Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 41
Found at i:6170183 original size:33 final size:33
Alignment explanation
Indices: 6170130--6170228 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
6170120 TTTGTTTCAA
6170130 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
6170162 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
6170195 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
6170228 T
1 T
6170229 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:6170257 original size:13 final size:13
Alignment explanation
Indices: 6170214--6170268 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
6170204 TTGGAAGTAT
6170214 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
6170227 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
6170241 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
6170254 TTAAGTATTTGAA
1 TTAAGTATTTCAA
6170267 TT
1 TT
6170269 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:6170516 original size:21 final size:22
Alignment explanation
Indices: 6170464--6170516 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
6170454 TGGAGCGTGG
6170464 GGGAATCGG-TACACTCTCATA
1 GGGAATCGGTTACACTCTCATA
*
6170485 GGGAATCGGTTTC-CTCTCATA
1 GGGAATCGGTTACACTCTCATA
6170506 GGGAATCGGTT
1 GGGAATCGGTT
6170517 CCCTAAGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (22 bp):
GGGAATCGGTTACACTCTCATA
Found at i:6171754 original size:10 final size:10
Alignment explanation
Indices: 6171719--6171759 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
6171709 AAAATAACAT
6171719 TTTATATAT-
1 TTTATATATA
6171728 TTTAATATATA
1 TTT-ATATATA
*
6171739 TATATATATA
1 TTTATATATA
6171749 TTTATAT-TA
1 TTTATATATA
6171758 TT
1 TT
6171760 AAAAATCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 7 0.25
10 19 0.68
11 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTATATATA
Found at i:6172302 original size:36 final size:35
Alignment explanation
Indices: 6172232--6172336 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 35
6172222 AAAAATGAAC
** *
6172232 ACTTGAATCGAAAGTGCGACACCTCCTTCCGTTGG
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTGG
*
6172267 ACTTGAATTGAAAGTGTCGATGCTTCCTTCCGTTGG
1 ACTTGAATCGAAAGTG-CGATGCTTCCTTCCGTTGG
* * *
6172303 ACTTGAATCAAAAGTGCCGATGTTTCCTTTCGTT
1 ACTTGAATCGAAAGTG-CGATGCTTCCTTCCGTT
6172337 CTTCTTATTC
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 15 0.25
36 45 0.75
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (35 bp):
ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTGG
Found at i:6174070 original size:21 final size:22
Alignment explanation
Indices: 6174046--6174086 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6174036 TTTTTATTTA
* *
6174046 TTTTTATATTTTTA-ACGAATG
1 TTTTAATATTTATATACGAATG
6174067 TTTTAATATTTATATACGAA
1 TTTTAATATTTATATACGAA
6174087 ATTTGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (22 bp):
TTTTAATATTTATATACGAATG
Found at i:6184806 original size:165 final size:165
Alignment explanation
Indices: 6184527--6184910 Score: 523
Period size: 165 Copynumber: 2.4 Consensus size: 165
6184517 TATTTAAATG
* * * ** * * *
6184527 ACGGGTCTGCTCCCTATTCTTTCA-AGGAGTATAAGACTCGAACAATCTTCGGCGAACGTGTCTG
1 ACGGGTCCGCTCTCTATTCCTTCAGA-GAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCG
* * *
6184591 CTCCATATTCATTCAGGGAGTATAAGACTCGAACAATATTCAATAAACGGGTCCGCTCCCTATTC
65 CTCCATATTCATTCAGAGAGTATAAGACTCGAACAATATTCAACAAACGGGTCCGCTCCCTATCC
*
6184656 GTTCAGGGAGTATATAACTCGAACAATCTTCATAAA
130 GTTCAGGGAGTATAAAACTCGAACAATCTTCATAAA
6184692 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAACGGGTCCG
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCCG
* * *
6184756 CTCTATATT-ACTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTAT
65 CTCCATATTCA-TTCAGAGAGTATAAG-ACTCGAACAATATTCAACAAACGGGTCCGCTCCCTAT
6184819 CCGTTCAGGGAGTATAAAACTCGAACAATCTTCATAAA
128 CCGTTCAGGGAGTATAAAACTCGAACAATCTTCATAAA
* *
6184857 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTACATGACT---A-AATCTTCAACAAACG
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACG
6184911 AGTTTGCTTC
Statistics
Matches: 197, Mismatches: 17, Indels: 14
0.86 0.07 0.06
Matches are distributed among these distances:
161 15 0.08
162 1 0.01
164 5 0.03
165 174 0.88
166 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (165 bp):
ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGC
TCCATATTCATTCAGAGAGTATAAGACTCGAACAATATTCAACAAACGGGTCCGCTCCCTATCCG
TTCAGGGAGTATAAAACTCGAACAATCTTCATAAA
Found at i:6184881 original size:55 final size:55
Alignment explanation
Indices: 6184527--6184887 Score: 431
Period size: 55 Copynumber: 6.6 Consensus size: 55
6184517 TATTTAAATG
* * * * ** *
6184527 ACGGGTCTGCTCCCTATTCTTTCAAGGAGTATAAGACTCGAACAATCTTCGGCGA
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAAACTCGAACAATCTTCAACAA
* * * * * * *
6184582 ACGTGTCTGCTCCATATTCATTCAGGGAGTATAAGACTCGAACAATATTCAATAA
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAAACTCGAACAATCTTCAACAA
* *
6184637 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATATAACTCGAACAATCTTCATA-AA
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAAACTCGAACAATCTTCA-ACAA
* * *
6184692 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAAACTCGAACAATCTTCAACAA
** * * *
6184747 ACGGGTCCGCTCTATATTACTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAAACTCGAACAATCTTCAACAA
*
6184802 ACGGGTCTGCTCCCTA-TCCGTTCAGGGAGTATAAAACTCGAACAATCTTCATA-AA
1 ACGGGTCCGCTCCCTATTCC-TTCAGGGAGTATAAAACTCGAACAATCTTCA-ACAA
* *
6184857 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTA
1 ACGGGTCCGCTCCCTATTCCTTCAGGGAGTA
6184888 CATGACTAAA
Statistics
Matches: 270, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
54 3 0.01
55 262 0.97
56 5 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (55 bp):
ACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAAAACTCGAACAATCTTCAACAA
Found at i:6185002 original size:37 final size:37
Alignment explanation
Indices: 6184917--6185023 Score: 117
Period size: 37 Copynumber: 2.9 Consensus size: 37
6184907 AACGAGTTTG
* * * * *
6184917 CTTCACTATTCTTCCATGAAGGCTTATAG-ATGACTTA
1 CTTCACAACTCTTCCGTGAAGGCTTA-AGTTTGAATTA
* *
6184954 CTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAATTG
1 CTTCACAACTCTTCCGTGAAGGCTTAAGTTTGAATTA
* *
6184991 CTTTACAACTCTTTCGTGAAGGCTTAAGTTTGA
1 CTTCACAACTCTTCCGTGAAGGCTTAAGTTTGA
6185024 CTTGTTTCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 2 0.03
37 59 0.97
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (37 bp):
CTTCACAACTCTTCCGTGAAGGCTTAAGTTTGAATTA
Found at i:6186287 original size:45 final size:44
Alignment explanation
Indices: 6186212--6186296 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 44
6186202 TAAACAAAAC
* * *
6186212 TCAAGTCGTCCTTTGCGGGTTTTCAACTTGAGACCTCCTTTGGTT
1 TCAAGACGTCCTTTGCGGATTTTCAACTTGA-ACCCCCTTTGGTT
* * *
6186257 TCAAGACGTTCTTTTCGGATTTTCATCTTGAACCCCCTTT
1 TCAAGACGTCCTTTGCGGATTTTCAACTTGAACCCCCTTT
6186297 TTATTTTTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 8 0.24
45 26 0.76
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (44 bp):
TCAAGACGTCCTTTGCGGATTTTCAACTTGAACCCCCTTTGGTT
Found at i:6186316 original size:19 final size:20
Alignment explanation
Indices: 6186294--6186345 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
6186284 TTGAACCCCC
*
6186294 TTTTTATTTTTCTC-T-ATT
1 TTTTTTTTTTTCTCATCATT
6186312 TTTTTTCTTTTT-TCATCATT
1 TTTTTT-TTTTTCTCATCATT
6186332 TTTTTCTTTTTTCT
1 TTTTT-TTTTTTCT
6186346 TCCATTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.25
19 6 0.21
20 13 0.46
21 2 0.07
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTTTCTCATCATT
Found at i:6186355 original size:7 final size:7
Alignment explanation
Indices: 6186345--6186374 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
6186335 TTCTTTTTTC
6186345 TTCCATT
1 TTCCATT
6186352 TTCCATT
1 TTCCATT
6186359 TTCCATT
1 TTCCATT
*
6186366 TTCTATT
1 TTCCATT
6186373 TT
1 TT
6186375 TTTTCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (7 bp):
TTCCATT
Found at i:6186383 original size:7 final size:7
Alignment explanation
Indices: 6186373--6186434 Score: 81
Period size: 7 Copynumber: 8.9 Consensus size: 7
6186363 ATTTTCTATT
6186373 TTTTTTC
1 TTTTTTC
6186380 TTTTTTTC
1 -TTTTTTC
6186388 TTTTTTC
1 TTTTTTC
6186395 TTTTTTC
1 TTTTTTC
6186402 TTTTTTC
1 TTTTTTC
6186409 TTTTTT-
1 TTTTTTC
* *
6186415 TCTTTCC
1 TTTTTTC
*
6186422 TTTTCTC
1 TTTTTTC
6186429 TTTTTT
1 TTTTTT
6186435 TCATTTCTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
6 4 0.09
7 36 0.77
8 7 0.15
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:6186388 original size:19 final size:19
Alignment explanation
Indices: 6186294--6186435 Score: 76
Period size: 21 Copynumber: 7.2 Consensus size: 19
6186284 TTGAACCCCC
* *
6186294 TTTTTATTTTTCTCTATTT
1 TTTTTCTTTTTTTCTATTT
6186313 TTTTTC-TTTTTTC-ATCATT
1 TTTTTCTTTTTTTCTAT--TT
*
6186332 TTTTTCTTTTTTCTTCCATTT
1 TTTTTC-TTTTT-TTCTATTT
**
6186353 TCCATTTTC-CATTTTCTATTT
1 T---TTTTCTTTTTTTCTATTT
*
6186374 TTTTTCTTTTTTTCTTTTT
1 TTTTTCTTTTTTTCTATTT
* *
6186393 TCTTTTTTCTTTTTTCTTTTT
1 T-TTTTCT-TTTTTTCTATTT
* *
6186414 TTCTTTCCTTTTCTCT-TTT
1 TT-TTTCTTTTTTTCTATTT
6186433 TTT
1 TTT
6186436 CATTTCTTCT
Statistics
Matches: 98, Mismatches: 12, Indels: 27
0.72 0.09 0.20
Matches are distributed among these distances:
17 2 0.02
18 12 0.12
19 28 0.29
20 13 0.13
21 31 0.32
22 5 0.05
23 2 0.02
24 5 0.05
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTCTTTTTTTCTATTT
Found at i:6186391 original size:15 final size:15
