Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 32
Found at i:1394528 original size:2 final size:2
Alignment explanation
Indices: 1394521--1394550 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1394511 GTTGTTCCTA
1394521 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
1394551 GAATATTTTT
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:1394975 original size:22 final size:20
Alignment explanation
Indices: 1394950--1395001 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
1394940 TACTCAAGAT
1394950 AGTATCGATACTACAAACCAGA
1 AGTATCGATACT-CAAACCA-A
*
1394972 AGTATC-AGTACTCAAACTAA
1 AGTATCGA-TACTCAAACCAA
1394992 AGTATCGATA
1 AGTATCGATA
1395002 ATATTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 9 0.33
21 8 0.30
22 10 0.37
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.23
Consensus pattern (20 bp):
AGTATCGATACTCAAACCAA
Found at i:1397494 original size:40 final size:40
Alignment explanation
Indices: 1397450--1397529 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1397440 GTCAATCAAT
1397450 AGATCAACCTGAAAATAAAATATTTTAGTTAAACAAAATA
1 AGATCAACCTGAAAATAAAATATTTTAGTTAAACAAAATA
1397490 AGATCAACCTGAAAATAAAATATTTTAGTTAAACAAAATA
1 AGATCAACCTGAAAATAAAATATTTTAGTTAAACAAAATA
1397530 TTTTCACTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (40 bp):
AGATCAACCTGAAAATAAAATATTTTAGTTAAACAAAATA
Found at i:1398739 original size:32 final size:31
Alignment explanation
Indices: 1398662--1398758 Score: 142
Period size: 31 Copynumber: 3.1 Consensus size: 31
1398652 GTCCCGAAGG
1398662 ACCTATCCATATGT-CTCGAAGGACATAGGTA
1 ACCTATCCATATGTCCT-GAAGGACATAGGTA
*
1398693 ACCTGTCCATATGTCCTGAAGGACATAGGTA
1 ACCTATCCATATGTCCTGAAGGACATAGGTA
* *
1398724 ATCCTATCCATATGTCCCGAAGGACATAAGTA
1 A-CCTATCCATATGTCCTGAAGGACATAGGTA
1398756 ACC
1 ACC
1398759 CTTGACTCTT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
31 30 0.50
32 30 0.50
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (31 bp):
ACCTATCCATATGTCCTGAAGGACATAGGTA
Found at i:1410233 original size:19 final size:19
Alignment explanation
Indices: 1410209--1410249 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1410199 ATTTTTTAAT
*
1410209 ATTATAATT-TTATTCATAA
1 ATTATAATTCTCATTC-TAA
1410228 ATTATAATTCTCATTCTAA
1 ATTATAATTCTCATTCTAA
1410247 ATT
1 ATT
1410250 GGTCTTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTATAATTCTCATTCTAA
Found at i:1411302 original size:22 final size:22
Alignment explanation
Indices: 1411245--1411303 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1411235 ACGCGATTCT
*
1411245 GACTATTGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* *
1411267 -AATATCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
1411288 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
1411304 ATATGTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:1411335 original size:20 final size:20
Alignment explanation
Indices: 1411320--1411425 Score: 149
Period size: 20 Copynumber: 5.3 Consensus size: 20
1411310 AAATCGTAAT
1411320 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
*
1411340 GAGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
*
1411360 GCGATTCTGACTGTCGCAAC
1 GCGATTCTGACTATCGCAAC
* * *
1411380 GCGATGCTGACTGTTGCAAC
1 GCGATTCTGACTATCGCAAC
* *
1411400 GCGATGCTGACTATCGCAAT
1 GCGATTCTGACTATCGCAAC
1411420 GCGATT
1 GCGATT
1411426 TTCAAAGCGC
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:1412096 original size:20 final size:20
Alignment explanation
Indices: 1412007--1412113 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
1411997 AGAATCGCAA
*
1412007 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
1412026 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
1412045 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
1412065 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1412085 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1412105 TGAGATTTT
1 TGCGATTTT
1412114 AAGTTTCAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
19 26 0.34
20 51 0.66
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1412120 original size:20 final size:20
Alignment explanation
Indices: 1412077--1412120 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1412067 CGATAGTCAT
* * *
1412077 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGAGATTTTAAG
1412097 TTTCGTGTTGAGATTTTAAG
1 TTTCGTGTTGAGATTTTAAG
1412117 TTTC
1 TTTC
1412121 AGAAACTATT
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:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGAGATTTTAAG
Found at i:1414075 original size:20 final size:19
Alignment explanation
Indices: 1414050--1414116 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
1414040 GCGATTCTTT
1414050 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
*
1414070 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-ATTCG
1414090 CGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
1414108 TGTTGCGAT
1 CGTTGCGAT
1414117 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 12 0.28
19 1 0.02
20 30 0.70
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:1414646 original size:18 final size:19
Alignment explanation
Indices: 1414607--1414648 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1414597 CTCATCTGTC
1414607 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1414628 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1414646 ATC
1 ATC
1414649 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1414702 original size:42 final size:42
Alignment explanation
Indices: 1414631--1414712 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1414621 CTCCCCTATC
*
1414631 GTTCAAGAGGCCCCTATCATCCCTCAAGAG-TCCCCTCCCACA
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGAT-CCCTCCCACA
* ** *
1414673 GTTCAAGAGGCCACTGTCATCGTTGAAGAGATCCCTCCCA
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGATCCCTCCCA
1414713 ACATTCTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (42 bp):
GTTCAAGAGGCCACTATCATCCCTCAAGAGATCCCTCCCACA
Found at i:1416903 original size:14 final size:14
Alignment explanation
Indices: 1416866--1416927 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
1416856 CCACTTGTTT
*
1416866 AATTGATTTATAAA
1 AATTGATTTGTAAA
1416880 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1416894 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1416909 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1416923 TAATT
1 -AATT
1416928 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1417051 original size:20 final size:20
Alignment explanation
Indices: 1417026--1417078 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1417016 AGGTACACTT
* *
1417026 TCGCAATGCTAAACTCAAAA
1 TCGCAATGCGAAACACAAAA
*
1417046 TCGCAATGCGAAAGACAAAA
1 TCGCAATGCGAAACACAAAA
*
1417066 TCGCAACGCGAAA
1 TCGCAATGCGAAA
1417079 GTCAATTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAATGCGAAACACAAAA
Found at i:1417220 original size:74 final size:74
Alignment explanation
Indices: 1417142--1417295 Score: 177
Period size: 74 Copynumber: 2.1 Consensus size: 74
1417132 GTAAAATACC
* *
1417142 CGTTGCGATAATCAAAT-TTGAGTTGCGATACTCAAATCCACGTTGCGATAGTCAAATTCGCATT
1 CGTTGCGATAATCAAATAGT-AGTTGCGATACTCAAATCCACGTTGCGATAGACAAATTCGCATT
*
1417206 GCGATTTTCT-
65 GCAATTTT-TG
* * * * *** *
1417216 CGTTGCGATAGTCAAATAGTCGTTGCGATAGTCAAATTCGTTTTGCGATAGACAAATTCGCGTTG
1 CGTTGCGATAATCAAATAGTAGTTGCGATACTCAAATCCACGTTGCGATAGACAAATTCGCATTG
1417281 CAATTTTTG
66 CAATTTTTG
1417290 CGTTGC
1 CGTTGC
1417296 ATTCGCGTTG
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
73 1 0.01
74 65 0.97
75 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (74 bp):
CGTTGCGATAATCAAATAGTAGTTGCGATACTCAAATCCACGTTGCGATAGACAAATTCGCATTG
CAATTTTTG
Found at i:1417262 original size:94 final size:94
Alignment explanation
Indices: 1417088--1417265 Score: 266
Period size: 94 Copynumber: 1.9 Consensus size: 94
1417078 AGTCAATTCG
* *
1417088 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTAAAATACCCGTTGCGATAA
1 CGTTGCGATAGTCAAATACGCATTGCGATTTTCTCGTTGCGATAGTAAAATACCCGTTGCGATAA
*
1417153 TCAAATTTGAGTTGCGATACTCAAATCCA
66 TCAAATTCGAGTTGCGATACTCAAATCCA
* * ** *
1417182 CGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCGTTGCGATAGTCAAATAGTCGTTGCGATAG
1 CGTTGCGATAGTCAAATACGCATTGCGATTTTCTCGTTGCGATAGTAAAATACCCGTTGCGATAA
**
1417247 TCAAATTCGTTTTGCGATA
66 TCAAATTCGAGTTGCGATA
1417266 GACAAATTCG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 74 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (94 bp):
CGTTGCGATAGTCAAATACGCATTGCGATTTTCTCGTTGCGATAGTAAAATACCCGTTGCGATAA
TCAAATTCGAGTTGCGATACTCAAATCCA
Found at i:1417281 original size:20 final size:20
Alignment explanation
Indices: 1417073--1417281 Score: 131
Period size: 20 Copynumber: 11.1 Consensus size: 20
1417063 AAATCGCAAC
*
1417073 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
