Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold118
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: 1286304
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:1178142 original size:101 final size:101
Alignment explanation
Indices: 1177965--1178502 Score: 713
Period size: 101 Copynumber: 5.3 Consensus size: 101
1177955 ACGTTGGCAC
* *
1177965 AAGTCCAATATCGCTGACCTTGACTCAGCATATTGGCGCCTTTGTCATCTTTAAAACCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAAACCAATGTCG
*
1178030 CTGGCCATGAATCAGCACATTGGCATCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCATCTTCATCTTT
** * *
1178066 AAGTCCGGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATTTTTAAGACCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAAACCAATGTCG
1178131 CTGGCCTTGAATCAGCACATTGGCATCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCATCTTCATCTTT
** * *
1178167 AAGTCCGGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCAATGTCA
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAAACCAATGTCG
*
1178232 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCATCTTCATCTTT
* * ** **
1178268 AAGTCCAATATCGTTGGCCTTGAATTAGCATATTAACGCCTTCATCATCTTTAAAACCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAAACCAATGTCG
* *
1178333 CTGGCCTTGAATCAGCACATTGGCACCTTCATCCTT
66 CTGGCCTTGAATCAGCACATTGGCATCTTCATCTTT
* ** ** ** *
1178369 AAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACAT-TTCTAAGCCCAATGTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT-TAAAACCAATGTC
* ** * *
1178433 GCTAGCCTTGTCTCAGCACATTGGCA--TTCTTCTTC
65 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTT
* * * *
1178468 AAGTCTAATGTCGCTGGCCTTGAATTAGCACATTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1178503 TCATTCTTCG
Statistics
Matches: 394, Mismatches: 42, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
99 36 0.09
100 2 0.01
101 356 0.90
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (101 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAAACCAATGTCG
CTGGCCTTGAATCAGCACATTGGCATCTTCATCTTT
Found at i:1178218 original size:202 final size:201
Alignment explanation
Indices: 1177675--1178502 Score: 853
Period size: 202 Copynumber: 4.2 Consensus size: 201
1177665 TCCGTGGCAC
*
1177675 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACC-TTGTC---TTTAAGACCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATTTTTAAGACCAAT
* * * * * *
1177736 GTCACTAGCCTTGACTCAGCACATTGGCACCTTAACCATCTTTAAGACCAATGTCGTTGGCCTTG
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGTCCAATATCGCTGGCCTTG
* * * ** * *
1177801 AATCAG-----T---GCATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
128 AATCAGCATATTGGCGCCTTGTCATCTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGG
* *
1177858 CACCTTTACC
193 CACCTTCA-T
* * * * *
1177868 CTCTTGAGTCCAATATTGCTGGCCTTGAATCAGCGTATTGGCACCCTTCTCATCTTTTAAGACCA
1 CT-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT-TTTTAAGACCA
* *
1177933 ATGTCGCTGGCCTTGAATCAGCACGTTGG------CA-C---AAGTCCAATATCGCTGACCTTGA
64 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGA
* *
1177988 CTCAGCATATTGGCGCCTTTGTCATCTTTAAAACCAATGTCGCTGGCCATGAATCAGCACATTGG
129 ATCAGCATATTGGCGCC-TTGTCATCTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGG
*
1178053 CATCTTCAT
193 CACCTTCAT
** *
1178062 CTTTAAGTCCGGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATTTTTAAGACCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATTTTTAAGACCAAT
* **
1178127 GTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGGTATCGCTGGCCTTGAAT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
*
1178192 CAGCATATTGGCGCCTTCGTCATCTTTAAAACCAATGTCACTGGCCTTGAATCAGCACATTGGCA
131 CAGCATATTGGCGCCTT-GTCATCTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1178257 CCTTCAT
195 CCTTCAT
* * ** * ** * *
1178264 CTTTAAGTCCAATATCGTTGGCCTTGAATTAGCATATTAACGCCTTCATCATCTTTAAAACCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATTTTTAAGACCAAT
* *
1178329 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCCTTAAGTCCAATATCGTTGGCCTTGAAT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
** ** * * **
1178394 CAGCATATTGGCATCTT-TAACAT-TTCTAAGCCCAATGTTGCTAGCCTTGTCTCAGCACATTGG
131 CAGCATATTGGCGCCTTGT--CATCTT-TAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGG
*
1178457 CA--TTCTT
193 CACCTTCAT
* * * * *
1178464 CTTCAAGTCTAATGTCGCTGGCCTTGAATTAGCACATTG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1178503 TCATTCTTCG
Statistics
Matches: 534, Mismatches: 72, Indels: 51
0.81 0.11 0.08
Matches are distributed among these distances:
186 23 0.04
189 1 0.00
190 2 0.00
191 1 0.00
192 39 0.07
193 44 0.08
194 42 0.08
195 50 0.09
198 2 0.00
199 36 0.07
200 38 0.07
201 4 0.01
202 252 0.47
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (201 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATTTTTAAGACCAAT
GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
CAGCATATTGGCGCCTTGTCATCTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
CTTCAT
Found at i:1179244 original size:13 final size:13
Alignment explanation
Indices: 1179226--1179250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1179216 ACATAAGTGT
1179226 TGTATCGATACAA
1 TGTATCGATACAA
1179239 TGTATCGATACA
1 TGTATCGATACA
1179251 TAAGTTTTGT
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:1179255 original size:32 final size:31
Alignment explanation
Indices: 1179206--1179277 Score: 126
Period size: 32 Copynumber: 2.3 Consensus size: 31
1179196 ACAAACAGTA
1179206 AATGTATCGTACATAAGTGTTGTATCGATAC
1 AATGTATCGTACATAAGTGTTGTATCGATAC
*
1179237 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCG-TACATAAGTGTTGTATCGATAC
1179269 AATGTATCG
1 AATGTATCG
1179278 CAACTGTAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 9 0.23
32 30 0.77
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (31 bp):
AATGTATCGTACATAAGTGTTGTATCGATAC
Found at i:1179263 original size:19 final size:19
Alignment explanation
Indices: 1179185--1179269 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
1179175 ATTTCAACAA
*
1179185 TTTGTATCGATACAAACAGT
1 TTTGTATCGATACATA-AGT
**
1179205 AAATGTATCG-TACATAAGT
1 -TTTGTATCGATACATAAGT
*
1179224 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1179239 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1179256 TTTGTATCGATACA
1 TTTGTATCGATACA
1179270 ATGTATCGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
13 11 0.21
15 2 0.04
17 2 0.04
18 7 0.13
19 18 0.35
20 5 0.10
21 7 0.13
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1179605 original size:33 final size:33
Alignment explanation
Indices: 1179568--1179634 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1179558 TTCAACGATT
1179568 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1179601 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1179634 T
1 T
1179635 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1179606 original size:13 final size:13
Alignment explanation
Indices: 1179588--1179612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1179578 CATAAAATGT
1179588 TGTATCGATACAA
1 TGTATCGATACAA
1179601 TGTATCGATACA
1 TGTATCGATACA
1179613 TATTTTTTTG
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:1179693 original size:13 final size:13
Alignment explanation
Indices: 1179675--1179702 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1179665 ATTACTTAAA
1179675 TGTATCGATACAT
1 TGTATCGATACAT
1179688 TGTATCGATACAT
1 TGTATCGATACAT
1179701 TG
1 TG
1179703 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1179751 original size:51 final size:52
Alignment explanation
Indices: 1179708--1179831 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1179698 CATTGATCTT
1179708 TGTATCGATACATGCAGGCAAATTTG-CCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* *
1179759 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
1179811 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1179832 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 26 0.38
52 43 0.62
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:1182399 original size:20 final size:21
Alignment explanation
Indices: 1182366--1182407 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
1182356 TTGGGAAATT
1182366 TTACTCAGATGTATCGATACA
1 TTACTCAGATGTATCGATACA
1182387 TTACTCA-ATGTATCGATACA
1 TTACTCAGATGTATCGATACA
1182407 T
1 T
1182408 GCAGGCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (21 bp):
TTACTCAGATGTATCGATACA
Found at i:1184537 original size:2 final size:2
Alignment explanation
