Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009586.1 Hibiscus syriacus cultivar Beakdansim tig00116964_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: 3773412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 19
Found at i:1463006 original size:182 final size:182
Alignment explanation
Indices: 1462699--1463361 Score: 967
Period size: 182 Copynumber: 3.6 Consensus size: 182
1462689 TACACATACT
* * **
1462699 TATTAAAGTATCGACACATTT-AAAATATCTGGTAGCACTTTACCGGTTTTGTCATTTCAAGACC
1 TATTAAAGTATCGACAC-TTTCAATATATCCGGTAGCACTTTACCGGTTTTGTCATTTTGAGACC
1462763 GGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACAC
*
1462828 TTTATAAGCGCTATTACTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTA
130 TTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTA
* * *
1462881 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGATCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCGGTTTTGTCATTTTGAGACCG
* *
1462946 GTTTTATCATATTTTTACCTTTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACT
*
1463011 TTATAGGCGCTATTACTACTTCTCTTTTAAATTCCCAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTA
* *
1463063 TATTAAAGTATCGACACTTTCAATATATCCAGTAGCACTTTACCAGTTTTGTC-TTTTCGAGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCGGTTTTGTCATTTT-GAGACC
* * *
1463127 GGTTTTGTCATATTTTTACCTGTTATGTTGTTATGGATCGATACATTTTTATAAAGTATCAACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACAC
* * *
1463192 TCTATAGGCGCT-TTACTGCTTCTCTTTTAAATTCTCAAAGTTTCGATACTTA
130 TTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTA
** * * ** * *
1463244 T-TTCAATCTAATCGATACTTTCAACATATCCGGTAGTGCTTTACCGGTTTTGTCATAATT-AAA
1 TATT-AAAGT-ATCGACACTTTCAATATATCCGGTAGCACTTTACCGGTTTTGTCAT-TTTGAGA
* * *
1463307 CCGGTTTTTTCATATTTTTACCTGTTATATTGATATGGATCGATACATATTTTAT
63 CCGGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACAT-TTTTAT
1463362 TTGGATCGAC
Statistics
Matches: 437, Mismatches: 37, Indels: 13
0.90 0.08 0.03
Matches are distributed among these distances:
180 2 0.00
181 48 0.11
182 378 0.86
183 7 0.02
184 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCGGTTTTGTCATTTTGAGACCG
GTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTA
Found at i:1464545 original size:22 final size:22
Alignment explanation
Indices: 1464520--1464566 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1464510 TATATTATTT
*
1464520 AAATTATTTACGTTTATGTGTA
1 AAATTATTTACATTTATGTGTA
1464542 AAATTATTTACATTTATGTGTA
1 AAATTATTTACATTTATGTGTA
1464564 AAA
1 AAA
1464567 AATTTATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (22 bp):
AAATTATTTACATTTATGTGTA
Found at i:1468792 original size:17 final size:18
Alignment explanation
Indices: 1468760--1468793 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1468750 TAGTTAAACA
1468760 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
1468778 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
1468794 ACCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:1471751 original size:24 final size:21
Alignment explanation
Indices: 1471693--1471753 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 21
1471683 GCTTTCCTTC
*
1471693 TTTTGACTTGATTTTTTTTAT
1 TTTTTACTTGATTTTTTTTAT
*
1471714 TTTTTATTTGGATTTCTTTTTAT
1 TTTTTACTT-GATTT-TTTTTAT
1471737 TTTTCTAACTTGATTTT
1 TTTT-T-ACTTGATTTT
1471754 GTTCCTTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 7 0.21
22 5 0.15
23 12 0.36
24 6 0.18
25 3 0.09
ACGTcount: A:0.15, C:0.07, G:0.08, T:0.70
Consensus pattern (21 bp):
TTTTTACTTGATTTTTTTTAT
Found at i:1472212 original size:2 final size:2
Alignment explanation
Indices: 1472205--1472234 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1472195 CTTAATTGAA
1472205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1472235 GAATATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1477426 original size:32 final size:32
Alignment explanation
Indices: 1477329--1477426 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 32
1477319 TACACCTTTA
* *
1477329 GGTACCTGAACTTGGC-TTTAATGTTCAATTT
1 GGTACCTGAACTTGTCTTTTAAGGTTCAATTT
* * * *
1477360 GGTGCCT-AGGCTT-T-TCTT--GGTTCAATTA
1 GGTACCTGA-ACTTGTCTTTTAAGGTTCAATTT
*
1477388 GCTACCTGAACTTGTCTTTTAAGGTTCAATTT
1 GGTACCTGAACTTGTCTTTTAAGGTTCAATTT
1477420 GGTACCT
1 GGTACCT
1477427 TAAGTTTTCT
Statistics
Matches: 48, Mismatches: 12, Indels: 13
0.66 0.16 0.18
Matches are distributed among these distances:
28 16 0.33
29 2 0.04
30 6 0.12
31 9 0.19
32 15 0.31
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (32 bp):
GGTACCTGAACTTGTCTTTTAAGGTTCAATTT
Found at i:1478223 original size:2 final size:2
Alignment explanation
Indices: 1478216--1478246 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1478206 CCAGCCAAGG
*
1478216 AC AC AC AC AC AC AC AC AC AC AC AA AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1478247 AAAGAAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1482933 original size:21 final size:20
Alignment explanation
Indices: 1482904--1482943 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1482894 ATACTTTATA
1482904 ACATTTAATAAAAAAAATTC
1 ACATTTAATAAAAAAAATTC
* *
1482924 ACATTATAATTAATAAAATT
1 ACATT-TAATAAAAAAAATT
1482944 AATATATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
ACATTTAATAAAAAAAATTC
Found at i:1485830 original size:16 final size:17
Alignment explanation
Indices: 1485799--1485835 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1485789 TATGCTAATA
1485799 TTCTCCTGTCTTTCTTC
1 TTCTCCTGTCTTTCTTC
*
1485816 TTCTCCT-TTTTTCTTC
1 TTCTCCTGTCTTTCTTC
1485832 TTCT
1 TTCT
1485836 TTATTCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (17 bp):
TTCTCCTGTCTTTCTTC
Found at i:1490139 original size:19 final size:20
Alignment explanation
Indices: 1490095--1490139 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
1490085 TAGTTTTCAT
*
1490095 AATAACAACATAATTTAATC
1 AATAACAACATAATTTAATA
1490115 AA-AAC-ACAATAATTTAA-A
1 AATAACAAC-ATAATTTAATA
1490133 AATAACA
1 AATAACA
1490140 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 4 0.19
19 15 0.71
20 2 0.10
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (20 bp):
AATAACAACATAATTTAATA
Found at i:1490561 original size:21 final size:21
Alignment explanation
Indices: 1490535--1490574 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1490525 CAGAACCCCA
*
1490535 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1490556 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1490575 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1497296 original size:23 final size:21
Alignment explanation
Indices: 1497256--1497297 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
1497246 TAATATATAT
*
1497256 ATATTTATTTTTATAAATAAA
1 ATATTTATTTTTAGAAATAAA
1497277 ATATTTATTTACTTAGAAATA
1 ATATTTATTT--TTAGAAATA
1497298 TCAGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTTATTTTTAGAAATAAA
Found at i:1497377 original size:18 final size:17
Alignment explanation
Indices: 1497338--1497379 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1497328 AACTCATTTC
1497338 TTAAAATTAATAAATAA
1 TTAAAATTAATAAATAA
*
1497355 ATAAATATTAATAAA-ACA
1 TTAAA-ATTAATAAATA-A
1497373 TTAAAAT
1 TTAAAAT
1497380 AAATTAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATTAATAAATAA
Found at i:1497665 original size:2 final size:2
Alignment explanation
Indices: 1497658--1497699 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1497648 ATTTAAACAA
1497658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1497700 TTATTTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1497735 original size:11 final size:11
Alignment explanation
Indices: 1497719--1497780 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 11
1497709 AGGCTAAGGT
1497719 AATAATAATAA
1 AATAATAATAA
1497730 AATAATAATTAA
1 AATAATAA-TAA
**
1497742 AGCAATAATTAA
1 AATAATAA-TAA
1497754 AAT-AT-A-AA
1 AATAATAATAA
*
1497762 AGTAATAA-AA
1 AATAATAATAA
1497772 AATAATAAT
1 AATAATAAT
1497781 GCAAATAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 11 0.27
11 10 0.24
12 14 0.34
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (11 bp):
AATAATAATAA
Found at i:1498996 original size:16 final size:15
Alignment explanation
Indices: 1498960--1499010 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1498950 GGGTTTAGAT
*
1498960 ATTCTG-TTGGGCTG
1 ATTCTGATTGGGCCG
* *
1498974 GTTCTGATCTGGTCCG
1 ATTCTGAT-TGGGCCG
1498990 ATTCTGATTGGGCCG
1 ATTCTGATTGGGCCG
*
1499005 GTTCTG
1 ATTCTG
1499011 TTGTAAACGG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 5 0.17
15 12 0.41
16 12 0.41
ACGTcount: A:0.08, C:0.20, G:0.33, T:0.39
Consensus pattern (15 bp):
ATTCTGATTGGGCCG
Found at i:1499063 original size:3 final size:3
Alignment explanation
Indices: 1499051--1499106 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
1499041 GATTTGTATT
**
1499051 TAA T-A TAA TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1499098 TAA TAA TAA
1 TAA TAA TAA
1499107 AACGAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1499301 original size:45 final size:45
Alignment explanation
Indices: 1499228--1499862 Score: 640
Period size: 45 Copynumber: 13.8 Consensus size: 45
1499218 GATGGAAATG
* *
