Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000254.1 Hibiscus syriacus cultivar Beakdansim tig00000465_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: 114919
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5126 original size:17 final size:17
Alignment explanation
Indices: 5104--5136 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5094 AACTGAATGA
5104 ATAACTTATAAAGAAAT
1 ATAACTTATAAAGAAAT
5121 ATAACTTATAAAGAAA
1 ATAACTTATAAAGAAA
5137 GATGCAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (17 bp):
ATAACTTATAAAGAAAT
Found at i:7167 original size:29 final size:29
Alignment explanation
Indices: 7129--7217 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
7119 ATATATTTTA
*
7129 TTTTAGTCTTTTAATTTCACTACTTTAATT
1 TTTTA-TCTTTTAATTTCAATACTTTAATT
* *
7159 TTTTATCTTTTTAATTT--TTGCTTTACATT
1 TTTTATC-TTTTAATTTCAATACTTTA-ATT
* *
7188 TTTCAATATTTTAATTTCAATACTTTAATT
1 TTT-TATCTTTTAATTTCAATACTTTAATT
7218 ATTACATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
28 6 0.12
29 17 0.35
30 19 0.40
31 6 0.12
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTATCTTTTAATTTCAATACTTTAATT
Found at i:7205 original size:14 final size:14
Alignment explanation
Indices: 7188--7217 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7178 GCTTTACATT
*
7188 TTTCAATATTTTAA
1 TTTCAATACTTTAA
7202 TTTCAATACTTTAA
1 TTTCAATACTTTAA
7216 TT
1 TT
7218 ATTACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTCAATACTTTAA
Found at i:9155 original size:194 final size:195
Alignment explanation
Indices: 8812--9202 Score: 775
Period size: 194 Copynumber: 2.0 Consensus size: 195
8802 CAGTTAGGTT
8812 AATTTTTCCAAACAAAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
1 AATTTTTCCAAACAAAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
8877 ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
66 ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
8942 TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
131 TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
9007 AATTTTTCCAAAC-AAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
1 AATTTTTCCAAACAAAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
9071 ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
66 ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
9136 TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
131 TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
9201 AA
1 AA
9203 AGGTGTTGAC
Statistics
Matches: 196, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
194 183 0.93
195 13 0.07
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (195 bp):
AATTTTTCCAAACAAAGCATGGAACTAGAATGCATGATGTTAGGATTTATACCTTAATAAATAGA
ATTTTTTTCTTTCCATTAATTGGTACTAACCATTTTATTTTTTCTTATTTTATTTTTTTCATGCA
TGTTATTTTTGCTCTAATTTGTTTATATTGATTTCTTTTTGCATTGCATGATCATGGAATAACCA
Found at i:9771 original size:30 final size:30
Alignment explanation
Indices: 9735--9792 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
9725 AGAATGTCAT
9735 GGAAGAAGTTGCAATCCAGACAAGCAATAC
1 GGAAGAAGTTGCAATCCAGACAAGCAATAC
* *
9765 GGAAGAAGTTGCAGTCTAGACAAGCAAT
1 GGAAGAAGTTGCAATCCAGACAAGCAAT
9793 TTGGCTCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.16
Consensus pattern (30 bp):
GGAAGAAGTTGCAATCCAGACAAGCAATAC
Found at i:10021 original size:14 final size:14
Alignment explanation
Indices: 9998--10045 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
9988 TGCATTTGCA
9998 TTTTGCATTTTTAC
1 TTTTGCATTTTTAC
* *
10012 TTTTGTATTTATA-
1 TTTTGCATTTTTAC
10025 TTTT-CATTTTTAC
1 TTTTGCATTTTTAC
*
10038 ATTTGCAT
1 TTTTGCAT
10046 CTTTGCATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 6 0.22
13 7 0.26
14 14 0.52
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTGCATTTTTAC
Found at i:10392 original size:29 final size:29
Alignment explanation
Indices: 10350--10405 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
10340 CCATGGAGAG
10350 AAACCCTTATAGGATCTTGTTGTGAAAAA
1 AAACCCTTATAGGATCTTGTTGTGAAAAA
10379 AAACCCTTATAGGATCTTGTTGTGAAA
1 AAACCCTTATAGGATCTTGTTGTGAAA
10406 GATTTGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (29 bp):
AAACCCTTATAGGATCTTGTTGTGAAAAA
Found at i:12494 original size:72 final size:72
Alignment explanation
Indices: 12398--12531 Score: 223
Period size: 72 Copynumber: 1.9 Consensus size: 72
12388 TACAATAAAG
*
12398 CTTGAGTTATCCCCCTAAAGCAATTGGTTAGTAGCCCCAGCTTTATGGATAATATTCAGCTAGTT
1 CTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAGTT
12463 TGTTATT
66 TGTTATT
* * **
12470 CTTGAGTTGTCCCCCTAAAGCAATTGGTTAATCGCCCTGGCTTTATGGATAATATTCAGCTA
1 CTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTA
12532 ACCTATTATA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (72 bp):
CTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAGTT
TGTTATT
Found at i:15351 original size:30 final size:27
Alignment explanation
Indices: 15290--15343 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
15280 ATTACTTCTT
15290 AAGTTTGTGACAACATGAAGAGAATTC
1 AAGTTTGTGACAACATGAAGAGAATTC
15317 AAGTTTGTGACAACATGAAGAGAATTC
1 AAGTTTGTGACAACATGAAGAGAATTC
15344 CTCAAGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (27 bp):
AAGTTTGTGACAACATGAAGAGAATTC
Found at i:15646 original size:35 final size:35
Alignment explanation
Indices: 15595--15661 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
15585 TTCAACCAGA
15595 AATAGAATATTGGGGCATT-TT-GAAGGCTCATAGT
1 AATAGAATATTGGGGCATTCTTGGAA-GCTCATAGT
*
15629 AATATGAATATTTGGGCATTCTTGGAAGCTCAT
1 AATA-GAATATTGGGGCATTCTTGGAAGCTCAT
15662 CTCAGCAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 4 0.14
35 14 0.48
36 8 0.28
37 3 0.10
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (35 bp):
AATAGAATATTGGGGCATTCTTGGAAGCTCATAGT
Found at i:17208 original size:22 final size:22
Alignment explanation
Indices: 17174--17249 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
17164 TCTACATTCC
*
17174 TCAAAGATGATAGATTCTCTCT
1 TCAAAAATGATAGATTCTCTCT
*
17196 TCAAAAATTATAGATTCTCT-T
1 TCAAAAATGATAGATTCTCTCT
* * * *
17217 TCCAAATATGATGGATTATCTTT
1 T-CAAAAATGATAGATTCTCTCT
*
17240 TCAAAGATGA
1 TCAAAAATGA
17250 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
21 2 0.04
22 41 0.91
23 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
TCAAAAATGATAGATTCTCTCT
Found at i:17859 original size:112 final size:113
Alignment explanation
Indices: 17595--18044 Score: 534
Period size: 112 Copynumber: 3.9 Consensus size: 113
17585 TAACAAATAT
* * * *
17595 TCGAATCCATCACTCAATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATATGA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGA
* *
17660 AGAA-GAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTCGC
66 AGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * *
17707 TCGAATTCATCACTCGGTGAATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGA
*
17772 AGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC
66 AGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
17820 TCGAATTCATCACTCGATGGATCAACATTTCCA-GAAGAGTTCATAATGAGAAAAATTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGA
* *
17884 AAAATG-AGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTTTGC
66 AGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * *
17931 TCGACGCTATCA-CAAAAGAAGATAGATCAGCATCAACATTTCCA-GAAGAGTTCATAATGAGAA
1 TCGA--AT-TCATC------A-CTCGAT--GGATCAACATTGCCAGGAAGAGTTCATAATGAGAA
* * *
17994 GAACTCATCTGAAGAAT-AAGAAGAATTTCATAATGAGAAGAATTTATTCAA
54 GAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
18045 ACTTGCCTTA
Statistics
Matches: 294, Mismatches: 30, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
111 43 0.15
112 96 0.33
113 71 0.24
114 3 0.01
119 1 0.00
120 4 0.01
122 76 0.26
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (113 bp):
TCGAATTCATCACTCGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGA
AGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:27626 original size:35 final size:34
Alignment explanation
Indices: 27541--27627 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
27531 ATTTGGTATT
*
27541 TAAATACAACAAACTTACAATAAGAATTAAATAG
1 TAAATACAACAAAATTACAATAAGAATTAAATAG
* * *
27575 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATAG
27613 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
27628 ACTGAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATAG
Found at i:29947 original size:18 final size:17
Alignment explanation
Indices: 29915--29956 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
29905 GAATTATATT
*
29915 AGTAAAATATTAAATAA
1 AGTAAATTATTAAATAA
29932 AGTAAATTACTTAAATAA
1 AGTAAATTA-TTAAATAA
*
29950 ATTAAAT
1 AGTAAAT
29957 ACATAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (17 bp):
AGTAAATTATTAAATAA
Found at i:30499 original size:33 final size:32
Alignment explanation
Indices: 30462--30554 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 32
30452 ATATCAAATG
30462 ATTAAATTATTAAATTTTAAAAATATAAAATTT
1 ATTAAA-TATTAAATTTTAAAAATATAAAATTT
30495 ATTAAATATTTAAATTTTAAAAA-AT--AATTT
1 ATTAAATA-TTAAATTTTAAAAATATAAAATTT
**
30525 ATTTGATATTAAATTTTTTAAAAATATAAA
1 ATTAAATATTAAA--TTTTAAAAATATAAA
30555 TATAAATTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
29 5 0.10
30 11 0.21
31 9 0.17
32 6 0.12
33 20 0.38
34 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
ATTAAATATTAAATTTTAAAAATATAAAATTT
Found at i:30519 original size:18 final size:18
Alignment explanation
Indices: 30471--30525 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
30461 GATTAAATTA
30471 TTAAATTTT-AAAAATA-