Indices: 1184532--1184557 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1184522 CACAATTGTA
1184532 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
1184558 TCGACTAGAC
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):
AT
Found at i:1185567 original size:27 final size:23
Alignment explanation
Indices: 1185504--1185568 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
1185494 TTTGTTCATC
*
1185504 CATATAAACGTAACAAAAGCATT
1 CATATAAACGTAACAAAAGCATA
*
1185527 CGTATAAACGTAACAAAAGCAGAAATA
1 CATATAAACGTAACAAAAGC----ATA
1185554 CATATAAACGTAACA
1 CATATAAACGTAACA
1185569 TAAGTTACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 19 0.54
27 16 0.46
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.18
Consensus pattern (23 bp):
CATATAAACGTAACAAAAGCATA
Found at i:1187592 original size:2 final size:2
Alignment explanation
Indices: 1187585--1187621 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1187575 GGGGGATTTT
1187585 AG AG AG AG 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 AG AG AG AG A
1187622 CTGATGCTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1187821 original size:75 final size:75
Alignment explanation
Indices: 1187698--1187848 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
1187688 AAGCACCATC
1187698 AATTGCTGAGTGCTGAAATGACATCTATACTTGGACTAAGGAAATCAGACATTGTTGCAATTCGT
1 AATTGCTGAGTGCTGAAATGACATCTATACTTGGACTAAGGAAATCAGACATTGTTGCAATTCGT
1187763 TTAGAAAAAG
66 TTAGAAAAAG
* *
1187773 AATTGCTGAGTGCTGAAATGACATCTATACTTGGACTAAGGATATCAGACATTTTTGCAATTCGT
1 AATTGCTGAGTGCTGAAATGACATCTATACTTGGACTAAGGAAATCAGACATTGTTGCAATTCGT
1187838 TTAGAAAAAG
66 TTAGAAAAAG
1187848 A
1 A
1187849 CTTTTGTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (75 bp):
AATTGCTGAGTGCTGAAATGACATCTATACTTGGACTAAGGAAATCAGACATTGTTGCAATTCGT
TTAGAAAAAG
Found at i:1190405 original size:102 final size:102
Alignment explanation
Indices: 1190229--1190432 Score: 372
Period size: 102 Copynumber: 2.0 Consensus size: 102
1190219 AAATAGCCTT
* * *
1190229 ATCTATTGAGCCTTTTCATTATTGGAGGTTTAACTTGGTACCTCCAAGTTTGAGCTTTATTTGTC
1 ATCTATTCAGCCTCTTCATTATTGGAAGTTTAACTTGGTACCTCCAAGTTTGAGCTTTATTTGTC
*
1190294 CACTTAGCATTGAAGTATCTTCACTCTCAAAAGAACC
66 CACTTAGCATTGAAGTATCTTCACTCCCAAAAGAACC
1190331 ATCTATTCAGCCTCTTCATTATTGGAAGTTTAACTTGGTACCTCCAAGTTTGAGCTTTATTTGTC
1 ATCTATTCAGCCTCTTCATTATTGGAAGTTTAACTTGGTACCTCCAAGTTTGAGCTTTATTTGTC
1190396 CACTTAGCATTGAAGTATCTTCACTCCCAAAAGAACC
66 CACTTAGCATTGAAGTATCTTCACTCCCAAAAGAACC
1190433 TTAGTCCTAA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (102 bp):
ATCTATTCAGCCTCTTCATTATTGGAAGTTTAACTTGGTACCTCCAAGTTTGAGCTTTATTTGTC
CACTTAGCATTGAAGTATCTTCACTCCCAAAAGAACC
Found at i:1190512 original size:21 final size:21
Alignment explanation
Indices: 1190488--1190527 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1190478 TCTTTGTCCT
1190488 TTAACATCAATAAATTGTTCC
1 TTAACATCAATAAATTGTTCC
1190509 TTAACATCAATAAATTGTT
1 TTAACATCAATAAATTGTT
1190528 GAGAATAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (21 bp):
TTAACATCAATAAATTGTTCC
Found at i:1198516 original size:2 final size:2
Alignment explanation
Indices: 1198509--1198558 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1198499 GAAAACTAAA
* * *
1198509 AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG AC AG AG AG AC AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1198551 AG AG AG AG
1 AG AG AG AG
1198559 GTACTTGTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.06, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1199790 original size:11 final size:10
Alignment explanation
Indices: 1199770--1199805 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
1199760 TCTTTATCTT
1199770 TCTTTCTTTTC
1 TCTTT-TTTTC
1199781 TCTTTTTTT-
1 TCTTTTTTTC
1199790 TCTTTTTTTC
1 TCTTTTTTTC
1199800 TCTTTT
1 TCTTTT
1199806 CTTTTCTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 10 0.42
11 5 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TCTTTTTTTC
Found at i:1199798 original size:19 final size:21
Alignment explanation
Indices: 1199760--1199822 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
1199750 AAAAAAAATT
1199760 TCTTTATC-TTTCTTTCTTTTC
1 TCTTT-TCTTTTCTTTCTTTTC
1199781 TCTTTT-TTTTCTTT-TTTTC
1 TCTTTTCTTTTCTTTCTTTTC
* *
1199800 TCTTTTCTTTTCTTCCTTCTC
1 TCTTTTCTTTTCTTTCTTTTC
1199821 TC
1 TC
1199823 CCTTCATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 11 0.30
20 15 0.41
21 11 0.30
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTCTTTTC
Found at i:1199813 original size:10 final size:10
Alignment explanation
Indices: 1199758--1199813 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
1199748 ACAAAAAAAA
1199758 TTTCTTTATC-
1 TTTCTTT-TCT
1199768 TTTC-TTTCT
1 TTTCTTTTCT
*
1199777 TTTCTCTTTTT
1 TTTCT-TTTCT
1199788 TTTCTTTT-T
1 TTTCTTTTCT
1199797 TTCTCTTTTCT
1 TT-TCTTTTCT
1199808 TTTCTT
1 TTTCTT
1199814 CCTTCTCTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 2 0.05
9 9 0.22
10 17 0.43
11 12 0.30
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTTCT
Found at i:1200369 original size:15 final size:15
Alignment explanation
Indices: 1200345--1200393 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1200335 ATAAAATAAA
*
1200345 ATAAATTATTAATAT
1 ATAAAATATTAATAT
*
1200360 ATAAAATATTTATAT
1 ATAAAATATTAATAT
1200375 A-AAAATA-TAATATT
1 ATAAAATATTAATA-T
1200389 ATAAA
1 ATAAA
1200394 TAAAAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAATATTAATAT
Found at i:1201796 original size:33 final size:32
Alignment explanation
Indices: 1201737--1201801 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
1201727 TTTGAGTCAA
1201737 TGTATCGATACAATTCTTCATATATCGATACAT
1 TGTATCGATACAATTC-TCATATATCGATACAT
*
1201770 TGTATCGATACAATGTGC-CATGTATCGATACA
1 TGTATCGATACAAT-T-CTCATATATCGATACA
1201802 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAATTCTCATATATCGATACAT
Found at i:1201854 original size:20 final size:20
Alignment explanation
Indices: 1201829--1201881 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1201819 TACTACCAAT
* *
1201829 TTCATGTATTGATACCTTTG
1 TTCATGTATCGATACATTTG
1201849 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACATTTG
*
1201869 -ACATGTATCGATA
1 TTCATGTATCGATA
1201882 TAATGTATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TTCATGTATCGATACATTTG
Found at i:1201875 original size:19 final size:19
Alignment explanation
Indices: 1201831--1201913 Score: 88
Period size: 19 Copynumber: 4.6 Consensus size: 19
1201821 CTACCAATTT
* * *
1201831 CATGTATTGATACCTTTGTT
1 CATGTATCGATACATTTG-A
1201851 CATGTATCGATACATTTGA
1 CATGTATCGATACATTTGA
1201870 CATGTATCGAT--A--T-A
1 CATGTATCGATACATTTGA
1201884 -ATGTATCGATACATTTGA
1 CATGTATCGATACATTTGA
1201902 CATGTATCGATA
1 CATGTATCGATA
1201914 TAATGTATCG
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
13 10 0.19
14 1 0.02
15 2 0.04
17 2 0.04
18 1 0.02
19 22 0.41
20 16 0.30
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (19 bp):
CATGTATCGATACATTTGA
Found at i:1201888 original size:32 final size:32
Alignment explanation
Indices: 1201852--1201928 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
1201842 ACCTTTGTTC
1201852 ATGTATCGATACATTTGACATGTATCGATATA
1 ATGTATCGATACATTTGACATGTATCGATATA
1201884 ATGTATCGATACATTTGACATGTATCGATATA
1 ATGTATCGATACATTTGACATGTATCGATATA
1201916 ATGTATCGATACA
1 ATGTATCGATACA
1201929 AAGCATAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (32 bp):
ATGTATCGATACATTTGACATGTATCGATATA
Found at i:1201889 original size:13 final size:13
Alignment explanation
Indices: 1201871--1201926 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 13
1201861 TACATTTGAC
1201871 ATGTATCGATATA
1 ATGTATCGATATA
1201884 ATGTATCGATACATTTGA
1 ATGTATCGAT--A--T-A
1201902 CATGTATCGATATA
1 -ATGTATCGATATA
1201916 ATGTATCGATA
1 ATGTATCGATA
1201927 CAAAGCATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.57
14 1 0.03
15 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:1208979 original size:3 final size:3
Alignment explanation
Indices: 1208971--1209010 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
1208961 TCTGAGTCAA
* *
1208971 CAT CAT CAT CAT CAT CAT CAT CAC CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1209011 TTTGATGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1210627 original size:13 final size:13
Alignment explanation
Indices: 1210609--1210633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1210599 CAATTCTTCA
1210609 TGTATCGATACAT
1 TGTATCGATACAT
1210622 TGTATCGATACA
1 TGTATCGATACA
1210634 ATGTGCCATG
