335 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1442274 TAATAGTACA
* *
1442284 TATTACAATAATATGATTATAAT
1 TATTAAAATAATATCATTAT-AT
1442307 TA-TAAAATAATA-CATTATAT
1 TATTAAAATAATATCATTATAT
1442327 TATTAAAAT
1 TATTAAAAT
1442336 TATCAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 11 0.42
22 9 0.35
23 2 0.08
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
TATTAAAATAATATCATTATAT
Found at i:1449445 original size:22 final size:22
Alignment explanation
Indices: 1449415--1449496 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
1449405 TGGTGTAGAA
*
1449415 GGAATCGATCCCCCCTCATGAG
1 GGAACCGATCCCCCCTCATGAG
* *
1449437 GGAACCGATTCCCCCT-TTGAAAG
1 GGAACCGATCCCCCCTCATG--AG
*
1449460 GGAACCGATTCCCCCCACA-G-G
1 GGAACCGA-TCCCCCCTCATGAG
* *
1449481 GGAATCGATACCCCCT
1 GGAACCGATCCCCCCT
1449497 GGGGTTCTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
20 6 0.13
21 10 0.21
22 14 0.30
23 10 0.21
24 7 0.15
ACGTcount: A:0.24, C:0.37, G:0.22, T:0.17
Consensus pattern (22 bp):
GGAACCGATCCCCCCTCATGAG
Found at i:1454435 original size:35 final size:35
Alignment explanation
Indices: 1454389--1454462 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
1454379 CGTCACGAAT
* *
1454389 AGTAAGGCCCTGAGCACAAAGCCAATGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCTCCA
*
1454424 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCTCCA
1454459 AGTA
1 AGTA
1454463 TTCTTCCTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.28, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCTCCA
Found at i:1454568 original size:24 final size:24
Alignment explanation
Indices: 1454541--1454631 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
1454531 CATAATTCAA
1454541 GTCAAGTATCAGATCAAAATCCAT
1 GTCAAGTATCAGATCAAAATCCAT
** *
1454565 GTCATTTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAT
* *
1454589 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAAAATCCAT
* * *
1454612 GTCAGGTATCATAACAAAAT
1 GTCAAGTATCAGATCAAAAT
1454632 TCAAATCAGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 21 0.37
24 36 0.63
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAT
Found at i:1454601 original size:23 final size:23
Alignment explanation
Indices: 1454541--1454615 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
1454531 CATAATTCAA
*
1454541 GTCAAGTATCAGATCAAAATCCAT
1 GTCAA-TATCAGATCAGAATCCAT
*
1454565 GTCATTTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAT
*
1454589 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAT
1454612 GTCA
1 GTCA
1454616 GGTATCATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAT
Found at i:1459769 original size:42 final size:41
Alignment explanation
Indices: 1459718--1459798 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 41
1459708 TATTTTTATT
1459718 TTTTAATATAA-TTTAT-TATTT-TATAAATTATATATATTAAAA
1 TTTTAATATAACTTT-TGTATTTCTA-AAA-TATATAT-TTAAAA
1459760 TTTTAATATAACTTTTGTATTTCTAAAATATATATTTAA
1 TTTTAATATAACTTTTGTATTTCTAAAATATATATTTAA
1459799 TTTTTCAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
41 4 0.11
42 19 0.53
43 11 0.31
44 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (41 bp):
TTTTAATATAACTTTTGTATTTCTAAAATATATATTTAAAA
Found at i:1459848 original size:15 final size:15
Alignment explanation
Indices: 1459793--1459847 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
1459783 TAAAATATAT
1459793 ATTTAATTTTTCAGTA
1 ATTTAATTTTT-AGTA
*
1459809 ATTTAATTTTCAGTA
1 ATTTAATTTTTAGTA
1459824 ATTTAATTTTT--TA
1 ATTTAATTTTTAGTA
1459837 ATTTAATTTTT
1 ATTTAATTTTT
1459848 TGATTATTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 13 0.35
15 14 0.38
16 10 0.27
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (15 bp):
ATTTAATTTTTAGTA
Found at i:1460190 original size:16 final size:16
Alignment explanation
Indices: 1460139--1460203 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
1460129 ATTTTAGTTA
* *
1460139 ATGTATTATTTATATA
1 ATGTATAATTTATATT
*
1460155 AT-TA-AATTTTATGTT
1 ATGTATAA-TTTATATT
*
1460170 GTGTATAATTTATATT
1 ATGTATAATTTATATT
*
1460186 ATGTATACTTTATATT
1 ATGTATAATTTATATT
1460202 AT
1 AT
1460204 TAAACCTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
14 1 0.03
15 9 0.23
16 27 0.69
17 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (16 bp):
ATGTATAATTTATATT
Found at i:1460212 original size:16 final size:16
Alignment explanation
Indices: 1460147--1460213 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
1460137 TAATGTATTA
* *
1460147 TTTATATAAT-TAAAT
1 TTTATATTATGTAAAC
* *
1460162 TTTATGTTGTGTATAA-
1 TTTATATTATGTA-AAC
*
1460178 TTTATATTATGTATAC
1 TTTATATTATGTAAAC
1460194 TTTATATTAT-TAAACC
1 TTTATATTATGTAAA-C
1460210 TTTA
1 TTTA
1460214 CTTTATCCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
15 11 0.27
16 28 0.68
17 2 0.05
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTATATTATGTAAAC
Found at i:1461374 original size:109 final size:109
Alignment explanation
Indices: 1461209--1461433 Score: 326
Period size: 109 Copynumber: 2.1 Consensus size: 109
1461199 TTAGGTTGAG
* * * * *
1461209 CCTAAAATGTTATCAAATTTTAAGCTAATAGAGCATTGGATTTTCTCATGATAAGAAAATAAGTT
1 CCTAAAATGTTACCAAAGTTTAAGCTAATAGAACATTGGATTTTCCCAAGATAAGAAAATAAGTT
* * *
1461274 AAAAATTGAA-AATATTATGAATATATATAAGAAATACGGTTGCC
66 AAAAACT-AAGAATATTATGAATATACATAAGAAATACGGTTGCA
* * *
1461318 CCTAAAATGTTACCAAAGTTTGAGCTGATGGAACATTGGATTTTCCCAAGATAAGAAAATAAGTT
1 CCTAAAATGTTACCAAAGTTTAAGCTAATAGAACATTGGATTTTCCCAAGATAAGAAAATAAGTT
*
1461383 AAAAACTAAGAATGTTATGAATATACATAAGAAATACGGTTGCA
66 AAAAACTAAGAATATTATGAATATACATAAGAAATACGGTTGCA
1461427 CCTAAAA
1 CCTAAAA
1461434 ATGTCATTGT
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
108 2 0.02
109 101 0.98
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (109 bp):
CCTAAAATGTTACCAAAGTTTAAGCTAATAGAACATTGGATTTTCCCAAGATAAGAAAATAAGTT
AAAAACTAAGAATATTATGAATATACATAAGAAATACGGTTGCA
Found at i:1461501 original size:77 final size:76
Alignment explanation
Indices: 1461420--1461877 Score: 498
Period size: 77 Copynumber: 6.0 Consensus size: 76
1461410 TAAGAAATAC
* * *
1461420 GGTTGCACCTAAAAATGTCATTGTTCACTAAGAAATAAGCTGCGAA-CTGGAATGTTAATATTTT
1 GGTTGCACC-AAGAATGTCATGGTTCACTAAGAAATAAGTTGC-AATCTGGAATGTTAATATTTT
1461484 TATTAATAAAATG
64 TATTAATAAAATG
* * * * * *
1461497 GGTTGCACCCAAGAATATCATGGTTCACTAATAAATAGGTTGCGATTTGGAATGTTAATAGTTTT
1 GGTTGCA-CCAAGAATGTCATGGTTCACTAAGAAATAAGTTGCAATCTGGAATGTTAATATTTTT
1461562 ATTAATAAAATG
65 ATTAATAAAATG
* * * * * *
1461574 AGTTTTGC-CCAAGAATGCCATGGTTCATTAGGAAATATGTTGCAATCTGAAATGTTAATATTTT
1 -G-GTTGCACCAAGAATGTCATGGTTCACTAAGAAATAAGTTGCAATCTGGAATGTTAATA-TTT
*
1461638 TTAATAATAAAAT-
63 TTATTAATAAAATG
* * * *
1461651 AGTTACACTCAAGAATGTCATGGTTCACTAAGAAAT-AGATTGCAATATGAAATGTTAATATTTT
1 GGTTGCAC-CAAGAATGTCATGGTTCACTAAGAAATAAG-TTGCAATCTGGAATGTTAATATTTT
*
1461715 TATTAATAAAATA
64 TATTAATAAAATG
* * * **
1461728 GGTTGCGTCCAAGATTGTCTTGGTTCACTAAGAAATAAGTTGTGATCTGGAATGTTAATATTTTT
1 GGTTGC-ACCAAGAATGTCATGGTTCACTAAGAAATAAGTTGCAATCTGGAATGTTAATATTTTT
