Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_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: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 40
Found at i:1084228 original size:41 final size:41
Alignment explanation
Indices: 1084142--1084276 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1084132 GAATAAGTAA
** *
1084142 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1084183 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
1084224 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1084265 TTCGCAACGCGA
1 ATCGCAACGCGA
1084277 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1084229 original size:20 final size:20
Alignment explanation
Indices: 1084204--1084297 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1084194 AATTGGGAAA
*
1084204 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
1084224 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
1084245 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
1084265 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
1084285 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1084298 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:1084875 original size:19 final size:19
Alignment explanation
Indices: 1084815--1084895 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
1084805 TTCGAGAATG
1084815 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
1084835 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
1084851 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1084868 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1084887 AAAATCGCA
1 AAAATCGCA
1084896 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1084913 original size:19 final size:19
Alignment explanation
Indices: 1084891--1085074 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
1084881 GAAACCAAAA
*
1084891 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1084910 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1084929 TCGCGTTGCGATTTT-ATT
1 TCGCGTTGCGATTTTCATT
1084947 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1084967 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1084983 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1085000 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1085014 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1085033 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1085053 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1085073 TC
1 TC
1085075 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 8 0.06
19 64 0.46
20 38 0.28
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1084999 original size:33 final size:33
Alignment explanation
Indices: 1084962--1085049 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1084952 GTTGCGATTT
* *
1084962 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1084995 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1085028 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1085050 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1085051 original size:20 final size:20
Alignment explanation
Indices: 1085017--1085074 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1085007 GCGATTCTCT
**
1085017 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1085037 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1085057 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1085075 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1087124 original size:42 final size:42
Alignment explanation
Indices: 1087064--1087156 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1087054 GCCCGACTCG
* * *
1087064 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1087106 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
1087148 ACTGTCATC
1 CCTATCATC
1087157 GTTAAAGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1088562 original size:14 final size:14
Alignment explanation
Indices: 1088543--1088578 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1088533 ATTGTTTAAT
1088543 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1088557 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1088571 TGATTTGT
1 TGATTTGT
1088579 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1089355 original size:33 final size:33
Alignment explanation
Indices: 1089318--1089437 Score: 186
Period size: 33 Copynumber: 3.5 Consensus size: 33
1089308 GAAATGAAAA
1089318 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1089351 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
1089389 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
1089422 TCGCATTGCGTTTTTC
1 TCGCATTGCGATTTTC
1089438 ATTTCGCGTT
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
35 3 0.04
36 3 0.04
38 30 0.37
ACGTcount: A:0.12, C:0.22, G:0.17, T:0.48
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:1089359 original size:19 final size:19
Alignment explanation
Indices: 1089318--1089471 Score: 193
Period size: 19 Copynumber: 8.6 Consensus size: 19
1089308 GAAATGAAAA
1089318 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1089334 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1089351 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1089370 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1089389 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1089405 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1089422 TCGCATTGCGTTTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
1089441 TCGCGTTGCAATTTCCATT
1 TCGCATTGCGATTTTCATT
*
1089460 TCGCGTTGCGAT
1 TCGCATTGCGAT
1089472 ATTCTGTTTT
Statistics
Matches: 122, Mismatches: 6, Indels: 17
0.84 0.04 0.12
Matches are distributed among these distances:
14 22 0.18
16 6 0.05
17 6 0.05
19 88 0.72
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1089415 original size:71 final size:71
Alignment explanation
Indices: 1089318--1089476 Score: 264
Period size: 71 Copynumber: 2.2 Consensus size: 71
1089308 GAAATGAAAA
*
1089318 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATT
*
1089383 TTCATT
66 TCCATT
* *
1089389 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGTTTTTCATTTCGCGTTGCAATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATT
1089454 TCCATT
66 TCCATT
* *
1089460 TCGCGTTGCGATATTCT
1 TCGCATTGCGATTTTCT
1089477 GTTTTGCCTT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 82 1.00
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (71 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATT
TCCATT
Found at i:1089438 original size:52 final size:52
Alignment explanation
Indices: 1089356--1089454 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
1089346 TCATTTCGCA
*
1089356 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATTTTCTCG
* *
1089408 TTGCGATTTTCATTTCGCATTGCGTTTTTCATTTCGCGTTGCAATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATTT
1089455 CCATTTCGCG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.49
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATTTTCTCG
Found at i:1091486 original size:20 final size:19
Alignment explanation
Indices: 1091451--1091506 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
1091441 GAAACTTAAA
1091451 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1091470 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
1091490 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
1091507 AAAATCGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1091526 original size:14 final size:14
Alignment explanation
Indices: 1091507--1091546 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
1091497 TGCGAAATGA
1091507 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1091521 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1091535 AAAATCGCAACG
1 AAAATCGCAACG
1091547 CGAAACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1092154 original size:18 final size:18
Alignment explanation
Indices: 1092128--1092172 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1092118 GTCGATCAGA
* *
1092128 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
1092146 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1092164 TGATGGCTC
1 TGATGGCTC
1092173 CGAAGTGGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1094018 original size:20 final size:20
Alignment explanation
Indices: 1093905--1094018 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
1093895 CGCTTTGAAA
