Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004169.1 Hibiscus syriacus cultivar Beakdansim tig00009117_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: 295911
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:147362 original size:20 final size:20
Alignment explanation
Indices: 147330--147380 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
147320 TATAAACTAT
147330 ATAATAT-TATAGTTTATAC
1 ATAATATATATAGTTTATAC
**
147349 ATGGTATATATAGTTTATAC
1 ATAATATATATAGTTTATAC
147369 ATAATATATATA
1 ATAATATATATA
147381 AAAACTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (20 bp):
ATAATATATATAGTTTATAC
Found at i:147423 original size:2 final size:2
Alignment explanation
Indices: 147406--147537 Score: 72
Period size: 2 Copynumber: 63.0 Consensus size: 2
147396 ATATGTAAAT
*
147406 TA TA CTA TA TA GTA TA TA TA GTT TA TA TA TA TA TA -A TA TA TA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * ** * *
147448 GTA TA TA AA TA TA AA CTA TA GTA TA TA TA TA GG TCA TA TG TA AA
1 -TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA T-A TA TA TA TA
* * *
147492 CTA TA TA GTA TA TA AA CA TA -A AA TA TA -A 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
147534 TA TA
1 TA TA
147538 GGTCATATGT
Statistics
Matches: 100, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
1 3 0.03
2 83 0.83
3 14 0.14
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (2 bp):
TA
Found at i:147436 original size:20 final size:20
Alignment explanation
Indices: 147327--147479 Score: 69
Period size: 20 Copynumber: 7.3 Consensus size: 20
147317 ATATATAAAC
*
147327 TATATAATAT-TATAGTTTA
1 TATATAGTATATATAGTTTA
* *
147346 TACATGGTATATATAGTTTA
1 TATATAGTATATATAGTTTA
* * ***
147366 TACATAATATATATA-AAAA
1 TATATAGTATATATAGTTTA
* *
147385 CTATATAGTTCATATGTAAATTATA
1 -TATATAG-T-ATATAT-AGTT-TA
147410 CTATATAGTATATATAGTTTA
1 -TATATAGTATATATAGTTTA
* *
147431 TATATATATAATATATAGTATA
1 TATATA-GT-ATATATAGTTTA
* * *
147453 TAAATA-TAAACTATAGTATA
1 TATATAGTATA-TATAGTTTA
147473 TATATAG
1 TATATAG
147480 GTCATATGTA
Statistics
Matches: 102, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
19 10 0.10
20 48 0.47
21 4 0.04
22 24 0.24
23 6 0.06
24 1 0.01
25 9 0.09
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (20 bp):
TATATAGTATATATAGTTTA
Found at i:147572 original size:112 final size:114
Alignment explanation
Indices: 147406--147617 Score: 249
Period size: 112 Copynumber: 1.9 Consensus size: 114
147396 ATATGTAAAT
* *
147406 TATACTATATAGTATATATAGTTTATATATATATAATATATAGTATATAAATATAAACT-ATA-G
1 TATACTATATAGTATATATAGGTCATATATATATAATATATAGTATATAAATAT-AACTCATATG
147469 TATATA-TATAGGTCATATGTAAACTATATAGTATATAAACATAAAATATAA
65 TA-A-ACTATAGGTCATATGTAAACTATATAGTATATAAACATAAAATATAA
* * * **
147520 TATA-TATATA-TATATATAGGTCATATGTA-A-ACTATATAGTTTATATATATATAGTTCATAT
1 TATACTATATAGTATATATAGGTCATATATATATAATATATAG--TATATAAATATAACTCATAT
* *
147581 GTAAACTATAGTTCATATGTAAACTATATAGTTTATA
64 GTAAACTATAGGTCATATGTAAACTATATAGTATATA
147618 TATATAGTTC
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
110 8 0.10
111 4 0.05
112 59 0.70
113 9 0.11
114 4 0.05
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (114 bp):
TATACTATATAGTATATATAGGTCATATATATATAATATATAGTATATAAATATAACTCATATGT
AAACTATAGGTCATATGTAAACTATATAGTATATAAACATAAAATATAA
Found at i:147591 original size:33 final size:34
Alignment explanation
Indices: 147526--147598 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 34
147516 ATAATATATA
147526 TATATATATATAGGTCATATGTAAACTATATAGTT
1 TATATATATATAGGTCATATGTAAAC-ATATAGTT
*
147561 TATATATATATAGTTCATATGTAAAC-TATAGTT
1 TATATATATATAGGTCATATGTAAACATATAGTT
*
147594 CATAT
1 TATAT
147599 GTAAACTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 11 0.31
35 25 0.69
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.44
Consensus pattern (34 bp):
TATATATATATAGGTCATATGTAAACATATAGTT
Found at i:147592 original size:18 final size:18
Alignment explanation
Indices: 147534--147649 Score: 95
Period size: 18 Copynumber: 6.7 Consensus size: 18
147524 TATATATATA
*
147534 TATAGGTCATATGTAAAC
1 TATAGTTCATATGTAAAC
* *
147552 TATATAGTT--TATATATA-
1 --TATAGTTCATATGTAAAC
147569 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
147587 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
*
147605 TATATAGTT--TA--TATA-
1 --TATAGTTCATATGTAAAC
*
147620 TATAGTTCATATGTAAAT
1 TATAGTTCATATGTAAAC
147638 TATAGTTCATAT
1 TATAGTTCATAT
147650 ATATAGTATA
Statistics
Matches: 79, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
13 7 0.09
15 9 0.11
16 3 0.04
17 9 0.11
18 38 0.48
20 13 0.16
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:147623 original size:13 final size:13
Alignment explanation
Indices: 147605--147656 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
147595 ATATGTAAAC
*
147605 TATATAGTTTATA
1 TATATAGTTCATA
147618 TATATAGTTCATA
1 TATATAGTTCATA
147631 TGTAAATTATAGTTCATA
1 --T--A-TATAGTTCATA
147649 TATATAGT
1 TATATAGT
147657 ATATAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 18 0.55
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.33
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (13 bp):
TATATAGTTCATA
Found at i:147624 original size:33 final size:32
Alignment explanation
Indices: 147587--147689 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 32
147577 ATATGTAAAC
147587 TATAGTTCATATGTAAACTATATAGTTTATATA
1 TATAGTTCATATGTAAACT-TATAGTTTATATA
*
147620 TATAGTTCATATGTAAA-TTATAGTTCATATA
1 TATAGTTCATATGTAAACTTATAGTTTATATA
*
147651 TATAGTAT-ATAAATATAAAC-TATAGTTTATATA
1 TATAGT-TCAT--ATGTAAACTTATAGTTTATATA
*
147684 AATAGT
1 TATAGT
147690 ATATAAATAG
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
31 20 0.32
32 2 0.03
33 40 0.65
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.44
Consensus pattern (32 bp):
TATAGTTCATATGTAAACTTATAGTTTATATA
Found at i:147650 original size:31 final size:33
Alignment explanation
Indices: 147587--147656 Score: 117
Period size: 31 Copynumber: 2.2 Consensus size: 33
147577 ATATGTAAAC
*
147587 TATAGTTCATATGTAAACTATATAGTTTATATA
1 TATAGTTCATATGTAAACTATATAGTTCATATA
147620 TATAGTTCATATGTAAA-T-TATAGTTCATATA
1 TATAGTTCATATGTAAACTATATAGTTCATATA
147651 TATAGT
1 TATAGT
147657 ATATAAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 18 0.50
32 1 0.03
33 17 0.47
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.46
Consensus pattern (33 bp):
TATAGTTCATATGTAAACTATATAGTTCATATA
Found at i:147661 original size:51 final size:53
Alignment explanation
Indices: 147534--147649 Score: 200
Period size: 51 Copynumber: 2.2 Consensus size: 53
147524 TATATATATA
*
147534 TATAGGTCATATGTAAACTATATAGTTTATATATATATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAACTATATAGTTTATATATATATAGTTCATATGTAAAC
*
147587 TATAGTTCATATGTAAACTATATAG-TT-TATATATATAGTTCATATGTAAAT
1 TATAGTTCATATGTAAACTATATAGTTTATATATATATAGTTCATATGTAAAC
147638 TATAGTTCATAT
1 TATAGTTCATAT
147650 ATATAGTATA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 35 0.57
52 2 0.03
53 24 0.39
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (53 bp):
TATAGTTCATATGTAAACTATATAGTTTATATATATATAGTTCATATGTAAAC
Found at i:147675 original size:51 final size:49
Alignment explanation
Indices: 147441--147686 Score: 147
Period size: 51 Copynumber: 4.8 Consensus size: 49
147431 TATATATATA
** * *
147441 ATATATAGTATATAAATATAAACTATAGTATATATATAGGTCATA-TGT-AA
1 ATATATAGTATATAAATATAAA-TATAGT-TATATATAAATTATAGT-TCAT
* * * *
147491 ACTATATAGTATATAAACATAAAATATAATATATATATATATATATAGGTCAT
1 A-TATATAGTATATAAATAT-AAATATAGT-TATATATAAAT-TATAGTTCAT
* * * * * * *
147544 ATGTAAACTATATAGTTTATATATATATAGTTCATATGTAAACTATAGTTCAT
1 ATATATAGTATATA---AATATAAATATAGTT-ATATATAAATTATAGTTCAT
* * * ** * *
147597 ATGTAAACTATATAGTTTATATATATAGTTCATATGTAAATTATAGTTCAT
1 ATATATAGTATATA-AATATAAATATAGTT-ATATATAAATTATAGTTCAT
147648 ATATATAGTATATAAATATAAACTATAGTT-TATATAAAT
1 ATATATAGTATATAAATATAAA-TATAGTTATATATAAAT
147687 AGTATATAAA
Statistics
Matches: 158, Mismatches: 28, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
49 8 0.05
50 6 0.04
51 84 0.53
52 17 0.11
53 26 0.16
54 14 0.09
55 3 0.02
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (49 bp):
ATATATAGTATATAAATATAAATATAGTTATATATAAATTATAGTTCAT
Found at i:147770 original size:14 final size:14
Alignment explanation
Indices: 147750--147788 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
147740 AATATACACC
147750 CTAAACCCTAATA-
1 CTAAACCCTAATAT
147763 CTTAAACCCTAATAT
1 C-TAAACCCTAATAT
147778 CTAAACCCTAA
1 CTAAACCCTAA
147789 ACCATATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.26
Consensus pattern (14 bp):
CTAAACCCTAATAT
Found at i:147864 original size:29 final size:31
Alignment explanation
Indices: 147832--147889 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
147822 AGTATATATT
*
147832 TATAAATTATAGTATGT-AGTT-TATATAAA