1499228 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
1499273 TTGAAAACATCATGCACTTAAGGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
1499318 TTGAAAACATCATGCACTGAA-GTCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
1499362 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
1499407 TTGAAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
1499452 TTGAAAACATCATGCACTGAAAGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* * *
1499497 TTGAAAACATCATGTATTGAAGGACTTACAGATGGCCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* * * * ** * **
1499542 TTGAAAATATCAAAAAGCTCCCGAAGG-CTTTTTGAAAACATCCTG-CACTGAAGGGC
1 TTGAAAACATC---ATGC-ACTGAAGGAC---TT----ACA-GATGAC-CCGAAGGTT
* * ** * * *
1499598 TT----ACA-GATG-ACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTT
1 TTGAAAACATCATGCA-CTGAA-G----G-ACTTA-C-AGATG-ACCCGAAGG-TT
* * * ** *
1499648 TTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCTGAAGGTT
1 TT-GAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* *
1499694 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
1499739 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* *
1499784 TTGAAAACATCATGCACTGAAGGGCTTACAGATGGCCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
1499829 TTGAAAACATCATGCACTGAAGGTCTTACAGATG
1 TTGAAAACATCATGCACTGAAGGACTTACAGATG
1499863 TGGGAAATAG
Statistics
Matches: 498, Mismatches: 58, Indels: 68
0.80 0.09 0.11
Matches are distributed among these distances:
44 43 0.09
45 380 0.76
46 4 0.01
47 13 0.03
48 10 0.02
49 12 0.02
50 5 0.01
51 4 0.01
52 3 0.01
55 8 0.02
56 15 0.03
57 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
Found at i:1499383 original size:25 final size:25
Alignment explanation
Indices: 1499311--1499384 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
1499301 CAGATGACCC
1499311 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
* * *
1499336 GAA-GTCTT----ACA-GATG-ACCC
1 GAAGGTTTTGAAAACATCATGCA-CT
1499355 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
1499380 GAAGG
1 GAAGG
1499385 GCTTACAGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 16
0.61 0.11 0.28
Matches are distributed among these distances:
18 1 0.03
19 7 0.20
20 7 0.20
24 7 0.20
25 12 0.34
26 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (25 bp):
GAAGGTTTTGAAAACATCATGCACT
Found at i:1499468 original size:134 final size:135
Alignment explanation
Indices: 1499228--1499553 Score: 573
Period size: 134 Copynumber: 2.4 Consensus size: 135
1499218 GATGGAAATG
* *
1499228 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTTA
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAA
*
1499293 AGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTG-AAGTCTTACAGATGACCCGA
66 AGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAAGACTTACAGATGACCCGA
1499357 AGGTT
131 AGGTT
1499362 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAA
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAA
1499427 AGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAAGACTTACAGATGACCCGA
66 AGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAAGACTTACAGATGACCCGA
1499492 AGGTT
131 AGGTT
* * * * *
1499497 TTGAAAACATCATGTATTGAAGGACTTACAGATGGCCCGAAGGTTTTGAAAATATCA
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
1499554 AAAAGCTCCC
Statistics
Matches: 183, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
134 107 0.58
135 76 0.42
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (135 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAA
AGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAAGACTTACAGATGACCCGA
AGGTT
Found at i:1499583 original size:76 final size:76
Alignment explanation
Indices: 1499487--1499705 Score: 325
Period size: 76 Copynumber: 2.9 Consensus size: 76
1499477 TTACAGATGA
* * * *
1499487 CCCGAAGG--TTTTGAAAACATCATGTATTGAAGGACTTACAGATGGCCCGAAGGTTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAT
1499550 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1499561 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAT
1499626 ATCAAAAAGCT
66 ATCAAAAAGCT
* * ** * *
1499637 CCCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCTGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAT
1499702 ATCA
66 ATCA
1499706 TGCACTGAAG
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
74 8 0.06
76 124 0.94
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAT
ATCAAAAAGCT
Found at i:1500554 original size:22 final size:22
Alignment explanation
Indices: 1500526--1500583 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1500516 AATAAAGCTT
1500526 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* * * *
1500548 TCATCTTCGGAGAGAGAATGTA
1 TCATCTTTGAAAAGAGAATCTA
1500570 TCATCTTTGAAAAG
1 TCATCTTTGAAAAG
1500584 TATAGATGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1504502 original size:65 final size:64
Alignment explanation
Indices: 1504313--1504504 Score: 203
Period size: 65 Copynumber: 3.0 Consensus size: 64
1504303 GGACCCTTAG
* ** *
1504313 TGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAA
1 TGCATTCGATGTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAA
*
1504377 TGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT-GTGCATCGATGCATGAA
1 TGCATTCGATG-TTTCATAAAATCCTCAGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAA
1504441 A
64 A
** * * * *
1504442 TGCATTCGATG-TTCAATTTATTCCAT-GGTGCATCGATGCATGGATTGGTGTATCGGTGCATCA
1 TGCATTCGATGTTTC-ATAAAATCC-TCAGTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
1504505 CTTTGAAAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.03
64 34 0.31
65 68 0.62
66 4 0.04
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (64 bp):
TGCATTCGATGTTTCATAAAATCCTCAGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAA
Found at i:1511075 original size:41 final size:41
Alignment explanation
Indices: 1511037--1511295 Score: 286
Period size: 41 Copynumber: 6.3 Consensus size: 41
1511027 CGTTTTTTCA
* * *
1511037 ACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
* * *
1511078 ACAAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTCTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
* * * *
1511119 ACAAACGCCGCTATAGAATTGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
1511160 ACAAACGCCGCTAAAGACTCA-TACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACT-AGTACTTTAGTGGCATTTTTAT
* * **
1511201 ACAAACTCCACTAAAGACGCGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
* * * * * * * *
1511242 TCAAACGCCGTTATACACTTGTACTATAGTGGCGTTTGTGTTT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTT-T-TAT
1511285 ACAAACGCCGC
1 ACAAACGCCGC
1511296 AAGTTTACAA
Statistics
Matches: 181, Mismatches: 33, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
41 169 0.93
42 1 0.01
43 11 0.06
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (41 bp):
ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
Found at i:1511157 original size:123 final size:122
Alignment explanation
Indices: 1511020--1511297 Score: 360
Period size: 123 Copynumber: 2.2 Consensus size: 122
1511010 AGGTTCATCG
* *
1511020 ATAGTGGCGTTTTTTCAACAAACGCCGCAAAAGAGT-AGTACTTTAGTGGCGTTTTTATACAAAC
1 ATAGTGGCG-TTTTT-AACAAACGCCGCAAAAGACTCA-TACTTTAGTGGCATTTTTATACAAAC
* * *
1511084 GCCGCTAAAGACTCGTAATTTAGTGGCATTTCTATACAAACGCCGCTATAGAATTGTACT
63 GCCACTAAAGACGCGTAATTTAGTGGCATTTCTATACAAACGCCGCTATACAATTGTACT
* * *
1511144 TTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAACTC
1 ATAGTGGCGTTTTTA-ACAAACGCCGCAAAAGACTCATACTTTAGTGGCATTTTTATACAAACGC
* * * * *
1511209 CACTAAAGACGCGTACTTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACT
65 CACTAAAGACGCGTAATTTAGTGGCATTTCTATACAAACGCCGCTATACAATTGTACT
*
1511267 ATAGTGGCGTTTGTGTTTACAAACGCCGCAA
1 ATAGTGGCG-TT-T-TTAACAAACGCCGCAA
1511298 GTTTACAAAT
Statistics
Matches: 133, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
122 1 0.01
123 106 0.80
124 11 0.08
125 13 0.10
126 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (122 bp):
ATAGTGGCGTTTTTAACAAACGCCGCAAAAGACTCATACTTTAGTGGCATTTTTATACAAACGCC
ACTAAAGACGCGTAATTTAGTGGCATTTCTATACAAACGCCGCTATACAATTGTACT
Found at i:1514774 original size:85 final size:86
Alignment explanation
Indices: 1514578--1514891 Score: 338
Period size: 85 Copynumber: 3.7 Consensus size: 86
1514568 TAATTAGCGA
* *
1514578 CGTTTGTATCCAAAAACGCCGATATAGATCTGACTTTTTGCGGCGTTTGAGTTC-ATAAACGCCG
1 CGTTTGTATCCAAAAACGCCGATATAGATCTGACCTTTTGCGGCGTTT--GTTCTAAAAACGCCG
* * *
1514642 TTATAGGTCTGAC-CTTTTGCGG
64 CTATATGTCTAACTCTTTTGCGG
* * * *
1514664 CGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAATGCCAG-
1 CGTTTGTATCCAAAAACGCCGATATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCC-GC
* *
1514728 TATATGTCT-TCTCTTTTGTGG
65 TATATGTCTAACTCTTTTGCGG
* * * *
1514749 CGTTTTTATCCAAAAACGCC-ACTATAGATCTGATCTTTTGCGGCGTTT-TTTTAGAAACGCCGC
1 CGTTTGTATCCAAAAACGCCGA-TATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGC
*
1514812 TATATATCATAACT-TTTTGCGG
65 TATATGTC-TAACTCTTTTGCGG
* * * *
1514834 CGTTTAT-TCCAAAAACGCCGATATAGATATCGACCTTTTACGGCGTTTGTTCAAAAAA
1 CGTTTGTATCCAAAAACGCCGATATAGATCT-GACCTTTTGCGGCGTTTGTTCTAAAAA
1514892 TGTCGTAATA
Statistics
Matches: 191, Mismatches: 27, Indels: 20
0.80 0.11 0.08
Matches are distributed among these distances:
