Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_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: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 25
Found at i:6840842 original size:24 final size:24
Alignment explanation
Indices: 6840791--6840897 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
6840781 ATGTTTTATT
* * * *
6840791 TGATTTCCGATTTGAATTCTATTT
1 TGATTTCTGATCTGAATTCTGTTA
*
6840815 TGATTTCTGATCTGAATTTTGTTA
1 TGATTTCTGATCTGAATTCTGTTA
* * *
6840839 TGATTTCTAATCTGGATTATGTTA
1 TGATTTCTGATCTGAATTCTGTTA
* * * *
6840863 TGATATATGATATGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTA
*
6840887 TGATTTATGAT
1 TGATTTCTGAT
6840898 ATCTCCGTTT
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.52
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTA
Found at i:6843179 original size:34 final size:34
Alignment explanation
Indices: 6843136--6843204 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
6843126 CAGAAGTGTC
6843136 AAGGTAGATAGAACCATATCAATTAATTCACAAA
1 AAGGTAGATAGAACCATATCAATTAATTCACAAA
6843170 AAGGTAGATAGAACCATATCAATTAATTCACAAA
1 AAGGTAGATAGAACCATATCAATTAATTCACAAA
6843204 A
1 A
6843205 CAAAATTTGC
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:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (34 bp):
AAGGTAGATAGAACCATATCAATTAATTCACAAA
Found at i:6844402 original size:11 final size:12
Alignment explanation
Indices: 6844386--6844422 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
6844376 TTCGATCCGA
6844386 TTTACC-AAAAT
1 TTTACCTAAAAT
*
6844397 TTTACCTGAAAT
1 TTTACCTAAAAT
6844409 TTT-CCTAAAAT
1 TTTACCTAAAAT
6844420 TTT
1 TTT
6844423 TATTCTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.35, C:0.16, G:0.03, T:0.46
Consensus pattern (12 bp):
TTTACCTAAAAT
Found at i:6848526 original size:59 final size:59
Alignment explanation
Indices: 6848423--6848550 Score: 166
Period size: 59 Copynumber: 2.2 Consensus size: 59
6848413 GTAGTGCTAA
* * * * * *
6848423 CCCGAGTATGACACATAAGGGCGTGCTCACCATCTGCACTAGTTATACTTTAATGCAGT
1 CCCGAATATGACACATAAGGGCGTGCCCACCATATGAACTAGTTATAATTTAATGCAAT
* * * *
6848482 CTCGAATATGTCACATAAGGTCGTGCCCACCATATGAACTAGTTATAATTTAGTGCAAT
1 CCCGAATATGACACATAAGGGCGTGCCCACCATATGAACTAGTTATAATTTAATGCAAT
6848541 CCCGAATATG
1 CCCGAATATG
6848551 CAGCCTTCTG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (59 bp):
CCCGAATATGACACATAAGGGCGTGCCCACCATATGAACTAGTTATAATTTAATGCAAT
Found at i:6856391 original size:27 final size:27
Alignment explanation
Indices: 6856361--6856420 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
6856351 ACTTAAGAGA
*
6856361 GGGATTATCCCAATTTGTGTTCAGATT
1 GGGATTATCCCAATTTGGGTTCAGATT
*
6856388 GGGATTATCCCAATTTGGGTTTAGATT
1 GGGATTATCCCAATTTGGGTTCAGATT
6856415 GGGATT
1 GGGATT
6856421 GGTTTGGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.40
Consensus pattern (27 bp):
GGGATTATCCCAATTTGGGTTCAGATT
Found at i:6860199 original size:21 final size:21
Alignment explanation
Indices: 6860153--6860199 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6860143 AAAAATAAAT
*
6860153 TATAATAGTATTATAATATAC
1 TATAATAGTAATATAATATAC
6860174 T-TAATATGTAATATAATATA-
1 TATAATA-GTAATATAATATAC
6860194 TATAAT
1 TATAAT
6860200 TTCAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
TATAATAGTAATATAATATAC
