Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1373533 original size:194 final size:197
Alignment explanation
Indices: 1373279--1373645 Score: 461
Period size: 195 Copynumber: 1.9 Consensus size: 197
1373269 AATATTTTTT
* * ** * *
1373279 TTATAATTTATTATTGTGAAAAAATATTATTTTTCATAATTTTTTTATAATGAGAAATTAATATT
1 TTATAAATGATTATTGTGAAAAAATATTATTTGCCATAATCTTTTTATAATAAGAAATTAATATT
* * * * * *
1373344 TGTTATAAATTATTATTTTGATTAAATAAATTTATCAAAAGATGTT-TTTTGAGAAAATATTGTG
66 TATTATAAATTATTATTATAACTAAATAAAATTATCAAAAGATGTTATTTTGAAAAAATATTGTG
* *
1373408 ACAAAATAAATTTAACATAATTTTTTATTTTGACTAAATTTAAAGTTATTGTGACTAAATAAATT
131 ACAAAACAAATTTAACATAATTTTTTATTTTAACTAAATTTAAAGTTATTGTGACTAAATAAATT
1373473 TG
196 TG
*
1373475 TTATAAATGATTATTGT-AAAAAATATTATTTGCCATAA-CTTTTTATATTAAGAAATTAATATT
1 TTATAAATGATTATTGTGAAAAAATATTATTTGCCATAATCTTTTTATAATAAGAAATTAATATT
* * * * * * ** *
1373538 TATTATAATTTGTTGTTATAACTAATTAAAATTGTCATAATTTGTTATTTTGAAAAAATATTTTG
66 TATTATAAATTATTATTATAACTAAATAAAATTATCAAAAGATGTTATTTTGAAAAAATATTGTG
* * **
1373603 ACTAAACACATTTGTCATAATTTTTTATTTTAACTAAATTTAA
131 ACAAAACAAATTTAACATAATTTTTTATTTTAACTAAATTTAA
1373646 TTTGTTCTTT
Statistics
Matches: 142, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
194 55 0.39
195 72 0.51
196 15 0.11
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (197 bp):
TTATAAATGATTATTGTGAAAAAATATTATTTGCCATAATCTTTTTATAATAAGAAATTAATATT
TATTATAAATTATTATTATAACTAAATAAAATTATCAAAAGATGTTATTTTGAAAAAATATTGTG
ACAAAACAAATTTAACATAATTTTTTATTTTAACTAAATTTAAAGTTATTGTGACTAAATAAATT
TG
Found at i:1373681 original size:31 final size:31
Alignment explanation
Indices: 1373643--1373707 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1373633 TAACTAAATT
* * *
1373643 TAATTTGTTCTTTTGTTTATATAAATTATCA
1 TAATTTGTTATTTTGTCTAAATAAATTATCA
1373674 TAATTTGTTATTTTGTCTAAATAAATTATCA
1 TAATTTGTTATTTTGTCTAAATAAATTATCA
1373705 TAA
1 TAA
1373708 ATTATCTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (31 bp):
TAATTTGTTATTTTGTCTAAATAAATTATCA
Found at i:1381728 original size:3 final size:3
Alignment explanation
Indices: 1381703--1381773 Score: 110
Period size: 3 Copynumber: 24.0 Consensus size: 3
1381693 TTTGGGTTTT
*
1381703 TTA TTT TTA TT- TTA TTA TT- TTA TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1381747 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1381774 CATGCCCAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 4 0.06
3 56 0.89
4 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1390446 original size:75 final size:75
Alignment explanation
Indices: 1390323--1390571 Score: 331
Period size: 75 Copynumber: 3.3 Consensus size: 75
1390313 TCAACAAAAA
* * * * * *
1390323 AGCAAATGTTGGGGTATGTTGAAAACCCATTTCAATCATAATCAGGAATATTGACGCATTTTGAA
1 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAATGAGGAATATTGACGCATTTTGAA
1390388 CGTTTGTATC
66 CGTTTGTATC
* *
1390398 AGCAAATGCTGGGGCATGCTGAAAGCCCAATTCAATCAGAATGAGGAATATTGACGTATTTTGAA
1 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAATGAGGAATATTGACGCATTTTGAA
1390463 CGTTTGTATC
66 CGTTTGTATC
* * * *
1390473 AGCAAATGCTGGGGTATGCTGAAAAGCCCATTTCAATCAGAATGAAGAATGTTGGCGCATTTTGA
1 AGCAAATGCTGGGGCATGCTG-AAAGCCCATTTCAATCAGAATGAGGAATATTGACGCATTTTGA
*
1390538 ACG-TTGTATT
65 ACGTTTGTATC
* * *
1390548 AACAAATGTTAGGGCATGCT-AAAG
1 AGCAAATGCTGGGGCATGCTGAAAG
1390572 GCTCATATTA
Statistics
Matches: 154, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
73 4 0.03
75 109 0.71
76 41 0.27
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (75 bp):
AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAATGAGGAATATTGACGCATTTTGAA
CGTTTGTATC
Found at i:1398043 original size:21 final size:22
Alignment explanation
Indices: 1398019--1398100 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
1398009 TTGGTGCAGA
* * *
1398019 GGGAATCGATCCCCCCCCTGA-
1 GGGAACCGATTCCCCCCATGAG
**
1398040 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATG-AG
1398063 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGATTCCCCCCATGAG
* *
1398084 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
1398101 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 33 0.65
22 1 0.02
23 17 0.33
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCATGAG
Found at i:1401534 original size:22 final size:22
Alignment explanation
Indices: 1401506--1401565 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
1401496 TCAACAACAT
*
1401506 TCTTCAAATATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1401528 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAGATTCTC
1401550 TCTTCAAAGATGATAG
1 TCTTCAAAGATGATAG
1401566 GTTTTCTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1402406 original size:245 final size:249
Alignment explanation
Indices: 1402002--1402554 Score: 873
Period size: 245 Copynumber: 2.2 Consensus size: 249
1401992 TATTTAATAG
*
1402002 TGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
1 TGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
1402067 ATGACTCTATCACAGAAGGAGATAGATCAACATACACTTTGCCAGAGAAAGTTCACAATAAGAAG
66 ATGACTCTATCACAGAAGGAGATAGATCAACATACACTTTGCCAGAGAAAGTTCACAATAAGAAG
* * * * * *
1402132 AATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAACAACTTGTTCAACTTTTTGCTTGATTC
131 AAATTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAACAACTTGTTCAACCTTTTGCGTAACTC
*
1402197 TATCACAGAAGGAGATAGATCAACATCAACA-T-TTT-CAAA-AGTGTTCATAA
196 TATCACAGAAGGAGATAGATCAACATCAACATTATTTCCAAAGAGAGTTCATAA
*
1402247 TGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
1 TGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * *
1402312 ATGATTCTATCACAGAAGGAGATAGATCAGCATACACTTTTCCAGAGAAAGTTCATAATGAGAAG
66 ATGACTCTATCACAGAAGGAGATAGATCAACATACACTTTGCCAGAGAAAGTTCACAATAAGAAG
* *
1402377 AAATTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCGTAACTC
131 AAATTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAACAACTTGTTCAACCTTTTGCGTAACTC
*
1402442 TATCACAGAAGGAGATAGATCAGCATCAACATTCATTTCCCAAAGAGAGTTCATAA
196 TATCACAGAAGGAGATAGATCAACATCAACATT-ATTT-CCAAAGAGAGTTCATAA
* *
1402498 TGAGAAGAGCTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
1 TGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1402555 GATTGCCTTA
Statistics
Matches: 281, Mismatches: 20, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
245 210 0.75
246 1 0.00
248 3 0.01
250 4 0.01
251 60 0.21
252 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (249 bp):
TGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
ATGACTCTATCACAGAAGGAGATAGATCAACATACACTTTGCCAGAGAAAGTTCACAATAAGAAG
AAATTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAACAACTTGTTCAACCTTTTGCGTAACTC
TATCACAGAAGGAGATAGATCAACATCAACATTATTTCCAAAGAGAGTTCATAA
Found at i:1402407 original size:123 final size:124
Alignment explanation
Indices: 1402002--1402554 Score: 760
Period size: 123 Copynumber: 4.5 Consensus size: 124
1401992 TATTTAATAG
* *
1402002 TGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
1 TGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
1402067 ATGACTCTATCACAGAAGGAGATAGATCAACATACAC-TTTGCCAGAGAAAGTTCACAA
66 ATGACTCTATCACAGAAGGAGATAGATCAACATACACATTTTCCAGAGAAAGTTCATAA
* * * * *
1402125 TAAGAAGAATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAACAACTTGTTCAACTTTTTGC
1 TGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
1402190 TTGATTCTATCACAGAAGGAGATAGATCAACAT-CAACATTTT-CA-A-AAGTGTTCATAA
66 ATGACTCTATCACAGAAGGAGATAGATCAACATAC-ACATTTTCCAGAGAA-AGTTCATAA
1402247 TGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
1 TGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
1402312 ATGATTCTATCACAGAAGGAGATAGATCAGCATACAC-TTTTCCAGAGAAAGTTCATAA
66 ATGACTCTATCACAGAAGGAGATAGATCAACATACACATTTTCCAGAGAAAGTTCATAA
* * *
1402370 TGAGAAGAAATTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGC
1 TGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * *
1402435 GTAACTCTATCACAGAAGGAGATAGATCAGCATCAACATTCATTTCCCAAAGAGAGTTCATAA
66 ATGACTCTATCACAGAAGGAGATAGATCAACAT--ACA--CATTTTCCAGAGAAAGTTCATAA
** *
1402498 TGAGAAGAGCTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
1 TGAGAAGAAATCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1402555 GATTGCCTTA
Statistics
Matches: 385, Mismatches: 32, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
121 6 0.02
122 104 0.27
123 196 0.51
124 5 0.01
125 3 0.01
127 1 0.00
128 67 0.17
129 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (124 bp):
TGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
ATGACTCTATCACAGAAGGAGATAGATCAACATACACATTTTCCAGAGAAAGTTCATAA
Found at i:1402919 original size:3 final size:3
Alignment explanation
Indices: 1402905--1402967 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
1402895 TTTGGGTTTT
* *
1402905 TTA TTT TTA TTA TTA TT- TTA TTTA TTA CTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
1402949 TTTA TTA TTA TTA TTA TTA
1 -TTA TTA TTA TTA TTA TTA
1402968 CAGGCCCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1402943 original size:24 final size:24
Alignment explanation
Indices: 1402911--1402967 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
1402901 TTTTTTATTT
*
1402911 TTATTATTATTTTATTTATTACTA
1 TTATTATTATATTATTTATTACTA
*
1402935 TTATTATTATATTATTTATTATTA
1 TTATTATTATATTATTTATTACTA
1402959 TTATTATTA
1 TTATTATTA
1402968 CAGGCCCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTATTATTATATTATTTATTACTA
Found at i:1404524 original size:17 final size:18
Alignment explanation
Indices: 1404504--1404539 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1404494 TTTATAAAAA
1404504 TATAAAAAAT-ATATATT
1 TATAAAAAATAATATATT
*
1404521 TATAAAAATTAATATATT