1461793 -TTAATAAAATG
65 ATTAATAAAATG
* * * *
1461804 GGTCGCACACAAGAATGTTATGGTTCACTAAGAAACAAGTTGCAATATGGAATGTTAAT-TTTTC
1 GGTTGCAC-CAAGAATGTCATGGTTCACTAAGAAATAAGTTGCAATCTGGAATGTTAATATTTT-
1461868 TATT-ATAAAA
64 TATTAATAAAA
1461878 AATTCGAAAG
Statistics
Matches: 318, Mismatches: 49, Indels: 29
0.80 0.12 0.07
Matches are distributed among these distances:
75 8 0.03
76 83 0.26
77 203 0.64
78 20 0.06
79 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (76 bp):
GGTTGCACCAAGAATGTCATGGTTCACTAAGAAATAAGTTGCAATCTGGAATGTTAATATTTTTA
TTAATAAAATG
Found at i:1462238 original size:37 final size:36
Alignment explanation
Indices: 1462195--1462316 Score: 100
Period size: 37 Copynumber: 3.2 Consensus size: 36
1462185 ATAAAAACAT
1462195 TAACATTCCAGATCACAATCTATTTCTTAATGAACCA
1 TAACATTCCAGATCACAA-CTATTTCTTAATGAACCA
* * ** * * **
1462232 TGACATTCTAGGGCACAACCTATTTTATTAATAAAAATA
1 TAACATTCCAGATCACAA-CTA-TTTCTTAAT-GAACCA
*
1462271 TTAACCTTCCAGATCACAACATATTTCTTAATGAACCA
1 -TAACATTCCAGATCACAAC-TATTTCTTAATGAACCA
*
1462309 TTACATTC
1 TAACATTC
1462317 TTGGGCGCAA
Statistics
Matches: 61, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
37 23 0.38
38 11 0.18
39 12 0.20
40 15 0.25
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.34
Consensus pattern (36 bp):
TAACATTCCAGATCACAACTATTTCTTAATGAACCA
Found at i:1462290 original size:40 final size:40
Alignment explanation
Indices: 1462168--1462373 Score: 136
Period size: 40 Copynumber: 5.3 Consensus size: 40
1462158 TATTCTTGGG
*
1462168 CACAACCCATTTTATTAATAAAAACATTAACATTCCAGAT
1 CACAACCTATTTTATTAATAAAAACATTAACATTCCAGAT
* * * * * * **
1462208 CACAATCTA-TTTCTTAAT-GAACCA-TGACATTCTAGGG
1 CACAACCTATTTTATTAATAAAAACATTAACATTCCAGAT
* *
1462245 CACAACCTATTTTATTAATAAAAATATTAACCTTCCAGAT
1 CACAACCTATTTTATTAATAAAAACATTAACATTCCAGAT
* * * * ** **
1462285 CACAACATA-TTTCTTAAT-GAACCATT-ACATTCTTGGG
1 CACAACCTATTTTATTAATAAAAACATTAACATTCCAGAT
* * * * * *
1462322 CGCAACTTATTATATTAATAAAAATATTAACATTCTAAAT
1 CACAACCTATTTTATTAATAAAAACATTAACATTCCAGAT
*
1462362 CTCAACCTATTT
1 CACAACCTATTT
1462374 CTTAATGAAC
Statistics
Matches: 117, Mismatches: 43, Indels: 12
0.68 0.25 0.07
Matches are distributed among these distances:
37 30 0.26
38 24 0.21
39 24 0.21
40 39 0.33
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.34
Consensus pattern (40 bp):
CACAACCTATTTTATTAATAAAAACATTAACATTCCAGAT
Found at i:1462406 original size:77 final size:77
Alignment explanation
Indices: 1462024--1462404 Score: 437
Period size: 77 Copynumber: 5.0 Consensus size: 77
1462014 ACTTTTGAAG
* * * * * * *
1462024 TTTTA-TAATAGAAAA-ATTAACATTTCGGATCGCAACTTGCTTTCTTAGTGAACCATAACATTC
1 TTTTATTAATA-AAAATATTAACATTCCAGATCACAACAT-ATTTCTTAATGAACCATGACATTC
** **
1462087 TTTTGTGCAACCTA
64 TTGGGCACAACCTA
* * * *
1462101 -TTTATTAATAAAAATATTAATATACCAGATCACAACATATTTCTTAGTGAACCATGATATTCTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAATGAACCATGACATTCTT
*
1462165 GGGCACAACCCA
66 GGGCACAACCTA
*
1462177 TTTTATTAATAAAAACATTAACATTCCAGATCACAATC-TATTTCTTAATGAACCATGACATTCT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAA-CATATTTCTTAATGAACCATGACATTCT
*
1462241 AGGGCACAACCTA
65 TGGGCACAACCTA
* *
1462254 TTTTATTAATAAAAATATTAACCTTCCAGATCACAACATATTTCTTAATGAACCATTACATTCTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAATGAACCATGACATTCTT
* *
1462319 GGGCGCAACTTA
66 GGGCACAACCTA
* * * * * * *
1462331 TTATATTAATAAAAATATTAACATTCTAAATCTCAACCTATTTCTTAATGAACCATAACATTATT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAATGAACCATGACATTCTT
*
1462396 GGACACAAC
66 GGGCACAAC
1462405 TTTATTTTTT
Statistics
Matches: 262, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
76 39 0.15
77 222 0.85
78 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (77 bp):
TTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAATGAACCATGACATTCTT
GGGCACAACCTA
Found at i:1462873 original size:20 final size:22
Alignment explanation
Indices: 1462830--1462871 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1462820 ATATACAAAT
1462830 TAGGTATAAAAAGAATAAAAAA
1 TAGGTATAAAAAGAATAAAAAA
1462852 TAGGTATAAAAAG-ATAAAAA
1 TAGGTATAAAAAGAATAAAAA
1462872 TAAAAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (22 bp):
TAGGTATAAAAAGAATAAAAAA
Found at i:1463166 original size:2 final size:2
Alignment explanation
Indices: 1463155--1463197 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1463145 GTTAATTTTG
1463155 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1463196 AT
1 AT
1463198 TCACCTAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1464639 original size:22 final size:20
Alignment explanation
Indices: 1464595--1464639 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1464585 TAAACTGGCA
* *
1464595 TTACGAACACCTGAAGCAGT
1 TTACGAACACCTGAAGAACT
1464615 TTACGAACACCATGGAAGAACT
1 TTACGAACACC-T-GAAGAACT
1464637 TTA
1 TTA
1464640 TATATAGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 1 0.05
22 9 0.43
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
TTACGAACACCTGAAGAACT
Found at i:1475593 original size:13 final size:13
Alignment explanation
Indices: 1475575--1475618 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1475565 TTCCTTAACT
1475575 TCAAACTCCTTTA
1 TCAAACTCCTTTA
*
1475588 TCAAAC-CATTCT-
1 TCAAACTCCTT-TA
1475600 TCAAACTCCTTTA
1 TCAAACTCCTTTA
1475613 TCAAAC
1 TCAAAC
1475619 AAATGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (13 bp):
TCAAACTCCTTTA
Found at i:1475627 original size:25 final size:25
Alignment explanation
Indices: 1475573--1475631 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
1475563 AGTTCCTTAA
* *
1475573 CTTCAAACTCCTTTATCAAACCATT
1 CTTCAAACTCCTTTATCAAACAAAT
1475598 CTTCAAACTCCTTTATCAAACAAAT
1 CTTCAAACTCCTTTATCAAACAAAT
*
1475623 GTTCAAACT
1 CTTCAAACT
1475632 GCCAATCCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.34
Consensus pattern (25 bp):
CTTCAAACTCCTTTATCAAACAAAT
Found at i:1483407 original size:18 final size:19
Alignment explanation
Indices: 1483372--1483408 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1483362 CACGGAATGT
1483372 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1483392 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1483409 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1490571 original size:2 final size:2
Alignment explanation
Indices: 1490564--1490611 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1490554 TTGTCATTCT
1490564 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1490606 AG AG AG
1 AG AG AG
1490612 GGATGGAGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1494131 original size:37 final size:37
Alignment explanation
Indices: 1494081--1494158 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
1494071 CAAGAAATTA
1494081 AAGAAAAAAAAGTTGAAATGCAATAAATTTTACAGTT
1 AAGAAAAAAAAGTTGAAATGCAATAAATTTTACAGTT
1494118 AAGAAAAAAAAGTTGAAATGCAATAAATTTTACAGTT
1 AAGAAAAAAAAGTTGAAATGCAATAAATTTTACAGTT
1494155 AAGA
1 AAGA
1494159 TGCTTAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.26