1417092 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
1417112 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
1417126 GCGATAGTAAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
1417146 GCGATAATCAAATTTGAGTT
1 GCGATAGTCAAATTCGCGTT
* * *
1417166 GCGATACTCAAATCCACGTT
1 GCGATAGTCAAATTCGCGTT
*
1417186 GCGATAGTCAAATTCGCATT
1 GCGATAGTCAAATTCGCGTT
*
1417206 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
1417220 GCGATAGTCAAA-TAGTCGTT
1 GCGATAGTCAAATTCG-CGTT
**
1417240 GCGATAGTCAAATTCGTTTT
1 GCGATAGTCAAATTCGCGTT
*
1417260 GCGATAGACAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
1417280 GC
1 GC
1417282 AATTTTTGCG
Statistics
Matches: 142, Mismatches: 33, Indels: 29
0.70 0.16 0.14
Matches are distributed among these distances:
14 21 0.15
16 2 0.01
18 2 0.01
19 9 0.06
20 106 0.75
21 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:1417548 original size:140 final size:140
Alignment explanation
Indices: 1417296--1417557 Score: 479
Period size: 140 Copynumber: 1.9 Consensus size: 140
1417286 TTTGCGTTGC
* * *
1417296 ATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAATATATCATAGCAATG
1 ATTCGCATTGCGATATTCAAATGAATCTGTAATAAGTGATAACAACTGAACATATCATAGCAATG
1417361 TTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATACACA
66 TTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATACACA
1417426 TAATAGTCAA
131 TAATAGTCAA
*
1417436 ATTCGCATTGCGATATTCAAATGAATCTGTAATAAGTGATAACAATTGAACATATCATAGCAATG
1 ATTCGCATTGCGATATTCAAATGAATCTGTAATAAGTGATAACAACTGAACATATCATAGCAATG
*
1417501 TTCAAACTCAAGTTACTAATACATGCCTAACTGTAAATGTTAAAAGTTTACACATAA
66 TTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1417558 TACAACGTTT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 117 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (140 bp):
ATTCGCATTGCGATATTCAAATGAATCTGTAATAAGTGATAACAACTGAACATATCATAGCAATG
TTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATACACA
TAATAGTCAA
Found at i:1419699 original size:14 final size:15
Alignment explanation
Indices: 1419679--1419713 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1419669 CCGTGGCATT
1419679 TTCTTCGGGGACTTC
1 TTCTTCGGGGACTTC
*
1419694 -TCTTCGGGGATTTC
1 TTCTTCGGGGACTTC
1419708 TTCTTC
1 TTCTTC
1419714 TTCTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.06, C:0.26, G:0.23, T:0.46
Consensus pattern (15 bp):
TTCTTCGGGGACTTC
Found at i:1420811 original size:20 final size:20
Alignment explanation
Indices: 1420786--1420873 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
1420776 GAAATTCAGT
*
1420786 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1420806 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
1420826 GTTACGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
1420846 ATTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1420866 ATTGCGAT
1 GTTGCGAT
1420874 TTATATATTC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1421096 original size:16 final size:16
Alignment explanation
Indices: 1421075--1421114 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
1421065 ATTATAAGAC
1421075 ATTTTTTATCAGTGAG
1 ATTTTTTATCAGTGAG
*
1421091 ATTTTTTGTCAGTGAG
1 ATTTTTTATCAGTGAG
1421107 ATTATTTT
1 ATT-TTTT
1421115 CTCTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.23, C:0.05, G:0.17, T:0.55
Consensus pattern (16 bp):
ATTTTTTATCAGTGAG
Found at i:1427390 original size:28 final size:30
Alignment explanation
Indices: 1427336--1427391 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
1427326 GTTAAGATAT
1427336 ATATGAAATATATTTAAAATACAATAAAAA
1 ATATGAAATATATTTAAAATACAATAAAAA
1427366 ATAT-AAATAT-TTTAAGAATAC-ATAAA
1 ATATGAAATATATTTAA-AATACAATAAA
1427392 GATATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 10 0.40
29 11 0.44
30 4 0.16
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (30 bp):
ATATGAAATATATTTAAAATACAATAAAAA
Found at i:1438168 original size:34 final size:30
Alignment explanation
Indices: 1438065--1438214 Score: 201
Period size: 30 Copynumber: 4.9 Consensus size: 30
1438055 AAATAAAATA
*
1438065 ACTAAGTGTCCTTACACACCATAGTGTTGC
1 ACTAAGTGTCCTTACACACTATAGTGTTGC
* * *
1438095 ACTGAGTGTCCTTACACACTACAGTGTTGT
1 ACTAAGTGTCCTTACACACTATAGTGTTGC
*
1438125 ACTAAGTGTCCTTACACACTATAGTACCATATGC
1 ACTAAGTGTCCTTACACACTATAGT---GT-TGC
* *
1438159 ACTAAGTGTCCTTACACACCATAGTGTTGT
1 ACTAAGTGTCCTTACACACTATAGTGTTGC
1438189 ACTAAGTGTCCTTACACACTATAGTG
1 ACTAAGTGTCCTTACACACTATAGTG
1438215 CTAATCTGAT
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
30 76 0.73
31 1 0.01
33 1 0.01
34 26 0.25
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (30 bp):
ACTAAGTGTCCTTACACACTATAGTGTTGC
Found at i:1438185 original size:64 final size:64
Alignment explanation
Indices: 1438092--1438213 Score: 217
Period size: 64 Copynumber: 1.9 Consensus size: 64
1438082 ACCATAGTGT
* *
1438092 TGCACTGAGTGTCCTTACACACTACAGTGTTGTACTAAGTGTCCTTACACACTATAGTACCATA
1 TGCACTAAGTGTCCTTACACACCACAGTGTTGTACTAAGTGTCCTTACACACTATAGTACCATA
*
1438156 TGCACTAAGTGTCCTTACACACCATAGTGTTGTACTAAGTGTCCTTACACACTATAGT
1 TGCACTAAGTGTCCTTACACACCACAGTGTTGTACTAAGTGTCCTTACACACTATAGT
1438214 GCTAATCTGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (64 bp):
TGCACTAAGTGTCCTTACACACCACAGTGTTGTACTAAGTGTCCTTACACACTATAGTACCATA
Found at i:1438398 original size:22 final size:22
Alignment explanation
Indices: 1438364--1438432 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
1438354 CATACCTGAA
*
1438364 ATAT-TATACATGATAAATATC
1 ATATATATTCATGATAAATATC
1438385 ATATATATTCATGATAAATATC
1 ATATATATTCATGATAAATATC
1438407 ATATATATTCATGATAAATATC
1 ATATATATTCATGATAAATATC
1438429 ATAT
1 ATAT
1438433 GTAACGATCA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 4 0.09
22 42 0.91
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (22 bp):
ATATATATTCATGATAAATATC
Found at i:1447172 original size:17 final size:17
Alignment explanation
Indices: 1447139--1447172 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1447129 TTAAATTTTT
* *
1447139 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
1447156 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
1447173 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:1453278 original size:20 final size:20
Alignment explanation
Indices: 1453242--1453279 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1453232 ATCCTATTCC
**
1453242 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1453262 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1453280 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1454462 original size:19 final size:20
Alignment explanation
Indices: 1454433--1454472 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
1454423 TTAAAGGGTG
1454433 ACGACGGTATCACTTTCTGA
1 ACGACGGTATCACTTTCTGA
1454453 ACGA-GGTATCACTTTCTGA
1 ACGACGGTATCACTTTCTGA
1454472 A
1 A
1454473 TCCGTGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
ACGACGGTATCACTTTCTGA
Found at i:1455017 original size:19 final size:19
Alignment explanation
Indices: 1454993--1455043 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
1454983 ACAAACTAAA
1454993 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
1455012 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
* *
1455031 TCGTAACGCGATC
1 TCGCAATGCGATC
1455044 TTCGGTATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (19 bp):
TCGCAATGCGATCGATAAT
Found at i:1455120 original size:21 final size:21
Alignment explanation
Indices: 1455091--1455143 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1455081 ATTCTGACTA
1455091 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1455112 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1455133 TCGCAATGCGA
1 TCGCATTGCGA
1455144 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1455160 original size:20 final size:20
Alignment explanation
Indices: 1455133--1455240 Score: 126
Period size: 20 Copynumber: 5.3 Consensus size: 20
1455123 TTTTCCTAAT
1455133 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1455153 TTGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1455173 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1455194 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1455214 TCGCAATGTGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1455235 TCGCAA
1 TCGCAA
1455241 CGAGATTCTG
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
20 44 0.60
21 29 0.40
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1455212 original size:41 final size:41
Alignment explanation
Indices: 1455133--1455240 Score: 155
Period size: 41 Copynumber: 2.7 Consensus size: 41
1455123 TTTTCCTAAT
* * * *
1455133 TCGCAATGCGAA-TACGTAAATTGCAATGTGAATACGTAAA
1 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
*
1455173 TCGCAATGCGAATTAGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
*
1455214 TCGCAATGTGAATTAGGAAAATCGCAA
1 TCGCAATGCGAATTAGGAAAATCGCAA