1 TATAAAAAATAATATATT
1404539 T
1 T
1404540 TCTTGGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAAAATAATATATT
Found at i:1404531 original size:149 final size:147
Alignment explanation
Indices: 1404256--1404522 Score: 362
Period size: 149 Copynumber: 1.8 Consensus size: 147
1404246 TAATAATATT
* * * *
1404256 TATTTATTTATTTTTAAATTTTAAGAAATGGGATGTCTTAAAGCAACTAGAAGTCATTTTCTGAT
1 TATTTATTTATTTTTAAATATTAAGAAAGGGGATGTCTTAAAGCAACTAGAAATCATTTTCTAAT
* ** *
1404321 ATTTTTAAAAATAAATAATATCCTACTTTTATAAATTATATATATTAATTTATTTTTAATTATTT
66 ATTTTT-AAAATAAATAATATCCTAC-TTTATAAATAATATATAAAAATTTATTTTAAATTATTT
1404386 TTAGAAAATATTTTATTAA
129 TTAGAAAATATTTTATTAA
*
1404405 TATTTATTTATTTTTAAATATTAAGAAAGGGGATGTCTTAAAGCAACTAGAAATCCTTTTCTAAT
1 TATTTATTTATTTTTAAATATTAAGAAAGGGGATGTCTTAAAGCAACTAGAAATCATTTTCTAAT
* * *
1404470 ATTTTT-AAGTAAATAAATATCTTA-TTTATAAA-AATATA-AAAAATATATATTTA
66 ATTTTTAAAATAAAT-AATATCCTACTTTATAAATAATATATAAAAATTTAT-TTTA
1404523 TAAAAATTAA
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
144 7 0.07
145 8 0.08
146 8 0.08
147 7 0.07
148 8 0.08
149 66 0.63
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (147 bp):
TATTTATTTATTTTTAAATATTAAGAAAGGGGATGTCTTAAAGCAACTAGAAATCATTTTCTAAT
ATTTTTAAAATAAATAATATCCTACTTTATAAATAATATATAAAAATTTATTTTAAATTATTTTT
AGAAAATATTTTATTAA
Found at i:1406440 original size:34 final size:35
Alignment explanation
Indices: 1406395--1406484 Score: 139
Period size: 34 Copynumber: 2.6 Consensus size: 35
1406385 CAACTTTGAA
1406395 AAAATGG-TTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1406429 -AAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
*
1406463 AAAAATAGTTTTTCAAAGTTTG
1 -AAAAT-GGTTTTCAAAGTTTG
1406485 TAGATGCTTG
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
33 6 0.12
34 27 0.53
36 4 0.08
37 14 0.27
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:1407271 original size:17 final size:17
Alignment explanation
Indices: 1407249--1407283 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1407239 ACTAACACAA
1407249 TCACAACCCAGTTGAGT
1 TCACAACCCAGTTGAGT
*
1407266 TCACAACCTAGTTGAGT
1 TCACAACCCAGTTGAGT
1407283 T
1 T
1407284 TCAGTGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (17 bp):
TCACAACCCAGTTGAGT
Found at i:1410931 original size:36 final size:36
Alignment explanation
Indices: 1410818--1410936 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
1410808 TGGTAACCAA
1410818 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1410854 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
1410889 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGCTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
1410926 -GTTGAAAAATG
1 CTTTGAAAAATG
1410937 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 36 0.47
36 19 0.25
37 22 0.29
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1412207 original size:29 final size:27
Alignment explanation
Indices: 1412151--1412211 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
1412141 AATATAATTG
*
1412151 ATTATTTTATATAATATTAAAAATATA
1 ATTATATTATATAATATTAAAAATATA
1412178 ATTATATTATA-AATATTAATAAATA-A
1 ATTATATTATATAATATTAA-AAATATA
*
1412204 ATAATATT
1 ATTATATT
1412212 TTGATGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTATATTATATAATATTAAAAATATA
Found at i:1412959 original size:31 final size:31
Alignment explanation
Indices: 1412933--1412994 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1412923 TATAATTGAT
1412933 TATT-TTATATAATATTAAAAATATAATATTA
1 TATTATTATA-AATATTAAAAATATAATATTA
*
1412964 TATTATTATAAATATTAAAATAAATAATATT
1 TATTATTATAAATATTAAAA-ATATAATATT
1412995 TTGATGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
TATTATTATAAATATTAAAAATATAATATTA
Found at i:1413560 original size:785 final size:780
Alignment explanation
Indices: 1411998--1413701 Score: 3119
Period size: 785 Copynumber: 2.2 Consensus size: 780
1411988 AAAATCTTAT
1411998 CAAATTAATAGAATTTCTAGATATTAAAAATCATTGAATTATTTTTGAATTGCGACAAATTTGAT
1 CAAATTAATAGAATTTCTAGATATTAAAAATCATTGAATTATTTTTGAATTGCGACAAATTTGAT
1412063 AGAATGTATAAATGTACACCCAGAATCATTAAGGATGGGCATGAGACCCGAATTCGACGAGTTTC
66 AGAATGTATAAATGTACACCCAGAATCATTAAGGATGGGCATGAGACCCGAATTCGACGAGTTTC
1412128 GACCTAATCTGATAATATAATTGATTATTTTATATAATATTAAAAATATAATTATATTATAAATA
131 GACCTAATCTGATAATATAATTGATTATTTTATATAATATTAAAAATATAATTATATTATAAATA
1412193 TTAATAAATAAATAATATTTTGATGAAAATGATATTAAAAATATTTATTAATATTAAATTCATAA
196 TTAATAAATAAATAATATTTTGATGAAAATGATATTAAAAATATTTATTAATATTAAATTCATAA
1412258 AATAAAATTATTTTAAGTATTTATTCTTTGAAGTGAAAAGTTCGGAAAATGATTTACGGAAAATG
261 AATAAAATTATTTTAAGTATTTATTCTTTGAAGTGAAAAGTTCGGAAAATGATTTACGGAAAATG
* *
1412323 AATCTGTAAGTCATTTTACAGAAAACACAAAGGAAATTCTGTTACTAGAAAAATGAATTACATTC
326 AATCTGTAAGTCATTTTACAGAAAACACAAAGGAAATTATGTTACTAGAAAAATAAATTACATTC
1412388 CGGAAAACCAATTACGTGAAACAAACACGGGAAAACATTTTCCAGAAAACGAATTACGTGAAACA
391 CGGAAAACCAATTACGTGAAACAAACACGGGAAAACATTTTCCAGAAAACGAATTACGTGAAACA
* ** * *
1412453 AATATGGGAATTTAGGGAAAACCAATTCTGTAATTCCAAATCGTCAAGCAACACACCCTAAATTT
456 AACACAGAAATTTAGGGAAAACCAATTCTGTAATTCCAAATCGACAAGCAACACACCCTAAATTT
** *
1412518 AGCGTTTATACGTAGTGGTGCTCAAAATCGAGTATCCAAAAATTTTCAGGTACCAAAATGTCGGT
521 AGCGTTTATACGTAGTGGTGCTCAAAATCGAGTATCCAAAAATTTTCAAATACCAAAATGCCGGT
1412583 CGGTGTCTCGGCTTATTACATTTAGCTACCCATAAGTCAGATACATGTATTTTCAGATCAGTATC
586 CGGTGTCTCGGCTTATTACATTTAGCTACCCATAAGTCAGATACATGTATTTTCAGATCAGTATC
1412648 CGGTTCATAATTTTTTTATTTAAAAAATTATATAAAAATTTAAAATTACATTTGGCTAAACATCG
651 CGGTTCATAATTTTTTTATTTAAAAAATTATATAAAAATTTAAAATTACATTTGGCTAAACATCG
* *
1412713 ATGTAAGGGACCGATAAGGGATGTGACTGACATAGAGAGGCGATGATGGTGATTTTATGTTCGAC
716 ATGTAAGGGACCGACAAGGGATGCGACTGACATAGAGAGGCGATGATGGTGATTTTATGTTCGAC
1412778 CAAATTAATAGAATTTCTAGATATTAAAAATCATTGAATTATTTTTGAATTGCGACAAATTTGAT
1 CAAATTAATAGAATTTCTAGATATTAAAAATCATTGAATTATTTTTGAATTGCGACAAATTTGAT
1412843 AGAATGTATAAATGTACACCCAGAATCATTAAGGATGGGCATGAGACCCGAATTCGACGAGTTTC
66 AGAATGTATAAATGTACACCCAGAATCATTAAGGATGGGCATGAGACCCGAATTCGACGAGTTTC
1412908 GACCTAATCTGATAATATAATTGATTATTTTATATAATATTAAAAATATAATATTATATTATTAT
131 GACCTAATCTGATAATATAATTGATTATTTTATATAATATTAAAAATAT-A-A-T-TA-TATTAT
1412973 AAATATT-A-AAATAAATAATATTTTGATGAAAATGATATT-AAAATATTTTATTAATATTAAAT
191 AAATATTAATAAATAAATAATATTTTGATGAAAATGATATTAAAAATA-TTTATTAATATTAAAT
1413035 TCATAAAATAAAATTATTTTAAGTATTTATTCTTTGAAGTGAAAAGTTCGGAAAATGATTTACGG
255 TCATAAAATAAAATTATTTTAAGTATTTATTCTTTGAAGTGAAAAGTTCGGAAAATGATTTACGG
1413100 AAAATGAATCTGTAAGTCATTTTACAGAAAACACAAAGGAAATTATGTTACTAGAAAAATAAATT
320 AAAATGAATCTGTAAGTCATTTTACAGAAAACACAAAGGAAATTATGTTACTAGAAAAATAAATT
* *
1413165 ACATTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAATATTTTCCGGAAAACGAATTACGT
385 ACATTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATTTTCCAGAAAACGAATTACGT
1413230 GAAACAAACACAGAAATTTAGGGAAAACCAATT-TCGTAATTCCAAATACGACAAGCAAACACAC
450 GAAACAAACACAGAAATTTAGGGAAAACCAATTCT-GTAATTCCAAAT-CGACAAGC-AACACAC
*
1413294 CCTAAATTTAGCGTTTATACGTAGTGGTGTTCAAAATCGAGTATCCAAAAATTTTCAAATACCAA
512 CCTAAATTTAGCGTTTATACGTAGTGGTGCTCAAAATCGAGTATCCAAAAATTTTCAAATACCAA
*
1413359 AATGCCGGTCGGTGTCTCGGCTTATTACATTTAGCTACCCATAAGTCAGATACATGTATTTTCAT
577 AATGCCGGTCGGTGTCTCGGCTTATTACATTTAGCTACCCATAAGTCAGATACATGTATTTTCAG
1413424 ATCAGTATCCGGTTCATAATTTTTTTATTTAAAAAATTATATAAAAATTTAAAATTACATTTGGC
642 ATCAGTATCCGGTTCATAATTTTTTTATTTAAAAAATTATATAAAAATTTAAAATTACATTTGGC
*
1413489 TAAACATCGATGTAAGGGACCGACAAGGGATGCGACTGACATAGAGGGGCGATGATGGTGATTTT
707 TAAACATCGATGTAAGGGACCGACAAGGGATGCGACTGACATAGAGAGGCGATGATGGTGATTTT
1413554 ATGTTCGAC
772 ATGTTCGAC
*
1413563 CAAATTAATAGAATTTCTAGATATTAAAATTCATTGAATTATTTTTGAATTGCGACAAATTTGAT
1 CAAATTAATAGAATTTCTAGATATTAAAAATCATTGAATTATTTTTGAATTGCGACAAATTTGAT
* *
1413628 AGAATGTATAAATGTACACCCAGAATCATTAAGGATGGGCATGAGACCCGAACTCGACGAATTTC
66 AGAATGTATAAATGTACACCCAGAATCATTAAGGATGGGCATGAGACCCGAATTCGACGAGTTTC
1413693 GACCTAATC
131 GACCTAATC
1413702 CGATCGGATT
Statistics
Matches: 895, Mismatches: 20, Indels: 13
0.96 0.02 0.01
Matches are distributed among these distances:
780 179 0.20
781 1 0.00
782 8 0.01
783 280 0.31
784 10 0.01
785 417 0.47
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (780 bp):
CAAATTAATAGAATTTCTAGATATTAAAAATCATTGAATTATTTTTGAATTGCGACAAATTTGAT
AGAATGTATAAATGTACACCCAGAATCATTAAGGATGGGCATGAGACCCGAATTCGACGAGTTTC
GACCTAATCTGATAATATAATTGATTATTTTATATAATATTAAAAATATAATTATATTATAAATA
TTAATAAATAAATAATATTTTGATGAAAATGATATTAAAAATATTTATTAATATTAAATTCATAA
AATAAAATTATTTTAAGTATTTATTCTTTGAAGTGAAAAGTTCGGAAAATGATTTACGGAAAATG
AATCTGTAAGTCATTTTACAGAAAACACAAAGGAAATTATGTTACTAGAAAAATAAATTACATTC
CGGAAAACCAATTACGTGAAACAAACACGGGAAAACATTTTCCAGAAAACGAATTACGTGAAACA
AACACAGAAATTTAGGGAAAACCAATTCTGTAATTCCAAATCGACAAGCAACACACCCTAAATTT
AGCGTTTATACGTAGTGGTGCTCAAAATCGAGTATCCAAAAATTTTCAAATACCAAAATGCCGGT
CGGTGTCTCGGCTTATTACATTTAGCTACCCATAAGTCAGATACATGTATTTTCAGATCAGTATC
CGGTTCATAATTTTTTTATTTAAAAAATTATATAAAAATTTAAAATTACATTTGGCTAAACATCG
ATGTAAGGGACCGACAAGGGATGCGACTGACATAGAGAGGCGATGATGGTGATTTTATGTTCGAC
Found at i:1419649 original size:18 final size:18
Alignment explanation
Indices: 1419626--1419673 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1419616 AAATTGTCCT
* *
1419626 TATTATATATTTGTATAA
1 TATTATATATTTATAAAA
*
1419644 TATTATA-AATTATAAAA
1 TATTATATATTTATAAAA
1419661 TATTTATATATTT
1 TA-TTATATATTT
1419674 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTATATATTTATAAAA
Found at i:1419731 original size:32 final size:31
Alignment explanation
Indices: 1419650--1419731 Score: 83
Period size: 37 Copynumber: 2.4 Consensus size: 31
1419640 ATAATATTAT
1419650 AAATTATAAAATATTTATATATTTTCTTTAAA