1093905 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
1093925 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
1093945 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
1093965 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
1093986 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
1094006 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1094019 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 56 0.73
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:1094036 original size:21 final size:21
Alignment explanation
Indices: 1094007--1094099 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
1093997 ATAGTAAGTA
1094007 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1094028 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1094048 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1094069 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1094089 TCGCATTGCGA
1 TCGCATTGCGA
1094100 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1094037 original size:41 final size:41
Alignment explanation
Indices: 1093946--1094080 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1093936 AAAGTCAGTA
* * * ** *
1093946 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
1093986 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1094028 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1094069 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1094081 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1094081 original size:41 final size:41
Alignment explanation
Indices: 1094007--1094099 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1093997 ATAGTAAGTA
1094007 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1094048 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1094089 TCGCATTGCGA
1 TCGCATTGCGA
1094100 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1095665 original size:38 final size:38
Alignment explanation
Indices: 1095597--1095670 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1095587 GGTCGGATCT
* * *
1095597 AGTGAAAAATATATATTTTTGTATTCGAGTCAAATTCA
1 AGTGAAAAATATATATTTTTGAAGTAGAGTCAAATTCA
*
1095635 AGTGAATAATATATATATTTT-AAGTAGAGTCAAATT
1 AGTGAAAAATATATAT-TTTTGAAGTAGAGTCAAATT
1095671 GACCAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 27 0.87
39 4 0.13
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (38 bp):
AGTGAAAAATATATATTTTTGAAGTAGAGTCAAATTCA
Found at i:1096080 original size:22 final size:22
Alignment explanation
Indices: 1096055--1096102 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1096045 CTATGGTGAC
1096055 ATCCTTCCCCATCTCCAACGAA
1 ATCCTTCCCCATCTCCAACGAA
**
1096077 ATCCTTCCCCATCTCCGGCGAA
1 ATCCTTCCCCATCTCCAACGAA
1096099 ATCC
1 ATCC
1096103 GTCTATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.46, G:0.08, T:0.23
Consensus pattern (22 bp):
ATCCTTCCCCATCTCCAACGAA
Found at i:1096553 original size:20 final size:20
Alignment explanation
Indices: 1096471--1096576 Score: 155
Period size: 19 Copynumber: 5.5 Consensus size: 20
1096461 AAAAACGCAA
*
1096471 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
*
1096490 TGCGATTTTCA-TTTCGTGT
1 TGCGATTTTCATTTTCGCGT
1096509 TGCGATTTTCATTTT-GCGT
1 TGCGATTTTCATTTTCGCGT
*
1096528 TACGATTTTCATTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
1096548 TGCGATTTTCATTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
*
1096568 TACGATTTT
1 TGCGATTTT
1096577 AAGTTTCAGA
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
19 44 0.56
20 35 0.44
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.51
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1098340 original size:21 final size:23
Alignment explanation
Indices: 1098316--1098413 Score: 50
Period size: 21 Copynumber: 4.6 Consensus size: 23
1098306 TGGTGCATGG
1098316 CGTGATGAGGTA-CGGT-CTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* * *
1098337 CGTGGTGAGATAGAGGT--TTTA
1 CGTGATGAGGTAGCGGTACTTTA
* * ** *
1098358 CGCGATGA--CAATGGTGCTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* *
1098379 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTAGCGGTACTTTA
1098400 CGTGATGAGGTAGC
1 CGTGATGAGGTAGC
1098414 CGCTCTACGT
Statistics
Matches: 56, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
19 4 0.07
21 48 0.86
22 3 0.05
23 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.34, T:0.32
Consensus pattern (23 bp):
CGTGATGAGGTAGCGGTACTTTA
Found at i:1098727 original size:21 final size:21
Alignment explanation
Indices: 1098698--1098877 Score: 141
Period size: 21 Copynumber: 8.6 Consensus size: 21
1098688 AGCACCTGTC
*
1098698 ATCGTTCAAGAGGCCACTCCT
1 ATCGTTCAAGAGGCCCCTCCT
* *
1098719 ATTGTTCAAGAGGCCCCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
* *
1098739 CATCCTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
1098761 ACCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
* * *
1098782 ATCGTTTAAGAGGCCCAT-AT
1 ATCGTTCAAGAGGCCCCTCCT
* *
1098802 CATCCTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
1098824 ACCGTTCAAGAGGCCCCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
* * * *
1098844 CATCGTTCAAGTGGTCCTTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
*
1098866 ACCGTTCAAGAG
1 ATCGTTCAAGAG
1098878 CCCGATTTAC
Statistics
Matches: 120, Mismatches: 33, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
20 2 0.02
21 118 0.98
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:1098850 original size:63 final size:63
Alignment explanation
Indices: 1098700--1098838 Score: 242
Period size: 63 Copynumber: 2.2 Consensus size: 63
1098690 CACCTGTCAT
* *
1098700 CGTTCAAGAGGCCACTCCTATTGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCACTCCTATCGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
* *
1098763 CGTTCAAGAGGCCTCTCCTATCGTTTAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCACTCCTATCGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
1098826 CGTTCAAGAGGCC
1 CGTTCAAGAGGCC
1098839 CCTGTCATCG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 72 1.00
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (63 bp):
CGTTCAAGAGGCCACTCCTATCGTTCAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
Found at i:1098877 original size:63 final size:63
Alignment explanation
Indices: 1098700--1098854 Score: 222
Period size: 63 Copynumber: 2.5 Consensus size: 63
1098690 CACCTGTCAT
* * * *
1098700 CGTTCAAGAGGCCACTCCTATTGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCTATCGTTCAAGAGGCCCATACCATCCTTCAAGAGGCCCCTCCCAC
* * *
1098763 CGTTCAAGAGGCCTCTCCTATCGTTTAAGAGGCCCATATCATCCTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCTATCGTTCAAGAGGCCCATACCATCCTTCAAGAGGCCCCTCCCAC
*
1098826 CGTTCAAGAGGCCCCT-GTCATCGTTCAAG
1 CGTTCAAGAGGCCCCTCCT-ATCGTTCAAG
1098855 TGGTCCTTCC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
62 1 0.01
63 83 0.99
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (63 bp):
CGTTCAAGAGGCCCCTCCTATCGTTCAAGAGGCCCATACCATCCTTCAAGAGGCCCCTCCCAC
Found at i:1100253 original size:13 final size:14
Alignment explanation
Indices: 1100228--1100260 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1100218 AAATTGATGT
1100228 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
1100242 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
1100255 ATTTGT
1 ATTTGT
1100261 TTAATAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:1101971 original size:25 final size:25
Alignment explanation
Indices: 1101943--1101992 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1101933 CATTATTTTC
*
1101943 CAAATAATATACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
*
1101968 CAAATAATGTACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
1101993 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:1104691 original size:24 final size:24
Alignment explanation
Indices: 1104664--1104717 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
1104654 CTGAAACATC
1104664 ATCAAAATCC-GAGTATTGACCAAG
1 ATCAAAATCCTG-GTATTGACCAAG
*
1104688 ATCAAAGTCCTGGTATTGACCAAG
1 ATCAAAATCCTGGTATTGACCAAG
1104712 ATCAAA
1 ATCAAA
1104718 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCTGGTATTGACCAAG
Found at i:1104864 original size:12 final size:12
Alignment explanation
Indices: 1104843--1104876 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1104833 GGTTGTGGGT
*
1104843 TTTGAGATTGTG
1 TTTGATATTGTG
1104855 TTTGATATTGTG
1 TTTGATATTGTG
*
1104867 TTTGGTATTG
1 TTTGATATTG
