Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004693.1 Hibiscus syriacus cultivar Beakdansim tig00010533_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: 2620943
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 7 of 12
Found at i:1332705 original size:18 final size:18
Alignment explanation
Indices: 1332682--1332716 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1332672 ATTTTTATTG
1332682 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
1332700 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
1332717 AGGTCATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:1337100 original size:13 final size:13
Alignment explanation
Indices: 1337079--1337124 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1337069 ATAAAAGTAA
*
1337079 AATATTAATCTAT
1 AATATTAATATAT
* *
1337092 AATACTAATTTCAT
1 AATATTAATAT-AT
1337106 AATATTAATATAT
1 AATATTAATATAT
1337119 AATATT
1 AATATT
1337125 TTAAGTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATTAATATAT
Found at i:1337167 original size:32 final size:33
Alignment explanation
Indices: 1337103--1337172 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
1337093 ATACTAATTT
*
1337103 CATAATATTAATATATAATATTTTAAGTAAAAA
1 CATAATATTAATATATAATATTTTAAGAAAAAA
* *
1337136 CATATATATTAA-A-ATATTATTTTTAGAAAAAA
1 CATA-ATATTAATATATAATATTTTAAGAAAAAA
*
1337168 AATAA
1 CATAA
1337173 AATAGAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 1 0.03
32 19 0.59
33 5 0.16
34 7 0.22
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (33 bp):
CATAATATTAATATATAATATTTTAAGAAAAAA
Found at i:1341400 original size:43 final size:43
Alignment explanation
Indices: 1341339--1341424 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1341329 TTCGTCACTC
*
1341339 CCAGCTCGCCCCTGTCCGAACCACTGAGACATAGTTTCATATG
1 CCAGCTCGCCCCAGTCCGAACCACTGAGACATAGTTTCATATG
1341382 CCAGCTCGCCCCAGTCCGAACCACTGAGACATAGTTTCATATG
1 CCAGCTCGCCCCAGTCCGAACCACTGAGACATAGTTTCATATG
1341425 AATATAGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (43 bp):
CCAGCTCGCCCCAGTCCGAACCACTGAGACATAGTTTCATATG
Found at i:1344753 original size:2 final size:2
Alignment explanation
Indices: 1344746--1344772 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1344736 AGTCTTGTTT
1344746 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1344773 GGGAAACTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1347438 original size:10 final size:9
Alignment explanation
Indices: 1347417--1347446 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1347407 ATATCTCTCC
1347417 AAATATTAA
1 AAATATTAA
1347426 AAATATATAA
1 AAATAT-TAA
1347436 AAATATTAA
1 AAATATTAA
1347445 AA
1 AA
1347447 CAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAATATTAA
Found at i:1347454 original size:19 final size:19
Alignment explanation
Indices: 1347417--1347458 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1347407 ATATCTCTCC
*
1347417 AAATATTAAAAATATATAA
1 AAATATTAAAAATAAATAA
1347436 AAATATTAAAACA-AAATAA
1 AAATATTAAAA-ATAAATAA
1347455 AAAT
1 AAAT
1347459 TAAATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATATTAAAAATAAATAA
Found at i:1347485 original size:15 final size:15
Alignment explanation
Indices: 1347448--1347488 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1347438 ATATTAAAAC
1347448 AAAATAAAAATTAAA
1 AAAATAAAAATTAAA
** *
1347463 TTATTAAAAATTAAA
1 AAAATAAAAATTAAA
1347478 AAAATAAAAAT
1 AAAATAAAAAT
1347489 ACCATAAATT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAAATTAAA
Found at i:1348295 original size:15 final size:15
Alignment explanation
Indices: 1348275--1348331 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1348265 AATCGGGTAT
*
1348275 CGGGTATCCGATTAC
1 CGGGTACCCGATTAC
**
1348290 CGGGTACCCGTAAAATC
1 CGGGTACCCG-ATTA-C
1348307 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
*
1348322 CGGATACCCG
1 CGGGTACCCG
1348332 TAACATCCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 19 0.56
16 4 0.12
17 11 0.32
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:1348311 original size:17 final size:17
Alignment explanation
Indices: 1348289--1348343 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
1348279 TATCCGATTA
1348289 CCGGGTACCCGTAAAAT
1 CCGGGTACCCGTAAAAT
**
1348306 CCGGGTACCCG-ATTA-
1 CCGGGTACCCGTAAAAT
* *
1348321 CCGGATACCCGTAACAT
1 CCGGGTACCCGTAAAAT
1348338 CCGGGT
1 CCGGGT
1348344 CGGGACACGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 10 0.33
16 4 0.13
17 16 0.53
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (17 bp):
CCGGGTACCCGTAAAAT
Found at i:1348318 original size:32 final size:32
Alignment explanation
Indices: 1348275--1348343 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
1348265 AATCGGGTAT
* *
1348275 CGGGTATCCGATTACCGGGTACCCGTAAAATC
1 CGGGTACCCGATTACCGGATACCCGTAAAATC
*
1348307 CGGGTACCCGATTACCGGATACCCGTAACATC
1 CGGGTACCCGATTACCGGATACCCGTAAAATC
1348339 CGGGT
1 CGGGT
1348344 CGGGACACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.20
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGATACCCGTAAAATC
Found at i:1356553 original size:26 final size:26
Alignment explanation
Indices: 1356496--1356553 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1356486 GCGTACCACT
*
1356496 ATTTTCACATTATTTTTTTAATATAA
1 ATTTTCACATTATTTTTTTAAGATAA
* *
1356522 AATTTCACATTATTTTATTT-CGATAA
1 ATTTTCACATTATTTT-TTTAAGATAA
1356548 ATTTTC
1 ATTTTC
1356554 CTTTTTGACG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTTCACATTATTTTTTTAAGATAA
Found at i:1356976 original size:21 final size:22
Alignment explanation
Indices: 1356947--1356987 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1356937 ATTATCTTTT
* *
1356947 AATATATATATAAT-TTTAAAA
1 AATAAATATAAAATGTTTAAAA
1356968 AATAAATATAAAATGTTTAA
1 AATAAATATAAAATGTTTAA
1356988 TAATATTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AATAAATATAAAATGTTTAAAA
Found at i:1356992 original size:21 final size:21
Alignment explanation
Indices: 1356946--1356992 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1356936 AATTATCTTT
* *
1356946 TAATATATATATAATTTTAAA
1 TAATAAATATAAAATTTTAAA
*
1356967 AAATAAATATAAAATGTTT-AA
1 TAATAAATATAAAAT-TTTAAA
1356988 TAATA
1 TAATA
1356993 TTCCAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAATAAATATAAAATTTTAAA
Found at i:1364643 original size:30 final size:29
Alignment explanation
Indices: 1364609--1364675 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
1364599 CGACAAGGTC
1364609 ATTAAGTAGGAAAAATAACTCAAAAACATT
1 ATTAAGTAGG-AAAATAACTCAAAAACATT
*
1364639 ATTAAGAAGGAAAATAACTCAAAAACATT
1 ATTAAGTAGGAAAATAACTCAAAAACATT
1364668 ATTAAGTA
1 ATTAAGTA
1364676 CCGTTTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 26 0.74
30 9 0.26
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (29 bp):
ATTAAGTAGGAAAATAACTCAAAAACATT
Found at i:1364998 original size:16 final size:16
Alignment explanation
Indices: 1364982--1365050 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
1364972 ATATATTTTA
1364982 AAAAAT-ATATTAATT
1 AAAAATAATATTAATT
1364997 AAAAATAATATTAA--
1 AAAAATAATATTAATT
* *
1365011 AAAATTAA-A-TAAAT
1 AAAAATAATATTAATT
1365025 ATAAAATAAT-TTAATT
1 A-AAAATAATATTAATT
1365041 ACAAAA-AATA
1 A-AAAATAATA
1365051 ATAAAATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
12 3 0.07
13 1 0.02
14 8 0.19
15 15 0.35
16 16 0.37
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATAATATTAATT
Found at i:1365035 original size:19 final size:21
Alignment explanation
Indices: 1364992--1365035 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1364982 AAAAATATAT
1364992 TAATTAAAAATAATATTAAAA
1 TAATTAAAAATAATATTAAAA
*
1365013 -AATTAAATA-AATA-TAAAA
1 TAATTAAAAATAATATTAAAA
1365031 TAATT
1 TAATT
1365036 TAATTACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATTAAAAATAATATTAAAA
Found at i:1365054 original size:26 final size:24
Alignment explanation
Indices: 1365013--1365061 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
1365003 AATATTAAAA
*
1365013 AATTAAATAAATATAAAATAATTT
1 AATTAAAAAAATATAAAATAATTT
1365037 AATTACAAAAAATAATAAAATAATT
1 AATTA-AAAAAAT-ATAAAATAATT
1365062 CTTACTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 6 0.27
26 11 0.50
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTAAAAAAATATAAAATAATTT
Found at i:1368725 original size:2 final size:2
Alignment explanation
Indices: 1368718--1368767 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1368708 ACATACATAC
1368718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1368760 AT AT AT AT
1 AT AT AT AT