1 AAATTA-AAAATATTTATATATTTTCTTTAAA
* *
1419682 AAATTAAATTCATAATATTTATATAATTTTTTTTACA
1 AAATT-AA---A-AATATTTATAT-ATTTTCTTTAAA
1419719 AAATTAAAAATAT
1 AAATTAAAAATAT
1419732 AAAAAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
32 11 0.26
33 2 0.05
35 1 0.02
36 13 0.31
37 15 0.36
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATTAAAAATATTTATATATTTTCTTTAAA
Found at i:1420370 original size:21 final size:21
Alignment explanation
Indices: 1420344--1420419 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1420334 ATGCGTAAGT
1420344 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1420365 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1420385 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
1420406 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1420420 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1420389 original size:41 final size:40
Alignment explanation
Indices: 1420329--1420421 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 40
1420319 TTTTCCCAAT
1420329 TCGCAATGCG-TAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGATAAGTAAATCGCAACGCGAATTGGGAAAA
1420368 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCG-ATAAGTAAATCGCAACGCGAATTGGGAAAA
1420409 TCGCAATGCGATA
1 TCGCAATGCGATA
1420422 CTGACTATCG
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
39 10 0.19
40 3 0.06
41 39 0.75
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (40 bp):
TCGCAATGCGATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1420432 original size:41 final size:41
Alignment explanation
Indices: 1420346--1420480 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
1420336 GCGTAAGTAA
* *
1420346 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1420387 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1420428 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1420469 TTCGCAACGCGA
1 ATCGCAACGCGA
1420481 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1420433 original size:20 final size:20
Alignment explanation
Indices: 1420408--1420502 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1420398 AATTGGGAAA
*
1420408 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1420428 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1420449 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1420469 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1420489 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1420503 ACATAATCGC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1420796 original size:144 final size:142
Alignment explanation
Indices: 1420533--1420818 Score: 506
Period size: 144 Copynumber: 2.0 Consensus size: 142
1420523 TCAAAGCGCC
1420533 ATTATATCTGGCCAAGTATTTTATTTTTAAATTCCAAATGAATATTAATATATTGGAACACTGAA
1 ATTATATCTGGCCAAGTATTTTATTTTTAAATTCCAAATGAATATTAATATATTGGAACACTGAA
1420598 CTGTCCACAGTAATCCCGTAATCGCAACTCATAACCTAAAACCTAAAATCACAACTCAGTCCCAT
66 CTGTCCACAGTAATCCCGTAATCGCAACTCATAACCTAAAACCTAAAATCACAACTCAGTCCCAT
1420663 CTCCATCTCTCA
131 CTCCATCTCTCA
1420675 ATTAGTATCTGGCCAAGTATTTTA-TTTTAAATTCCAAACATGAATA-TAATAATATTGGAACAC
1 ATTA-TATCTGGCCAAGTATTTTATTTTTAAATTCC-AA-ATGAATATTAAT-ATATTGGAACAC
1420738 TGAACTGTCCACAGT-ATCCCCGTAATCGCAACTCATAACCTAAAACCTAAAATCACAACTCAGT
62 TGAACTGTCCACAGTAAT-CCCGTAATCGCAACTCATAACCTAAAACCTAAAATCACAACTCAGT
1420802 CCCATCTCCATCTCTCA
126 CCCATCTCCATCTCTCA
1420819 CTCTCTCACC
Statistics
Matches: 139, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
142 15 0.11
143 27 0.19
144 97 0.70
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (142 bp):
ATTATATCTGGCCAAGTATTTTATTTTTAAATTCCAAATGAATATTAATATATTGGAACACTGAA
CTGTCCACAGTAATCCCGTAATCGCAACTCATAACCTAAAACCTAAAATCACAACTCAGTCCCAT
CTCCATCTCTCA
Found at i:1420855 original size:22 final size:22
Alignment explanation
Indices: 1420827--1420870 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1420817 CACTCTCTCA
1420827 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1420849 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1420871 TATCTCCATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1422474 original size:18 final size:18
Alignment explanation
Indices: 1422453--1422497 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1422443 TCCACTTCGG
*
1422453 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1422471 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1422489 GAGCCATCA
1 GAGCCATCA
1422498 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1423046 original size:14 final size:14
Alignment explanation
Indices: 1423027--1423083 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
1423017 ATGCGAAATG
1423027 AAATCGCAACGACA
1 AAATCGCAACGACA
*
1423041 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
1423057 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
1423073 AAATCGCAACG
1 AAATCGCAACG
1423084 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:1423055 original size:32 final size:32
Alignment explanation
Indices: 1423011--1423100 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
1423001 GGAAATGGCT
*
1423011 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1423043 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1423075 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATG-AAATCGCAA
1423101 TGCGATTTGG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 47 0.84
33 9 0.16
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:1423094 original size:19 final size:19
Alignment explanation
Indices: 1422972--1423105 Score: 76
Period size: 20 Copynumber: 7.6 Consensus size: 19
1422962 TAGTTTACTT
* **
1422972 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1422992 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1423012 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1423030 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1423044 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1423062 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1423076 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1423095 TCGCAATGCGA
1 TCGCAACGCGA
1423106 TTTGGTGTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
14 20 0.22
16 8 0.09
18 18 0.20
19 20 0.22
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1423137 original size:14 final size:14
Alignment explanation
Indices: 1423118--1423175 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1423108 TGGTGTTTCG
1423118 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1423132 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1423148 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1423164 CGTTGCGATTTT
1 CGTTGCGATTTT
1423176 CATTTTGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1423152 original size:32 final size:33
Alignment explanation
Indices: 1423113--1423180 Score: 129
Period size: 32 Copynumber: 2.1 Consensus size: 33
1423103 CGATTTGGTG
1423113 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1423145 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1423178 TTT
1 TTT
1423181 TGCATTGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 27 0.77
33 8 0.23
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.50
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1423223 original size:20 final size:20
Alignment explanation
Indices: 1423185--1423225 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1423175 TCATTTTGCA
1423185 TTGCATAGCCATTTCCGCGT
1 TTGCATAGCCATTTCCGCGT
*
1423205 TTGCAATAGTCATTT-CGCGT
1 TTGC-ATAGCCATTTCCGCGT
1423225 T
1 T
1423226 GCGATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCATAGCCATTTCCGCGT
Found at i:1425086 original size:14 final size:14
Alignment explanation
Indices: 1425067--1425102 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1425057 ATTGTTTAAT
1425067 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1425081 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1425095 TGATTTGT
1 TGATTTGT
1425103 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1425212 original size:19 final size:18
Alignment explanation
Indices: 1425188--1425257 Score: 58
Period size: 19 Copynumber: 4.0 Consensus size: 18
1425178 GCAAAACAGA
1425188 CTATCGCAATGCGAAATGG
1 CTATCGCAATGCGAAAT-G
* *
1425207 CTATCGCAACGAGAAA--
1 CTATCGCAATGCGAAATG
1425223 --ATCGCAATGCGAAATG
1 CTATCGCAATGCGAAATG
**
1425239 AAAATCGCAATGCGAAATG
1 -CTATCGCAATGCGAAATG
1425258 AAAATCGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 12 0.29
19 30 0.71
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (18 bp):
CTATCGCAATGCGAAATG
Found at i:1425228 original size:14 final size:17
Alignment explanation
Indices: 1425219--1425281 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 17
1425209 ATCGCAACGA
1425219 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAA-GCG-AAT
1425238 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAA-GCG-AAT
1425257 GAAAATCGCAA-CG-A-
1 GAAAATCGCAAGCGAAT
1425271 GAAAATCGCAA
1 GAAAATCGCAA
1425282 TGTGATTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
17 2 0.05
19 30 0.68
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.13
Consensus pattern (17 bp):
GAAAATCGCAAGCGAAT
Found at i:1425274 original size:19 final size:19
Alignment explanation
Indices: 1425219--1425267 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1425209 ATCGCAACGA
1425219 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1425238 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1425257 GAAAATCGCAA
1 GAAAATCGCAA
1425268 CGAGAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1425338 original size:20 final size:20
Alignment explanation
