Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007931.1 Hibiscus syriacus cultivar Beakdansim tig00110339_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: 2341804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:340 original size:24 final size:23
Alignment explanation
Indices: 312--383 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
302 GACAAATATA
312 TGGCACTTTTGGTGCAACCCTATG
1 TGGCAC-TTTGGTGCAACCCTATG
**
336 TGGCACTTCAGTGCAACCCTATG
1 TGGCACTTTGGTGCAACCCTATG
* *
359 TGGTACTTTGGTGCAA-ACTATG
1 TGGCACTTTGGTGCAACCCTATG
381 TGG
1 TGG
384 TCATTCGGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.19
23 28 0.67
24 6 0.14
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTTGGTGCAACCCTATG
Found at i:420 original size:20 final size:21
Alignment explanation
Indices: 377--421 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
367 TGGTGCAAAC
377 TATGTGGTCATTCGGGACAAT
1 TATGTGGTCATTCGGGACAAT
*
398 TATGTGG-CACTTCGGTA-AAT
1 TATGTGGTCA-TTCGGGACAAT
418 TATG
1 TATG
422 AGTTGTGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACAAT
Found at i:1550 original size:198 final size:201
Alignment explanation
Indices: 1024--1675 Score: 832
Period size: 201 Copynumber: 3.3 Consensus size: 201
1014 AGGGGTGTTA
* ** *
1024 CTACAATGCGGTTGATACACCCTCGAGCTGAATGGAATCAAACTCAAAAGTGGTCATTGAGAGAT
1 CTACAATGCGGTTGATACACCCTCGAGATGAATGGAATCAAACTCAAAAGTCTTCATTGATAGAT
* *
1089 AACCCTTATCGCATTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTATTGCTAAATCGC
66 AACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTGTTGCTAAATCGC
* * *
1154 ATCCAAACCGGGTCTTCTTCTGGACTTAAAGACCTCAGTTTAAACTTCAACCGAAAAGTAGTTCC
131 ATCCAACCCGGGTCTTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCC
*
1219 TCT-TTG
196 T-TGCTG
* * *
1225 CTAC-ATGCGGTTGATACACCCTCAAGATTAATGGAATCGAAACTCGAAAGTCTTCATTGATAGA
1 CTACAATGCGGTTGATACACCCTCGAGATGAATGGAATC-AAACTCAAAAGTCTTCATTGATAGA
* * * * *
1289 TATCCTTTATCGCCTTGAGCTATGCTATGAATTTGGCTGGGATATAGTTCATTGTTTCTAAATCG
65 TAACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTGTTGCTAAATCG
* * * *
1354 CATCCAACCCGGGTCTTTTTTTCGACTTAAATACCTCAGTTT-AACTTC-ACCGGAAAGTAGTTC
130 CATCCAACCCGGGTCTTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTC
1417 CTTGCTG
195 CTTGCTG
* * * ** **
1424 CTACAATGCAGTTGATACACCATCGAG-TGAATGGAATCAAATTTGAAAGTCTTTGTTGATAGAT
1 CTACAATGCGGTTGATACACCCTCGAGATGAATGGAATCAAACTCAAAAGTCTTCATTGATAGAT
* * **
1488 AACCCTTATCTCCTTGAGCTATGCTGTGAATTTAGCTGAAATATAGTTCCTTGTTGCTAAATCGC
66 AACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTGTTGCTAAATCGC
* ** * * * *
1553 AGCCAACCCAAGTATTCTTCTAGACTTAAAGACCTCAATTTAAACTTCAACAGGAAAGTAGTTCA
131 ATCCAACCCGGGTCTTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCC
* *
1618 TCGCTA
196 TTGCTG
* * *
1624 C-ACAATACGGTTGATAC-CCCTCGAGTTGAATGGAATCGAACTCAAAAGTCTT
1 CTACAATGCGGTTGATACACCCTCGAGATGAATGGAATCAAACTCAAAAGTCTT
1676 TGTTAACAGA
Statistics
Matches: 387, Mismatches: 58, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
198 118 0.30
199 74 0.19
200 75 0.19
201 120 0.31
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (201 bp):
CTACAATGCGGTTGATACACCCTCGAGATGAATGGAATCAAACTCAAAAGTCTTCATTGATAGAT
AACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTGTTGCTAAATCGC
ATCCAACCCGGGTCTTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCC
TTGCTG
Found at i:7430 original size:54 final size:54
Alignment explanation
Indices: 7354--7722 Score: 544
Period size: 54 Copynumber: 6.9 Consensus size: 54
7344 AGTGCCAAAA
* * *
7354 TTATTCATCCACGTTGGATGAATTCCGTGAAATGCACACTTAGTGCCGAGACGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGG
* * * * * **
7408 TTATTCATCTATATAGGATGAATTCCGTGAAGTGCACAATTAGTGTCGAAACAA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGG
*
7462 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGG
* **
7516 TTATTCATCCACATATGATGAATTCCGTGAAATGCACACTTAGTTTCGAAACGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGG
*
7570 TTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAACGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGG
* * **
7624 TTATT--TCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCTGAAACAA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGG
*
7676 TTATTCATCCACATAGGATGAATTCCGTGAAATGTACACTTAGTGCC
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCC
7723 TATTTGATAA
Statistics
Matches: 281, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
52 49 0.17
54 232 0.83
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (54 bp):
TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGG
Found at i:8085 original size:22 final size:22
Alignment explanation
Indices: 8043--8113 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
8033 TAGTCCCTCA
*
8043 GTATCGATA--ACCATACCATG
1 GTATCGATACTACCATACTATG
*
8063 GTATCGATACTACCATTCTATG
1 GTATCGATACTACCATACTATG
* *
8085 GTACCGATACT---ATGCTATG
1 GTATCGATACTACCATACTATG
8104 GTATCGATAC
1 GTATCGATAC
8114 CATTTTTGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.36
20 9 0.20
22 19 0.43
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (22 bp):
GTATCGATACTACCATACTATG
Found at i:17237 original size:3 final size:3
Alignment explanation
Indices: 17231--17295 Score: 73
Period size: 3 Copynumber: 22.7 Consensus size: 3
17221 TTTATTATTC
* * *
17231 AAT AAT AAT GAT AAT AAT AAT -AT AAT ATT AAT AA- AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
17277 AAT AAT AAT ATT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AA
17296 AATGGGGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 6 0.12
3 45 0.88
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:17255 original size:17 final size:17
Alignment explanation
Indices: 17242--17287 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
17232 ATAATAATGA
17242 TAATAATAATATAATAT
1 TAATAATAATATAATAT
17259 TAATAA-AATAATAATAT
1 TAATAATAAT-ATAATAT
17276 TAATAATAATAT
1 TAATAATAATAT
17288 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAATAATATAATAT
Found at i:17298 original size:31 final size:28
Alignment explanation
Indices: 17226--17290 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
17216 AAATATTTAT
*
17226 TATTCAATAATAATGATAATAATAATATAA
1 TATT-AATAA-AATAATAATAATAATATAA
*
17256 TATTAATAAAATAATAATATTAATAATAA
1 TATTAATAAAATAATAATAATAAT-ATAA
17285 TATTAA
1 TATTAA
17291 AATAAAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 13 0.41
29 15 0.47
30 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (28 bp):
TATTAATAAAATAATAATAATAATATAA
Found at i:17626 original size:123 final size:121
Alignment explanation
Indices: 17414--17835 Score: 564
Period size: 123 Copynumber: 3.5 Consensus size: 121
17404 TTGATTCTGA
* * * * *
17414 TCTATCTCCTTCTGCGAT-GAATCGATCAAAAGGTTGAATAAGTTCTTTAGATTGTGAACTTTTT
1 TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTATGAACTTCTT
* *
17478 CTTCCTCTTCAGATGAGTTTATCTTATTACGAACTCCT-TCTGGAAAT-TTTGATGCTAC
66 CTTCCTCTTCAGATGAGTTT-TCTTATTACGAACT-CTATCTGGAAATGGTT--TGCTGC
* *
17536 TCTATTTCCTTCTGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTTAGACTATGAACTTCTT
1 TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTATGAACTTCTT
* * *
17601 CTTCCTCTTCAGATGAGTTCTTCTTATTACAAACTCTGTCTGGAAATGGTTCTGTTGC
66 CTTCCTCTTCAGATGAGTT-TTCTTATTACGAACTCTATCTGGAAATGGTT-TGCTGC
* * *
17659 TCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTAAACAAGTTCTTCAGACTATGAACTTCTT
1 TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTATGAACTTCTT
* *
17724 CTTCCTCTTCAGATGAGTTTTTCTTATTACGAACTCTATGTGGAAATGGTTTGCTGG
66 CTTCCTCTTCAGATGAG-TTTTCTTATTACGAACTCTATCTGGAAATGGTTTGCTGC
* * * *
17781 TCTATCT-CTTTTGTGATTGAATAGAGCAAAAGGTTGAACAAGTTCTTTAGACTAT
1 TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTAT
17836 AAATGTTGAG
Statistics
Matches: 268, Mismatches: 27, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
121 43 0.16
122 30 0.11
123 190 0.71
124 5 0.02
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (121 bp):
TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTATGAACTTCTT
CTTCCTCTTCAGATGAGTTTTCTTATTACGAACTCTATCTGGAAATGGTTTGCTGC
Found at i:21240 original size:23 final size:23
Alignment explanation
Indices: 21208--21268 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
21198 ATTCCCCTGT
21208 GGGGGAAATCGGTTCCCCTTCAA-A
1 GGGGG-AATCGGTTCCCC-TCAAGA
21232 GGGGGAATCGGTT-CCCTCAAGA
1 GGGGGAATCGGTTCCCCTCAAGA
*
21254 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
21269 TCTGCACCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 10 0.29
22 11 0.32
23 8 0.24
24 5 0.15
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.20
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTCAAGA
Found at i:21257 original size:21 final size:21
Alignment explanation
Indices: 21208--21270 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
21198 ATTCCCCTGT
21208 GGGGGAAATCGGTTCCCCTTCAAA
1 GGGGG-AATCGGTT-CCC-TCAAA
21232 GGGGGAATCGGTTCCCTCAAGA
1 GGGGGAATCGGTTCCCTCAA-A
*