Consensus pattern (37 bp):
AAGAAAAAAAAGTTGAAATGCAATAAATTTTACAGTT
Found at i:1495071 original size:150 final size:151
Alignment explanation
Indices: 1494792--1495392 Score: 823
Period size: 150 Copynumber: 4.0 Consensus size: 151
1494782 GATTGTATCT
* * * * *
1494792 TGAGAAACATTCATTGTTTTCCTCTTCC-TACAACTACCATAATAAGGTCTCTTCTCCCAAGGAA
1 TGAGAATCATTCAATGTTTTCCTCTTCCGGACAACTACCATAATAGGGTCTCTTCTCCAAAGGAA
* * * *
1494856 TACTTTGGAATCTGGGGCTAACTCTAGCATTTGATGTCTTTCCCGAGTCAAGCACATCCTGTATC
66 TACTTTGGAATCTGGGGCTAACTCTAGCATTTGATATCTTTCCTGAGTCAAGTACATTCTGTATC
1494921 TTCTCAATGTTTGAGTTACCA
131 TTCTCAATGTTTGAGTTACCA
* * *
1494942 TGAGAATCATTCAATGTTTTCCTCTTAC-GACAACTACCATAATAGGGTTTCTTCTCCCAAGGAA
1 TGAGAATCATTCAATGTTTTCCTCTTCCGGACAACTACCATAATAGGGTCTCTTCTCCAAAGGAA
* * * * *
1495006 TACTTTGGAATCTGGGGCTGACTCTAGCATTTGATGTCTTTCTTGAATCAAGTACATTCTCTATC
66 TACTTTGGAATCTGGGGCTAACTCTAGCATTTGATATCTTTCCTGAGTCAAGTACATTCTGTATC
*
1495071 TTCTCAATGTTTGAGTTATCA
131 TTCTCAATGTTTGAGTTACCA
* *
1495092 TGAGAATCATTCAATGTTTTCCTCTCCCGGA-AACTACCATAATAGGGTCTCTTTTCCAAAGGAA
1 TGAGAATCATTCAATGTTTTCCTCTTCCGGACAACTACCATAATAGGGTCTCTTCTCCAAAGGAA
* * ** ** * *
1495156 TACTTTGGAGTCTGGGGCTAACTCTAGTATCCGATATCTTTAATGACTCAATTACATTCTGTATC
66 TACTTTGGAATCTGGGGCTAACTCTAGCATTTGATATCTTTCCTGAGTCAAGTACATTCTGTATC
*
1495221 TTCTTAATGTTTGAGTTACCA
131 TTCTCAATGTTTGAGTTACCA
* * *
1495242 TGAGAATCATTCAATGTTTTCCTATT-CTGACAACTACCATAATAGGGTCTCTTTTCCAAAGGAA
1 TGAGAATCATTCAATGTTTTCCTCTTCCGGACAACTACCATAATAGGGTCTCTTCTCCAAAGGAA
* ** * *
1495306 CACTTTGGAGCCTGGGGCTAACTCTAGTATTTGATATCTTTCCTGAGTCAAGTACATTATGTATC
66 TACTTTGGAATCTGGGGCTAACTCTAGCATTTGATATCTTTCCTGAGTCAAGTACATTCTGTATC
* *
1495371 TTCTCAGTGTTTGAGCTACCA
131 TTCTCAATGTTTGAGTTACCA
1495392 T
1 T
1495393 TGTTTGGTAA
Statistics
Matches: 402, Mismatches: 47, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
149 3 0.01
150 397 0.99
151 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (151 bp):
TGAGAATCATTCAATGTTTTCCTCTTCCGGACAACTACCATAATAGGGTCTCTTCTCCAAAGGAA
TACTTTGGAATCTGGGGCTAACTCTAGCATTTGATATCTTTCCTGAGTCAAGTACATTCTGTATC
TTCTCAATGTTTGAGTTACCA
Found at i:1495701 original size:33 final size:33
Alignment explanation
Indices: 1495655--1495785 Score: 217
Period size: 33 Copynumber: 4.0 Consensus size: 33
1495645 CCTTCCGTAT
1495655 ATTTTGAAACCTTGGACTAACTCTTCGCTGTAG
1 ATTTTGAAACCTTGGACTAACTCTTCGCTGTAG
* *
1495688 ATTGTGAAACCTTGGACTAACTCTTCTCTGTAG
1 ATTTTGAAACCTTGGACTAACTCTTCGCTGTAG
*
1495721 ATTTTGAAACCTTGGACTAACTCTTCGCTGCAG
1 ATTTTGAAACCTTGGACTAACTCTTCGCTGTAG
* *
1495754 ATTTTGAAACCTTGGACCATCTCTTCGCTGTA
1 ATTTTGAAACCTTGGACTAACTCTTCGCTGTA
1495786 TTGCCATTCA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (33 bp):
ATTTTGAAACCTTGGACTAACTCTTCGCTGTAG
Found at i:1497152 original size:31 final size:31
Alignment explanation
Indices: 1497117--1497178 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1497107 TAAATAACTA
*
1497117 GAGGTTATATCTAATAATACTTGTTTTTAAT
1 GAGGTTAAATCTAATAATACTTGTTTTTAAT
*
1497148 GAGGTTAAATTTAATAATACTTGTTTTTAAT
1 GAGGTTAAATCTAATAATACTTGTTTTTAAT
1497179 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (31 bp):
GAGGTTAAATCTAATAATACTTGTTTTTAAT
Found at i:1497184 original size:2 final size:2
Alignment explanation
Indices: 1497177--1497220 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1497167 CTTGTTTTTA
1497177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1497219 AT
1 AT
1497221 CGAATCCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1502436 original size:33 final size:33
Alignment explanation
Indices: 1502394--1502461 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
1502384 GTCATCGCCA
* *
1502394 TCAGAAATGGGAATGGACACAGAATACTCCGTT
1 TCAGAAATGGGAATGGACACAGAAGACTCCATT
1502427 TCAGAAATGGGAATGGACACAGAAGACTCCATT
1 TCAGAAATGGGAATGGACACAGAAGACTCCATT
1502460 TC
1 TC
1502462 CCCATCAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.21
Consensus pattern (33 bp):
TCAGAAATGGGAATGGACACAGAAGACTCCATT
Found at i:1505353 original size:31 final size:31
Alignment explanation
Indices: 1505318--1505404 Score: 77
Period size: 32 Copynumber: 2.8 Consensus size: 31
1505308 GTAACCGGTC
*
1505318 CATATGCTCCTTAGAACATAGGTATACTGTA
1 CATATGCTCCATAGAACATAGGTATACTGTA
* * * *
1505349 CATATGTCTCAAAAG-ACATAGGTAATTCTGTC
1 CATATG-CTCCATAGAACATAGGT-ATACTGTA
* * *
1505381 CATATGTTCCGTAGAATATAGGTA
1 CATATGCTCCATAGAACATAGGTA
1505405 AACCCTCGAC
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
31 19 0.44
32 24 0.56
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (31 bp):
CATATGCTCCATAGAACATAGGTATACTGTA
Found at i:1505572 original size:14 final size:14
Alignment explanation
Indices: 1505553--1505579 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1505543 TTGTACGTAC
1505553 CACATATACACATT
1 CACATATACACATT
1505567 CACATATACACAT
1 CACATATACACAT
1505580 AGACATATGG
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:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
CACATATACACATT
Found at i:1505585 original size:14 final size:14
Alignment explanation
Indices: 1505553--1505587 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1505543 TTGTACGTAC
*
1505553 CACATATACACATT
1 CACATATACACATA
1505567 CACATATACACATA
1 CACATATACACATA
*
1505581 GACATAT
1 CACATAT
1505588 GGTTCACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.26, G:0.03, T:0.26
Consensus pattern (14 bp):
CACATATACACATA
Found at i:1509262 original size:25 final size:27
Alignment explanation
Indices: 1509216--1509266 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
1509206 AACATCATAT
1509216 TTATTTATTCATTTATTTTTAAAATTA
1 TTATTTATTCATTTATTTTTAAAATTA
1509243 TTATTTA-T-ATTT-TTTATTAAAATT
1 TTATTTATTCATTTATTT-TTAAAATT
1509267 TACACCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.13
25 12 0.52
26 1 0.04
27 7 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTTATTCATTTATTTTTAAAATTA
Found at i:1520417 original size:20 final size:20
Alignment explanation
Indices: 1520392--1520447 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1520382 TTTCAGAGTG
*
1520392 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCA
1520412 ATGCACCGATGCACCAATCA
1 ATGCACCGATGCACCAATCA
* *
1520432 ATGCATCGGTGCACCA
1 ATGCACCGATGCACCA
1520448 TGGAATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.16
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCA
Found at i:1526144 original size:20 final size:20
Alignment explanation
Indices: 1526107--1526144 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1526097 TCACTTAGTG
*
1526107 TTTAAAATAAATTTAAAATT
1 TTTAAAATAAATTGAAAATT
1526127 TTTAAGAATAAA-TGAAAA
1 TTTAA-AATAAATTGAAAA
1526145 ATGCTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
TTTAAAATAAATTGAAAATT
Found at i:1526145 original size:21 final size:20
Alignment explanation
Indices: 1526107--1526146 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1526097 TCACTTAGTG
**
1526107 TTTAAAATAAATTTAAAATT
1 TTTAAAATAAATGAAAAATT