Indices: 1425313--1425383 Score: 142
Period size: 20 Copynumber: 3.5 Consensus size: 20
1425303 CGATTTTCCT
1425313 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1425333 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1425353 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1425373 CGTTGCGATAG
1 CGTTGCGATAG
1425384 TCAAATGAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:1425339 original size:35 final size:36
Alignment explanation
Indices: 1425293--1425382 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 36
1425283 GTGATTTTCA
* *
1425293 TTTCGCATTGCGAT-TTTCCTCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATATTTCCGCGTTGCGATAGCCAT
*
1425328 TTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGAT----ATTTCCGCGTTGCGATAGCCAT
1425368 TTTCGCGTTGCGATA
1 TTTCGCGTTGCGATA
1425383 GTCAAATGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
35 13 0.28
36 1 0.02
40 33 0.70
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.38
Consensus pattern (36 bp):
TTTCGCGTTGCGATATTTCCGCGTTGCGATAGCCAT
Found at i:1426442 original size:24 final size:24
Alignment explanation
Indices: 1426391--1426444 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1426381 GTATTCGAAA
* * *
1426391 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACAGAC
*
1426415 TTTGATATTGGTCAATACACAGAT
1 TTTGATATTGGTCAATACACAGAC
1426439 TTTGAT
1 TTTGAT
1426445 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:1428911 original size:33 final size:33
Alignment explanation
Indices: 1428869--1428994 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
1428859 GGAAATTACT
1428869 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1428902 ATCGCAATGCGAAATG-AAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1428933 TTTCGCAATGCGAAATGAAATTCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1428967 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1428995 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
31 1 0.01
32 27 0.34
33 51 0.64
34 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1428975 original size:65 final size:66
Alignment explanation
Indices: 1428870--1429001 Score: 221
Period size: 65 Copynumber: 2.0 Consensus size: 66
1428860 GAAATTACTA
* *
1428870 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG-AAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1428934 T
66 T
* *
1428935 TCGCAATGCGAAATGAAATTCGCAACGAGGGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1429000 T
66 T
1429001 T
1 T
1429002 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
65 45 0.73
66 17 0.27
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1429016 original size:19 final size:20
Alignment explanation
Indices: 1428994--1429036 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1428984 AAATCGCAAC
1428994 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1429013 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1429033 GCGA
1 GCGA
1429037 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1429021 original size:14 final size:14
Alignment explanation
Indices: 1429022--1429055 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1429012 TGCGATTTTC
1429022 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1429036 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1429050 ATTTTC
1 ATTTTC
1429056 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1429196 original size:14 final size:14
Alignment explanation
Indices: 1429177--1429213 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1429167 CATCAATTAA
1429177 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1429191 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1429205 ACAAATCAA
1 ACAAATCAA
1429214 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1430628 original size:21 final size:21
Alignment explanation
Indices: 1430562--1430628 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1430552 GTGAATCGGG
*
1430562 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1430582 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1430604 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1430625 CTCT
1 CTCT
1430629 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1430647 original size:42 final size:41
Alignment explanation
Indices: 1430562--1430684 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1430552 GTGAATCGGG
* * * * *
1430562 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1430604 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1430646 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1430685 CGAGCCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1432706 original size:20 final size:19
Alignment explanation
Indices: 1432675--1432735 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1432665 TCTTTTGGTT
1432675 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1432694 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1432715 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
1432734 GA
1 GA
1432736 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1432743 original size:34 final size:33
Alignment explanation
Indices: 1432700--1432795 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 33
1432690 ACGAGATAAT
*
1432700 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
1432734 GAGAATCGCAACGCGAAATGACTAT--C-ACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1432764 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1432796 GCGAAATAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
30 25 0.45
31 1 0.02
32 1 0.02
33 14 0.25
34 14 0.25
ACGTcount: A:0.41, C:0.26, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1432800 original size:20 final size:19
Alignment explanation
Indices: 1432767--1432837 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
1432757 ATCACCAGAC
1432767 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1432786 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
1432806 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1432825 AATCGCAATGCGA
1 AATCGCAACGCGA
1432838 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 30 0.62
20 18 0.38
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1432866 original size:19 final size:19
Alignment explanation
Indices: 1432833--1432899 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1432823 AAAATCGCAA
**
1432833 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1432852 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1432871 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1432891 TGCGATTTT
1 TGCGATTTT
1432900 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1433441 original size:20 final size:20
Alignment explanation
Indices: 1433416--1433468 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1433406 GCGCTATGTA
1433416 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1433436 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1433456 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1433469 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1433502 original size:20 final size:20
Alignment explanation
Indices: 1433477--1433530 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1433467 GATTTTGTAT
1433477 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1433497 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1433517 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1433531 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1433515 original size:61 final size:61
Alignment explanation
Indices: 1433417--1433533 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1433407 CGCTATGTAA
* * * * *
1433417 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1433478 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1433534 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1433549 original size:61 final size:61
Alignment explanation
Indices: 1433417--1433551 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1433407 CGCTATGTAA
* * * * * ** *
1433417 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1433478 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1433540 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1433552 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1434123 original size:60 final size:59
Alignment explanation
Indices: 1434012--1434161 Score: 137
Period size: 59 Copynumber: 2.5 Consensus size: 59
1434002 TATTGAAATG
* * * * * * **
1434012 TTAAAAGTTTGGGGATCAATATAGAATGAATGTTATATTTTAGGAATAAATTTGGAATAT
1 TTAAAACTTTAGGGATCAATTTAAAATGAAAGTCATATTTTAGGAATAAA-TTAAAATAT
*
1434072 TTAAAA-TTTTGGGATCAATTTAAAATGAAAGTCATGATTTT--GAGATGAAATTAAAATAT
1 TTAAAACTTTAGGGATCAATTTAAAATGAAAGTCAT-ATTTTAGGA-AT-AAATTAAAATAT
* *
1434131 TTAAAACTTTAAGAATCAATTTAAAAT-AAAG
1 TTAAAACTTTAGGGATCAATTTAAAATGAAAG
1434162 GGAATAGTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.03
59 43 0.57
60 31 0.41
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (59 bp):
TTAAAACTTTAGGGATCAATTTAAAATGAAAGTCATATTTTAGGAATAAATTAAAATAT
Found at i:1434746 original size:2 final size:2
Alignment explanation
Indices: 1434739--1434768 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1434729 AACTAAAAGA
1434739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1434769 GTATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1435497 original size:31 final size:30
Alignment explanation
Indices: 1435445--1435540 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
1435435 ATATATACTA
*
1435445 TAGGG-TTCAATTATTTTTAATATTTATTAT
1 TAGGGATTC-ATTTTTTTTAATATTTATTAT
1435475 TAGGGATTCATTTTTTCTTAATATTTATTAT
