Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 175 of 410
Found at i:53809412 original size:12 final size:12
Alignment explanation
Indices: 53809381--53809405 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53809371 TTTTTCAATC
53809381 TCATTTTCTTTT
1 TCATTTTCTTTT
53809393 TCATTTTCTTTT
1 TCATTTTCTTTT
53809405 T
1 T
53809406 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:53809483 original size:5 final size:5
Alignment explanation
Indices: 53809473--53809527 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
53809463 CTCTTGCCTC
*
53809473 TCTTT TCTTT T-TATT T-TTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TCTTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
53809518 TCTTT TCTTT
1 TCTTT TCTTT
53809528 ATTTTCTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
4 7 0.16
5 30 0.70
6 2 0.05
7 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:53809534 original size:14 final size:14
Alignment explanation
Indices: 53809473--53809527 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
53809463 CTCTTGCCTC
53809473 TCTTTTCTTTTTAT
1 TCTTTTCTTTTTAT
* *
53809487 TTTTTTCTTTTTCT
1 TCTTTTCTTTTTAT
*
53809501 TCTTTTGCTTTTTCTTT
1 TCTTTT-C-TTTT-TAT
53809518 TCTTTTCTTT
1 TCTTTTCTTT
53809528 ATTTTCTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 17 0.50
15 4 0.12
16 5 0.15
17 8 0.24
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (14 bp):
TCTTTTCTTTTTAT
Found at i:53809537 original size:21 final size:20
Alignment explanation
Indices: 53809471--53809538 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
53809461 GCCTCTTGCC
*
53809471 TCTCTTTTCTTTTTATTTTTT
1 TCTCTTTTCTTTTT-TTATTT
**
53809492 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
53809512 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
53809532 TCTCTTT
1 TCTCTTT
53809539 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.08
20 25 0.64
21 11 0.28
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:53812176 original size:30 final size:30
Alignment explanation
Indices: 53812091--53812187 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
53812081 TAAACTAAAA
* * *
53812091 TGAGCTAAGCTTTACCTCGTAAGCTAAAGT
1 TGAGCTAAGGTTTAACTCGTAAGCTGAAGT
* * * *
53812121 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAACTCGTAAGCTGAAGT
* *
53812151 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAACTCGTAAGCTGAAGT
53812180 ATGAGCTA
1 -TGAGCTA
53812188 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAACTCGTAAGCTGAAGT
Found at i:53821123 original size:15 final size:15
Alignment explanation
Indices: 53821100--53821130 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53821090 CCAAAAATTC
53821100 CAATACAAAACATAT
1 CAATACAAAACATAT
*
53821115 CAATCCAAAACATAT
1 CAATACAAAACATAT
53821130 C
1 C
53821131 TTTCATAATT
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:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:53827441 original size:23 final size:23
Alignment explanation
Indices: 53827397--53827445 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
53827387 TGAGTATTTA
*
53827397 AATGTATATATTTAATTGAATTG
1 AATGTATATATTTAATTAAATTG
*
53827420 AATGTATATCATTT-GTTAAATTG
1 AATGTATAT-ATTTAATTAAATTG
53827443 AAT
1 AAT
53827446 TATTGATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (23 bp):
AATGTATATATTTAATTAAATTG
Found at i:53837318 original size:46 final size:46
Alignment explanation
Indices: 53837268--53837443 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
53837258 TGGTTGAGCA
*
53837268 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
53837314 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
53837361 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * **
53837407 CCCGAGCTCGTTGATTTGAGTCTAAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53837444 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:53837435 original size:93 final size:93
Alignment explanation
Indices: 53837265--53837435 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
53837255 GGATGGTTGA
* * *
53837265 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
*
53837330 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCAAGTTCGTGAGATGTAACTAG
* * *
53837358 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGATT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
*
53837423 TGAGTCTAAGTTC
66 TGAGTCCAAGTTC
53837436 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAGATGTAACTAG
Found at i:53840015 original size:31 final size:31
Alignment explanation
Indices: 53839977--53840055 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
53839967 TTAAACGATT
53839977 ACTGGGCCGAAGCCTTTTCATAACTCATATC
1 ACTGGGCCGAAGCCTTTTCATAACTCATATC
* * *
53840008 ACTGGGCCAAAGCCTTTTCATTATTCATATC
1 ACTGGGCCGAAGCCTTTTCATAACTCATATC
*
53840039 ACTGGGCTGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
53840056 ACTATAAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAACTCATATC
Found at i:53840479 original size:25 final size:25
Alignment explanation
Indices: 53840451--53840498 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
53840441 ATAATTAAAC
* *
53840451 CCTAGGGGTACAATGGTCATTTTTA
1 CCTAGGGGTAAAATAGTCATTTTTA
53840476 CCTAGGGGTAAAATAGTCATTTT
1 CCTAGGGGTAAAATAGTCATTTT
53840499 CCATATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGTAAAATAGTCATTTTTA
Found at i:53845289 original size:55 final size:55
Alignment explanation
Indices: 53845203--53845331 Score: 177
Period size: 55 Copynumber: 2.3 Consensus size: 55
53845193 GCAATCTTGC
* * *
53845203 CAAAATAACACGTGCGTGTGACACGCCCGTGCCAACCACCCGTGGTCAAAATTGT
1 CAAAATAACACGGGCGTGCGACACGCCCGTGCCAACCACCCGTGGTCAAAACTGT
* * * **
53845258 CAAAATAACATGGGCGTGCGACACGCTCGTGCCCACCACCCGTGGTTGAAACTGT
1 CAAAATAACACGGGCGTGCGACACGCCCGTGCCAACCACCCGTGGTCAAAACTGT
*
53845313 CAAAATAAGACGGGCGTGC
1 CAAAATAACACGGGCGTGC
53845332 ACATATATAC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (55 bp):
CAAAATAACACGGGCGTGCGACACGCCCGTGCCAACCACCCGTGGTCAAAACTGT
Found at i:53850386 original size:27 final size:27
Alignment explanation
Indices: 53850356--53850474 Score: 184
Period size: 27 Copynumber: 4.4 Consensus size: 27
53850346 GGGGCAAAAT
* * *
53850356 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53850383 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53850410 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53850437 GGTAATTCTATCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
53850464 GGTAATTCTAC
1 GGTAATTCTAC
53850475 AACTTATCCA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:53857719 original size:53 final size:54
Alignment explanation
Indices: 53857650--53857855 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 54
53857640 TTCCTTTTTA
* * * *
53857650 AACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
53857703 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * * *
53857757 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGGTTTCCTTGCCTTGTAA
1 -AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
53857812 AACTCACCGA-TGCCATGCCTTGGCATGGTCTTACTTGGTGTCCT
1 AACTCACC-ATTGCCATGCCTTGACATGGTCTTACATGGTATCCT
53857856 GAAACCCTAA
Statistics
Matches: 122, Mismatches: 28, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
53 45 0.37
54 35 0.29
55 42 0.34
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.37
Consensus pattern (54 bp):
AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:53857805 original size:55 final size:53
Alignment explanation
Indices: 53857662--53857855 Score: 199
Period size: 55 Copynumber: 3.6 Consensus size: 53
53857652 CTTACCATTT
* *
53857662 CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCATTG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
* * * * ** * *
53857715 CCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCGTAGTTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G-AACTCACCAATG
* * * *
53857770 CCATGTCTTGACATGGTCTTACATGGTTTCCTTGCCTTGTAAAACTCACCGATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATG
* * * *
53857824 CCATGCCTTGGCATGGTCTTACTTGGTGTCCT
1 CCATGTCTTGACATGGTCTTACATGGTATCCT
53857856 GAAACCCTAA
Statistics
Matches: 112, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 35 0.31
54 36 0.32
55 41 0.37
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.37
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
Found at i:53862496 original size:14 final size:14
Alignment explanation
Indices: 53862449--53862496 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
53862439 GTATGAATGG
*