1455241 CGAGATTCTG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 12 0.20
41 49 0.80
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (41 bp):
TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
Found at i:1458707 original size:19 final size:20
Alignment explanation
Indices: 1458665--1458719 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1458655 CAATCATCTT
*
1458665 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
*
1458685 AATGACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
**
1458704 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
1458720 AGAGAATTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:1458737 original size:33 final size:33
Alignment explanation
Indices: 1458692--1458818 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
1458682 GGAAATGACT
1458692 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1458725 ATTGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1458758 GTCGCAATGCGAAATAAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1458791 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1458819 CGAATTTAGT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1458814 original size:19 final size:19
Alignment explanation
Indices: 1458672--1458822 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
1458662 CTTAATGTCT
* **
1458672 ATCGCAACGCGGAAATGACT
1 ATCGCAAAGC-GAAATGAAA
*
1458692 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
1458711 ATCGC-AA-CG--A-GAGA
1 ATCGCAAAGCGAAATGAAA
* *
1458725 ATTGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
1458744 ATCGC-AA-CG--A-GAGA
1 ATCGCAAAGCGAAATGAAA
* * *
1458758 GTCGCAATGCGAAATAAAA
1 ATCGCAAAGCGAAATGAAA
**
1458777 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
1458791 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
1458810 ATCGCAACGCGAA
1 ATCGCAAAGCGAA
1458823 TTTAGTTTCG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 20 0.22
15 7 0.08
16 6 0.06
17 6 0.06
18 6 0.06
19 39 0.42
20 9 0.10
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.13
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:1458853 original size:19 final size:19
Alignment explanation
Indices: 1458818--1458912 Score: 87
Period size: 19 Copynumber: 5.3 Consensus size: 19
1458808 AAATCGCAAC
*
1458818 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1458837 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
1458856 GTGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
1458870 GCAATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
1458889 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCGTT
1458908 GCGAT
1 GCGAT
1458913 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.16
16 1 0.02
17 1 0.02
18 1 0.02
19 51 0.80
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1458877 original size:33 final size:33
Alignment explanation
Indices: 1458833--1458896 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1458823 TTTAGTTTCG
* *
1458833 CGTTGCGATTTT-AGTTTCGCGTTGTGATTTTGT
1 CGTTGCAATTTTCA-TTTCGCGTTGCGATTTTGT
1458866 CGTTGCAATTTTCATTTCGCGTTGCGATTTT
1 CGTTGCAATTTTCATTTCGCGTTGCGATTTT
1458897 CATTTCGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (33 bp):
CGTTGCAATTTTCATTTCGCGTTGCGATTTTGT
Found at i:1458918 original size:19 final size:19
Alignment explanation
Indices: 1458877--1458920 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1458867 GTTGCAATTT
* **
1458877 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
1458896 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
1458915 TCATTT
1 TCATTT
1458921 TTGCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1459038 original size:14 final size:14
Alignment explanation
Indices: 1459019--1459055 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1459009 CATCAATTAA
1459019 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1459033 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1459047 ACAAATCAA
1 ACAAATCAA
1459056 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1460471 original size:21 final size:21
Alignment explanation
Indices: 1460405--1460471 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1460395 GTGAATCGGG
*
1460405 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1460425 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1460447 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1460468 CTCT
1 CTCT
1460472 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1460980 original size:19 final size:19
Alignment explanation
Indices: 1460924--1460998 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
1460914 TCTGGAACAT
*
1460924 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAAC--GAGAAATG
**
1460945 ACTATCGCAAC-ATGAAATG
1 AAAATCGCAACGA-GAAATG
*
1460964 AAAATCGCAACGAGAAATAA
1 AAAATCGCAACGAGAAAT-G
*
1460984 AAAATTGCAACGAGA
1 AAAATCGCAACGAGA
1460999 GAATCGCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.02
19 19 0.43
20 15 0.34
21 9 0.20
ACGTcount: A:0.52, C:0.16, G:0.17, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGAGAAATG
Found at i:1467757 original size:20 final size:20
Alignment explanation
Indices: 1467734--1467776 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1467724 AATCCACCAC
*
1467734 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
1467754 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
1467774 ATG
1 ATG
1467777 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:1467872 original size:20 final size:20
Alignment explanation
Indices: 1467843--1467880 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1467833 GGAGTTATCA
*
1467843 GTTTCGCGTTGCGATTTTTG
1 GTTTCACGTTGCGATTTTTG
1467863 GTTTCACGTTGCGATTTT
1 GTTTCACGTTGCGATTTT
1467881 GTCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.16, G:0.26, T:0.50
Consensus pattern (20 bp):
GTTTCACGTTGCGATTTTTG
Found at i:1467888 original size:14 final size:14
Alignment explanation
Indices: 1467869--1467908 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1467859 TTTGGTTTCA
*
1467869 CGTTGCGATTTTGT
1 CGTTGCGATTTTAT
*
1467883 CGTTGCGATTCTAT
1 CGTTGCGATTTTAT
1467897 CGTTGCGATTTT
1 CGTTGCGATTTT
1467909 CGTTTCGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:1467943 original size:20 final size:19
Alignment explanation
Indices: 1467899--1467953 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1467889 GATTCTATCG
* *
1467899 TTGCGATTTTCGTTTCGCG
1 TTGCGATTTTCATTTCGCA
*
1467918 TTGCGATTTTCATTCTCTCA
1 TTGCGATTTTCATT-TCGCA
1467938 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1467954 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1468161 original size:94 final size:95
Alignment explanation
Indices: 1468044--1468420 Score: 599
Period size: 94 Copynumber: 4.1 Consensus size: 95
1468034 ATGGATTGCA
* *
1468044 TTAC-TTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCAGAGTTTTAAAGAATACACAG
1 TTACTTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1468107 TTTAGCAGAATTTGCAGCAAACGAACAAAT
66 TTTAGCAGAATTGGCAGCAACCGAACAAAT
* *
1468137 TTACTTTCAACCAAAAGACAAAACAAAAGATAAATACTAACTTCACAATGTTAAAGAATACACAG
1 TTACTTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
1468202 TTTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTTAGCAGAATTGGCAGCAACCGAACAAAT
*
1468232 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAA
1 TTACTTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
*
1468296 TTTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTTAGCAGAATTGGCAGCAACCGAACAAAT
*
1468326 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1468386 TTTAGCAGTATTGGCAGCAACCGAATAAAT
66 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1468416 TTACT
1 TTACT
1468421 AAGCAATCTA
Statistics
Matches: 267, Mismatches: 13, Indels: 10
0.92 0.04 0.03
Matches are distributed among these distances:
90 40 0.15
93 23 0.09
94 116 0.43
95 88 0.33
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (95 bp):
TTACTTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
TTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1468272 original size:189 final size:184
Alignment explanation
Indices: 1468044--1468420 Score: 603
Period size: 189 Copynumber: 2.0 Consensus size: 184
1468034 ATGGATTGCA
* * *
1468044 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTTTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
* *
1468108 TTAGCAGAATTTGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAAGATAAATA
66 TTAGCAGAATTGGCAGCAAACGAACAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATA
*
1468173 CTAACTTCACAATGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
130 CTAACTTCACAATGTT----AATAAACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
1468232 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
* *
1468297 TTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATAC
66 TTAGCAGAATTGGCAGCAAACGAACAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATAC
* * *
1468362 TAACTTCACAGTGTTAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATAAAT
131 TAACTTCACAATGTTAATAAACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
1468416 TTACT
1 TTACT
1468421 AAGCAATCTA
Statistics
Matches: 177, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
184 41 0.23
188 49 0.28
189 87 0.49
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (184 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
TTAGCAGAATTGGCAGCAAACGAACAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATAC
TAACTTCACAATGTTAATAAACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1470126 original size:20 final size:20
Alignment explanation
Indices: 1470101--1470163 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
1470091 TTTTGGTTGA
1470101 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
1470121 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
1470140 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
1470161 AAT
1 AAT
1470164 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1470223 original size:14 final size:14
Alignment explanation
Indices: 1470204--1470260 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1470194 TTTGGTTTCG
1470204 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
1470218 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
1470237 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
1470251 CGTTGCGATT
1 CGTTGCGATT
1470261 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:1470236 original size:33 final size:33
Alignment explanation
Indices: 1470188--1470268 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1470178 AAAATCGCAA
**
1470188 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
1470221 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
1470254 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1470269 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:1470242 original size:19 final size:19
Alignment explanation
Indices: 1470218--1470321 Score: 76
Period size: 21 Copynumber: 5.6 Consensus size: 19
1470208 GCGATTATCT
1470218 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1470237 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
1470251 CGTTGCGATTTTCATTTCTCT
1 CGTTGCGATTTTCA-TT-TCG
**
1470272 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
* *
1470292 TGTTGCGA-TTTCATTTCA
1 CGTTGCGATTTTCATTTCG
*
1470310 TGTTGCGATTTT
1 CGTTGCGATTTT
1470322 AAGTTTAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
18 12 0.17
19 14 0.20
20 9 0.13
21 18 0.26
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1470271 original size:21 final size:20
Alignment explanation
Indices: 1470215--1470321 Score: 83
Period size: 19 Copynumber: 5.8 Consensus size: 20
1470205 GTTGCGATTA
1470215 TCTC-GTTGCGATTTTCATT
1 TCTCTGTTGCGATTTTCATT
*
1470234 TCGC-GTTGCGA--TTC---
1 TCTCTGTTGCGATTTTCATT
1470248 TCTC-GTTGCGATTTTCATT
1 TCTCTGTTGCGATTTTCATT
**
1470267 TCTCTCGTTGCGATAGTCATT
1 TCTCT-GTTGCGATTTTCATT
1470288 T-TCGTGTTGCGA-TTTCATT
1 TCTC-TGTTGCGATTTTCATT
*
1470307 TC-ATGTTGCGATTTT
1 TCTCTGTTGCGATTTT
1470322 AAGTTTAGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
18 8 0.11
19 23 0.32
20 9 0.13
21 15 0.21
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.49
Consensus pattern (20 bp):
TCTCTGTTGCGATTTTCATT
Found at i:1470298 original size:20 final size:18
Alignment explanation
Indices: 1470273--1470318 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1470263 CATTTCTCTC
*
1470273 GTTGCGATAGTCATTTTCGT
1 GTTGCGAT-GTCA-TTTCAT
*
1470293 GTTGCGATTTCATTTCAT
1 GTTGCGATGTCATTTCAT
1470311 GTTGCGAT
1 GTTGCGAT
1470319 TTTAAGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
19 3 0.12
20 8 0.33
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (18 bp):
GTTGCGATGTCATTTCAT
Found at i:1470884 original size:20 final size:20
Alignment explanation
Indices: 1470861--1470953 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
1470851 CGATAGTCAG
1470861 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1470881 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1470901 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
1470921 AATCGCGTTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
1470941 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1470954 ATTAGGAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1470967 original size:21 final size:21
Alignment explanation
Indices: 1470943--1470995 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1470933 ATTTACGTAT
*
1470943 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
1470964 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
*
1470985 TCACAATGCGA
1 TCGCAATGCGA
1470996 TAGTCAGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:1475497 original size:16 final size:16
Alignment explanation
Indices: 1475473--1475503 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1475463 TATATATATA
1475473 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
1475489 ATATTATGAATTATT
1 ATATAATGAATTATT
1475504 AGATTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:1475820 original size:21 final size:21
Alignment explanation
Indices: 1475794--1475838 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1475784 CCGGAAATGT
*
1475794 TAAAAACATTAATGTTTTAGG
1 TAAAAACAATAATGTTTTAGG
*
1475815 TAAAAATAATAATGTTTTAGG
1 TAAAAACAATAATGTTTTAGG
1475836 TAA
1 TAA
1475839 TTTTTTGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (21 bp):
TAAAAACAATAATGTTTTAGG
Found at i:1476896 original size:11 final size:11
Alignment explanation
Indices: 1476880--1476942 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
1476870 AAAATTACAT
1476880 TATTAAAAATA
1 TATTAAAAATA
1476891 TATTAAAAATA
1 TATTAAAAATA
* ***
1476902 CATTATTGATA
1 TATTAAAAATA
1476913 -ATTATAAAAT-
1 TATTA-AAAATA
1476923 T-TTAAAAATA
1 TATTAAAAATA
1476933 TATTAAAAAT
1 TATTAAAAAT
1476943 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:1477085 original size:21 final size:21
Alignment explanation
Indices: 1477059--1477123 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1477049 AACCCTAAGA
1477059 CCTAAAACCTAAA-CTATAAAT
1 CCTAAAACCTAAACCT-TAAAT
*
1477080 CCTAAACCCTAAACCTTAAAT
1 CCTAAAACCTAAACCTTAAAT
* * *
1477101 CCTAAATCATAAACCCTAAAT
1 CCTAAAACCTAAACCTTAAAT
1477122 CC
1 CC
1477124 GATTATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 37 0.95
22 2 0.05
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (21 bp):
CCTAAAACCTAAACCTTAAAT
Found at i:1477092 original size:14 final size:14
Alignment explanation
Indices: 1477059--1477123 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
1477049 AACCCTAAGA
*
1477059 CCTAAAACCTAAAC
1 CCTAAATCCTAAAC
**
1477073 TATAAATCCTAAAC
1 CCTAAATCCTAAAC
*
1477087 CCTAAA-CCTTAAAT
1 CCTAAATCC-TAAAC
*
1477101 CCTAAATCATAAAC
1 CCTAAATCCTAAAC
1477115 CCTAAATCC
1 CCTAAATCC
1477124 GATTATATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
13 2 0.05
14 37 0.93
15 1 0.03
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (14 bp):
CCTAAATCCTAAAC
Found at i:1479171 original size:181 final size:181
Alignment explanation
Indices: 1478851--1479230 Score: 717
Period size: 181 Copynumber: 2.1 Consensus size: 181
1478841 CAATGGTCCA
*
1478851 AAGCAGAAATAAATAGAAGCCTGTTGATCAATAATGAAAGAGTAAACAACCATTCATAACACATA
1 AAGCAGAAAT-AA-ACAAGCCTGTTGATCAATAATGAAAGAGTAAACAACCATTCATAACACATA
1478916 AAAAGAGGGCTAATTCCAATTTCAGGATGCCATAAAAGAAATGCAGAATGTTAAGAATTTTACTG
64 AAAAGAGGGCTAATTCCAATTTCAGGATGCCATAAAAGAAATGCAGAATGTTAAGAATTTTACTG
1478981 AGCAAAGGCTATGATGCTGTCGAAAAACAAAAAACCCAATGAAATGGATCAAAC
129 AGCAAAGGCTATGATGCTGTCGAAAAAC-AAAAACCCAATGAAATGGATCAAAC
1479035 AAGCAGAAA-AAACAAGCCTGTTGATCAATAATGAAAGAGTAAACAACCATTCATAACACATAAA
1 AAGCAGAAATAAACAAGCCTGTTGATCAATAATGAAAGAGTAAACAACCATTCATAACACATAAA
1479099 AAGAGGGCTAATTCCAATTTCAGGATGCCATAAAAGAAATGCAGAATGTTAAGAATTTTACTGAG
66 AAGAGGGCTAATTCCAATTTCAGGATGCCATAAAAGAAATGCAGAATGTTAAGAATTTTACTGAG
1479164 CAAAGGCTATGATGCTGTCGAAAAACAAAAACCCAATGAAATGGATCAAAC
131 CAAAGGCTATGATGCTGTCGAAAAACAAAAACCCAATGAAATGGATCAAAC
1479215 AAGCAGAAATAAACAA
1 AAGCAGAAATAAACAA
1479231 ACCTTACAAA
Statistics
Matches: 194, Mismatches: 1, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
180 34 0.18
181 149 0.77
182 2 0.01
184 9 0.05
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.20
Consensus pattern (181 bp):
AAGCAGAAATAAACAAGCCTGTTGATCAATAATGAAAGAGTAAACAACCATTCATAACACATAAA
AAGAGGGCTAATTCCAATTTCAGGATGCCATAAAAGAAATGCAGAATGTTAAGAATTTTACTGAG
CAAAGGCTATGATGCTGTCGAAAAACAAAAACCCAATGAAATGGATCAAAC
Found at i:1479928 original size:12 final size:12
Alignment explanation
Indices: 1479911--1479949 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1479901 AATAAACCCG
1479911 TCGAGCTTAGAA
1 TCGAGCTTAGAA
* *
1479923 TCGAGCTCAAAA
1 TCGAGCTTAGAA
1479935 TCGAGCTT-GAA
1 TCGAGCTTAGAA