1526127 TTTAAGAATAAATGAAAAAT
1 TTTAA-AATAAATGAAAAAT
1526147 GCTTATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTAAAATAAATGAAAAATT
Found at i:1532923 original size:19 final size:19
Alignment explanation
Indices: 1532899--1532937 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1532889 ACAAACAAAA
*
1532899 TAAATAAAAAGTCTACAAT
1 TAAATAAAAACTCTACAAT
*
1532918 TAAATAAAAACTTTACAAT
1 TAAATAAAAACTCTACAAT
1532937 T
1 T
1532938 GATGGTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAATAAAAACTCTACAAT
Found at i:1539559 original size:19 final size:19
Alignment explanation
Indices: 1539537--1539573 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1539527 ACAACATAAT
1539537 TTTTA-TATTTATCAACATC
1 TTTTACTATTTAT-AACATC
1539556 TTTTACTATTTATAACAT
1 TTTTACTATTTATAACAT
1539574 TATAGTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTACTATTTATAACATC
Found at i:1564419 original size:64 final size:64
Alignment explanation
Indices: 1564318--1564446 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
1564308 TTTTTTTCTC
*
1564318 TGGTTTTTGGACAAATTTTCTCTTGTGAATTATCTGTTGGAACTAGCTTGCAAGATAATCGTTA
1 TGGTTTTTGGACAAATTTTCTCTTGTGAATTATCTGTTAGAACTAGCTTGCAAGATAATCGTTA
* *
1564382 TGGTTTTTGGACGAATTTTCTCTTGTGAATTATCTGTTAGAACTAGCTTGCAGGATAATCGTTA
1 TGGTTTTTGGACAAATTTTCTCTTGTGAATTATCTGTTAGAACTAGCTTGCAAGATAATCGTTA
1564446 T
1 T
1564447 TCTGTCTGGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (64 bp):
TGGTTTTTGGACAAATTTTCTCTTGTGAATTATCTGTTAGAACTAGCTTGCAAGATAATCGTTA
Found at i:1565501 original size:10 final size:10
Alignment explanation
Indices: 1565478--1565510 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1565468 ATTCTTTTAA
1565478 AAATAAAC--
1 AAATAAACAT
1565486 AAATAAACAT
1 AAATAAACAT
1565496 AAATAAACAT
1 AAATAAACAT
1565506 AAATA
1 AAATA
1565511 GAGTATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
10 15 0.65
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (10 bp):
AAATAAACAT
Found at i:1574096 original size:33 final size:32
Alignment explanation
Indices: 1574051--1574130 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 32
1574041 TCCAGCACCG
* *
1574051 CCTAGGGCCGAGGCCTT-CGCATACTAAGGGTCA
1 CCTAGGGTCGAGG--TTCCGCACACTAAGGGTCA
1574084 CCTAGGGTCGAGGTTGCCGCACACTAAGGGTCA
1 CCTAGGGTCGAGGTT-CCGCACACTAAGGGTCA
*
1574117 TCTAGGGTCGAGGT
1 CCTAGGGTCGAGGT
1574131 CGACGTATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 2 0.05
33 40 0.95
ACGTcount: A:0.20, C:0.26, G:0.34, T:0.20
Consensus pattern (32 bp):
CCTAGGGTCGAGGTTCCGCACACTAAGGGTCA
Found at i:1574145 original size:33 final size:33
Alignment explanation
Indices: 1574068--1574135 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
1574058 CCGAGGCCTT
* * *
1574068 CGCATACTAAGGGTCACCTAGGGTCGAGGTTGC
1 CGCACACTAAGGGTCACCTAGGGTCGAGGTCGA
*
1574101 CGCACACTAAGGGTCATCTAGGGTCGAGGTCGA
1 CGCACACTAAGGGTCACCTAGGGTCGAGGTCGA
1574134 CG
1 CG
1574136 TATATTAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (33 bp):
CGCACACTAAGGGTCACCTAGGGTCGAGGTCGA
Found at i:1577486 original size:55 final size:55
Alignment explanation
Indices: 1577426--1577533 Score: 207
Period size: 55 Copynumber: 2.0 Consensus size: 55
1577416 AGAAATGTAG
1577426 TTTGATTAAAAGTAGAGAACTCTATTAAATTAGGTTTCCACTTTATTTAGTTTAT
1 TTTGATTAAAAGTAGAGAACTCTATTAAATTAGGTTTCCACTTTATTTAGTTTAT
*
1577481 TTTGATTAAAAGTAGAGAACTTTATTAAATTAGGTTTCCACTTTATTTAGTTT
1 TTTGATTAAAAGTAGAGAACTCTATTAAATTAGGTTTCCACTTTATTTAGTTT
1577534 CTTTGTAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.46
Consensus pattern (55 bp):
TTTGATTAAAAGTAGAGAACTCTATTAAATTAGGTTTCCACTTTATTTAGTTTAT
Found at i:1577935 original size:23 final size:23
Alignment explanation
Indices: 1577909--1577957 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1577899 AGCCCTTGAA
1577909 AGAGTATCTCGTGGTGCATGGAT
1 AGAGTATCTCGTGGTGCATGGAT
1577932 AGAGTATCTCGTGGTGCATGGAT
1 AGAGTATCTCGTGGTGCATGGAT
1577955 AGA
1 AGA
1577958 CTAACTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (23 bp):
AGAGTATCTCGTGGTGCATGGAT
Found at i:1580630 original size:22 final size:22
Alignment explanation
Indices: 1580604--1580677 Score: 121
Period size: 22 Copynumber: 3.3 Consensus size: 22
1580594 TATACTTATC
*
1580604 TCATATTAATAAAAAAATGTGT
1 TCATATTATTAAAAAAATGTGT
1580626 TCATATTATTAAAAAAATGTGT
1 TCATATTATTAAAAAAATGTGT
1580648 TCATATTATTAAAAAAAAGTGTGT
1 TCATATTATT-AAAAAAA-TGTGT
1580672 TCATAT
1 TCATAT
1580678 ACATGCTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 31 0.63
23 7 0.14
24 11 0.22
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.39
Consensus pattern (22 bp):
TCATATTATTAAAAAAATGTGT
Found at i:1581817 original size:12 final size:12
Alignment explanation
Indices: 1581800--1581824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1581790 CTCAAACAGA
1581800 GAGAATGAACAT
1 GAGAATGAACAT
1581812 GAGAATGAACAT
1 GAGAATGAACAT
1581824 G
1 G
1581825 TTGCATGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (12 bp):
GAGAATGAACAT
Found at i:1582007 original size:20 final size:20
Alignment explanation
Indices: 1581982--1582055 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
1581972 ATGGCCTTGG
1581982 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
1582002 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
1582022 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
1582042 TCGGATGACCTCGG
1 TCGGATGGCCTCGG
1582056 TCGGATGGCC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:1582071 original size:10 final size:10
Alignment explanation
Indices: 1581982--1582055 Score: 91
Period size: 10 Copynumber: 7.4 Consensus size: 10
1581972 ATGGCCTTGG
1581982 TCGGATGGCC
1 TCGGATGGCC
1581992 TCGGAT-GCTC
1 TCGGATGGC-C
1582002 TCGGATGGCC
1 TCGGATGGCC
1582012 TCGGAT-GCTC
1 TCGGATGGC-C
1582022 TCGGATGGCC
1 TCGGATGGCC
1582032 TCGGAT-GCTC
1 TCGGATGGC-C
*
1582042 TCGGATGACC
1 TCGGATGGCC
1582052 TCGG
1 TCGG
1582056 TCGGATGGCC
Statistics
Matches: 57, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
9 6 0.11
10 46 0.81
11 5 0.09
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:1589571 original size:2 final size:2
Alignment explanation
Indices: 1589564--1589608 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1589554 TCACCTCGAT
* *
1589564 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1589603 TA TA TA
1 TA TA TA
1589609 AAATATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1589608 original size:25 final size:26
Alignment explanation
Indices: 1589566--1589617 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1589556 ACCTCGATTA
*
1589566 TATATATATATATATATATAATATTT
1 TATATATATATATATATAAAATATTT
*
1589592 TATATAT-TTTATATATAAAATATTT
1 TATATATATATATATATAAAATATTT
1589617 T
1 T
1589618 TGAATTTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TATATATATATATATATAAAATATTT
Found at i:1611250 original size:183 final size:183
Alignment explanation
Indices: 1610935--1611280 Score: 611
Period size: 183 Copynumber: 1.9 Consensus size: 183
1610925 TTAAATCCGT