53862449 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
53862463 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
53862477 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
53862491 ATTGGT
1 AATGGT
53862497 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:53868306 original size:55 final size:54
Alignment explanation
Indices: 53868151--53868357 Score: 218
Period size: 53 Copynumber: 3.8 Consensus size: 54
53868141 TTCCTTTTTA
* * * *
53868151 AACTTACCATTGCTATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * *
53868204 AACTCACCATTGTCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * *
53868258 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* *
53868313 AACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
53868358 AAACCCCAAT
Statistics
Matches: 122, Mismatches: 30, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 44 0.36
54 38 0.31
55 40 0.33
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:53872915 original size:29 final size:29
Alignment explanation
Indices: 53872882--53872984 Score: 152
Period size: 29 Copynumber: 3.6 Consensus size: 29
53872872 CCTTCGAGCT
** * *
53872882 CGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
53872911 TGCACAGTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
53872940 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
53872969 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
53872985 ATCTTGTCAC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:53872916 original size:58 final size:58
Alignment explanation
Indices: 53872853--53872984 Score: 147
Period size: 58 Copynumber: 2.3 Consensus size: 58
53872843 AATTTAAGCC
* * * * * *
53872853 CGCACAAATAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACAATTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
* * * * **
53872911 TGCACAGTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACAATTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
*
53872969 CGCACACTTAGTGCCA
1 CGCACAATTAGTGCCA
53872985 ATCTTGTCAC
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
CGCACAATTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
Found at i:53876328 original size:19 final size:19
Alignment explanation
Indices: 53876304--53876343 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53876294 AGCTCCCATG
53876304 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
53876323 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
53876342 TA
1 TA
53876344 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:53881097 original size:30 final size:30
Alignment explanation
Indices: 53881012--53881108 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
53881002 TAAACTAAAA
* *
53881012 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
53881042 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53881072 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53881101 ATGAGCTA
1 -TGAGCTA
53881109 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:53883287 original size:30 final size:30
Alignment explanation
Indices: 53883216--53883298 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
53883206 CTTTTGTTTC
* *
53883216 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
53883247 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
53883276 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
53883299 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:53883298 original size:18 final size:18
Alignment explanation
Indices: 53883249--53883304 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
53883239 CACTCTCAAA
* *
53883249 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
53883266 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
53883284 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
53883303 TT
1 TT
53883305 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:53883305 original size:12 final size:12
Alignment explanation
Indices: 53883274--53883298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53883264 TTTTTCAATC
53883274 TCATTTTCTTTT
1 TCATTTTCTTTT
53883286 TCATTTTCTTTT
1 TCATTTTCTTTT
53883298 T
1 T
53883299 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:53886032 original size:30 final size:30
Alignment explanation
Indices: 53885947--53886043 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
53885937 TAAACTAAAA
* *
53885947 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
53885977 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53886007 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53886036 ATGAGCTA
1 -TGAGCTA
53886044 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:53886787 original size:9 final size:10
Alignment explanation
Indices: 53886780--53886836 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
53886770 AAGAGAAAAT
53886780 AAAGAAAAGA
1 AAAGAAAAGA
53886790 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
53886802 AAAGAAGA-A
1 AAAGAAAAGA
53886811 AAAGAAAATGA
1 AAAGAAAA-GA
53886822 AATA-AAAAGA
1 AA-AGAAAAGA
53886832 AAAGA
1 AAAGA
53886837 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:53886804 original size:6 final size:5
Alignment explanation
Indices: 53886780--53886836 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
53886770 AAGAGAAAAT
*
53886780 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
53886827 AAAGA AAAGA
1 AAAGA AAAGA
53886837 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:53886811 original size:15 final size:14
Alignment explanation
Indices: 53886780--53886836 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
53886770 AAGAGAAAAT
53886780 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
53886796 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
53886811 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
53886827 AAAGAAAAGA
1 AAAGAAAAGA
53886837 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:53895903 original size:2 final size:2
Alignment explanation
Indices: 53895891--53895933 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
53895881 AACAAATCAG
*
53895891 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53895933 T
1 T
53895934 CAACCATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53899142 original size:43 final size:43
Alignment explanation
Indices: 53899043--53899143 Score: 98
Period size: 43 Copynumber: 2.3 Consensus size: 43
53899033 CTTGGATAAT
* *
53899043 CACACATATCATACAATGCCAATGTCCCAAACGTGGTCTTACATG
1 CACACATAT-AT-CAATGCCAACGTACCAAACGTGGTCTTACATG
* * **
53899088 TA-ATCACATATCAATGCCAACGTATTAAACGTGGTCTTAC-TCG
1 CACA-CATATATCAATGCCAACGTACCAAACGTGGTCTTACAT-G
53899131 CACACATATATCA
1 CACACATATATCA
53899144 GAATCACATA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
42 1 0.02
43 35 0.78
44 4 0.09
45 5 0.11
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (43 bp):
CACACATATATCAATGCCAACGTACCAAACGTGGTCTTACATG
Found at i:53899178 original size:56 final size:55
Alignment explanation
Indices: 53899089--53899254 Score: 251
Period size: 56 Copynumber: 3.0 Consensus size: 55
53899079 TCTTACATGT
* *
53899089 AATCACATATCAATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
1 AATCACATATCGATG-CAACGTATTAAATGTGGTCTTACTCGCACACATATATCAG
* * *
53899145 AATCACATATCGATGCGAACGTATTAAATGTGGTCTTGCTCGCACACATATACCGG
1 AATCACATATCGATGC-AACGTATTAAATGTGGTCTTACTCGCACACATATATCAG
* *
53899201 AATCACATATCGATGCCACGTATTAAATGTGGTTTTACTCGCACACATATATCA
1 AATCACATATCGATGCAACGTATTAAATGTGGTCTTACTCGCACACATATATCA
53899255 ATGCCATGGT
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
55 34 0.34
56 65 0.66
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (55 bp):
AATCACATATCGATGCAACGTATTAAATGTGGTCTTACTCGCACACATATATCAG
Found at i:53903178 original size:20 final size:21
Alignment explanation
Indices: 53903153--53903210 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
53903143 TCAGTTTCCA
53903153 TCAGCTCGCTTGAGCTCG-AT
1 TCAGCTCGCTTGAGCTCGAAT
**
53903173 TCAGCTCATTTGAGCTCGAAT
1 TCAGCTCGCTTGAGCTCGAAT
* * *
53903194 TTAGCTCGTTTCAGCTC
1 TCAGCTCGCTTGAGCTC
53903211 ATTTCTTCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (21 bp):
TCAGCTCGCTTGAGCTCGAAT
Found at i:53905623 original size:7 final size:6
Alignment explanation
Indices: 53905602--53905708 Score: 53
Period size: 6 Copynumber: 17.2 Consensus size: 6
53905592 ATGAATGTGA
* *
53905602 AAAAAG -AAAAG AAAATG AAAAAG -AAAAG AAAAA- AACAAG AAAAA-
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * *
53905646 AATACAA- AAATAG CAAAAG AAAAAA AACAAAGTG AGAAAAG AAAAAG
1 AA-A-AAG AAAAAG AAAAAG AAAAAG AA-AAA--G A-AAAAG AAAAAG