Found at i:6860219 original size:22 final size:23
Alignment explanation
Indices: 6860189--6860241 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
6860179 ATGTAATATA
6860189 ATATATATAATTTCAA-AAAA-T
1 ATATATATAATTTCAATAAAACT
* *
6860210 ATAATATATATTTTTAATAAAACT
1 AT-ATATATAATTTCAATAAAACT
6860234 ATATATAT
1 ATATATAT
6860242 TTTATAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 12 0.44
23 10 0.37
24 3 0.11
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATATATAATTTCAATAAAACT
Found at i:6860238 original size:19 final size:18
Alignment explanation
Indices: 6860213--6860277 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
6860203 AAAAAATATA
6860213 ATATATATTTTTAATAAAACT
1 ATATATA-TTTT-AT-AAACT
6860234 ATATATATTTTATAAACT
1 ATATATATTTTATAAACT
* * *
6860252 ATACATATATATATATA-T
1 ATATATAT-TTTATAAACT
6860270 ATATATAT
1 ATATATAT
6860278 ATAAATATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
18 20 0.51
19 8 0.21
20 4 0.10
21 7 0.18
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATATATTTTATAAACT
Found at i:6860261 original size:20 final size:20
Alignment explanation
Indices: 6860213--6860259 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
6860203 AAAAAATATA
6860213 ATATATATTTTTAATAAAACT
1 ATATATA-TTTTAATAAAACT
6860234 ATATATATTTT-AT-AAACT
1 ATATATATTTTAATAAAACT
*
6860252 ATACATAT
1 ATATATAT
6860260 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 12 0.48
19 2 0.08
20 4 0.16
21 7 0.28
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATATTTTAATAAAACT
Found at i:6860304 original size:21 final size:23
Alignment explanation
Indices: 6860282--6860340 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
6860272 ATATATATAA
*
6860282 ATATAATATATATTTTCAAAAAT
1 ATATATTATATATTTTCAAAAAT
*
6860305 ATATATTATATATTTTTAAAAACT
1 ATATATTATATATTTTCAAAAA-T
*
6860329 ACAT-TTATATAT
1 ATATATTATATAT
6860341 ATATATTCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 28 0.88
24 4 0.12
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATTATATATTTTCAAAAAT
Found at i:6860310 original size:2 final size:2
Alignment explanation
Indices: 6860233--6860294 Score: 65
Period size: 2 Copynumber: 31.5 Consensus size: 2
6860223 TTAATAAAAC
* * *
6860233 TA TA TA TA T- TT TA TA AA CTA TA CA 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 TA TA TA TA TA
*
6860275 TA TA TA AA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
6860295 TTTCAAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.94
3 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6861281 original size:43 final size:43
Alignment explanation
Indices: 6861091--6861301 Score: 135
Period size: 43 Copynumber: 4.9 Consensus size: 43
6861081 TAAATGATTC
* * *
6861091 TTTGGATGACTTCCCTTCATGGGTTTAAGCCAAGTGA-ACTATT
1 TTTGGATGACTCCCCTTCACGAGTTTAAGCCAAGTGAGA-TATT
* * ** * *
6861134 TTCGAATGACTCATCTT--CGTAGGTTTAAGCCAAGGGAAATGATT
1 TTTGGATGACTCCCCTTCACG-A-GTTTAAGCCAAGTGAGAT-ATT
* * * * *
6861178 CTTCGTATGACTCCCCTTCACGA-TCTAATCCAAGTGAAGGAT-TC
1 -TTTGGATGACTCCCCTTCACGAGTTTAAGCCAAGTG-A-GATATT
* * *
6861222 TTTGGATAATTTCCCTTCACGAGTTTAAGCCAAGTGAGATATT
1 TTTGGATGACTCCCCTTCACGAGTTTAAGCCAAGTGAGATATT
** * *
6861265 TTTGGATGACTCCCCTTTGCGGGTTTAAGCTAAGTGA
1 TTTGGATGACTCCCCTTCACGAGTTTAAGCCAAGTGA
6861302 AATGATTCTT
Statistics
Matches: 126, Mismatches: 31, Indels: 22
