Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009596.1 Hibiscus syriacus cultivar Beakdansim tig00116975_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1846166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1194705 original size:24 final size:24
Alignment explanation
Indices: 1194654--1194701 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1194644 AATAATTTGA
*
1194654 TAATAATGATTTAGTAATTATTAT
1 TAATAATGATTTAGTAATTAATAT
*
1194678 TAATAATGATTTA-TTATTAATAT
1 TAATAATGATTTAGTAATTAATAT
1194701 T
1 T
1194702 TAATTATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
TAATAATGATTTAGTAATTAATAT
Found at i:1194708 original size:17 final size:17
Alignment explanation
Indices: 1194668--1194709 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1194658 AATGATTTAG
1194668 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
1194685 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
1194702 TAATTATT
1 TAATTATT
1194710 TGATTTTATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:1197285 original size:21 final size:21
Alignment explanation
Indices: 1197261--1197300 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1197251 TTTCTATATG
1197261 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1197282 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1197301 ACTAATTTTT
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:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1197341 original size:18 final size:18
Alignment explanation
Indices: 1197320--1197380 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
1197310 TTGTTTTACC
1197320 CTAATTTATAATAATAAA
1 CTAATTTATAATAATAAA
*
1197338 CTAA--T-T-A-ACT-AA
1 CTAATTTATAATAATAAA
1197350 -TAATTTATAATAATAAA
1 CTAATTTATAATAATAAA
1197367 CTAATTTA-AATAAT
1 CTAATTTATAATAAT
1197381 TATTCTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
11 3 0.09
12 2 0.06
13 3 0.09
14 2 0.06
15 2 0.06
16 3 0.09
17 8 0.24
18 11 0.32
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (18 bp):
CTAATTTATAATAATAAA
Found at i:1197349 original size:26 final size:27
Alignment explanation
Indices: 1197320--1197381 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 27
1197310 TTGTTTTACC
1197320 CTAATTTATAATAATAAACTAA-TTAA
1 CTAATTTATAATAATAAACTAATTTAA
1197346 CTAATAATTTATAATAATAAACTAATTTAA
1 C---TAATTTATAATAATAAACTAATTTAA
*
1197376 ATAATT
1 CTAATT
1197382 ATTCTTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 1 0.03
27 5 0.16
29 21 0.68
30 4 0.13
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (27 bp):
CTAATTTATAATAATAAACTAATTTAA
Found at i:1197668 original size:21 final size:21
Alignment explanation
Indices: 1197615--1197654 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1197605 TTTATGTATC
1197615 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1197636 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1197655 ACTAATTAAC
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:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1197947 original size:12 final size:11
Alignment explanation
Indices: 1197917--1197951 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1197907 AGCTGAACGA
1197917 CTGCAATAATG
1 CTGCAATAATG
*
1197928 CAGCAATAAGTG
1 CTGCAATAA-TG
1197940 CTGCAATAATG
1 CTGCAATAATG
1197951 C
1 C
1197952 AGTTGAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (11 bp):
CTGCAATAATG
Found at i:1198144 original size:29 final size:29
Alignment explanation
Indices: 1198066--1198150 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
1198056 CAAAACATGC
* * * *
1198066 ATGTCGCTCGGATGCCCTGACGGCCTACC
1 ATGTCGCTGGGATGCCCTGGCGACCTACA
* *
1198095 ATGTCGCTGGGATGCCATGGCGTCCTACA
1 ATGTCGCTGGGATGCCCTGGCGACCTACA
1198124 ATGTCGCTGGGATGCCCTGGCGACCTA
1 ATGTCGCTGGGATGCCCTGGCGACCTA
1198151 TCCATTCACG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.32, G:0.31, T:0.22
Consensus pattern (29 bp):
ATGTCGCTGGGATGCCCTGGCGACCTACA
Found at i:1201174 original size:16 final size:16
Alignment explanation
Indices: 1201127--1201180 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
1201117 CAATTAGTTT
*
1201127 TTATTTATA-TATATA
1 TTATTTATATTATAGA
* *
1201142 TATATATAATATAATAGA
1 T-TAT-TTATATTATAGA
1201160 TTATTTATATTATAGA
1 TTATTTATATTATAGA
1201176 TTATT
1 TTATT
1201181 AGATTTTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.03
16 18 0.58
17 7 0.23
18 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (16 bp):
TTATTTATATTATAGA
Found at i:1213521 original size:15 final size:15
Alignment explanation
Indices: 1213501--1213531 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1213491 AATAAGAATG
1213501 AATTAATGAATCTTA
1 AATTAATGAATCTTA
*
1213516 AATTAATGACTCTTA
1 AATTAATGAATCTTA
1213531 A
1 A
1213532 CAGAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (15 bp):
AATTAATGAATCTTA
Found at i:1224102 original size:31 final size:31
Alignment explanation
Indices: 1224064--1224135 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
1224054 CAGTTACATC
**
1224064 GGGACCATATTGCAAATGGACTAAATGTTGG
1 GGGACCATATTGCAAACAGACTAAATGTTGG
1224095 GGGACCATATTGCAAACAGACTAAATGTTGG
1 GGGACCATATTGCAAACAGACTAAATGTTGG
*
1224126 GGGACTATAT
1 GGGACCATAT
1224136 AGTAAGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATGTTGG
Found at i:1224807 original size:30 final size:30
Alignment explanation
Indices: 1224771--1224834 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
1224761 CAGTTACGTC
*
1224771 GGGGACCATATTGCAAAT-GAACTAAATGTT
1 GGGGACCATATTACAAATAG-ACTAAATGTT
*
1224801 GGGGACCATATTACAAATAGACTAATTGTT
1 GGGGACCATATTACAAATAGACTAAATGTT
1224831 GGGG
1 GGGG
1224835 GACTTTATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (30 bp):
GGGGACCATATTACAAATAGACTAAATGTT
Found at i:1225054 original size:3 final size:3
Alignment explanation
Indices: 1225046--1225074 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1225036 ACGTGGTGTT
1225046 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1225075 TGTCAACCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1225140 original size:27 final size:27
Alignment explanation
Indices: 1225102--1225170 Score: 124
Period size: 25 Copynumber: 2.6 Consensus size: 27
1225092 TAATTAAACA
1225102 AAGGAAAAGTTAATGTTTTTTTATCAG
1 AAGGAAAAGTTAATGTTTTTTTATCAG
1225129 AAGGAAAAGTTAA--TTTTTTTATCAG
1 AAGGAAAAGTTAATGTTTTTTTATCAG
1225154 AAGGAAAAGTTAATGTT
1 AAGGAAAAGTTAATGTT
1225171 AAAGACAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
25 25 0.62
27 15 0.38
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.38
Consensus pattern (27 bp):
AAGGAAAAGTTAATGTTTTTTTATCAG
Found at i:1227372 original size:21 final size:22
Alignment explanation
Indices: 1227330--1227377 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1227320 CTAAAATCAT
** *
1227330 TTTAAAAAAAATATGCTTTAAA
1 TTTAAAAAAAATAAACTATAAA
1227352 TTTAAAAAAAA-AAACTATAAA
1 TTTAAAAAAAATAAACTATAAA
*
1227373 ATTAA
1 TTTAA
1227378 CATCGTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
TTTAAAAAAAATAAACTATAAA
Found at i:1228111 original size:14 final size:14
Alignment explanation
Indices: 1228092--1228119 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1228082 AGACAAACCG
1228092 GTCGAAATTTCTAT
1 GTCGAAATTTCTAT
1228106 GTCGAAATTTCTAT
1 GTCGAAATTTCTAT
1228120 TTTCTCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
GTCGAAATTTCTAT
Found at i:1231603 original size:6 final size:6
Alignment explanation
Indices: 1231588--1231918 Score: 599
Period size: 6 Copynumber: 54.8 Consensus size: 6
1231578 ATGATTGGCC
* * * *
1231588 CATATA CATATG CATATG CATATA CATATA CATATA CATATG CATATG
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1231636 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
*
1231684 CATATATA TATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 C--ATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1231734 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1231782 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1231830 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1231878 CATATA CATATA CATATA CATATA CATATA CATATA CATAT
1 CATATA CATATA CATATA CATATA CATATA CATATA CATAT
1231919 CATCTTCTAA
Statistics
Matches: 317, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
6 312 0.98
8 5 0.02
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.34
Consensus pattern (6 bp):
CATATA
Found at i:1232060 original size:20 final size:20
Alignment explanation
Indices: 1232035--1232083 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1232025 GATCTATGAT
*
1232035 ATTTATTATAATATTTTAGA
1 ATTTATTACAATATTTTAGA
*
1232055 ATTTATTACAGTATTTTAGA
1 ATTTATTACAATATTTTAGA
1232075 ATTTATTAC
1 ATTTATTAC
1232084 GTGGGCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (20 bp):
ATTTATTACAATATTTTAGA
Found at i:1233429 original size:12 final size:12
Alignment explanation
Indices: 1233412--1233436 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1233402 CATCTTCCCC
1233412 CTTTCCAAATCA
