Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 186 of 205
Found at i:55214917 original size:42 final size:42
Alignment explanation
Indices: 55214865--55215007 Score: 171
Period size: 42 Copynumber: 3.4 Consensus size: 42
55214855 AGTTACATGT
* * *
55214865 CCTGGACACACACCCATGCCTTTGCCCGTGTGGCTCACACGG
1 CCTGGACACACACCCATGACTTTGCTCGTGTAGCTCACACGG
* * * *
55214907 CCTGGGCACACACCCATGTCGTTGCTCGTGTATCTCACACGG
1 CCTGGACACACACCCATGACTTTGCTCGTGTAGCTCACACGG
* * *
55214949 CCTGGACACACGCTCATGACTTTGCTCGTGTAGCTCACACAG
1 CCTGGACACACACCCATGACTTTGCTCGTGTAGCTCACACGG
*
55214991 CCTAGG-CACACGCCCAT
1 CCT-GGACACACACCCAT
55215008 ATCCCTGGGC
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 84 0.98
43 2 0.02
ACGTcount: A:0.19, C:0.38, G:0.22, T:0.21
Consensus pattern (42 bp):
CCTGGACACACACCCATGACTTTGCTCGTGTAGCTCACACGG
Found at i:55215021 original size:84 final size:84
Alignment explanation
Indices: 55214865--55215021 Score: 197
Period size: 84 Copynumber: 1.9 Consensus size: 84
55214855 AGTTACATGT
* * * * * **
55214865 CCTGGACACACACCCATGCCTTTGCCCGTGTGGCTCACACGGCCTGGGCACACACCCATGTCGTT
1 CCTGGACACACACCCATGACTTTGCCCGTGTAGCTCACACAGCCTAGGCACACACCCATATCCCT
*
55214930 GCTCGTGTATCTCACACGG
66 GCGCGTGTATCTCACACGG
* * * *
55214949 CCTGGACACACGCTCATGACTTTGCTCGTGTAGCTCACACAGCCTAGGCACACGCCCATATCCCT
1 CCTGGACACACACCCATGACTTTGCCCGTGTAGCTCACACAGCCTAGGCACACACCCATATCCCT
*
55215014 GGGCGTGT
66 GCGCGTGT
55215022 GGTTCTAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
84 60 1.00
ACGTcount: A:0.18, C:0.37, G:0.24, T:0.22
Consensus pattern (84 bp):
CCTGGACACACACCCATGACTTTGCCCGTGTAGCTCACACAGCCTAGGCACACACCCATATCCCT
GCGCGTGTATCTCACACGG
Found at i:55220552 original size:47 final size:47
Alignment explanation
Indices: 55220498--55220611 Score: 174
Period size: 47 Copynumber: 2.4 Consensus size: 47
55220488 AGTCGCAAAT
* *
55220498 AAACTGCCAGAATAGATATGGGTGGTCGAGCCACCATAATTGCAGTC
1 AAACTGCCAGAATAGATATGAGTGGTCGAGCCACCATAATTGCAATC
*
55220545 AAGCTGCCAGAATAGATATGAGTGGTCGAGCCACCATAATTGCAATC
1 AAACTGCCAGAATAGATATGAGTGGTCGAGCCACCATAATTGCAATC
* * *
55220592 AAACTACTAGAACAGATATG
1 AAACTGCCAGAATAGATATG
55220612 TGGTTAAACC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (47 bp):
AAACTGCCAGAATAGATATGAGTGGTCGAGCCACCATAATTGCAATC
Found at i:55223413 original size:16 final size:17
Alignment explanation
Indices: 55223392--55223426 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
55223382 TATACTTGAA
55223392 ATATTATAAATAT-ATT
1 ATATTATAAATATAATT
*
55223408 ATATTATTAATATAATT
1 ATATTATAAATATAATT
55223425 AT
1 AT
55223427 GAAGTACGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATAAATATAATT
Found at i:55224160 original size:21 final size:21
Alignment explanation
Indices: 55224075--55224162 Score: 56
Period size: 21 Copynumber: 4.1 Consensus size: 21
55224065 TAGTTAAGTA
*
55224075 ATATTATTTATATTTATAAATAT
1 ATATTA-TTATATTTAAAAAT-T
* *
55224098 ATATTATTATACTT-AACA-T
1 ATATTATTATATTTAAAAATT
* **
55224117 -GATTATCTATACTTTTATCAATT
1 ATATTAT-TATA--TTTAAAAATT
55224140 ATATTATTATATTTAAAAATT
1 ATATTATTATATTTAAAAATT
55224161 AT
1 AT
55224163 CTAAATCTTG
Statistics
Matches: 48, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
18 5 0.10
19 5 0.10
21 14 0.29
22 8 0.17
23 11 0.23
24 5 0.10
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (21 bp):
ATATTATTATATTTAAAAATT
Found at i:55224180 original size:40 final size:42
Alignment explanation
Indices: 55224090--55224181 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 42
55224080 ATTTATATTT
* * *
55224090 ATAAATATATATTATTATACTTAACATGATTATCTATACTTTT
1 ATAAAT-TATATTATTATACTTAACATAATTATCTAAACTTTG
* *
55224133 ATCAATTATATTATTATATTTAA-A-AATTATCTAAA-TCTTG
1 ATAAATTATATTATTATACTTAACATAATTATCTAAACT-TTG
55224173 ATAAATTAT
1 ATAAATTAT
55224182 TTTAAATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
39 1 0.02
40 19 0.45
41 1 0.02
42 16 0.38
43 5 0.12
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (42 bp):
ATAAATTATATTATTATACTTAACATAATTATCTAAACTTTG
Found at i:55224414 original size:7 final size:7
Alignment explanation
Indices: 55224404--55224429 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55224394 GATTATAGAT
55224404 TAATTAA
1 TAATTAA
55224411 TAATTAA
1 TAATTAA
55224418 TAATTAA
1 TAATTAA
55224425 TAATT
1 TAATT
55224430 TATCAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TAATTAA
Found at i:55231232 original size:16 final size:16
Alignment explanation
Indices: 55231211--55231243 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55231201 CTAAAACCAG
*
55231211 GACAACTTAGCTTAGA
1 GACAACCTAGCTTAGA
55231227 GACAACCTAGCTTAGA
1 GACAACCTAGCTTAGA
55231243 G
1 G
55231244 TCGCTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (16 bp):
GACAACCTAGCTTAGA
Found at i:55231947 original size:16 final size:16
Alignment explanation
Indices: 55231926--55231957 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55231916 ACTTCTACGA
55231926 ACAAAGAAAACACACC
1 ACAAAGAAAACACACC
55231942 ACAAAGAAAACACACC
1 ACAAAGAAAACACACC
55231958 TCTCAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.31, G:0.06, T:0.00
Consensus pattern (16 bp):
ACAAAGAAAACACACC
Found at i:55234108 original size:16 final size:16
Alignment explanation
Indices: 55234087--55234123 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
55234077 GCAAAAAATT
55234087 TTCTTGAACCGTAAAA
1 TTCTTGAACCGTAAAA
55234103 TTCTTGAACCGTAAAA
1 TTCTTGAACCGTAAAA
55234119 TTCTT
1 TTCTT
55234124 TTACAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (16 bp):
TTCTTGAACCGTAAAA
Found at i:55234636 original size:18 final size:18
Alignment explanation
Indices: 55234613--55234652 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
55234603 TAATTACTCA
*
55234613 ATAATTAAATGTCATTCT
1 ATAATTAAATGTCATTAT
55234631 ATAATTAAATGTCATTAT
1 ATAATTAAATGTCATTAT
55234649 ATAA
1 ATAA
55234653 CCTTATGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (18 bp):
ATAATTAAATGTCATTAT
Found at i:55240726 original size:408 final size:408
Alignment explanation
Indices: 55239971--55240775 Score: 1547
Period size: 408 Copynumber: 2.0 Consensus size: 408
55239961 TTTCATGCAT
*
55239971 TAATCCTTAAGTCCTTTATCTTTGGATTGGACACAAGTCATGGAATAGTCACACTTGCATAGTCC
1 TAATCCTTAAGTCCTTTATCTCTGGATTGGACACAAGTCATGGAATAGTCACACTTGCATAGTCC
* *
55240036 ATCCCATGTTTCTTGATATCTTGAGTAGACTATGATATACAAATAAGTATGACATCTCATATCAA
66 ATCCCATGTTCCTTGATATCTTAAGTAGACTATGATATACAAATAAGTATGACATCTCATATCAA
55240101 CTTATTTGAGCATGGCCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCA
131 CTTATTTGAGCATGGCCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCA
55240166 TTATGTAGGAGGGACTTATCCTATATCGATCAGCCATATCCCTCTACATAGATCGTGGTATATCC
196 TTATGTAGGAGGGACTTATCCTATATCGATCAGCCATATCCCTCTACATAGATCGTGGTATATCC
55240231 AACATCTGCCTTTATAGAACAACCGGTTACGGTGTACGTTTGACTGTATCAAAATATACAACTCA
261 AACATCTGCCTTTATAGAACAACCGGTTACGGTGTACGTTTGACTGTATCAAAATATACAACTCA
55240296 CAATGTTAGGATTATGATGATCTCAAGTCTGAGGATCATATACATATTAATCACTATGAGTAATG
326 CAATGTTAGGATTATGATGATCTCAAGTCTGAGGATCATATACATATTAATCACTATGAGTAATG
*
55240361 TTGTGACTTTTTATGTAA
391 TCGTGACTTTTTATGTAA
*
55240379 TAATCCTTAAGTTCTTTATCTCTGGATTGGACACAAGTCATGGAATAGTCACACTTGCATAGTCC
1 TAATCCTTAAGTCCTTTATCTCTGGATTGGACACAAGTCATGGAATAGTCACACTTGCATAGTCC
* *
55240444 ATTCCATGTTCCTTGATATCTTAAGTAGACTATGATATACAAATAAGTATGACATCTCATATCAG
66 ATCCCATGTTCCTTGATATCTTAAGTAGACTATGATATACAAATAAGTATGACATCTCATATCAA
55240509 CTTATTTGAGCATGGCCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCA
131 CTTATTTGAGCATGGCCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCA
55240574 TTATGTAGGAGGGACTTATCCTATATCGATCAGCCATATCCCTCTACATAGATCGTGGTATATCC
196 TTATGTAGGAGGGACTTATCCTATATCGATCAGCCATATCCCTCTACATAGATCGTGGTATATCC
55240639 AACATCTGCCTTTATAGAACAACCGGTTACGGTGTACGTTTGACTGTATCAAAATATACAACTCA
261 AACATCTGCCTTTATAGAACAACCGGTTACGGTGTACGTTTGACTGTATCAAAATATACAACTCA
55240704 CAATGTTAGGATTATGATGATCTCAAGTCTGAGGATCATATACATATTAATCACTATGAGTAATG
326 CAATGTTAGGATTATGATGATCTCAAGTCTGAGGATCATATACATATTAATCACTATGAGTAATG
55240769 TCGTGAC
391 TCGTGAC
55240776 AATTACATAA
Statistics
Matches: 390, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
408 390 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (408 bp):
TAATCCTTAAGTCCTTTATCTCTGGATTGGACACAAGTCATGGAATAGTCACACTTGCATAGTCC
ATCCCATGTTCCTTGATATCTTAAGTAGACTATGATATACAAATAAGTATGACATCTCATATCAA
CTTATTTGAGCATGGCCATGCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATATTACTCCCA
TTATGTAGGAGGGACTTATCCTATATCGATCAGCCATATCCCTCTACATAGATCGTGGTATATCC
AACATCTGCCTTTATAGAACAACCGGTTACGGTGTACGTTTGACTGTATCAAAATATACAACTCA
CAATGTTAGGATTATGATGATCTCAAGTCTGAGGATCATATACATATTAATCACTATGAGTAATG
TCGTGACTTTTTATGTAA
Found at i:55247830 original size:24 final size:24
Alignment explanation
Indices: 55247780--55247832 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
55247770 TTTCTAGAAG
* * *
55247780 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTACTAGCATAATAT
* *
55247804 ATTTAGCATTTACTAGCATAGTTT