1 TAGGGATTCATTTTTT-TTAATATTTATTAT
* **
1435506 TATGGACTT-AGATTTTTTAATATTTATTAT
1 TAGGGA-TTCATTTTTTTTAATATTTATTAT
1435536 TAGGG
1 TAGGG
1435541 TCTACTCTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 29 0.50
31 27 0.47
32 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.12, T:0.55
Consensus pattern (30 bp):
TAGGGATTCATTTTTTTTAATATTTATTAT
Found at i:1438188 original size:30 final size:30
Alignment explanation
Indices: 1438153--1438219 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
1438143 CTCGAGCTCG
1438153 ACTCGATTTCTTAACGAGCCGAAACGAGCT
1 ACTCGATTTCTTAACGAGCCGAAACGAGCT
1438183 ACTCGATTTCTTAACGAGCCGAAACGAGCT
1 ACTCGATTTCTTAACGAGCCGAAACGAGCT
1438213 ACTCGAT
1 ACTCGAT
1438220 ATTCGATTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (30 bp):
ACTCGATTTCTTAACGAGCCGAAACGAGCT
Found at i:1438407 original size:7 final size:7
Alignment explanation
Indices: 1438391--1438559 Score: 76
Period size: 7 Copynumber: 24.7 Consensus size: 7
1438381 ATGTGATAGA
*
1438391 GTTTATG
1 GTTTAGG
1438398 GTTTAGG
1 GTTTAGG
**
1438405 GTTTAAT
1 GTTTAGG
*
1438412 G-TTAAG
1 GTTTAGG
*
1438418 G-TTAAG
1 GTTTAGG
*
1438424 GTTTATG
1 GTTTAGG
**
1438431 GTTTATA
1 GTTTAGG
1438438 GTTTAGG
1 GTTTAGG
1438445 GTTTAGG
1 GTTTAGG
1438452 GTTTAGG
1 GTTTAGG
**
1438459 GTTTAAA
1 GTTTAGG
*
1438466 GTTTATG
1 GTTTAGG
* *
1438473 ATTTAGA
1 GTTTAGG
1438480 GTTTAGG
1 GTTTAGG
*
1438487 GGTTAGG
1 GTTTAGG
* *
1438494 GTTAAGT
1 GTTTAGG
1438501 G-TT-GG
1 GTTTAGG
*
1438506 GTTAAGG
1 GTTTAGG
* *
1438513 CTTTATG
1 GTTTAGG
*
1438520 ATTTAGG
1 GTTTAGG
* *
1438527 GTTGAAG
1 GTTTAGG
*
1438534 ATTTAGG
1 GTTTAGG
* *
1438541 ATTCAGG
1 GTTTAGG
*
1438548 GTTTATG
1 GTTTAGG
1438555 GTTTA
1 GTTTA
1438560 AGTTATACAC
Statistics
Matches: 120, Mismatches: 39, Indels: 6
0.73 0.24 0.04
Matches are distributed among these distances:
5 2 0.02
6 13 0.11
7 105 0.88
ACGTcount: A:0.22, C:0.01, G:0.32, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:1438485 original size:28 final size:27
Alignment explanation
Indices: 1438391--1438487 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 27
1438381 ATGTGATAGA
*
1438391 GTTTATGGTTTAGGGTTTAATG-TTAAG
1 GTTTA-GGTTTAGGGTTTAAAGTTTAAG
* * * *
1438418 GTTAAGGTTTATGGTTTATAGTTTAGG
1 GTTTAGGTTTAGGGTTTAAAGTTTAAG
*
1438445 GTTTAGGGTTTAGGGTTTAAAGTTTATG
1 GTTTA-GGTTTAGGGTTTAAAGTTTAAG
*
1438473 ATTTAGAGTTTAGGG
1 GTTTAG-GTTTAGGG
1438488 GTTAGGGTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
26 13 0.23
27 13 0.23
28 31 0.54
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (27 bp):
GTTTAGGTTTAGGGTTTAAAGTTTAAG
Found at i:1438878 original size:17 final size:17
Alignment explanation
Indices: 1438849--1438881 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1438839 AATTAAAATT
1438849 ACAAGACACAATTGAAA
1 ACAAGACACAATTGAAA
1438866 ACAAG-CACAAATTGAA
1 ACAAGACAC-AATTGAA
1438882 GGAACACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (17 bp):
ACAAGACACAATTGAAA
Found at i:1439358 original size:19 final size:18
Alignment explanation
Indices: 1439334--1439372 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1439324 GAAAGCCATC
1439334 TCTTTGGATTAATGATGTG
1 TCTTTGGATTAATGA-GTG
*
1439353 TCTTTGTATTAATGAGTG
1 TCTTTGGATTAATGAGTG
1439371 TC
1 TC
1439373 AAAAGGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.49
Consensus pattern (18 bp):
TCTTTGGATTAATGAGTG
Found at i:1441129 original size:12 final size:12
Alignment explanation
Indices: 1441082--1441169 Score: 56
Period size: 12 Copynumber: 7.5 Consensus size: 12
1441072 ATGCTGATTA
1441082 GAGCTTGAGTTC
1 GAGCTTGAGTTC
* *
1441094 AAGCTTGA-ATC
1 GAGCTTGAGTTC
** *
1441105 GAGCTCAAATTC
1 GAGCTTGAGTTC
*
1441117 GAGTTTGAGTTC
1 GAGCTTGAGTTC
*
1441129 GAGCTTGA-ATC
1 GAGCTTGAGTTC
* *
1441140 GAGCTGGAATT-
1 GAGCTTGAGTTC
*
1441151 GAGCTCGAGTCTC
1 GAGCTTGAGT-TC
1441164 GAGCTT
1 GAGCTT
1441170 CAATCGAGCT
Statistics
Matches: 55, Mismatches: 17, Indels: 7
0.70 0.22 0.09
Matches are distributed among these distances:
11 24 0.44
12 26 0.47
13 5 0.09
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (12 bp):
GAGCTTGAGTTC
Found at i:1441134 original size:35 final size:34
Alignment explanation
Indices: 1441082--1441181 Score: 128
Period size: 35 Copynumber: 2.9 Consensus size: 34
1441072 ATGCTGATTA
*
1441082 GAGCTTGAGTTCAAGCTTGAATCGAGCTCAAATT
1 GAGCTTGAGTTCGAGCTTGAATCGAGCTCAAATT
* **
1441116 CGAGTTTGAGTTCGAGCTTGAATCGAGCTGGAATT
1 -GAGCTTGAGTTCGAGCTTGAATCGAGCTCAAATT
* *
1441151 GAGCTCGAGTCTCGAGCTTCAATCGAGCTCA
1 GAGCTTGAGT-TCGAGCTTGAATCGAGCTCA
1441182 TGATTTTTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 8 0.15
35 47 0.85
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (34 bp):
GAGCTTGAGTTCGAGCTTGAATCGAGCTCAAATT
Found at i:1441143 original size:11 final size:11
Alignment explanation
Indices: 1441095--1441179 Score: 53
Period size: 11 Copynumber: 7.4 Consensus size: 11
1441085 CTTGAGTTCA
1441095 AGCTTGAATCG
1 AGCTTGAATCG
**
1441106 AGCTCAAATTCG
1 AGCTTGAA-TCG
* *
1441118 AGTTTGAGTTCG
1 AGCTTGA-ATCG
1441130 AGCTTGAATCG
1 AGCTTGAATCG
* *
1441141 AGCTGGAATTG
1 AGCTTGAATCG
* *
1441152 AGCTCGAGTCTCG
1 AGCTTGA--ATCG
*
1441165 AGCTTCAATCG
1 AGCTTGAATCG
1441176 AGCT
1 AGCT
1441180 CATGATTTTT
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
11 31 0.57
12 16 0.30
13 7 0.13
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (11 bp):
AGCTTGAATCG
Found at i:1442184 original size:19 final size:19
Alignment explanation
Indices: 1442160--1442196 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1442150 ATGACCAACA
*
1442160 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1442179 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1442197 CAGTATCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1442266 original size:40 final size:40
Alignment explanation
Indices: 1442222--1442353 Score: 137
Period size: 40 Copynumber: 3.3 Consensus size: 40
1442212 GTTTCCGGAT
1442222 TCGCAACGCGATTTTGACTATCGCAATGCGAATATGTAAA
1 TCGCAACGCGATTTTGACTATCGCAATGCGAATATGTAAA
* * * * *
1442262 TCGCAACGCGATTCTGACTATCGCAACGCGATTCTG-ACTA
1 TCGCAACGCGATTTTGACTATCGCAATGCGAATATGTA-AA
*
1442302 TCGCAACGCGATTCTT-ACTATCGCATTGCG-ATA-GTAACTA
1 TCGCAACGCGATT-TTGACTATCGCAATGCGAATATGTAA--A
*
1442342 TCGCAATGCGAT
1 TCGCAACGCGAT
1442354 AATACAAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
38 1 0.01
39 3 0.04
40 70 0.93
41 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
TCGCAACGCGATTTTGACTATCGCAATGCGAATATGTAAA
Found at i:1442325 original size:60 final size:60
Alignment explanation
Indices: 1442222--1442353 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 60
1442212 GTTTCCGGAT
* * * *
1442222 TCGCAACGCGATTTTGACTATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTATCGCAACGCGAATATGTAAATCGCAACGCGATACTAACTA
* * * ** *
1442282 TCGCAACGCGATTCTGACTATCGCAACGCGATTCT-TACTATCGCATTGCGATAGTAACTA
1 TCGCAACGCGATTCTGACTATCGCAACGCGAATATGTA-AATCGCAACGCGATACTAACTA
*
1442342 TCGCAATGCGAT
1 TCGCAACGCGAT
1442354 AATACAAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.03
60 58 0.97
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (60 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGAATATGTAAATCGCAACGCGATACTAACTA
Found at i:1442333 original size:20 final size:20
Alignment explanation
Indices: 1442222--1442326 Score: 140
Period size: 20 Copynumber: 5.2 Consensus size: 20
1442212 GTTTCCGGAT
*
1442222 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * * *
1442242 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
1442262 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
1442282 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
1442302 TCGCAACGCGATTCTTACTA
1 TCGCAACGCGATTCTGACTA
1442322 TCGCA
1 TCGCA
1442327 TTGCGATAGT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 72 0.97
21 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1442537 original size:22 final size:22
Alignment explanation
Indices: 1442512--1442576 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
1442502 TCACTCTCTA
*
1442512 CGACGACATCCGTCCCTATCTC
1 CGACGAAATCCGTCCCTATCTC
*
1442534 CGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCTATCTC
1442556 C-AGCGAAATCCGT--CTATCTC
1 CGA-CGAAATCCGTCCCTATCTC
1442576 C
1 C
1442577 ATCTCTCAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 7 0.18
21 1 0.03
22 31 0.79
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
CGACGAAATCCGTCCCTATCTC
Found at i:1442993 original size:20 final size:20
Alignment explanation
Indices: 1442944--1443060 Score: 77
Period size: 20 Copynumber: 6.2 Consensus size: 20
1442934 AAAATCGCAA
**
1442944 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
*
1442964 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
** **
1442984 CGATTTTCA-TTTCATGTTG
1 CGATAGTCATTTTCGCGTTG
* *
1443003 C---A---ATTATCTCGTTG
1 CGATAGTCATTTTCGCGTTG
**
1443017 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
*
1443037 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
1443057 CGAT
1 CGAT
1443061 TTTAAGTTTC
Statistics
Matches: 73, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
13 1 0.01
14 8 0.11
17 1 0.01
19 10 0.14
20 53 0.73
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
CGATAGTCATTTTCGCGTTG
Found at i:1443082 original size:73 final size:73
Alignment explanation
Indices: 1442944--1443082 Score: 217
Period size: 73 Copynumber: 1.9 Consensus size: 73
1442934 AAAATCGCAA
* ***
1442944 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCATGTTGCAATTA
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTTCATGAAACAATTA
1443009 TCTCGTTG
66 TCTCGTTG