0.70 0.17 0.12
Matches are distributed among these distances:
41 1 0.01
42 3 0.02
43 76 0.60
44 26 0.21
45 15 0.12
46 3 0.02
47 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (43 bp):
TTTGGATGACTCCCCTTCACGAGTTTAAGCCAAGTGAGATATT
Found at i:6861406 original size:131 final size:131
Alignment explanation
Indices: 6861026--6861425 Score: 396
Period size: 131 Copynumber: 3.0 Consensus size: 131
6861016 CGCTAATAAG
* * * * * * * *
6861026 TTAAGCCAAGTGAAATGATTATTCA-AATAACTCCCATTCGTGGGTCGAAGCCAGGTAAATGATT
1 TTAAGCCAAGTGAAATGATTCTTCAGAAGAA-TCCCCTTCGCGGGTCTAAACCAGGTGAAGGATT
* * * * * * **
6861090 CTTTGGATGACTTCCCTTCATGGGTTTAAGCCAAGTGAACTATTTTCGAATGACTCATCTTCGTA
65 CTTTGGATGACTTTCCTTCACGGGTTTAAGCCAAGTGAAATATTTTCG-GTGACTCACCTTTGCG
6861155 GGT
129 GGT
* * * * * * *
6861158 TTAAGCCAAGGGAAATGATTCTTC-GTATGACTCCCCTTCAC-GATCTAATCCAAGTGAAGGATT
1 TTAAGCCAAGTGAAATGATTCTTCAG-AAGAATCCCCTTCGCGGGTCTAAACCAGGTGAAGGATT
* * * * *
6861221 CTTTGGAT-AATTTCCCTTCACGAGTTTAAGCCAAGTGAGATATTTTTGGATGACTCCCCTTTGC
65 CTTTGGATGACTTT-CCTTCACGGGTTTAAGCCAAGTGAAATATTTTCGG-TGACTCACCTTTGC
6861285 GGGT
128 GGGT
* * *
6861289 TTAAGCTAAGTGAAATGATTCTTCAGAGGAATCCCCTTCGCGGGTCTAAACCAGGGGAAGGATTC
1 TTAAGCCAAGTGAAATGATTCTTCAGAAGAATCCCCTTCGCGGGTCTAAACCAGGTGAAGGATTC
* * * *
6861354 TTTGGATGACTTTCTTTCA-GGGTTTAAGCCAAGTGAAATGTTTTCAGGTGACTCTCCGTTGCGG
66 TTTGGATGACTTTCCTTCACGGGTTTAAGCCAAGTGAAATATTTTC-GGTGACTCACCTTTGCGG
6861418 GT
130 GT
6861420 TTAAGC
1 TTAAGC
6861426 TAGTCTTGTA
Statistics
Matches: 216, Mismatches: 44, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
130 3 0.01
131 144 0.67
132 63 0.29
133 6 0.03
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (131 bp):
TTAAGCCAAGTGAAATGATTCTTCAGAAGAATCCCCTTCGCGGGTCTAAACCAGGTGAAGGATTC
TTTGGATGACTTTCCTTCACGGGTTTAAGCCAAGTGAAATATTTTCGGTGACTCACCTTTGCGGG
T
Found at i:6861933 original size:28 final size:28
Alignment explanation
Indices: 6861901--6861959 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
6861891 CTTCCTATAA
6861901 AATATTATAATCATTACTATCAATCCAT
1 AATATTATAATCATTACTATCAATCCAT
6861929 AATATTATAATCATTACTATCAATCCAT
1 AATATTATAATCATTACTATCAATCCAT
6861957 AAT
1 AAT
6861960 TCTTCTACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (28 bp):
AATATTATAATCATTACTATCAATCCAT
Found at i:6875495 original size:2 final size:2
Alignment explanation
Indices: 6875488--6875515 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6875478 TACAATTACA
6875488 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
6875516 TGTCTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6875983 original size:12 final size:12
Alignment explanation
Indices: 6875966--6875991 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6875956 AGTGGATTGG
6875966 ATGACTACTAAC
1 ATGACTACTAAC
6875978 ATGACTACTAAC
1 ATGACTACTAAC
6875990 AT
1 AT
6875992 CGCTTGCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (12 bp):
ATGACTACTAAC
Found at i:6883258 original size:23 final size:23
Alignment explanation
Indices: 6883232--6883279 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
6883222 CTGACCCGAT
6883232 CCGACCCGA-CCTATTGACTTTGA
1 CCGACCCGATCC-ATTGACTTTGA
*
6883255 CCGACCCGATCCGTTGACTTTGA
1 CCGACCCGATCCATTGACTTTGA
6883278 CC
1 CC
6883280 AGAGTTGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.25