83 1 0.01
84 42 0.22
85 95 0.50
86 53 0.28
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (86 bp):
CGTTTGTATCCAAAAACGCCGATATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCT
ATATGTCTAACTCTTTTGCGG
Found at i:1514872 original size:128 final size:130
Alignment explanation
Indices: 1514586--1514881 Score: 293
Period size: 128 Copynumber: 2.3 Consensus size: 130
1514576 GACGTTTGTA
* * * * ** *
1514586 TCCAAAAACGCCGATATAGATCT-GACTTTTTGCGGCG-TTTGAGTTCATAAACGCCGTTATAGG
1 TCCAAAAACGCCGATATAGATATCGACCTTTTGCGGCGTTTTGAGTCCAAAAACGCCACTATAGA
* * *
1514649 TCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGT
66 TCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTAT
* * * ** * *
1514714 TCTAAAAATGCC-AGTAT--ATGTCTTCTCTTTTGTGGCGTTTTTA-TCCAAAAACGCCACTATA
1 TCCAAAAACGCCGA-TATAGATATCGAC-CTTTTGCGGCGTTTTGAGTCCAAAAACGCCACTATA
* ** * * *
1514775 GATCTGATCTTTTGCGGCGTTT-T-TTTAGAAACGCCGCTATATATCATAACTTTTTGCGGCGTT
64 GATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGCTATAGATC-TAACCTTTTGCGGCGTT
1514838 TAT
128 TAT
*
1514841 TCCAAAAACGCCGATATAGATATCGACCTTTTACGGCGTTT
1 TCCAAAAACGCCGATATAGATATCGACCTTTTGCGGCGTTT
1514882 GTTCAAAAAA
Statistics
Matches: 131, Mismatches: 29, Indels: 16
0.74 0.16 0.09
Matches are distributed among these distances:
126 20 0.15
127 33 0.25
128 69 0.53
129 9 0.07
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (130 bp):
TCCAAAAACGCCGATATAGATATCGACCTTTTGCGGCGTTTTGAGTCCAAAAACGCCACTATAGA
TCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTAT
Found at i:1514891 original size:43 final size:42
Alignment explanation
Indices: 1514578--1514891 Score: 280
Period size: 43 Copynumber: 7.4 Consensus size: 42
1514568 TAATTAGCGA
*
1514578 CGTTTGTATCCAAAAACGCCGATATAGATCTGACTTTTTGCGG
1 CGTTTGT-TCCAAAAACGCCGATATAGATCTGACCTTTTGCGG
* * *
1514621 CGTTTGAGTT-CATAAACGCCGTTATAGGTCTGACCTTTTGCGG
1 CGTTT--GTTCCAAAAACGCCGATATAGATCTGACCTTTTGCGG
* *
1514664 CGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGG
1 CGTTTGT-TCCAAAAACGCCGATATAGATCTGACCTTTTGCGG
* * * *
1514707 CGTTTGTTCTAAAAATGCC-AGTATATG-TCT-TCTCTTTTGTGG
1 CGTTTGTTCCAAAAACGCCGA-TATA-GATCTGAC-CTTTTGCGG
* *
1514749 CGTTTTTATCCAAAAACGCC-ACTATAGATCTGATCTTTTGCGG
1 CGTTTGT-TCCAAAAACGCCGA-TATAGATCTGACCTTTTGCGG
** * * * * *
1514792 CGTTT-TTTTAGAAACGCCGCTATATATCATAACTTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGATATAGATC-TGACCTTTTGCGG
* * *
1514834 CGTTTATTCCAAAAACGCCGATATAGATATCGACCTTTTACGG
1 CGTTTGTTCCAAAAACGCCGATATAGATCT-GACCTTTTGCGG
*
1514877 CGTTTGTTCAAAAAA
1 CGTTTGTTCCAAAAA
1514892 TGTCGTAATA
Statistics
Matches: 220, Mismatches: 37, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
41 19 0.09
42 50 0.23
43 148 0.67
44 1 0.00
45 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
CGTTTGTTCCAAAAACGCCGATATAGATCTGACCTTTTGCGG
Found at i:1515209 original size:21 final size:21
Alignment explanation
Indices: 1515185--1515224 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1515175 AAGACTATTT
1515185 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTGAAACA
1515206 TCATTTTTATATTTTGAAA
1 TCATTTTTATATTTTGAAA
1515225 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTATATTTTGAAACA
Found at i:1517366 original size:65 final size:64
Alignment explanation
Indices: 1517168--1517377 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 64
1517158 TGCACTAAGA
* * * * *
1517168 GTGCATTGATGCATCAAGTGCATTCGATGTTTCAAAATAGT-CGGAGTGCATCGATGCATGGCTG
1 GTGCATTGATGCATCAAATGCATTCGATGTTTCAATATAATCCTG-GTGCATCGATGCATGGTTG
* * * * *
1517232 GTGCATCGATACATCAAATGCATTCGATGTTTTC-ATAAAATCCTCAGTGCATCGATGGATGGTA
1 GTGCATTGATGCATCAAATGCATTCGATG-TTTCAATATAATCCT-GGTGCATCGATGCATGGT-
1517296 T-
63 TG
* * *
1517297 GTGCATTGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATGGTGCATCGATGCATGGATT
1 GTGCATTGATGCATCAAATGCATTCGATGTTTCAATATAATCC-TGGTGCATCGATGCATGG-TT
1517361 G
64 G
* *
1517362 GTGCATCGGTGCATCA
1 GTGCATTGATGCATCA
1517378 CTTTGAAAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
63 3 0.03
64 52 0.44
65 61 0.52
66 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (64 bp):
GTGCATTGATGCATCAAATGCATTCGATGTTTCAATATAATCCTGGTGCATCGATGCATGGTTG
Found at i:1529352 original size:21 final size:21
Alignment explanation
Indices: 1529315--1529354 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1529305 CCCCCTTTGA
*
1529315 AGGGGAACTGATTCCCCCCAC
1 AGGGGAACTGATACCCCCCAC
1529336 AGGGGAA-TCGATACCCCCC
1 AGGGGAACT-GATACCCCCC
1529355 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAACTGATACCCCCCAC
Found at i:1529396 original size:8 final size:8
Alignment explanation
Indices: 1529383--1529407 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1529373 GGGCAAGAAC
1529383 ACCCCAAA
1 ACCCCAAA
1529391 ACCCCAAA
1 ACCCCAAA
1529399 ACCCCAAA
1 ACCCCAAA
1529407 A
1 A
1529408 TCTATTCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (8 bp):
ACCCCAAA
Found at i:1531356 original size:19 final size:19
Alignment explanation
Indices: 1531334--1531379 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1531324 AATTTATGGA
1531334 TGGTGTGAACTTATATGTT
1 TGGTGTGAACTTATATGTT
1531353 TGGTGTGAACTTATATGTT
1 TGGTGTGAACTTATATGTT
1531372 TGGTGTGA
1 TGGTGTGA
1531380 TTTATTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.04, G:0.30, T:0.46
Consensus pattern (19 bp):
TGGTGTGAACTTATATGTT
Found at i:1533436 original size:11 final size:11
Alignment explanation
Indices: 1533415--1533458 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
1533405 GTCGGGTCAG
1533415 ACCGG-TCAAA
1 ACCGGTTCAAA
*
1533425 ATCGGTTCAAA
1 ACCGGTTCAAA
1533436 ACCGG-TCAAA
1 ACCGGTTCAAA
1533446 ACCGGTTCAAA
1 ACCGGTTCAAA
1533457 AC
1 AC
1533459 TGGTCAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 14 0.47
11 16 0.53
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (11 bp):
ACCGGTTCAAA
Found at i:1533440 original size:21 final size:21
Alignment explanation
Indices: 1533415--1533466 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1533405 GTCGGGTCAG
*
1533415 ACCGGTCAAAATCGGTTCAAA
1 ACCGGTCAAAACCGGTTCAAA
1533436 ACCGGTCAAAACCGGTTCAAA
1 ACCGGTCAAAACCGGTTCAAA
*
1533457 ACTGGTCAAA
1 ACCGGTCAAA
1533467 TTGGTTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (21 bp):
ACCGGTCAAAACCGGTTCAAA
Found at i:1533444 original size:10 final size:10
Alignment explanation
Indices: 1533415--1533466 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
1533405 GTCGGGTCAG
1533415 ACCGGTCAAA
1 ACCGGTCAAA
*
1533425 ATCGGTTCAAA
1 ACCGG-TCAAA
1533436 ACCGGTCAAA
1 ACCGGTCAAA
1533446 ACCGGTTCAAA
1 ACCGG-TCAAA
*
1533457 ACTGGTCAAA
1 ACCGGTCAAA
1533467 TTGGTTTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 19 0.51
11 18 0.49
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1546243 original size:14 final size:14
Alignment explanation
Indices: 1546224--1546252 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1546214 CAACGGTCAA
1546224 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
1546238 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
1546252 C
1 C
1546253 AGACCGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.55, T:0.21
Consensus pattern (14 bp):
CGGTCGGGTCGGGT
Found at i:1549066 original size:23 final size:21
Alignment explanation
Indices: 1549026--1549067 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
1549016 ATTAATATAT
*
1549026 ATATTTATTTTTATAAATAAA
1 ATATTTATTTTTAGAAATAAA
1549047 ATATTTATTTAATTAGAAATA
1 ATATTTATTT--TTAGAAATA
1549068 TCAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTTATTTTTAGAAATAAA
Found at i:1550836 original size:3 final size:3
Alignment explanation
Indices: 1550828--1550875 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1550818 GTATTTAATT
* **
1550828 TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1550876 AACGAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1550844 original size:12 final size:12
Alignment explanation
Indices: 1550823--1550871 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
1550813 GATTTGTATT
1550823 TAAT-TTAATAA
1 TAATATTAATAA
1550834 TAATATTAATAA
1 TAATATTAATAA
1550846 T-A-A-TAATAA
1 TAATATTAATAA
*
1550855 TAATTTTAATAA
1 TAATATTAATAA
1550867 TAATA
1 TAATA
1550872 ATAAAACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 7 0.22
10 2 0.06
11 5 0.16
12 18 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:1570638 original size:22 final size:24
Alignment explanation
Indices: 1570593--1570643 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1570583 TTTTGTGTTT
*
1570593 TTATATAAAATGATAGTATATTTA
1 TTATATAAAATGATAGAATATTTA
*
1570617 TTATATAAAATTATA-AAT-TTTA
1 TTATATAAAATGATAGAATATTTA
1570639 TTATA
1 TTATA
1570644 AATGCAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 2 0.08
24 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TTATATAAAATGATAGAATATTTA
Found at i:1570951 original size:15 final size:15
Alignment explanation
Indices: 1570931--1570963 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1570921 TGGTTGTATT
1570931 GGGGGATGACGGTGA
1 GGGGGATGACGGTGA
*
1570946 GGGGGATGATGGTGA
1 GGGGGATGACGGTGA
1570961 GGG
1 GGG
1570964 AAAATAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.64, T:0.15