*
1443017 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAAGTTTCA-GAAACTATT
1 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAA-TTTCATGAAACAATT
1443081 AT
65 AT
1443083 TCTTCTGCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 55 0.92
74 5 0.08
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (73 bp):
CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTTCATGAAACAATTA
TCTCGTTG
Found at i:1443757 original size:20 final size:20
Alignment explanation
Indices: 1443732--1443776 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1443722 TTGTCCGAGT
1443732 ATGCCTTTTAGTACTTTTGC
1 ATGCCTTTTAGTACTTTTGC
1443752 ATGCCTTTTAGTACTTTTGC
1 ATGCCTTTTAGTACTTTTGC
1443772 ATGCC
1 ATGCC
1443777 GGCTTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (20 bp):
ATGCCTTTTAGTACTTTTGC
Found at i:1444991 original size:20 final size:20
Alignment explanation
Indices: 1444966--1445032 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
1444956 CGAAACTTAA
1444966 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1444986 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1445006 ATCGCAACGCGAAGTTGACT
1 ATCGCAACGCGAAAATGACT
1445026 ATCGCAA
1 ATCGCAA
1445033 TGGGATAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1445123 original size:19 final size:19
Alignment explanation
Indices: 1445101--1445245 Score: 95
Period size: 19 Copynumber: 7.7 Consensus size: 19
1445091 CTATCGCAAC
*
1445101 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
1445120 GCGATTTTGGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
1445139 GCGATTTTTA-TTTCGCTTT
1 GCGA-TTTTAGTTTCGCGTT
*
1445158 GCGA--TTA---TCCCGTT
1 GCGATTTTAGTTTCGCGTT
* * *
1445172 GCGATAGTCATTTTCGCGTT
1 GCGAT-TTTAGTTTCGCGTT
* * *
1445192 GCGATAGTCATTTTCGCGTT
1 GCGAT-TTTAGTTTCGCGTT
* **
1445212 GCGATTTAAGTTTCATGTT
1 GCGATTTTAGTTTCGCGTT
1445231 GCGATTTTAAGTTTC
1 GCGATTTT-AGTTTC
1445246 AGAAATTATT
Statistics
Matches: 104, Mismatches: 14, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
14 9 0.09
16 3 0.03
17 2 0.02
19 49 0.47
20 41 0.39
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1445193 original size:20 final size:20
Alignment explanation
Indices: 1445168--1445216 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1445158 GCGATTATCC
1445168 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1445188 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1445208 CGTTGCGAT
1 CGTTGCGAT
1445217 TTAAGTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1445241 original size:20 final size:19
Alignment explanation
Indices: 1445209--1445246 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1445199 TCATTTTCGC
1445209 GTTGCGATTTAAGTTTCAT
1 GTTGCGATTTAAGTTTCAT
1445228 GTTGCGATTTTAAGTTTCA
1 GTTGCGA-TTTAAGTTTCA
1445247 GAAATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (19 bp):
GTTGCGATTTAAGTTTCAT
Found at i:1445375 original size:20 final size:20
Alignment explanation
Indices: 1445347--1445402 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1445337 AAATTTTTGA
1445347 GTTGCGATAATCAAATTCGC
1 GTTGCGATAATCAAATTCGC
* * *
1445367 GTTGTGATAGTCAAATTTGC
1 GTTGCGATAATCAAATTCGC
*
1445387 GTTGCGATATTCAAAT
1 GTTGCGATAATCAAAT
1445403 GAATGTGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGCGATAATCAAATTCGC
Found at i:1445630 original size:140 final size:140
Alignment explanation
Indices: 1445373--1445655 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
1445363 TCGCGTTGTG
*
1445373 ATAGTCAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1445438 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGATAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGATAAAAGTTTACACATAA
1445503 AATACACATA
131 AATACACATA
1445513 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
* *
1445578 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAATTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGATAAAAGTTTACACATAA
1445643 AATACACATA
131 AATACACATA
1445653 ATA
1 ATA
1445656 CAACGTTTGC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGATAAAAGTTTACACATAA
AATACACATA
Found at i:1445734 original size:18 final size:18
Alignment explanation
Indices: 1445708--1445748 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1445698 AGGTGAAGCC
*
1445708 GATTGTGATTGGGATTTT
1 GATTGTGATTGCGATTTT
*
1445726 GATTTTGATTGCGATTTT
1 GATTGTGATTGCGATTTT
1445744 GATTG
1 GATTG
1445749 CCTTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.29, T:0.51
Consensus pattern (18 bp):
GATTGTGATTGCGATTTT
Found at i:1447966 original size:24 final size:24
Alignment explanation
Indices: 1447932--1447985 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1447922 CTGAAACATC
1447932 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
1447956 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1447980 ATCAAA
1 ATCAAA
1447986 TTTCGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1447999 original size:24 final size:24
Alignment explanation
Indices: 1447932--1447999 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1447922 CTGAAACATC
* * *
1447932 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1447956 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1447980 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1448000 TAGTACTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1448843 original size:21 final size:21
Alignment explanation
Indices: 1448813--1448887 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
1448803 GACAGTCAGA
*
1448813 ATCGCTTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
1448834 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
*
1448854 ATCGCGTTGTGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* *
1448875 ATCACATTGCGAT
1 ATCGCGTTGCGAT
1448888 AGTCAGAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
19 2 0.05
20 14 0.33
21 24 0.57
22 2 0.05
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:1448843 original size:41 final size:41
Alignment explanation
Indices: 1448798--1448908 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
1448788 GAAATTCAGT
* * *
1448798 GTTGCGACAGTCAGAATCGCTTTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCATTGCGATTATGTATTATCAC
* *
1448839 GTTGCGATAGTCAGAATCGCGTTGTGATTATGTATTATCAC
1 GTTGCGATAGTCAGAATCGCATTGCGATTATGTATTATCAC
*
1448880 ATTGCGATAGTCAGAATCGCATTGCGATT
1 GTTGCGATAGTCAGAATCGCATTGCGATT
1448909 TACATATTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (41 bp):
GTTGCGATAGTCAGAATCGCATTGCGATTATGTATTATCAC
Found at i:1448859 original size:20 final size:20
Alignment explanation
Indices: 1448798--1448907 Score: 80
Period size: 20 Copynumber: 5.4 Consensus size: 20
1448788 GAAATTCAGT
*
1448798 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* **
1448818 TTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
1448839 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* ** *
1448859 GTTGTGATTATGT-ATTATCAC
1 GTTGCGA-TA-GTCAGAATCGC
*
1448880 ATTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1448900 ATTGCGAT
1 GTTGCGAT
1448908 TTACATATTC
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
19 4 0.06
20 35 0.51
21 25 0.37
22 4 0.06
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1457583 original size:17 final size:17
Alignment explanation
Indices: 1457537--1457583 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
1457527 ATAGATAATG
*
1457537 AGAAAAAGAGAGAAAAAA
1 AGAAAAA-AGAGGAAAAA
1457555 AGAAAAAAGAGGAAAAA
1 AGAAAAAAGAGGAAAAA
*
1457572 AGAAAATAGAGG
1 AGAAAAAAGAGG
1457584 GACATGAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (17 bp):
AGAAAAAAGAGGAAAAA
Found at i:1460764 original size:2 final size:2
Alignment explanation
Indices: 1460759--1460824 Score: 105
Period size: 2 Copynumber: 32.5 Consensus size: 2
1460749 AGAGAATCCA
* *
1460759 AT AT AT AT AT AT AT AT AT GAG AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
1460802 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1460825 CACACACACA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 58 0.98
3 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1463695 original size:68 final size:69
Alignment explanation
Indices: 1463586--1463723 Score: 269
Period size: 68 Copynumber: 2.0 Consensus size: 69
1463576 CTGGATTCTA
1463586 AACGAGGGAGATAAAAGAACAGATGATTGAACTCGTGGCTTCCG-AAAAAAATATGTATATATAT
1 AACGAGGGAGATAAAAGAACAGATGATTGAACTCGTGGCTTCCGAAAAAAAATATGTATATATAT
1463650 GTAC
66 GTAC
1463654 AACGAGGGAGATAAAAGAACAGATGATTGAACTCGTGGCTTCCGAAAAAAAATATGTATATATAT
1 AACGAGGGAGATAAAAGAACAGATGATTGAACTCGTGGCTTCCGAAAAAAAATATGTATATATAT
1463719 GTAC
66 GTAC
1463723 A
1 A
1463724 CTGATATATA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 44 0.64
69 25 0.36
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (69 bp):
AACGAGGGAGATAAAAGAACAGATGATTGAACTCGTGGCTTCCGAAAAAAAATATGTATATATAT
GTAC
Found at i:1469122 original size:47 final size:48
Alignment explanation
Indices: 1469065--1469346 Score: 173
Period size: 51 Copynumber: 5.5 Consensus size: 48
1469055 GATTATAGTA
*
1469065 ATTTGATAGTAATGA-TTAGTAATACTGAATATTAT-TAATTATGTATG
1 ATTTGATAGTAATGATTTAGTAATA-TAAATATTATATAATTATGTATG
* * * *
1469112 ATTTGATAGTAATGATTTAGT-ATGATTAGTATAATGA-AATTAGTTTTAATG
1 ATTTGATAGTAATGATTTAGTAAT-ATAAATATTAT-ATAATTA--TGT-ATG
* * *
1469163 A-TTGATAGTAATGATTTAGTTATAGTAAAAGAATTATATTATTATGTATG
1 ATTTGATAGTAATGATTTAGTAATA-T-AAA-TATTATATAATTATGTATG
* ** *
1469213 ATTTGATAGTAATGACTTAGTAATGATAATAATAATTCAT-TTTTTATTTTAATG
1 ATTTGATAGTAATGATTTAGTAAT-AT-A-AAT-ATT-ATATAATTA-TGT-ATG
1469267 ATTTGATAGTAATGATTTAGTAATGATTAGTAAATGAATTATTATTAA-TATGTATG