Consensus pattern (23 bp):
CCGACCCGATCCATTGACTTTGA
Found at i:6883317 original size:17 final size:17
Alignment explanation
Indices: 6883295--6883328 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6883285 TGACTTTGAC
*
6883295 CCAAAAAGTCAAATTTT
1 CCAAAAAATCAAATTTT
*
6883312 CCAAAAAATCATATTTT
1 CCAAAAAATCAAATTTT
6883329 AGGTTTTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (17 bp):
CCAAAAAATCAAATTTT
Found at i:6884498 original size:15 final size:15
Alignment explanation
Indices: 6884478--6884516 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
6884468 TGACATGTGC
6884478 CTTATTTTTGAAGTA
1 CTTATTTTTGAAGTA
6884493 CTTATTTTTGAAGTA
1 CTTATTTTTGAAGTA
6884508 CTTATTTTT
1 CTTATTTTT
6884517 ATGATGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.59
Consensus pattern (15 bp):
CTTATTTTTGAAGTA
Found at i:6885003 original size:18 final size:18
Alignment explanation
Indices: 6884980--6885025 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
6884970 AAGATGAGTG
*
6884980 CTAGACGTGGTCCTTGAA
1 CTAGACGTGGTCATTGAA
6884998 CTAGACGTGGTCATTGAA
1 CTAGACGTGGTCATTGAA
*
6885016 CTAGCCGTGG
1 CTAGACGTGG
6885026 GCAAGGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (18 bp):
CTAGACGTGGTCATTGAA
Found at i:6886308 original size:19 final size:20
Alignment explanation
Indices: 6886281--6886318 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6886271 AAGGCAAGCA
*
6886281 AATCTATGCAAGT-ATATAC
1 AATCGATGCAAGTAATATAC
6886300 AATCGATGCAAGTAATATA
1 AATCGATGCAAGTAATATA
6886319 GTAGTGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (20 bp):
AATCGATGCAAGTAATATAC
Found at i:6894586 original size:14 final size:14
Alignment explanation
Indices: 6894569--6894618 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
6894559 TTAAAACAAC
6894569 AAATAAAAAAATAA
1 AAATAAAAAAATAA
*
6894583 AAATAAAAACATTAA
1 AAATAAAAA-AATAA
* *
6894598 AAA-AACAACAT-A
1 AAATAAAAAAATAA
6894610 AAATAAAAA
1 AAATAAAAA
6894619 TAAAACAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.14
13 5 0.17
14 13 0.45
15 7 0.24
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:6894590 original size:35 final size:35
Alignment explanation
Indices: 6894532--6894623 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 35
6894522 AAATATCAAT
** * * *
6894532 ACAAATAAAAAAGCATAATTAAAATA-ATTAAAACA
1 ACAAATAAAAAAATAAAAATAAAA-ACATTAAAAAA
6894567 ACAAATAAAAAAATAAAAATAAAAACATTAAAAAA
1 ACAAATAAAAAAATAAAAATAAAAACATTAAAAAA
6894602 ACAACAT---AAAATAAAAATAAAA
1 ACAA-ATAAAAAAATAAAAATAAAA
6894624 CAAGTACAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 15 0.30
34 1 0.02
35 32 0.64
36 2 0.04
ACGTcount: A:0.75, C:0.08, G:0.01, T:0.16
Consensus pattern (35 bp):
ACAAATAAAAAAATAAAAATAAAAACATTAAAAAA
Found at i:6894739 original size:20 final size:20
Alignment explanation
Indices: 6894714--6894767 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
6894704 CAAAATGCAA
6894714 AAATCAAAATAACAGTAG-CT
1 AAATCAAAATAACA-TAGACT
*
6894734 AAATCAGAAACTAACATTGACT
1 AAATCA-AAA-TAACATAGACT
*
6894756 AAATTAAAATAA
1 AAATCAAAATAA
6894768 AACAAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 9 0.31
21 8 0.28
22 12 0.41
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.22
Consensus pattern (20 bp):
AAATCAAAATAACATAGACT
Found at i:6895813 original size:21 final size:21
