Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold34
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: 1758877
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
File 9 of 12
Found at i:1250670 original size:17 final size:16
Alignment explanation
Indices: 1250639--1250672 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1250629 TTTTTATGTA
*
1250639 AATATATAAATAATAT
1 AATATATAAAAAATAT
1250655 AATATATTAAAAAATAT
1 AATATA-TAAAAAATAT
1250672 A
1 A
1250673 TGATATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATATAAAAAATAT
Found at i:1250795 original size:94 final size:97
Alignment explanation
Indices: 1250653--1250895 Score: 273
Period size: 94 Copynumber: 2.5 Consensus size: 97
1250643 TATAAATAAT
* * * *
1250653 ATAATATATTAA-AAAATATATGATATGTTATAAATAAAATTATACTAACAATTTCCACTTTTTC
1 ATAA-ATATTAATATAATATATAATATATTATAAATAAAATTATACTAACAATTTCC-CTTTTTA
*
1250717 ATATAATAATATGATATATT-AAT-AT-AT-TAGA
64 ATATAATAA-ATAATATATTAAATAATGATATAGA
* * * * * *
1250748 AT-AATTTTAATATAATATGTAATATATTATAAATGAAACTATTCTAACAAATTTTCCTTTTTAA
1 ATAAATATTAATATAATATATAATATATTATAAATAAAATTATACTAAC-AATTTCCCTTTTTAA
**
1250812 TATAATAAATAATATATTAAAATAATGATATATT
65 TATAATAAATAATATATT-AAATAATGATATAGA
*
1250846 ATAAATATTAATATAGTATATAATATATTATAAATAAAATTATACTAACA
1 ATAAATATTAATATAATATATAATATATTATAAATAAAATTATACTAACA
1250896 TTTTTTTCTT
Statistics
Matches: 121, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
93 15 0.12
94 46 0.38
95 11 0.09
96 2 0.02
97 2 0.02
98 5 0.04
99 40 0.33
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (97 bp):
ATAAATATTAATATAATATATAATATATTATAAATAAAATTATACTAACAATTTCCCTTTTTAAT
ATAATAAATAATATATTAAATAATGATATAGA
Found at i:1250907 original size:99 final size:95
Alignment explanation
Indices: 1250652--1250908 Score: 268
Period size: 99 Copynumber: 2.7 Consensus size: 95
1250642 ATATAAATAA
* * * **
1250652 TATAATATATTAA-AAAATATATGATATGTTATAAATAAAATTATACTAACAATTTCCACTTTTT
1 TATAA-ATATTAATATAATATATAATATATTATAAATAAAATTATACTAACAATTTTTACTTTTT
* *
1250716 CATATAATAATATGATATATTAATATATTAG
65 AATATAATAATATAATATATTAATATATTAG
* * * * * * * *
1250747 AAT-AATTTTAATATAATATGTAATATATTATAAATGAAACTATTCTAACAAATTTTCCTTTTTA
1 TATAAATATTAATATAATATATAATATATTATAAATAAAATTATACTAACAATTTTTACTTTTTA
*
1250811 ATATAATAA-ATAATATATTAAAATAATGATATAT
66 ATATAATAATATAATATATT--AAT-AT-AT-TAG
* * *
1250845 TATAAATATTAATATAGTATATAATATATTATAAATAAAATTATACTAACATTTTTTTCTTTTT
1 TATAAATATTAATATAATATATAATATATTATAAATAAAATTATACTAACAATTTTTACTTTTT
1250909 TGATGTAAAT
Statistics
Matches: 129, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
93 15 0.12
94 50 0.39
95 5 0.04
96 2 0.02
97 2 0.02
98 4 0.03
99 51 0.40
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (95 bp):
TATAAATATTAATATAATATATAATATATTATAAATAAAATTATACTAACAATTTTTACTTTTTA
ATATAATAATATAATATATTAATATATTAG
Found at i:1255299 original size:20 final size:19
Alignment explanation
Indices: 1255272--1255332 Score: 86
Period size: 20 Copynumber: 3.1 Consensus size: 19
1255262 ACCGATATAA
1255272 ATAGTAAATATATCGATAC
1 ATAGTAAATATATCGATAC
1255291 ATAAGTAAATATATCGATAC
1 AT-AGTAAATATATCGATAC
*
1255311 ATAGCTGAAATGTATCGATAC
1 ATAG-T-AAATATATCGATAC
1255332 A
1 A
1255333 AAACCATCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
19 4 0.11
20 20 0.53
21 14 0.37
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (19 bp):
ATAGTAAATATATCGATAC
Found at i:1262641 original size:13 final size:13
Alignment explanation
Indices: 1262623--1262679 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1262613 CATAAGGTGT
1262623 TGTATCGATACAA
1 TGTATCGATACAA
1262636 TGTATCGATACATAA
1 TGTATCGATAC--AA
1262651 GTGTTATATCGATACAA
1 -TG---TATCGATACAA
1262668 TGTATCGATACA
1 TGTATCGATACA
1262680 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
15 2 0.05
16 4 0.11
17 2 0.05
19 9 0.24
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1262661 original size:32 final size:32
Alignment explanation
Indices: 1262603--1262701 Score: 162
Period size: 32 Copynumber: 3.1 Consensus size: 32
1262593 TTCAACGATT
*
1262603 TGTATCCATACATAAGGTGTTGTATCGATACAA
1 TGTATCGATACATAA-GTGTTGTATCGATACAA
*
1262636 TGTATCGATACATAAGTGTTATATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1262668 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1262700 TG
1 TG
1262702 CAAGCTACTG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 48 0.77
33 14 0.23
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1262662 original size:19 final size:18
Alignment explanation
Indices: 1262605--1262698 Score: 64
Period size: 19 Copynumber: 5.6 Consensus size: 18
1262595 CAACGATTTG
*
1262605 TATCCATACATAAGGTGTT
1 TATCGATACATAA-GTGTT
1262624 GTATCGATAC--AA-TG--
1 -TATCGATACATAAGTGTT
1262638 TATCGATACATAAGTGTT
1 TATCGATACATAAGTGTT
1262656 ATATCGATAC--AA-TG--
1 -TATCGATACATAAGTGTT
*
1262670 TATCGATACATAAGTTTT
1 TATCGATACATAAGTGTT
1262688 GTATCGATACA
1 -TATCGATACA
1262699 ATGCAAGCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
13 18 0.30
15 4 0.07
16 7 0.12
17 2 0.03
18 2 0.03
19 19 0.32
20 8 0.13
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (18 bp):
TATCGATACATAAGTGTT
Found at i:1262759 original size:13 final size:13
Alignment explanation
Indices: 1262741--1262765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1262731 ATTACTCAAA
1262741 TGTATCGATACAT
1 TGTATCGATACAT
1262754 TGTATCGATACA
1 TGTATCGATACA
1262766 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1262869 original size:52 final size:52
Alignment explanation
Indices: 1262774--1262903 Score: 233
Period size: 52 Copynumber: 2.5 Consensus size: 52
1262764 CACTGATCTT
*
1262774 TGTATCGATACATGGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACAT-GCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1262827 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1262879 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1262904 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 62 0.83
53 13 0.17
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1269587 original size:12 final size:12
Alignment explanation
Indices: 1269570--1269605 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1269560 CACAAACAAA
*
1269570 AGTAAAAAAAAT
1 AGTAAAAAAAAG
1269582 AGTAAAAAAAAAG
1 AGT-AAAAAAAAG
1269595 AGTAAAAAAAA
1 AGTAAAAAAAA
1269606 AAGTGCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (12 bp):
AGTAAAAAAAAG
Found at i:1269608 original size:14 final size:13
Alignment explanation
Indices: 1269573--1269606 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1269563 AAACAAAAGT
*
1269573 AAAAAAAATAGTA
1 AAAAAAAAGAGTA
1269586 AAAAAAAAGAGTA
1 AAAAAAAAGAGTA
1269599 AAAAAAAA
1 AAAAAAAA
1269607 AGTGCAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAAAAAAGAGTA
Found at i:1270980 original size:32 final size:30
Alignment explanation
Indices: 1270910--1270994 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 30
1270900 ATACCTTTTT
*
1270910 AAAGTCCACGACTCAGTGGAAATCTCTTCTC
1 AAAGTCCACGACTCAGTGG-CATCTCTTCTC
* *
1270941 AAAGTCCACGACTTAGTGGCATCCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCAT-CTCTTC-TC
*
1270973 AAAGTCCACGACTCATTGGCAT
1 AAAGTCCACGACTCAGTGGCAT
1270995 TTGTCGTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
30 2 0.04
31 23 0.49
32 22 0.47
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTCTTCTC
Found at i:1274135 original size:52 final size:52
Alignment explanation
Indices: 1274057--1274183 Score: 254
Period size: 52 Copynumber: 2.4 Consensus size: 52
1274047 TGAAATATGA
1274057 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1274109 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1274161 AAATTTGCCTGCATGTATCGATA
1 AAATTTGCCTGCATGTATCGATA
1274184 TAATGTATTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:1274265 original size:19 final size:18
Alignment explanation
Indices: 1274241--1274338 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1274231 TAGCTTAAAT
1274241 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1274260 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1274273 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1274292 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1274305 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
*
1274325 TGTGTCGATACAAA
1 TGTATCGATACAAA
1274339 TCGTTAAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.37
20 12 0.18
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1274278 original size:13 final size:13
Alignment explanation
Indices: 1274260--1274316 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1274250 ACAAAACTTA
1274260 TGTATCGATACAT
1 TGTATCGATACAT
1274273 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1274291 ATGTATCGATACAT
1 -TGTATCGATACAT
1274305 TGTATCGATACA
1 TGTATCGATACA
1274317 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1274280 original size:32 final size:32
Alignment explanation
Indices: 1274239--1274336 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
1274229 AGTAGCTTAA
*
1274239 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
1274271 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
1274303 ATTGTATCGATACAACACTTTATGTGTCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
1274336 A
1 A
1274337 AATCGTTAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 49 0.78
33 14 0.22
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:1274655 original size:30 final size:31
Alignment explanation
Indices: 1274621--1274887 Score: 105
Period size: 34 Copynumber: 8.1 Consensus size: 31
1274611 AGTGTCTACA
* *
1274621 GCATTTTGTC-TCAAAGTCCACGACTCAGTG
1 GCATTTTGTCTTCAAAGCCCACAACTCAGTG
* *
1274651 GCATTTTTTCTTCAAAGCCCACAACTCCGTG
1 GCATTTTGTCTTCAAAGCCCACAACTCAGTG
* * * *
1274682 GCACCTTTTCCTTTTTAAAGCCCACAACTCCGTG
1 GCA--TTTT-GTCTTCAAAGCCCACAACTCAGTG
* *
1274716 GCACCTTTT-TCTTTTTAAAGCCCACAACTCCGTG
1 GCA--TTTTGTC--TTCAAAGCCCACAACTCAGTG
* ** * *
1274750 GCATCTTGTTCCTTTTAAGTCCACAACTCCGTG
1 GCATTTTG-T-CTTCAAAGCCCACAACTCAGTG
*
1274783 GCACCTTTT-TCTTTTTAAAGCCCACAACTTC-GTG
1 GCA--TTTTGTC--TTCAAAGCCCACAAC-TCAGTG
* * *
1274817 GTACCTTTT-TCTTTTTAAAGCCCACAACTCCGTG
1 G--CATTTTGTC--TTCAAAGCCCACAACTCAGTG
* *
1274851 GCACCTTTT-TCTTTTCAAAGCCCACCACTCCGTG
1 GCA--TTTTGTC--TTCAAAGCCCACAACTCAGTG
1274885 GCA
1 GCA
1274888 CCTTTTCTTT
Statistics
Matches: 200, Mismatches: 18, Indels: 34
0.79 0.07 0.13
Matches are distributed among these distances:
30 9 0.05
31 20 0.10
32 6 0.03
33 29 0.14
34 129 0.64
35 6 0.03
36 1 0.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (31 bp):
GCATTTTGTCTTCAAAGCCCACAACTCAGTG
Found at i:1274707 original size:34 final size:34
Alignment explanation
Indices: 1274664--1275677 Score: 1057
Period size: 34 Copynumber: 30.3 Consensus size: 34
1274654 TTTTTTCTTC
1274664 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
*
1274698 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
*
1274732 AAAGCCCACAACTCCGTGGCATCTTGTTCC-TTTT
1 AAAGCCCACAACTCCGTGGCACCTT-TTCCTTTTT
* *
1274766 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* * *
1274799 AAAGCCCACAACTTCGTGGTACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* *
1274833 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
*
1274867 AAAGCCCACCACTCCGTGGCACCTTTT-CTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* * *
1274900 GAAGTCCACAACCCCGTGGCACCTTGTTCC-TTTT