1 ATTTAGCATTTACTAGCATAATAT
55247828 ATTTA
1 ATTTA
55247833 ACTTACTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (24 bp):
ATTTAGCATTTACTAGCATAATAT
Found at i:55252125 original size:4 final size:4
Alignment explanation
Indices: 55252116--55252145 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
55252106 AATTTAAAAC
55252116 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
55252146 CATGCATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:55252908 original size:21 final size:21
Alignment explanation
Indices: 55252884--55252931 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
55252874 GATCAAGTAA
55252884 TTATATTATAAAGACATAATT
1 TTATATTATAAAGACATAATT
* * **
55252905 TTATTTTATAAATATGTAATT
1 TTATATTATAAAGACATAATT
55252926 TTATAT
1 TTATAT
55252932 AAAGTTGTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
TTATATTATAAAGACATAATT
Found at i:55255979 original size:19 final size:17
Alignment explanation
Indices: 55255931--55255980 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
55255921 TGTGCAGGTG
55255931 AAATAAAAAAAATCCTA
1 AAATAAAAAAAATCCTA
*
55255948 AAATAGAAGAAAAATTCTAA
1 AAATA-AA-AAAAATCCT-A
*
55255968 AAATATAAAAAAT
1 AAATAAAAAAAAT
55255981 TAAAAAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 9 0.32
20 6 0.21
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAAAAAAAATCCTA
Found at i:55265121 original size:21 final size:22
Alignment explanation
Indices: 55265091--55265137 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
55265081 TTTAGTCATT
55265091 TTTTTAAATTTTAA-TATTTTTA
1 TTTTTAAA-TTTAATTATTTTTA
*
55265113 TTTTT-AATTTAATTTTTTTTA
1 TTTTTAAATTTAATTATTTTTA
55265134 TTTT
1 TTTT
55265138 GTGTGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTAAATTTAATTATTTTTA
Found at i:55273319 original size:57 final size:56
Alignment explanation
Indices: 55273256--55273433 Score: 160
Period size: 57 Copynumber: 3.1 Consensus size: 56
55273246 CCTAAAAGTG
* * ***
55273256 AGCCTTTATGGCTATCCCTGTTAAAGGAAGCCTTTATGGCTGTTTCTGTTAAAAGAA
1 AGCCTTTATGGCTATCTCTATTAAAGGAAGCCTTTATGGCTAACTCTGTTAAAAG-A
** * * * * *
55273313 AGCCTTTATAACGATTTCTATTAAAGGAAGCATTTATGGCTAACTCTGTTAAATGG
1 AGCCTTTATGGCTATCTCTATTAAAGGAAGCCTTTATGGCTAACTCTGTTAAAAGA
* * * * *
55273369 AGCCTTTGTGGCTATCTCTATTAAAAGGATA-CCTTTATGGTTATCTTTATTAAAAGA
1 AGCCTTTATGGCTATCTCTATT-AAAGGA-AGCCTTTATGGCTAACTCTGTTAAAAGA
55273426 ATGCCTTT
1 A-GCCTTT
55273434 GTGGTGAGAC
Statistics
Matches: 94, Mismatches: 24, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
56 17 0.18
57 70 0.74
58 7 0.07
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (56 bp):
AGCCTTTATGGCTATCTCTATTAAAGGAAGCCTTTATGGCTAACTCTGTTAAAAGA
Found at i:55273414 original size:29 final size:28
Alignment explanation
Indices: 55273248--55273424 Score: 124
Period size: 28 Copynumber: 6.2 Consensus size: 28
55273238 GCAATTCCCC
* * *
55273248 TAAAAGTGAGCCTTTATGGCTATCCCTGT
1 TAAAAG-GAACCTTTATGGCTATCTCTAT
* * *
55273277 T-AAAGGAAGCCTTTATGGCTGTTTCTGT
1 TAAAAGGAA-CCTTTATGGCTATCTCTAT
* ** * *
55273305 TAAAAGAAAGCCTTTATAACGATTTCTAT
1 TAAAAGGAA-CCTTTATGGCTATCTCTAT
* * *
55273334 T-AAAGGAAGCATTTATGGCTAACTCTGT
1 TAAAAGGAA-CCTTTATGGCTATCTCTAT
* * *
55273362 TAAATGGAGCCTTTGTGGCTATCTCTAT
1 TAAAAGGAACCTTTATGGCTATCTCTAT
* *
55273390 TAAAAGGATACCTTTATGGTTATCTTTAT
1 TAAAAGGA-ACCTTTATGGCTATCTCTAT
55273419 TAAAAG
1 TAAAAG
55273425 AATGCCTTTG
Statistics
Matches: 115, Mismatches: 29, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
27 2 0.02
28 63 0.55
29 50 0.43
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (28 bp):
TAAAAGGAACCTTTATGGCTATCTCTAT
Found at i:55273432 original size:29 final size:29
Alignment explanation
Indices: 55273370--55273438 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
55273360 GTTAAATGGA
* *
55273370 GCCTTTGTGGCTATCTCTATTAAAAGGAT
1 GCCTTTGTGGTTATCTCTATTAAAAGAAT
* * *
55273399 ACCTTTATGGTTATCTTTATTAAAAGAAT
1 GCCTTTGTGGTTATCTCTATTAAAAGAAT
55273428 GCCTTTGTGGT
1 GCCTTTGTGGT
55273439 GAGACTCTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (29 bp):
GCCTTTGTGGTTATCTCTATTAAAAGAAT
Found at i:55286756 original size:20 final size:20
Alignment explanation
Indices: 55286731--55286810 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
55286721 ACGTGTAAAC
55286731 AGGGGTACCGAAGTACAAAT
1 AGGGGTACCGAAGTACAAAT
*
55286751 AGGGGTACCGAAGTACAATT
1 AGGGGTACCGAAGTACAAAT
* *
55286771 AGGGGTATCGAA-TGATAAAT
1 AGGGGTACCGAAGT-ACAAAT
55286791 AGGGGGTACCGAAGTACAAA
1 A-GGGGTACCGAAGTACAAA
55286811 CAGTGTAACA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 35 0.69
21 14 0.27
22 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.31, T:0.17
Consensus pattern (20 bp):
AGGGGTACCGAAGTACAAAT
Found at i:55288535 original size:25 final size:25
Alignment explanation
Indices: 55288446--55288538 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 25
55288436 TATGTACATG
* * * *
55288446 TATGCTCATACAAGCTGTGAATCGG
1 TATGCTCATACGAGCTATAAATCGA
* *
55288471 TATGCTCACT-CGAGCTGA-AGACCGA
1 TATGCTCA-TACGAGCT-ATAAATCGA
*
55288496 TATGCTC-TCATGAGCTATAAATCGA
1 TATGCTCAT-ACGAGCTATAAATCGA
55288521 TATGCTCATACGAGCTAT
1 TATGCTCATACGAGCTAT
55288539 GGGTCAAGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 48 0.92
26 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (25 bp):
TATGCTCATACGAGCTATAAATCGA
Found at i:55295002 original size:25 final size:25
Alignment explanation
Indices: 55294912--55295003 Score: 64
Period size: 25 Copynumber: 3.7 Consensus size: 25
55294902 TTATGTACAT
* * * * *
55294912 GTATGCTCATATGAGCTGTGAACCG
1 GTATGCTCATACGAGCTATAAATCA
*
55294937 GTATGCTCA-ATCGAGCTGA-AGATCA
1 GTATGCTCATA-CGAGCT-ATAAATCA
* *
55294962 ATATGCTC-TCATGAGCTATAAATCA
1 GTATGCTCAT-ACGAGCTATAAATCA
55294987 GTATGCTCATACGAGCT
1 GTATGCTCATACGAGCT
55295004 GTGGGTCGTG
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
24 2 0.04
25 46 0.92
26 2 0.04
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATAAATCA
Found at i:55296335 original size:20 final size:20
Alignment explanation
Indices: 55296312--55296350 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55296302 GTTACAAATA
55296312 GGGGTACCGAAGTACAAGCT
1 GGGGTACCGAAGTACAAGCT
*
55296332 GGGGTACTGAAGTACAAGC
1 GGGGTACCGAAGTACAAGC
55296351 AAGGCACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.18, G:0.36, T:0.15
Consensus pattern (20 bp):
GGGGTACCGAAGTACAAGCT
Found at i:55300503 original size:42 final size:42
Alignment explanation
Indices: 55300423--55300510 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
55300413 TCTGAGAGAT
* ** *
55300423 GTTTATTATCTCCTGTGATGACATATTATGAATGCATGTTTA
1 GTTTATTATCTCCTGTGATGACATATGACAAATACATGTTTA
* * * *
55300465 GTTTATTTTCTCTTGTGATGACTTATGACAAATACATGTTTT
1 GTTTATTATCTCCTGTGATGACATATGACAAATACATGTTTA
55300507 GTTT
1 GTTT
55300511 TGAGAAGTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (42 bp):
GTTTATTATCTCCTGTGATGACATATGACAAATACATGTTTA
Found at i:55314887 original size:12 final size:12
Alignment explanation
Indices: 55314870--55314909 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
55314860 AATACTTCGA
55314870 AATTTTTTTTTC
1 AATTTTTTTTTC
55314882 AA-TTTTTTTT-
1 AATTTTTTTTTC
55314892 AATTTTTTTTTC
1 AATTTTTTTTTC
55314904 GAATTT
1 -AATTT
55314910 CCTCTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 16 0.64
12 2 0.08
13 5 0.20
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (12 bp):
AATTTTTTTTTC
Found at i:55314901 original size:10 final size:11
Alignment explanation
Indices: 55314873--55314901 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
55314863 ACTTCGAAAT
55314873 TTTTTTTTCAA
1 TTTTTTTTCAA
55314884 TTTTTTTT-AA
1 TTTTTTTTCAA
55314894 TTTTTTTT
1 TTTTTTTT
55314902 TCGAATTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:55315772 original size:44 final size:44
Alignment explanation
Indices: 55315660--55316199 Score: 250
Period size: 44 Copynumber: 11.6 Consensus size: 44
55315650 ATTATACAGG
** ** **
55315660 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAGGAATTA-TAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGA--AGCTAGTA-A
55315706 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAA
* * * * *
55315750 TCCTATCTCCCTGAGATTACAGTGGAGC-GAATTAAAACAAAG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAG-ATTGAAGC-TAGTAA
* * * *
55315794 TCTTATCTCTCTTA-AGTTACAGTAAAGTAGATCGCGTCAGATTGAAGCCAGAAA
1 TCTTATCTCCCTGAGA-TTACAGT---G--GA----G-CAGATTGAAGCTAGTAA
* *
55315848 TCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAA
* * * * * *
55315892 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGC-TAGTAA
* * * * *
55315936 TCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCGTCAGATTGAAGCCAGAAA
1 TCTTATCTCCCTG-AG--AT--TACAGT-G---GAG-CAGATTGAAGCTAGTAA
** *
55315990 TCTTATCTCCCTGAGATTACAGCAGAGCAGGTTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAA
* * * ** **
55316034 TCCTATCTCCCTGAGATTATAGTGGAGCGGATT-AAAATAAAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTA-A