*
1610935 AAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGAA
1 AAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGAA
* *
1611000 TAGATTACATTCAAACCATGGCATTGCTTAGACACTTGGCAATTCGGTGTTTGCTCCACTACTTT
66 TAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCGGTGTTTGCTCCACTACTTT
*
1611065 TGTCAGGCCAAAGACTTTGTGATTAGACGAACCTTTCAATGATTTGTCCCTCC
131 TGTCAGGCCAAAGACTTTGTGATGAGACGAACCTTTCAATGATTTGTCCCTCC
*
1611118 AAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGAA
1 AAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGAA
* * *
1611183 TAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCTACTGCTTT
66 TAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCGGTGTTTGCTCCACTACTTT
*
1611248 TGTCAGGCTAAAGACTTTGTGATGAGACGAACC
131 TGTCAGGCCAAAGACTTTGTGATGAGACGAACC
1611281 CTTTAGGTAA
Statistics
Matches: 154, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
183 154 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
AAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGAA
TAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCGGTGTTTGCTCCACTACTTT
TGTCAGGCCAAAGACTTTGTGATGAGACGAACCTTTCAATGATTTGTCCCTCC
Found at i:1612475 original size:36 final size:36
Alignment explanation
Indices: 1612422--1612584 Score: 166
Period size: 36 Copynumber: 4.5 Consensus size: 36
1612412 TAGATGATTA
* * *
1612422 TCTCACTTGTGATTGTTTTTCTTAAAGCATACTTTG
1 TCTCACTTGAGACTGTTTTTCTTAAAGCAGACTTTG
*
1612458 TCTCACTTGAGACTGTTTTTCTTAAAGCACACTTTG
1 TCTCACTTGAGACTGTTTTTCTTAAAGCAGACTTTG
* * * * *
1612494 TCTCACTTGAGACTATTTTACTCGAAAGAAGA-TTTA
1 TCTCACTTGAGACTGTTTTTCT-TAAAGCAGACTTTG
* ** ** * *
1612530 TTTCACTCAAGTTTGTTTTGCTTAAAACAGACTTTG
1 TCTCACTTGAGACTGTTTTTCTTAAAGCAGACTTTG
1612566 TCTCACTTGAGACTGTTTT
1 TCTCACTTGAGACTGTTTT
1612585 ACTCGAAAGA
Statistics
Matches: 100, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
35 6 0.06
36 88 0.88
37 6 0.06
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTCACTTGAGACTGTTTTTCTTAAAGCAGACTTTG
Found at i:1612619 original size:36 final size:36
Alignment explanation
Indices: 1612509--1612620 Score: 104
Period size: 36 Copynumber: 3.1 Consensus size: 36
1612499 CTTGAGACTA
* *
1612509 TTTTACTCGAAAGAAGATTTATTTCACTCAAGTTTG
1 TTTTACTCGAAAGAAGATTTATTCCACTCAAGATTG
* * * ** *
1612545 TTTTGCT-TAAA-ACAGACTTT-GTCTCACTTGAGACTG
1 TTTTACTCGAAAGA-AGA-TTTATTC-CACTCAAGATTG
1612581 TTTTACTCGAAAGAAGATTTATTCCACTCAAGATTG
1 TTTTACTCGAAAGAAGATTTATTCCACTCAAGATTG
1612617 TTTT
1 TTTT
1612621 TCTTAAAACC
Statistics
Matches: 56, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
34 1 0.02
35 7 0.12
36 39 0.70
37 8 0.14
38 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTACTCGAAAGAAGATTTATTCCACTCAAGATTG
Found at i:1612635 original size:36 final size:35
Alignment explanation
Indices: 1612523--1612636 Score: 88
Period size: 36 Copynumber: 3.2 Consensus size: 35
1612513 ACTCGAAAGA
* * *
1612523 AGATTTATTTCACTCAAGTTTGTTTTGCTTAAAAC
1 AGATTTATTCCACTCAAGATTGTTTTACTTAAAAC
* ** * *
1612558 AGACTTT-GTCTCACTTGAGACTGTTTTACTCGAAAGA-
1 AGA-TTTATTC-CACTCAAGATTGTTTTACT-TAAA-AC
*
1612595 AGATTTATTCCACTCAAGATTGTTTTTCTTAAAACC
1 AGATTTATTCCACTCAAGATTGTTTTACTTAAAA-C
1612631 AGATTT
1 AGATTT
1612637 GTCTCTCTTG
Statistics
Matches: 58, Mismatches: 14, Indels: 13
0.68 0.16 0.15
Matches are distributed among these distances:
34 1 0.02
35 7 0.12
36 41 0.71
37 8 0.14
38 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (35 bp):
AGATTTATTCCACTCAAGATTGTTTTACTTAAAAC
Found at i:1612656 original size:72 final size:72
Alignment explanation
Indices: 1612471--1612646 Score: 264
Period size: 72 Copynumber: 2.4 Consensus size: 72
1612461 CACTTGAGAC
* * * * *
1612471 TGTTTTTCTTAAAGCACACTTTGTCTCACTTGAGACTATTTTACTCGAAAGAAGATTTATTTCAC
1 TGTTTTGCTTAAAACAGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTCCAC
*
1612536 TCAAGTT
66 TCAAGAT
1612543 TGTTTTGCTTAAAACAGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTCCAC
1 TGTTTTGCTTAAAACAGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTCCAC
1612608 TCAAGAT
66 TCAAGAT
* *
1612615 TGTTTTTCTTAAAACCAGA-TTTGTCTCTCTTG
1 TGTTTTGCTTAAAA-CAGACTTTGTCTCACTTG
1612647 GGAACGTTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
72 91 0.96
73 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (72 bp):
TGTTTTGCTTAAAACAGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTCCAC
TCAAGAT
Found at i:1613582 original size:23 final size:23
Alignment explanation
Indices: 1613556--1613622 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
1613546 CTACAGCTCA
1613556 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* *
1613579 TATAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
* *
1613602 TAGAATTGCACCGTAGTGCCA
1 TATAATTGCACCGAAGTGCCA
1613623 TATAATAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:1613811 original size:103 final size:103
Alignment explanation
Indices: 1613638--1613855 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
1613628 TAATGTCCAT
* * * *
1613638 AAGGACCACATATTATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1613703 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1613741 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1613806 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1613844 AAAGACCACATA
1 AAGGACCACATA
1613856 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1619303 original size:23 final size:23
Alignment explanation
Indices: 1619277--1619343 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
1619267 CTACAGCTCA
1619277 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* * *
1619300 TATAATTTCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
* *
1619323 TAGAATTGCACCGTAGTGCCA
1 TATAATTGCACCGAAGTGCCA
1619344 TATAATAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:1619530 original size:103 final size:103
Alignment explanation
Indices: 1619359--1619576 Score: 375
Period size: 103 Copynumber: 2.1 Consensus size: 103
1619349 TAATGTCCAT
**
1619359 AAGGACCACATATCATTCCTTAAGAATCATATACATATATTAGAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
*
1619424 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1619462 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGTGTCTCACT
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGAGATCAAGTATGTGTCTCACC
1619526 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1619565 AAGGACCACATA
1 AAGGACCACATA
1619577 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 107 0.98
104 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1621487 original size:2 final size:2
Alignment explanation
Indices: 1621480--1621505 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1621470 CGTTGATGCA
1621480 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1621506 TAATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1622700 original size:24 final size:22
Alignment explanation
Indices: 1622673--1622716 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
1622663 GATAGTTAAA
1622673 ATTTTTGATATAATTATACATTTG