1 TTAAATTTTAAAAAATAT
* **
30487 -TAAAATTTATTAAATAT
1 TTAAATTTTAAAAAATAT
30504 TTAAATTTTAAAAAATAAT
1 TTAAATTTTAAAAAAT-AT
30523 TTA
1 TTA
30526 TTTGATATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 7 0.24
16 5 0.17
18 12 0.41
19 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAATTTTAAAAAATAT
Found at i:30526 original size:30 final size:30
Alignment explanation
Indices: 30462--30550 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 30
30452 ATATCAAATG
30462 ATTAAAT-TATTAAATTTTAAAAATATAAAATTT
1 ATTAAATAT-TTAAATTTTAAAAA-AT--AATTT
30495 ATTAAATATTTAAATTTTAAAAAATAATTT
1 ATTAAATATTTAAATTTTAAAAAATAATTT
** *
30525 ATTTGATA-TTAAATTTTTTAAAAATA
1 ATTAAATATTTAAA-TTTTAAAAAATA
30551 TAAATATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
29 5 0.10
30 22 0.43
32 2 0.04
33 21 0.41
34 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
ATTAAATATTTAAATTTTAAAAAATAATTT
Found at i:33615 original size:15 final size:16
Alignment explanation
Indices: 33589--33618 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33579 ATAATCATTT
33589 TATTATAAATAATTAA
1 TATTATAAATAATTAA
33605 TATTA-AAATAATTA
1 TATTATAAATAATTA
33619 TAACTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTATAAATAATTAA
Found at i:34222 original size:4 final size:4
Alignment explanation
Indices: 34213--34269 Score: 60
Period size: 4 Copynumber: 13.2 Consensus size: 4
34203 CTAAACAAGG
* *
34213 ATAA ATAA ATAAA ATAA CTAA ATGAA GATAA ATAA ATAA ATAC ATGAA
1 ATAA ATAA AT-AA ATAA ATAA AT-AA -ATAA ATAA ATAA ATAA AT-AA
34261 ATAA ATAA A
1 ATAA ATAA A
34270 AAGGAATGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 32 0.71
5 11 0.24
6 2 0.04
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:34232 original size:27 final size:27
Alignment explanation
Indices: 34201--34252 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
34191 AATATAATAA
34201 AACTAAA-CAAGGATAAATAAATAAAAT
1 AACTAAATCAA-GATAAATAAATAAAAT
*
34228 AACTAAATGAAGATAAATAAATAAA
1 AACTAAATCAAGATAAATAAATAAA
34253 TACATGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (27 bp):
AACTAAATCAAGATAAATAAATAAAAT
Found at i:34307 original size:2 final size:2
Alignment explanation
Indices: 34300--34333 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
34290 AATAATTATG
*
34300 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34334 CATTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:34338 original size:14 final size:14
Alignment explanation
Indices: 34295--34339 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
34285 ATTAAAATAA
*
34295 TTATGTATATATAT
1 TTATATATATATAT
*
34309 ATATATATATATAT
1 TTATATATATATAT
*
34323 TTATATATATACAT
1 TTATATATATATAT
34337 TTA
1 TTA
34340 AAAAAATAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (14 bp):
TTATATATATATAT
Found at i:34548 original size:12 final size:12
Alignment explanation
Indices: 34531--34555 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34521 TGTCTAAAAC
34531 ATTTATATATAT
1 ATTTATATATAT
34543 ATTTATATATAT
1 ATTTATATATAT
34555 A
1 A
34556 ATAAAATAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:35918 original size:3 final size:3
Alignment explanation
Indices: 35910--35965 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
35900 AATAAAATAA
*
35910 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAA AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
35958 AAC AAC AA
1 AAC AAC AA
35966 TAATAATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:35970 original size:3 final size:3
Alignment explanation
Indices: 35964--35996 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
35954 CAACAACAAC
35964 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35997 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:36001 original size:3 final size:3
Alignment explanation
Indices: 35995--36025 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35985 AATAATAATA
35995 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
36026 ATAATGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:37865 original size:30 final size:30
Alignment explanation
Indices: 37831--37899 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
37821 CTTGGTTCTG
37831 ATACTATTTAACA-TGAGTGGCCAAGTCCCT
1 ATACTATTTAACATTG-GTGGCCAAGTCCCT
**
37861 ATACTATTTGGCATTGGTGGCCAAGTCCCT
1 ATACTATTTAACATTGGTGGCCAAGTCCCT
*
37891 GTACTATTT
1 ATACTATTT
37900 GGTGCTTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (30 bp):
ATACTATTTAACATTGGTGGCCAAGTCCCT
Found at i:38253 original size:24 final size:23
Alignment explanation
Indices: 38221--38270 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
38211 TCAAAAGGTG
* *
38221 AAAAAGCTTTATTAAAAAGTTTT
1 AAAAAGCTTTATGAAAAAATTTT
38244 AAAAATGCTTTATGAAAAAATTTT