1104877 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1105493 original size:16 final size:16
Alignment explanation
Indices: 1105471--1105510 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1105461 GAAATCATTG
*
1105471 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
1105487 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
1105503 AAAAATTA
1 AAAAATTA
1105511 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:1105656 original size:20 final size:20
Alignment explanation
Indices: 1105631--1105740 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
1105621 AAATAAAACC
1105631 TGTTGCGAAATT-AAAATTCG
1 TGTTGCGAAATTCAAAA-TCG
1105651 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATTC-AAAATCG
*
1105671 AGTTGCG-AATTCAGAAATCG
1 TGTTGCGAAATTCA-AAATCG
* * * *
1105691 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTCAAAATC-G
* **
1105712 TGTTGCGAATTTGGAAATCG
1 TGTTGCGAAATTCAAAATCG
*
1105732 CGTTGCGAA
1 TGTTGCGAA
1105741 TTTGGAAATC
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
19 5 0.06
20 47 0.61
21 25 0.32
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTCAAAATCG
Found at i:1105741 original size:20 final size:20
Alignment explanation
Indices: 1105652--1105882 Score: 166
Period size: 20 Copynumber: 11.6 Consensus size: 20
1105642 TAAAATTCGT
* * *
1105652 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGGAAATCGC
** *
1105672 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTTGGAAATCGC
*
1105692 GTTGCGAATTT-GAAATTCAGT
1 GTTGCGAATTTGGAAA-TC-GC
1105713 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGGAAATCGC
*
1105733 GTTGCGAATTTGGAAATCAC
1 GTTGCGAATTTGGAAATCGC
*
1105753 ATTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGGAAATCGC
** *
1105773 GTTGCGAATTT-GACTTCTGT
1 GTTGCGAATTTGGAAATC-GC
** *
1105793 GTTGCG-ATTTACATATTCGC
1 GTTGCGAATTTGGA-AATCGC
* *
1105813 GTTGCGAATTTAGAAA-CTGA
1 GTTGCGAATTTGGAAATC-GC
* * ** *
1105833 GTTACGAAATTGGAGTTTGC
1 GTTGCGAATTTGGAAATCGC
* *
1105853 GTTGCGAA-TTCGAGATCGC
1 GTTGCGAATTTGGAAATCGC
1105872 GTTGCGAATTT
1 GTTGCGAATTT
1105883 ATTGGTCATT
Statistics
Matches: 172, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
19 29 0.17
20 116 0.67
21 23 0.13
22 4 0.02
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGGAAATCGC
Found at i:1105798 original size:40 final size:39
Alignment explanation
Indices: 1105631--1105823 Score: 165
Period size: 40 Copynumber: 4.8 Consensus size: 39
1105621 AAATAAAACC
* * * *
1105631 TGTTGCGAAATTA-AAATTCGTGTTGCGAATTCGAAAATCG
1 TGTTGCGAATTTAGAAA-TCGCGTTGCGAATTTG-AATTCG
* * *
1105671 AGTTGCGAATTCAGAAATCGAGTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTAGAAATCGCGTTGCGAATTTG-AATTC-G
* * *
1105712 TGTTGCGAATTTGGAAATCGCGTTGCGAATTTGGAAATCA
1 TGTTGCGAATTTAGAAATCGCGTTGCGAATTT-GAATTCG
** * *
1105752 CATTGCGAATTTGGAAATCGCGTTGCGAATTTGACTTCTG
1 TGTTGCGAATTTAGAAATCGCGTTGCGAATTTGAATTC-G
* *
1105792 TGTTGCG-ATTTACATATTCGCGTTGCGAATTT
1 TGTTGCGAATTTAGA-AATCGCGTTGCGAATTT
1105824 AGAAACTGAG
Statistics
Matches: 126, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
39 9 0.07
40 80 0.63
41 36 0.29
42 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.34
Consensus pattern (39 bp):
TGTTGCGAATTTAGAAATCGCGTTGCGAATTTGAATTCG
Found at i:1105846 original size:80 final size:81
Alignment explanation
Indices: 1105684--1105883 Score: 194
Period size: 80 Copynumber: 2.5 Consensus size: 81
1105674 TGCGAATTCA
* ** *
1105684 GAAATCGAGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGGAAATCGCGTTGCGAATTTGGAAA
1 GAAATCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTACAAATCGCGTTGCGAATTTAGAAA
* *
1105749 TCACATTGCGAATTTG
66 TCACATTACGAAATTG
* * *
1105765 GAAATCGCGTTGCGAATTTG-ACTTCTGTGTTGCG-ATTTACATATTCGCGTTGCGAATTTAGAA
1 GAAATCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTACA-AATCGCGTTGCGAATTTAGAA
* *
1105828 ACTGA-GTTACGAAATTG
65 A-TCACATTACGAAATTG
** * * * *
1105845 GAGTTTGCGTTGCGAATTCGAGA-TC-GCGTTGCGAATTTA
1 GAAATCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTA
1105884 TTGGTCATTT
Statistics
Matches: 97, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
79 12 0.12
80 64 0.66
81 21 0.22
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (81 bp):
GAAATCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTACAAATCGCGTTGCGAATTTAGAAA
TCACATTACGAAATTG
Found at i:1113655 original size:14 final size:14
Alignment explanation
Indices: 1113636--1113668 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1113626 AGCACTCAAA
1113636 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
1113650 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
1113664 AAAAG
1 AAAAG
1113669 TTTAAGCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:1121032 original size:20 final size:21
Alignment explanation
Indices: 1121008--1121077 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
1120998 ATATCTAGAG
1121008 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATATGTTTTAA
* * *
1121029 -TAATCTCAAATATTTAATTTCAA
1 TTAAT-T-AAATATAT-GTTTTAA
*
1121052 TTAATTAAATATA-GATTTAA
1 TTAATTAAATATATGTTTTAA
1121072 TTAATT
1 TTAATT
1121078 TCAAAAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 14 0.37
21 1 0.03
22 13 0.34
23 6 0.16
24 4 0.11
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (21 bp):
TTAATTAAATATATGTTTTAA
Found at i:1121221 original size:89 final size:89
Alignment explanation
Indices: 1121039--1121300 Score: 409
Period size: 89 Copynumber: 2.9 Consensus size: 89
1121029 TAATCTCAAA
* * * * *
1121039 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTCAAAAAATAAAATTCCTAATATT-A
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-ACCTAAT-TTGA
1121103 TTAGGGTAACTTGGATATAAGAGGAT
64 TTAGGGTAACTTGGATATAAGAGGAT
*
1121129 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCTAATTTGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCTAATTTGATT
*
1121194 AGTGTAACTTGGATATAAGAGGAT
66 AGGGTAACTTGGATATAAGAGGAT
* *
1121218 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCTAATTTGATT
*
1121283 AGGGTAACTTGGCTATAA
66 AGGGTAACTTGGATATAA
1121301 AAGGGTGTGT
Statistics
Matches: 159, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
88 2 0.01
89 110 0.69
90 47 0.30
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCTAATTTGATT
AGGGTAACTTGGATATAAGAGGAT
Found at i:1128013 original size:20 final size:21
Alignment explanation
Indices: 1127989--1128058 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
1127979 ATATCTAGAG
1127989 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATATGTTTTAA
* * *
1128010 -TAATCCTGAATATTTAATTTTAA
1 TTAAT--TAAATATAT-GTTTTAA
*
1128033 TTAATTAAATATA-GATTTAA
1 TTAATTAAATATATGTTTTAA
1128053 TTAATT
1 TTAATT
1128059 TCAAATAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 15 0.39
22 13 0.34
23 6 0.16
24 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (21 bp):
TTAATTAAATATATGTTTTAA
Found at i:1134015 original size:13 final size:13
Alignment explanation
Indices: 1133993--1134030 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1133983 AAGCACTCAT
1133993 AAAG-AAGAAAA-
1 AAAGAAAGAAAAG
1134004 AAAGAAAAGAAAAG
1 AAAG-AAAGAAAAG
1134018 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
1134031 TTGAAGCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.17
13 16 0.67
14 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAG
Found at i:1135321 original size:24 final size:25
Alignment explanation
Indices: 1135294--1135345 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1135284 TTGACATTTC
* *
1135294 AAAGGATGTACCACTTGAAG-TCCA
1 AAAGAATGTACCAATTGAAGATCCA
*
1135318 AAAGAATGTGCCAATTGAAGATCCA
1 AAAGAATGTACCAATTGAAGATCCA
1135343 AAA
1 AAA
1135346 ATTGTGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.19
Consensus pattern (25 bp):
AAAGAATGTACCAATTGAAGATCCA
Found at i:1142406 original size:16 final size:16
Alignment explanation
Indices: 1142381--1142422 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1142371 GTGATGGCTG
* **
1142381 GTGGAAACAAAGTTAA
1 GTGGAGACAAAGCCAA
1142397 GTGGAGACAAAGCCAA
1 GTGGAGACAAAGCCAA
1142413 GTGGAGACAA
1 GTGGAGACAA
1142423 GCAATCTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.31, T:0.12
Consensus pattern (16 bp):
GTGGAGACAAAGCCAA
Found at i:1146583 original size:35 final size:35
Alignment explanation
Indices: 1146536--1146602 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1146526 AGACAAGTAA
1146536 TCTTCCAAGCACATGGGCTGTTT-ATAGTGCATTG