1 TATAAATTATACTATGTAAGTTCTATATAAA
147861 TATAAATTATACTATGTAAGTTCTATATA
1 TATAAATTATACTATGTAAGTTCTATATA
147890 GTTCAATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 16 0.62
30 4 0.15
31 6 0.23
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (31 bp):
TATAAATTATACTATGTAAGTTCTATATAAA
Found at i:147958 original size:27 final size:28
Alignment explanation
Indices: 147884--147972 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 28
147874 ATGTAAGTTC
* * * *
147884 TATATAGTTCAATAGTTCATATATAA-A
1 TATATAGTACTATAGTTTATACATAATA
* **
147911 CTATATAGTATTATAGTTTATACATGGTA
1 -TATATAGTACTATAGTTTATACATAATA
147940 TATATAG-ACTATAGTTTATACATAATA
1 TATATAGTACTATAGTTTATACATAATA
147967 TATATA
1 TATATA
147973 CAAACTATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
27 23 0.46
28 26 0.52
29 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.43
Consensus pattern (28 bp):
TATATAGTACTATAGTTTATACATAATA
Found at i:147971 original size:2 final size:2
Alignment explanation
Indices: 147964--148060 Score: 63
Period size: 2 Copynumber: 47.0 Consensus size: 2
147954 TTTATACATA
* * * *
147964 AT AT AT AT AC AA ACT AT AT AGT TT AT AT AT AT A- AT AC AT AT ACT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * * *
148008 TT TT AT AT AA ACT AT AT AGT TT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
148051 AT AT AT AT AT
1 AT AT AT AT AT
148061 TAGTTGTTTT
Statistics
Matches: 75, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
1 2 0.03
2 68 0.91
3 5 0.07
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:148043 original size:20 final size:19
Alignment explanation
Indices: 147978--148065 Score: 81
Period size: 22 Copynumber: 4.5 Consensus size: 19
147968 ATATACAAAC
147978 TATATAGTTTATATATATAA
1 TATATAGTTTATATATAT-A
* * *
147998 TACATATACTTTTTATATAAA
1 T--ATATAGTTTATATATATA
148019 CTATATAGTTTATAT-TATA
1 -TATATAGTTTATATATATA
*
148038 TATATA-TATATATATATA
1 TATATAGTTTATATATATA
148056 TATATTAGTT
1 TATA-TAGTT
148066 GTTTTAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
17 6 0.11
18 14 0.26
19 5 0.09
20 13 0.24
21 1 0.02
22 15 0.28
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATAGTTTATATATATA
Found at i:148747 original size:215 final size:213
Alignment explanation
Indices: 148142--148835 Score: 1080
Period size: 207 Copynumber: 3.3 Consensus size: 213
148132 TTGGTCCCTT
* * * * *
148142 TTGTGTTGTTTAATTTATTAAAAATTTTATTTGTAATTTCATATTTTTTTAATTTAGTCCTCCAT
1 TTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAA
148207 ATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTATTAATTGGCCCATAA
66 ATTTTATTTGCATCTGAAATTGA-CCATACTTATTACTTATTTCTATTT-TTAATTGGCCCATAA
* * * *
148272 CTTTTTAAATGAGTATAATTTAGTACATTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATT
129 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
148337 TCGATTTGATCCCT--T---
194 TCGATTTGATCCCTCATCAA
* * * *
148352 TTGTGTTGTTTAGTTTATTT-AA-TTTT-TTTGTTATTTTATATTTTTTCAATTTAGTCCTCCAA
1 TTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAA
148414 ATTTTATTTGCATCTGAAATTGACTCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAA
66 ATTTTATTTGCATCTGAAATTGAC-CATACTTATTACTTATTTCTATTTTT-AATTGGCCCATAA
*
148479 CTTTTTAAATGGGTATAATTTAGTATTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
129 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
148544 TCGATTTGATCCCTCATCAA
194 TCGATTTGATCCCTCATCAA
* * *
148564 TGTGTGTTGTTTAATTAATTTAAATTTTTATTTTTAATTTCATATTTGTTCAATTCAGTCCTCCA
1 T-TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCA
* * * *
148629 AATTTTATTTGCATATGAAATTGATCCATACTTTTTACTTAATTCTATTTTTAATTGGCACATAA
65 AATTTTATTTGCATCTGAAATTGA-CCATACTTATTACTTATTTCTATTTTTAATTGGCCCATAA
148694 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
129 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
148759 TCGATTTGATCCCTCATCAA
194 TCGATTTGATCCCTCATCAA
148779 TATGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1 T-TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
148836 ATTCTTAAAT
Statistics
Matches: 445, Mismatches: 27, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
206 3 0.01
207 166 0.37
208 4 0.01
209 3 0.01
210 18 0.04
212 1 0.00
213 17 0.04
214 2 0.00
215 153 0.34
216 77 0.17
217 1 0.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (213 bp):
TTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAA
ATTTTATTTGCATCTGAAATTGACCATACTTATTACTTATTTCTATTTTTAATTGGCCCATAACT
TTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTC
GATTTGATCCCTCATCAA
Found at i:149548 original size:13 final size:13
Alignment explanation
Indices: 149530--149555 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
149520 ACTTCTGCAC
149530 TAATCTAATTTAA
1 TAATCTAATTTAA
149543 TAATCTAATTTAA
1 TAATCTAATTTAA
149556 GGTTAAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATCTAATTTAA
Found at i:150164 original size:15 final size:15
Alignment explanation
Indices: 150144--150188 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
150134 AAAAAAAAGT
150144 AATAAAAATAAAGAA
1 AATAAAAATAAAGAA
*
150159 AATAAAAATAAATCAA
1 AATAAAAATAAA-GAA
*
150175 AGTAAAAATAAAGA
1 AATAAAAATAAAGA
150189 GGAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (15 bp):
AATAAAAATAAAGAA
Found at i:150180 original size:16 final size:15
Alignment explanation
Indices: 150144--150186 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
150134 AAAAAAAAGT
*
150144 AATAAAAATAAAGAA
1 AATAAAAATAAACAA
150159 AATAAAAATAAATCAA
1 AATAAAAATAAA-CAA
*
150175 AGTAAAAATAAA
1 AATAAAAATAAA
150187 GAGGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (15 bp):
AATAAAAATAAACAA
Found at i:150270 original size:6 final size:6
Alignment explanation
Indices: 150233--150350 Score: 59
Period size: 6 Copynumber: 19.3 Consensus size: 6
150223 ATATGTATGT
* * *
150233 AAAATA AATAAT- TAAATA AAAACA AGAATA AAAATA AAAAT- -AAATA
1 AAAATA AA-AATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * *
150279 AAGAGATA AAAATA AATATAA AAGCAATA AAAGT- AAGATA AAGATA AAAGA-A
1 AA-A-ATA AAAATA AAAAT-A AA--AATA AAAATA AAAATA AAAATA AAA-ATA
150331 ATAAATA AAAAT- AAAATA AA
1 A-AAATA AAAATA AAAATA AA
150351 GAAAAAGACA
Statistics
Matches: 86, Mismatches: 12, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
4 4 0.05
5 11 0.13
6 48 0.56
7 13 0.15
8 8 0.09
9 2 0.02
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:150273 original size:24 final size:24
Alignment explanation
Indices: 150246--150301 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
150236 ATAAATAATT
150246 AAATAAAAACAAGA-ATAAAAATAA
1 AAATAAAAA-AAGAGATAAAAATAA
*
150270 AAATAAATAAAGAGATAAAAATAA
1 AAATAAAAAAAGAGATAAAAATAA
*
150294 ATATAAAA
1 AAATAAAA
150302 GCAATAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (24 bp):
AAATAAAAAAAGAGATAAAAATAA
Found at i:150300 original size:36 final size:35
Alignment explanation
Indices: 150233--150350 Score: 98
Period size: 36 Copynumber: 3.2 Consensus size: 35
150223 ATATGTATGT
** *
150233 AAAATAAATAATTAAATAAAAACAAGAATAAAAATA
1 AAAATAAATAAAGAAATAAAAATAA-AATAAAAATA
*
150269 AAAATAAATAAAGAGATAAAAATAAATATAAAAGCAATA
1 AAAATAAATAAAGAAATAAAAATAAA-AT-AAA--AATA
*
150308 AAAGTAAGATAAAGATAA-AAGAAAT-AAATAAAAAT-
1 AAAATAA-ATAAAGA-AATAA-AAATAAAATAAAAATA
150343 AAAATAAA
1 AAAATAAA
150351 GAAAAAGACA
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
34 1 0.01
35 7 0.10
36 26 0.38
37 3 0.04
38 3 0.04
39 12 0.18
40 11 0.16
41 5 0.07
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.18
Consensus pattern (35 bp):
AAAATAAATAAAGAAATAAAAATAAAATAAAAATA
Found at i:150308 original size:21 final size:19
Alignment explanation
Indices: 150265--150341 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 19
150255 CAAGAATAAA
*
150265 AATAAAAATAAATAAAGAG
1 AATAAAAATAAATAAAAAG
150284 -ATAAAAATAAATATAAAAG
1 AATAAAAATAAATA-AAAAG
* * *
150303 CAATAAAAGTAAGATAAAGAT
1 -AATAAAAATAA-ATAAAAAG
150324 AA-AAGAAATAAATAAAAA
1 AATAA-AAATAAATAAAAA
150342 TAAAATAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
18 13 0.28
19 12 0.26
20 7 0.15
21 12 0.26
22 3 0.06
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (19 bp):
AATAAAAATAAATAAAAAG
Found at i:150339 original size:39 final size:39
Alignment explanation
Indices: 150265--150341 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
150255 CAAGAATAAA
*
150265 AATAAAAATAAATAAAGAGATAAAAATAAATATAAAAGC
1 AATAAAAATAAATAAAGAGAAAAAAATAAATATAAAAGC
* *
150304 AATAAAAGTAAGATAAAGATAAAAGAAATAAATA-AAAA
1 AATAAAAATAA-ATAAAGAGAAAA-AAATAAATATAAAA
150342 TAAAATAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 10 0.30
40 14 0.42
41 9 0.27
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (39 bp):
AATAAAAATAAATAAAGAGAAAAAAATAAATATAAAAGC
Found at i:150340 original size:30 final size:30
Alignment explanation