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:1210631 original size:33 final size:33
Alignment explanation
Indices: 1210589--1210653 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1210579 TTTGAGTCAA
1210589 TGTATCGATACAAT-T-CTTCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
1210622 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
1210654 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:1212473 original size:154 final size:152
Alignment explanation
Indices: 1212308--1212912 Score: 510
Period size: 154 Copynumber: 4.0 Consensus size: 152
1212298 TTGCATTTTC
* * * *
1212308 TTTTAAATTTTTTTATTTTCAAAATATGGAGTTTTTTACTTTATAAATTTCTCCGGTAGGATTTT
1 TTTTAAATTTTTTTTTTTTCAAAATATAGAGTTTTCTACTTTATAAATTTCTCAGGTAGGATTTT
* * * *
1212373 TCTAAATTTATAATTTTTACAATTCTTTAAATATTATTGTTTAGCTCATATTAATTCAGTTTTGA
66 TCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCATATTAATTCAGTTTTGA
*
1212438 AAATTTTAATTTATTTTAAGAG
131 AAAATTTAATTTATTTTAAGAG
* * * * **
1212460 TTTTAGAATTTTTTCTGTTACAAAAATATAGAATTTTCTACTCCATAAATTTCTCAGGTAGGATT
1 TTTTA-AATTTTTTTTTTTTC-AAAATATAGAGTTTTCTACTTTATAAATTTCTCAGGTAGGATT
* * * * * *
1212525 TTTCTGAGTTTATAATTTTCAAAATTCTTCAGATATTATGGTTTAATTCATATTAAATT-ATTTT
64 TTTCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCATATT-AATTCAGTTT
*
1212589 TGAAAAAATTAATTTATTTTATA-AG
128 TGAAAAATTTAATTTATTTTA-AGAG
* * * ** * * * *
1212614 TTTTAAAAATTTTCTTTTTATCAAGATCCAAAGTTTTCTA-TTCTGTAATTTTCTCTA-GTCGGA
1 TTTT--AAATTTTTTTTTTTTCAAAATATAGAGTTTTCTACTT-TATAAATTTCTC-AGGTAGGA
* *
1212677 -TTTTCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCACATTTAA-TC-GG
62 TTTTTCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCATA-TTAATTCAGT
* *
1212739 TTTGAAAAATTCAATTTATTTTATGAG
126 TTTGAAAAATTTAATTTATTTTAAGAG
* * ** ** * * * * * *
1212766 TTTTAAAAATTTTCTAATACCAAGATACAGAGTGTTT-TACTCTATAAATTTTTTC-GATTGGAT
1 TTTT-AAATTTTTTTTTTTTCAAAATATAGAGT-TTTCTACTTTATAAA-TTTCTCAGGTAGGAT
* * * * * * * *
1212829 TTTTCTCAGCTTAAAATTTTTAAAATTCATCAAATATTTTTATTAAATTCATATTAAATT-AGTT
63 TTTTCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCATATT-AATTCAGTT
* *
1212893 TTTAAAAATTCAATTTATTT
127 TTGAAAAATTTAATTTATTT
1212913 GATAAGTTTT
Statistics
Matches: 361, Mismatches: 73, Indels: 37
0.77 0.15 0.08
Matches are distributed among these distances:
151 33 0.09
152 88 0.24
153 83 0.23
154 140 0.39
155 16 0.04
156 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (152 bp):
TTTTAAATTTTTTTTTTTTCAAAATATAGAGTTTTCTACTTTATAAATTTCTCAGGTAGGATTTT
TCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCATATTAATTCAGTTTTGA
AAAATTTAATTTATTTTAAGAG
Found at i:1212910 original size:305 final size:306
Alignment explanation
Indices: 1212370--1212922 Score: 722
Period size: 305 Copynumber: 1.8 Consensus size: 306
1212360 CCGGTAGGAT
* * * * *
1212370 TTTTCTAAATTTATAATTTTTACAATTCTTTAAATATTATTGTTTAGCTCATATTAATTCAGTTT
1 TTTTCTAAATTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCACATTAATTCAGGTT
* * ** ** *
1212435 TGAAAATTTTAATTTATTTTAAGAGTTTTAGAATTTTTTCTGTTACAAAAATATAGAATTTTCTA
66 TGAAAAATTCAATTTATTTTAAGAGTTTTAGAAAATTTTCTAATACAAAAATACAGAATTTTCTA
* * * * * *
1212500 CTCCATAAATTTCTCAGGTAGGATTTTTCTGAGTTTATAATTTTCAAAATTCTTCAGATATTATG
131 CTCCATAAATTTCTCAGATAGGATTTTTCTCAGCTTAAAATTTTCAAAATTCATCAAATATTATG
* * *
1212565 GTTTAATTCATATTAAATTATTTTTGAAAAAATTAATTTATTTTATAAGTTTTAAAAATTTTCTT
196 ATTAAATTCATATTAAATTATTTTT-AAAAAATTAATTTATTTGATAAGTTTTAAAAATTTTCTT
1212630 TTTATCAAGATCCAAAGTTTTCTATTCTGTAATTTTCTCTAGTCGGA
260 TTTATCAAGATCCAAAGTTTTCTATTCTGTAATTTTCTCTAGTCGGA
*
1212677 TTTTCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCACATTTAA-TC-GGT
1 TTTTCTAAATTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCACA-TTAATTCAGGT
* * * *
1212740 TTGAAAAATTCAATTTATTTTATGAGTTTTA-AAAATTTTCTAATACCAAGATACAGAGTGTTT-
65 TTGAAAAATTCAATTTATTTTAAGAGTTTTAGAAAATTTTCTAATACAAAAATACAGAAT-TTTC
* * * *
1212803 TACTCTATAAATTTTTTC-GATTGGATTTTTCTCAGCTTAAAATTTTTAAAATTCATCAAATATT
129 TACTCCATAAA-TTTCTCAGATAGGATTTTTCTCAGCTTAAAATTTTCAAAATTCATCAAATATT
* *
1212867 TTTATTAAATTCATATTAAATTAGTTTTT-AAAAATTCAATTTATTTGATAAGTTTT
193 ATGATTAAATTCATATTAAATTA-TTTTTAAAAAATT-AATTTATTTGATAAGTTTT
1212923 GCATTTTTTT
Statistics
Matches: 209, Mismatches: 32, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
304 7 0.03
305 105 0.50
306 43 0.21
307 50 0.24
308 4 0.02
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (306 bp):
TTTTCTAAATTTATAATTTTTAAAATTCTTCAAATATTATTGTTTAACTCACATTAATTCAGGTT
TGAAAAATTCAATTTATTTTAAGAGTTTTAGAAAATTTTCTAATACAAAAATACAGAATTTTCTA
CTCCATAAATTTCTCAGATAGGATTTTTCTCAGCTTAAAATTTTCAAAATTCATCAAATATTATG
ATTAAATTCATATTAAATTATTTTTAAAAAATTAATTTATTTGATAAGTTTTAAAAATTTTCTTT
TTATCAAGATCCAAAGTTTTCTATTCTGTAATTTTCTCTAGTCGGA
Found at i:1213129 original size:2 final size:2
Alignment explanation
Indices: 1213122--1213151 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1213112 TAATTTTACA
*
1213122 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1213152 CTCAAAAATC
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1214409 original size:79 final size:78
Alignment explanation
Indices: 1214292--1214496 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 78
1214282 GATAATAACG
* * * * * * * * *
1214292 GGGTTGGAGTGTTCCCTTGAAAATGACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-T
1 GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATT
1214356 TA-GAAAAAAA-CA
65 TAGGAAAAAAACCA
*
1214368 TCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA
1 --GGG-TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA
* *
1214433 TTTTAGGAATAAAGCCA
63 -TTTAGGAAAAAAACCA
**
1214450 GGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGAT
1 GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT
1214497 GAAATAACGA
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
78 4 0.04
79 89 0.83
80 6 0.06
81 6 0.06
82 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTT
AGGAAAAAAACCA
Found at i:1214504 original size:28 final size:28
Alignment explanation
Indices: 1214450--1214524 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 28
1214440 AATAAAGCCA
*** **
1214450 GGGTTGGAGTATCCCCTCGGAGGTAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
1214478 GGGTTGGAGTATCCCCGATGAAATAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
* * *
1214506 AGGTTGAAGTATCCTCGAT
1 GGGTTGGAGTATCCCCGAT
1214525 TATGAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACG
Found at i:1214572 original size:53 final size:52
Alignment explanation
Indices: 1214507--1214686 Score: 211
Period size: 52 Copynumber: 3.4 Consensus size: 52
1214497 GAAATAACGA
* * *
1214507 GGTTGAAGTATCCTCGATTATGAAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAAATTGGTG-TTTTGGAAATAAAACCGG
* * * *
1214560 AGCTGGAGTATCCCTGATTA--AAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAA--AAAATTGGTGTTTTGGAAATAAAACCGG
* * * * *
1214612 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAAATTGGTGTTTTGGAAATAAAACCGG
1214664 GGTTGGAGTATCCCCGATTATGA
1 GGTTGGAGTATCCCCGATTATGA
1214687 GAAATCAATA
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
51 2 0.02
52 77 0.73
53 25 0.24
54 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATGAAAAAATTGGTGTTTTGGAAATAAAACCGG
Found at i:1214724 original size:51 final size:52
Alignment explanation
Indices: 1214601--1214729 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 52
1214591 GTGTTTTGAA
* * * *
1214601 AATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGC
1 AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAGC
*
1214653 AATAAAACCGGGGTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTTAAG-
1 AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTT-AGC
* * *
1214704 AATAAAGCAGGGGTTAGAGTATCCCC
1 AATAAAACCGGGGTTGGAGTATCCCC
1214730 TCGGAAATAA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 35 0.51
52 33 0.49
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (52 bp):
AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAGC
Found at i:1214751 original size:28 final size:27
Alignment explanation
Indices: 1214713--1214786 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
1214703 GAATAAAGCA
* ** *
1214713 GGGGTTAGAGTATCCCCTCGGAAATAAT
1 GGGGTTGGAGTATCCCCGAGG-AATAAC
* *
1214741 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGAGGAATAAC
1214768 GGGGTTGGAGTATCCCCGA
1 GGGGTTGGAGTATCCCCGA
1214787 TTGTGAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGAGGAATAAC
Found at i:1214834 original size:53 final size:51
Alignment explanation
Indices: 1214771--1214893 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 51