1 TCTTCCAAGCACATGGGCTGTTTCATAGTGCATTG
* **
1146570 TCTTCTAATGCACATGGTTTGTTTCATAGTGCA
1 TCTTCCAA-GCACATGGGCTGTTTCATAGTGCA
1146603 ATGGTATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.25
35 13 0.46
36 8 0.29
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (35 bp):
TCTTCCAAGCACATGGGCTGTTTCATAGTGCATTG
Found at i:1155641 original size:16 final size:16
Alignment explanation
Indices: 1155605--1155646 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1155595 ATAAGAATAT
*
1155605 ATGAAATAATAAGGAA
1 ATGAAATAGTAAGGAA
1155621 ATGAAATAGTAA-GAA
1 ATGAAATAGTAAGGAA
1155636 AGTGAAGATAG
1 A-TGAA-ATAG
1155647 CTTACCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 15 0.65
17 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (16 bp):
ATGAAATAGTAAGGAA
Found at i:1159936 original size:21 final size:21
Alignment explanation
Indices: 1159897--1159936 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1159887 AGGAGTCTTT
*
1159897 TTCTTTCTCTTTTTGTTTTTC
1 TTCTTTCTCTTTCTGTTTTTC
1159918 TTCTTTCTTCTTTCT-TTTT
1 TTCTTTC-TCTTTCTGTTTT
1159937 AATGCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (21 bp):
TTCTTTCTCTTTCTGTTTTTC
Found at i:1162037 original size:10 final size:10
Alignment explanation
Indices: 1162022--1162047 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1162012 TTCAACTTTC
1162022 TTTCTTTTAT
1 TTTCTTTTAT
1162032 TTTCTTTTAT
1 TTTCTTTTAT
1162042 TTTCTT
1 TTTCTT
1162048 CTTTTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTTAT
Found at i:1166425 original size:24 final size:23
Alignment explanation
Indices: 1166381--1166425 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1166371 TTTATAGGTT
**
1166381 TACAAGGGGTTTGGACGAATATA
1 TACAAGGGGTTTGGAAAAATATA
*
1166404 TACAAGGGTTTTTGGAAAAATA
1 TACAAGGG-GTTTGGAAAAATA
1166426 CATGACTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (23 bp):
TACAAGGGGTTTGGAAAAATATA
Found at i:1168536 original size:19 final size:20
Alignment explanation
Indices: 1168496--1168536 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
1168486 TGTTGTAGGA
1168496 TTCTTTCTTTTCTTTTTGAT
1 TTCTTTCTTTTCTTTTTGAT
1168516 TTCTTT-TTTTCTTTTTGAT
1 TTCTTTCTTTTCTTTTTGAT
1168535 TT
1 TT
1168537 GCACACCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (20 bp):
TTCTTTCTTTTCTTTTTGAT
Found at i:1169099 original size:19 final size:19
Alignment explanation
Indices: 1169035--1169096 Score: 106
Period size: 19 Copynumber: 3.2 Consensus size: 19
1169025 GAAACCCCTT
1169035 TGAAAATACATGATTTTTAA
1 TGAAAATACATGA-TTTTAA
1169055 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
1169074 TGAAGATACATGATTTTAA
1 TGAAAATACATGATTTTAA
1169093 TGAA
1 TGAA
1169097 GATTCATGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:1169104 original size:19 final size:19
Alignment explanation
Indices: 1169035--1169104 Score: 104
Period size: 19 Copynumber: 3.6 Consensus size: 19
1169025 GAAACCCCTT
*
1169035 TGAAAATACATGATTTTTAA
1 TGAAGATACATGA-TTTTAA
*
1169055 TGAAAATACATGATTTTAA
1 TGAAGATACATGATTTTAA
1169074 TGAAGATACATGATTTTAA
1 TGAAGATACATGATTTTAA
*
1169093 TGAAGATTCATG
1 TGAAGATACATG
1169105 CTCTTGCTCG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (19 bp):
TGAAGATACATGATTTTAA
Found at i:1170233 original size:16 final size:16
Alignment explanation
Indices: 1170194--1170235 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1170184 GCATCTCGAC
1170194 AATAAGCA-TTTATGT
1 AATAAGCACTTTATGT
*
1170209 AACAAGCACTTATATGT
1 AATAAGCACTT-TATGT
1170226 -ATAAGCACTT
1 AATAAGCACTT
1170236 GTTTTTGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 11 0.48
17 5 0.22
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (16 bp):
AATAAGCACTTTATGT
Found at i:1174052 original size:5 final size:5
Alignment explanation
Indices: 1174038--1174092 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
1174028 TCTTTTTGAA
* *
1174038 TTTTC TTTTTC TTTTC TTTTC --TAC TTTTC TTTCTT TTTGTC TTTTC
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTT-TC TTT-TC TTTTC
1174084 TTTTC TTTT
1 TTTTC TTTT
1174093 TGCACTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
3 2 0.05
5 26 0.63
6 13 0.32
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:1174064 original size:13 final size:11
Alignment explanation
Indices: 1174038--1174093 Score: 62
Period size: 11 Copynumber: 4.9 Consensus size: 11
1174028 TCTTTTTGAA
1174038 TTTTCTTTTTC
1 TTTTCTTTTTC
1174049 TTTTCTTTTCTAC
1 TTTTCTTTT-T-C
1174062 TTTTCTTTCTT-
1 TTTTCTTT-TTC
1174073 TTTGTC-TTTTC
1 TTT-TCTTTTTC
1174084 TTTTCTTTTT
1 TTTTCTTTTT
1174094 GCACTCCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.10
11 21 0.54
12 3 0.08
13 10 0.26
14 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:1174072 original size:17 final size:18
Alignment explanation
Indices: 1174044--1174094 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
1174034 TGAATTTTCT
1174044 TTTTCTTTTCTTTTCT-AC
1 TTTTCTTTTCTTTT-TGAC
*
1174062 TTTTC-TTTCTTTTTGTC
1 TTTTCTTTTCTTTTTGAC
1174079 TTTTCTTTTCTTTTTG
1 TTTTCTTTTCTTTTTG
1174095 CACTCCAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 14 0.47
18 15 0.50
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTGAC
Found at i:1187970 original size:10 final size:10
Alignment explanation
Indices: 1187957--1187983 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1187947 CAGAGTTCTC
1187957 TTCTTCTCCT
1 TTCTTCTCCT
1187967 TTCTTCTCCT
1 TTCTTCTCCT
1187977 TTCTTCT
1 TTCTTCT
1187984 TCTTCACGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (10 bp):
TTCTTCTCCT
Found at i:1189381 original size:20 final size:21
Alignment explanation
Indices: 1189349--1189405 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
1189339 AGGGTTCATA
* *
1189349 GGTCCTTCAGGACA-TACAGT
1 GGTCATTCGGGACATTACAGT
*
1189369 GGTCATTCGGGACATTTTATAGT
1 GGTCATTCGGGACA--TTACAGT
1189392 GGTCATTCGGGACA
1 GGTCATTCGGGACA
1189406 AATTCATAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.39
23 19 0.61
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
GGTCATTCGGGACATTACAGT
Found at i:1192839 original size:20 final size:20
Alignment explanation
Indices: 1192814--1192869 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
1192804 GAAACCCCTT
1192814 TGAAAATTCATGATTTTTAA
1 TGAAAATTCATGATTTTTAA
*
1192834 TGAAAATACATGA-TTTTAA
1 TGAAAATTCATGATTTTTAA
* *
1192853 TGAAGATTCATGCTTTT
1 TGAAAATTCATGATTTT
1192870 GGCCGAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (20 bp):
TGAAAATTCATGATTTTTAA
Found at i:1192852 original size:19 final size:20
Alignment explanation
Indices: 1192814--1192856 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1192804 GAAACCCCTT
*
1192814 TGAAAATTCATGATTTTTAA
1 TGAAAATACATGATTTTTAA
1192834 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
1192853 TGAA
1 TGAA
1192857 GATTCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1194826 original size:104 final size:104
Alignment explanation
Indices: 1194702--1194919 Score: 418
Period size: 104 Copynumber: 2.1 Consensus size: 104
1194692 TTGTTTATTG
*
1194702 AAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
1 AAACATGCTTGAATGCATAACAAGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
*
1194767 AGATATTAATATGCATGACATGAATTTGAGAATGAATGA
66 AGATATTAATATGCATGACATGAATTTGAAAATGAATGA
1194806 AAACATGCTTGAATGCATAACAAGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
1 AAACATGCTTGAATGCATAACAAGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
1194871 AGATATTAATATGCATGACATGAATTTGAAAATGAATGA
66 AGATATTAATATGCATGACATGAATTTGAAAATGAATGA
1194910 AAACATGCTT
1 AAACATGCTT
1194920 AATATGTATG
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 112 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (104 bp):
AAACATGCTTGAATGCATAACAAGTGAATCATCTTAAATGCTAAGATGAATGCAAAACTACTATG
AGATATTAATATGCATGACATGAATTTGAAAATGAATGA
Found at i:1194908 original size:51 final size:50
Alignment explanation
Indices: 1194747--1194913 Score: 144
Period size: 51 Copynumber: 3.2 Consensus size: 50
1194737 AAATGCTAAG
*
1194747 ATGAATGCAAAACTACTATGAGATATTAATATGCATGACATGAATTTGAGA
1 ATGAATG-AAAACTACTATGAGATATTAATATGCATGACATGAATTTGAAA
* * * * * * * *
1194798 ATGAATGAAAACATGCT-TGA-ATGCA-TAACAAGTGAATCATCTTAAATGCT-AAG
1 ATGAATGAAAAC-TACTATGAGAT--ATTAA-TA-TGCATGA-CATGAAT-TTGAAA
1194851 ATGAATGCAAAACTACTATGAGATATTAATATGCATGACATGAATTTGAAA
1 ATGAATG-AAAACTACTATGAGATATTAATATGCATGACATGAATTTGAAA
1194902 ATGAATGAAAAC