1479946 TCGA
1 TCGA
1479950 ACTCAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (12 bp):
TCGAGCTTAGAA
Found at i:1479954 original size:23 final size:24
Alignment explanation
Indices: 1479911--1479965 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
1479901 AATAAACCCG
*
1479911 TCGAGCTTAGAATCGAGCTCAAAA
1 TCGAGCTTAGAATCGAACTCAAAA
1479935 TCGAGCTT-GAATCGAACTCAAAA
1 TCGAGCTTAGAATCGAACTCAAAA
*
1479958 TTGAGCTT
1 TCGAGCTT
1479966 CAATTGAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (24 bp):
TCGAGCTTAGAATCGAACTCAAAA
Found at i:1480022 original size:16 final size:16
Alignment explanation
Indices: 1480001--1480032 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1479991 CTCTTGAATT
1480001 TTTTTGAGTTCGAGTC
1 TTTTTGAGTTCGAGTC
1480017 TTTTTGAGTTCGAGTC
1 TTTTTGAGTTCGAGTC
1480033 GAGTTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TTTTTGAGTTCGAGTC
Found at i:1483673 original size:18 final size:18
Alignment explanation
Indices: 1483647--1483686 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1483637 ACCTGTCATA
* *
1483647 ACCCGACCCGACCCGTTT
1 ACCCAACCCGACCCGTTG
1483665 ACCCAACCCGACCCGTTG
1 ACCCAACCCGACCCGTTG
1483683 ACCC
1 ACCC
1483687 GTTGACTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.53, G:0.15, T:0.12
Consensus pattern (18 bp):
ACCCAACCCGACCCGTTG
Found at i:1486204 original size:24 final size:24
Alignment explanation
Indices: 1486177--1486291 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
1486167 ATTTGAATTA
1486177 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
1486201 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
* * *
1486225 TGATATAATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
1486249 TGATCTGTTACTTGACCT-GATTTC
1 TGATCTGATACTTGACATGGA-TTC
* *
1486273 TTATATGATACTTGACATG
1 TGATCTGATACTTGACATG
1486292 ATTTATGTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
23 3 0.04
24 72 0.95
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:1488359 original size:15 final size:16
Alignment explanation
Indices: 1488328--1488361 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1488318 AACCCGACCC
1488328 GACTCGTTGACCCGTT
1 GACTCGTTGACCCGTT
1488344 GACTCGTTGA-CCGTT
1 GACTCGTTGACCCGTT
1488359 GAC
1 GAC
1488362 CACTGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.15, C:0.29, G:0.26, T:0.29
Consensus pattern (16 bp):
GACTCGTTGACCCGTT
Found at i:1490829 original size:24 final size:24
Alignment explanation
Indices: 1490802--1490917 Score: 164
Period size: 24 Copynumber: 4.8 Consensus size: 24
1490792 TTCGATTTGA
1490802 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
1490826 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
1490850 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
1490874 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
1490897 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
1490918 TGATTTATGT
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 80 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1490933 original size:23 final size:24
Alignment explanation
Indices: 1490854--1490926 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
1490844 ACATGGATTC
* * *
1490854 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
1490878 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
1490902 TGATATGATACTTGA-CTGATTTA
1 TGATATGATACTTGACCTGATTTA
1490925 TG
1 TG
1490927 TTTTGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.26
24 32 0.74
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:1503915 original size:33 final size:36
Alignment explanation
Indices: 1503844--1503918 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 36
1503834 CAATCCTTTT
*
1503844 AAACTAATGTTAGATCATTCCAACTTATTCAACTTCCTA
1 AAACTAATGTTAGAGCATTCCAACTTATT--A-TTCCTA
1503883 AAACT-ATGTTAGAGCATTCCAACTTA-T-TTCCTA
1 AAACTAATGTTAGAGCATTCCAACTTATTATTCCTA
1503916 AAA
1 AAA
1503919 TGTTGGAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
33 9 0.26
37 1 0.03
38 20 0.57
39 5 0.14
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (36 bp):
AAACTAATGTTAGAGCATTCCAACTTATTATTCCTA
Found at i:1509416 original size:18 final size:19
Alignment explanation
Indices: 1509393--1509429 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1509383 CACCTGACAT
1509393 CTGCAGCA-GGGCAGCATG
1 CTGCAGCATGGGCAGCATG
*
1509411 CTGCAGCATGGGCGGCATG
1 CTGCAGCATGGGCAGCATG
1509430 GTATTTGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.27, G:0.41, T:0.14
Consensus pattern (19 bp):
CTGCAGCATGGGCAGCATG
Found at i:1516260 original size:23 final size:23
Alignment explanation
Indices: 1516204--1516253 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1516194 GGATTCCCCT
*
1516204 AGGGGGAATCGGCTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
1516227 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
1516249 AGGGG
1 AGGGG
1516254 TATATCGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.20, C:0.26, G:0.36, T:0.18
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:1516267 original size:22 final size:23
Alignment explanation
Indices: 1516204--1516266 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
1516194 GGATTCCCCT
**
1516204 AGGGGGAATCGGCTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTCAA
*
1516227 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGATTCCCCTTCAA
*
1516249 AGGGGTATATCGATTCCC
1 AGGGGGA-ATCGATTCCC
1516267 TCTGCCTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 7 0.19
23 29 0.81
ACGTcount: A:0.21, C:0.27, G:0.30, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGATTCCCCTTCAA
Found at i:1543931 original size:67 final size:67
Alignment explanation
Indices: 1543847--1544097 Score: 299
Period size: 67 Copynumber: 3.8 Consensus size: 67
1543837 AGACAAGTGA
* *
1543847 AACAAATCTATCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCTCGAT
1 AACAAATCAAACTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCTCGAT
1543912 TC
66 TC
***
1543914 AACAAATCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCTCGAT
1 AACAAATCAAACTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCTCGAT
1543979 TC
66 TC
*** ** * * * * *
1543981 AATGGATCAAACTCCTCCAATATTTGTTATTCCTTTCAAAGTAAGTGGAACAAGTCTGCCCCGAT
1 AACAAATCAAACTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCTCGAT
1544046 TC
66 TC
*** * * *
1544048 AATGGATCAAACTTTT--TAGATCTGATATTCCCTTCAGAGTAAGCGGAACA
1 AACAAATCAAACTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACA
1544098 GATCTTTCTT
Statistics
Matches: 161, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
65 27 0.17
67 134 0.83
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (67 bp):
AACAAATCAAACTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCTCGAT
TC
Found at i:1544239 original size:115 final size:115
Alignment explanation
Indices: 1543997--1544497 Score: 606
Period size: 115 Copynumber: 4.4 Consensus size: 115
1543987 TCAAACTCCT
* * * * * * *
1543997 CCAATATTTGTTATTCCTTTCAAAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTT
1 CCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTCAGTGGATCAAACTT
* *
1544062 -TTT-AGATCTGATATTCCCTTCAGAGTAAGCGGAAC-AG-ATCTTTCTTTT
66 CTTTAAGATCTGATATTCCCTTCAGAGTAAGCGAAACAAGTATC--TCTTTC
*
1544110 CTAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTCAGTGGATCAAA-TT
1 CCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTCAGTGGATCAAACTT
*
1544174 CCTTTAAGATCTGATATTCCCTTCAGAGTAAGCGAAACAAGTATCTATTTC
66 -CTTTAAGATCTGATATTCCCTTCAGAGTAAGCGAAACAAGTATCTCTTTC
* * *** * *
1544225 CCAAGATTTGATATTCCCTTCAAAGTAAGTGGAACAAGTCTGCCCTGTTTCAAG-GAATCGAACT
1 CCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTC-AGTGGATCAAACT
* * * * * *
1544289 CCTTCAAAATCTGATATTCCTTTCAGAGTAAGTGAAACATA-TCTCTCTTTC
65 TCTTTAAGATCTGATATTCCCTTCAGAGTAAGCGAAACA-AGTATCTCTTTC
*
1544340 CCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCCTCCATTCAGTGGATCAAACTT
1 CCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTCAGTGGATCAAACTT
* * * * *
1544405 CTCTAAGATCTGATATTCCCTTCAGAGTAAG-TAGAACAGGTCTCT-TTTT
66 CTTTAAGATCTGATATTCCCTTCAGAGTAAGCGA-AACAAGTATCTCTTTC
*
1544454 TCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCC
1 CCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCC
1544498 TCAATTCAAT
Statistics
Matches: 334, Mismatches: 43, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
112 2 0.01
113 54 0.16
114 52 0.16
115 217 0.65
116 6 0.02
117 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (115 bp):
CCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTCAGTGGATCAAACTT
CTTTAAGATCTGATATTCCCTTCAGAGTAAGCGAAACAAGTATCTCTTTC
Found at i:1544416 original size:230 final size:227
Alignment explanation
Indices: 1543997--1544507 Score: 704
Period size: 230 Copynumber: 2.2 Consensus size: 227
1543987 TCAAACTCCT
* * *
1543997 CCAATATTTGTTATTCCTTTCAAAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTT
1 CCAAGATTTGATATTCCCTTCAAAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTT
** * * * * *
1544062 TTTAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGATCTTTCTTTTCTAAGATTTGATATTCC
66 TCAAAATCTGATATTCCCTTCAGAGTAAGCGAAACAGATCTCTCTTTCCCAAGATTTGATATTCC
*
1544127 CTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTCAGTGGATCAAATTCCTTTAAGATCTGATATT
131 CTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTCAGTGGATCAAATTCCTCTAAGATCTGATATT
1544192 CCCTTCAGAGTAAGCGA-AACAAGTATCTATTTC
196 CCCTTCAGAGTAAG-GAGAACAAGTATCT-TTTC
* * *
1544225 CCAAGATTTGATATTCCCTTCAAAGTAAGTGGAACAAGTCTGCCCTGTTTCAA-GGAATCGAACT
1 CCAAGATTTGATATTCCCTTCAAAGTAAGTGGAACAAGTCTGCCCCGATTCAATGG-ATCAAACT
* * *
1544289 CCTTCAAAATCTGATATTCCTTTCAGAGTAAGTGAAACATATCTCTCTTTCCCAAGATTTGATAT
65 --TTCAAAATCTGATATTCCCTTCAGAGTAAGCGAAACAGATCTCTCTTTCCCAAGATTTGATAT
*
1544354 TCCCTTCAGAGTAAGTGGAATAAGTCTGCCTCCATTCAGTGGATCAAACTT-CTCTAAGATCTGA
128 TCCCTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTCAGTGGATCAAA-TTCCTCTAAGATCTGA
* * * *
1544418 TATTCCCTTCAGAGTAAGTAGAACAGGTCTCTTTTT
192 TATTCCCTTCAGAGTAAGGAGAACAAGTATCTTTTC
* * * * *
1544454 TCAAGATTTGATATTCCCTTCAGAGTAAGTGGAATAAGTCTGCCTCAATTCAAT
1 CCAAGATTTGATATTCCCTTCAAAGTAAGTGGAACAAGTCTGCCCCGATTCAAT
1544508 TTTCCCTGAA
Statistics
Matches: 248, Mismatches: 29, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
227 2 0.01
228 55 0.22
229 50 0.20
230 139 0.56
231 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (227 bp):
CCAAGATTTGATATTCCCTTCAAAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTT
TCAAAATCTGATATTCCCTTCAGAGTAAGCGAAACAGATCTCTCTTTCCCAAGATTTGATATTCC
CTTCAGAGTAAGTGGAATAAGTCTGCCCCCATTCAGTGGATCAAATTCCTCTAAGATCTGATATT
CCCTTCAGAGTAAGGAGAACAAGTATCTTTTC
Found at i:1545075 original size:24 final size:24
Alignment explanation
Indices: 1545038--1545106 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
1545028 TCCAGAACAA
1545038 GCCACCACCACTTGGACCACTCAT
1 GCCACCACCACTTGGACCACTCAT
* * *
1545062 GCCACCGCCGCTTGGACCACTCAACA
1 GCCACCACCACTTGGACCACTC-A-T
*
1545088 GCCACCACCATTTGGACCA
1 GCCACCACCACTTGGACCA
1545107 TTCAACAGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 20 0.54
25 1 0.03
26 16 0.43
ACGTcount: A:0.25, C:0.45, G:0.16, T:0.14
Consensus pattern (24 bp):
GCCACCACCACTTGGACCACTCAT
Found at i:1545102 original size:26 final size:26
Alignment explanation
Indices: 1545037--1545173 Score: 152
Period size: 26 Copynumber: 5.3 Consensus size: 26
1545027 TTCCAGAACA
*
1545037 AGCCACCACCACTTGGACCACTC-A-
1 AGCCACCACCGCTTGGACCACTCAAC
* *
1545061 TGCCACCGCCGCTTGGACCACTCAAC
1 AGCCACCACCGCTTGGACCACTCAAC
** *
1545087 AGCCACCACCATTTGGACCATTCAAC
1 AGCCACCACCGCTTGGACCACTCAAC
* *
1545113 AGTCACCACCGCTTGGACTACTCAAC
1 AGCCACCACCGCTTGGACCACTCAAC
* * *
1545139 AACCACCGCTGCTTGGACCACTCAAC
1 AGCCACCACCGCTTGGACCACTCAAC
*
1545165 AACCACCAC
1 AGCCACCAC
1545174 TACTTCCAAC
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
24 20 0.22
25 1 0.01
26 71 0.77
ACGTcount: A:0.28, C:0.43, G:0.14, T:0.15
Consensus pattern (26 bp):
AGCCACCACCGCTTGGACCACTCAAC
Found at i:1550699 original size:26 final size:26
Alignment explanation
Indices: 1550626--1550699 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
1550616 GTGGTGGTTA
* *
1550626 TTGAGTGGTCCAAGCGGCGGTAGTTG
1 TTGAGTGGTCCAAGCGGCGGTGGCTG
*
1550652 TTGAGTGGTCCAAGCGGTGGTGGCTG
1 TTGAGTGGTCCAAGCGGCGGTGGCTG
*
1550678 TTGAGTGGTCCAAGCGACGGTG
1 TTGAGTGGTCCAAGCGGCGGTG
1550700 ACATGAGTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.15, C:0.16, G:0.43, T:0.26
Consensus pattern (26 bp):
TTGAGTGGTCCAAGCGGCGGTGGCTG
Found at i:1550991 original size:25 final size:25
Alignment explanation
Indices: 1550924--1551001 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 25
1550914 TGTAAAATAA
* *
1550924 AATATAATTATAAATTATTAT-TTTT
1 AATATAATTAT-AATTATAATATATT
* *
1550949 AATATTA-T-TAATAATAATATATT
1 AATATAATTATAATTATAATATATT
1550972 AATATAATTATAATTATAATA-A-T
1 AATATAATTATAATTATAATATATT
1550995 AATATAA
1 AATATAA
1551002 ATAATGACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
22 7 0.16
23 18 0.41
24 3 0.07
25 16 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATATAATTATAATTATAATATATT
Found at i:1552559 original size:183 final size:184
Alignment explanation
Indices: 1552238--1552623 Score: 611
Period size: 183 Copynumber: 2.1 Consensus size: 184
1552228 TTTTCTAATT
* *
1552238 TATATAA-A-ATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAAT
*
1552301 TATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
1552366 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAACCCATATGTTA
*
1552420 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATAAATAA
* *
1552484 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* *
1552548 TTGATCTTAAATTATTAATTGGGTTTTTAATGATTTGGGTTGAACCCATATGTTA
130 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAACCCATATGTTA
1552603 TATATAATATATGTTATATAT
1 TATATAATATAT-TTA-ATAT
1552624 AATATATTTA
Statistics
Matches: 188, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
182 9 0.05
183 108 0.57
184 67 0.36
185 4 0.02
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAAT
TATAAAATAAAAAATTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAACCCATATGTTA
Found at i:1552616 original size:16 final size:16
Alignment explanation
Indices: 1552595--1552630 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1552585 GGTTGAACCC
1552595 ATATGTTATATATAAT
1 ATATGTTATATATAAT
1552611 ATATGTTATATATAAT
1 ATATGTTATATATAAT
1552627 ATAT
1 ATAT
1552631 TTAATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
ATATGTTATATATAAT
Found at i:1552637 original size:16 final size:16
Alignment explanation
Indices: 1552602--1552649 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1552592 CCCATATGTT
1552602 ATATATAATATATGTT-
1 ATATATAATATAT-TTA
1552618 ATATATAATATATTTA
1 ATATATAATATATTTA
*
1552634 ATATTTAA-A-ATTTA
1 ATATATAATATATTTA
1552648 AT
1 AT
1552650 TTCGGTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 7 0.23
15 3 0.10
16 20 0.67
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATATAATATATTTA
Found at i:1557172 original size:27 final size:25
Alignment explanation
Indices: 1557137--1557191 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
1557127 ATTTTAAATA
*
1557137 AAAATAAAAATATTATTATATTTTATT
1 AAAATAAAAATATTA-TA-ATTATATT
1557164 AAAATAAAAATATTATAATTATATT
1 AAAATAAAAATATTATAATTATATT
1557189 AAA
1 AAA
1557192 TATTTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 10 0.37
26 2 0.07
27 15 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAAATAAAAATATTATAATTATATT
Found at i:1557212 original size:42 final size:43
Alignment explanation
Indices: 1557164--1557249 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
1557154 ATATTTTATT
* *
1557164 AAAATAAAAATATTA-TAATTATATTAAATATTTATTAAAATA
1 AAAATAAAAATATTATTAAGTATATTAAATACTTATTAAAATA
* *
1557206 AAAATAAATATATTATTAAGTATATTAATTACTTATTAAAATA
1 AAAATAAAAATATTATTAAGTATATTAAATACTTATTAAAATA
1557249 A
1 A
1557250 TATTATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 14 0.36
43 25 0.64
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (43 bp):
AAAATAAAAATATTATTAAGTATATTAAATACTTATTAAAATA
Found at i:1557231 original size:36 final size:35
Alignment explanation
Indices: 1557132--1557236 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 35
1557122 CTACAATTTT
*
1557132 AAATAAAAATAAAAATATTATT-ATAT-TTTATTA
1 AAATAAAAATAAATATATTATTAATATATTTATTA
*
1557165 AAATAAAAAT-ATTATAATTATATTAA-ATATTTATTA
1 AAATAAAAATAAATAT-A-T-TATTAATATATTTATTA
*
1557201 AAATAAAAATAAATATATTATTAAGTATATTAATTA
1 AAATAAAAATAAATATATTATTAA-TATATTTATTA
1557237 CTTATTAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
32 3 0.05
33 11 0.18
34 7 0.12
35 7 0.12
36 28 0.47
37 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (35 bp):
AAATAAAAATAAATATATTATTAATATATTTATTA
Found at i:1557491 original size:30 final size:28
Alignment explanation
Indices: 1557457--1557512 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 28
1557447 TTAATATTTT
1557457 TATTAAAATGATATTAAAATAAT-ATATTAA
1 TATT-AAAT-ATA-TAAAATAATGATATTAA
1557487 TATTAAATATATAAAATAATGATATT
1 TATTAAATATATAAAATAATGATATT
1557513 TTAAATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
28 8 0.32
29 4 0.16
30 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (28 bp):
TATTAAATATATAAAATAATGATATTAA
Found at i:1557506 original size:19 final size:19
Alignment explanation
Indices: 1557460--1557506 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1557450 ATATTTTTAT
*
1557460 TAAAATGATATTAAAATAA
1 TAAAATAATATTAAAATAA
* *
1557479 TATATTAATATT-AAATATA
1 TAAAATAATATTAAAATA-A
1557498 TAAAATAAT
1 TAAAATAAT
1557507 GATATTTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAAATAATATTAAAATAA
Found at i:1557863 original size:21 final size:21
Alignment explanation