Consensus pattern (15 bp):
GGGGGATGACGGTGA
Found at i:1571105 original size:21 final size:21
Alignment explanation
Indices: 1571046--1571110 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
1571036 TAGACAATCA
* *
1571046 AGAGTCGAATAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
1571067 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* * *
1571088 AGAGTTGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1571109 AG
1 AG
1571111 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1571181 original size:33 final size:33
Alignment explanation
Indices: 1571144--1571207 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1571134 AAATAGATGG
*
1571144 AGTGGTGAAAGAAGTAGAGATGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGATGTTAAGGGGTGA
* *
1571177 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGT
1 AGTGGTGAAAGAAGTAGAGATGTTAAGGGGT
1571208 AATCTTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGATGTTAAGGGGTGA
Found at i:1573022 original size:6 final size:6
Alignment explanation
Indices: 1572955--1573018 Score: 83
Period size: 6 Copynumber: 10.7 Consensus size: 6
1572945 CAAGCGGTCA
* * *
1572955 ATGAAG ATGAAG ATGACG ATGAAG ATGACG ATGAAG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* *
1573003 ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGA
1573019 TGATCCAAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:1573022 original size:12 final size:12
Alignment explanation
Indices: 1572955--1573018 Score: 101
Period size: 12 Copynumber: 5.3 Consensus size: 12
1572945 CAAGCGGTCA
*
1572955 ATGAAGATGAAG
1 ATGACGATGAAG
1572967 ATGACGATGAAG
1 ATGACGATGAAG
1572979 ATGACGATGAAG
1 ATGACGATGAAG
1572991 ATGACGATGAAG
1 ATGACGATGAAG
* *
1573003 ATGATGATGATG
1 ATGACGATGAAG
1573015 ATGA
1 ATGA
1573019 TGATCCAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1574872 original size:179 final size:179
Alignment explanation
Indices: 1574557--1574926 Score: 503
Period size: 179 Copynumber: 2.1 Consensus size: 179
1574547 TTCATACATT
* * * **
1574557 TAAAATGTCGATCCCAAAAACATCGAAACCCATAATAATAATGTAATAGGTAATTTTGTAATATA
1 TAAAGTGTCGATCCCAAAAACATCGAAACCCATAATAATAATATAATAGGTAAATTTACAATATA
* * *
1574622 ACCAGTATACATATACCAGTTTTATGAGAGAATATGTCTATAATATGTATCGACACTTCTTAATA
66 ACCAGTATAAATATACCAGTTTTATGAGAGAATATGTCTATAACATGTAGCGACACTTCTTAATA
* * *
1574687 TTGTGTCGATAATTTATGTTT-ATAATGGATGCCAAAAAGGGTGAACGCA
131 TTGTGTCGATAATTT-TGTTTCAGAATGGATGCCAAAAAGGATGAACACA
* * *
1574736 TAAAGTGTCGATCCCAAAAATATCGAAACCCATAATTATAATATAATAGGTAAATTTACAATGTA
1 TAAAGTGTCGATCCCAAAAACATCGAAACCCATAATAATAATATAATAGGTAAATTTACAATATA
* * *
1574801 A-CAGGTATAAATATACCGGTTTTATGAGAGAATATGTCTATAACATGTAGCGACATTTGTTAA-
66 ACCA-GTATAAATATACCAGTTTTATGAGAGAATATGTCTATAACATGTAGCGACACTTCTTAAT
* *
1574864 ATTTGTGTCGATACTTTTTTTTCAGAATGGATGCCAAAAAGGATGAACACA
130 A-TTGTGTCGATAATTTTGTTTCAGAATGGATGCCAAAAAGGATGAACACA
* *
1574915 CAAAGTATCGAT
1 TAAAGTGTCGAT
1574927 ACATTTATTA
Statistics
Matches: 167, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
178 7 0.04
179 160 0.96
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (179 bp):
TAAAGTGTCGATCCCAAAAACATCGAAACCCATAATAATAATATAATAGGTAAATTTACAATATA
ACCAGTATAAATATACCAGTTTTATGAGAGAATATGTCTATAACATGTAGCGACACTTCTTAATA
TTGTGTCGATAATTTTGTTTCAGAATGGATGCCAAAAAGGATGAACACA
Found at i:1579144 original size:24 final size:24
Alignment explanation
Indices: 1579117--1579181 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
1579107 GTAAACGGAG
* *
1579117 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATCC
*
1579141 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATCC
*
1579165 AGATCAG-AATCAGAACA
1 ATATCAGAAATCAGAACA
1579182 ATTCAGGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 9 0.25
24 27 0.75
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.18
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATCC
Found at i:1579160 original size:12 final size:11
Alignment explanation
Indices: 1579125--1579181 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
1579115 AGATATCAGA
*
1579125 AATCAAAACAG
1 AATCAGAACAG
* *
1579136 AATTCATATCAG
1 AA-TCAGAACAG
1579148 ATATCAGAACAG
1 A-ATCAGAACAG
*
1579160 AATCCAGATCAG
1 AAT-CAGAACAG
1579172 AATCAGAACA
1 AATCAGAACA
1579182 ATTCAGGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 10 0.27
12 26 0.70
13 1 0.03
ACGTcount: A:0.51, C:0.19, G:0.12, T:0.18
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:1580318 original size:18 final size:18
Alignment explanation
Indices: 1580297--1580331 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1580287 TGCCATCCGG
*
1580297 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1580315 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1580332 GTCCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1581666 original size:18 final size:18
Alignment explanation
Indices: 1581643--1581681 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1581633 ACGGGTCAAC
*
1581643 GGTCGGTTCAACAAGTCG
1 GGTCGGGTCAACAAGTCG
*
1581661 GGTCGGGTCAACGAGTCG
1 GGTCGGGTCAACAAGTCG
1581679 GGT
1 GGT
1581682 AAACGGGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.41, T:0.21
Consensus pattern (18 bp):
GGTCGGGTCAACAAGTCG
Found at i:1581678 original size:13 final size:13
Alignment explanation
Indices: 1581662--1581695 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1581652 AACAAGTCGG
1581662 GTCGGGTCAACGA
1 GTCGGGTCAACGA
* *
1581675 GTCGGGTAAACGG
1 GTCGGGTCAACGA
1581688 GTCGGGTC
1 GTCGGGTC
1581696 GGGTCTGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.44, T:0.18
Consensus pattern (13 bp):
GTCGGGTCAACGA
Found at i:1581692 original size:31 final size:30
Alignment explanation
Indices: 1581634--1581700 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
1581624 CAACGGTCAA
* *
1581634 CGGGTCAACGGTCGGTTCAACAAGTCGGGT
1 CGGGTCAACGGTCGGGTAAACAAGTCGGGT
**
1581664 CGGGTCAACGAGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACG-GTCGGGTAAACAAGTCGGGT
1581695 CGGGTC
1 CGGGTC
1581701 TGGTTGTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 10 0.31
31 22 0.69
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (30 bp):
CGGGTCAACGGTCGGGTAAACAAGTCGGGT
Found at i:1583848 original size:24 final size:24
Alignment explanation
Indices: 1583821--1583927 Score: 105
Period size: 24 Copynumber: 4.5 Consensus size: 24
1583811 GTAAACGGAG
*
1583821 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
1583845 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
1583869 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
1583892 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
1583916 A-ATTCAGAAATC
1 ATA-TCAGAAATC
1583928 GGATAAAATA
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 16 0.24
24 47 0.70
25 2 0.03
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:1583852 original size:12 final size:12
Alignment explanation
Indices: 1583825--1583916 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
1583815 ACGGAGATAT
* *
1583825 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
1583837 CAGAATTCATAT
1 CAGAATTCAGAA
1583849 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1583861 CAGAATCCAGAT
1 CAGAATTCAGAA
1583873 CAGAA-TCAGAA
1 CAGAATTCAGAA
1583884 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
1583898 C-GTA-TCAGAA
1 CAGAATTCAGAA
1583908 CAGAATTCA
1 CAGAATTCA
1583917 ATTCAGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1583904 original size:47 final size:48
Alignment explanation
Indices: 1583823--1583927 Score: 128
Period size: 47 Copynumber: 2.2 Consensus size: 48
1583813 AAACGGAGAT
*
1583823 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
* *
1583871 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAATTCA-
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAATCCAG
1583917 ATTCAGAAATC
1 A-TCAGAAATC
1583928 GGATAAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
46 1 0.02
47 36 0.72
48 10 0.20
49 3 0.06
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:1585032 original size:18 final size:18
Alignment explanation
Indices: 1585011--1585045 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1585001 TGCCATCTGG
*
1585011 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1585029 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1585046 GTTCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1587847 original size:23 final size:23
Alignment explanation
Indices: 1587821--1587865 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1587811 TCACACAGCT
*
1587821 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1587844 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1587866 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1588010 original size:26 final size:26
Alignment explanation
Indices: 1587981--1588044 Score: 112
Period size: 25 Copynumber: 2.5 Consensus size: 26
1587971 ATATATCCCG
1587981 AGGACCGCGTAGAAATATTGTCCCAA
1 AGGACCGCGTAGAAATATTGTCCCAA
*
1588007 AGGACCGCGTAG-AATATTGTCCCGA
1 AGGACCGCGTAGAAATATTGTCCCAA
1588032 AGGACCGCGTAGA
1 AGGACCGCGTAGA
1588045 CCTCTACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 24 0.67
26 12 0.33
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.17