1368768 TTGCTTTCAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1370038 original size:18 final size:18
Alignment explanation
Indices: 1370017--1370059 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1370007 GTTTTTTTAA
* *
1370017 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1370035 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1370053 AAATAAA
1 AAATAAA
1370060 TAATCTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1373276 original size:15 final size:15
Alignment explanation
Indices: 1373256--1373285 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1373246 GCACATTATT
*
1373256 TTTTAAAGATTAAAA
1 TTTTAAAGATCAAAA
1373271 TTTTAAAGATCAAAA
1 TTTTAAAGATCAAAA
1373286 AAATATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (15 bp):
TTTTAAAGATCAAAA
Found at i:1375212 original size:6 final size:6
Alignment explanation
Indices: 1375201--1375241 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
1375191 CACGTATTAT
1375201 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
1375242 GACGGGACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:1375639 original size:41 final size:42
Alignment explanation
Indices: 1375589--1375671 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 42
1375579 AGTATTGGGA
* ** *
1375589 ACAAGTGTAGACTATCGCAACG-AATTTGAAATATCGCAACG
1 ACAACTGTAGACTATCGCAACGCAAAATGAAAAATCGCAACG
1375630 ACAACTGTAGACTATCGCAACGCAAAATGAAAAATCGCAACG
1 ACAACTGTAGACTATCGCAACGCAAAATGAAAAATCGCAACG
1375672 CGAAATGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 21 0.57
42 16 0.43
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (42 bp):
ACAACTGTAGACTATCGCAACGCAAAATGAAAAATCGCAACG
Found at i:1375648 original size:22 final size:22
Alignment explanation
Indices: 1375589--1375651 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 22
1375579 AGTATTGGGA
*
1375589 ACAAGTGTAGACTATCGCAACG
1 ACAACTGTAGACTATCGCAACG
** *
1375611 A-ATTTG-A-AATATCGCAACG
1 ACAACTGTAGACTATCGCAACG
1375630 ACAACTGTAGACTATCGCAACG
1 ACAACTGTAGACTATCGCAACG
1375652 CAAAATGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 12 0.38
20 4 0.12
21 4 0.12
22 12 0.38
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (22 bp):
ACAACTGTAGACTATCGCAACG
Found at i:1375668 original size:20 final size:20
Alignment explanation
Indices: 1375643--1375694 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1375633 ACTGTAGACT
1375643 ATCGCAACGCAAAATGAAAA
1 ATCGCAACGCAAAATGAAAA
* *
1375663 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCAAAATGAAAA
1375683 ATCGCAACGCAA
1 ATCGCAACGCAA
1375695 CGCGAAATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCAAAATGAAAA
Found at i:1400052 original size:21 final size:22
Alignment explanation
Indices: 1400014--1400054 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1400004 TATTAAATAC
1400014 TAAATTATATTCTGCTAAAATT
1 TAAATTATATTCTGCTAAAATT
* *
1400036 TAAA-TATTTTCTTCTAAAA
1 TAAATTATATTCTGCTAAAA
1400055 ACATCGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAATTATATTCTGCTAAAATT
Found at i:1407429 original size:2 final size:2
Alignment explanation
Indices: 1407422--1407493 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1407412 ATGAAAACCT
1407422 TA TA TA 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
1407464 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
1407494 AAAATTAACA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1411208 original size:42 final size:42
Alignment explanation
Indices: 1411133--1411300 Score: 308
Period size: 42 Copynumber: 4.1 Consensus size: 42
1411123 AAGACACCCA
1411133 CACTCCCAA-TT-TCTC-T-CTTTGTCTGTTTCACTTGGAGC
1 CACTCCCAATTTCTCTCTTACTTTGTCTGTTTCACTTGGAGC
1411171 CACTCCCAATTTCTCTCTTACTTTGTCTGTTTCACTTGGAGC
1 CACTCCCAATTTCTCTCTTACTTTGTCTGTTTCACTTGGAGC
1411213 CACTCCCAATTTCTCTCTTACTTTGTCTGTTTCACTTGGAGC
1 CACTCCCAATTTCTCTCTTACTTTGTCTGTTTCACTTGGAGC
1411255 CACTCCCAATTTCTCTCTTACTTTGTCTGTTTCACTTGGAGC
1 CACTCCCAATTTCTCTCTTACTTTGTCTGTTTCACTTGGAGC
1411297 CACT
1 CACT
1411301 TGAAGACGCT
Statistics
Matches: 126, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
38 9 0.07
39 2 0.02
40 4 0.03
41 1 0.01
42 110 0.87
ACGTcount: A:0.14, C:0.32, G:0.12, T:0.42
Consensus pattern (42 bp):
CACTCCCAATTTCTCTCTTACTTTGTCTGTTTCACTTGGAGC
Found at i:1411594 original size:40 final size:40
Alignment explanation
Indices: 1411535--1411612 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
1411525 TAATTTCATG
* *
1411535 AACCCTAAATTATAGGTATAGTTAT-GTATATATACATATT
1 AACCCTAAATTATACGTATAGTT-TCATATATATACATATT
1411575 AACCCTAAATTATACGTATAGTTTCATATATATACATA
1 AACCCTAAATTATACGTATAGTTTCATATATATACATA
1411613 GCATCGCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 1 0.03
40 34 0.97
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (40 bp):
AACCCTAAATTATACGTATAGTTTCATATATATACATATT
Found at i:1413026 original size:54 final size:54
Alignment explanation
Indices: 1412954--1413109 Score: 195
Period size: 63 Copynumber: 2.7 Consensus size: 54
1412944 GGTGTGGCTC
*
1412954 CGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGCGGATGCAACTGGTCTTGGTCAT
1 CGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGAGGATGCAACTGGTCTTGGTCAT
* * *
1413008 CTTGTAAAGGGTGTGGTAGCTCTTCTTGTGGAGGATGCAGCGGCAACAACTGGTCTTGGTCAT
1 CGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGAGGAT------G---CAACTGGTCTTGGTCAT
1413071 CGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGAGGATGCA
1 CGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGAGGATGCA
1413110 GCGGCGGCGG
Statistics
Matches: 86, Mismatches: 7, Indels: 18
0.77 0.06 0.16
Matches are distributed among these distances:
54 34 0.40
57 1 0.01
60 1 0.01
63 50 0.58
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (54 bp):
CGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGAGGATGCAACTGGTCTTGGTCAT
Found at i:1413090 original size:63 final size:64
Alignment explanation
Indices: 1412991--1413152 Score: 227
Period size: 63 Copynumber: 2.5 Consensus size: 64
1412981 GTGGCGGATG
* * *
1412991 CAACTGGTCTTGGTCATCTTGTAAAGGGTGTGGTAGCTCTTCTTGTGGAGGATGCA-GCGGCAA
1 CAACTGGTCTTGGTCATCGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGAGGATGCAGGCGGCAA
*
1413054 CAACTGGTCTTGGTCATCGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGAGGATGCAGCGGCGGCG
1 CAACTGGTCTTGGTCATCGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGAGGATGCA--GGCGGCA
*
1413119 G
64 A
** *
1413120 CAACTGGAATTGGTCATCGTGCAGAGGGTGCGG
1 CAACTGGTCTTGGTCATCGTGCAAAGGGTGCGG
1413153 CAACATGTCT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
63 53 0.60
66 35 0.40
ACGTcount: A:0.18, C:0.19, G:0.37, T:0.26
Consensus pattern (64 bp):
CAACTGGTCTTGGTCATCGTGCAAAGGGTGCGGTAGCTCTTCTTGTGGAGGATGCAGGCGGCAA
Found at i:1414264 original size:34 final size:34
Alignment explanation
Indices: 1414211--1414331 Score: 174
Period size: 34 Copynumber: 3.6 Consensus size: 34
1414201 GGTTTTTTGG
*
1414211 TCCACCC--GACCCGACCCGAGAACAAGAGAGTC
1 TCCACCCGAGACCCAACCCGAGAACAAGAGAGTC
*
1414243 TCCACCCGAGACCCAATCCGAGAACAAGAGAGTC
1 TCCACCCGAGACCCAACCCGAGAACAAGAGAGTC
* *
1414277 TCCACCCGAGACCCGACCCGAGAACAAGAGAGTT
1 TCCACCCGAGACCCAACCCGAGAACAAGAGAGTC
* *
1414311 TCCACCCGAGATCCGACCCGA
1 TCCACCCGAGACCCAACCCGA
1414332 CCAAAACAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 7 0.09
34 74 0.91
ACGTcount: A:0.31, C:0.39, G:0.21, T:0.08
Consensus pattern (34 bp):
TCCACCCGAGACCCAACCCGAGAACAAGAGAGTC
Found at i:1416242 original size:17 final size:17
Alignment explanation
Indices: 1416220--1416263 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1416210 ATGTAAAAAT
1416220 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
1416237 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
1416254 AAATATTTAA
1 AAATATTTAA
1416264 TCAAATATAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:1417956 original size:18 final size:18
Alignment explanation
Indices: 1417935--1418035 Score: 112
Period size: 18 Copynumber: 5.6 Consensus size: 18
1417925 ACCGGCGAAA
* *
1417935 CCGAAAGAACCAGAGAAG
1 CCGAAAGAACCCGAAAAG
* *
1417953 CCGAAAGAGCCCGAAAAA
1 CCGAAAGAACCCGAAAAG
* **
1417971 CCTAAAGCTCCCGAAAAG
1 CCGAAAGAACCCGAAAAG
*
1417989 CCGAAAGAACCGGAAAAG
1 CCGAAAGAACCCGAAAAG
*
1418007 CCGAAAGAACCCGAGAAG
1 CCGAAAGAACCCGAAAAG
*
1418025 CCCAAAGAACC
1 CCGAAAGAACC
1418036 AAAGAAACCG
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.47, C:0.29, G:0.23, T:0.02
Consensus pattern (18 bp):
CCGAAAGAACCCGAAAAG
Found at i:1418041 original size:18 final size:18
Alignment explanation
