Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001965.1 Hibiscus syriacus cultivar Beakdansim tig00003969_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: 250570
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:993 original size:23 final size:25
Alignment explanation
Indices: 962--1033 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 25
952 TGCATTATAA
962 AAAATTAAA-ATTAATAATAAAT-TT
1 AAAATTAAACA-TAATAATAAATATT
986 -AAATTAAACATAATAATAAATATT
1 AAAATTAAACATAATAATAAATATT
**
1010 AAAATTAATTATAA-AA-AAATATT
1 AAAATTAAACATAATAATAAATATT
1033 A
1 A
1034 CCATATCGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 27 0.63
24 5 0.12
25 11 0.26
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAATTAAACATAATAATAAATATT
Found at i:998 original size:17 final size:17
Alignment explanation
Indices: 958--992 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
948 AATATGCATT
*
958 ATAAAAAATTAAAATTA
1 ATAATAAATTAAAATTA
*
975 ATAATAAATTTAAATTA
1 ATAATAAATTAAAATTA
992 A
1 A
993 ACATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAAATTAAAATTA
Found at i:1195 original size:31 final size:31
Alignment explanation
Indices: 1129--1228 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
1119 TAATTAGCAC
* * *
1129 AAAAATAATTA-ATTAATA-AATTTAAAT-A
1 AAAAATAATTATATAAATATTATTTTAATAA
*
1157 AATAATAATTATATAAATATTATTTTAATAA
1 AAAAATAATTATATAAATATTATTTTAATAA
* * *
1188 AAAAATAA-TATTTATATAATTATATTAATATA
1 AAAAATAATTATATAAAT-ATTATTTTAATA-A
*
1220 AAATATAAT
1 AAAAATAAT
1229 AACTATTTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 10 0.18
29 6 0.11
30 14 0.25
31 19 0.33
32 8 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAAATAATTATATAAATATTATTTTAATAA
Found at i:1239 original size:24 final size:23
Alignment explanation
Indices: 1203--1248 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1193 TAATATTTAT
* *
1203 ATAATTATATTAATATAAAATATA
1 ATAACTATATTAA-AAAAAATATA
*
1227 ATAACTATTTTAAAAAAAATAT
1 ATAACTATATTAAAAAAAATAT
1249 TAACTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAACTATATTAAAAAAAATATA
Found at i:1546 original size:60 final size:60
Alignment explanation
Indices: 1438--1585 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 60
1428 CATTTAATGA
* * *
1438 AAGGCGCGTCCCCAGGGATACGCCTTTCACACGTGACAACCGAATCAGC-AAAACCCCGT
1 AAGGCGCGTCCCCGGGGATGCGCCTTTCACACGTGACAACCGAATCAGCGAAAACCACGT
* * * *
1497 GAAGGCGCATCCCCGGGGATGCGCCTTTCACACGT-AGCATCC-AACTCAGCGTAAAATCAGGT
1 -AAGGCGCGTCCCCGGGGATGCGCCTTTCACACGTGA-CAACCGAA-TCAGCG-AAAACCACGT
*
1559 AAAGCGCGT-CCCGGGGATGCGCCTTTC
1 AAGGCGCGTCCCCGGGGATGCGCCTTTC
1586 TCCACCTCAG
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
59 3 0.04
60 58 0.77
61 7 0.09
62 7 0.09
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (60 bp):
AAGGCGCGTCCCCGGGGATGCGCCTTTCACACGTGACAACCGAATCAGCGAAAACCACGT
Found at i:4112 original size:21 final size:21
Alignment explanation
Indices: 4083--4126 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
4073 ATAATTTAAA
**
4083 TAAAGCAATTCATTTTAAAAAT
1 TAAAGCAA-TCATGATAAAAAT
4105 TAAA-CAATCATGATAAAAAT
1 TAAAGCAATCATGATAAAAAT
4125 TA
1 TA
4127 GAACCCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 3 0.15
22 4 0.20
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.32
Consensus pattern (21 bp):
TAAAGCAATCATGATAAAAAT
Found at i:4625 original size:82 final size:84
Alignment explanation
Indices: 4539--4718 Score: 215
Period size: 82 Copynumber: 2.2 Consensus size: 84
4529 ATTTTTTAAC
** ****
4539 AAACGCCGCAATAGAAT-GGTAAATTAGCAGCGTTTATACCACAAACGCTGTGATAGATTA-ACA
1 AAACGCCGCAATAG-ATCAATAAATTAGCAGCGTTTATACCACAAACGCCACAATAGATTACACA
4602 TATAGTGACGTTT-TAGCC-A
65 TATAGTGACGTTTAT-GCCTA
* * *
4621 AAACGCTGTAATAGATCAATAAATTAGCGGCGTTTATACCACAAACGCCACAATAGATTACACAT
1 AAACGCCGCAATAGATCAATAAATTAGCAGCGTTTATACCACAAACGCCACAATAGATTACACAT
* *
4686 ATAGTGGCGTTTATTCCTA
66 ATAGTGACGTTTATGCCTA
4705 AAACGCCGCAATAG
1 AAACGCCGCAATAG
4719 TGATAATAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
81 2 0.02
82 48 0.59
83 17 0.21
84 14 0.17
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (84 bp):
AAACGCCGCAATAGATCAATAAATTAGCAGCGTTTATACCACAAACGCCACAATAGATTACACAT
ATAGTGACGTTTATGCCTA
Found at i:4676 original size:42 final size:41
Alignment explanation
Indices: 4537--4759 Score: 154
Period size: 42 Copynumber: 5.4 Consensus size: 41
4527 ACATTTTTTA
** **
4537 ACAAACGCCGCAATAGAATGGTAAATTAGCAGCGTTTATACC
1 ACAAACGCCGCAATAG-ATAATAAATTAGTGGCGTTTATACC
* ** *
4579 ACAAACGCTGTGATAGAT--TAACATATAGTGACGTTT-TAGCC
1 ACAAACGCCGCAATAGATAATAA-AT-TAGTGGCGTTTATA-CC
* * *
4620 A-AAACGCTGTAATAGATCAATAAATTAGCGGCGTTTATACC
1 ACAAACGCCGCAATAGAT-AATAAATTAGTGGCGTTTATACC
* * * * *
4661 ACAAACGCCACAATAGATTACACATATAGTGGCGTTTATTCC
1 ACAAACGCCGCAATAGATAATAAAT-TAGTGGCGTTTATACC
* *
4703 TA-AAACGCCGCAATAGTGATAATAAA-TAGTGGCGTTTTTA-G
1 -ACAAACGCCGCAATA--GATAATAAATTAGTGGCGTTTATACC
4744 ACAAACGCCGCAATAG
1 ACAAACGCCGCAATAG
4760 TGTTAATCAA
Statistics
Matches: 144, Mismatches: 24, Indels: 29
0.73 0.12 0.15
Matches are distributed among these distances:
39 4 0.03
40 20 0.14
41 42 0.29
42 68 0.47
43 4 0.03
44 6 0.04
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (41 bp):
ACAAACGCCGCAATAGATAATAAATTAGTGGCGTTTATACC
Found at i:4750 original size:83 final size:79
Alignment explanation
Indices: 4591--4864 Score: 225
Period size: 83 Copynumber: 3.3 Consensus size: 79
4581 AAACGCTGTG
* * * * *
4591 ATAGATTAACATATAGTGACGTTTTAGCCAAAACGCTGTAATA--GATCAATAAATTAGCGGCGT
1 ATAGATTAACATATAGTGGCGTTTT-TCCAAAACGCCGCAATAGTGAT-AATAAA-TAGTGGCGT
*
4654 TTATACCACAAACGCCACA
63 TTTTA--ACAAACGCCACA
4673 ATAGATTACACATATAGTGGCGTTTATTCCTAAAACGCCGCAATAGTGATAATAAATAGTGGCGT
1 ATAGATTA-ACATATAGTGGCGTTT-TTCC-AAAACGCCGCAATAGTGATAATAAATAGTGGCGT
*
4738 TTTTAGACAAACGCCGCA
63 TTTTA-ACAAACGCCACA
* ** * ** *
4756 ATAGTGTTAATCA-ATAGTGGCGTTTTTAGAAAAACACCGCAATAGTTTTAATCAATAGTGGCGT
1 ATAG-ATTAA-CATATAGTGGCGTTTTT-CCAAAACGCCGCAATAGTGATAATAAATAGTGGCG-
*
4820 TGTTTTAACAAACGTCACA
62 T-TTTTAACAAACGCCACA
*
4839 ATAG-TGTAATCA-ATAGTGGCATTTTT
1 ATAGAT-TAA-CATATAGTGGCGTTTTT
4865 TTGTATAAAT
Statistics
Matches: 163, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
81 1 0.01
82 58 0.36
83 60 0.37
84 35 0.21
85 6 0.04
86 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (79 bp):
ATAGATTAACATATAGTGGCGTTTTTCCAAAACGCCGCAATAGTGATAATAAATAGTGGCGTTTT
TAACAAACGCCACA
Found at i:4760 original size:41 final size:41
Alignment explanation
Indices: 4705--4864 Score: 216
Period size: 41 Copynumber: 3.9 Consensus size: 41
4695 TTTATTCCTA
* *
4705 AAACGCCGCAATAGTGATAATAAATAGTGGCGTTTTTAGAC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
*
4746 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAA
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
* *
4787 AAACACCGCAATAGTTTTAATCAATAGTGGCGTTGTTTTA-AC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCG-T-TTTTAGAC
* * *
4829 AAACGTCACAATAGTG-TAATCAATAGTGGCATTTTT
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
4865 TTGTATAAAT
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 1 0.01
41 82 0.77
42 14 0.13
43 5 0.05
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (41 bp):
AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
Found at i:4820 original size:82 final size:83
Alignment explanation
Indices: 4661--4864 Score: 238
Period size: 82 Copynumber: 2.5 Consensus size: 83
4651 CGTTTATACC
* * * *
4661 ACAAACGCCACAATAG-ATTACA-CATATAGTGGCGTTTATTCCTAAAACGCCGCAATAGTGATA
1 ACAAACGCCACAATAGTGTTA-ATCA-ATAGTGGCGTTT-TTACAAAAACACCGCAATAGTGATA
4724 ATAAATAGTGGCG-T-TTTTA
63 ATAAATAGTGGCGTTGTTTTA
* * **
4743 GACAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAACACCGCAATAGTTTTAAT
1 -ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTACAAAAACACCGCAATAGTGATAAT
*
4808 CAATAGTGGCGTTGTTTTA
65 AAATAGTGGCGTTGTTTTA
* *
4827 ACAAACGTCACAATAGTG-TAATCAATAGTGGCATTTTT
1 ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTT
4865 TTGTATAAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
82 50 0.48
83 45 0.43
84 10 0.10
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (83 bp):
ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTACAAAAACACCGCAATAGTGATAATA
AATAGTGGCGTTGTTTTA
Found at i:6242 original size:41 final size:42
Alignment explanation
Indices: 6197--6293 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 42
6187 TAGAGAGTAA
*
6197 TACTTTAGTGGCGTTTTTTAAC-AAACGCCGCTAA-AAAGTTG
1 TACTTTAGTGGCGTTTTTTAACAAAACCCCGC-AATAAAGTTG
*
6238 TACTTTAGTGGCG-TTTTTAACATAAACCCCGCAATAGAGTTG
1 TACTTTAGTGGCGTTTTTTAACA-AAACCCCGCAATAAAGTTG
*
6280 TAATTTAGTGGCGT
1 TACTTTAGTGGCGT
6294 AATATGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
40 8 0.16
41 15 0.31
42 26 0.53
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (42 bp):
TACTTTAGTGGCGTTTTTTAACAAAACCCCGCAATAAAGTTG
Found at i:9142 original size:16 final size:16
Alignment explanation
Indices: 9107--9149 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
9097 ATAAAATTTG
9107 AAATAAATACAAATAATA
1 AAATAAAT--AAATAATA
*
9125 AAATAAATAAATATTA
1 AAATAAATAAATAATA
*
9141 AAAAAAATA
1 AAATAAATA
9150 GATTACCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
18 8 0.35
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAATAAATAATA
Found at i:9503 original size:155 final size:155
Alignment explanation
Indices: 9278--9587 Score: 611
Period size: 155 Copynumber: 2.0 Consensus size: 155
9268 TCACCTGAAA
9278 CTGATTGTTAGTTGTTATTCATGTTGAATGTTTTACATAAACTAGAAGCCCTTGTCCTTTTGTAC
1 CTGATTGTTAGTTGTTATTCATGTTGAATGTTTTACATAAACTAGAAGCCCTTGTCCTTTTGTAC
9343 TTTTTGTAGAACATGAATGTCGATATTTTCTACAATAAAGAAGCCATTTCCCCCCTTTTTTGCAT
66 TTTTTGTAGAACATGAATGTCGATATTTTCTACAATAAAGAAGCCATTTCCCCCCTTTTTTGCAT
*
9408 AACATGAATGTCGATATTTTCTTGC
131 AACATAAATGTCGATATTTTCTTGC
9433 CTGATTGTTAGTTGTTATTCATGTTGAATGTTTTACATAAACTAGAAGCCCTTGTCCTTTTGTAC
1 CTGATTGTTAGTTGTTATTCATGTTGAATGTTTTACATAAACTAGAAGCCCTTGTCCTTTTGTAC
9498 TTTTTGTAGAACATGAATGTCGATATTTTCTACAATAAAGAAGCCATTTCCCCCCTTTTTTGCAT
66 TTTTTGTAGAACATGAATGTCGATATTTTCTACAATAAAGAAGCCATTTCCCCCCTTTTTTGCAT
9563 AACATAAATGTCGATATTTTCTTGC
131 AACATAAATGTCGATATTTTCTTGC
9588 ATATTTTGTT
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 154 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (155 bp):