53905693 AAGAGCAAG AAAAAG A
1 AA-A--AAG AAAAAG A
53905709 GATTAGAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
5 17 0.22
6 40 0.51
7 10 0.13
8 1 0.01
9 9 0.12
10 1 0.01
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:53905646 original size:11 final size:10
Alignment explanation
Indices: 53905601--53905647 Score: 58
Period size: 11 Copynumber: 4.4 Consensus size: 10
53905591 AATGAATGTG
53905601 AAAAAAGAAA
1 AAAAAAGAAA
*
53905611 AGAAAATGAAA
1 A-AAAAAGAAA
53905622 AAGAAAAGAAA
1 AA-AAAAGAAA
53905633 AAAACAAGAAA
1 AAAA-AAGAAA
53905644 AAAA
1 AAAA
53905648 TACAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 4 0.12
11 28 0.88
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:53908685 original size:21 final size:20
Alignment explanation
Indices: 53908641--53908698 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
53908631 TCAGTTTCCA
* *
53908641 TCAGCTCGCTTGAGCTTGAT
1 TCAGCTCGTTTGAGCTCGAT
53908661 TCAGCTCGTTTGAGCTCGAAT
1 TCAGCTCGTTTGAGCTCG-AT
*
53908682 TCAGCTCGTTTCAGCTC
1 TCAGCTCGTTTGAGCTC
53908699 ATTTCTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.16, C:0.28, G:0.22, T:0.34
Consensus pattern (20 bp):
TCAGCTCGTTTGAGCTCGAT
Found at i:53908694 original size:10 final size:10
Alignment explanation
Indices: 53908641--53908703 Score: 54
Period size: 10 Copynumber: 6.2 Consensus size: 10
53908631 TCAGTTTCCA
*
53908641 TCAGCTCGCT
1 TCAGCTCGTT
* * *
53908651 TGAGCTTGAT
1 TCAGCTCGTT
53908661 TCAGCTCGTT
1 TCAGCTCGTT
* *
53908671 TGAGCTCGAAT
1 TCAGCTCG-TT
53908682 TCAGCTCGTT
1 TCAGCTCGTT
*
53908692 TCAGCTCATT
1 TCAGCTCGTT
53908702 TC
1 TC
53908704 TTCTTCATCT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
10 33 0.80
11 8 0.20
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.37
Consensus pattern (10 bp):
TCAGCTCGTT
Found at i:53911335 original size:22 final size:22
Alignment explanation
Indices: 53911309--53911371 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
53911299 AAATACGTTG
*
53911309 GGCACATAGCCATAATCAGGTT
1 GGCACAAAGCCATAATCAGGTT
* *
53911331 GGCACAGAGCCAT-ATGTAGGTT
1 GGCACAAAGCCATAAT-CAGGTT
*
53911353 GGCGCAAAGCCATAATCAG
1 GGCACAAAGCCATAATCAG
53911372 AATAATTGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (22 bp):
GGCACAAAGCCATAATCAGGTT
Found at i:53911571 original size:41 final size:41
Alignment explanation
Indices: 53911514--53911636 Score: 201
Period size: 41 Copynumber: 3.0 Consensus size: 41
53911504 AAAAGCCACC
* *
53911514 GGTGGATCCACGGTCGTCAAGCAACCATACGATCCTTAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
53911555 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
* * *
53911596 GGTGGATCCACGATCGTCAATCAACCATGCGATCCCCAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
53911637 TCTTCCTCCG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 77 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (41 bp):
GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATT
Found at i:53911923 original size:27 final size:27
Alignment explanation
Indices: 53911891--53912286 Score: 259
Period size: 27 Copynumber: 14.7 Consensus size: 27
53911881 TTTGTAAATC
*
53911891 TACAAACCAAGGGTATTTCGATAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
* * *
53911918 TGCAAA-CTAATGGTATTGCTG-TAATTT
1 TACAAATC-AAGGGTATTTC-GATAATTT
**
53911945 TTGAAAGTCAAGGGTATTTCTG-TAATTT
1 TACAAA-TCAAGGGTATTTC-GATAATTT
** * *
53911973 TGTAAATCAAAGGTATTTCTATAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
* *
53912000 TCCAAATCAAAGGTATTTC-AGTAATTT
1 TACAAATCAAGGGTATTTCGA-TAATTT
* * *
53912027 TCCAAATCAAGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
** *
53912054 TACAAATTGAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
* * * *
53912081 TATAAGTCGAGGGTATTTTGATAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
** * * *
53912108 TACAGGTCGAGAGTATTTCGTTAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
* *
53912135 CACAAAT-TAGGAGTATTTTCG-TAATTT
1 TACAAATCAAGG-GTA-TTTCGATAATTT
* * * *
53912162 TACAAACCAGGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
* *
53912189 TACAAA-CTAAGGGTATTTTGGTAATTT
1 TACAAATC-AAGGGTATTTCGATAATTT
* * * *
53912216 TACTAATCGAGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
* * *
53912243 TATAAACCAAGGGTA-TTCAATAATTT
1 TACAAATCAAGGGTATTTCGATAATTT
** *
53912269 TGTAAACCAAGGGTATTT
1 TACAAATCAAGGGTATTT
53912287 TAGTAATTCT
Statistics
Matches: 304, Mismatches: 51, Indels: 28
0.79 0.13 0.07
Matches are distributed among these distances:
26 31 0.10
27 242 0.80
28 30 0.10
29 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
TACAAATCAAGGGTATTTCGATAATTT
Found at i:53912079 original size:81 final size:81
Alignment explanation
Indices: 53911891--53912294 Score: 307
Period size: 81 Copynumber: 5.0 Consensus size: 81
53911881 TTTGTAAATC
* * * * * * * * **
53911891 TACAAACCAAGGGTATTTCGATAATTTTGCAAACTAATGGTATTGCTGTAATTTTTGAAAGTCAA
1 TACAAATCGAGGGTATTTCGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTACAAA-TCAA
53911956 GGGTATTTCT-GTAATTT
65 GGGTATTT-TGGTAATTT
** * * ** * * * *
53911973 TGTAAATCAAAGGTATTTCTATAATTTTCCAAATCAAAGGTATTTCAGTAATTTTCCAAATCAAG
1 TACAAATCGAGGGTATTTCGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTACAAATCAAG
53912038 GGTATTTTGGTAATTT
66 GGTATTTTGGTAATTT
* * ** * * ** *
53912054 TACAAATTGAGGGTATTTCGGTAATTTTATAAGTCGAGGGTATTT-TGATAATTTTACAGGTCGA
1 TACAAATCGAGGGTATTTCGGTAATTTTACAAACCAAGGGTATTTCAG-TAATTTTACAAATCAA
* * *
53912118 GAGTATTTCGTTAATTT
65 GGGTATTTTGGTAATTT
* * * **
53912135 CACAAAT-TAGGAGTATTTTC-GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAA-CT
1 TACAAATCGAGG-GTA-TTTCGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTACAAATC-
53912197 AAGGGTATTTTGGTAATTT
63 AAGGGTATTTTGGTAATTT
* * * * ** *
53912216 TACTAATCGAGGGTATTTTGGTAATTTTATAAACCAAGGGTA-TTCAATAATTTTGTAAACCAAG
1 TACAAATCGAGGGTATTTCGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTACAAATCAAG
*
53912280 GGTATTTTAGTAATT
66 GGTATTTTGGTAATT
53912295 CTACCCTACA
Statistics
Matches: 254, Mismatches: 59, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
80 38 0.15
81 161 0.63
82 55 0.22
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (81 bp):
TACAAATCGAGGGTATTTCGGTAATTTTACAAACCAAGGGTATTTCAGTAATTTTACAAATCAAG
GGTATTTTGGTAATTT
Found at i:53912307 original size:26 final size:26
Alignment explanation
Indices: 53912278--53912358 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
53912268 TTGTAAACCA
53912278 AGGGTATTTTAGTAATTCTACCCTAC
1 AGGGTATTTTAGTAATTCTACCCTAC
* **
53912304 AGGGGCATTTTAGTAATTCTATGCTAC
1 A-GGGTATTTTAGTAATTCTACCCTAC
* *
53912331 AGGGTATTTTAGTAATACTAGCCTAC
1 AGGGTATTTTAGTAATTCTACCCTAC
53912357 AG
1 AG
53912359 ATATGAGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 24 0.51
27 23 0.49
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (26 bp):
AGGGTATTTTAGTAATTCTACCCTAC
Found at i:53914119 original size:13 final size:13
Alignment explanation
Indices: 53914101--53914129 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53914091 AATAGTTGTG
53914101 TGTTATTTAATTA
1 TGTTATTTAATTA
53914114 TGTTATTTAATTA
1 TGTTATTTAATTA
53914127 TGT
1 TGT
53914130 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:53923868 original size:12 final size:12
Alignment explanation
Indices: 53923853--53923883 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
53923843 TTCTTTTTGC
53923853 TTTTCAAAGGCT
1 TTTTCAAAGGCT
53923865 TTTTCAAAGGCT
1 TTTTCAAAGGCT
53923877 TTTTCAA
1 TTTTCAA
53923884 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:53923986 original size:20 final size:20
Alignment explanation
Indices: 53923948--53923996 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
53923938 TTTTATTTCG
53923948 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTCTTCTTTTG-T
53923969 TTTTC-TTTTCTT-TCTTTGT
1 TTTTCTTTTTCTTCT-TTTGT
53923988 TTTCTCTTT
1 TTT-TCTTT
53923997 ACAAGAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.20
20 13 0.52
21 7 0.28
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTTCTTCTTTTGT
Found at i:53923995 original size:15 final size:15
Alignment explanation
Indices: 53923929--53923996 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
53923919 GCCTCTTGCC
*
53923929 TCTCTTTCTTTTTAT
1 TCTCTTTCTTTTTCT
53923944 T-TCGTTTTCTTTTTCT
1 TCTC--TTTCTTTTTCT
53923960 TCT-TTTGCTTTTTCT
1 TCTCTTT-CTTTTTCT
*
53923975 TTTCTTTCTTTGTT-T
1 TCTCTTTCTTT-TTCT
53923990 TCTCTTT
1 TCTCTTT
53923997 ACAAGAATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.11
15 22 0.50
16 16 0.36
17 1 0.02