1 CTTTCCAAATCA
1233424 CTTTCCAAATCA
1 CTTTCCAAATCA
1233436 C
1 C
1233437 AGCACATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (12 bp):
CTTTCCAAATCA
Found at i:1242466 original size:23 final size:23
Alignment explanation
Indices: 1242418--1242467 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1242408 TCATTTTTGC
* **
1242418 TTTTATTTTTTTTAATAATAGTA
1 TTTTATTTTTTTGAATAATAAAA
1242441 TTTTATTTTTTTGAA-AAGTAAAA
1 TTTTATTTTTTTGAATAA-TAAAA
1242464 TTTT
1 TTTT
1242468 CAAAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (23 bp):
TTTTATTTTTTTGAATAATAAAA
Found at i:1244719 original size:14 final size:13
Alignment explanation
Indices: 1244694--1244756 Score: 53
Period size: 14 Copynumber: 5.0 Consensus size: 13
1244684 TTAAAATATC
*
1244694 ATATATTTATTTT
1 ATATAATTATTTT
1244707 ATATAAATTATTTT
1 ATAT-AATTATTTT
*
1244721 -T-T-ATTA-TTC
1 ATATAATTATTTT
*
1244730 ATATATTTATTTT
1 ATATAATTATTTT
1244743 ATATAAATTATTTT
1 ATAT-AATTATTTT
1244757 TTATTATTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
9 2 0.05
10 5 0.13
11 1 0.03
12 4 0.10
13 11 0.28
14 16 0.41
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
ATATAATTATTTT
Found at i:1244723 original size:21 final size:22
Alignment explanation
Indices: 1244699--1244742 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1244689 ATATCATATA
1244699 TTTATT-TT-ATATAAATTATTT
1 TTTATTATTCATAT-AATTATTT
*
1244720 TTTATTATTCATATATTTATTT
1 TTTATTATTCATATAATTATTT
1244742 T
1 T
1244743 ATATAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATTATTCATATAATTATTT
Found at i:1244732 original size:36 final size:36
Alignment explanation
Indices: 1244692--1244767 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
1244682 CTTTAAAATA
1244692 TCATATATTTATTTTATATAAATTATTTTTTATTAT
1 TCATATATTTATTTTATATAAATTATTTTTTATTAT
1244728 TCATATATTTATTTTATATAAATTATTTTTTATTAT
1 TCATATATTTATTTTATATAAATTATTTTTTATTAT
1244764 TCAT
1 TCAT
1244768 GAATAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (36 bp):
TCATATATTTATTTTATATAAATTATTTTTTATTAT
Found at i:1244776 original size:21 final size:19
Alignment explanation
Indices: 1244715--1244777 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 19
1244705 TTATATAAAT
1244715 TATTTTTTATTATTCAT-A
1 TATTTTTTATTATTCATAA
*
1244733 TATTTATT-TTA-T-ATAAA
1 TATTTTTTATTATTCAT-AA
1244750 TTATTTTTTATTATTCATGAA
1 -TATTTTTTATTATTCAT-AA
1244771 TAATTTT
1 T-ATTTT
1244778 AATACTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
15 2 0.06
16 1 0.03
17 4 0.11
18 14 0.40
19 3 0.09
20 2 0.06
21 9 0.26
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTTTTATTATTCATAA
Found at i:1258760 original size:31 final size:31
Alignment explanation
Indices: 1258722--1258783 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1258712 CATTCGTTCA
*
1258722 ATAATTAGAAATCAATATAAAATTAAAGAAT
1 ATAATTAGAAATCAATATAAAACTAAAGAAT
1258753 ATAATTAGAAATCAATATAAAACTAAAGAAT
1 ATAATTAGAAATCAATATAAAACTAAAGAAT
1258784 TTTATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.27
Consensus pattern (31 bp):
ATAATTAGAAATCAATATAAAACTAAAGAAT
Found at i:1258771 original size:16 final size:16
Alignment explanation
Indices: 1258722--1258772 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1258712 CATTCGTTCA
1258722 ATAATTAGAAATCAAT
1 ATAATTAGAAATCAAT
*
1258738 ATAAAATT--AAA-GAAT
1 AT--AATTAGAAATCAAT
1258753 ATAATTAGAAATCAAT
1 ATAATTAGAAATCAAT
1258769 ATAA
1 ATAA
1258773 AACTAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 4 0.14
15 8 0.29
16 12 0.43
18 4 0.14
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (16 bp):
ATAATTAGAAATCAAT
Found at i:1258815 original size:2 final size:2
Alignment explanation
Indices: 1258808--1258836 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1258798 CCAGATCGTG
1258808 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1258837 TTATGTACCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1267595 original size:17 final size:16
Alignment explanation
Indices: 1267559--1267593 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1267549 GAAATTTTTT
*
1267559 AAATTTTTTAAATTTA
1 AAATTTTTTAAATTAA
*
1267575 AAATTTTTTTAATTAA
1 AAATTTTTTAAATTAA
1267591 AAA
1 AAA
1267594 ATAGTTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATTTTTTAAATTAA
Found at i:1267765 original size:23 final size:23
Alignment explanation
Indices: 1267735--1267779 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1267725 GCAGAACTGG
1267735 AAGCATAATTCAGTATACAAACC
1 AAGCATAATTCAGTATACAAACC
1267758 AAGCATAATTCAGTATACAAAC
1 AAGCATAATTCAGTATACAAAC
1267780 AGTTTACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.22
Consensus pattern (23 bp):
AAGCATAATTCAGTATACAAACC
Found at i:1272652 original size:18 final size:18
Alignment explanation
Indices: 1272631--1272667 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1272621 ATTTTATTTA
1272631 GTTTTAAAATTTAAATGG
1 GTTTTAAAATTTAAATGG
1272649 GTTTTAAAATTTAAATGG
1 GTTTTAAAATTTAAATGG
1272667 G
1 G
1272668 CAGTGGGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (18 bp):
GTTTTAAAATTTAAATGG
Found at i:1278086 original size:41 final size:42
Alignment explanation
Indices: 1277982--1278220 Score: 143
Period size: 42 Copynumber: 5.8 Consensus size: 42
1277972 AATCATACTT
* * *
1277982 TAGCAGCGTTTTTTAAACAAACGCCGTAATAGAGTGGTAATT-
1 TAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTGGT-ATTA
* * * *
1278024 TAGCGGCGTTTTTAGC-TCAAACGCCGCAATTGAGTTGT-TTA
1 TAGCGGCGTTTTT-TCAACAAACGCCGCAATAGAGTGGTATTA
* * * *
1278065 TAGTGGCGTTTTTTCAACAAACACCGAAATAGAGTGGTAATA
1 TAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTATTA
* * *
1278107 TAGCGGCGTTTTTGT--ACAAACGCCACGATA-A-TGTTATTTA
1 TAGCGGCGTTTTT-TCAACAAACGCCGCAATAGAGTGGTA-TTA
* * * * ** * *
1278147 TAGTGGCGTTTGTTCAAAAAACGACGGTATAGATTAGTAATT-
1 TAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTGGT-ATTA
* * * *
1278189 TAGCTGCGTTTATTAAATAAACGCCGCAATAG
1 TAGCGGCGTTTTTTCAACAAACGCCGCAATAG
1278221 TATTGTTTAT
Statistics
Matches: 147, Mismatches: 39, Indels: 22
0.71 0.19 0.11
Matches are distributed among these distances:
39 5 0.03
40 17 0.12
41 50 0.34
42 69 0.47
43 5 0.03
44 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (42 bp):
TAGCGGCGTTTTTTCAACAAACGCCGCAATAGAGTGGTATTA
Found at i:1278086 original size:83 final size:83
Alignment explanation
Indices: 1277987--1278323 Score: 303
Period size: 83 Copynumber: 4.1 Consensus size: 83
1277977 TACTTTAGCA
*
1277987 GCGTTTTTT-AAACAAACGCCGTAATAGAGTGGTAATTTAGCGGCGTTTTTAGCT-CAAACGCCG
1 GCGTTTTTTCAAA-AAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTT-GCTACAAACGCCG
1278050 CAATTGA-GTTGTTTATAGTG
64 CAA-TGATGTTGTTTATAGTG
* * * * * * *
1278070 GCGTTTTTTCAACAAACACCGAAATAGAGTGGTAATATAGCGGCGTTTTTG-TACAAACGCCACG
1 GCGTTTTTTCAAAAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTGCTACAAACGCCGCA
* *
1278134 ATAATGTTATTTATAGTG
66 ATGATGTTGTTTATAGTG
* * * * ** *
1278152 GCGTTTGTTCAAAAAACGACGGT-ATAGATTAGTAATTTAGCTGCGTTTATT-AAATAAACGCCG
1 GCGTTTTTTCAAAAAACG-CCGTAATAGAGTAGTAATTTAGCGGCGTTT-TTGCTACAAACGCCG
*
1278215 CAAT-AGTATTGTTTATAGTG
64 CAATGA-TGTTGTTTATAGTG
* * * * * * * * *
1278235 ACATTTGTGCAAAAAATGCAGTAATAGAGTAATAATTTAGCGGCGTTTGTCCTACAAACGCCGCA
1 GCGTTTTTTCAAAAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTGCTACAAACGCCGCA
*
1278300 AT-ATGTTGTTTATCGTG
66 ATGATGTTGTTTATAGTG
*
1278317 GCATTTT
1 GCGTTTT
1278324 ATAAAAACGC
Statistics
Matches: 206, Mismatches: 39, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
81 3 0.01
82 81 0.39
83 120 0.58
84 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (83 bp):
GCGTTTTTTCAAAAAACGCCGTAATAGAGTAGTAATTTAGCGGCGTTTTTGCTACAAACGCCGCA
ATGATGTTGTTTATAGTG
Found at i:1279554 original size:14 final size:14
Alignment explanation
Indices: 1279535--1279561 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1279525 TTTATTATTT
1279535 CTAGATATATTATA
1 CTAGATATATTATA
1279549 CTAGATATATTAT
1 CTAGATATATTAT
1279562 GCCATTTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
CTAGATATATTATA
Found at i:1281075 original size:17 final size:17
Alignment explanation
Indices: 1281041--1281078 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1281031 AATTTTATCT
*
1281041 ATATTATTAGCAATTAA
1 ATATTATTAGCAACTAA
1281058 ATATTATTATGC-ACTAA
1 ATATTATTA-GCAACTAA
1281075 ATAT
1 ATAT
1281079 GATAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (17 bp):
ATATTATTAGCAACTAA
Found at i:1281451 original size:43 final size:45
Alignment explanation
Indices: 1281404--1281515 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 45
1281394 CATATATTTA
*
1281404 GCGGCGTTTGTGATAAAAACGTCGCGAAATCTCAAGACATA-T-T
1 GCGGCGTTTGTGACAAAAACGTCGCGAAATCTCAAGACATACTCT
* * *
1281447 GCGGCGTTT-TCGACGAAAATG-CTGCTAAATCTCAAGACATACTCT
1 GCGGCGTTTGT-GACAAAAACGTC-GCGAAATCTCAAGACATACTCT
* *
1281492 GCGGAGTTTGT-AGGAAAAACGTCG
1 GCGGCGTTTGTGA-CAAAAACGTCG
1281516 GTAAAAATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
42 2 0.04
43 33 0.61
44 2 0.04
45 15 0.28