Indices: 1557839--1557882 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1557829 AAATATGTTA
* * *
1557839 AAAAATATTACTATTTTATAT
1 AAAAATAATAATATTTTAAAT
1557860 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
1557881 AA
1 AA
1557883 TTTTTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:1562296 original size:37 final size:39
Alignment explanation
Indices: 1562218--1562297 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
1562208 AATAAGTTGA
* *
1562218 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAATTAAAAATCAT
*
1562257 AAAAT-TTATATATATTTT-TTTACAAAATTAAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAATTAAAAATCAT
1562294 AAAA
1 AAAA
1562298 AAGTTTAACG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 6 0.16
38 16 0.43
39 15 0.41
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:1570930 original size:7 final size:7
Alignment explanation
Indices: 1570918--1570942 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1570908 GGGCTGACCA
1570918 CTTTGTT
1 CTTTGTT
1570925 CTTTGTT
1 CTTTGTT
1570932 CTTTGTT
1 CTTTGTT
1570939 CTTT
1 CTTT
1570943 TTTACTACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.12, T:0.72
Consensus pattern (7 bp):
CTTTGTT
Found at i:1572803 original size:21 final size:21
Alignment explanation
Indices: 1572777--1572831 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1572767 TCACTATTGT
*
1572777 AGTGCTAACGTGACGGTCTAC
1 AGTGCTAACGTGACGATCTAC
1572798 AGTGCTAACGTGACGATCTAC
1 AGTGCTAACGTGACGATCTAC
*
1572819 AGTACTAACGTGA
1 AGTGCTAACGTGA
1572832 TAGTCAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (21 bp):
AGTGCTAACGTGACGATCTAC
Found at i:1572982 original size:16 final size:14
Alignment explanation
Indices: 1572961--1573027 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 14
1572951 ATTTAAATTA
1572961 TAAATATAAAAATATT
1 TAAATAT-AAAATA-T
* *
1572977 TAAATATTCAAAAAAA
1 TAAATA-T-AAAATAT
*
1572993 TAAATATAAAACAT
1 TAAATATAAAATAT
*
1573007 TAAAAATAAAATAT
1 TAAATATAAAATAT
1573021 TAAATAT
1 TAAATAT
1573028 TCATATTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
14 23 0.55
15 1 0.02
16 12 0.29
17 6 0.14
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATATAAAATAT
Found at i:1573380 original size:31 final size:30
Alignment explanation
Indices: 1573334--1573420 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
1573324 TTCGATAATA
*
1573334 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAA-TATTTTATAATATTTTA-ATAAATT
*
1573365 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTTAATAAATT
*
1573396 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATATTTTAA
1573421 ACTTTATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.88
32 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:1574168 original size:11 final size:10
Alignment explanation
Indices: 1574148--1574227 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 10
1574138 AGTTTAAAAA
*
1574148 ATTATAAAAT
1 ATTATTAAAT
1574158 ACTTATTAAAT
1 A-TTATTAAAT
1574169 -TTATTAAAAT
1 ATTATT-AAAT
*
1574179 ATTATAAAATT
1 ATTATTAAA-T
*
1574190 ATTAATAAAT
1 ATTATTAAAT
1574200 -TTATCTAAAT
1 ATTAT-TAAAT
* *
1574210 ACTATAAAAT
1 ATTATTAAAT
1574220 AATTATTA
1 -ATTATTA
1574228 TATTATCGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
9 8 0.15
10 18 0.33
11 28 0.52
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTATTAAAT
Found at i:1574176 original size:31 final size:30
Alignment explanation
Indices: 1574141--1574227 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
1574131 TCAATAAAGT
*
1574141 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAATATTATAAAATA-TTATTAAATTTA
*
1574172 TTAAAATATTATAAAATTATTAATAAATTTA
1 TTAAAATATTATAAAA-TATTATTAAATTTA
*
1574203 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAATATTATAAAAT-ATTATTA
1574228 TATTATCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAAAATATTATAAAATATTATTAAATTTA
Found at i:1574186 original size:19 final size:21
Alignment explanation
Indices: 1574145--1574194 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
1574135 TAAAGTTTAA
1574145 AAAATTA-TAAAATACTTATT
1 AAAATTATTAAAATACTTATT
*
1574165 AAATTTATTAAAATA-TTA-T
1 AAAATTATTAAAATACTTATT
1574184 AAAATTATTAA
1 AAAATTATTAA
1574195 TAAATTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTATTAAAATACTTATT
Found at i:1576437 original size:62 final size:62
Alignment explanation
Indices: 1576340--1576459 Score: 231
Period size: 62 Copynumber: 1.9 Consensus size: 62
1576330 TTCCTTCCGT
1576340 ACTAGTGTGCTATTGTTTCTCCTGATCAAGGATCGGCCAATCCTCCTATTGGAATCAAGCCA
1 ACTAGTGTGCTATTGTTTCTCCTGATCAAGGATCGGCCAATCCTCCTATTGGAATCAAGCCA
*
1576402 ACTAGTGTGCTATTGTTTCTCCTGATCAGGGATCGGCCAATCCTCCTATTGGAATCAA
1 ACTAGTGTGCTATTGTTTCTCCTGATCAAGGATCGGCCAATCCTCCTATTGGAATCAA
1576460 TCTGGTGGCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (62 bp):
ACTAGTGTGCTATTGTTTCTCCTGATCAAGGATCGGCCAATCCTCCTATTGGAATCAAGCCA
Found at i:1589830 original size:20 final size:20
Alignment explanation
Indices: 1589805--1589845 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1589795 TAAGAGAATG
1589805 TAAGATTATCAATGAA-AATA
1 TAAGATTATCAA-GAATAATA
1589825 TAAGATTATCAAGAATAATA
1 TAAGATTATCAAGAATAATA
1589845 T
1 T
1589846 TACTGGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.32
Consensus pattern (20 bp):
TAAGATTATCAAGAATAATA
Found at i:1589906 original size:35 final size:35
Alignment explanation
Indices: 1589866--1589945 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
1589856 GTTGTATTTT
* *
1589866 GTGTTTGGTTGGCTTAGCAAGAATGTAAGATTATC
1 GTGTTTGGTTGGATTAACAAGAATGTAAGATTATC
*
1589901 GTGTTTGGTTGGATTAACAGGAATGTAAGATTATC
1 GTGTTTGGTTGGATTAACAAGAATGTAAGATTATC
1589936 GTGTTTGGTT
1 GTGTTTGGTT
1589946 AAAAGAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.24, C:0.06, G:0.30, T:0.40
Consensus pattern (35 bp):
GTGTTTGGTTGGATTAACAAGAATGTAAGATTATC
Found at i:1594902 original size:23 final size:23
Alignment explanation
Indices: 1594868--1594952 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
1594858 AAATCTTATA
*
1594868 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
1594891 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* **
1594914 CGGTTCTTCGG-G-ATAAATTCTACG
1 TGGCACTTCGGTGCAT---TTCTACG
1594938 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1594953 ATTTATATGA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 29 0.60
24 15 0.31
25 1 0.02
26 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1594946 original size:24 final size:24
Alignment explanation
Indices: 1594884--1594948 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
1594874 TACGGTGCAT
*
1594884 TTCTACGTGGCACTTC-GGTGCAA
1 TTCTACGTGGCACTTCGGGTGAAA
* **
1594907 TTCTACGCGGTTCTTCGGGAT-AAA
1 TTCTACGTGGCACTTCGGG-TGAAA
1594931 TTCTACGTGGCACTTCGG
1 TTCTACGTGGCACTTCGG
1594949 TGCAATTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 13 0.39
24 19 0.58
25 1 0.03
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (24 bp):
TTCTACGTGGCACTTCGGGTGAAA
Found at i:1595670 original size:12 final size:12
Alignment explanation
Indices: 1595653--1595695 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1595643 ACATTTGGGC
1595653 ACTGTTCATAGT
1 ACTGTTCATAGT
1595665 ACTGTTCAT--T
1 ACTGTTCATAGT
*
1595675 ACTGTTCACAGT
1 ACTGTTCATAGT
1595687 ACTGTTCAT
1 ACTGTTCAT
1595696 TAATGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (12 bp):
ACTGTTCATAGT
Found at i:1595679 original size:10 final size:10
Alignment explanation
Indices: 1595653--1595704 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 10
1595643 ACATTTGGGC
1595653 ACTGTTCATAGT
1 ACTGTTCAT--T
1595665 ACTGTTCATT
1 ACTGTTCATT
*
1595675 ACTGTTCACAGT
1 ACTGTT--CATT
1595687 ACTGTTCATT
1 ACTGTTCATT
*
1595697 AATGTTCA
1 ACTGTTCA
1595705 AACGTTACTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 17 0.49
12 18 0.51
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.42
Consensus pattern (10 bp):
ACTGTTCATT
Found at i:1595681 original size:22 final size:22
Alignment explanation
Indices: 1595653--1595719 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
1595643 ACATTTGGGC
*
1595653 ACTGTTCATAGTACTGTTCATT
1 ACTGTTCAAAGTACTGTTCATT
*
1595675 ACTGTTCACAGTACTGTTCATT
1 ACTGTTCAAAGTACTGTTCATT
*
1595697 AATGTTCAAACGTTACTGTTCAT
1 ACTGTTCAAA-G-TACTGTTCAT
1595720 ACCATATGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 29 0.73
23 1 0.03
24 10 0.25
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.42
Consensus pattern (22 bp):
ACTGTTCAAAGTACTGTTCATT
Found at i:1600444 original size:16 final size:17
Alignment explanation
Indices: 1600410--1600449 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1600400 TTATATGAAC
*
1600410 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
1600427 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
1600443 TGATATG
1 TGATATG