ACGTcount: A:0.01, C:0.19, G:0.04, T:0.75
Consensus pattern (15 bp):
TCTCTTTCTTTTTCT
Found at i:53924917 original size:11 final size:11
Alignment explanation
Indices: 53924901--53924955 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 11
53924891 CATAAATCAC
53924901 TTTTTTTTAAT
1 TTTTTTTTAAT
53924912 TTTTTTTTAAT
1 TTTTTTTTAAT
53924923 TATTTTTTTCAAAT
1 T-TTTTTTT--AAT
*
53924937 TTTTTTTCGAAT
1 TTTTTTT-TAAT
53924949 TTTTTTT
1 TTTTTTT
53924956 CGGTTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
11 12 0.31
12 17 0.44
13 6 0.15
14 4 0.10
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:53924918 original size:12 final size:12
Alignment explanation
Indices: 53924901--53924955 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
53924891 CATAAATCAC
53924901 TTTTTTTTAA-T
1 TTTTTTTTAATT
53924912 TTTTTTTTAATT
1 TTTTTTTTAATT
*
53924924 ATTTTTTTCAAATT
1 -TTTTTTT-TAATT
**
53924938 TTTTTTCGAATT
1 TTTTTTTTAATT
53924950 TTTTTT
1 TTTTTT
53924956 CGGTTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
11 10 0.26
12 11 0.29
13 13 0.34
14 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTTAATT
Found at i:53924967 original size:12 final size:12
Alignment explanation
Indices: 53924925--53924966 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
53924915 TTTTTAATTA
*
53924925 TTTTTTTCAAAT
1 TTTTTTTCGAAT
53924937 TTTTTTTCGAAT
1 TTTTTTTCGAAT
*
53924949 TTTTTTTCG-GT
1 TTTTTTTCGAAT
53924960 TTTTTTT
1 TTTTTTT
53924967 TTCAAACTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:53927101 original size:13 final size:13
Alignment explanation
Indices: 53927083--53927107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53927073 ATTCTTATCA
53927083 ATTTAATTATGTT
1 ATTTAATTATGTT
53927096 ATTTAATTATGT
1 ATTTAATTATGT
53927108 AGGTTAGCCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
ATTTAATTATGTT
Found at i:53929404 original size:16 final size:16
Alignment explanation
Indices: 53929383--53929413 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53929373 TTCACATCAT
53929383 ACTAAATATACCATAC
1 ACTAAATATACCATAC
53929399 ACTAAATATACCATA
1 ACTAAATATACCATA
53929414 TGCATATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (16 bp):
ACTAAATATACCATAC
Found at i:53930832 original size:56 final size:56
Alignment explanation
Indices: 53930699--53930833 Score: 234
Period size: 56 Copynumber: 2.4 Consensus size: 56
53930689 TCCCAGATAG
* * * *
53930699 GGTCTTTCTCGCACACATATAACGAAATCACATATCGATGCCAACGTATTAAACGT
1 GGTCTTACTCACACACATATATCAAAATCACATATCGATGCCAACGTATTAAACGT
53930755 GGTCTTACTCACACACATATATCAAAATCACATATCGATGCCAACGTATTAAACGT
1 GGTCTTACTCACACACATATATCAAAATCACATATCGATGCCAACGTATTAAACGT
53930811 GGTCTTACTCACACACATATATC
1 GGTCTTACTCACACACATATATC
53930834 GATGCCATGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 75 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (56 bp):
GGTCTTACTCACACACATATATCAAAATCACATATCGATGCCAACGTATTAAACGT
Found at i:53941474 original size:42 final size:41
Alignment explanation
Indices: 53941366--53941477 Score: 102
Period size: 44 Copynumber: 2.6 Consensus size: 41
53941356 TTTCGATATG
* *
53941366 TGATTTTGTGTAAGAGCAC-GTCTAGGACGTTGGCATCAATT
1 TGATTTTGTGTAAGAGC-CTGTCTGGGACATTGGCATCAATT
*** *
53941407 TGAGAATTACATGTAAGA-CCATGTCTGGGACATTGGCATCGTATT
1 T--G-ATTTTGTGTAAGAGCC-TGTCTGGGACATTGGCATC-AATT
53941452 TGATTTTGTGTAAGAGCCTGTCTGGG
1 TGATTTTGTGTAAGAGCCTGTCTGGG
53941478 GCAGTGTGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
41 1 0.02
42 19 0.35
43 5 0.09
44 26 0.47
45 4 0.07
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (41 bp):
TGATTTTGTGTAAGAGCCTGTCTGGGACATTGGCATCAATT
Found at i:53941700 original size:10 final size:10
Alignment explanation
Indices: 53941685--53941711 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
53941675 TACTCCTTCA
53941685 AGCTCAAATC
1 AGCTCAAATC
53941695 AGCTCAAATC
1 AGCTCAAATC
53941705 AGCTCAA
1 AGCTCAA
53941712 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:53952778 original size:16 final size:16
Alignment explanation
Indices: 53952757--53952791 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53952747 TGTACTCTTA
53952757 TAACATATAATCCATG
1 TAACATATAATCCATG
* *
53952773 TAACATGTAATTCATG
1 TAACATATAATCCATG
53952789 TAA
1 TAA
53952792 AGTATATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (16 bp):
TAACATATAATCCATG
Found at i:53953025 original size:22 final size:23
Alignment explanation
Indices: 53952969--53953027 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
53952959 TCTGAGCTGA
*
53952969 TAAATGGTAAGCTCTGTAGAGCG
1 TAAATGGTAAGCTCTGAAGAGCG
* *
53952992 AAAATGGTAAGCTTTGAAGAGC-
1 TAAATGGTAAGCTCTGAAGAGCG
*
53953014 TAAACGGTAAGCTC
1 TAAATGGTAAGCTC
53953028 ATAAAAGCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.24
Consensus pattern (23 bp):
TAAATGGTAAGCTCTGAAGAGCG
Found at i:53954679 original size:13 final size:13
Alignment explanation
Indices: 53954661--53954695 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
53954651 ATTATATGAA
*
53954661 TAATTATTTTATT
1 TAATTATGTTATT
53954674 TAATTATGTTATT
1 TAATTATGTTATT
53954687 TAATTATGT
1 TAATTATGT
53954696 AGGTTAGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (13 bp):
TAATTATGTTATT
Found at i:53956250 original size:25 final size:26
Alignment explanation
Indices: 53956217--53956266 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
53956207 TTTACCCACA
* *
53956217 AGGGCAAAATAGTCATTTTACTCTTT
1 AGGGAAAAATAATCATTTTACTCTTT
53956243 AGGGAAAAATAATCATTTTACTCT
1 AGGGAAAAATAATCATTTTACTCT
53956267 ACAAGGGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (26 bp):
AGGGAAAAATAATCATTTTACTCTTT
Found at i:53956356 original size:26 final size:27
Alignment explanation
Indices: 53956304--53956364 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 27
53956294 TCGAGGGTAG
53956304 TAATTTCATAAATTAGGGGTATTTCGA
1 TAATTTCATAAATTAGGGGTATTTCGA
* *
53956331 TCATTTCATAAATTA-GGGTTTTTCGA
1 TAATTTCATAAATTAGGGGTATTTCGA
53956357 TAATTTCA
1 TAATTTCA
53956365 CAATCCGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (27 bp):
TAATTTCATAAATTAGGGGTATTTCGA
Found at i:53956428 original size:27 final size:27
Alignment explanation
Indices: 53956357--53956428 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
53956347 GGTTTTTCGA
* * * *
53956357 TAATTTCACAATCCGGAGATATTTCAG
1 TAATTTTACAAACCGGGGGTATTTCAG
*
53956384 TAATTTTACAAACTGGGGGTATTTCAG
1 TAATTTTACAAACCGGGGGTATTTCAG
*
53956411 TAATTTTATAAACCGGGG
1 TAATTTTACAAACCGGGG
53956429 TCTTAACGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (27 bp):
TAATTTTACAAACCGGGGGTATTTCAG
Found at i:53959533 original size:14 final size:14
Alignment explanation
Indices: 53959486--53959533 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
53959476 GTACGAATGG
*
53959486 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
53959500 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
53959514 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
53959528 ATTGGT
1 AATGGT
53959534 CGATTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:53962115 original size:322 final size:323
Alignment explanation
Indices: 53961507--53962152 Score: 996
Period size: 322 Copynumber: 2.0 Consensus size: 323
53961497 AAACTTTCAC
* *
53961507 CAAATAATTCTATCATGCTGTAAACCTTAATAAAATAATAAAATAAATATTTTGACTTCAGATTT
1 CAAATAATTATATCATACTGTAAACCTTAATAAAATAATAAAATAAATATTTTGACTTCAGATTT
* * * ** * *
53961572 GTGGTCCCAAAACTAATATTTTGATTTGACCTAAAAACGGGCTATTATAACTCTCCCCTCTTTAG
66 GGGGTCCCAAAACCAATATTTCGATTAAACCTAAAAACGGACTATTACAACTCTCCCCTCTTTAG
* *
53961637 GGATTTTCGTCCTCGAAAATCTTACAGGTAAAAATGTTAGGGTACTGTTTTCACATAGCTTCCTC
131 GGATTTTCGTCCTCGAAAATCTTACAGGTAAAAAGGTTAGGGTACTATTTTCACATAGCTTCCTC
* * * *
53961702 AGATTCCCATGTAGCTTCCTCTATCCTGTGTTTATGCCAAAGAATCTTCACAAGTGCTATACGTT
196 AGATTCCCACGTAGCATCCTCTATCCTGTGTTTATGCCAAAGAACCTTCACAAGCGCTATACGTT
*
53961767 TATTTCTCAATTCTTTGATTTCTCGAGCCAGATTTCTAATCGGTTCTTCATTATACGACAAAT
261 TATTTCTCAATTCTTTGATTTCTCGAGCCAGAATTCTAATCGGTTCTTCATTATACGACAAAT
53961830 CAAACTAATTATATCATACTGTAAACCTTAATAAAATAATAAAATAAATATTTTGACTTCAGATT
1 CAAA-TAATTATATCATACTGTAAACCTTAATAAAATAATAAAATAAATATTTTGACTTCAGATT
*
53961895 TGGGGTCCCGAAACCAATATTTCGATTAAACCTAAAAACGGACTATTACAACTCTCCCC-CTTTA
65 TGGGGTCCCAAAACCAATATTTCGATTAAACCTAAAAACGGACTATTACAACTCTCCCCTCTTTA
* * **
53961959 GGGATTTTTGTCCTTGAAAATCTTACAGGT-AAAAGGTTAGGGTACTATTTTCGTATAGCTTCCT
130 GGGATTTTCGTCCTCGAAAATCTTACAGGTAAAAAGGTTAGGGTACTATTTTCACATAGCTTCCT
53962023 C-GAGTTCCCACGTAGCATCCTCTATCCCT-TGTTTATGCCAAAGAACCGTT-ACAAGCGCTATA