CTGATTGTTAGTTGTTATTCATGTTGAATGTTTTACATAAACTAGAAGCCCTTGTCCTTTTGTAC
TTTTTGTAGAACATGAATGTCGATATTTTCTACAATAAAGAAGCCATTTCCCCCCTTTTTTGCAT
AACATAAATGTCGATATTTTCTTGC
Found at i:15604 original size:21 final size:21
Alignment explanation
Indices: 15580--15622 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15570 AAAGAAGTAG
15580 CGGCAACACAGAGAGAAGCAA
1 CGGCAACACAGAGAGAAGCAA
* *
15601 CGGCAGCACAGAGAGAATCAA
1 CGGCAACACAGAGAGAAGCAA
15622 C
1 C
15623 ATATCAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.28, T:0.02
Consensus pattern (21 bp):
CGGCAACACAGAGAGAAGCAA
Found at i:16067 original size:43 final size:41
Alignment explanation
Indices: 16020--16236 Score: 238
Period size: 42 Copynumber: 5.1 Consensus size: 41
16010 AGACCTTTAC
* *
16020 CGGCGTTTTTAGCAACAACGCCGCAAAACATCAATACCTACTG
1 CGGCGTTTTGAG-AA-AACGCCGCAAAACATCAACACCTACTG
*
16063 CGGCGTTTGTGAGAAAACGCCGCAAAACATCAAAACCTACTG
1 CGGCGTTT-TGAGAAAACGCCGCAAAACATCAACACCTACTG
* * *
16105 CGGCATTTGTGGGAAAACGCCGCAAAATATCAACACCTACTG
1 CGGCGTTT-TGAGAAAACGCCGCAAAACATCAACACCTACTG
* * *
16147 CGACGTTTGTGAGAAAAACGTCGCAAAACATTAACACCTACTG
1 CGGCGTTT-TGAG-AAAACGCCGCAAAACATCAACACCTACTG
* * *
16190 CGGCGTTTTAGAGAAAAACGCTGCTAAACATCATA-ACCTATTG
1 CGGCGTTTT-GAG-AAAACGCCGCAAAACATCA-ACACCTACTG
16233 CGGC
1 CGGC
16237 ATTTGTCTAA
Statistics
Matches: 152, Mismatches: 18, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
42 75 0.49
43 73 0.48
44 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (41 bp):
CGGCGTTTTGAGAAAACGCCGCAAAACATCAACACCTACTG
Found at i:16085 original size:42 final size:42
Alignment explanation
Indices: 16036--16315 Score: 251
Period size: 43 Copynumber: 6.6 Consensus size: 42
16026 TTTTAGCAAC
16036 AACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTGAGAA
1 AACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTGAGAA
* * *
16078 AACGCCGCAAAACATCAAAACCTACTGCGGCATTTGTGGGAA
1 AACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTGAGAA
* * *
16120 AACGCCGCAAAATATCAACACCTACTGCGACGTTTGTGAGAAA
1 AACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTGAG-AA
* * *
16163 AACGTCGCAAAACATTAACACCTACTGCGGCGTTT-TAGAGAAA
1 AACGCCGCAAAACATCAATACCTACTGCGGCGTTTGT-GAG-AA
* * * * *
16206 AACGCTGCTAAACATC-ATAACCTATTGCGGCATTTGTCTA-AA
1 AACGCCGCAAAACATCAAT-ACCTACTGCGGCGTTTGT-GAGAA
* * * * * * * * *
16248 AATTGCCGCTAAATATCAAAACCTATTACAGCGTTTGTCACACA
1 AA-CGCCGCAAAACATCAATACCTACTGCGGCGTTTGTGAGA-A
* *
16292 AACGCCGCTAAATATCAATACCTA
1 AACGCCGCAAAACATCAATACCTA
16316 TTACGGCATT
Statistics
Matches: 199, Mismatches: 31, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
42 81 0.41
43 112 0.56
44 6 0.03
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (42 bp):
AACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTGAGAA
Found at i:17892 original size:20 final size:19
Alignment explanation
Indices: 17854--17896 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
17844 AGGGTTATAT
*
17854 TCAACTTCTCAACTCACTC
1 TCAACTTCACAACTCACTC
*
17873 TCAACATTCACAATTCACTC
1 TCAAC-TTCACAACTCACTC
17893 TCAA
1 TCAA
17897 AGTGTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (19 bp):
TCAACTTCACAACTCACTC
Found at i:20350 original size:28 final size:27
Alignment explanation
Indices: 20297--20353 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
20287 TATTAGGTAC
* *
20297 AAAAAATATATATAAAATATATTTTCA
1 AAAAAATATATATAAAATAAAATTTCA
**
20324 AAAAAATATATGATAATTTAAAATTTCA
1 AAAAAATATAT-ATAAAATAAAATTTCA
20352 AA
1 AA
20354 GCGGTGACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
AAAAAATATATATAAAATAAAATTTCA
Found at i:20492 original size:31 final size:32
Alignment explanation
Indices: 20454--20521 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
20444 AAAAATTGTA
* *
20454 AAGCTCGACTCAAGCT-TAAAATCAGAAATTG
1 AAGCTCGACTCAAACTCAAAAATCAGAAATTG
* *
20485 AAGCTCGAGTGAAACTCAAAAATCAGAAATTG
1 AAGCTCGACTCAAACTCAAAAATCAGAAATTG
*
20517 GAGCT
1 AAGCT
20522 GATGCATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (32 bp):
AAGCTCGACTCAAACTCAAAAATCAGAAATTG
Found at i:21016 original size:389 final size:382
Alignment explanation
Indices: 20503--21272 Score: 1173
Period size: 389 Copynumber: 2.0 Consensus size: 382
20493 GTGAAACTCA
* * * *
20503 AAAATCAGAAATTGGAGCTGATGCATGTTCAAAAAAACTTAAACTCTAAATATTCTTAAACTTAA
1 AAAATCAGAAATTGGAGCTCAAGCAAGTTCAAAAAAACATAAACTCTAAATATTCTTAAACTTAA
* * *
20568 CTTGATTGAAGCTCAAACTCGAACTAAGTTCAAGCTCGAGCGTGAACCTAAATCGTAAGTACATG
66 CTCGATTGAAACTCAAACTCGAACTAAGTTCAAGCTCGAGCGCGAACCTAAATCGTAAGTACATG
20633 AAAACCTTATATTGTAATTTTTAAAATAATATATAAATGTTAATATTATTAAACATTTAACTTAA
131 AAAACCTTATATTGTAATTTTTAAAATAATATATAAATGTTAATATTATTAAACATTTAACTTAA
20698 AAATTAAAATTTTAATATATATATATATATATAGTTGCTTGTAATC-TTTTCAAGTCGAATATTA
196 AAATTAAAATTTTAATATATATA-AT-TATATAGTTGCTTGTAATCTTTTTCAAGTCGAATATTA
* * * * * ** *
20762 AGTAATTCGCTTCGACTCGTCAAAAATTCGAGTCATGTTCAAGCTCATATCTCTTGTTCATTCAG
259 AATAACTCGCTTCGACTCGTAAAAAATTCGAGTC--GTTCAAACTCA-A-ATCGAGTTCATTCAA
*
20827 TTTGAGAGTTGACCGAACTTTAATGAAATCAAACTTGAATAGTTTAAAATTTGTCTCGTCTCG
320 TTTGAGAGTTGACCGAACTTTAATGAAATCAAACTTGAATAGTTTAAAATCTGTCTCGTCTCG
* * * *
20890 AAAATCAGAAATTGGAGCTCAAGCTAGAGTTCGAAAAAACATCACCTCTAAATATTCTTAGACTT
1 AAAATCAGAAATTGGAGCTCAAGC-A-AGTTCAAAAAAACATAAACTCTAAATATTCTTAAACTT
*
20955 AACTCGATTGAAACTCAAACTCGAGCTAAGTTCAAGCTCGAGCGCGAACCTAAATCGTAAGTACA
64 AACTCGATTGAAACTCAAACTCGAACTAAGTTCAAGCTCGAGCGCGAACCTAAATCGTAAGTACA
* * * *
21020 TGAAAATCTTATATTTTAATTTTTAAAATAATATATAAATGTTAATATTATTAAACGTTTAATTT
129 TGAAAACCTTATATTGTAATTTTTAAAATAATATATAAATGTTAATATTATTAAACATTTAACTT
* *
21085 AAAAATTAAAATTTTAATATATATAATTTTTTAGTTGCTTGTAATCTTTTTCAAGTCGAATATTA
194 AAAAATTAAAATTTTAATATATATAATTATATAGTTGCTTGTAATCTTTTTCAAGTCGAATATTA
* *
21150 AATAACTCGTTTCGACTCGTAAAAAATTTGAGTCGTTCAAACTCAAATCGAGTTCATTCAATTTG
259 AATAACTCGCTTCGACTCGTAAAAAATTCGAGTCGTTCAAACTCAAATCGAGTTCATTCAATTTG
** *
21215 AGAGTTGACCGAACTTTAATGAAATTGAACTTGAATAGTTTCAAATCTGTCTCGTCTC
324 AGAGTTGACCGAACTTTAATGAAATCAAACTTGAATAGTTTAAAATCTGTCTCGTCTC
21273 ATTTAGTGTT
Statistics
Matches: 348, Mismatches: 32, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
384 69 0.20
385 1 0.00
386 10 0.03
387 39 0.11
388 50 0.14
389 179 0.51
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.35
Consensus pattern (382 bp):
AAAATCAGAAATTGGAGCTCAAGCAAGTTCAAAAAAACATAAACTCTAAATATTCTTAAACTTAA
CTCGATTGAAACTCAAACTCGAACTAAGTTCAAGCTCGAGCGCGAACCTAAATCGTAAGTACATG
AAAACCTTATATTGTAATTTTTAAAATAATATATAAATGTTAATATTATTAAACATTTAACTTAA
AAATTAAAATTTTAATATATATAATTATATAGTTGCTTGTAATCTTTTTCAAGTCGAATATTAAA
TAACTCGCTTCGACTCGTAAAAAATTCGAGTCGTTCAAACTCAAATCGAGTTCATTCAATTTGAG
AGTTGACCGAACTTTAATGAAATCAAACTTGAATAGTTTAAAATCTGTCTCGTCTCG
Found at i:27266 original size:19 final size:20
Alignment explanation
Indices: 27230--27277 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
27220 TCTAAATCCT
* *
27230 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
27250 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
*
27269 ATTTCAAAA
1 TTTTCAAAA
27278 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:29364 original size:22 final size:22
Alignment explanation
Indices: 29324--29374 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
29314 ATATATTTAG
*
29324 ACTAATTTATACTTTTTTTTGT
1 ACTAATTTATACTTTTTTTGGT
*
29346 ACTAATTTTTA-TTTATTTTGGT
1 ACTAATTTATACTTT-TTTTGGT
*
29368 TCTAATT
1 ACTAATT
29375 CCGATTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.63
Consensus pattern (22 bp):
ACTAATTTATACTTTTTTTGGT
Found at i:34218 original size:20 final size:20
Alignment explanation
Indices: 34189--34240 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
34179 GATTCAATTG
* * **
34189 GTATCAATACCGAAGGGGGA
1 GTATCGATACCAAAGGGAAA
34209 GTATCGATACCAAAGGGAAA
1 GTATCGATACCAAAGGGAAA
*
34229 GTATTGATACCA
1 GTATCGATACCA
34241 TTCAAAACAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.19
Consensus pattern (20 bp):
GTATCGATACCAAAGGGAAA
Found at i:35097 original size:54 final size:54
Alignment explanation
Indices: 34658--35089 Score: 598
Period size: 54 Copynumber: 8.0 Consensus size: 54
34648 TTACCAAATA
* * * **
34658 GGCACTAAGTGTGCATTTCACGGAATTCACCCTATGTGGATGAATAGCTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTC
* * *
34712 GACACTAAGTGTGTATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTC
* * *
34766 GGCACTAAGTGTGCATTTCAAGGAATTCATCCTAGGTAGATCAATAA-CAGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCA-TTTC
**
34820 TACACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTC
** *** * *
34874 GGCTTTAAGTGTGCATTTCAAATAATTCATTCTAGGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTC
* *
34928 GGCACTAAGTGTGCATTTCATGGAATTCATCCTAGGTGGATGAATAACCGTTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACC-ATTTC
* *
34983 GGCACTAAGTGTGCATTTCACGGAATTCATCCTGGGTGGATGAATAACTATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTC
*
35037 GGCACTAAGTGTTG-ATTTCACGGAATTCATCCTATGTGGATGAATAACCATTT
1 GGCACTAAGTG-TGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTT
35090 TGACACTATG
Statistics
Matches: 334, Mismatches: 40, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
53 2 0.01
54 278 0.83
55 54 0.16
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTC
Found at i:41148 original size:54 final size:53
Alignment explanation
Indices: 41066--41620 Score: 741
Period size: 54 Copynumber: 10.3 Consensus size: 53
41056 TTACCAAATA
* * ** * *
41066 GGCACTAAGTGTTCATTTCACGAAATTCATCATATTTGGATGAATAATCATTTT
1 GGCACTAAGTGTGCATTTCACG-AATTCATCCTAGGTGGATGAATAACCATTTC
* *
41120 GGCACTAAGTGTGTATTTCACAGAATTCATCCTAGGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCAC-GAATTCATCCTAGGTGGATGAATAACCATTTC
* * *
41174 AGCACTAAGTGTGCATTTCACGAAATTCATCATATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACG-AATTCATCCTAGGTGGATGAATAACCATTTC
* *
41228 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCAC-GAATTCATCCTAGGTGGATGAATAACCATTTC
* **
41282 GGCACTAAGTGTGCATTTCACGGAATTCATCTTAGGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCAC-GAATTCATCCTAGGTGGATGAATAACCATTTC
*
41336 GACACTAAGTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACG-AATTCATCCTAGGTGGATGAATAACCATTTC
* *