46 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (45 bp):
GCGGCGTTTGTGACAAAAACGTCGCGAAATCTCAAGACATACTCT
Found at i:1281593 original size:43 final size:43
Alignment explanation
Indices: 1281537--1281629 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 43
1281527 CATCTACGGT
* * *
1281537 GGCGTTTGTCTGCCAAATGTCGTTAAATATCAACACCTATTGC
1 GGCGTTTGTCTGCCAAACGCCGCTAAATATCAACACCTATTGC
* * * *
1281580 GGTGTTTTTCTGCCAAACGCCGCTAAATATCAATACCTTTTGC
1 GGCGTTTGTCTGCCAAACGCCGCTAAATATCAACACCTATTGC
1281623 GGCGTTT
1 GGCGTTT
1281630 ATTCAACAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (43 bp):
GGCGTTTGTCTGCCAAACGCCGCTAAATATCAACACCTATTGC
Found at i:1281644 original size:43 final size:43
Alignment explanation
Indices: 1281560--1281674 Score: 106
Period size: 43 Copynumber: 2.7 Consensus size: 43
1281550 CAAATGTCGT
* **
1281560 TAAATATCAACACCTATTGCGGTGTTTTTCTGCCAAACGCCGC
1 TAAATATCAACACCTATTGCGGCGTTTTTCTAACAAACGCCGC
* * *
1281603 TAAATATCAATACCTTTTGCGGCGTTTATTC-AACAATCGCCGC
1 TAAATATCAACACCTATTGCGGCGTTT-TTCTAACAAACGCCGC
* * *** *
1281646 TATATGTTGTCACCTATTGCGACGTTTTT
1 TAAATATCAACACCTATTGCGGCGTTTTT
1281675 TTTGTTGAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
42 2 0.04
43 52 0.91
44 3 0.05
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (43 bp):
TAAATATCAACACCTATTGCGGCGTTTTTCTAACAAACGCCGC
Found at i:1285996 original size:2 final size:2
Alignment explanation
Indices: 1285989--1286029 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1285979 TCGTACAAAT
1285989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1286030 TCTAAGATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1290372 original size:23 final size:23
Alignment explanation
Indices: 1290338--1290418 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
1290328 CACCCCTACG
1290338 GTGCAT-GAATGCACCTGCCACTA
1 GTGCATCG-ATGCACCTGCCACTA
1290361 GTGCATCGATGCACCATG---C-A
1 GTGCATCGATGCACC-TGCCACTA
1290381 GTGCATTC-ATGCACCTGCCACTA
1 GTGCA-TCGATGCACCTGCCACTA
1290404 GTGCATCGATGCACC
1 GTGCATCGATGCACC
1290419 ATGCAGTGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.04
20 13 0.26
21 3 0.06
22 3 0.06
23 26 0.52
24 3 0.06
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.22
Consensus pattern (23 bp):
GTGCATCGATGCACCTGCCACTA
Found at i:1290385 original size:20 final size:20
Alignment explanation
Indices: 1290360--1290437 Score: 88
Period size: 20 Copynumber: 3.8 Consensus size: 20
1290350 ACCTGCCACT
1290360 AGTGCATCGATGCACCATGC
1 AGTGCATCGATGCACCATGC
1290380 AGTGCATTC-ATGCACC-TGCCAC
1 AGTGCA-TCGATGCACCATG---C
1290402 TAGTGCATCGATGCACCATGC
1 -AGTGCATCGATGCACCATGC
*
1290423 AGTGCATTGATGCAC
1 AGTGCATCGATGCAC
1290438 TCCATTTCGA
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
19 2 0.04
20 27 0.54
21 3 0.06
22 3 0.06
23 13 0.26
24 2 0.04
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.23
Consensus pattern (20 bp):
AGTGCATCGATGCACCATGC
Found at i:1290393 original size:43 final size:43
Alignment explanation
Indices: 1290346--1290437 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
1290336 CGGTGCATGA
1290346 ATGCACCTGCCACTAGTGCATCGATGCACCATGCAGTGCATTC
1 ATGCACCTGCCACTAGTGCATCGATGCACCATGCAGTGCATTC
*
1290389 ATGCACCTGCCACTAGTGCATCGATGCACCATGCAGTGCATTG
1 ATGCACCTGCCACTAGTGCATCGATGCACCATGCAGTGCATTC
1290432 ATGCAC
1 ATGCAC
1290438 TCCATTTCGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.23
Consensus pattern (43 bp):
ATGCACCTGCCACTAGTGCATCGATGCACCATGCAGTGCATTC
Found at i:1291742 original size:21 final size:20
Alignment explanation
Indices: 1291709--1291750 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1291699 ATTTGAGACC
*
1291709 ATGAATTCCAAATATAAGAAA
1 ATGAATTCAAAATATAA-AAA
*
1291730 ATGATTTCAAAATATAAAAA
1 ATGAATTCAAAATATAAAAA
1291750 A
1 A
1291751 GAAAACAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (20 bp):
ATGAATTCAAAATATAAAAA
Found at i:1291805 original size:20 final size:19
Alignment explanation
Indices: 1291764--1291807 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1291754 AACAATTTTC
* *
1291764 TTTTGAAAGCAAAAATGGA
1 TTTTGAAAACAAAAATGAA
*
1291783 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATG-AA
1291803 TTTTG
1 TTTTG
1291808 TGAAAGGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (19 bp):
TTTTGAAAACAAAAATGAA
Found at i:1293164 original size:21 final size:21
Alignment explanation
Indices: 1293138--1293216 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
1293128 AGGGTGTCAA
1293138 AGTGCATCCATGCACCTCTAC
1 AGTGCATCCATGCACCTCTAC
* *
1293159 AGTGCATCCATGCACCTGCCATT
1 AGTGCATCCATGCACCT-CTA-C
* * *
1293182 AGTGCATCGATGCACC-ATGC
1 AGTGCATCCATGCACCTCTAC
1293202 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1293217 TCCATTTCGA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 14 0.29
21 17 0.35
22 2 0.04
23 15 0.31
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCTCTAC
Found at i:1293353 original size:21 final size:21
Alignment explanation
Indices: 1293324--1293374 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1293314 GAAGGGGTAT
*
1293324 CGATGCACCTTAATAGTGCAC
1 CGATACACCTTAATAGTGCAC
1293345 CGATACACCTTAATAGTGCAC
1 CGATACACCTTAATAGTGCAC
*
1293366 TGATACACC
1 CGATACACC
1293375 ATGTTATGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (21 bp):
CGATACACCTTAATAGTGCAC
Found at i:1308642 original size:4 final size:4
Alignment explanation
Indices: 1308633--1309020 Score: 760
Period size: 4 Copynumber: 97.2 Consensus size: 4
1308623 CGAGATCAGC
*
1308633 TACA TACA TACA TACA TACA TACA TACA TACA TGCA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1308681 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1308729 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1308777 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1308825 TAC- TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1308872 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1308920 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1308968 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1309016 TACA T
1 TACA T
1309021 CTATCTTTGG
Statistics
Matches: 381, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
3 3 0.01
4 378 0.99
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:1317689 original size:11 final size:12
Alignment explanation
Indices: 1317661--1317694 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1317651 TATTTAAACG
1317661 GGTATTGGGCTA
1 GGTATTGGGCTA
*
1317673 GGTATTGGG-TC
1 GGTATTGGGCTA
1317684 GGTATTGGGCT
1 GGTATTGGGCT
1317695 GGGAATCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.09, G:0.44, T:0.35
Consensus pattern (12 bp):
GGTATTGGGCTA
Found at i:1317770 original size:24 final size:25
Alignment explanation
Indices: 1317710--1317793 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 25
1317700 TCAGGCCGGG
1317710 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
1317733 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
1317757 T-T-TATTAATATTATATATATATATA
1 TATATATT-ATATTATTTAAAT-TAAA
1317782 TATATATATATA
1 TATATAT-TATA
1317794 AATAATTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 4 0.08
23 8 0.17
24 24 0.50
25 4 0.08
26 1 0.02
27 6 0.12
28 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:1317775 original size:2 final size:2
Alignment explanation
Indices: 1317764--1317793 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1317754 AAATTTATTA
1317764 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1317794 AATAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1317830 original size:12 final size:13
Alignment explanation
Indices: 1317814--1317858 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1317804 TTTAATATTT
1317814 ATCGGGTCGGGT-
1 ATCGGGTCGGGTA
*
1317826 ATCGGGACGGGTA
1 ATCGGGTCGGGTA
* *
1317839 ATTGGGGCGGGTA
1 ATCGGGTCGGGTA
1317852 ATCGGGT
1 ATCGGGT
1317859 AATCGGGGCG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.16, C:0.13, G:0.49, T:0.22
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:1323382 original size:30 final size:31
Alignment explanation
Indices: 1323310--1323382 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1323300 AAATTCATGG
1323310 TCAAATTGAA-ATTTTATAAAAAGTTTAAGGA
1 TCAAATT-AATATTTTATAAAAAGTTTAAGGA
* * *
1323341 TTAAATTAATATTTTATATAAAGTTTAATG-
1 TCAAATTAATATTTTATAAAAAGTTTAAGGA
*
1323371 TCAAGTTAATAT
1 TCAAATTAATAT
1323383 GCAATCCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (31 bp):
TCAAATTAATATTTTATAAAAAGTTTAAGGA
Found at i:1326530 original size:21 final size:21
Alignment explanation
Indices: 1326504--1326543 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1326494 GTCGAGGGTT
1326504 TCATAGGTCATTCAGGACAAC
1 TCATAGGTCATTCAGGACAAC
* *
1326525 TCATAGGTCCTTCGGGACA
1 TCATAGGTCATTCAGGACA
1326544 TATTCACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
TCATAGGTCATTCAGGACAAC
Found at i:1327416 original size:19 final size:19
Alignment explanation
Indices: 1327371--1327487 Score: 130