Indices: 150304--150368 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
150294 ATATAAAAGC
* *
150304 AATAAAAGTAAGATAAAGATAAAAG-AAATA
1 AATAAAAATAAAATAAAGA-AAAAGAAAATA
150334 AATAAAAATAAAATAAAGAAAAAGACAAATA
1 AATAAAAATAAAATAAAGAAAAAGA-AAATA
150365 AATA
1 AATA
150369 TTTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 5 0.16
30 17 0.55
31 9 0.29
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (30 bp):
AATAAAAATAAAATAAAGAAAAAGAAAATA
Found at i:150487 original size:2 final size:2
Alignment explanation
Indices: 150482--150527 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
150472 TATGTGTGTG
150482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
150524 TA TA
1 TA TA
150528 GTATTTAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:152760 original size:86 final size:85
Alignment explanation
Indices: 152449--153391 Score: 1087
Period size: 84 Copynumber: 11.1 Consensus size: 85
152439 CGACAGCTTT
* ** * * * * ** *
152449 TTTTGTTGACAGATAGCTTTTCTCGACTTAAGTTATACTGTAAAGTTGACATGCCCTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAA-TTGATGTGCCTTTGAGCTGA
* *
152514 ATGGAATCGAACTCGAAGGT-
65 GTGTAATCGAACTCGAAGGTC
* * * * * *
152534 ATTTCTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATTTGCCTCTGAGATGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATT-GATGTGCCTTTGAGCTGA
* *
152599 ATGTAATCGAACTCGAAGGAC
65 GTGTAATCGAACTCGAAGGTC
* ** * * *
152620 -TTGGTTGACAGATAACCCTTCTCGTATTGAGTTATGCTGTAAAATTGATATGCCTTTGAGTTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTG-CAAATTGATGTGCCTTTGAGCTGA
*
152684 ATGTAATCGAACTCGAAGGTC
65 GTGTAATCGAACTCGAAGGTC
* * * * * *
152705 TTTTGTTGGCAGATAGCCCTTCTCACCTTGAGCTATGTTACAAATTTGATGTGCCTTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAA-TTGATGTGCCTTTGAGCTGA
*
152770 GTGTAATTGAACTCGAAGGTC
65 GTGTAATCGAACTCGAAGGTC
*
152791 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATACTGCAAA-TGATGTGCCTTTGAGCTGAG
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATTGATGTGCCTTTGAGCTGAG
152855 TGTAATCGAACTCGAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * * * *
152875 -TTGGTTGATAGATAACCCTTCTCACCTTGAGTTATACTGTAAATTGGATGTGCCTTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATT-GATGTGCCTTTGAGCTGA
*
152939 GTGTAATCGAACTTGAAGGTC
65 GTGTAATCGAACTCGAAGGTC
* * * **
152960 TTTTGTTGGCCA-ATAGCCCTTCTCGCCTTGAGCTATAATGCAAA-TGATGTGCCTTTGAGCTGA
1 TTTTGTT-GACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATTGATGTGCCTTTGAGCTGA
153023 GTGTAATCGAACTCGAAGGTC
65 GTGTAATCGAACTCGAAGGTC
* *
153044 -TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATT-GATGTGCCTTTGAGCTGA
* *
153108 GTGTAATCAAACTTGAAGGTC
65 GTGTAATCGAACTCGAAGGTC
* * * * *
153129 TTTTGTTGGTC-GATAGCCCTTCTCGCCTTGAGCTATGCTACAAA-TGATATGCCTTTGAGCTGA
1 TTTTGTT-GACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATTGATGTGCCTTTGAGCTGA
153192 GTGTAATCGAACTCGAAGGTC
65 GTGTAATCGAACTCGAAGGTC
* ** * * * *
153213 TTTTATTGGTAGATAACCCTTCTCGACTTGAGATATGCTACAAA-AGATGTGCCTTTGAGCTGAG
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATTGATGTGCCTTTGAGCTGAG
* *
153277 TGTAATCAAACTCAAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * * ** * *
153297 TTTTGTTGGCAGATAGCCCTTCTCACCTTGAGCCATGTTGCAAATTTGATGCGCCTTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAA-TTGATGTGCCTTTGAGCTGA
*
153362 GTGTAATCGAACTCGAAGGCC
65 GTGTAATCGAACTCGAAGGTC
153383 TTTTGTTGA
1 TTTTGTTGA
153392 AGGTACTTTT
Statistics
Matches: 738, Mismatches: 103, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
82 3 0.00
83 72 0.10
84 224 0.30
85 217 0.29
86 218 0.30
87 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (85 bp):
TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATTGATGTGCCTTTGAGCTGAG
TGTAATCGAACTCGAAGGTC
Found at i:152936 original size:169 final size:170
Alignment explanation
Indices: 152449--153391 Score: 1121
Period size: 169 Copynumber: 5.5 Consensus size: 170
152439 CGACAGCTTT
** * * * * * *
152449 TTTTGTTGACAGATAGCTTTTCTCGACTTAAGTTATACTGTAAAGTTGACATGCCCTTGAGCTGA
1 TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATACTGCAAA-TTGATATGCCTTTGAGCTGA
* * * * *
152514 ATGGAATCGAACTCGAAGGTATTTCTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
65 GTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAAT
* * * * *
152579 TGGATTTGCCTCTGAGATGAATGTAATCGAACTCGAAGGAC
130 TGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* * ** * * * *
152620 -TTGGTTGACAGATAACCCTTCTCGTATTGAGTTATGCTGTAAAATTGATATGCCTTTGAGTTGA
1 TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATACTG-CAAATTGATATGCCTTTGAGCTGA
* * * * * **
152684 ATGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCACCTTGAGCTATGTTACAAA
65 GTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAA
* *
152749 TTTGATGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC
129 TTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* * *
152791 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATACTGCAAA-TGATGTGCCTTTGAGCTGAG
1 TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATACTGCAAATTGATATGCCTTTGAGCTGAG
* * *
152855 TGTAATCGAACTCGAAGGTCTTGGTTGATAGATAACCCTTCTCACCTTGAGTTATACTGTAAATT
66 TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATT
*
152920 GGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTC
131 GGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* * *
152960 TTTTGTTGGCCA-ATAGCCCTTCTCGCCTTGAGCTATAATGCAAA-TGATGTGCCTTTGAGCTGA
1 TTTTGTT-GACAGATAGCCCTTCTCGCCTTGAGCTATACTGCAAATTGATATGCCTTTGAGCTGA
* *
153023 GTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
65 GTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAAT
* *
153088 TGGATGTGCCTTTGAGCTGAGTGTAATCAAACTTGAAGGTC
130 TGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* * *
153129 TTTTGTTGGTC-GATAGCCCTTCTCGCCTTGAGCTATGCTACAAA-TGATATGCCTTTGAGCTGA
1 TTTTGTT-GACAGATAGCCCTTCTCGCCTTGAGCTATACTGCAAATTGATATGCCTTTGAGCTGA
* ** * **
153192 GTGTAATCGAACTCGAAGGTCTTTTATTGGTAGATAACCCTTCTCGA-CTTGAGATATGCTACAA
65 GTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTC-ACCTTGAGTTATGCTGTAA
* * *
153256 A--AGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTC
128 ATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
* * * ** **
153297 TTTTGTTGGCAGATAGCCCTTCTCACCTTGAGCCATGTTGCAAATTTGATGCGCCTTTGAGCTGA
1 TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATACTGCAAA-TTGATATGCCTTTGAGCTGA
*
153362 GTGTAATCGAACTCGAAGGCCTTTTGTTGA
65 GTGTAATCGAACTCGAAGGTC-TTTGTTGA
153392 AGGTACTTTT
Statistics
Matches: 679, Mismatches: 83, Indels: 21
0.87 0.11 0.03
Matches are distributed among these distances:
167 2 0.00
168 73 0.11
169 308 0.45
170 185 0.27
171 76 0.11
172 35 0.05
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (170 bp):
TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATACTGCAAATTGATATGCCTTTGAGCTGAG
TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATT
GGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
Found at i:154404 original size:95 final size:94
Alignment explanation
Indices: 154271--154468 Score: 306
Period size: 95 Copynumber: 2.1 Consensus size: 94
154261 TTGTATAGAT
* * *
154271 ATTATAATCATCTTATCAGGTTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTGCT
1 ATTATAATCACCTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGAGTTTAACCAATTGCT
154336 CTAGAGGGACAACTCAAGCTTTATTGTAC
66 CTAGAGGGACAACTCAAGCTTTATTGTAC
* *
154365 ATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGAGGAGTTTAACCAATTGC
1 ATTATAATCACC-TTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGAGTTTAACCAATTGC
* * *
154430 TTTAGAGGGACAGCTCAAGCTTTATTGTAT
65 TCTAGAGGGACAACTCAAGCTTTATTGTAC
154460 ATATATAAT
1 AT-TATAAT
154469 ATTATAATAT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 11 0.12
95 77 0.82
96 6 0.06
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (94 bp):
ATTATAATCACCTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGAGTTTAACCAATTGCT
CTAGAGGGACAACTCAAGCTTTATTGTAC
Found at i:167878 original size:12 final size:11
Alignment explanation
Indices: 167861--167916 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
167851 ATATACATAT
167861 AATAAATAAATA
1 AATAAATAAA-A
167873 AATAAATAAAA
1 AATAAATAAAA
*
167884 ACATGAAT-AAA
1 A-ATAAATAAAA
*
167895 AATAAATATAA
1 AATAAATAAAA
**
167906 AGGAAATAAAA
1 AATAAATAAAA
167917 GTAAGATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
10 5 0.14
11 16 0.44
12 15 0.42
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:167945 original size:30 final size:30
Alignment explanation
Indices: 167909--167973 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
167899 AATATAAAGG
* * * *
167909 AAATAAAAGTAAGATAAAGATAAAG-GAAAT
1 AAATAAAAATAAAAT-AAGAAAAAGACAAAT
167939 AAATAAAAATAAAATAAGAAAAAGACAAAT
1 AAATAAAAATAAAATAAGAAAAAGACAAAT
167969 AAATA
1 AAATA
167974 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (30 bp):
AAATAAAAATAAAATAAGAAAAAGACAAAT