1214761 GATTAACGGG
* *
1214771 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTTTCG-AAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAG-AAAATTAGTG--TTTT-GAAAATAAAATCAGA
* *
1214824 GTTGGGGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTAGAAAATTAGTGTTTTGAAAATAAAATCAGA
* *
1214875 GATGGAATATCCCCGATTG
1 GTTGGAGTATCCCCGATTG
1214894 CGGAGAATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
50 1 0.02
51 31 0.52
53 27 0.45
54 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTAGAAAATTAGTGTTTTGAAAATAAAATCAGA
Found at i:1217183 original size:13 final size:13
Alignment explanation
Indices: 1217165--1217190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1217155 CAAAGAATAG
1217165 ATGTATCGATACA
1 ATGTATCGATACA
1217178 ATGTATCGATACA
1 ATGTATCGATACA
1217191 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1217187 original size:34 final size:33
Alignment explanation
Indices: 1217144--1217210 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
1217134 AACTTCCTAG
*
1217144 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
1217178 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
1217211 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:1217266 original size:19 final size:19
Alignment explanation
Indices: 1217242--1217293 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1217232 AGCGATACAT
1217242 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
1217261 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1217280 TGTATCGATACAAA
1 TGTATCGATACAAA
1217294 TCGCTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1217355 original size:21 final size:20
Alignment explanation
Indices: 1217329--1217426 Score: 135
Period size: 21 Copynumber: 4.7 Consensus size: 20
1217319 GTTGGGACCC
*
1217329 TGTATCGATACATT-AGTAGAA
1 TGTATCGATACATTCA-CA-AA
1217350 TGTATCGATACATTCCACAAA
1 TGTATCGATACATT-CACAAA
1217371 TGTATCGATACATTCCACAAA
1 TGTATCGATACATT-CACAAA
1217392 TGTATCGATACATTCCACAAA
1 TGTATCGATACATT-CACAAA
1217413 TGTATCGATACATT
1 TGTATCGATACATT
1217427 TGGATAAAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
21 72 0.97
22 1 0.01
23 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATTCACAAA
Found at i:1218854 original size:157 final size:158
Alignment explanation
Indices: 1218577--1218908 Score: 402
Period size: 157 Copynumber: 2.1 Consensus size: 158
1218567 TAGTTGATAT
* * * *
1218577 TTAACTTTGTGTTTTAATTATATAAGGACCAATTTGCAAATTTAGAAAGTTTAGGGGGTTCATTT
1 TTAATTTTGTGTTTTAATTATATAAGGACCAATTTGCAAAATTAGAAAGTTTAGCGGGTTCATTC
* * ** *
1218642 GAAAATTTTGTTCTAAAGCCAAAAGTACTTGCCTAAATTTTCCTTGTAATGTTT-GGATATGTTT
66 AAAAATTTTGTTCTAAAGCCAAAAGTACTAGCCTAAATCCTCCTTGTAATGTTTGGGATATGCTT
** *
1218706 TGGATGCTGATTTCCATTTCTTTGATGC
131 AAGATGCTGATTTCCATTTCTTCGATGC
* *
1218734 TTAATTTTGTGTTTTAATTATATAAGGACTAATTTGCAAAATTAGAAAGTTTAGCGGGTTTATTC
1 TTAATTTTGTGTTTTAATTATATAAGGACCAATTTGCAAAATTAGAAAGTTTAGCGGGTTCATTC
* * *
1218799 AAAAATTTTGTTCT-AAGTCTAAAAGTACTAAGCC-GAATCCTCCTTGTAACT-TTTGGGATGTG
66 AAAAATTTTGTTCTAAAG-CCAAAAGTACT-AGCCTAAATCCTCCTTGTAA-TGTTTGGGATATG
* ** ** *
1218861 CTTAATATTTTGATTTTGATTTCTTCGATGT
128 CTTAAGATGCTGATTTCCATTTCTTCGATGC
1218892 TTAATTTTGTGTTTTAA
1 TTAATTTTGTGTTTTAA
1218909 CTAGGTTCGA
Statistics
Matches: 148, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
156 3 0.02
157 97 0.66
158 48 0.32
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (158 bp):
TTAATTTTGTGTTTTAATTATATAAGGACCAATTTGCAAAATTAGAAAGTTTAGCGGGTTCATTC
AAAAATTTTGTTCTAAAGCCAAAAGTACTAGCCTAAATCCTCCTTGTAATGTTTGGGATATGCTT
AAGATGCTGATTTCCATTTCTTCGATGC
Found at i:1218944 original size:158 final size:155
Alignment explanation
Indices: 1218577--1218953 Score: 384
Period size: 157 Copynumber: 2.4 Consensus size: 155
1218567 TAGTTGATAT
* * * * *
1218577 TTAACTTTGTGTTTTAATTATATAAGGACCAATTTGCAAATTTAGAAAGTTTAGGGGGTTCATTT
1 TTAATTTTGTGTTTTAACTAGATAAGGA-CAATTTGCAAATTTAGAAAGTTTA-GGGGTTTATTC
* * ** * *
1218642 GAAAATTTTGTTCTAAAGCCAAAAGTACTTGCCTAAATTTTCCTTGTAATGTTTGGATATGTTTT
64 AAAAATTTTGTTCTAAAGCCAAAAGTACTAGCCTAAATCCTCCTTGTAATGTTTGGATATGCTTA
* *
1218707 GGATGCTGATTTCCATTTCTTTGATGC
129 AGATGCTGATTTCCATTTCTTCGATGC
* * *
1218734 TTAATTTTGTGTTTTAATTATATAAGGACTAATTTGCAAAATTAGAAAGTTTAGCGGGTTTATTC
1 TTAATTTTGTGTTTTAACTAGATAAGGAC-AATTTGCAAATTTAGAAAGTTTAG-GGGTTTATTC
* * *
1218799 AAAAATTTTGTTCT-AAGTCTAAAAGTACTAAGCC-GAATCCTCCTTGTAACT-TTTGGGATGTG
64 AAAAATTTTGTTCTAAAG-CCAAAAGTACT-AGCCTAAATCCTCCTTGTAA-TGTTT-GGATATG
* ** ** *
1218861 CTTAATATTTTGATTTTGATTTCTTCGATGT
125 CTTAAGATGCTGATTTCCATTTCTTCGATGC
* **
1218892 TTAATTTTGTGTTTTAACTAGGTTCGAGAGC-ATTTGCAAATTTAGAAAGTTTAGGGGTTTAT
1 TTAATTTTGTGTTTTAACTAGATAAG-GA-CAATTTGCAAATTTAGAAAGTTTAGGGGTTTAT
1218954 CTATAAATAT
Statistics
Matches: 185, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
156 5 0.03
157 103 0.56
158 74 0.40
159 2 0.01
160 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (155 bp):
TTAATTTTGTGTTTTAACTAGATAAGGACAATTTGCAAATTTAGAAAGTTTAGGGGTTTATTCAA
AAATTTTGTTCTAAAGCCAAAAGTACTAGCCTAAATCCTCCTTGTAATGTTTGGATATGCTTAAG
ATGCTGATTTCCATTTCTTCGATGC
Found at i:1223672 original size:19 final size:18
Alignment explanation
Indices: 1223648--1223745 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
1223638 TAGCTTACAT
1223648 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1223667 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1223680 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1223699 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1223712 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
1223732 TGTATCGATACAAA
1 TGTATCGATACAAA
1223746 TCATTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1223684 original size:32 final size:32
Alignment explanation
Indices: 1223643--1223743 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
1223633 GGCAGTAGCT
*
1223643 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1223675 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1223707 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1223740 TACA
1 TACA
1223744 AATCATTGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 52 0.78
33 15 0.22
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1223685 original size:13 final size:13
Alignment explanation
Indices: 1223667--1223723 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1223657 ACAAAACTTA
1223667 TGTATCGATACAT
1 TGTATCGATACAT
1223680 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1223698 ATGTATCGATACAT
1 -TGTATCGATACAT
1223712 TGTATCGATACA
1 TGTATCGATACA
1223724 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:1228845 original size:20 final size:19
Alignment explanation
Indices: 1228799--1228855 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1228789 TTATATCGAT
*
1228799 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
1228818 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
1228837 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1228856 AAACTGGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1228918 original size:13 final size:13
Alignment explanation
Indices: 1228900--1228952 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
1228890 CGATACATGG
1228900 TACATTGTATCGA
1 TACATTGTATCGA
1228913 TACATTGTATCGA
1 TACATTGTATCGA
1228926 TACA-TG-AT-G-
1 TACATTGTATCGA
1228935 -A-ATTGTATCGA
1 TACATTGTATCGA
1228946 TACATTG
1 TACATTG
1228953 CTTGTAACAG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1228926 original size:33 final size:33
Alignment explanation
Indices: 1228884--1228952 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1228874 CTACCACTAT
*
1228884 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
1228917 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
1228950 TTG
1 TTG
1228953 CTTGTAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:1237682 original size:20 final size:20
Alignment explanation
Indices: 1237642--1237692 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1237632 CGATAGATTC
* *
1237642 TATCGATACAT-GTTCATTG
1 TATCGATACATGGATAATTG
1237661 TATCGATACATGGATAATTG
1 TATCGATACATGGATAATTG
1237681 TATCGATACATG
1 TATCGATACATG
1237693 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (20 bp):
TATCGATACATGGATAATTG
Found at i:1239360 original size:26 final size:25
Alignment explanation
Indices: 1239337--1239388 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1239327 ACATATTATA
1239337 TAAAT-AAT-TAAAT-TTTTAAAAT
1 TAAATAAATATAAATATTTTAAAAT
* *
1239359 TAAATTAATATAACTATTTTAAAAT
1 TAAATAAATATAAATATTTTAAAAT