195 CAGA-TTCCCACGTAGCATCCTCTAT-CCTGTGTTTATGCCAAAGAACC-TTCACAAGCGCTATA
* * * *
53962085 TGTTTATTTCTCAATTCTTTGATTTCTCGAGCCAGAATTCTGATCTGTTCTTCGTTATACGACAA
257 CGTTTATTTCTCAATTCTTTGATTTCTCGAGCCAGAATTCTAATCGGTTCTTCATTATACGACAA
53962150 AT
322 AT
53962152 C
1 C
53962153 GGATTGTATC
Statistics
Matches: 294, Mismatches: 25, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
321 2 0.01
322 141 0.48
323 42 0.14
324 109 0.37
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (323 bp):
CAAATAATTATATCATACTGTAAACCTTAATAAAATAATAAAATAAATATTTTGACTTCAGATTT
GGGGTCCCAAAACCAATATTTCGATTAAACCTAAAAACGGACTATTACAACTCTCCCCTCTTTAG
GGATTTTCGTCCTCGAAAATCTTACAGGTAAAAAGGTTAGGGTACTATTTTCACATAGCTTCCTC
AGATTCCCACGTAGCATCCTCTATCCTGTGTTTATGCCAAAGAACCTTCACAAGCGCTATACGTT
TATTTCTCAATTCTTTGATTTCTCGAGCCAGAATTCTAATCGGTTCTTCATTATACGACAAAT
Found at i:53966329 original size:30 final size:30
Alignment explanation
Indices: 53966244--53966340 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
53966234 TAAACTAAAA
* *
53966244 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * * *
53966274 TGAGTTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53966304 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53966333 ATGAGCTA
1 -TGAGCTA
53966341 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:53967007 original size:689 final size:689
Alignment explanation
Indices: 53965690--53967061 Score: 2690
Period size: 689 Copynumber: 2.0 Consensus size: 689
53965680 GGTCAATTCA
53965690 AAGTGTGAACATGTTCAAGGAGCTCTATGGTCAACATAGAATTAGTTAGCAGCTACTTCTTGGCC
1 AAGTGTGAACATGTTCAAGGAGCTCTATGGTCAACATAGAATTAGTTAGCAGCTACTTCTTGGCC
*
53965755 GAATAAGTGCCTTGGAAAGTTAGGAGACAGCCACCATACATGCACTTAAGCCATTCATGCATTCT
66 AAATAAGTGCCTTGGAAAGTTAGGAGACAGCCACCATACATGCACTTAAGCCATTCATGCATTCT
53965820 ATCATCCCATGCATTTGATCCATTCATGGACTAGCCTTTAATGTCCATACATGCATTCGACACAT
131 ATCATCCCATGCATTTGATCCATTCATGGACTAGCCTTTAATGTCCATACATGCATTCGACACAT
53965885 GCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACCAGCATTTAATACTTCTTCATTCA
196 GCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACCAGCATTTAATACTTCTTCATTCA
*
53965950 TGAGTGTGGAATTCCCAAAAGAGATGTTTCTTCATCCATACATTGTACCGTCCAAAGGAATGTAC
261 TGAGTGTGGAATTCCCAAAAAAGATGTTTCTTCATCCATACATTGTACCGTCCAAAGGAATGTAC
53966015 CTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCATAAATTCGGCATGATGTGAAC
326 CTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCATAAATTCGGCATGATGTGAAC
*
53966080 ACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCAATTTATATAATGACAATGACATA
391 ACATTAATATCATGCATTAATTCGGCTATGTGAACATAATCAATTTATATAATGACAATGACATA
*
53966145 TTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAAAATGTGTAAATTTTTATTTA
456 TTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAAAATGTGCAAATTTTTATTTA
53966210 ATCTATTAAAGACAAAACCGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
521 ATCTATTAAAGACAAAACCGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
*
53966275 GAGTTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTGAATATGAGCT
586 GAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTGAATATGAGCT
*
53966340 AGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGCCGAAT
651 AGCAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGCCGAAT
53966379 AAGTGTGAACATGTTCAAGGAGCTCTATGGTCAACATAGAATTAGTTAGCAGCTACTTCTTGGCC
1 AAGTGTGAACATGTTCAAGGAGCTCTATGGTCAACATAGAATTAGTTAGCAGCTACTTCTTGGCC
53966444 AAATAAGTGCCTTGGAAAGTTAGGAGACAGCCACCATACATGCACTTAAGCCATTCATGCATTCT
66 AAATAAGTGCCTTGGAAAGTTAGGAGACAGCCACCATACATGCACTTAAGCCATTCATGCATTCT
53966509 ATCATCCCATGCATTTGATCCATTCATGGACTAGCCTTTAATGTCCATACATGCATTCGACACAT
131 ATCATCCCATGCATTTGATCCATTCATGGACTAGCCTTTAATGTCCATACATGCATTCGACACAT
53966574 GCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACCAGCATTTAATACTTCTTCATTCA
196 GCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACCAGCATTTAATACTTCTTCATTCA
53966639 TGAGTGTGGAATTCCCAAAAAAGATGTTTCTTCATCCATACATTGTACCGTCCAAAGGAATGTAC
261 TGAGTGTGGAATTCCCAAAAAAGATGTTTCTTCATCCATACATTGTACCGTCCAAAGGAATGTAC
53966704 CTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCATAAATTCGGCATGATGTGAAC
326 CTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCATAAATTCGGCATGATGTGAAC
53966769 ACATTAATATCATGCATTAATTCGGCTATGTGAACATAATCAATTTATATAATGACAATGACATA
391 ACATTAATATCATGCATTAATTCGGCTATGTGAACATAATCAATTTATATAATGACAATGACATA
53966834 TTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAAAATGTGCAAATTTTTATTTA
456 TTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAAAATGTGCAAATTTTTATTTA
53966899 ATCTATTAAAGACAAAACCGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
521 ATCTATTAAAGACAAAACCGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
53966964 GAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTGAATATGAGCT
586 GAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTGAATATGAGCT
53967029 AGCAGTGAGCTCGGTTTAGCTCAGGCAAGTTGG
651 AGCAGTGAGCTCGGTTTAGCTCAGGCAAGTTGG
53967062 ATTGAGCTCG
Statistics
Matches: 677, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
689 677 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (689 bp):
AAGTGTGAACATGTTCAAGGAGCTCTATGGTCAACATAGAATTAGTTAGCAGCTACTTCTTGGCC
AAATAAGTGCCTTGGAAAGTTAGGAGACAGCCACCATACATGCACTTAAGCCATTCATGCATTCT
ATCATCCCATGCATTTGATCCATTCATGGACTAGCCTTTAATGTCCATACATGCATTCGACACAT
GCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACCAGCATTTAATACTTCTTCATTCA
TGAGTGTGGAATTCCCAAAAAAGATGTTTCTTCATCCATACATTGTACCGTCCAAAGGAATGTAC
CTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCATAAATTCGGCATGATGTGAAC
ACATTAATATCATGCATTAATTCGGCTATGTGAACATAATCAATTTATATAATGACAATGACATA
TTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAAAATGTGCAAATTTTTATTTA
ATCTATTAAAGACAAAACCGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
GAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTGAATATGAGCT
AGCAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGCCGAAT
Found at i:53967018 original size:30 final size:30
Alignment explanation
Indices: 53966933--53967029 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
53966923 TAAACTAAAA
* *
53966933 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
53966963 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53966993 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
53967022 ATGAGCTA
1 -TGAGCTA
53967030 GCAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:53967262 original size:9 final size:10
Alignment explanation
Indices: 53967255--53967326 Score: 58
Period size: 11 Copynumber: 6.9 Consensus size: 10
53967245 ACGAGAAAAC
53967255 AAAGAAAAGA
1 AAAGAAAAGA
53967265 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
53967277 AAAGAAGA-A
1 AAAGAAAAGA
53967286 AAAGAAAATGA
1 AAAGAAAA-GA
53967297 AATA-AAAAGA
1 AA-AGAAAAGA
* *
53967307 AAAGAGAGGCA
1 AAAGAAAAG-A
53967318 AAAGAAAAG
1 AAAGAAAAG
53967327 TAAGAGAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
9 9 0.18
10 11 0.22
11 23 0.47
12 6 0.12
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:53967279 original size:6 final size:5
Alignment explanation
Indices: 53967255--53967326 Score: 58
Period size: 5 Copynumber: 13.8 Consensus size: 5
53967245 ACGAGAAAAC
*
53967255 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
* *
53967302 AAAGA AAAGA GAGGCA AAAGA AAAG
1 AAAGA AAAGA AAAG-A AAAGA AAAG
53967327 TAAGAGAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.07
5 32 0.59
6 17 0.31
7 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:53967286 original size:15 final size:14
Alignment explanation
Indices: 53967255--53967331 Score: 64
Period size: 16 Copynumber: 4.9 Consensus size: 14
53967245 ACGAGAAAAC
53967255 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
53967271 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
53967286 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
*
53967302 AAAGAAAAGAGAGGCA
1 AAAGAAAAGA-A-GAA
53967318 AAAGAAAAGTAAGA
1 AAAGAAAAG-AAGA
53967332 GAGAAAATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.10
15 13 0.25
16 27 0.53
17 6 0.12
ACGTcount: A:0.73, C:0.03, G:0.21, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:53967291 original size:31 final size:31
Alignment explanation
Indices: 53967255--53967331 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
53967245 ACGAGAAAAC
53967255 AAAGAAAAGAAAAGAAAAAGCAAAAGA-A-GAA
1 AAAGAAAAG-AAAGAAAAAG-AAAAGAGAGGAA
* *
53967286 AAAGAAAATGAAATAAAAAGAAAAGAGAGGCA
1 AAAGAAAA-GAAAGAAAAAGAAAAGAGAGGAA
*
53967318 AAAGAAAAGTAAGA
1 AAAGAAAAGAAAGA
53967332 GAGAAAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 6 0.15