* * ** * * * *
55316078 TCTTATCTCTCT-AAAGTTACAGCAGAGTAGATCGCATCAGATTGAGGTCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTG-A--AG-CT-A-GT-A-A
* *
55316130 TCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAA
55316174 T-TCTATCTCCCTGAGATTACAGTGGA
1 TCT-TATCTCCCTGAGATTACAGTGGA
55316200 TCGAAGCGCC
Statistics
Matches: 370, Mismatches: 83, Indels: 84
0.69 0.15 0.16
Matches are distributed among these distances:
43 10 0.03
44 200 0.54
45 12 0.03
46 34 0.09
47 4 0.01
48 2 0.01
49 15 0.04
50 2 0.01
51 4 0.01
52 27 0.07
53 11 0.03
54 47 0.13
55 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAA
Found at i:55315965 original size:142 final size:142
Alignment explanation
Indices: 55315705--55316199 Score: 807
Period size: 142 Copynumber: 3.5 Consensus size: 142
55315695 GGAATTATAG
* *
55315705 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* * *
55315770 AGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTTAAGTTACAGTAAAGTAGATCGCGTCAGA
66 AGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCGTCAGA
55315835 TTGAAGCCAGAA
131 TTGAAGCCAGAA
55315847 ATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* *
55315912 AGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCGTCAGA
66 AGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCGTCAGA
55315977 TTGAAGCCAGAA
131 TTGAAGCCAGAA
*
55315989 ATCTTATCTCCCTGAGATTACAGC-AGAGCAGGTTGAAGCTAGTAATCCTATCTCCCTGAGATTA
1 ATCTTATCTCCCTGAGATTACAGCGA-AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA
* * * * *
55316053 TAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGCATCAG
65 CAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCGTCAG
* *
55316118 ATTGAGGTCAG--
130 ATTGAAGCCAGAA
* *
55316129 GTCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATTCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
55316194 AGTGGA
66 AGTGGA
55316200 TCGAAGCGCC
Statistics
Matches: 331, Mismatches: 20, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
140 65 0.20
141 2 0.01
142 264 0.80
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (142 bp):
ATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
AGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCGTCAGA
TTGAAGCCAGAA
Found at i:55316054 original size:98 final size:98
Alignment explanation
Indices: 55315875--55316056 Score: 217
Period size: 98 Copynumber: 1.9 Consensus size: 98
55315865 TACAGCGAAG
* * ** * *
55315875 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAGGATCTT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCAGAGCGGATTAAAACAAAGAATCCT
*
55315940 ATCTCTCTGAAGTTATAGTAGAGTAGATCGCGT
66 ATCTCCCTGAAGTTATAGTAGAGTAGATCGCGT
* * * *
55315973 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCAGAGCAGG-TTGAAGC-TAGTAATC
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCAGAGC-GGATTAAAACAAAG-AATC
55316036 CTATCTCCCTG-AGATTATAGT
64 CTATCTCCCTGAAG-TTATAGT
55316057 GGAGCGGATT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
97 4 0.06
98 64 0.91
99 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (98 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCAGAGCGGATTAAAACAAAGAATCCT
ATCTCCCTGAAGTTATAGTAGAGTAGATCGCGT
Found at i:55319162 original size:11 final size:11
Alignment explanation
Indices: 55319146--55319184 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55319136 AATACTTCGA
55319146 AATTTTTTTTC
1 AATTTTTTTTC
55319157 AATTTTTTTTTC
1 AA-TTTTTTTTC
* *
55319169 GATTTTTTTTG
1 AATTTTTTTTC
55319180 AATTT
1 AATTT
55319185 CCTCTTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:55319165 original size:12 final size:12
Alignment explanation
Indices: 55319148--55319178 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55319138 TACTTCGAAA
55319148 TTTTTTTTCAAT
1 TTTTTTTTCAAT
*
55319160 TTTTTTTTCGAT
1 TTTTTTTTCAAT
55319172 TTTTTTT
1 TTTTTTT
55319179 GAATTTCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:55319838 original size:33 final size:34
Alignment explanation
Indices: 55319801--55319872 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
55319791 GAGTTAGTTT
*
55319801 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
* *
55319834 ATTAATTTTAGTTCAACTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
55319868 ATTAA
1 ATTAA
55319873 TTTGTTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
Found at i:55322282 original size:27 final size:27
Alignment explanation
Indices: 55322231--55322282 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
55322221 CTCATCTTAG
** *
55322231 TTTAATTAATAAGTATTTTTGTTAAAC
1 TTTAATTAATAAGTATTGCTCTTAAAC
*
55322258 TTTAATTAATAAGTGTTGCTCTTAA
1 TTTAATTAATAAGTATTGCTCTTAA
55322283 TTAATCTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (27 bp):
TTTAATTAATAAGTATTGCTCTTAAAC
Found at i:55325760 original size:17 final size:18
Alignment explanation
Indices: 55325733--55325768 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
55325723 AGGCAACAAT
55325733 AGAAGAAAAACATGGAGA
1 AGAAGAAAAACATGGAGA
*
55325751 AGAA-AAAAACATTGAGA
1 AGAAGAAAAACATGGAGA
55325768 A
1 A
55325769 AATGAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.64, C:0.06, G:0.22, T:0.08
Consensus pattern (18 bp):
AGAAGAAAAACATGGAGA
Found at i:55328208 original size:32 final size:32
Alignment explanation
Indices: 55328164--55328224 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
55328154 TCATAGGAGT
* *
55328164 TTCTCGTGACTTGGCAACTCGATCTTGGTCCG
1 TTCTCGTAACTTGACAACTCGATCTTGGTCCG
*
55328196 TTCTCGTAACTTGACGACTCGATCTTGGT
1 TTCTCGTAACTTGACAACTCGATCTTGGT
55328225 TCGCGTGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (32 bp):
TTCTCGTAACTTGACAACTCGATCTTGGTCCG
Found at i:55329632 original size:23 final size:23
Alignment explanation
Indices: 55329606--55329671 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
55329596 TTGGTTTAGG
*
55329606 TTTGTTACGAAATGGTAATGTGA
1 TTTGTTACGAAATGGTAATGCGA
* *
55329629 TTTGGTTA-GAAATGGTATTACGA
1 TTT-GTTACGAAATGGTAATGCGA
*
55329652 TTTGGTACGAAATGGTAATG
1 TTTGTTACGAAATGGTAATG
55329672 GTTCAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 3 0.09
23 28 0.80
24 4 0.11
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (23 bp):
TTTGTTACGAAATGGTAATGCGA
Found at i:55333857 original size:20 final size:20
Alignment explanation
Indices: 55333808--55333863 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
55333798 TCTCGCTTTC
* *
55333808 TTTTCATTTTCATTTTTTGAA
1 TTTTC-TTTTCTTTTTTTCAA
*
55333829 TTTTC-TTTCTTTTTTTCAT
1 TTTTCTTTTCTTTTTTTCAA
55333848 TTTTCTTTTCTTTTTT
1 TTTTCTTTTCTTTTTT
55333864 ATTTTCGCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.52
20 10 0.32
21 5 0.16
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTCAA
Found at i:55335434 original size:72 final size:72
Alignment explanation
Indices: 55335317--55335461 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
55335307 GATCCTTGAT
* * * *
55335317 CACTTTCGGCTTCATTCGGATCATATAGGTCGTCTTGATTGATTTCCAATTGGTCTCGCCTTCTT
1 CACTTTCGACTTCATTCGGATCACATAGGTCGTCTTGATTGATTTCCAATTGGTCTCACCCTCTT
55335382 TGCGGCC
66 TGCGGCC
55335389 CACTTTCGACTTCATTCGGATCACATAGGTCGTCTTGATTGATTTCCAATTGGTCTCACCCTCTT
1 CACTTTCGACTTCATTCGGATCACATAGGTCGTCTTGATTGATTTCCAATTGGTCTCACCCTCTT
55335454 TGCGGCC
66 TGCGGCC
55335461 C
1 C
55335462 TTGGGGTGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.37
Consensus pattern (72 bp):
CACTTTCGACTTCATTCGGATCACATAGGTCGTCTTGATTGATTTCCAATTGGTCTCACCCTCTT
TGCGGCC
Found at i:55336474 original size:23 final size:23
Alignment explanation
Indices: 55336448--55336513 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
55336438 TCGGTTTAGG
*
55336448 TTTGTTACGAAATGGTAATGTGA
1 TTTGTTACGAAATGGTAATGCGA
* *
55336471 TTTGGTT-CGAAATGGTATTACGA
1 TTT-GTTACGAAATGGTAATGCGA
*
55336494 TTTGGTACGAAATGGTAATG
1 TTTGTTACGAAATGGTAATG
55336514 GTTCAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 2 0.06
23 30 0.86
24 3 0.09
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (23 bp):
TTTGTTACGAAATGGTAATGCGA
Found at i:55341183 original size:22 final size:22
Alignment explanation
Indices: 55341153--55341196 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55341143 TTTGGTATTT
55341153 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
55341175 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
55341197 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:55343439 original size:10 final size:10
Alignment explanation
Indices: 55343415--55343463 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
55343405 AGCTTGTTTC
*
55343415 CAGCTCACTT
1 CAGCTCAATT
* *
55343425 GAGCTCAAGT
1 CAGCTCAATT
55343435 CAGCTC-ATT
1 CAGCTCAATT
55343444 CGAGCTCAATT
1 C-AGCTCAATT
55343455 CAGCTCAAT
1 CAGCTCAAT
55343464 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:55343440 original size:20 final size:20
Alignment explanation
Indices: 55343415--55343461 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
55343405 AGCTTGTTTC
55343415 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