Indices: 1417986--1418041 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1417976 AGCTCCCGAA
*
1417986 AAGCCGAAAGAACCGGAA-
1 AAGCCGAAAGAACC-AAAG
**
1418004 AAGCCGAAAGAACCCGAG
1 AAGCCGAAAGAACCAAAG
*
1418022 AAGCCCAAAGAACCAAAG
1 AAGCCGAAAGAACCAAAG
1418040 AA
1 AA
1418042 ACCGGCACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.52, C:0.25, G:0.23, T:0.00
Consensus pattern (18 bp):
AAGCCGAAAGAACCAAAG
Found at i:1418084 original size:24 final size:24
Alignment explanation
Indices: 1418052--1418099 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1418042 ACCGGCACCA
1418052 CCACCAGCTCTA-CCTCCAGCGCCG
1 CCACCAGCTC-AGCCTCCAGCGCCG
1418076 CCACCAGCTCAGCCTCCAGCGCCG
1 CCACCAGCTCAGCCTCCAGCGCCG
1418100 AATCCTCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.17, C:0.54, G:0.19, T:0.10
Consensus pattern (24 bp):
CCACCAGCTCAGCCTCCAGCGCCG
Found at i:1419505 original size:2 final size:2
Alignment explanation
Indices: 1419498--1419531 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1419488 CACCCCCTAA
1419498 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
1419532 TAATCAAACT
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:1420397 original size:41 final size:41
Alignment explanation
Indices: 1420312--1420409 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 41
1420302 ACAACGGTAG
*
1420312 ACTATCGCAAC-GAATTTGGAAAATCGCAACGACAACTTGC
1 ACTATCGCAACGGAATATGGAAAATCGCAACGACAACTTGC
* * *
1420352 ACTATCGCAACGTGAA-ATGGAAAATCGCAACG-CGATTTTC
1 ACTATCGCAACG-GAATATGGAAAATCGCAACGACAACTTGC
1420392 AACTATCGCAACGCGAAT
1 -ACTATCGCAACG-GAAT
1420410 TTGCGATATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
40 16 0.33
41 30 0.61
42 3 0.06
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGGAATATGGAAAATCGCAACGACAACTTGC
Found at i:1420445 original size:19 final size:20
Alignment explanation
Indices: 1420411--1420455 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1420401 AACGCGAATT
*
1420411 TGCGATATTGGAGATCGCAA
1 TGCGATATTAGAGATCGCAA
*
1420431 TGCGA-ATTAGAGATCGCAT
1 TGCGATATTAGAGATCGCAA
1420450 TGCGAT
1 TGCGAT
1420456 TTTATTGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (20 bp):
TGCGATATTAGAGATCGCAA
Found at i:1428962 original size:32 final size:32
Alignment explanation
Indices: 1428900--1428962 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1428890 GGAGCTGATT
**
1428900 ATTAAGCACATTAATCCAACATAATTACATTA
1 ATTAAGCACATTAATCCAACATAACAACATTA
1428932 ATTAAGCACATTAATCCAACATAACAACATT
1 ATTAAGCACATTAATCCAACATAACAACATT
1428963 GAAAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.29
Consensus pattern (32 bp):
ATTAAGCACATTAATCCAACATAACAACATTA
Found at i:1433498 original size:6 final size:6
Alignment explanation
Indices: 1433480--1433613 Score: 236
Period size: 6 Copynumber: 22.7 Consensus size: 6
1433470 TGCTAAGTAC
*
1433480 TAATCT T-ATCT TAATCT TAATCT TAATCT TAATCT TAATCT TAAT-A
1 TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT
*
1433526 TAATAT TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT
1 TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT
1433574 TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT TAAT
1 TAATCT TAATCT TAATCT TAATCT TAATCT TAATCT TAAT
1433614 TTCAATGAAA
Statistics
Matches: 123, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
5 9 0.07
6 114 0.93
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATCT
Found at i:1435565 original size:16 final size:16
Alignment explanation
Indices: 1435544--1435594 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
1435534 AATTAGCATC
1435544 ATGCATGAATGTATGT
1 ATGCATGAATGTATGT
*
1435560 ATGCATGCATGTATGT
1 ATGCATGAATGTATGT
* *
1435576 ATGTATGTATGTATGT
1 ATGCATGAATGTATGT
1435592 ATG
1 ATG
1435595 TATGTGCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.41
Consensus pattern (16 bp):
ATGCATGAATGTATGT
Found at i:1435575 original size:4 final size:4
Alignment explanation
Indices: 1435552--1435599 Score: 78
Period size: 4 Copynumber: 12.0 Consensus size: 4
1435542 TCATGCATGA
* *
1435552 ATGT ATGT ATGC ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1435600 GCAATATACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:1437668 original size:12 final size:11
Alignment explanation
Indices: 1437638--1437672 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1437628 ACATCATCAA
1437638 AAAATATTTTT
1 AAAATATTTTT
*
1437649 AAACTATTTTT
1 AAAATATTTTT
1437660 AAATATATTTTT
1 AAA-ATATTTTT
1437672 A
1 A
1437673 TAAGAGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:1439171 original size:18 final size:18
Alignment explanation
Indices: 1439137--1439171 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1439127 GAAATAAAAA
*
1439137 CAATGACAACAACAAGAG
1 CAATGACAACAAAAAGAG
*
1439155 CAATGACAATAAAAAGA
1 CAATGACAACAAAAAGA
1439172 TCCAAAATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.14, T:0.09
Consensus pattern (18 bp):
CAATGACAACAAAAAGAG
Found at i:1443405 original size:35 final size:37
Alignment explanation
Indices: 1443338--1443409 Score: 112
Period size: 35 Copynumber: 2.0 Consensus size: 37
1443328 TATGTGCAAG
*
1443338 GGGAACAGATTCCCCCACTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCACCCACTGGGGGGTATCGATTCCCC
*
1443375 GGGAACAGATT-ACCC-CTGTGGGGTATCGATTCCCC
1 GGGAACAGATTCACCCACTGGGGGGTATCGATTCCCC
1443410 CCTAAATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 19 0.58
36 3 0.09
37 11 0.33
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (37 bp):
GGGAACAGATTCACCCACTGGGGGGTATCGATTCCCC
Found at i:1444013 original size:31 final size:31
Alignment explanation
Indices: 1443975--1444069 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
1443965 AGGGTTGAGG
1443975 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1444006 GTTTACCTATGTTATTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1444037 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1444068 GT
1 GT
1444070 AACACCCCAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1445006 original size:23 final size:23
Alignment explanation
Indices: 1444980--1445066 Score: 138
Period size: 23 Copynumber: 3.8 Consensus size: 23
1444970 CAGCTCATAT
*
1444980 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACGTAG
1445003 AATTGCACCGGAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACGTAG
**
1445026 AATTGCACCGGAGTGCCGTGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
1445049 AATTGCACCGTAGTGCCA
1 AATTGCACCGGAGTGCCA
1445067 TATAATAATG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCACGTAG
Found at i:1445207 original size:103 final size:103
Alignment explanation
Indices: 1445082--1445299 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1445072 TAATGTCCAT
** * *
1445082 AAGGACCACATATCATTCCTTAAGAATCATATACATATATTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTACGTGTCTCACCA
1445147 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1445185 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTACGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTACGTGTCTCACCA
1445250 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1445288 AAGGACCACATA
1 AAGGACCACATA
1445300 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTACGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1446141 original size:64 final size:64
Alignment explanation
Indices: 1446069--1446225 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
1446059 TTCCCTATCG
* * **
1446069 GTGCATCGATGCACTACCTGTGCATCGGTGCA-TAAAATACATTCGATGTTTATT-TATT-ACTG
1 GTGCATCGATGCACTACCTGTGCATCGATGCACT-AAATACATTCGATGTTT-TTAGATTAAAAG
*
1446131 G
64 A
* * * *
1446132 GATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTAGATTAAAAG
1 G-TGCATCGATGCACTACC-TGTGCATCGATGCACTAAATACATTCGATGTTTTTAGATTAAAAG
1446196 A
64 A
*
1446197 GTGCATCGGTGCACTACCTGTGCATCGAT
1 GTGCATCGATGCACTACCTGTGCATCGAT
1446226 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
63 6 0.08
64 63 0.83
65 7 0.09
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTGTGCATCGATGCACTAAATACATTCGATGTTTTTAGATTAAAAGA
Found at i:1447426 original size:25 final size:25
Alignment explanation
Indices: 1447392--1447448 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
1447382 AAATCTTCAT
1447392 CATAACTGATTAAACATACACTTTG
1 CATAACTGATTAAACATACACTTTG
1447417 CATAACTGATTAAACATACACTTTG
1 CATAACTGATTAAACATACACTTTG
1447442 CATAACT
1 CATAACT
1447449 AAACAATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (25 bp):
CATAACTGATTAAACATACACTTTG
Found at i:1450784 original size:23 final size:23
Alignment explanation