21254 GGGGG-ATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
21271 TGCACCAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 15 0.41
22 9 0.24
23 8 0.22
24 5 0.14
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:27239 original size:123 final size:123
Alignment explanation
Indices: 27023--27447 Score: 660
Period size: 123 Copynumber: 3.5 Consensus size: 123
27013 GTTTTCAACA
*
27023 ATGAACTTCTTCTTCCTCTTCAGATGA--T-TTCTTATTACGAACTCTGTCTGGAAATGGTTCTG
1 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGGTTATG
*
27085 TTGCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
66 TTTCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
* *
27143 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTTTGTCTGGAAATGGTTTTG
1 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGGTTATG
* * *
27208 TTTCTCTATCTCCTTTTGCGATAAAATCGAGCAAAAGGTTGAACAAGTTCTTCAGACT
66 TTTCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
* * *
27266 ATGAACTTCTTCTTCCTCTTAAGATAAGTTCTTCTTATTATGAACTCTGTCTGGAAATGGTTATG
1 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGGTTATG
* * * *
27331 ATGT-TCTATCTCCTTCTACGATAGAATCGAGCAAAAGTTTGAACAAGTTCTTCAGACT
66 -TTTCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
* * *
27389 ATTAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTATCTGGCAATG
1 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATG
27448 TTGATCTCTT
Statistics
Matches: 279, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
120 27 0.10
122 1 0.00
123 249 0.89
124 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (123 bp):
ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGGTTATG
TTTCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
Found at i:29834 original size:10 final size:10
Alignment explanation
Indices: 29813--29864 Score: 65
Period size: 9 Copynumber: 5.5 Consensus size: 10
29803 CAACTTATTC
29813 TCTTTC-TTT
1 TCTTTCTTTT
*
29822 TCTGTCTTTT
1 TCTTTCTTTT
*
29832 TCTTTTTTTT
1 TCTTTCTTTT
29842 TC-TTCTTTT
1 TCTTTCTTTT
29851 T-TTTCTTTT
1 TCTTTCTTTT
29860 TCTTT
1 TCTTT
29865 TTTCTATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (10 bp):
TCTTTCTTTT
Found at i:29835 original size:6 final size:6
Alignment explanation
Indices: 29826--29866 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
29816 TTCTTTTCTG
29826 TCTTTT TC-TTT T-TTTT TCTTCTT T-TTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT TCTTTT T
29867 TCTATTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 11 0.35
6 17 0.55
7 3 0.10
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TCTTTT
Found at i:29835 original size:15 final size:13
Alignment explanation
Indices: 29810--29869 Score: 59
Period size: 15 Copynumber: 4.3 Consensus size: 13
29800 TAGCAACTTA
*
29810 TTCTCTTTCTTTT
1 TTCTTTTTCTTTT
29823 CTGTCTTTTTCTTTT
1 -T-TCTTTTTCTTTT
29838 TT-TTTCTTCTTTTTT
1 TTCTTT-TTC--TTTT
29853 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
29866 TTCT
1 TTCT
29870 ATTTGAAACT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
12 3 0.08
13 12 0.30
14 2 0.05
15 20 0.50
16 3 0.08
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:29841 original size:19 final size:18
Alignment explanation
Indices: 29813--29867 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
29803 CAACTTATTC
*
29813 TCTTTCTTTTCTGTCTTTT
1 TCTTTTTTTTCT-TCTTTT
29832 TCTTTTTTTTTCTTCTTTT
1 TC-TTTTTTTTCTTCTTTT
29851 T-TTTCTTTTTCTT-TTTT
1 TCTTT-TTTTTCTTCTTTT
29868 CTATTTGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.21
18 8 0.24
19 9 0.27
20 9 0.27
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (18 bp):
TCTTTTTTTTCTTCTTTT
Found at i:29856 original size:22 final size:22
Alignment explanation
Indices: 29819--29869 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
29809 ATTCTCTTTC
*
29819 TTTTCTGTCTTTTTCTTTTT-TT
1 TTTTCT-TTTTTTTCTTTTTCTT
29841 TTCTTCTTTTTTTTCTTTTTCTT
1 TT-TTCTTTTTTTTCTTTTTCTT
29864 TTTTCT
1 TTTTCT
29870 ATTTGAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (22 bp):
TTTTCTTTTTTTTCTTTTTCTT
Found at i:32190 original size:26 final size:26
Alignment explanation
Indices: 32161--32215 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
32151 GTTTGAAACA
* *
32161 AAATGTAAATGCAAAGATGCAAATGC
1 AAATGCAAATACAAAGATGCAAATGC
**
32187 AAATGCAAATACAAAGATGTGAATGC
1 AAATGCAAATACAAAGATGCAAATGC
32213 AAA
1 AAA
32216 ATAAAAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (26 bp):
AAATGCAAATACAAAGATGCAAATGC
Found at i:32254 original size:26 final size:25
Alignment explanation
Indices: 32208--32256 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
32198 CAAAGATGTG
*
32208 AATGCAAAATAAAAATACAAATGAA
1 AATGAAAAATAAAAATACAAATGAA
*
32233 AATGAAAATATAAAAATGCAAATG
1 AATGAAAA-ATAAAAATACAAATG
32257 CAAACATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.18
Consensus pattern (25 bp):
AATGAAAAATAAAAATACAAATGAA
Found at i:32255 original size:20 final size:19
Alignment explanation
Indices: 32208--32295 Score: 61
Period size: 20 Copynumber: 4.5 Consensus size: 19
32198 CAAAGATGTG
*
32208 AATGCAAAAT-AAAAATACA
1 AATGC-AAATGAAAAATAAA
*
32227 AATGAAAATGAAAATATAAA
1 AATGCAAATGAAAA-ATAAA
*
32247 AATGCAAATGCAAACATAAA
1 AATGCAAATG-AAAAATAAA
* * * * *
32267 AGTACGAATGCAAAATGAA
1 AATGCAAATGAAAAATAAA
*
32286 AATACAAATG
1 AATGCAAATG
32296 CAACGAAGGA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
18 4 0.07
19 22 0.41
20 25 0.46
21 3 0.06
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.17
Consensus pattern (19 bp):
AATGCAAATGAAAAATAAA
Found at i:32297 original size:19 final size:19
Alignment explanation
Indices: 32245--32298 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
32235 TGAAAATATA
*
32245 AAAATGCAAATGCAAACAT
1 AAAATACAAATGCAAACAT
*
32264 AAAAGTACGAATGCAAA-AT
1 AAAA-TACAAATGCAAACAT
32283 GAAAATACAAATGCAA
1 -AAAATACAAATGCAA
32299 CGAAGGAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (19 bp):
AAAATACAAATGCAAACAT
Found at i:34268 original size:20 final size:20
Alignment explanation
Indices: 34194--34562 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
34184 GATTTTCCAT
* ** *
34194 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
34214 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
34234 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34254 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* **
34274 AATCACAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
34294 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34314 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34334 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
34354 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34374 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34394 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34414 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34434 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
34454 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34474 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
34494 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
34514 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
34534 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
34554 AATCACAAC
1 AATCGCAAC
34563 ACTAAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:35483 original size:12 final size:12
Alignment explanation
Indices: 35466--35490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35456 ATATAATCCT
35466 GAAGAAGAAAAA
1 GAAGAAGAAAAA
35478 GAAGAAGAAAAA
1 GAAGAAGAAAAA
35490 G
1 G
35491 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:37794 original size:19 final size:19
Alignment explanation
Indices: 37772--38092 Score: 369
Period size: 19 Copynumber: 18.4 Consensus size: 19
37762 CGGAAAATAC
*
37772 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37791 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
37805 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
37825 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
37839 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37858 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37877 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
37891 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37910 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37929 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37948 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
37962 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
37981 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38000 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
38014 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38033 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
38047 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38066 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38085 AATCGCAA
1 AATCGCAA
38093 CGAGATAATC
Statistics