Alignment explanation
Indices: 6186373--6186419 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
6186363 ATTTTCTATT
6186373 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
6186388 TTTTTTC-TTTTTTC
1 TTTTTTCTTTTTTTC
6186402 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
6186417 TTT
1 TTT
6186420 CCTTTTCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 14 0.45
15 17 0.55
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:6196156 original size:45 final size:48
Alignment explanation
Indices: 6196088--6196198 Score: 158
Period size: 45 Copynumber: 2.4 Consensus size: 48
6196078 CCATACTTTG
*
6196088 TTATTC-ACAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-
1 TTATTCGA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
*
6196135 TTATTCG-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCA
1 TTATTCGAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
6196181 TTTATTCGAAAAAATAAA
1 -TTATTCGAAAAAATAAA
6196199 AATAAACGAC
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
45 28 0.48
46 8 0.14
47 13 0.22
48 9 0.16
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (48 bp):
TTATTCGAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
Found at i:6201345 original size:3 final size:3
Alignment explanation
Indices: 6201337--6201401 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
6201327 CATTTAAAAT
6201337 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
6201384 GT- ATA TATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA
6201402 GTAAGAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6201427 original size:17 final size:20
Alignment explanation
Indices: 6201392--6201428 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
6201382 AAGTATATAT
6201392 AATAATAATAGTAAGAAAAA
1 AATAATAATAGTAAGAAAAA
6201412 AATAA-AATA-TAA-AAAAA
1 AATAATAATAGTAAGAAAAA
6201429 TGAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 4 0.24
20 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (20 bp):
AATAATAATAGTAAGAAAAA
Found at i:6201809 original size:37 final size:37
Alignment explanation
Indices: 6201759--6201870 Score: 161
Period size: 37 Copynumber: 3.0 Consensus size: 37
6201749 AATGCTTGTG
6201759 TATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTC
1 TATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTC
* * * *
6201796 TATCCTATTTTTAGTAGTTTAAATCTTAGTAAAATTC
1 TATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTC
* * *
6201833 TATCATATTTTTAGGAGTTTGAATCCTAATAAAACTC
1 TATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTC
6201870 T
1 T
6201871 TATTGAGAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (37 bp):
TATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTC
Found at i:6208452 original size:3 final size:3
Alignment explanation
Indices: 6208444--6208509 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
6208434 TAAAATTATT
*
6208444 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TATT TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA
**
6208488 TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
6208510 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 6 0.12
3 41 0.79
4 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:6208472 original size:22 final size:24
Alignment explanation
Indices: 6208444--6208497 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
6208434 TAAAATTATT
6208444 TAATAATAATATAATATAT-ATAA
1 TAATAATAATATAATATATAATAA
*
6208467 T-ATAAT-A-ATAATATTTAATAA
1 TAATAATAATATAATATATAATAA
6208488 TAATAATAAT
1 TAATAATAAT
6208498 TTTAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 8 0.31
21 6 0.23
22 10 0.38
23 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAATAATAATATAATATATAATAA
Found at i:6208793 original size:76 final size:76
Alignment explanation
Indices: 6208667--6209732 Score: 1908
Period size: 76 Copynumber: 14.1 Consensus size: 76
6208657 GGTCTTATGA
* *
6208667 ATGACCCCG-AGGGTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGA-CCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
6208731 CAGGACTTACAG
65 AAGGACTTACAG
*
6208743 ATGACCCTG-AGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
6208807 AAGGACTTACAG
65 AAGGACTTACAG
* * *
6208819 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGAAGGTTTTTTTGGAAACATCATGCACTG
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGG-CTTTTTGGAAACATCATGCACTG
6208884 AAGGACTTACAG
65 AAGGACTTACAG
*
6208896 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6208961 AGGACTTACAG
66 AGGACTTACAG
*
6208972 ATGACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6209036 AGGACTTACAG
66 AGGACTTACAG
6209047 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6209112 AGGACTTACAG
66 AGGACTTACAG
6209123 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6209188 AGGACTTACAG
66 AGGACTTACAG
6209199 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6209264 AGGACTTACAG
66 AGGACTTACAG
6209275 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6209340 AGGACTTACAG
66 AGGACTTACAG
6209351 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
6209416 AGGGCTTACAG
66 AGGACTTACAG
* *
6209427 ATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6209492 AGGACTTACAG
66 AGGACTTACAG
** * *
6209503 ATGACCTTAAGGTTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6209568 AGGACTTACAG
66 AGGACTTACAG
*
6209579 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6209644 AGGACTT--AG
66 AGGACTTACAG
*
6209653 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6209718 AGGACTTACAG
66 AGGACTTACAG
6209729 ATGA
1 ATGA
6209733 GGGAAATAGT
Statistics
Matches: 964, Mismatches: 20, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
74 74 0.08
75 78 0.08
76 738 0.77
77 74 0.08
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:6210436 original size:22 final size:22
Alignment explanation
Indices: 6210411--6210465 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
6210401 CATAAAGCTT
6210411 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
6210433 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
6210455 TCATCTTTGAA
1 TCATCTTTGAA
6210466 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:6211903 original size:75 final size:73
Alignment explanation
Indices: 6211810--6211981 Score: 211
Period size: 74 Copynumber: 2.3 Consensus size: 73
6211800 ATTGTGGGCC
* *
6211810 TTCAGCATGCCCCAACA-TTGACTAATACAAGTGTTCAAAATGCATCAACAGTTCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTG-CTAATA-AA-TATTCAAAATACATCAACAGTTCTGATTCTGAT
*
6211874 TGAAATGGGTT
63 TGAAAAGGGTT
* * ** * *
6211885 TTCAGCATGCCCCAACATTTTGCTGATAAATATTCAGAATATTTCAACATTTCTGATTCTGTTTG
1 TTCAGCATGCCCCAACA-TTTGCTAATAAATATTCAAAATACATCAACAGTTCTGATTCTGATTG
6211950 AAAAGGGTT
65 AAAAGGGTT
*
6211959 TTCAGCATGCCCCAATATTTGCT
1 TTCAGCATGCCCCAACATTTGCT
6211982 TCTTGTTAAT
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
73 6 0.07
74 52 0.61
75 19 0.22
76 5 0.06
77 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (73 bp):
TTCAGCATGCCCCAACATTTGCTAATAAATATTCAAAATACATCAACAGTTCTGATTCTGATTGA
AAAGGGTT
Found at i:6213510 original size:92 final size:92
Alignment explanation
Indices: 6213274--6213696 Score: 675
Period size: 92 Copynumber: 4.6 Consensus size: 92
6213264 TGATTTTAGA
* * * * *
6213274 GTTCATACCAAATCATATCAGATAATTCAAAGAATACTTCCAAAAGATGCTATGAGCACATTCAT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
* * *
6213339 CTTCCAAATTCAATGATTGATTCTGTG
66 CTTCCAAATTCAATAACTGGTTCTGTG
* *
6213366 GTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAATATGCTATGAGCACATTCA
1 G-TTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCA
* * *
6213431 TCTTCCAAATTCAATGATTAGTTCTGTG
65 TCTTCCAAATTCAATAACTGGTTCTGTG
*
6213459 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
6213524 CTTCCAAATTCAATAACTGGTTCTGTG
66 CTTCCAAATTCAATAACTGGTTCTGTG
* * * *
6213551 GTTCATACCAATCCAGATTAGATAACTCAAAGAACACTTCCAGAAGATTCTATGAGCACATTCCT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
6213616 CTTCCAAATTCAATAACTGGTTCTGTG
66 CTTCCAAATTCAATAACTGGTTCTGTG
6213643 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
6213697 GGTCTCCTTA
Statistics
Matches: 311, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
92 226 0.73
93 85 0.27
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (92 bp):
GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
CTTCCAAATTCAATAACTGGTTCTGTG
Found at i:6220620 original size:26 final size:23
Alignment explanation
Indices: 6220574--6220624 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 23
6220564 TTAATACTTG
*
6220574 AATAAATAAAAATATATTAATAA
1 AATAAATAAAAATATAGTAATAA
6220597 AATAATATAAAAATAATAAGTAATAA
1 AATAA-ATAAAAAT-AT-AGTAATAA
6220623 AA
1 AA
6220625 ATTTAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 8 0.33
25 2 0.08
26 9 0.38
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAAATAAAAATATAGTAATAA
Found at i:6222803 original size:3 final size:3
Alignment explanation
Indices: 6222797--6222852 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
6222787 AAAATTATTA
*
6222797 AAT AAT AAT -AT AAT -AT ATAT AAT -AT AAT AAT AAT ATTT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A-AT AAT AAT
6222841 AAT AAT AAT AAT
1 AAT AAT AAT AAT
6222853 TTAAGTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
2 6 0.13
3 35 0.76
4 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:6222823 original size:22 final size:24
Alignment explanation
Indices: 6222799--6222850 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
6222789 AATTATTAAA