Period size: 19 Copynumber: 6.1 Consensus size: 19
1327361 GGCTGCTGGA
* *
1327371 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
*
1327391 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
1327411 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
1327430 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
1327449 AATCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
1327468 AATCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
1327487 A
1 A
1327488 CTCGACCCGA
Statistics
Matches: 88, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.02
19 59 0.67
20 20 0.23
21 7 0.08
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:1327434 original size:29 final size:30
Alignment explanation
Indices: 1327371--1327445 Score: 127
Period size: 29 Copynumber: 2.5 Consensus size: 30
1327361 GGCTGCTGGA
1327371 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
1327402 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
1327430 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1327446 CTGAATCGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.65
30 14 0.33
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:1327455 original size:29 final size:28
Alignment explanation
Indices: 1327372--1327464 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 28
1327362 GCTGCTGGAA
1327372 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
1327402 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * * *
1327430 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
1327459 ACCGGT
1 ACCGGT
1327465 CTGAATCGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.12
29 37 0.64
30 14 0.24
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:1327511 original size:5 final size:5
Alignment explanation
Indices: 1327503--1327565 Score: 72
Period size: 5 Copynumber: 11.8 Consensus size: 5
1327493 CCCGACCGTT
* *
1327503 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC
1327552 GACCC GACCC GACC
1 GACCC GACCC GACC
1327566 GTTGACCGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 42 0.84
7 8 0.16
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:1327516 original size:22 final size:22
Alignment explanation
Indices: 1327490--1327572 Score: 166
Period size: 22 Copynumber: 3.8 Consensus size: 22
1327480 CGGTCTGACT
1327490 CGACCCGACCGTTGACCCGACC
1 CGACCCGACCGTTGACCCGACC
1327512 CGACCCGACCGTTGACCCGACC
1 CGACCCGACCGTTGACCCGACC
1327534 CGACCCGACCGTTGACCCGACC
1 CGACCCGACCGTTGACCCGACC
1327556 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
1327573 GTTGACCGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.10
Consensus pattern (22 bp):
CGACCCGACCGTTGACCCGACC
Found at i:1327574 original size:7 final size:7
Alignment explanation
Indices: 1327562--1327599 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1327552 GACCCGACCC
1327562 GACCGTT
1 GACCGTT
1327569 GACCGTT
1 GACCGTT
1327576 GACCGTT
1 GACCGTT
1327583 GACCGTT
1 GACCGTT
1327590 GACCGTT
1 GACCGTT
1327597 GAC
1 GAC
1327600 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1328544 original size:32 final size:31
Alignment explanation
Indices: 1328497--1328584 Score: 79
Period size: 32 Copynumber: 2.8 Consensus size: 31
1328487 ATCATTCTCG
** *
1328497 GGTAGGCCCTGCGGCCCTAAGATGTGTTCTTA
1 GGTAGGCCCCACGGCCCTAAGATGT-ATCTTA
* * * *
1328529 GGTAGGCCCCACGGCCCCAAAATCTATCTTG
1 GGTAGGCCCCACGGCCCTAAGATGTATCTTA
*
1328560 GGTAGGCTCTCA-GGCCCTAAGATGT
1 GGTAGGC-CCCACGGCCCTAAGATGT
1328585 TCCCTTAGGG
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
31 21 0.48
32 23 0.52
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.24
Consensus pattern (31 bp):
GGTAGGCCCCACGGCCCTAAGATGTATCTTA
Found at i:1334530 original size:19 final size:19
Alignment explanation
Indices: 1334506--1334560 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
1334496 TGCTGGAAAC
*
1334506 CGGTTTGACTGGTCTGAAT
1 CGGTTTGACCGGTCTGAAT
1334525 CGGTTTGACCGGTCTGAAT
1 CGGTTTGACCGGTCTGAAT
1334544 CGGTTTGACCGGTCTGA
1 CGGTTTGACCGGTCTGA
1334561 CCCGACCCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.15, C:0.20, G:0.33, T:0.33
Consensus pattern (19 bp):
CGGTTTGACCGGTCTGAAT
Found at i:1334580 original size:17 final size:17
Alignment explanation
Indices: 1334558--1334596 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1334548 TTGACCGGTC
1334558 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1334575 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1334592 TGACC
1 TGACC
1334597 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1337946 original size:2 final size:2
Alignment explanation
Indices: 1337939--1337968 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1337929 GCCAATTGAT
1337939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1337969 GCTGCTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1345136 original size:22 final size:21
Alignment explanation
Indices: 1345092--1345149 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
1345082 ACTATTCAGA
*
1345092 GGGGAATCGGTACCCCCTTGG
1 GGGGAATCGGTTCCCCCTTGG
1345113 GGGGAATCGGTTCCCCCTTGG
1 GGGGAATCGGTTCCCCCTTGG
1345134 GGGAGAATCGGTTCCC
1 GGG-GAATCGGTTCCC
1345150 TCTGGACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGAATCGGTTCCCCCTTGG
Found at i:1348896 original size:14 final size:14
Alignment explanation
Indices: 1348867--1348911 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
1348857 TATTCGTGAA
1348867 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
1348883 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
1348897 TGTTCATTTATGTT
1 CGTTCATTTATGTT
1348911 C
1 C
1348912 AAACAAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 19 0.70
15 3 0.11
16 5 0.19
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.56
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:1349809 original size:21 final size:21
Alignment explanation
Indices: 1349785--1349838 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1349775 TCTCTCTGAA
*
1349785 TTCTCTCCTATT-TTCTCATAT
1 TTCTCTCCAATTCTTCTC-TAT
* *
1349806 TTCTTTCGAATTCTTCTCTAT
1 TTCTCTCCAATTCTTCTCTAT
*
1349827 TTCTCTTCAATT
1 TTCTCTCCAATT
1349839 TATAACAACT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.57
Consensus pattern (21 bp):
TTCTCTCCAATTCTTCTCTAT
Found at i:1354009 original size:21 final size:21
Alignment explanation
Indices: 1353983--1354027 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1353973 GATTTCTGGG
* *
1353983 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1354004 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1354025 CAA
1 CAA
1354028 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1354900 original size:32 final size:32
Alignment explanation
Indices: 1354859--1354954 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
1354849 GAGTCGAGGG
1354859 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
1354891 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
1354922 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
1354954 T
1 T
1354955 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:1355041 original size:29 final size:30
Alignment explanation
Indices: 1354946--1355038 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
1354936 AAGGAACATA
1354946 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1354976 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
1355006 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1355035 TGGA
1 TGGA
1355039 TAGGTCCTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
29 18 0.30
30 42 0.70
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1358892 original size:21 final size:21
Alignment explanation
Indices: 1358866--1358910 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1358856 GATTTCTGGG
* *
1358866 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1358887 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1358908 CAA
1 CAA
1358911 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1359785 original size:32 final size:32
Alignment explanation
Indices: 1359744--1359839 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
1359734 GAGTCGAGGG
1359744 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
1359776 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
1359807 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
1359839 T
1 T
1359840 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:1359867 original size:30 final size:30
Alignment explanation
Indices: 1359831--1359923 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
1359821 AAGGAACATA
1359831 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1359861 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * * *
1359891 TGGATAGTTATCG-GGGTCTTTGTGACCTT
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1359920 TGGA
1 TGGA
1359924 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 17 0.29
30 41 0.71
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.33
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1360204 original size:2 final size:2