Matches: 261, Mismatches: 10, Indels: 62
0.78 0.03 0.19
Matches are distributed among these distances:
14 56 0.21
15 2 0.01
16 22 0.08
17 20 0.08
18 3 0.01
19 145 0.56
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:37859 original size:33 final size:33
Alignment explanation
Indices: 37772--38073 Score: 243
Period size: 33 Copynumber: 8.8 Consensus size: 33
37762 CGGAAAATAC
* *
37772 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
37805 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
37839 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
37877 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
37910 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
37948 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
37981 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
38013 GAATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 -AATCGCAATGCGAAATGAAAATCGCAACGAGAA
38046 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
38074 TGCGAAATGA
Statistics
Matches: 242, Mismatches: 9, Indels: 36
0.84 0.03 0.13
Matches are distributed among these distances:
32 2 0.01
33 141 0.58
34 31 0.13
35 10 0.04
36 9 0.04
37 2 0.01
38 47 0.19
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:38019 original size:14 final size:14
Alignment explanation
Indices: 38000--38054 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
37990 GCGAAATGAA
38000 AATCGCAACGAAAG
1 AATCGCAACGAAAG
38014 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
38031 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
38047 AATCGCAA
1 AATCGCAA
38055 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.44
16 6 0.17
17 6 0.17
19 8 0.22
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:38130 original size:52 final size:52
Alignment explanation
Indices: 37800--38114 Score: 412
Period size: 52 Copynumber: 6.0 Consensus size: 52
37790 AAATCCCAAC
37800 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
37853 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
37905 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* * *
37955 ACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
38012 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
38061 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
38113 AT
1 AT
38115 TATAAACGCA
Statistics
Matches: 232, Mismatches: 15, Indels: 31
0.83 0.05 0.11
Matches are distributed among these distances:
47 9 0.04
48 1 0.00
49 5 0.02
50 10 0.04
51 7 0.03
52 170 0.73
53 16 0.07
54 1 0.00
56 1 0.00
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:38230 original size:19 final size:19
Alignment explanation
Indices: 38121--38222 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
38111 AAATTATAAA
38121 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
38140 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
38160 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
38176 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
38193 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
38212 CGCATTGCGAT
1 CGCATTGCGAT
38223 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:38348 original size:14 final size:14
Alignment explanation
Indices: 38329--38365 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
38319 CATCAATTAC
38329 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
38343 ACAAATCATCTTTT
1 ACAAATCAACTTTT
38357 ACAAATCAA
1 ACAAATCAA
38366 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:40365 original size:14 final size:14
Alignment explanation
Indices: 40346--40402 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
40336 GCGAAATGAA
*
40346 AATCGCAACGACAG
1 AATCGCAACGAAAG
40360 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
40377 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
40393 AATCGCAACG
1 AATCGCAACG
40403 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:40373 original size:33 final size:33
Alignment explanation
Indices: 40327--40419 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
40317 GCGAAACCAA
*
40327 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
40360 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
40393 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
40420 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:40384 original size:19 final size:19
Alignment explanation
Indices: 40290--40424 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
40280 TAGTTTACTT
* *
40290 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
40310 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
40329 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
40348 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
40362 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
40381 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
40395 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
40414 TCGCAATGCGA
1 TCGCAACGCGA
40425 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:40442 original size:19 final size:19
Alignment explanation
Indices: 40420--40548 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
40410 AAAATCGCAA
40420 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
40439 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
40453 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
40472 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
40486 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
40505 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
40524 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
40544 TGCGA
1 TGCGA
40549 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:40462 original size:33 final size:33
Alignment explanation
Indices: 40420--40511 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
40410 AAAATCGCAA
40420 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
40453 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
40486 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
40512 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:40739 original size:93 final size:93
Alignment explanation
Indices: 40580--41046 Score: 918
Period size: 93 Copynumber: 5.0 Consensus size: 93
40570 GCAAATTGAA
40580 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
40645 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
40673 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
40738 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
40766 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
40831 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
40859 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
40923 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
40951 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
41016 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
41044 ACT
1 ACT
41047 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.25
93 280 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:41017 original size:185 final size:186
Alignment explanation
Indices: 40580--41046 Score: 918
Period size: 185 Copynumber: 2.5 Consensus size: 186
40570 GCAAATTGAA
40580 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
40645 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
40710 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
40766 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
40831 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
40895 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
40951 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
41016 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
41047 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 154 0.55
186 126 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:42771 original size:14 final size:14
Alignment explanation
Indices: 42752--42841 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
42742 TTGAAATGAA
42752 AATCGCAACGAGAG
1 AATCGCAACGAGAG
42766 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
42783 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
42799 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
42818 AATCGCAACGAGAG
1 AATCGCAACGAGAG
42832 AATCGCAACG
1 AATCGCAACG
42842 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:42789 original size:33 final size:33
Alignment explanation
Indices: 42744--42858 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
42734 TCTTTTGGTT
42744 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
42777 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
42810 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
42843 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
42859 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:42790 original size:19 final size:18
Alignment explanation
Indices: 42751--42863 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
42741 GTTGAAATGA
42751 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