41390 GGCACTAAGTGTGCATTTCACGAAATTCATCCTAGGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACG-AATTCATCCTAGGTGGATGAATAACCATTTC
** *
41444 GAAACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTT
1 GGCACTAAGTGTGCATTTCAC-GAATTCATCCTAGGTGGATGAATAACCATTTC
* * * * * *
41498 GGCACTAAGTGTGCATATCACAGAATTTATCCAATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCAC-GAATTCATCCTAGGTGGATGAATAACCATTTC
* *
41552 GGCACTAAGTGTGCATTTTACGGAATTCATCCTAGGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCAC-GAATTCATCCTAGGTGGATGAATAACCATTTC
*
41606 GGCACTATGTGTGCA
1 GGCACTAAGTGTGCA
41621 AACCATGTAG
Statistics
Matches: 450, Mismatches: 46, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
53 2 0.00
54 445 0.99
55 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (53 bp):
GGCACTAAGTGTGCATTTCACGAATTCATCCTAGGTGGATGAATAACCATTTC
Found at i:43300 original size:12 final size:12
Alignment explanation
Indices: 43279--43310 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
43269 AATATGATCT
*
43279 AAAACGCTCCTA
1 AAAACACTCCTA
43291 AAAACACTCCTA
1 AAAACACTCCTA
43303 AAAACACT
1 AAAACACT
43311 TGAGTTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.31, G:0.03, T:0.16
Consensus pattern (12 bp):
AAAACACTCCTA
Found at i:44159 original size:12 final size:12
Alignment explanation
Indices: 44142--44178 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
44132 ACGAACAACC
44142 AAAACTAAAACA
1 AAAACTAAAACA
*
44154 AAAACTAACACA
1 AAAACTAAAACA
44166 ATAAACTAAAACA
1 A-AAACTAAAACA
44179 TGAGAAAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.70, C:0.19, G:0.00, T:0.11
Consensus pattern (12 bp):
AAAACTAAAACA
Found at i:48258 original size:21 final size:22
Alignment explanation
Indices: 48229--48272 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
48219 ATAAAACAAT
*
48229 TTATAAATA-AAAAAGTAAAAC
1 TTATAAATATAAAAAATAAAAC
*
48250 TTATCAATATTAAAAAATAAAAC
1 TTATAAATA-TAAAAAATAAAAC
48273 AGAATTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (22 bp):
TTATAAATATAAAAAATAAAAC
Found at i:57348 original size:23 final size:22
Alignment explanation
Indices: 57280--57341 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
57270 AACAATACTC
57280 TTCATG-AAAAAGTTAAGTCTT
1 TTCATGAAAAAAGTTAAGTCTT
* *
57301 TTTAT-AAGAAAGGTTAAGTCTT
1 TTCATGAA-AAAAGTTAAGTCTT
57323 TTCATGAAAAAATGTTAAG
1 TTCATGAAAAAA-GTTAAG
57342 CCGTTTCGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.15
22 20 0.61
23 8 0.24
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.37
Consensus pattern (22 bp):
TTCATGAAAAAAGTTAAGTCTT
Found at i:59792 original size:27 final size:27
Alignment explanation
Indices: 59731--59800 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 27
59721 TTTTTATTGT
*
59731 TTTTAATTTTTATTAATGGAAGAAATAA
1 TTTTAATTTTTATTAAT-GAAAAAATAA
*
59759 TTCTTAACTTTTATTAAT-AAAAAATAA
1 TT-TTAATTTTTATTAATGAAAAAATAA
59786 TATTTAATTTTTATT
1 T-TTTAATTTTTATT
59801 TATTAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 20 0.54
28 3 0.08
29 14 0.38
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (27 bp):
TTTTAATTTTTATTAATGAAAAAATAA
Found at i:61111 original size:54 final size:53
Alignment explanation
Indices: 61021--61156 Score: 186
Period size: 54 Copynumber: 2.5 Consensus size: 53
61011 TCTTACTATT
* *
61021 GTGTTCGTTTATTGT-TTTTGAAGGTGCTCGTTTAAATTTTTAATATCATG-TC
1 GTGTTCGTTTATT-TATTTTGAAGGTGTTCATTTAAATTTTTAATATCATGCTC
*
61073 GGTGTTCGTTTATTTATATTTTAAGGTGTTCATTTAAATTTTTAATATCATGCTC
1 -GTGTTCGTTTATTTAT-TTTGAAGGTGTTCATTTAAATTTTTAATATCATGCTC
* *
61128 GTGATCATTTATTTATTTTGAAGGTGTTC
1 GTGTTCGTTTATTTATTTTGAAGGTGTTC
61157 GTTCATTTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
52 1 0.01
53 26 0.35
54 45 0.61
55 2 0.03
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.52
Consensus pattern (53 bp):
GTGTTCGTTTATTTATTTTGAAGGTGTTCATTTAAATTTTTAATATCATGCTC
Found at i:62503 original size:2 final size:2
Alignment explanation
Indices: 62496--62523 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62486 TTTATTTTTC
62496 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
62524 TTCCCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65735 original size:14 final size:14
Alignment explanation
Indices: 65716--65742 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65706 CCTAAACCAT
65716 TTTTTTCTAAGTAA
1 TTTTTTCTAAGTAA
65730 TTTTTTCTAAGTA
1 TTTTTTCTAAGTA
65743 TAAAAAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTTTTCTAAGTAA
Found at i:69946 original size:61 final size:61
Alignment explanation
Indices: 69871--70005 Score: 243
Period size: 61 Copynumber: 2.2 Consensus size: 61
69861 GGGCTTGTCT
* *
69871 AGTATCGATACCAGGTTTTATGTATCAACACTACTATGTAAAGTAGTATTGGTACTCTTTG
1 AGTACCGATACCAGGTTTCATGTATCAACACTACTATGTAAAGTAGTATTGGTACTCTTTG
*
69932 AGTACCGATACCAGGTTTCATGTATCAATACTACTATGTAAAGTAGTATTGGTACTCTTTG
1 AGTACCGATACCAGGTTTCATGTATCAACACTACTATGTAAAGTAGTATTGGTACTCTTTG
69993 AGTACCGATACCA
1 AGTACCGATACCA
70006 ATTTTGCTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (61 bp):
AGTACCGATACCAGGTTTCATGTATCAACACTACTATGTAAAGTAGTATTGGTACTCTTTG
Found at i:71033 original size:22 final size:22
Alignment explanation
Indices: 71005--71050 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
70995 CTTTCTCACT
71005 AAGTCTACCCTCTCAGAGTACA
1 AAGTCTACCCTCTCAGAGTACA
71027 AAGTCTACCCTCTCAGAGTACA
1 AAGTCTACCCTCTCAGAGTACA
71049 AA
1 AA
71051 CAAAGAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (22 bp):
AAGTCTACCCTCTCAGAGTACA
Found at i:83077 original size:23 final size:24
Alignment explanation
Indices: 83051--83182 Score: 98
Period size: 23 Copynumber: 5.4 Consensus size: 24
83041 TTGAAGAAGA
83051 GATG-AAAAAATGAAATGAAAAAT
1 GATGAAAAAAATGAAATGAAAAAT
*
83074 GATGAAAAAAAAGAAA--AAGAAAT
1 GATGAAAAAAATGAAATGAA-AAAT
83097 GATGAAAAAAATGAAAAATGAAAAAT
1 GATGAAAAAAATG--AAATGAAAAAT
*
83123 GAAAATGAAAAAAATGAAAAAGTGAAAAAA
1 G---ATGAAAAAAATG--AAA-TGAAAAAT
*
83153 GAAGAAAAAGAA--AAATG-AAAAT
1 GATGAAAAA-AATGAAATGAAAAAT
83175 GA-GAAAAA
1 GATGAAAAA
83183 GAAAATAAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 24
0.76 0.04 0.20
Matches are distributed among these distances:
21 6 0.06
22 8 0.09
23 22 0.24
24 13 0.14
25 3 0.03
26 5 0.05
27 9 0.10
28 2 0.02
29 17 0.18
30 8 0.09
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (24 bp):
GATGAAAAAAATGAAATGAAAAAT
Found at i:83080 original size:15 final size:13
Alignment explanation
Indices: 83052--83141 Score: 52
Period size: 12 Copynumber: 7.1 Consensus size: 13
83042 TGAAGAAGAG
83052 ATGAAAAAATGAA
1 ATGAAAAAATGAA
83065 ATG-AAAAATG--
1 ATGAAAAAATGAA
*
83075 ATGAAAAAAAAGAA
1 ATG-AAAAAATGAA
*
83089 A--AAGAAATG--
1 ATGAAAAAATGAA
83098 ATGAAAAAAATGAAAA
1 ATG-AAAAAATG--AA
83114 ATG-AAAAATGAAA
1 ATGAAAAAATG-AA
83127 ATGAAAAAAATGAA
1 ATG-AAAAAATGAA
83141 A
1 A
83142 AAGTGAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 25
0.67 0.04 0.28
Matches are distributed among these distances:
9 1 0.02
10 3 0.05
11 6 0.10
12 20 0.33
13 9 0.15
14 11 0.18
15 7 0.12
16 3 0.05
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (13 bp):
ATGAAAAAATGAA
Found at i:83089 original size:9 final size:10
Alignment explanation
Indices: 83063--83143 Score: 55
Period size: 10 Copynumber: 8.0 Consensus size: 10
83053 TGAAAAAATG
83063 AAATGAAAAA
1 AAATGAAAAA
**
83073 TGATGAAAAA
1 AAATGAAAAA
83083 AAA-GAAAAA
1 AAATGAAAAA
83092 GAAATGATGAAAA
1 -AAATGA--AAAA
83105 AAATG---AA
1 AAATGAAAAA
83112 AAATGAAAAATGA
1 AAATG-AAAA--A
83125 AAATG-AAAA
1 AAATGAAAAA
83134 AAATGAAAAA
1 AAATGAAAAA
83144 GTGAAAAAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 22
0.68 0.05 0.27
Matches are distributed among these distances:
7 7 0.12
9 12 0.21
10 16 0.29
11 6 0.11
12 5 0.09
13 10 0.18
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (10 bp):
AAATGAAAAA
Found at i:83114 original size:30 final size:29
Alignment explanation
Indices: 83080--83186 Score: 101
Period size: 31 Copynumber: 3.6 Consensus size: 29
83070 AAATGATGAA
83080 AAAAAAGAAAAAGAAATGATGAAAAAAATG
1 AAAAAAGAAAAAGAAA-GATGAAAAAAATG
*
83110 AAAAATGAAAAATGAAA-ATGAAAAAAATG
1 AAAAAAGAAAAA-GAAAGATGAAAAAAATG
* **
83139 AAAAAGTGAAAAA-AGAAGAAAAAGAAAAATG
1 AAAAA-AGAAAAAGA-AAGATGAA-AAAAATG
*
83170 AAAATGAGAAAAAGAAA
1 AAAA-AAGAAAAAGAAA
83187 ATAAAAGAGG
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
28 1 0.02
29 19 0.29
30 21 0.32
31 23 0.35
32 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (29 bp):
AAAAAAGAAAAAGAAAGATGAAAAAAATG
Found at i:83125 original size:46 final size:45
Alignment explanation
Indices: 83044--83186 Score: 118
Period size: 46 Copynumber: 3.1 Consensus size: 45
83034 ATTTTGCTTG
83044 AAGAAGAGATG-AAAAAATG--AAATGAAAAATGATGAAAAAAAAGAAA
1 AAGAA-AGATGAAAAAAATGAAAAATG-AAAA--ATGAAAAAAAAGAAA
*
83090 AAGAAATGATGAAAAAAATGAAAAATGAAAAATGAAAATGAAA-AAA
1 AAGAAA-GATGAAAAAAATGAAAAATGAAAAATGAAAA-AAAAGAAA
* * * **
83136 ATGAAAAAGTGAAAAAAGAAGAAAAA-GAAAAATG-AAAATGAGAAA
1 AAGAAAGA-TGAAAAAA-ATGAAAAATGAAAAATGAAAAAAAAGAAA
83181 AAGAAA
1 AAGAAA
83187 ATAAAAGAGG
Statistics
Matches: 81, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
44 1 0.01
45 13 0.16
46 40 0.49
47 18 0.22
48 4 0.05
49 5 0.06
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.10
Consensus pattern (45 bp):
AAGAAAGATGAAAAAAATGAAAAATGAAAAATGAAAAAAAAGAAA
Found at i:83182 original size:9 final size:8
Alignment explanation
Indices: 83052--83173 Score: 68
Period size: 8 Copynumber: 15.9 Consensus size: 8
83042 TGAAGAAGAG
83052 ATGAAAAA
1 ATGAAAAA
83060 ATG---AA
1 ATGAAAAA
83065 ATGAAAAA
1 ATGAAAAA
83073 TGATGAAAAA
1 --ATGAAAAA
83083 A--AAGAAA
1 ATGAA-AAA
* **
83090 AAGAAATG
1 ATGAAAAA
83098 ATGAAAAAA
1 ATG-AAAAA
83107 ATG-AAAA
1 ATGAAAAA
83114 ATG-AAAA
1 ATGAAAAA
83121 ATG--AAA
1 ATGAAAAA
83127 ATGAAAAAA
1 ATG-AAAAA
83136 ATGAAAAA
1 ATGAAAAA
*
83144 GTGAAAAA
1 ATGAAAAA
83152 A-GAAGAAA
1 ATGAA-AAA
*
83160 AAG-AAAA
1 ATGAAAAA
83167 ATGAAAA
1 ATGAAAA
83174 TGAGAAAAAG
Statistics
Matches: 91, Mismatches: 8, Indels: 30
0.71 0.06 0.23
Matches are distributed among these distances:
5 5 0.05
6 8 0.09
7 26 0.29
8 29 0.32
9 15 0.16
10 8 0.09
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.11
Consensus pattern (8 bp):
ATGAAAAA
Found at i:84081 original size:37 final size:36
Alignment explanation