1 AAAAA-GCTTTATGAAAAAATTTT
38268 AAA
1 AAA
38271 TAACGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (23 bp):
AAAAAGCTTTATGAAAAAATTTT
Found at i:43722 original size:27 final size:26
Alignment explanation
Indices: 43691--43750 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
43681 AATATTGTCA
*
43691 AACTAAAC-AAGTATAAGTAAATAACAT
1 AACTAAACGAAG-ATAAATAAATAA-AT
43718 AACTAAACGAAGATAAATAAATAAAT
1 AACTAAACGAAGATAAATAAATAAAT
*
43744 AAATAAA
1 AACTAAA
43751 TATATGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 8 0.27
27 19 0.63
28 3 0.10
ACGTcount: A:0.65, C:0.08, G:0.07, T:0.20
Consensus pattern (26 bp):
AACTAAACGAAGATAAATAAATAAAT
Found at i:43739 original size:4 final size:4
Alignment explanation
Indices: 43730--43767 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
43720 CTAAACGAAG
*
43730 ATAA ATAA ATAA ATAA ATAA ATAT ATGAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA A
43768 AAGAATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 28 0.90
5 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:44038 original size:2 final size:2
Alignment explanation
Indices: 44026--44085 Score: 111
Period size: 2 Copynumber: 29.5 Consensus size: 2
44016 ATACATACAA
44026 AT AT CAT 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
44069 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
44086 ATAAAATAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 55 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44260 original size:29 final size:29
Alignment explanation
Indices: 44204--44261 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
44194 TACACATATG
* * * * *
44204 AAAATATAAGGGCTAAATAAAGATAAATA
1 AAAATATAAGGACCAAAGAAAAAAAAATA
44233 AAAATATAAGGACCAAAGAAAAAAAAATA
1 AAAATATAAGGACCAAAGAAAAAAAAATA
44262 GTAACATAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (29 bp):
AAAATATAAGGACCAAAGAAAAAAAAATA
Found at i:46810 original size:12 final size:12
Alignment explanation
Indices: 46793--46820 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
46783 TGCATGGGAT
46793 GGTGGTGTTCAG
1 GGTGGTGTTCAG
46805 GGTGGTGTTCAG
1 GGTGGTGTTCAG
46817 GGTG
1 GGTG
46821 TTGCTACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.54, T:0.32
Consensus pattern (12 bp):
GGTGGTGTTCAG
Found at i:49603 original size:66 final size:65
Alignment explanation
Indices: 49497--49657 Score: 295
Period size: 66 Copynumber: 2.5 Consensus size: 65
49487 GTTGAGCTTC
49497 TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGCAGCAGTAATATATGTTT
1 TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGCAGCAGTAATATATG-TT
49562 T
65 T
*
49563 TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGTAGCAGTAATATATGTTT
1 TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGCAGCAGTAATATATGTTT
*
49628 TTTTTGTGTATGGCAAATATATGCCTAACT
1 TTTTTGTGTATGGCAAATATCTGCCTAACT
49658 CAAGAATCAA
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
65 32 0.34
66 61 0.66
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (65 bp):
TTTTTGTGTATGGCAAATATCTGCCTAACTTCATATGATATACCTTGCAGCAGTAATATATGTTT
Found at i:51497 original size:25 final size:25
Alignment explanation
Indices: 51469--51522 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
51459 TATAATATGT
51469 TTTATTC-CTTCTAAAATTTTATAAG
1 TTTATTCTC-TCTAAAATTTTATAAG
*
51494 TTTATTTTCTCTAAAATTTTATAAG
1 TTTATTCTCTCTAAAATTTTATAAG
51519 TTTA
1 TTTA
51523 CCTCTAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTATTCTCTCTAAAATTTTATAAG
Found at i:52117 original size:341 final size:331
Alignment explanation
Indices: 51452--52410 Score: 1450
Period size: 341 Copynumber: 2.9 Consensus size: 331
51442 GCATTATGCC
*
51452 TTTTATTTATAATATGTTTTATTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
1 TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
* *
51517 AGTTTACCTCTAACATAAAATCTTGAATTAAG-----TTTTT--TTTT-C-TCTAGCTTGAGATT
66 AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTTTTTTCATTTTCCTTCTATCTTGAGATT
51573 AATTTGAAAATCCACAAATTTATAATCTAGAAAAAAATAATTGATTTGAGGTTTTTTCGATTTCT
131 AATTTGAAAATCCACAAATTTATAATCTAGAAAAAAATAA-TGATTTGAGGTTTTTTCGATTTCT
** * * *
51638 TTATTTTTTTCCTAGTCCTGTTCTCCTAAATTATTCAGTCTTCCTAATTTGTTTATCTATAAGTT
195 TTA--TTTTTCCCGGTCCTATTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAGTT
* * *
51703 TTACTTGCAATCTTTTTGTTTCTTCTTCTCTTCGAATATGTTATCAATAATTAAGTAAGGACGAA
258 TTACTTGCAATCTTTTTGTTTCTTCTGCTGTTTGAATATGTTATCAATAATTAAGTAAGGACGAA
51768 TCTTATTATTTTTAT
323 --TT-TTA---TTAT
* * *
51783 TTTTATTTATAATATGTTTTCCTCTTTTTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
1 TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
* *
51848 AGTTTACCTTTAACATAAAATCTTGAATTTAGTTTTTTTTTTCATTTTCCTTCTATCTTGAGATT