42766 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
42783 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
42799 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
42816 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
42832 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
42849 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
42864 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:42894 original size:14 final size:14
Alignment explanation
Indices: 42875--42929 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
42865 TTTGGTTTCG
42875 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
42889 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
42908 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
42922 CGTTGCGA
1 CGTTGCGA
42930 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:42907 original size:33 final size:33
Alignment explanation
Indices: 42859--42929 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
42849 AAAATCGCAA
**
42859 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
42892 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
42925 TGCGA
1 TGCGA
42930 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:42937 original size:33 final size:33
Alignment explanation
Indices: 42870--42951 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
42860 GCGATTTTGG
***
42870 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
42903 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
42936 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
42952 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:42956 original size:20 final size:20
Alignment explanation
Indices: 42882--42970 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
42872 TCGCGTTGCG
42882 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
42902 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
42915 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
42935 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
42955 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
42971 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:43092 original size:33 final size:33
Alignment explanation
Indices: 43050--43120 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
43040 AATACTAACT
*
43050 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
43083 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
43116 TGAAA
1 TGAAA
43121 TCTAATTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:43354 original size:22 final size:22
Alignment explanation
Indices: 43302--43356 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
43292 TGGTTGTGAG
**
43302 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
43324 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
43346 GGATTTCTTCG
1 GGATTTCTTCG
43357 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:43527 original size:20 final size:20
Alignment explanation
Indices: 43502--43694 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
43492 CTTTAAATAT
43502 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
43522 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
43544 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
43563 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
43583 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
43603 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
43623 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
43643 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
43663 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
43683 CGCGTTGCGATT
1 CGCGTTGCGATT
43695 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:43689 original size:60 final size:60
Alignment explanation
Indices: 43502--43694 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
43492 CTTTAAATAT
**
43502 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
43563 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
43623 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
43683 CGCGTTGCGATT
1 CGCGTTGCGATT
43695 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:43775 original size:20 final size:20
Alignment explanation
Indices: 43750--43802 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
43740 AAGAATCGCG
*
43750 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
43770 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
43790 TTGCGATTCTGGA
1 TTGCGATTCTGGA
43803 GATCGCGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:45957 original size:23 final size:22
Alignment explanation
Indices: 45918--45961 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
45908 CTGTGGGTTG
*
45918 CTTGTTGTTGGTTTTGTATTTTT
1 CTTGTTGTTGGTATTGT-TTTTT
45941 CTTGTTG-TGTGTATTGTTTTT
1 CTTGTTGTTG-GTATTGTTTTT
45962 CTCTCCATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.05, C:0.05, G:0.23, T:0.68
Consensus pattern (22 bp):
CTTGTTGTTGGTATTGTTTTTT
Found at i:46456 original size:3 final size:3
Alignment explanation
Indices: 46450--46520 Score: 85
Period size: 3 Copynumber: 24.7 Consensus size: 3
46440 TTTATTATTC
* *
46450 AAT AAT AAT GAT AAT AAT AAT AAT AAT -AT AAT ATT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
46496 AAT ATT AAT AAT AAT ATT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
46521 AATGGGAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
2 6 0.11
3 51 0.89
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:54364 original size:2 final size:2
Alignment explanation
Indices: 54357--54382 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54347 CAGTTCACTC
54357 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
54383 TCCCCCACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54690 original size:15 final size:16
Alignment explanation
Indices: 54665--54694 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54655 AAGTTAACGC
54665 CGTTAAACTTTGACGG
1 CGTTAAACTTTGACGG
54681 CGTT-AACTTTGACG
1 CGTTAAACTTTGACG
54695 TGTGAGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (16 bp):
CGTTAAACTTTGACGG
Found at i:56503 original size:15 final size:15
Alignment explanation
Indices: 56479--56513 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
56469 ATGATCCAAT
* *
56479 TCTTTTAGCTGAATC
1 TCTTTCAGCTAAATC
56494 TCTTTCAGCTAAATC
1 TCTTTCAGCTAAATC
56509 TCTTT
1 TCTTT
56514 ACATATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.49
Consensus pattern (15 bp):
TCTTTCAGCTAAATC
Found at i:62861 original size:21 final size:22
Alignment explanation
Indices: 62822--62862 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
62812 ATTTATTTTA
*
62822 TTTATTTAAATTGAGAATTAAG
1 TTTATTTAAATTGACAATTAAG
*
62844 TTTATTT-ATTTGACAATTA
1 TTTATTTAAATTGACAATTA
62863 CGATGTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (22 bp):
TTTATTTAAATTGACAATTAAG
Found at i:65566 original size:3 final size:3
Alignment explanation
Indices: 65558--65642 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
65548 TCCCGACACC
65558 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
65606 ATT ATT ATT ATT ATT ATT ATT ATT AAT GTT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
65643 ATGGGTTTTC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:67146 original size:17 final size:17
Alignment explanation
Indices: 67121--67163 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
67111 GATTTGATTG
*
67121 TTTATATTTTAGTCTTA
1 TTTAAATTTTAGTCTTA
*
67138 TTTAAA-TTTAGTTTTA
1 TTTAAATTTTAGTCTTA
*
67154 TTTTAATTTT
1 TTTAAATTTT
67164 GGTATGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTAAATTTTAGTCTTA
Found at i:67817 original size:131 final size:130
Alignment explanation
Indices: 67573--67937 Score: 473
Period size: 131 Copynumber: 2.8 Consensus size: 130
67563 CTCGATATTG
* * * *
67573 AAAATAATAATATCTTTTCATTTCGGTTGGAGTAATAAATGATTGGTTTAAGACATAAGAGGTCA
1 AAAATAATGATATC-TTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGACATGAGAGGTCA
* * * *
67638 TTTATTCTCGATT-GAATATAATTAGATATTACCGTTTTCTCCCGAATCAATATTGATTTTTAAG
65 TTTATTCTCGATTGGAA-ATAATTAGATATTATCGTTTTCACCAGAATCAATATTGAATTTTAAG
67702 AC
129 AC
** * * * *
67704 GGAATAATGGCATATC-TTCATTTCGATTGGAGTAATAAATAAATGTTTTAAGACATGAGATGTC
1 AAAATAAT-G-ATATCTTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGACATGAGAGGTC
* * *
67768 ATTTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTATAATCAATATTGAATTTTAAG
64 ATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACCAGAATCAATATTGAATTTTAAG
67833 AC
129 AC
* * * * *
67835 AAAATAGTGATATCTTTTCATTTTGATCGGAGTAATAAATGATTGCTTTAAGGCCTGAGAGGTCA
1 AAAATAATGATATC-TTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGACATGAGAGGTCA
67900 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTT
65 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTT
67938 TTCTTAAAAT
Statistics
Matches: 201, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
129 5 0.02
130 1 0.00