1 ATGAATGAAAAC
1194914 ATGCTTAATA
Statistics
Matches: 87, Mismatches: 17, Indels: 25
0.67 0.13 0.19
Matches are distributed among these distances:
49 2 0.02
50 17 0.20
51 26 0.30
52 10 0.11
53 18 0.21
54 12 0.14
55 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.28
Consensus pattern (50 bp):
ATGAATGAAAACTACTATGAGATATTAATATGCATGACATGAATTTGAAA
Found at i:1197562 original size:63 final size:63
Alignment explanation
Indices: 1197463--1197601 Score: 226
Period size: 63 Copynumber: 2.2 Consensus size: 63
1197453 AGATAGAAAT
**
1197463 CACAAGTATCAAGGTGAAAGGAATGATTCCACAAGCATAAGCTTGA-TAAGTCGGGTTTGACGC
1 CACAAGTATCAAGGTGAAAGGAATGACGCCACAAGCATAAGCTT-ACTAAGTCGGGTTTGACGC
*
1197526 CACAAGTATCAAGGTGAATGGAATGACGCCACAAGCATAAGCTTACTAAGTCGGGTTTGACGC
1 CACAAGTATCAAGGTGAAAGGAATGACGCCACAAGCATAAGCTTACTAAGTCGGGTTTGACGC
*
1197589 CACAAGTAACAAG
1 CACAAGTATCAAG
1197602 TTACTTGATA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 1 0.01
63 70 0.99
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.20
Consensus pattern (63 bp):
CACAAGTATCAAGGTGAAAGGAATGACGCCACAAGCATAAGCTTACTAAGTCGGGTTTGACGC
Found at i:1197592 original size:34 final size:33
Alignment explanation
Indices: 1197491--1197594 Score: 101
Period size: 34 Copynumber: 3.2 Consensus size: 33
1197481 AGGAATGATT
1197491 CCACAAGCATAAGCTTGATAAGTCGGGTTTGACG
1 CCACAAGCATAAGCTT-ATAAGTCGGGTTTGACG
* * * **
1197525 CCACAAGTATCAAG-GT-GAA-T--GGAATGACG
1 CCACAAGCAT-AAGCTTATAAGTCGGGTTTGACG
1197554 CCACAAGCATAAGCTTACTAAGTCGGGTTTGACG
1 CCACAAGCATAAGCTTA-TAAGTCGGGTTTGACG
1197588 CCACAAG
1 CCACAAG
1197595 TAACAAGTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
28 3 0.06
29 17 0.32
31 3 0.06
32 3 0.06
34 24 0.45
35 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (33 bp):
CCACAAGCATAAGCTTATAAGTCGGGTTTGACG
Found at i:1197606 original size:34 final size:34
Alignment explanation
Indices: 1197509--1197606 Score: 82
Period size: 34 Copynumber: 3.0 Consensus size: 34
1197499 ATAAGCTTGA
* *
1197509 TAAGTCGGGTTTGACGCCACAAGTATCAAGGT--
1 TAAGTCGGGTTTGACGCCACAAGTAACAAGTTAC
* ** * *
1197541 GAA-T--GGAATGACGCCACAAG-CATAAGCTTAC
1 TAAGTCGGGTTTGACGCCACAAGTAACAAG-TTAC
1197572 TAAGTCGGGTTTGACGCCACAAGTAACAAGTTAC
1 TAAGTCGGGTTTGACGCCACAAGTAACAAGTTAC
1197606 T
1 T
1197607 TGATAAGTCG
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
28 3 0.06
29 15 0.32
31 3 0.06
32 3 0.06
34 19 0.40
35 4 0.09
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (34 bp):
TAAGTCGGGTTTGACGCCACAAGTAACAAGTTAC
Found at i:1198885 original size:117 final size:117
Alignment explanation
Indices: 1198679--1198913 Score: 443
Period size: 117 Copynumber: 2.0 Consensus size: 117
1198669 ATGTTGTTTA
* * *
1198679 TTGAAACATGTTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGCATGCAAAACTACT
1 TTGAAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAAATACT
1198744 ATGAGATATTAATATGCATGACATGAATTTGAGAATGAATGAAAACATGCTT
66 ATGAGATATTAATATGCATGACATGAATTTGAGAATGAATGAAAACATGCTT
1198796 TTGAAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAAATACT
1 TTGAAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAAATACT
1198861 ATGAGATATTAATATGCATGACATGAATTTGAGAATGAATGAAAACATGCTT
66 ATGAGATATTAATATGCATGACATGAATTTGAGAATGAATGAAAACATGCTT
1198913 T
1 T
1198914 GATACAGTTC
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (117 bp):
TTGAAACATGCTTGAATGCATAACACGTGAATCATCTTAAATGCTAAGATGAATGCAAAAATACT
ATGAGATATTAATATGCATGACATGAATTTGAGAATGAATGAAAACATGCTT
Found at i:1199723 original size:10 final size:10
Alignment explanation
Indices: 1199708--1199736 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1199698 TTTGGCTTCT
1199708 TGCATGAATA
1 TGCATGAATA
1199718 TGCATGAATA
1 TGCATGAATA
1199728 TGCATGAAT
1 TGCATGAAT
1199737 GGATGAATTT
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:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (10 bp):
TGCATGAATA
Found at i:1200870 original size:60 final size:59
Alignment explanation
Indices: 1200777--1200896 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 59
1200767 ACAATGTGAA
*
1200777 TGAACGTACAGGATTCATTAAAGTTCATGAATGGAAGTTGGTTCGTTTGACACTTCCCTT
1 TGAACATACAGGATTCATTAAAGTTCATGAATGGAAGTTGGTTCG-TTGACACTTCCCTT
* *
1200837 TGAACATACAGGATTCATTAAATTTCATGAATGGAATTTGGTTCGTTGACACTTCCCTT
1 TGAACATACAGGATTCATTAAAGTTCATGAATGGAAGTTGGTTCGTTGACACTTCCCTT
1200896 T
1 T
1200897 CATAAGGTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
59 15 0.26
60 42 0.74
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (59 bp):
TGAACATACAGGATTCATTAAAGTTCATGAATGGAAGTTGGTTCGTTGACACTTCCCTT
Found at i:1204595 original size:20 final size:19
Alignment explanation
Indices: 1204548--1204596 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
1204538 ATAAGAGAAA
1204548 AAAG-TAAAAGTTAAAATG
1 AAAGATAAAAGTTAAAATG
* * *
1204566 AAATAGAAAAGTTAAGGATG
1 AAAGATAAAAGTTAA-AATG
1204586 AAAGATAAAAG
1 AAAGATAAAAG
1204597 AAAAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 3 0.12
19 9 0.38
20 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.18
Consensus pattern (19 bp):
AAAGATAAAAGTTAAAATG
Found at i:1213198 original size:18 final size:18
Alignment explanation
Indices: 1213175--1213243 Score: 120
Period size: 18 Copynumber: 3.8 Consensus size: 18
1213165 GTTCTTAAGG
*
1213175 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
*
1213193 AGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1213211 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1213229 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
1213244 TAATTTCTAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1227039 original size:42 final size:42
Alignment explanation
Indices: 1226980--1227071 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
1226970 GTGGATTGGA
1226980 TTAAGGATCCAGGCGGTTGTCTGGCTTTTGTTTCTTTCCTAG
1 TTAAGGATCCAGGCGGTTGTCTGGCTTTTGTTTCTTTCCTAG
*
1227022 TTAAGGATCCAGGCGGTTGTTTGGCTTTTGTTTCTTTCCTAG
1 TTAAGGATCCAGGCGGTTGTCTGGCTTTTGTTTCTTTCCTAG
1227064 TTAAGGAT
1 TTAAGGAT
1227072 ATTGCTAGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.43
Consensus pattern (42 bp):
TTAAGGATCCAGGCGGTTGTCTGGCTTTTGTTTCTTTCCTAG
Found at i:1244718 original size:20 final size:20
Alignment explanation
Indices: 1244693--1244737 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1244683 GTCATCTAAT
* *
1244693 TTTTTAAACCCTAGATCGGA
1 TTTTTAAACCCCAGACCGGA
1244713 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
1244733 TTTTT
1 TTTTT
1244738 TTCCGGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:1247236 original size:20 final size:21
Alignment explanation
Indices: 1247194--1247238 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1247184 TTGGTTTTTA
1247194 TTATGGAGTTCAAGTTGGTTG
1 TTATGGAGTTCAAGTTGGTTG
* *
1247215 TTATGGATTTCAA-TTTGTTG
1 TTATGGAGTTCAAGTTGGTTG
1247235 TTAT
1 TTAT
1247239 AGATGTCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.51
Consensus pattern (21 bp):
TTATGGAGTTCAAGTTGGTTG
Found at i:1251290 original size:12 final size:12
Alignment explanation
Indices: 1251273--1251305 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1251263 CATTAAAGGC
1251273 TTATAATCTGAA
1 TTATAATCTGAA
*
1251285 TTATAATATGAA
1 TTATAATCTGAA
1251297 TTATAATCT
1 TTATAATCT
1251306 TTAATGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (12 bp):
TTATAATCTGAA
Found at i:1253525 original size:24 final size:24
Alignment explanation
Indices: 1253508--1253593 Score: 145
Period size: 24 Copynumber: 3.6 Consensus size: 24
1253498 CGTTCATGAA
*
1253508 CGTTCGGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATGTG
1253532 CGTTCAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATGTG
*
1253556 CGTTCAGTTATGTTCATTTATGTG
1 CGTTCAGTTATGTTCGTTTATGTG
*
1253580 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
1253594 TAACCCGATA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.51
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATGTG
Found at i:1258607 original size:65 final size:64
Alignment explanation
Indices: 1258409--1258618 Score: 232
Period size: 65 Copynumber: 3.2 Consensus size: 64
1258399 AGTGCTAAGA
* * ** *
1258409 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* *
1258473 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
1258536 AT-
63 -TG
* *
1258538 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
1258602 G
64 G
*
1258603 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1258619 CTTTGAAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 51 0.41
