Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002881.1 Hibiscus syriacus cultivar Beakdansim tig00005939_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: 1746118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1256500 original size:18 final size:18
Alignment explanation
Indices: 1256477--1256570 Score: 107
Period size: 18 Copynumber: 5.0 Consensus size: 18
1256467 ACTGAATATT
1256477 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1256495 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
** *
1256514 TTGTTTCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
1256533 TGTCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
*
1256553 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
1256571 ATAATCCCTC
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
18 31 0.49
19 2 0.03
20 30 0.48
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1256568 original size:38 final size:37
Alignment explanation
Indices: 1256475--1256570 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 37
1256465 GCACTGAATA
1256475 TTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
1 TTTGTCCCGAA-GACCACTATGTCCCGAAGGACCACTG
* **
1256513 ATTGTTTCGAAGAACCACTATGTCCCGAAGGACCACTG
1 TTTGTCCCGAAG-ACCACTATGTCCCGAAGGACCACTG
1256551 TTTGTCCCGAATGACCACTA
1 TTTGTCCCGAA-GACCACTA
1256571 ATAATCCCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 1 0.02
38 48 0.96
39 1 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (37 bp):
TTTGTCCCGAAGACCACTATGTCCCGAAGGACCACTG
Found at i:1257257 original size:154 final size:153
Alignment explanation
Indices: 1257052--1257358 Score: 525
Period size: 159 Copynumber: 2.0 Consensus size: 153
1257042 ATATTACTTG
1257052 ATAACATATATCATATAGTATATAAATTCTATCATATCTACCTTATGCTCCA-TTCTTTATACTC
1 ATAACATATATCATATAGTATATAAATTCTATCATATCTACCTTATGCTCCATTTCTTTATACTC
1257116 CCATAGATTTCATAAA-TATATCGTATTTCT-AA-ATATGTCA-TTAATAGTATTTTATTTATGT
66 CCATAGATTTCATAAATTATATCGTATTTCTAAATATATGTCATTTAATAGTATTTTATTTATGT
1257177 ATTAATTTAATCCATTTACTTAA
131 ATTAATTTAATCCATTTACTTAA
1257200 ATAACATATATCATATATGTATATATAACTTCTATCATATCATCTACCTTATGCTCCATTTCTTT
1 ATAACATATATCATATA-GTATATA-AA-TTCTATC--AT-ATCTACCTTATGCTCCATTTCTTT
1257265 ATACTCCCATAGATTTCATAAATTATATCGTATTTCTAAATATATGTCATTTAATAGTATTTTAT
60 ATACTCCCATAGATTTCATAAATTATATCGTATTTCTAAATATATGTCATTTAATAGTATTTTAT
1257330 TTATGTATTAATTTAATCCATTTACTTAA
125 TTATGTATTAATTTAATCCATTTACTTAA
1257359 TTCAATTTCA
Statistics
Matches: 148, Mismatches: 0, Indels: 11
0.93 0.00 0.07
Matches are distributed among these distances:
148 17 0.11
149 7 0.05
150 2 0.01
151 7 0.05
153 2 0.01
154 17 0.11
155 28 0.19
156 14 0.09
157 2 0.01
158 8 0.05
159 44 0.30
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.46
Consensus pattern (153 bp):
ATAACATATATCATATAGTATATAAATTCTATCATATCTACCTTATGCTCCATTTCTTTATACTC
CCATAGATTTCATAAATTATATCGTATTTCTAAATATATGTCATTTAATAGTATTTTATTTATGT
ATTAATTTAATCCATTTACTTAA
Found at i:1263460 original size:19 final size:19
Alignment explanation
Indices: 1263438--1263476 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1263428 ATTTTGGAAG
1263438 CTCCTCATTATTTGTAAAC
1 CTCCTCATTATTTGTAAAC
1263457 CTCCTCATTATTTGTAAAC
1 CTCCTCATTATTTGTAAAC
1263476 C
1 C
1263477 CAGTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41
Consensus pattern (19 bp):
CTCCTCATTATTTGTAAAC
Found at i:1264622 original size:2 final size:2
Alignment explanation
Indices: 1264579--1264606 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1264569 AACCATTTTC
1264579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1264607 ACATGTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1268863 original size:42 final size:42
Alignment explanation
Indices: 1268776--1268935 Score: 281
Period size: 42 Copynumber: 3.9 Consensus size: 42
1268766 ATAAATGCAG
*
1268776 TATTGGAGTATCTGATTTCCAAGCTATC--AGTGTCAGTCAA
1 TATTGGAGTATCTGATTTCCAAGCTATCAGAGTGTTAGTCAA
*
1268816 TATTGGAGTATCTGATTTCGAAGCTATCAGAGTGTTAGTCAA
1 TATTGGAGTATCTGATTTCCAAGCTATCAGAGTGTTAGTCAA
1268858 TATTGGAGTATCTGATTTCCAAGCTATCAGAGTGTTAGTCAA
1 TATTGGAGTATCTGATTTCCAAGCTATCAGAGTGTTAGTCAA
1268900 TATTGGAGTATCTGA-TTCCAAGCTATCAGAGTGTTA
1 TATTGGAGTATCTGATTTCCAAGCTATCAGAGTGTTA
1268936 ATCTTTTAAA
Statistics
Matches: 115, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
40 27 0.23
41 21 0.18
42 67 0.58
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (42 bp):
TATTGGAGTATCTGATTTCCAAGCTATCAGAGTGTTAGTCAA
Found at i:1269650 original size:14 final size:14
Alignment explanation
Indices: 1269633--1269670 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1269623 TTCTTTTTTG
*
1269633 TGGAAAATGGCTTT
1 TGGAAAATGGATTT
1269647 TGGAAAAT-GATTT
1 TGGAAAATGGATTT
*
1269660 TGGAGAATGGA
1 TGGAAAATGGA
1269671 ATTATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.32
Consensus pattern (14 bp):
TGGAAAATGGATTT
Found at i:1274789 original size:20 final size:20
Alignment explanation
Indices: 1274760--1274797 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1274750 CAAACCCCAG
*