1239384 TAAAT
1 TAAAT
1239389 TTATAGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 3 0.12
24 4 0.15
25 14 0.54
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAATAAATATAAATATTTTAAAAT
Found at i:1240408 original size:2 final size:2
Alignment explanation
Indices: 1240401--1240426 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1240391 ACGTGCAAGA
1240401 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
1240427 TTAATGTCCT
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):
AT
Found at i:1240436 original size:53 final size:53
Alignment explanation
Indices: 1240373--1240477 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
1240363 AAAGGAAAAC
1240373 TTTAATGTCCTTGGTGCAACGTGCAAGAATATATATATATATATATATATATA
1 TTTAATGTCCTTGGTGCAACGTGCAAGAATATATATATATATATATATATATA
*
1240426 TTTAATGTCCTTGGTGTAACGTGCAAGAATATATATATATATATATATATAT
1 TTTAATGTCCTTGGTGCAACGTGCAAGAATATATATATATATATATATATAT
1240478 TTATTTATCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (53 bp):
TTTAATGTCCTTGGTGCAACGTGCAAGAATATATATATATATATATATATATA
Found at i:1242808 original size:21 final size:21
Alignment explanation
Indices: 1242784--1242823 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1242774 TCACATTTTT
*
1242784 ACTTATATATATCGATACATG
1 ACTTACATATATCGATACATG
* *
1242805 ACTTCCATGTATCGATACA
1 ACTTACATATATCGATACA
1242824 AGGTCCCAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (21 bp):
ACTTACATATATCGATACATG
Found at i:1243029 original size:20 final size:20
Alignment explanation
Indices: 1243004--1243098 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
1242994 TTTTACCCAG
*
1243004 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTAGTCA
* *
1243024 ATGTATCGATACATGCAGGCAA
1 ATGTATCGATACAT-TAGTC-A
* ** *
1243046 AT-TTTC-ATATTTTAGCCA
1 ATGTATCGATACATTAGTCA
*
1243064 GATGTATCGATACATTATTCA
1 -ATGTATCGATACATTAGTCA
1243085 ATGTATCGATACAT
1 ATGTATCGATACAT
1243099 GCAGACAAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
18 1 0.02
19 5 0.09
20 35 0.61
21 13 0.23
22 3 0.05
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTAGTCA
Found at i:1243087 original size:61 final size:61
Alignment explanation
Indices: 1242992--1243118 Score: 236
Period size: 61 Copynumber: 2.1 Consensus size: 61
1242982 ACGCGTGTGG
*
1242992 TATTTTACCCAGATGTATCGATACATTATTCAATGTATCGATACATGCAGGCAAATTTTCA
1 TATTTTACCCAGATGTATCGATACATTATTCAATGTATCGATACATGCAGACAAATTTTCA
*
1243053 TATTTTAGCCAGATGTATCGATACATTATTCAATGTATCGATACATGCAGACAAATTTTCA
1 TATTTTACCCAGATGTATCGATACATTATTCAATGTATCGATACATGCAGACAAATTTTCA
1243114 TATTT
1 TATTT
1243119 CAGGATGTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (61 bp):
TATTTTACCCAGATGTATCGATACATTATTCAATGTATCGATACATGCAGACAAATTTTCA
Found at i:1243978 original size:20 final size:20
Alignment explanation
Indices: 1243940--1243978 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1243930 TAGCCCTTAA
*
1243940 TCATGCATTTTTACTATGTT
1 TCATGCATTTTAACTATGTT
1243960 TCATGCATTTATAAC-ATGT
1 TCATGCATTT-TAACTATGT
1243979 CCAGCACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TCATGCATTTTAACTATGTT
Found at i:1247389 original size:144 final size:144
Alignment explanation
Indices: 1247125--1247414 Score: 490
Period size: 144 Copynumber: 2.0 Consensus size: 144
1247115 GTGAGCCCAT
* * * * *
1247125 CACGGTTCCATGACTTTCCTAAGATTATCATGCATTATTGGGGCCTTGGATGTGGTAGTTTTAGA
1 CACGGTTCCATGACTCTCCTAAGATTATCATGCATTATTAGGGCCTGGGATGTGGTACTTTTAAA
* *
1247190 ATTGTTTTGATGTCTTGATGTCATTTGTGTGACTAAAATGCCATGTTCATCTCCATCATCTTAAC
66 ATTGTTTTGATGTCTTGATGTCATTTGTCTGACCAAAATGCCATGTTCATCTCCATCATCTTAAC
* *
1247255 AGCCTATGTTCAAG
131 AACCCATGTTCAAG
1247269 CACGGTTCCATGACTCTCCTAAGATTATCATGCATTATTAGGGCCTGGGATGTGGTACTTTTAAA
1 CACGGTTCCATGACTCTCCTAAGATTATCATGCATTATTAGGGCCTGGGATGTGGTACTTTTAAA
*
1247334 ATTGTTTTGATGTCTTGATGTCATTTGTCTGACCAAAATGCCATGTTCATTTCCATCATCTTAAC
66 ATTGTTTTGATGTCTTGATGTCATTTGTCTGACCAAAATGCCATGTTCATCTCCATCATCTTAAC
1247399 AACCCATGTTCAAG
131 AACCCATGTTCAAG
1247413 CA
1 CA
1247415 TTTTTTCCAT
Statistics
Matches: 136, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 136 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (144 bp):
CACGGTTCCATGACTCTCCTAAGATTATCATGCATTATTAGGGCCTGGGATGTGGTACTTTTAAA
ATTGTTTTGATGTCTTGATGTCATTTGTCTGACCAAAATGCCATGTTCATCTCCATCATCTTAAC
AACCCATGTTCAAG
Found at i:1258890 original size:21 final size:20
Alignment explanation
Indices: 1258842--1258897 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1258832 ATATAAATAG
1258842 CAAATGTATCGATACATAAA
1 CAAATGTATCGATACATAAA
* ***
1258862 CGAATGTATCGATACATGCCT
1 CAAATGTATCGATACAT-AAA
1258883 CAAATGTATCGATAC
1 CAAATGTATCGATAC
1258898 CAAACTACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
CAAATGTATCGATACATAAA
Found at i:1262420 original size:52 final size:51
Alignment explanation
Indices: 1262335--1262458 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 51
1262325 ATATGAAAAG
* *
1262335 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
1262386 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAA
1262438 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1262459 AAGATCGGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 21 0.30
52 43 0.62
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:1262471 original size:51 final size:52
Alignment explanation
Indices: 1262335--1262478 Score: 168
Period size: 52 Copynumber: 2.8 Consensus size: 52
1262325 ATATGAAAAG
* **
1262335 TTGCTTGCATGTATCGATAC-ATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACAAGATAA-AGTGTATCGATACATCTGGGCAAAT
*** *
1262387 TTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACAAGATAAAGTGTATCGATACATCTGGGCAAAT
**
1262438 TTGCCTGCATGTATCGATACAAAGAT-CGGTGTATCGATACA
1 TTGCCTGCATGTATCGATAC-AAGATAAAGTGTATCGATACA
1262479 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
51 32 0.40
52 44 0.54
53 5 0.06
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACAAGATAAAGTGTATCGATACATCTGGGCAAAT
Found at i:1262485 original size:13 final size:13
Alignment explanation
Indices: 1262467--1262491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1262457 CAAAGATCGG
1262467 TGTATCGATACAA
1 TGTATCGATACAA
1262480 TGTATCGATACA
1 TGTATCGATACA
1262492 TTTGAGTAAT
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:1262569 original size:33 final size:33
Alignment explanation
Indices: 1262532--1262598 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1262522 AGTAGCTTAA
1262532 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1262565 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1262598 A
1 A
1262599 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1262572 original size:13 final size:13
Alignment explanation
Indices: 1262554--1262578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1262544 CAAAAAAATA
1262554 TGTATCGATACAT
1 TGTATCGATACAT
1262567 TGTATCGATACA
1 TGTATCGATACA
1262579 ACATTTTATG
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:1262930 original size:32 final size:31
Alignment explanation
Indices: 1262889--1262960 Score: 117
Period size: 32 Copynumber: 2.3 Consensus size: 31
1262879 TCTACAGTAG
*
1262889 CGATACATTGTATTGATACAAAACTTATGTA
1 CGATACATTGTATCGATACAAAACTTATGTA
*
1262920 TCGATACATTGTATCGATACAACACTTATGTA
1 -CGATACATTGTATCGATACAAAACTTATGTA
1262952 CGATACATT
1 CGATACATT
1262961 TACTGTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 9 0.24
32 29 0.76
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (31 bp):
CGATACATTGTATCGATACAAAACTTATGTA
Found at i:1262934 original size:13 final size:13
Alignment explanation
Indices: 1262916--1262940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1262906 ACAAAACTTA
1262916 TGTATCGATACAT
1 TGTATCGATACAT
1262929 TGTATCGATACA
1 TGTATCGATACA
1262941 ACACTTATGT
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:1263154 original size:160 final size:160
Alignment explanation
Indices: 1262968--1263276 Score: 514
Period size: 160 Copynumber: 1.9 Consensus size: 160
1262958 ATTTACTGTT
* *
1262968 TGTATCGATACAAATTGTTAAAATTCAAAATTTTTGACCTTTGGGACCTTGTATCGATACATTCT
1 TGTATCGATACAAATCGTTAAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTCT
*
1263033 AGA-AATGTATCGATACATTTGAACAAAAATGTGATTTTTTCATCCCTTTTGCCTTCCG-AACAC
66 A-ACAATGTATCGATACATTTGAACAAAAATGTAATTTTTTCATCCCTTTTGCCTT-CGAAACAC
*
1263096 CCTATCTTGACTAGGGACGATACAACATTTTA
129 CCTATCTCGACTAGGGACGATACAACATTTTA
*
1263128 TGTATCGATACAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTCT
1 TGTATCGATACAAATCGTTAAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTCT
* *
1263193 AACAATGTATCGATACATTTGGACAAAAATGTAATTTTTTCATCCTTTTTGCCTTCGAAACACCC
66 AACAATGTATCGATACATTTGAACAAAAATGTAATTTTTTCATCCCTTTTGCCTTCGAAACACCC
*
1263258 TATCTCGATTAGGGACGAT
131 TATCTCGACTAGGGACGAT
1263277 GGGAAATTGA
Statistics
Matches: 139, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
159 3 0.02
160 136 0.98
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (160 bp):
TGTATCGATACAAATCGTTAAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTCT
AACAATGTATCGATACATTTGAACAAAAATGTAATTTTTTCATCCCTTTTGCCTTCGAAACACCC
TATCTCGACTAGGGACGATACAACATTTTA
Found at i:1265697 original size:51 final size:51
Alignment explanation
Indices: 1265586--1265698 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
1265576 CTGAGGGAAA
* * *
1265586 ACTCTAACCCTAATTTTATTTTCAAAATATTAAAATTTTTATCTCGGGGAT
1 ACTCTAACCCTAATTTTATTTTCAAAATATTAAAAATTTCATCTCGGAGAT
* * ** *
1265637 ACTCAAACCCTATTTTTATTTTGGAAATATTAAAAATTTCATCTTGGAGAT
1 ACTCTAACCCTAATTTTATTTTCAAAATATTAAAAATTTCATCTCGGAGAT
*
1265688 ACTTTAACCCT
1 ACTCTAACCCT
1265699 GTTATTTTCA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (51 bp):
ACTCTAACCCTAATTTTATTTTCAAAATATTAAAAATTTCATCTCGGAGAT
Found at i:1265731 original size:79 final size:78
Alignment explanation
Indices: 1265631--1265916 Score: 385
Period size: 79 Copynumber: 3.6 Consensus size: 78
1265621 TTTTTATCTC
* * * * *
1265631 GGGGATACTCAAACCCTATTTTTATTTTGGAAATATTAAAAATTTCATCTTGGAGATACTTTAAC
1 GGGGATACTCCAACCCCATTTTTATTTTCGAAATATTAAAATTTTCATCTTGG-GATACTCTAAC
* *
1265696 CCTGTTATTTTCAA
65 CATGTTATTTTCGA
* *
1265710 GGGGATACTCCAACTCCATTTTTATTTTCGAAATATTAAAATTTTCATCTTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCATTTTTATTTTCGAAATATTAAAATTTTCATCTT-GGGATACTCTAAC
1265775 CATGTTATTTTCGA
65 CATGTTATTTTCGA
* * *
1265789 GGGGATACTCCAACCCCATTTTTA-TTTCTAAAATATTAAAATTTTCATTTTAGGGATAATCTAA
1 GGGGATACTCCAACCCCATTTTTATTTTC-GAAATATTAAAATTTTCATCTT-GGGATACTCTAA
*
1265853 CGATGTTATTTTCGA
64 CCATGTTATTTTCGA
* * *
1265868 GGGGATATTCCAACCCCATTTTTATTTCCTAAATATTAAAATTTTCATC
1 GGGGATACTCCAACCCCATTTTTATTTTCGAAATATTAAAATTTTCATC
1265917 GGGTACTCCA
Statistics
Matches: 184, Mismatches: 20, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
78 4 0.02
79 175 0.95
80 5 0.03
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (78 bp):
GGGGATACTCCAACCCCATTTTTATTTTCGAAATATTAAAATTTTCATCTTGGGATACTCTAACC
ATGTTATTTTCGA
Found at i:1265860 original size:158 final size:152
Alignment explanation
Indices: 1265631--1265955 Score: 402
Period size: 158 Copynumber: 2.1 Consensus size: 152
1265621 TTTTTATCTC
* * * * *
1265631 GGGGATACTCAAACCCTATTTTTATTTTGGAAATATTAAAAATTTCATCTTGGAGATACTTTAAC
1 GGGGATACTCCAACCCCATTTTTATTTTGAAAATATTAAAAATTTCATCTTGGAGATAATCTAAC
* * *
1265696 CCTGTTATTTTCAAGGGGATACTCCAACTCCATTTTTATTTTCGAAATATTAAAATTTTCATCTT
66 CATGTTATTTTCAAGGGGATACTCCAACCCCATTTTTATTTCCGAAATATTAAAATTTTCATC--
*
1265761 GGGGATACTCCAACCATGTTATTTTCGA
129 -GGG-TACTCCAACCATG-TA-TTTAGA
* *
1265789 GGGGATACTCCAACCCCATTTTTATTTCT-AAAATATTAAAATTTTCATTTTAGG-GATAATCTA
1 GGGGATACTCCAACCCCATTTTTATTT-TGAAAATATTAAAAATTTCATCTT-GGAGATAATCTA
* * * *
1265852 ACGATGTTATTTTCGAGGGGATATTCCAACCCCATTTTTATTTCCTAAATATTAAAATTTTCATC
64 ACCATGTTATTTTCAAGGGGATACTCCAACCCCATTTTTATTTCCGAAATATTAAAATTTTCATC
*
1265917 GGGTACTCCAACCCTGTATTTAGA
129 GGGTACTCCAACCATGTATTTAGA
* *
1265941 AGGGACACTCCAACC
1 GGGGATACTCCAACC
1265956 TTGTTTCTTT
Statistics
Matches: 147, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
152 18 0.12
153 2 0.01
154 12 0.08
155 3 0.02
158 109 0.74
159 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (152 bp):
GGGGATACTCCAACCCCATTTTTATTTTGAAAATATTAAAAATTTCATCTTGGAGATAATCTAAC
CATGTTATTTTCAAGGGGATACTCCAACCCCATTTTTATTTCCGAAATATTAAAATTTTCATCGG
GTACTCCAACCATGTATTTAGA
Found at i:1270189 original size:20 final size:20
Alignment explanation
Indices: 1270164--1270288 Score: 144
Period size: 20 Copynumber: 6.7 Consensus size: 20
1270154 TTTGCCTGCA
1270164 TGTATCGATACATTTCATGG
1 TGTATCGATACATTTCATGG
1270184 TGTATCGATACATTTCATGG
1 TGTATCGATACATTTCATGG
1270204 TGTATCGATACA--TC-TGG
1 TGTATCGATACATTTCATGG
* *
1270221 -G---C-A-A-ATTTACCTGCA
1 TGTATCGATACATTT-CATG-G
1270236 TGTATCGATACATTTCATGG
1 TGTATCGATACATTTCATGG
1270256 TGTATCGATACATTTCATGG
1 TGTATCGATACATTTCATGG
1270276 TGTATCGATACAT
1 TGTATCGATACAT
1270289 CTGGGCAAAT
Statistics
Matches: 90, Mismatches: 3, Indels: 24
0.77 0.03 0.21
Matches are distributed among these distances:
10 1 0.01
11 1 0.01
12 2 0.02
13 2 0.02
14 2 0.02
16 2 0.02
17 3 0.03
18 2 0.02
19 1 0.01
20 66 0.73
21 4 0.04
22 4 0.04
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTCATGG
Found at i:1270268 original size:72 final size:72
Alignment explanation
Indices: 1270151--1270340 Score: 344
Period size: 72 Copynumber: 2.6 Consensus size: 72
1270141 CAAAATATGA
*
1270151 AAATTTGCCTGCATGTATCGATACATTTCATGGTGTATCGATACATTTCATGGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTTCATGGTGTATCGATACATTTCATGGTGTATCGATACA
1270216 TCTGGGC
66 TCTGGGC
1270223 AAATTTACCTGCATGTATCGATACATTTCATGGTGTATCGATACATTTCATGGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTTCATGGTGTATCGATACATTTCATGGTGTATCGATACA
1270288 TCTGGGC
66 TCTGGGC
* * *
1270295 AAATTTACCTGTATGTATTGATACATTTCATAGTGTATCGATACAT
1 AAATTTACCTGCATGTATCGATACATTTCATGGTGTATCGATACAT
1270341 CTGGGCAAAT
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 114 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (72 bp):
AAATTTACCTGCATGTATCGATACATTTCATGGTGTATCGATACATTTCATGGTGTATCGATACA
TCTGGGC
Found at i:1270312 original size:52 final size:52
Alignment explanation
Indices: 1270256--1270371 Score: 187
Period size: 52 Copynumber: 2.2 Consensus size: 52
1270246 CATTTCATGG
* *
1270256 TGTATCGATACATTTCATGGTGTATCGATACATCTGGGCAAATTTACCTGTA
1 TGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTACCTGCA
* * *
1270308 TGTATTGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGCTTGCA
1 TGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTACCTGCA
1270360 TGTATCGATACA
1 TGTATCGATACA
1270372 AAGATCAGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (52 bp):
TGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTACCTGCA
Found at i:1270382 original size:52 final size:52
Alignment explanation
Indices: 1270256--1270391 Score: 166
Period size: 52 Copynumber: 2.6 Consensus size: 52
1270246 CATTTCATGG
** * *
1270256 TGTATCGATACATTTCATGGTGTATCGATACATCTGGGCAAATTTACCTGTA
1 TGTATCGATACATAACATAGTGTATCGATACATCTGGGCAAATTTACCTGCA
* ** * *
1270308 TGTATTGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGCTTGCA
1 TGTATCGATACATAACATAGTGTATCGATACATCTGGGCAAATTTACCTGCA
*
1270360 TGTATCGATACA-AAGATCAGTGTATCGATACA
1 TGTATCGATACATAACAT-AGTGTATCGATACA
1270392 ATGTATTGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 2 0.03
52 72 0.97
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (52 bp):
TGTATCGATACATAACATAGTGTATCGATACATCTGGGCAAATTTACCTGCA
Found at i:1271956 original size:19 final size:19
Alignment explanation
Indices: 1271912--1271984 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
1271902 CTGCCAGTTT
**
1271912 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1271932 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1271951 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
1271972 -ATGTATCGATACA
1 CATGTATCGATACA
1271985 TCTGGGTGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.60
21 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1277471 original size:30 final size:30
Alignment explanation
Indices: 1277435--1277545 Score: 163
Period size: 30 Copynumber: 3.7 Consensus size: 30
1277425 ATACCTTCTT
*
1277435 AAAGTCCACGACTCAGTGGCATTTTGTCCC
1 AAAGTCCACGAATCAGTGGCATTTTGTCCC
1277465 AAAGTCCACGAATCAGTGGCATTTTGTCCC
1 AAAGTCCACGAATCAGTGGCATTTTGTCCC
* *
1277495 AAA-TCCATGAATCAGTGGCATTTTTTCTCC
1 AAAGTCCACGAATCAGTGGCATTTTGTC-CC
1277525 AAAGTCCAC-AACTCAGTGGCA
1 AAAGTCCACGAA-TCAGTGGCA
1277546 ATCTCTTTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
29 22 0.30
30 39 0.53
31 13 0.18
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (30 bp):
AAAGTCCACGAATCAGTGGCATTTTGTCCC
Found at i:1277544 original size:31 final size:31
Alignment explanation
Indices: 1277435--1277616 Score: 171
Period size: 31 Copynumber: 5.9 Consensus size: 31
1277425 ATACCTTCTT
* *
1277435 AAAGTCCACGACTCAGTGGCATTTTGTC-CC
1 AAAGTCCACAACTCAGTGGCATTTTTTCTCC
*
1277465 AAAGTCCACGAA-TCAGTGGCATTTTGTC-CC
1 AAAGTCCAC-AACTCAGTGGCATTTTTTCTCC
*
1277495 AAA-TCCATGAA-TCAGTGGCATTTTTTCTCC