65 63 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:1265411 original size:65 final size:65
Alignment explanation
Indices: 1265278--1265437 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
1265268 TGCACTAAGA
* * *
1265278 GTGCATCGATGCATCAAGTGCATTCAATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
1265342 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
1265405 AT
65 -G
*
1265407 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
1265438 CAATTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 28 0.33
65 54 0.64
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:1265476 original size:65 final size:63
Alignment explanation
Indices: 1265278--1265487 Score: 205
Period size: 65 Copynumber: 3.3 Consensus size: 63
1265268 TGCACTAAGA
* * * *
1265278 GTGCATCGATGCATCAAGTGCATTCAATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
1265341 G
63 G
*
1265342 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
1265407 -
63 G
* ** *
1265407 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGTATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
1265470 TG
62 TG
*
1265472 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1265488 CTCTGAAAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 47 0.38
65 65 0.52
66 5 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:1265866 original size:16 final size:16
Alignment explanation
Indices: 1265845--1265895 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
1265835 GTCTCCAACG
1265845 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1265861 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
1265877 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1265891 TTTAT
1 TTTAT
1265896 TAAATGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.15
15 2 0.06
16 26 0.79
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1266264 original size:40 final size:38
Alignment explanation
Indices: 1266219--1266304 Score: 95
Period size: 41 Copynumber: 2.2 Consensus size: 38
1266209 CTGACTCGAA
*
1266219 TATATTAATATT-TTAAAATAATATATT-TATAATTATTTAT
1 TATATTAA-ATTATTAAAA-AATATATTATAT-ATAATTT-T
1266259 TATATTTTAAATTATTAAAAAATATATTATATATAATTTT
1 TATA--TTAAATTATTAAAAAATATATTATATATAATTTT
1266299 TATATT
1 TATATT
1266305 TTTAATAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
38 2 0.05
40 9 0.22
41 17 0.41
42 13 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (38 bp):
TATATTAAATTATTAAAAAATATATTATATATAATTTT
Found at i:1266278 original size:42 final size:40
Alignment explanation
Indices: 1266218--1266334 Score: 132
Period size: 40 Copynumber: 2.9 Consensus size: 40
1266208 TCTGACTCGA
* *
1266218 ATATATTAATATT-TTAAAATAATATATTTATAATTATTTATT
1 ATATTTTAA-ATTATTAAAA-AATATATTTATAATAATTT-TT
1266260 ATATTTTAAATTATTAAAAAATATA-TTATATATAATTTTT
1 ATATTTTAAATTATTAAAAAATATATTTATA-ATAATTTTT
* * *
1266300 ATATTTTTAATAATTAAAGAATATATTT-TAATAAT
1 ATATTTTAAATTATTAAAAAATATATTTATAATAAT
1266335 ATAAAAATAA
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
39 5 0.07
40 31 0.46
41 17 0.25
42 14 0.21
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (40 bp):
ATATTTTAAATTATTAAAAAATATATTTATAATAATTTTT
Found at i:1266330 original size:21 final size:22
Alignment explanation
Indices: 1266299--1266343 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1266289 ATATAATTTT
1266299 TATATTTTTAATAAT-TAAAGAA
1 TATATTTTTAATAATATAAA-AA
1266321 TATA-TTTTAATAATATAAAAA
1 TATATTTTTAATAATATAAAAA
1266342 TA
1 TA
1266344 AAAATCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATTTTTAATAATATAAAAA
Found at i:1276312 original size:36 final size:36
Alignment explanation
Indices: 1276265--1276338 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1276255 TCAAATAAAG
1276265 TACAAGTATTTTAGACAAAGCTTTTGTCTAATTATT
1 TACAAGTATTTTAGACAAAGCTTTTGTCTAATTATT
1276301 TACAAGTATTTTAGACAAAGCTTTTGTCTAATTATT
1 TACAAGTATTTTAGACAAAGCTTTTGTCTAATTATT
1276337 TA
1 TA
1276339 TCCAAATCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (36 bp):
TACAAGTATTTTAGACAAAGCTTTTGTCTAATTATT
Found at i:1276601 original size:20 final size:17
Alignment explanation
Indices: 1276559--1276600 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1276549 ATCTTCCCCC
1276559 TCTTCTTCAACGCTGTT
1 TCTTCTTCAACGCTGTT
1276576 TCTTCTTCAACGCTGTT
1 TCTTCTTCAACGCTGTT
*
1276593 TCGTCTTC
1 TCTTCTTC
1276601 TATGTTGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.10, C:0.31, G:0.12, T:0.48
Consensus pattern (17 bp):
TCTTCTTCAACGCTGTT
Found at i:1278047 original size:80 final size:80
Alignment explanation
Indices: 1277914--1278074 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
1277904 ATGTCAGCAG
*
1277914 TCTAGTCTTCGATGACGTTGCAGCTGCTATTCTACAATAAGAAAATCGGCGCAAGAACAAGGAAG
1 TCTAGTCTTCGATGACGTTGCAACTGCTATTCTACAATAAGAAAATCGGCGCAAGAACAAGGAAG
1277979 ACAGACAAGTAAATC
66 ACAGACAAGTAAATC
*
1277994 TCTAGTCTTCTATGACGTTGCAACTGCTATTCTACAATAAGAAAATCGGCGCAAGAACAAGGAAG
1 TCTAGTCTTCGATGACGTTGCAACTGCTATTCTACAATAAGAAAATCGGCGCAAGAACAAGGAAG
1278059 ACAGACAAGTAAATC
66 ACAGACAAGTAAATC
1278074 T
1 T
1278075 GCAACAAGTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (80 bp):
TCTAGTCTTCGATGACGTTGCAACTGCTATTCTACAATAAGAAAATCGGCGCAAGAACAAGGAAG
ACAGACAAGTAAATC
Found at i:1282941 original size:3 final size:3
Alignment explanation
Indices: 1282933--1282966 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1282923 TTTCATCCGA
1282933 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1282967 TTCTTTTCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1283258 original size:18 final size:18
Alignment explanation
Indices: 1283235--1283269 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1283225 TACTCCACGC
*
1283235 CAACCAAATGAGCAAAAT
1 CAACCAAATCAGCAAAAT
1283253 CAACCAAATCAGCAAAA
1 CAACCAAATCAGCAAAA
1283270 ATATATGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.26, G:0.09, T:0.09
Consensus pattern (18 bp):
CAACCAAATCAGCAAAAT
Found at i:1284392 original size:21 final size:21
Alignment explanation
Indices: 1284344--1284421 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 21
1284334 AAGTTTCCTT
* *
1284344 TTCGCAACAAG-ATTTTCTAA
1 TTCGCAACACGAATTTTCGAA
* * * *
1284364 ATCACAACACGAATTTTTGAT
1 TTCGCAACACGAATTTTCGAA
*
1284385 TTCGCAACTCG-ATTTTCGAA
1 TTCGCAACACGAATTTTCGAA
1284405 TTCGCAACACGAATTTT
1 TTCGCAACACGAATTTT
1284422 AATTTCACAA
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 25 0.57
21 19 0.43
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
TTCGCAACACGAATTTTCGAA
Found at i:1284392 original size:41 final size:41
Alignment explanation
Indices: 1284343--1284421 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
1284333 CAAGTTTCCT
*
1284343 TTTCGCAACAAGATTTTCTAAATCACAACACGAATTTTTGA
1 TTTCGCAACAAGATTTTCGAAATCACAACACGAATTTTTGA
** * *
1284384 TTTCGCAACTCGATTTTCGAATTCGCAACACGAATTTT
1 TTTCGCAACAAGATTTTCGAAATCACAACACGAATTTT
1284422 AATTTCACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (41 bp):
TTTCGCAACAAGATTTTCGAAATCACAACACGAATTTTTGA
Found at i:1284609 original size:14 final size:15
Alignment explanation
Indices: 1284590--1284627 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1284580 TCCCCATCTC
1284590 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1284604 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1284620 TAATTTTT
1 TAATTTTT
1284628 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1285252 original size:12 final size:12
Alignment explanation
Indices: 1285219--1285253 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1285209 CACCACATTT
*
1285219 ACAATACCAAAC
1 ACAATATCAAAC
1285231 ACAATATCAAAC
1 ACAATATCAAAC
*
1285243 ACAATCTCAAA
1 ACAATATCAAA
1285254 ACCCACAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (12 bp):
ACAATATCAAAC
Found at i:1285432 original size:24 final size:24
Alignment explanation
Indices: 1285379--1285425 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1285369 GTATTCAAAA
*
1285379 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCAGAAC
1285403 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTGGTCAATAC-CAGA
1285426 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGAAC
Found at i:1287724 original size:18 final size:18
Alignment explanation
Indices: 1287701--1287736 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1287691 AAGCAAAAGG
*