6222799 TAATAATATAATATAT-ATAAT-A
1 TAATAATATAATATATAATAATAA
*
6222821 TAAT-A-ATAATATTTAATAATAA
1 TAATAATATAATATATAATAATAA
6222843 TAATAATA
1 TAATAATA
6222851 ATTTAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 8 0.32
21 6 0.24
22 9 0.36
23 1 0.04
24 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAATAATATAATATATAATAATAA
Found at i:6222825 original size:19 final size:19
Alignment explanation
Indices: 6222792--6222856 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
6222782 CCTGTAAAAT
*
6222792 TATTAAATAATAAT-ATAA
1 TATTTAATAATAATAATAA
6222810 TATATATAAT-ATAATAATAA
1 TAT-T-TAATAATAATAATAA
6222830 TATTTAATAATAATAATAA
1 TATTTAATAATAATAATAA
6222849 TAATTTAA
1 T-ATTTAA
6222857 GTAAAATGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 7 0.17
19 18 0.44
20 16 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTTAATAATAATAATAA
Found at i:6222830 original size:25 final size:22
Alignment explanation
Indices: 6222797--6222852 Score: 82
Period size: 20 Copynumber: 2.7 Consensus size: 22
6222787 AAAATTATTA
*
6222797 AATAATAAT-ATAATATAT-AT
1 AATAATAATAATAATATTTAAT
6222817 AAT-ATAATAATAATATTTAAT
1 AATAATAATAATAATATTTAAT
6222838 AATAATAATAATAAT
1 AATAATAATAATAAT
6222853 TTAAGTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 5 0.16
20 11 0.34
21 5 0.16
22 11 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAATAATAATAATATTTAAT
Found at i:6224369 original size:14 final size:16
Alignment explanation
Indices: 6224350--6224406 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
6224340 TAGATAAATA
*
6224350 AAATATCTATA-AT-T
1 AAATATATATATATAT
6224364 AAATATATATATATAT
1 AAATATATATATATAT
*
6224380 ATATATATATATATAT
1 AAATATATATATATAT
*
6224396 ATATATATATA
1 AAATATATATA
6224407 ATTAACATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.26
15 2 0.05
16 27 0.69
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATATATATATAT
Found at i:6224373 original size:2 final size:2
Alignment explanation
Indices: 6224366--6224406 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6224356 CTATAATTAA
6224366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6224407 ATTAACATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6225222 original size:21 final size:21
Alignment explanation
Indices: 6225180--6225222 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6225170 TTTCTAGGCT
* *
6225180 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
6225201 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
6225222 A
1 A
6225223 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:6226146 original size:4 final size:4
Alignment explanation
Indices: 6226137--6226161 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6226127 AAATGATGAC
6226137 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
6226162 ATGGTTATAT
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:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:6226447 original size:30 final size:30
Alignment explanation
Indices: 6226413--6226575 Score: 308
Period size: 30 Copynumber: 5.4 Consensus size: 30
6226403 GGTTCTTCGG
*
6226413 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
6226443 GACCTCTGGATAGTTAGCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
6226473 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
6226503 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
6226533 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
6226563 GACCTCTGGATAG
1 GACCTCTGGATAG
6226576 GTCATTCGGA
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 130 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:6229956 original size:21 final size:21
Alignment explanation
Indices: 6229914--6229956 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6229904 TTTCTAGGCT
* *
6229914 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
6229935 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
6229956 A
1 A
6229957 AACGAATATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:6231101 original size:31 final size:30
Alignment explanation
Indices: 6231063--6231158 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
6231053 GTCAAAGAAC
6231063 TACCTATGTCTTTCGAGACATATGGACAGT
1 TACCTATGTCTTTCGAGACATATGGACAGT
*** *
6231093 ATACCTATGTTCTAAGGA-ACATATGGATAGTT
1 -TACCTATG-TCTTTCGAGACATATGGACAG-T
* * *
6231125 TACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTCT-TTCGAGACATATGGACAGT
6231155 TACC
1 TACC
6231159 GAGGATCTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
29 1 0.02
30 7 0.14
31 36 0.72
32 6 0.12
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (30 bp):
TACCTATGTCTTTCGAGACATATGGACAGT
Found at i:6231175 original size:30 final size:30
Alignment explanation
Indices: 6231141--6231333 Score: 359
Period size: 30 Copynumber: 6.4 Consensus size: 30
6231131 GGTTCTTCGG
* *
6231141 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
6231171 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
6231201 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
6231231 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
6231261 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
6231291 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
6231321 GACCTCTGAATAG
1 GACCTCTGGATAG
6231334 GTCCTTCGGA
Statistics
Matches: 160, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 160 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:6233734 original size:31 final size:31
Alignment explanation
Indices: 6233670--6233730 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
6233660 TTATTATTTA
*
6233670 ATTATAAAATTATAATTAATTTATAATTTTT
1 ATTATAAAAATATAATTAATTTATAATTTTT
*
6233701 ATTA-AAAAATATAATTATTTTA-AGATTTTT
1 ATTATAAAAATATAATTAATTTATA-ATTTTT
6233731 TATTTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 1 0.04
30 22 0.81
31 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (31 bp):
ATTATAAAAATATAATTAATTTATAATTTTT
Found at i:6234176 original size:13 final size:13
Alignment explanation
Indices: 6234158--6234188 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
6234148 ATGAATTTGG
6234158 GGTTGTTTATAAA
1 GGTTGTTTATAAA
6234171 GGTTGTTTATAAA
1 GGTTGTTTATAAA
6234184 GGTTG
1 GGTTG
6234189 CTTAGAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (13 bp):
GGTTGTTTATAAA
Found at i:6235052 original size:23 final size:23
Alignment explanation
Indices: 6235026--6235069 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
6235016 TTTGAATTAG
6235026 TTTATATTTTAAATA-ATTTTAAA
1 TTTA-ATTTTAAATATATTTTAAA
* *
6235049 TTTACTTTTGAATATATTTTA
1 TTTAATTTTAAATATATTTTA
6235070 GATTCAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTAATTTTAAATATATTTTAAA
Found at i:6235491 original size:3 final size:3
Alignment explanation
Indices: 6235483--6235508 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6235473 CGTCATAAGA
6235483 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6235509 AAACATTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6238894 original size:17 final size:17
Alignment explanation
Indices: 6238874--6238921 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
6238864 TGAAAATTTG
*
6238874 AAAATT-TAGAAAAATAT
1 AAAATTATA-AAAAAGAT
6238891 AAAATTATAAAAAAGAT
1 AAAATTATAAAAAAGAT
* *
6238908 AAAAATACAAAAAA
1 AAAATTATAAAAAA
6238922 AAAATCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 25 0.93
18 2 0.07
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (17 bp):
AAAATTATAAAAAAGAT
Found at i:6239729 original size:30 final size:28
Alignment explanation
Indices: 6239662--6239737 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 28
6239652 GTTATTTTAA
6239662 ATATTTAAATATT-ATTATTATTATTATT
1 ATATTTAAA-ATTAATTATTATTATTATT
6239690 ATATTTAAAATGTTAATTATTA-TATT-TT
1 ATATTTAAAA--TTAATTATTATTATTATT
6239718 ATATTCATAAAATTAATTAT
1 ATATT--TAAAATTAATTAT
6239738 CTTTTTATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
27 1 0.02
28 24 0.56
29 6 0.14
30 12 0.28
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
ATATTTAAAATTAATTATTATTATTATT
Found at i:6241589 original size:15 final size:14
Alignment explanation
Indices: 6241560--6241586 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6241550 TTCATCGTGT
6241560 TGTTGATATTTTTA
1 TGTTGATATTTTTA
6241574 TGTTGATATTTTT
1 TGTTGATATTTTT
6241587 TATAATTCAC
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:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (14 bp):
TGTTGATATTTTTA
Found at i:6246935 original size:35 final size:34
Alignment explanation
Indices: 6246850--6246936 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
6246840 AAAATAATTT
*
6246850 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
6246884 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
6246922 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
6246937 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:6265088 original size:2 final size:2
Alignment explanation
Indices: 6265081--6265112 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
6265071 AAATCTTCTT
6265081 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
6265113 TTAAAACTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6274121 original size:2 final size:2
Alignment explanation
Indices: 6274114--6274213 Score: 200
Period size: 2 Copynumber: 50.0 Consensus size: 2
6274104 CTATTAATCA
6274114 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
6274156 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
6274198 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