55343435 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
55343455 CAGCTCA
1 CAGCTCA
55343462 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:55349002 original size:12 final size:12
Alignment explanation
Indices: 55348985--55349009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55348975 TCGTGTCATC
55348985 AAATCATGTGTA
1 AAATCATGTGTA
55348997 AAATCATGTGTA
1 AAATCATGTGTA
55349009 A
1 A
55349010 CTAGAGATAG
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
AAATCATGTGTA
Found at i:55354189 original size:54 final size:54
Alignment explanation
Indices: 55354107--55354215 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
55354097 AGGAATAAAA
*
55354107 TGTGCCATCTTGGAAAACCTGTCAACAACAACAGATATACTATCTCTTCCTTTC
1 TGTGCCATCTTGGAAAACCTGTCAACAACAACAAATATACTATCTCTTCCTTTC
55354161 TGTGCCATCTTGGAAAACCTGTCAACAACAACAAATATACTATCTCTTCCTTTC
1 TGTGCCATCTTGGAAAACCTGTCAACAACAACAAATATACTATCTCTTCCTTTC
55354215 T
1 T
55354216 TAGTTCGTGG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (54 bp):
TGTGCCATCTTGGAAAACCTGTCAACAACAACAAATATACTATCTCTTCCTTTC
Found at i:55357021 original size:18 final size:20
Alignment explanation
Indices: 55357000--55357049 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
55356990 AAAGGAAGAT
55357000 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
55357018 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
55357038 AGCAAAAAGAGA
1 AG-AAAAAGAGA
55357050 TTGGGAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:55358298 original size:33 final size:34
Alignment explanation
Indices: 55358261--55358332 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
55358251 GAGTTAGTTT
*
55358261 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
* *
55358294 ATTAATTTTAGTTCAACTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
55358328 ATTAA
1 ATTAA
55358333 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
Found at i:55360463 original size:68 final size:68
Alignment explanation
Indices: 55360354--55360492 Score: 269
Period size: 68 Copynumber: 2.0 Consensus size: 68
55360344 ATCTACAAGG
*
55360354 TAAAACTTCTCAAAAGTAGTATTTCCATAATTACTATAGATATGGCCGAATTCAGCATCATCATT
1 TAAAACTTCTCAAAAGTAGTATTTCCATAATTACTATAGATATAGCCGAATTCAGCATCATCATT
55360419 ATA
66 ATA
55360422 TAAAACTTCTCAAAAGTAGTATTTCCATAATTACTATAGATATAGCCGAATTCAGCATCATCATT
1 TAAAACTTCTCAAAAGTAGTATTTCCATAATTACTATAGATATAGCCGAATTCAGCATCATCATT
55360487 ATA
66 ATA
55360490 TAA
1 TAA
55360493 CTCTTTAATA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (68 bp):
TAAAACTTCTCAAAAGTAGTATTTCCATAATTACTATAGATATAGCCGAATTCAGCATCATCATT
ATA
Found at i:55367356 original size:13 final size:13
Alignment explanation
Indices: 55367338--55367384 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
55367328 AATACTTCGA
55367338 AATTTTTTTTTTC
1 AATTTTTTTTTTC
55367351 AATTTTTTTTTT-
1 AATTTTTTTTTTC
55367363 AA-TTTTTTTTTC
1 AATTTTTTTTTTC
*
55367375 GATTTTTTTT
1 AATTTTTTTT
55367385 CGAATTTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 9 0.29
12 3 0.10
13 19 0.61
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (13 bp):
AATTTTTTTTTTC
Found at i:55367387 original size:11 final size:12
Alignment explanation
Indices: 55367341--55367384 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
55367331 ACTTCGAAAT
55367341 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
55367353 TTTTTTTTTTAA
1 TTTTTTTTTCAA
*
55367365 TTTTTTTTTCGA
1 TTTTTTTTTCAA
55367377 TTTTTTTT
1 TTTTTTTT
55367385 CGAATTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.11, C:0.05, G:0.02, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:55367390 original size:24 final size:24
Alignment explanation
Indices: 55367341--55367391 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
55367331 ACTTCGAAAT
**
55367341 TTTTTTTTTCAATTTTTTTTTTAA
1 TTTTTTTTTCAATTTTTTTTCGAA
*
55367365 TTTTTTTTTCGATTTTTTTTCGAA
1 TTTTTTTTTCAATTTTTTTTCGAA
55367389 TTT
1 TTT
55367392 CAACTTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTTTTTTCAATTTTTTTTCGAA
Found at i:55367391 original size:12 final size:12
Alignment explanation
Indices: 55367342--55367391 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
55367332 CTTCGAAATT
55367342 TTTTTTTTC-AA
1 TTTTTTTTCGAA
**
55367353 TTTTTTTTTTAA
1 TTTTTTTTCGAA
55367365 TTTTTTTTTCG-A
1 -TTTTTTTTCGAA
55367377 TTTTTTTTCGAA
1 TTTTTTTTCGAA
55367389 TTT
1 TTT
55367392 CAACTTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 18 0.55
12 7 0.21
13 8 0.24
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:55369816 original size:11 final size:11
Alignment explanation
Indices: 55369800--55369829 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
55369790 TTGGAGTAAC
55369800 AAAAAAATCAA
1 AAAAAAATCAA
*
55369811 AAAAAATTCAA
1 AAAAAAATCAA
55369822 AAAAAAAT
1 AAAAAAAT
55369830 TTGATTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:55369854 original size:12 final size:13
Alignment explanation
Indices: 55369838--55369872 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
55369828 ATTTGATTGA
55369838 AAAAAAAAAATTC
1 AAAAAAAAAATTC
* *
55369851 AAAAAAAAAAGTG
1 AAAAAAAAAATTC
55369864 AAAAAAAAA
1 AAAAAAAAA
55369873 TCGAGCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:55369881 original size:28 final size:28
Alignment explanation
Indices: 55369850--55369924 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
55369840 AAAAAAAATT
*
55369850 CAAAAAAAAAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAAAGTGAAAAAAAAATCAAG
*
55369878 CAAAAAAAAAAGGTGACCAAAAAAATCAAG
1 CAAAAAAAAAA-GTGA-AAAAAAAATCAAG
**
55369908 -TTAAAAAAAAGTGAAAA
1 CAAAAAAAAAAGTGAAAA
55369925 GTCTTGCGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.05
28 15 0.38
29 12 0.30
30 11 0.28
ACGTcount: A:0.69, C:0.08, G:0.13, T:0.09
Consensus pattern (28 bp):
CAAAAAAAAAAGTGAAAAAAAAATCAAG
Found at i:55369914 original size:30 final size:29
Alignment explanation
Indices: 55369851--55369924 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
55369841 AAAAAAATTC
*
55369851 AAAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAAAAGTGAAAAAAAAATCAAGCA
* *
55369880 AAAAAAAAAGGTGACCAAAAAAATCAAG--
1 AAAAAAAAAAGTGA-AAAAAAAATCAAGCA
**
55369908 TTAAAAAAAAGTGAAAA
1 AAAAAAAAAAGTGAAAA
55369925 GTCTTGCGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 2 0.05
28 11 0.30
29 13 0.35
30 11 0.30
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (29 bp):
AAAAAAAAAAGTGAAAAAAAAATCAAGCA
Found at i:55373949 original size:11 final size:11
Alignment explanation
Indices: 55373933--55373979 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 11
55373923 AGAAGTGAGC
55373933 AAAAAAAGT-A
1 AAAAAAAGTAA
55373943 AAAAAAAGTAA
1 AAAAAAAGTAA
*
55373954 AAAAAAAGAACA
1 AAAAAAAGTA-A
55373966 AAAAAAAGTGAA
1 AAAAAAAGT-AA
55373978 AA
1 AA
55373980 GTCTTGTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 9 0.28
11 10 0.31
12 12 0.38
13 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (11 bp):
AAAAAAAGTAA
Found at i:55373951 original size:23 final size:23
Alignment explanation
Indices: 55373918--55373979 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
55373908 AATTCAAAAA
* *
55373918 AAAAAAGAAGTGAGCAAAAAAAG-T
1 AAAAAA-AAGTGA-AAAAAAAAGAC
55373942 AAAAAAAAGT-AAAAAAAAAGAAC
1 AAAAAAAAGTGAAAAAAAAAG-AC
55373965 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
55373980 GTCTTGTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 8 0.24
22 1 0.03
23 14 0.42
24 10 0.30
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (23 bp):
AAAAAAAAGTGAAAAAAAAAGAC
Found at i:55373970 original size:10 final size:10
Alignment explanation
Indices: 55373933--55373959 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55373923 AGAAGTGAGC
55373933 AAAAAAAGTA
1 AAAAAAAGTA
55373943 AAAAAAAGTA
1 AAAAAAAGTA
55373953 AAAAAAA
1 AAAAAAA
55373960 AGAACAAAAA
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:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (10 bp):
AAAAAAAGTA
Found at i:55378127 original size:7 final size:7
Alignment explanation
Indices: 55378110--55378143 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
55378100 TTCGCAATTT
55378110 CAAAAAA
1 CAAAAAA
55378117 -AAAAAA
1 CAAAAAA
55378123 CAAAAAAA
1 C-AAAAAA
55378131 CAAAAAA
1 CAAAAAA
55378138 CAAAAA
1 CAAAAA
55378144 GAGAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:55378135 original size:15 final size:14
Alignment explanation
Indices: 55378111--55378143 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
55378101 TCGCAATTTC
55378111 AAAAAAAAAAAACA
1 AAAAAAAAAAAACA
55378125 AAAAAACAAAAAACA
1 AAAAAA-AAAAAACA
55378140 AAAA
1 AAAA
55378144 GAGAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:55381609 original size:20 final size:20
Alignment explanation
Indices: 55381584--55381638 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
55381574 TGTGGTTCAA
*
55381584 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