1 AAAGCCCACAACTCCGTGGCACCTT-TTCCTTTTT
* * *
1274934 -AAGTCCACAACTCCGTGGTACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* *
1274967 AAAGCCCACAACTTCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* *
1275001 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
*
1275035 AAAGCCCACCACTCCGTGGCACCTTTT-CTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* *
1275068 AAAGTCCACAACCCCGTGGCACCTTGTTCC-TTTT
1 AAAGCCCACAACTCCGTGGCACCTT-TTCCTTTTT
* *
1275102 -AAGTCCACAACTCCGTGGCACC--TT-CTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
*
1275132 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-C-TTTTCCTTTTT
* *
1275168 AAAGTCCACAACCCCGTGGCACCTTGTTCC-TTTT
1 AAAGCCCACAACTCCGTGGCACCTT-TTCCTTTTT
* *
1275202 -AAGTCCACAACTCCGTGGCACC--TT-CTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* *
1275232 AAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-C-TTTTCCTTTTT
* *
1275268 AAAGTCCACAAC-CTCGTGGCACTTTGTTCC-TTTT
1 AAAGCCCACAACTC-CGTGGCACCTT-TTCCTTTTT
* * *
1275302 -AAGTCCACGACTCCGTGGCACC--TTCC-TTTC
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
** * * *
1275332 AAAGTTCGCGACTCCGTGGCACC--TT-CTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
*
1275363 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-C-TTTTCCTTTTT
** * * *
1275399 AAAGTTCACAACTCCATGGCATCTTGTTTC-TTTT
1 AAAGCCCACAACTCCGTGGCACCTT-TTCCTTTTT
* * *
1275433 -AAGTCCACAACTCTGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
*
1275466 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* * *
1275500 AAAGCCCACAACTACGTGGCACCTTTTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* *
1275534 AAAGCCCACCACTCCGTAGCACCTTTT-CTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* **
1275567 -AAGTCCACAACTTTGTGGCACTCTTTTTCC-TTTT
1 AAAGCCCACAACTCCGTGGCAC-C-TTTTCCTTTTT
* *
1275601 AAAGTCCACAACTCCGTGGCACCTGTTCC-TTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
* * * * *
1275634 -AAGTCCACAACTTCGTGGCATCTTTCACCCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTT-TCCTTTTT
1275668 AAAGCCCACA
1 AAAGCCCACA
1275678 CAAGTCGGTG
Statistics
Matches: 848, Mismatches: 88, Indels: 87
0.83 0.09 0.09
Matches are distributed among these distances:
29 2 0.00
30 18 0.02
31 83 0.10
32 51 0.06
33 206 0.24
34 367 0.43
35 52 0.06
36 69 0.08
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACCTTTTCCTTTTT
Found at i:1274787 original size:67 final size:67
Alignment explanation
Indices: 1274634--1275677 Score: 1079
Period size: 67 Copynumber: 15.6 Consensus size: 67
1274624 TTTTGTCTCA
* * * *
1274634 AAGTCCACGACTCAGTGGCA--TTTTT-TCTTCAAAGCCCACAACTCCGTGGCACCTT-TTCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCC-T
1274695 TTT
65 TTT
* *
1274698 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCATCTTGTTCCT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
1274763 TTT
65 TTT
* * * *
1274766 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTTCGTGGTACCTTTTTCTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTT
1274831 TT
66 TT
* * * *
1274833 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACCACTCCGTGGCACCTT-TTCTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
1274897 TTT
65 TTT
* * * * * * *
1274900 GAAGTCCACAACCCCGTGGCACCTTGTTCCTTTT-AAGTCCACAACTCCGTGGTACCTTTTTCTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
1274964 TTT
65 TTT
* * *
1274967 AAAGCCCACAACTTCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTT-TTTCT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
1275031 TTT
65 TTT
* * * *
1275034 CAAAGCCCACCACTCCGTGGCACC-TTTTCTTTTTAAAGTCCACAACCCCGTGGCACCTTGTTCC
1 --AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCC
1275098 TTTT
64 TTTT
* *
1275102 AAGTCCACAACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTGTT-CC
1275164 TTTT
64 TTTT
* * * * *
1275168 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTT-AAGTCCACAACTCCGTGGCACCTTCTT--T
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
**
1275230 TCA
65 TTT
* * * * *
1275233 AAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAAC-CTCGTGGCACTTTGTTC
1 AAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTTTAAAGCCCACAACTC-CGTGGCACCTTGTTC
1275297 CTTTT
63 CTTTT
* * * ** * * *
1275302 AAGTCCACGACTCCGTGGCACC---TTCCTTTCAAAGTTCGCGACTCCGTGGCACCTTCTT--TT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTT
**
1275362 CA
66 TT
* * ** * * *
1275364 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTTCACAACTCCATGGCATCTTGTTTC
1 AAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCC
1275429 TTTT
64 TTTT
* * *
1275433 AAGTCCACAACTCTGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTT
1275498 TT
66 TT
* * * * * *
1275500 AAAGCCCACAACTACGTGGCACCTTTTTCTTTTCAAAGCCCACCACTCCGTAGCACCTT-TTCTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
1275564 TTT
65 TTT
** * *
1275567 AAGTCCACAACTTTGTGGCACTCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACC-TGTTCCT
1 AAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
1275631 TTT
65 TTT
* * ** *
1275634 AAGTCCACAACTTCGTGGCATCTTTCACCCTTTTAAAGCCCACA
1 AAGTCCACAACTCCGTGGCACCTTT-TTCTTTTTAAAGCCCACA
1275678 CAAGTCGGTG
Statistics
Matches: 833, Mismatches: 113, Indels: 64
0.82 0.11 0.06
Matches are distributed among these distances:
62 21 0.03
63 1 0.00
64 71 0.09
65 32 0.04
66 79 0.09
67 360 0.43
68 198 0.24
69 65 0.08
70 6 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (67 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTT
TT
Found at i:1274972 original size:100 final size:100
Alignment explanation
Indices: 1274664--1275677 Score: 1082
Period size: 100 Copynumber: 10.1 Consensus size: 100
1274654 TTTTTTCTTC
* *
1274664 AAAGCCCACAACTCCGTGGCACC-TTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCC-TTTTAAAGTCCACAACTCCGTGGCACC-TTTTCC
* * *
1274728 TTTTAAAGCCCACAACTCCGTGGCATCTTGTTCCTTTT
64 TTTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* * * * * *
1274766 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTTCGTGGTACCTTTTTCTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACC-TTTTCCT
*
1274830 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTC
65 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* * * *
1274867 AAAGCCCACCACTCCGTGGCACC-TTTTCTTTTTGAAGTCCACAACCCCGTGGCACCTTGTTCCT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTT-TTCCT
* *
1274931 TTTAAGTCCACAACTCCGTGGTACCTTTTTCTTTTT
65 TTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* * * *
1274967 AAAGCCCACAACTTCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTCCTT
*
1275032 TTCAAAGCCCACCACTCCGTGGCACC-TTTTCTTTTT
66 TT--AAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* * *
1275068 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTT-AAGTCCACAACTCCGTGGCACC--TT-CTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTCCTT
*
1275129 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
66 TT--AAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* * *
1275168 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTT-AAGTCCACAACTCCGTGGCACC--TT-CTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTCCTT
* *
1275229 TTCAAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTT
66 TT--AAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* *
1275268 AAAGTCCACAAC-CTCGTGGCA-CTTTGTTCCTTTT-AAGTCCACGACTCCGTGGCACC--TTCC
1 AAAGCCCACAACTC-CGTGGCACCTTT-TTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTCC
* ** * * *
1275328 TTTCAAAGTTCGCGACTCCGTGGCACC---TTCTTTTC
64 TTT-TAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* * * *
1275363 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTTCACAACTCCATGGCATCTTGTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAAGTCCACAACTCCGTGGCACCTT-TTC
* *
1275428 CTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTT
63 CTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* * * *
1275466 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTACGTGGCACCTTTTTCTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTCCTT
* *
1275531 TTCAAAGCCCACCACTCCGTAGCACC-TTTTCTTTTT
66 TT--AAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* ** *
1275567 -AAGTCCACAACTTTGTGGCACTCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTGTTCCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTCCT
* * * ** *
1275631 TTTAAGTCCACAACTTCGTGGCATCTTTCACCCTTTT
65 TTTAAGCCCACAACTCCGTGGCACCTTT-TTCTTTTT
1275668 AAAGCCCACA
1 AAAGCCCACA
1275678 CAAGTCGGTG
Statistics
Matches: 796, Mismatches: 86, Indels: 60
0.85 0.09 0.06
Matches are distributed among these distances:
95 22 0.03
96 5 0.01
97 37 0.05
98 21 0.03
99 26 0.03
100 297 0.37
101 283 0.36
102 76 0.10
103 29 0.04
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (100 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTCCTT
TTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
Found at i:1275703 original size:31 final size:31
Alignment explanation
Indices: 1275668--1275853 Score: 237
Period size: 32 Copynumber: 5.9 Consensus size: 31
1275658 TCACCCTTTT
1275668 AAAGCCCACACAAGTCGGTGGCAACCCCCCC
1 AAAGCCCACACAAGTCGGTGGCAACCCCCCC
*
1275699 AAAGCCCACACAAGTTGGTGGCAACCCCCTCC
1 AAAGCCCACACAAGTCGGTGGCAACCCCC-CC
* * *
1275731 AAAGCTCACACAAGTCGGTGGTAACCCCCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCCCCC
* * *
1275762 AAAGCCCACACAAGTTGGTGGCAATCCCCTCT
1 AAAGCCCACACAAGTCGGTGGCAA-CCCCCCC
* * * *
1275794 AAAGCCCACACAAGTTGGTGGCAACCATTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACC--CCCCC
1275827 AAAGCCCACACAAGTCGGTGGCAACCC
1 AAAGCCCACACAAGTCGGTGGCAACCC
1275854 TTCGAAGCCC
Statistics
Matches: 137, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
31 52 0.38
32 56 0.41
33 29 0.21
ACGTcount: A:0.30, C:0.37, G:0.19, T:0.14
Consensus pattern (31 bp):
AAAGCCCACACAAGTCGGTGGCAACCCCCCC
Found at i:1275741 original size:32 final size:32
Alignment explanation
Indices: 1275668--1275853 Score: 259
Period size: 31 Copynumber: 5.8 Consensus size: 32
1275658 TCACCCTTTT
1275668 AAAGCCCACACAAGTCGGTGGCAACCCCC-CC
1 AAAGCCCACACAAGTCGGTGGCAACCCCCTCC
*
1275699 AAAGCCCACACAAGTTGGTGGCAACCCCCTCC
1 AAAGCCCACACAAGTCGGTGGCAACCCCCTCC
* *
1275731 AAAGCTCACACAAGTCGGTGGTAACCCCCT-C
1 AAAGCCCACACAAGTCGGTGGCAACCCCCTCC
* * *
1275762 AAAGCCCACACAAGTTGGTGGCAATCCCCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCCCTCC
* ** *
1275794 AAAGCCCACACAAGTTGGTGGCAACCATTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACC-CCCTCC
1275827 AAAGCCCACACAAGTCGGTGGCAACCC
1 AAAGCCCACACAAGTCGGTGGCAACCC
1275854 TTCGAAGCCC
Statistics
Matches: 138, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
31 55 0.40
32 54 0.39
33 29 0.21
ACGTcount: A:0.30, C:0.37, G:0.19, T:0.14
Consensus pattern (32 bp):
AAAGCCCACACAAGTCGGTGGCAACCCCCTCC
Found at i:1275742 original size:63 final size:63
Alignment explanation
Indices: 1275668--1275853 Score: 264
Period size: 63 Copynumber: 2.9 Consensus size: 63
1275658 TCACCCTTTT
1275668 AAAGCCCACACAAGTCGGTGGCAACCCCCCCAAAGCCCACACAAGTTGGTGGCAACCCCCTCC
1 AAAGCCCACACAAGTCGGTGGCAACCCCCCCAAAGCCCACACAAGTTGGTGGCAACCCCCTCC
* * * * *
1275731 AAAGCTCACACAAGTCGGTGGTAACCCCCTCAAAGCCCACACAAGTTGGTGGCAATCCCCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCCCCCAAAGCCCACACAAGTTGGTGGCAACCCCCTCC
* * * * *
1275794 AAAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCC
1 AAAGCCCACACAAGTCGGTGGCAACC--CCCCCAAAGCCCACACAAGTTGGTGGCAACCC