31 22 0.56
32 11 0.28
ACGTcount: A:0.73, C:0.03, G:0.21, T:0.04
Consensus pattern (31 bp):
AAAGAAAAGAAAGAAAAAGAAAAGAGAGGAA
Found at i:53970555 original size:30 final size:31
Alignment explanation
Indices: 53970521--53970617 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
53970511 AGCTCACTCC
*
53970521 TAGCTC-ACTTTCAACTTACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * * *
53970551 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * *
53970581 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
53970611 TAGCTCA
1 TAGCTCA
53970618 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 48 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTTACGAGCTAAACCT
Found at i:53972915 original size:93 final size:93
Alignment explanation
Indices: 53972803--53972974 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
53972793 CGCCCATAAG
* *
53972803 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53972868 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
53972896 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53972961 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
53972975 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:53972971 original size:46 final size:46
Alignment explanation
Indices: 53972796--53972971 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
53972786 TGTAACCCGC
* * *
53972796 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
53972842 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
53972892 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
53972935 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
53972972 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:53975060 original size:178 final size:178
Alignment explanation
Indices: 53974758--53975115 Score: 689
Period size: 178 Copynumber: 2.0 Consensus size: 178
53974748 CATAAGATTT
*
53974758 CTGTCTATCTGAAGCAGCTTTCAAACAATCTTGAATCACTTTCACCTTTTCTTCGGTTTCTTTTA
1 CTGTCTATCTGAAGCAGCTTTCAAACAATCTCGAATCACTTTCACCTTTTCTTCGGTTTCTTTTA
*
53974823 TTAAATCAACTCCATAAATCTGATTTTCCTTGAGTTCAGTCCAATACAATGGTGTCCGACATTTA
66 TTAAATCAACTCCATAAATCTGATTTTCCTTGAGTTCAGTCCAATACAATGGCGTCCGACATTTA
53974888 CGACCATATAATGCTTCATAAGGTGCCATCTTCAAACTCGTCTGATAA
131 CGACCATATAATGCTTCATAAGGTGCCATCTTCAAACTCGTCTGATAA
53974936 CTGTCTATCTGAAGCAGCTTTCAAACAATCTCGAATCACTTTCACCTTTTCTTCGGTTTCTTTTA
1 CTGTCTATCTGAAGCAGCTTTCAAACAATCTCGAATCACTTTCACCTTTTCTTCGGTTTCTTTTA
*
53975001 TTAAATCAACTCCATAAATTTGATTTTCCTTGAGTTCAGTCCAATACAATGGCGTCCGACATTTA
66 TTAAATCAACTCCATAAATCTGATTTTCCTTGAGTTCAGTCCAATACAATGGCGTCCGACATTTA
53975066 CGACCATATAATGCTTCATAAGGTGCCATCTTCAAACTCGTCTGATAA
131 CGACCATATAATGCTTCATAAGGTGCCATCTTCAAACTCGTCTGATAA
53975114 CT
1 CT
53975116 ATTATTATAA
Statistics
Matches: 177, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
178 177 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (178 bp):
CTGTCTATCTGAAGCAGCTTTCAAACAATCTCGAATCACTTTCACCTTTTCTTCGGTTTCTTTTA
TTAAATCAACTCCATAAATCTGATTTTCCTTGAGTTCAGTCCAATACAATGGCGTCCGACATTTA
CGACCATATAATGCTTCATAAGGTGCCATCTTCAAACTCGTCTGATAA
Found at i:53980583 original size:45 final size:46
Alignment explanation
Indices: 53980519--53980693 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
53980509 TGTAACCCGC
*
53980519 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* *
53980564 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* *
53980614 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
53980657 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
53980694 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 36 0.32
46 29 0.26
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:53980684 original size:93 final size:92
Alignment explanation
Indices: 53980526--53980696 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 92
53980516 CGCCCATAAG
*
53980526 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53980591 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
53980618 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53980683 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
53980697 TCAACCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 28 0.37
93 48 0.63
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Found at i:53983923 original size:13 final size:13
Alignment explanation
Indices: 53983894--53983932 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
53983884 TTTTATTTTG
53983894 TTTTCTTTTTCTTC
1 TTTTC-TTTTCTTC
53983908 TTTTGCTTTT-TTC
1 TTTT-CTTTTCTTC
53983921 TTTTCTTTTCTT
1 TTTTCTTTTCTT
53983933 TGTTTTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.22
13 9 0.39
14 8 0.35
15 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTCTTC
Found at i:53984865 original size:11 final size:12
Alignment explanation
Indices: 53984847--53984904 Score: 82
Period size: 12 Copynumber: 4.8 Consensus size: 12
53984837 TGCATAAATC
53984847 ATTTTTTTTTGA
1 ATTTTTTTTTGA
53984859 ATTTTTTTTTGA
1 ATTTTTTTTTGA
53984871 ATTTTTTTTTCGA
1 ATTTTTTTTT-GA
*
53984884 A-TTTTTTTCGAA
1 ATTTTTTTTTG-A
53984896 ATTTTTTTT
1 ATTTTTTTT
53984905 CGGTTTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
11 1 0.02
12 31 0.74
13 10 0.24
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.72
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:53984866 original size:13 final size:13
Alignment explanation
Indices: 53984848--53984891 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
53984838 GCATAAATCA
53984848 TTTTTTTTTGAA-
1 TTTTTTTTTGAAT
53984860 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
53984873 TTTTTTTTCGAAT
1 TTTTTTTTTGAAT
53984886 TTTTTT
1 TTTTTT
53984892 CGAAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 12 0.40
13 18 0.60
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:53984901 original size:13 final size:12
Alignment explanation
Indices: 53984847--53984917 Score: 81
Period size: 12 Copynumber: 5.8 Consensus size: 12
53984837 TGCATAAATC
*
53984847 ATTTTTTTTTGA
1 ATTTTTTTTCGA
*
53984859 ATTTTTTTTTGA
1 ATTTTTTTTCGA
53984871 ATTTTTTTTTCGA
1 A-TTTTTTTTCGA
53984884 A-TTTTTTTCGAA
1 ATTTTTTTTCG-A
*
53984896 ATTTTTTTTCGG
1 ATTTTTTTTCGA
*
53984908 TTTTTTTTTC
1 ATTTTTTTTC
53984918 AAACTTGTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
11 9 0.17
12 24 0.45
13 20 0.38
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (12 bp):
ATTTTTTTTCGA
Found at i:53984911 original size:11 final size:11
Alignment explanation
Indices: 53984847--53984915 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 11
53984837 TGCATAAATC
*
53984847 ATTTTTTTTTG
1 ATTTTTTTTCG
*
53984858 AATTTTTTTTTG
1 -ATTTTTTTTCG
53984870 AATTTTTTTTTCG
1 -A-TTTTTTTTCG
*
53984883 AATTTTTTTCG
1 ATTTTTTTTCG
53984894 AAATTTTTTTTCG
1 --ATTTTTTTTCG
*
53984907 GTTTTTTTT
1 ATTTTTTTT
53984916 TCAAACTTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
11 17 0.34
12 14 0.28
13 19 0.38
ACGTcount: A:0.14, C:0.04, G:0.09, T:0.72
Consensus pattern (11 bp):
ATTTTTTTTCG
Found at i:53988085 original size:30 final size:30
Alignment explanation
Indices: 53987999--53988096 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
53987989 TTAAACTAAA
* *
53987999 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
53988029 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
53988059 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
53988089 ATGAGCTA
1 ATGAGCTA
53988097 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:53993591 original size:39 final size:39
Alignment explanation
Indices: 53993518--53993643 Score: 153
Period size: 39 Copynumber: 3.2 Consensus size: 39
53993508 GACTTAATGT
* * * *
53993518 CTAGCAAGCCTCGTGCCGATGATAAATTTAGGTTTATAC
1 CTAGCAGGCCTCGTACCGGTGATAAATTCAGGTTTATAC
* *
53993557 CTAGTAGGCCTTGTACCGGTGATAAATTCAGGTTTATAC
1 CTAGCAGGCCTCGTACCGGTGATAAATTCAGGTTTATAC
* * * *
53993596 CTAGCAGGCCTCGTGCCGGTGTTAAGTTCGGGTTTATAC
1 CTAGCAGGCCTCGTACCGGTGATAAATTCAGGTTTATAC
*
53993635 TTAGCAGGC
1 CTAGCAGGC
53993644 AAATTACTGG
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (39 bp):
CTAGCAGGCCTCGTACCGGTGATAAATTCAGGTTTATAC
Found at i:53997381 original size:5 final size:5
Alignment explanation
Indices: 53997371--53997427 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
53997361 CTCTTGCCGC
*
53997371 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
53997418 TCTTT TCTTT
1 TCTTT TCTTT
53997428 GTTTTCTCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:53997411 original size:15 final size:14
Alignment explanation
Indices: 53997371--53997427 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