1 ATTTTT-A-ATAATTATACATTTG
*
1622697 ATTTTTAATATTTATACATT
1 ATTTTTAATAATTATACATT
1622717 ACATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 1 0.05
24 6 0.32
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (22 bp):
ATTTTTAATAATTATACATTTG
Found at i:1628197 original size:91 final size:92
Alignment explanation
Indices: 1628039--1628209 Score: 274
Period size: 91 Copynumber: 1.9 Consensus size: 92
1628029 TTATTTATGA
*
1628039 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAATTGTTTGACATCTTT
1 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAATTGTTTGACATCATT
1628104 TGTTGCTG-TATTTTATGATCTTTCAT
66 TGTTGCTGCTATTTTATGATCTTTCAT
* * * *
1628130 TCTTTTATGTAGGCCTTAAACAAATATGTTAAGTA-TATATTCCTTGTCAATTGTTTTACATCAT
1 TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTA-ATTCCATGTCAATTGTTTGACATCAT
1628194 TTGTTGCTGCTATTTT
65 TTGTTGCTGCTATTTT
1628210 CTTGAAGGTG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
90 2 0.03
91 65 0.89
92 6 0.08
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (92 bp):
TCTTTTATGCAGGCCTTAAACAAATATGTTAAATATTAATTCCATGTCAATTGTTTGACATCATT
TGTTGCTGCTATTTTATGATCTTTCAT
Found at i:1630155 original size:2 final size:2
Alignment explanation
Indices: 1630148--1630178 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1630138 CTTGGCAGAC
1630148 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1630179 GCACCAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1631784 original size:76 final size:77
Alignment explanation
Indices: 1631680--1631880 Score: 264
Period size: 75 Copynumber: 2.6 Consensus size: 77
1631670 GACCGTTGAA
* * * *
1631680 CAGGGGGGAATCGGTACCCCCT-TGGGGGGGAATCGGTTCCCTTCGAGCATACTGGAATTCTCGG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
**
1631744 AACAAAAATGTT
66 AACAAAAACATT
** *
1631756 TTGGGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
* * *
1631819 AGCCAAACCATT
66 AACAAAAACATT
*
1631831 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCA
1631881 ATCTGTAATT
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
75 65 0.61
76 18 0.17
77 24 0.22
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (77 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
AACAAAAACATT
Found at i:1634500 original size:21 final size:21
Alignment explanation
Indices: 1634474--1634513 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1634464 CAGAACCCCA
*
1634474 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1634495 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1634514 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1640437 original size:75 final size:75
Alignment explanation
Indices: 1640324--1640525 Score: 251
Period size: 75 Copynumber: 2.6 Consensus size: 75
1640314 GACCGTTGAA
* * * *
1640324 CAGGGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGT-TCCTCTTAGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
**
1640389 ACAAAAATGTT
65 ACAAAAACATT
* * * *
1640400 TAGGGGGGAATCGGTTCCTCTTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 CAGGGGGGAATCGGTTCCTCTTAGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
* *
1640465 CCAAACCATT
66 CAAAAACATT
*
1640475 CAGGGGGGAATCGGTTCCTCCTATGAGGGGGGAATCGGTTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCT-CT-T-AGGGGGGAATCGGTTCCCTCCGAGCA
1640526 ATCTGTAATT
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
75 67 0.62
76 16 0.15
77 1 0.01
78 24 0.22
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (75 bp):
CAGGGGGGAATCGGTTCCTCTTAGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
CAAAAACATT
Found at i:1641816 original size:85 final size:84
Alignment explanation
Indices: 1641725--1641882 Score: 203
Period size: 85 Copynumber: 1.9 Consensus size: 84
1641715 ATGACCCCTG
* * * *
1641725 AATGTGTGTCATCCTT-TTTAATGGCG-GGAGCTTCAATGATGCTCAATGTAAGTCATAAATGCG
1 AATGTGTGTCAT-CTTATTT-ATGACGAGG-GCTTCAATGACGCTCAATGCAAGTCATAAATGAG
*
1641788 TGTCATAAATTTATGACACATA
63 CGTCATAAATTTATGACACATA
**
1641810 AATGTGTGTCATCTTAATTTATGACGAGGGCTTCAATGACGCTCAATGCGCGTCATAAATGAGCG
1 AATGTGTGTCATCTT-ATTTATGACGAGGGCTTCAATGACGCTCAATGCAAGTCATAAATGAGCG
1641875 TCATAAAT
65 TCATAAAT
1641883 GAGCGTCATA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 3 0.05
85 55 0.87
86 5 0.08
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (84 bp):
AATGTGTGTCATCTTATTTATGACGAGGGCTTCAATGACGCTCAATGCAAGTCATAAATGAGCGT
CATAAATTTATGACACATA
Found at i:1641875 original size:13 final size:13
Alignment explanation
Indices: 1641854--1641918 Score: 87
Period size: 13 Copynumber: 5.0 Consensus size: 13
1641844 AATGACGCTC
*
1641854 AATGCGCGTCATA
1 AATGAGCGTCATA
1641867 AATGAGCGTCATA
1 AATGAGCGTCATA
1641880 AATGAGCGTCATA
1 AATGAGCGTCATA
* *
1641893 AATGCGTGTCATA
1 AATGAGCGTCATA
1641906 AATGTA-CGTCATA
1 AATG-AGCGTCATA
1641919 GATTTATGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (13 bp):
AATGAGCGTCATA
Found at i:1644003 original size:24 final size:25
Alignment explanation
Indices: 1643933--1644003 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 25
1643923 CAATCTTATA
*
1643933 TGGCACTACGGTGC-ATTTCTACGC
1 TGGCACTTCGGTGCAATTTCTACGC
*
1643957 T-GCACTTCGGTGCAAATTCTACG-
1 TGGCACTTCGGTGCAATTTCTACGC
*
1643980 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
1644004 AGCTATGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.29
24 29 0.71
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (25 bp):
TGGCACTTCGGTGCAATTTCTACGC
Found at i:1645299 original size:12 final size:12
Alignment explanation
Indices: 1645269--1645303 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1645259 TATATTTTAT
1645269 TTATCTTGTTT-
1 TTATCTTGTTTC
*
1645280 TAATCTTGTTTC
1 TTATCTTGTTTC
1645292 TTATCTTGTTTC
1 TTATCTTGTTTC
1645304 CAGCACCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:1646037 original size:21 final size:22
Alignment explanation
Indices: 1645998--1646041 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1645988 TATTTTACTG
*
1645998 TAGCAGGGGAATCGGTTCCCTA
1 TAGCAGGGGAATCGATTCCCTA
*
1646020 TAGCA-GGGTATCGATTCCCTA
1 TAGCAGGGGAATCGATTCCCTA
1646041 T
1 T
1646042 TTGTAATCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (22 bp):
TAGCAGGGGAATCGATTCCCTA
Found at i:1646101 original size:25 final size:25
Alignment explanation
Indices: 1646067--1646116 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1646057 TTTGTGTAAT
* * *
1646067 CGGTACTGTAGTATGGTACTGTTCA
1 CGGTACTGTAGCAAGGTACAGTTCA
1646092 CGGTACTGTAGCAAGGTACAGTTCA
1 CGGTACTGTAGCAAGGTACAGTTCA
1646117 TTACTATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (25 bp):
CGGTACTGTAGCAAGGTACAGTTCA
Found at i:1666242 original size:21 final size:21
Alignment explanation
Indices: 1666218--1666271 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1666208 CAAATGACTA
1666218 ATAAAAA-AAAGAAAATGTGTC
1 ATAAAAATAAA-AAAATGTGTC
1666239 ATAAAAATAAAAAAATGTGTC
1 ATAAAAATAAAAAAATGTGTC
* *
1666260 ACAAATATAAAA
1 ATAAAAATAAAA
1666272 TTATTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.20