Alignment explanation
Indices: 1360194--1360229 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1360184 GTATGTGTGG
* *
1360194 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1360230 GAAAGGTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1361850 original size:24 final size:24
Alignment explanation
Indices: 1361806--1361852 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1361796 AAATTATATA
*
1361806 AAAATTTTAAGGACATAAAATTAT
1 AAAATTTTAAGAACATAAAATTAT
* *
1361830 AAAATTTTAAGAATATGAAATTA
1 AAAATTTTAAGAACATAAAATTA
1361853 AATCATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (24 bp):
AAAATTTTAAGAACATAAAATTAT
Found at i:1365570 original size:93 final size:93
Alignment explanation
Indices: 1365379--1365611 Score: 236
Period size: 93 Copynumber: 2.4 Consensus size: 93
1365369 TTCATACTCC
* * * * * *
1365379 ACTTCGTTGAATTCGATTCAAAATTTAGATTTAATTCTTTTCTTTTTTGTACAATTTTTGTTCTA
1 ACTTAGTTGAATTCGATTC-AAATTTAGCTTTAATTC-TTTCATATATGTACAATTTTTGTTATA
* *
1365444 ACTAATTGTTTAATCTTTGGCATCAACAGT
64 ACTAATTGTTTAATCTTAGGCATCAACAAT
*
1365474 ACTTAGTTGAATTCGATTCAAATTTAGCTTTAATTCTTT-ATATATGTATATTATTTTT-TTATA
1 ACTTAGTTGAATTCGATTCAAATTTAGCTTTAATTCTTTCATATATGTACA--ATTTTTGTTATA
* *
1365537 ATTAATTGTTTAATCTTAGGCATCGACAAT
64 ACTAATTGTTTAATCTTAGGCATCAACAAT
* * *
1365567 ACTTCACTTCGCTGAATCCGATTCAAATTTAAGCTTTAGTTCTTT
1 ACTT-A----GTTGAATTCGATTCAAATTT-AGCTTTAATTCTTT
1365612 TCTTTTATAT
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
92 7 0.06
93 37 0.32
94 23 0.20
95 18 0.16
98 18 0.16
99 13 0.11
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (93 bp):
ACTTAGTTGAATTCGATTCAAATTTAGCTTTAATTCTTTCATATATGTACAATTTTTGTTATAAC
TAATTGTTTAATCTTAGGCATCAACAAT
Found at i:1379412 original size:22 final size:22
Alignment explanation
Indices: 1379386--1379447 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 22
1379376 TATAAAAAAT
1379386 ATAAATTTTATAAAAAATATTA
1 ATAAATTTTATAAAAAATATTA
* *
1379408 ATAAA-TTAAT-AAGAATA-TA
1 ATAAATTTTATAAAAAATATTA
* *
1379427 ATAAATTAT-TAAAAATTATTA
1 ATAAATTTTATAAAAAATATTA
1379448 TGATCCATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 12 0.39
21 6 0.19
22 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATAAATTTTATAAAAAATATTA
Found at i:1382167 original size:2 final size:2
Alignment explanation
Indices: 1382158--1382200 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1382148 ATTATTAGTT
1382158 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1382199 TA
1 TA
1382201 ACATAAAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1384195 original size:16 final size:17
Alignment explanation
Indices: 1384171--1384205 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1384161 TGCCTCTGTA
*
1384171 AAATTTGTCC-ACATGC
1 AAATGTGTCCTACATGC
1384187 AAATGTGTCCTACATGC
1 AAATGTGTCCTACATGC
1384204 AA
1 AA
1384206 CTAAAATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (17 bp):
AAATGTGTCCTACATGC
Found at i:1389489 original size:15 final size:15
Alignment explanation
Indices: 1389469--1389499 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1389459 CAACAAATAG
1389469 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1389484 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1389499 A
1 A
1389500 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1389672 original size:18 final size:19
Alignment explanation
Indices: 1389649--1389690 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1389639 CCAGTAATCC
*
1389649 TATTCT-CTGGTAATCTTT
1 TATTCTACTGATAATCTTT
1389667 TATTCTCACTGATAATCTTT
1 TATTCT-ACTGATAATCTTT
1389687 TATT
1 TATT
1389691 TCCACTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (19 bp):
TATTCTACTGATAATCTTT
Found at i:1389703 original size:20 final size:20
Alignment explanation
Indices: 1389660--1389705 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1389650 ATTCTCTGGT
* *
1389660 AATCTTTTATTCTCACTGAT
1 AATCTTTTATTCTCACTAAC
1389680 AATCTTTTATT-TCCACTAAC
1 AATCTTTTATTCT-CACTAAC
1389700 AATCTT
1 AATCTT
1389706 ACATTCTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.28, C:0.22, G:0.02, T:0.48
Consensus pattern (20 bp):
AATCTTTTATTCTCACTAAC
Found at i:1392290 original size:26 final size:28
Alignment explanation
Indices: 1392228--1392290 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
1392218 CGAGTATTGC
*
1392228 TGAGCTCGACTCGACTTGAAAACTCTGAAA
1 TGAGCTCGACTCGACTCGAAAACTCTG--A
1392258 TGAAGCTCGACTCGACTCGAAAACTC-G-
1 TG-AGCTCGACTCGACTCGAAAACTCTGA
1392285 TGAGCT
1 TGAGCT
1392291 TAAAATTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 2 0.06
30 3 0.10
31 22 0.71
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (28 bp):
TGAGCTCGACTCGACTCGAAAACTCTGA
Found at i:1402069 original size:35 final size:35
Alignment explanation
Indices: 1402023--1402091 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
1402013 CACTGAGCCG
*
1402023 GATTCGGTCTCAGTTCCTTCATCTCCTTCATACCA
1 GATTCGATCTCAGTTCCTTCATCTCCTTCATACCA
* *
1402058 GATTCGATCTCAGTTCCTTCATCTTCTTCGTACC
1 GATTCGATCTCAGTTCCTTCATCTCCTTCATACC
1402092 GGACAAACAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.16, C:0.33, G:0.12, T:0.39
Consensus pattern (35 bp):
GATTCGATCTCAGTTCCTTCATCTCCTTCATACCA
Found at i:1417425 original size:92 final size:92
Alignment explanation
Indices: 1417268--1417452 Score: 370
Period size: 92 Copynumber: 2.0 Consensus size: 92
1417258 TTGTACCAAA
1417268 TCCGAGTTTATTGAGGGAGCGTGGTCGTCCAAAATCCAATCTGTTGAAAACATTTTGATGTTTCG
1 TCCGAGTTTATTGAGGGAGCGTGGTCGTCCAAAATCCAATCTGTTGAAAACATTTTGATGTTTCG
1417333 ATATAACAAATTAAGTTAAATGAATTT
66 ATATAACAAATTAAGTTAAATGAATTT
1417360 TCCGAGTTTATTGAGGGAGCGTGGTCGTCCAAAATCCAATCTGTTGAAAACATTTTGATGTTTCG
1 TCCGAGTTTATTGAGGGAGCGTGGTCGTCCAAAATCCAATCTGTTGAAAACATTTTGATGTTTCG
1417425 ATATAACAAATTAAGTTAAATGAATTT
66 ATATAACAAATTAAGTTAAATGAATTT
1417452 T
1 T
1417453 AAGATTTTAC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (92 bp):
TCCGAGTTTATTGAGGGAGCGTGGTCGTCCAAAATCCAATCTGTTGAAAACATTTTGATGTTTCG
ATATAACAAATTAAGTTAAATGAATTT
Found at i:1417751 original size:64 final size:64
Alignment explanation
Indices: 1417648--1417854 Score: 258
Period size: 64 Copynumber: 3.2 Consensus size: 64
1417638 TTTCAGAGGG
* * *
1417648 ATGCACCGATGCACCAATCCATGCATCGATGCACCATTGAATAAATTGAACATCGAATGCATTTT
1 ATGCATCGATGCA-CAAGCCATGCATCGATGCACTATTGAATAAATTGAACATCGAATGCATTTT
* *
1417713 ATGCATCAATGCATATA-CCATGCATCGATGCACTATTGAATAAATTGAACATCGAATGCATTTT
1 ATGCATCGATGCACA-AGCCATGCATCGATGCACTATTGAATAAATTGAACATCGAATGCATTTT
* * * ** *
1417777 ATGCATCGATGCACAAGACATGCATTGATGCACTCA--GACTATTTTGAAACATCGAATGCACTT
1 ATGCATCGATGCACAAGCCATGCATCGATGCACT-ATTGAATAAATTG-AACATCGAATGCATTT
1417840 T
64 T
1417841 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1417855 TCTTAGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
63 8 0.06
64 105 0.83
65 13 0.10
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCACTATTGAATAAATTGAACATCGAATGCATTTT
Found at i:1417849 original size:18 final size:19
Alignment explanation
Indices: 1417826--1417874 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1417816 TATTTTGAAA
1417826 CATCGAATGCACT-TTA-TG
1 CATCG-ATGCACTCTTAGTG
1417844 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTTAGTG
*
1417863 CACCGATGCACT
1 CATCGATGCACT
1417875 AAGGCTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.25
18 8 0.29
19 13 0.46
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCTTAGTG
Found at i:1417988 original size:13 final size:13
Alignment explanation
Indices: 1417970--1417995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1417960 CTGATTTTAT
1417970 TAATTATTTTCAC
1 TAATTATTTTCAC
1417983 TAATTATTTTCAC
1 TAATTATTTTCAC
1417996 ACTCAAACGG
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:0.00, T:0.54
Consensus pattern (13 bp):
TAATTATTTTCAC
Found at i:1419753 original size:28 final size:29
Alignment explanation
Indices: 1419713--1419770 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
1419703 CCACACATGA
1419713 AAAAAGAACGGGTAA-CTCTAAACTTAAT
1 AAAAAGAACGGGTAACCTCTAAACTTAAT
1419741 AAAAAGAACGGGTAACCTCTAAACTTAAT
1 AAAAAGAACGGGTAACCTCTAAACTTAAT
1419770 A
1 A
1419771 TTTTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.21
Consensus pattern (29 bp):
AAAAAGAACGGGTAACCTCTAAACTTAAT
Found at i:1425059 original size:22 final size:22
Alignment explanation
Indices: 1425034--1425081 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1425024 ATGCTTATTT
*
1425034 ATTTGGTTTGGTTTTAACTTTC
1 ATTTGGTTTGATTTTAACTTTC
1425056 ATTTGGTTTGATTTTAACTTTC
1 ATTTGGTTTGATTTTAACTTTC
1425078 ATTT
1 ATTT
1425082 TGAGCTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.08, G:0.15, T:0.60
Consensus pattern (22 bp):
ATTTGGTTTGATTTTAACTTTC
Found at i:1425365 original size:12 final size:12
Alignment explanation
Indices: 1425348--1425375 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1425338 AGGGGGAGTA
1425348 ATTTCAAAATTT
1 ATTTCAAAATTT
1425360 ATTTCAAAATTT
1 ATTTCAAAATTT
