Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_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: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 18
Found at i:3310911 original size:3 final size:3
Alignment explanation
Indices: 3310896--3310952 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
3310886 TTTTATTTAT
* * *
3310896 TTA TTA CTA TTA TTA TTTA TTA TTA TTT TTA TT- TTA ATA CTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
3310942 TTA CTA TTA TT
1 TTA TTA TTA TT
3310953 TTTTTATACA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.84
4 5 0.12
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3310913 original size:16 final size:16
Alignment explanation
Indices: 3310892--3310944 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3310882 TCTTTTTTAT
3310892 TTATTTATTACTATTA
1 TTATTTATTACTATTA
* *
3310908 TTATTTATTATTATTT
1 TTATTTATTACTATTA
*
3310924 TTATTTTAATACTTATTA
1 TTA-TTTATTAC-TATTA
3310942 TTA
1 TTA
3310945 CTATTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 17 0.57
17 6 0.20
18 7 0.23
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTATTACTATTA
Found at i:3310914 original size:24 final size:22
Alignment explanation
Indices: 3310888--3310959 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 22
3310878 TGTTTCTTTT
3310888 TTATTTA-T-TTATTACTATTA
1 TTATTTATTATTATTACTATTA
**
3310908 TTATTTATTATTATTTTTATT-
1 TTATTTATTATTATTACTATTA
*
3310929 TTA-ATACTTATTATTACTATTA
1 TTATTTA-TTATTATTACTATTA
3310951 TT-TTT-TTAT
1 TTATTTATTAT
3310960 ACATTGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
20 13 0.32
21 16 0.39
22 12 0.29
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTTATTATTATTACTATTA
Found at i:3325803 original size:21 final size:21
Alignment explanation
Indices: 3325777--3325821 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3325767 GATTTCTGGG
* *
3325777 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3325798 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3325819 CAA
1 CAA
3325822 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3326844 original size:2 final size:2
Alignment explanation
Indices: 3326837--3326870 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3326827 GAACATGTGA
3326837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3326871 GTTTAAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3327551 original size:22 final size:23
Alignment explanation
Indices: 3327519--3327577 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
3327509 ATCATTATAT
*
3327519 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
3327541 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
3327564 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3327578 TTTACGAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:3331123 original size:18 final size:17
Alignment explanation
Indices: 3331102--3331136 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3331092 TGATTATACG
3331102 TATATGAATGACATGAAT
1 TATATGAATG-CATGAAT
*
3331120 TATATGTATGCATGAAT
1 TATATGAATGCATGAAT
3331137 ATGTGTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (17 bp):
TATATGAATGCATGAAT
Found at i:3331134 original size:26 final size:24
Alignment explanation
Indices: 3331079--3331137 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
3331069 CTATGTTAGA
*
3331079 ATGCATGAATATATGATTATACGT
1 ATGCATGAATACATGATTATACGT
*
3331103 AT--ATGAATGACATGAATTATATGT
1 ATGCATGAAT-ACATG-ATTATACGT
3331127 ATGCATGAATA
1 ATGCATGAATA
3331138 TGTGTTGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
22 6 0.21
23 4 0.14
24 12 0.41
25 1 0.03
26 6 0.21
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (24 bp):
ATGCATGAATACATGATTATACGT
Found at i:3331761 original size:2 final size:2
Alignment explanation
Indices: 3331754--3331785 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3331744 GAACATGTGA
3331754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3331786 GTTTAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3332498 original size:23 final size:23
Alignment explanation
Indices: 3332432--3332490 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
3332422 ATCATTATAT
*
3332432 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
3332454 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
3332477 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3332491 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:3335633 original size:21 final size:21
Alignment explanation
Indices: 3335607--3335651 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3335597 GATTTCTGGG
* *
3335607 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3335628 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3335649 CAA
1 CAA
3335652 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3336659 original size:2 final size:2
Alignment explanation
Indices: 3336652--3336680 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3336642 GAACATGTGA
3336652 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3336681 GTTTAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3336669 original size:13 final size:13
Alignment explanation
Indices: 3336651--3336677 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3336641 TGAACATGTG
3336651 AATATATATATAT
1 AATATATATATAT
3336664 AATATATATATAT
1 AATATATATATAT
3336677 A
1 A
3336678 TATGTTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATATATATAT
Found at i:3337367 original size:21 final size:21
Alignment explanation
Indices: 3337327--3337385 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
3337317 ATCATTATAT
*
3337327 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGC-ATTCTACG
3337349 GGCACTTCGGTGCATTCTACG
1 GGCACTTCGGTGCATTCTACG
3337370 GGCACTTCGGTGCATT
1 GGCACTTCGGTGCATT
3337386 TATACGAGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (21 bp):
GGCACTTCGGTGCATTCTACG
Found at i:3340567 original size:21 final size:21
Alignment explanation
Indices: 3340541--3340585 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3340531 GATTTCTGGG
* *
3340541 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3340562 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3340583 CAA
1 CAA
3340586 ACGAACAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3341602 original size:2 final size:2
Alignment explanation
Indices: 3341595--3341627 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3341585 GAACATGTGA
3341595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3341628 GTTTAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3342345 original size:23 final size:23
Alignment explanation
Indices: 3342279--3342337 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
3342269 ATCATTATAT
*
3342279 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
3342301 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
3342324 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3342338 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:3345521 original size:21 final size:21
Alignment explanation
Indices: 3345495--3345539 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3345485 GATTTCTGGG
* *
3345495 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3345516 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3345537 CAA
1 CAA
3345540 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3346547 original size:2 final size:2
Alignment explanation
Indices: 3346540--3346569 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3346530 GAACATGTGA
3346540 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
3346570 GTTTAAGAGA
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:3347283 original size:22 final size:22
Alignment explanation
Indices: 3347218--3347275 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
3347208 ATCATTATAT
*
3347218 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
3347240 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
3347262 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3347276 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:3350460 original size:21 final size:21
Alignment explanation
Indices: 3350434--3350478 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3350424 GATTTCTGGG
* *
3350434 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3350455 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3350476 CAA
1 CAA
3350479 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:3351485 original size:2 final size:2
Alignment explanation
Indices: 3351478--3351524 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3351468 GAACATGTGA
3351478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
3351519 AT AT AT
1 AT AT AT