6274214 GTACTGCTTC
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6279794 original size:31 final size:31
Alignment explanation
Indices: 6279756--6279877 Score: 176
Period size: 31 Copynumber: 3.9 Consensus size: 31
6279746 AGGGTCGAGG
6279756 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
* *
6279787 GTTTACCTAGGTTCTTCGGGACATATGAATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
**
6279818 GTTTACCTATGTTCTTCGGGACATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGATT
6279849 GTTTACCTA-GATTCTTCGGGATC-TATGGA
1 GTTTACCTATG-TTCTTCGGGA-CATATGGA
6279878 CTGGTCCTTC
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
30 1 0.01
31 81 0.98
32 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGATT
Found at i:6281040 original size:19 final size:19
Alignment explanation
Indices: 6281013--6281050 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6281003 GGTTAGTCGG
6281013 TACAAGGCAAATCCAGGCA
1 TACAAGGCAAATCCAGGCA
*
6281032 TACATGGCAAATCCAGGCA
1 TACAAGGCAAATCCAGGCA
6281051 AAGAGCATTG
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:0.39, C:0.26, G:0.21, T:0.13
Consensus pattern (19 bp):
TACAAGGCAAATCCAGGCA
Found at i:6281745 original size:17 final size:17
Alignment explanation
Indices: 6281723--6281760 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
6281713 TTTAAGCAAA
6281723 TGTTGGAAATATTTTGT
1 TGTTGGAAATATTTTGT
6281740 TGTTGGAAATATTTTGT
1 TGTTGGAAATATTTTGT
6281757 TGTT
1 TGTT
6281761 ATCATGGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (17 bp):
TGTTGGAAATATTTTGT
Found at i:6285484 original size:22 final size:24
Alignment explanation
Indices: 6285456--6285500 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6285446 AGAGAAGAAA
6285456 AGGAAGA-AAAAA-TAGATGAATG
1 AGGAAGAGAAAAAGTAGATGAATG
6285478 AGGAAGAGAAAAAGTAGATGAAT
1 AGGAAGAGAAAAAGTAGATGAAT
6285501 AACGTGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.33
23 5 0.24
24 9 0.43
ACGTcount: A:0.58, C:0.00, G:0.29, T:0.13
Consensus pattern (24 bp):
AGGAAGAGAAAAAGTAGATGAATG
Found at i:6301821 original size:2 final size:2
Alignment explanation
Indices: 6301814--6301841 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6301804 CGAATTTCCA
6301814 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
6301842 TGGTACACTA
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:6306596 original size:24 final size:24
Alignment explanation
Indices: 6306564--6306609 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
6306554 TCTTCCAGAT
6306564 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
6306588 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
6306610 CATATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:6308014 original size:3 final size:3
Alignment explanation
Indices: 6308008--6308032 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6307998 GGTTATAATA
6308008 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
6308033 ACATTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:6311904 original size:55 final size:55
Alignment explanation
Indices: 6311838--6311950 Score: 172
Period size: 55 Copynumber: 2.1 Consensus size: 55
6311828 GCGTTCAGAT
* *
6311838 GATTCATGAAGAAGAACATTCGACGAATGAAGAAATTTGAACCTGACTGAAGAAC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
* * * *
6311893 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGACC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
6311948 GAT
1 GAT
6311951 CCACAAAGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.21
Consensus pattern (55 bp):
GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
Found at i:6311960 original size:55 final size:55
Alignment explanation
Indices: 6311846--6311968 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 55
6311836 ATGATTCATG
* * * * **
6311846 AAGAAGAACATTCGACGAATGAAGAAATTTGAACCTGACTGAAGAACGATTCATG
1 AAGAAGGACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAACGATCCACA
* * *
6311901 AAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGACCGATCCACA
1 AAGAAGGACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAACGATCCACA
*
6311956 AAGAAAGACATCC
1 AAGAAGGACATCC
6311969 TAAAGATGTT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (55 bp):
AAGAAGGACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAACGATCCACA
Found at i:6312747 original size:72 final size:72
Alignment explanation
Indices: 6312630--6312779 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
6312620 CCCTATTACA
*
6312630 CAAGAAAATATGAAGACTTCAGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
1 CAAGAAAAGATGAAGACTTCAGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
6312695 AAATGAT
66 AAATGAT
*
6312702 CAAGAATAGATGAAGACTTC-GAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAG
1 CAAGAAAAGATGAAGACTTCAG-GTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAG
*
6312766 CAACTGAT
65 CAAATGAT
6312774 CAAGAA
1 CAAGAA
6312780 CCTGTTAGGG
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
71 1 0.01
72 73 0.99
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (72 bp):
CAAGAAAAGATGAAGACTTCAGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
AAATGAT
Found at i:6316221 original size:125 final size:125
Alignment explanation
Indices: 6316061--6316286 Score: 371
Period size: 125 Copynumber: 1.8 Consensus size: 125
6316051 ATACCCACAC
* ** * * *
6316061 TGGGGCATGACTGAACCCCCATCATTTTGAGATGACATGATTCGGACGAAGAAGGCATTGAGAAT
1 TGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACGAAGAAGGCATTGAGAAT
6316126 GAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGACTCATACCAGTAAAAGATTATAT
66 GAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGACTCATACCAGTAAAAGATTATAT
* *
6316186 TGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACTAAGAAGGCTTTGAGAAT
1 TGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACGAAGAAGGCATTGAGAAT
*
6316251 GAGCCTTACAATTTGAGGTGTTGGGGTATTTTGAAG
66 GAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAG
6316287 GCCCGTATCA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 92 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (125 bp):
TGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACGAAGAAGGCATTGAGAAT
GAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGACTCATACCAGTAAAAGATTATAT
Found at i:6317581 original size:36 final size:36
Alignment explanation
Indices: 6317503--6317634 Score: 201
Period size: 36 Copynumber: 3.6 Consensus size: 36
6317493 AAAGCCAAGT
* *
6317503 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAA-CCATCTTGAGC
*
6317540 ATTCACCAAAGAGTAGTGAAGCAAACCATCTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTGAGC
*
6317576 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTGAGC
* *
6317612 TTTCACCGAAGAGTAGTGAAGCA
1 CTTCACCAAAGAGTAGTGAAGCA
6317635 TATCCTTTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 65 0.74
37 23 0.26
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (36 bp):
CTTCACCAAAGAGTAGTGAAGCAAACCATCTTGAGC
Found at i:6317650 original size:73 final size:73
Alignment explanation
Indices: 6317503--6317652 Score: 203
Period size: 73 Copynumber: 2.1 Consensus size: 73
6317493 AAAGCCAAGT
* *
6317503 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTGAGCATTCACCAAAGAGTAGTGAAGCAAACCA
1 CTTCACCAAAGAGTAATGAAGCAAATCCATCTTAAGCATTCACCAAAGAGTAGTGAAGCAAACCA
*
6317568 TCTTGAGC
66 TCTTAAGC
* * * *
6317576 CTTCACCAAAGAGTAGTGAAGCAAA-CCATCTTAAGCTTTCACCGAAGAGTAGTGAAGCATATCC
1 CTTCACCAAAGAGTAATGAAGCAAATCCATCTTAAGCATTCACCAAAGAGTAGTGAAGCA-AACC
* *
6317640 TTTTTAAGC
65 ATCTTAAGC
6317649 CTTC
1 CTTC
6317653 TCGGAAGAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
72 30 0.45
73 37 0.55
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (73 bp):
CTTCACCAAAGAGTAATGAAGCAAATCCATCTTAAGCATTCACCAAAGAGTAGTGAAGCAAACCA
TCTTAAGC
Found at i:6317662 original size:37 final size:36
Alignment explanation
Indices: 6317503--6317652 Score: 192
Period size: 36 Copynumber: 4.1 Consensus size: 36
6317493 AAAGCCAAGT
* * *
6317503 CTTCACCAAAGAGTAATGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAA-CCATCTTAAGC
* *
6317540 ATTCACCAAAGAGTAGTGAAGCAAACCATCTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
6317576 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
* * * * *
6317612 TTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCA-AACCATCTTAAGC
6317649 CTTC
1 CTTC
6317653 TCGGAAGAGT
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
36 65 0.64
37 36 0.36
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (36 bp):
CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
Found at i:6318094 original size:54 final size:54
Alignment explanation
Indices: 6318035--6318326 Score: 470
Period size: 54 Copynumber: 5.5 Consensus size: 54
6318025 GAAAGTGGTA
6318035 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
*
6318089 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
*
6318143 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
* * *
6318197 AAGAAGAAGATGCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAATCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
*
6318251 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGA-TAA-A--GA--GAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
* *
6318299 AAGAAGAAGACGTTTGAGTTCCATACTC
1 AAGAAGAAGATGTTCGAGTTCCATACTC
6318327 TTTGAAGCAA
Statistics
Matches: 225, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
48 32 0.14
50 2 0.01
52 1 0.00
53 2 0.01
54 188 0.84
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.18
Consensus pattern (54 bp):
AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
Found at i:6318426 original size:52 final size:51
Alignment explanation
Indices: 6318321--6318501 Score: 220
Period size: 51 Copynumber: 3.5 Consensus size: 51
6318311 TTTGAGTTCC
* * * *
6318321 ATACTCTTTGAAGCAATAGGGAGC-GGCACGTTTATTGAAGATCGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTGAAGATCGAGTCCT
* * * * *
6318371 ATACTCTCTGAAGGAATATGGAGCATACACATTTTATTGAAAATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACAC-GTTTATTGAAGATCGAGTCCT
* * *
6318423 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATCAAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTGAAGATCGAGTCCT
* *
6318474 ATATTCTCTGAAGAAATAGGGAGCAGAC
1 ATACTCTCTGAAGGAATAGGGAGCAGAC
6318502 TTATCATTTG
Statistics
Matches: 109, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
50 21 0.19
51 44 0.40
52 44 0.40
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (51 bp):
ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTGAAGATCGAGTCCT
Found at i:6318483 original size:51 final size:51
Alignment explanation
Indices: 6318321--6318497 Score: 221
Period size: 52 Copynumber: 3.5 Consensus size: 51
6318311 TTTGAGTTCC
* * *
6318321 ATACTCTTTGAAGCAATAGGGAGCGG-CACGTTTATTGAAGATCGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGATCGAGTCCT
* ** * * *
6318371 ATACTCTCTGAAGGAATATGGAGCATACACATTTTATTGAAAATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACAC-GTTTATTGAAGATCGAGTCCT
* *
6318423 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATCAAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGATCGAGTCCT
* *
6318474 ATATTCTCTGAAGAAATAGGGAGC
1 ATACTCTCTGAAGGAATAGGGAGC
6318498 AGACTTATCA
Statistics
Matches: 106, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
50 21 0.20
51 41 0.39
52 44 0.42
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (51 bp):
ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGATCGAGTCCT
Found at i:6318497 original size:103 final size:102
Alignment explanation
Indices: 6318312--6318498 Score: 277
Period size: 103 Copynumber: 1.8 Consensus size: 102
6318302 AAGAAGACGT
* * *
6318312 TTGAGTTCCATACTCTTTGAAGCAATAGGGAGCGGCACGTTTATTGAAGATCGAGTCTTATACTC
1 TTGAGTTCCATACTCTCTGAAGCAATAGGGAGCGGCACGTTTATTGAAGATCAAGTCCTATACTC
* *
6318377 TCTGAAGGAATATGGAGCATACACATTTTATTGAAAA
66 TCTGAAGAAATAGGGAGCATACACATTTTATTGAAAA
* * *
6318414 TTGAG-TCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATCAAGTCCTATAT
1 TTGAGTTCC-ATACTCTCTGAAGCAATAGGGAGCGG-CACGTTTATTGAAGATCAAGTCCTATAC
6318478 TCTCTGAAGAAATAGGGAGCA
64 TCTCTGAAGAAATAGGGAGCA
6318499 GACTTATCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
101 3 0.04
102 29 0.39
103 43 0.57
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (102 bp):
TTGAGTTCCATACTCTCTGAAGCAATAGGGAGCGGCACGTTTATTGAAGATCAAGTCCTATACTC
TCTGAAGAAATAGGGAGCATACACATTTTATTGAAAA
Found at i:6320177 original size:27 final size:27
Alignment explanation
Indices: 6320137--6320188 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
6320127 TTATTTATGT
*
6320137 GTATTTTATATTTAGGTCACTAATTTA
1 GTATTTCATATTTAGGTCACTAATTTA
*
6320164 GTATTTCATGTTTAGGTCACTAATT
1 GTATTTCATATTTAGGTCACTAATT
6320189 CATTTCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (27 bp):
GTATTTCATATTTAGGTCACTAATTTA
Found at i:6320201 original size:24 final size:27
Alignment explanation
Indices: 6320146--6320201 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
6320136 TGTATTTTAT
*
6320146 ATTTAGGTCACTAATTTAGTATTTCATG
1 ATTTAGGTCACTAATTTA-CATTTCATG
6320174 -TTTAGGTCACTAA-TT-CATTTC-TG
1 ATTTAGGTCACTAATTTACATTTCATG
6320197 ATTTA
1 ATTTA
6320202 TAAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.08
24 9 0.35
26 2 0.08
27 13 0.50
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (27 bp):
ATTTAGGTCACTAATTTACATTTCATG
Found at i:6323618 original size:15 final size:14
Alignment explanation
Indices: 6323600--6323637 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
6323590 TCAAAAGGAG
6323600 AAAAATAAATAAATA
1 AAAAATAAATAAA-A
6323615 AAAAATAAATAAAA
1 AAAAATAAATAAAA
*
6323629 TAAAATAAA
1 AAAAATAAA
6323638 CCAAAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAATAAATAAAA
Found at i:6323622 original size:34 final size:34
Alignment explanation
Indices: 6323557--6323628 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
6323547 AATAAAAAGA
*
6323557 AAAAGGAAAAAATAATAATAATAAGAGAATAAAT
1 AAAAGGAAAAAATAATAATAATAAGAAAATAAAT
6323591 CAAAAGGAGAAAAAT-A-AATAAATAA-AAAATAAAT
1 -AAAAGGA-AAAAATAATAAT-AATAAGAAAATAAAT
6323625 AAAA
1 AAAA
6323629 TAAAATAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 4 0.12
34 11 0.32
35 13 0.38
36 6 0.18
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.15
Consensus pattern (34 bp):
AAAAGGAAAAAATAATAATAATAAGAAAATAAAT
Found at i:6324796 original size:3 final size:3
Alignment explanation
Indices: 6324785--6324820 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
6324775 AAAACAAATA
6324785 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6324821 CTATATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6324932 original size:25 final size:26
Alignment explanation
Indices: 6324891--6324960 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
6324881 TTTTAAATAC
*
6324891 TATATAA-TTTTCAAAAATTAGATAT
1 TATATAAGTTTTCAAAAACTAGATAT
*
6324916 TATATAAGTTTTCAAAAACTATATAT
1 TATATAAGTTTTCAAAAACTAGATAT
*
6324942 TATATAAGTTTTTAAAAAC
1 TATATAAGTTTTCAAAAAC
6324961 GTTTTCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 7 0.17
26 34 0.83
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (26 bp):
TATATAAGTTTTCAAAAACTAGATAT
Found at i:6325008 original size:72 final size:73
Alignment explanation
Indices: 6324923--6325132 Score: 222
Period size: 72 Copynumber: 2.8 Consensus size: 73
6324913 TATTATATAA
6324923 GTTTTCAAAAACTATATATTATATAAGTTTTTAAAAACGTTTTCAAAAACTATATATTATGTA-A
1 GTTTT-AAAAACTATATATTATATAAGTTTTTAAAAACGTTTTC-AAAACTATATATTATGTACA
6324987 G-TCAAAAAG-
64 GTTC-AAAAGT
*
6324996 GTTTTAAAAACTATATATTATATATA-TTTTCT-AAAATGTTTT-AAAACTATATATTA--TACA
1 GTTTTAAAAACTATATATTATATA-AGTTTT-TAAAAACGTTTTCAAAACTATATATTATGTACA
6325056 GTTTTCAAAAGT
64 G--TTCAAAAGT
* *
6325068 GTTTTAAAAACTATATATTATATATGTATTTTCAAAAACCGTTTGC-AAACTATATAATTTATGT
1 GTTTTAAAAACTATATATTATATAAGT-TTTT-AAAAA-CGTTTTCAAAACTATAT-A-TTATGT
6325132 A
61 A
6325133 TATATAGATA
Statistics
Matches: 116, Mismatches: 4, Indels: 28
0.78 0.03 0.19
Matches are distributed among these distances:
68 2 0.02
69 2 0.02
70 14 0.12
71 5 0.04
72 60 0.52
73 10 0.09
74 4 0.03
75 13 0.11
76 1 0.01
77 3 0.03
79 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (73 bp):
GTTTTAAAAACTATATATTATATAAGTTTTTAAAAACGTTTTCAAAACTATATATTATGTACAGT
TCAAAAGT
Found at i:6325042 original size:36 final size:36
Alignment explanation
Indices: 6324923--6325091 Score: 186
Period size: 36 Copynumber: 4.7 Consensus size: 36
6324913 TATTATATAA
*
6324923 GTTTTCAAAAACTATATATTATATAAGTTTT-TAAAAAC
1 GTTTT-AAAAACTATATATTATATAA-TTTTCT-AAAAT
* * * *
6324961 GTTTTCAAAAACTATATATTATGTAA--GTCAAAAAG
1 GTTTT-AAAAACTATATATTATATAATTTTCTAAAAT
6324996 GTTTTAAAAACTATATATTATATATATTTTCTAAAAT
1 GTTTTAAAAACTATATATTATATA-ATTTTCTAAAAT
* *
6325033 GTTTT-AAAACTATATATTATACAGTTTTC-AAAAGT
1 GTTTTAAAAACTATATATTATATAATTTTCTAAAA-T
6325068 GTTTTAAAAACTATATATTATATA
1 GTTTTAAAAACTATATATTATATA
6325092 TGTATTTTCA
Statistics
Matches: 114, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
34 22 0.19
35 22 0.19
36 34 0.30
37 11 0.10
38 25 0.22
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (36 bp):
GTTTTAAAAACTATATATTATATAATTTTCTAAAAT
Found at i:6332063 original size:16 final size:17
Alignment explanation
Indices: 6332026--6332072 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
6332016 GTTTATGAGA
6332026 GAATTGAAATCTGTGAAG
1 GAATTGAAATCTGT-AAG
6332044 GAATTGAAATCTGT-AG
1 GAATTGAAATCTGTAAG
*
6332060 GAATTGGAATCTG
1 GAATTGAAATCTG
6332073 AAACATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 14 0.50
18 14 0.50
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (17 bp):
GAATTGAAATCTGTAAG
Found at i:6332685 original size:39 final size:36
Alignment explanation
Indices: 6332600--6332704 Score: 135
Period size: 39 Copynumber: 2.9 Consensus size: 36
6332590 CACCCTAAAT
* *
6332600 CCGAACTCGACCTGAATATCACACTT--AAAAAAAC
1 CCGAACCCGACCCGAATATCACACTTAAAAAAAAAC
6332634 CCG-ACCCGACCCGAATATCACACTTAAAACAATAAGAC
1 CCGAACCCGACCCGAATATCACACTTAAAA-AA-AA-AC
*
6332672 CCGAACCCGACCCGAATATCACACTTTAAAAAA
1 CCGAACCCGACCCGAATATCACACTTAAAAAAA
6332705 CCTGATTCGA
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
33 20 0.32
34 3 0.05
35 2 0.03
36 2 0.03
37 3 0.05
38 7 0.11
39 25 0.40
ACGTcount: A:0.43, C:0.32, G:0.10, T:0.15
Consensus pattern (36 bp):
CCGAACCCGACCCGAATATCACACTTAAAAAAAAAC
Found at i:6332689 original size:72 final size:72
Alignment explanation
Indices: 6332600--6332757 Score: 192
Period size: 72 Copynumber: 2.1 Consensus size: 72
6332590 CACCCTAAAT
* * *
6332600 CCGAACTCGACCTGAATATCACACTTAAAAAAACC-CGACCCGACCCGAATATCACACTTAAAAC
1 CCGAACCCGACCCGAATATCACACTTAAAAAAACCTCGACCCGACCCGAATATCAAACTTAAAA-
*
6332664 AATAAGAC
65 AACAAGAC
* *
6332672 CCGAACCCGACCCGAATATCACACTTTAAAAAACCTGATTCGACCCGACCCGAATATTAAACTTA
1 CCGAACCCGACCCGAATATCACACTTAAAAAAACC----TCGACCCGACCCGAATATCAAACTTA
**
6332737 AAAAACCTGAC
62 AAAAACAAGAC
6332748 CCGAACCCGA
1 CCGAACCCGA
6332758 TTTTTTTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
72 32 0.44
76 15 0.21
77 26 0.36
ACGTcount: A:0.41, C:0.33, G:0.11, T:0.16
Consensus pattern (72 bp):