131 187 0.93
132 3 0.01
133 5 0.02
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.40
Consensus pattern (130 bp):
AAAATAATGATATCTTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGACATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACCAGAATCAATATTGAATTTTAAGAC
Found at i:70760 original size:18 final size:17
Alignment explanation
Indices: 70739--70783 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
70729 ACATTAAATG
*
70739 ATATTAAAATTATAATAA
1 ATATTAAAATT-TAAGAA
70757 ATATTAAAAATTTAAGAA
1 ATATT-AAAATTTAAGAA
*
70775 ATATGAAAA
1 ATATTAAAA
70784 ACGTTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 14 0.58
19 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
ATATTAAAATTTAAGAA
Found at i:70784 original size:18 final size:19
Alignment explanation
Indices: 70744--70784 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
70734 AAATGATATT
* *
70744 AAAATTATAATAAATATTA
1 AAAATTATAAGAAATATGA
70763 AAAATT-TAAGAAATATGA
1 AAAATTATAAGAAATATGA
70781 AAAA
1 AAAA
70785 CGTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATTATAAGAAATATGA
Found at i:70851 original size:18 final size:17
Alignment explanation
Indices: 70825--70880 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
70815 ATATGGAATT
* *
70825 ATTTTTTAAAATCTTGAA
1 ATTTATTAAAAT-TTAAA
70843 ATTTATTAAAAATTTAAA
1 ATTTATT-AAAATTTAAA
70861 ATATTATTAAAATTGTAAA
1 AT-TTATTAAAATT-TAAA
70880 A
1 A
70881 AAAGGATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 18 0.55
19 15 0.45
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (17 bp):
ATTTATTAAAATTTAAA
Found at i:71099 original size:17 final size:18
Alignment explanation
Indices: 71062--71108 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
71052 TGTTTATGAG
*
71062 GGAATTGGAATTTGTTCA
1 GGAATTGGAATCTGTTCA
71080 GGAATTGGAATCTG-TCA
1 GGAATTGGAATCTGTTCA
71097 GGAATTGGAATC
1 GGAATTGGAATC
71109 CAATTCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (18 bp):
GGAATTGGAATCTGTTCA
Found at i:72022 original size:259 final size:250
Alignment explanation
Indices: 71466--72069 Score: 937
Period size: 259 Copynumber: 2.4 Consensus size: 250
71456 CTCTATCCGA
* * *
71466 GACCCAACCCGAACAAAATAAAGTTTCACCCGACCCAACCCGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
* *
71531 CCGAAATAAT-AAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAATATATATATAG
66 CCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATATAG
* *
71595 AGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGGTCGGGT
131 AGAGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTCGGGTCGGGT
* * *
71660 ATTTTTCACCCTAAACCCGAACCTGACTCGAGCCGAATATCACACTCAAAAAACT
196 ATTTTTCACCCTAAACCCGAACCTGACCCGACCCGAATATCACACTAAAAAAACT
* *
71715 GACCTGACCCGACCAAAATAAAGTTTCACCCGAACCGACCCGAATATATGAATTAGAAATCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA--C--C
*
71780 CTGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGGCTTAATTGAAAAAAAAA
62 C-GACCCGAAATAATAAAAAAA-TATTTTTATTCAATAAAAACAGTGACTTAATTG-AAAAAAAA
*
71845 TTATATATAGAGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTC
124 -TATATAGAGAGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATAT-TTTTC
71910 GGGTCGGGTATTTTTCACCCTAAACCCGAA-CTCGACCCGACCCGAATATCACACTTAAAAAAAC
187 GGGTCGGGTATTTTTCACCCTAAACCCGAACCT-GACCCGACCCGAATATCACAC-TAAAAAAAC
71974 T
250 T
*
71975 GACCCGACCCGACCAAAATAAAGTTTCA-CCGACCCGACCCAAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
*
72039 CCGAAATAATAAAAATAT-TTTTTATTCAATA
66 CCGAAATAATAAAAAAATATTTTTATTCAATA
72070 TATGAATAAG
Statistics
Matches: 325, Mismatches: 18, Indels: 21
0.89 0.05 0.06
Matches are distributed among these distances:
249 54 0.17
251 1 0.00
252 13 0.04
253 3 0.01
254 32 0.10
255 8 0.02
256 32 0.10
257 7 0.02
258 58 0.18
259 81 0.25
260 36 0.11
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (250 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
CCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATATAG
AGAGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTCGGGTCGGGT
ATTTTTCACCCTAAACCCGAACCTGACCCGACCCGAATATCACACTAAAAAAACT
Found at i:75282 original size:3 final size:3
Alignment explanation
Indices: 75274--75300 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
75264 CAAATAAGGA
75274 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
75301 TACAGAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:76122 original size:3 final size:3
Alignment explanation
Indices: 76114--76157 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
76104 TCCTTTTTAA
* *
76114 ATT ATT ATT ATT ATT ATT AAT ATCA ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT A
76158 AAAAATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:79970 original size:4 final size:4
Alignment explanation
Indices: 79961--79985 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
79951 ATTGATTTTT
79961 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
79986 TTGGACTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:83053 original size:198 final size:200
Alignment explanation
Indices: 82653--83065 Score: 492
Period size: 198 Copynumber: 2.1 Consensus size: 200
82643 ATATTAAATG
* ** * * *
82653 AGAAACTTTGAAAATTGCTTTTCTCATTTTTTACAAGCATCATATGAAAACATCATGCCTAAAGG
1 AGAAACTTTGGAAATCACTTTTCTCATTTTTGACAAACATCATATGAAAACATCATGCCCAAAGG
* * * * ** *
82718 TCTTATAGATGACCCGGATGATTTATCTTCTCACTCGAAATACTGTTAGACAACCTGAATGATTT
66 TCTTATAGATGACCCGAATGACTTATCATCTCACTCGAAAGACTGACAGACAACCTGAAGGATTT
* * * * *
82783 AATCATCATGCTCGAAAGACTTATTGATAGCTCGAATGACTTACCAGTTATGGAAATAGTCTATT
131 AATCATCATGCTCGAAAGACTTATTGATAGCTCAAAGGACTTACCAATTATGAAAATAGTCTACT
*
82848 GGGTA
196 AGGTA
* * *
82853 AGAAACTTTGGAAATCAC-TTTCTCATTTTTGA-AAACATCATTTGAAAGCATCTTGCCCAAAGG
1 AGAAACTTTGGAAATCACTTTTCTCATTTTTGACAAACATCATATGAAAACATCATGCCCAAAGG
** * ** **
82916 TCTTATAGATGGTCCGAATGACTTATGATCTTGCTCGAAAGACTGACAGATGA-CTCGAAGGATT
66 TCTTATAGATGACCCGAATGACTTATCATCTCACTCGAAAGACTGACAGACAACCT-GAAGGATT
* * *
82980 TAATCATCATGCTCGAAAGACTTATTGATGGAC-CAAAGGACTTACCAATTTTGAAAATAGTTTA
130 TAATCATCATGCTCGAAAGACTTATTGATAG-CTCAAAGGACTTACCAATTATGAAAATAGTCTA
83044 CTAGGTA
194 CTAGGTA
83051 AGAAACTTTGGAAAT
1 AGAAACTTTGGAAAT
83066 TGCTTTCTTA
Statistics
Matches: 179, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
197 2 0.01
198 148 0.83
199 14 0.08
200 15 0.08
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (200 bp):
AGAAACTTTGGAAATCACTTTTCTCATTTTTGACAAACATCATATGAAAACATCATGCCCAAAGG
TCTTATAGATGACCCGAATGACTTATCATCTCACTCGAAAGACTGACAGACAACCTGAAGGATTT
AATCATCATGCTCGAAAGACTTATTGATAGCTCAAAGGACTTACCAATTATGAAAATAGTCTACT
AGGTA
Found at i:84649 original size:2 final size:2
Alignment explanation
Indices: 84642--84673 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
84632 ACATGCATAC
84642 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
84674 GTTAACGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84986 original size:18 final size:18
Alignment explanation
Indices: 84924--84994 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
84914 GGATTATCAA
* *
84924 TGGTCCTTTGGGATATAG
1 TGGTCCTTCGGGACATAG
* * *
84942 TGGTTCTTCAGAACAATCAG
1 TGGTCCTTCGGGAC-AT-AG
*
84962 TGGTCCTTTGGGACATAG
1 TGGTCCTTCGGGACATAG
*
84980 TGTTCCTTCGGGACA
1 TGGTCCTTCGGGACA
84995 AATATTCAGT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
18 24 0.60
19 4 0.10
20 12 0.30
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:88747 original size:21 final size:21
Alignment explanation
Indices: 88721--88762 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
88711 CCAGAATGGG
*
88721 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
88742 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
88763 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:88896 original size:19 final size:19
Alignment explanation
Indices: 88868--88933 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
88858 AGCCTCGGGG
*
88868 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAATT
* *
88887 TACTGCTCAAATAGTAATT
1 TACTGTTCAAACAGTAATT
* *
88906 TACTGTTCAAATAGTAAAT
1 TACTGTTCAAACAGTAATT
*
88925 TACTATTCA
1 TACTGTTCA
88934 TAAAAACATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TACTGTTCAAACAGTAATT
Found at i:89030 original size:29 final size:31
Alignment explanation
Indices: 88998--89057 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
88988 AAATTTTGAA
*
88998 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
89027 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
89058 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:90371 original size:54 final size:54
Alignment explanation
Indices: 90307--90809 Score: 718
Period size: 54 Copynumber: 9.3 Consensus size: 54
90297 TTGCCAAATA
*
90307 GGCACTAAGTGTGCATTTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * ** *
90361 AGCACTAAGTGTGCATTTTACATAATTCATCATATGTTGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* *
90415 AGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* *