Found at i:168089 original size:2 final size:2
Alignment explanation
Indices: 168077--168119 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
168067 ATGCCAGGTA
*
168077 AT AT AT GT 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
168119 A
1 A
168120 GTATTAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:168724 original size:2 final size:2
Alignment explanation
Indices: 168717--168745 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
168707 CGGCGAACTT
168717 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
168746 TACTTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:169759 original size:15 final size:16
Alignment explanation
Indices: 169734--169765 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
169724 TGTTGGTTCA
169734 TTTTGTTATATTGCAG
1 TTTTGTTATATTGCAG
169750 TTTT-TTATATTGCAG
1 TTTTGTTATATTGCAG
169765 T
1 T
169766 ATGGAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.59
Consensus pattern (16 bp):
TTTTGTTATATTGCAG
Found at i:171735 original size:20 final size:20
Alignment explanation
Indices: 171689--171736 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 20
171679 TGCCATGGAG
171689 GAGGAAGATGAAGGAAGAAAA
1 GAGGAA-ATGAAGGAAGAAAA
*
171710 GA-GAAATGAA-GAAGAGAA
1 GAGGAAATGAAGGAAGAAAA
171728 GATGGAAAT
1 GA-GGAAAT
171737 ATAAGACACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 8 0.33
21 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.35, T:0.08
Consensus pattern (20 bp):
GAGGAAATGAAGGAAGAAAA
Found at i:173040 original size:14 final size:14
Alignment explanation
Indices: 173023--173055 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
173013 ATTTCTATGT
173023 AGGGAATTATTTAC
1 AGGGAATTATTTAC
*
173037 AGGGAATTATTTAT
1 AGGGAATTATTTAC
173051 AGGGA
1 AGGGA
173056 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:175155 original size:29 final size:28
Alignment explanation
Indices: 175100--175187 Score: 70
Period size: 32 Copynumber: 2.9 Consensus size: 28
175090 GTTGACCTTG
*
175100 AAAATTGAGTTTTTATCATTGAT-TTTTCAA
1 AAAATT-A-TTTTTATTATT-ATATTTTCAA
*
175130 AAAATTATTTTTTATTATTATATTTTTAATTAA
1 AAAATTA-TTTTTATTATTATA--TTT--TCAA
*
175163 AAAATTATTATTATTATTATATTTT
1 AAAATTATTTTTATTATTATATTTT
175188 TAATTCATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
28 3 0.06
29 11 0.22
30 9 0.18
31 3 0.06
32 13 0.27
33 10 0.20
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (28 bp):
AAAATTATTTTTATTATTATATTTTCAA
Found at i:175177 original size:32 final size:33
Alignment explanation
Indices: 175128--175192 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
175118 TTGATTTTTC
*
175128 AAAAAATTATTTTTTATTATTATATTTTTAATT
1 AAAAAATTATTTATTATTATTATATTTTTAATT
175161 AAAAAATTA-TTATTATTATTATATTTTTAATT
1 AAAAAATTATTTATTATTATTATATTTTTAATT
175193 CATTTTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 22 0.71
33 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
AAAAAATTATTTATTATTATTATATTTTTAATT
Found at i:175665 original size:20 final size:20
Alignment explanation
Indices: 175628--175667 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
175618 AGGATTTAAT
*
175628 GAAAAAAAATTATTAAAAAA
1 GAAAAAAAATTATGAAAAAA
175648 GAAAAAAATATT-TGAAAAAA
1 GAAAAAAA-ATTATGAAAAAA
175668 ATGATAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
GAAAAAAAATTATGAAAAAA
Found at i:176105 original size:2 final size:2
Alignment explanation
Indices: 176098--176151 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
176088 AGGAATTCTA
176098 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
176140 AT AT AT AT AT AT
1 AT AT AT AT AT AT
176152 CGGTTAAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176586 original size:31 final size:31
Alignment explanation
Indices: 176549--176629 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
176539 AACAAAATTT
*
176549 CTTGTTCGTGTTCGGTCATTAAGAAATTTAG
1 CTTGTTCGTGTTCGTTCATTAAGAAATTTAG
* * *
176580 TTTGTTCGTGCTCCTTCATTAAGAAATTTAG
1 CTTGTTCGTGTTCGTTCATTAAGAAATTTAG
*
176611 CTTGTTCGTTTTCGTTCAT
1 CTTGTTCGTGTTCGTTCAT
176630 GTTTGTTCGG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.47
Consensus pattern (31 bp):
CTTGTTCGTGTTCGTTCATTAAGAAATTTAG
Found at i:177014 original size:40 final size:41
Alignment explanation
Indices: 176969--177051 Score: 123
Period size: 40 Copynumber: 2.0 Consensus size: 41
176959 ATGAACGAGC
176969 ATTTTGTTCATGTTCGTTCATTTAAT-TAAACGAACATAAA
1 ATTTTGTTCATGTTCGTTCATTTAATATAAACGAACATAAA
* *
177009 ATTTTGTTTATGTTCGTTCGTTTAATAAATAAACGAACATAAA
1 ATTTTGTTCATGTTCGTTCATTTAAT--ATAAACGAACATAAA
177052 TGAACTTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 24 0.63
43 14 0.37
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (41 bp):
ATTTTGTTCATGTTCGTTCATTTAATATAAACGAACATAAA
Found at i:177931 original size:14 final size:14
Alignment explanation
Indices: 177911--177958 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
177901 AATGTATAAT
177911 AAAATAATAAATTA
1 AAAATAATAAATTA
*
177925 TAAATAATAAAATTA
1 AAAATAAT-AAATTA
177940 AAAATAATAAATTA
1 AAAATAATAAATTA
177954 AAAAT
1 AAAAT
177959 TAAAAATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATAATAAATTA
Found at i:177934 original size:22 final size:22
Alignment explanation
Indices: 177906--177966 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
177896 TTAAAAATGT
*
177906 ATAATAAAA-TAATAAATTATAA
1 ATAATAAAATTAA-AAATAATAA
177928 ATAATAAAATTAAAAATAATAA
1 ATAATAAAATTAAAAATAATAA
*
177950 ATTA-AAAATTAAAAATA
1 ATAATAAAATTAAAAATA
177967 GTAATAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 13 0.36
22 20 0.56
23 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAATAAAATTAAAAATAATAA
Found at i:177959 original size:21 final size:23
Alignment explanation
Indices: 177924--177974 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 23
177914 ATAATAAATT
177924 ATAAA-TAATAAAATTAAAAA-TA
1 ATAAATTAA-AAAATTAAAAATTA
177946 ATAAATT-AAAAATTAAAAATAGTA
1 ATAAATTAAAAAATTAAAAAT--TA
177970 ATAAA
1 ATAAA
177975 GATAAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 11 0.44
22 6 0.24
23 1 0.04
24 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
ATAAATTAAAAAATTAAAAATTA
Found at i:178040 original size:17 final size:17
Alignment explanation
Indices: 178020--178053 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
178010 AATGAGATAA
*
178020 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
178037 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
178054 TGGGATAAAG
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:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:178752 original size:69 final size:73
Alignment explanation
Indices: 178668--178857 Score: 219
Period size: 76 Copynumber: 2.6 Consensus size: 73
178658 AAATCCTAAT
* * *
178668 TAAAA-CTATTTAAACTAAAATACCTAAAAA-ATAATATTTAAAAAT-AT-T-CTAAATCCTAAT
1 TAAAACCTATTTAAACTAAAATACCTAAAAAGATAAAATATAAAAATAATATCCTAAAACCTAAT
*
178728 TGAAATAA
66 TAAAATAA
* *
178736 TAAAACCTATTTAAACTAAAATACCAAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTT
1 TAAAACCTATTTAAACTAAAATACC--TAA-AAAGATAAAATATAAAAATAATATCCTAAAACCT
*
178801 AATTAAAATAC
63 AATTAAAATAA
*
178812 TAAAACCTATTTAAACTAAAATACATAAAACAAAGATAAAATATAA
1 TAAAACCTATTTAAACTAAAATACCT--AA-AAAGATAAAATATAA
178858 TGTTTAAAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
68 5 0.05
69 19 0.18
71 2 0.02
72 3 0.03
73 13 0.13
74 2 0.02
75 1 0.01
76 58 0.56
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (73 bp):
TAAAACCTATTTAAACTAAAATACCTAAAAAGATAAAATATAAAAATAATATCCTAAAACCTAAT
TAAAATAA
Found at i:178804 original size:76 final size:76
Alignment explanation
Indices: 178710--178857 Score: 235
Period size: 76 Copynumber: 1.9 Consensus size: 76
178700 AATATTTAAA
* * *
178710 AATATTCTAAATCCTAATTGAAATAATAAAACCTATTTAAACTAAAATACCA-AAAACAAAGATA
1 AATATCCTAAAACCTAATTAAAATAATAAAACCTATTTAAACTAAAATA-CATAAAACAAAGATA
178774 AAATATAAAAAT
65 AAATATAAAAAT
* *
178786 AATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACATAAAACAAAGATAA
1 AATATCCTAAAACCTAATTAAAATAATAAAACCTATTTAAACTAAAATACATAAAACAAAGATAA
178851 AATATAA
66 AATATAA
178858 TGTTTAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 2 0.03
76 64 0.97
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.26
Consensus pattern (76 bp):
AATATCCTAAAACCTAATTAAAATAATAAAACCTATTTAAACTAAAATACATAAAACAAAGATAA
AATATAAAAAT
Found at i:180922 original size:5 final size:5
Alignment explanation
Indices: 180912--181001 Score: 78
Period size: 5 Copynumber: 18.2 Consensus size: 5
180902 GTTCAGAGAA
* * *
180912 AAAAT AAAAT AAAAT -TAAT CAAAAT AAAAT AAAAT -TAAT AAAAT AAAGT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
****
180961 TTGCT AAAAT AAAAT AAAAT GAAAAT AAAAT AAAA- AAAAT A
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT A
181002 GAACGAAATG