CCGAACCCGACCCGAATATCACACTTAAAAAAACCTCGACCCGACCCGAATATCAAACTTAAAAA
ACAAGAC
Found at i:6332717 original size:44 final size:38
Alignment explanation
Indices: 6332607--6332739 Score: 134
Period size: 39 Copynumber: 3.6 Consensus size: 38
6332597 AATCCGAACT
*
6332607 CGACCTGAATATCACACTT--AA-AA-AA-ACCCGACC
1 CGACCCGAATATCACACTTAAAACAATAAGACCCGACC
6332640 CGACCCGAATATCACACTTAAAACAATAAGACCCGAACC
1 CGACCCGAATATCACACTTAAAACAATAAGACCCG-ACC
*** **
6332679 CGACCCGAATATCACACTTTAAAA-AACCTGATTCGACC
1 CGACCCGAATATCACAC-TTAAAACAATAAGACCCGACC
* *
6332717 CGACCCGAATATTAAACTTAAAA
1 CGACCCGAATATCACACTTAAAA
6332740 AACCTGACCC
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
33 18 0.21
35 2 0.02
36 2 0.02
37 8 0.09
38 23 0.27
39 26 0.31
40 6 0.07
ACGTcount: A:0.42, C:0.31, G:0.10, T:0.17
Consensus pattern (38 bp):
CGACCCGAATATCACACTTAAAACAATAAGACCCGACC
Found at i:6332756 original size:38 final size:38
Alignment explanation
Indices: 6332600--6332757 Score: 175
Period size: 38 Copynumber: 4.3 Consensus size: 38
6332590 CACCCTAAAT
* *
6332600 CCGAACTCGACCTGAATATCACACTTAAAAAA----AC
1 CCGAACCCGACCCGAATATCACACTTAAAAAACCTGAC
***
6332634 CCG-ACCCGACCCGAATATCACACTTAAAACAATAAGAC
1 CCGAACCCGACCCGAATATCACACTTAAAA-AACCTGAC
*
6332672 CCGAACCCGACCCGAATATCACACTTTAAAAAACCTGAT
1 CCGAACCCGACCCGAATATCACAC-TTAAAAAACCTGAC
* * *
6332711 TCG-ACCCGACCCGAATATTAAACTTAAAAAACCTGAC
1 CCGAACCCGACCCGAATATCACACTTAAAAAACCTGAC
6332748 CCGAACCCGA
1 CCGAACCCGA
6332758 TTTTTTTTTT
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
33 24 0.23
34 5 0.05
37 15 0.14
38 29 0.28
39 26 0.25
40 6 0.06
ACGTcount: A:0.41, C:0.33, G:0.11, T:0.16
Consensus pattern (38 bp):
CCGAACCCGACCCGAATATCACACTTAAAAAACCTGAC
Found at i:6336157 original size:3 final size:3
Alignment explanation
Indices: 6336151--6336256 Score: 196
Period size: 3 Copynumber: 35.7 Consensus size: 3
6336141 TTTTTATCCA
*
6336151 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6336199 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6336246 TAT TAT TAT TA
1 TAT TAT TAT TA
6336257 AATATATATT
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 98 0.98
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:6336765 original size:26 final size:25
Alignment explanation
Indices: 6336736--6336785 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
6336726 GAAACCAGAG
*
6336736 ACAGA-AACAGAAAACGGAAAAAAAAT
1 ACAGAGAA-AGAAAA-GAAAAAAAAAT
6336762 ACAGAGAAAGAAAAGAAAAAAAAA
1 ACAGAGAAAGAAAAGAAAAAAAAA
6336786 ACAACAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 11 0.50
27 2 0.09
ACGTcount: A:0.74, C:0.08, G:0.16, T:0.02
Consensus pattern (25 bp):
ACAGAGAAAGAAAAGAAAAAAAAAT
Found at i:6338106 original size:561 final size:563
Alignment explanation
Indices: 6337042--6338152 Score: 2181
Period size: 561 Copynumber: 2.0 Consensus size: 563
6337032 CCACCGAAGA
6337042 CGGTGGCCGGCGGCAGAACTCGCAGCGGCAGACGGCTGCCGGATTCCCTCCGGGGAGGGAATCTA
1 CGGTGGCCGGCGGCAGAACTCGCAGCGGCAGACGGCTGCCGGATTCCCTCCGGGGAGGGAATCTA
6337107 GAGAGAGGCCAGAGAGAATTCTCTCTCTCTCTCTCTCTGCTTTGAAAAAAAAAAGAAATGAAATG
66 GAGAGAGGCCAGAGAGAATTCTCTCTCTCTCTCTCTCTGCTTTGAAAAAAAAAAGAAATGAAATG
6337172 GTTGGCCCTTCGGGCCAGCCGGTTTGGACTCTTATAGTCCTTCCCGAACGACGTCGTTTCGGGAA
131 GTTGGCCCTTCGGGCCAGCCGGTTTGGACTCTTATAGTCCTTCCCGAACGACGTCGTTTCGGGAA
*
6337237 GGACTATGCGCGTAATTATGAAATAGTTAAACCCCGTCCATAGTCCTTCGTATTTGTAAATTTTA
196 GGACTATGCGCGTAATTATGAAATAGTTAAACCCCGTCCACAGTCCTTCGTATTTGTAAATTTTA
*
6337302 TATTTTGGTCACTAAACTGAATTTATAATAATTTTAATTCAGTCTTTAAATTTTAATTTTATTCA
261 CATTTTGGTCACTAAACTGAATTTATAATAATTTTAATTCAGTCTTTAAATTTTAATTTTATTCA
6337367 TTTTAGTCCTTTTTATTAAAATAATATATTTAGGATAAATGACAAATTTAATCCCTTAATTTTAA
326 TTTTAGTCCTTTTTATTAAAATAATATATTTAGGATAAATGACAAATTTAATCCCTTAATTTTAA
6337432 TAAATAATTTTTTAATCCCTAGTTCATATTTTTAATTTATTTTATTATAAAATTCGAATTTTAAA
391 TAAATAATTTTTTAATCCCTAGTTCATATTTTTAATTTATTTTATTATAAAATTCGAATTTTAAA
6337497 TAATTTTATTTTGGTCACTAAATTATTAAATTAGAAAATAAAATATTTAATCCCTATAATTTCAA
456 TAATTTTATTTTGGTCACTAAATTATTAAATTAGAAAATAAAATATTTAATCCCTATAATTTCAA
6337562 TTAATTAGGAATTAGATTTAGTTTTATTTTTATTGGCCGGCGG
521 TTAATTAGGAATTAGATTTAGTTTTATTTTTATTGGCCGGCGG
6337605 CGGTGGCCGGCGGCAGAACTCGCAGCGGCAGACGGCTGCCGGATTCCCTCCGGGGAGGGAATCTA
1 CGGTGGCCGGCGGCAGAACTCGCAGCGGCAGACGGCTGCCGGATTCCCTCCGGGGAGGGAATCTA
6337670 GAGAGAGGCCAGAGAGAA-T-TCTCTCTCTCTCTCTCTGCTTTGAAAAAAAAAAGAAATGAAATG
66 GAGAGAGGCCAGAGAGAATTCTCTCTCTCTCTCTCTCTGCTTTGAAAAAAAAAAGAAATGAAATG
6337733 GTTGGCCCTTCGGGCCAGCCGGTTTGGACTCTTATAGTCCTTCCCGAACGACGTCGTTTCGGGAA
131 GTTGGCCCTTCGGGCCAGCCGGTTTGGACTCTTATAGTCCTTCCCGAACGACGTCGTTTCGGGAA
6337798 GGACTATGCGCGTAATTATGAAATAGTTAAACCCCGTCCACAGTCCTTCGTATTTGTAAATTTTA
196 GGACTATGCGCGTAATTATGAAATAGTTAAACCCCGTCCACAGTCCTTCGTATTTGTAAATTTTA
6337863 CATTTTGGTCACTAAACTGAATTTATAATAATTTTAATTCAGTCTTTAAATTTTAATTTTATTCA
261 CATTTTGGTCACTAAACTGAATTTATAATAATTTTAATTCAGTCTTTAAATTTTAATTTTATTCA
*
6337928 TTTTAGTCCTTTTTATTAAAATAATATATTTAGGATAAATGACAGATTTAATCCCTTAATTTTAA
326 TTTTAGTCCTTTTTATTAAAATAATATATTTAGGATAAATGACAAATTTAATCCCTTAATTTTAA
6337993 TAAATAATTTTTTAATCCCTAGTTCATATTTTTAATTTATTTTATTATAAAATTCGAATTTTAAA
391 TAAATAATTTTTTAATCCCTAGTTCATATTTTTAATTTATTTTATTATAAAATTCGAATTTTAAA
6338058 TAATTTTATTTTGGTCACTAAATTATTAAATTAGAAAATAAAATATTTAATCCCTATAATTTCAA
456 TAATTTTATTTTGGTCACTAAATTATTAAATTAGAAAATAAAATATTTAATCCCTATAATTTCAA
6338123 TTAATTAGGAATTAGATTTAGTTTTATTTT
521 TTAATTAGGAATTAGATTTAGTTTTATTTT
6338153 ATTATAATTT
Statistics
Matches: 545, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
561 461 0.85
562 1 0.00
563 83 0.15
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (563 bp):
CGGTGGCCGGCGGCAGAACTCGCAGCGGCAGACGGCTGCCGGATTCCCTCCGGGGAGGGAATCTA
GAGAGAGGCCAGAGAGAATTCTCTCTCTCTCTCTCTCTGCTTTGAAAAAAAAAAGAAATGAAATG
GTTGGCCCTTCGGGCCAGCCGGTTTGGACTCTTATAGTCCTTCCCGAACGACGTCGTTTCGGGAA
GGACTATGCGCGTAATTATGAAATAGTTAAACCCCGTCCACAGTCCTTCGTATTTGTAAATTTTA
CATTTTGGTCACTAAACTGAATTTATAATAATTTTAATTCAGTCTTTAAATTTTAATTTTATTCA
TTTTAGTCCTTTTTATTAAAATAATATATTTAGGATAAATGACAAATTTAATCCCTTAATTTTAA
TAAATAATTTTTTAATCCCTAGTTCATATTTTTAATTTATTTTATTATAAAATTCGAATTTTAAA
TAATTTTATTTTGGTCACTAAATTATTAAATTAGAAAATAAAATATTTAATCCCTATAATTTCAA
TTAATTAGGAATTAGATTTAGTTTTATTTTTATTGGCCGGCGG
Found at i:6338260 original size:20 final size:21
Alignment explanation
Indices: 6338223--6338263 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6338213 GATATTTTTA
**
6338223 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
6338244 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
6338264 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:6340437 original size:8 final size:7
Alignment explanation
Indices: 6340413--6340454 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
6340403 TTTTCATACA
6340413 TGCA-TT
1 TGCATTT
6340419 TGCATTT
1 TGCATTT
6340426 TGCATCTT
1 TGCAT-TT
6340434 TGCATTT
1 TGCATTT
* *
6340441 TTCATTG
1 TGCATTT
6340448 TGCATTT
1 TGCATTT
6340455 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:6340437 original size:15 final size:14
Alignment explanation
Indices: 6340413--6340454 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
6340403 TTTTCATACA
6340413 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
6340426 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
6340441 TTCATTGTGCATTT
1 TGCATTTTGCATTT
6340455 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:6340539 original size:27 final size:26
Alignment explanation
Indices: 6340508--6340567 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
6340498 CATTCACATA
*
6340508 TTTACATTTGAATTTGCATTTGCATTT
1 TTTACATTTGAATTTACATTTGCA-TT
* * *
6340535 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
6340561 TTTACAT
1 TTTACAT
6340568 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:6342531 original size:11 final size:10
Alignment explanation
Indices: 6342513--6342542 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6342503 GCAAAGAAAG
6342513 AAGAAAAAAA
1 AAGAAAAAAA
*
6342523 AAGGAAAAAA
1 AAGAAAAAAA
6342533 AAGAAAAAAA
1 AAGAAAAAAA
6342543 GGAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:6342532 original size:9 final size:9
Alignment explanation
Indices: 6342518--6342548 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6342508 GAAAGAAGAA
6342518 AAAAAAAGG
1 AAAAAAAGG
*
6342527 AAAAAAAAG
1 AAAAAAAGG
6342536 AAAAAAAGG
1 AAAAAAAGG
6342545 AAAA
1 AAAA
6342549 TTAATTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:6342532 original size:10 final size:10
Alignment explanation
Indices: 6342517--6342548 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
6342507 AGAAAGAAGA
6342517 AAAAAAAAGG
1 AAAAAAAAGG
6342527 AAAAAAAA-G
1 AAAAAAAAGG
6342536 -AAAAAAAGG
1 AAAAAAAAGG
6342545 AAAA
1 AAAA
6342549 TTAATTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.35
9 2 0.10
10 11 0.55
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:6344988 original size:114 final size:114
Alignment explanation
Indices: 6344780--6345005 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
6344770 AAGTGCCATG
*
6344780 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * *
6344845 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
*
6344894 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
6344959 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
6345006 CTGCATGATC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:6347605 original size:22 final size:22
Alignment explanation
Indices: 6347574--6347628 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
6347564 ATCTACACTC
*