90469 GGCACTAAGTATGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* *
90523 GGCACTAAATGTGCATTTCATGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
*
90577 GGTACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * **
90631 GGCACTAAGTGTGAATTTCATGGAATTCATCATATGTTGATGAATAACCGTTAA
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* *
90685 GGCACTAAGTGTGTATTTCACGGAATTCATCATATGTCGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * *** * * * * * *
90739 GGCACTATGTGTGTAAAACAAGGAATTCATAATATGTTTATGAATGACCGTATG
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* *
90793 GGCACTACGGGTGCATT
1 GGCACTAAGTGTGCATT
90810 ACAAAGAAAT
Statistics
Matches: 402, Mismatches: 47, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 402 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:91379 original size:11 final size:11
Alignment explanation
Indices: 91363--91393 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
91353 GTTTAAATAA
91363 ACAAATGCAAT
1 ACAAATGCAAT
*
91374 ACAAATGCGAT
1 ACAAATGCAAT
91385 ACAAATGCA
1 ACAAATGCA
91394 TGTATGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.16
Consensus pattern (11 bp):
ACAAATGCAAT
Found at i:93180 original size:19 final size:19
Alignment explanation
Indices: 93158--93195 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
93148 TAAAATAAAT
93158 AAATAAGAAAGCAAATGCA
1 AAATAAGAAAGCAAATGCA
*
93177 AAATAAGAATGCAAATGCA
1 AAATAAGAAAGCAAATGCA
93196 CAAGGTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.13
Consensus pattern (19 bp):
AAATAAGAAAGCAAATGCA
Found at i:94403 original size:5 final size:5
Alignment explanation
Indices: 94395--94425 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
94385 GTATGATGTG
94395 ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA A
1 ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA A
94426 ACAAAACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATGCA
Found at i:95772 original size:2 final size:2
Alignment explanation
Indices: 95760--95792 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
95750 TATAGGCTAC
*
95760 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
95793 CACCATATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:97181 original size:3 final size:3
Alignment explanation
Indices: 97173--97271 Score: 81
Period size: 3 Copynumber: 31.0 Consensus size: 3
97163 AAACATGTAG
* * *
97173 TAA TAA TAAA TGAA TAA TAA TAG TAG TAA TAA TAAA TGAA TAA TAA TAG
1 TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA
* * * *
97222 TAG TAA TAT TAAA TAA TAA TAA TAA TAA TAT TAAA TAT TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
97269 TAA
1 TAA
97272 CCCGAACAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
3 64 0.80
4 16 0.20
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:97190 original size:11 final size:11
Alignment explanation
Indices: 97174--97218 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 11
97164 AACATGTAGT
97174 AATAATAAATG
1 AATAATAAATG
97185 AATAATAATAGTAG
1 AATAATAA-A-T-G
97199 TAATAATAAATG
1 -AATAATAAATG
97211 AATAATAA
1 AATAATAA
97219 TAGTAGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 16 0.53
12 2 0.07
13 2 0.07
14 2 0.07
15 8 0.27
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (11 bp):
AATAATAAATG
Found at i:97205 original size:26 final size:26
Alignment explanation
Indices: 97169--97245 Score: 138
Period size: 26 Copynumber: 3.0 Consensus size: 26
97159 CAAAAAACAT
97169 GTAGTAATAATAAATGAATAATAATA
1 GTAGTAATAATAAATGAATAATAATA
97195 GTAGTAATAATAAATGAATAATAATA
1 GTAGTAATAATAAATGAATAATAATA
*
97221 GTAGTAATATTAAAT-AATAATAATA
1 GTAGTAATAATAAATGAATAATAATA
97246 ATAATATTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 10 0.20
26 40 0.80
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.32
Consensus pattern (26 bp):
GTAGTAATAATAAATGAATAATAATA
Found at i:97265 original size:22 final size:22
Alignment explanation
Indices: 97173--97271 Score: 103
Period size: 22 Copynumber: 4.4 Consensus size: 22
97163 AAACATGTAG
*
97173 TAATAATAA-A-TGAATAATAA
1 TAATAATAATATTAAATAATAA
* * *
97193 TAGTAGTAATAATAAATGAATAA
1 TAATAATAATATTAAAT-AATAA
97216 TAATAGTAGTAATATTAAATAATAA
1 TAATA--A-TAATATTAAATAATAA
*
97241 TAATAATAATATTAAATATTAA
1 TAATAATAATATTAAATAATAA
97263 TAATAATAA
1 TAATAATAA
97272 CCCGAACAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
20 7 0.11
21 1 0.02
22 28 0.42
23 10 0.15
25 10 0.15
26 10 0.15
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (22 bp):
TAATAATAATATTAAATAATAA
Found at i:97717 original size:41 final size:41
Alignment explanation
Indices: 97489--97750 Score: 145
Period size: 41 Copynumber: 6.4 Consensus size: 41
97479 TTTTAACAAA
* * * *
97489 GCCGCTAAAAACTCGTACTTT-GATTGCATTTCTATATAAAC
1 GCCGCTAAAGACTCGTACTTTAG-TGGCGTTTTTATATAAAC
* * * * * *
97530 GCTGCTAAAGA-TTGTACTTTAGTGGCATTTCTATACAAAG
1 GCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATATAAAC
* * * *
97570 GCCGCTAAAAACTCATACTTTAGTGGCGTTTTTAGACAAAC
1 GCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATATAAAC
** * * * *
97611 GCCGCTTTAGACTCGTACATTAATGGTGTTTTT-TAATAAAT
1 GCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT-ATAAAC
** *** * ** *
97652 GTTG-TAATTTCTAAGTACAATAGTGGTGTTTTTATATAAAC
1 GCCGCTAAAGACT-CGTACTTTAGTGGCGTTTTTATATAAAC
* * * * *
97693 GTCGCTAAAGACTCGTACTTTAGTGACGCTTTTAGACAAAC
1 GCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATATAAAC
* *
97734 GCCGCCATAGACTCGTA
1 GCCGCTAAAGACTCGTA
97751 ATGGCTTTTT
Statistics
Matches: 165, Mismatches: 50, Indels: 12
0.73 0.22 0.05
Matches are distributed among these distances:
40 35 0.21
41 124 0.75
42 6 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (41 bp):
GCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATATAAAC
Found at i:100151 original size:21 final size:21
Alignment explanation
Indices: 100125--100183 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
100115 TGATTTATTA
100125 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
100146 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
100167 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
100184 ATTGGATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:104890 original size:15 final size:15
Alignment explanation
Indices: 104872--104903 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
104862 CTTTAACCCT
104872 CTTTTGTTTAAGTAC
1 CTTTTGTTTAAGTAC
104887 CTTTTGTTTAAGTAC
1 CTTTTGTTTAAGTAC
104902 CT
1 CT
104904 AACATGGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (15 bp):
CTTTTGTTTAAGTAC
Found at i:104994 original size:31 final size:31
Alignment explanation
Indices: 104948--105015 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
104938 AACGGCCTAT
* * *
104948 GGACCAAAATTGAACAAATCGATAACGTTAG
1 GGACTAAAATCGAACAAATCAATAACGTTAG
* *
104979 GGACTAAAATCGAACATATCAATAATGTTAG
1 GGACTAAAATCGAACAAATCAATAACGTTAG
105010 GGACTA
1 GGACTA
105016 TTTCCCCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (31 bp):
GGACTAAAATCGAACAAATCAATAACGTTAG
Found at i:106054 original size:60 final size:58
Alignment explanation
Indices: 105977--106146 Score: 232
Period size: 60 Copynumber: 2.8 Consensus size: 58
105967 GAACATATGA
*
105977 ATAGTTAGGTGATCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAACAATGTCCC
1 ATAGTTAGG-GACCATTTTGTAA-TTTTAATAGTTGAGGGACTCAACAAAACAATGTCCC
* * * *
106037 ATAGTTAGGAGACCATTTTGTAATTTTGAATAGTCGAGGGACACAACAAAATATTGTCCC
1 ATAGTTAGG-GACCATTTTGTAATTTT-AATAGTTGAGGGACTCAACAAAACAATGTCCC
*
106097 ATAGTTAAGGGAGCATTTTGTAATTTTTAATAGTTGAGGGACTCAACAAA
1 ATAGTT-AGGGACCATTTTGTAA-TTTTAATAGTTGAGGGACTCAACAAA
106147 GATATACTCT
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
59 4 0.04
60 87 0.89
61 7 0.07
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (58 bp):
ATAGTTAGGGACCATTTTGTAATTTTAATAGTTGAGGGACTCAACAAAACAATGTCCC
Found at i:107747 original size:36 final size:36
Alignment explanation
Indices: 107700--107771 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
107690 ATACCTGAAA
*
107700 GTGTGTTGCAGAGAACCCCTGGGGATAATGGAAGGC
1 GTGTGTTGCAGAGAACCCCTGCGGATAATGGAAGGC
107736 GTGTGTTGCAGAGAACCCCTGCGGATAATGGAAGGC
1 GTGTGTTGCAGAGAACCCCTGCGGATAATGGAAGGC
107772 ACTTTCCTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.19
Consensus pattern (36 bp):
GTGTGTTGCAGAGAACCCCTGCGGATAATGGAAGGC
Found at i:108959 original size:30 final size:31
Alignment explanation
Indices: 108919--108981 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 31
108909 TAATTATTTC
*
108919 TTAATTATTAACATATGTAAAC-AGTTTTTT
1 TTAACTATTAACATATGTAAACAAGTTTTTT
108949 TTAACTATTAACATATGTAAACATAGTTTTTT
1 TTAACTATTAACATATGTAAACA-AGTTTTTT
108981 T
1 T
108982 CAGAAAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 21 0.70
32 9 0.30
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (31 bp):
TTAACTATTAACATATGTAAACAAGTTTTTT
Found at i:116187 original size:47 final size:48