Indices: 1450711--1450775 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
1450701 CAGCTCATAT
*
1450711 AATTGCACCGGAGTGCCACGTAG
1 AATTGCACCGGAGTGCCATGTAG
*
1450734 AATTGCACCGGAGTGCCGTGTAG
1 AATTGCACCGGAGTGCCATGTAG
*
1450757 AATTGCACCGTAGTGCCAT
1 AATTGCACCGGAGTGCCAT
1450776 ATAATATTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.22
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCATGTAG
Found at i:1450962 original size:103 final size:102
Alignment explanation
Indices: 1450790--1451006 Score: 362
Period size: 103 Copynumber: 2.1 Consensus size: 102
1450780 TATTGTCCAT
* * *
1450790 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATAAAGTATGTGTCTCACCA
* *
1450855 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAA-AAAACATATATATCCCG
* *
1450893 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATAAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATAAAGTATGTGTCTCACCA
1450958 GACTTCACACATGTTCCAAAAAAACATATATATCCCG
66 GACTTCACACATGTTCCAAAAAAACATATATATCCCG
1450995 AAGGACCACATA
1 AAGGACCACATA
1451007 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
102 27 0.25
103 80 0.75
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATAAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAAAAACATATATATCCCG
Found at i:1452773 original size:31 final size:31
Alignment explanation
Indices: 1452708--1452777 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1452698 AGGATGTTAC
* * *
1452708 ATGGACTGTTTACCTATGTTCTTCGGGACAT
1 ATGGACTGATTACCTAGGTTCTTCGGAACAT
*
1452739 ATGGACTGATTACCTAGGTTCTTTGGAATC-T
1 ATGGACTGATTACCTAGGTTCTTCGGAA-CAT
1452770 ATGGACTG
1 ATGGACTG
1452778 GTCCTTCGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.37
Consensus pattern (31 bp):
ATGGACTGATTACCTAGGTTCTTCGGAACAT
Found at i:1454576 original size:18 final size:18
Alignment explanation
Indices: 1454532--1454592 Score: 115
Period size: 18 Copynumber: 3.4 Consensus size: 18
1454522 TTTGGGGATC
1454532 AAAGAACCCAATTATCTA
1 AAAGAACCCAATTATCTA
1454550 AAA-AACCCAATTATCTA
1 AAAGAACCCAATTATCTA
1454567 AAAGAACCCAATTATCTA
1 AAAGAACCCAATTATCTA
1454585 AAAGAACC
1 AAAGAACC
1454593 GGGGCTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.40
18 25 0.60
ACGTcount: A:0.52, C:0.23, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAGAACCCAATTATCTA
Found at i:1456633 original size:36 final size:36
Alignment explanation
Indices: 1456577--1456645 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
1456567 TGTGCAGGGG
1456577 GAACAGATTCTCCCCTGGGGGGTATCGATTCCCCAT
1 GAACAGATTCTCCCCTGGGGGGTATCGATTCCCCAT
1456613 GAACAGATTC-CCCCTGGGGGGTATCGATTCCCC
1 GAACAGATTCTCCCCTGGGGGGTATCGATTCCCC
1456646 CCTAAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (36 bp):
GAACAGATTCTCCCCTGGGGGGTATCGATTCCCCAT
Found at i:1457287 original size:62 final size:62
Alignment explanation
Indices: 1457211--1457332 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
1457201 AGGGTCGAGG
* * *
1457211 GTTTACCTATGTTCTTCGGGACATATGGAATGTTTACCTATGTTCTTCGGGATATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGAATGATTACCTAGGTTCTTCGGAATATATGGATT
* *
1457273 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGGAATCTATGGA
1 GTTTACCTATGTTCTTCGGGACATATGGAATGATTACCTAGGTTCTTCGGAATATATGGA
1457333 CTGGTCCTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.39
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGAATGATTACCTAGGTTCTTCGGAATATATGGATT
Found at i:1457331 original size:31 final size:31
Alignment explanation
Indices: 1457211--1457335 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
1457201 AGGGTCGAGG
*
1457211 GTTTACCTATGTTCTTCGGGACATATGGAAT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1457242 GTTTACCTATGTTCTTCGGGATATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1457273 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1457304 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1457335 G
1 G
1457336 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1460544 original size:2 final size:2
Alignment explanation
Indices: 1460537--1460566 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1460527 TTAAATTTAA
1460537 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
1460567 GTATGTATTC
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:1463463 original size:8 final size:8
Alignment explanation
Indices: 1463442--1463473 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
1463432 ATTTAATTAA
1463442 AAAATAATT
1 AAAATAA-T
1463451 AAAATAAT
1 AAAATAAT
1463459 AAAATAAT
1 AAAATAAT
1463467 AAAATAA
1 AAAATAA
1463474 ACACTTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAATAAT
Found at i:1465552 original size:3 final size:3
Alignment explanation
Indices: 1465546--1465643 Score: 178
Period size: 3 Copynumber: 32.7 Consensus size: 3
1465536 TTTTTATCCA
*
1465546 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1465594 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1465642 TA
1 TA
1465644 AATATATATT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1465655 original size:11 final size:11
Alignment explanation
Indices: 1465639--1465670 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1465629 TTATTATTAT
1465639 TATTAAATATA
1 TATTAAATATA
1465650 TATTAAATATA
1 TATTAAATATA
1465661 TATATAAATA
1 TAT-TAAATA
1465671 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1466099 original size:21 final size:19
Alignment explanation
Indices: 1466074--1466111 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1466064 AACCTGAAAA
1466074 AAAAACACAGAGAGACAGAG
1 AAAAA-ACAGAGAGACAGAG
*
1466094 AAAAAAGAGAGAGACAGA
1 AAAAAACAGAGAGACAGA
1466112 ACCGGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.63, C:0.11, G:0.26, T:0.00
Consensus pattern (19 bp):
AAAAAACAGAGAGACAGAG
Found at i:1478378 original size:9 final size:8
Alignment explanation
Indices: 1478357--1478424 Score: 86
Period size: 9 Copynumber: 8.2 Consensus size: 8
1478347 ATGCTTGAAG
1478357 AAAAAAG-
1 AAAAAAGA
1478364 AAAAAAGA
1 AAAAAAGA
1478372 AAGAAAAGA
1 AA-AAAAGA
1478381 AAAAATAGA
1 AAAAA-AGA
1478390 AAAAAAGA
1 AAAAAAGA
1478398 AAAAAGAGA
1 AAAAA-AGA
1478407 AAAAAA-A
1 AAAAAAGA
1478414 AGAAAAAGA
1 A-AAAAAGA
1478423 AA
1 AA
1478425 GGGGGTCAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
7 9 0.16
8 20 0.36
9 26 0.47
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1478378 original size:17 final size:17
Alignment explanation
Indices: 1478357--1478422 Score: 89
Period size: 17 Copynumber: 3.9 Consensus size: 17
1478347 ATGCTTGAAG
1478357 AAAAAAGAAAAAAGA-A
1 AAAAAAGAAAAAAGAGA
* *
1478373 AGAAAAGAAAAAATAGA
1 AAAAAAGAAAAAAGAGA
1478390 AAAAAAGAAAAAAGAGA
1 AAAAAAGAAAAAAGAGA
*
1478407 AAAAAAAAGAAAAAGA
1 AAAAAAGA-AAAAAGA
1478423 AAGGGGGTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
16 13 0.30
17 23 0.53
18 7 0.16
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAGA
Found at i:1478424 original size:33 final size:33
Alignment explanation
Indices: 1478357--1478424 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1478347 ATGCTTGAAG
*
1478357 AAAAAAGAAAAAAGAAAGAAAAGAAAAAATAGA
1 AAAAAAGAAAAAAGAAAGAAAAGAAAAAAAAGA
1478390 AAAAAAGAAAAAAGAGAA-AAAA-AAAGAAAAAGA
1 AAAAAAGAAAAAAGA-AAGAAAAGAAA-AAAAAGA
1478423 AA
1 AA
1478425 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 3 0.09
33 27 0.84
34 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (33 bp):
AAAAAAGAAAAAAGAAAGAAAAGAAAAAAAAGA
Found at i:1479707 original size:82 final size:82
Alignment explanation
Indices: 1479568--1480305 Score: 1343
Period size: 82 Copynumber: 9.0 Consensus size: 82
1479558 GAAAGAGACT
* *
1479568 CAATAGCATCTTCTGGAATTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGACCAATCATTGAAT
1479633 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
* *
1479650 CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGGTGGACAGACCAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGACCAATCATTGAAT
1479715 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
*
1479732 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGGTGGACAGACCAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGACCAATCATTGAAT
1479797 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
*
1479814 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGACCAATCATTGAAT
1479879 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
*
1479896 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGACCAATCATTGAAT
1479961 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
*