1274760 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
1274780 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
1274798 TCAAAGGGGG
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:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:1274833 original size:21 final size:21
Alignment explanation
Indices: 1274759--1274841 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
1274749 GCAAACCCCA
*
1274759 GGGGGGTATCGATTCCC-C-T
1 GGGGGGAATCGATTCCCTCAT
* *
1274778 GTGGGGGAATCGGTTCCCCTTCAA
1 G-GGGGGAATCGATT-CCC-TCAT
* *
1274802 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGAATCGATTCCCTCAT
*
1274823 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
1274842 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.02
20 11 0.22
21 22 0.43
22 3 0.06
23 14 0.27
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.24
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAT
Found at i:1278684 original size:22 final size:21
Alignment explanation
Indices: 1278642--1278681 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1278632 GAGTTTGTTT
*
1278642 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1278663 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1278682 ACAATTTCTC
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:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1281044 original size:30 final size:31
Alignment explanation
Indices: 1280993--1281054 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 31
1280983 GCAACCACAT
1280993 GTGCTGGTGCTGGTAAGTGGAGCATGTGCTG
1 GTGCTGGTGCTGGTAAGTGGAGCATGTGCTG
1281024 GTGCTGGTG-TGG-AGAGTGGAGCATGTGCTG
1 GTGCTGGTGCTGGTA-AGTGGAGCATGTGCTG
1281054 G
1 G
1281055 AGTGGATAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 1 0.03
30 20 0.67
31 9 0.30
ACGTcount: A:0.13, C:0.11, G:0.48, T:0.27
Consensus pattern (31 bp):
GTGCTGGTGCTGGTAAGTGGAGCATGTGCTG
Found at i:1281521 original size:95 final size:95
Alignment explanation
Indices: 1281411--1281714 Score: 285
Period size: 95 Copynumber: 3.2 Consensus size: 95
1281401 GTGACACTGC
*
1281411 TCCTTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAG
1 TCCTTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACCGCTCATCCGCGATGAAG
*
1281476 AGATCGGGTCGTTTTCGAGTATGACGTTGT
66 AGATCGGGTCGTTTTCGAGTATGACGATGT
* ** * * ** * * * * * * *
1281506 TCCTTCGTGATGAGGAAAT-TGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCCTTCGTG
1 TCCTTCGTGATGAGGAGATCT-GGTCGGT-T--TGAT--GTTGAAGACGACACCGCTCATCCGCG
* * * * * ** *
1281570 ATGAGGA-AGTCTGATTG-TCT-GAGGGTGAC-ACTGC
60 ATGAAGAGA-TCGGGTCGTTTTCGAGTATGACGA-TGT
1281604 TCCTTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACCGCTCATCCGCGATGAAG
1 TCCTTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACCGCTCATCCGCGATGAAG
1281669 AGATCGGGTCGTTTTCGAGTATGACGATGT
66 AGATCGGGTCGTTTTCGAGTATGACGATGT
1281699 TCCTTCGTGATGAGGA
1 TCCTTCGTGATGAGGA
1281715 AATTAGGTCA
Statistics
Matches: 151, Mismatches: 45, Indels: 26
0.68 0.20 0.12
Matches are distributed among these distances:
93 27 0.18
94 4 0.03
95 51 0.34
96 2 0.01
97 1 0.01
98 35 0.23
99 4 0.03
100 27 0.18
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (95 bp):
TCCTTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACCGCTCATCCGCGATGAAG
AGATCGGGTCGTTTTCGAGTATGACGATGT
Found at i:1281570 original size:193 final size:193
Alignment explanation
Indices: 1281241--1281812 Score: 993
Period size: 193 Copynumber: 3.0 Consensus size: 193
1281231 CTTCGATTAA
* * * *
1281241 TCGGTTTGATATTGAAGACGACATTGCTCATCCGCGATGAAGAGATCGGGTCGCTTTCGATTATG
1 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAGTATG
* * * *
1281306 AC-TATGTTCCTTCGTGATGAGGAAATCGGGTCAATCAAGAGATAATTTGGGGATAATATGGTTC
66 ACGT-TGTTCCTTCGTGATGAGGAAATTGGGTCAATCTAGAGATAATTTGGGGACAATACGGTTC
*
1281370 CTTCGTGATGAGGAAGTCTTATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
130 CTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
1281434 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAGTATG
1 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAGTATG
*
1281499 ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTGGAGATAATTTGGGGACAATACGGTTCC
66 ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTAGAGATAATTTGGGGACAATACGGTTCC
1281564 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
131 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
*
1281627 TCGGTTTGATGTTGAAGACGACACCGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAGTATG
1 TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAGTATG
* *
1281692 ACGATGTTCCTTCGTGATGAGGAAATTAGGTCAATCTAGAGATAATTTGGGGACAATACGGTTCC
66 ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTAGAGATAATTTGGGGACAATACGGTTCC
* *
1281757 TTCGTGATGAGAAAGCCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGA
131 TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGA
1281813 AATTGGGTCA
Statistics
Matches: 362, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
193 361 1.00
194 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (193 bp):
TCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGATCGGGTCGTTTTCGAGTATG
ACGTTGTTCCTTCGTGATGAGGAAATTGGGTCAATCTAGAGATAATTTGGGGACAATACGGTTCC
TTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCCTTCGTGATGAGGAGATCTGG
Found at i:1282457 original size:15 final size:15
Alignment explanation
Indices: 1282437--1282467 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1282427 TTTCTATCAT
*
1282437 TTTGTCTCAAGTCTC
1 TTTGTCTCAAGCCTC
1282452 TTTGTCTCAAGCCTC
1 TTTGTCTCAAGCCTC
1282467 T
1 T
1282468 CCTGAGAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.29, G:0.13, T:0.45
Consensus pattern (15 bp):
TTTGTCTCAAGCCTC
Found at i:1295032 original size:18 final size:18
Alignment explanation
Indices: 1295009--1295043 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1294999 TGCTGGTAAG
1295009 TGGAGCATGTGCTGGTGC
1 TGGAGCATGTGCTGGTGC
1295027 TGGAGCATGTGCTGGTG
1 TGGAGCATGTGCTGGTG
1295044 TTGGTGTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.14, G:0.46, T:0.29
Consensus pattern (18 bp):
TGGAGCATGTGCTGGTGC
Found at i:1298360 original size:52 final size:52
Alignment explanation
Indices: 1298298--1298401 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
1298288 GAAGCGCATA
1298298 AAATCTACCCCCGGAGCAACTCTGATACGCATATTACTTTGAGGTCATCTAC
1 AAATCTACCCCCGGAGCAACTCTGATACGCATATTACTTTGAGGTCATCTAC
1298350 AAATCTACCCCCGGAGCAACTCTGATACGCATATTACTTTGAGGTCATCTAC
1 AAATCTACCCCCGGAGCAACTCTGATACGCATATTACTTTGAGGTCATCTAC
1298402 TTACAATGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (52 bp):
AAATCTACCCCCGGAGCAACTCTGATACGCATATTACTTTGAGGTCATCTAC
Found at i:1302411 original size:32 final size:31
Alignment explanation
Indices: 1302373--1302449 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
1302363 CGGGGCCGTG
1302373 GGGCCTACCTAAGAACACATCTTAGGG-CTGCA
1 GGGCCTACCTAAGAA-ACATCTTAGGGTC-GCA
** **
1302405 GGGCCTACCCGAGAATGATCTTAGGGTCGCA
1 GGGCCTACCTAAGAAACATCTTAGGGTCGCA
*
1302436 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1302450 GTCACATTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTTAGGGTCGCA
Found at i:1306515 original size:7 final size:7
Alignment explanation
Indices: 1306505--1306542 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1306495 AGGATTTATA
1306505 ATTTAAG
1 ATTTAAG
1306512 ATTTAAG
1 ATTTAAG
*
1306519 GTTTAAG
1 ATTTAAG
1306526 ATTTAAG
1 ATTTAAG
*
1306533 GTTTAAG
1 ATTTAAG
1306540 ATT
1 ATT
1306543 AAGGGTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (7 bp):
ATTTAAG
Found at i:1306550 original size:14 final size:14
Alignment explanation
Indices: 1306506--1306546 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
1306496 GGATTTATAA
1306506 TTTAAGATTTAAGG
1 TTTAAGATTTAAGG
1306520 TTTAAGATTTAAGG
1 TTTAAGATTTAAGG
1306534 TTTAAGA-TTAAGG
1 TTTAAGATTTAAGG
1306547 GTTTGATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (14 bp):
TTTAAGATTTAAGG
Found at i:1308910 original size:2 final size:2
Alignment explanation
Indices: 1308905--1308958 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1308895 ATTTTTTCTA
1308905 AT AT AT AT AT AT AT AT AT -T 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
1308946 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1308959 CACATGTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1322092 original size:6 final size:6
Alignment explanation
Indices: 1322081--1322105 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1322071 TCATACTATG
1322081 CTTCTC CTTCTC CTTCTC CTTCTC C
1 CTTCTC CTTCTC CTTCTC CTTCTC C
1322106 ACTTTCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CTTCTC
Found at i:1326802 original size:12 final size:11
Alignment explanation
Indices: 1326781--1326813 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
1326771 AAGTCATCAA
1326781 AAAATATTTTT
1 AAAATATTTTT
1326792 AAAATATTTTT
1 AAAATATTTTT
1326803 AAATATATTTT
1 AAA-ATATTTT
1326814 AGAAGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:1328020 original size:38 final size:38
Alignment explanation
Indices: 1327977--1328068 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
1327967 GACTCAATCA
* *
1327977 GAAAATTGTACACCCTACACGCGACTTGAACCCGAATT
1 GAAAATTATACACCCTACACGCGACCTGAACCCGAATT
* * * **
1328015 GAAAATTATACACCCTCCACTCGACCTGAACTCGAACA
1 GAAAATTATACACCCTACACGCGACCTGAACCCGAATT
* *
1328053 AAAAACTATACACCCT
1 GAAAATTATACACCCT
1328069 CCACTTGACA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.20
Consensus pattern (38 bp):
GAAAATTATACACCCTACACGCGACCTGAACCCGAATT
Found at i:1330367 original size:23 final size:23
Alignment explanation
Indices: 1330318--1330380 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1330308 GTGTTATATT
* **
1330318 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
*
1330341 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTAATTAAA
1330364 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
1330381 AAATAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 22 0.65
24 1 0.03
25 11 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:1330374 original size:12 final size:12
Alignment explanation