Alignment explanation
Indices: 116125--116246 Score: 201
Period size: 47 Copynumber: 2.6 Consensus size: 48
116115 TTATAGCACA
116125 AGTCTGACATCTGTGTGACGGTGGTGCTATTATATGATATTGAG-CCG
1 AGTCTGACATCTGTGTGACGGTGGTGCTATTATATGATATTGAGCCCG
* *
116172 AGTTTGACGTCTGTGTGACGGTGGTGCTATTATATGATATTGAGCCCG
1 AGTCTGACATCTGTGTGACGGTGGTGCTATTATATGATATTGAGCCCG
* *
116220 AGTCTGACTTCTATGTGACGGTGGTGC
1 AGTCTGACATCTGTGTGACGGTGGTGC
116247 GTTGGTATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 42 0.61
48 27 0.39
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (48 bp):
AGTCTGACATCTGTGTGACGGTGGTGCTATTATATGATATTGAGCCCG
Found at i:118446 original size:30 final size:31
Alignment explanation
Indices: 118387--118446 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
118377 AAATTACACA
118387 TTTAGTACCTAAACTATTACTTTTGTTCCAT
1 TTTAGTACCTAAACTATTACTTTTGTTCCAT
* *
118418 TTTAGTATCC-AAACT-TTATTTTTTTTCCA
1 TTTAGTA-CCTAAACTATTACTTTTGTTCCA
118447 AATCATACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 12 0.46
32 2 0.08
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTAGTACCTAAACTATTACTTTTGTTCCAT
Found at i:118626 original size:38 final size:35
Alignment explanation
Indices: 118575--118650 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 35
118565 AACTAAACGT
*
118575 CAAGTATAATTTTGGAAGAAACAA-ATAAGTTTGGGTAC
1 CAAGTATAATTTT-GAA-AAA-AATA-AAGTTTGAGTAC
**
118613 CAAGTATGGTTTTGAAAAAAATAAAGTTTGAGTAC
1 CAAGTATAATTTTGAAAAAAATAAAGTTTGAGTAC
118648 CAA
1 CAA
118651 ATGAAACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 16 0.47
36 4 0.12
37 3 0.09
38 11 0.32
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (35 bp):
CAAGTATAATTTTGAAAAAAATAAAGTTTGAGTAC
Found at i:121758 original size:11 final size:11
Alignment explanation
Indices: 121720--121789 Score: 61
Period size: 11 Copynumber: 5.9 Consensus size: 11
121710 TTTTACTTAA
121720 ATTATTATTATT
1 ATTATTATTA-T
121732 ATTATT-TTAAAT
1 ATTATTATT--AT
121744 ATTATTATTAT
1 ATTATTATTAT
121755 ATTATACATATTAT
1 ATTAT---TATTAT
*
121769 ATTATTATTAA
1 ATTATTATTAT
*
121780 ATAATTATTA
1 ATTATTATTA
121790 CAAGCCCAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
11 23 0.46
12 13 0.26
13 3 0.06
14 11 0.22
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:121789 original size:3 final size:3
Alignment explanation
Indices: 121720--121778 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
121710 TTTTACTTAA
* *
121720 ATT ATT ATT ATT ATT ATT -TT AAAT ATT ATT ATT A-T ATT A-T ACAT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT A-TT
121764 ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
121779 AATAATTATT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
2 8 0.17
3 36 0.77
4 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:123187 original size:3 final size:3
Alignment explanation
Indices: 123181--123245 Score: 73
Period size: 3 Copynumber: 21.3 Consensus size: 3
123171 TGTTTTGCAA
123181 TAT TAT T-T TAT TAT TAT TAT TAT T-T T-T TAAT TAT TACT TCCAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T T--AT TAT
123227 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
123246 TTCATCTTAG
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.11
3 43 0.77
4 4 0.07
5 2 0.04
6 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:123265 original size:2 final size:2
Alignment explanation
Indices: 123258--123333 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
123248 CATCTTAGTC
123258 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
123300 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
123334 TTGTTTAAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123610 original size:29 final size:28
Alignment explanation
Indices: 123557--123614 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
123547 ATATTTCTAA
*
123557 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTACTTATAAAT-TAT
123586 ATAAATAAATAGATTTT-CTTA-AAATTAT
1 ATAAATAAAT--ATTTTACTTATAAATTAT
123614 A
1 A
123615 AATTTGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 4 0.15
29 14 0.54
30 3 0.12
31 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
ATAAATAAATATTTTACTTATAAATTAT
Found at i:129415 original size:7 final size:7
Alignment explanation
Indices: 129403--129483 Score: 81
Period size: 7 Copynumber: 10.3 Consensus size: 7
129393 TCCAATAAAG
129403 AAAGAAA
1 AAAGAAA
129410 AAAGAAAA
1 AAAG-AAA
129418 AAAGAAA
1 AAAGAAA
129425 AAAGAAA
1 AAAGAAA
129432 AAAGATGAA
1 AAAGA--AA
129441 AAAGGAAA
1 AAA-GAAA
129449 AATGAGAAAAA
1 AA--AG--AAA
129460 AAAGAAA
1 AAAGAAA
129467 AAAGAGAA
1 AAAGA-AA
129475 AAAGAAA
1 AAAGAAA
129482 AA
1 AA
129484 GGGGAGAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 18
0.78 0.00 0.22
Matches are distributed among these distances:
7 31 0.48
8 18 0.28
9 8 0.12
10 3 0.05
11 5 0.08
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:129423 original size:15 final size:15
Alignment explanation
Indices: 129403--129483 Score: 90
Period size: 17 Copynumber: 5.1 Consensus size: 15
129393 TCCAATAAAG
129403 AAAGAAAAAAGAAAA
1 AAAGAAAAAAGAAAA
129418 AAAGAAAAAAGAAAA
1 AAAGAAAAAAGAAAA
*
129433 AAGATGAAAAAGGAAAA
1 AA-A-GAAAAAAGAAAA
* *
129450 ATGAGAAAAAAAAGAAA
1 A-AAGAAAAAAGA-AAA
129467 AAAGAGAAAAAGAAAA
1 AAAGA-AAAAAGAAAA
129483 A
1 A
129484 GGGGAGAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
15 17 0.31
16 15 0.27
17 23 0.42
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAAGAAAA
Found at i:129426 original size:9 final size:9
Alignment explanation
Indices: 129403--129477 Score: 53
Period size: 9 Copynumber: 8.0 Consensus size: 9
129393 TCCAATAAAG
129403 AAAGAAAAA
1 AAAGAAAAA
129412 AGAA-AAAAA
1 A-AAGAAAAA
*
129421 GAAAAAAGAAA
1 -AAAGAA-AAA
*
129432 AAAGATGAAA
1 AAAGA-AAAA
*
129442 AAGGAAAAA
1 AAAGAAAAA
**
129451 TGAGAAAAA
1 AAAGAAAAA
129460 AAAGAAAAA
1 AAAGAAAAA
*
129469 AGAGAAAAA
1 AAAGAAAAA
129478 GAAAAAGGGG
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
9 32 0.63
10 16 0.31
11 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:134277 original size:22 final size:22
Alignment explanation
Indices: 134248--134302 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
134238 ATCTATACTC
134248 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
134270 TTTAAAGATGATAGATTTTCTT
1 TTCAAAGATGATAGATTCTCTT
134292 TTCAAAGATGA
1 TTCAAAGATGA
134303 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:135771 original size:76 final size:76
Alignment explanation
Indices: 134980--135770 Score: 1321
Period size: 76 Copynumber: 10.4 Consensus size: 76
134970 CTATTTCTCA
*
134980 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135045 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
135056 CATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCTTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135121 AGCCTTAGGGT
66 AGCCTTAGGGT
** *
135132 CATCTACAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135197 AGCCTTAGGGT
66 AGCCTTAGGGT
135208 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135273 AGCCTTAGGGT
66 AGCCTTAGGGT
*
135284 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
135349 AGCCATAGGGT
66 AGCCTTAGGGT
**
135360 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGGAGCTTTTTGAAATTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC-GGGAGCTTTTTGATGTTTTCA
*
135425 AAACCTTAGGGT
65 AAGCCTTAGGGT
* * *
135437 CATCTTTAAGTCCTACAATGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
135502 AACCTTTGGGT
66 AGCCTTAGGGT
* *
135513 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135578 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
135589 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
135654 AACCTTAGGGT
66 AGCCTTAGGGT
*
135665 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
135730 AACCTTCGGGT
66 AGCCTTAGGGT
* * * *
135741 AATCCGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
135771 TTAAGACCTC
Statistics
Matches: 670, Mismatches: 44, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
76 602 0.90
77 68 0.10
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:135942 original size:15 final size:14
Alignment explanation
Indices: 135920--135993 Score: 94
Period size: 15 Copynumber: 5.0 Consensus size: 14
135910 TTCATTTTAC
135920 TTAAATTATTATTA
1 TTAAATTATTATTA
135934 TTAAAATTATTATTA
1 TT-AAATTATTATTA
135949 TTATAATTATTATTA
1 TTA-AATTATTATTA
*
135964 TTATATATATATATTA
1 TTAAAT-TAT-TATTA
*
135980 TTAAATAATTATTA
1 TTAAATTATTATTA
135994 CAAGCCCAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
14 10 0.19
15 33 0.62
16 10 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAATTATTATTA
Found at i:135993 original size:3 final size:3
Alignment explanation
Indices: 135924--135982 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
135914 TTTTACTTAA
** *
135924 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATA ATT ATT ATT ATT A-T ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