66 AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTTTTTTCATTTTCCTTCTATCTTGAGATT
*
51913 AATTTGAAAATCCACAAATTTATAACCTAGAAAAAAAAATGAATGATTTGAGGTTTTTTCGATTT
131 AATTTGAAAATCCACAAATTTATAATCTAG--AAAAAAAT-AATGATTTGAGGTTTTTTCGATTT
*
51978 CTTTATTTTTCCCCGGTCCTCTTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAGT
193 CTTTATTTTT-CCCGGTCCTATTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAGT
* *
52043 TTTACTTGCAATCTTTTTGTTTCTTCTGCTGTTTGAATCTGTTATCAATAATTAAGTAAGGACGG
257 TTTACTTGCAATCTTTTTGTTTCTTCTGCTGTTTGAATATGTTATCAATAATTAAGTAAGGACGA
52108 ATTTTATTAT
322 ATTTTATTAT
* *
52118 TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATGAGTTTACTTTCTCTAAAATTTTATA
1 TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
* *
52183 AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTTATTTTCATTTTCCTTCTCTATTGAGAT
66 AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTT-TTTTCATTTTCCTTCTATCTTGAGAT
*
52248 TAAGTTGAAAATCCACAAATTTATAATCTAGAAAAAAATAAATGATTTGAGGTTTTTTCGATTTC
130 TAATTTGAAAATCCACAAATTTATAATCTAGAAAAAAAT-AATGATTTGAGGTTTTTTCGATTTC
* *
52313 TTTATTTTTCCCGGTTCTATTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAATTT
194 TTTATTTTTCCCGGTCCTATTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAGTTT
* * *
52378 CAATTGCAATCTTTTTGTTTCTCCTGCTGTTTG
259 TACTTGCAATCTTTTTGTTTCTTCTGCTGTTTG
52411 TCAAAAATTT
Statistics
Matches: 578, Mismatches: 36, Indels: 26
0.90 0.06 0.04
Matches are distributed among these distances:
331 91 0.16
333 83 0.14
334 42 0.07
335 100 0.17
336 58 0.10
338 7 0.01
339 3 0.01
340 47 0.08
341 110 0.19
342 35 0.06
343 2 0.00
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (331 bp):
TTTTATTTATAATATGTTTTCTTCCTTCTAAAATTTTATAAGTTTATTTTCTCTAAAATTTTATA
AGTTTACCTATAACATAAAATCTTGAATTAAGTTTTTTTTTTCATTTTCCTTCTATCTTGAGATT
AATTTGAAAATCCACAAATTTATAATCTAGAAAAAAATAATGATTTGAGGTTTTTTCGATTTCTT
TATTTTTCCCGGTCCTATTCTCCCAAATTCTTCAGTCTTCCTAATTTGTTTATCTATAAGTTTTA
CTTGCAATCTTTTTGTTTCTTCTGCTGTTTGAATATGTTATCAATAATTAAGTAAGGACGAATTT
TATTAT
Found at i:55839 original size:6 final size:6
Alignment explanation
Indices: 55828--55852 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55818 AGCTTTGAAG
55828 GCGAGA GCGAGA GCGAGA GCGAGA G
1 GCGAGA GCGAGA GCGAGA GCGAGA G
55853 AGGGGGTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.52, T:0.00
Consensus pattern (6 bp):
GCGAGA
Found at i:72575 original size:20 final size:20
Alignment explanation
Indices: 72525--72593 Score: 52
Period size: 20 Copynumber: 3.5 Consensus size: 20
72515 CGTAACGCGA
* *
72525 TTTCAAATTTGCAACAT-GG
1 TTTCAAATTCGCAACATAGT
* *
72544 ATTCTAATTTCGCAACATAGT
1 TTTC-AAATTCGCAACATAGT
*
72565 TTTCAAATTCGTAAC-TCAGT
1 TTTCAAATTCGCAACAT-AGT
*
72585 TTTAAAATT
1 TTTCAAATT
72594 TGGAACTCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 4 0.10
20 31 0.79
21 4 0.10
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTCAAATTCGCAACATAGT
Found at i:72600 original size:20 final size:20
Alignment explanation
Indices: 72562--72602 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
72552 TTCGCAACAT
* *
72562 AGTTTTCAAATTCGTAACTC
1 AGTTTTAAAATTCGGAACTC
*
72582 AGTTTTAAAATTTGGAACTC
1 AGTTTTAAAATTCGGAACTC
72602 A
1 A
72603 AATTTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
AGTTTTAAAATTCGGAACTC
Found at i:73243 original size:14 final size:14
Alignment explanation
Indices: 73220--73251 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
73210 CGATTTTAGT
73220 TTTCGCGTTGCGAA
1 TTTCGCGTTGCGAA
*
73234 TTTCGTGTTGCGAA
1 TTTCGCGTTGCGAA
73248 TTTC
1 TTTC
73252 ATTTTCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (14 bp):
TTTCGCGTTGCGAA
Found at i:73257 original size:34 final size:34
Alignment explanation
Indices: 73219--73284 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
73209 GCGATTTTAG
* *
73219 TTTTCGCGTTGCGAATTTCGTGTTGCGAATTTCA
1 TTTTCGAGTTGCGAATTTCATGTTGCGAATTTCA
*
73253 TTTTCGAGTTGCGATTTTCATGTTGCGAATTT
1 TTTTCGAGTTGCGAATTTCATGTTGCGAATTT
73285 AAGTTTCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.47
Consensus pattern (34 bp):
TTTTCGAGTTGCGAATTTCATGTTGCGAATTTCA
Found at i:73263 original size:20 final size:20
Alignment explanation
Indices: 73234--73273 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
73224 GCGTTGCGAA
*
73234 TTTCGTGTTGCGAATTTCAT
1 TTTCGAGTTGCGAATTTCAT
*
73254 TTTCGAGTTGCGATTTTCAT
1 TTTCGAGTTGCGAATTTCAT
73274 GTTGCGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGAGTTGCGAATTTCAT
Found at i:74841 original size:42 final size:42
Alignment explanation
Indices: 74787--74934 Score: 197
Period size: 42 Copynumber: 3.5 Consensus size: 42
74777 ACCCCCCACT
* * ** * *
74787 TCGACACCGAGATTCATCACCTCATCGAGCCTCTTCTCCACT
1 TCGACACCGAGATCCATCACCTGATCGAGCCGATTCTACACC
74829 TCGACACCGAGATCCATCACCTGATCGAGCCGATTCTACACC