3351525 GTTTAAGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3352197 original size:13 final size:13
Alignment explanation
Indices: 3352179--3352241 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
3352169 TTATATGGCA
3352179 CTACGGTGCAATT
1 CTACGGTGCAATT
3352192 CTACGG-GC-A--
1 CTACGGTGCAATT
*
3352201 CTTCGGTGCAATT
1 CTACGGTGCAATT
3352214 CTACGG-GC-A--
1 CTACGGTGCAATT
*
3352223 CTTCGGTGCAATT
1 CTACGGTGCAATT
3352236 CTACGG
1 CTACGG
3352242 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:3352207 original size:22 final size:22
Alignment explanation
Indices: 3352175--3352255 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
3352165 ATCATTATAT
*
3352175 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
3352197 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
3352219 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
3352242 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3352256 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:3354154 original size:7 final size:7
Alignment explanation
Indices: 3354139--3354178 Score: 53
Period size: 8 Copynumber: 5.3 Consensus size: 7
3354129 GCCCTAAATT
3354139 GAAAAAA
1 GAAAAAA
3354146 GAGAAAAGA
1 GA-AAAA-A
3354155 GAAAAAA
1 GAAAAAA
3354162 GAACAAAA
1 GAA-AAAA
3354170 GAAAAAA
1 GAAAAAA
3354177 GA
1 GA
3354179 GAAGAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 12 0.40
8 15 0.50
9 3 0.10
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:3354169 original size:17 final size:17
Alignment explanation
Indices: 3354139--3354186 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
3354129 GCCCTAAATT
3354139 GAAAAAAG-AGAAAAGA
1 GAAAAAAGAAGAAAAGA
*
3354155 GAAAAAAGAACAAAAGA
1 GAAAAAAGAAGAAAAGA
3354172 -AAAAAGAGAAGAAAA
1 GAAAAA-AGAAGAAAA
3354187 ATAAGGTGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAGAAAAGA
Found at i:3354172 original size:15 final size:16
Alignment explanation
Indices: 3354139--3354181 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
3354129 GCCCTAAATT
3354139 GAAAAAAGAGAAAAGA
1 GAAAAAAGAGAAAAGA
3354155 GAAAAAAGA-ACAAA-A
1 GAAAAAAGAGA-AAAGA
3354170 GAAAAAAGAGAA
1 GAAAAAAGAGAA
3354182 GAAAAATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (16 bp):
GAAAAAAGAGAAAAGA
Found at i:3357456 original size:6 final size:6
Alignment explanation
Indices: 3357425--3357488 Score: 51
Period size: 6 Copynumber: 11.0 Consensus size: 6
3357415 TCCATTATTA
* * * *
3357425 TTATTT TTATAT TT-TAT TT-CAT TTATAT TTATAT ATATAT ATATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
* * *
3357471 ATATAT ATATAT ATATAT
1 TTATAT TTATAT TTATAT
3357489 ATGTTTTTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
5 9 0.17
6 44 0.83
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (6 bp):
TTATAT
Found at i:3357461 original size:2 final size:2
Alignment explanation
Indices: 3357448--3357490 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3357438 TTATTTCATT
*
3357448 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3357490 T
1 T
3357491 GTTTTTACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3357535 original size:20 final size:21
Alignment explanation
Indices: 3357486--3357540 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
3357476 TATATATATA
*
3357486 TATATGTTTTTACTTATGTTTT
1 TATAT-TTTTTATTTATGTTTT
3357508 TATATTTTTTATTTATGTTTCT
1 TATATTTTTTATTTATGTTT-T
3357530 T-T-TTTTTTATT
1 TATATTTTTTATT
3357541 ATTACTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 9 0.29
21 15 0.48
22 7 0.23
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (21 bp):
TATATTTTTTATTTATGTTTT
Found at i:3357542 original size:3 final size:3
Alignment explanation
Indices: 3357536--3357595 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
3357526 TTCTTTTTTT
* * *
3357536 TTA TTA TTA CTA TTA TTA TTTA TTA TTA TTT TTA TT- TTA ATA TTTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
3357582 TTA TTA CTA TTA TT
1 TTA TTA TTA TTA TT
3357596 TTTTATACCT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3357584 original size:24 final size:24
Alignment explanation
Indices: 3357535--3357597 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 24
3357525 TTTCTTTTTT
3357535 TTTATTATTACTATTATTATT--TA
1 TTTATTATTACTATTATT-TTAATA
3357558 -TTATTATT--T-TTATTTTAATA
1 TTTATTATTACTATTATTTTAATA
3357578 TTTATTATTACTATTATTTT
1 TTTATTATTACTATTATTTT
3357598 TTATACCTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 3 0.09
21 8 0.24
22 8 0.24
23 1 0.03
24 7 0.21
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTATTATTACTATTATTTTAATA
Found at i:3357763 original size:21 final size:20
Alignment explanation
Indices: 3357736--3357797 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 20
3357726 CAGCGTTTAC
*
3357736 TTTTATTTTCTGTGTTTTTT
1 TTTTATTTTCTATGTTTTTT
* *
3357756 TATTTATTTAACATATGTTTTAT
1 T-TTTATTT-TC-TATGTTTTTT
*
3357779 TTTTATTTTCTTTGTTTTT
1 TTTTATTTTCTATGTTTTT
3357798 ATATAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 8 0.24
21 8 0.24
22 8 0.24
23 9 0.27
ACGTcount: A:0.15, C:0.05, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTTATTTTCTATGTTTTTT
Found at i:3357794 original size:20 final size:20
Alignment explanation
Indices: 3357731--3357796 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
3357721 TATTTCAGCG
* *
3357731 TTTACTTTTATTTTCTGTGT
1 TTTATTTTTATTTTCTATGT
* *
3357751 TTTTTTATTTATTTAACATATGT
1 TTTATT-TTTATTT-TC-TATGT
*
3357774 TTTATTTTTATTTTCTTTGT
1 TTTATTTTTATTTTCTATGT
3357794 TTT
1 TTT
3357797 TATATAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
20 11 0.31
21 8 0.22
22 8 0.22
23 9 0.25
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (20 bp):
TTTATTTTTATTTTCTATGT
Found at i:3357799 original size:21 final size:21
Alignment explanation
Indices: 3357731--3357799 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
3357721 TATTTCAGCG
* *
3357731 TTTACTTTTATTTTCTGTGTT
1 TTTATTTTTATTTTCTATGTT
*
3357752 TTT-TTATTTATTTAACATATG-T
1 TTTATT-TTTATTT-TC-TATGTT
*
3357774 TTTATTTTTATTTTCTTTGTT
1 TTTATTTTTATTTTCTATGTT
3357795 TTTAT
1 TTTAT
3357800 ATAATTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 4 0.11
21 17 0.45
22 12 0.32
23 5 0.13
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (21 bp):
TTTATTTTTATTTTCTATGTT
Found at i:3357822 original size:41 final size:42
Alignment explanation
Indices: 3357736--3357840 Score: 97
Period size: 41 Copynumber: 2.5 Consensus size: 42
3357726 CAGCGTTTAC
* * * * *
3357736 TTTTATTTTCTGTGTTTTTTTATTTATTTAACATATGTTTTA
1 TTTTATTTTCTTTGTTTTTATATTAATTTAACATATCTTTGA
* *
3357778 TTTTTATTTTCTTTGTTTTTATA-TAATTT-TCATTTCTTTGA
1 -TTTTATTTTCTTTGTTTTTATATTAATTTAACATATCTTTGA
* *
3357819 TTTTATGTTTGTTTTTTTTTAT
1 TTTTAT-TTTCTTTGTTTTTAT
3357841 TTTATTACTA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
40 6 0.12
41 21 0.40
42 5 0.10
43 20 0.38
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (42 bp):
TTTTATTTTCTTTGTTTTTATATTAATTTAACATATCTTTGA
Found at i:3360928 original size:22 final size:22
Alignment explanation
Indices: 3360895--3360953 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
3360885 TAAAATCCAT
**
3360895 GCAGCT-ACATCGTTAACAGCC
1 GCAGCTGACATCGCCAACAGCC
3360916 GCAGCTGACATCGCCAACAGCC
1 GCAGCTGACATCGCCAACAGCC
3360938 GCAGCTGACATCGCCA
1 GCAGCTGACATCGCCA
3360954 TTCTTCCGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 6 0.17
22 29 0.83
ACGTcount: A:0.27, C:0.37, G:0.22, T:0.14
Consensus pattern (22 bp):
GCAGCTGACATCGCCAACAGCC
Found at i:3379488 original size:379 final size:381
Alignment explanation
Indices: 3378778--3379542 Score: 1417
Period size: 379 Copynumber: 2.0 Consensus size: 381
3378768 CTGAGATTTC
* * *
3378778 TGATATGCCGGAGATATGTGCAGCCCACCTTGGACGAGGGATCAACGGATTTGGTAGTTGGATCC
1 TGATATACCAGAGATATGTGCAGCCCACCTTAGACGAGGGATCAACGGATTTGGTAGTTGGATCC
*
3378843 TAGTTTGAAACTAAGAATGATGCCCAATTAGCAGTAAAGGAGTTTTTTTTATCAAAGCTCATATA
66 TAGTTTGAAACTAAGAAGGATGCCCAATTAGCAGTAAAGGAGTTTTTTTTATCAAAGCTCATATA
*
3378908 TAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTGTTAAGTGTATAAACAATAATGTCGG
131 GAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTGTTAAGTGTATAAACAATAATGTCGG
*
3378973 TTGTATGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGACAAGATTCC
196 TTGTAAGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGACAAGATTCC
*
3379038 ACTCCCAGTACAGTTGTACGTTGAGCTCCTTGACACAAGACCACAAACACTTAGATTCTGATGTC
261 ACTCCCAGTACAGTTGTACGTTGAGCTCCTTGACACAAGACCACAAACACTTAGATTCTGATGGC
3379103 ATATATGCACATGTCAAGC-TTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
326 ATATATGCACATGTCAAGCTTTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
3379158 TGATATACCAGAGATATGTGCAGCCCACCTTAGACGAGGGATCAACGGATTTGGTAGTTGGATCC