1275854 TTCGAAGCCC
Statistics
Matches: 107, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 81 0.76
65 26 0.24
ACGTcount: A:0.30, C:0.37, G:0.19, T:0.14
Consensus pattern (63 bp):
AAAGCCCACACAAGTCGGTGGCAACCCCCCCAAAGCCCACACAAGTTGGTGGCAACCCCCTCC
Found at i:1275969 original size:49 final size:49
Alignment explanation
Indices: 1275862--1276580 Score: 672
Period size: 43 Copynumber: 15.0 Consensus size: 49
1275852 CCTTCGAAGC
* *
1275862 CCAATATCGCTGGCCTTGAATTAGCACATTGG---CA-C--CTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
1275905 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
* * *
1275954 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
* * *
1276003 CCAATGTAGCTGGCCTTGAATCAGCACATTGG---CA-C--CTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
* *
1276046 CCAATATAGCTGGCCTTGAATCAGCATATTGGCA-AATTTTCCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCA---T-CATCTTTAAGT
* * * * * * * *
1276098 TCAATGTAGTTGGCCTTGAATCAGCACATTGACATCATTTTTTTCACCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCA------TCATCTTTAAGT
*
1276153 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
* * * *
1276202 CCAATGTAGCTGGCCTTGAATTAGCACATTGG---CA-C--CTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
1276245 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
* * *
1276294 CCAATGTAGCTGGCCTTGAATCAGCACATTGG---CA-C--CTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
* * * * *
1276337 CTAATATCGCTGGCCATGAATTAGCATATTGGCACCCTCATCTTTTAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATC-TTTAAGT
* *
1276387 CCAATGTCGCTGGCCTTGAATCAGCACATTGG---CA-C--CTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
** *
1276430 CCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC---ATCATCTTTAAGT
* **
1276482 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC--CATCATCTTTAAGT
* * * * *
1276534 CCAATGTCGCTGGTCTTGAATCAGCACATTAGCACCTTCATCTTTAA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAA
1276581 CATTCCTAAG
Statistics
Matches: 565, Mismatches: 67, Indels: 82
0.79 0.09 0.11
Matches are distributed among these distances:
43 174 0.31
44 1 0.00
45 4 0.01
46 11 0.02
47 4 0.01
49 171 0.30
50 35 0.06
51 1 0.00
52 119 0.21
53 2 0.00
55 39 0.07
56 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGT
Found at i:1276042 original size:92 final size:92
Alignment explanation
Indices: 1275862--1276580 Score: 811
Period size: 92 Copynumber: 7.5 Consensus size: 92
1275852 CCTTCGAAGC
* * * *
1275862 CCAATATCGCTGGCCTTGAATTAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
*
1275921 TGAATCAGCATATTGGCACCATCATCTTTAAGT
66 TGAATCAGCACATTGG---CA-C--CTTTAAGT
* *
1275954 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
1276019 TGAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
* ** * *
1276046 CCAATATAGCTGGCCTTGAATCAGCATATTGGCAAATTTTCCATCTTTAAGTTCAATGTAGTTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGC--ACCTT-CATCTTTAAGTCCAATGTAGCTGG
*
1276111 CCTTGAATCAGCACATTGACATCATTTTTTTCACCTTTAAGT
63 CCTTGAATCAGCACATTG------------GCACCTTTAAGT
1276153 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
*
1276218 TGAATTAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
*
1276245 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
1276310 TGAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
* * * * * *
1276337 CTAATATCGCTGGCCATGAATTAGCATATTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAATGTAGCTGGCC
1276402 TTGAATCAGCACATTGGCACCTTTAAGT
65 TTGAATCAGCACATTGGCACCTTTAAGT
** * *
1276430 CCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGTCCAATATCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATGTAGCTGG
* *
1276495 CCTTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAGT
63 CCTTGAATCAGCACATT---G-----G-CACCTTTAAGT
* * * *
1276534 CCAATGTCGCTGGTCTTGAATCAGCACATTAGCACCTTCATCTTTAA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAA
1276581 CATTCCTAAG
Statistics
Matches: 550, Mismatches: 43, Indels: 59
0.84 0.07 0.09
Matches are distributed among these distances:
92 211 0.38
93 79 0.14
94 4 0.01
95 75 0.14
96 6 0.01
98 38 0.07
101 10 0.02
102 1 0.00
103 1 0.00
104 79 0.14
105 3 0.01
107 43 0.08
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (92 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
TGAATCAGCACATTGGCACCTTTAAGT
Found at i:1276500 original size:52 final size:52
Alignment explanation
Indices: 1276422--1276559 Score: 240
Period size: 52 Copynumber: 2.7 Consensus size: 52
1276412 ACATTGGCAC
*
1276422 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
*
1276474 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
* *
1276526 CTTTAAGTCCAATGTCGCTGGTCTTGAATCAGCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
1276560 CATTAGCACC
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 82 1.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
Found at i:1277463 original size:13 final size:13
Alignment explanation
Indices: 1277445--1277577 Score: 158
Period size: 13 Copynumber: 9.3 Consensus size: 13
1277435 CATAAAGTGT
1277445 TGTATCGATACAA
1 TGTATCGATACAA
1277458 TGTATCGATACATAA
1 TGTATCGATAC--AA
1277473 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1277490 TGTATCGATACAA
1 TGTATCGATACAA
1277503 TGTATCGATACAA
1 TGTATCGATACAA
1277516 TGTATCGATACATAA
1 TGTATCGATAC--AA
1277531 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1277548 TGTATCGATACAA
1 TGTATCGATACAA
1277561 TGTATCGATACAA
1 TGTATCGATACAA
1277574 TGTA
1 TGTA
1277578 AGCTACTGCC
Statistics
Matches: 108, Mismatches: 0, Indels: 24
0.82 0.00 0.18
Matches are distributed among these distances:
13 78 0.72
15 4 0.04
17 4 0.04
19 22 0.20
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1277480 original size:32 final size:32
Alignment explanation
Indices: 1277425--1277559 Score: 210
Period size: 32 Copynumber: 4.4 Consensus size: 32
1277415 TTCAACGATT
*
1277425 TGTATCCATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1277458 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1277490 TGTATCGATAC--AA----TGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1277516 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1277548 TGTATCGATACA
1 TGTATCGATACA
1277560 ATGTATCGAT
Statistics
Matches: 95, Mismatches: 1, Indels: 13
0.87 0.01 0.12
Matches are distributed among these distances:
26 24 0.25
28 2 0.02
30 2 0.02
32 55 0.58
33 12 0.13
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1277535 original size:58 final size:58
Alignment explanation
Indices: 1277445--1277577 Score: 266
Period size: 58 Copynumber: 2.3 Consensus size: 58
1277435 CATAAAGTGT
1277445 TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
1 TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
1277503 TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
1 TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
1277561 TGTATCGATACAATGTA
1 TGTATCGATACAATGTA
1277578 AGCTACTGCC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 75 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (58 bp):
TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
Found at i:1277539 original size:45 final size:45
Alignment explanation
Indices: 1277425--1277572 Score: 182
Period size: 45 Copynumber: 3.3 Consensus size: 45
1277415 TTCAACGATT
*
1277425 TGTATCCATACATAAAGTGTTGTATCGATACAATGTATCGATACATAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAATGTATCGATAC--AA
1277473 GTGTTGTATCGATAC--AA----TGTATCGATACAATGTATCGATACAA
1 ----TGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
1277516 TGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
1277561 TGTATCGATACA
1 TGTATCGATACA
1277573 ATGTAAGCTA
Statistics
Matches: 89, Mismatches: 1, Indels: 19
0.82 0.01 0.17
Matches are distributed among these distances:
39 11 0.12
41 2 0.02
43 2 0.02
45 62 0.70
49 2 0.02
52 10 0.11
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (45 bp):
TGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACAA
Found at i:1277633 original size:13 final size:13
Alignment explanation
Indices: 1277615--1277639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1277605 ATTACTCAAA
1277615 TGTATCGATACAT
1 TGTATCGATACAT
1277628 TGTATCGATACA
1 TGTATCGATACA
1277640 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1277740 original size:52 final size:51
Alignment explanation
Indices: 1277628--1277829 Score: 323
Period size: 52 Copynumber: 3.9 Consensus size: 51
1277618 ATCGATACAT
***
1277628 TGTATCGATACACTGATCTTTGTATCGATACATGGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATAAATGTATCGATACAT-GCAGGCAAATTTGCCCAGA
1277681 TGTATCGATACACTATAAGATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATAA-ATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
1277733 TGTATCGATACACTATAAAATGTATCGATACATGCAAGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-AAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1277785 TGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTAT-AAATGTATCGATACATGCAGGCAAATTT
1277830 TCATATTTCG
Statistics
Matches: 141, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
52 112 0.79
53 29 0.21
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (51 bp):
TGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1281994 original size:21 final size:21
Alignment explanation
Indices: 1281970--1282014 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1281960 AAGCTCATAG
1281970 AAGACTAAAAAATAAAAATAA
1 AAGACTAAAAAATAAAAATAA
* * **
1281991 AAGAGTAATAAATTCAAATAA
1 AAGACTAAAAAATAAAAATAA
1282012 AAG
1 AAG
1282015 TAAACTCCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (21 bp):
AAGACTAAAAAATAAAAATAA
Found at i:1282364 original size:2 final size:2
Alignment explanation
Indices: 1282357--1282386 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1282347 TTTCATTTCA
*
1282357 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1282387 GTAAACATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1282469 original size:14 final size:13
Alignment explanation
Indices: 1282426--1282495 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
1282416 CATTTTTTTG
*
1282426 TCAAAATCAACT-
1 TCAAAGTCAACTA
* *
1282438 TCAAAAATCAACAA
1 TC-AAAGTCAACTA
1282452 TCAAAGTCAACTA
1 TCAAAGTCAACTA
* *
1282465 GTCAAGGTCAATTA
1 -TCAAAGTCAACTA
* *
1282479 TGAAAGTCAACAA
1 TCAAAGTCAACTA
1282492 TCAA
1 TCAA
1282496 TGATTAACCA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
12 2 0.04
13 30 0.67
14 13 0.29
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.21
Consensus pattern (13 bp):
TCAAAGTCAACTA
Found at i:1285635 original size:12 final size:13
Alignment explanation
Indices: 1285607--1285639 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
1285597 GAATCCGGAC
1285607 TTAAAAAGTACCAA
1 TTAAAAAGTA-CAA
1285621 TTAAAAAGT-CAA
1 TTAAAAAGTACAA
1285633 TTAAAAA
1 TTAAAAA
1285640 CTCGAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
14 9 0.47
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (13 bp):
TTAAAAAGTACAA
Found at i:1286457 original size:86 final size:86
Alignment explanation
Indices: 1286312--1286484 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
1286302 TTGTTGTCAA
1286312 TCTGGTCAAGTGAAATTGGTTAGCACTTCAGTTCTTAAACAATTATATCATTTGTTTGCATCTCA
1 TCTGGTCAAGTGAAATTGGTTAGCACTTCAGTTCTTAAACAATTATATCATTTGTTTGCATCTCA