53997361 CTCTTGCCGC
*
53997371 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
53997386 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
53997401 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
53997418 TCTTTTCTTT
1 TCTTTTCTTT
53997428 GTTTTCTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:53997428 original size:21 final size:21
Alignment explanation
Indices: 53997371--53997432 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
53997361 CTCTTGCCGC
* *
53997371 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
53997392 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
53997413 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
53997433 CTCATTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 7 0.21
21 22 0.65
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:54002630 original size:13 final size:13
Alignment explanation
Indices: 54002612--54002640 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54002602 CGGCTAACCT
54002612 ACATAATTAAATA
1 ACATAATTAAATA
54002625 ACATAATTAAATA
1 ACATAATTAAATA
54002638 ACA
1 ACA
54002641 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:54002897 original size:10 final size:10
Alignment explanation
Indices: 54002864--54002912 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
54002854 AAAAAGGAAT
*
54002864 GAGCTGAAAC
1 GAGCTCAAAC
54002874 GAGCT-AAATTC
1 GAGCTCAAA--C
54002885 GAGCTCAAAC
1 GAGCTCAAAC
*
54002895 GAGCTAAAAC
1 GAGCTCAAAC
54002905 GAGCTCAA
1 GAGCTCAA
54002913 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:54002919 original size:20 final size:21
Alignment explanation
Indices: 54002864--54002912 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
54002854 AAAAAGGAAT
* *
54002864 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
54002885 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
54002905 GAGCTCAA
1 GAGCTCAA
54002913 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Found at i:54004667 original size:30 final size:30
Alignment explanation
Indices: 54004633--54004729 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
54004623 TAAACTAAAA
54004633 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
54004663 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
54004693 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
54004723 TGAGCTA
1 TGAGCTA
54004730 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:54008966 original size:13 final size:13
Alignment explanation
Indices: 54008948--54008976 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54008938 CGGCTAACCT
54008948 ACATAATTAAATA
1 ACATAATTAAATA
54008961 ACATAATTAAATA
1 ACATAATTAAATA
54008974 ACA
1 ACA
54008977 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:54011621 original size:10 final size:10
Alignment explanation
Indices: 54011608--54011634 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54011598 TTTTTTCAGT
54011608 TTTTTTTGAA
1 TTTTTTTGAA
54011618 TTTTTTTGAA
1 TTTTTTTGAA
54011628 TTTTTTT
1 TTTTTTT
54011635 AACTTGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:54017903 original size:19 final size:19
Alignment explanation
Indices: 54017879--54017918 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
54017869 AGCTCCCATG
54017879 TAGCTC-AACACCAGCTCAT
1 TAGCTCGAA-ACCAGCTCAT
*
54017898 TAGCTCGGAACCAGCTCAT
1 TAGCTCGAAACCAGCTCAT
54017917 TA
1 TA
54017919 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGAAACCAGCTCAT
Found at i:54019176 original size:14 final size:14
Alignment explanation
Indices: 54019154--54019201 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
54019144 ACCTAAACCG
* *
54019154 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
54019168 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
54019182 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
54019196 ACCATT
1 ACCATT
54019202 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:54024807 original size:14 final size:14
Alignment explanation
Indices: 54024785--54024832 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
54024775 ACCTAAACCG
* *
54024785 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
54024799 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
54024813 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
54024827 ACCATT
1 ACCATT
54024833 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:54027166 original size:30 final size:30
Alignment explanation
Indices: 54027095--54027177 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
54027085 CTTTTGTTTC
* *
54027095 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
54027126 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
54027155 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
54027178 TCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:54027177 original size:18 final size:18
Alignment explanation
Indices: 54027128--54027183 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
54027118 CACTCTCAAA
* *
54027128 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
54027145 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
54027163 TTTCATTTTCTTTTTTCTT
1 TTTCATTTTC-ATTTTCTT
54027182 TT
1 TT
54027184 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 17 0.57
19 9 0.30
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:54027184 original size:12 final size:12
Alignment explanation
Indices: 54027153--54027177 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54027143 TTTTTCAATC
54027153 TCATTTTCTTTT
1 TCATTTTCTTTT
54027165 TCATTTTCTTTT
1 TCATTTTCTTTT
54027177 T
1 T
54027178 TCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:54028243 original size:19 final size:18
Alignment explanation
Indices: 54028216--54028255 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
54028206 CATTAAACAC
54028216 TTTTTTTTTC-AGATTTTT
1 TTTTTTTTTCGA-ATTTTT
54028234 TTTTTCTTTTCGAATTTTT
1 TTTTT-TTTTCGAATTTTT
54028253 TTT
1 TTT
54028256 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 14 0.70
20 1 0.05
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTTTTTTCGAATTTTT
Found at i:54028251 original size:18 final size:18
Alignment explanation
Indices: 54028216--54028255 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
54028206 CATTAAACAC
*
54028216 TTTTTTTTTCAGATTTTT
1 TTTTTTTTTCAGAATTTT
54028234 TTTTTCTTTTC-GAATTTT
1 TTTTT-TTTTCAGAATTTT
54028252 TTTT
1 TTTT
54028256 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTTTTTTCAGAATTTT
Found at i:54028255 original size:12 final size:12
Alignment explanation
Indices: 54028235--54028279 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
54028225 CAGATTTTTT
54028235 TTTTCTTTTCGAA
1 TTTT-TTTTCGAA
54028248 TTTTTTTT-GAA
1 TTTTTTTTCGAA
*
54028259 TTTTTTTTTCAAA
1 -TTTTTTTTCGAA
54028272 TTTTTTTT
1 TTTTTTTT
54028280 GACTTGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 3 0.10
12 20 0.69
13 6 0.21
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:54028262 original size:24 final size:24
Alignment explanation
Indices: 54028235--54028281 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
54028225 CAGATTTTTT
*
54028235 TTTTCTTTTCGAATTTTTTTTGAA
1 TTTTCTTTTCAAATTTTTTTTGAA
*
54028259 TTTTTTTTTCAAATTTTTTTTGA
1 TTTTCTTTTCAAATTTTTTTTGA
54028282 CTTGTATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.70
Consensus pattern (24 bp):
TTTTCTTTTCAAATTTTTTTTGAA
Found at i:54028296 original size:43 final size:43
Alignment explanation
Indices: 54028216--54028298 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
54028206 CATTAAACAC
* ** * * *
54028216 TTTTTTTTTCAGATTTTTTTTTTCTTTTCGAATTTTTTTTGAA
1 TTTTTTTTTCAAATTTTTTTTGACTTGTAGAACTTTTTTTGAA
*
54028259 TTTTTTTTTCAAATTTTTTTTGACTTGTATAACTTTTTTT
1 TTTTTTTTTCAAATTTTTTTTGACTTGTAGAACTTTTTTT
54028299 TGTACTATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.16, C:0.07, G:0.06, T:0.71
Consensus pattern (43 bp):
TTTTTTTTTCAAATTTTTTTTGACTTGTAGAACTTTTTTTGAA
Found at i:54040936 original size:18 final size:20
Alignment explanation
Indices: 54040915--54040952 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54040905 TTCACTTTCG
54040915 TTTT-TTTATTT-TTCTCTC
1 TTTTCTTTATTTCTTCTCTC
*
54040933 TTTTCTTTGTTTCTTCTCTC
1 TTTTCTTTATTTCTTCTCTC
54040953 GATTTCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTCTTTATTTCTTCTCTC
Found at i:54041996 original size:17 final size:15
Alignment explanation
Indices: 54041962--54041992 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54041952 TTCTTTTTCT
54041962 CTTCGATTTTTTTAA