1 TGATATACCAGAGATATGTGCAGCCCACCTTAGACGAGGGATCAACGGATTTGGTAGTTGGATCC
* *
3379223 TAGTTTTAAACTAAGAAGGATGCCCAATTAGCAGTAAAGGAG-TTTTTTTATCAGAGCTCATATA
66 TAGTTTGAAACTAAGAAGGATGCCCAATTAGCAGTAAAGGAGTTTTTTTTATCAAAGCTCATATA
*
3379287 GAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTGTTAAGTGTATAAACAATAATGTTGG
131 GAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTGTTAAGTGTATAAACAATAATGTCGG
*
3379352 TTGTAAGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGACAAGGTTCC
196 TTGTAAGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGACAAGATTCC
3379417 ACTCCCAGTACAGTTGTACGTTGAGCTCCTTGACACAAGACCACAAACACTTAGATTCTGATGGC
261 ACTCCCAGTACAGTTGTACGTTGAGCTCCTTGACACAAGACCACAAACACTTAGATTCTGATGGC
3379482 ATATATGCACATGTCAAGCTTTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
326 ATATATGCACATGTCAAGCTTTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
3379538 TGATA
1 TGATA
3379543 GTGGCATCAA
Statistics
Matches: 373, Mismatches: 11, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
379 230 0.62
380 143 0.38
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (381 bp):
TGATATACCAGAGATATGTGCAGCCCACCTTAGACGAGGGATCAACGGATTTGGTAGTTGGATCC
TAGTTTGAAACTAAGAAGGATGCCCAATTAGCAGTAAAGGAGTTTTTTTTATCAAAGCTCATATA
GAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTGTTAAGTGTATAAACAATAATGTCGG
TTGTAAGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGACAAGATTCC
ACTCCCAGTACAGTTGTACGTTGAGCTCCTTGACACAAGACCACAAACACTTAGATTCTGATGGC
ATATATGCACATGTCAAGCTTTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
Found at i:3383210 original size:2 final size:2
Alignment explanation
Indices: 3383203--3383234 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3383193 CCAGAAACAA
3383203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3383235 GGGAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3383675 original size:16 final size:17
Alignment explanation
Indices: 3383635--3383678 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3383625 CCCTATTTGA
3383635 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
3383652 TTTTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
3383668 TTAAATATTTA
1 TTAAATATTTA
3383679 GTTTTTGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:3384857 original size:125 final size:125
Alignment explanation
Indices: 3384635--3384882 Score: 451
Period size: 125 Copynumber: 2.0 Consensus size: 125
3384625 TTAGGTGGGA
* * *
3384635 GTTATGACCCCCACTAATTTAGGGTATAATAAAAATAAATTAATTAAATGCACCTGCACTGATTT
1 GTTATGACCCCCACTAATTTAGAGTATAATAAAAATAAATTAATTAAATGCAACTACACTGATTT
3384700 GGACAACAATTTCAATTAGAAATTATGTAAGCACGATGTTGGTTTCTTTAGTACACAAGT
66 GGACAACAATTTCAATTAGAAATTATGTAAGCACGATGTTGGTTTCTTTAGTACACAAGT
* *
3384760 GTTATGACCCCTACTAATTTAGAGTATAATAAAAATAAATTAATTAAATGCAACTACACTGTTTT
1 GTTATGACCCCCACTAATTTAGAGTATAATAAAAATAAATTAATTAAATGCAACTACACTGATTT
3384825 GGACAACAATTTCAATTAGAAATTATGTAAGCACGATGTTGGTTTCTTTAGTACACAA
66 GGACAACAATTTCAATTAGAAATTATGTAAGCACGATGTTGGTTTCTTTAGTACACAA
3384883 ATTCAATACT
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 118 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (125 bp):
GTTATGACCCCCACTAATTTAGAGTATAATAAAAATAAATTAATTAAATGCAACTACACTGATTT
GGACAACAATTTCAATTAGAAATTATGTAAGCACGATGTTGGTTTCTTTAGTACACAAGT
Found at i:3390717 original size:66 final size:65
Alignment explanation
Indices: 3390647--3390803 Score: 162
Period size: 65 Copynumber: 2.4 Consensus size: 65
3390637 CCATTCAACA
* * * *
3390647 GGTACCGATACCCTCTCAAATGAGAAAATTTCAGAATGTAAT-AGGGGTACCGATACCCCCCAGG
1 GGTACCGATACCCCCTCAAACGA-AAAATTACAAAATGTAATGA-GGGTACCGATACCCCCCAGG
3390711 TG
64 TG
** *
3390713 GGTACCGATACCCCCTTGAACGAAAAATTACAAAATGTTATGAGGGTACCGATA--CCCCA-GTA
1 GGTACCGATACCCCCTCAAACGAAAAATTACAAAATGTAATGAGGGTACCGATACCCCCCAGGT-
3390775 G
65 G
* * *
3390776 GGTATCGATACCTCCT-AAAGGAAAAATT
1 GGTACCGATACCCCCTCAAACGAAAAATT
3390804 TGAATATTGG
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
62 12 0.15
63 20 0.26
65 26 0.33
66 20 0.26
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (65 bp):
GGTACCGATACCCCCTCAAACGAAAAATTACAAAATGTAATGAGGGTACCGATACCCCCCAGGTG
Found at i:3391668 original size:23 final size:23
Alignment explanation
Indices: 3391600--3391668 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3391590 ACATCTTATA
* *
3391600 TGGCACTACGGTGCATTTCTACA
1 TGGCACTTCGGTGCATTTCTACG
* *
3391623 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
3391646 TGGCACTTCGATGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
3391669 AGTTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:3397138 original size:23 final size:22
Alignment explanation
Indices: 3397112--3397174 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 22
3397102 CATCTTATAT
3397112 GGCACTTACGTGCATTTCTATGC
1 GGCACTT-CGTGCATTTCTATGC
* *
3397135 GGCACTTCGGTGCAATTCTATGT
1 GGCACTTC-GTGCATTTCTATGC
3397158 GGCACTTCGATGCATTT
1 GGCACTTCG-TGCATTT
3397175 ATACGAGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (22 bp):
GGCACTTCGTGCATTTCTATGC
Found at i:3399226 original size:15 final size:15
Alignment explanation
Indices: 3399191--3399227 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3399181 AATTTATGTG
*
3399191 ATTTTATTTTCTTGT
1 ATTTTATTTTCTTCT
*
3399206 ACTTTATTTTCTTCT
1 ATTTTATTTTCTTCT
3399221 ATTTTAT
1 ATTTTAT
3399228 GTATTTTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.70
Consensus pattern (15 bp):
ATTTTATTTTCTTCT
Found at i:3399267 original size:10 final size:11
Alignment explanation
Indices: 3399251--3399283 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
3399241 ATATTTTATC
3399251 ATATAAATATT
1 ATATAAATATT
3399262 AT-TAAATATT
1 ATATAAATATT
*
3399272 ATATATATATT
1 ATATAAATATT
3399283 A
1 A
3399284 ATGTCTAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATAAATATT
Found at i:3399483 original size:49 final size:49
Alignment explanation
Indices: 3399426--3399587 Score: 127
Period size: 49 Copynumber: 3.2 Consensus size: 49
3399416 CAGCTATGAT
*
3399426 ATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCCAATC
1 ATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCTAATC
* * * ** * *
3399475 ATTTGCCAGA-CATGAT-TCA-AATATCATAGCCACAGC-TAGCAGTACAGCTTTGAT-
1 ATTTGCCAGATTAT-ATAT-ATAATAT--TTG-TACAGCTTA--A--ATTG-TCTAATC
3399529 ATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCTAATC
1 ATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCTAATC
3399578 ATTTGCCAGA
1 ATTTGCCAGA
3399588 CATGATTCAA
Statistics
Matches: 83, Mismatches: 15, Indels: 30
0.65 0.12 0.23
Matches are distributed among these distances:
48 12 0.14
49 25 0.30
50 4 0.05
51 6 0.07
52 6 0.07
53 4 0.05
54 15 0.18
55 11 0.13
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (49 bp):
ATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCTAATC
Found at i:3399539 original size:103 final size:103
Alignment explanation
Indices: 3399413--3399626 Score: 401
Period size: 103 Copynumber: 2.1 Consensus size: 103
3399403 TTTGCCAGCG
3399413 GTACAGCTATGATATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCCAATCATT
1 GTACAGCTATGATATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCCAATCATT
3399478 TGCCAGACATGATTCAAATATCATAGCCACAGCTAGCA
66 TGCCAGACATGATTCAAATATCATAGCCACAGCTAGCA
* *
3399516 GTACAGCTTTGATATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCTAATCATT
1 GTACAGCTATGATATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCCAATCATT
*
3399581 TGCCAGACATGATTCAAATATCATAGCCACAGCTAGCG
66 TGCCAGACATGATTCAAATATCATAGCCACAGCTAGCA
3399619 GTACAGCT
1 GTACAGCT
3399627 GCTTAAGTCG
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (103 bp):
GTACAGCTATGATATTTGCCAGATTATATATATAATATTTGTACAGCTTAAATTGTCCAATCATT
TGCCAGACATGATTCAAATATCATAGCCACAGCTAGCA
Found at i:3401480 original size:20 final size:20
Alignment explanation
Indices: 3401455--3401492 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3401445 ATTGAGAAGG
3401455 GATGCACCAATGCACTCATT
1 GATGCACCAATGCACTCATT
* *
3401475 GATGCATCGATGCACTCA
1 GATGCACCAATGCACTCA
3401493 CCATATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (20 bp):
GATGCACCAATGCACTCATT
Found at i:3401567 original size:63 final size:64
Alignment explanation
Indices: 3401500--3401648 Score: 223
Period size: 64 Copynumber: 2.3 Consensus size: 64
3401490 TCACCATATT
* *
3401500 GAATGCATTTTATGCATTGATGCAC-TACCATGCATCGATGCACTCAGG-TT-TTATGAAAACAT
1 GAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTT-T-AAAACAT
3401562 C
64 C
**
3401563 GAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTTTGGCTTGTTTAAAACATC
1 GAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTTTAAAACATC
3401627 GAATGCATTTTATGCATCGATG
1 GAATGCATTTTATGCATCGATG
3401649 TACTCTTAGT