1286377 AATTGAAGAGACCATTGAATT
66 AATTGAAGAGACCATTGAATT
1286398 TCTGGTCAAGTGAAATTGGTTAGCACTTCAGTTCTTAAACAATTATATCATTTGTTTGCATCTCA
1 TCTGGTCAAGTGAAATTGGTTAGCACTTCAGTTCTTAAACAATTATATCATTTGTTTGCATCTCA
1286463 AATTGAAGAGACCATTGAATT
66 AATTGAAGAGACCATTGAATT
1286484 T
1 T
1286485 TGGAAGAACA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (86 bp):
TCTGGTCAAGTGAAATTGGTTAGCACTTCAGTTCTTAAACAATTATATCATTTGTTTGCATCTCA
AATTGAAGAGACCATTGAATT
Found at i:1287499 original size:23 final size:22
Alignment explanation
Indices: 1287454--1287507 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
1287444 CAAATATAAA
1287454 ATTATTGTATTTTTTTTCAAATT
1 ATTATT-TATTTTTTTTCAAATT
*
1287477 -TTATTTATATTTTTTTCTTAATT
1 ATTATTTAT-TTTTTTTC-AAATT
1287500 ATT-TTTAT
1 ATTATTTAT
1287508 CATGAATACC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.11
22 13 0.48
23 9 0.33
24 2 0.07
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTATTTATTTTTTTTCAAATT
Found at i:1290927 original size:51 final size:50
Alignment explanation
Indices: 1290870--1291015 Score: 168
Period size: 50 Copynumber: 2.9 Consensus size: 50
1290860 TTTTAACTAG
*
1290870 ATGTATCGATACATTGAAAAATGTACAGATATATCTGGGTAAAAAGACAAA
1 ATGTATCGATACATTGAAAAATGTAC-GATACATCTGGGTAAAAAGACAAA
* * * * * *
1290921 ATGTATCGATACATTCATACATGTATTGATACATCTGAGT-AAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTA-CGATACATCTGGGTAAAAAGACAAA
* * *
1290971 ATGTATTGATACATCGAAAAATGTATCGATACATTTGGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTA-CGATACATCTGGGTAAAAA
1291016 TGTGACTTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
50 41 0.53
51 37 0.47
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATGTACGATACATCTGGGTAAAAAGACAAA
Found at i:1296760 original size:16 final size:16
Alignment explanation
Indices: 1296739--1296769 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1296729 TATCCAATAC
*
1296739 TCAAAATTAAATCAGA
1 TCAAAACTAAATCAGA
1296755 TCAAAACTAAATCAG
1 TCAAAACTAAATCAG
1296770 TTGGATGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.23
Consensus pattern (16 bp):
TCAAAACTAAATCAGA
Found at i:1302901 original size:32 final size:32
Alignment explanation
Indices: 1302849--1302922 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
1302839 GCAGTAGCTT
*
1302849 TGTAGCGATACATTGCATCGATACAACACTTA
1 TGTATCGATACATTGCATCGATACAACACTTA
* *
1302881 TGTATTGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGCATCGATACAACACTTA
1302913 TGTATCGATA
1 TGTATCGATA
1302923 TAGTTACTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGCATCGATACAACACTTA
Found at i:1302918 original size:19 final size:19
Alignment explanation
Indices: 1302865--1302922 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1302855 GATACATTGC
1302865 ATCGATACAACACTTATGT
1 ATCGATACAACACTTATGT
*
1302884 ATTGAT---ACA--T-TGT
1 ATCGATACAACACTTATGT
1302897 ATCGATACAACACTTATGT
1 ATCGATACAACACTTATGT
1302916 ATCGATA
1 ATCGATA
1302923 TAGTTACTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
13 8 0.26
14 1 0.03
16 6 0.19
18 1 0.03
19 15 0.48
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (19 bp):
ATCGATACAACACTTATGT
Found at i:1303415 original size:19 final size:19
Alignment explanation
Indices: 1303371--1303426 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1303361 CTACCAGTTT
**
1303371 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
1303391 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1303410 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1303427 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1303429 original size:13 final size:13
Alignment explanation
Indices: 1303411--1303437 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1303401 TACAATGAAC
1303411 ATGTATCGATACA
1 ATGTATCGATACA
1303424 ATGTATCGATACA
1 ATGTATCGATACA
1303437 A
1 A
1303438 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1303448 original size:20 final size:20
Alignment explanation
Indices: 1303423--1303502 Score: 106
Period size: 20 Copynumber: 3.7 Consensus size: 20
1303413 GTATCGATAC
1303423 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
1303443 AATGTATCGATACAAAGCACAAT
1 AATGTATCGATACAAAG--C-AT
1303466 GAACATGTATCGATACAAAGCAT
1 --A-ATGTATCGATACAAAGCAT
1303489 AATGTATCGATACA
1 AATGTATCGATACA
1303503 TCTGAGTGTG
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
20 30 0.56
21 1 0.02
22 1 0.02
23 4 0.07
24 1 0.02
25 1 0.02
26 16 0.30
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACAAAGCAT
Found at i:1304083 original size:29 final size:29
Alignment explanation
Indices: 1304037--1304097 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
1304027 AAGGCTCTCG
*
1304037 TTAAAAAATTTCTCCCCCTTGATAATTGT
1 TTAAAAAATTTCTCCCCCTTGATAATCGT
*
1304066 TTAAAAGATTTTCTCCCCCTTGATAATCGT
1 TTAAAA-AATTTCTCCCCCTTGATAATCGT
1304096 TT
1 TT
1304098 TTTAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (29 bp):
TTAAAAAATTTCTCCCCCTTGATAATCGT
Found at i:1305998 original size:13 final size:13
Alignment explanation
Indices: 1305977--1306016 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1305967 ATAGTAACCC
1305977 ATGTATCGATACA
1 ATGTATCGATACA
*
1305990 ATTTATCGATACA
1 ATGTATCGATACA
1306003 ATGTATCGATACA
1 ATGTATCGATACA
1306016 A
1 A
1306017 AGAATAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1312201 original size:13 final size:13
Alignment explanation
Indices: 1312183--1312286 Score: 88
Period size: 13 Copynumber: 8.9 Consensus size: 13
1312173 CAATTCATCA
1312183 TGTATCGATACAT
1 TGTATCGATACAT
1312196 TGTATCGATACA-
1 TGTATCGATACAT
* *
1312208 -AT-TC-AT-C-G
1 TGTATCGATACAT
1312216 TGTATCGATACAT
1 TGTATCGATACAT
1312229 TGTATCGATACAT
1 TGTATCGATACAT
1312242 TGTATCGATACA-
1 TGTATCGATACAT
* *
1312254 -AT-TC-AT-C-G
1 TGTATCGATACAT
1312262 TGTATCGATACAT
1 TGTATCGATACAT
1312275 TGTATCGATACA
1 TGTATCGATACA
1312287 ATATGCCATG
Statistics
Matches: 73, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
8 2 0.03
9 6 0.08
10 8 0.11
11 6 0.08
12 2 0.03
13 49 0.67
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1312210 original size:33 final size:33
Alignment explanation
Indices: 1312163--1312240 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
1312153 TTTGAAGCAA
*
1312163 TGTAGCGATACAATTCATCATGTATCGATACAT
1 TGTATCGATACAATTCATCATGTATCGATACAT
*
1312196 TGTATCGATACAATTCATCGTGTATCGATACAT
1 TGTATCGATACAATTCATCATGTATCGATACAT
1312229 TGTATCGATACA
1 TGTATCGATACA
1312241 TTGTATCGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATTCATCATGTATCGATACAT
Found at i:1312250 original size:46 final size:46
Alignment explanation
Indices: 1312183--1312286 Score: 208
Period size: 46 Copynumber: 2.3 Consensus size: 46
1312173 CAATTCATCA
1312183 TGTATCGATACATTGTATCGATACAATTCATCGTGTATCGATACAT
1 TGTATCGATACATTGTATCGATACAATTCATCGTGTATCGATACAT
1312229 TGTATCGATACATTGTATCGATACAATTCATCGTGTATCGATACAT
1 TGTATCGATACATTGTATCGATACAATTCATCGTGTATCGATACAT
1312275 TGTATCGATACA
1 TGTATCGATACA
1312287 ATATGCCATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (46 bp):
TGTATCGATACATTGTATCGATACAATTCATCGTGTATCGATACAT
Found at i:1312299 original size:33 final size:32
Alignment explanation
Indices: 1312229--1312306 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 32
1312219 ATCGATACAT
*
1312229 TGTATCGATACATTGTATCGATACAATTCATCG
1 TGTATCGATACATTGTATCGATACAATTCA-CA
1312262 TGTATCGATACATTGTATCGATACAATATGC-CA
1 TGTATCGATACATTGTATCGATACAAT-T-CACA
1312295 TGTATCGATACA
1 TGTATCGATACA
1312307 AACAGTGGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 40 0.95
34 1 0.02
35 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAATTCACA
Found at i:1312380 original size:19 final size:19
Alignment explanation
Indices: 1312336--1312391 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1312326 CTGCCAGTTT
* **
1312336 CATGTAACGATACAATTGTG
1 CATGTATCGATACAA-TGAA
1312356 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1312375 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1312392 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1312394 original size:13 final size:13
Alignment explanation
Indices: 1312376--1312402 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1312366 TACAATGAAC
1312376 ATGTATCGATACA
1 ATGTATCGATACA
1312389 ATGTATCGATACA
1 ATGTATCGATACA
1312402 A
1 A
1312403 CGCGTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1320117 original size:23 final size:23
Alignment explanation
Indices: 1320090--1320135 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1320080 TTTCTTTTTA
*
1320090 TATGTTCAAATATTAATTTTAAT
1 TATGTTCAAATATTAAGTTTAAT
* *
1320113 TATGTTTAAGTATTAAGTTTAAT
1 TATGTTCAAATATTAAGTTTAAT
1320136 GTCAAATAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (23 bp):
TATGTTCAAATATTAAGTTTAAT
Found at i:1321361 original size:153 final size:153
Alignment explanation
Indices: 1321083--1321393 Score: 622
Period size: 153 Copynumber: 2.0 Consensus size: 153
1321073 AAATAAACTC
1321083 TAAATAATCACTTCTAGGGTAAATTAAAAACCTTAAGCTACAGCACACCACAATTAATGACCGCA
1 TAAATAATCACTTCTAGGGTAAATTAAAAACCTTAAGCTACAGCACACCACAATTAATGACCGCA
1321148 ATAATGATAGTAAAGAATAGAACTGAGTCAGAACATGATATCTATCCATTTTTTTATACAAATCT
66 ATAATGATAGTAAAGAATAGAACTGAGTCAGAACATGATATCTATCCATTTTTTTATACAAATCT
1321213 CACCTTAAGGTTCCCAGCAACAT
131 CACCTTAAGGTTCCCAGCAACAT
1321236 TAAATAATCACTTCTAGGGTAAATTAAAAACCTTAAGCTACAGCACACCACAATTAATGACCGCA
1 TAAATAATCACTTCTAGGGTAAATTAAAAACCTTAAGCTACAGCACACCACAATTAATGACCGCA
1321301 ATAATGATAGTAAAGAATAGAACTGAGTCAGAACATGATATCTATCCATTTTTTTATACAAATCT
66 ATAATGATAGTAAAGAATAGAACTGAGTCAGAACATGATATCTATCCATTTTTTTATACAAATCT
1321366 CACCTTAAGGTTCCCAGCAACAT
131 CACCTTAAGGTTCCCAGCAACAT
1321389 TAAAT
1 TAAAT
1321394 GTGACGGCAG
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 158 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (153 bp):
TAAATAATCACTTCTAGGGTAAATTAAAAACCTTAAGCTACAGCACACCACAATTAATGACCGCA
ATAATGATAGTAAAGAATAGAACTGAGTCAGAACATGATATCTATCCATTTTTTTATACAAATCT
CACCTTAAGGTTCCCAGCAACAT
Found at i:1324430 original size:2 final size:2
Alignment explanation
Indices: 1324425--1324451 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1324415 CTCCACCACC
1324425 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1324452 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1325089 original size:42 final size:42
Alignment explanation
Indices: 1325041--1325149 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
1325031 TTAAATACTT
*
1325041 TAATTTATTTTA-TTATTACAAATATGAGTTTTATTTTTTATG
1 TAATTTATATTATTTA-TACAAATATGAGTTTTATTTTTTATG
*
1325083 TAATTTATATTATTTATACATATATGAGTTTTATTTTTTATG
1 TAATTTATATTATTTATACAAATATGAGTTTTATTTTTTATG
*
1325125 TAATTTATATTATTTATACATATAT
1 TAATTTATATTATTTATACAAATAT
1325150 TATATAATAA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
42 61 0.95
43 3 0.05
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.59
Consensus pattern (42 bp):
TAATTTATATTATTTATACAAATATGAGTTTTATTTTTTATG
Found at i:1325093 original size:18 final size:18
Alignment explanation
Indices: 1325072--1325141 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1325062 ATATGAGTTT
1325072 TATTTTTTATGTAATTTA
1 TATTTTTTATGTAATTTA
*
1325090 TATTATTTATACATATATGAGTTT-
1 TATT-TTT-T--ATGTA--A-TTTA
1325114 TATTTTTTATGTAATTTA
1 TATTTTTTATGTAATTTA
*
1325132 TATTATTTAT
1 TATTTTTTAT
1325142 ACATATATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