1 ATTTGATAGTAATGATTTAGT-A--A-TA-TAAAT--ATTA-TA-TAATTATGTATG
*
1469323 CTTTGATAGTAATGATTTAGTAAT
1 ATTTGATAGTAATGATTTAGTAAT
1469347 GATTAGTAAT
Statistics
Matches: 187, Mismatches: 20, Indels: 51
0.72 0.08 0.20
Matches are distributed among these distances:
47 24 0.13
48 11 0.06
50 26 0.14
51 32 0.17
52 14 0.07
53 13 0.07
54 23 0.12
55 2 0.01
56 27 0.14
57 10 0.05
58 4 0.02
59 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.45
Consensus pattern (48 bp):
ATTTGATAGTAATGATTTAGTAATATAAATATTATATAATTATGTATG
Found at i:1469181 original size:27 final size:25
Alignment explanation
Indices: 1469108--1469183 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 25
1469098 ATTAATTATG
1469108 TATGATTTGATAGTAATGATTTAG--
1 TATGA-TTGATAGTAATGATTTAGTT
*
1469132 TATGATT-AGTA-TAATGAAATTAGTTT
1 TATGATTGA-TAGTAATG-ATTTAG-TT
1469158 TAATGATTGATAGTAATGATTTAGTT
1 T-ATGATTGATAGTAATGATTTAGTT
1469184 ATAGTAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
22 6 0.14
23 9 0.21
24 5 0.12
26 3 0.07
27 13 0.31
28 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (25 bp):
TATGATTGATAGTAATGATTTAGTT
Found at i:1469233 original size:101 final size:107
Alignment explanation
Indices: 1469071--1469453 Score: 393
Period size: 103 Copynumber: 3.6 Consensus size: 107
1469061 AGTAATTTGA
*
1469071 TAGTAATGATTAGTAATACTGAA-TATTATTAATTATGTATGATTTGATAGTAATGATTTAGT-A
1 TAGT-ATGATTAGTAA-A-AGAATTATTATT-ATTATGTATGATTTGATAGTAATGATTTAGTAA
1469134 TGATTAGT-ATAATGAAATTAGTTTTAATGA-TTGATAGTAATGATT
62 TGATTAGTAATAATGAAATTA-TTTTAATGATTTGATAGTAATGATT
*
1469179 TAGT-T-A-TAGTAAAAGAATTA-TATTATTATGTATGATTTGATAGTAATGACTTAGTAATGA-
1 TAGTATGATTAGTAAAAGAATTATTATTATTATGTATGATTTGATAGTAATGATTTAGTAATGAT
* * **
1469239 TAATAATAATTCATTTTTTATTTTAATGATTTGATAGTAATGATT
66 TAGTAATAA-TGA--AATTATTTTAATGATTTGATAGTAATGATT
* * *
1469284 TAGTAATGATTAGTAAATGAATTATTATTAATATGTATGCTTTGATAGTAATGATTTAGTAATGA
1 TAGT-ATGATTAGTAAAAGAATTATTATTATTATGTATGATTTGATAGTAATGATTTAGTAATGA
* * *
1469349 TTAGTAATAATGAAATTATTATTAAT-TTTTAAT-G-ATTTGA--
65 TTAGTAATAATGAAATTATT-TTAATGATTTGATAGTA-ATGATT
* * * * *
1469389 TAGTATGATTAGTAATA-ATTTATTA-TAATATTTAATGATTTGATATTAATGATTTAGTAATGA
1 TAGTATGATTAGTAAAAGAATTATTATTATTATGT-ATGATTTGATAGTAATGATTTAGTAATGA
1469452 TT
65 TT
1469454 TGATAGTAAT
Statistics
Matches: 236, Mismatches: 23, Indels: 37
0.80 0.08 0.12
Matches are distributed among these distances:
101 33 0.14
102 22 0.09
103 41 0.17
104 26 0.11
105 27 0.11
106 2 0.01
107 5 0.02
108 15 0.06
109 18 0.08
110 39 0.17
111 8 0.03
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.46
Consensus pattern (107 bp):
TAGTATGATTAGTAAAAGAATTATTATTATTATGTATGATTTGATAGTAATGATTTAGTAATGAT
TAGTAATAATGAAATTATTTTAATGATTTGATAGTAATGATT
Found at i:1469298 original size:10 final size:11
Alignment explanation
Indices: 1469273--1469356 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 11
1469263 AATGATTTGA
1469273 TAGTAATGATT
1 TAGTAATGATT
1469284 TAGTAATGA-T
1 TAGTAATGATT
*
1469294 TAGTAAATGAAT
1 TAGT-AATGATT
* * * *
1469306 TATTATTAATA
1 TAGTAATGATT
*
1469317 T-GT-ATGCTTT
1 TAGTAATG-ATT
1469327 GATAGTAATGATT
1 --TAGTAATGATT
1469340 TAGTAATGA-T
1 TAGTAATGATT
1469350 TAGTAAT
1 TAGTAAT
1469357 AATGAAATTA
Statistics
Matches: 55, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
9 1 0.02
10 15 0.27
11 27 0.49
12 5 0.09
13 4 0.07
14 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.44
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:1469335 original size:56 final size:56
Alignment explanation
Indices: 1469017--1469404 Score: 330
Period size: 56 Copynumber: 7.2 Consensus size: 56
1469007 TGTATTTTAA
* *
1469017 GATTTAGT-ATGA-TA-T-AATG-ATAATTATTTAATATTTATGA-TT-ATAGTAAT
1 GATTTAGTAATGATTAGTAAATGAATTATTA-TTAATATGTATGATTTGATAGTAAT
1469067 --TTGATAGTAATGATTAGTAATACTGAA-TATTATTAATTATGTATGATTTGATAGTAAT
1 GATT--TAGTAATGATTAGTAA-A-TGAATTATTATTAA-TATGTATGATTTGATAGTAAT
*
1469125 GATTTAGT-ATGATTAGTATAATGAA--ATTAGTT--T-T-AATGA-TTGATAGTAAT
1 GATTTAGTAATGATTAGTA-AATGAATTATTA-TTAATATGTATGATTTGATAGTAAT
* *
1469175 GATTTAGT--T-A-TAGTAAAAGAATTA-TATTATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAAATGAATTATTATTAATATGTATGATTTGATAGTAAT
* * * * *
1469226 GACTTAGTAATGA-TAAT-AAT-AATTCATTTTTTAT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAAATGAATT-ATTATTAATATGT-ATGATTTGATAGTAAT
*
1469280 GATTTAGTAATGATTAGTAAATGAATTATTATTAATATGTATGCTTTGATAGTAAT
1 GATTTAGTAATGATTAGTAAATGAATTATTATTAATATGTATGATTTGATAGTAAT
* *
1469336 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGT-AT
1 GATTTAGTAATGATTAGT-A-AATG-AATTATTATTAATATGT-ATGATTTGATAGTAAT
1469395 GA-TTAGTAAT
1 GATTTAGTAAT
1469405 AATTTATTAT
Statistics
Matches: 280, Mismatches: 21, Indels: 66
0.76 0.06 0.18
Matches are distributed among these distances:
46 7 0.03
47 7 0.03
48 5 0.02
49 2 0.01
50 27 0.10
51 26 0.09
52 7 0.03
53 8 0.03
54 37 0.13
55 12 0.04
56 63 0.22
57 21 0.08
58 25 0.09
59 19 0.07
60 14 0.05
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.46
Consensus pattern (56 bp):
GATTTAGTAATGATTAGTAAATGAATTATTATTAATATGTATGATTTGATAGTAAT
Found at i:1469427 original size:43 final size:45
Alignment explanation
Indices: 1469340--1469454 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 45
1469330 AGTAATGATT
*
1469340 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAAT----TTATTATTAATATTTAATGATTTGA
1469389 TAGT-ATGATTAGTAATAATTTATTA-TAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATTTATTATTAATATTTAATGATTTGA
* *
1469432 TATTAATGATTTAGTAATGATTT
1 TAGTAATGA-TTAGTAATAATTT
1469455 GATAGTAATG
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
43 20 0.33
44 10 0.16
45 12 0.20
48 15 0.25
49 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (45 bp):
TAGTAATGATTAGTAATAATTTATTATTAATATTTAATGATTTGA
Found at i:1469439 original size:14 final size:14
Alignment explanation
Indices: 1469421--1469468 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1469411 TTATAATATT
*
1469421 TAATGATTTGATAT
1 TAATGATTTGATAG
1469435 TAATGA-TT--TAG
1 TAATGATTTGATAG
1469446 TAATGATTTGATAG
1 TAATGATTTGATAG
1469460 TAATGATTT
1 TAATGATTT
1469469 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:1469469 original size:25 final size:24
Alignment explanation
Indices: 1469378--1469467 Score: 102
Period size: 25 Copynumber: 3.9 Consensus size: 24
1469368 TATTAATTTT
1469378 TAATGATTTGATAGT-ATGATTAG
1 TAATGATTTGATAGTAATGATTAG
*
1469401 TAATAATTT-ATTA-TAAT-ATT--
1 TAATGATTTGA-TAGTAATGATTAG
*
1469421 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGA-TTAG
1469446 TAATGATTTGATAGTAATGATT
1 TAATGATTTGATAGTAATGATT
1469468 TACGACTTGA
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
20 10 0.18
21 5 0.09
22 6 0.11
23 14 0.25
24 2 0.04
25 19 0.34
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (24 bp):
TAATGATTTGATAGTAATGATTAG
Found at i:1471758 original size:30 final size:31
Alignment explanation
Indices: 1471721--1471795 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
1471711 TTTCCCTTAA
1471721 ACAACTAATAAACTATTCTTTAA-TATAAATT
1 ACAACTAATAAACTATT-TTTAATTATAAATT
*
1471752 A-AACTAATAAA-TGATTTTTAATTATAATTT
1 ACAACTAATAAACT-ATTTTTAATTATAAATT
*
1471782 ACTACTAA-AAACTA
1 ACAACTAATAAACTA
1471796 ATTAACTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 6 0.16
30 25 0.66
31 7 0.18
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (31 bp):
ACAACTAATAAACTATTTTTAATTATAAATT
Found at i:1471996 original size:21 final size:21
Alignment explanation
Indices: 1471972--1472011 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1471962 TTTCTATATG
1471972 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1471993 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1472012 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1472234 original size:27 final size:29
Alignment explanation
Indices: 1472204--1472268 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
1472194 CAAATATAAC
*
1472204 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
1472231 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
1472259 TTAATTATTT
1 TTAAATATTT
1472269 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:1472392 original size:22 final size:24
Alignment explanation
Indices: 1472348--1472392 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1472338 CTAACAAACT
*
1472348 AATAATTTAAAATAATAAACTTAA
1 AATAATTTAAAATAAAAAACTTAA
1472372 AATAA-TTAAAA-AAAAAACTTA
1 AATAATTTAAAATAAAAAACTTA
1472393 CCTCGATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 6 0.30
24 5 0.25
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
AATAATTTAAAATAAAAAACTTAA
Found at i:1472578 original size:12 final size:11
Alignment explanation
Indices: 1472547--1472582 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1472537 ACGTTCACGG
1472547 GCTGCAATAAT
1 GCTGCAATAAT
*
1472558 GCAGCAATAAGT
1 GCTGCAATAA-T
1472570 GCTGCAATAAT
1 GCTGCAATAAT
1472581 GC
1 GC
1472583 AGTTGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (11 bp):
GCTGCAATAAT
Found at i:1472851 original size:10 final size:10
Alignment explanation
Indices: 1472827--1472861 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1472817 CTTTGGCGAG
*
1472827 ATGGGCGAG-
1 ATGGGCGTGC
1472836 ATGGGCGTGC
1 ATGGGCGTGC
1472846 ATGGGCGTGC
1 ATGGGCGTGC
1472856 ATGGGC
1 ATGGGC
1472862 ATGGAGGTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.14, C:0.17, G:0.51, T:0.17
Consensus pattern (10 bp):
ATGGGCGTGC
Found at i:1472916 original size:29 final size:29
Alignment explanation
Indices: 1472881--1472967 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