1479978 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGGTGGACAGACCAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGACCAATCATTGAAT
1480043 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
*
1480060 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGGTGGACAGACCAATCATTGAAT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGACCAATCATTGAAT
1480125 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
* *
1480142 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGACCAATCATTGAAT
1480207 TTAGAAGATGAATTTGC
66 TTAGAAGATGAATTTGC
*
1480224 CAATAGCATCATCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA-AGACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGACCAATCATTGAA
*
1480288 TTTGGAAGATGAATTTGC
65 TTTAGAAGATGAATTTGC
1480306 TCATAGTAAA
Statistics
Matches: 639, Mismatches: 16, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
82 634 0.99
83 5 0.01
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (82 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGACCAATCATTGAAT
TTAGAAGATGAATTTGC
Found at i:1481325 original size:113 final size:113
Alignment explanation
Indices: 1481113--1481662 Score: 933
Period size: 113 Copynumber: 4.9 Consensus size: 113
1481103 TCGAATCCAC
* *
1481113 TTGATGGATCAGT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 TTGATGGATTA-TCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
** *
1481177 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACCCATCAT
64 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
* * *
1481227 TTGATGGATCATCTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
1481292 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATTCATCAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
*
1481340 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1481405 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
*
1481453 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1481518 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
*
1481566 TTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
1481630 AGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTT
1481663 GCATAATTCT
Statistics
Matches: 420, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
112 69 0.16
113 337 0.80
114 14 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (113 bp):
TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
Found at i:1481988 original size:3 final size:3
Alignment explanation
Indices: 1481982--1482097 Score: 223
Period size: 3 Copynumber: 38.7 Consensus size: 3
1481972 TTTTTATCCA
1481982 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1482030 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1482078 CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1482098 AATATATATT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 111 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1482109 original size:11 final size:11
Alignment explanation
Indices: 1482093--1482124 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1482083 TTATTATTAT
1482093 TATTAAATATA
1 TATTAAATATA
1482104 TATTAAATATA
1 TATTAAATATA
1482115 TATATAAATA
1 TAT-TAAATA
1482125 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1482568 original size:21 final size:19
Alignment explanation
Indices: 1482545--1482582 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1482535 ACCTGAAAAA
1482545 AAAAACACAGAGAGACAGAG
1 AAAAA-ACAGAGAGACAGAG
*
1482565 AAAAAAGAGAGAGACAGA
1 AAAAAACAGAGAGACAGA
1482583 ACCGGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.63, C:0.11, G:0.26, T:0.00
Consensus pattern (19 bp):
AAAAAACAGAGAGACAGAG
Found at i:1483569 original size:17 final size:18
Alignment explanation
Indices: 1483547--1483587 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
1483537 AAGTATATAA
1483547 TAAATAAATATTTA-TTT
1 TAAATAAATATTTAGTTT
1483564 TAAATAAATATTTAGTTT
1 TAAATAAATATTTAGTTT
*
1483582 TCAATA
1 TAAATA
1483588 TCAAAGAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TAAATAAATATTTAGTTT
Found at i:1487416 original size:94 final size:92
Alignment explanation
Indices: 1487248--1487434 Score: 320
Period size: 94 Copynumber: 2.0 Consensus size: 92
1487238 GGCATATTTG
* *
1487248 GAGCAATGTAGGTTGAGGGATGCTCTCTTGTCGGGAATATCTTAGCTTGCCCTCAATCCAATGCT
1 GAGCAATGTAGGTTGAGGGATGCTCTCTTGTCAGGAATATCATAGCTTGCCCTCAATCCAATGCT
1487313 TCTTTTCTAGCTTTGAAGATACCAAGTA
66 TCTTTTCTAGCTTTGAAGAT-CCAAGTA
*
1487341 GAGCAATAGTAGGTTGAGGGATGCTCTCTTGTCAGGACTATCATAGCTTGCCCTCAATCCAATGC
1 GAGCAAT-GTAGGTTGAGGGATGCTCTCTTGTCAGGAATATCATAGCTTGCCCTCAATCCAATGC
*
1487406 TTCTTTTCTAGCTTTGAAGATGCAAGTA
65 TTCTTTTCTAGCTTTGAAGATCCAAGTA
1487434 G
1 G
1487435 GGAAGGCACA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
93 14 0.16
94 75 0.84
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (92 bp):
GAGCAATGTAGGTTGAGGGATGCTCTCTTGTCAGGAATATCATAGCTTGCCCTCAATCCAATGCT
TCTTTTCTAGCTTTGAAGATCCAAGTA
Found at i:1489145 original size:33 final size:33
Alignment explanation
Indices: 1489103--1489170 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
1489093 TGTATTTTCA
1489103 TTGATCTACATCACCTACGTGATAATTGGAGTC
1 TTGATCTACATCACCTACGTGATAATTGGAGTC
*
1489136 TTGATCTACATCACCTTCGTGATAATTGGAGTC
1 TTGATCTACATCACCTACGTGATAATTGGAGTC
1489169 TT
1 TT
1489171 TCTCTGGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (33 bp):
TTGATCTACATCACCTACGTGATAATTGGAGTC
Found at i:1491133 original size:2 final size:2
Alignment explanation
Indices: 1491126--1491190 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1491116 CCTTTGTTAC
1491126 TA TA TA 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
1491168 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1491191 GCATGCATGC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1491427 original size:2 final size:2
Alignment explanation
Indices: 1491422--1491446 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1491412 AAAATTTGTA
1491422 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1491447 AACGCACGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1492593 original size:2 final size:2
Alignment explanation
Indices: 1492586--1492617 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1492576 TTCACGCATG
*
1492586 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1492618 ATTCCACCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1499053 original size:60 final size:60
Alignment explanation
Indices: 1498976--1499096 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
1498966 TAATTATGTA
*
1498976 TTATTTTTAAGTACCAAAAT-TTTGAGAGATGTACATACTTACACGGGTGTAAGTATGTGT
1 TTATTTTTAAGTACCAAAATATTT-AGAAATGTACATACTTACACGGGTGTAAGTATGTGT
* **
1499036 TTATTTTTAGGTACCAAAATATTTAGAAATGTACATACTTACATTGGTGTAAGTATGTGT
1 TTATTTTTAAGTACCAAAATATTTAGAAATGTACATACTTACACGGGTGTAAGTATGTGT
1499096 T
1 T
1499097 ATGTAACATC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
60 53 0.95
61 3 0.05
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (60 bp):
TTATTTTTAAGTACCAAAATATTTAGAAATGTACATACTTACACGGGTGTAAGTATGTGT
Found at i:1499825 original size:21 final size:21
Alignment explanation
Indices: 1499799--1499843 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1499789 GATTTCTGGG
* *
1499799 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1499820 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1499841 CAA
1 CAA
1499844 ACGAACAACA
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:1501246 original size:30 final size:31
Alignment explanation
Indices: 1501140--1501325 Score: 317
Period size: 31 Copynumber: 6.1 Consensus size: 31
1501130 TCGAGACATA
1501140 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
1501171 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
1501202 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
1501233 TGGACAG-TTACCGAGGATCTTTATGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
1501263 TGGACAG-TTACCGAGGATCTTTATGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
* **
1501293 TGGACAG-TTACCG-GGGTCTTGGTGACCTC
1 TGGACAGTTTACCGAGGATCTTTATGACCTC
1501322 TGGA
1 TGGA
1501326 TAGGTCCTTC
Statistics
Matches: 152, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
29 17 0.11
30 66 0.43
31 69 0.45
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (31 bp):
TGGACAGTTTACCGAGGATCTTTATGACCTC
Found at i:1501346 original size:60 final size:61
Alignment explanation
Indices: 1501152--1501336 Score: 245
Period size: 60 Copynumber: 3.0 Consensus size: 61
1501142 GACAGTTTAC
1501152 CGAGGATCTTTATGACCTCTGGACAGTTTACCGAGGATCTTTATGACCTCTGGACA-GT-TT