Indices: 1330340--1330380 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1330330 TATTAATTAG
1330340 TATA-TTTTAAA
1 TATATTTTTAAA
1330351 TATATTTATTAAA
1 TATATTT-TTAAA
1330364 -ATATTATTTAAA
1 TATATT-TTTAAA
1330376 TATAT
1 TATAT
1330381 AAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.15
12 12 0.46
13 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATTTTTAAA
Found at i:1330393 original size:25 final size:26
Alignment explanation
Indices: 1330364--1330443 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 26
1330354 ATTTATTAAA
1330364 ATATTATTTAAATATATAAATAATAT-T
1 ATATTATTTAAATATA-AAA-AATATAT
1330391 ATTCATTA-TTAAATATAAAAAATATAT
1 A-T-ATTATTTAAATATAAAAAATATAT
1330418 ATATTA-TTAAA-AT-AAAAATATA-
1 ATATTATTTAAATATAAAAAATATAT
1330440 ATAT
1 ATAT
1330444 CTTATATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.08
23 9 0.18
24 2 0.04
25 9 0.18
26 6 0.12
27 6 0.12
28 10 0.20
29 4 0.08
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATTATTTAAATATAAAAAATATAT
Found at i:1330405 original size:28 final size:26
Alignment explanation
Indices: 1330364--1330463 Score: 96
Period size: 29 Copynumber: 3.6 Consensus size: 26
1330354 ATTTATTAAA
1330364 ATATTATTTAAATATATAAATAATAT-T
1 ATATTA-TTAAATATA-AAATAATATAT
1330391 ATTCATTATTAAATATAAAA-AATATAT
1 A-T-ATTATTAAATATAAAATAATATAT
* *
1330418 ATATTATTAAAATAAAAATATAATATCTT
1 ATATTATT-AAATATAAA-ATAATAT-AT
1330447 ATATTATTATAATATAA
1 ATATTATTA-AATATAA
1330464 TTGATTATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
25 6 0.10
26 14 0.23
27 7 0.11
28 16 0.26
29 19 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATTATTAAATATAAAATAATATAT
Found at i:1330422 original size:22 final size:23
Alignment explanation
Indices: 1330361--1330443 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 23
1330351 TATATTTATT
1330361 AAAATAT-TAT-TTAAATATATA
1 AAAATATATATATTAAATATATA
1330382 AATAATATTATTCATTATTAAATATA-A
1 AA-AATA-TA-T-A-TATTAAATATATA
1330409 AAAATATATATATTATTAA-A-ATA
1 AAAATATATATATTA--AATATATA
1330432 AAAATATA-ATAT
1 AAAATATATATAT
1330444 CTTATATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 19
0.73 0.00 0.27
Matches are distributed among these distances:
21 2 0.04
22 14 0.27
23 12 0.23
24 3 0.06
25 3 0.06
26 5 0.10
27 4 0.08
28 9 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATATATATATTAAATATATA
Found at i:1330531 original size:34 final size:31
Alignment explanation
Indices: 1330469--1330534 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
1330459 TATAATTGAT
1330469 TATTTTATATAATATTAAAAATACAATATTA
1 TATTTTATATAATATTAAAAATACAATATTA
1330500 TATTATTATA-AATATTAATAAATA-AATA--A
1 TATT-TTATATAATATTAA-AAATACAATATTA
1330529 TATTTT
1 TATTTT
1330535 GATAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
28 2 0.06
29 5 0.15
31 16 0.48
32 10 0.30
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
TATTTTATATAATATTAAAAATACAATATTA
Found at i:1330544 original size:31 final size:31
Alignment explanation
Indices: 1330479--1330544 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
1330469 TATTTTATAT
* *
1330479 AATATTAAAAATACAATATTATATTATTATA
1 AATATTAAAAATACAATAATATATTATTAAA
*
1330510 AATATTAATAAATA-AATAATATTTTGA-TAAA
1 AATATTAA-AAATACAATAATATATT-ATTAAA
1330541 AATA
1 AATA
1330545 ATATTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (31 bp):
AATATTAAAAATACAATAATATATTATTAAA
Found at i:1331053 original size:42 final size:42
Alignment explanation
Indices: 1330994--1331106 Score: 190
Period size: 42 Copynumber: 2.7 Consensus size: 42
1330984 AATTACGTTC
*
1330994 CGAAAAACGAATTACGTGAAACAAACACGGGAAAATATTTTT
1 CGAAAAACGAATTACGTGAAACAAACACGGAAAAATATTTTT
*
1331036 CGAAAAACGACTTACGTGAAACAAACACGGAAAAATATTTTT
1 CGAAAAACGAATTACGTGAAACAAACACGGAAAAATATTTTT
* *
1331078 CAAAAAACGAATTACATGAAACAAACACG
1 CGAAAAACGAATTACGTGAAACAAACACG
1331107 AAATTTCAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (42 bp):
CGAAAAACGAATTACGTGAAACAAACACGGAAAAATATTTTT
Found at i:1333683 original size:24 final size:24
Alignment explanation
Indices: 1333650--1333698 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1333640 TAAAATTTAG
*
1333650 ATATATACATA-AATATACTAATTT
1 ATATACACATACAATATA-TAATTT
*
1333674 ATATACACATACAATGTATAATTT
1 ATATACACATACAATATATAATTT
1333698 A
1 A
1333699 ATTATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (24 bp):
ATATACACATACAATATATAATTT
Found at i:1336133 original size:41 final size:41
Alignment explanation
Indices: 1336076--1336153 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1336066 CCAAAGTTAG
1336076 ATGTGCCACGAGAGTCATTCCAGATTAATCAGATAAAACTT
1 ATGTGCCACGAGAGTCATTCCAGATTAATCAGATAAAACTT
*
1336117 ATGTGCCACGCGAGTCATTCCAGATTAATCAGATAAA
1 ATGTGCCACGAGAGTCATTCCAGATTAATCAGATAAA
1336154 GCTTTGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (41 bp):
ATGTGCCACGAGAGTCATTCCAGATTAATCAGATAAAACTT
Found at i:1340020 original size:41 final size:40
Alignment explanation
Indices: 1339975--1340130 Score: 145
Period size: 40 Copynumber: 3.9 Consensus size: 40
1339965 GATTTTGACT
* * * *
1339975 ATCGCATTGCGATTTTCCTAATTCGTAATGCGAATACGTAA