1600450 CCATATGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:1601069 original size:24 final size:23
Alignment explanation
Indices: 1600991--1601078 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
1600981 AAATTTTATA
* *
1600991 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1601014 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1601037 CGGTC-CTTCGG-GACAAATTCTTCG
1 TGG-CACTTCGGTG-C-AATTCTACG
1601061 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
1601079 TATATGAGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 1 0.02
23 35 0.64
24 18 0.33
25 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1606413 original size:17 final size:18
Alignment explanation
Indices: 1606380--1606413 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1606370 TGATTATTTA
*
1606380 TTTATTATTTCTCATATT
1 TTTATTATTTCTAATATT
1606398 TTTATT-TTTCTAATAT
1 TTTATTATTTCTAATAT
1606414 AACTTTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTTCTAATATT
Found at i:1607121 original size:31 final size:30
Alignment explanation
Indices: 1607053--1607121 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 30
1607043 AAGAATTAAG
* *
1607053 ATATATAAAATATTATATTCATATTTTTTG
1 ATATATAAAATATTATATTCATATTTATTA
1607083 ATAATATAAAATATTATATTCATATTATATTA
1 AT-ATATAAAATATTATATTCATATT-TATTA
1607115 ATATATA
1 ATATATA
1607122 TATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 2 0.06
31 28 0.80
32 5 0.14
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (30 bp):
ATATATAAAATATTATATTCATATTTATTA
Found at i:1607125 original size:25 final size:24
Alignment explanation
Indices: 1607083--1607148 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
1607073 ATATTTTTTG
*
1607083 ATAATATAAAATAT-TATAT-TCAT
1 ATAATATTAAATATATATATAT-AT
*
1607106 ATTATATTAATATATATATATATAT
1 ATAATATTAA-ATATATATATATAT
1607131 ATAATATTAAACTATATA
1 ATAATATTAAA-TATATA
1607149 ATTAAAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 8 0.22
24 5 0.14
25 22 0.61
26 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAATATTAAATATATATATATAT
Found at i:1609119 original size:291 final size:297
Alignment explanation
Indices: 1608600--1609296 Score: 1050
Period size: 291 Copynumber: 2.3 Consensus size: 297
1608590 TGATAACTTG
1608600 AAAGGCTTGTTTCTC-AAAACATTCGCAGTGGCCGCCTAAGAGCTTTCGCCTTTGCCGGGCTTGA
1 AAAGGCTTGTTTCTCAAAAACATTCGCAGTGG-CGCCTAAGAGCTTTCGCCTTTGCCGGGCTTGA
*
1608664 GAGCTTGTGCTGCTTCAATCCTTCCTTGGATGTCTGAGACCTTATAATATTTGTGTTTGTGTCTT
65 GAGCTTGTGCTGCTTCAATCCTTCCTTGGATGTCTGAGACCTTATAATATTTGTGTTCGTGTCTT
1608729 GTGCTTGAAAGGGCTGCTATTTCATTTAGTCTTTTGCTTAGTTACTTCATTAATTCAATTTTGGT
130 GTGCTTGAAAGGGCTGCTATTTCATTTAGTCTTTTGCTTAGTTACTTCATTAATTCAATTTTGGT
* *
1608794 ACACTTTCTTACATGCTATGATACAACTCTGTATACTTGGGTAT-T-T-G-TTAACATCATTAAA
195 ACACTTTCTTACATGCTATGATACAACCCTGTATACTTGGGTATCTCTAGATTAACACCATTAAA
* *
1608855 TTTATGTGTTTTGATGGTTTTG-T-TGATGATAAATCC
260 TTTATGCGTTTTGATGGTTTTGTTATGATGATAAAACC
* * *
1608891 AAAGGCTTGTTTCTCAAAAACATTGGCAGTGGTCGCCTAAGAGCTTTCGCCTTAG-CTGGCTTGA
1 AAAGGCTTGTTTCTCAAAAACATTCGCAGTGG-CGCCTAAGAGCTTTCGCCTTTGCCGGGCTTGA
*
1608955 GAGCTTGTGCTGCTTCAATCCTTCCTTGGATGCCTGAGACCTTATAATATTTGTGTTCGTGTCTT
65 GAGCTTGTGCTGCTTCAATCCTTCCTTGGATGTCTGAGACCTTATAATATTTGTGTTCGTGTCTT
* * *
1609020 GTGCTTGAAAGGGCTGCTATTTTATTTAGTCTTTTGCTTAGTTACTTCCTTGATTCAATTTTGGT
130 GTGCTTGAAAGGGCTGCTATTTCATTTAGTCTTTTGCTTAGTTACTTCATTAATTCAATTTTGGT
* * **
1609085 TCACTTTCTTACATGCTATGATGCCGCCCTGTATACTTGGGTATCTGCTAACAGTACTTAACACC
195 ACACTTTCTTACATGCTATGATACAACCCTGTATACTTGGGTATCT-CT---AG-A-TTAACACC
* *
1609150 ATTATATTTATGCGTTTTGATGGTTTTGTTGATGATGATAAAAGC
254 ATTAAATTTATGCGTTTTGATGGTTTTGTT-ATGATGATAAAACC
*
1609195 AAAGGCTTGTTTCTCAAAAACATTTGCAGTGGCTGCCTAAGAGCTTTCGCCTTTGCCGGGCTTGA
1 AAAGGCTTGTTTCTCAAAAACATTCGCAGTGGC-GCCTAAGAGCTTTCGCCTTTGCCGGGCTTGA
* **
1609260 GAGCTTGTGCTGCTTCATTAGTTCCTTGGATGTCTGA
65 GAGCTTGTGCTGCTTCAATCCTTCCTTGGATGTCTGA
1609297 AACTTTGAAC
Statistics
Matches: 364, Mismatches: 26, Indels: 18
0.89 0.06 0.04
Matches are distributed among these distances:
291 187 0.51
292 37 0.10
294 1 0.00
298 1 0.00
301 33 0.09
302 1 0.00
303 1 0.00
304 62 0.17
305 41 0.11
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (297 bp):
AAAGGCTTGTTTCTCAAAAACATTCGCAGTGGCGCCTAAGAGCTTTCGCCTTTGCCGGGCTTGAG
AGCTTGTGCTGCTTCAATCCTTCCTTGGATGTCTGAGACCTTATAATATTTGTGTTCGTGTCTTG
TGCTTGAAAGGGCTGCTATTTCATTTAGTCTTTTGCTTAGTTACTTCATTAATTCAATTTTGGTA
CACTTTCTTACATGCTATGATACAACCCTGTATACTTGGGTATCTCTAGATTAACACCATTAAAT
TTATGCGTTTTGATGGTTTTGTTATGATGATAAAACC
Found at i:1610660 original size:22 final size:21
Alignment explanation
Indices: 1610621--1610667 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
1610611 ATTTTACTGG
1610621 TTTTATAAAACTTAATAATTA
1 TTTTATAAAACTTAATAATTA
*
1610642 TTTTATAATAATTTAATAATTA
1 TTTTATAA-AACTTAATAATTA
1610664 TTTT
1 TTTT
1610668 GTAACTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATAAAACTTAATAATTA
Found at i:1612650 original size:90 final size:90
Alignment explanation
Indices: 1612497--1612675 Score: 322
Period size: 90 Copynumber: 2.0 Consensus size: 90
1612487 GAACCTGCTC
*
1612497 AACCTGATCACAAGCTTAACTTGTCAGCAGTTGAGATAATGCATTGCCGCAAAAGCACTTATAGA
1 AACCTGATCACAAGCTTAACTTGTCAGCAGTTCAGATAATGCATTGCCGCAAAAGCACTTATAGA
1612562 TGAATGAAAATCCCCCCCCCCCCAA
66 TGAATGAAAATCCCCCCCCCCCCAA
*
1612587 AACCTGATCACAAGCTTAACTTGTCAGCAGTTCAGATAATGCATTGCTGCAAAAGCACTTATAGA
1 AACCTGATCACAAGCTTAACTTGTCAGCAGTTCAGATAATGCATTGCCGCAAAAGCACTTATAGA
* *
1612652 TGAATGACAATTCCCCCCCCCCCA
66 TGAATGAAAATCCCCCCCCCCCCA
1612676 TGTCAAATTA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (90 bp):
AACCTGATCACAAGCTTAACTTGTCAGCAGTTCAGATAATGCATTGCCGCAAAAGCACTTATAGA
TGAATGAAAATCCCCCCCCCCCCAA
Found at i:1631524 original size:37 final size:37
Alignment explanation
Indices: 1631448--1631524 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1631438 TTTTTATGTT
*
1631448 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
1631485 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
1631522 TTT
1 TTT
1631525 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:1632275 original size:22 final size:23
Alignment explanation
Indices: 1632245--1632291 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1632235 AAAATATATT
1632245 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
1632268 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
1632290 TA
1 TA
1632292 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:1632305 original size:32 final size:32
Alignment explanation
Indices: 1632239--1632318 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
1632229 ATATTAAAAA
* *
1632239 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
1632271 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
1632303 TATATTATAATAATAT
1 TATATT-TATTAATAT
1632319 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:1632344 original size:29 final size:31
Alignment explanation
Indices: 1632305--1632369 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
1632295 TAATCAATTA
*
1632305 TATTATAATAATATAAGATATTATT-TT-TT
1 TATTATAATAATATAAGAAATTATTATTATT
* *
1632334 TATTTTAATAATATAATAAATTATTATTATT
1 TATTATAATAATATAAGAAATTATTATTATT
1632365 TATTA
1 TATTA
1632370 ATTTCATAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 22 0.73
30 2 0.07
31 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
TATTATAATAATATAAGAAATTATTATTATT
Found at i:1632418 original size:19 final size:18
Alignment explanation
Indices: 1632394--1632462 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
1632384 ATATTATTAA
1632394 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
1632413 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
1632431 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
1632453 ATT-TTAATAA
1 ATTATTAATAA
1632463 GGCTATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:1632437 original size:27 final size:27
Alignment explanation
Indices: 1632349--1632442 Score: 68
Period size: 27 Copynumber: 3.4 Consensus size: 27
1632339 TAATAATATA
* *
1632349 ATAAATTATTATTATTTAT-TAATTTCAT
1 ATAAA-TAATATTATTTATAT-ATTTAAT
* *
1632377 AGAAATAATATTA-TTAAAT-TATTAAT
1 ATAAATAATATTATTTATATAT-TTAAT
*
1632403 AATGAATAATATTATTTATATATTTAAT
1 -ATAAATAATATTATTTATATATTTAAT
1632431 ATTAATATAATA
1 A-TAA-ATAATA
1632443 ATCTAATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
25 1 0.02
26 7 0.14
27 20 0.39
28 16 0.31
29 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAAATAATATTATTTATATATTTAAT
Found at i:1632620 original size:20 final size:19
Alignment explanation
Indices: 1632583--1632621 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1632573 TAATAAAATT
1632583 ATAAAAAAATATTGTAATA
1 ATAAAAAAATATTGTAATA
* *
1632602 ATAAATAAATTATTTTAATA
1 ATAAA-AAAATATTGTAATA
1632622 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAAAAAAATATTGTAATA
Done.