Indices: 84017--84091 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
84007 AAACAAGTCA
* *
84017 ATCTTAAGCCTTCACAAAGAGTGGTGAAGTAAA-TC
1 ATCTTAAGCCTTCACAAAGAGTAGTGAAGCAAACTC
*
84052 ATCTATAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
1 ATCT-TAAGCCTTCAC-AAAGAGTAGTGAAGCAAACTC
84090 AT
1 AT
84092 TTTATGAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 4 0.12
36 11 0.32
37 15 0.44
38 4 0.12
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (36 bp):
ATCTTAAGCCTTCACAAAGAGTAGTGAAGCAAACTC
Found at i:84151 original size:51 final size:51
Alignment explanation
Indices: 84096--84204 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
84086 ACTCATTTTA
* *
84096 TGAAGATCGAGTCCTATACTCTCTGAAGAAATAGGGAGTGGACACGTTTGT
1 TGAAGATCAAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACGTTTGT
* * *
84147 TGAAGATCAAGTCTTATACTCTTTGAAGGAATAGGGAGCGGACACGTTTGT
1 TGAAGATCAAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACGTTTGT
*
84198 TAAAGAT
1 TGAAGAT
84205 TGTTTGAGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (51 bp):
TGAAGATCAAGTCCTATACTCTCTGAAGAAATAGGGAGCGGACACGTTTGT
Found at i:84244 original size:55 final size:55
Alignment explanation
Indices: 84161--84414 Score: 249
Period size: 55 Copynumber: 4.6 Consensus size: 55
84151 GATCAAGTCT
** * * * *
84161 TATACTCTTTGAAGGAATAGGGAGCGGACACGTTTGTTAAAGATTGTTTGAGTTC
1 TATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTTAAAGATTGTTCGAGTTC
* * * * *
84216 TATACTCCCTTAACGAATAGGGAACGGACCCGTTTTGCTGAAGATTGTTCGAGTTC
1 TATACTCCCTGAACGAATAGGGAGCGGACCC-ATTTGTTAAAGATTGTTCGAGTTC
* * * * * *
84272 TATATTCCCTAAACGAATAAGGAGCGAACCCATTT-TCAGAAGATTGTTCAAGTTC
1 TATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTTA-AAGATTGTTCGAGTTC
* * ** * * *
84327 TATACTCCCTGAACTAATAGGGAGCGAACTTATTTTTTGAAGATTGTTCGAGTCC
1 TATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTTAAAGATTGTTCGAGTTC
* *
84382 TATACTCCCTGAAGGAAAAGGGAGCGGACCCAT
1 TATACTCCCTGAACGAATAGGGAGCGGACCCAT
84415 CATTTAAAGT
Statistics
Matches: 160, Mismatches: 36, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
55 113 0.71
56 47 0.29
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (55 bp):
TATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTTAAAGATTGTTCGAGTTC
Found at i:94002 original size:20 final size:20
Alignment explanation
Indices: 93977--94022 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
93967 ACGGGATGAA
*
93977 TATCGACACTGGTCCCTCGG
1 TATCGACACTGGTCCCTCAG
* *
93997 TATCGATATTGGTCCCTCAG
1 TATCGACACTGGTCCCTCAG
94017 TATCGA
1 TATCGA
94023 TATTGAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (20 bp):
TATCGACACTGGTCCCTCAG
Found at i:94023 original size:20 final size:20
Alignment explanation
Indices: 93986--94027 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
93976 ATATCGACAC
*
93986 TGGTCCCTCGGTATCGATAT
1 TGGTCCCTCAGTATCGATAT
94006 TGGTCCCTCAGTATCGATAT
1 TGGTCCCTCAGTATCGATAT
94026 TG
1 TG
94028 AAGGTTATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (20 bp):
TGGTCCCTCAGTATCGATAT
Found at i:100808 original size:20 final size:20
Alignment explanation
Indices: 100785--100825 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
100775 TATCATACTA
100785 TGGTATCGGAGTATCAATAC
1 TGGTATCGGAGTATCAATAC
* *
100805 TGGTATGGGAGTATCGATAC
1 TGGTATCGGAGTATCAATAC
100825 T
1 T
100826 ACCCTTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (20 bp):
TGGTATCGGAGTATCAATAC
Found at i:104393 original size:31 final size:30
Alignment explanation
Indices: 104355--104435 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
104345 TAATTTGAAA
* *
104355 ATATTTTATTTTTATTTTAATCCAGAAATAT
1 ATATTTTATTATTATTTTAAACCAGAAA-AT
* * ***
104386 ATATTTTATTCTTA-TCTAAACTTTAAAAT
1 ATATTTTATTATTATTTTAAACCAGAAAAT
104415 ATATTTTATTATTATTTTAAA
1 ATATTTTATTATTATTTTAAA
104436 TTTTCAAAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 15 0.37
30 13 0.32
31 13 0.32
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (30 bp):
ATATTTTATTATTATTTTAAACCAGAAAAT
Found at i:104501 original size:30 final size:30
Alignment explanation
Indices: 104411--104510 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 30
104401 CTAAACTTTA
* *
104411 AAATATATTTTATTATTATTTTAAATT-TT
1 AAATATATTATATTATTACTTTAAATTATT
* *
104440 CAAAGTA-ATTAT-TTA-T-CTTT-ATTTACT
1 -AAA-TATATTATATTATTACTTTAAATTATT
104467 AAATATATTATATTATTACTTTAAATTATT
1 AAATATATTATATTATTACTTTAAATTATT
*
104497 AAATATATTTTATT
1 AAATATATTATATT
104511 CTTATTATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
25 2 0.04
26 11 0.20
27 7 0.12
28 2 0.04
29 7 0.12
30 25 0.45
31 2 0.04
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (30 bp):
AAATATATTATATTATTACTTTAAATTATT
Found at i:104532 original size:16 final size:16
Alignment explanation
Indices: 104513--104546 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
104503 ATTTTATTCT
*
104513 TATTATAACTTAAAAA
1 TATTATAACATAAAAA
*
104529 TATTTTAACATAAAAA
1 TATTATAACATAAAAA
104545 TA
1 TA
104547 AAATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TATTATAACATAAAAA
Found at i:104597 original size:27 final size:26
Alignment explanation
Indices: 104546--104595 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
104536 ACATAAAAAT
104546 AAAATATTTTTAATAAGTTAATATAA
1 AAAATATTTTTAATAAGTTAATATAA
*
104572 AAAATATTTTTTA-AAGTTAATATA
1 AAAATATTTTTAATAAGTTAATATA
104596 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
AAAATATTTTTAATAAGTTAATATAA
Found at i:106924 original size:10 final size:10
Alignment explanation
Indices: 106909--106938 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
106899 TATTATGTTC
*
106909 GTTCGTTTGT
1 GTTCGTTTAT
106919 GTTCGTTTAT
1 GTTCGTTTAT
106929 GTTCGTTTAT
1 GTTCGTTTAT
106939 CATTTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.10, G:0.23, T:0.60
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:107027 original size:16 final size:16
Alignment explanation
Indices: 107002--107034 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
106992 AAAGAAATTT
107002 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
107018 TGTTCTTTTATGTTCG
1 TGTTCGTTTATGTTCG
107034 T
1 T
107035 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.21, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:107901 original size:10 final size:10
Alignment explanation
Indices: 107886--107911 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
107876 ACATAAAATT
107886 TCATGAAAAG
1 TCATGAAAAG
107896 TCATGAAAAG
1 TCATGAAAAG
107906 TCATGA
1 TCATGA
107912 TTTTCACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (10 bp):
TCATGAAAAG
Found at i:117197 original size:23 final size:23
Alignment explanation
Indices: 117182--117280 Score: 144
Period size: 23 Copynumber: 4.3 Consensus size: 23
117172 AATGTCCTGC
* * *
117182 AGGACCACGTAGAAATGTCCGGA
1 AGGACCACATAGAATTGTCCCGA
* * *
117205 AGGACCACGTAGAATTATCCTGA
1 AGGACCACATAGAATTGTCCCGA
117228 AGGACCACATAGAATTGTCCCGA
1 AGGACCACATAGAATTGTCCCGA
117251 AGGACCACATAGAATTGTCCCGA
1 AGGACCACATAGAATTGTCCCGA
117274 AGGACCA
1 AGGACCA
117281 TATATATGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (23 bp):
AGGACCACATAGAATTGTCCCGA
Found at i:117327 original size:21 final size:20
Alignment explanation
Indices: 117303--117365 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
117293 AAAAAACCAA
117303 ATATATGTCCTGAAGGACCGC
1 ATATATGTCC-GAAGGACCGC
* *
117324 ATATATGTTCCAAAGGACCAC
1 ATATATG-TCCGAAGGACCGC
117345 ATATATGTCCCGAAGGACCGC
1 ATATATGT-CCGAAGGACCGC
117366 GTAGAACCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.89
22 3 0.08
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (20 bp):
ATATATGTCCGAAGGACCGC
Found at i:117364 original size:42 final size:42
Alignment explanation
Indices: 117250--117365 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 42
117240 AATTGTCCCG
* ** *
117250 AAGGACCACATAGAATTGTCCCGAAGGACCATATATATGTTATA
1 AAGGACCACATA-TA-TGTCCCGAAGGACCGCATATATGTTACA
** * * *
117294 AAAAACCAAATATATGTCCTGAAGGACCGCATATATGTTCCA
1 AAGGACCACATATATGTCCCGAAGGACCGCATATATGTTACA
117336 AAGGACCACATATATGTCCCGAAGGACCGC
1 AAGGACCACATATATGTCCCGAAGGACCGC
117366 GTAGAACCCT
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
42 49 0.83
43 1 0.02
44 9 0.15
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (42 bp):
AAGGACCACATATATGTCCCGAAGGACCGCATATATGTTACA
Found at i:136630 original size:18 final size:19
Alignment explanation
Indices: 136607--136642 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
136597 TCTTTTTTTT
136607 TATACATATATA-TATATC
1 TATACATATATATTATATC
136625 TATACATATATATTATAT
1 TATACATATATATTATAT
136643 AGTTCGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (19 bp):
TATACATATATATTATATC
Found at i:136753 original size:38 final size:36
Alignment explanation
Indices: 136669--136852 Score: 147
Period size: 38 Copynumber: 4.9 Consensus size: 36
136659 TTTGAAAAAT
136669 ACATATATAATATA-AGATTTTTTAAAAAACATTTTGAAA
1 ACATATATAATATATAG---TTTT-AAAAACATTTTGAAA
** *
136708 ATGTATATAATATATAGTTTTAAAAAAATACCTTTGAAA
1 ACATATATAATATATAGTTTTAAAAACAT---TTTGAAA
* *
136747 AC-TATATAATATATAATTTTTAAAACATTTTTAGAAA
1 ACATATATAATATATAGTTTTAAAAACA-TTTT-GAAA
* * *
136784 GCATATATAATATATAATTTTTAAAACCATTTTGAAA
1 ACATATATAATATAT-AGTTTTAAAAACATTTTGAAA
* * * * *
136821 GCTTATATAAAATATAGTTTTAAGATCATTTT
1 ACATATATAATATATAGTTTTAAAAACATTTT
136853 TGTTGAGTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
36 24 0.20
37 26 0.21
38 38 0.31
39 31 0.26
40 2 0.02
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (36 bp):
ACATATATAATATATAGTTTTAAAAACATTTTGAAA
Found at i:137689 original size:65 final size:65
Alignment explanation
Indices: 137565--137715 Score: 191
Period size: 65 Copynumber: 2.3 Consensus size: 65
137555 GCACTAAGAG
* *
137565 TGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTGCATCAA
1 TGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTGCATCAA
* * * *
137629 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TATGTGCATC
1 TGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-GGTGCATC
*
137692 GA
64 AA
*
137694 TGCATGAAATGCATTCGATGTT
1 TGCATCAAATGCATTCGATGTT
137716 CAATTTAATT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 20 0.26
65 53 0.70
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (65 bp):
TGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTGCATCAA
Found at i:138815 original size:21 final size:21
Alignment explanation
Indices: 138768--138816 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
138758 AGGAGCACGA
* *
138768 GAAGAGCTAGGAGCATCTTGT
1 GAAGAGCTAGGAGCAGCTCGT
*
138789 GTAGAGCTAGGAGCAGCTCGT
1 GAAGAGCTAGGAGCAGCTCGT
138810 GAAGAGC
1 GAAGAGC
138817 CAGCTCCCGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.37, T:0.18
Consensus pattern (21 bp):
GAAGAGCTAGGAGCAGCTCGT
Found at i:140400 original size:23 final size:22
Alignment explanation
Indices: 140370--140449 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
140360 GCATGGTCTT
140370 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
140392 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
140414 GTGTATTGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
140436 ATGCATCGATGCAC
1 GTGCATCGATGCAC
140450 TGTTAGGTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 14 0.31
22 15 0.33
23 16 0.36
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:140489 original size:20 final size:20
Alignment explanation
Indices: 140440--140490 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
140430 TCAAGGATGC
*
140440 ATCGATGCACTGTTAGGTAT
1 ATCGATGCATTGTTAGGTAT
140460 ATCGATGCATTGTTAGGTAT
1 ATCGATGCATTGTTAGGTAT
140480 ATCGATGCATT
1 ATCGATGCATT
140491 AAGCACAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (20 bp):
ATCGATGCATTGTTAGGTAT
Found at i:144753 original size:37 final size:36
Alignment explanation
Indices: 144682--144753 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 36
144672 TATTAGACTT
* * * *
144682 ATAAGTAAAATATTAAAGAAATATATATATATAATA
1 ATAAGTAAAATATTAAAAAAATAAATAAAAATAATA
144718 ATAA-TAAAATATAGTAAAAAAATAAATAAAAATAAT
1 ATAAGTAAAATAT--TAAAAAAATAAATAAAAATAAT
144754 TTAATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
35 8 0.27
36 4 0.13
37 18 0.60
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (36 bp):
ATAAGTAAAATATTAAAAAAATAAATAAAAATAATA
Found at i:144798 original size:18 final size:17
Alignment explanation
Indices: 144775--144817 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
144765 ATATATACAT
144775 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
144793 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
144810 ATAA-AATA
1 ATAATAATA
144818 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:145225 original size:37 final size:37
Alignment explanation
Indices: 145175--145279 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
145165 GTGCTTGTGG
* * * *
145175 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
145212 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
145249 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
145280 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:146126 original size:105 final size:105
Alignment explanation
Indices: 145822--146452 Score: 864
Period size: 105 Copynumber: 6.0 Consensus size: 105
145812 GCATTGTTCT
* ** ** * *
145822 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * * *
145886 ACCAGCCGTCCCTTCGTTGTGAAATTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
145928 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--AAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * *
145988 CAGTGGTCCATTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
146028 GAGTCCAATATCCTTCGTTGTGAAGTTGTAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
146093 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
146133 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
146198 CAGCGGTCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
146238 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AAATTTGAGAAGTTGTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGA-TTGGGAAGTTGTTGTTGACAA
146302 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
146343 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * *
146408 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
146449 GAGT
1 GAGT
146453 GTCACGATAT
Statistics
Matches: 478, Mismatches: 37, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
100 79 0.17
101 1 0.00
102 6 0.01
104 6 0.01
105 296 0.62
106 89 0.19
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:146699 original size:36 final size:36
Alignment explanation
Indices: 146652--146727 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
146642 TGTTTGGAGA
* * *
146652 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
146688 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
146724 GAAA
1 GAAA
146728 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:146848 original size:106 final size:105
Alignment explanation
Indices: 146627--146946 Score: 506
Period size: 106 Copynumber: 3.1 Consensus size: 105
146617 TTCGTTAAAT
* ** *
146627 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
146689 AAACTATCTCA-AGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
*
146728 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
146793 AAACTATCTCAAGAGAGAGAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTC-AGAGAGAGAAAAAATTCATTTCAAGGGAAA
*
146834 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTATCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
146899 AAACTATCTCAG-GAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
146938 TGTTTTCAA
1 TGTTTTCAA
146947 GAGAAACTGT
Statistics
Matches: 202, Mismatches: 12, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
101 45 0.22
103 3 0.01
104 53 0.26
105 3 0.01
106 98 0.49
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (105 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:147107 original size:36 final size:36
Alignment explanation
Indices: 147062--147176 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
147052 AGTCTCAAGC
*
147062 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* * ** * **
147098 GAAATAAATCTTCTTTCGAGAAAAACAGTCTCAAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* *
147134 GAGACAAAGT-ATGTTTTAAGAAAAACAAAT-TTGAGT
1 GAGATAAA-TCTTGTTTTAAGAAAAAC-AATCTTGAGT
147170 GAGATAA
1 GAGATAA
147177 TCATCTGCAT
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
36 56 0.95
37 3 0.05
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.28
Consensus pattern (36 bp):
GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
Found at i:147138 original size:72 final size:74
Alignment explanation
Indices: 147015--147176 Score: 208
Period size: 72 Copynumber: 2.2 Consensus size: 74
147005 AAAAAAAAGC
*
147015 CTTGAGTGAAATGAAATGCCTTATTTCGACTGAAAACAGTCTCAAGCGAGACAAA-TCTTGTTTT
1 CTTGAGTGAAAT-AAAT-CCTTATTTCGAC-GAAAACAGTCTCAAGCGAGACAAAGT-ATGTTTT
147079 AAGAAAAAC-AAT
62 AAGAAAAACAAAT
* *
147091 CTTGAGTGAAATAAAT-CTTCTTTCGA-GAAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAG
1 CTTGAGTGAAATAAATCCTTATTTCGACG-AAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAG
147154 AAAAACAAAT
65 AAAAACAAAT
*
147164 -TTGAGTGAGATAA
1 CTTGAGTGAAATAA
147177 TCATCTGCAT
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
71 1 0.01
72 49 0.62
73 13 0.16
75 4 0.05
76 12 0.15
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (74 bp):
CTTGAGTGAAATAAATCCTTATTTCGACGAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAGA
AAAACAAAT
Found at i:148624 original size:183 final size:183
Alignment explanation
Indices: 148316--148852 Score: 923
Period size: 183 Copynumber: 2.9 Consensus size: 183
148306 ATCAGGTTTA
*
148316 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* ** *
148381 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGACAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
148445 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGAAAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGAAAAATC
* *
148499 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
148564 GCCAAGTGTCCTAGCAGTGTCATAGTTTGAACATAATTTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
148629 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGAAAAATC
* * *
148682 ACTGAAGGGTTCATCTCATCAAAAAGTCTTTGGCCTGACAAAAACAGTGGAGCAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
148747 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTTATAAAGCTAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
148812 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
148853 CGGATTTAAT
Statistics
Matches: 334, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 333 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGAAAAATC
Found at i:154246 original size:36 final size:33
Alignment explanation
Indices: 154195--154269 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
154185 ATAAACAAGG
*
154195 TAAAGAAAACAAATAAGATACAAGGGAAAAATAAAA
1 TAAATAAAACAAATAAGAT--AA-GGAAAAATAAAA
* *
154231 TAAATAAAATAAATAAGATAAGGAAAAATAATA
1 TAAATAAAACAAATAAGATAAGGAAAAATAAAA
154264 TAAATA
1 TAAATA
154270 TATAAAGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 17 0.47
34 2 0.06
36 17 0.47
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (33 bp):
TAAATAAAACAAATAAGATAAGGAAAAATAAAA
Found at i:154547 original size:18 final size:17
Alignment explanation
Indices: 154524--154566 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
154514 ATATATACAT
154524 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
154542 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
154559 ATAA-AATA
1 ATAATAATA
154567 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:155007 original size:37 final size:37
Alignment explanation
Indices: 154925--155026 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
154915 GTGCTTGTGG
* * * * * *
154925 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
154962 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
154999 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
155027 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:155535 original size:117 final size:117
Alignment explanation
Indices: 155316--155535 Score: 266
Period size: 117 Copynumber: 1.9 Consensus size: 117
155306 TTTCAAATTA
* * * *
155316 AAATTTTCTTTTTCAATATTTTCAAATTTCATTTGTGAAAGTTCTAAATCCTTCTTCAAGAGTTC
1 AAATTTTCTTTTTCAAAAATTTCAAATTTCATTTGTAAAAGTTCTAAATCCTTCTTCAACAGTTC
* *