1425372 ATTT
1 ATTT
1425376 TTAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTCAAAATTT
Found at i:1425807 original size:65 final size:63
Alignment explanation
Indices: 1425738--1425860 Score: 158
Period size: 65 Copynumber: 1.9 Consensus size: 63
1425728 AATGCATTTT
* *
1425738 ATGCATCGATGCACTTAGGAT-TTTATGAAAACATCAAATGAATTTGATGCATCGATGCACAAGA
1 ATGCATCGATGCACTCAGGATATTT-TG-AAACATCAAATGAATTT-ATGCATCAATGCACAAGA
1425802 C
63 C
* * * *
1425803 ATGCATTGATGCACTCAGGCTATTTTGAAACATCGAATGACTTTATGCATCAATGCAC
1 ATGCATCGATGCACTCAGGATATTTTGAAACATCAAATGAATTTATGCATCAATGCAC
1425861 TCTTAGTGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
63 13 0.25
64 15 0.29
65 20 0.39
66 3 0.06
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (63 bp):
ATGCATCGATGCACTCAGGATATTTTGAAACATCAAATGAATTTATGCATCAATGCACAAGAC
Found at i:1426963 original size:34 final size:33
Alignment explanation
Indices: 1426925--1426991 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
1426915 GTAATAAACA
1426925 AAATTAAGCAAAATAAATTAACAA-AAAGTCCAAC
1 AAATTAAGCAAAATAAATTAA-AATAAA-TCCAAC
* *
1426959 AAATTTATCAAAATAAATTAAAATAAATCCAAC
1 AAATTAAGCAAAATAAATTAAAATAAATCCAAC
1426992 CATATTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.22
Consensus pattern (33 bp):
AAATTAAGCAAAATAAATTAAAATAAATCCAAC
Found at i:1429313 original size:21 final size:21
Alignment explanation
Indices: 1429284--1429362 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
1429274 ATCTGTAAAA
*
1429284 AAATTAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
*
1429305 AAATAAATTAAAT---A-CTT
1 AAATAAATTAAATAAAATATT
1429322 AAATAAATTAAATACAAAATATT
1 AAATAAATTAAAT--AAAATATT
1429345 -AA-AAA-TATAATAAAATAT
1 AAATAAATTA-AATAAAATAT
1429363 ACCTTAGACA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
17 15 0.31
18 1 0.02
19 7 0.15
20 2 0.04
21 18 0.38
22 3 0.06
23 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:1429314 original size:9 final size:9
Alignment explanation
Indices: 1429279--1429335 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
1429269 TTTATATCTG
*
1429279 TAAAAAAAT
1 TAAATAAAT
*
1429288 TAATTAAA-
1 TAAATAAAT
*
1429296 TAAA-ATAT
1 TAAATAAAT
1429304 TAAATAAAT
1 TAAATAAAT
*
1429313 TAAAT-ACT
1 TAAATAAAT
1429321 TAAATAAAT
1 TAAATAAAT
1429330 TAAATA
1 TAAATA
1429336 CAAAATATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
7 2 0.05
8 14 0.37
9 22 0.58
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAATAAAT
Found at i:1429316 original size:17 final size:17
Alignment explanation
Indices: 1429281--1429333 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
1429271 TATATCTGTA
* *
1429281 AAAAAATTAATTAAA-T
1 AAAATATTAAATAAATT
1429297 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
1429314 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
1429331 AAA
1 AAA
1429334 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
17 12 0.38
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:1429334 original size:17 final size:17
Alignment explanation
Indices: 1429287--1429336 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1429277 TGTAAAAAAA
* *
1429287 TTAATTAAATAAAATA-
1 TTAAATAAATTAAATAC
1429303 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
1429320 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
1429337 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:1429395 original size:10 final size:10
Alignment explanation
Indices: 1429389--1429417 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1429379 ATAAGAGTAT
1429389 TTGAGAGAAG
1 TTGAGAGAAG
1429399 TTGAGAGAAG
1 TTGAGAGAAG
1429409 TTGAGAGAA
1 TTGAGAGAA
1429418 TTTGGTGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:1436807 original size:176 final size:177
Alignment explanation
Indices: 1436508--1436864 Score: 707
Period size: 176 Copynumber: 2.0 Consensus size: 177
1436498 ATACTCTTCT
1436508 GCACAAGGTTTTGGACTGGAATGCCTCTCGTTTACCACACCAGGCATTTCAGTCAAGTGTAATTG
1 GCACAAGGTTTTGGACTGGAATGCCTCTCGTTTACCACACCAGGCATTTCAGTCAAGTGTAATTG
1436573 ATCTCCTGTATGTACAGCAGCATTAGCTAAATCACTTGCAGATTGAGAGCAACCAATCATATTCG
66 ATCTCCTGTATGTACAGCAGCATTAGCTAAATCACTTGCAGATTGAGAGCAACCAATCATATTCG
1436638 ACTCTTGACTGCATTCTGATATGTCTTCTGCTTCTTTCATACATTTC
131 ACTCTTGACTGCATTCTGATATGTCTTCTGCTTCTTTCATACATTTC
1436685 GCAC-AGGTTTTGGACTGGAATGCCTCTCGTTTACCACACCAGGCATTTCAGTCAAGTGTAATTG
1 GCACAAGGTTTTGGACTGGAATGCCTCTCGTTTACCACACCAGGCATTTCAGTCAAGTGTAATTG
1436749 ATCTCCTGTATGTACAGCAGCATTAGCTAAATCACTTGCAGATTGAGAGCAACCAATCATATTCG
66 ATCTCCTGTATGTACAGCAGCATTAGCTAAATCACTTGCAGATTGAGAGCAACCAATCATATTCG
1436814 ACTCTTGACTGCATTCTGATATGTCTTCTGCTTCTTTCATACATTTC
131 ACTCTTGACTGCATTCTGATATGTCTTCTGCTTCTTTCATACATTTC
1436861 GCAC
1 GCAC
1436865 CACTATCATC
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 176 0.98
177 4 0.02
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (177 bp):
GCACAAGGTTTTGGACTGGAATGCCTCTCGTTTACCACACCAGGCATTTCAGTCAAGTGTAATTG
ATCTCCTGTATGTACAGCAGCATTAGCTAAATCACTTGCAGATTGAGAGCAACCAATCATATTCG
ACTCTTGACTGCATTCTGATATGTCTTCTGCTTCTTTCATACATTTC
Found at i:1441492 original size:2 final size:2
Alignment explanation
Indices: 1441485--1441515 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1441475 GTATTGAAGA
1441485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1441516 CTTAATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1458563 original size:32 final size:32
Alignment explanation
Indices: 1458519--1458598 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
1458509 ATTTTAATTA
* *
1458519 ATATT-AAATTTTACATAATTTATGTTAAAAT
1 ATATTAAAATTTTACATAATTTATATAAAAAT
1458550 ATATTAAAATTTTACATAATTTATATAAAAAT
1 ATATTAAAATTTTACATAATTTATATAAAAAT
1458582 ATATTAAAATTTTACAT
1 ATATTAAAATTTTACAT
1458599 CAACATTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 5 0.11
32 41 0.89
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (32 bp):
ATATTAAAATTTTACATAATTTATATAAAAAT
Found at i:1458799 original size:23 final size:22
Alignment explanation
Indices: 1458773--1458833 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 22
1458763 GTTATCTAAG
1458773 ATATAATATTTATTATATCTTCT
1 ATATAATATTTATT-TATCTTCT
*
1458796 ATATACAATAATTTATTTATCTTTT
1 ATAT--AAT-ATTTATTTATCTTCT
*
1458821 ATATTTATATTTA
1 ATA-TAATATTTA
1458834 ATTCTACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 9 0.28
24 2 0.06
25 13 0.41
26 8 0.25
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATAATATTTATTTATCTTCT
Found at i:1468809 original size:22 final size:21
Alignment explanation
Indices: 1468783--1468830 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1468773 TTTTAAATTT
1468783 ATTAAATTAGATTAAAAT-TAAG
1 ATTAAATTA-A-TAAAATATAAG
*
1468805 ATTAAATTAATAAAATATATG
1 ATTAAATTAATAAAATATAAG
1468826 ATTAA
1 ATTAA
1468831 TAAAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 9 0.38
22 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (21 bp):
ATTAAATTAATAAAATATAAG
Found at i:1468866 original size:23 final size:21
Alignment explanation
Indices: 1468818--1468877 Score: 93
Period size: 21 Copynumber: 2.8 Consensus size: 21
1468808 AAATTAATAA
1468818 AATATATGATTAATAAAAATT
1 AATATATGATTAATAAAAATT
*
1468839 AATATATGATTATTAAAAATT
1 AATATATGATTAATAAAAATT
*
1468860 AATATATAATTATATAAA
1 AATATATGATTA-ATAAA
1468878 TGTATTTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 31 0.89
22 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AATATATGATTAATAAAAATT
Found at i:1469392 original size:14 final size:13
Alignment explanation
Indices: 1469375--1469443 Score: 88
Period size: 12 Copynumber: 5.2 Consensus size: 13
1469365 TGTGTGGTGT
1469375 TATATGTATATATA
1 TATAT-TATATATA
1469389 TATA-TATATATA
1 TATATTATATATA
1469401 TATATATATATATA
1 TATAT-TATATATA
1469415 TATATTA-ATATA
1 TATATTATATATA
*
1469427 TATATTAGTGTATA
1 TATATTA-TATATA
1469441 TAT
1 TAT
1469444 CTTCATCTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
12 24 0.48
13 2 0.04
14 24 0.48
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (13 bp):
TATATTATATATA
Found at i:1469440 original size:12 final size:12
Alignment explanation
Indices: 1469382--1469443 Score: 70
Period size: 14 Copynumber: 4.8 Consensus size: 12
1469372 TGTTATATGT
1469382 ATATATATATATA
1 ATATATATAT-TA
1469395 TATATATATATATA
1 -ATATATATAT-TA
1469409 TATATATATATTA
1 -ATATATATATTA
1469422 ATATATATATTA
1 ATATATATATTA
* *
1469434 GTGTATATAT
1 ATATATATAT
1469444 CTTCATCTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
12 20 0.43
13 2 0.04
14 24 0.52
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
ATATATATATTA
Found at i:1469443 original size:2 final size:2
Alignment explanation
Indices: 1469375--1469431 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
1469365 TGTGTGGTGT
*
1469375 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1469417 TA T- TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1469432 TAGTGTATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1474155 original size:181 final size:182
Alignment explanation