Consensus pattern (26 bp):
AGGACCGCGTAGAAATATTGTCCCAA
Found at i:1588644 original size:22 final size:19
Alignment explanation
Indices: 1588614--1588656 Score: 50
Period size: 22 Copynumber: 2.1 Consensus size: 19
1588604 CAGAAATCCT
*
1588614 ATTTGAGCTCGAAAATCATCTC
1 ATTTCAGCTC-AAAA-CAT-TC
1588636 ATTTCAGCTCAAAACATTC
1 ATTTCAGCTCAAAACATTC
1588655 AT
1 AT
1588657 ATTTCACTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 4 0.20
22 9 0.45
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (19 bp):
ATTTCAGCTCAAAACATTC
Found at i:1591039 original size:48 final size:48
Alignment explanation
Indices: 1590968--1591063 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1590958 CATAATTCTC
1590968 TTTAAAACTTCGAAACTTTCTTGACATTCAGAAGTCCAAACAAATGGT
1 TTTAAAACTTCGAAACTTTCTTGACATTCAGAAGTCCAAACAAATGGT
1591016 TTTAAAACTTCGAAACTTTCTTGACATTCAGAAGTCCAAACAAATGGT
1 TTTAAAACTTCGAAACTTTCTTGACATTCAGAAGTCCAAACAAATGGT
1591064 ACGTTATTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (48 bp):
TTTAAAACTTCGAAACTTTCTTGACATTCAGAAGTCCAAACAAATGGT
Found at i:1592658 original size:29 final size:30
Alignment explanation
Indices: 1592600--1592659 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
1592590 CAACAATCAA
1592600 TGGACAATCCCTGATAAAATGTTCGGCATC
1 TGGACAATCCCTGATAAAATGTTCGGCATC
1592630 TGGACAATCCCTGAT-AAATGTTCGGCATC
1 TGGACAATCCCTGATAAAATGTTCGGCATC
1592659 T
1 T
1592660 CCGCATCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (30 bp):
TGGACAATCCCTGATAAAATGTTCGGCATC
Found at i:1594416 original size:23 final size:23
Alignment explanation
Indices: 1594390--1594434 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1594380 CACCACAGCT
*
1594390 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1594413 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1594435 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1594579 original size:25 final size:25
Alignment explanation
Indices: 1594551--1594617 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
1594541 TATATATATA
1594551 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
1594576 TCCCAAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
1594601 TCCCGAAGGACCGCGTA
1 TCCCGAAGGACCGCGTA
1594618 TACCCTCTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:1615992 original size:20 final size:20
Alignment explanation
Indices: 1615967--1616028 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
1615957 AATCAGATTG
1615967 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACCGATTCCC
* *
1615987 CCCAGGGGGAACAGATTCCCC
1 CCCAGGGGGTACCGATT-CCC
*
1616008 CCCAAGGGGTACCGATTCCC
1 CCCAGGGGGTACCGATTCCC
1616028 C
1 C
1616029 ATGTCTAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.13
Consensus pattern (20 bp):
CCCAGGGGGTACCGATTCCC
Found at i:1616008 original size:21 final size:21
Alignment explanation
Indices: 1615967--1616028 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1615957 AATCAGATTG
1615967 CCCAGGGGGTACCGATT-CCC
1 CCCAGGGGGTACCGATTCCCC
* *
1615987 CCCAGGGGGAACAGATTCCCC
1 CCCAGGGGGTACCGATTCCCC
*
1616008 CCCAAGGGGTACCGATTCCCC
1 CCCAGGGGGTACCGATTCCCC
1616029 ATGTCTAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACCGATTCCCC
Found at i:1619363 original size:21 final size:21
Alignment explanation
Indices: 1619323--1619406 Score: 118
Period size: 22 Copynumber: 4.0 Consensus size: 21
1619313 TCAGATTGCC
1619323 CAGGGGGTACAGATTCCCCCCT
1 CAGGGGGTACAGATT-CCCCCT
1619345 CAGGGGGTACAGATTCCCCC-
1 CAGGGGGTACAGATTCCCCCT
*
1619365 CAGGGGGAACAGA-TCCCCCT
1 CAGGGGGTACAGATTCCCCCT
*
1619385 CCAGGGGGTACCGATTCCCCCT
1 -CAGGGGGTACAGATTCCCCCT
1619407 GTCTAACGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.11
20 12 0.21
21 16 0.29
22 22 0.39
ACGTcount: A:0.19, C:0.37, G:0.29, T:0.15
Consensus pattern (21 bp):
CAGGGGGTACAGATTCCCCCT
Found at i:1619394 original size:41 final size:42
Alignment explanation
Indices: 1619321--1619405 Score: 129
Period size: 41 Copynumber: 2.0 Consensus size: 42
1619311 AATCAGATTG
*
1619321 CCCAGGGGGTACAGATTCCCCCCTCAGGGGGTACAGATTCCC
1 CCCAGGGGGAACAGATTCCCCCCTCAGGGGGTACAGATTCCC
*
1619363 CCCAGGGGGAACAGA-T-CCCCCTCCAGGGGGTACCGATTCCC
1 CCCAGGGGGAACAGATTCCCCCCT-CAGGGGGTACAGATTCCC
1619404 CC
1 CC
1619406 TGTCTAACGG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 6 0.15
41 20 0.50
42 14 0.35
ACGTcount: A:0.19, C:0.39, G:0.28, T:0.14
Consensus pattern (42 bp):
CCCAGGGGGAACAGATTCCCCCCTCAGGGGGTACAGATTCCC
Found at i:1619819 original size:31 final size:32
Alignment explanation
Indices: 1619754--1619819 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
1619744 TTTGTAAAGG
* *
1619754 GGAAAGGTTCTAGCTAATCCCGTGTAAAAGCTA
1 GGAAAGGTTCTAGCTAAGCCCG-GTAAAAACTA
* *
1619787 GGAAAGGTTCTAGTTTAGCCC-GTAAAAACTA
1 GGAAAGGTTCTAGCTAAGCCCGGTAAAAACTA
1619818 GG
1 GG
1619820 GAGTTTGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 11 0.38
33 18 0.62
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (32 bp):
GGAAAGGTTCTAGCTAAGCCCGGTAAAAACTA
Found at i:1633202 original size:3 final size:3
Alignment explanation
Indices: 1633194--1633228 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1633184 TCAATTCAAA
1633194 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1633229 GAGAAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1633390 original size:20 final size:20
Alignment explanation
Indices: 1633310--1633403 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1633300 AAATGACCAA
* * *
1633310 TAAATTCGCAACGCGAACTC
1 TAAATTCGCAACACGAATTT
* * *
1633330 CAATTTCGCAACGCG-ATTT
1 TAAATTCGCAACACGAATTT
*
1633349 CCAAATTCGCAACACTGAATTT
1 -TAAATTCGCAACAC-GAATTT
1633371 TAAATTCGCAACACGAATTT
1 TAAATTCGCAACACGAATTT
*
1633391 TAATTTCGCAACA
1 TAAATTCGCAACA
1633404 GGTTTTATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.68
21 14 0.22
22 4 0.06
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.28
Consensus pattern (20 bp):
TAAATTCGCAACACGAATTT
Found at i:1634640 original size:20 final size:20
Alignment explanation
Indices: 1634617--1634655 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1634607 TCGCGTTGCG
*
1634617 ATTTTCGTGTTGTGAATTTC
1 ATTTTCGTGTTGCGAATTTC
1634637 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1634656 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:1634662 original size:20 final size:20
Alignment explanation
Indices: 1634619--1634662 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1634609 GCGTTGCGAT
* * *
1634619 TTTCGTGTTGTGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
1634639 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
1634659 TTTC
1 TTTC
1634663 AAAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:1635037 original size:22 final size:22
Alignment explanation
Indices: 1634980--1635037 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1634970 GATGGAGCTA
*
1634980 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1635002 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1635024 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1635038 TAGAGAGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.43, T:0.17
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1635227 original size:20 final size:20
Alignment explanation
Indices: 1635204--1635255 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
1635194 ACAAATTCGC
1635204 GTTGCGAATTTGGAAACT-GT
1 GTTGCGAATTTGG-AACTCGT
* * **
1635224 GTTGTGAAATTGGAGTTCGT
1 GTTGCGAATTTGGAACTCGT
1635244 GTTGCGAATTTG
1 GTTGCGAATTTG
1635256 TTGGTTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.21, C:0.08, G:0.33, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGGAACTCGT
Found at i:1635953 original size:59 final size:59
Alignment explanation
Indices: 1635821--1635980 Score: 189
Period size: 59 Copynumber: 2.7 Consensus size: 59
1635811 GTGTTGTTCA
* * * * * *
1635821 AAAGTTTGGAGACTAATTTAGAAT-GGGGTCATA-TTTGGGGATGAGTTTGGAATGTTT
1 AAAGTTTGGAGACTAATTTAGAATAAGGGTCATAGTTTAGGAATAAATTTGGAATATTT
*
1635878 ATAAGTTTGGACACTAATTTAGAATAAGGGTCATAGTTTAGGAATAAATTTGGAATATTT
1 A-AAGTTTGGAGACTAATTTAGAATAAGGGTCATAGTTTAGGAATAAATTTGGAATATTT
** **
1635938 AAAGTTTAAAGACTAATTTAGAATAAAAGTCATAGTTTGAGGA
1 AAAGTTTGGAGACTAATTTAGAATAAGGGTCATAGTTT-AGGA
1635981 TTATGATGCA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
57 1 0.01
58 22 0.25
59 40 0.46
60 24 0.28
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (59 bp):
AAAGTTTGGAGACTAATTTAGAATAAGGGTCATAGTTTAGGAATAAATTTGGAATATTT
Found at i:1638887 original size:23 final size:23
Alignment explanation
Indices: 1638851--1638909 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
1638841 TTCTCTATCA
* *
1638851 AGTGCAGAATATATTACCTGCAC
1 AGTGCACAACATATTACCTGCAC
*
1638874 AGTGCACAACATATTACTTGCAC
1 AGTGCACAACATATTACCTGCAC
1638897 AGTGCACAACATA
1 AGTGCACAACATA
1638910 GAAATAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (23 bp):
AGTGCACAACATATTACCTGCAC
Found at i:1641433 original size:2 final size:2
Alignment explanation
Indices: 1641424--1641452 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1641414 ACAACAACAA
1641424 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1641453 TACATGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1642696 original size:2 final size:2