17 3 0.07
18 14 0.34
19 3 0.07
20 5 0.12
22 5 0.12
23 3 0.07
24 5 0.12
25 3 0.07
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (18 bp):
TATTTTTTATGTAATTTA
Found at i:1325095 original size:21 final size:21
Alignment explanation
Indices: 1325071--1325139 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1325061 AATATGAGTT
1325071 TTATTTTTTATGTAATTTATA
1 TTATTTTTTATGTAATTTATA
* ** * *
1325092 TTA-TTTATACAT-ATATGAGTT
1 TTATTTTTTATGTAAT-TTA-TA
1325113 TTATTTTTTATGTAATTTATA
1 TTATTTTTTATGTAATTTATA
1325134 TTATTT
1 TTATTT
1325140 ATACATATAT
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
19 2 0.06
20 8 0.24
21 14 0.41
22 8 0.24
23 2 0.06
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (21 bp):
TTATTTTTTATGTAATTTATA
Found at i:1328128 original size:13 final size:13
Alignment explanation
Indices: 1328110--1328134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1328100 ATAAACCCAA
1328110 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1328123 AAAAAATAAAAA
1 AAAAAATAAAAA
1328135 CCAATCTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:1328353 original size:28 final size:27
Alignment explanation
Indices: 1328300--1328357 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1328290 ATTGAATATA
1328300 ATATAAAAAATTAAAATATGACATAAAT
1 ATATAAAAAATTAAAATATGACAT-AAT
* *
1328328 ATATAAAAATTTTAAAATAT-ATATAAT
1 ATATAAAAA-ATTAAAATATGACATAAT
1328355 ATA
1 ATA
1328358 AATTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 6 0.22
28 12 0.44
29 9 0.33
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (27 bp):
ATATAAAAAATTAAAATATGACATAAT
Found at i:1328369 original size:24 final size:22
Alignment explanation
Indices: 1328326--1328371 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
1328316 TATGACATAA
1328326 ATATATAAAAATTTTAAAATAT
1 ATATATAAAAATTTTAAAATAT
*
1328348 ATATAATATAAATTATTAAAATAT
1 ATAT-ATAAAAATT-TTAAAATAT
1328372 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 8 0.38
24 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATAAAAATTTTAAAATAT
Found at i:1328372 original size:8 final size:8
Alignment explanation
Indices: 1328323--1328378 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
1328313 AAATATGACA
1328323 TAAATATAT
1 TAAA-ATAT
* *
1328332 AAAAATTT
1 TAAAATAT
1328340 TAAAATAT
1 TAAAATAT
*
1328348 ATATAATA-
1 -TAAAATAT
*
1328356 TAAATTAT
1 TAAAATAT
1328364 TAAAATAT
1 TAAAATAT
1328372 TAAAATA
1 TAAAATA
1328379 AAATACTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
7 5 0.14
8 23 0.62
9 9 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TAAAATAT
Found at i:1328378 original size:23 final size:22
Alignment explanation
Indices: 1328333--1328382 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
1328323 TAAATATATA
*
1328333 AAAATTTTAAAATATATATAAT
1 AAAATTTTAAAATATATAAAAT
1328355 ATAAATTATTAAAATAT-TAAAAT
1 A-AAATT-TTAAAATATATAAAAT
1328378 AAAAT
1 AAAAT
1328383 ACTTTATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 11 0.44
24 9 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTTTAAAATATATAAAAT
Found at i:1329507 original size:2 final size:2
Alignment explanation
Indices: 1329500--1329525 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1329490 AAATAAATTT
1329500 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
1329526 CATTTAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1330034 original size:16 final size:17
Alignment explanation
Indices: 1330008--1330039 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1329998 TATGTTTACT
1330008 ATTATAAAAATAAAATA
1 ATTATAAAAATAAAATA
1330025 ATTA-AAAAATAAAAT
1 ATTATAAAAATAAAAT
1330040 TTAATTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATTATAAAAATAAAATA
Found at i:1330197 original size:2 final size:2
Alignment explanation
Indices: 1330190--1330227 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1330180 CATCACCATC
1330190 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
1330228 CCACCAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1330897 original size:2 final size:2
Alignment explanation
Indices: 1330892--1330923 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1330882 TGTGTGTGTG
1330892 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
1330924 TGTAGCCGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1335184 original size:14 final size:14
Alignment explanation
Indices: 1335162--1335192 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1335152 TAAGTGGCTC
1335162 AACCCTATGAGGTT
1 AACCCTATGAGGTT
*
1335176 AACCTTATGAGGTT
1 AACCCTATGAGGTT
1335190 AAC
1 AAC
1335193 ACCAGTAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (14 bp):
AACCCTATGAGGTT
Found at i:1341102 original size:13 final size:13
Alignment explanation
Indices: 1341084--1341109 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1341074 CAATTTTTTG
1341084 TGTATCGATACAT
1 TGTATCGATACAT
1341097 TGTATCGATACAT
1 TGTATCGATACAT
1341110 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1341174 original size:21 final size:21
Alignment explanation
Indices: 1341148--1341223 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1341138 CTGCCAAGAA
1341148 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
1341169 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1341189 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1341210 ATGTATCGATACAT
1 ATGTATCGATACAT
1341224 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1341193 original size:20 final size:20
Alignment explanation
Indices: 1341168--1341241 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1341158 ACATCTTTTT
1341168 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
1341188 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
1341209 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
1341229 CATGTATCGATAC
1 CATGTATCGATAC
1341242 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:1341205 original size:41 final size:41
Alignment explanation
Indices: 1341148--1341241 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1341138 CTGCCAAGAA
1341148 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1341189 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1341230 ATGTATCGATAC
1 ATGTATCGATAC
1341242 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1341327 original size:21 final size:21
Alignment explanation
Indices: 1341301--1341341 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1341291 GTCAACCTTG
1341301 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1341322 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1341342 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1342057 original size:79 final size:79
Alignment explanation
Indices: 1341890--1342065 Score: 201
Period size: 79 Copynumber: 2.2 Consensus size: 79
1341880 GAGATAATAA
* * * ** * *
1341890 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGCTGGAGTATCCCCAATTATGAGAAATCAATGA
*
1341955 TTAGAAAAAAAAAT
66 TTAGAAAAAAAAAC
* *
1341969 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGCTGGAGTATCCCCAATTATGAGAAATCAATGA
* ** * *
1342033 TTTTGGGAATAAAGC
66 -TTAGAAAAAAAAAC
1342048 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1342066 GATTGTGGGA
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 1 0.01
79 79 0.99
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGCTGGAGTATCCCCAATTATGAGAAATCAATGA
TTAGAAAAAAAAAC
Found at i:1342065 original size:51 final size:51
Alignment explanation
Indices: 1341997--1342272 Score: 264
Period size: 52 Copynumber: 5.4 Consensus size: 51
1341987 TCGAAAATAA
* * * * * * *
1341997 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGGAAATAAAAC
* * ***
1342048 CGGGGTTGGAGTATCCCCGATTGTGGGAAAATTGGTGTTTCAAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGGAAATAAAAC
* * * * *
1342100 CGGGGTTGAAGTATCCCCGATTGTGGGAAAATTGGTGTTTCGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGGAAATAAAAC
* * * *
1342152 CGGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGT-GAGAAATTAGTGTTTTGGAAATAAAAC
* * * * * * **
1342204 CGGGGTTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGGAAATAAAAC
1342255 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1342273 TCGGAAATAA
Statistics
Matches: 189, Mismatches: 34, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
51 61 0.32
52 127 0.67
53 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGGAAATAAAAC
Found at i:1342113 original size:52 final size:52
Alignment explanation
Indices: 1342040--1342225 Score: 266
Period size: 52 Copynumber: 3.6 Consensus size: 52
1342030 ATATTTTGGG
* *
1342040 AATAAAGCCGGGGTTGGAGTATCCCCGATTGTGGGAAAATTGGTGTTTCAAA
1 AATAAAACCGGGGTTGAAGTATCCCCGATTGTGGGAAAATTGGTGTTTCAAA
*
1342092 AATAAAACCGGGGTTGAAGTATCCCCGATTGTGGGAAAATTGGTGTTTCGAA
1 AATAAAACCGGGGTTGAAGTATCCCCGATTGTGGGAAAATTGGTGTTTCAAA
* * * * * **
1342144 AATAAAACCGGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGC
1 AATAAAACCGGGGTTGAAGTATCCCCGATTGTGGGAAAATTGGTGTTTCAAA
1342196 AATAAAACCGGGGTTGGAA-TATCCCCGATT
1 AATAAAACCGGGGTT-GAAGTATCCCCGATT
1342226 ATGAAAAATC
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
52 118 0.98
53 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (52 bp):
AATAAAACCGGGGTTGAAGTATCCCCGATTGTGGGAAAATTGGTGTTTCAAA
Found at i:1342356 original size:55 final size:52
Alignment explanation
Indices: 1342287--1342413 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 52
1342277 AAATAACGGG
* *
1342287 GTTGGAGTATCCCCGATTGTGA-AGAAATTGGTGTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGA-AAATTAGTG---TTTTGAAAATAAAATCGGA
*
1342342 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
*
1342393 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1342414 GGGAATTGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
51 36 0.55
54 9 0.14
55 20 0.31
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:1342384 original size:134 final size:131
Alignment explanation
Indices: 1342152--1342406 Score: 325
Period size: 134 Copynumber: 1.9 Consensus size: 131
1342142 AAAATAAAAC
* *
1342152 CGGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAATA
1 CGGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAATA
* * * *
1342217 TCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCGGAAATA
66 TCCCCGATTATGAAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCCTCGGAAATA
1342282 A
131 A
* * * *
1342283 CGGGGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGG
1 CGGGATTGGAGTATCCCCGATTGTGGAA-AAATTAGTG---TTTTAGAAATAAAACCGGAGTTGG
* * * *
1342347 AGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCC
62 AATATCCCCGATTATGA-AAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCC
1342407 GATTGTGGGG
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
130 3 0.03
131 31 0.30
133 1 0.01
134 70 0.67
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (131 bp):
CGGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAATA
TCCCCGATTATGAAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCCTCGGAAATA
A
Found at i:1344802 original size:33 final size:33
Alignment explanation
Indices: 1344756--1344822 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1344746 AAAATTTCCA
* ***
1344756 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCAATACAAAGAAAAATGTATCGATAC
*
1344789 AATGTATCAATACACAGAAAAATGTATCGATAC
1 AATGTATCAATACAAAGAAAAATGTATCGATAC