Alignment explanation
Indices: 6895787--6895829 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6895777 TGGGGCAGGA
*
6895787 GAATGTGGCTTCTGGTTGGGG
1 GAATGTGGCTTCTGATTGGGG
* *
6895808 GAATGTGGGTTTTGATTGGGG
1 GAATGTGGCTTCTGATTGGGG
6895829 G
1 G
6895830 CTAGTTAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.05, G:0.49, T:0.35
Consensus pattern (21 bp):
GAATGTGGCTTCTGATTGGGG
Found at i:6896895 original size:22 final size:22
Alignment explanation
Indices: 6896870--6896914 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
6896860 TTTGTAGATG
*
6896870 TTTA-CTCTAAATATACAAAAGA
1 TTTATCTCTAAAGAT-CAAAAGA
*
6896892 TTTATCTCTTAAGATCAAAAGA
1 TTTATCTCTAAAGATCAAAAGA
6896914 T
1 T
6896915 GAAACCAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (22 bp):
TTTATCTCTAAAGATCAAAAGA
Found at i:6899310 original size:94 final size:94
Alignment explanation
Indices: 6899149--6899336 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
6899139 TGCCCTCCAT
6899149 GAACATATGCATGTGATGCTTAGAAGAGGAAAATTCCAATAATAGTTGCAACACTAACAATGTTG
1 GAACATATGCATGTGATGCTTAGAAGAGGAAAATTCCAATAATAGTTGCAACACTAACAATGTTG
6899214 TTTGCTTTGATAGAAACGACATTAGAGGG
66 TTTGCTTTGATAGAAACGACATTAGAGGG
6899243 GAACATATGCATGTGATGCTTAGAAGAGGAAAATTCCAATAATAGTTGCAACACTAACAATGTTG
1 GAACATATGCATGTGATGCTTAGAAGAGGAAAATTCCAATAATAGTTGCAACACTAACAATGTTG
6899308 TTTGCTTTGATAGAAACGACATTAGAGGG
66 TTTGCTTTGATAGAAACGACATTAGAGGG
6899337 TGTAGGTGCT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (94 bp):
GAACATATGCATGTGATGCTTAGAAGAGGAAAATTCCAATAATAGTTGCAACACTAACAATGTTG
TTTGCTTTGATAGAAACGACATTAGAGGG
Found at i:6899941 original size:33 final size:33
Alignment explanation
Indices: 6899904--6899971 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
6899894 AATGAGTTGA
6899904 AAGAATTGATTACATCTCATTTAAATAGAAAAC
1 AAGAATTGATTACATCTCATTTAAATAGAAAAC
6899937 AAGAATTGATTACATCTCATTTAAATAGAAAAC
1 AAGAATTGATTACATCTCATTTAAATAGAAAAC
6899970 AA
1 AA
6899972 ACGATAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (33 bp):
AAGAATTGATTACATCTCATTTAAATAGAAAAC
Found at i:6908302 original size:26 final size:25
Alignment explanation
Indices: 6908253--6908304 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
6908243 CCAATTCTCA
6908253 TAATTCTTTTTCTACAACACATATT
1 TAATTCTTTTTCTACAACACATATT
*
6908278 TAATTCCTTTTTGCTTCAACA-ATATT
1 TAATT-CTTTTT-CTACAACACATATT
6908304 T
1 T
6908305 TCCTTGTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 12 0.50
27 7 0.29
ACGTcount: A:0.29, C:0.19, G:0.02, T:0.50
Consensus pattern (25 bp):
TAATTCTTTTTCTACAACACATATT
Found at i:6909135 original size:21 final size:20
Alignment explanation
Indices: 6909106--6909163 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
6909096 AAATATCAAT
*
6909106 ACAAATAAAAACATAATTAAA
1 ACAATTAAAAACATAA-TAAA
*
6909127 ATAATTAAAACAACA-AATAAA
1 ACAATT-AAA-AACATAATAAA
*
6909148 ACAATAAAAAACATAA
1 ACAATTAAAAACATAA
6909164 AATAAAAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.13
20 5 0.17
21 12 0.40
22 5 0.17
23 4 0.13
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (20 bp):
ACAATTAAAAACATAATAAA
Found at i:6909149 original size:12 final size:11
Alignment explanation
Indices: 6909132--6909185 Score: 56
Period size: 12 Copynumber: 4.7 Consensus size: 11
6909122 TTAAAATAAT
6909132 TAAAACAACAAA