1 ATCGCAATGCGA-TTTCGTAAATCGCAATGCGAATACGTAA
* * * * *
1340016 ATCGCAACGCGAATTTGGAAAATCGCAATACGATTACGTAA
1 ATCGCAATGCG-ATTTCGTAAATCGCAATGCGAATACGTAA
* * *
1340057 ATCACAATGCGAATACGTAAATCGCAATGCGAATACGTAA
1 ATCGCAATGCGATTTCGTAAATCGCAATGCGAATACGTAA
*
1340097 ATCGCAATGCGAATTT-G-ACTATCGCAATGCGAAT
1 ATCGCAATGCG-ATTTCGTA-AATCGCAATGCGAAT
1340131 CTGACTATCG
Statistics
Matches: 91, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
39 1 0.01
40 48 0.53
41 41 0.45
42 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (40 bp):
ATCGCAATGCGATTTCGTAAATCGCAATGCGAATACGTAA
Found at i:1340029 original size:20 final size:20
Alignment explanation
Indices: 1340001--1340110 Score: 148
Period size: 20 Copynumber: 5.5 Consensus size: 20
1339991 CCTAATTCGT
1340001 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* ** *
1340021 AACGCGAATTTGGAAAATCGC
1 AATGCGAA-TACGTAAATCGC
* * *
1340042 AATACGATTACGTAAATCAC
1 AATGCGAATACGTAAATCGC
1340062 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
1340082 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
1340102 AATGCGAAT
1 AATGCGAAT
1340111 TTGACTATCG
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
20 61 0.81
21 14 0.19
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:1340094 original size:40 final size:40
Alignment explanation
Indices: 1340001--1340130 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
1339991 CCTAATTCGT
* **
1340001 AATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGC
1 AATGCGAATACGTAAATCGCAATGCGAA-TACGAAAATCGC
* * * *
1340042 AATACGATTACGTAAATCACAATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGCAATGCGAATACGAAAATCGC
** **
1340082 AATGCGAATACGTAAATCGCAATGCGAATTTGACTATCGC
1 AATGCGAATACGTAAATCGCAATGCGAATACGAAAATCGC
1340122 AATGCGAAT
1 AATGCGAAT
1340131 CTGACTATCG
Statistics
Matches: 74, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 50 0.68
41 24 0.32
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (40 bp):
AATGCGAATACGTAAATCGCAATGCGAATACGAAAATCGC
Found at i:1340120 original size:20 final size:21
Alignment explanation
Indices: 1340097--1340184 Score: 105
Period size: 20 Copynumber: 4.4 Consensus size: 21
1340087 GAATACGTAA
1340097 ATCGCAATGCGAATT-TGACT
1 ATCGCAATGCGAATTATGACT
*
1340117 ATCGCAATGCGAA-TCTGACT
1 ATCGCAATGCGAATTATGACT
* *
1340137 ATCGCAATGAG-ATTCTGACT
1 ATCGCAATGCGAATTATGACT
1340157 ATCGCAA--CGAGATTATGACT
1 ATCGCAATGCGA-ATTATGACT
1340177 ATCGCAAT
1 ATCGCAAT
1340185 ACTAAATTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.02
19 2 0.03
20 57 0.95
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (21 bp):
ATCGCAATGCGAATTATGACT
Found at i:1341051 original size:24 final size:24
Alignment explanation
Indices: 1341024--1341077 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1341014 GTATTCGAAA
1341024 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1341048 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1341072 TTTGAT
1 TTTGAT
1341078 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1343511 original size:20 final size:20
Alignment explanation
Indices: 1343486--1343576 Score: 139
Period size: 20 Copynumber: 4.5 Consensus size: 20
1343476 ACATTTATTG
1343486 GACTATCGCAACGC-GAATAT
1 GACTATCGCAACGCGGAA-AT
**
1343506 GACTATCGCAACAAGGAAAT
1 GACTATCGCAACGCGGAAAT
*
1343526 GACTATCGCAACGCGGAATT
1 GACTATCGCAACGCGGAAAT
1343546 GACTATCGCAACGCGGAAAT
1 GACTATCGCAACGCGGAAAT
1343566 GACTATCGCAA
1 GACTATCGCAA
1343577 TGAGAGTATC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 61 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (20 bp):
GACTATCGCAACGCGGAAAT
Found at i:1343607 original size:33 final size:33
Alignment explanation
Indices: 1343561--1343646 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
1343551 TCGCAACGCG
** * *
1343561 GAAATGACTATCGCAATGAGAGTATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
* *
1343594 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
1343627 GAAAATGAAAAATCGCAACG
1 G-AAATG-AAAATCGCAACG
1343647 CGAAACTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 28 0.62
34 5 0.11
35 12 0.27
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGC
Found at i:1343718 original size:33 final size:33
Alignment explanation
Indices: 1343662--1343756 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
1343652 CTAAATTTGT
*
1343662 GTTGCGATTTTCATTTTCGCATTGTGATTCACTC
1 GTTGCGATTTTCA-TTTCGCATTGCGATTCACTC
*
1343696 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCACTC
** *
1343729 GTTGCGATAGTCATTTCCGCGTTGCGAT
1 GTTGCGATTTTCATTT-CGCATTGCGAT
1343757 AGTCATTTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 32 0.58
34 23 0.42
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCACTC
Found at i:1343753 original size:20 final size:20
Alignment explanation
Indices: 1343728--1343780 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1343718 GCGATTCTCT
1343728 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1343748 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCG
1343768 CGTTGCGATAGTC
1 CGTTGCGATAGTC