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
63 24 0.30
64 50 0.63
65 3 0.04
66 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (64 bp):
GAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTTTAAAACATC
Found at i:3401667 original size:64 final size:62
Alignment explanation
Indices: 3401500--3401671 Score: 204
Period size: 64 Copynumber: 2.7 Consensus size: 62
3401490 TCACCATATT
*
3401500 GAATGCATTTTATGCATTGATGCACTACCATGCATCGATGCACTCAGGTTTTATGAAAACATC
1 GAATGCATTTTATGCATCGATGCACT-CCATGCATCGATGCACTCAGGTTTTATGAAAACATC
* **
3401563 GAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTTTGGCTTGTT-T-AAAACAT
1 GAATGCATTTTATGCATCGATGCAC--TCCATGCATCGATGCACTCAGG-TT-TTATGAAAACAT
3401626 C
62 C
* * *
3401627 GAATGCATTTTATGCATCGATGTACTCTTAGTGCACCGATGCACT
1 GAATGCATTTTATGCATCGATGCACTC-CA-TGCATCGATGCACT
3401672 AAGGGTCCAA
Statistics
Matches: 95, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
62 1 0.01
63 25 0.26
64 64 0.67
65 3 0.03
66 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (62 bp):
GAATGCATTTTATGCATCGATGCACTCCATGCATCGATGCACTCAGGTTTTATGAAAACATC
Found at i:3404887 original size:5 final size:5
Alignment explanation
Indices: 3404877--3404911 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
3404867 TAACAAATTA
3404877 ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT
3404912 TTCATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:3405367 original size:22 final size:22
Alignment explanation
Indices: 3405323--3405367 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3405313 GAGTTTTTAG
* *
3405323 TGAGTTTTTATTTAATGGGTAT
1 TGAGTTTTTATTGAATGAGTAT
* *
3405345 TGAGTTTTTATTGGATGATTAT
1 TGAGTTTTTATTGAATGAGTAT
3405367 T
1 T
3405368 TAATAGGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (22 bp):
TGAGTTTTTATTGAATGAGTAT
Found at i:3405377 original size:33 final size:33
Alignment explanation
Indices: 3405300--3405386 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 33
3405290 GTTTTCTTTG
* **
3405300 TTTAATAGGTAGTGAGTTTTTAGTGAGTTTTTA
1 TTTAATAGGTATTGAGTTTTTAGTGAGTGATTA
* *
3405333 TTTAATGGGTATTGAGTTTTTATTG-GATGATTA
1 TTTAATAGGTATTGAGTTTTTAGTGAG-TGATTA
3405366 TTTAATAGGTATT-AGGTTTTT
1 TTTAATAGGTATTGA-GTTTTT
3405387 TAGATTAGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 2 0.04
33 44 0.96
ACGTcount: A:0.24, C:0.00, G:0.23, T:0.53
Consensus pattern (33 bp):
TTTAATAGGTATTGAGTTTTTAGTGAGTGATTA
Found at i:3405410 original size:3 final size:3
Alignment explanation
Indices: 3405396--3405460 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
3405386 TTAGATTAGG
* * *
3405396 TAA TAT TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3405444 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
3405461 TTTAATAGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3409081 original size:22 final size:22
Alignment explanation
Indices: 3409054--3409115 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
3409044 TTTTGTATAT
3409054 TATAATATATTAGATTATTATC
1 TATAATATATTAGATTATTATC
*
3409076 TATAATAT-TCTAAATTATTATC
1 TATAATATAT-TAGATTATTATC
*
3409098 TAT-ATA-ATTAGATAATTA
1 TATAATATATTAGATTATTA
3409116 AATTAGAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 8 0.23
21 5 0.14
22 22 0.63
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (22 bp):
TATAATATATTAGATTATTATC
Found at i:3409188 original size:18 final size:19
Alignment explanation
Indices: 3409143--3409188 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
3409133 AATTATTTCT
3409143 TTTCTATTTTTATTAAAAAA
1 TTTCTA-TTTTATTAAAAAA
* *
3409163 TAT-AATTTTATT-AAAAA
1 TTTCTATTTTATTAAAAAA
3409180 TTTCTATTT
1 TTTCTATTT
3409189 AAATTTAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
17 7 0.33
18 11 0.52
19 1 0.05
20 2 0.10
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTCTATTTTATTAAAAAA
Found at i:3412881 original size:16 final size:15
Alignment explanation
Indices: 3412850--3412889 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
3412840 TTTTTTATAT
3412850 TTATAA-AATTAATA
1 TTATAATAATTAATA
3412864 TTATAATAATTAAATA
1 TTATAATAATT-AATA
3412880 TTATGAATAA
1 TTAT-AATAA
3412890 AGTAGAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 8 0.35
17 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TTATAATAATTAATA
Found at i:3413532 original size:15 final size:16
Alignment explanation
Indices: 3413495--3413539 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
3413485 CAAAAAGAAT
* *
3413495 ATTAAA-AAAATAATA
1 ATTAAATAAATTATTA
3413510 ATTAAATAAATTATTA
1 ATTAAATAAATTATTA
3413526 ATT-AATAAATTATT
1 ATTAAATAAATTATT
3413540 TTTTAAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAATAAATTATTA
Found at i:3418690 original size:14 final size:14
Alignment explanation
Indices: 3418671--3418709 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
3418661 AGACTTGTTG
3418671 TTTTCTACAGTCTA
1 TTTTCTACAGTCTA
*
3418685 TTTTCTACACAGTCTG
1 TTTTCT--ACAGTCTA
3418701 TTTTCTACA
1 TTTTCTACA
3418710 TGGTATCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 9 0.41
16 13 0.59
ACGTcount: A:0.21, C:0.23, G:0.08, T:0.49
Consensus pattern (14 bp):
TTTTCTACAGTCTA
Found at i:3418698 original size:16 final size:16
Alignment explanation
Indices: 3418677--3418709 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3418667 GTTGTTTTCT
3418677 ACAGTCTATTTTCTAC
1 ACAGTCTATTTTCTAC
*
3418693 ACAGTCTGTTTTCTAC
1 ACAGTCTATTTTCTAC
3418709 A
1 A
3418710 TGGTATCATA
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:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (16 bp):
ACAGTCTATTTTCTAC
Found at i:3420514 original size:51 final size:51
Alignment explanation
Indices: 3420455--3420555 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
3420445 TCAGGGGGGG
* *
3420455 AGTTACAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
3420506 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
3420556 CCTTTCCTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
Found at i:3427612 original size:2 final size:2
Alignment explanation
Indices: 3427605--3427644 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3427595 TACTTTTACA
3427605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3427645 TGGATTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3428080 original size:29 final size:29
Alignment explanation
Indices: 3428047--3428104 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3428037 TCCTTTTGAT
3428047 CACTGAAATCATTTTATCCGTGCTCAGTA
1 CACTGAAATCATTTTATCCGTGCTCAGTA
3428076 CACTGAAATCATTTTATCCGTGCTCAGTA
1 CACTGAAATCATTTTATCCGTGCTCAGTA
3428105 TAGAAGCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (29 bp):
CACTGAAATCATTTTATCCGTGCTCAGTA
Found at i:3430722 original size:10 final size:10
Alignment explanation
Indices: 3430707--3430735 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3430697 AAAGGAAAGG
3430707 ATTCAAAATA
1 ATTCAAAATA
3430717 ATTCAAAATA
1 ATTCAAAATA
3430727 ATTCAAAAT
1 ATTCAAAAT
3430736 GAGTTGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (10 bp):
ATTCAAAATA
Found at i:3433145 original size:22 final size:22
Alignment explanation
Indices: 3433120--3433226 Score: 60
Period size: 24 Copynumber: 4.6 Consensus size: 22
3433110 AAATATAGTG
3433120 AAAATAAATAAATAGTATAAAT
1 AAAATAAATAAATAGTATAAAT
* * *
3433142 AAAAT-AATAAAAAAATATATAT
1 AAAATAAAT-AAATAGTATAAAT
*
3433164 AAAAATAAA-AATGTATGTATAATAT
1 -AAAATAAATAA-ATA-GTATAA-AT
3433189 AATAA-AATACTAAATAGTA-ATAAT
1 AA-AATAA-A-TAAATAGTATA-AAT
3433213 AATAATAAATAAAT
1 AA-AATAAATAAAT
3433227 GAAAAAAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 23
0.68 0.08 0.24
Matches are distributed among these distances:
21 3 0.05
22 17 0.26
23 11 0.17
24 19 0.29
25 11 0.17
26 2 0.03
27 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAATAAATAAATAGTATAAAT
Found at i:3433184 original size:20 final size:22
Alignment explanation
Indices: 3433135--3433195 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 22
3433125 AAATAAATAG
* *
3433135 TATAAATAAAATAATAAAAAAA
1 TATATATAATATAATAAAAAAA
**
3433157 TATATATAA-A-AATAAAAATG
1 TATATATAATATAATAAAAAAA
*
3433177 TATGTATAATATAATAAAA
1 TATATATAATATAATAAAA
3433196 TACTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
22 15 0.45
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (22 bp):
TATATATAATATAATAAAAAAA
Found at i:3433452 original size:27 final size:26
Alignment explanation
Indices: 3433410--3433491 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 26
3433400 AACGCAAAGA
3433410 AAATAAAAAAAT-TATAATAAATAAT
1 AAATAAAAAAATATATAATAAATAAT
3433435 AAATAAAAAAATAATATAATAAATAAAT
1 AAATAAAAAAAT-ATATAATAAAT-AAT
* *
3433463 AAA-ATAATAAATATACATATAAATAAT
1 AAATA-AAAAAATATATA-ATAAATAAT
3433490 AA
1 AA