1 AAAGTCCA-CAACTCAGTGGCATTTTTTCTCC
*
1277525 AAAGTCCACAACTCAGTGGCAATCTCTTT-T-C
1 AAAGTCCACAACTCAGTGGC-AT-TTTTTCTCC
* * *
1277556 AAAGTCCACAACTCAATGGCATCTTTTCTTC
1 AAAGTCCACAACTCAGTGGCATTTTTTCTCC
* * *
1277587 AAAGCCCACAACTCCGTGGCACCTTTTTCT
1 AAAGTCCACAACTCAGTGGCA-TTTTTTCT
1277617 TTTCAAAGCC
Statistics
Matches: 129, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
29 24 0.19
30 40 0.31
31 52 0.40
32 9 0.07
33 4 0.03
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (31 bp):
AAAGTCCACAACTCAGTGGCATTTTTTCTCC
Found at i:1277627 original size:34 final size:34
Alignment explanation
Indices: 1277549--1277713 Score: 219
Period size: 35 Copynumber: 4.9 Consensus size: 34
1277539 AGTGGCAATC
* ** *
1277549 TCTTTTCAAAGTCCACAACTCAATGGCATC-TTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
1277582 TC--TTCAAAGCCCACAACTCCGTGGCACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
*
1277614 TCTTTTCAAAGCCCACAATTCCGTGGCACCCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCA-CCTTTT
*
1277649 TCTTTTCAAAGCCCACCACTCCGTGGCACTCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTT
* *
1277684 TCTTTTTAAAGTCCACAACTCCGTGGCACC
1 TCTTTTCAAAGCCCACAACTCCGTGGCACC
1277714 CCCTCTAAAG
Statistics
Matches: 117, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.19
32 5 0.04
33 2 0.02
34 25 0.21
35 63 0.54
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.33
Consensus pattern (34 bp):
TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
Found at i:1277754 original size:33 final size:33
Alignment explanation
Indices: 1277716--1277849 Score: 214
Period size: 33 Copynumber: 4.1 Consensus size: 33
1277706 GTGGCACCCC
*
1277716 CTCTAAAGCCCATACAAGTTGGTGGCAACCATT
1 CTCTAAAGCCCACACAAGTTGGTGGCAACCATT
1277749 CTCTAAAGCCCACACAAGTTGGTGGCAACCATT
1 CTCTAAAGCCCACACAAGTTGGTGGCAACCATT
* * *
1277782 CTTTAAAGCCCACACAAGTCGGTGGCAACCACT
1 CTCTAAAGCCCACACAAGTTGGTGGCAACCATT
* *
1277815 CTTTAAAGCCCACACAAGTTGGTGGCAACCCTT
1 CTCTAAAGCCCACACAAGTTGGTGGCAACCATT
1277848 CT
1 CT
1277850 AAGCCCAATA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 94 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (33 bp):
CTCTAAAGCCCACACAAGTTGGTGGCAACCATT
Found at i:1277765 original size:64 final size:66
Alignment explanation
Indices: 1277697--1277831 Score: 166
Period size: 66 Copynumber: 2.1 Consensus size: 66
1277687 TTTTAAAGTC
* * *
1277697 CACAACTCCGTGGC-ACC-CCCTCTAAAGCCCATACAAGTTGGTGGCAACCATTCTCTAAAGCCC
1 CACAACTCCGTGGCAACCACCCTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAAGCCC
1277760 A
66 A
* ** ** * *
1277761 CACAAGTTGGTGGCAACCATTCTTTAAAGCCCACACAAGTCGGTGGCAACCACTCTTTAAAGCCC
1 CACAACTCCGTGGCAACCACCCTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAAGCCC
1277826 A
66 A
1277827 CACAA
1 CACAA
1277832 GTTGGTGGCA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 11 0.19
65 3 0.05
66 45 0.76
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.19
Consensus pattern (66 bp):
CACAACTCCGTGGCAACCACCCTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAAGCCC
A
Found at i:1278010 original size:43 final size:43
Alignment explanation
Indices: 1277944--1278486 Score: 654
Period size: 43 Copynumber: 12.1 Consensus size: 43
1277934 GCACCTTCAT
*
1277944 CTTTCAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1277987 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
*
1278030 CTTTATCTTTCAATCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTA------AGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
1278079 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1278122 CTTTATCTTTCAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTA------AGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1278171 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C
* ** *
1278215 TTTATCTTTAAGACCAATGTCCCTGGCCTTGAATAAGCACATTGGCAC
1 -----CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1278263 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C
*
1278307 TTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAT
1 -----CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
1278355 CTTTAAGTCCAATGTAGTTGGCCTTGAATCAGTACATTGGCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
*
1278398 CTTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * **
1278441 CTTTATGTCCAATGTAGCTAGCCTTGAATCAATACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1278484 CTT
1 CTT
1278487 CATCTTTAAG
Statistics
Matches: 435, Mismatches: 41, Indels: 48
0.83 0.08 0.09
Matches are distributed among these distances:
43 276 0.63
44 2 0.00
48 1 0.00
49 156 0.36
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1278023 original size:92 final size:92
Alignment explanation
Indices: 1277893--1278502 Score: 955
Period size: 92 Copynumber: 6.7 Consensus size: 92
1277883 TGGCACCTTT
* * * *
1277893 ACCTTTAAGTCCAATATAGCTGGCATTGAATCAACATATTGGCACCTTCATCTTTCAGTCCAATG
1 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1277958 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
1277985 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTCAA-TCCAAT
1 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT-AAGTCCAAT
1278049 GTAGCTGGCCTTGAATCAGCACATTGGC
65 GTAGCTGGCCTTGAATCAGCACATTGGC
* *
1278077 ACCTTTAAGTCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTCAGTCCAATG
1 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1278142 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
*
1278169 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATG
1 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
** *
1278234 TCCCTGGCCTTGAATAAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
1278261 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1278326 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
* * * * *
1278353 ATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGTACATTGG---C---ATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
*
1278412 TAGCTGGCCTTGAATTAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
* * * ** * *
1278439 ACCTTTATGTCCAATGTAGCTAGCCTTGAATCAATACATTGGCACCTTCATCTTTAAGTCCAAT
1 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
1278503 ATCGCTAGTG
Statistics
Matches: 483, Mismatches: 27, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
86 79 0.16
89 2 0.00
91 1 0.00
92 400 0.83
93 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (92 bp):
ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGGC
Found at i:1278081 original size:21 final size:20
Alignment explanation
Indices: 1278057--1278124 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
1278047 ATGTAGCTGG
1278057 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCA-ATTGGCA
* *
1278078 CCTTTAAGTC--CAATATAGCTA
1 CCTTGAA-TCAGCAAT-TGGC-A
1278099 GCCTTGAATCAGCATATTGGCA
1 -CCTTGAATCAGCA-ATTGGCA
1278121 CCTT
1 CCTT
1278125 TATCTTTCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (20 bp):
CCTTGAATCAGCAATTGGCA
Found at i:1279602 original size:52 final size:51
Alignment explanation
Indices: 1279542--1279929 Score: 279
Period size: 52 Copynumber: 7.4 Consensus size: 51
1279532 AAATAACGAG
* *
1279542 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGGAAATAAAATCGGA
** * *
1279594 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATC-GA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* * * * *
1279645 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGG
1 -GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAATCGGA
* *** * *
1279698 GTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCAGG-
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATC-GGA
* * * *** * * *
1279749 GTTGGAGTATGCCC--TCG-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTGT-T-TTGGA-AATAAAATCGGA
*
1279804 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTCTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTG-TTT-TGGAAATAAAATCGGA
* * *
1279858 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGGAAATAAAATCGGA
*
1279909 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1279930 GAGAATTGAG
Statistics
Matches: 258, Mismatches: 53, Indels: 50
0.71 0.15 0.14
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 68 0.26
52 98 0.38
53 30 0.12
54 27 0.10
55 15 0.06
56 3 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:1279782 original size:28 final size:26
Alignment explanation
Indices: 1279747--1279819 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 26
1279737 AATAAAGTCA
1279747 GGGTTGGAGTATGCCCTCG-GAAATAACG
1 GGGTTGGAGTAT-CCC-CGAG-AATAACG
*
1279775 GGGTTGGAGTATCCCCGATGATTAACG