1287701 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1287719 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1287737 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1288104 original size:60 final size:60
Alignment explanation
Indices: 1288030--1288144 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
1288020 AGGTACACTT
* *
1288030 TCGCAACACGAAAATCAAATTCGCAACATGAAAGACAAAATCGCAACGCGAAAGTCAAAA
1 TCGCAACACGAAAATCAAAATCGCAACACGAAAGACAAAATCGCAACGCGAAAGTCAAAA
* * * *
1288090 TCGCAACGCGAAAATCAAAATCGCAACGCGAAAGTCAAAATCGTAACGCGAAAGT
1 TCGCAACACGAAAATCAAAATCGCAACACGAAAGACAAAATCGCAACGCGAAAGT
1288145 GTACCTTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (60 bp):
TCGCAACACGAAAATCAAAATCGCAACACGAAAGACAAAATCGCAACGCGAAAGTCAAAA
Found at i:1288143 original size:20 final size:20
Alignment explanation
Indices: 1288030--1288144 Score: 158
Period size: 20 Copynumber: 5.8 Consensus size: 20
1288020 AGGTACACTT
* * *
1288030 TCGCAACACGAAAATCAAAT
1 TCGCAACGCGAAAGTCAAAA
** *
1288050 TCGCAACATGAAAGACAAAA
1 TCGCAACGCGAAAGTCAAAA
1288070 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
1288090 TCGCAACGCGAAAATCAAAA
1 TCGCAACGCGAAAGTCAAAA
1288110 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
1288130 TCGTAACGCGAAAGT
1 TCGCAACGCGAAAGT
1288145 GTACCTTATG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:1288326 original size:20 final size:20
Alignment explanation
Indices: 1288303--1288346 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1288293 AAAATCAAAA
1288303 TCGCAATGCGAATTTGACTT
1 TCGCAATGCGAATTTGACTT
** * *
1288323 TCGCGTTGTGAATTTGATTT
1 TCGCAATGCGAATTTGACTT
1288343 TCGC
1 TCGC
1288347 GTTACGAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCAATGCGAATTTGACTT
Found at i:1288347 original size:20 final size:20
Alignment explanation
Indices: 1288312--1288349 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1288302 ATCGCAATGC
1288312 GAATTTGACTTTCGCGTTGT
1 GAATTTGACTTTCGCGTTGT
*
1288332 GAATTTGATTTTCGCGTT
1 GAATTTGACTTTCGCGTT
1288350 ACGAAAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.24, T:0.47
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGT
Found at i:1289873 original size:21 final size:21
Alignment explanation
Indices: 1289847--1289943 Score: 108
Period size: 21 Copynumber: 4.6 Consensus size: 21
1289837 GTGAATCGGG
* *
1289847 CTCTTGAACGGTGGAAGAGAC
1 CTCTTGAACGATGGAAGAGGC
*
1289868 CTCTTGAACGAT-GATAGGGGC
1 CTCTTGAACGATGGA-AGAGGC
* * *
1289889 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGAAGAGGC
1289910 CTCTTGAACGATAGG-AGAGGC
1 CTCTTGAACGAT-GGAAGAGGC
1289931 CTCTTGAACGATG
1 CTCTTGAACGATG
1289944 ACAGGTGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.05
21 60 0.91
22 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGAAGAGGC
Found at i:1289913 original size:42 final size:42
Alignment explanation
Indices: 1289847--1289940 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
1289837 GTGAATCGGG
* *
1289847 CTCTTGAACGGTGGAAGAGACCTCTTGAACGAT-GATAGGGGC
1 CTCTTGAACGGTGGAAGAGACCTCTTGAACGATAG-GAGAGGC
* * *
1289889 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGAAGAGACCTCTTGAACGATAGGAGAGGC
1289931 CTCTTGAACG
1 CTCTTGAACG
1289941 ATGACAGGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGAAGAGACCTCTTGAACGATAGGAGAGGC
Found at i:1290540 original size:21 final size:21
Alignment explanation
Indices: 1290516--1290576 Score: 122
Period size: 21 Copynumber: 2.9 Consensus size: 21
1290506 GTGATGGAAT
1290516 AGGTGATGGCTCTCGTTGTGG
1 AGGTGATGGCTCTCGTTGTGG
1290537 AGGTGATGGCTCTCGTTGTGG
1 AGGTGATGGCTCTCGTTGTGG
1290558 AGGTGATGGCTCTCGTTGT
1 AGGTGATGGCTCTCGTTGT
1290577 AGAGCTGTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.10, C:0.15, G:0.41, T:0.34
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTGG
Found at i:1292152 original size:19 final size:20
Alignment explanation
Indices: 1292093--1292164 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
1292083 TCTTAAACTT
1292093 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
*
1292113 AAAATCGTAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
1292133 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
1292152 AAAATCGCAACGC
1 AAAATCGCAACGC
1292165 AAATTTCATT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 18 0.36
20 32 0.64
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1292722 original size:18 final size:19
Alignment explanation
Indices: 1292701--1292738 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1292691 AATATTGTGT
1292701 TTCGAATT-CGAAAATAAA
1 TTCGAATTACGAAAATAAA
*
1292719 TTCGAGTTACGAAAATAAA
1 TTCGAATTACGAAAATAAA
1292738 T
1 T
1292739 GCGCTTTGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (19 bp):
TTCGAATTACGAAAATAAA
Found at i:1292769 original size:20 final size:20
Alignment explanation
Indices: 1292744--1292789 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1292734 TAAATGCGCT
*
1292744 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
1292764 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
1292784 TTGCGA
1 TTGCGA
1292790 TTTAACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:1292807 original size:20 final size:20
Alignment explanation
Indices: 1292783--1292849 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1292773 TGACTTATGT
1292783 GTTGCGATTTAACTATTCGC
1 GTTGCGATTTAACTATTCGC
* **
1292803 ATTGCGATTT-ACATATTATC
1 GTTGCGATTTAAC-TATTCGC
1292823 GTTGCGATTTAACTATTCGC
1 GTTGCGATTTAACTATTCGC
1292843 GTTGCGA
1 GTTGCGA
1292850 ATTTGGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.05
20 35 0.90
21 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTAACTATTCGC
Found at i:1292808 original size:40 final size:42
Alignment explanation
Indices: 1292764--1292854 Score: 127
Period size: 40 Copynumber: 2.3 Consensus size: 42
1292754 GACTTCTGTG
* *
1292764 TTGCGAATTTGACTTA-TGT-GTTGCGATTTAACTATTCGCA
1 TTGCGAATTTGACATATTATCGTTGCGATTTAACTATTCGCA
*
1292804 TTGCG-ATTT-ACATATTATCGTTGCGATTTAACTATTCGCG
1 TTGCGAATTTGACATATTATCGTTGCGATTTAACTATTCGCA
1292844 TTGCGAATTTG
1 TTGCGAATTTG
1292855 GAAAATTGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 4 0.09
39 6 0.14
40 30 0.68
41 4 0.09
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (42 bp):
TTGCGAATTTGACATATTATCGTTGCGATTTAACTATTCGCA
Found at i:1298091 original size:19 final size:20
Alignment explanation
Indices: 1298067--1298114 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1298057 AATGTTTTTC
*
1298067 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1298086 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1298106 TTTTGAAAA
1 TTTTGAAAA
1298115 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1299692 original size:22 final size:21
Alignment explanation
Indices: 1299639--1299714 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
1299629 CATTCAAGGC
* * *
1299639 GTGCATCGGTGCACCTTCATG
1 GTGCATCGATGCACTTTCAAG
*
1299660 GTGTATCGATGCACTTTCAAG
1 GTGCATCGATGCACTTTCAAG
1299681 GATGCATCGATGCACTGTT--AG
1 G-TGCATCGATGCACT-TTCAAG
*
1299702 GTGTATCGATGCA
1 GTGCATCGATGCA
1299715 TTAAGCACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
20 11 0.23
21 21 0.45
22 13 0.28
23 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (21 bp):
GTGCATCGATGCACTTTCAAG
Found at i:1299695 original size:43 final size:43
Alignment explanation
Indices: 1299631--1299714 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
1299621 ATCATACCCA
* *
1299631 TTCAAGGCGTGCATCGGTGCACCT-TCATGGTGTATCGATGCACT
1 TTCAAGGCATGCATCGATGCA-CTGTCA-GGTGTATCGATGCACT
*
1299675 TTCAAGG-ATGCATCGATGCACTGTTAGGTGTATCGATGCA
1 TTCAAGGCATGCATCGATGCACTGTCAGGTGTATCGATGCA
1299715 TTAAGCACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 16 0.44
43 13 0.36
44 7 0.19
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (43 bp):
TTCAAGGCATGCATCGATGCACTGTCAGGTGTATCGATGCACT
Found at i:1299711 original size:20 final size:20
Alignment explanation
Indices: 1299659--1299714 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
1299649 GCACCTTCAT
1299659 GGTGTATCGATGCACTTTCAA
1 GGTGTATCGATGCACTTT-AA
*
1299680 GGATGCATCGATGCACTGTT-A
1 GG-TGTATCGATGCACT-TTAA
1299701 GGTGTATCGATGCA
1 GGTGTATCGATGCA
1299715 TTAAGCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.35
21 5 0.16
22 13 0.42
23 2 0.06
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (20 bp):
GGTGTATCGATGCACTTTAA
Found at i:1300638 original size:21 final size:19
Alignment explanation