1 TAAAACAA-AAA
*
6909144 TAAAACAATAA
1 TAAAACAAAAA
6909155 -AAAACATAAAA
1 TAAAACA-AAAA
*
6909166 TAAAAGTAAAAA
1 TAAAA-CAAAAA
6909178 TAAAACAA
1 TAAAACAA
6909186 GTACAATGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 6 0.17
11 7 0.20
12 21 0.60
13 1 0.03
ACGTcount: A:0.76, C:0.09, G:0.02, T:0.13
Consensus pattern (11 bp):
TAAAACAAAAA
Found at i:6909166 original size:22 final size:21
Alignment explanation
Indices: 6909109--6909170 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
6909099 TATCAATACA
* *
6909109 AATAAAAACAT-AATTAAAAT
1 AATAAAAACATAAAATAAAAC
*
6909129 AATTAAAACA-ACAAATAAAAC
1 AATAAAAACATA-AAATAAAAC
6909150 AATAAAAAACATAAAATAAAA
1 AAT-AAAAACATAAAATAAAA
6909171 GTAAAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 9 0.26
21 10 0.29
22 14 0.41
23 1 0.03
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (21 bp):
AATAAAAACATAAAATAAAAC
Found at i:6911078 original size:42 final size:41
Alignment explanation
Indices: 6911006--6911095 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 41
6910996 TGGATAGTCT
* * *
6911006 GAAGGTCTTATCATCTTGCTCAAAAGACTTA-TAAATGGCCC
1 GAAGGACTTATCATCATGCTCAAAAGACTTACT-AATGGCCA
* *
6911047 GAAGGACTTATGCATCATGCTCGAAAGACTTACTGATGGCCA
1 GAAGGACTTAT-CATCATGCTCAAAAGACTTACTAATGGCCA
6911089 GAAGGAC
1 GAAGGAC
6911096 ATACTCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 10 0.24
42 31 0.74
43 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (41 bp):
GAAGGACTTATCATCATGCTCAAAAGACTTACTAATGGCCA
Found at i:6911315 original size:41 final size:42
Alignment explanation
Indices: 6911270--6911356 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
6911260 GTCCGAAGGT
* * * *
6911270 CTTATGGATGGCCCGAATGACTT-ATCAT-CTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCCTT-CTCGAAAGA
*
6911311 CTTATAGATGACCCGAAGGATTTAAGCATCCTTCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCCTTCTCGAAAGA
6911353 CTTA
1 CTTA
6911357 CTGATGCCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 19 0.49
42 17 0.44
43 3 0.08
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGACTTAAGCATCCTTCTCGAAAGA
Found at i:6913327 original size:10 final size:9
Alignment explanation
Indices: 6913311--6913378 Score: 70
Period size: 8 Copynumber: 7.7 Consensus size: 9
6913301 ATTTGATCGT
6913311 TTTTTTCTC
1 TTTTTTCTC
6913320 TCTTTTTCTC
1 T-TTTTTCTC
* *
6913330 -TTTTTATG
1 TTTTTTCTC
*
6913338 TTTTTTCTT
1 TTTTTTCTC
6913347 TCTTTTTC-C
1 T-TTTTTCTC
6913356 TTTTTTC-C
1 TTTTTTCTC
6913364 TTTTTTCTC
1 TTTTTTCTC
6913373 TTTTTT
1 TTTTTT
6913379 ATTTCCTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
8 20 0.40
9 16 0.32
10 14 0.28
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:6913367 original size:26 final size:27
Alignment explanation
Indices: 6913311--6913378 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
6913301 ATTTGATCGT
*
6913311 TTTTTTCTCTCTTTTTCTCTTTTTATG
1 TTTTTTCTCTCTTTTTCTCTTTTTATC
*
6913338 TTTTTTCTTTCTTTTTC-CTTTTT-TCC
1 TTTTTTCTCTCTTTTTCTCTTTTTAT-C
6913364 TTTTTTCTCT-TTTTT
1 TTTTTTCTCTCTTTTT
6913379 ATTTCCTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 6 0.16
26 15 0.41
27 16 0.43
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (27 bp):
TTTTTTCTCTCTTTTTCTCTTTTTATC
Found at i:6913385 original size:21 final size:22
Alignment explanation