6347574 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
6347596 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
6347618 TTCAAAGATGA
1 TTCAAAGATGA
6347629 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:6348226 original size:113 final size:112
Alignment explanation
Indices: 6348028--6348312 Score: 412
Period size: 113 Copynumber: 2.5 Consensus size: 112
6348018 TTAGCAAAGA
* * * *
6348028 TTCAAATCCATCATTCAATGGATCAACATTTCAAGAG-AGAGTTCATAATGAGAAGAACTCATCT
1 TTCAAATCCATCATT-GATGGATCATCATTGCCAGAGAAG-GTTCATAATGAGAAGAACTCATCT
* *
6348092 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTG
6348141 TTCAAATCCATCATATGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
1 TTCAAATCCATCAT-TGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
*
6348206 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTG
** * *
6348254 TTTGAATTCATCACTTGATGGATTATCATTGCCAGAAGAA-GTTCATAATGAGAAGAACT
1 TTCAAATCCATCA-TTGATGGATCATCATTGCCAG-AGAAGGTTCATAATGAGAAGAACT
6348313 TGTTCAACTT
Statistics
Matches: 157, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
113 149 0.95
114 8 0.05
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (112 bp):
TTCAAATCCATCATTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTG
Found at i:6348339 original size:73 final size:73
Alignment explanation
Indices: 6348214--6348385 Score: 240
Period size: 73 Copynumber: 2.4 Consensus size: 73
6348204 TGAAGAAGGA
* * ** * *
6348214 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACT-TGATGGATT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTCAAATCCATCA-TATGATGGATC
6348278 ATCATTGCC
65 ATCATTGCC
*
6348287 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCATATGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTCAAATCCATCATATGATGGATCA
6348352 TCATTGCC
66 TCATTGCC
*
6348360 AG-AGAAGGTTTATAATGAGAAGAACT
1 AGAAGAA-GTTCATAATGAGAAGAACT
6348386 CATCTGAAGA
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
72 5 0.06
73 84 0.94
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (73 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTCAAATCCATCATATGATGGATCA
TCATTGCC
Found at i:6348414 original size:113 final size:114
Alignment explanation
Indices: 6348287--6348762 Score: 712
Period size: 113 Copynumber: 4.2 Consensus size: 114
6348277 TATCATTGCC
* * * * *
6348287 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTC-AAATCCATCA-TATGATGGAT
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGATCTGAATTCATCACT-TGATGGAT
* * * *
6348350 CATCATTGCCAGAGAAGGTTTATAATGAGAAGAACTCATCTGAAGAAGGA
65 TATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
6348400 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG-TTTGAATTCATCACTTGATGGATT
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGATCTGAATTCATCACTTGATGGATT
*
6348464 ATTTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 ATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
6348513 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACC-TTTAATCTGAATTCATCACTGGATGGATT
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGATCTGAATTCATCACTTGATGGATT
* *
6348577 ATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 ATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
6348626 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-ACCTGAATTCATCAATTGATGGATT
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGATCTGAATTCATCACTTGATGGATT
*
6348690 ATCTTTTCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGAA
66 ATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
6348738 AGAAGAAAGTTCATAATGAGAAGAA
1 AGAAG-AAGTTCATAATGAGAAGAA
6348763 CTCATCAAGA
Statistics
Matches: 335, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
112 41 0.12
113 290 0.87
114 4 0.01
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (114 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGATCTGAATTCATCACTTGATGGATT
ATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:6348415 original size:186 final size:186
Alignment explanation
Indices: 6348101--6348498 Score: 744
Period size: 186 Copynumber: 2.1 Consensus size: 186
6348091 TGAAGAAGGA
6348101 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCATATGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCATATGATGGATCA
6348166 TCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
6348231 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCC
131 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCC
6348287 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCATATGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCATATGATGGATCA
*
6348352 TCATTGCCAGAGAAGGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 TCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
** *
6348417 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTATTTTTTCC
131 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCC
6348473 AG-AGAAGGTTCATAATGAGAAGAACT
1 AGAAGAA-GTTCATAATGAGAAGAACT
6348499 CATCTGAAGA
Statistics
Matches: 207, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
185 4 0.02
186 203 0.98
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.31
Consensus pattern (186 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCATATGATGGATCA
TCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCC
Found at i:6348566 original size:299 final size:299
Alignment explanation
Indices: 6348028--6348611 Score: 888
Period size: 299 Copynumber: 2.0 Consensus size: 299
6348018 TTAGCAAAGA
*
6348028 TTCAAATCCATCATTCAATGGATCAACATTTCAAGAGAGAGTTCATAATGAGAAGAACTCATCTG
1 TTCAAATCCATCATTCAATGGATCAACATTGCAAGAGAGAGTTCATAATGAGAAGAACTCATCTG
* *
6348093 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCATATG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGTTCAAATCCATCATATG
6348158 ATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
131 ATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
* ** * *
6348223 TCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCA
196 TCATAATAAGAAGAATTTGTTCAACCTTTAATCTGAATTCATCACTGGATGGATTATCATTGCCA
6348288 GA-AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
261 GAGA-AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
* * * *
6348327 TTCAAATCCATCATAT-GATGGATCATCATTGCCAGAGA-AGGTTTATAATGAGAAGAACTCATC
1 TTCAAATCCATCAT-TCAATGGATCAACATTGCAAGAGAGA-GTTCATAATGAGAAGAACTCATC
* ** *
6348390 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACT
64 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGTTCAAATCCATCA-T
* ** *
6348455 -TGATGGATTATTTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
128 ATGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* ** *
6348519 AGTTCATAATAAGAAGAATTTGTTCAACCTTTAATCTGAATTCATCACTGGATGGATTATTTTTT
193 AATTCATAATAAGAAGAATTTGTTCAACCTTTAATCTGAATTCATCACTGGATGGATTATCATTG
6348584 CCAGAGAAAGTTCATAATGAGAAGAACT
258 CCAGAGAAAGTTCATAATGAGAAGAACT
6348612 CATCTGAAGA
Statistics
Matches: 257, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
298 1 0.00
299 253 0.98
300 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (299 bp):
TTCAAATCCATCATTCAATGGATCAACATTGCAAGAGAGAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGTTCAAATCCATCATATG
ATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
TCATAATAAGAAGAATTTGTTCAACCTTTAATCTGAATTCATCACTGGATGGATTATCATTGCCA
GAGAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
Found at i:6349018 original size:3 final size:3
Alignment explanation
Indices: 6349012--6349124 Score: 190
Period size: 3 Copynumber: 37.7 Consensus size: 3
6349002 TTTTTATCCA
* * *
6349012 TAT TAT TAT TAT TAA TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
6349060 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6349108 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
6349125 AATATATATT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:6349631 original size:26 final size:25
Alignment explanation
Indices: 6349602--6349651 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
6349592 GAAACCAGAG
*
6349602 ACAGA-AACAGAAAACGGAAAAAAAAT
1 ACAGAGAA-AGAAAA-GAAAAAAAAAT
6349628 ACAGAGAAAGAAAAGAAAAAAAAA
1 ACAGAGAAAGAAAAGAAAAAAAAA
6349652 ACAACAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 11 0.50
27 2 0.09
ACGTcount: A:0.74, C:0.08, G:0.16, T:0.02
Consensus pattern (25 bp):
ACAGAGAAAGAAAAGAAAAAAAAAT
Found at i:6349925 original size:13 final size:13
Alignment explanation
Indices: 6349907--6349933 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6349897 CCACCGAAGA
6349907 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
6349920 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
6349933 C
1 C
6349934 AGAACTCGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.33, G:0.59, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:6350573 original size:20 final size:21
Alignment explanation
Indices: 6350536--6350576 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6350526 GATATTTTTA
**
6350536 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
6350557 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
6350577 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:6353454 original size:7 final size:7
Alignment explanation
Indices: 6353444--6353468 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6353434 ATTCTAAATC
6353444 TTAAACT
1 TTAAACT
6353451 TTAAACT
1 TTAAACT
6353458 TTAAACT
1 TTAAACT
6353465 TTAA
1 TTAA
6353469 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAAACT
Found at i:6353484 original size:15 final size:15
Alignment explanation
Indices: 6353464--6353493 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6353454 AACTTTAAAC