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
4 10 0.15
5 49 0.73
6 8 0.12
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:180952 original size:34 final size:35
Alignment explanation
Indices: 180912--180995 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 35
180902 GTTCAGAGAA
180912 AAAATAAAATAAAATTAAT-C-AAAATAAAATAAAAT
1 AAAATAAAATAAAATT--TGCTAAAATAAAATAAAAT
* *
180947 -TAATAAAATAAAGTTTGCTAAAATAAAATAAAAT
1 AAAATAAAATAAAATTTGCTAAAATAAAATAAAAT
180981 GAAAATAAAATAAAA
1 -AAAATAAAATAAAA
180996 AAAATAGAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
32 1 0.02
33 1 0.02
34 28 0.68
36 11 0.27
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (35 bp):
AAAATAAAATAAAATTTGCTAAAATAAAATAAAAT
Found at i:185983 original size:20 final size:20
Alignment explanation
Indices: 185960--186037 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 20
185950 AGAACCCCAG
*
185960 GGGGGTATCGATTCCCCT-A
1 GGGGGAATCGATTCCCCTCA
*
185979 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC--A
*
186002 GGGGGAATCGGTT-CCCTCA
1 GGGGGAATCGATTCCCCTCA
*
186021 TGGGGGTATCGATTCCC
1 -GGGGGAATCGATTCCC
186038 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 16 0.33
20 12 0.24
21 4 0.08
22 3 0.06
23 14 0.29
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTCA
Found at i:186038 original size:20 final size:20
Alignment explanation
Indices: 185960--186039 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
185950 AGAACCCCAG
*
185960 GGGGGTATCGATTCCC-C-T
1 GGGGGAATCGATTCCCTCAT
* *
185978 AGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TC-AT
*
186002 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
186022 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
186040 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.22
20 20 0.40
21 2 0.04
22 4 0.08
23 13 0.26
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:188971 original size:20 final size:20
Alignment explanation
Indices: 188930--188972 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
188920 TCTAAGAGCC
*
188930 CATTTAGGACTATTTAGATG
1 CATTTAGGACTATATAGATG
*
188950 CATTTAGGAGC-ATATAGTTG
1 CATTTAGGA-CTATATAGATG
188970 CAT
1 CAT
188973 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGACTATATAGATG
Found at i:193859 original size:20 final size:20
Alignment explanation
Indices: 193834--193876 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
193824 TCTAAGAGCC
*
193834 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
193854 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
193874 CAT
1 CAT
193877 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:196635 original size:22 final size:21
Alignment explanation
Indices: 196593--196632 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
196583 GAGTTTATTT
*
196593 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
196614 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
196633 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:200325 original size:14 final size:15
Alignment explanation
Indices: 200308--200336 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
200298 AAATAATTAT
200308 AAATAA-AAAAGGAA
1 AAATAATAAAAGGAA
200322 AAATAATAAAAGGAA
1 AAATAATAAAAGGAA
200337 TTAAAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (15 bp):
AAATAATAAAAGGAA
Found at i:200422 original size:17 final size:16
Alignment explanation
Indices: 200395--200426 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
200385 AAGTATAATG
200395 AAATAATAAATAAATA
1 AAATAATAAATAAATA
200411 AAATACATAAATAAAT
1 AAATA-ATAAATAAAT
200427 TGGGATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAATAAATAAATA
Found at i:201199 original size:19 final size:18
Alignment explanation
Indices: 201175--201218 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
201165 GAGTATATAT
201175 TAATATAATATTAAAAATA
1 TAATAT-ATATTAAAAATA
*
201194 TAATAT-TATTAAAATTA
1 TAATATATATTAAAAATA
*
201211 TATTATAT
1 TAATATAT
201219 GCATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATATATTAAAAATA
Found at i:201753 original size:16 final size:17
Alignment explanation
Indices: 201734--201768 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
201724 ATAAAAAAGG
*
201734 AAAATAAAT-AAAATAA
1 AAAACAAATAAAAATAA
201750 AAAACAAATAAAAATAA
1 AAAACAAATAAAAATAA
201767 AA
1 AA
201769 GGTGAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAACAAATAAAAATAA
Found at i:202032 original size:2 final size:2
Alignment explanation
Indices: 202025--202051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
202015 ATAATAGTAA
202025 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 A
202052 ATAAAATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:202134 original size:2 final size:2
Alignment explanation
Indices: 202098--202126 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
202088 ACAAAAGGTA
202098 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 A
202127 GGTATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:202619 original size:19 final size:19
Alignment explanation
Indices: 202595--202637 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
202585 GGGTCGTATT
202595 TTCCAGAAACCAGAGGATG
1 TTCCAGAAACCAGAGGATG
* * *
202614 TTCCAGAAATCGGCGGATG
1 TTCCAGAAACCAGAGGATG
202633 TTCCA
1 TTCCA
202638 CCTCGCACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (19 bp):
TTCCAGAAACCAGAGGATG
Found at i:204238 original size:31 final size:32
Alignment explanation
Indices: 204197--204266 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
204187 GTCGAACTCG
* * *
204197 AAGGTCTTT-TGTTTCAAGAGAAACATTTTCT
1 AAGGTTTTTGTGTTTCAAGAGAAACAATTTCA
204228 AAGGTTTTTTGTGTTTCAAGAGAAACAATTTCA
1 AAGG-TTTTTGTGTTTCAAGAGAAACAATTTCA
204261 AAGGTT
1 AAGGTT
204267 ATATTTCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 4 0.12
32 6 0.18
33 24 0.71
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (32 bp):
AAGGTTTTTGTGTTTCAAGAGAAACAATTTCA
Found at i:206473 original size:95 final size:95
Alignment explanation
Indices: 206310--206491 Score: 278
Period size: 95 Copynumber: 1.9 Consensus size: 95
206300 ATATGTAAAT
* *
206310 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAACCAAGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCAAGGCGTTTAACCAATTGCCTTAGAGGG
*
206375 ACAACTCAGGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
* **
206405 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTATG-C-TAGAG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCAAGGCGTTTAACCAA-T-TGCCTTAGAG
206468 GGACAACTCAAGCTTTATTGTATA
64 GGACAACTCAAGCTTTATTGTATA
206492 TAAATAATAT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
95 75 0.95
96 2 0.03
97 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCAAGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:210423 original size:16 final size:17
Alignment explanation
Indices: 210404--210438 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
210394 ATAAAAAAGG
*
210404 AAAATAAAT-AAAATAA
1 AAAACAAATAAAAATAA
210420 AAAACAAATAAAAATAA
1 AAAACAAATAAAAATAA
210437 AA
1 AA
210439 GGTGAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAACAAATAAAAATAA
Found at i:214513 original size:12 final size:12
Alignment explanation
Indices: 214498--214522 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
214488 TAAAAAAAGT
214498 TAAAAAATTATA
1 TAAAAAATTATA
214510 TAAAAAATTATA
1 TAAAAAATTATA
214522 T
1 T
214523 TATATATATA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAAATTATA
Found at i:214567 original size:23 final size:23
Alignment explanation
Indices: 214523--214567 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
214513 AAAATTATAT
* * *
214523 TATATATATAATATATTTAATCA
1 TATAAATATAATAAATTCAATCA
*
214546 TATAAATATTATAAATTCAATC
1 TATAAATATAATAAATTCAATC
214568 CGATTACACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAAATATAATAAATTCAATCA
Found at i:215500 original size:21 final size:21
Alignment explanation
Indices: 215453--215503 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
215443 TGAAAATCAA
215453 ACAATAAAAGAAAATAAAGGT
1 ACAATAAAAGAAAATAAAGGT
** *
215474 GTAATATAAGAAAATAAAAGG-
1 ACAATAAAAGAAAAT-AAAGGT
215495 ACAATAAAA
1 ACAATAAAA
215504 AATATCGACG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.67, C:0.04, G:0.14, T:0.16
Consensus pattern (21 bp):
ACAATAAAAGAAAATAAAGGT
Found at i:216758 original size:198 final size:198
Alignment explanation
Indices: 216357--216770 Score: 688
Period size: 199 Copynumber: 2.1 Consensus size: 198
216347 ATTTCTAGAA
* *
216357 ATTGTTAGAAGGATTTGAGGGACCATATTATTGTTAGAATGACCACATTGAGAGTATTTTCTAAC
1 ATTGTTAGAAGGATTTGAGGGACCATATTATTGTTAAAAGGACCACATTGAGAGTATTTTCTAAC
* * *
216422 AATATTTTGGACACTCAATATTCAAACTCTTAAAAAATAGTTTAAATACCACATTGAGTGCAAAA
66 AATAATTTGGACAATCAATATTCAAACTCTTAAAAAATAGTTTAAAGACCACATTGAGTGCAAAA