Indices: 1473700--1474168 Score: 764
Period size: 181 Copynumber: 2.6 Consensus size: 182
1473690 ATTAAAAATG
* * * * * *
1473700 TATCGATCCATATCAATATAACAGGTAAAAA-ATGATAAAACCGGTCA-CGAAAAGACAATACCG
1 TATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGT-ATCGAAATGATAAAACCG
*
1473763 GTAAAGCGCTACCGGATATATTGAAAGTGACGATACTTTAATATAAGTATCGACACTTTGTGAAT
65 GTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAAT
**
1473828 TTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAACG
130 TTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAAAA
* * *
1473881 TATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCGGTATCGAAATGATAAAATCGG
1 TATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATGATAAAACCGG
*
1473946 TAAAGTGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATT
66 TAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATT
*
1474011 TAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATTCTTTA-AAAAAAA
131 TAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAAAA
* *
1474062 TATCGATCCACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCGAAATGATAAAACCGA
1 TATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATGATAAAACCGG
1474127 TAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
66 TAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
1474169 AGTACGTGTA
Statistics
Matches: 266, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
181 134 0.50
182 132 0.50
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (182 bp):
TATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATGATAAAACCGG
TAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATT
TAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAAAA
Found at i:1476386 original size:21 final size:21
Alignment explanation
Indices: 1476362--1476405 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1476352 AAGACAATCA
1476362 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
1476383 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1476404 AG
1 AG
1476406 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1476490 original size:33 final size:33
Alignment explanation
Indices: 1476453--1476518 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1476443 AAATAGATGG
*
1476453 AGTGGTAAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTAAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1476486 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTAAAAGAAGTAGAGGTGTTAAGGGGTGA
1476519 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTAAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1476729 original size:21 final size:21
Alignment explanation
Indices: 1476703--1476743 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1476693 GAAAAAATAT
1476703 GAAGAAGAAAAGAGGGAGGAG
1 GAAGAAGAAAAGAGGGAGGAG
1476724 GAAGAAGAAAAGAGGGAGGA
1 GAAGAAGAAAAGAGGGAGGA
1476744 AATGAGGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (21 bp):
GAAGAAGAAAAGAGGGAGGAG
Found at i:1478140 original size:10 final size:10
Alignment explanation
Indices: 1478125--1478153 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1478115 TAGGATCATG
1478125 TAGTTGCATA
1 TAGTTGCATA
1478135 TAGTTGCATA
1 TAGTTGCATA
1478145 TAGTTGCAT
1 TAGTTGCAT
1478154 TTTTGGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (10 bp):
TAGTTGCATA
Found at i:1479421 original size:17 final size:16
Alignment explanation
Indices: 1479390--1479423 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1479380 CACGTGAGGA
1479390 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1479406 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1479423 T
1 T
1479424 ACTGTTTTTA
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:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1489632 original size:16 final size:16
Alignment explanation
Indices: 1489596--1489629 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1489586 CACGTGAGGA
1489596 TTATTTTCTTTTTATT
1 TTATTTTCTTTTTATT
1489612 TTATTTATCTTTTTATT
1 TTATTT-TCTTTTTATT
1489629 T
1 T
1489630 ATTGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTCTTTTTATT
Found at i:1490212 original size:29 final size:29
Alignment explanation
Indices: 1490156--1490212 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1490146 AAATCAACGA
* * *
1490156 ACACAGGAGATAACAAAAGCTGCCATGAG
1 ACACAAGAGATAACAAAAGATGCAATGAG
1490185 ACACAAGA-ATAACAAAAGGATGCAATGA
1 ACACAAGAGATAACAAAA-GATGCAATGA
1490213 TGTAAATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.11
Consensus pattern (29 bp):
ACACAAGAGATAACAAAAGATGCAATGAG
Found at i:1490251 original size:19 final size:19
Alignment explanation
Indices: 1490227--1490275 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1490217 AATGTAGGGT
1490227 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1490246 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTTA
1490265 TAATTTTGTAT
1 TAATTTTGTAT
1490276 GTAAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1490292 original size:18 final size:18
Alignment explanation
Indices: 1490265--1490315 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
1490255 ATATGATTTA
*
1490265 TAATTTTGTATGTA-AATG
1 TAATTATGTATG-AGAATG
1490283 TAATTATGTATGAGAATG
1 TAATTATGTATGAGAATG
1490301 TAATTATGTATGAGA
1 TAATTATGTATGAGA
1490316 TGAGAAAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (18 bp):
TAATTATGTATGAGAATG
Found at i:1491126 original size:200 final size:201
Alignment explanation
Indices: 1490643--1491604 Score: 1414
Period size: 201 Copynumber: 4.8 Consensus size: 201
1490633 GTAAGCATAT
*
1490643 GTGTCGATCCATATATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * *
1490708 GGTAAATTTTCAATCTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCTACAACATGT
66 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
* *
1490773 ATCGACACTTTTTAATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCACAAAAAGGGTGCAAC
131 ATCGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCACAAAAAGGGTGCACC
1490838 CATAAA
196 CATAAA
*
1490844 GTGTCGATCCATTTATAAAAAGTATCGATCTCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * ** *
1490909 GGTAATTTTTTAATGTAACCGGTATAAATATACCATTTTTATGAGAGAATAGGTCTACAATATGT
66 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
*
1490974 ATCGACACTTTTTAATTTTGTGTCGATACTTTTGGTTCAGAATGAATGC-CAAAAAGGGTGCACC
131 ATCGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCACAAAAAGGGTGCACC
1491038 CATAAA
196 CATAAA
*
1491044 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCTATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
** * *
1491109 GGTAAATTTTCAATGTAACCGGTATAAATATACCTATCTTATTAGAGAATAGGTCTACAACATGT
66 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
* *
1491174 ATCGATACTTTTTAATTTTGTGTCGAATAATTTTGGTCCAGAATGAATGCA-AAAAAGGGTGCAC
131 ATCGACACTTTTTAATTTTGTGTCG-ATACTTTTGGTCCAGAATGAATGCACAAAAAGGGTGCAC
1491238 CCATAAA
195 CCATAAA
* * * *
1491245 GTGTCAATACATTTATAAAAAGTATCGATCCCAGCAACATCAAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1491310 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
66 GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
* *
1491375 ATCGACACTTTTTAAATTTTGTGTTGATACTTTTTGTCCA-AGATGAATGCACAAAAAGGGTGCA
131 ATCGACACTTTTT-AATTTTGTGTCGATACTTTTGGTCCAGA-ATGAATGCACAAAAAGGGTGCA
*
1491439 CCCATGAA
194 CCCATAAA
* * *** * ** *
1491447 GTGTCGATACATTTTTAAAAAGTATCGATATAAAAAACATCGAAATTCATAATTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * * * * *
1491512 GGT-AATTTTGTAATATAACCAGTATAACTATACCGGTTTTATGAGAAAATATGTC-ATCATA-A
66 GGTAAATTTT-CAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CA-ACA
* * * *
1491574 AGTATCGACAATTGTTAAATTTGTGTCGATA
128 TGTATCGACACTTTTTAATTTTGTGTCGATA
1491605 TTATTTTAAT
Statistics
Matches: 692, Mismatches: 61, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
200 166 0.24
201 383 0.55
202 142 0.21
203 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (201 bp):
GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
ATCGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCACAAAAAGGGTGCACC
CATAAA
Found at i:1491386 original size:401 final size:403
Alignment explanation
Indices: 1490643--1491604 Score: 1400
Period size: 401 Copynumber: 2.4 Consensus size: 403
1490633 GTAAGCATAT
* *
1490643 GTGTCGATCCATATATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCTATAAGTATAATGTAATA
* * * *
1490708 GGTAAATTTTCAATCTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCTACAACATGT
66 GGTAAATTTTCAATATAACCGGTATAAATATACCGATCTTATGAGAAAATAGGTCTACAACATGT
* *
1490773 ATCGACACTTTTTAATTTTGTGTCGATACTTTTTGTCCAGAATGAATGCACAAAAAGGGTGCAAC
131 ATCGACACTTTTTAATTTTGTGTCGATAATTTTGGTCCAGAATGAATGCACAAAAAGGGTGCAAC
* * * *
1490838 CATAAAGTGTCGATCCATTTATAAAAAGTATCGATCTCAGAAACATCGAAACCCATAAGTATAAT
196 CATAAAGTGTCAATACATTTATAAAAAGTATCGATCCCAGAAACATCAAAACCCATAAGTATAAT
* * *
1490903 GTAATAGGTAATTTTTTAATGTAACCGGTATAAATATACCATTTTTATGAGAGAATAGGTCTACA
261 GTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACA
* *