1 CGAGGATCTTTATGACCTCTGGACAG-TTACCGAGGATCTTTATGACCTCTGGACAGGTCTT
*
1501212 ACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACA-GT-TAC
1 --CGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGGTCT-T
* ** *
1501274 CGAGGATCTTTATGACCTCTGGACAGTTACCG-GGGTCTTGGTGACCTCTGGATAGGTCCTT
1 CGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGGT-CTT
1501335 CG
1 CG
1501337 GGACATTTAT
Statistics
Matches: 113, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
59 18 0.16
60 34 0.30
61 34 0.30
62 27 0.24
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (61 bp):
CGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGGTCTT
Found at i:1502997 original size:7 final size:7
Alignment explanation
Indices: 1502985--1503023 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
1502975 GTCTTTGCAA
1502985 TAAACCT
1 TAAACCT
1502992 TAAACCT
1 TAAACCT
1502999 TAAA-CT
1 TAAACCT
1503005 CTAAACCT
1 -TAAACCT
*
1503013 TAAACCC
1 TAAACCT
1503020 TAAA
1 TAAA
1503024 ATTGATTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 25 0.86
8 2 0.07
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAACCT
Found at i:1503009 original size:14 final size:14
Alignment explanation
Indices: 1502985--1503023 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1502975 GTCTTTGCAA
*
1502985 TAAACCTTAAACCT
1 TAAACCCTAAACCT
*
1502999 TAAACTCTAAACCT
1 TAAACCCTAAACCT
1503013 TAAACCCTAAA
1 TAAACCCTAAA
1503024 ATTGATTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:1504611 original size:12 final size:12
Alignment explanation
Indices: 1504585--1504660 Score: 68
Period size: 12 Copynumber: 6.6 Consensus size: 12
1504575 TAATCTGTCT
*
1504585 TCGAGCTT-GAA
1 TCGAGCTTAAAA
*
1504596 TCGAGTTTAAAA
1 TCGAGCTTAAAA
*
1504608 TCGAGCTCAAAA
1 TCGAGCTTAAAA
*
1504620 TCGAGCTT-GAA
1 TCGAGCTTAAAA
*
1504631 TCGAGCTAAAAA
1 TCGAGCTTAAAA
**
1504643 TCGAG-TTTCAA
1 TCGAGCTTAAAA
1504654 TCGAGCT
1 TCGAGCT
1504661 CGAGTCTTGA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
11 24 0.47
12 27 0.53
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (12 bp):
TCGAGCTTAAAA
Found at i:1504632 original size:23 final size:23
Alignment explanation
Indices: 1504606--1504661 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1504596 TCGAGTTTAA
*
1504606 AATCGAGCTCAAAATCGAGCTTG
1 AATCGAGCTCAAAATCGAGCTTC
* *
1504629 AATCGAGCTAAAAATCGAGTTTC
1 AATCGAGCTCAAAATCGAGCTTC
1504652 AATCGAGCTC
1 AATCGAGCTC
1504662 GAGTCTTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (23 bp):
AATCGAGCTCAAAATCGAGCTTC
Found at i:1508844 original size:20 final size:20
Alignment explanation
Indices: 1508821--1508860 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1508811 AAAACGAAGG
1508821 TAAGCTGGAAAAGGAAGCTA
1 TAAGCTGGAAAAGGAAGCTA
*
1508841 TAAGCTGGAGAAGGAAGCTA
1 TAAGCTGGAAAAGGAAGCTA
1508861 AAGTAGGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.33, T:0.15
Consensus pattern (20 bp):
TAAGCTGGAAAAGGAAGCTA
Found at i:1511125 original size:2 final size:2
Alignment explanation
Indices: 1511120--1511163 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1511110 TCACATGCCA
*
1511120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1511162 AT
1 AT
1511164 CTTCACAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1515522 original size:11 final size:10
Alignment explanation
Indices: 1515501--1515547 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
1515491 TAAATAACTT
1515501 TAAAATATTA
1 TAAAATATTA
1515511 TAAAATAGTTA
1 TAAAATA-TTA
* *
1515522 TTAAATATTC
1 TAAAATATTA
1515532 TAAACA-ATTA
1 TAAA-ATATTA
1515542 TAAAAT
1 TAAAAT
1515548 GATCCGTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 1 0.03
10 19 0.63
11 10 0.33
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (10 bp):
TAAAATATTA
Found at i:1515635 original size:29 final size:31
Alignment explanation
Indices: 1515597--1515668 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 31
1515587 GTTTAAGGAC
*
1515597 TATTTTATAATATTTTAATAAATTT-AA-CA
1 TATTTTATAATAATTTAATAAATTTGAATCA
* *
1515626 TATTTTATAATAATTTGATAAATTTGAATGA
1 TATTTTATAATAATTTAATAAATTTGAATCA
1515657 TCATTTTATAAT
1 T-ATTTTATAAT
1515669 TGTTTGAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.62
30 2 0.05
31 2 0.05
32 10 0.27
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (31 bp):
TATTTTATAATAATTTAATAAATTTGAATCA
Found at i:1515695 original size:32 final size:32
Alignment explanation
Indices: 1515598--1515705 Score: 84
Period size: 32 Copynumber: 3.5 Consensus size: 32
1515588 TTTAAGGACT
* * * *
1515598 ATTTTATAATATTTTAATAAATTT-AA-CAT-
1 ATTTTATAATAATTTGAGAAATTTGAATAATA
* * *
1515627 ATTTTATAATAATTTGATAAATTTGAATGATC
1 ATTTTATAATAATTTGAGAAATTTGAATAATA
**
1515659 ATTTTATAATTGTTTGAGAAATTT-AATAACTA
1 ATTTTATAATAATTTGAGAAATTTGAATAA-TA
1515691 ATTTT-TAAT-ATTTGA
1 ATTTTATAATAATTTGA
1515706 AAGATCACTC
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
29 22 0.33
30 7 0.11
31 10 0.15
32 27 0.41
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (32 bp):
ATTTTATAATAATTTGAGAAATTTGAATAATA
Found at i:1516543 original size:22 final size:22
Alignment explanation
Indices: 1516494--1516604 Score: 90
Period size: 22 Copynumber: 5.2 Consensus size: 22
1516484 TTGCATTTCG
* *
1516494 CGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATAGTCT-ACAATTGT
*
1516515 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATTGT
* *
1516537 CGTTGCGAT--TTTTCAAATT-T
1 CGTTGCGATAGTCTAC-AATTGT
1516557 -GTTGCGATAGTCTACAATTGT
1 CGTTGCGATAGTCTACAATTGT
* * *
1516578 TGTTGCCATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATTGT
1516600 CGTTG
1 CGTTG
1516605 AGATTTTCCA
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
19 8 0.11
20 8 0.11
21 23 0.32
22 33 0.46
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAATTGT
Found at i:1516593 original size:63 final size:63
Alignment explanation
Indices: 1516516--1516635 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 63
1516506 TGAAAATCGC
* * * *
1516516 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATTTGTTGCGATAGTCTACAATTGTT
1 GTTGCCATAGTCTACAGTTGTCGTTGAGATTTTCCAAATTCGTTGCGATAGTCTACAATTGTT
*
1516579 GTTGCCATAGTCTACAGTTGTCGTTGAGATTTTCCAAATTCGTTGTGATAGTCTACA
1 GTTGCCATAGTCTACAGTTGTCGTTGAGATTTTCCAAATTCGTTGCGATAGTCTACA
1516636 GTCGTGGTCG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (63 bp):
GTTGCCATAGTCTACAGTTGTCGTTGAGATTTTCCAAATTCGTTGCGATAGTCTACAATTGTT
Found at i:1516810 original size:41 final size:42
Alignment explanation
Indices: 1516734--1516848 Score: 114
Period size: 41 Copynumber: 2.8 Consensus size: 42
1516724 TTAACTATCG
* * *
1516734 CAACGACAACTGTAGACTATCACAA--CGAATTTGGAAAATCA
1 CAACGACAATTGTAGACTATCGCAACGCGAA-ATGGAAAATCA
* *
1516775 CAACGAC-ATTGTAGACTATCGCAACGCGAAATGGAATATCG
1 CAACGACAATTGTAGACTATCGCAACGCGAAATGGAAAATCA
* *
1516816 CAAC-ACGATTTTCA-ACTATCGCAACGCGAAATG
1 CAACGACAATTGT-AGACTATCGCAACGCGAAATG
1516849 CAACGCGAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.27
41 42 0.66
42 5 0.08
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (42 bp):
CAACGACAATTGTAGACTATCGCAACGCGAAATGGAAAATCA
Found at i:1516852 original size:21 final size:21
Alignment explanation
Indices: 1516789--1516852 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1516779 GACATTGTAG
*
1516789 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
1516810 A-TATCGCAACACGATTTTCA
1 ACTATCGCAACGCGAAATGCA
1516830 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
1516851 AC
1 AC
1516853 GCGAATTTGC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:1517109 original size:24 final size:22
Alignment explanation
Indices: 1517077--1517122 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1517067 TCTACTGATT
1517077 TTTTATTATCGTACACTTTACCGG
1 TTTTATTAT--TACACTTTACCGG
*
1517101 TTTTGTTATTACACTTTACCGG
1 TTTTATTATTACACTTTACCGG
1517123 AAATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
24 8 0.38
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.48
Consensus pattern (22 bp):
TTTTATTATTACACTTTACCGG
Found at i:1526577 original size:18 final size:17
Alignment explanation
Indices: 1526556--1526590 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1526546 CATTCGTAAA
1526556 TTTTTAAGTACTTTATTT
1 TTTTTAA-TACTTTATTT
*
1526574 TTTTTAATATTTTATTT
1 TTTTTAATACTTTATTT
1526591 CAGTCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAATACTTTATTT
Found at i:1538947 original size:44 final size:44
Alignment explanation
Indices: 1538832--1538952 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 44
1538822 TCTTCAACAT