1 CTTCGATTTTTTTAA
54041977 CTTCGATTTTTTTAA
1 CTTCGATTTTTTTAA
54041992 C
1 C
54041993 ACTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.58
Consensus pattern (15 bp):
CTTCGATTTTTTTAA
Found at i:54042088 original size:9 final size:9
Alignment explanation
Indices: 54042074--54042100 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
54042064 TTTTGTTACA
54042074 AAAAATAAT
1 AAAAATAAT
54042083 AAAAATAAT
1 AAAAATAAT
54042092 AAAAATAAT
1 AAAAATAAT
54042101 TTTTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAATAAT
Found at i:54047299 original size:93 final size:93
Alignment explanation
Indices: 54047187--54047358 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
54047177 CGCCCATAAG
* *
54047187 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
54047252 ATGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
54047280 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54047345 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
54047359 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54047355 original size:46 final size:46
Alignment explanation
Indices: 54047180--54047355 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
54047170 TGTAACCCGC
* * *
54047180 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
54047226 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
54047276 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54047319 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
54047356 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.57
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54048912 original size:43 final size:43
Alignment explanation
Indices: 54048864--54048975 Score: 208
Period size: 43 Copynumber: 2.6 Consensus size: 43
54048854 GCTGGTATTA
54048864 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCA-GTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTG-CAGGTGATGTG
54048907 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCAGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCAGGTGATGTG
54048950 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
54048976 GTAATGCCGG
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
42 2 0.03
43 66 0.97
ACGTcount: A:0.12, C:0.26, G:0.33, T:0.29
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCAGGTGATGTG
Found at i:54049371 original size:45 final size:45
Alignment explanation
Indices: 54049307--54049427 Score: 208
Period size: 45 Copynumber: 2.7 Consensus size: 45
54049297 TTGATTTGAT
54049307 TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
1 TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
54049352 TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
1 TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
* *
54049397 TATTCGGG-CTTTCGAGCCTAGCAGGCTATAA
1 TATTCGGGCCTTT-GAGCTTAGCAGACTATAA
54049428 AGCCGGTGAA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
44 4 0.05
45 69 0.95
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCTTAGCAGACTATAATGTCGGTAAGATAC
Found at i:54052505 original size:13 final size:13
Alignment explanation
Indices: 54052487--54052511 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54052477 TGGTCATCAT
54052487 GGTGTGAACACAA
1 GGTGTGAACACAA
54052500 GGTGTGAACACA
1 GGTGTGAACACA
54052512 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:54053074 original size:30 final size:30
Alignment explanation
Indices: 54052989--54053085 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
54052979 TAAACTAAAA
* * *
54052989 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
54053019 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
54053049 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
54053078 ATGAGCTA
1 -TGAGCTA
54053086 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:54055046 original size:28 final size:27
Alignment explanation
Indices: 54055009--54055130 Score: 145
Period size: 28 Copynumber: 4.3 Consensus size: 27
54054999 AAGTCTACAT
*
54055009 ACATGCATATGGCCCACTAGGCCCAATC
1 ACATTCATATGGCCCA-TAGGCCCAATC
* *
54055037 TCATTCATATAGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCA-TAGGCCC-AATC
* *
54055066 ACATTCATATGGCCCATCGACCCCAATC
1 ACATTCATATGGCCCATAG-GCCCAATC
*
54055094 ACATTCATATGGCCCGTCAGGCCCAATC
1 ACATTCATATGGCCCAT-AGGCCCAATC
54055122 ACATTCATA
1 ACATTCATA
54055131 GTCATGCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
28 58 0.73
29 22 0.28
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (27 bp):
ACATTCATATGGCCCATAGGCCCAATC
Found at i:54055075 original size:57 final size:56
Alignment explanation
Indices: 54055009--54055130 Score: 156
Period size: 57 Copynumber: 2.2 Consensus size: 56
54054999 AAGTCTACAT
* * * *
54055009 ACATGCATATGGCCCACTAG-GCCCAATCTCATTCATATAGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCA-TAGACCCCAATCACATTCATATAGCCCATCAGGCCC-AATC
* * *
54055066 ACATTCATATGGCCCATCGACCCCAATCACATTCATATGGCCCGTCAGGCCCAATC
1 ACATTCATATGGCCCATAGACCCCAATCACATTCATATAGCCCATCAGGCCCAATC
54055122 ACATTCATA
1 ACATTCATA
54055131 GTCATGCAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
56 15 0.26
57 42 0.74
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (56 bp):
ACATTCATATGGCCCATAGACCCCAATCACATTCATATAGCCCATCAGGCCCAATC
Found at i:54057255 original size:26 final size:26
Alignment explanation
Indices: 54057226--54057333 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
54057216 TGGTACAAAT
54057226 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
54057252 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54057278 TGATAATGGGTTAGGTAAAAGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54057304 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54057330 TGAT
1 TGAT
54057334 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54066625 original size:12 final size:14
Alignment explanation
Indices: 54066608--54066643 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
54066598 CATAAATCAC
54066608 TTTTTTTTTC-G-A
1 TTTTTTTTTCGGAA
54066620 TTTTTTTTTCGGAA
1 TTTTTTTTTCGGAA
54066634 TTTTTTTTTC
1 TTTTTTTTTC
54066644 AAACTTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 1 0.05
14 11 0.50
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTCGGAA
Found at i:54068231 original size:10 final size:10
Alignment explanation
Indices: 54068216--54068242 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54068206 TAAGTTGAAG
54068216 TTGAGCTGAT
1 TTGAGCTGAT
54068226 TTGAGCTGAT
1 TTGAGCTGAT
54068236 TTGAGCT
1 TTGAGCT
54068243 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:54069851 original size:30 final size:30
Alignment explanation
Indices: 54069780--54069862 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
54069770 CTTTTGTTTC
* *
54069780 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
54069811 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
54069840 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
54069863 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:54069862 original size:18 final size:18
Alignment explanation
Indices: 54069813--54069868 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
54069803 CACTCTCAAA
* *
54069813 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
54069830 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
54069848 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
54069867 TT
1 TT
54069869 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:54069869 original size:12 final size:12
Alignment explanation
Indices: 54069838--54069862 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54069828 TTTTTCAATC
54069838 TCATTTTCTTTT
1 TCATTTTCTTTT
54069850 TCATTTTCTTTT
1 TCATTTTCTTTT
54069862 T
1 T
54069863 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:54069934 original size:5 final size:5
Alignment explanation
Indices: 54069924--54069980 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54069914 TACTTGCCTC
*
54069924 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
54069971 TCTTT TCTTT
1 TCTTT TCTTT
54069981 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:54069964 original size:15 final size:14
Alignment explanation
Indices: 54069924--54069980 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
54069914 TACTTGCCTC
*
54069924 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
54069939 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
54069954 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
54069971 TCTTTTCTTT
1 TCTTTTCTTT
54069981 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Done.