135972 ATAT ATT ATT A
1 AT-T ATT ATT A
135983 AATAATTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 39 0.81
4 7 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:137377 original size:3 final size:3
Alignment explanation
Indices: 137364--137428 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
137354 TTATTTGCAA
* *
137364 TAT TAT T-T TAT TAT TAT TTT TAT T-T T-T TAAT TAT TACT T-T CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT
137407 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
137429 TCTTTCATCT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 7 0.13
3 42 0.79
4 4 0.08
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:137451 original size:2 final size:2
Alignment explanation
Indices: 137444--137483 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
137434 CATCTTAGTC
137444 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
137484 TTGTTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:139514 original size:15 final size:15
Alignment explanation
Indices: 139496--139546 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
139486 CGCAAGGCTA
*
139496 TCCTCAGGGTTATCC
1 TCCTCAGGGATATCC
*
139511 TCCTCAGGGATACCC
1 TCCTCAGGGATATCC
*
139526 GCCTCAGGGATATCC
1 TCCTCAGGGATATCC
139541 TCCTCA
1 TCCTCA
139547 ATATGCTCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.18, C:0.37, G:0.20, T:0.25
Consensus pattern (15 bp):
TCCTCAGGGATATCC
Found at i:139621 original size:2 final size:2
Alignment explanation
Indices: 139608--139645 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
139598 CTGGTCAGTA
* *
139608 CT CT CC CT CT CT CT CT CG CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
139646 ATATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.03, T:0.45
Consensus pattern (2 bp):
CT
Found at i:140116 original size:26 final size:26
Alignment explanation
Indices: 140080--140129 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
140070 TGGATCAGTA
*
140080 ATCATCTAAAATTTTATAAGTTTGTT
1 ATCATCTAAAATTTTATAAATTTGTT
140106 ATCATCTAAAATTTTATAAATTTG
1 ATCATCTAAAATTTTATAAATTTG
140130 CCTTAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (26 bp):
ATCATCTAAAATTTTATAAATTTGTT
Found at i:142302 original size:25 final size:24
Alignment explanation
Indices: 142248--142328 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 24
142238 ATAAATTGCA
* * *
142248 CCGAAGTGCCGTGTAGAGTTTTTGC
1 CCGAAGTGCCGCGTAGAATTTGT-C
142273 ACCGAAGTGCCGCGTAGAAATTTGTC
1 -CCGAAGTGCCGCGTAG-AATTTGTC
142299 CCGAAG-GACCGCGTAGAATTTGTC
1 CCGAAGTG-CCGCGTAGAATTTGTC
142323 CCGAAG
1 CCGAAG
142329 GACACATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
24 15 0.30
25 14 0.28
26 16 0.32
27 5 0.10
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (24 bp):
CCGAAGTGCCGCGTAGAATTTGTC
Found at i:142323 original size:24 final size:25
Alignment explanation
Indices: 142274--142331 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 25
142264 AGTTTTTGCA
142274 CCGAAGTG-CCGCGTAGAAATTTGTC
1 CCGAAG-GACCGCGTAGAAATTTGTC
142299 CCGAAGGACCGCGTAG-AATTTGTC
1 CCGAAGGACCGCGTAGAAATTTGTC
142323 CCGAAGGAC
1 CCGAAGGAC
142332 ACATATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (25 bp):
CCGAAGGACCGCGTAGAAATTTGTC
Found at i:142342 original size:24 final size:24
Alignment explanation
Indices: 142290--142342 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
142280 TGCCGCGTAG
* *
142290 AAATTTGTCCCGAAGGACCGCGTA
1 AAATTTGTCCCGAAGGACCACATA
*
142314 GAATTTGTCCCGAAGGA-CACATA
1 AAATTTGTCCCGAAGGACCACATA
142337 TAAATT
1 -AAATT
142343 CCTTAAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
AAATTTGTCCCGAAGGACCACATA
Found at i:142571 original size:30 final size:31
Alignment explanation
Indices: 142522--142592 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
142512 ACATAATTTA
* *
142522 TATCGCATAGACATATCA-TTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
*
142552 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
142583 TATCACATAA
1 TATCACATAA
142593 TTCATATAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (31 bp):
TATCACATAAACATATCATTTTCCATACCTT
Found at i:143026 original size:21 final size:21
Alignment explanation
Indices: 143002--143043 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
142992 TTCATATTCG
* *
143002 TTTGAGGGGGTATCGATTCCC
1 TTTGAAGGGGTACCGATTCCC
*
143023 TTTGAATGGGTACCGATTCCC
1 TTTGAAGGGGTACCGATTCCC
143044 CTAGCCCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (21 bp):
TTTGAAGGGGTACCGATTCCC
Found at i:148753 original size:2 final size:2
Alignment explanation
Indices: 148746--148831 Score: 57
Period size: 2 Copynumber: 48.0 Consensus size: 2
148736 GAAAATATTT
* *
148746 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA TA -A AA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
148782 TA TA TA TA -A T- TA -A TA TA AA AA TA TA TA AA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
148820 TA TA TA TA TA TA
1 TA TA TA TA TA TA
148832 ATCGGGGCGG
Statistics
Matches: 68, Mismatches: 6, Indels: 20
0.72 0.06 0.21
Matches are distributed among these distances:
1 10 0.15
2 58 0.85
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:148779 original size:25 final size:25
Alignment explanation
Indices: 148751--148825 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 25
148741 TATTTTATAT
148751 ATAATTAATATAAAATATATATAAA
1 ATAATTAATATAAAATATATATAAA
*
148776 ATAA-TATATATATAAT-TAATATAAAA
1 ATAATTA-ATATAAAATAT-ATAT-AAA
* * *
148802 ATATATAAATATTATATATATATA
1 ATA-ATTAATATAAAATATATATA
148826 TATATAATCG
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
24 3 0.08
25 16 0.41
26 7 0.18
27 11 0.28
28 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAATTAATATAAAATATATATAAA
Found at i:148786 original size:36 final size:35
Alignment explanation
Indices: 148737--148825 Score: 133
Period size: 36 Copynumber: 2.5 Consensus size: 35
148727 CCCGAACCCG
* *
148737 AAAATATTTTATATATAATTAATATAAAATATATAT
1 AAAATAATATATATATAATTAATATAAAA-ATATAT
148773 AAAATAATATATATATAATTAATATAAAAATATAT
1 AAAATAATATATATATAATTAATATAAAAATATAT
*
148808 AAATATTATATATATATA
1 AAA-ATAATATATATATA
148826 TATATAATCG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
35 9 0.18
36 40 0.82
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
AAAATAATATATATATAATTAATATAAAAATATAT
Found at i:148804 original size:23 final size:21
Alignment explanation
Indices: 148765--148831 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
148755 TTAATATAAA
148765 ATATA-TATA-AAATAATATAT
1 ATATATTATATAAA-AATATAT
148785 ATATAATTAATATAAAAATATAT
1 ATAT-ATT-ATATAAAAATATAT
* * *
148808 AAATATTATATATATATATAT
1 ATATATTATATAAAAATATAT
148829 ATA
1 ATA
148832 ATCGGGGCGG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.10
21 15 0.38
22 4 0.10
23 13 0.33
24 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATATTATATAAAAATATAT
Found at i:148830 original size:25 final size:23
Alignment explanation
Indices: 148745--148832 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 23
148735 CGAAAATATT
*
148745 TTATATATAATTA-ATATAAA-A
1 TTATATATAAATATATATAAATA
*
148766 -TATATATAAAATAATATATATATAA
1 TTATATAT-AAAT-ATATATAAAT-A
*
148791 TTA-ATATAAAAATATATAAATA
1 TTATATATAAATATATATAAATA
*
148813 TTATATATATATATATATAA
1 TTATATATAAATATATATAA
148833 TCGGGGCGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
20 7 0.13
21 3 0.06
22 5 0.09
23 29 0.54
24 3 0.06
25 5 0.09
26 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TTATATATAAATATATATAAATA
Found at i:149603 original size:25 final size:24
Alignment explanation
Indices: 149575--149625 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
149565 AGTTTTTGCA
149575 CCGAAGTG-CCGCATAGAAATTTGTC
1 CCGAA-TGACCGCATAG-AATTTGTC
*
149600 CCGAATGACCGCGTAGAATTTGTC
1 CCGAATGACCGCATAGAATTTGTC
149624 CC
1 CC
149626 AAAGGACCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (24 bp):
CCGAATGACCGCATAGAATTTGTC
Found at i:149624 original size:24 final size:24
Alignment explanation
Indices: 149552--149625 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 24
149542 AATTGCACCA
* *
149552 AAGTGCCGCGTAGAGTTTTTGCACCG
1 AAGTGCCGCGTAGAATTTGT-C-CCG
*
149578 AAGTGCCGCATAGAAATTTGTCCCG
1 AAGTGCCGCGTAG-AATTTGTCCCG
149603 AA-TGACCGCGTAGAATTTGTCCC
1 AAGTG-CCGCGTAGAATTTGTCCC
149626 AAAGGACCAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 12 0.29
25 12 0.29
26 13 0.31
27 5 0.12
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (24 bp):
AAGTGCCGCGTAGAATTTGTCCCG
Found at i:149633 original size:24 final size:25
Alignment explanation
Indices: 149583--149644 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
149573 CACCGAAGTG
* *
149583 CCGCATAGAAATTTGTCCCGAATGA
1 CCGCATAGAAATTTGTCCCAAAGGA
*
149608 CCGCGTAG-AATTTGTCCCAAAGGA
1 CCGCATAGAAATTTGTCCCAAAGGA
* *
149632 CCACATATAAATT
1 CCGCATAGAAATT
149645 CCTTAAGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (25 bp):
CCGCATAGAAATTTGTCCCAAAGGA
Done.