1344822 A
1 A
1344823 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCAATACAAAGAAAAATGTATCGATAC
Found at i:1344882 original size:18 final size:18
Alignment explanation
Indices: 1344842--1344895 Score: 99
Period size: 18 Copynumber: 2.9 Consensus size: 18
1344832 CAGTAGCTAA
1344842 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1344861 TTATGTATCGATACAAAC
1 TTATGTATCGATACAAAC
1344879 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1344896 TTGTTGAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 19 0.54
19 16 0.46
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1346063 original size:59 final size:59
Alignment explanation
Indices: 1345754--1346911 Score: 1507
Period size: 59 Copynumber: 20.0 Consensus size: 59
1345744 GTGGGGTTTG
* *
1345754 AAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG-
1 AAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * **
1345811 --AGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----A
1 AAAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * * *
1345864 AAAGGTGTTCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GA
1 AAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * ** * *
1345920 AATGGGGTCCTACTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTCTGAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCT-TTAAAAGA
* * * * *
1345981 AAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
1346040 AAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
1346099 AAAGGCGTTCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
1346158 AAAGGGGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
1346217 AAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
** *
1346276 AAAGGCGTCCCGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTT-----A
1 AAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * **
1346331 AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-
1 AAAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* *
1346386 AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGA
* * * * *
1346447 AAAAGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
1346506 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGATTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* *
1346565 AAAGGTGTCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
1346624 AAAGGCGTCCCACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1346683 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
1346742 AAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACCTTGTGTGGGCTTT-AAAG-
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAA-CTTGTGTGGGCTTTAAAAGA
** *
1346800 AAAGGCGT-CCGCTCTTTGAGGACTGAAAATGCCACCAACCTGTGTGGGCTTT-----A
1 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * * * ** *
1346853 AAAGGTGTTCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 AAAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
1346912 GTGTCCTGCT
Statistics
Matches: 1001, Mismatches: 70, Indels: 57
0.89 0.06 0.05
Matches are distributed among these distances:
53 7 0.01
54 16 0.02
55 219 0.22
56 64 0.06
57 29 0.03
58 7 0.01
59 527 0.53
60 88 0.09
61 44 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (59 bp):
AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
Found at i:1346487 original size:466 final size:464
Alignment explanation
Indices: 1345754--1346910 Score: 1896
Period size: 466 Copynumber: 2.5 Consensus size: 464
1345744 GTGGGGTTTG
*
1345754 AAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGG
1 AAAGGCATCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
* * * *
1345814 TGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTTCTGCTC
65 CGTCCCGCTCTTTGAGGACT-GAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTC
* * * * *
1345879 TTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAATGGGGTCCTACTCTTTGGGGAC
129 TTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAA-GGTGTCCTGCTCTTTGAGGAC
* *
1345944 TGAAAGGTGCCACCAACTTGTGTGGGCTCTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAA
192 TGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAAA
1346009 GGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCC
257 GGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCC
* * *
1346074 ACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTTCCGCTCTTTGAGGACTGAAGGTGCCACCAAC
322 ACCAACTTGTGTGGGATTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCCACCAAC
* *
1346139 TTGTGTGGGCTTTAAAAGAAAAGGGGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGT
387 TTGTGTGGGCTTTAAAAGAAAAGGCGTCCCACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGT
1346204 GGGCTTTAAAAGA
452 GGGCTTTAAAAGA
1346217 AAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
1 AAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
1346282 GTCCCGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
66 GTCCCGCTCTTTGAGGACTG-AAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1346347 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
130 TTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
1346412 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAAAGG
194 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAAAGG
* *
1346477 TGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCAC
259 TGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCCAC
*
1346542 CAACTTGTGTGGGATTTAAAAGAAAAGGTGTCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTT
324 CAACTTGTGTGGGATTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTT
1346607 GTGTGGGCTTTAAAAGAAAAGGCGTCCCACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGG
389 GTGTGGGCTTTAAAAGAAAAGGCGTCCCACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGG
1346672 GCTTTAAAAGA
454 GCTTTAAAAGA
*
1346683 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
1 AAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
* ** *
1346748 ATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACCTTGTGTGGGCTTTAAAGAAAGGCGTCC-GC
66 GTCCCGCTCTTTGAGGACTGAAAATGCCACCAACC-TGTGTGGGCTTT--A-AAAGGTGTCCTGC
* * * *
1346812 TCTTTGAGGACTGAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTTCTGCTTTTTGAGGAC
127 TCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGAC
*
1346877 TGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAA
192 T-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA
1346911 GGTGTCCTGC
Statistics
Matches: 652, Mismatches: 30, Indels: 20
0.93 0.04 0.03
Matches are distributed among these distances:
462 27 0.04
463 25 0.04
464 3 0.00
465 13 0.02
466 377 0.58
467 175 0.27
468 23 0.04
469 9 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (464 bp):
AAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
GTCCCGCTCTTTGAGGACTGAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
TGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAA
AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAAAGGTG
CCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCCACCA
ACTTGTGTGGGATTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGT
GTGGGCTTTAAAAGAAAAGGCGTCCCACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGC
TTTAAAAGA
Found at i:1347931 original size:5 final size:5
Alignment explanation
Indices: 1347923--1347980 Score: 59
Period size: 5 Copynumber: 11.6 Consensus size: 5
1347913 TCTCTTTTTC
*
1347923 TTTGT TTTGTTT TTTGT TTTGT TTTGT TTT-T TTT-T TTTGCT TTTTT
1 TTTGT TTTG--T TTTGT TTTGT TTTGT TTTGT TTTGT TTTG-T TTTGT
1347969 TTTGT TTT-T TTT
1 TTTGT TTTGT TTT
1347981 TAAGAGAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
4 12 0.26
5 26 0.55
6 4 0.09
7 5 0.11
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (5 bp):
TTTGT
Found at i:1347940 original size:12 final size:11
Alignment explanation
Indices: 1347917--1347981 Score: 78
Period size: 11 Copynumber: 5.7 Consensus size: 11
1347907 CTTTTCTCTC
*
1347917 TTTTTCTTTGT
1 TTTTTTTTTGT
1347928 TTTGTTTTTTGT
1 TTT-TTTTTTGT
1347940 TTTGTTTTGTT-T
1 TTT-TTTT-TTGT
*
1347952 TTTTTTTTTGC
1 TTTTTTTTTGT
1347963 TTTTTTTTTGT
1 TTTTTTTTTGT
1347974 TTTTTTTT
1 TTTTTTTT
1347982 AAGAGAAGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
10 2 0.04
11 25 0.52
12 19 0.40
13 2 0.04
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:1347943 original size:17 final size:17
Alignment explanation
Indices: 1347923--1347980 Score: 75
Period size: 18 Copynumber: 3.5 Consensus size: 17
1347913 TCTCTTTTTC
1347923 TTTGTTTTGTTTTTTGT
1 TTTGTTTTGTTTTTTGT
*
1347940 TTTGTTTTGTTTTTTTTT
1 TTTGTTTTG-TTTTTTGT
*
1347958 TTTGCTTT-TTTTTTGT
1 TTTGTTTTGTTTTTTGT
1347974 TTT-TTTT
1 TTTGTTTT
1347981 TAAGAGAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.08
16 10 0.28
17 9 0.25
18 14 0.39
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (17 bp):
TTTGTTTTGTTTTTTGT
Found at i:1360500 original size:81 final size:79
Alignment explanation
Indices: 1360393--1360586 Score: 210
Period size: 79 Copynumber: 2.4 Consensus size: 79
1360383 TTAGAGTGTT
* * * * *
1360393 CCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGAAAAAAAAAA
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG--AAAAAAAA
*
1360457 ATCGGGATTGGAGTATC
63 ACCGGGATTGGAGTATC
* * * ** * *
1360474 CCCTCGAAAATAACGGGGTTGGAGTATCCACAATTATGAGAAATCAATATTTTGGGAATAAAGCC
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGAAAAAAAAACC
*
1360539 GGGGTTGGAGTATC
66 GGGATTGGAGTATC
* *
1360553 CCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1360587 GAAATAGCGA
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
79 49 0.52
80 1 0.01
81 44 0.47
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (79 bp):
CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGAAAAAAAAACC
GGGATTGGAGTATC
Found at i:1360600 original size:28 final size:28
Alignment explanation
Indices: 1360541--1360609 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
1360531 ATAAAGCCGG
** * *
1360541 GGTTGGAGTATCCCCTCGGAAGTAACGG
1 GGTTGGAGTATCCCCGAGGAAATAACGA
* *
1360569 GGTTGGAGTATCCCCGATGAAATAGCGA
1 GGTTGGAGTATCCCCGAGGAAATAACGA
1360597 GGTTGGAGTATCC
1 GGTTGGAGTATCC
1360610 TCGACTGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGAGGAAATAACGA
Found at i:1360662 original size:52 final size:51
Alignment explanation
Indices: 1360597--1360866 Score: 245
Period size: 52 Copynumber: 5.2 Consensus size: 51
1360587 GAAATAGCGA
* * *
1360597 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGGAAATAAAATCGG
* ** ** * * *
1360649 AGTTGGAGTATCCTAGATTAAAGGAAAATTGGTGTTTCGAAAATAAAA-CAGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAATC-GG
* * * *
1360701 GGTTGGAGTATCCCCGATTGTGGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAATCGG
* * *
1360753 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAATCGG
* * *** * **
1360805 GGTTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAGGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGG
*
1360856 GGTTTGAGTAT
1 GGTTGGAGTAT
1360867 TCCCTCGGAA
Statistics
Matches: 182, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
51 33 0.18
52 138 0.76
53 11 0.06
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGG
Found at i:1360996 original size:51 final size:54
Alignment explanation
Indices: 1360885--1361008 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 54
1360875 AAATAACGGG
* * *
1360885 GTTGGAGTATCCCCGATTACGAAGAAATTGGTGTTTTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAGAAATTAGTG-TTTTTGAGAAATAAAATCGGA