3433492 GGGTTAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
25 12 0.24
27 20 0.40
28 18 0.36
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (26 bp):
AAATAAAAAAATATATAATAAATAAT
Found at i:3433453 original size:24 final size:24
Alignment explanation
Indices: 3433410--3433488 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
3433400 AACGCAAAGA
*
3433410 AAATAAAAAAATTATAATAAATAAT
1 AAATAAAAAAATAAT-ATAAATAAT
3433435 AAATAAAAAAATAATAT-AATAAAT
1 AAATAAAAAAATAATATAAAT-AAT
* *
3433459 AAATAAAATAATAAATATACAT-AT
1 AAATAAAAAAAT-AATATAAATAAT
3433483 AAATAA
1 AAATAA
3433489 TAAGGGTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
23 3 0.06
24 24 0.50
25 19 0.40
26 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATAAAAAAATAATATAAATAAT
Found at i:3433457 original size:16 final size:16
Alignment explanation
Indices: 3433428--3433473 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
3433418 AAATTATAAT
3433428 AAATAATA-AATAAAA
1 AAATAATATAATAAAA
*
3433443 AAATAATATAATAAAT
1 AAATAATATAATAAAA
*
3433459 AAATAAAATAATAAA
1 AAATAATATAATAAA
3433474 TATACATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAATATAATAAAA
Found at i:3433488 original size:4 final size:4
Alignment explanation
Indices: 3433410--3433475 Score: 57
Period size: 4 Copynumber: 16.2 Consensus size: 4
3433400 AACGCAAAGA
* *
3433410 AAAT AAAA AAATT ATAAT AAAT -AAT AAAT AAAA AAAT -AAT ATAAT AAAT
1 AAAT AAAT AAA-T A-AAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT
3433459 AAAT AAA- ATAAT AAAT A
1 AAAT AAAT A-AAT AAAT A
3433476 TACATATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
3 7 0.14
4 34 0.67
5 8 0.16
6 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:3433929 original size:37 final size:37
Alignment explanation
Indices: 3433888--3433972 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
3433878 GGATCACATC
* *
3433888 TTTAGGAGTTTAAATAATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
* ** *
3433925 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
3433962 TTTAGGAGTTT
1 TTTAGGAGTTT
3433973 GAATCTTAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
Found at i:3434927 original size:106 final size:106
Alignment explanation
Indices: 3434732--3436040 Score: 2008
Period size: 106 Copynumber: 12.3 Consensus size: 106
3434722 GCATTGTTCC
* * * * * *
3434732 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * *
3434797 CCAGTC-GTCTCTTCGTTGTAAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3434838 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** *
3434903 CCAGCGGTCCCTTCACCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
3434944 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3435009 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3435050 GAGTCCAACATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
3435115 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3435156 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3435221 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3435262 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3435327 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3435368 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3435433 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3435474 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3435539 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3435580 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
3435645 CCAGCGGTCCTTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3435686 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3435751 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3435792 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
3435857 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3435898 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * *
3435963 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3436004 GAGTGGCACGATATCCTCCGTCGTGGAGTTGAAATTG
1 GAGT--C-CAATATCCTTCGTTGTGAAGTTGAAATTG
3436041 CGGATAGTCA
Statistics
Matches: 1110, Mismatches: 89, Indels: 5
0.92 0.07 0.00
Matches are distributed among these distances:
105 1 0.00
106 1084 0.98
108 1 0.00
109 24 0.02
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3437620 original size:16 final size:16
Alignment explanation
Indices: 3437601--3437664 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
3437591 TTGTCCCTTT
3437601 TTCTTTTTGATTTTTG
1 TTCTTTTTGATTTTTG
* *
3437617 TTCTTTCTT-TTTTTTC
1 TTCTTT-TTGATTTTTG
* *
3437633 TTCTTTTTTGCTTCTT-
1 TTC-TTTTTGATTTTTG
*
3437649 TTCTTTTTTATTTTTG
1 TTCTTTTTGATTTTTG
3437665 CCCTTTTTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
15 9 0.24
16 19 0.51
17 9 0.24
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.78
Consensus pattern (16 bp):
TTCTTTTTGATTTTTG
Found at i:3441131 original size:19 final size:20
Alignment explanation
Indices: 3441102--3441139 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3441092 TCTCCTTACC
3441102 GGTGCCCCCTTGGGCTTGCT
1 GGTGCCCCCTTGGGCTTGCT
3441122 GGTG-CCCCTTGGGCTTGC
1 GGTGCCCCCTTGGGCTTGC
3441140 CAGACCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.00, C:0.34, G:0.37, T:0.29
Consensus pattern (20 bp):
GGTGCCCCCTTGGGCTTGCT
Found at i:3442006 original size:20 final size:19
Alignment explanation
Indices: 3441956--3442011 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
3441946 AACCAATAAT
3441956 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
3441975 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
3441995 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
3442012 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:3442149 original size:2 final size:2
Alignment explanation
Indices: 3442142--3442193 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
3442132 AAATAATAAA
*
3442142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
*
3442184 GT AT A- AT AT A
1 AT AT AT AT AT A
3442194 ATAAAATACT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3442396 original size:11 final size:11
Alignment explanation
Indices: 3442380--3442425 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
3442370 ATAGATAAAA
3442380 ATAATAATAAT
1 ATAATAATAAT
3442391 ATAATAA-ATAT
1 ATAATAATA-AT
*
3442402 ATAATAATAAG
1 ATAATAATAAT
3442413 A-AATAAT-AT
1 ATAATAATAAT
3442422 ATAA
1 ATAA
3442426 CGCAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 2 0.07
10 9 0.30
11 18 0.60
12 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:3442406 original size:22 final size:20
Alignment explanation
Indices: 3442380--3442425 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
3442370 ATAGATAAAA
*
3442380 ATAATAATAATATAATAAATAT
1 ATAATAATAAGA-AAT-AATAT
3442402 ATAATAATAAGAAATAATAT
1 ATAATAATAAGAAATAATAT
3442422 ATAA
1 ATAA
3442426 CGCAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.39
21 3 0.13
22 11 0.48
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAATAATAAGAAATAATAT
Found at i:3442407 original size:19 final size:17
Alignment explanation
Indices: 3442374--3442425 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
3442364 GTAAACATAG
3442374 ATAAAAATAATAATAAT
1 ATAAAAATAATAATAAT
3442391 ATAATAAATATATAATAAT
1 ATAA-AAATA-ATAATAAT
*
3442410 A-AGAAATAATATATAA
1 ATAAAAATAATA-ATAA
3442426 CGCAAAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 3 0.10
17 13 0.42
18 6 0.19
19 9 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAAAAATAATAATAAT
Found at i:3442472 original size:15 final size:16
Alignment explanation
Indices: 3442435--3442474 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3442425 ACGCAAAGAA
*
3442435 AAATAAAAAAAATAAT
1 AAATAAATAAAATAAT
3442451 AAATAAATAAAAT-AT
1 AAATAAATAAAATAAT
*
3442466 AATTAAATA
1 AAATAAATA
3442475 TATACATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAATAAAATAAT
Found at i:3442986 original size:37 final size:37
Alignment explanation
Indices: 3442894--3442994 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
3442884 TGCTTGTAGG
* * ** * *
3442894 TCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCTA
1 TCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCTA
* *
3442931 TTCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCTA
1 TCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCTA
3442968 TCCTATTTTTAGGAGTTTGAATCCTAG
1 TCCTATTTTTAGGAGTTTGAATCCTAG
3442995 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.42
Consensus pattern (37 bp):
TCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCTA
Found at i:3446151 original size:83 final size:85
Alignment explanation
Indices: 3446032--3446196 Score: 214
Period size: 83 Copynumber: 2.0 Consensus size: 85
3446022 TTATAAACAC
* *