1 TCGACACCGAGATCCATCACCTGATCGAGCCGATTCTACACC
* * *
74871 TCAACACTGAGAACCATCACCTGATCGAGCCGATTCTACACC
1 TCGACACCGAGATCCATCACCTGATCGAGCCGATTCTACACC
* *
74913 TCGACACCGAGAGCCATTACCT
1 TCGACACCGAGATCCATCACCT
74935 ATTTCATCAC
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (42 bp):
TCGACACCGAGATCCATCACCTGATCGAGCCGATTCTACACC
Found at i:75056 original size:21 final size:21
Alignment explanation
Indices: 75030--75073 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
75020 CTTCACCTCC
*
75030 ACATGATGAGTTAGGTGCTTT
1 ACATGATGAGGTAGGTGCTTT
*
75051 ACATGATGAGGTCGGTGCTTT
1 ACATGATGAGGTAGGTGCTTT
75072 AC
1 AC
75074 GTGACGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.34
Consensus pattern (21 bp):
ACATGATGAGGTAGGTGCTTT
Found at i:75132 original size:21 final size:21
Alignment explanation
Indices: 75107--75199 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
75097 GAGGTAGGGT
*
75107 CTTTACGTGGCGAGGTAGCTG
1 CTTTACGTGGTGAGGTAGCTG
* * ** *
75128 TTTTACGTGATGA-CAATGGTG
1 CTTTACGTGGTGAGGTA-GCTG
*
75149 CTTTACGTGGTGAGGTATCTG
1 CTTTACGTGGTGAGGTAGCTG
75170 CTTTACGTGGTGAGGTAGCTG
1 CTTTACGTGGTGAGGTAGCTG
*
75191 CTCTACGTG
1 CTTTACGTG
75200 AGATTGTTTC
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.96
22 1 0.02
ACGTcount: A:0.16, C:0.16, G:0.33, T:0.34
Consensus pattern (21 bp):
CTTTACGTGGTGAGGTAGCTG
Found at i:75318 original size:4 final size:4
Alignment explanation
Indices: 75309--75346 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
75299 TTTTTTGGTA
* *
75309 TTAT TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
75347 TTAGCGGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:75536 original size:21 final size:21
Alignment explanation
Indices: 75512--75562 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
75502 ATTCACCTGT
*
75512 CATCGTTCAAGAGGCTCATCC
1 CATCGTTCAAGAGGCCCATCC
*
75533 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCATCC
75554 CATCGTTCA
1 CATCGTTCA
75563 GGATACACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCATCC
Found at i:75573 original size:21 final size:21
Alignment explanation
Indices: 75530--75587 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
75520 AAGAGGCTCA
* ** *
75530 TCCCATCGTTCAAGAGGCCCC
1 TCCCATCGTTCAGGATACACC
75551 TCCCATCGTTCAGGATACACC
1 TCCCATCGTTCAGGATACACC
*
75572 TCCCACCGTTCAGGAT
1 TCCCATCGTTCAGGAT
75588 CCATATGGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.22
Consensus pattern (21 bp):
TCCCATCGTTCAGGATACACC
Found at i:77049 original size:13 final size:13
Alignment explanation
Indices: 77031--77067 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
77021 TTTGGTAATC
77031 CCCGCCCCGATTA
1 CCCGCCCCGATTA
*
77044 CCCGCCCCAATTA
1 CCCGCCCCGATTA
*
77057 CCCGACCCGAT
1 CCCGCCCCGAT
77068 AAATATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.54, G:0.14, T:0.14
Consensus pattern (13 bp):
CCCGCCCCGATTA
Found at i:77208 original size:12 final size:12
Alignment explanation
Indices: 77191--77216 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
77181 ACCCGATTCT
77191 CGGCCCAATACC
1 CGGCCCAATACC
77203 CGGCCCAATACC
1 CGGCCCAATACC
77215 CG
1 CG
77217 TTTAAATAAC
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:0.23, C:0.50, G:0.19, T:0.08
Consensus pattern (12 bp):
CGGCCCAATACC
Found at i:77634 original size:14 final size:15
Alignment explanation
Indices: 77615--77645 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
77605 GAAAATAAAA
77615 TTCGTGTTGCG-ATT
1 TTCGTGTTGCGAATT
77629 TTCGTGTTGCGAATT
1 TTCGTGTTGCGAATT
77644 TT
1 TT
77646 ATTTTCGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.10, C:0.13, G:0.26, T:0.52
Consensus pattern (15 bp):
TTCGTGTTGCGAATT
Found at i:77928 original size:18 final size:18
Alignment explanation
Indices: 77905--77940 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
77895 AAGGCGGTTG
*
77905 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
77923 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
77941 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:80238 original size:24 final size:24
Alignment explanation
Indices: 80204--80257 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
80194 CTAAAACATA
80204 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
80228 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
80252 ATCAAA
1 ATCAAA
80258 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:81195 original size:21 final size:20
Alignment explanation
Indices: 81169--81323 Score: 102
Period size: 20 Copynumber: 7.7 Consensus size: 20
81159 CAAAACATTT
81169 GTGTTGCGAATTTGAAATTCC
1 GTGTTGCGAATTTGAAATT-C
**
81190 GTGTTGCGTAA-AAGAAATTC
1 GTGTTGCG-AATTTGAAATTC
* **
81210 GAGTTGCGAAATCAGAAA-TC
1 GTGTTGCG-AATTTGAAATTC