* * * *
1538832 CAAATTGATCCGATCTCCTCAACACGAAGGAGCAGTGTCATCCT
1 CAAATTGATCCGATTTCCTCAACACGAAGGAACAGTATCATCCC
* * * * * * *
1538876 CAGA-TAATCAGACTTCCTCATCACGAAGGAACCGTATTATCCC
1 CAAATTGATCCGATTTCCTCAACACGAAGGAACAGTATCATCCC
*
1538919 CAAATTGATCCGATTTCCTCAACGCGAAGGAACA
1 CAAATTGATCCGATTTCCTCAACACGAAGGAACA
1538953 ATGTCACAAT
Statistics
Matches: 58, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
43 32 0.55
44 26 0.45
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (44 bp):
CAAATTGATCCGATTTCCTCAACACGAAGGAACAGTATCATCCC
Found at i:1539056 original size:186 final size:185
Alignment explanation
Indices: 1538736--1539301 Score: 965
Period size: 186 Copynumber: 3.0 Consensus size: 185
1538726 TCATCTCCAG
1538736 ATTGACCCGATTTCCTCAACGCGAAGGAA-AAGTGTCATAATTTATCGAAAATGACCCGATCTCT
1 ATTGA-CCGATTTCCTCAACGCGAAGGAACAA-TGTCATAATTTATCGAAAATGACCCGATCTCT
* * *
1538800 TCAACACGGATGAGCAGTGACGTCTTCAACATCAAATTGATCCGATCTCCTCAACACGAAGGAGC
64 TCAACACGGATGAGCAGTGTCGTCTTCAACATCAAATTGAACTGATCTCCTCAACACGAAGGAGC
*
1538865 AGTGTCATCCTCAGATAATCAGACTTCCTCATCACGAAGGAACCGTATTATCCCCAA
129 AGTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTATCCCCAA
* *
1538922 ATTGATCCGATTTCCTCAACGCGAAGGAACAATGTCACAATTTATCGAAAATGACCTGATCTCTT
1 ATTGA-CCGATTTCCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAATGACCCGATCTCTT
* *
1538987 CAACACGGATGAGCAGTGTCGTCTTCAATATCAAATTGAACTGATCTCCTCAACACGAAGGAACA
65 CAACACGGATGAGCAGTGTCGTCTTCAACATCAAATTGAACTGATCTCCTCAACACGAAGGAGCA
1539052 GTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTATCCCCAA
130 GTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTATCCCCAA
* *
1539108 ATTGACCTGATTTCCTCAACACGAAGGAACAATGTCATAATTTATCGAAAACGACCCGATCTCTT
1 ATTGACC-GATTTCCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAATGACCCGATCTCTT
1539173 CAACACGGATGAGCAGTGTCGTCTTCAACATCAAATTG-ACATGATCTCCTCAACACGAAGGAGC
65 CAACACGGATGAGCAGTGTCGTCTTCAACATCAAATTGAAC-TGATCTCCTCAACACGAAGGAGC
*
1539237 AGTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCCAA
129 AGTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTAT-CCCCAA
1539295 ATTGACC
1 ATTGACC
1539302 CTTAGATAGC
Statistics
Matches: 360, Mismatches: 16, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
185 4 0.01
186 341 0.95
187 15 0.04
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (185 bp):
ATTGACCGATTTCCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAATGACCCGATCTCTTC
AACACGGATGAGCAGTGTCGTCTTCAACATCAAATTGAACTGATCTCCTCAACACGAAGGAGCAG
TGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTATCCCCAA
Found at i:1539666 original size:18 final size:18
Alignment explanation
Indices: 1539643--1539681 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1539633 TTTCTGTCCA
1539643 CCAGCACCAGCACATGCT
1 CCAGCACCAGCACATGCT
*
1539661 CCAGCAGCAGCACATGCT
1 CCAGCACCAGCACATGCT
1539679 CCA
1 CCA
1539682 CTTACCAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.44, G:0.18, T:0.10
Consensus pattern (18 bp):
CCAGCACCAGCACATGCT
Found at i:1540575 original size:18 final size:17
Alignment explanation
Indices: 1540554--1540588 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1540544 CATTCGTAAA
1540554 TTTTTAAGTACTTTATTT
1 TTTTTAA-TACTTTATTT
*
1540572 TTTTTAATATTTTATTT
1 TTTTTAATACTTTATTT
1540589 CAGTCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAATACTTTATTT
Found at i:1546331 original size:10 final size:10
Alignment explanation
Indices: 1546318--1546354 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
1546308 ATTGGGTTAA
1546318 ATTATATTAG
1 ATTATATTAG
*
1546328 ATTATAGTTAA
1 ATTATA-TTAG
1546339 ATTATATTAG
1 ATTATATTAG
1546349 ATTATA
1 ATTATA
1546355 GTCAAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (10 bp):
ATTATATTAG
Found at i:1546337 original size:21 final size:21
Alignment explanation
Indices: 1546313--1546362 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1546303 TTAAAATTGG
1546313 GTTAAATTATATTAGATTATA
1 GTTAAATTATATTAGATTATA
1546334 GTTAAATTATATTAGATTATA
1 GTTAAATTATATTAGATTATA
*
1546355 GTCAAATT
1 GTTAAATT
1546363 TCAGAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (21 bp):
GTTAAATTATATTAGATTATA
Found at i:1552043 original size:30 final size:30
Alignment explanation
Indices: 1552009--1552091 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
1551999 GATTTGACAT
* * *
1552009 AACTAACACCGTTTGAGTCTAATTTGCCTG
1 AACTAACACCGTTTGAGCCTAATATGCATG
** *
1552039 AACTAACTTCGTTTGAGCCTAATATGTATG
1 AACTAACACCGTTTGAGCCTAATATGCATG
1552069 AACTAACACCGTTTGA-CC-AATAT
1 AACTAACACCGTTTGAGCCTAATAT
1552092 TTCCCGAAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
28 5 0.11
29 2 0.04
30 38 0.84
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (30 bp):
AACTAACACCGTTTGAGCCTAATATGCATG
Found at i:1556577 original size:139 final size:138
Alignment explanation
Indices: 1556150--1556924 Score: 1023
Period size: 139 Copynumber: 5.6 Consensus size: 138
1556140 ACTATTCACG
* * * * *
1556150 TGAAAACGCGTTTCAGAGGGTGCGTCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTTCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * ** * *
1556215 TTATGTCACTCATGTCCCCCGGGGGAATTATTTATGTCAGTACCTATCATGTTTGAATGAACACA
66 TTATGTCACTCATGT-CCCCGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
*
1556280 TCAAAGTGA
130 ACAAAGTGA
* * * * *
1556289 TGAAAGTGCATTTTAGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCCCTA
1 TGAAAGCGCGTTTCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * * * **
1556354 TTATGTGAGTCATGTCCCTC-GTGGCACTATTCCTGTCAGTACATATCATGTTTGAGATGACGCA
66 TTATGTCACTCATGTCCC-CGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
1556418 ACAAAGTGA
130 ACAAAGTGA
* * *
1556427 TGAAAGCGTGTTTCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTGCACTA
1 TGAAAGCGCGTTTCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1556492 TTATGTCACTCATGTCTCCCGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
66 TTATGTCACTCATGTC-CCCGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
1556557 ACAAAGTGA
130 ACAAAGTGA
* * *
1556566 TGAAAGTGTGTTTCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCTCTA
1 TGAAAGCGCGTTTCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * ** * *
1556631 TTTTGTCACTTATGTCCCTCGGGGAAACTATTCATGTCAGTACATATCATGTTTGAGGGGACACA
66 TTATGTCACTCATGTCCC-CGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
* *
1556696 TCAAAGTGG
130 ACAAAGTGA
* * *
1556705 TGAAAGCGCGTTTCAGGGGGCACACATTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTTCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * * *
1556770 TTATGTGAGTCATGTCCCCCGGGGCACTATTCATATAAGTACCTATCATGTTTGAGGGGACGCAA
66 TTATGTCACTCATGTCCCCGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAA
*
1556835 CAAAGTGG
131 CAAAGTGA
* * * *
1556843 TGAAAGCACGTTTCA-GGGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATAATTGCCTTA
1 TGAAAGCGCGTTTCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1556907 TTATGTGACTCATGTCCC
66 TTATGTCACTCATGTCCC
1556925 TGGAGACACA
Statistics
Matches: 557, Mismatches: 75, Indels: 10
0.87 0.12 0.02
Matches are distributed among these distances:
137 60 0.11
138 179 0.32
139 318 0.57
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (138 bp):
TGAAAGCGCGTTTCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCCGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAA
CAAAGTGA
Found at i:1556796 original size:277 final size:275
Alignment explanation
Indices: 1556176--1556925 Score: 1070
Period size: 277 Copynumber: 2.7 Consensus size: 275
1556166 AGGGTGCGTC
* *
1556176 TTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGGA
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCC-GGGGC
* * ** * * * * *
1556241 ATTATTTATGTCAGTACCTATCATGTTTGAATGAACACATCAAAGTGATGAAAGTGCATTTTAGG
65 ACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGATGAAAGTGCGTTTCAGG
* *
1556306 GGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGAGTCATGTCC
130 GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTG-CCTATTATGTGACTCATGTCC
* * * * * *
1556371 CTCGTGGCACTATTCCTGTCAGTACATATCATGTTTGAGATGACGCAACAAAGTGATGAAAGCGT
194 CTCGGGGAACTATTCATGTCAGTACATATCATGTTTGAGAGGACACAACAAAGTGATGAAAGCGC
* * *
1556436 GTTTCAGGGGGCGCGCC
259 GTTTCAGGGGGCACACA
* * *
1556453 TTCCATTATTTTGTCAGAGAATATATTATCATTGCACTATTATGTCACTCATGTCTCCCGGGGGC
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTC-CCCCGGGGC
*
1556518 ACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGATGAAAGTGTGTTTCAGG
65 ACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGATGAAAGTGCGTTTCAGG
* * * *