3446032 CGTAATAGGGTTAACCTATAGTGGCGTTTCTGCAAT-AACTGTCGCACCATATTAGTACTTTAGC
1 CGTAATAGGGTTAACCTATAGTGGCGTTTCTGCAATAAAC-GCCGCAACATATTAGTACTTTAGC
*
3446096 GGC-TTT-TTTATACAAATGT
65 GGCATTTGTGTATACAAATGT
* * *
3446115 CGTAATAGGGTTTAA-CTATAGTGGTGTTAT-TTCAATAAACGCCGTAACATATTAGTACTTTAG
1 CGTAATAGGG-TTAACCTATAGTGGCGTT-TCTGCAATAAACGCCGCAACATATTAGTACTTTAG
3446178 CGGCATTTGTGTATACAAA
64 CGGCATTTGTGTATACAAA
3446197 CACCGTGATA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
83 51 0.72
84 11 0.15
85 9 0.13
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (85 bp):
CGTAATAGGGTTAACCTATAGTGGCGTTTCTGCAATAAACGCCGCAACATATTAGTACTTTAGCG
GCATTTGTGTATACAAATGT
Found at i:3452188 original size:45 final size:46
Alignment explanation
Indices: 3452097--3452201 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 46
3452087 TGCACATACC
* *
3452097 ATGCATCGATGCACTCAAGTTTTTATGAAAACATCGAATGCTTTTT
1 ATGCATCGATGCACTCAAGTATTTATGAAAACATCGAATGCATTTT
* *
3452143 ATGCATCGATGCACTTAGGCTATTT-T-AAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAAG-TATTTATGAAAACATCGAATGCATTTT
*
3452188 ATGAATCGATGCAC
1 ATGCATCGATGCAC
3452202 CCTTAGTGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 31 0.58
46 18 0.34
47 4 0.08
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (46 bp):
ATGCATCGATGCACTCAAGTATTTATGAAAACATCGAATGCATTTT
Found at i:3460943 original size:64 final size:65
Alignment explanation
Indices: 3460790--3460947 Score: 214
Period size: 65 Copynumber: 2.4 Consensus size: 65
3460780 GAATAAATTG
* * *
3460790 AACATCTAATGCATTTTATGCATCAATGCACATACCATGCATCAATACACTCAGGTTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCAATACACTCAGGTATTTATGAA
* *
3460855 AACATCGAATGCATTTTATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTATTT-T-
1 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCAATACACTCAGG-TATTTATG
3460917 AA
64 AA
* *
3460919 AACATTGAATGTATTTTATGCATCGATGC
1 AACATCGAATGCATTTTATGCATCGATGC
3460948 CCTTAGTGCA
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 30 0.36
65 50 0.60
66 4 0.05
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCAATACACTCAGGTATTTATGAA
Found at i:3462594 original size:22 final size:24
Alignment explanation
Indices: 3462552--3462596 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3462542 GTCATCGAAT
3462552 ATATATATTACTAGTATTGTTGTCA
1 ATATATATTAC-AGTATTGTTGTCA
3462577 ATATATATTA-A-TATTGTTGT
1 ATATATATTACAGTATTGTTGT
3462597 TTGTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
25 10 0.50
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (24 bp):
ATATATATTACAGTATTGTTGTCA
Found at i:3464205 original size:21 final size:21
Alignment explanation
Indices: 3464144--3464192 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3464134 CCGAAGCTGA
*
3464144 AGCGAGAGAAGCAGAAAGAGT
1 AGCGAGAGAAGCAGAAAGAGC
3464165 AGCGAGAGAAGCAGAAAGAGC
1 AGCGAGAGAAGCAGAAAGAGC
3464186 AGCGAGA
1 AGCGAGA
3464193 TATGCAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.12, G:0.39, T:0.02
Consensus pattern (21 bp):
AGCGAGAGAAGCAGAAAGAGC
Found at i:3468077 original size:23 final size:22
Alignment explanation
Indices: 3468044--3468099 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
3468034 ATTTTTAGTG
3468044 TTTTTTATTTTTAGTAATTTAA
1 TTTTTTATTTTTAGTAATTTAA
* *
3468066 TTTTTTATTTTTAGTAGTTTTA
1 TTTTTTATTTTTAGTAATTTAA
* *
3468088 TATTTGATTTTT
1 TTTTTTATTTTT
3468100 TTAATATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (22 bp):
TTTTTTATTTTTAGTAATTTAA
Found at i:3468108 original size:16 final size:16
Alignment explanation
Indices: 3468083--3468120 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3468073 TTTTTAGTAG
3468083 TTTT-ATATTTGATTT
1 TTTTAATATTTGATTT
3468098 TTTTAATATTTGATTT
1 TTTTAATATTTGATTT
3468114 TTTTAAT
1 TTTTAAT
3468121 TTTAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTTAATATTTGATTT
Found at i:3477849 original size:5 final size:5
Alignment explanation
Indices: 3477841--3477872 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
3477831 TTTTTTATCG
3477841 AATTA AATTA AATTA AATTGA AATTA AATTA A
1 AATTA AATTA AATTA AATT-A AATTA AATTA A
3477873 TTTATTTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:3477866 original size:16 final size:15
Alignment explanation
Indices: 3477841--3477872 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3477831 TTTTTTATCG
3477841 AATTAAATTAAATTA
1 AATTAAATTAAATTA
3477856 AATTGAAATTAAATTA
1 AATT-AAATTAAATTA
3477872 A
1 A
3477873 TTTATTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AATTAAATTAAATTA
Found at i:3483394 original size:22 final size:22
Alignment explanation
Indices: 3483346--3483388 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3483336 TGACTTTTTG
*
3483346 GTCAAAGTAAACGGTCATACCA
1 GTCAAAGTAAACGGTCAGACCA
* *
3483368 GTCAAAGTCAATGGTCAGACC
1 GTCAAAGTAAACGGTCAGACC
3483389 GATCAACGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (22 bp):
GTCAAAGTAAACGGTCAGACCA
Found at i:3485381 original size:15 final size:15
Alignment explanation
Indices: 3485343--3485377 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3485333 ATGATTATAC
*
3485343 ATAATGTTACCATAT
1 ATAATGTAACCATAT
3485358 ATAATGTAACCA-AT
1 ATAATGTAACCATAT
3485372 ATAATG
1 ATAATG
3485378 GTAAAACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (15 bp):
ATAATGTAACCATAT
Found at i:3492244 original size:102 final size:100
Alignment explanation
Indices: 3492068--3492365 Score: 333
Period size: 102 Copynumber: 3.0 Consensus size: 100
3492058 TATTAGAATA
** * * * * *
3492068 TGACATTGAGTATGCGAGTTAAAAGAAGATTGAAAAGAAGTGTCGTAACATATTTTCTAGCTAGT
1 TGACATTGAGTATGCGAACTAAAAGAAGATCGAAAAGAAGTGTCGTAGCAGATTTTCTGGCCAGT
3492133 CATGCATCAGATGATTATGAGTCCCTCAGTTTTAATT
66 CAT--ATCAGATGATTATGAGTCCCTCAGTTTTAATT
** * * *
3492170 TGACATTTTGTATGCGAACTAAAAGATGATCGAAAAGAAATGTCATAGCAGATTTTCTGGCCAGT
1 TGACATTGAGTATGCGAACTAAAAGAAGATCGAAAAGAAGTGTCGTAGCAGATTTTCTGGCCAGT
*
3492235 CATTTATCAGATGATTATGAGTCCCTCTGTTTTAATT
66 CA--TATCAGATGATTATGAGTCCCTCAGTTTTAATT
* * * * *
3492272 TGACATTGCGTATAC-AAGCTAAAAGACGCTCGAAAAGAAGTGCCGTAGCAGATTTTCTGG-CA-
1 TGACATTGAGTATGCGAA-CTAAAAGAAGATCGAAAAGAAGTGTCGTAGCAGATTTTCTGGCCAG
3492334 -C----CAGATGATTATGAGTCCCTCAGTTTTAATT
65 TCATATCAGATGATTATGAGTCCCTCAGTTTTAATT
3492365 T
1 T
3492366 TCCAGATGAG
Statistics
Matches: 171, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
93 30 0.18
99 1 0.01
101 4 0.02
102 135 0.79
104 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (100 bp):
TGACATTGAGTATGCGAACTAAAAGAAGATCGAAAAGAAGTGTCGTAGCAGATTTTCTGGCCAGT
CATATCAGATGATTATGAGTCCCTCAGTTTTAATT
Found at i:3493068 original size:9 final size:8
Alignment explanation
Indices: 3493033--3493115 Score: 58
Period size: 9 Copynumber: 9.4 Consensus size: 8
3493023 AACGAAAACG
3493033 AAAAAGAA
1 AAAAAGAA
*
3493041 AAAGAAAAA
1 AAA-AAGAA
3493050 GAAAAAGAA
1 -AAAAAGAA
3493059 AAAAATGAA
1 AAAAA-GAA
*
3493068 AAAAGTGAA
1 AAAA-AGAA
3493077 AAAAAGAA
1 AAAAAGAA
*
3493085 AGAAAACAA
1 A-AAAAGAA
*
3493094 AGGATAAGAA
1 A--AAAAGAA
3493104 TAAAAAGAA
1 -AAAAAGAA
3493113 AAA
1 AAA
3493116 TAAAAAACTG
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
8 15 0.25
9 35 0.58
10 9 0.15
11 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.05
Consensus pattern (8 bp):
AAAAAGAA
Found at i:3493069 original size:6 final size:6
Alignment explanation
Indices: 3492999--3493061 Score: 81
Period size: 6 Copynumber: 10.0 Consensus size: 6
3492989 AAAGACAGAG
* *
3492999 GAAAAA GAAAAA GAAAAAA TGGAAAAC GAAAAC GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA G-AAAAA --GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
3493050 GAAAAA GAAAAA
1 GAAAAA GAAAAA
3493062 AATGAAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
6 42 0.81
7 5 0.10
8 4 0.08
9 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:3495316 original size:36 final size:36
Alignment explanation
Indices: 3495274--3495451 Score: 123
Period size: 36 Copynumber: 5.3 Consensus size: 36
3495264 TGAGGTTGTT
* *
3495274 TCTTGAAACAAATTTTGTCTCGCATGAGACAGTTTC
1 TCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTC
* * * *
3495310 TCTTGAAACATAA-----AC-C-TTTGAGATTGTTTA
1 TCTTGAAACA-AATTTTGTCTCGCTTGAGATAGTTTC
*
3495340 TCTTGAAACAAATTTTGTCTCGCTTAAGATAGTTTC
1 TCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTC
* * * * *
3495376 TCTTGAAACATAA-----AC-C-TTTAAGATTGTTTA
1 TCTTGAAACA-AATTTTGTCTCGCTTGAGATAGTTTC
*
3495406 TCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTC
1 TCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTC
3495442 TCTTGAAACA
1 TCTTGAAACA
3495452 TAAACATTTG
Statistics
Matches: 105, Mismatches: 21, Indels: 32
0.66 0.13 0.20
Matches are distributed among these distances:
29 4 0.04
30 40 0.38
31 2 0.02