Indices: 1300590--1300699 Score: 79
Period size: 21 Copynumber: 5.8 Consensus size: 19
1300580 ATATAAGAGA
* *
1300590 GAGAAAGAAGATATAAAAAT
1 GAGAAAAAAGA-AAAAAAAT
*
1300610 -AAAAAAAAGAAAAAATAAT
1 GAGAAAAAAGAAAAAA-AAT
1300629 CGAGAAAAAAGAAAAAAAA-
1 -GAGAAAAAAGAAAAAAAAT
* *
1300648 GA-AGAAAAG-AAAAAGAT
1 GAGAAAAAAGAAAAAAAAT
1300665 -AG-AAAAAGAATAAAAGAAT
1 GAGAAAAAAGAA-AAAA-AAT
1300684 AGAGAAAAAAGAAAAA
1 -GAGAAAAAAGAAAAA
1300700 GAGAGAAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
16 12 0.17
17 7 0.10
18 10 0.14
19 13 0.18
20 2 0.03
21 19 0.27
22 8 0.11
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.07
Consensus pattern (19 bp):
GAGAAAAAAGAAAAAAAAT
Found at i:1300646 original size:8 final size:8
Alignment explanation
Indices: 1300633--1300699 Score: 53
Period size: 9 Copynumber: 7.5 Consensus size: 8
1300623 AATAATCGAG
1300633 AAAAAAGAA
1 AAAAAAG-A
1300642 AAAAAAGA
1 AAAAAAGA
*
1300650 AGAAAAGA
1 AAAAAAGA
1300658 AAAAGATAGA
1 AAAA-A-AGA
*
1300668 AAAAGAATA
1 AAAA-AAGA
1300677 AAAGAATAGA
1 AAA-AA-AGA
1300687 GAAAAAAGA
1 -AAAAAAGA
1300696 AAAA
1 AAAA
1300700 GAGAGAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
8 15 0.31
9 17 0.35
10 14 0.29
11 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1300660 original size:23 final size:23
Alignment explanation
Indices: 1300634--1300693 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
1300624 ATAATCGAGA
1300634 AAAAAGAAAAAAAAGAAGAAAAG
1 AAAAAGAAAAAAAAGAAGAAAAG
* *
1300657 AAAAAGATAGAAAAAGAATAAAAG
1 AAAAAGA-AAAAAAAGAAGAAAAG
*
1300681 AATAGAGAAAAAA
1 AA-AAAGAAAAAA
1300694 GAAAAAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 7 0.23
24 20 0.65
25 4 0.13
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (23 bp):
AAAAAGAAAAAAAAGAAGAAAAG
Found at i:1300662 original size:14 final size:13
Alignment explanation
Indices: 1300633--1300698 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 13
1300623 AATAATCGAG
1300633 AAAAAAGAAAA-A
1 AAAAAAGAAAAGA
*
1300645 AAAGAAGAAAAGA
1 AAAAAAGAAAAGA
1300658 AAAAGATAGAAAAAGA
1 AAAA-A-AG-AAAAGA
* *
1300674 ATAAAAGAATAGA
1 AAAAAAGAAAAGA
1300687 GAAAAAAGAAAA
1 -AAAAAAGAAAA
1300699 AGAGAGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
12 10 0.23
13 9 0.21
14 12 0.28
15 3 0.07
16 9 0.21
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (13 bp):
AAAAAAGAAAAGA
Found at i:1300708 original size:10 final size:9
Alignment explanation
Indices: 1300633--1300708 Score: 52
Period size: 8 Copynumber: 8.3 Consensus size: 9
1300623 AATAATCGAG
1300633 AAAA-AAGA
1 AAAAGAAGA
*
1300641 AAAAAAAGA
1 AAAAGAAGA
*
1300650 AGAA-AAGA
1 AAAAGAAGA
1300658 AAAAGATAGA
1 AAAAGA-AGA
*
1300668 AAAAGAA-T
1 AAAAGAAGA
1300676 AAAAGAATAGA
1 AAAAG-A-AGA
1300687 GAAAA-AAGA
1 -AAAAGAAGA
1300696 AAAAGAGAGA
1 AAAAGA-AGA
1300706 AAA
1 AAA
1300709 TAAATCAAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
8 20 0.36
9 14 0.25
10 17 0.31
12 4 0.07
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:1302892 original size:134 final size:132
Alignment explanation
Indices: 1302614--1302968 Score: 425
Period size: 134 Copynumber: 2.7 Consensus size: 132
1302604 TACAAATATA
* * * *
1302614 ATATTCCATTAAGAAGAAGCGAAACATGTCCCTCTTTTCCAAGATTTGATATTCCCT--GTGACA
1 ATATTCCCTTCAGAAGAAGCGGAATATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGACA
* * * *
1302677 GCAGAACAAGTCTGCCTGATTCAATCTTTCCTTAGTGACAGCGAATGGATCAACTTCTCCAGATC
66 GCAGAACAAGTCTCCCTGATTCAATCTTTCCTTAGTAACAACGAATGGATCAACTTCCCCAGATC
*
1302742 TT
131 TG
* * *
1302744 ATATTTCCTTCAGAAGAAGAGGAATATGTCCCTCTTTTCCAAGACTTGATATTCCCTGAGTGACA
1 ATATTCCCTTCAGAAGAAGCGGAATATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGACA
* * *
1302809 G-TGAAACAAGTTTACCCTGATTCAATC-TTCCTTGAGTAACAACGGAATGGGTCAAC-TCCCCT
66 GCAG-AACAAGTCT-CCCTGATTCAATCTTTCCTT-AGTAACAAC-GAATGGATCAACTTCCCC-
1302871 AGATCTG
126 AGATCTG
* * *
1302878 ATATTCCCTTCAGAAGAAGCGG-GTCATGTCCCACTTTTCCAAGATTTGATATTCCTTGAGTGAC
1 ATATTCCCTTCAGAAGAAGCGGAAT-ATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGAC
* *
1302942 AGCAGAACAAGTGTGCCCCGATTCAAT
65 AGCAGAACAAGTCT-CCCTGATTCAAT
1302969 GATAAACTCC
Statistics
Matches: 191, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
130 50 0.26
131 1 0.01
132 21 0.11
133 24 0.13
134 94 0.49
135 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
ATATTCCCTTCAGAAGAAGCGGAATATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGACA
GCAGAACAAGTCTCCCTGATTCAATCTTTCCTTAGTAACAACGAATGGATCAACTTCCCCAGATC
TG
Found at i:1303060 original size:111 final size:113
Alignment explanation
Indices: 1302862--1303192 Score: 452
Period size: 111 Copynumber: 2.9 Consensus size: 113
1302852 GGAATGGGTC
** *
1302862 AACTCCCCTAGATCTGATATTCCCTTCAGAAGAAGCGGGTCATGTCCCACTTTTCCAAGATTTGA
1 AACTCCCCTAGATCTGATATTCCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGA
* *
1302927 TATTCCTTGAGTGACAGC-AGAACAAGTGTGCCCCGATTCAAT-GAT-A
66 TATTCCCTGAGTGACA-CTAGAACAAGTCTGCCCCGATTCAATAGATCA
* * *
1302973 AACTCCCCCAGATCTGATATTCCCTTCAGAAGAAGCGAAACATATCCCTCTTTTCCAAGATTTGA
1 AACTCCCCTAGATCTGATATTCCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGA
1303038 TATTCCCTGAGTGACACTAGAACAAGTCTGCCCCGATTCAATAGATCA
66 TATTCCCTGAGTGACACTAGAACAAGTCTGCCCCGATTCAATAGATCA
* * * * * * * **
1303086 ACCTCTCCTAGATCTGATATTCCCTTTAGAAAAAACGGAACAGGTCCATCTTTTTTAAGATTTGA
1 AACTCCCCTAGATCTGATATTCCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGA
* * *
1303151 TATTCCCTGAGTGACAGTAGAACAAGTCTACCCCAATTCAAT
66 TATTCCCTGAGTGACACTAGAACAAGTCTGCCCCGATTCAAT
1303193 CTTCCCTAAG
Statistics
Matches: 194, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
110 1 0.01
111 97 0.50
112 3 0.02
113 93 0.48
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (113 bp):
AACTCCCCTAGATCTGATATTCCCTTCAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGA
TATTCCCTGAGTGACACTAGAACAAGTCTGCCCCGATTCAATAGATCA
Found at i:1303674 original size:3 final size:3
Alignment explanation
Indices: 1303662--1303725 Score: 112
Period size: 3 Copynumber: 21.3 Consensus size: 3
1303652 CCATTCGATA
1303662 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1303708 TAT TA- TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
1303726 TTTCATATCC
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1304018 original size:18 final size:18
Alignment explanation
Indices: 1303984--1304018 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1303974 CAATCCACGG
*
1303984 CAACCAAATGAGCAAAAT
1 CAACCAAATCAGCAAAAT
*
1304002 CAACCAAATCAGTAAAA
1 CAACCAAATCAGCAAAA
1304019 AAATATGATA
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:0.57, C:0.23, G:0.09, T:0.11
Consensus pattern (18 bp):
CAACCAAATCAGCAAAAT
Found at i:1305638 original size:13 final size:13
Alignment explanation
Indices: 1305620--1305645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1305610 CGGTAAAATA
1305620 AATTGAACATCCT
1 AATTGAACATCCT
1305633 AATTGAACATCCT
1 AATTGAACATCCT
1305646 TAGAAACGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
AATTGAACATCCT
Found at i:1307607 original size:22 final size:22
Alignment explanation
Indices: 1307576--1307628 Score: 88
Period size: 23 Copynumber: 2.4 Consensus size: 22
1307566 AGGTTTCGTT
*
1307576 GGTTTGCCCCTGCCGCTATTCC
1 GGTTTCCCCCTGCCGCTATTCC
1307598 GGTTTCCCCCCTGCCGCTATTCC
1 GGTTT-CCCCCTGCCGCTATTCC
1307621 GGTTTCCC
1 GGTTTCCC
1307629 TGTTAGCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.04, C:0.43, G:0.21, T:0.32
Consensus pattern (22 bp):
GGTTTCCCCCTGCCGCTATTCC
Found at i:1307612 original size:23 final size:23
Alignment explanation
Indices: 1307582--1307628 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1307572 CGTTGGTTTG
1307582 CCCCTGCCGCTATTCCGGTTTCC
1 CCCCTGCCGCTATTCCGGTTTCC
1307605 CCCCTGCCGCTATTCCGGTTTCC
1 CCCCTGCCGCTATTCCGGTTTCC
1307628 C
1 C
1307629 TGTTAGCCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.04, C:0.49, G:0.17, T:0.30
Consensus pattern (23 bp):
CCCCTGCCGCTATTCCGGTTTCC
Found at i:1310844 original size:23 final size:23
Alignment explanation
Indices: 1310787--1310835 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
1310777 AAGATATAAA
1310787 TATAAAATTTAAATTATTTTTATT
1 TATAAAATTTAAATTA-TTTTATT
1310811 TATAAAATTTAAATTATTTT-TT
1 TATAAAATTTAAATTATTTTATT
1310833 TAT
1 TAT
1310836 CATCATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.20
23 4 0.16
24 16 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATAAAATTTAAATTATTTTATT
Done.