55381604 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
55381624 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
55381639 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:55390852 original size:23 final size:22
Alignment explanation
Indices: 55390800--55390852 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55390790 TCCACGTCTT
55390800 TTTCTTTTATTTCTTTTTCTAA
1 TTTCTTTTATTTCTTTTTCTAA
*
55390822 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTAT-TTCTTT-TTCTAA
55390845 TTTCTTTT
1 TTTCTTTT
55390853 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTCTTTTATTTCTTTTTCTAA
Found at i:55390897 original size:18 final size:17
Alignment explanation
Indices: 55390796--55390899 Score: 52
Period size: 18 Copynumber: 5.8 Consensus size: 17
55390786 CCTTTCCACG
55390796 TCTTTTTC-TTTT-ATT
1 TCTTTTTCTTTTTCATT
**
55390811 TCTTTTTCTAATTCATT
1 TCTTTTTCTTTTTCATT
*
55390828 T-TCTCTTCTTTCTTCAATT
1 TCT-TTTTCTTT-TTC-ATT
** * *
55390847 TCTTTTTCACTCTCAATC
1 TCTTTTTCTTTTTC-ATT
55390865 TCTTTTTGCTCTTTTTCATT
1 TC-TTTT--TCTTTTTCATT
55390885 CTCTTTTTCTTTTTC
1 -TCTTTTTCTTTTTC
55390900 CTCACTTGTT
Statistics
Matches: 65, Mismatches: 14, Indels: 17
0.68 0.15 0.18
Matches are distributed among these distances:
15 8 0.12
16 3 0.05
17 9 0.14
18 18 0.28
19 13 0.20
20 7 0.11
21 7 0.11
ACGTcount: A:0.10, C:0.23, G:0.01, T:0.66
Consensus pattern (17 bp):
TCTTTTTCTTTTTCATT
Found at i:55398148 original size:33 final size:33
Alignment explanation
Indices: 55398110--55398172 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
55398100 GATTACTCAC
55398110 TTCACTCG-TTTCTTTTACAAACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CAAACTCTCTTTCTTT
* *
55398143 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAACTCTCTTTC
55398173 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 19 0.70
34 8 0.30
ACGTcount: A:0.14, C:0.27, G:0.05, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAACTCTCTTTCTTT
Found at i:55398199 original size:14 final size:15
Alignment explanation
Indices: 55398175--55398254 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 15
55398165 TCTCTTTCAA
*
55398175 TTTCTTTTTTCACTT
1 TTTCTTTTTTCAATT
55398190 TTTC-TTTTTCAATT
1 TTTCTTTTTTCAATT
55398204 TTT-TTTCATTCTCAA--
1 TTTCTTT--TT-TCAATT
55398219 TTTC-TTTTTCAA-T
1 TTTCTTTTTTCAATT
55398232 TTTCTTTTCTTC-A-T
1 TTTCTTTT-TTCAATT
55398246 TTTCTTTTT
1 TTTCTTTTT
55398255 CTCTCACCTT
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
12 4 0.07
13 7 0.12
14 27 0.48
15 12 0.21
16 2 0.04
17 4 0.07
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCTTTTTTCAATT
Found at i:55398199 original size:27 final size:27
Alignment explanation
Indices: 55398169--55398255 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
55398159 TCAAGCTCTC
55398169 TTTCAATTTCTTTT-TTCACTTTTTCTT
1 TTTCAATTTCTTTTCTTCAC-TTTTCTT
* * *
55398196 TTTCAATTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTCAC-TTTTCTT
55398225 TTTCAATTTTCTTTTCTTCA-TTTTCTT
1 TTTCAA-TTTCTTTTCTTCACTTTTCTT
55398252 TTTC
1 TTTC
55398256 TCTCACCTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 23 0.46
29 19 0.38
30 8 0.16
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTCTTCACTTTTCTT
Found at i:55398239 original size:12 final size:12
Alignment explanation
Indices: 55398151--55398344 Score: 58
Period size: 12 Copynumber: 16.7 Consensus size: 12
55398141 TTTTCACTTG
55398151 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
55398162 AGCTCTCTTTCA
1 ATTTCTTTTTCA
55398174 ATTTCTTTTTTCA
1 ATTTC-TTTTTCA
*
55398187 CTTTTTCTTTTTCA
1 --ATTTCTTTTTCA
55398201 ATTT-TTTTTC-
1 ATTTCTTTTTCA
55398211 A-TTC----TCA
1 ATTTCTTTTTCA
55398218 ATTTCTTTTTCA
1 ATTTCTTTTTCA
55398230 ATTTTCTTTTCTTCA
1 A-TTTC-TTT-TTCA
* *
55398245 TTTTCTTTTTCT
1 ATTTCTTTTTCA
* ** * *
55398257 CTCACCTTTTCG
1 ATTTCTTTTTCA
55398269 ATTTCTTTTTC-
1 ATTTCTTTTTCA
*
55398280 TTTTGCAATTTTT--
1 ATTT-C--TTTTTCA
55398293 -TTTCTTTTTCA
1 ATTTCTTTTTCA
*
55398304 TTTTCTTTTT--
1 ATTTCTTTTTCA
* *
55398314 GTTT-TCTTTCA
1 ATTTCTTTTTCA
55398325 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
55398337 ATCTCTTT
1 ATTTCTTT
55398345 CTCCTTTTCT
Statistics
Matches: 135, Mismatches: 25, Indels: 45
0.66 0.12 0.22
Matches are distributed among these distances:
6 2 0.01
7 1 0.01
8 3 0.02
9 11 0.08
10 4 0.03
11 16 0.12
12 58 0.43
13 13 0.10
14 19 0.14
15 8 0.06
ACGTcount: A:0.12, C:0.20, G:0.02, T:0.66
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:55398240 original size:18 final size:17
Alignment explanation
Indices: 55398187--55398312 Score: 60
Period size: 17 Copynumber: 7.0 Consensus size: 17
55398177 TCTTTTTTCA
* *
55398187 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTTTC-TTTT
* *
55398205 -TTTTTCATTCTCAATTT
1 CTTTTTCATTTTC-TTTT
55398222 CTTTTTCAATTTTCTTTT
1 CTTTTTC-ATTTTCTTTT
* **
55398240 CTTCATTTTCTTTTTCTCTCA
1 C-T--TTTTCATTTTCT-TTT
*
55398261 CCTTTTCGA-TTTCTTTTT
1 CTTTTTC-ATTTTC-TTTT
*
55398279 CTTTTGCAATTTT-TTTT
1 CTTTTTC-ATTTTCTTTT
55398296 CTTTTTCATTTTCTTTT
1 CTTTTTCATTTTCTTTT
55398313 TGTTTTCTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 21
0.70 0.13 0.18
Matches are distributed among these distances:
16 5 0.06
17 29 0.35
18 26 0.31
19 10 0.12
20 6 0.07
21 7 0.08
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (17 bp):
CTTTTTCATTTTCTTTT
Found at i:55398318 original size:23 final size:22
Alignment explanation
Indices: 55398270--55398334 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
55398260 ACCTTTTCGA
*
55398270 TTTCTTTTTC-TTTTGCAATTTTT
1 TTTCTTTTTCATTTT-C-TTTTTT
55398293 TTTCTTTTTCATTTTCTTTTTGT
1 TTTCTTTTTCATTTTCTTTTT-T
*
55398316 TTTC--TTTCAATTTCTTTTT
1 TTTCTTTTTCATTTTCTTTTT
55398335 CAATCTCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 14 0.37
22 4 0.11
23 16 0.42
24 4 0.11
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.75
Consensus pattern (22 bp):
TTTCTTTTTCATTTTCTTTTTT
Found at i:55398319 original size:17 final size:17
Alignment explanation
Indices: 55398270--55398319 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
55398260 ACCTTTTCGA
55398270 TTTCTTTTTCTTTTGCAAT
1 TTTCTTTTT-TTTT-CAAT
55398289 TTT-TTTTCTTTTTC-AT
1 TTTCTTTT-TTTTTCAAT
55398305 TTTCTTTTTGTTTTC
1 TTTCTTTTT-TTTTC
55398320 TTTCAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.21
17 10 0.36
18 8 0.29
19 4 0.14
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTCTTTTTTTTTCAAT
Found at i:55398335 original size:6 final size:6
Alignment explanation
Indices: 55398187--55398322 Score: 53
Period size: 6 Copynumber: 22.7 Consensus size: 6
55398177 TCTTTTTTCA
** * * ** *
55398187 CTTTTT CTTTTT CAATTT -TTTTT CATTCT CAATTT CTTTTT CAATTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT
* * ** * ** *
55398235 CTTTTCTT CATTTT CTTTTT CTCTCA CCTTTT CGATTT CTTTTT CTTTTG
1 C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
** * *
55398285 CAATTT -TTTTT CTTTTT CATTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
55398323 CAATTTCTTT
Statistics
Matches: 89, Mismatches: 36, Indels: 10
0.66 0.27 0.07
Matches are distributed among these distances:
5 10 0.11
6 67 0.75
7 9 0.10
8 3 0.03
ACGTcount: A:0.10, C:0.18, G:0.02, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:55398351 original size:86 final size:85
Alignment explanation
Indices: 55398187--55398353 Score: 185
Period size: 86 Copynumber: 1.9 Consensus size: 85
55398177 TCTTTTTTCA
* **
55398187 CTTTTTCTTTTTCAATTTTTTTTCATTCTCAATTTCTTTTTCAATTTTCTTTTCTTCATTTTCTT
1 CTTTTTCTTTTGCAATTTTTTTTCATTCTCAATTTCTTTTT-AATTTTCTTTTCTTCATTTTCAA
*
55398252 TTTCTCTCACCTTTTCGATTT
65 TCTCTCTCACCTTTTCGATTT
* * * * *
55398273 CTTTTTCTTTTGCAATTTTTTTTCTTTTTCATTTTCTTTTT-GTTTTC-TTTCAATTTCTTTTTC
1 CTTTTTCTTTTGCAATTTTTTTTCATTCTCAATTTCTTTTTAATTTTCTTTTC---TTCATTTTC
* *
55398336 AATCTCTTTCTCCTTTTC
63 AATCTCTCTCACCTTTTC
55398354 TCGCTCAATG
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
83 4 0.06
84 5 0.07
86 58 0.87
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.68
Consensus pattern (85 bp):
CTTTTTCTTTTGCAATTTTTTTTCATTCTCAATTTCTTTTTAATTTTCTTTTCTTCATTTTCAAT
CTCTCTCACCTTTTCGATTT
Found at i:55400060 original size:14 final size:14
Alignment explanation
Indices: 55400015--55400067 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
55400005 AAAAAACTCG
55400015 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
* ***
55400029 AAAAAAAATTTTTG
1 AAAAAAAAATTCAA
55400043 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
55400057 AAAAAAAAATT
1 AAAAAAAAATT
55400068 TGGTTTCCAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (14 bp):
AAAAAAAAATTCAA
Found at i:55400064 original size:13 final size:13
Alignment explanation
Indices: 55400003--55400064 Score: 70
Period size: 13 Copynumber: 4.6 Consensus size: 13
55399993 TAGTTTCTCG
* *
55400003 AAAAAAAACTCGA
1 AAAAAAAATTCAA
55400016 AAAAAAAATTCAA
1 AAAAAAAATTCAA
**
55400029 AAAAAAAATTTTTGA
1 AAAAAAAA--TTCAA
55400044 AAAAAAAATTCAA
1 AAAAAAAATTCAA
55400057 AAAAAAAA
1 AAAAAAAA