32 2 0.02
34 2 0.02
35 2 0.02
36 49 0.47
37 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (36 bp):
TCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTC
Found at i:3495344 original size:30 final size:30
Alignment explanation
Indices: 3495305--3495415 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 30
3495295 GCATGAGACA
* *
3495305 GTTTCTCTTGAAACATAAACCTTTGAGATT
1 GTTTATCTTGAAACATAAACCTTTAAGATT
* * *
3495335 GTTTATCTTGAAACA-AATTTTGTCTCGCTTAAGATA
1 GTTTATCTTGAAACATAA-----AC-C-TTTAAGATT
*
3495371 GTTTCTCTTGAAACATAAACCTTTAAGATT
1 GTTTATCTTGAAACATAAACCTTTAAGATT
3495401 GTTTATCTTGAAACA
1 GTTTATCTTGAAACA
3495416 AATTTTGTCT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
29 2 0.03
30 35 0.56
31 1 0.02
32 1 0.02
34 1 0.02
35 1 0.02
36 20 0.32
37 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (30 bp):
GTTTATCTTGAAACATAAACCTTTAAGATT
Found at i:3495380 original size:66 final size:66
Alignment explanation
Indices: 3495224--3495508 Score: 421
Period size: 66 Copynumber: 4.3 Consensus size: 66
3495214 AGAAGATTGC
* * *
3495224 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAAATTTGAGGTTG-TT-TCTTGAAACAAAT
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAAT
3495287 T
66 T
* *
3495288 TTGTCTCGCATGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTATCTTGAAACAAAT
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAAT
3495353 T
66 T
* * * *
3495354 TTGTCTCGCTTAAGATAGTTTCTCTTGAAACATAAACCTTTAAGATTGTTTATCTTGAAACAAAT
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAAT
3495419 T
66 T
*
3495420 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAAG
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAA-
3495485 TT
65 TT
** * *
3495487 ACGTCTCACTTGAGACAATTTC
1 TTGTCTCGCTTGAGACAGTTTC
3495509 CCATAAAAAC
Statistics
Matches: 200, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
64 43 0.22
65 2 0.01
66 135 0.68
67 20 0.10
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (66 bp):
TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAAT
T
Found at i:3495535 original size:67 final size:66
Alignment explanation
Indices: 3495226--3495546 Score: 211
Period size: 66 Copynumber: 4.9 Consensus size: 66
3495216 AAGATTGCTT
* * * ** * ** *
3495226 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAAATTTGAGGTTG-TT-TCTTGAAACAAATTT
1 GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAAATTGTTTCTCTTGAAACAAATTA
*
3495289 T
66 C
* * * * ** * * * *
3495290 GTCTCGCATGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTATCTTGAAACAAATTT
1 GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAAATTGTTTCTCTTGAAACAAATTA
*
3495355 T
66 C
* * * * * ** * *
3495356 GTCTCGCTTAAGATAGTTTCTCTTGAAACATAAACCTTT-AAGATTGTTTATCTTGAAACAAATT
1 GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAA-ATTGTTTCTCTTGAAACAAATT
**
3495420 TT
65 AC
* * * ** *
3495422 GTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAAGTT
1 GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAAATTGTTTCTCTTGAAACAAA-TT
3495487 AC
65 AC
* *
3495489 GTCTCACTTGAGACAATTTCCCATAAAAAC-TCAAA-TTTTGAAATTGTTTCACTTGAAA
1 GTCTCACTTGAGACAATTTCCC-TAAAAACAT-AAACATTTGAAATTGTTTCTCTTGAAA
3495547 AAAAAATAAT
Statistics
Matches: 226, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
64 41 0.18
65 3 0.01
66 131 0.58
67 43 0.19
68 8 0.04
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (66 bp):
GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAAATTGTTTCTCTTGAAACAAATTA
C
Found at i:3495573 original size:103 final size:103
Alignment explanation
Indices: 3495456--3495689 Score: 253
Period size: 103 Copynumber: 2.3 Consensus size: 103
3495446 GAAACATAAA
3495456 CATTTGAGATTGTTTCTCTTGAAACAAAGT-TACGTCTCACTTGAGACA-ATTTCCCATAAAAAC
1 CATTTGAGATTGTTTCTCTTGAAACAAA-TAT-CGTCTCACTTGAGACAGATTTCCC-TAAAAAC
* *
3495519 TCAAATTTTGAAATTGTTTCACTTGAAA-AAAAAATAATCT
63 ACAAATTTTGAAATTATTTCACTTGAAACAAAAAATAATCT
* * * * **
3495559 CATTTGAGATTGTTT-TC-CGAAAAACAAATATCGTCTCGCTTGAGGCAGTTTTCCCTTGAAACA
1 CATTTGAGATTGTTTCTCTTG--AAACAAATATCGTCTCACTTGAGACAGATTTCCCTAAAAACA
** *
3495622 CAAATTTTGAAATTATTTCACTTGAAACAAAATTTTATCT
64 CAAATTTTGAAATTATTTCACTTGAAACAAAAAATAATCT
* * * *
3495662 CACTTGATATAGCTTCTCTTGAAACAAA
1 CATTTGAGATTGTTTCTCTTGAAACAAA
3495690 ATTCTTTCCA
Statistics
Matches: 108, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
101 1 0.01
102 48 0.44
103 56 0.52
104 2 0.02
105 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (103 bp):
CATTTGAGATTGTTTCTCTTGAAACAAATATCGTCTCACTTGAGACAGATTTCCCTAAAAACACA
AATTTTGAAATTATTTCACTTGAAACAAAAAATAATCT
Found at i:3498994 original size:24 final size:25
Alignment explanation
Indices: 3498967--3499017 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
3498957 TGATTTTATT
*
3498967 TTTTTATAATTA-GTTTACCTTTTA
1 TTTTTATAATTATGTTTACATTTTA
* *
3498991 -TTTTATATTTATGTTTATATTTTA
1 TTTTTATAATTATGTTTACATTTTA
3499015 TTT
1 TTT
3499018 AATTGTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
23 10 0.45
24 10 0.45
25 2 0.09
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTTATAATTATGTTTACATTTTA
Found at i:3500439 original size:16 final size:16
Alignment explanation
Indices: 3500420--3500452 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3500410 AAATCATTCA
3500420 TAAATAAAATAACCCT
1 TAAATAAAATAACCCT
*
3500436 TAAATAAAATAATCCT
1 TAAATAAAATAACCCT
3500452 T
1 T
3500453 CTTCAACTTA
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:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAATAAAATAACCCT
Found at i:3501696 original size:29 final size:29
Alignment explanation
Indices: 3501626--3501851 Score: 260
Period size: 29 Copynumber: 7.8 Consensus size: 29
3501616 GGACAAACCT
* * *
3501626 TTATCGTAATATATAAATAGTTTTGTA-C
1 TTATTGTAATTTAGAAATAGTTTTGTACC
* *
3501654 TTATTATAATTTAGAAATAGTTTTGTACT
1 TTATTGTAATTTAGAAATAGTTTTGTACC
* *
3501683 TTATTGTATTTTAGAAATAGTTTTGTACT
1 TTATTGTAATTTAGAAATAGTTTTGTACC
* * *
3501712 TTATTTTAATTTAGAAATAGTTTTGCACT
1 TTATTGTAATTTAGAAATAGTTTTGTACC
*
3501741 TTATTGTAATTTAGAAATAGTTATGTACC
1 TTATTGTAATTTAGAAATAGTTTTGTACC
* * *
3501770 TTATTGTAATTTATAAATACTTTTTTACC
1 TTATTGTAATTTAGAAATAGTTTTGTACC
*
3501799 TTATTGTAATTTA-ATAA-AATTTATGTACC
1 TTATTGTAATTTAGA-AATAGTTT-TGTACC
* *
3501828 TTATTGTAATTTATAAATACTTTT
1 TTATTGTAATTTAGAAATAGTTTT
3501852 ATCTTTGATT
Statistics
Matches: 172, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
28 28 0.16
29 139 0.81
30 5 0.03
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.51
Consensus pattern (29 bp):
TTATTGTAATTTAGAAATAGTTTTGTACC
Found at i:3501893 original size:27 final size:27
Alignment explanation
Indices: 3501853--3501930 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
3501843 AATACTTTTA
*
3501853 TCTTTGATTATAATTTCTAAAACGTTG
1 TCTTTTATTATAATTTCTAAAACGTTG
* *
3501880 TCTTTTATTGTAATTTCTAAAAAGATATG
1 TCTTTTATTATAATTTCTAAAACG-T-TG
* *
3501909 TCCTTCATTATAATTTCTAAAA
1 TCTTTTATTATAATTTCTAAAA
3501931 TATTTTGTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 21 0.49
28 1 0.02
29 21 0.49
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (27 bp):
TCTTTTATTATAATTTCTAAAACGTTG
Found at i:3501895 original size:56 final size:58
Alignment explanation
Indices: 3501762--3501900 Score: 160
Period size: 58 Copynumber: 2.4 Consensus size: 58
3501752 TAGAAATAGT
* * **
3501762 TATGTACCTTATTGTAATTTATAAATACTTTTTTACCTTATTGTAATTTAATAAAATT
1 TATGTACCTTATTGTAATTTATAAATACTTTTATACCTTATTATAATTTAATAAAACG
* *
3501820 TATGTACCTTATTGTAATTTATAAATACTTTTAT-CTTTGATTATAATTT-CTAAAACG
1 TATGTACCTTATTGTAATTTATAAATACTTTTATACCTT-ATTATAATTTAATAAAACG
* *
3501877 T-TGT-CTTTTATTGTAATTTCTAAA
1 TATGTAC-CTTATTGTAATTTATAAA
3501901 AAGATATGTC
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 1 0.01
56 19 0.27
57 9 0.13
58 42 0.59
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.52
Consensus pattern (58 bp):
TATGTACCTTATTGTAATTTATAAATACTTTTATACCTTATTATAATTTAATAAAACG
Found at i:3501923 original size:29 final size:27
Alignment explanation
Indices: 3501859--3501930 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 27
3501849 TTTATCTTTG
* * *
3501859 ATTATAATTTCTAAAACGTTGTCTTTT
1 ATTATAATTTCTAAAAAGTTGTCCTTC
*
3501886 ATTGTAATTTCTAAAAAGATATGTCCTTC
1 ATTATAATTTCTAAAAAG-T-TGTCCTTC
3501915 ATTATAATTTCTAAAA
1 ATTATAATTTCTAAAA
3501931 TATTTTGTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 16 0.42
28 1 0.03
29 21 0.55
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (27 bp):
ATTATAATTTCTAAAAAGTTGTCCTTC
Found at i:3501939 original size:29 final size:28
Alignment explanation
Indices: 3501859--3501942 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 28
3501849 TTTATCTTTG
** * *
3501859 ATTATAATTTCT-AAAACGTTGTCTTTT