Alignment explanation
Indices: 1642689--1642721 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1642679 TCATATTATT
1642689 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 T
1642722 GAAGATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1644930 original size:43 final size:44
Alignment explanation
Indices: 1644863--1644949 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
1644853 TGGCTTTAGA
* * *
1644863 GAAGTTAGGAGGGAAGGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
* *
1644906 GAAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
1644950 TGATGCACGG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 27 0.71
44 11 0.29
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.34
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
Found at i:1645066 original size:14 final size:13
Alignment explanation
Indices: 1645026--1645094 Score: 61
Period size: 13 Copynumber: 5.2 Consensus size: 13
1645016 TTCATACATA
*
1645026 CATTTGCATTTTG
1 CATTTTCATTTTG
1645039 CATTTTCATTTTG
1 CATTTTCATTTTG
1645052 CATTCTT-ATTTTTG
1 CATT-TTCA-TTTTG
**
1645066 CATCATCA-TTTG
1 CATTTTCATTTTG
*
1645078 CATTTGCATCTTTG
1 CATTTTCAT-TTTG
1645092 CAT
1 CAT
1645095 AGTTACATCT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 9 0.20
13 18 0.40
14 18 0.40
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (13 bp):
CATTTTCATTTTG
Found at i:1645091 original size:26 final size:26
Alignment explanation
Indices: 1645026--1645094 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
1645016 TTCATACATA
**
1645026 CATTTGCATTTTGCATTTTCATTTTG
1 CATTTGCATTTTGCATCATCATTTTG
*
1645052 CATTCT-TATTTTTGCATCATCA-TTTG
1 CATT-TGCA-TTTTGCATCATCATTTTG
1645078 CATTTGCATCTTTGCAT
1 CATTTGCAT-TTTGCAT
1645095 AGTTACATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
25 2 0.06
26 21 0.60
27 12 0.34
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (26 bp):
CATTTGCATTTTGCATCATCATTTTG
Found at i:1645724 original size:90 final size:90
Alignment explanation
Indices: 1645571--1645752 Score: 364
Period size: 90 Copynumber: 2.0 Consensus size: 90
1645561 ATTTTGTACT
1645571 GATAATGAGATCTCTGACCCAAATGAATTAGTTGAGAAGAAAAAACTCATCCAACAACTGAAAAA
1 GATAATGAGATCTCTGACCCAAATGAATTAGTTGAGAAGAAAAAACTCATCCAACAACTGAAAAA
1645636 TGTAGAAGAGGTAATAAAATCTAGA
66 TGTAGAAGAGGTAATAAAATCTAGA
1645661 GATAATGAGATCTCTGACCCAAATGAATTAGTTGAGAAGAAAAAACTCATCCAACAACTGAAAAA
1 GATAATGAGATCTCTGACCCAAATGAATTAGTTGAGAAGAAAAAACTCATCCAACAACTGAAAAA
1645726 TGTAGAAGAGGTAATAAAATCTAGA
66 TGTAGAAGAGGTAATAAAATCTAGA
1645751 GA
1 GA
1645753 GACGGTTAAG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 92 1.00
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (90 bp):
GATAATGAGATCTCTGACCCAAATGAATTAGTTGAGAAGAAAAAACTCATCCAACAACTGAAAAA
TGTAGAAGAGGTAATAAAATCTAGA
Found at i:1648333 original size:9 final size:9
Alignment explanation
Indices: 1648319--1648361 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1648309 ATTCATCAGG
1648319 AAAAAAGGAA
1 AAAAAAGG-A
*
1648329 AAAAAAGAAA
1 AAAAAAG-GA
*
1648339 AAAAAAAGA
1 AAAAAAGGA
1648348 AAAAAAGGA
1 AAAAAAGGA
1648357 AAAAA
1 AAAAA
1648362 TTAAATCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 14 0.50
10 14 0.50
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAGGA
Found at i:1648341 original size:11 final size:11
Alignment explanation
Indices: 1648327--1648353 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1648317 GGAAAAAAGG
1648327 AAAAAAAAGAA
1 AAAAAAAAGAA
1648338 AAAAAAAAGAA
1 AAAAAAAAGAA
1648349 AAAAA
1 AAAAA
1648354 GGAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:1648344 original size:20 final size:20
Alignment explanation
Indices: 1648319--1648361 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1648309 ATTCATCAGG
*
1648319 AAAAAAGGAAAAAAAAGAAA
1 AAAAAAAGAAAAAAAAGAAA
*
1648339 AAAAAAAGAAAAAAAGGAAA
1 AAAAAAAGAAAAAAAAGAAA
1648359 AAA
1 AAA
1648362 TTAAATCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAAGAAA
Found at i:1652339 original size:22 final size:22
Alignment explanation
Indices: 1652311--1652367 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
1652301 ACATCCACAT
1652311 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
1652333 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1652355 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1652368 AAGCTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1652729 original size:10 final size:11
Alignment explanation
Indices: 1652714--1652746 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
1652704 ACAGGAATTT
1652714 CAAAGATT-AA
1 CAAAGATTCAA
1652724 CAAAGATTTCAA
1 CAAAGA-TTCAA
1652736 CAAAGATTCAA
1 CAAAGATTCAA
1652747 ATTCACCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 7 0.33
12 8 0.38
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (11 bp):
CAAAGATTCAA
Found at i:1653097 original size:122 final size:122
Alignment explanation
Indices: 1652879--1653304 Score: 653
Period size: 122 Copynumber: 3.5 Consensus size: 122
1652869 CACTCGATGG
* *
1652879 ATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGATGAATAAGAAGTTCAT
1 ATCAACATTTCCA-A-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
*
1652943 AATAAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
64 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* *
1653002 ATCAACTTTTCCAGAGAA-AGTTCATAATGAGAA-AACTTATCTGAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCA-A-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* *
1653065 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAATGAGATAGATCAGC
64 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* *
1653124 ATCAACATTTCCAAAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAA
1 ATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
**
1653189 TGAGAAGAACTTGTTCAACCTTTTGC-TCGACTCTATCGTAGAAGGAGATAGATCAGC
66 TGAGAAGAACTTGTTCAACCTTTTGCAT-GACTCTATCACAGAAGGAGATAGATCAGC
* *
1653246 ATCAACATTTCCAAAAGGAGTTCATAACGAGAAGAACTCATCTGAAGAAGAAGAAGAAG
1 ATCAACATTTCCAAAA-GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAG
1653305 AAGAAGTTCA
Statistics
Matches: 280, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
120 2 0.01
121 16 0.06
122 192 0.69
123 70 0.25
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.24
Consensus pattern (122 bp):
ATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:1655538 original size:24 final size:23
Alignment explanation
Indices: 1655510--1655557 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1655500 TGATATTTTT
*
1655510 AAGTAAATAAATATCTTATTTATA
1 AAGTAAATAAATATC-TATATATA
* *
1655534 AAGTATATATATATCTATATATA
1 AAGTAAATAAATATCTATATATA
1655557 A
1 A
1655558 GTTAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (23 bp):
AAGTAAATAAATATCTATATATA
Found at i:1655615 original size:155 final size:153
Alignment explanation
Indices: 1655281--1655615 Score: 344
Period size: 155 Copynumber: 2.2 Consensus size: 153
1655271 TGATTAAATA
* * * * *
1655281 ATAATATTTATTTATT-TTTAATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTCATTTTC
1 ATAATATATATTTATTCTTAAATTTTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCATTTTA
* * **
1655345 TGATATTTTTAATAAACTAAATATCCTACTTTTATAAATTATATATATATTAATTTATTTTATTT
66 TGATATTTTTAATAAACTAAATATCCTAC-TTTATAAAGTATATATATATTAATTAATTAAATTT
* **
1655410 TTGTTACTTTTAGAAAAAATGTTTT
130 TTGTTAC-TTTACAAAAAATGAATT
* * * *
1655435 ATTAATATTTATTTATTTTTTAATTTTAAGAAAATGACTGTCTTAAAGCAACTA-AAGTCTTTTT
1 A-TAATATATATTTATTCTTAAATTTTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCATTTT
*
1655499 ATGATATTTTTAAGTAAA-TAAATATCTTA-TTTATAAAGTATATATATATCTATATATAAGTTA
65 ATGATATTTTTAA-TAAACTAAATATCCTACTTTATAAAGTATATATATAT-TA-AT-TAA-TTA
*
1655562 AATTATTT-TT-C-TTACAAAATTATGAATT
125 AATT-TTTGTTACTTTACAAAA-AATGAATT
1655590 A-AATATATATTTGAATTCTTAAATTT
1 ATAATATATATTT--ATTCTTAAATTT
1655616 CTAAATAATA
Statistics
Matches: 154, Mismatches: 16, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
153 29 0.19
154 10 0.06
155 64 0.42
156 41 0.27
157 7 0.05
158 3 0.02
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (153 bp):
ATAATATATATTTATTCTTAAATTTTAAGAAAATGACTGTCTTAAAGCAACTAGAAGTCATTTTA
TGATATTTTTAATAAACTAAATATCCTACTTTATAAAGTATATATATATTAATTAATTAAATTTT
TGTTACTTTACAAAAAATGAATT
Found at i:1660005 original size:27 final size:26
Alignment explanation
Indices: 1659964--1660017 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 26
1659954 GAGAACAAAG
1659964 AAAAGTTAAGATGAAAG-AGAAATAAGA
1 AAAAGTTAAGATG-AAGCA-AAATAAGA
1659991 AAAAGTTAA-AGTGAAGCAAAATAAGA
1 AAAAGTTAAGA-TGAAGCAAAATAAGA
1660017 A
1 A
1660018 GATACGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.63, C:0.02, G:0.20, T:0.15
Consensus pattern (26 bp):
AAAAGTTAAGATGAAGCAAAATAAGA
Found at i:1673641 original size:24 final size:24
Alignment explanation
Indices: 1673605--1673723 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
1673595 GAGAATACTT
1673605 TGGAAAGTATGTGTATAAACAGAG
1 TGGAAAGTATGTGTATAAACAGAG
*
1673629 TGGAAAGTGTGTGTATAAACAGAG
1 TGGAAAGTATGTGTATAAACAGAG
* *
1673653 TAG-AAGTATGTATATAAACAGAG
1 TGGAAAGTATGTGTATAAACAGAG
*
1673676 TGGAAAGTATATGTATAAACAGAG
1 TGGAAAGTATGTGTATAAACAGAG
* *