1556583 GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCTCTATTTTGTCACTTATGTCC
130 GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGC-CTATTATGTGACTCATGTCC
* * *
1556648 CTCGGGGAAACTATTCATGTCAGTACATATCATGTTTGAGGGGACACATCAAAGTGGTGAAAGCG
194 CTCGGGG-AACTATTCATGTCAGTACATATCATGTTTGAGAGGACACAACAAAGTGATGAAAGCG
1556713 CGTTTCAGGGGGCACACA
258 CGTTTCAGGGGGCACACA
* *
1556731 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTGAGTCATGTCCCCCGGGGCA
1 TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGCA
* * * **
1556796 CTATTCATATAAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGGTGAAAGCACGTTTCA-GG
66 CTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGATGAAAGTGCGTTTCAGGG
*
1556860 GGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATAATTGCCTTATTATGTGACTCATGTCCC
131 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCC-TATTATGTGACTCATGTCCC
1556925 T
195 T
1556926 GGAGACACAA
Statistics
Matches: 420, Mismatches: 49, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
275 1 0.00
276 62 0.15
277 239 0.57
278 118 0.28
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (275 bp):
TTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGCA
CTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAGTGATGAAAGTGCGTTTCAGGG
GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAATTGCCTATTATGTGACTCATGTCCCT
CGGGGAACTATTCATGTCAGTACATATCATGTTTGAGAGGACACAACAAAGTGATGAAAGCGCGT
TTCAGGGGGCACACA
Found at i:1558022 original size:21 final size:21
Alignment explanation
Indices: 1557934--1558024 Score: 121
Period size: 21 Copynumber: 4.3 Consensus size: 21
1557924 GGTGTCATAA
* * *
1557934 AACCCTGCGGACTAGGCATGT
1 AACCCTGTGGGCTAGGAATGT
*
1557955 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GTGGGCTAGGAATGT
1557976 AACCCTGTGGGCTAGGAATGT
1 AACCCTGTGGGCTAGGAATGT
*
1557997 AACCCTGTGGGCTAGGAATAT
1 AACCCTGTGGGCTAGGAATGT
1558018 AACCCTG
1 AACCCTG
1558025 CGGAGATTGC
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
20 3 0.05
21 58 0.91
22 3 0.05
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (21 bp):
AACCCTGTGGGCTAGGAATGT
Found at i:1559884 original size:34 final size:31
Alignment explanation
Indices: 1559832--1559907 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1559822 TTAATAAATT
* *
1559832 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATAT--A-ATTATATTAA
*
1559866 TAAAAAAATAATATTTATATAATTATATTAA
1 TAAAAAAATAATAATTATATAATTATATTAA
*
1559897 TAAAAATATAA
1 TAAAAAAATAA
1559908 CAACTATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 19 0.50
32 1 0.03
34 18 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAATTATATTAA
Found at i:1564691 original size:22 final size:23
Alignment explanation
Indices: 1564660--1564706 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1564650 TAATCGCGAG
1564660 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* *
1564682 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
1564705 TT
1 TT
1564707 ATTTAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:1569109 original size:18 final size:18
Alignment explanation
Indices: 1569086--1569120 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1569076 TACTTCACGA
1569086 TTTATAAGTTAATATATG
1 TTTATAAGTTAATATATG
* *
1569104 TTTATAATTTTATATAT
1 TTTATAAGTTAATATAT
1569121 ATTTTACGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTATAAGTTAATATATG
Found at i:1573508 original size:31 final size:32
Alignment explanation
Indices: 1573460--1573524 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
1573450 TCAATATGAC
*
1573460 ATTTCATGCAAAATTAATTAGAGATTTGATTG
1 ATTTCATGCAAAATTAATAAGAGATTTGATTG
*
1573492 ATTTCATG-TAAATTAATAAGAGATTTGATTG
1 ATTTCATGCAAAATTAATAAGAGATTTGATTG
1573523 AT
1 AT
1573525 ATGATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (32 bp):
ATTTCATGCAAAATTAATAAGAGATTTGATTG
Found at i:1573759 original size:20 final size:19
Alignment explanation
Indices: 1573715--1573759 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1573705 AACAATTAAT
1573715 AAAAAAAAATTAAATTTCA
1 AAAAAAAAATTAAATTTCA
**
1573734 AGAAAAAAAATTGTTATTTCA
1 A-AAAAAAAATT-AAATTTCA
1573755 AAAAA
1 AAAAA
1573760 TTATAAGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 14 0.64
21 7 0.32
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAAAAAATTAAATTTCA
Found at i:1576630 original size:6 final size:6
Alignment explanation
Indices: 1576619--1576645 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1576609 ACTGTTTTTA
1576619 TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTT
1576646 CTACTTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:1581200 original size:2 final size:2
Alignment explanation
Indices: 1581193--1581272 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1581183 CATGTCTTTG
1581193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1581235 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
1581273 GCTCCTTATC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1589994 original size:17 final size:19
Alignment explanation
Indices: 1589972--1590020 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1589962 ACTCATTTAT
1589972 TATTATTTTGT-ATGGT-A
1 TATTATTTTGTGATGGTGA
*
1589989 TATTATTTCTGTGATGTTGA
1 TATTATTT-TGTGATGGTGA
1590009 TATTATATTTGT
1 TATTAT-TTTGT
1590021 TTGAGAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 8 0.30
18 3 0.11
19 4 0.15
20 10 0.37
21 2 0.07
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.59
Consensus pattern (19 bp):
TATTATTTTGTGATGGTGA
Found at i:1595963 original size:23 final size:23
Alignment explanation
Indices: 1595933--1595980 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1595923 AAGCTGAGGA
1595933 TATTATTGACAGAATGATAAAAC
1 TATTATTGACAGAATGATAAAAC
1595956 TATTATTGACAGAATGATAAAAC
1 TATTATTGACAGAATGATAAAAC
1595979 TA
1 TA
1595981 GTCATTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (23 bp):
TATTATTGACAGAATGATAAAAC
Found at i:1604140 original size:26 final size:26
Alignment explanation
Indices: 1604110--1604167 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1604100 TTATACATGC
*
1604110 AGTGTCTTTCATTGACATGGCATGAA
1 AGTGTCTTTCACTGACATGGCATGAA
**
1604136 AGTGTCTTTCACTGGTATGGCATGAA
1 AGTGTCTTTCACTGACATGGCATGAA
1604162 ATGTGT
1 A-GTGT
1604168 TCTATAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (26 bp):
AGTGTCTTTCACTGACATGGCATGAA
Found at i:1608669 original size:20 final size:20
Alignment explanation
Indices: 1608644--1608687 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1608634 CATTAGAAAT
1608644 GAAACAGTTTTAGCATCATA
1 GAAACAGTTTTAGCATCATA
*
1608664 GAAACAGTTTTAGCATTATA
1 GAAACAGTTTTAGCATCATA
1608684 GAAA
1 GAAA
1608688 GGGGTCTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (20 bp):
GAAACAGTTTTAGCATCATA
Found at i:1612467 original size:72 final size:77
Alignment explanation
Indices: 1612372--1612554 Score: 205
Period size: 83 Copynumber: 2.4 Consensus size: 77
1612362 AGGGATATTA
*
1612372 TTTACACAAACGCCGCTAAAGTACTA-TTTT-T-TTTG-ACAAAA-CGCTACTATAGTCGAAACC
1 TTTATACAAACGCCGCTAAAGTACTACTTTTGTGTTTGTACAAAAGCGCTACTATAGTCGAAACC
* **
1612432 TATTGCGGTGTT
66 TATGGCGGACTT
**
1612444 TTTATACAAACGCCGCTAAAGTACTACTCTTTTGCGGTGTTTGTTGGAAAAGCGCTACTATAGTC
1 TTTATACAAACGCCGCTAAAGTACTA--CTTTT---GTGTTTG-TACAAAAGCGCTACTATAGTC
1612509 GAAACCTATGGCGGACTT
60 GAAACCTATGGCGGACTT
* *
1612527 TTAATACAAACGCTGCTAAAGTACTACT
1 TTTATACAAACGCCGCTAAAGTACTACT
1612555 CTCTTACGTT
Statistics
Matches: 92, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
72 25 0.27
75 4 0.04
79 1 0.01
80 4 0.04
81 2 0.02
82 4 0.04
83 52 0.57
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (77 bp):
TTTATACAAACGCCGCTAAAGTACTACTTTTGTGTTTGTACAAAAGCGCTACTATAGTCGAAACC
TATGGCGGACTT
Found at i:1613337 original size:17 final size:17
Alignment explanation
Indices: 1613315--1613357 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1613305 CAATTTTTTA
1613315 TATATCTTTATATATTT
1 TATATCTTTATATATTT
* *
1613332 TATATCGATAATATATTT
1 TATATC-TTTATATATTT
1613350 T-TATCTTT
1 TATATCTTT
1613358 CTTAAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
16 1 0.05
17 10 0.48
18 10 0.48
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (17 bp):
TATATCTTTATATATTT
Found at i:1614992 original size:2 final size:2
Alignment explanation
Indices: 1614985--1615018 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1614975 AAGCTAAATA
1614985 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
1615019 TAAATATTTA
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
Done.