1 ATTATAATTTCTAAAAAATTTGTCCTTC
* *
3501886 ATTGTAATTTCTAAAAAGATATGTCCTTC
1 ATTATAATTTCTAAAAA-ATTTGTCCTTC
*
3501915 ATTATAATTTCTAAAATATTTTGTCCTT
1 ATTATAATTTCTAAAA-AATTTGTCCTT
3501943 TTTTATAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
27 11 0.24
28 4 0.09
29 29 0.64
30 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (28 bp):
ATTATAATTTCTAAAAAATTTGTCCTTC
Found at i:3507574 original size:27 final size:27
Alignment explanation
Indices: 3507520--3507575 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
3507510 CCGCCATCAC
*
3507520 CACTTTGAACTTGAAACTCCATAACAT
1 CACTTTGAACTTGAAACTCCACAACAT
* *
3507547 CACTTTGAACTTGAAATTCCACAGCAT
1 CACTTTGAACTTGAAACTCCACAACAT
3507574 CA
1 CA
3507576 AAATCTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.29
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAACAT
Found at i:3507875 original size:20 final size:19
Alignment explanation
Indices: 3507832--3507877 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3507822 AACAGAACCT
* *
3507832 TCGGTTCACACCGGTTTTG
1 TCGGTTCACACCGGTTCTA
*
3507851 CCGGTTCACAACCGGTTCTA
1 TCGGTTCAC-ACCGGTTCTA
3507871 TCGGTTC
1 TCGGTTC
3507878 TTTAGCGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.13, C:0.30, G:0.24, T:0.33
Consensus pattern (19 bp):
TCGGTTCACACCGGTTCTA
Found at i:3521186 original size:21 final size:21
Alignment explanation
Indices: 3521160--3521202 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3521150 ATCTGGTTCT
*
3521160 GAGCCCTAGGCAGAGGGTCTC
1 GAGCCCCAGGCAGAGGGTCTC
3521181 GAGCCCCAGGCAGAGGGTCTC
1 GAGCCCCAGGCAGAGGGTCTC
3521202 G
1 G
3521203 TGGTGCATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.40, T:0.12
Consensus pattern (21 bp):
GAGCCCCAGGCAGAGGGTCTC
Found at i:3522060 original size:15 final size:15
Alignment explanation
Indices: 3522042--3522087 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
3522032 GTTGTGCTTG
3522042 ATATTATTTGTGGTA
1 ATATTATTTGTGGTA
*
3522057 ATATTATTTGTGGTG
1 ATATTATTTGTGGTA
3522072 ATA-TATTTGTGAGTA
1 ATATTATTTGTG-GTA
3522087 A
1 A
3522088 AGTTGACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 8 0.29
15 20 0.71
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (15 bp):
ATATTATTTGTGGTA
Found at i:3526575 original size:3 final size:3
Alignment explanation
Indices: 3526563--3526599 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3526553 CAAAAATTTG
3526563 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3526600 GTCATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3527110 original size:134 final size:134
Alignment explanation
Indices: 3526820--3527163 Score: 440
Period size: 134 Copynumber: 2.6 Consensus size: 134
3526810 AGTTCGGGTC
* * * * *
3526820 ATCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACATTGCTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACA-CGCTCATACG
* ** *
3526885 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATAAGGATGGC
65 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACAAGGTTCCTACGCGATAAGGACGGC
3526950 TGGTT
130 TGGTT
*
3526955 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTAGTCGGGGGATGACACGACTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACG-CTCATACG
* * * *
3527020 TGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGCGATAACAAGGTTCCTATGTGATGAGGACGTC
65 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACAAGGTTCCTACGCGATAAGGACGGC
3527084 TGGTT
130 TGGTT
* * * * * * * *
3527089 ATCTAGGGGTGACATGACTCCTACATGATGA-AATGATTTGGTCAGGAGATGACACGGCTCATAT
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGA-GATCTGGTCGGGGGATGACAC-GCTCATAC
3527153 GTGATGAAGAG
64 GTGATGAAGAG
3527164 GGCCATCTTT
Statistics
Matches: 183, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
133 1 0.01
134 111 0.61
135 71 0.39
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (134 bp):
ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGCTCATACGT
GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACAAGGTTCCTACGCGATAAGGACGGCT
GGTT
Found at i:3527476 original size:29 final size:30
Alignment explanation
Indices: 3527427--3527484 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
3527417 ACAAAACTTT
3527427 GTTTCAAAAGAAACAAACTCAAAGATTTTG
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
**
3527457 GTTTCAAAAGAAA-TGACTCAAAGATTTT
1 GTTTCAAAAGAAACAAACTCAAAGATTTT
3527485 TTCACGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (30 bp):
GTTTCAAAAGAAACAAACTCAAAGATTTTG
Found at i:3527505 original size:91 final size:94
Alignment explanation
Indices: 3527363--3527542 Score: 242
Period size: 91 Copynumber: 1.9 Consensus size: 94
3527353 GTCAAAGATT
*
3527363 TTTCAAAAGGAACAGACTCAAAGATTTGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAAAGGAACAGACTCAAAGATTTGTTTCAAG-AAAACTGTCTCAAGAGAAACAAAACTTTG
*
3527428 TTTCAAAAGAAACAAACTCAAAGATTTTGG
65 GTTCAAAAGAAACAAACTCAAAGATTTTGG
* * * * *
3527458 TTTCAAAA-GAA-ATGACTCAAAGATTT-TTTCACG-AAATTTTCTTAAGAGAAATAAAACTTTG
1 TTTCAAAAGGAACA-GACTCAAAGATTTGTTTCAAGAAAACTGTCTCAAGAGAAACAAAACTTTG
*
3527519 GTTCAAAAGAAACAGACTCAAAGA
65 GTTCAAAAGAAACAAACTCAAAGA
3527543 ATTTAAAGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
91 45 0.59
93 7 0.09
94 16 0.21
95 8 0.11
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (94 bp):
TTTCAAAAGGAACAGACTCAAAGATTTGTTTCAAGAAAACTGTCTCAAGAGAAACAAAACTTTGG
TTCAAAAGAAACAAACTCAAAGATTTTGG
Found at i:3527595 original size:29 final size:29
Alignment explanation
Indices: 3527558--3527671 Score: 120
Period size: 29 Copynumber: 3.8 Consensus size: 29
3527548 AAGAATTTTG
*
3527558 TCAAAAGAAATAACTCAAAGATTTTTATT
1 TCAAAAGAAACAACTCAAAGATTTTTATT
* *
3527587 TCAAAAGAAACAACTCACATATTTTTATT
1 TCAAAAGAAACAACTCAAAGATTTTTATT
* *
3527616 TCAAGAGAAACAGACTCAAAGATAGGTTTTGTT
1 TCAAAAGAAACA-ACTCAAAGAT---TTTTATT
**
3527649 TCAAGGGAAACAATCTCAAAGAT
1 TCAAAAGAAACAA-CTCAAAGAT
3527672 GTTTGTTTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
29 37 0.51
30 8 0.11
32 1 0.01
33 26 0.36
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (29 bp):
TCAAAAGAAACAACTCAAAGATTTTTATT
Found at i:3527653 original size:33 final size:31
Alignment explanation
Indices: 3527558--3527688 Score: 112
Period size: 29 Copynumber: 4.3 Consensus size: 31
3527548 AAGAATTTTG
* * *
3527558 TCAAAAGAAATAA-CTCAAAGAT-TTTTATT
1 TCAAGAGAAACAATCTCAAAGATGTTTTGTT
* * * *
3527587 TCAAAAGAAACAA-CTCACATAT-TTTTATT
1 TCAAGAGAAACAATCTCAAAGATGTTTTGTT
3527616 TCAAGAGAAACAGA-CTCAAAGATAGGTTTTGTT
1 TCAAGAGAAACA-ATCTCAAAGAT--GTTTTGTT
*
3527649 TCAAGGGAAACAATCTCAAAGATG-TTTGTT
1 TCAAGAGAAACAATCTCAAAGATGTTTTGTT
*
3527679 TTAAGAGAAA
1 TCAAGAGAAA
3527689 TTGTCTCAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
29 37 0.43
30 22 0.25
31 1 0.01
32 1 0.01
33 26 0.30
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (31 bp):
TCAAGAGAAACAATCTCAAAGATGTTTTGTT
Found at i:3527841 original size:64 final size:66
Alignment explanation
Indices: 3527684--3527868 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 66
3527674 TTGTTTTAAG
* * * *
3527684 AGAAA-TTGTCTCAAAAGAGACAAAACTTTGTTTTCATAA-AATCAAACTCAAAGATTTTTCTTC
1 AGAAACTT-TCTCAAAAGAGACAAAATTTTGTTTACA-AAGAAACAAACTCAAAGA-TTCTCTTC
3527747 ACAA
63 ACAA
* * * * * *
3527751 TG-ATCTGTCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAATTCAAAGATTCT-TTCA-A
1 AGAAACTTTCTCAAAAGAGACAAAATTTTGTTTACAAAGAAACAAACTCAAAGATTCTCTTCACA
3527813 A
66 A
* *
3527814 AGAAACTTTCTCAAAAGAGACAAAATTTTGTTAACAAAGAAACATACTCAAAGAT
1 AGAAACTTTCTCAAAAGAGACAAAATTTTGTTTACAAAGAAACAAACTCAAAGAT
3527869 ATTTCATTTT
Statistics
Matches: 98, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
63 3 0.03
64 49 0.50
65 5 0.05
66 39 0.40
67 2 0.02
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.29
Consensus pattern (66 bp):
AGAAACTTTCTCAAAAGAGACAAAATTTTGTTTACAAAGAAACAAACTCAAAGATTCTCTTCACA
A
Found at i:3527952 original size:99 final size:100
Alignment explanation
Indices: 3527788--3527967 Score: 229
Period size: 99 Copynumber: 1.8 Consensus size: 100
3527778 TGTTTCCAAA
* * *
3527788 GAAACAAATTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTAACAAAG
1 GAAACAAACTCAAAGATTCTTTCAAAACAAACTGTCTCAAAAGAGACAAAATTTTGTTAACAAAG
*
3527853 AAACATACTCAAAGATATTTCATTTTGTTTTAAGT
66 AAACAGACTCAAAGATATTTCATTTTGTTTTAAGT
* * * * * *
3527888 GAAACAGACTCAAAGATT-TTTCAAGACAATCTGTCTCAAGAGAGACAAAGTTTTGTT-TCAAAA
1 GAAACAAACTCAAAGATTCTTTCAAAACAAACTGTCTCAAAAGAGACAAAATTTTGTTAAC-AAA
* *
3527951 GAGATAGACTCAAAGAT
65 GAAACAGACTCAAAGAT
3527968 CCTTTGTTTC
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
98 1 0.01
99 50 0.75
100 16 0.24
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (100 bp):
GAAACAAACTCAAAGATTCTTTCAAAACAAACTGTCTCAAAAGAGACAAAATTTTGTTAACAAAG
AAACAGACTCAAAGATATTTCATTTTGTTTTAAGT
Done.