155381 ATTTTGATTTTCAAGATCCATTTTTGTTTCTAGAAGAAGTTTGTTTAATTTG
66 ATTTTGATTTTCAAGATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * * *
155433 AAATTTTCTTTTTCAAAAATTTCAGATTTTAGTTT-TAAAAGTTCTAACTCCTTTTTCAACATTT
1 AAATTTTCTTTTTCAAAAATTTCAAATTTCA-TTTGTAAAAGTTCTAAATCCTTCTTCAACAGTT
* **
155497 CATTTTGTTTTTCCAAG-TCTGTTTTAGCTTTC-AAAAGAA
65 CATTTTGATTTT-CAAGATCCATTTTAG-TTTCTAAAAGAA
155536 TATCATTTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
117 75 0.87
118 11 0.13
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (117 bp):
AAATTTTCTTTTTCAAAAATTTCAAATTTCATTTGTAAAAGTTCTAAATCCTTCTTCAACAGTTC
ATTTTGATTTTCAAGATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:157459 original size:36 final size:35
Alignment explanation
Indices: 157386--157464 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 35
157376 TAACATATAG
* **
157386 TTTGAAAACATTTTTAAAATTATATAATATATGGT
1 TTTGAAAACATCTTTAAAATTATATAATATAAAGT
* * *
157421 TTTGAAAATATCTTTGAAATATATATTATATAAAGT
1 TTTGAAAACATCTTTAAAAT-TATATAATATAAAGT
157457 TTT-AAAAC
1 TTTGAAAAC
157465 TTTTTTTCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 21 0.58
36 15 0.42
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (35 bp):
TTTGAAAACATCTTTAAAATTATATAATATAAAGT
Found at i:157514 original size:7 final size:7
Alignment explanation
Indices: 157492--157543 Score: 65
Period size: 7 Copynumber: 7.9 Consensus size: 7
157482 CATATAGTAT
*
157492 TTTATTC
1 TTTATTA
157499 TTT-TTA
1 TTTATTA
157505 TTTATTA
1 TTTATTA
157512 TTTATTA
1 TTTATTA
157519 TTTATT-
1 TTTATTA
*
157525 TTTGTT-
1 TTTATTA
157531 TTTATTA
1 TTTATTA
157538 TTTATT
1 TTTATT
157544 TAATCATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
6 15 0.38
7 25 0.62
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (7 bp):
TTTATTA
Found at i:158894 original size:9 final size:9
Alignment explanation
Indices: 158882--158930 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
158872 TATTTAGCCT
158882 TTTTATTTA
1 TTTTATTTA
158891 TTTTATTTA
1 TTTTATTTA
158900 TTTTATTT-
1 TTTTATTTA
158908 TTATT-TTTA
1 TT-TTATTTA
158917 TTCTTCATTTA
1 TT-TT-ATTTA
158928 TTT
1 TTT
158931 ATCCATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
8 5 0.14
9 23 0.66
10 1 0.03
11 6 0.17
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTTA
Found at i:158926 original size:24 final size:23
Alignment explanation
Indices: 158881--158930 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
158871 ATATTTAGCC
*
158881 TTTTTATTTATTTTATTTATTTTA
1 TTTTTATTTATTTTATTCA-TTTA
*
158905 TTTTTATTT-TTATTCTTCATTTA
1 TTTTTATTTATT-TTATTCATTTA
158928 TTT
1 TTT
158931 ATCCATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTATTTATTTTATTCATTTA
Found at i:158931 original size:32 final size:36
Alignment explanation
Indices: 158892--158987 Score: 94
Period size: 37 Copynumber: 2.7 Consensus size: 36
158882 TTTTATTTAT
158892 TTTATTTATTTTATTTTTATTTTTA-TTC-T-TC-A
1 TTTATTTATTTTATTTTTATTTTTATTTCATCTCTA
* *
158924 TTTATTTATCCATTT-TTTCTCTTTTTATTTCATCTCTA
1 TTTATTTAT---TTTATTTTTATTTTTATTTCATCTCTA
*
158962 TTTCATTTATTTTATTATTATTTTTA
1 TTT-ATTTATTTTATTTTTATTTTTA
158988 ATTATCGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
32 9 0.18
34 10 0.20
35 6 0.12
36 4 0.08
37 11 0.22
38 4 0.08
39 6 0.12
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (36 bp):
TTTATTTATTTTATTTTTATTTTTATTTCATCTCTA
Found at i:159996 original size:15 final size:16
Alignment explanation
Indices: 159968--160012 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
159958 TAGGAATTAA
159968 AGCATGTGGGGTAGAT
1 AGCATGTGGGGTAGAT
159984 AGCATGT-GGGTAGAT
1 AGCATGTGGGGTAGAT
**
159999 ATAATGTGGGGTAG
1 AGCATGTGGGGTAG
160013 GATTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.27, C:0.04, G:0.42, T:0.27
Consensus pattern (16 bp):
AGCATGTGGGGTAGAT
Found at i:162538 original size:90 final size:89
Alignment explanation
Indices: 162385--162619 Score: 331
Period size: 90 Copynumber: 2.7 Consensus size: 89
162375 ATTATATATA
* * *
162385 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
*
162450 ATTCAGCTAGCCTGATAAAGGTAAT
66 ATTCAGCTAACCTGATAAAGGT-AT
162475 TATACAATAAAGCTTGAGTTGTCCCTCTA-AGACAATTGGTTAAACGCCCCGACTTTATGGATAA
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAG-CAATTGGTTAAACGCCCCGACTTTATGGATAA
*
162539 GATTCAGCTAACCTGATAAAGGTGT
65 GATTCAGCTAACCTGATAAAGGTAT
* * *
162564 T-T---ATATA--TTAAGTTGTCTCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGAT
162620 TCAGCTAGCC
Statistics
Matches: 135, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
83 44 0.33
84 2 0.01
85 4 0.03
88 1 0.01
89 4 0.03
90 80 0.59
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (89 bp):
TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTAT
Found at i:163775 original size:38 final size:36
Alignment explanation
Indices: 163715--163975 Score: 209
Period size: 38 Copynumber: 7.3 Consensus size: 36
163705 ATTTTTTAAA
* **
163715 AAAAACATTTTGGAAATGTATATAATATATAGTTTT
1 AAAAACATTTTTGAAACCTATATAATATATAGTTTT
* * * *
163751 AAAAAAATACCTTTGAAACCTATATAATATGTAATTTT
1 AAAAACAT--TTTTGAAACCTATATAATATATAGTTTT
* * *
163789 TAAAACATTTTTAGAAAGCATATATAATATATAATTTTT
1 AAAAACATTTTT-GAAA-CCTATATAATATAT-AGTTTT
* *
163828 AAAACCA-TTTTGAAAGCTTATATAATATATAGTTTT
1 AAAAACATTTTTGAAA-CCTATATAATATATAGTTTT
* * **
163864 AAGATCA-TTTTGAAATTTATATAATATATAGTCTTT
1 AAAAACATTTTTGAAACCTATATAATATATAGT-TTT
163900 AAAAACATTTTTGAAA-C-ATAT-A-ATATAGTTTT
1 AAAAACATTTTTGAAACCTATATAATATATAGTTTT
* * *
163932 -AAAACGTTTTTGAAAAC--TATAACATATAG-TTT
1 AAAAACATTTTTGAAACCTATATAATATATAGTTTT
*
163964 GAAAACATTTTT
1 AAAAACATTTTT
163976 AAAATTATAT
Statistics
Matches: 189, Mismatches: 25, Indels: 25
0.79 0.10 0.10
Matches are distributed among these distances:
31 17 0.09
32 8 0.04
33 23 0.12
34 1 0.01
35 20 0.11
36 36 0.19
37 30 0.16
38 44 0.23
39 10 0.05
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (36 bp):
AAAAACATTTTTGAAACCTATATAATATATAGTTTT
Found at i:163852 original size:37 final size:36
Alignment explanation
Indices: 163716--164047 Score: 185
Period size: 38 Copynumber: 9.3 Consensus size: 36
163706 TTTTTTAAAA
* * *
163716 AAAACATTTTGGAAA-TGTATATAATATATAGTTTTA
1 AAAACATTTTTGAAACT-TATATAATATATAATTTTT
* * * *
163752 AAAAAATACCTTTGAAACCTATATAATATGTAATTTTT
1 AAAACAT--TTTTGAAACTTATATAATATATAATTTTT
*
163790 AAAACATTTTTAGAAAGCATATATAATATATAATTTTT
1 AAAACATTTTT-GAAA-CTTATATAATATATAATTTTT
*
163828 AAAACCA-TTTTGAAAGCTTATATAATATAT-AGTTTT
1 AAAA-CATTTTTGAAA-CTTATATAATATATAATTTTT
* * * *
163864 AAGATCA-TTTTGAAATTTATATAATATATAGTCTTTA
1 AA-AACATTTTTGAAACTTATATAATATATAAT-TTTT
*
163901 AAAACATTTTTGAAAC--ATAT-A-ATAT-AGTTTT
1 AAAACATTTTTGAAACTTATATAATATATAATTTTT
* * * *
163932 AAAACGTTTTTGAAA---ACTATAACATAT-AGTTTG
1 AAAACATTTTTGAAACTTA-TATAATATATAATTTTT
* *
163965 AAAACATTTTT-AAAATTATATAAAATA-AATGGTTTT
1 AAAACATTTTTGAAACTTATATAATATATAAT--TTTT
* * ** *
164001 GAAAATATCTTTGAAA--TATATGTTATATAAAGTTTT
1 -AAAACATTTTTGAAACTTATATAATATAT-AATTTTT
*
164037 AAAACTTTTTT
1 AAAACATTTTT
164048 CGTTATATAT
Statistics
Matches: 235, Mismatches: 38, Indels: 47
0.73 0.12 0.15
Matches are distributed among these distances:
30 1 0.00
31 20 0.09
32 4 0.02
33 23 0.10
34 10 0.04
35 26 0.11
36 44 0.19
37 45 0.19
38 60 0.26
39 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (36 bp):
AAAACATTTTTGAAACTTATATAATATATAATTTTT
Found at i:163942 original size:31 final size:33
Alignment explanation
Indices: 163786--163984 Score: 115
Period size: 33 Copynumber: 5.8 Consensus size: 33
163776 AATATGTAAT
* * *
163786 TTTTAAAACATTTTTAGAAAGCATATATAATATATAAT
1 TTTTAAAACATTTTT-GAAA--A-CTATAACATAT-AG
* *
163824 TTTTAAAACCA-TTTTGAAAGCTTATATAATATATAG
1 TTTTAAAA-CATTTTTGAAAAC---TATAACATATAG
* *
163860 TTTTAAGATCA-TTTTGAAATTTA-TATAATATATAG
1 TTTTAA-AACATTTTTGAAA---ACTATAACATATAG
163895 TCTTTAAAAACATTTTTG-AAAC-ATATA-ATATAG
1 T-TTT-AAAACATTTTTGAAAACTATA-ACATATAG
*
163928 TTTTAAAACGTTTTTGAAAACTATAACATATAG
1 TTTTAAAACATTTTTGAAAACTATAACATATAG
* *
163961 TTTGAAAACATTTTT-AAAATTATA
1 TTTTAAAACATTTTTGAAAACTATA
163985 TAAAATAAAT
Statistics
Matches: 135, Mismatches: 10, Indels: 38
0.74 0.05 0.21
Matches are distributed among these distances:
31 11 0.08
32 16 0.12
33 33 0.24
34 1 0.01
35 13 0.10
36 25 0.19
37 22 0.16
38 12 0.09
39 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (33 bp):
TTTTAAAACATTTTTGAAAACTATAACATATAG
Found at i:164089 original size:21 final size:22
Alignment explanation
Indices: 164065--164111 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
164055 TATCATATAG
164065 TATTTTA-TTCTTTTTAATTA-T
1 TATTTTACTT-TTTTTAATTATT
*
164086 TA-TTTACTTTTTTTTATTATT
1 TATTTTACTTTTTTTAATTATT
164107 TATTT
1 TATTT
164112 AATCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 13 0.59
21 7 0.32
22 2 0.09
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTTACTTTTTTTAATTATT
Found at i:166657 original size:15 final size:17
Alignment explanation
Indices: 166626--166657 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
166616 ATGTATTTTT
166626 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
166643 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
166658 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:172092 original size:29 final size:29
Alignment explanation
Indices: 172059--172114 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
172049 CATACTAAAT
172059 ATATTATCAAAATACATATTAT-ACATTTA
1 ATATTATCAAAATACATA-TATCACATTTA
* *
172088 ATATTTTTAAAATACATATATCACATT
1 ATATTATCAAAATACATATATCACATT
172115 AAAGATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTATCAAAATACATATATCACATTTA
Found at i:172122 original size:29 final size:29
Alignment explanation
Indices: 172067--172122 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
172057 ATATATTATC
* *
172067 AAAATACATATTATACATTTAATATTTTT
1 AAAATACATATTATACATTAAAGATTTTT
172096 AAAATACATA-TATCACATTAAAGATTT
1 AAAATACATATTAT-ACATTAAAGATTT
172123 AAAAATATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (29 bp):
AAAATACATATTATACATTAAAGATTTTT
Found at i:172128 original size:28 final size:29
Alignment explanation
Indices: 172067--172129 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
172057 ATATATTATC
* * *
172067 AAAATACATATTATACATTTAATATTTTT
1 AAAATACATATTATACATTAAAGATTTTA