1360940 GTTGGAGTATCCCCGATTATAG-A-AAATTAGTG-TTTTGA-AAATAAAATCGGA
1 GTTGGAGTATCCCCGATTA-AGAAGAAATTAGTGTTTTTGAGAAATAAAATCGGA
*
1360991 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
1361009 GTGGAGAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
51 30 0.47
52 5 0.08
54 8 0.12
55 20 0.31
56 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (54 bp):
GTTGGAGTATCCCCGATTAAGAAGAAATTAGTGTTTTTGAGAAATAAAATCGGA
Found at i:1363389 original size:33 final size:33
Alignment explanation
Indices: 1363343--1363409 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1363333 AAAATTTCCA
* ***
1363343 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCAATACAAAGAAAAATGTATCGATAC
*
1363376 AATGTATCAATACACAGAAAAATGTATCGATAC
1 AATGTATCAATACAAAGAAAAATGTATCGATAC
1363409 A
1 A
1363410 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCAATACAAAGAAAAATGTATCGATAC
Found at i:1363544 original size:21 final size:21
Alignment explanation
Indices: 1363520--1363576 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1363510 CATTTGTAGG
1363520 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1363541 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1363562 ATGTATCGATACATT
1 ATGTATCGATACATT
1363577 TGGATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1367628 original size:93 final size:92
Alignment explanation
Indices: 1367464--1367645 Score: 249
Period size: 93 Copynumber: 2.0 Consensus size: 92
1367454 TGCCATCGGT
* * * *
1367464 GATAATGGGGTTGGAGTATCCTCGAAGATGAAAATTTGATGTTTTCATAAATTGAATTTTAGTGT
1 GATAATGGGGTTGGAGTATCCTCAAAGATGAAAATTTGATGTTTTCATAAATCGAATTTTACTGC
*
1367529 AAAATCGTGATTAAAGTATCCCCTTAGA
66 AAAATCGGGATTAAAGTA-CCCCTTAGA
* * *
1367557 GATAGTGGGGTTGGATTATCC-CTAAAGTTGAAAATTTGATGTTTTCATAAATCGAATTTTACTG
1 GATAATGGGGTTGGAGTATCCTC-AAAGATGAAAATTTGATGTTTTCATAAATCGAATTTTACTG
* *
1367621 CAAAATCGGGGTTAGAGTACCCCTT
65 CAAAATCGGGATTAAAGTACCCCTT
1367646 TCGATATTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
92 7 0.09
93 71 0.91
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (92 bp):
GATAATGGGGTTGGAGTATCCTCAAAGATGAAAATTTGATGTTTTCATAAATCGAATTTTACTGC
AAAATCGGGATTAAAGTACCCCTTAGA
Found at i:1367985 original size:20 final size:20
Alignment explanation
Indices: 1367960--1367998 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1367950 CGATATAATT
*
1367960 AGTGAATGTATTGATACATA
1 AGTGAATATATTGATACATA
1367980 AGTGAATATATTGATACAT
1 AGTGAATATATTGATACAT
1367999 GTCTCAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (20 bp):
AGTGAATATATTGATACATA
Found at i:1373909 original size:112 final size:114
Alignment explanation
Indices: 1373710--1373944 Score: 339
Period size: 112 Copynumber: 2.1 Consensus size: 114
1373700 ATACAATTAA
* *
1373710 GTATCGATACTTGCTATCCAAAAAATCAAATTTTAGCTACTATCAAGGCCATGTATCGATACAAT
1 GTATCGATACTTGCTATCCAAAAAATCAAATTTTAGCTACTACCAAGGCCATGTATCAATACAAT
* * * * * *
1373775 CACACTAGGTATCGATATCACACCCTGGGTATTGATACCAAGTCTTCAT
66 CACACCAGGTATCAATACCACACCCTAGGTATCGATACCAAGCCTTCAT
* * * *
1373824 GTATCGATACTTGCTGTCC-AAAAATTAAATTTTAGCTACTGCCAAGG-CTTGTATCAATACAAT
1 GTATCGATACTTGCTATCCAAAAAATCAAATTTTAGCTACTACCAAGGCCATGTATCAATACAAT
1373887 CACACCAGGTATCAATACCACACCCTAGGTATCGATACCAAGCCTTCAT
66 CACACCAGGTATCAATACCACACCCTAGGTATCGATACCAAGCCTTCAT
*
1373936 GTATTGATA
1 GTATCGATA
1373945 TATTGCATGG
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
112 65 0.60
113 25 0.23
114 18 0.17
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (114 bp):
GTATCGATACTTGCTATCCAAAAAATCAAATTTTAGCTACTACCAAGGCCATGTATCAATACAAT
CACACCAGGTATCAATACCACACCCTAGGTATCGATACCAAGCCTTCAT
Found at i:1373918 original size:20 final size:21
Alignment explanation
Indices: 1373874--1373926 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1373864 GCCAAGGCTT
*
1373874 GTATCAATACAATCACACCAG
1 GTATCAATACCATCACACCAG
1373895 GTATCAATACCA-CAC-CCTAG
1 GTATCAATACCATCACACC-AG
*
1373915 GTATCGATACCA
1 GTATCAATACCA
1373927 AGCCTTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.55
21 11 0.38
ACGTcount: A:0.38, C:0.30, G:0.11, T:0.21
Consensus pattern (21 bp):
GTATCAATACCATCACACCAG
Found at i:1373968 original size:112 final size:111
Alignment explanation
Indices: 1373730--1373968 Score: 277
Period size: 112 Copynumber: 2.1 Consensus size: 111
1373720 TTGCTATCCA
* * * * * *
1373730 AAAAATCAAATTTTAGCTACTATCAAGGCCATGTATCGATACAATCACACTAGGTATCGATATCA
1 AAAATTCAAATTTTAGCTACTACCAAGGCCATGTATCAATACAATCACACCAGGTATCAATACCA
* * * *
1373795 CACCCTGGGTATTGATACCAAGTCTTCATGTATCGATACTTGCTGTCC
66 CACCCTAGGTATCGATACCAAGCCTTCATGTATCGATAATTGCTG--C
* *
1373843 AAAAATT-AAATTTTAGCTACTGCCAAGG-CTTGTATCAATACAATCACACCAGGTATCAATACC
1 -AAAATTCAAATTTTAGCTACTACCAAGGCCATGTATCAATACAATCACACCAGGTATCAATACC
*
1373906 ACACCCTAGGTATCGATACCAAGCCTTCATGTATTGATATATTGCATG-
65 ACACCCTAGGTATCGATACCAAGCCTTCATGTATCGATA-ATTGC-TGC
*
1373954 GAAATTCAATATTTT
1 AAAATTCAA-ATTTT
1373969 GGCAACGTAT
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
110 5 0.05
111 2 0.02
112 70 0.65
113 23 0.21
114 7 0.07
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (111 bp):
AAAATTCAAATTTTAGCTACTACCAAGGCCATGTATCAATACAATCACACCAGGTATCAATACCA
CACCCTAGGTATCGATACCAAGCCTTCATGTATCGATAATTGCTGC
Found at i:1375175 original size:12 final size:12
Alignment explanation
Indices: 1375158--1375188 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1375148 GCTCACATCA
*
1375158 AAACATTTTATC
1 AAACATTTTAAC
1375170 AAACATTTTAAC
1 AAACATTTTAAC
1375182 AAACATT
1 AAACATT
1375189 ATATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (12 bp):
AAACATTTTAAC
Found at i:1377199 original size:110 final size:107
Alignment explanation
Indices: 1377033--1377238 Score: 270
Period size: 110 Copynumber: 1.9 Consensus size: 107
1377023 AAATTGGCCC
* * * * *
1377033 AATATAATTAAATAAAATAAGCCTCAAATTAATTTAATATGCACGTGGGTCCTATTTTATTTAAT
1 AATATAATTAAATAAAATAAGCCTAAAATTAATTAAATAAGCACGTGGGACCTATTTTATCTAAT
* * * *
1377098 ATTTTTTATGAGGTTTAGCTTTAAATTAAATAATTTATGACCT
66 -TTTTTTATAAGATTGAACTTTAAATTAAATAATTTATGACCT
* *
1377141 AATAT-ATTCAAATAAAATAGGCCTAAAAAATTAATTAAATAAGCACGTGGGACTTATTTTATCT
1 AATATAATT-AAATAAAATAAGCCT--AAAATTAATTAAATAAGCACGTGGGACCTATTTTATCT
1377205 AATTTTTTTATAAGATTGAACTTTAAATTAAATA
63 AATTTTTTTATAAGATTGAACTTTAAATTAAATA
1377239 TTCAATGACC
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
107 3 0.04
108 19 0.23
109 27 0.32
110 35 0.42
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (107 bp):
AATATAATTAAATAAAATAAGCCTAAAATTAATTAAATAAGCACGTGGGACCTATTTTATCTAAT
TTTTTTATAAGATTGAACTTTAAATTAAATAATTTATGACCT
Found at i:1382452 original size:28 final size:29
Alignment explanation
Indices: 1382421--1382478 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
1382411 TACTCATGTG
1382421 TAAAA-ATTCTAATTAAAATTTT-TATATA
1 TAAAATATT-TAATTAAAATTTTATATATA
*
1382449 TAAAATATTTAATTAAGATTTTATATATA
1 TAAAATATTTAATTAAAATTTTATATATA
1382478 T
1 T
1382479 GTATACGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
TAAAATATTTAATTAAAATTTTATATATA
Found at i:1383096 original size:6 final size:6
Alignment explanation
Indices: 1383085--1383117 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1383075 CGCATGAATT
1383085 AAATAA AAAT-A AAATAAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAAT-AA AAATAA AAATAA AAA
1383118 ATCTCAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:1385513 original size:30 final size:30
Alignment explanation
Indices: 1385479--1385539 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
1385469 TAATATTATT
1385479 AAAAATTTACATAAAA-TATT-TATTTTTTAA
1 AAAAATTTA-A-AAAATTATTATATTTTTTAA
1385509 AAAAATTTAAAAAATTTATTATATTTTTTAA
1 AAAAATTTAAAAAA-TTATTATATTTTTTAA
1385540 TATTTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 4 0.14
29 1 0.04
30 13 0.46
31 10 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AAAAATTTAAAAAATTATTATATTTTTTAA
Found at i:1386138 original size:3 final size:3
Alignment explanation
Indices: 1386130--1386157 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1386120 AAGCAGAAAT
1386130 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1386158 CTTTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1392195 original size:112 final size:112
Alignment explanation
Indices: 1391998--1392221 Score: 448
Period size: 112 Copynumber: 2.0 Consensus size: 112
1391988 GCACCTGACC
1391998 GAATATTGAAAAATCAACATCCAAAGATAAGAAAATTTTGAAGCTGGGTTTTTTCACCCAATTTT
1 GAATATTGAAAAATCAACATCCAAAGATAAGAAAATTTTGAAGCTGGGTTTTTTCACCCAATTTT
1392063 CTGATTGGGATATATCTTAGCTGGATTCTGCTTGGTATCTCATCCTT
66 CTGATTGGGATATATCTTAGCTGGATTCTGCTTGGTATCTCATCCTT
1392110 GAATATTGAAAAATCAACATCCAAAGATAAGAAAATTTTGAAGCTGGGTTTTTTCACCCAATTTT
1 GAATATTGAAAAATCAACATCCAAAGATAAGAAAATTTTGAAGCTGGGTTTTTTCACCCAATTTT
1392175 CTGATTGGGATATATCTTAGCTGGATTCTGCTTGGTATCTCATCCTT
66 CTGATTGGGATATATCTTAGCTGGATTCTGCTTGGTATCTCATCCTT
1392222 TCTGTGTCGA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (112 bp):
GAATATTGAAAAATCAACATCCAAAGATAAGAAAATTTTGAAGCTGGGTTTTTTCACCCAATTTT
CTGATTGGGATATATCTTAGCTGGATTCTGCTTGGTATCTCATCCTT
Found at i:1401958 original size:2 final size:2
Alignment explanation
Indices: 1401951--1402000 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1401941 TGTTCAAAGA
1401951 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
1401993 AT AT AT AT
1 AT AT AT AT
1402001 TTCTGCAATT
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:1405917 original size:2 final size:2
Alignment explanation
Indices: 1405910--1405938 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1405900 AAAAATGAAA
1405910 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1405939 AAAAAGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1409536 original size:17 final size:17
Alignment explanation
Indices: 1409498--1409537 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1409488 TTAAAATAAA
*
1409498 TTAA-ATATATTCGTGT
1 TTAATATATATTCGTAT
*
1409514 TGAATATATATTCGTAT
1 TTAATATATATTCGTAT
1409531 TTAATAT
1 TTAATAT
1409538 TCACATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (17 bp):
TTAATATATATTCGTAT
Found at i:1415443 original size:79 final size:79
Alignment explanation
Indices: 1415305--1415547 Score: 285
Period size: 79 Copynumber: 3.1 Consensus size: 79
1415295 CTAAAGACTC
* * * *
1415305 TATTTCT-CATAAAATTCCCT-AAATGACCTTAATGCACATATCTCTATATAAAAACACTAATAT
1 TATTTCTCCA-AAAATTCTCTAAAATGACCTTAATGCACATGTCTCGATATAAAAATACTAATAT
1415368 GCTCTTAAGGACTTA
65 GCTCTTAAGGACTTA
* * * * * * *
1415383 AATTTTTCCAAAAATTTTCTAAAATGACCTTAATGTACATGTCTAGATATGAAAATACTAATGTG
1 TATTTCTCCAAAAATTCTCTAAAATGACCTTAATGCACATGTCTCGATATAAAAATACTAATATG
1415448 CTCTTGAA-GACTTA
66 CTCTT-AAGGACTTA
** * * * *
1415462 TATTTCTCGTAAAATTCTCTAAAATAACTTTAATGCACATGTCTCGATATAAAAATATTAACATG
1 TATTTCTCCAAAAATTCTCTAAAATGACCTTAATGCACATGTCTCGATATAAAAATACTAATATG
*
1415527 CTCCTAAGGACTTA
66 CTCTTAAGGACTTA
1415541 TATTTCT
1 TATTTCT
1415548 TATGAATTCA
Statistics
Matches: 136, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
78 15 0.11
79 119 0.88
80 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (79 bp):
TATTTCTCCAAAAATTCTCTAAAATGACCTTAATGCACATGTCTCGATATAAAAATACTAATATG
CTCTTAAGGACTTA
Found at i:1415593 original size:157 final size:156
Alignment explanation
Indices: 1415305--1415597 Score: 340
Period size: 158 Copynumber: 1.9 Consensus size: 156
1415295 CTAAAGACTC