55400065 ATTTGGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 30 0.73
15 11 0.27
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.16
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:55400129 original size:15 final size:16
Alignment explanation
Indices: 55400109--55400144 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
55400099 TCAAGTTGAC
55400109 AAAAAAA-TTCGTGAA
1 AAAAAAATTTCGTGAA
55400124 AAAAAAATTTCGTGAA
1 AAAAAAATTTCGTGAA
55400140 AAAAA
1 AAAAA
55400145 GAAGAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.19
Consensus pattern (16 bp):
AAAAAAATTTCGTGAA
Found at i:55403001 original size:58 final size:58
Alignment explanation
Indices: 55402911--55403697 Score: 1565
Period size: 58 Copynumber: 13.6 Consensus size: 58
55402901 AAAGTCATGC
55402911 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55402969 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403027 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403085 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403143 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403201 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403259 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403317 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403375 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403433 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403491 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403549 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
55403607 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
*
55403665 ATTATGTAACTTTCATGTTAGTTAAATTTGCAT
1 ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
55403698 TTCAAAACCA
Statistics
Matches: 728, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 728 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (58 bp):
ATTATGTAACTTTCATGTTAGTTAAGTTTGCATCATTAAATTAAGTCAAGTTAGTTTA
Found at i:55408798 original size:15 final size:14
Alignment explanation
Indices: 55408778--55408816 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
55408768 TTTTCACTCA
55408778 CTTTTTCTTTTTCAT
1 CTTTTTCTTTTTC-T
55408793 CTTTTTC-TTTTCT
1 CTTTTTCTTTTTCT
*
55408806 CATTTTCTTTT
1 CTTTTTCTTTT
55408817 CATTTCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 7 0.32
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (14 bp):
CTTTTTCTTTTTCT
Found at i:55408813 original size:13 final size:14
Alignment explanation
Indices: 55408780--55408819 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
55408770 TTCACTCACT
*
55408780 TTTTCTTTTTCATCT
1 TTTTC-TTTTCATCA
55408795 TTTTCTTTTC-TCA
1 TTTTCTTTTCATCA
55408808 TTTTCTTTTCAT
1 TTTTCTTTTCAT
55408820 TTCATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 12 0.52
14 6 0.26
15 5 0.22
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTTTTCATCA
Found at i:55408846 original size:19 final size:20
Alignment explanation
Indices: 55408813--55408865 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
55408803 TCTCATTTTC
* *
55408813 TTTTCATTTCATTTTTTGAA
1 TTTTCATTTCTTTTTTTCAA
*
55408833 TTTTC-TTTCTTTTTTTCAT
1 TTTTCATTTCTTTTTTTCAA
*
55408852 TTTTCTTTTCTTTT
1 TTTTCATTTCTTTT
55408866 GTATTTTCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTCATTTCTTTTTTTCAA
Found at i:55411317 original size:23 final size:23
Alignment explanation
Indices: 55411280--55411345 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
55411270 TCAGTTTAGG
* * *
55411280 TTTGTTACAAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
55411303 TTTGGTTA-GATATGGTATTACGA
1 TTTGG-TACGAAATGGTAATGCGA
55411326 TTTGGTACGAAATGGTAATG
1 TTTGGTACGAAATGGTAATG
55411346 GTTCAAAAAG
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
22 2 0.06
23 28 0.88
24 2 0.06
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.39
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:55413282 original size:19 final size:19
Alignment explanation
Indices: 55413258--55413350 Score: 70
Period size: 19 Copynumber: 5.1 Consensus size: 19
55413248 AATAAATTAC
*
55413258 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
55413277 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
* * *
55413296 T--GC-TAGAATAAATT-A-C
1 TCATCTTAG--TTAATTAAGT
* * *
55413312 TCATCTTGGTTAATTGAGC
1 TCATCTTAGTTAATTAAGT
55413331 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
55413350 T
1 T
55413351 GCTGGAATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
16 4 0.07
17 7 0.12
18 7 0.12
19 39 0.68
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:55413305 original size:54 final size:54
Alignment explanation
Indices: 55413239--55413392 Score: 263
Period size: 54 Copynumber: 2.9 Consensus size: 54
55413229 ATAAGTATTT
55413239 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
* * *
55413293 AGTTGCTAGAATAAATTACTCATCTTGGTTAATTGAGCTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
* *
55413347 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCAACTTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTA
55413393 ATTCACTTAG
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (54 bp):
AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
Found at i:55413705 original size:91 final size:90
Alignment explanation
Indices: 55413565--55413750 Score: 309
Period size: 91 Copynumber: 2.1 Consensus size: 90
55413555 TAGGTCAATT
*
55413565 AATTATTTAAAATCAGCTGTTACATGATTGGAATTAAAGGGAGGAATGAATTCAACTGTTATGAA
1 AATTATTTAAAATCAGCTATTACATGATTGGAATTAAAGGGAGGAATGAATTCAACTGTTATGAA
* *
55413630 GATTTAATTAAAGGCTAACAAGTTG
66 GATTGAATTAAAGGCCAACAAGTTG
* * *
55413655 AATTATTTAAAATCAGCTATTACATGGTTTGGCATTAAAGGGAGGAATGAATTCAGCTGTTATGA
1 AATTATTTAAAATCAGCTATTACAT-GATTGGAATTAAAGGGAGGAATGAATTCAACTGTTATGA
55413720 AGATTGAATTAAAGGCCAACAAGTTG
65 AGATTGAATTAAAGGCCAACAAGTTG
55413746 AATTA
1 AATTA
55413751 AAGGCCAGCA
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 24 0.27
91 65 0.73
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (90 bp):
AATTATTTAAAATCAGCTATTACATGATTGGAATTAAAGGGAGGAATGAATTCAACTGTTATGAA
GATTGAATTAAAGGCCAACAAGTTG
Found at i:55414540 original size:30 final size:30
Alignment explanation
Indices: 55414504--55414576 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
55414494 ACGAAGGAAA
*
55414504 AAGAAAATCAGGATTCACTTTCTTGTTTTC
1 AAGAAAATCAAGATTCACTTTCTTGTTTTC
55414534 AAGAAAATCAAGATTCACTTTCTTGTTTTC
1 AAGAAAATCAAGATTCACTTTCTTGTTTTC
55414564 AAGAAAATCAAGA
1 AAGAAAATCAAGA
55414577 AACCGAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (30 bp):
AAGAAAATCAAGATTCACTTTCTTGTTTTC
Found at i:55414588 original size:30 final size:30
Alignment explanation
Indices: 55414524--55414588 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
55414514 GGATTCACTT
** **
55414524 TCTTGTTTTCAAGAAAATCAAGATTCACTT
1 TCTTGTTTTCAAGAAAATCAAGAAACACAA
55414554 TCTTGTTTTCAAGAAAATCAAGAAAC-CGAA
1 TCTTGTTTTCAAGAAAATCAAGAAACAC-AA
55414584 TCTTG
1 TCTTG
55414589 GTCCAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (30 bp):
TCTTGTTTTCAAGAAAATCAAGAAACACAA
Found at i:55428043 original size:20 final size:20
Alignment explanation
Indices: 55428018--55428072 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
55428008 ACGAGTTAAA
* *
55428018 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
55428038 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
55428058 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
55428073 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:55435767 original size:11 final size:11
Alignment explanation
Indices: 55435751--55435806 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
55435741 CAAGTGAGGA
55435751 AAAAGAAAAAG
1 AAAAGAAAAAG
*
55435762 AAAAGAAAAAT
1 AAAAGAAAAAG
55435773 AAAAGTGAAAAAG
1 AAAA--GAAAAAG
*
55435786 --AAGAAAATG
1 AAAAGAAAAAG
55435795 AAAATGAAAAAG
1 AAAA-GAAAAAG
55435807 GCGAAAAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
9 6 0.17
11 18 0.50
12 6 0.17
13 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:55435818 original size:21 final size:22
Alignment explanation
Indices: 55435747--55435818 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 22
55435737 AAAACAAGTG
*
55435747 AGGAAAA-AGAAAAAGAAAAGAAA
1 AGGAAAAGTGAAAAAG--AAGAAA
**
55435770 AATAAAAGTGAAAAAGAAGAAA
1 AGGAAAAGTGAAAAAGAAGAAA
* **
55435792 ATGAAAA-TGAAAAAGGCGAAA
1 AGGAAAAGTGAAAAAGAAGAAA
55435813 AGGAAA
1 AGGAAA
55435819 GCGAGAGAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 17 0.43
22 11 0.28
23 5 0.12
24 7 0.17
ACGTcount: A:0.71, C:0.01, G:0.22, T:0.06
Consensus pattern (22 bp):
AGGAAAAGTGAAAAAGAAGAAA
Found at i:55438474 original size:38 final size:38
Alignment explanation
Indices: 55438422--55438497 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
55438412 TTATCACTGG
*
55438422 TGGCAAACCGTTTTGAGGGGTACCCAGGCTGAGAGACT
1 TGGCAAACCATTTTGAGGGGTACCCAGGCTGAGAGACT
* *
55438460 TGGCAAGCCATTTTGAGGGGTTCCCAGGCTGAGAGACT
1 TGGCAAACCATTTTGAGGGGTACCCAGGCTGAGAGACT