216487 AAGTTTAGGGATCATATTATTTTTTTCAAAAGTTTGAGGGTTTTAGATATCATTAAATAAAAAAA
131 AAGTTTAGGGATCATATTATTTTTTTCAAAAGTTTGAGGGTTTTAGATATCATTAAATAAAAAAA
216552 ATT
196 ATT
* *
216555 ATTGTTAGAAGGATTTGAGGGACCATATTATTGTTAAAAGGACCACGTTGAGTGTATTTTTCTAA
1 ATTGTTAGAAGGATTTGAGGGACCATATTATTGTTAAAAGGACCACATTGAGAGTA-TTTTCTAA
* * *
216620 TAATAATTTGGACAATCAATATTCAAACTCTTAAAAAATTAGTTTAAGGATCACATTGAGTGCAA
65 CAATAATTTGGACAATCAATATTCAAACTCTTAAAAAA-TAGTTTAAAGACCACATTGAGTGCAA
*
216685 AAAAGTTTAGGGATCATA-TATTTTTTTCAAAAGTTTGAGGGTTTTAGATATCATTAAAT-CAAA
129 AAAAGTTTAGGGATCATATTATTTTTTTCAAAAGTTTGAGGGTTTTAGATATCATTAAATAAAAA
216748 AAATT
194 AAATT
*
216753 ATTGTTAGAATGATTTGA
1 ATTGTTAGAAGGATTTGA
216771 ACATGTGTAA
Statistics
Matches: 202, Mismatches: 12, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
198 77 0.38
199 84 0.42
200 41 0.20
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (198 bp):
ATTGTTAGAAGGATTTGAGGGACCATATTATTGTTAAAAGGACCACATTGAGAGTATTTTCTAAC
AATAATTTGGACAATCAATATTCAAACTCTTAAAAAATAGTTTAAAGACCACATTGAGTGCAAAA
AAGTTTAGGGATCATATTATTTTTTTCAAAAGTTTGAGGGTTTTAGATATCATTAAATAAAAAAA
ATT
Found at i:219078 original size:34 final size:34
Alignment explanation
Indices: 219029--219095 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
219019 GTTAGATAGG
* * *
219029 AAAATAAGTAAAAAATATAAAT-AAATGAAAAGAC
1 AAAAAAAGGAAAAAATA-AAATAAAATAAAAAGAC
219063 AAAAAAAGGAAAAAATAAAATAAAATAAAAAGA
1 AAAAAAAGGAAAAAATAAAATAAAATAAAAAGA
219096 ATAAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.76, C:0.01, G:0.09, T:0.13
Consensus pattern (34 bp):
AAAAAAAGGAAAAAATAAAATAAAATAAAAAGAC
Found at i:219082 original size:16 final size:17
Alignment explanation
Indices: 219029--219086 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
219019 GTTAGATAGG
*
219029 AAAAT-AAGTAAAAAAT
1 AAAATAAAGGAAAAAAT
* * *
219045 ATAAATAAATGAAAAGAC
1 A-AAATAAAGGAAAAAAT
219063 AAAA-AAAGGAAAAAAT
1 AAAATAAAGGAAAAAAT
219079 AAAATAAA
1 AAAATAAA
219087 ATAAAAAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
16 14 0.44
17 10 0.31
18 8 0.25
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.14
Consensus pattern (17 bp):
AAAATAAAGGAAAAAAT
Found at i:219143 original size:3 final size:3
Alignment explanation
Indices: 219135--219181 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
219125 ATCAAAGGAA
*
219135 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
219182 ATAAAACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:220602 original size:39 final size:39
Alignment explanation
Indices: 220513--220729 Score: 159
Period size: 35 Copynumber: 5.9 Consensus size: 39
220503 TTTAAAAACG
* *
220513 TTTTTCAAAACTATATATTATAT-AGTTTTCAAAAATG-
1 TTTTTTAAAACTATATATTATATAAGTTTTCCAAAATGT
* *
220550 -ATTTT-AAA--A-ATATTATATAAGCTTTCCAAAATGT
1 TTTTTTAAAACTATATATTATATAAGTTTTCCAAAATGT
*
220584 TTTTTTAAAACTATATATTATATAAATTTTCCAAAAATGT
1 TTTTTTAAAACTATATATTATATAAGTTTTCC-AAAATGT
*
220624 TTTTTTAAAAACTAAATA-T-TAT-A-TTTT-CAAAATG-
1 TTTTTT-AAAACTATATATTATATAAGTTTTCCAAAATGT
* *
220658 -ATTTCAAAACTATATATTGA-ATAA-TTTT-CAAAATG-
1 TTTTTTAAAACTATATATT-ATATAAGTTTTCCAAAATGT
*
220693 --TTTTAAAACTTATATATTGTATATAAGTTTTCAAAAA
1 TTTTTTAAAAC-TATATA-T-TATATAAGTTTTCCAAAA
220730 AAGTTTTAAA
Statistics
Matches: 148, Mismatches: 13, Indels: 36
0.75 0.07 0.18
Matches are distributed among these distances:
32 19 0.13
33 17 0.11
34 10 0.07
35 31 0.21
36 9 0.06
37 9 0.06
38 6 0.04
39 23 0.16
40 14 0.09
41 10 0.07
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (39 bp):
TTTTTTAAAACTATATATTATATAAGTTTTCCAAAATGT
Found at i:220643 original size:41 final size:39
Alignment explanation
Indices: 220557--220647 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
220547 ATGATTTTAA
*
220557 AAATATTATATAAGCTTTCCAAAATGTTTTTTTAAAACT
1 AAATATTATATAAACTTTCCAAAATGTTTTTTTAAAACT
* *
220596 ATATATTATATAAATTTTCCAAAAATGTTTTTTTAAAAACT
1 AAATATTATATAAACTTTCC-AAAATGTTTTTTT-AAAACT
220637 AAATATTATAT
1 AAATATTATAT
220648 TTTCAAAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 17 0.37
40 13 0.28
41 16 0.35
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (39 bp):
AAATATTATATAAACTTTCCAAAATGTTTTTTTAAAACT
Found at i:220667 original size:73 final size:72
Alignment explanation
Indices: 220488--220696 Score: 225
Period size: 73 Copynumber: 2.9 Consensus size: 72
220478 CAAAAAAATT
* * *
220488 AAACTATATATTATA-TTTAAAAACGTTTTTCAAAACTATATATTATATAGTTTTCAAAAATG--
1 AAACTATATATTATATTTTCAAAATGTTTTTCAAAACTATATATTATATAATTTTCAAAAATGTT
*
220550 ATTTTAA
66 TTTTTAA
* ** * *
220557 AAA-TATTATATAAGCTTTCCAAAATGTTTTTTTAAAACTATATATTATATAAATTTTCCAAAAA
1 AAACTA-TATATTATATTTTCAAAATG-TTTTTCAAAACTATATATTATAT-AATTTT-CAAAAA
220621 TGTTTTTTTAA
62 TGTTTTTTTAA
* *
220632 AAACTAAATATTATATTTTCAAAATG-ATTTCAAAACTATATATTGA-ATAATTTTC-AAAATGT
1 AAACTATATATTATATTTTCAAAATGTTTTTCAAAACTATATATT-ATATAATTTTCAAAAATGT
220694 TTT
65 TTT
220697 AAAACTTATA
Statistics
Matches: 115, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
68 2 0.02
69 9 0.08
70 17 0.15
71 23 0.20
72 11 0.10
73 26 0.23
74 1 0.01
75 24 0.21
76 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (72 bp):
AAACTATATATTATATTTTCAAAATGTTTTTCAAAACTATATATTATATAATTTTCAAAAATGTT
TTTTTAA
Found at i:221567 original size:84 final size:84
Alignment explanation
Indices: 221469--222440 Score: 1100
Period size: 84 Copynumber: 11.7 Consensus size: 84
221459 TGAAATGTAA
* * * * *
221469 TCGAACTCGGAGGTCTTCGGTTGGCACATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
221534 GCCTTAGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * *
221553 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * *
221617 TGCCCTCGAAGCTGAGTGTAA
65 TG-CCTTGGAGCTGAGCGTAG
* * * *
221638 TCGAACTCG-AGAGTC--T--TTGGCAGATAGCCCTTCTCGATTTAAGCTATACTGCAAATGATG
1 TCGAACTCGAAG-GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
*
221698 TGCCTTGAAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
* * * * *
221718 TTGAACTCAAAGGTCTTTAGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
221783 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
221802 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * ** *
221867 GCCCTCGAAGCTGAGTATAA
66 G-CCTTGGAGCTGAGCGTAG
* * * * *
221887 TCGAACTTGAGGGTC--T--TTGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
221948 GCCTTGGAGCTGAGAGTAG
66 GCCTTGGAGCTGAGCGTAG
* * *
221967 TCAAACTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
222032 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* *
222051 TCGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * * *
222116 ACCCTCGAAGCTGAGTGTAA
66 -GCCTTGGAGCTGAGCGTAG
* * * * * *
222136 TCGAACTTGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACCTAAGCTATGCTGCAAATGACGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
222197 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * *
222216 TCGTACTCAAATGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
222281 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * *
222300 TCGAAATCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * *
222364 TGCCCTCGAAGCTGAGTGTAA
65 TG-CCTTGGAGCTGAGCGTAG
* * * * *
222385 TCGAACTCGAGGGTC--T--TTGGAAGATAGCCCTTCTCGACTTAAGCTATACTGCAAAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
222441 AGTTTGTATA
Statistics
Matches: 742, Mismatches: 124, Indels: 47
0.81 0.14 0.05
Matches are distributed among these distances:
80 72 0.10
81 150 0.20
82 5 0.01
83 2 0.00
84 399 0.54
85 114 0.15
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:221923 original size:249 final size:249
Alignment explanation
Indices: 221469--222440 Score: 1534
Period size: 249 Copynumber: 3.9 Consensus size: 249
221459 TGAAATGTAA
** * * * *
221469 TCGAACTCGGAGGTCTTCGGTTGGCACATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * *
221534 GCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAA
* *
221599 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTTTGGCAGATA
131 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATA
* *
221664 GCCCTTCTCGATTTAAGCTATACTGCAAATGATGTGCCTTGAAGCTGAGCGTAG
196 GCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * *
221718 TTGAACTCAAAGGTCTTTAGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* *
221783 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTA
* *
221847 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTATAATCGAACTTGAGGGTCTTTGGCAGAT
130 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
* * *
221912 AGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGAGTAG
195 AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* *
221967 TCAAACTCGAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
** *
222032 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGTAGATAACCCTTCTCGACTTA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTA
* * *
222096 AGTTATGCTACAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGAT
130 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
* * *
222161 AGCCCTTCTCGACCTAAGCTATGCTGCAAATGACGTGCCTTGGAGCTGAGCGTAG
195 AGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* *
222216 TCGTACTCAAATGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
* * *
222281 GCCTTGGAGCTGAGCGTAGTCGAAATCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAA
* *
222346 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGAAGATA
131 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATA
222411 GCCCTTCTCGACTTAAGCTATACTGCAAAT
196 GCCCTTCTCGACTTAAGCTATACTGCAAAT
222441 AGTTTGTATA
Statistics
Matches: 668, Mismatches: 53, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
248 5 0.01
249 658 0.99
250 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (249 bp):
TCGAACTCAAAGGCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAA
GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATA
GCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
Found at i:227468 original size:15 final size:15
Alignment explanation
Indices: 227435--227476 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
227425 AATAAGTAAA
*
227435 AAAAAATAAATAAATG
1 AAAAAATAAA-AAAGG
*
227451 AAAAGATAAAAAAGG
1 AAAAAATAAAAAAGG
227466 AAAAAATAAAA
1 AAAAAATAAAA
227477 TAAAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (15 bp):
AAAAAATAAAAAAGG
Found at i:227545 original size:15 final size:15
Alignment explanation
Indices: 227423--227571 Score: 53
Period size: 15 Copynumber: 9.7 Consensus size: 15
227413 GTTAGATAGG
*
227423 AAAATAAGTAAAA-A
1 AAAATAAATAAAATA
227437 AAAATAAAT-AAATGA
1 AAAATAAATAAAAT-A
227452 AAAGATAAA-AAAGGA-A
1 AAA-ATAAATAAA--ATA
227468 AAAATAAAATAAAAATA
1 AAAAT-AAAT-AAAATA
* * *
227485 ATAGT-AATATAAA-G
1 AAAATAAATA-AAATA
**
227499 AAAATAAATCAAAGGA
1 AAAATAAAT-AAAATA
227515 AAAATAATAATAAAAATA
1 AAAAT-A-AAT-AAAATA
*
227533 AAAATAAATAAAACA
1 AAAATAAATAAAATA
* *
227548 AAGA-AATTAAAAT-
1 AAAATAAATAAAATA
*
227561 TAAATAAATAA
1 AAAATAAATAA
227572 GAAAAAATTA
Statistics
Matches: 100, Mismatches: 18, Indels: 34
0.66 0.12 0.22
Matches are distributed among these distances:
13 5 0.05
14 24 0.24
15 25 0.25
16 24 0.24
17 6 0.06
18 16 0.16
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (15 bp):
AAAATAAATAAAATA
Found at i:228947 original size:71 final size:70
Alignment explanation
Indices: 228847--229059 Score: 233
Period size: 73 Copynumber: 3.0 Consensus size: 70
228837 AAAAAAATTT
* * * *
228847 AAACTATATATTATA-TTTAAAAACGTTTTTCAAAACTATATATTATATAGTTTTCAAAAATGAT
1 AAACTAAATATTATAGTTTCAAAATGTTTTTCAAAACTATATATTATATAATTTTCAAAAATGAT
228911 TTTAA
66 TTTAA
* *
228916 AAA-T-ATTA-TATAAGCTTTCCAAAATGTTTTTTTAAAACTATATATTATATAAATTTTCCAAA
1 AAACTAAATATTAT-AG-TTT-CAAAATG-TTTTTCAAAACTATATATTATAT-AATTTT-CAAA
228978 AATGTTATTTTAA
60 AATG--ATTTTAA
* *
228991 AAACTAAATATTATAGTTTCAAAATG-ATTTCAAAACTATATTTTATATAATTTTC-AAAATG-T
1 AAACTAAATATTATAGTTTCAAAATGTTTTTCAAAACTATATATTATATAATTTTCAAAAATGAT
229053 TTTAA
66 TTTAA
229058 AA
1 AA
229060 CTTACATATT
Statistics
Matches: 122, Mismatches: 10, Indels: 26
0.77 0.06 0.16
Matches are distributed among these distances:
66 3 0.02
67 11 0.09
68 1 0.01
69 6 0.05
70 11 0.09
71 23 0.19
72 11 0.09
73 27 0.22
75 17 0.14
76 4 0.03
77 5 0.04
78 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (70 bp):
AAACTAAATATTATAGTTTCAAAATGTTTTTCAAAACTATATATTATATAATTTTCAAAAATGAT
TTTAA
Found at i:236164 original size:30 final size:29
Alignment explanation
Indices: 236125--236188 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
236115 TAATTTTATA
236125 TAAAATAATTTA-CGTAAAATGAATTAGTTG
1 TAAAATAATTTATC-TAAAATGAATTA-TTG
236155 -AAAATTAATTTATCTAAAATGAATTATTG
1 TAAAA-TAATTTATCTAAAATGAATTATTG
236184 TAAAA
1 TAAAA
236189 AGTTTCCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
29 7 0.23
30 23 0.74
31 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (29 bp):
TAAAATAATTTATCTAAAATGAATTATTG
Found at i:236187 original size:15 final size:15
Alignment explanation
Indices: 236138--236188 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
236128 AATAATTTAC
236138 GTAAAATGAATTAGTT
1 GTAAAATGAATTA-TT
*
236154 G-AAAATTAATT-TAT
1 GTAAAATGAATTAT-T
*
236168 CTAAAATGAATTATT
1 GTAAAATGAATTATT
236183 GTAAAA
1 GTAAAA
236189 AGTTTCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
13 1 0.04
14 1 0.04
15 24 0.86
16 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (15 bp):
GTAAAATGAATTATT
Found at i:236784 original size:42 final size:41
Alignment explanation
Indices: 236732--236810 Score: 122
Period size: 42 Copynumber: 1.9 Consensus size: 41
236722 TTCATTTAGG
* * *
236732 AAAATCAATTACAACTATTAAACACTGGAAAATATTTTCCTT
1 AAAACCAATTACAACTATCAAACACT-GAAAACATTTTCCTT
236774 AAAACCAATTACAACTATCAAACACTGAAAACATTTT
1 AAAACCAATTACAACTATCAAACACTGAAAACATTTT
236811 TCAGCTACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 10 0.29
42 24 0.71
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.29
Consensus pattern (41 bp):
AAAACCAATTACAACTATCAAACACTGAAAACATTTTCCTT
Found at i:242792 original size:16 final size:16
Alignment explanation
Indices: 242771--242803 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
242761 TAATAAATAA
242771 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
242787 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
242803 A
1 A
242804 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:242890 original size:16 final size:16
Alignment explanation
Indices: 242869--242922 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
242859 CATTTAATAA
242869 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
242885 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
* *
242901 ATAAATGAACACGAAC
1 ATAAACGAACACAAAC
242917 ATAAAC
1 ATAAAC
242923 ATTGGAGACC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.61, C:0.22, G:0.07, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:243651 original size:24 final size:24
Alignment explanation
Indices: 243577--243645 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
243567 GATTGGCTTA
243577 AACATAAATGAA-TGAACATAAACG
1 AACATAAATGAACT-AACATAAACG
** *
243601 AACATAACCGAACAAACATAAACG
1 AACATAAATGAACTAACATAAACG
*
243625 AACATAATTGAACTAACATAA
1 AACATAAATGAACTAACATAA
243646 CTGAACGTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.58, C:0.17, G:0.09, T:0.16
Consensus pattern (24 bp):
AACATAAATGAACTAACATAAACG
Found at i:244890 original size:14 final size:14
Alignment explanation
Indices: 244868--244897 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
244858 GTTTTCTGGA
*
244868 TCCGTAAGTCATTT
1 TCCGAAAGTCATTT
244882 TCCGAAAGTCATTT
1 TCCGAAAGTCATTT
244896 TC
1 TC
244898 TGAACCTTTT
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:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (14 bp):
TCCGAAAGTCATTT
Found at i:245032 original size:12 final size:12
Alignment explanation
Indices: 244997--245056 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 12
244987 TAATTATTAA
*
244997 AATATTTAAAAT
1 AATATTTATAAT
245009 -ATATTTAT--T
1 AATATTTATAAT
245018 AATATTTATAAT
1 AATATTTATAAT
*
245030 AATA--TAAAAT
1 AATATTTATAAT
*
245040 AATATTTTTAAT
1 AATATTTATAAT
245052 AATAT
1 AATAT
245057 AATAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
9 1 0.03
10 17 0.44
11 7 0.18
12 14 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATATTTATAAT
Found at i:245067 original size:25 final size:22
Alignment explanation
Indices: 245017--245058 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
245007 ATATATTTAT
245017 TAATATTTATAATAATATAAAA
1 TAATATTTATAATAATATAAAA
*
245039 TAATATTTTTAATAATATAA
1 TAATATTTATAATAATATAA
245059 TAAAATAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATTTATAATAATATAAAA
Found at i:245153 original size:19 final size:19
Alignment explanation
Indices: 245107--245201 Score: 70
Period size: 19 Copynumber: 5.0 Consensus size: 19
245097 TATTTTTATT
*
245107 TTAATAA-ATATATAATAA
1 TTAATAATATATTTAATAA
** *
245125 TTTTTTATATATTTAATAA
1 TTAATAATATATTTAATAA
* *
245144 TGAATAATATTATTTATATAT
1 TTAATAATA-TATTTA-ATAA
* *
245165 TTAATATTA-ATATAATAA
1 TTAATAATATATTTAATAA
245183 TCTAATAATAT-TTTAATAA
1 T-TAATAATATATTTAATAA
245202 AGATATTTAA
Statistics
Matches: 57, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
18 8 0.14
19 33 0.58
20 6 0.11
21 10 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTAATAATATATTTAATAA
Found at i:245168 original size:28 final size:29
Alignment explanation
Indices: 245041--245201 Score: 109
Period size: 29 Copynumber: 5.4 Consensus size: 29
245031 ATATAAAATA
* * *
245041 ATATTTTTAATAATATAATAAAATAATCAATT
1 ATATATTTAATAATAT-AT--AATAATTATTT
* *
245073 ATAT-TATAATAATATA-AGATATTATATTT
1 ATATATTTAATAATATATA-ATAAT-TATTT
* *
245102 TTAT-TTTAATAAATATATAATAATTTTTT
1 ATATATTTAAT-AATATATAATAATTATTT