1673700 TAG-AAGTATATGTATAAACAGAG
1 TGGAAAGTATGTGTATAAACAGAG
1673723 T
1 T
1673724 AGAATGATTA
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
23 41 0.48
24 45 0.52
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (24 bp):
TGGAAAGTATGTGTATAAACAGAG
Found at i:1673668 original size:23 final size:23
Alignment explanation
Indices: 1673609--1673727 Score: 166
Period size: 23 Copynumber: 5.1 Consensus size: 23
1673599 ATACTTTGGA
*
1673609 AAGTATGTGTATAAACAGAGTGG
1 AAGTATGTGTATAAACAGAGTAG
*
1673632 AAAGTGTGTGTATAAACAGAGTAG
1 -AAGTATGTGTATAAACAGAGTAG
* *
1673656 AAGTATGTATATAAACAGAGTGG
1 AAGTATGTGTATAAACAGAGTAG
*
1673679 AAAGTATATGTATAAACAGAGTAG
1 -AAGTATGTGTATAAACAGAGTAG
*
1673703 AAGTATATGTATAAACAGAGTAG
1 AAGTATGTGTATAAACAGAGTAG
1673726 AA
1 AA
1673728 TGATTAGTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
23 45 0.52
24 41 0.48
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.25
Consensus pattern (23 bp):
AAGTATGTGTATAAACAGAGTAG
Found at i:1673678 original size:47 final size:47
Alignment explanation
Indices: 1673609--1673723 Score: 194
Period size: 47 Copynumber: 2.4 Consensus size: 47
1673599 ATACTTTGGA
* *
1673609 AAGTATGTGTATAAACAGAGTGGAAAGTGTGTGTATAAACAGAGTAG
1 AAGTATGTGTATAAACAGAGTGGAAAGTATATGTATAAACAGAGTAG
*
1673656 AAGTATGTATATAAACAGAGTGGAAAGTATATGTATAAACAGAGTAG
1 AAGTATGTGTATAAACAGAGTGGAAAGTATATGTATAAACAGAGTAG
*
1673703 AAGTATATGTATAAACAGAGT
1 AAGTATGTGTATAAACAGAGT
1673724 AGAATGATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.44, C:0.04, G:0.25, T:0.26
Consensus pattern (47 bp):
AAGTATGTGTATAAACAGAGTGGAAAGTATATGTATAAACAGAGTAG
Found at i:1673944 original size:11 final size:11
Alignment explanation
Indices: 1673928--1673952 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1673918 AGGAAAGGCG
1673928 GACTAATATAC
1 GACTAATATAC
1673939 GACTAATATAC
1 GACTAATATAC
1673950 GAC
1 GAC
1673953 GTTACCGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (11 bp):
GACTAATATAC
Found at i:1674486 original size:223 final size:223
Alignment explanation
Indices: 1674091--1674551 Score: 778
Period size: 223 Copynumber: 2.1 Consensus size: 223
1674081 TTGTCGGTTT
* * *
1674091 GTGTCGATACTTTATAAAAATATATTGATTCATAACAATATAACAGGTAAAAAATGACAAGACCG
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
*
1674156 ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCGATACTTTATAAAA
66 ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCAATACTTTATAAAA
*
1674221 ATGTATCGATTCATAACAATATAACAGGTAAAAAAATGACAAAACCGATCTATAAATGACAAAAC
131 ATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATCTATAAATGACAAAAC
* *
1674286 AGGTAAAGTGCTACCGGATATATTGAAA
196 AGGTAAAGCGCTACCAGATATATTGAAA
* * *
1674314 GTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAATATGACAAAACCG
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
* *
1674379 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCAATACTTTATAAAA
66 ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCAATACTTTATAAAA
* *
1674444 ATGTATCGATCCATAACAATATAACAGGTAAAAAACTGACAAAACCGGTCTATAAATGACAAAAC
131 ATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATCTATAAATGACAAAAC
* *
1674509 AGGTAAAGCGCTACCAGATATGTTGATA
196 AGGTAAAGCGCTACCAGATATATTGAAA
1674537 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
1674552 TATAAGTATC
Statistics
Matches: 221, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
223 221 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (223 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTATCAATACTTTATAAAA
ATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGATCTATAAATGACAAAAC
AGGTAAAGCGCTACCAGATATATTGAAA
Found at i:1674563 original size:111 final size:111
Alignment explanation
Indices: 1674091--1674551 Score: 769
Period size: 112 Copynumber: 4.1 Consensus size: 111
1674081 TTGTCGGTTT
* * * *
1674091 GTGTCGATACTTTATAAAAATATATTGATTCATAACAATATAACAGGTAAAAAATGACAAGACCG
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
1674156 ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1674202 GTATCGATACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
*
1674267 GATCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
65 GATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1674314 GTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAATATGACAAAACCG
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
*
1674379 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1674425 GTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAACTGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAA-TGACAAAACC
* * * *
1674490 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATGTTGATA
65 GATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
1674537 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
1674552 TATAAGTATC
Statistics
Matches: 332, Mismatches: 16, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
111 158 0.48
112 174 0.52
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (111 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1674721 original size:178 final size:180
Alignment explanation
Indices: 1674422--1674873 Score: 766
Period size: 178 Copynumber: 2.5 Consensus size: 180
1674412 GGATATATTG
*
1674422 AAAGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAA-ACTGACAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATA-TGACAA
** * * *
1674486 AACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATGTTGATAGTGTCGATACTTTA
65 AACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTA
*
1674551 TTATAAGTATCGACAC-TTTGGAATTTAAAAG-AGAAGTTATAGCGCTAAT
130 TTATAAGTATCGACACTTTTGGAATTTAAAAGAAGAAGTTATAGCGCGAAT
1674600 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1674665 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
1674730 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCGAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAG--AAGAAGTTATAGCGCGAAT
*
1674782 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
1674847 ATCGGTCTCGAAATGAAAAAACCGGTA
66 ACCGGTCTCGAAATGACAAAACCGGTA
1674874 GTAAAAAAGT
Statistics
Matches: 259, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
178 137 0.53
179 16 0.06
182 106 0.41
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (180 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAAGAAGTTATAGCGCGAAT
Found at i:1676499 original size:44 final size:44
Alignment explanation
Indices: 1676436--1676522 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
1676426 TTAAGTTCAA
1676436 TTTTGATATGTATTAATGAAAAAGATTATTTAGAAAATAAAATC
1 TTTTGATATGTATTAATGAAAAAGATTATTTAGAAAATAAAATC
* * *
1676480 TTTTGATATGTATTAATGAAGAAGCTTATTTGGAAAATAAAAT
1 TTTTGATATGTATTAATGAAAAAGATTATTTAGAAAATAAAAT
1676523 ATATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (44 bp):
TTTTGATATGTATTAATGAAAAAGATTATTTAGAAAATAAAATC
Found at i:1676695 original size:15 final size:15
Alignment explanation
Indices: 1676675--1676707 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1676665 TCAAACACGT
1676675 AGTTGCTTAAATCCG
1 AGTTGCTTAAATCCG
1676690 AGTTGCTTAAATCCG
1 AGTTGCTTAAATCCG
1676705 AGT
1 AGT
1676708 CATTTAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (15 bp):
AGTTGCTTAAATCCG
Found at i:1681140 original size:2 final size:2
Alignment explanation
Indices: 1681133--1681161 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1681123 GATTAAACAA
1681133 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 A
1681162 CTTTTTATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1681397 original size:14 final size:16
Alignment explanation
Indices: 1681365--1681402 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1681355 GTTCCATTCA
1681365 AAAATAATATGAGGTG
1 AAAATAATATGAGGTG
1681381 AAAA-AATATGA-GTG
1 AAAATAATATGAGGTG
1681395 AAATATAA
1 AAA-ATAA
1681403 ATATTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 8 0.40
16 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (16 bp):
AAAATAATATGAGGTG
Found at i:1681626 original size:16 final size:17
Alignment explanation
Indices: 1681594--1681626 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1681584 TTGACAAAAC
*
1681594 TATCATTTTTGTTATTA
1 TATCATTTTTGTAATTA
1681611 TATCATTTTTG-AATTA
1 TATCATTTTTGTAATTA
1681627 ATAGTCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (17 bp):
TATCATTTTTGTAATTA
Found at i:1683592 original size:15 final size:15
Alignment explanation
Indices: 1683572--1683622 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
1683562 TTCCAGAAAA
1683572 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1683587 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
1683602 TGAATTACTGGAATT
1 TGAATTACTGGAATT
1683617 TGAATT
1 TGAATT
1683623 CTAGAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:1683601 original size:30 final size:29
Alignment explanation
Indices: 1683566--1683638 Score: 128
Period size: 30 Copynumber: 2.5 Consensus size: 29
1683556 TTGATTTTCC
1683566 AGAAAATGAATTACTGGAATTTGAATTACT
1 AGAAAATGAATTACTGGAATTTGAATT-CT
*
1683596 GGAAAATGAATTACTGGAATTTGAATTCT
1 AGAAAATGAATTACTGGAATTTGAATTCT
1683625 AGAAAATGAATTAC
1 AGAAAATGAATTAC
1683639 ATTTCTGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (29 bp):
AGAAAATGAATTACTGGAATTTGAATTCT