55438498 GACTTGGGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (38 bp):
TGGCAAACCATTTTGAGGGGTACCCAGGCTGAGAGACT
Found at i:55443686 original size:27 final size:27
Alignment explanation
Indices: 55443652--55444122 Score: 545
Period size: 27 Copynumber: 17.6 Consensus size: 27
55443642 CGAAAAGGTT
*
55443652 GTAAAATGACTGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* ** *
55443679 GTAAAATGACCGTAATGCATCTATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* **
55443706 ATAAAATGACCGTAATACCATTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
**
55443733 GTAAAATGACTATAATACCCCT-TAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
55443759 GTAAAATGACCGTAATACCCCTATAGC
1 GTAAAATGACCGTAATACCCCTGTAGG
* * *
55443786 GTAAAATGACCATAATACCCTTATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* * **
55443813 ATAAAATAATTGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
55443840 GTAAAATGACCGTAATACCCTTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* * * *
55443867 GTAAAATGACCATAATGCTCC-ATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* * *
55443893 ATAAAATGACCGTAATACCCTTATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
55443920 GTAAAATGACTGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
55443947 GTAAAATG-TCGTAATA-CCTTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
55443972 GTAAAATGACCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
55443999 GTAAAATGACCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
55444026 GTAAAATGACTGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* ** *
55444053 GTAAAATGATCGTAATGTCGCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
***
55444080 GTAAAATGATAATAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
55444107 GTAAAATGACCGTAAT
1 GTAAAATGACCGTAAT
55444123 TCCCTGGTGG
Statistics
Matches: 369, Mismatches: 71, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
25 16 0.04
26 55 0.15
27 298 0.81
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTGTAGG
Found at i:55443838 original size:107 final size:108
Alignment explanation
Indices: 55443652--55444127 Score: 577
Period size: 107 Copynumber: 4.4 Consensus size: 108
55443642 CGAAAAGGTT
* * *
55443652 GTAAAATGACTGTAATACCCCTGTAGGGTAAAATGACCGTAAT-GCATCTATAGGATAAAATGAC
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCT-TATAGGATAAAATGAC
* ** *
55443716 CGTAATACCATTGTAGGGTAAAATGACTATAATACCCCT-TAGG
65 TGTAATACCCCTGTAGGGTAAAATGACTGTAATACCCCTGTAGG
* * * * *
55443759 GTAAAATGACCGTAATACCCCTATAGCGTAAAATGACCATAATACCCTTATAGGATAAAATAATT
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGATAAAATGACT
* *
55443824 GTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTGTAGG
66 GTAATACCCCTGTAGGGTAAAATGACTGTAATACCCCTGTAGG
* * * * * *
55443867 GTAAAATGACCATAATGCTCC-ATAGGATAAAATGACCGTAATACCCTTATAGGGTAAAATGACT
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGATAAAATGACT
* * *
55443931 GTAATGCCCCTGTAGGGTAAAATGTC-GTAATA-CCTTGTAGG
66 GTAATACCCCTGTAGGGTAAAATGACTGTAATACCCCTGTAGG
* * * * *
55443972 GTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACT
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGATAAAATGACT
** *
55444037 GTAATACCCCTGTAGGGTAAAATGA-TCGTAATGTCGCTGTAGG
66 GTAATACCCCTGTAGGGTAAAATGACT-GTAATACCCCTGTAGG
*** *
55444080 GTAAAATGATAATAATACCCCTGTAGGGTAAAATGACCGTAATTCCCT
1 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCT
55444128 GGTGGGTAAA
Statistics
Matches: 320, Mismatches: 43, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
105 28 0.09
106 67 0.21
107 152 0.47
108 73 0.23
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (108 bp):
GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGATAAAATGACT
GTAATACCCCTGTAGGGTAAAATGACTGTAATACCCCTGTAGG
Found at i:55444194 original size:24 final size:24
Alignment explanation
Indices: 55444162--55444221 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
55444152 CTCAAGGTCA
55444162 AATGACTGATTTGTCTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
*
55444186 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
55444210 AATGACTGATTT
1 AATGACTGATTT
55444222 TGAGCATGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.20, C:0.08, G:0.25, T:0.47
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:55444401 original size:26 final size:26
Alignment explanation
Indices: 55444336--55444395 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
55444326 CTGGCCGTAT
*
55444336 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTACTACTGGCAGCTTTGCTGCG
*
55444362 ATACTGCTACTGGCAGCTTTGCTGCG
1 ATACTACTACTGGCAGCTTTGCTGCG
*
55444388 ATGCTACT
1 ATACTACT
55444396 GATGGCTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.33
Consensus pattern (26 bp):
ATACTACTACTGGCAGCTTTGCTGCG
Found at i:55444433 original size:32 final size:32
Alignment explanation
Indices: 55444392--55444530 Score: 163
Period size: 32 Copynumber: 4.4 Consensus size: 32
55444382 GCTGCGATGC
* *
55444392 TACTGATGGCTTTGTGCTGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
55444424 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * * *
55444456 TACTGATGGCTGTGTTCTGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
55444488 TACTGATGGATTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
55444519 TACTTATGGCTT
1 TACTGATGGCTT
55444531 GTAGCCATTC
Statistics
Matches: 91, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
31 10 0.11
32 81 0.89
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:55444755 original size:28 final size:28
Alignment explanation
Indices: 55444722--55444775 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
55444712 CAAACTGATA
* *
55444722 CTGTATCGGGCTTAGGCCCATACTGTTT
1 CTGTATCGGGCTAAGGCCCACACTGTTT
*
55444750 CTGTATTGGGCTAAGGCCCACACTGT
1 CTGTATCGGGCTAAGGCCCACACTGT
55444776 ACTATTACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (28 bp):
CTGTATCGGGCTAAGGCCCACACTGTTT
Found at i:55450676 original size:126 final size:126
Alignment explanation
Indices: 55450451--55450697 Score: 431
Period size: 126 Copynumber: 2.0 Consensus size: 126
55450441 GCTCACCCCT
* * * *
55450451 TTTAAATTTTAATTTCTCATATAATCGAGGTTAGGATGGGCTCAGTTTACGGTGGTGCTCTTGAT
1 TTTAAATTCTAATTTCTCATATAATCAAGGTTAGGATGGGCTCAGTTTACGGAGGTGCACTTGAT
55450516 CATTTTTCAGTAAACTATTTGTTTTGGGTATTTGATAATGTGGGATGTGTTTATGATGATA
66 CATTTTTCAGTAAACTATTTGTTTTGGGTATTTGATAATGTGGGATGTGTTTATGATGATA
* *
55450577 TTTAAATTCTAATTTCTCATATAATTAAGGTTAGGATGGGCTCGGTTTACGGAGGTGCACTTGAT
1 TTTAAATTCTAATTTCTCATATAATCAAGGTTAGGATGGGCTCAGTTTACGGAGGTGCACTTGAT
*
55450642 CATTTTTCAGTAAACTATTTGTTTTGGGTATTTGATAATTTGGGATGTGTTTATGA
66 CATTTTTCAGTAAACTATTTGTTTTGGGTATTTGATAATGTGGGATGTGTTTATGA
55450698 CGTGATCCTG
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 114 1.00
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.44
Consensus pattern (126 bp):
TTTAAATTCTAATTTCTCATATAATCAAGGTTAGGATGGGCTCAGTTTACGGAGGTGCACTTGAT
CATTTTTCAGTAAACTATTTGTTTTGGGTATTTGATAATGTGGGATGTGTTTATGATGATA
Found at i:55450941 original size:35 final size:35
Alignment explanation
Indices: 55450894--55450967 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
55450884 ATAAGTTTTT
*
55450894 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTA
1 AGTTGCTAGAATAAATTACTCATCTTAGTTAATTA
55450929 AGTTGCTAGAATAAATTACTCATCTTAGTTAATTA
1 AGTTGCTAGAATAAATTACTCATCTTAGTTAATTA
55450964 AGTT
1 AGTT
55450968 CATCTTAGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (35 bp):
AGTTGCTAGAATAAATTACTCATCTTAGTTAATTA
Found at i:55450972 original size:19 final size:19
Alignment explanation
Indices: 55450948--55450986 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
55450938 AATAAATTAC
55450948 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
55450967 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
55450986 T
1 T
55450987 TCTTAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:55455594 original size:18 final size:18
Alignment explanation
Indices: 55455571--55455605 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55455561 AGGAGAGAAT
55455571 GCCATCAGAGATAGTTGC
1 GCCATCAGAGATAGTTGC
*
55455589 GCCATCAGAGATGGTTG
1 GCCATCAGAGATAGTTG
55455606 TGAGGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (18 bp):
GCCATCAGAGATAGTTGC
Found at i:55468612 original size:13 final size:13
Alignment explanation
Indices: 55468594--55468618 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55468584 GTATTGATCA
55468594 TGTGTTCACACCT
1 TGTGTTCACACCT
55468607 TGTGTTCACACC
1 TGTGTTCACACC
55468619 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:55470713 original size:27 final size:27
Alignment explanation
Indices: 55470683--55470745 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
55470673 GAATGAATTT
* * *
55470683 CCTTTGTGGCATACTCTGTATATATAA
1 CCTTTGTGGCATACACTATATAGATAA
** * *
55470710 CCTTCATGGCCTACACTATATAGATCA
1 CCTTTGTGGCATACACTATATAGATAA
55470737 CCTTTGTGG
1 CCTTTGTGG
55470746 AATATTATAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (27 bp):