* * *
1415305 TATTTCTCATAAAATTCCCTAAATGACCTTAATGCACATATCTCTATATAAAAACACTAATATGC
1 TATTTCTCATAAAATTCCCTAAATAACCTTAATGCACATATCTCGATATAAAAACACTAACATGC
* * * * * *
1415370 TCTTAAGGACTTAAATTTTTCCAAAAATTTTCTAAAATGACCTTAATGTACATGTCTAGATATGA
66 TCCTAAGGACTTAAATTTTT-CAAAAATTATCTAAAATAAACTTAATGTACATATATAGATATGA
1415435 AAATACTAATGTGCTCTTGAAGACTTA
130 AAATACTAATGTGCTCTTGAAGACTTA
* * * * * *
1415462 TATTTCTCGTAAAATTCTCTAAAATAACTTTAATGCACATGTCTCGATATAAAAATATTAACATG
1 TATTTCTCATAAAATTCCCT-AAATAACCTTAATGCACATATCTCGATATAAAAACACTAACATG
* ** * *
1415527 CTCCTAAGGACTTATATTTCTT-ATGAATTCAT-TAAAATAAACTTAATG-ACCATATATTGATG
65 CTCCTAAGGACTTAAATTT-TTCAAAAATT-ATCTAAAATAAACTTAATGTA-CATATATAGATA
1415589 TGAAAATAC
127 TGAAAATAC
1415598 CAACCTGGTC
Statistics
Matches: 112, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
156 1 0.01
157 54 0.48
158 55 0.49
159 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (156 bp):
TATTTCTCATAAAATTCCCTAAATAACCTTAATGCACATATCTCGATATAAAAACACTAACATGC
TCCTAAGGACTTAAATTTTTCAAAAATTATCTAAAATAAACTTAATGTACATATATAGATATGAA
AATACTAATGTGCTCTTGAAGACTTA
Found at i:1415989 original size:16 final size:16
Alignment explanation
Indices: 1415964--1415995 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1415954 ATACATTGGC
*
1415964 TTCAACATTTCAAATT
1 TTCAAAATTTCAAATT
1415980 TTCAAAATTTCAAATT
1 TTCAAAATTTCAAATT
1415996 CTAGAGTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (16 bp):
TTCAAAATTTCAAATT
Found at i:1416078 original size:21 final size:21
Alignment explanation
Indices: 1416052--1416099 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1416042 TAAATATATT
1416052 GATACAGTAGCCTAATGAATC
1 GATACAGTAGCCTAATGAATC
*
1416073 GATACAGTAGCTTAATGAATC
1 GATACAGTAGCCTAATGAATC
*
1416094 AATACA
1 GATACA
1416100 TAGGGTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (21 bp):
GATACAGTAGCCTAATGAATC
Found at i:1417474 original size:78 final size:78
Alignment explanation
Indices: 1417093--1417807 Score: 477
Period size: 79 Copynumber: 9.1 Consensus size: 78
1417083 TATTTTGGGG
* * * ** * * * * *
1417093 ATAAAAACGAGGTCGGAGTACTCCCTCAGAAATAACGGGGTTGGAGTATCACCAATGGT-ACAAA
1 ATAAAACCGGGGTTGGAGTA-TCCCTTGGAAATAATGGGGTTAGAGTATCCCCGATTGTGA-AAA
* *
1417157 ATCGATATTTTAGAC
64 ATCGATGTTTTAGAA
* * * ** * ** * *
1417172 ATAAAACTGGGGTTAGAGTGTCCTCTCAGAAATAACGGACTTGGAGTATTCCCGATTGTGAAAAA
1 ATAAAACCGGGGTTGGAGTATCC-CTTGGAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAA
**
1417237 TTAATGTTTTAGAA
65 TCGATGTTTTAGAA
* * * *
1417251 ATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTAGAGTATCCTCGATTGTAAAAAA
1 ATAAAACCGGGGTTGGAGTAT-CCCTTGGAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAA
*
1417316 TTGATGTTTTAGAA
65 TCGATGTTTTAGAA
* * * * * * *
1417330 ATAAAGCTGGGCTTAGAGTATCCCTTTGGAAATAATGAGGTTGGAGTATCTCCGATTGTGAAAAA
1 ATAAAACCGGGGTTGGAGTATCCC-TTGGAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAA
* * *
1417395 TCGGTATTTTAAAA
65 TCGATGTTTTAGAA
* * *
1417409 ATAAAACCGGGGTTGGACTATCTCCTTGGGAA-AATGGGGTTAGAGTATCCCCGATTGTGGAAAA
1 ATAAAACCGGGGTTGGAGTATC-CCTTGGAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAA
* *
1417473 TCGATGCTTTGGAA
65 TCGATGTTTTAGAA
* * * * *** * * * ** * *
1417487 TTAAAATCAGGGTTGGATTATCCCCTCAAAAATAATAGGGTTGGCGTATCTTCGGTTGTAAAAAA
1 ATAAAACCGGGGTTGGAGTAT-CCCTTGGAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAA
* * *
1417552 TTGGTG-TTTCGAAA
65 TCGATGTTTTAG-AA
* * * * * *
1417566 ATAAAA-CTGGGTTGGAGTATCCCTTCGGAAATAATAGGGTTGGAGTATCCTCGGTTGTAAAAAA
1 ATAAAACCGGGGTTGGAGTATCCCTT-GGAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAA
*
1417630 TCGGTGTTTT-GAAA
65 TCGATGTTTTAG-AA
*** * * * * * * * *
1417644 ATAAAACTAAGGTTGGAGTATCCCCTAGGAAATAACGAGATTGGAGTATCCTCGATTATGGAAAA
1 ATAAAACCGGGGTTGGAGTAT-CCCTTGGAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAA
1417709 TCGATGTTTTAGAA
65 TCGATGTTTTAGAA
* * * ** * * ** *
1417723 ATAAAGCCGGGTTTGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGACGGTGAAGAA
1 ATAAAACCGGGGTTGGAGTAT-CCCTTGGAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAA
*
1417788 TCGATGTTTTGGAA
65 TCGATGTTTTAGAA
1417802 ATAAAA
1 ATAAAA
1417808 ACATAAATGA
Statistics
Matches: 505, Mismatches: 118, Indels: 26
0.78 0.18 0.04
Matches are distributed among these distances:
77 4 0.01
78 130 0.26
79 361 0.71
80 10 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (78 bp):
ATAAAACCGGGGTTGGAGTATCCCTTGGAAATAATGGGGTTAGAGTATCCCCGATTGTGAAAAAT
CGATGTTTTAGAA
Found at i:1417548 original size:236 final size:236
Alignment explanation
Indices: 1417200--1417773 Score: 665
Period size: 236 Copynumber: 2.4 Consensus size: 236
1417190 TGTCCTCTCA
* * * ** *
1417200 GAAATAACG-GACTTGGAGTATTCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAACCGGGGT
1 GAAATAACGAGA-TTAGAGTATCCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAACCAGGGT
* *
1417264 TGGAGTATCCCCTCGAAAATAATGGGGTTAGAGTATCCTCGATTGTAAAAAATTGATGTTTTAG-
65 TGGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCTCGATTGTAAAAAATTGATG-TTTAGA
* * *
1417328 AAATAAAGCTGGGCTTAGAGTATCCCTTTGGAAATAAT-GAGGTTGGAGTAT-CTCCGATTGTGA
129 AAATAAAACTGGG-TTAGAGTATCCCTTCGGAAATAATAG-GGTTGGAGTATCCT-CGATTGTAA
** * *
1417391 AAAATCGGTATTTTAAAAATAAAACCGGGGTTGGACTATCTCCTTG
191 AAAATCGGTATTTTAAAAATAAAACCAAGGTTGGACTATCCCCTAG
* * * * * * * *
1417437 GGAA-AATGGGGTTAGAGTATCCCCGATTGTGGAAAATCGATGCTTTGGAATTAAAATCAGGGTT
1 GAAATAACGAGATTAGAGTATCCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAACCAGGGTT
* * * * * * *
1417501 GGATTATCCCCTCAAAAATAATAGGGTTGGCGTATCTTCGGTTGTAAAAAATTGGTGTTTCGAAA
66 GGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCTCGATTGTAAAAAATTGATGTTTAGAAA
* *
1417566 ATAAAACTGGGTTGGAGTATCCCTTCGGAAATAATAGGGTTGGAGTATCCTCGGTTGTAAAAAAT
131 ATAAAACTGGGTTAGAGTATCCCTTCGGAAATAATAGGGTTGGAGTATCCTCGATTGTAAAAAAT
* * * *
1417631 CGGTGTTTTGAAAATAAAACTAAGGTTGGAGTATCCCCTAG
196 CGGTATTTTAAAAATAAAACCAAGGTTGGACTATCCCCTAG
* * * *
1417672 GAAATAACGAGATTGGAGTATCCTCGATTATGGAAAATCGATGTTTTAGAAATAAAGCC-GGGTT
1 GAAATAACGAGATTAGAGTATCCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAACCAGGG-T
* * *
1417736 TGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCC
65 TGGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCC
1417774 CCGACGGTGA
Statistics
Matches: 277, Mismatches: 54, Indels: 13
0.81 0.16 0.04
Matches are distributed among these distances:
235 88 0.32
236 185 0.67
237 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (236 bp):
GAAATAACGAGATTAGAGTATCCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAACCAGGGTT
GGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCTCGATTGTAAAAAATTGATGTTTAGAAA
ATAAAACTGGGTTAGAGTATCCCTTCGGAAATAATAGGGTTGGAGTATCCTCGATTGTAAAAAAT
CGGTATTTTAAAAATAAAACCAAGGTTGGACTATCCCCTAG
Found at i:1417807 original size:158 final size:158
Alignment explanation
Indices: 1417093--1417807 Score: 617
Period size: 158 Copynumber: 4.5 Consensus size: 158
1417083 TATTTTGGGG
* * * * * * * *
1417093 ATAAAAACGAGGTCGGAGTA-CTCCCTCAGAAATAACGGGGTTGGAGTATCACCAATGGTACAAA
1 ATAAAACCGGGGTTGGAGTATC-CCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTGTAAAAA
* * * * * *
1417157 ATCGATATTTTAGACATAAAACTGGGGTTAGAGTGTCCTCTCAGAAATAACG-GACTTGGAGTAT
65 ATCGATGTTTTGGAAATAAAACTAGGGTTAGAGTATCCCCTCAGAAATAACGAGA-TTGGAGTA-
**
1417221 TCC-CGATTGTGAAAAATTAATGTTTTAGAA
128 TCCTCGATTGTGAAAAATCGATGTTTTAGAA
* *
1417251 ATAAAACCGGGGTTGGAGTATCCCCTC-GAAAATAATGGGGTTAGAGTATCCTCGATTGTAAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAG-AAATAATGGGGTTGGAGTATCCCCGATTGTAAAAA
* * * * ** * *
1417315 ATTGATGTTTTAGAAATAAAGCT-GGGCTTAGAGTATCCCTTTGGAAATAATGAGGTTGGAGTAT
65 ATCGATGTTTTGGAAATAAAACTAGGG-TTAGAGTATCCCCTCAGAAATAACGAGATTGGAGTAT
* * *
1417379 -CTCCGATTGTGAAAAATCGGTATTTTAAAA
129 CCT-CGATTGTGAAAAATCGATGTTTTAGAA
* * ** * * **
1417409 ATAAAACCGGGGTTGGACTATCTCCTTGGGAA-AATGGGGTTAGAGTATCCCCGATTGTGGAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTGTAAAAAA
* * * * * * * *
1417473 TCGATGCTTTGGAATTAAAA-TCAGGGTTGGATTATCCCCTCAAAAATAA-TAGGGTTGGCGTAT
66 TCGATGTTTTGGAAATAAAACT-AGGGTTAGAGTATCCCCTCAGAAATAACGA-GATTGGAGTAT
* * * * * *
1417536 CTTCGGTTGTAAAAAATTGGTG-TTTCGAAA
129 CCTCGATTGTGAAAAATCGATGTTTTAG-AA
* * * * * *
1417566 ATAAAA-CTGGGTTGGAGTATCCCTTCGGAAATAATAGGGTTGGAGTATCCTCGGTTGTAAAAAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTGTAAAAAA
* * * *
1417630 TCGGTGTTTTGAAAATAAAACTAAGGTTGGAGTATCCCCT-AGGAAATAACGAGATTGGAGTATC
66 TCGATGTTTTGGAAATAAAACTAGGGTTAGAGTATCCCCTCA-GAAATAACGAGATTGGAGTATC
* *
1417694 CTCGATTATGGAAAATCGATGTTTTAGAA
130 CTCGATTGTGAAAAATCGATGTTTTAGAA
* * * * ** * *
1417723 ATAAAGCCGGGTTTGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGACGGTGAAGAA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTGTAAAAAA
1417788 TCGATGTTTTGGAAATAAAA
66 TCGATGTTTTGGAAATAAAA
1417808 ACATAAATGA
Statistics
Matches: 440, Mismatches: 99, Indels: 36
0.77 0.17 0.06
Matches are distributed among these distances:
156 26 0.06
157 194 0.44
158 217 0.49
159 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (158 bp):
ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTGTAAAAAA
TCGATGTTTTGGAAATAAAACTAGGGTTAGAGTATCCCCTCAGAAATAACGAGATTGGAGTATCC
TCGATTGTGAAAAATCGATGTTTTAGAA
Found at i:1420451 original size:17 final size:17
Alignment explanation
Indices: 1420429--1420464 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1420419 CCATGCCTTT
1420429 CAACCTTTTTACCTAAA
1 CAACCTTTTTACCTAAA
1420446 CAACCTTTTTACCTAAA
1 CAACCTTTTTACCTAAA
1420463 CA
1 CA
1420465 TGCTTCGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (17 bp):
CAACCTTTTTACCTAAA
Found at i:1426628 original size:13 final size:13
Alignment explanation
Indices: 1426612--1426636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1426602 CATAATACTT
1426612 TGTATCGATACAA
1 TGTATCGATACAA
1426625 TGTATCGATACA
1 TGTATCGATACA
1426637 TGAAACCGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1426706 original size:13 final size:13
Alignment explanation
Indices: 1426688--1426712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1426678 CATGGCACAT
1426688 TGTATCGATACAA
1 TGTATCGATACAA
1426701 TGTATCGATACA
1 TGTATCGATACA
1426713 TAATAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1426710 original size:33 final size:33
Alignment explanation
Indices: 1426668--1426732 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1426658 TACCACTGTT
** *
1426668 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATAACAAATTGTATCGATACAA
*
1426701 TGTATCGATACATAATAAATTGTATCGATACA
1 TGTATCGATACATAACAAATTGTATCGATACA
1426733 TTGTCCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATAACAAATTGTATCGATACAA
Found at i:1428344 original size:15 final size:15
Alignment explanation
Indices: 1428324--1428358 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1428314 AACCATCAAA
1428324 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
1428339 GATGATGATGATAAT
1 GATGATGAAGATAAT
1428354 GATGA
1 GATGA
1428359 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:1429576 original size:9 final size:9
Alignment explanation
Indices: 1429562--1429589 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1429552 TGAAGGAAAC
1429562 GGTACCATT
1 GGTACCATT
1429571 GGTACCATT
1 GGTACCATT
1429580 GGTACCATT
1 GGTACCATT
1429589 G
1 G
1429590 AAGCATAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (9 bp):
GGTACCATT
Done.