Indices: 6913359--6913415 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 22
6913349 TTTTTCCTTT
*
6913359 TTTCCTTTTTTC-TCTTTTTTA
1 TTTCCTTTTTTCATATTTTTTA
*
6913380 TTTCCTTTATTTTCTATATTTTTTC
1 TTTCC-TT-TTTTC-ATATTTTTTA
6913405 TTTCCTTTTTT
1 TTTCCTTTTTT
6913416 TGCTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 5 0.17
22 2 0.07
23 9 0.30
24 2 0.07
25 12 0.40
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTCCTTTTTTCATATTTTTTA
Found at i:6913392 original size:25 final size:24
Alignment explanation
Indices: 6913373--6913427 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
6913363 CTTTTTTCTC
6913373 TTTTTTATTTCCTTTATTTTCTATA
1 TTTTTTATTTCCTTT-TTTTCTATA
*
6913398 TTTTTTCTTTCCTTTTTTTGCTATA
1 TTTTTTATTTCCTTTTTTT-CTATA
6913423 TTTTT
1 TTTTT
6913428 CTTCTTTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTTTATTTCCTTTTTTTCTATA
Found at i:6917209 original size:28 final size:29
Alignment explanation
Indices: 6917138--6917211 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 29
6917128 TAAAATAATT
* *
6917138 AAAACAACAAATAAAA-AATATGAAAATA
1 AAAACAAAAAATAAAACAACATGAAAATA
**
6917166 AAAACAGTAAA-AAAACAACAT-AAAATA
1 AAAACAAAAAATAAAACAACATGAAAATA
*
6917193 AAAATAAAAAATAAAACAA
1 AAAACAAAAAATAAAACAA
6917212 GTACAAGTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
27 18 0.47
28 20 0.53
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.12
Consensus pattern (29 bp):
AAAACAAAAAATAAAACAACATGAAAATA
Found at i:6918183 original size:65 final size:65
Alignment explanation
Indices: 6918077--6918200 Score: 198
Period size: 65 Copynumber: 1.9 Consensus size: 65
6918067 GGGGTAGGAG
*
6918077 CAGGTGGCTCCTGATTGGGGGAAAAGGTGGGTTTTGATTGGGTAATTT-GGGGGCTAGTTAGAGC
1 CAGGTGGCTCCTGATTGGGGGAAAAGCTGGGTTTTGATTGGGTAATTTGGGGGGCTAGTTAGAGC
*
6918141 CAGGTGGCTCCTGCTTGGGGGGGAAAA-CTGGGTTTTGATTGGGTAATTTGGGGGGCTAGT
1 CAGGTGGCTCCTGATT--GGGGGAAAAGCTGGGTTTTGATTGGGTAATTTGGGGGGCTAGT
6918201 CAGACCCGGG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
64 15 0.27
65 21 0.38
66 19 0.35
ACGTcount: A:0.17, C:0.10, G:0.43, T:0.30
Consensus pattern (65 bp):
CAGGTGGCTCCTGATTGGGGGAAAAGCTGGGTTTTGATTGGGTAATTTGGGGGGCTAGTTAGAGC
Found at i:6921442 original size:20 final size:20
Alignment explanation
Indices: 6921417--6921470 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
6921407 CAAAATGCAA
6921417 AAATCAAAATAACAGTAG-CT
1 AAATCAAAATAACA-TAGACT
*
6921437 AAATCAGAAACTAACATTGACT
1 AAATCA-AAA-TAACATAGACT
*
6921459 AAATTAAAATAA
1 AAATCAAAATAA
6921471 AACAAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 9 0.31
21 8 0.28
22 12 0.41
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.22
Consensus pattern (20 bp):
AAATCAAAATAACATAGACT
Found at i:6936658 original size:40 final size:40
Alignment explanation
Indices: 6936581--6936663 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
6936571 TTTGGTATTA
* * ***
6936581 ATACTCATTGTGGTATCCATACTGAAGAAGGCGAGTATCG
1 ATACTCATTGGGGTATCAATACTGAAGAAGAAAAGTATCG
6936621 ATACTCATTGGGGTATCAATACTG-AGAATGAAAAGTATCG
1 ATACTCATTGGGGTATCAATACTGAAGAA-GAAAAGTATCG
6936661 ATA
1 ATA
6936664 TTCCCTGATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.11
40 33 0.89
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (40 bp):
ATACTCATTGGGGTATCAATACTGAAGAAGAAAAGTATCG
Done.