245131 ATATATTTAATAATGA-ATAAT-ATTATTT
1 ATATATTTAATAAT-ATATAATAATTATTT
* * *
245159 ATATATTTAATATTAATATAATAATCTAATA
1 ATATATTTAATAAT-ATATAATAAT-TATTT
245190 ATAT-TTTAATAA
1 ATATATTTAATAA
245202 AGATATTTAA
Statistics
Matches: 105, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.01
28 24 0.23
29 31 0.30
30 27 0.26
31 18 0.17
32 4 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
ATATATTTAATAATATATAATAATTATTT
Found at i:245368 original size:48 final size:48
Alignment explanation
Indices: 245316--245417 Score: 109
Period size: 49 Copynumber: 2.1 Consensus size: 48
245306 CCAATATTAA
*
245316 TATTTT-TATTAATAAAATTATAAAAATAATATTTAATAATAAATAA-AT
1 TATTTTATATT-ATAAAATAATAAAAATAA-ATTTAATAATAAATAATAT
* * * * *
245364 TATTTTAATATTTTAAAATAATAATATTAAATTTTATGATAAATAATAT
1 TATTTT-ATATTATAAAATAATAAAAATAAATTTAATAATAAATAATAT
245413 TATTT
1 TATTT
245418 ATTGTATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
48 20 0.44
49 21 0.47
50 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (48 bp):
TATTTTATATTATAAAATAATAAAAATAAATTTAATAATAAATAATAT
Found at i:245619 original size:26 final size:27
Alignment explanation
Indices: 245588--245639 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
245578 AGAAATGTAA
*
245588 TTCATTTTCCAG-ATTTCAAATTCCAG
1 TTCATTTTCCAGTAATTCAAATTCCAG
245614 TTCATTTTCCAGTAATTCAAATTCCA
1 TTCATTTTCCAGTAATTCAAATTCCA
245640 ATAATTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (27 bp):
TTCATTTTCCAGTAATTCAAATTCCAG
Found at i:245638 original size:15 final size:15
Alignment explanation
Indices: 245620--245662 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
245610 CCAGTTCATT
245620 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
*
245635 TTCCAATAATTCAAA
1 TTCCAGTAATTCAAA
*
245650 TTCCAGCAATTCA
1 TTCCAGTAATTCA
245663 TTTTCCAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:245668 original size:15 final size:14
Alignment explanation
Indices: 245594--245672 Score: 63
Period size: 15 Copynumber: 5.6 Consensus size: 14
245584 GTAATTCATT
*
245594 TTCCAGATTTCAAA
1 TTCCAGAATTCAAA
**
245608 TTCCAG--TTCATT
1 TTCCAGAATTCAAA
245620 TTCCAGTAATTCAAA
1 TTCCAG-AATTCAAA
*
245635 TTCCAATAATTCAAA
1 TTCC-AGAATTCAAA
**
245650 TTCCAGCAATTCATT
1 TTCCAG-AATTCAAA
245665 TTCCAGAA
1 TTCCAGAA
245673 AACCAATTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
12 10 0.19
14 9 0.17
15 32 0.62
16 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (14 bp):
TTCCAGAATTCAAA
Found at i:267437 original size:23 final size:23
Alignment explanation
Indices: 267389--267439 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
267379 TTTTGTCACT
* *
267389 TTCTCTTCATTTCCCTCTTTTCC
1 TTCTCTTCACTTCCCTCATTTCC
*
267412 TTCTCTTCCACTTCTCTCATTT-C
1 TTCTCTT-CACTTCCCTCATTTCC
267435 TTCTC
1 TTCTC
267440 CAAGAGCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (23 bp):
TTCTCTTCACTTCCCTCATTTCC
Found at i:269268 original size:31 final size:31
Alignment explanation
Indices: 269184--269363 Score: 234
Period size: 31 Copynumber: 5.8 Consensus size: 31
269174 CCAAATACTA
* *
269184 GTCAGGTTTGCGTTCAGATAATGCACAATAT
1 GTCAGGTTTGCATTCAGATAATGCACAGTAT
* **
269215 GTTCATGTTTGCATTCAGATAATGCATGGTAT
1 G-TCAGGTTTGCATTCAGATAATGCACAGTAT
* *
269247 GTCAGGTTTACATTCAAATAATGCACAGTAT
1 GTCAGGTTTGCATTCAGATAATGCACAGTAT
*
269278 GTCAAGTTTGCATTCAGATAATGCACAGTAT
1 GTCAGGTTTGCATTCAGATAATGCACAGTAT
* *
269309 GTCAAGTTTGCATTCATATAATGCACAGTAT
1 GTCAGGTTTGCATTCAGATAATGCACAGTAT
** *
269340 GTCAGGTTCACATTTAGATAATGC
1 GTCAGGTTTGCATTCAGATAATGC
269364 GTAGCAGTTC
Statistics
Matches: 129, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
31 103 0.80
32 26 0.20
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (31 bp):
GTCAGGTTTGCATTCAGATAATGCACAGTAT
Found at i:269353 original size:93 final size:94
Alignment explanation
Indices: 269184--269363 Score: 263
Period size: 93 Copynumber: 1.9 Consensus size: 94
269174 CCAAATACTA
* * * **
269184 GTCAGGTTTGCGTTCAGATAATGCACAATATGTTCATGTTTGCATTCAGATAATGCATGGTATGT
1 GTCAAGTTTGCATTCAGATAATGCACAATATGTTCAAGTTTGCATTCAGATAATGCACAGTATGT
*
269249 CAGGTTTACATTCAAATAATGCACAGTAT
66 CAGGTTCACATTCAAATAATGCACAGTAT
* *
269278 GTCAAGTTTGCATTCAGATAATGCACAGTATG-TCAAGTTTGCATTCATATAATGCACAGTATGT
1 GTCAAGTTTGCATTCAGATAATGCACAATATGTTCAAGTTTGCATTCAGATAATGCACAGTATGT
* *
269342 CAGGTTCACATTTAGATAATGC
66 CAGGTTCACATTCAAATAATGC
269364 GTAGCAGTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
93 47 0.62
94 29 0.38
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (94 bp):
GTCAAGTTTGCATTCAGATAATGCACAATATGTTCAAGTTTGCATTCAGATAATGCACAGTATGT
CAGGTTCACATTCAAATAATGCACAGTAT
Found at i:277581 original size:21 final size:21
Alignment explanation
Indices: 277555--277603 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
277545 TACCGAAATG
277555 CCACATATTTATCCC-AGAGGA
1 CCACATATTTATCCCGA-AGGA
* *
277576 CCACATATTTGTCCCGAATGA
1 CCACATATTTATCCCGAAGGA
277597 CCACATA
1 CCACATA
277604 AGACCCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.31, G:0.12, T:0.24
Consensus pattern (21 bp):
CCACATATTTATCCCGAAGGA
Found at i:280055 original size:11 final size:10
Alignment explanation
Indices: 280034--280126 Score: 57
Period size: 11 Copynumber: 8.8 Consensus size: 10
280024 AATATGTATT
*
280034 TAATATTATA
1 TAATAATATA
*
280044 TCATAATAATA
1 TAATAAT-ATA
280055 TAATAATGATA
1 TAATAAT-ATA
280066 TCAA-AATATAA
1 T-AATAATAT-A
*
280077 TAATATTATTA
1 TAATAATA-TA
*
280088 AAATAATAT-
1 TAATAATATA
280097 TAATAATATGA
1 TAATAATAT-A
280108 TACA-AATAATA
1 TA-ATAAT-ATA
280119 TAATAATA
1 TAATAATA
280127 CTATGATACG
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
9 8 0.12
10 12 0.18
11 39 0.60
12 6 0.09
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (10 bp):
TAATAATATA
Found at i:281251 original size:22 final size:22
Alignment explanation
Indices: 281225--281272 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
281215 TATTAAATAT
281225 TTAATACGATCGATTAATTCGG
1 TTAATACGATCGATTAATTCGG
281247 TTAATACGATCGATTAATTCGG
1 TTAATACGATCGATTAATTCGG
281269 TTAA
1 TTAA
281273 AACAGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (22 bp):
TTAATACGATCGATTAATTCGG
Found at i:287150 original size:24 final size:24
Alignment explanation
Indices: 287120--287165 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
287110 TTTGTTTAAA
**
287120 TTTATTTATTTAATAAATAAATTT
1 TTTATTTACATAATAAATAAATTT
*
287144 TTTATTTACATAATAATTAAAT
1 TTTATTTACATAATAAATAAAT
287166 AAACAATATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTATTTACATAATAAATAAATTT
Found at i:287159 original size:20 final size:21
Alignment explanation
Indices: 287116--287156 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
287106 TATGTTTGTT
287116 TAAATTTATTTATTTAATAAA
1 TAAATTTATTTATTTAATAAA
287137 TAAATTT-TTTATTTACATAA
1 TAAATTTATTTATTTA-ATAA
287157 TAATTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TAAATTTATTTATTTAATAAA
Found at i:289867 original size:130 final size:131
Alignment explanation
Indices: 289634--289997 Score: 428
Period size: 130 Copynumber: 2.8 Consensus size: 131
289624 ATCGATATTG
* * * * * * *
289634 AGAATATTAATATCTTTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGTATGAAATATCA
1 AGAATAATGATATCTTTTCATTTCGATTAGAGTAATAAATGACTGCTTTAAGGTATGAGATGTCG
* * * * *
289699 TTTATTCTCGATTGGAAATAATT-TGATATTACCGTTTTCGCTCGAATTAATATTGATTTTTAA-
66 TTTATTCTCGATTAGAAATAATTAT-ATATTATCATTTTCACTCGAATTAATATTGAATTTTAAG
*
289762 AT
130 AC
* * * * *
289764 AGAATAGTGATATCTTTGCATTTCGATTTGAGCAATAAATGACTGCTTTAAAGTATGAGATGTCG
1 AGAATAATGATATCTTTTCATTTCGATTAGAGTAATAAATGACTGCTTTAAGGTATGAGATGTCG
* * *
289829 TTTATTCTTGATTAGAAATTATTATATATTATCATTTTCACTCGAATTGATATTGAATTTTAAGA
66 TTTATTCTCGATTAGAAATAATTATATATTATCATTTTCACTCGAATTAATATTGAATTTTAAGA
289894 C
131 C
* * * *
289895 AGAATAATGATATTTTTTCATTTCGATTAGAGTAATAAATGATTG-TTTAGGGGTATGAGAGGTC
1 AGAATAATGATATCTTTTCATTTCGATTAGAGTAATAAATGACTGCTTTA-AGGTATGAGATGTC
* * * *
289959 GTTTATTCTCGATTTGAAAGAATTAGATATTATTATTTT
65 GTTTATTCTCGATTAGAAATAATTATATATTATCATTTT
289998 TTCTCTTAAA
Statistics
Matches: 197, Mismatches: 34, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
130 112 0.57
131 85 0.43
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (131 bp):
AGAATAATGATATCTTTTCATTTCGATTAGAGTAATAAATGACTGCTTTAAGGTATGAGATGTCG
TTTATTCTCGATTAGAAATAATTATATATTATCATTTTCACTCGAATTAATATTGAATTTTAAGA
C
Found at i:291065 original size:31 final size:31
Alignment explanation
Indices: 291024--291092 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
291014 TTGTGCCATT
* *
291024 TACCACTAAACTATAGGTGGTGTATCGTTTA
1 TACCATTAAACTATAGGTGGTGTATCATTTA
* * *
291055 TATCATTAAACTTTAGGTGTTGTATCATTTA
1 TACCATTAAACTATAGGTGGTGTATCATTTA
291086 TACCATT
1 TACCATT
291093 GAAATTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (31 bp):
TACCATTAAACTATAGGTGGTGTATCATTTA
Done.