Found at i:1683687 original size:20 final size:20
Alignment explanation
Indices: 1683621--1683690 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
1683611 GGAATTTGAA
*
1683621 TTCTAGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
1683641 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1683661 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1683681 TAT-TGGAAAA
1 T-TCTGGAAAA
1683691 CATCTGGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 45 0.98
21 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:1683889 original size:27 final size:26
Alignment explanation
Indices: 1683851--1683913 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
1683841 TTTACTAAAA
* *
1683851 TATTATTGAAATATATAATAATATTAT
1 TATTATT-AAATATATAAAAAAATTAT
1683878 TCATTATTAAATATATAAAAAAATTAT
1 T-ATTATTAAATATATAAAAAAATTAT
1683905 TATATATTA
1 TAT-TATTA
1683914 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.06
27 24 0.75
28 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
TATTATTAAATATATAAAAAAATTAT
Found at i:1683921 original size:58 final size:55
Alignment explanation
Indices: 1683850--1683994 Score: 134
Period size: 58 Copynumber: 2.6 Consensus size: 55
1683840 CTTTACTAAA
*
1683850 ATATTATTGAAATATATAATAATATTATTCATTATTAAATATATAAAAAAATTATTAT
1 ATATTATTAAAATATATAATAATATTATT-ATTATTAAA-ATAT-AAAAAATTATTAT
* * * *** *
1683908 ATATTATTAAAATAAAAATATAATATCT-TATATTATTATAATATAATTGATTATTTT
1 ATATTATTAAAATATATA-ATAATAT-TAT-TATTATTAAAATATAAAAAATTATTAT
1683965 ATATATATTAAAA-ATATAAT-ATATTATTAT
1 ATAT-TATTAAAATATATAATAATATTATTAT
1683995 AAATATTAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
54 4 0.06
55 5 0.07
56 2 0.03
57 16 0.22
58 27 0.38
59 16 0.22
60 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (55 bp):
ATATTATTAAAATATATAATAATATTATTATTATTAAAATATAAAAAATTATTAT
Found at i:1683981 original size:30 final size:28
Alignment explanation
Indices: 1683900--1684010 Score: 95
Period size: 28 Copynumber: 3.9 Consensus size: 28
1683890 ATATAAAAAA
*
1683900 ATTATTATATATTATTAA-AATAAAAATAT
1 ATTATTATATA-TATTAATAAT-ATAATAT
*
1683929 AATATCT-TATATTATT-ATAATATAAT-T
1 ATTAT-TATATA-TATTAATAATATAATAT
*
1683956 GATTATTTTATATATATTAAAAATATAATAT
1 -ATTA--TTATATATATTAATAATATAATAT
*
1683987 ATTATTATAAATATTAATAATATA
1 ATTATTATATATATTAATAATATA
1684011 TTTTAAATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 17
0.75 0.07 0.19
Matches are distributed among these distances:
27 1 0.01
28 26 0.38
29 21 0.31
30 19 0.28
31 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
ATTATTATATATATTAATAATATAATAT
Found at i:1684018 original size:20 final size:20
Alignment explanation
Indices: 1683965--1684028 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
1683955 TGATTATTTT
* *
1683965 ATATATATTAAAAATATAAT-
1 ATATATTTTAAATAT-TAATA
*
1683985 ATATTATTATAAATATTAATA
1 ATA-TATTTTAAATATTAATA
1684006 ATATATTTTAAATATTTAATA
1 ATATATTTTAAATA-TTAATA
1684027 AT
1 AT
1684029 TAATTTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATTTTAAATATTAATA
Found at i:1684034 original size:21 final size:21
Alignment explanation
Indices: 1683972--1684035 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1683962 TTTATATATA
* *
1683972 TTAAAAATATAATATATT-ATT
1 TTAAATATTTAATA-ATTAATT
*
1683993 ATAAATA-TTAATAA-TATATT
1 TTAAATATTTAATAATTA-ATT
1684013 TTAAATATTTAATAATTAATT
1 TTAAATATTTAATAATTAATT
1684034 TT
1 TT
1684036 TGATGAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 14 0.40
21 17 0.49
22 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAATATTTAATAATTAATT
Found at i:1684267 original size:42 final size:42
Alignment explanation
Indices: 1684208--1684327 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
1684198 ATGAATTACA
*
1684208 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1684250 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1684292 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1684328 TTCGGGGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1686873 original size:2 final size:2
Alignment explanation
Indices: 1686866--1686899 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1686856 CAGCTGGAAC
1686866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1686900 GCTTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1696759 original size:214 final size:219
Alignment explanation
Indices: 1696353--1696829 Score: 750
Period size: 223 Copynumber: 2.2 Consensus size: 219
1696343 GTTATATTGT
* * *
1696353 AAAGTATATATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTAACTGTGAAAACATATTTATTATTA
*
1696418 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
66 TATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC--AACAAT-AAA
1696483 TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-A
128 T-ATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
1696547 TTGAAACATAAATTACATAACTTTAAAA
192 TTGAAACATAAATTACATAACTTTAAAA
*
1696575 AAAGTATATATCATTTTTATAAAAGTGTTCATACTTATTTAACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTAACTGT-GAAAACATATTTATTATT
1696640 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-A-AAT-AAT-
65 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAACAATAAATA
1696701 TTTT-TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
130 TTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-----
1696765 AAATTGAAACATAAATTACATAACTTTAAAA
190 -AATTGAAACATAAATTACATAACTTTAAAA
* *
1696796 AAAGTATATATTATTTTTATAAAAGTGTCAATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1696830 GTATAAAAGT
Statistics
Matches: 239, Mismatches: 8, Indels: 17
0.91 0.03 0.06
Matches are distributed among these distances:
214 55 0.23
215 4 0.02
217 3 0.01
219 3 0.01
220 1 0.00
221 60 0.25
222 43 0.18
223 70 0.29
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (219 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTAACTGTGAAAACATATTTATTATTA
TATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAACAATAAATAT
TTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAATTGA
AACATAAATTACATAACTTTAAAA
Found at i:1697276 original size:181 final size:182
Alignment explanation
Indices: 1696899--1697372 Score: 693
Period size: 181 Copynumber: 2.6 Consensus size: 182
1696889 CAATCCAAAT
* * * *
1696899 AAAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGA
1 AAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGT-TACAAAATGA
* * * * * *
1696963 TAAAATCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
65 TAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
* *
1697028 TCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTT
130 TCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
* *
1697081 AAAAAATGTATCGATCCAAAATGATATACCAGGTAAAAATATGATAAAACCGGTTACAAAATGAT
1 AAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTACAAAATGAT
*
1697146 AAAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTT
66 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* ** *
1697210 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTA
131 CGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
* *
1697262 AAAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGG-TATCAAAATGA
1 AAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTA-CAAAATGA
* * *
1697326 TAAACCCGGTAAAATGATATCGGATATATTGAAAGTGTCGATACTTT
65 TAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1697373 CGTAAGTACG
Statistics
Matches: 264, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
180 2 0.01
181 166 0.63
182 96 0.36
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTACAAAATGAT
AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
CGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
Found at i:1697316 original size:20 final size:19
Alignment explanation
Indices: 1697293--1697339 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1697283 CGATATAACA
1697293 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
1697313 GGTATCAAAATGATAAACCC
1 GGTA-AAAAATGATAAAACC
1697333 GGTAAAA
1 GGTAAAA
1697340 TGATATCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1699579 original size:21 final size:21
Alignment explanation
Indices: 1699555--1699598 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1699545 AAGACAATCA
1699555 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1699576 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1699597 AG
1 AG
1699599 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1699673 original size:32 final size:32
Alignment explanation
Indices: 1699632--1699692 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1699622 AAATAGATTG
*
1699632 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
* *
1699664 AGTGGTGAAAGAAGTTGGGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
1699693 GTGATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:1701508 original size:19 final size:19
Alignment explanation
Indices: 1701484--1701532 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1701474 AATGTAGGGT
1701484 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1701503 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1701522 TATTTTTGTAT
1 TAATTTTGTAT
1701533 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Done.