1490968 ATATGTATCGACACTTTTT-AATTTTGTGTCGATACTTTTGGTTC-AGAATGAATGC-CAAAAAG
326 ACATGTATCGACACTTTTTAAATTTTGTGTCGATACTTTTGGTCCAAG-ATGAATGCACAAAAAG
1491030 GGTGCACCCATAAA
390 GGTGCACCCATAAA
1491044 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCTATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCTATAAGTATAATGTAATA
* * * *
1491109 GGTAAATTTTCAATGTAACCGGTATAAATATACCTATCTTATTAGAGAATAGGTCTACAACATGT
66 GGTAAATTTTCAATATAACCGGTATAAATATACCGATCTTATGAGAAAATAGGTCTACAACATGT
* *
1491174 ATCGATACTTTTTAATTTTGTGTCGAATAATTTTGGTCCAGAATGAATGCA-AAAAAGGGTGCAC
131 ATCGACACTTTTTAATTTTGTGTCG-ATAATTTTGGTCCAGAATGAATGCACAAAAAGGGTGCAA
*
1491238 CCATAAAGTGTCAATACATTTATAAAAAGTATCGATCCCAGCAACATCAAAACCCATAAGTATAA
195 CCATAAAGTGTCAATACATTTATAAAAAGTATCGATCCCAGAAACATCAAAACCCATAAGTATAA
*
1491303 TGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAC
260 TGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTAC
* *
1491368 AACATGTATCGACACTTTTTAAATTTTGTGTTGATACTTTTTGTCCAAGATGAATGCACAAAAAG
325 AACATGTATCGACACTTTTTAAATTTTGTGTCGATACTTTTGGTCCAAGATGAATGCACAAAAAG
*
1491433 GGTGCACCCATGAA
390 GGTGCACCCATAAA
* * *** * * *
1491447 GTGTCGATACATTTTTAAAAAGTATCGATATAAAAAACATCGAAA-TTCATAATTATAATGTAAT
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCT-ATAAGTATAATGTAAT
* * * * * *
1491511 AGGT-AATTTTGTAATATAACCAGTATAACTATACCGGTTTTATGAGAAAATATGTC-ATCATA-
65 AGGTAAATTTT-CAATATAACCGGTATAAATATACCGATCTTATGAGAAAATAGGTCTA-CA-AC
* * * *
1491573 AAGTATCGACAATTGTTAAATTTGTGTCGATA
127 ATGTATCGACACTTTTTAATTTTGTGTCGATA
1491605 TTATTTTAAT
Statistics
Matches: 503, Mismatches: 50, Indels: 15
0.89 0.09 0.03
Matches are distributed among these distances:
401 297 0.59
402 64 0.13
403 141 0.28
404 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (403 bp):
GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCTATAAGTATAATGTAATA
GGTAAATTTTCAATATAACCGGTATAAATATACCGATCTTATGAGAAAATAGGTCTACAACATGT
ATCGACACTTTTTAATTTTGTGTCGATAATTTTGGTCCAGAATGAATGCACAAAAAGGGTGCAAC
CATAAAGTGTCAATACATTTATAAAAAGTATCGATCCCAGAAACATCAAAACCCATAAGTATAAT
GTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACA
ACATGTATCGACACTTTTTAAATTTTGTGTCGATACTTTTGGTCCAAGATGAATGCACAAAAAGG
GTGCACCCATAAA
Found at i:1493134 original size:6 final size:6
Alignment explanation
Indices: 1493094--1493133 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1493084 CAAGCGGTCA
* * *
1493094 ATGAAG ATGAAG ATGACG ATGAAG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
1493134 TCCAAACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.42, C:0.03, G:0.33, T:0.23
Consensus pattern (6 bp):
ATGAAG
Found at i:1494818 original size:200 final size:199
Alignment explanation
Indices: 1494480--1495589 Score: 1407
Period size: 200 Copynumber: 5.7 Consensus size: 199
1494470 AGTAACGACC
* * *
1494480 CCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAATTTT-TCAATGTAACTGGTATAAA
1 CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGT-AATATAACTGGTATAAA
* * *
1494544 TATACCGGTTTTATGA-AAAATAGGTCTATAACATGTATCGACACTTTTTAATTTTGTGTCGATA
65 TATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACAC-TTTTAAATTTGTGTCGATA
1494608 CTTTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAAAGT
129 CTTTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAAAGT
*
1494673 GTTGAT
194 GTCGAT
* ** *
1494679 CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACTGGTATAAAT
1 CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACTGGTATAAAT
* * *
1494744 ATACCGGTTTTATGAGAGAATATGTCTATAATATGTATCGACACTTGTTAAATTTGTGTCGATAC
66 ATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT-TTAAATTTGTGTCGATAC
* *
1494809 GTTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTATTAAAAA-T
130 TTTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTT-TCAAAAAGT
1494873 GTCGAT
194 GTCGAT
* * *
1494879 TCCGAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAAAT
1 CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACTGGTATAAAT
* *
1494944 ATACGGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATATTGTGTCGATAC
66 ATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTAAAT-TTGTGTCGATAC
* * * * *
1495009 TTTTTGTTCAGAATGGATGCTAAAAAGGGTGAACGCACAAAGTGTCGAT-C----CCAAAAA---
130 TTTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAAAGTG
*
1495066 TCGAAA
195 TCG-AT
* ** **** ** * *
1495072 CCCATAATTAT--AATGTAATAGGTA-AAT-T--TA--CAA---TGT-A----ACCGGTATAAAT
1 CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACTGGTATAAAT
*
1495121 ATACCGGTTTTATGAGAGAATAGGTCTATAACATGTATCGACACTTGTTAAATTTGTGTCGATAC
66 ATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT-TTAAATTTGTGTCGATAC
*
1495186 TTTTTGT-CAAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTAT-TAAAAG
130 TTTTTGTCCAA-AATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTT-TCAAAAAG
1495249 TGTCGAT
193 TGTCGAT
* *
1495256 CCCAAAAAAATTGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACTGGTATAAAT
1 CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACTGGTATAAAT
* * *
1495321 ATATCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATATTGTGTCGATAC
66 ATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTAAAT-TTGTGTCGATAC
* * *
1495386 TTTATGTCCAGAATGGATGCCAAAAAGGGTGAACGCACAAAGTGTCGATACATTTTCAAAAAGTG
130 TTTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAAAGTG
1495451 TCGAT
195 TCGAT
*
1495456 CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTTAATATAA-TCGGTATAAA
1 CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACT-GGTATAAA
* * * * * *
1495520 TATACCGGTTTTATGAGAGATTAGGTATACAACATGTAGCGACATTTTTTTATTTTGTGTCGATA
65 TATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACA-CTTTTAAATTTGTGTCGATA
1495585 CTTTT
129 CTTTT
1495590 AAATAACACG
Statistics
Matches: 791, Mismatches: 82, Indels: 75
0.83 0.09 0.08
Matches are distributed among these distances:
176 2 0.00
177 111 0.14
178 6 0.01
181 1 0.00
182 7 0.01
184 9 0.01
185 5 0.01
186 7 0.01
187 5 0.01
188 1 0.00
189 1 0.00
190 5 0.01
191 7 0.01
192 5 0.01
193 7 0.01
194 5 0.01
195 3 0.00
196 1 0.00
199 90 0.11
200 498 0.63
201 15 0.02
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (199 bp):
CCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACTGGTATAAAT
ATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTAAATTTGTGTCGATACT
TTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAAAGTGT
CGAT
Found at i:1495382 original size:377 final size:379
Alignment explanation
Indices: 1494668--1495434 Score: 1353
Period size: 377 Copynumber: 2.0 Consensus size: 379
1494658 ACATTTTCAA
*
1494668 AAAGTGTTGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
* * *
1494733 CTGGTATAAATATACCGGTTTTATGAGAGAATATGTCTATAATATGTATCGACACTTGTTAAATT
66 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTATAACATGTATCGACACTTGTTAAATT
1494798 TGTGTCGATACGTTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATT
131 TGTGTCGATACGTTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATT
* * *
1494863 TATTAAAAATGTCGATTCCGAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAA
196 TATTAAAAATGTCGATCCCAAAAAAATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAA
*
1494928 TATAACCGGTATAAATATACGGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTT
261 TATAACCGGTATAAATATACGGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTT
* * *
1494993 AATATTGTGTCGATACTTTTTGTTCAGAATGGATGCTAAAAAGGGTGAACGCAC
326 AATATTGTGTCGATACTTTATGTCCAGAATGGATGCCAAAAAGGGTGAACGCAC
1495047 AAAGTGTCGATCCC-AAAA-ATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
1495110 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTATAACATGTATCGACACTTGTTAAATT
66 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTATAACATGTATCGACACTTGTTAAATT
*
1495175 TGTGTCGATACTTTTTGT-CAAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACAT
131 TGTGTCGATACGTTTTGTCCAA-AATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACAT
* *
1495239 TTATTAAAAGTGTCGATCCCAAAAAAATTGAAACCCATAATTATAATGTAATAGGTAATTTTGTA
195 TTATTAAAAATGTCGATCCCAAAAAAATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTA
*
1495304 ATATAACTGGTATAAATATATC-GATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTT
260 ATATAACCGGTATAAATATA-CGGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTT
1495368 TTAATATTGTGTCGATACTTTATGTCCAGAATGGATGCCAAAAAGGGTGAACGCAC
324 TTAATATTGTGTCGATACTTTATGTCCAGAATGGATGCCAAAAAGGGTGAACGCAC
1495424 AAAGTGTCGAT
1 AAAGTGTCGAT
1495435 ACATTTTCAA
Statistics
Matches: 371, Mismatches: 15, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
376 3 0.01
377 350 0.94
378 5 0.01
379 13 0.04
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (379 bp):
AAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTATAACATGTATCGACACTTGTTAAATT
TGTGTCGATACGTTTTGTCCAAAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATT
TATTAAAAATGTCGATCCCAAAAAAATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAA
TATAACCGGTATAAATATACGGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTT
AATATTGTGTCGATACTTTATGTCCAGAATGGATGCCAAAAAGGGTGAACGCAC
Done.