172096 AAAATACATA-TATCACATTAAAGA-TTTA
1 AAAATACATATTAT-ACATTAAAGATTTTA
172124 AAAATA
1 AAAATA
172130 TTGATATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATACATATTATACATTAAAGATTTTA
Found at i:172393 original size:3 final size:3
Alignment explanation
Indices: 172385--172481 Score: 194
Period size: 3 Copynumber: 32.3 Consensus size: 3
172375 AGTTAAAGCA
172385 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
172433 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
172481 A
1 A
172482 TGACATGAAA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:173092 original size:17 final size:17
Alignment explanation
Indices: 173070--173102 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
173060 TGAAGAGATA
173070 TGATTCATTCCGAATTT
1 TGATTCATTCCGAATTT
173087 TGATTCATTCCGAATT
1 TGATTCATTCCGAATT
173103 AAAGAATTCA
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:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (17 bp):
TGATTCATTCCGAATTT
Found at i:174055 original size:2 final size:2
Alignment explanation
Indices: 174048--174098 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
174038 AAACCATGCA
174048 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
174090 AT AT AT AT A
1 AT AT AT AT A
174099 GGTTAGGATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:178254 original size:23 final size:23
Alignment explanation
Indices: 178228--178275 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
178218 ATAAAGTACA
*
178228 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
178251 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
178274 AT
1 AT
178276 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:178679 original size:21 final size:22
Alignment explanation
Indices: 178654--178705 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
178644 ACACTTTACA
*
178654 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
178677 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
178700 ATATAA
1 ATATAA
178706 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:178690 original size:23 final size:23
Alignment explanation
Indices: 178664--178726 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
178654 ATATAACCAC
178664 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
178687 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
178710 TACCTATTACATCATAT
1 TACCTATTACATTATAT
178727 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:179183 original size:39 final size:39
Alignment explanation
Indices: 179129--179215 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
179119 TCAAGTTGTA
*
179129 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
179168 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
179207 GATTTTGAT
1 GATTTTGAT
179216 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:179497 original size:18 final size:18
Alignment explanation
Indices: 179474--179510 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
179464 CGAAATATAT
179474 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
179492 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
179510 A
1 A
179511 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:179787 original size:25 final size:25
Alignment explanation
Indices: 179759--179809 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
179749 TTAATCCAAA
*
179759 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
179784 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
179809 T
1 T
179810 GATTTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:180057 original size:20 final size:20
Alignment explanation
Indices: 180032--180070 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
180022 TTCCACAGTG
* *
180032 AAAAAGTATGGACACTTTAT
1 AAAAAGGATAGACACTTTAT
180052 AAAAAGGATAGACACTTTA
1 AAAAAGGATAGACACTTTA
180071 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAAAGGATAGACACTTTAT
Found at i:180098 original size:21 final size:22
Alignment explanation
Indices: 180073--180124 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
180063 ACACTTTACA
*
180073 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
180096 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
180119 ATATAA
1 ATATAA
180125 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:180109 original size:23 final size:23
Alignment explanation
Indices: 180083--180145 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
180073 ATATAACCAC
180083 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
180106 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
180129 TACCTATTACATCATAT
1 TACCTATTACATTATAT
180146 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:180524 original size:21 final size:22
Alignment explanation
Indices: 180499--180550 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
180489 ACACTTTACA
*
180499 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
180522 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
180545 ATATAA
1 ATATAA
180551 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:180535 original size:23 final size:23
Alignment explanation
Indices: 180509--180571 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
180499 ATATAACCAC
180509 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
180532 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
180555 TACCTATTACATCATAT
1 TACCTATTACATTATAT
180572 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:183452 original size:184 final size:184
Alignment explanation
Indices: 183143--183486 Score: 580
Period size: 184 Copynumber: 1.9 Consensus size: 184
183133 TTCAAATTAC
* *
183143 CGACACTTTTTTAAATGGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAC
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAC
* *
183208 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
183273 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
131 ATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
* * *
183327 CGACACTTTTTTAAATCGTATCGATACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAC
*
183392 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* **
183457 ATATTACAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTACCTATTACATTATAAT
183487 ATGTTGAAAG
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
184 148 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (184 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAC
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
Found at i:184938 original size:3 final size:3
Alignment explanation
Indices: 184930--185014 Score: 75
Period size: 3 Copynumber: 29.0 Consensus size: 3
184920 ACTTGTTTGG
* * **
184930 ATC ATC ATC TTC ATC ATC A-C ATC ATC ATC ATC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
184977 AGC TTC ATC GTC ATC ATC -TC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
185015 GTCAGCTTCA
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
2 4 0.06
3 59 0.94
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:184954 original size:17 final size:17
Alignment explanation
Indices: 184932--184965 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
184922 TTGTTTGGAT
*
184932 CATCATCTTCATCATCA
1 CATCATCATCATCATCA
184949 CATCATCATCATCATCA
1 CATCATCATCATCATCA
184966 TCTTCATCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (17 bp):
CATCATCATCATCATCA
Found at i:184955 original size:20 final size:20
Alignment explanation
Indices: 184930--184967 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
184920 ACTTGTTTGG
*
184930 ATCATCATCTTCATCATCAC
1 ATCATCATCATCATCATCAC
184950 ATCATCATCATCATCATC
1 ATCATCATCATCATCATC
184968 TTCATCGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (20 bp):
ATCATCATCATCATCATCAC
Found at i:184999 original size:41 final size:41
Alignment explanation
Indices: 184938--185026 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
184928 GGATCATCAT
184938 CTTCATCATCACATCATCATCATCATCATCTTCATCGCCAG
1 CTTCATCATCACATCATCATCATCATCATCTTCATCGCCAG
* * *
184979 CTTCATCGTCATCATC-TCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCA-CATCATCATCATCATCATCTTCATCGCCAG
185020 CTTCATC
1 CTTCATC
185027 TTGCGACCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 40 0.91
42 4 0.09
ACGTcount: A:0.22, C:0.36, G:0.07, T:0.35
Consensus pattern (41 bp):
CTTCATCATCACATCATCATCATCATCATCTTCATCGCCAG
Found at i:186798 original size:193 final size:197
Alignment explanation
Indices: 186469--187992 Score: 2569
Period size: 193 Copynumber: 7.9 Consensus size: 197
186459 TTTAAATTAG
*
186469 TATCGACACAAACTATATTAGTGTCG--ACATTATTTAGACCTAT-TCTCAT-AAACCGGTATAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCTCTCATAAAACCGGTATAA
186530 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
186594 GACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAAA
186658 AA
196 AA
186660 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-TCTCTCATAAAACCGGTATA
186725 ATTGTACC-GTTAGA-TGAAAAATTACATATTACATTATAC-TTT-GGTTCGATGA-TTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
186785 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG--A
186849 AAAAA
193 AAAAA
186854 TATCGACACAAA-TATATTAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-TCTCTCATAAAACCGGTATA
186915 ATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
186979 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGG-AA
187043 AAAA
194 AAAA
187047 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATAT-CTCTCATAAAACCGGTATA
187112 ATTGTACCGGTTAGATTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
187176 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
187240 AAA
195 AAA
*
187243 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATACCTCTCATAAAACCGGTATAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCTCTCATAAAACCGGTATAA
*
187308 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGAT
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGAT
* *
187373 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTT-AATTCATTCTGGAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
187437 AAA
195 AAA
187440 TATCGACACAAACTATATTAGTGTCGACACA-TATTTAGACATAT-TCTCATAAAACCGGTATAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCTCTCATAAAACCGGTATAA
*