Consensus pattern (21 bp):
ATAAAAATAAAAAAATGTGTC
Found at i:1666324 original size:21 final size:20
Alignment explanation
Indices: 1666277--1666324 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1666267 TAAAATTATT
*
1666277 AAAAATTTAAAAAACAAATG
1 AAAAATATAAAAAACAAATG
***
1666297 TGTAATATAAAAAACTAAATG
1 AAAAATATAAAAAAC-AAATG
1666318 AAAAATA
1 AAAAATA
1666325 AAGAATCTAG
Statistics
Matches: 20, Mismatches: 7, Indels: 1
0.71 0.25 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (20 bp):
AAAAATATAAAAAACAAATG
Found at i:1669494 original size:30 final size:30
Alignment explanation
Indices: 1669458--1669530 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1669448 TGCGAAGGAC
1669458 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1669488 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1669518 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1669531 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1671580 original size:103 final size:103
Alignment explanation
Indices: 1671355--1671572 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1671345 GTCGAGGGTC
1671355 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
* *
1671420 TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
*
1671458 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
* *
1671523 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
1671561 TATGTGGTCCTT
1 TATGTGGTCCTT
1671573 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
Found at i:1675791 original size:31 final size:30
Alignment explanation
Indices: 1675756--1675823 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
1675746 GACAACGAAT
*
1675756 TTATTTTATAAT-TGATTAAGAATTTTAAAAA
1 TTATTTTATAATAT--TTAAAAATTTTAAAAA
1675787 TTATTTTATAATATTTAAAAATTTTAAAAA
1 TTATTTTATAATATTTAAAAATTTTAAAAA
1675817 TATATTT
1 T-TATTT
1675824 AAACAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 16 0.47
31 17 0.50
32 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
TTATTTTATAATATTTAAAAATTTTAAAAA
Found at i:1675812 original size:30 final size:30
Alignment explanation
Indices: 1675756--1675823 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 30
1675746 GACAACGAAT
*
1675756 TTATTTTATAATTGATTAAGAATTTTAAAAA
1 TTATTTTATAATT-ATTAAAAATTTTAAAAA
1675787 TTATTTTATAA-TATTTAAAAATTTTAAAAA
1 TTATTTTATAATTA-TTAAAAATTTTAAAAA
1675817 TATATTT
1 T-TATTT
1675824 AAACAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.03
30 17 0.50
31 16 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
TTATTTTATAATTATTAAAAATTTTAAAAA
Found at i:1675923 original size:39 final size:39
Alignment explanation
Indices: 1675864--1675941 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
1675854 TATCTTATTA
*
1675864 TTTTGTTTAAATTAGTGTCTAAATAGTTTCAATCACACG
1 TTTTATTTAAATTAGTGTCTAAATAGTTTCAATCACACG
* * *
1675903 TTTTATTTAAATTGGTGTCTAAATTGTTTTAATCACACG
1 TTTTATTTAAATTAGTGTCTAAATAGTTTCAATCACACG
1675942 CTTAAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (39 bp):
TTTTATTTAAATTAGTGTCTAAATAGTTTCAATCACACG
Found at i:1680139 original size:3 final size:3
Alignment explanation
Indices: 1680127--1680177 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
1680117 TCTCCCTTAA
* * *
1680127 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT CAT TTT TAAT T-T CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
1680171 TAT TAT T
1 TAT TAT T
1680178 TTCCCCTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 3 0.08
3 34 0.87
4 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1680180 original size:12 final size:12
Alignment explanation
Indices: 1680127--1680180 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
1680117 TCTCCCTTAA
1680127 TATTTT-ATTAT
1 TATTTTCATTAT
1680138 TATTATT-ATTAT
1 TATT-TTCATTAT
* *
1680150 TATTATCATTTT
1 TATTTTCATTAT
*
1680162 TAATTTCATTAT
1 TATTTTCATTAT
1680174 TATTTTC
1 TATTTTC
1680181 CCCTTATTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
11 5 0.14
12 30 0.86
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTTCATTAT
Found at i:1680250 original size:2 final size:2
Alignment explanation
Indices: 1680245--1680276 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1680235 TTTTTTGTTA
1680245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1680277 TTTTTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1681149 original size:20 final size:19
Alignment explanation
Indices: 1681120--1681158 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1681110 TTTCAAATTT
*
1681120 AAATGTGATTTTTTTTATA
1 AAATGTGATTTTATTTATA
1681139 AAATAGTGATTTTATTTATA
1 AAAT-GTGATTTTATTTATA
1681159 TTTAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (19 bp):
AAATGTGATTTTATTTATA
Found at i:1681820 original size:30 final size:27
Alignment explanation
Indices: 1681769--1681824 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
1681759 TTTTAACTAA
*
1681769 ATTAATCGATCGAATCGAATTAATTCG
1 ATTAATCGATCGAACCGAATTAATTCG
1681796 ATTAATTCGATCGATCACCGAATTAATTC
1 ATTAA-TCGATCGA--ACCGAATTAATTC
1681825 AGTCAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 5 0.20
28 8 0.32
30 12 0.48
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (27 bp):
ATTAATCGATCGAACCGAATTAATTCG
Found at i:1682078 original size:20 final size:20
Alignment explanation
Indices: 1682034--1682090 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 20
1682024 TATTTGAATC
*
1682034 AAATTAATTAGATATTATTT
1 AAATTAATTATATATTATTT
1682054 --A-TAATTATATATTATTT
1 AAATTAATTATATATTATTT
* *
1682071 AAATTAATTGTAAATTATTT
1 AAATTAATTATATATTATTT
1682091 TTTAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 15 0.48
18 1 0.03
19 1 0.03
20 14 0.45
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
AAATTAATTATATATTATTT
Found at i:1682503 original size:24 final size:24
Alignment explanation
Indices: 1682463--1682523 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
1682453 AATTTTATTA
*
1682463 ATTTTATATCTAACATTAAATTTTT
1 ATTTTAT-TTTAACATTAAATTTTT
*
1682488 ATTTTATTTTAACATTTAATTTTT
1 ATTTTATTTTAACATTAAATTTTT
1682512 ATTTTATTTTAA
1 ATTTTATTTTAA
1682524 AATATATCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 27 0.79
25 7 0.21
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTATTTTAACATTAAATTTTT
Found at i:1682604 original size:24 final size:26
Alignment explanation
Indices: 1682568--1682617 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
1682558 AAACGATTAA
*
1682568 TTTAATTTATTTTAATACT-AATTTT
1 TTTAATTTATTTTAAAACTCAATTTT
1682593 TTTAA-TTATTTTAAAACTCAATTTT
1 TTTAATTTATTTTAAAACTCAATTTT
1682618 ATATTTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTAATTTATTTTAAAACTCAATTTT
Found at i:1682643 original size:14 final size:15
Alignment explanation
Indices: 1682615--1682647 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1682605 AAAACTCAAT
*
1682615 TTTATATTTTCAAAA
1 TTTATAATTTCAAAA
1682630 TTTATAATTT-AAAA
1 TTTATAATTTCAAAA
1682644 TTTA
1 TTTA