6353464 TTTAATTATTTTTAA
1 TTTAATTATTTTTAA
6353479 TTTAATTATTTTTAA
1 TTTAATTATTTTTAA
6353494 GACATTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTAATTATTTTTAA
Found at i:6353552 original size:69 final size:69
Alignment explanation
Indices: 6353462--6353595 Score: 166
Period size: 70 Copynumber: 1.9 Consensus size: 69
6353452 TAAACTTTAA
*
6353462 ACTTTAATTATTTTTAATTTAATTA-TTTTTAAGACATTATCAATTTTAAAATTAAATGAAATTA
1 ACTTTAATTATTTTTAATTTAATTATTTTTTAAGACATGAT-AATTTTAAAATT-AATGAAATTA
6353526 AGTTTT
64 AGTTTT
* * * * *
6353532 ACTTCTAATT-TTTTT-GTTTAATTATTTTTTAAGATATGATGATTTTGAAATTAGTGAAATTAA
1 ACTT-TAATTATTTTTAATTTAATTATTTTTTAAGACATGATAATTTTAAAATTAATGAAATTAA
6353595 G
65 G
6353596 CTTCAATTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
68 11 0.20
69 18 0.32
70 22 0.39
71 5 0.09
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (69 bp):
ACTTTAATTATTTTTAATTTAATTATTTTTTAAGACATGATAATTTTAAAATTAATGAAATTAAG
TTTT
Found at i:6353612 original size:69 final size:69
Alignment explanation
Indices: 6353466--6353621 Score: 172
Period size: 69 Copynumber: 2.2 Consensus size: 69
6353456 CTTTAAACTT
* *
6353466 TAATTATTTTTAATTTAATTATTTTTAAGACATTATCAATTTTAAAATTAAATGAAATTAAGTTT
1 TAATT-TTTTT-ATTTAATTATTTTTAAGACATGATCAATTTTAAAATTAAATGAAATTAAGCTT
* *
6353531 TACTTC
64 CAATTC
* * * * *
6353537 TAATTTTTTTGTTTAATTATTTTTTAAGATATGAT-GATTTTGAAATT-AGTGAAATTAAGCTTC
1 TAATTTTTTTATTTAATTA-TTTTTAAGACATGATCAATTTTAAAATTAAATGAAATTAAGCTTC
6353600 AATTC
65 AATTC
*
6353605 TCTATTTTTTTATTTAA
1 T-AATTTTTTTATTTAA
6353622 CTATCTCTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
68 18 0.25
69 31 0.43
70 18 0.25
71 5 0.07
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (69 bp):
TAATTTTTTTATTTAATTATTTTTAAGACATGATCAATTTTAAAATTAAATGAAATTAAGCTTCA
ATTC
Found at i:6356996 original size:6 final size:6
Alignment explanation
Indices: 6356985--6357059 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
6356975 TCTCGTCTCG
6356985 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
6357033 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
6357060 AATACGTGTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:6361964 original size:25 final size:27
Alignment explanation
Indices: 6361912--6361967 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
6361902 TAATATAATG
*
6361912 AATTTTTTTAATAATTATAGTTTAATTT
1 AATTTTGTTAATAA-TATAGTTTAATTT
* *
6361940 AATTTTGTTAATAA-ATATTTTATTTT
1 AATTTTGTTAATAATATAGTTTAATTT
6361966 AA
1 AA
6361968 AAAAATTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.48
28 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (27 bp):
AATTTTGTTAATAATATAGTTTAATTT
Found at i:6362576 original size:25 final size:25
Alignment explanation
Indices: 6362548--6362601 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
6362538 CGATTCAAAT
6362548 TACTTACCTCCGATAGATTAAAAAG
1 TACTTACCTCCGATAGATTAAAAAG
*
6362573 TACTTACCTCCGATCGATTAAAAAG
1 TACTTACCTCCGATAGATTAAAAAG
6362598 TACT
1 TACT
6362602 CCTAAAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (25 bp):
TACTTACCTCCGATAGATTAAAAAG
Found at i:6364196 original size:35 final size:37
Alignment explanation
Indices: 6364130--6364201 Score: 121
Period size: 35 Copynumber: 2.0 Consensus size: 37
6364120 TATGTGCAGG
*
6364130 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGAGGGGGTATCGATTCCCC
6364167 GGGAACAGATT-CCCCCT-AGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGAGGGGGTATCGATTCCCC
6364202 CTAAATGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 17 0.50
36 6 0.18
37 11 0.32
ACGTcount: A:0.18, C:0.32, G:0.31, T:0.19
Consensus pattern (37 bp):
GGGAACAGATTCCCCCCTGAGGGGGTATCGATTCCCC
Found at i:6364633 original size:22 final size:20
Alignment explanation
Indices: 6364608--6364649 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
6364598 CCAATGTGAA
6364608 ATGAAATAAGCTATATGAATAT
1 ATGAAATAA-C-ATATGAATAT
*
6364630 ATGAAATGACATATGAATAT
1 ATGAAATAACATATGAATAT
6364650 GCAATATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGAAATAACATATGAATAT
Found at i:6364827 original size:15 final size:15
Alignment explanation
Indices: 6364809--6364842 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6364799 GAGGGTATTT
*
6364809 TAGTCCTTCGGGACG
1 TAGTCCTTCGAGACG
6364824 TAGTCCTTCGAGACG
1 TAGTCCTTCGAGACG
6364839 TAGT
1 TAGT
6364843 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (15 bp):
TAGTCCTTCGAGACG
Found at i:6370190 original size:20 final size:18
Alignment explanation
Indices: 6370167--6370266 Score: 54
Period size: 20 Copynumber: 5.6 Consensus size: 18
6370157 AGGGGGAACA
6370167 GATTCCCCCTGGGGGGTATC
1 GATTCCCCCT--GGGGTATC
*
6370187 GATT-CCCC--GGG-AAC
1 GATTCCCCCTGGGGTATC
6370201 AGATTCCCCCTAGAGGGTATC
1 -GATTCCCCCT-G-GGGTATC
*
6370222 GATT-CCCC--GGG-AAC
1 GATTCCCCCTGGGGTATC
6370236 AGATTCCCCCTGGGGGGTATC
1 -GATTCCCCCT--GGGGTATC
6370257 GATTCCCCCT
1 GATTCCCCCT
6370267 AAATGAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 28
0.66 0.04 0.30
Matches are distributed among these distances:
14 4 0.06
15 14 0.23
16 8 0.13
19 8 0.13
20 24 0.39
21 4 0.06
ACGTcount: A:0.17, C:0.33, G:0.28, T:0.22
Consensus pattern (18 bp):
GATTCCCCCTGGGGTATC
Found at i:6370206 original size:35 final size:35
Alignment explanation
Indices: 6370160--6370264 Score: 192
Period size: 35 Copynumber: 3.0 Consensus size: 35
6370150 TATGTGCAGG
6370160 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
* *
6370195 GGGAACAGATTCCCCCTAGAGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
6370230 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
6370265 CTAAATGAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
Found at i:6370616 original size:5 final size:5
Alignment explanation
Indices: 6370606--6370638 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
6370596 AACATTAGAT
*
6370606 ATATG ATATG ATAT- ACATG ATATG ATATG ATAT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATAT
6370639 ACATGATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (5 bp):
ATATG
Found at i:6370630 original size:19 final size:19
Alignment explanation
Indices: 6370606--6370645 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
6370596 AACATTAGAT
6370606 ATATGATATGATATACATG
1 ATATGATATGATATACATG
6370625 ATATGATATGATATACATG
1 ATATGATATGATATACATG
6370644 AT
1 AT
6370646 TATATGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (19 bp):
ATATGATATGATATACATG
Found at i:6370908 original size:15 final size:15
Alignment explanation
Indices: 6370890--6370969 Score: 160
Period size: 15 Copynumber: 5.3 Consensus size: 15
6370880 CGAGGGTATT
6370890 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
6370905 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
6370920 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
6370935 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
6370950 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
6370965 GTAGT
1 GTAGT
6370970 GGTCCTACGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 65 1.00
ACGTcount: A:0.14, C:0.25, G:0.34, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:6379067 original size:30 final size:30
Alignment explanation
Indices: 6379026--6379094 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
6379016 ATGTACGTGG
*
6379026 GATTCAAGGAAGTTCCGTCACCGCACCTGC
1 GATTCAGGGAAGTTCCGTCACCGCACCTGC
* *
6379056 GATTCAGGGAAGTTCCGTCACTGCACCTTC
1 GATTCAGGGAAGTTCCGTCACCGCACCTGC
*
6379086 GGTTCAGGG
1 GATTCAGGG
6379095 GAGCTCAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.23
Consensus pattern (30 bp):
GATTCAGGGAAGTTCCGTCACCGCACCTGC
Found at i:6379139 original size:30 final size:30
Alignment explanation
Indices: 6379048--6379151 Score: 81
Period size: 30 Copynumber: 3.5 Consensus size: 30
6379038 TTCCGTCACC
* * *
6379048 GCACCTGCGATTCAGGGAAGTTCC-GTCACT
1 GCACCGGCGGTTCAGGGAGGTTCCAG-CACT
** * *
6379078 GCACCTTCGGTTCAGGG-GAGCT-CAACTACT
1 GCACCGGCGGTTCAGGGAG-GTTCCAGC-ACT
6379108 GCACCGGCGGTTCAGGGAGGTTCCAGCACT
1 GCACCGGCGGTTCAGGGAGGTTCCAGCACT
6379138 GCACCCGG-GGTTCA
1 GCA-CCGGCGGTTCA
6379152 AGGAAAATCC
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
29 2 0.03
30 49 0.83
31 8 0.14
ACGTcount: A:0.18, C:0.31, G:0.31, T:0.20
Consensus pattern (30 bp):
GCACCGGCGGTTCAGGGAGGTTCCAGCACT
Found at i:6380129 original size:15 final size:15
Alignment explanation
Indices: 6380109--6380139 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6380099 TTATTTAATC
6380109 TTTTAAAAAATAAAA
1 TTTTAAAAAATAAAA
*
6380124 TTTTAAAAACTAAAA
1 TTTTAAAAAATAAAA
6380139 T
1 T
6380140 ATTCAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
TTTTAAAAAATAAAA
Found at i:6380147 original size:15 final size:15
Alignment explanation
Indices: 6380111--6380149 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6380101 ATTTAATCTT
* *
6380111 TTAAAAAATAAAATT
1 TTAAAAACTAAAATA
6380126 TTAAAAACTAAAATA
1 TTAAAAACTAAAATA
*
6380141 TTCAAAACT
1 TTAAAAACT
6380150 TACTAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAAACTAAAATA
Found at i:6380245 original size:10 final size:9
Alignment explanation
Indices: 6380236--6380278 Score: 54
Period size: 8 Copynumber: 4.8 Consensus size: 9
6380226 AATTATAAAT
6380236 TATTAAAAA
1 TATTAAAAA
6380245 T-TTAAAAA
1 TATTAAAAA
6380253 TATTTATAAAA
1 TA-TTA-AAAA
6380264 TATTAAAAA
1 TATTAAAAA
6380273 -ATTAAA
1 TATTAAA
6380279 CAATTTTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 14 0.45
9 5 0.16
10 6 0.19
11 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TATTAAAAA
Done.