* **
81230 GAGTTGCGAATTCAAAATTCC
1 GTGTTGCGAATTTGAAATT-C
* *
81251 GTGTTGTGAATTTGGAAACT-
1 GTGTTGCGAATTT-GAAATTC
* * *
81271 GTGTTGCGAAATTGGAGTTC
1 GTGTTGCGAATTTGAAATTC
*
81291 GTGTTGCGAATTTGACA-TC
1 GTGTTGCGAATTTGAAATTC
*
81310 GCGTTGCGAATTTG
1 GTGTTGCGAATTTG
81324 TTGGTTATTT
Statistics
Matches: 105, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
19 24 0.23
20 45 0.43
21 30 0.29
22 6 0.06
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (20 bp):
GTGTTGCGAATTTGAAATTC
Found at i:81662 original size:22 final size:22
Alignment explanation
Indices: 81615--81662 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
81605 AAATTTAGCG
*
81615 AAATCGAAATCAACCAGAATCG
1 AAATCGAAATCAACCAGAATCA
* * *
81637 AAATCGAAATTATCCCGAATCA
1 AAATCGAAATCAACCAGAATCA
81659 AAAT
1 AAAT
81663 TTAACCCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.21, G:0.10, T:0.19
Consensus pattern (22 bp):
AAATCGAAATCAACCAGAATCA
Found at i:82448 original size:33 final size:33
Alignment explanation
Indices: 82411--82477 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
82401 GATCTAAAGG
82411 TTGACTTAAATCGAAAATC-AACC-GATCTAATAT
1 TTGACTTAAATC-AAAATCTAACCAG-TCTAATAT
* *
82444 TTGACTTGACTCAAAATCTAACCAGTCTAATAT
1 TTGACTTAAATCAAAATCTAACCAGTCTAATAT
82477 T
1 T
82478 AACCCGGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 6 0.20
33 23 0.77
34 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (33 bp):
TTGACTTAAATCAAAATCTAACCAGTCTAATAT
Found at i:87944 original size:23 final size:23
Alignment explanation
Indices: 87918--87986 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
87908 CACCACATCT
* *
87918 CGTATAAATGTACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
87941 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
87964 CATAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
87987 TATAAAGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:88129 original size:103 final size:103
Alignment explanation
Indices: 87995--88322 Score: 584
Period size: 103 Copynumber: 3.2 Consensus size: 103
87985 CATATAAAGT
* * * *
87995 TGTCCCTAAGGACCACATATCATTCCATAAGAATCATATACATATGCCAAAGATCAAGTATGTAT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATAAATATGCCAAAGATCAAGTATGTGT
*
88060 CTCAACAGACCTCACACCTATTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
*
88098 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATTTAAATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATAAATATGCCAAAGATCAAGTATGTGT
*
88163 CTCAATAGACCTCACACCTGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
*
88201 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATATATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATAAATATGCCAAAGATCAAGTATGTGT
88266 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
88304 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
88323 GACCCTCTAC
Statistics
Matches: 215, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 215 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.26
Consensus pattern (103 bp):
TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATAAATATGCCAAAGATCAAGTATGTGT
CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
Found at i:88850 original size:17 final size:19
Alignment explanation
Indices: 88828--88868 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
88818 TCTTTTTAAA
88828 TTAA-TGCATCGATGCA-C
1 TTAAGTGCATCGATGCACC
88845 TTAATGTGCATCGATGCACC
1 TTAA-GTGCATCGATGCACC
88865 TTAA
1 TTAA
88869 ACAATTTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
19 12 0.57
20 5 0.24
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (19 bp):
TTAAGTGCATCGATGCACC
Found at i:88919 original size:21 final size:21
Alignment explanation
Indices: 88893--88948 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
88883 TTATCATTGA
88893 TGCATCGGTGCACAATGAATG
1 TGCATCGGTGCACAATGAATG
88914 TGCATCGGTGCACAATGAATG
1 TGCATCGGTGCACAATGAATG
* *
88935 CGCATCGATGCACA
1 TGCATCGGTGCACA
88949 TTGCCCAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (21 bp):
TGCATCGGTGCACAATGAATG
Found at i:94991 original size:23 final size:23
Alignment explanation
Indices: 94965--95033 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
94955 CACCACAGCT
*
94965 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
94988 CGTAGAATTGCACTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
95011 CATAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
95034 TATAAAGTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:95264 original size:103 final size:103
Alignment explanation
Indices: 95085--95360 Score: 498
Period size: 103 Copynumber: 2.7 Consensus size: 103
95075 TCATATACAT
* *
95085 ATCAAGTATGTGTCTTAACAGACCTCACACCTGTTTCAAAGAATACATATATGTCCCGAAGGACC