1682648 AAGAGATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATAATTTCAAAA
Found at i:1683133 original size:6 final size:6
Alignment explanation
Indices: 1683122--1683175 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
1683112 CCCAACACCA
1683122 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
1683170 CTCTCC
1 CTCTCC
1683176 TTCCATCTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCC
Found at i:1690378 original size:32 final size:32
Alignment explanation
Indices: 1690342--1690402 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1690332 TACTTTTCAA
* *
1690342 TTTCTTATATTTTGGACATAGTTATCTTTTTT
1 TTTCTTATATTTTGAACAGAGTTATCTTTTTT
1690374 TTTCTTATATTTTGAACAGAGTTATCTTT
1 TTTCTTATATTTTGAACAGAGTTATCTTT
1690403 CAAATAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (32 bp):
TTTCTTATATTTTGAACAGAGTTATCTTTTTT
Found at i:1692776 original size:5 final size:5
Alignment explanation
Indices: 1692766--1692793 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1692756 GGCATTCATT
1692766 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
1692794 GGCAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1696715 original size:16 final size:16
Alignment explanation
Indices: 1696694--1696726 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1696684 GATATAGTAA
1696694 ATAGTATTAGATTTAT
1 ATAGTATTAGATTTAT
*
1696710 ATAGTATTATATTTAT
1 ATAGTATTAGATTTAT
1696726 A
1 A
1696727 CTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (16 bp):
ATAGTATTAGATTTAT
Found at i:1697805 original size:33 final size:33
Alignment explanation
Indices: 1697757--1697831 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 33
1697747 ATATGTTATT
1697757 GATTATATTAGGAGCAAAATAGAAAAGGGAATAG
1 GATTATA-TAGGAGCAAAATAGAAAAGGGAATAG
**
1697791 GATTATATAGGAGCAAAATATTAAAGGGAATAG
1 GATTATATAGGAGCAAAATAGAAAAGGGAATAG
*
1697824 GAATATAT
1 GATTATAT
1697832 TTGCAGAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 31 0.82
34 7 0.18
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (33 bp):
GATTATATAGGAGCAAAATAGAAAAGGGAATAG
Found at i:1703387 original size:30 final size:30
Alignment explanation
Indices: 1703349--1703455 Score: 128
Period size: 30 Copynumber: 3.6 Consensus size: 30
1703339 TAGAAAAGAA
* * *
1703349 TTTACGTAAGAT-AGATTACCTGAAAATTGT
1 TTTACGTAAAATGA-ATTACATGAAAAATGT
*
1703379 TTTTCGTAAAATGAATTACATGAAAAATGT
1 TTTACGTAAAATGAATTACATGAAAAATGT
** *
1703409 TTTACGTAAAATGAATTAC-CCAAAACTGT
1 TTTACGTAAAATGAATTACATGAAAAATGT
1703438 TTTACGTAAAATGAATTA
1 TTTACGTAAAATGAATTA
1703456 TATTTTTCAG
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
29 25 0.37
30 42 0.62
31 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACATGAAAAATGT
Found at i:1703448 original size:15 final size:14
Alignment explanation
Indices: 1703402--1703450 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1703392 AATTACATGA
1703402 AAAATGTTTTACGT
1 AAAATGTTTTACGT
** **
1703416 AAAATGAATTACCC
1 AAAATGTTTTACGT
1703430 AAAACTGTTTTACGT
1 AAAA-TGTTTTACGT
1703445 AAAATG
1 AAAATG
1703451 AATTATATTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (14 bp):
AAAATGTTTTACGT
Found at i:1704924 original size:84 final size:84
Alignment explanation
Indices: 1704825--1704994 Score: 232
Period size: 84 Copynumber: 2.0 Consensus size: 84
1704815 ATATCTGACG
* * * * *
1704825 AACGATGGTTGAAATTCGCGTAACGATTGATCTTACGAATGATGATTGAAATCCAAATAGATGTT
1 AACGATGATTGAAATTCGCATAACGATTGATCTGACGAATGATGATTGAAAGCCAAATAGATGTC
* *
1704890 TACATGTATAAAGAAAATT
66 GACATGAATAAAGAAAATT
* * * * *
1704909 AACGATGATTGAAATTCGTATAATGATTGATCTGACGAATGATTATTGAAAGCCGAATCGATGTC
1 AACGATGATTGAAATTCGCATAACGATTGATCTGACGAATGATGATTGAAAGCCAAATAGATGTC
1704974 GACATGAATAAAGAAAATT
66 GACATGAATAAAGAAAATT
1704993 AA
1 AA
1704995 AATAAATCGT
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (84 bp):
AACGATGATTGAAATTCGCATAACGATTGATCTGACGAATGATGATTGAAAGCCAAATAGATGTC
GACATGAATAAAGAAAATT
Found at i:1706175 original size:34 final size:34
Alignment explanation
Indices: 1706132--1706200 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1706122 ATAACTAATA
1706132 CTATCACGGATATAATAGGTATATCGAAAGGCAG
1 CTATCACGGATATAATAGGTATATCGAAAGGCAG
1706166 CTATCACGGATATAATAGGTATATCGAAAGGCAG
1 CTATCACGGATATAATAGGTATATCGAAAGGCAG
1706200 C
1 C
1706201 GCTATTGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (34 bp):
CTATCACGGATATAATAGGTATATCGAAAGGCAG
Found at i:1711293 original size:2 final size:2
Alignment explanation
Indices: 1711286--1711311 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1711276 ACGTTCTTTT
1711286 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
1711312 AATGTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1713577 original size:3 final size:3
Alignment explanation
Indices: 1713569--1713699 Score: 156
Period size: 3 Copynumber: 43.0 Consensus size: 3
1713559 TTATTTATTA
*
1713569 AAT AAT AAT AAT -AT ATAT AAT ATT AAT AAT AAT AAT AAAT AAAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT
* * *
1713616 AAT AAT AAT AAT TAT TAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * **
1713664 ACT AAT AGT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1713700 TTTAAATGAA
Statistics
Matches: 111, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
2 2 0.02
3 99 0.89
4 10 0.09
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1715747 original size:24 final size:23
Alignment explanation
Indices: 1715684--1715747 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 23
1715674 CGGGCCAGGT
1715684 ATATATATATATATATTTAAATTAA
1 ATATATA-ATAT-TATTTAAATTAA
*
1715709 ATATATAATTTTTATTTAAATTAA
1 ATATATAA-TATTATTTAAATTAA
*
1715733 ATTTATTAATATTAT
1 ATATA-TAATATTAT
1715748 ATATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 22 0.65
25 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATATAATATTATTTAAATTAA
Found at i:1715752 original size:2 final size:2
Alignment explanation
Indices: 1715741--1715774 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1715731 AAATTTATTA
1715741 AT AT -T 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 A
1715775 AATGATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1716673 original size:19 final size:20
Alignment explanation
Indices: 1716649--1716686 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1716639 ATCTTGCTTG
*
1716649 TTATAA-AAAAATATTAGAT
1 TTATAATAAAAATAATAGAT
1716668 TTATAATAAAAATAATAGA
1 TTATAATAAAAATAATAGA
1716687 AAACAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
TTATAATAAAAATAATAGAT
Found at i:1716853 original size:20 final size:20
Alignment explanation
Indices: 1716795--1716853 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
1716785 TTATTTTTTT
* *
1716795 AAAATTTAATAAAAATATTA
1 AAAATTTAATAAAAAAATAA
**
1716815 AAAATTT-ATAATTGGAAATAA
1 AAAATTTAATAA--AAAAATAA
1716836 AAAATTTAATAAAAAAAT
1 AAAATTTAATAAAAAAAT
1716854 TATTTCTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
21 11 0.37
22 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATTTAATAAAAAAATAA
Done.