187503 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTGTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* **
187568 GACACTTTTTATATCTGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT-GGAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAAA
187632 AA
196 AA
*
187634 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGAC-TATCTCTCATAAAACCGTTAT-A
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCTCTCATAAAACCGGTATAA
187696 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
*
187760 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACC-TG-TTTCCATTCATTCTGGAAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAAA
187823 AA
196 AA
187825 TATCGACACAAACTATATTAGTGTCGAC-CA-T-TTTAGACATATCCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATAT-CTCTCATAAAACCGGTATA
* *
187886 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
187951 TTGACACTTTTTTATATATGGATCGACAC-TTATGGGTGCACC
129 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACC
187993 CTGTGGCATA
Statistics
Matches: 1276, Mismatches: 22, Indels: 68
0.93 0.02 0.05
Matches are distributed among these distances:
189 7 0.01
190 38 0.03
191 136 0.11
192 135 0.11
193 252 0.20
194 208 0.16
195 141 0.11
196 121 0.09
197 195 0.15
198 43 0.03
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (197 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCTCTCATAAAACCGGTATAA
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAAA
AA
Found at i:187701 original size:583 final size:588
Alignment explanation
Indices: 186469--187992 Score: 2638
Period size: 583 Copynumber: 2.6 Consensus size: 588
186459 TTTAAATTAG
186469 TATCGACACAAACTATATTAGTGTCG--ACATTATTTAGACCTAT-TCTCAT-AAACCGGTATAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGA-CTATCTCTCATAAAACCGGTATAA
186530 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGATC
65 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* *
186594 GACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAAA
130 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAAA
*
186658 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
194 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTA
186723 TAATTGTACC-GTTAGA-TGAAAAATTACATATTACATTATAC-TTTGG--TTCGATGA-TTTGG
259 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGG
*
186782 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGA
324 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCAATTCATTCTGGGA
*
186847 AAAAAAATATCGACACAAATATATTAGTGTCGACATTATTTAGACATATTCTCTCATAAAACCGT
389 AAAAAAATATCGACACAAATATATTAGTGTCGACAATATTTAGACATATTCTCTCATAAAACCGT
*
186912 ATAATTGTACCGGTTAGATTGAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTGGG
454 ATAATTGTACCGGTTAGATTGAAAAATTACATATACATTATACTGTTGGGTTCGATGATTTTGGG
*
186977 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAA
519 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCAATTCATTCTGGGAA
187042 AAAAA
584 AAAAA
187047 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGAC-TAT-CTCTCATAAAACCGGTATA
187112 ATTGTACCGGTTAGATTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGGGAT
64 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
187176 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAA
129 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAA
187241 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-CCTCTCATAAAACCGGTA
194 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTA
187305 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGG
259 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGG
*
187370 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTAATTCATTCT-GG-
324 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCAATTCATTCTGGGA
187433 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATATTTAGACATA-T-TCTCATAAAACC
389 AAAAAAATATCGACACAAA-TATATTAGTGTCGACA-ATATTTAGACATATTCTCTCATAAAACC
187496 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTGTTGGGTTCGATGATTT
452 -GTATAATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTGTTGGGTTCGATGATTT
* *
187561 TGGGATCGACACTTTTTATATCTGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
515 TGGGATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCAATTCATTCT
187626 -GG-AAAAAA
579 GGGAAAAAAA
*
187634 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTATCTCTCATAAAACCGTTAT-AT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTATCTCTCATAAAACCGGTATAAT
187697 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGATCG
66 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
187761 ACACTTTTTATATATGGATCGACACTTTATGGGTGCA-CCTGTTTCCATTCATTCTGGAAAAAAA
131 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAAAA
187825 TATCGACACAAACTATATTAGTGTCGAC-CA-T-TTTAGACATATCCTCTCAT-AAACCGGTATA
196 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
*
187886 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
261 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
*
187951 TTGACACTTTTTTATATATGGATCGACAC-TTATGGGTGCACC
326 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACC
187993 CTGTGGCATA
Statistics
Matches: 911, Mismatches: 13, Indels: 43
0.94 0.01 0.04
Matches are distributed among these distances:
578 26 0.03
579 105 0.12
580 45 0.05
581 2 0.00
582 93 0.10
583 240 0.26
584 87 0.10
585 8 0.01
586 71 0.08
587 68 0.07
588 117 0.13
589 49 0.05
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (588 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTATCTCTCATAAAACCGGTATAAT
TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCATTCTGGAAAAAAA
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGATTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCAATTCATTCTGGGAAA
AAAAATATCGACACAAATATATTAGTGTCGACAATATTTAGACATATTCTCTCATAAAACCGTAT
AATTGTACCGGTTAGATTGAAAAATTACATATACATTATACTGTTGGGTTCGATGATTTTGGGAT
CGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCAATTCATTCTGGGAAAA
AAA
Found at i:188159 original size:19 final size:19
Alignment explanation
Indices: 188113--188161 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
188103 TTTTATTCAC
*
188113 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
188132 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
188151 ATACAAAATTA
1 ATACAAAATTA
188162 CTCGACATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:190247 original size:33 final size:33
Alignment explanation
Indices: 190210--190275 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
190200 CATCTTAATA
*
190210 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
190243 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
190276 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:192757 original size:19 final size:19
Alignment explanation
Indices: 192733--192791 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
192723 ACTTTTAAAT
192733 TTACCGGTTTTTCATTTTG
1 TTACCGGTTTTTCATTTTG
192752 TTACCGGTTTTATCATATTT-
1 TTACCGGTTTT-TCAT-TTTG
* *
192772 TTACCTGGTATATCATTTTG
1 TTACC-GGTTTTTCATTTTG
192792 GATCGATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 14 0.41
20 13 0.38
21 7 0.21
ACGTcount: A:0.17, C:0.15, G:0.14, T:0.54
Consensus pattern (19 bp):
TTACCGGTTTTTCATTTTG
Found at i:193249 original size:224 final size:222
Alignment explanation
Indices: 192841--193280 Score: 715
Period size: 224 Copynumber: 2.0 Consensus size: 222
192831 TTAAAACTGC
192841 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACTACAATAT
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACTACAATAT
** *
192906 TAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAATATTTAGA
66 TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTAAAAATATTTAGA
*
192971 ATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAGTATG
131 ATTTAAATTTAACAATATTAACCAAAGATAATAATAAATA-GTTTTCAACAGTGAAATAAGTATG
*
193036 GACACTTTTATAAAAATGATATATACTT
195 GACACTTTTATAAAAAGGATATATACTT
*
193064 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCA-CTACAAT
*
193129 ATTAATTTAATAA-TTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTATAAAATATTAT
64 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTT-TAAAA-A-TAT
* *
193193 TTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATA-TTTTC-ACAGTGAAATAAG
126 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATAGTTTTCAACAGTGAAATAAG
*
193256 TATGTACACTTTTATAAAAAGGATA
191 TATGGACACTTTTATAAAAAGGATA
193281 GATTTTACAA
Statistics
Matches: 202, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
223 4 0.02
224 123 0.61
225 29 0.14
226 1 0.00
227 45 0.22
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (222 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACTACAATAT
TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTAAAAATATTTAGA
ATTTAAATTTAACAATATTAACCAAAGATAATAATAAATAGTTTTCAACAGTGAAATAAGTATGG
ACACTTTTATAAAAAGGATATATACTT
Found at i:194143 original size:24 final size:25
Alignment explanation
Indices: 194116--194169 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
194106 AATAAAATAT
*
194116 AATACA-TATCACATCATCATTTTA
1 AATACATTATCACATCATCACTTTA
* *
194140 AATATATTTATCACATCATTACTTTA
1 AATACA-TTATCACATCATCACTTTA
194166 AATA
1 AATA
194170 TATGATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.20
26 20 0.80
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.41
Consensus pattern (25 bp):
AATACATTATCACATCATCACTTTA
Found at i:194154 original size:26 final size:26
Alignment explanation
Indices: 194122--194172 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
194112 ATATAATACA
*
194122 TATCACATCATCATTTTAAATATATT
1 TATCACATCATCACTTTAAATATATT
*
194148 TATCACATCATTACTTTAAATATAT
1 TATCACATCATCACTTTAAATATAT
194173 GATATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (26 bp):
TATCACATCATCACTTTAAATATATT
Found at i:194270 original size:24 final size:23
Alignment explanation
Indices: 194216--194276 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
194206 TATATATATT
* *
194216 TATCATCATTTTTAAAAATATGTCA
1 TATCATCA--TTTAAAAACATGACA
**
194241 CGTCATCACTTTAAAAACATGACA
1 TATCATCA-TTTAAAAACATGACA
194265 TATCATCATTTA
1 TATCATCATTTA
194277 TGTACACATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
23 4 0.14
24 19 0.66
25 6 0.21
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (23 bp):
TATCATCATTTAAAAACATGACA
Done.