1472871 GTTGGCTGGT
*
1472881 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
1472910 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* *
1472939 AGGTCGCCGGGCGTACATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
1472968 CCCCGGTACT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.16, C:0.30, G:0.38, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:1480800 original size:23 final size:23
Alignment explanation
Indices: 1480774--1480845 Score: 135
Period size: 23 Copynumber: 3.1 Consensus size: 23
1480764 TCTCCTACTT
*
1480774 AACTGAGATTTTCTTTTGAACCA
1 AACTGAGATTTTCTTTCGAACCA
1480797 AACTGAGATTTTCTTTCGAACCA
1 AACTGAGATTTTCTTTCGAACCA
1480820 AACTGAGATTTTCTTTCGAACCA
1 AACTGAGATTTTCTTTCGAACCA
1480843 AAC
1 AAC
1480846 AGTGTTTTCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (23 bp):
AACTGAGATTTTCTTTCGAACCA
Found at i:1480911 original size:42 final size:42
Alignment explanation
Indices: 1480852--1480940 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
1480842 AAACAGTGTT
1480852 TTCCTCTTTTCGCGGCAAATTCATACGAAATTTGCATTTGGA
1 TTCCTCTTTTCGCGGCAAATTCATACGAAATTTGCATTTGGA
1480894 TTCCTCTTTTCGCGGCAAATTCATACGAAATTTGCATTTGGA
1 TTCCTCTTTTCGCGGCAAATTCATACGAAATTTGCATTTGGA
1480936 TTCCT
1 TTCCT
1480941 TACCTAGGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (42 bp):
TTCCTCTTTTCGCGGCAAATTCATACGAAATTTGCATTTGGA
Found at i:1481761 original size:21 final size:21
Alignment explanation
Indices: 1481735--1481816 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
1481725 GCCATATAAA
1481735 ATGTCCCGAAAGACCACATAT
1 ATGTCCCGAAAGACCACATAT
* *
1481756 ATGTCCCG-AAGAACCTCATAGA
1 ATGTCCCGAAAG-ACCACATA-T
* *
1481778 ATTGTCCCGAAGGACCAAATAT
1 A-TGTCCCGAAAGACCACATAT
* *
1481800 ATGTCCCCAAGGACCAC
1 ATGTCCCGAAAGACCAC
1481817 GTAGAACCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 3 0.06
21 29 0.59
22 2 0.04
23 13 0.27
24 2 0.04
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.18
Consensus pattern (21 bp):
ATGTCCCGAAAGACCACATAT
Found at i:1481822 original size:44 final size:44
Alignment explanation
Indices: 1481736--1481822 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
1481726 CCATATAAAA
* * *
1481736 TGTCCCGAAAGACCACATATATGTCCCGAAGAACCTCATAGAAT
1 TGTCCCGAAAGACCAAATATATGTCCCCAAGAACCACATAGAAT
* * *
1481780 TGTCCCGAAGGACCAAATATATGTCCCCAAGGACCACGTAGAA
1 TGTCCCGAAAGACCAAATATATGTCCCCAAGAACCACATAGAA
1481823 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (44 bp):
TGTCCCGAAAGACCAAATATATGTCCCCAAGAACCACATAGAAT
Found at i:1485110 original size:19 final size:21
Alignment explanation
Indices: 1485088--1485133 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1485078 CTAATTTAGT
1485088 AATAT-ATATATATTTTTT-A
1 AATATCATATATATTTTTTGA
1485107 AATATGCATATATATTTTTTGA
1 AATAT-CATATATATTTTTTGA
1485129 AATAT
1 AATAT
1485134 TTTTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.21
21 13 0.54
22 6 0.25
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
AATATCATATATATTTTTTGA
Found at i:1485117 original size:23 final size:22
Alignment explanation
Indices: 1485093--1485133 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1485083 TTAGTAATAT
1485093 ATATATATTTTTT-AAATATGC
1 ATATATATTTTTTGAAATATGC
1485114 ATATATATTTTTTGAAATAT
1 ATATATATTTTTTGAAATAT
1485134 TTTTTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (22 bp):
ATATATATTTTTTGAAATATGC
Found at i:1485904 original size:19 final size:19
Alignment explanation
Indices: 1485880--1485923 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1485870 ACTAGGAGGG
1485880 GTTTTGGCTAAAATAAAGT
1 GTTTTGGCTAAAATAAAGT
1485899 GTTTTGGCTAAAATAAAGT
1 GTTTTGGCTAAAATAAAGT
1485918 GTTTTG
1 GTTTTG
1485924 AGCTTTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.41
Consensus pattern (19 bp):
GTTTTGGCTAAAATAAAGT
Found at i:1486197 original size:29 final size:31
Alignment explanation
Indices: 1486142--1486219 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
1486132 ATATATATAT
* *
1486142 TATTCATTTTAA-ATAATTTTTGTATTACCTA
1 TATT-ATTTTAATATAATTTTTGAATTACATA
*
1486173 T-TATATTTTAATA-AATTTTT-AATTAGATA
1 TAT-TATTTTAATATAATTTTTGAATTACATA
1486202 TATTATTTTAATATAATT
1 TATTATTTTAATATAATT
1486220 ATTTTAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
29 17 0.43
30 20 0.50
31 3 0.08
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (31 bp):
TATTATTTTAATATAATTTTTGAATTACATA
Found at i:1486222 original size:14 final size:14
Alignment explanation
Indices: 1486176--1486228 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
1486166 TTACCTATTA
1486176 TATTTTAATA-AAT
1 TATTTTAATATAAT
*
1486189 TTTTAATTAGATAT-AT
1 TATT--TTA-ATATAAT
1486205 TATTTTAATATAAT
1 TATTTTAATATAAT
1486219 TATTTTAATA
1 TATTTTAATA
1486229 AAAATAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 7 0.21
14 15 0.45
15 3 0.09
16 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TATTTTAATATAAT
Found at i:1492102 original size:97 final size:95
Alignment explanation
Indices: 1491905--1492100 Score: 216
Period size: 95 Copynumber: 2.0 Consensus size: 95
1491895 GATTTAATAC
* *
1491905 AAAATTGAATGAATAAATAAGAGAAATGGAAAAAGATGGTCAAAACTAAATATTTTATGAAATTA
1 AAAATTGAATGAATAAATAAGAGAAATAGAAAAAGATGGTCAAAACTAAATATTTTATAAAATTA
* *
1491970 TAAAAGTTAGGGCCCTAATTATAAATATAA
66 TAAAAATTAGGACCCTAATTATAAATATAA
* * * * *
1492000 AAAATT-AGATGAATTAATAAGAGAAATAGAGAAGGA-GGATCAAAAACTAATTTTTTTTATAAA
1 AAAATTGA-ATGAATAAATAAGAGAAATAGAAAAAGATGG-TC-AAAACTAA-ATATTTTATAAA
** * *
1492063 ATTATAAAAATTAGGTATTCTAGTTATCAATATAA
62 ATTATAAAAATTAGG-ACCCTAATTATAAATATAA
1492098 AAA
1 AAA
1492101 TTTGGGGTCC
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
94 3 0.04
95 32 0.39
96 8 0.10
97 23 0.28
98 17 0.20
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (95 bp):
AAAATTGAATGAATAAATAAGAGAAATAGAAAAAGATGGTCAAAACTAAATATTTTATAAAATTA
TAAAAATTAGGACCCTAATTATAAATATAA
Found at i:1493484 original size:27 final size:25
Alignment explanation
Indices: 1493424--1493485 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
1493414 TATTACTTCT
*
1493424 ATTTATTTTCAAATTTTAAAATTAA
1 ATTTATTTTAAAATTTTAAAATTAA
* **
1493449 ATTTTTTTTGAAAATTTTAATAATTTC
1 ATTTATTTT-AAAATTTTAA-AATTAA
1493476 ATTTATTTTA
1 ATTTATTTTA
1493486 TAAGTACTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 8 0.27
26 10 0.33
27 12 0.40
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTATTTTAAAATTTTAAAATTAA
Found at i:1497766 original size:15 final size:15
Alignment explanation
Indices: 1497746--1497785 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1497736 AGTTGCATCG
*
1497746 CATATCATATAGTTT
1 CATATCATATAATTT
*
1497761 CATATCAAATAATTT
1 CATATCATATAATTT
*
1497776 CATATTATAT
1 CATATCATAT
1497786 TTGATACTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (15 bp):
CATATCATATAATTT
Found at i:1497839 original size:18 final size:18
Alignment explanation
Indices: 1497813--1497849 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1497803 GTATATTACA
* *
1497813 TAGTTTATATTATATAGT
1 TAGTATATACTATATAGT
1497831 TAGTATATACTATATAGT
1 TAGTATATACTATATAGT
1497849 T
1 T
1497850 TGCATGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TAGTATATACTATATAGT
Found at i:1498716 original size:20 final size:20
Alignment explanation
Indices: 1498642--1498727 Score: 54
Period size: 20 Copynumber: 4.2 Consensus size: 20
1498632 TCAAATATAG
1498642 TATATAGTTTATATATA--A
1 TATATAGTTTATATATAGTA
*
1498660 AATATAGTTTTTATATATAGT-
1 TATATAG--TTTATATATAGTA
* **
1498681 TCAT-TTGTAAACTATATAGTA
1 T-ATATAGTTTA-TATATAGTA
1498702 TATATAGTTTATATATTTAGTA
1 TATATAGTTTATATA--TAGTA
1498724 TATA
1 TATA
1498728 CTATATAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 16
0.68 0.11 0.22
Matches are distributed among these distances:
18 6 0.12
19 2 0.04
20 24 0.48
21 7 0.14
22 11 0.22
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (20 bp):
TATATAGTTTATATATAGTA
Found at i:1499673 original size:62 final size:63
Alignment explanation
Indices: 1499539--1499686 Score: 226
Period size: 62 Copynumber: 2.4 Consensus size: 63
1499529 TGGTGTATAG
* * * *
1499539 GTACCGATACATAGGCAGTGTATCGATACCCCCCTAATAATGAAAAATTCAAATGTAATTTGT
1 GTACCGATACATAGGTAGTGTATCAATACCCCCCTAAAAATGAAAAACTCAAATGTAATTTGT
* * *
1499602 GTACCGATACATAGGTAGTGTATCAATA-CCCCTTAAAAATGAAAACCTCGAATGTAATTTGT
1 GTACCGATACATAGGTAGTGTATCAATACCCCCCTAAAAATGAAAAACTCAAATGTAATTTGT
1499664 GTACCGATACATAGGTAGTGTAT
1 GTACCGATACATAGGTAGTGTAT
1499687 TGATACACAC
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
62 52 0.67
63 26 0.33
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (63 bp):
GTACCGATACATAGGTAGTGTATCAATACCCCCCTAAAAATGAAAAACTCAAATGTAATTTGT
Found at i:1500938 original size:2 final size:2
Alignment explanation
Indices: 1500933--1501099 Score: 53
Period size: 2 Copynumber: 81.0 Consensus size: 2
1500923 TAAGTATAAA
*
1500933 AT AT AT -T AT AT A- AT AT AT A- AT AT AT AT AA ACT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT
* * *
1500974 A- AT AT AT AA AT AT CA- ACT AT AGT AT AT AGT TT AT AT AT AA ACT
1 AT AT AT AT AT AT AT -AT A-T AT A-T AT AT A-T AT AT AT AT AT A-T
* * * * *
1501017 AT AGT TT AT AT AGT TT AG AT AT AT AT A- AT TT TT AT AT AT AGT
1 AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
1501059 -T CAT AT GT AA ACT AT AT AT AT AT -T AT AT AGT AT AT AA AT AT
1 AT -AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
1501100 CAACTATAGT
Statistics
Matches: 122, Mismatches: 22, Indels: 42
0.66 0.12 0.23
Matches are distributed among these distances:
1 8 0.07
2 98 0.80
3 16 0.13
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Done.