1 GGGTTGGAGTATCCCCGA-GAATAACG
1279802 GGGTTGGAGTATCCCCGA
1 GGGTTGGAGTATCCCCGA
1279820 TTGTGAAGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.05
27 27 0.64
28 13 0.31
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (26 bp):
GGGTTGGAGTATCCCCGAGAATAACG
Found at i:1282304 original size:13 final size:13
Alignment explanation
Indices: 1282286--1282311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1282276 ACAAAGATCC
1282286 ATGTATCGATACA
1 ATGTATCGATACA
1282299 ATGTATCGATACA
1 ATGTATCGATACA
1282312 CAAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1282375 original size:19 final size:18
Alignment explanation
Indices: 1282351--1282418 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1282341 CAGTAGCTAA
1282351 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1282370 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1282385 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1282402 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1282419 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1282391 original size:13 final size:13
Alignment explanation
Indices: 1282373--1282397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1282363 ACAATACTTA
1282373 TGTATCGATACAT
1 TGTATCGATACAT
1282386 TGTATCGATACA
1 TGTATCGATACA
1282398 AAACTTATGT
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:1282395 original size:32 final size:32
Alignment explanation
Indices: 1282354--1282416 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1282344 TAGCTAATTA
*
1282354 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1282386 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1282417 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1282676 original size:55 final size:55
Alignment explanation
Indices: 1282592--1283164 Score: 616
Period size: 55 Copynumber: 10.0 Consensus size: 55
1282582 TAAAAGAGGT
* * * *
1282592 GTCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCATTAAAAGGT
1 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* * * * *
1282647 GTCTTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAACGGG
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
*
1282702 GTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGC
* *
1282762 GTCCCGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGT
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
*
1282817 GTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGC
* *
1282877 ATCCCGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGC
* * * *
1282936 GTCCCGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGAGCTTTAAAAGGG
1 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
* *
1282991 GTCCTGCTCTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----AAAAGGC
* * *
1283051 ATCCCGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT---A--A-AAGGC
*
1283112 GTCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG
1 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
1283165 AAAAAGCATC
Statistics
Matches: 453, Mismatches: 42, Indels: 46
0.84 0.08 0.09
Matches are distributed among these distances:
54 8 0.02
55 188 0.42
56 1 0.00
58 4 0.01
59 57 0.13
60 139 0.31
61 56 0.12
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.26
Consensus pattern (55 bp):
GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
Found at i:1282799 original size:115 final size:114
Alignment explanation
Indices: 1282592--1283164 Score: 675
Period size: 115 Copynumber: 5.0 Consensus size: 114
1282582 TAAAAGAGGT
* * * *
1282592 GTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCATT----AAAAGGTGTCTTG
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTG
* *
1282653 CTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAACGGG
66 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGG
* *
1282702 GTCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCGTCC
1 GTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCGTCC
* * *
1282766 CGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGT
64 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGG
* * *
1282817 GTCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCC
1 GTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCGTCC
* *
1282881 CGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGC
64 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGG
* * *
1282936 GTCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTT----AAAAGGGGTCCTG
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTG
* *
1282997 CTCTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGG
66 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG----GG
* * *
1283050 CATCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTC
1 -GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAA-GAAAAGGCGTC
* *
1283115 CTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG
63 CTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
1283165 AAAAAGCATC
Statistics
Matches: 405, Mismatches: 33, Indels: 39
0.85 0.07 0.08
Matches are distributed among these distances:
109 4 0.01
110 43 0.11
111 1 0.00
114 50 0.12
115 206 0.51
119 44 0.11
120 4 0.01
121 50 0.12
122 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.26
Consensus pattern (114 bp):
GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCTG
CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGG
Found at i:1282976 original size:174 final size:173
Alignment explanation
Indices: 1282598--1283164 Score: 869
Period size: 174 Copynumber: 3.3 Consensus size: 173
1282588 AGGTGTCCTA
* *
1282598 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCATTAAAAGGTGTCTTGCTCTTTGGGG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGGG
* ** * *
1282663 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---G-AACGGGGTCCTGCTCTTTGGGGACTGAA
66 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAA
1282724 AGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCGTCCCG
131 AGGTGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCGTCCCG
*
1282768 CTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGG
1 CTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGG
1282832 GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACT-
65 GACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCATCCCGCTCTTTGAGGACTG
1282896 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGCGTCCCG
129 AAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGAAAAGGCGTCCCG
* *
1282942 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTTAAAAGGGGTCCTGCTCTTTGGGG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGGG
*
1283007 ACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCATCCCGCTCTTTGAGGACTGG
66 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCATCCCGCTCTTTGAGGACT-G
* * *
1283072 AAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTG
129 AAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-GAAAAGGCGTCCCG
* *
1283118 CTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1283165 AAAAAGCATC
Statistics
Matches: 366, Mismatches: 19, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
169 4 0.01
170 89 0.24
173 2 0.01
174 162 0.44
175 48 0.13
176 61 0.17
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.26
Consensus pattern (173 bp):
CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGGG
ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAA
AGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGGCGTCCCG
Found at i:1284194 original size:12 final size:11
Alignment explanation
Indices: 1284171--1284226 Score: 67
Period size: 12 Copynumber: 4.9 Consensus size: 11
1284161 CTTTTCTCTC
*
1284171 TTTTTCTTTGT
1 TTTTTTTTTGT
1284182 TTTGTTTTTTGT
1 TTT-TTTTTTGT
*
1284194 TTTGTTTTTTCT
1 TTT-TTTTTTGT
*
1284206 TTTTTTTTTGC
1 TTTTTTTTTGT
1284217 TTTTTTTTTG
1 TTTTTTTTTG
1284227 AAGAGAAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 19 0.47
12 21 0.52
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:1284203 original size:19 final size:19
Alignment explanation
Indices: 1284156--1284222 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 19
1284146 AAGCAGGTTC
* *
1284156 TTTTCCTTTTCTCTCTTTTT
1 TTTTGCTTTTTTCT-TTTTT
* * *
1284176 CTTTG-TTTTGT-TTTTTG
1 TTTTGCTTTTTTCTTTTTT
1284193 TTTTG-TTTTTTCTTTTTT
1 TTTTGCTTTTTTCTTTTTT
1284211 TTTTGCTTTTTT
1 TTTTGCTTTTTT
1284223 TTTGAAGAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 13 0.34
18 11 0.29
19 11 0.29
20 3 0.08
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (19 bp):
TTTTGCTTTTTTCTTTTTT
Done.