CCTTTGTGGCATACACTATATAGATAA
Found at i:55473602 original size:23 final size:22
Alignment explanation
Indices: 55473550--55473602 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
55473540 TCCTTGTCTT
*
55473550 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
55473572 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
55473595 TTTCTTTT
1 TTTCTTTT
55473603 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55473616 original size:18 final size:18
Alignment explanation
Indices: 55473595--55473634 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55473585 CTTTCTTCAA
* * *
55473595 TTTCTTTTTCACTTTTCT
1 TTTCTATTTCACATTCCT
55473613 TTTCTATTTCACATTCCT
1 TTTCTATTTCACATTCCT
55473631 TTTC
1 TTTC
55473635 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCTATTTCACATTCCT
Found at i:55477792 original size:15 final size:14
Alignment explanation
Indices: 55477756--55477810 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
55477746 TCTATCGAGC
55477756 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
55477770 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
55477784 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
55477799 GAAAGAAAAGAA
1 GAGA-AAAAGAA
55477811 GGACGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:55496071 original size:37 final size:37
Alignment explanation
Indices: 55496020--55496090 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
55496010 CATTCTTGTA
55496020 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
55496057 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
55496091 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:55496090 original size:6 final size:6
Alignment explanation
Indices: 55496030--55496079 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
55496020 AAGAGAAAAC
*
55496030 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
55496079 A
1 A
55496080 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:55498373 original size:30 final size:30
Alignment explanation
Indices: 55498339--55498435 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
55498329 AGCTCACTCC
55498339 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
55498369 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
55498399 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
55498429 TAGCTCA
1 TAGCTCA
55498436 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:55503373 original size:31 final size:32
Alignment explanation
Indices: 55503338--55503403 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
55503328 GACAAATAAA
*
55503338 TATAATGCATGACATAATTAAA-ATGCAAACT
1 TATAATGCAAGACATAATTAAAGATGCAAACT
* *
55503369 TATAATGCAAGCCATTATTAAAGATGCAAACT
1 TATAATGCAAGACATAATTAAAGATGCAAACT
55503401 TAT
1 TAT
55503404 TAAATTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (32 bp):
TATAATGCAAGACATAATTAAAGATGCAAACT
Found at i:55522492 original size:17 final size:17
Alignment explanation
Indices: 55522467--55522503 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
55522457 GATAAGTATA
*
55522467 CATTTTCATTACATTTT
1 CATTGTCATTACATTTT
55522484 CATTGTCATTACATTTT
1 CATTGTCATTACATTTT
55522501 CAT
1 CAT
55522504 GTTAGTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.03, T:0.54
Consensus pattern (17 bp):
CATTGTCATTACATTTT
Found at i:55527929 original size:16 final size:16
Alignment explanation
Indices: 55527908--55527940 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55527898 AGGAAGACAG
55527908 AAAAAGA-AATCGAAAA
1 AAAAAGAGAAT-GAAAA
55527924 AAAAAGAGAATGAAAA
1 AAAAAGAGAATGAAAA
55527940 A
1 A
55527941 GAGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAAAGAGAATGAAAA
Found at i:55529673 original size:22 final size:24
Alignment explanation
Indices: 55529639--55529682 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
55529629 CTTGGACCAA
55529639 GATTTCCAAGA-T-TTGAAATCTT
1 GATTTCCAAGATTCTTGAAATCTT
* *
55529661 GATTTTCATGATTCTTGAAATC
1 GATTTCCAAGATTCTTGAAATC
55529683 GCTCCAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 1 0.06
24 8 0.44
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (24 bp):
GATTTCCAAGATTCTTGAAATCTT
Found at i:55529762 original size:22 final size:24
Alignment explanation
Indices: 55529728--55529771 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
55529718 CTTGGACCAA
55529728 GATTTCCAAGA-T-TTGAAATCTT
1 GATTTCCAAGATTCTTGAAATCTT
* *
55529750 GATTTTCATGATTCTTGAAATC
1 GATTTCCAAGATTCTTGAAATC
55529772 GCTCCAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 1 0.06
24 8 0.44
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (24 bp):
GATTTCCAAGATTCTTGAAATCTT
Found at i:55529767 original size:89 final size:89
Alignment explanation
Indices: 55529616--55529810 Score: 390
Period size: 89 Copynumber: 2.2 Consensus size: 89
55529606 GCTTTGGCTG
55529616 CAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCATGATTCTTGAAA
1 CAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCATGATTCTTGAAA
55529681 TCGCTCCAAACAACAAAATTGGGC
66 TCGCTCCAAACAACAAAATTGGGC
55529705 CAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCATGATTCTTGAAA
1 CAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCATGATTCTTGAAA
55529770 TCGCTCCAAACAACAAAATTGGGC
66 TCGCTCCAAACAACAAAATTGGGC
55529794 CAAGATTCGGTTTCTTG
1 CAAGATTCGGTTTCTTG
55529811 ATTTTCTTGA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 106 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (89 bp):
CAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCATGATTCTTGAAA
TCGCTCCAAACAACAAAATTGGGC
Found at i:55531238 original size:33 final size:34
Alignment explanation
Indices: 55531201--55531272 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
55531191 GAGTTGGTTT
55531201 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
* *
55531234 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
55531268 ATTAA
1 ATTAA
55531273 TTTGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:55532014 original size:89 final size:89
Alignment explanation
Indices: 55531863--55532057 Score: 390
Period size: 89 Copynumber: 2.2 Consensus size: 89
55531853 TCAAGAAAAT
55531863 CAAGAAACCGAATCTTGGTCCAATTTTGTTGTTTTGAGCCATTTCAAGAATCAAGAAAATCAAGA
1 CAAGAAACCGAATCTTGGTCCAATTTTGTTGTTTTGAGCCATTTCAAGAATCAAGAAAATCAAGA
55531928 TTTCAAATCTTGGAAATCTTGGTC
66 TTTCAAATCTTGGAAATCTTGGTC
55531952 CAAGAAACCGAATCTTGGTCCAATTTTGTTGTTTTGAGCCATTTCAAGAATCAAGAAAATCAAGA
1 CAAGAAACCGAATCTTGGTCCAATTTTGTTGTTTTGAGCCATTTCAAGAATCAAGAAAATCAAGA
55532017 TTTCAAATCTTGGAAATCTTGGTC
66 TTTCAAATCTTGGAAATCTTGGTC
55532041 CAAGAAACCGAATCTTG
1 CAAGAAACCGAATCTTG
55532058 CAGCTAAGGC
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 106 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (89 bp):
CAAGAAACCGAATCTTGGTCCAATTTTGTTGTTTTGAGCCATTTCAAGAATCAAGAAAATCAAGA
TTTCAAATCTTGGAAATCTTGGTC
Found at i:55534470 original size:23 final size:24
Alignment explanation
Indices: 55534424--55534472 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
55534414 TTTAAACTTT
*
55534424 AATTTCATTTTATCTGTTAGTTTA
1 AATTTCATTTTATCTGTTAATTTA
55534448 AATTT-ATTTTATCT-TTATATTTA
1 AATTTCATTTTATCTGTTA-ATTTA
55534471 AA
1 AA
55534473 AATTGAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 3 0.13
23 15 0.65
24 5 0.22
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (24 bp):
AATTTCATTTTATCTGTTAATTTA
Found at i:55535724 original size:16 final size:16
Alignment explanation
Indices: 55535678--55535727 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
55535668 TAAAATTAAA
55535678 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
55535695 A-A--AATAATAAATT
1 ATATTAATAATTTATT
55535708 ATATTAATAATTTATT
1 ATATTAATAATTTATT
55535724 ATAT
1 ATAT
55535728 GACAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:55538924 original size:50 final size:50
Alignment explanation
Indices: 55538809--55538993 Score: 253
Period size: 50 Copynumber: 3.7 Consensus size: 50
55538799 GATAATAACA
* **
55538809 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATATTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGG
* * ** *
55538860 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATTTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
55538910 TGCCAACGCCATGTCCAAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
55538960 TGCCAACGCCATGTCCCAAACATGGTCTTACATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
55538994 CTTTACCCAA
Statistics
Matches: 118, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 85 0.72
51 33 0.28
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:55540878 original size:20 final size:20
Alignment explanation
Indices: 55540853--55540893 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55540843 AATTAATTAA
55540853 TTTATTCTAAATTTTCAAAT
1 TTTATTCTAAATTTTCAAAT
* **
55540873 TTTATTTTATGTTTTCAAAT
1 TTTATTCTAAATTTTCAAAT
55540893 T
1 T
55540894 ATCATTAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTATTCTAAATTTTCAAAT
Done.