1 ATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATACATATATGTCCCGAAGGACC
*
95150 ACATATCATTCCTTAAGAATCATATACATATGCCAAAG
66 ACATATCATTCCTTAAAAATCATATACATATGCCAAAG
* * *
95188 ATCAAGTATGTGTCTCAACAGACCTCACACGTGTTCCAAAGAATACATGTATGTCACGAAGGACC
1 ATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATACATATATGTCCCGAAGGACC
95253 ACATATCATTCCTTAAAAATCATATACATATGCCAAAG
66 ACATATCATTCCTTAAAAATCATATACATATGCCAAAG
95291 ATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATACATATATGTCCCGAAGGACC
1 ATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATACATATATGTCCCGAAGGACC
95356 ACATA
66 ACATA
95361 GACCCTCTAC
Statistics
Matches: 164, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 164 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
ATCAAGTATGTGTCTCAACAGACCTCACACCTGTTCCAAAGAATACATATATGTCCCGAAGGACC
ACATATCATTCCTTAAAAATCATATACATATGCCAAAG
Found at i:101805 original size:21 final size:21
Alignment explanation
Indices: 101779--101820 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
101769 CCATAATGGG
*
101779 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
101800 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
101821 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:101987 original size:19 final size:19
Alignment explanation
Indices: 101927--101987 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
101917 AGCCTCGGGG
* * *
101927 TACTGTTCAAACAGTGATT
1 TACTGTTCAAATAGTAAAT
**
101946 TACTGTTCAAATAGTAAGG
1 TACTGTTCAAATAGTAAAT
101965 TACTGTTCAAATAGTAAAT
1 TACTGTTCAAATAGTAAAT
101984 TACT
1 TACT
101988 ATTTATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (19 bp):
TACTGTTCAAATAGTAAAT
Found at i:102089 original size:29 final size:31
Alignment explanation
Indices: 102048--102116 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 31
102038 TATTTTTGAA
*
102048 AATTTTGAATAAATTCAATT-AAGTCCAAATAC
1 AATTTTG--TAAATTCAATTCAAGTCCAAAAAC
102080 -ATTTTGTAAATTCAATTCAAGTCCAAAAAC
1 AATTTTGTAAATTCAATTCAAGTCCAAAAAC
102110 AATTTTG
1 AATTTTG
102117 CCTTAAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 11 0.32
30 11 0.32
31 12 0.35
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (31 bp):
AATTTTGTAAATTCAATTCAAGTCCAAAAAC
Found at i:102125 original size:34 final size:29
Alignment explanation
Indices: 102057--102116 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
102047 AAATTTTGAA
*
102057 TAAATTCAATTAAGTCCAAATACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
102086 TAAATTCAATTCAAGTCCAAAAACAATTTTG
1 TAAATTCAATT-AAGTCCAAAAAC-ATTTTG
102117 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:110869 original size:32 final size:33
Alignment explanation
Indices: 110798--110915 Score: 93
Period size: 31 Copynumber: 3.6 Consensus size: 33
110788 TTAAAAATTA
* * *
110798 TAAATAACTATT-AAGTTTAT-TAAATTATTAGT
1 TAAATAATTATTAAATTTTATAAAAATTATT-GT
110830 ATAAAATAATTATTAAATTTTA-AAAAATTATTGT
1 -T-AAATAATTATTAAATTTTATAAAAATTATTGT
** * * *
110864 TAAATAACCATTAAATTTTATTAGAA-T-TTAT
1 TAAATAATTATTAAATTTTATAAAAATTATTGT
*
110895 AAAATAATTATTAAATTTTAT
1 TAAATAATTATTAAATTTTAT
110916 CATATTTTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
31 21 0.30
32 18 0.26
33 5 0.07
34 12 0.17
35 14 0.20
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (33 bp):
TAAATAATTATTAAATTTTATAAAAATTATTGT
Found at i:110908 original size:31 final size:31
Alignment explanation
Indices: 110829--110953 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
110819 AAATTATTAG
110829 TATAAAATAATTATTAAATTTTA-AAAAATTAT
1 TATAAAATAATTATTAAATTTTATAAAAA-T-T
* * ** * *
110861 TGTTAAATAACCATTAAATTTTATTAGAATT
1 TATAAAATAATTATTAAATTTTATAAAAATT
* * *
110892 TATAAAATAATTATTAAATTTTATCATATTT
1 TATAAAATAATTATTAAATTTTATAAAAATT
* * * *
110923 TATAAAACATTTATT-AAGTTTATCAAAATT
1 TATAAAATAATTATTAAATTTTATAAAAATT
110953 T
1 T
110954 TACTCTTACT
Statistics
Matches: 74, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
30 13 0.18
31 38 0.51
32 20 0.27
33 3 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.46
Consensus pattern (31 bp):
TATAAAATAATTATTAAATTTTATAAAAATT
Found at i:110914 original size:21 final size:21
Alignment explanation
Indices: 110829--110915 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
110819 AAATTATTAG
110829 TATAAAATAATTATTAAATTT
1 TATAAAATAATTATTAAATTT
* * * **
110850 TAAAAAATTATTGTTAAATAAC
1 TATAAAATAATTATTAAAT-TT
* * *
110872 CATTAAAT-TTTATTAGAA-TT
1 TATAAAATAATTATTA-AATTT
110892 TATAAAATAATTATTAAATTT
1 TATAAAATAATTATTAAATTT
110913 TAT
1 TAT
110916 CATATTTTAT
Statistics
Matches: 47, Mismatches: 15, Indels: 8
0.67 0.21 0.11
Matches are distributed among these distances:
20 8 0.17
21 32 0.68
22 7 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
TATAAAATAATTATTAAATTT
Done.