1343781 TGTTTTGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1343901 original size:14 final size:14
Alignment explanation
Indices: 1343882--1343918 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1343872 TATCAATTAA
1343882 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1343896 ACAAATCATCTTTT
1 ACAAATCAACATTT
1343910 ACAAATCAA
1 ACAAATCAA
1343919 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1345333 original size:21 final size:21
Alignment explanation
Indices: 1345304--1345407 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 21
1345294 GAATGTTGGG
* *
1345304 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTGAACGATGAT
* **
1345325 AGTGGCCTCTTGAACGATGGG
1 AGGGGCCTCTTGAACGATGAT
* **
1345346 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAT
*
1345367 AGGGGCCTCTTGAACGAT-AG
1 AGGGGCCTCTTGAACGATGAT
*
1345387 GGGAGGCCTCTTGAACGATGA
1 AGG-GGCCTCTTGAACGATGA
1345408 CTTGTGAGTC
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 3 0.05
21 61 0.94
22 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAT
Found at i:1345407 original size:42 final size:42
Alignment explanation
Indices: 1345300--1345407 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
1345290 TCTAGAATGT
* *
1345300 TGGGAG-GGACCTCTTCAACGATGATAGTGGCCTCTTGAACGA
1 TGGGAGAGG-CCTCTTGAACGATGATAGGGGCCTCTTGAACGA
* * **
1345342 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
1345384 TAGGG-GAGGCCTCTTGAACGATGA
1 T-GGGAGAGGCCTCTTGAACGATGA
1345408 CTTGTGAGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:1345915 original size:20 final size:20
Alignment explanation
Indices: 1345892--1345940 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1345882 GAAACTTAAA
1345892 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
1345912 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
1345932 ATCGCAACG
1 ATCGCAACG
1345941 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1346027 original size:20 final size:20
Alignment explanation
Indices: 1346004--1346141 Score: 164
Period size: 20 Copynumber: 7.2 Consensus size: 20
1345994 TAAAATTCTT
1346004 ATTGCGATAGTCATTTTCGC
1 ATTGCGATAGTCATTTTCGC
*
1346024 ATTGCGATAGTCATTTTTGC
1 ATTGCGATAGTCATTTTCGC
1346044 ATTGCGATAGTCATTTTCGC
1 ATTGCGATAGTCATTTTCGC
* **
1346064 GTTGCGATTTTCA-TTTCGC
1 ATTGCGATAGTCATTTTCGC
*
1346083 ATTGCGAT--TC--TCTCG-
1 ATTGCGATAGTCATTTTCGC
*
1346098 -TTGCTATAGTCATTTTCGC
1 ATTGCGATAGTCATTTTCGC
*
1346117 GTTGCGATAGTCATTTTCGC
1 ATTGCGATAGTCATTTTCGC
1346137 ATTGC
1 ATTGC
1346142 AATAATAAAC
Statistics
Matches: 101, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
14 6 0.06
16 6 0.06
17 2 0.02
18 4 0.04
19 13 0.13
20 70 0.69
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (20 bp):
ATTGCGATAGTCATTTTCGC
Found at i:1348062 original size:20 final size:20
Alignment explanation
Indices: 1348039--1348127 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
1348029 CTGAAACTTT
1348039 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
1348059 AAATCGCAACACAAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
1348079 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
* *
1348099 CAATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
1348118 AAATCGCAAC
1 AAATCGCAAC
1348128 GACAGAATCG
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
19 13 0.22
20 45 0.78
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1348497 original size:22 final size:22
Alignment explanation
Indices: 1348467--1348540 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
1348457 TGACCGTGAA
*
1348467 TGATTTCGTCGGAGATGGAGAC
1 TGATATCGTCGGAGATGGAGAC
1348489 TGATATCGTCGGAGAT-GAGGAC
1 TGATATCGTCGGAGATGGA-GAC
* *
1348511 TGATTTCGTCGGAGATGGGGAC
1 TGATATCGTCGGAGATGGAGAC
*
1348533 GGATATCG
1 TGATATCG
1348541 CCTTAGAGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
21 2 0.04
22 42 0.93
23 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
TGATATCGTCGGAGATGGAGAC
Found at i:1348752 original size:20 final size:20
Alignment explanation
Indices: 1348729--1348842 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
1348719 CGATAGTCAG
*
1348729 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
*
1348749 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1348769 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1348789 AATCGCATTGCGATTTTTCAA
1 ATTCGCATTGCGA-TTTACGT
*
1348810 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1348830 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1348843 ATTAGGAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 65 0.81
21 15 0.19
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1348759 original size:40 final size:38
Alignment explanation
Indices: 1348711--1348842 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 38
1348701 GCTATGTAAA
*
1348711 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTATGTAT
1 TCGCATTGCGAT--TCAGATTCGCATTGCGATTTACGTAT
* * *
1348751 TCACATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTCA-G-ATTCGCATTGCGATTTACGTAT
* *
1348791 TCGCATTGCGATTTTTCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGA---TTCAGATTCGCATTGCGATTTACGTAT
1348832 TCGCATTGCGA
1 TCGCATTGCGA
1348843 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 41 0.53
41 31 0.40
43 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (38 bp):
TCGCATTGCGATTCAGATTCGCATTGCGATTTACGTAT
Found at i:1351950 original size:34 final size:34
Alignment explanation
Indices: 1351912--1352032 Score: 165
Period size: 34 Copynumber: 3.6 Consensus size: 34
1351902 AATCTTAATT
1351912 GAAAAAGAAAATAAGAAAGTCTGATTAAAAAAAG
1 GAAAAAGAAAATAAGAAAGTCTGATTAAAAAAAG
* *
1351946 GAAAAAGAGAATTAAGAAAGTCTGATT-AAAAAAT
1 GAAAAAGA-AAATAAGAAAGTCTGATTAAAAAAAG
*
1351980 GAAAAAGAGAATCAAGAAAGTCTGATTAAAAAAAG
1 GAAAAAGAAAAT-AAGAAAGTCTGATTAAAAAAAG
* *
1352015 GAAATAG-AAATAACAAAG
1 GAAAAAGAAAATAAGAAAG
1352033 AAAGAGGATA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
33 8 0.11
34 39 0.51
35 29 0.38
ACGTcount: A:0.62, C:0.04, G:0.18, T:0.16
Consensus pattern (34 bp):
GAAAAAGAAAATAAGAAAGTCTGATTAAAAAAAG
Found at i:1351965 original size:35 final size:35
Alignment explanation
Indices: 1351912--1352018 Score: 173
Period size: 34 Copynumber: 3.1 Consensus size: 35
1351902 AATCTTAATT
*
1351912 GAAAAAGA-AAATAAGAAAGTCTGATTAAAAAAAG
1 GAAAAAGAGAATTAAGAAAGTCTGATTAAAAAAAG
*
1351946 GAAAAAGAGAATTAAGAAAGTCTGATT-AAAAAAT
1 GAAAAAGAGAATTAAGAAAGTCTGATTAAAAAAAG
*
1351980 GAAAAAGAGAATCAAGAAAGTCTGATTAAAAAAAG
1 GAAAAAGAGAATTAAGAAAGTCTGATTAAAAAAAG
1352015 GAAA
1 GAAA
1352019 TAGAAATAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 40 0.60
35 27 0.40
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.16
Consensus pattern (35 bp):
GAAAAAGAGAATTAAGAAAGTCTGATTAAAAAAAG
Found at i:1357008 original size:20 final size:20
Alignment explanation
Indices: 1356983--1357032 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1356973 CATCCTTTGA
*
1356983 TTTCGAGACTCAGATTTAAG
1 TTTCGAAACTCAGATTTAAG
1357003 TTTCGAAACTCAGATTTAAG
1 TTTCGAAACTCAGATTTAAG
1357023 TTTCGAAACT
1 TTTCGAAACT
1357033 TACATGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (20 bp):
TTTCGAAACTCAGATTTAAG
Found at i:1359311 original size:25 final size:26
Alignment explanation
Indices: 1359274--1359330 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1359264 CTCAACTGTA
1359274 AGCTGCCCAGGAGAGGACCA-TGCCC
1 AGCTGCCCAGGAGAGGACCACTGCCC
** * *
1359299 AGCTGCCTTGGAGGGGACCACTGTCC
1 AGCTGCCCAGGAGAGGACCACTGCCC
1359325 AGCTGC
1 AGCTGC
1359331 TCACCCCCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.14
Consensus pattern (26 bp):
AGCTGCCCAGGAGAGGACCACTGCCC
Found at i:1363283 original size:5 final size:5
Alignment explanation
Indices: 1363273--1363305 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
1363263 AGTCAAGGTA
1363273 CATTG CATTG CATTG CATTG CATTG CATTG CAT
1 CATTG CATTG CATTG CATTG CATTG CATTG CAT
1363306 GTAGTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (5 bp):
CATTG
Found at i:1367364 original size:21 final size:24
Alignment explanation
Indices: 1367322--1367377 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
1367312 TTAAAGAATT
1367322 TTTTAATAATATATTTTAATTTTA
1 TTTTAATAATATATTTTAATTTTA
*
1367346 TTTTAATAACTAT-TTATTTATCTTTA
1 TTTTAATAA-TATATT-TTAAT-TTTA
1367372 TTTTAA
1 TTTTAA
1367378 AATTTCAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 11 0.39
25 7 0.25
26 10 0.36
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTAATAATATATTTTAATTTTA
Found at i:1367365 original size:26 final size:24
Alignment explanation
Indices: 1367322--1367377 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
1367312 TTAAAGAATT
1367322 TTTTAATAATATATTTTAAT-TTTA
1 TTTTAATAATATATTTT-ATCTTTA
*
1367346 TTTTAATAACTATTTATTTATCTTTA
1 TTTTAATAA-TATAT-TTTATCTTTA
1367372 TTTTAA
1 TTTTAA
1367378 AATTTCAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 9 0.32
25 6 0.21
26 13 0.46
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTAATAATATATTTTATCTTTA
Found at i:1369293 original size:12 final size:12
Alignment explanation
Indices: 1369256--1369306 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
1369246 TTTCTTTTCA
**
1369256 TTTTATTTCCTT
1 TTTTATTTTATT
1369268 TTTTATTTACTATT
1 TTTTATTT--TATT
1369282 TTTTATTTTATT
1 TTTTATTTTATT
1369294 TTATT-TTTTATT
1 TT-TTATTTTATT
1369306 T
1 T
1369307 GTTTTATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 22 0.65
13 2 0.06
14 10 0.29
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:1369548 original size:13 final size:13
Alignment explanation
Indices: 1369530--1369562 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1369520 TCGAATAGGG
1369530 TAATTTTAAATTC
1 TAATTTTAAATTC
*
1369543 TAATTTTAAATTT
1 TAATTTTAAATTC
1369556 TAATTTT
1 TAATTTT
1369563 CGCGATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TAATTTTAAATTC
Found at i:1373413 original size:95 final size:98
Alignment explanation
Indices: 1373244--1373494 Score: 350
Period size: 95 Copynumber: 2.6 Consensus size: 98
1373234 AATATTATAC
* *
1373244 ATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTATGGATAAGA
1 ATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAGA
*
1373309 TTCAGCTAGCCTGATAAAGGTGATTAT-TAT-T
66 TTCAACTAGCCTGATAAAGGTGATTATATATCT
* * *
1373340 -TACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAATA
1 ATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAGA
1373404 TTCAACTAGCCTGATAAAGGTGATTATAATATCT
66 TTCAACTAGCCTGATAAAGGTGATTAT-ATATCT
* * * * *
1373438 ATACAATGATA--TTAAGCTGTCCCTCTAGAGCAATTGGTTAAATGCTCCGGCTTTATG
1 ATACAAT-AAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
1373495 ATTCAGCTAG
Statistics
Matches: 137, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
95 85 0.62
97 3 0.02
98 41 0.30
99 6 0.04
100 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (98 bp):
ATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAGA
TTCAACTAGCCTGATAAAGGTGATTATATATCT
Found at i:1374744 original size:84 final size:84
Alignment explanation
Indices: 1374598--1375580 Score: 1268
Period size: 84 Copynumber: 11.7 Consensus size: 84
1374588 AGAAACCGTT
* *
1374598 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1374663 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* *
1374682 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACG
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
1374747 CTCAGCTCCAAGGCACATA
66 CTCAGCTCCAAGGCACATC
* ** * * * * * * * *
1374766 ATTTGCAACATAGCTCAAGGAAAGAAGGGCTATTTTCTAACAAAAGACCTTTGAGTTTGACTAAG
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
1374831 CTCAGCTCAAAGGCATATC
66 CTCAGCTCCAAGGCACATC
** * * *
1374850 ATTTGCTGCATAACTCAAGGCTATAAGTGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATG
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1374915 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * *
1374934 ATTTGCAACATAGCTCAAGGCTAGAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTTGACTACT
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
1374999 CTTAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * * * * *
1375018 ATTTACAACATAGCTCAAGGCAAGAAGGGCTATTTGCCATCAAAAGACCTTCGAGTTTGACTACG
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
1375083 CTCAGCTCCAAGGTACATC
66 CTCAGCTCCAAGGCACATC
* * *
1375102 ATTTGCACCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTATG
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
1375167 CTCAGCTCCAAGACACA-C
66 CTCAGCTCCAAGGCACATC
* * * *
1375185 ATTTGCAACATAACTCAAGGCAAGGAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
1375250 CTCAGCTCAAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* *
1375269 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTTGACTACG
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1375334 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* *** * *
1375353 ATTTGCAACATAGCTCAAGAAAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
1375418 CTTAACTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * *
1375437 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAAGACCTTCGAGTTCGATTCC
1 ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-CAAAGACCTTCGAGTTCGACTAC
** * *
1375502 ATTCAGCTCAAAGGCATATCC
65 GCTCAGCTCCAAGGCACAT-C
* * * * ** *
1375523 AATATACAGCATAACTCAAGGCGAGAAGGGTTATCTATCAA-TAAAGACCTTTCGAGTT
1 -ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACC-TTCGAGTT
1375581 TGATTTCATT
Statistics
Matches: 779, Mismatches: 115, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
83 73 0.09
84 621 0.80
85 41 0.05
86 9 0.01
87 35 0.04
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
ATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:1377235 original size:5 final size:5
Alignment explanation
Indices: 1377211--1377317 Score: 58
Period size: 5 Copynumber: 20.8 Consensus size: 5
1377201 ATACTTATTT
* * *
1377211 TTTTA GTTTC TTTTA TTTTTA TTTTA -TTTA TTACTA TTATTA TTTTA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TT-TTA TT-TTA TTTTA
* * * * * *
1377258 -TATA CTTCA TTATTA TTGTA TTTTA -TATG TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1377307 TCTTTTA TTTT
1 --TTTTA TTTT
1377318 TTTAATTTAT
Statistics
Matches: 77, Mismatches: 17, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
4 9 0.12
5 45 0.58
6 18 0.23
7 5 0.06
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (5 bp):
TTTTA
Found at i:1377250 original size:24 final size:24
Alignment explanation
Indices: 1377205--1377251 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1377195 ATTTCTATAC
* *
1377205 TTATTTTTTTAGTTTCTTTTATTT
1 TTATTTTTTTAGTTACTATTATTT
1377229 TTATTTTATTTA-TTACTATTATT
1 TTATTTT-TTTAGTTACTATTATT
1377252 ATTTTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (24 bp):
TTATTTTTTTAGTTACTATTATTT
Found at i:1377285 original size:25 final size:24
Alignment explanation
Indices: 1377251--1377307 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
1377241 TTACTATTAT
1377251 TATTTTATATACTTCATTATTATTG
1 TATTTTATATACTTCATT-TTATTG
** * *
1377276 TATTTTATATGTTTTATTTTATTT
1 TATTTTATATACTTCATTTTATTG
1377300 TATTTTAT
1 TATTTTAT
1377308 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (24 bp):
TATTTTATATACTTCATTTTATTG
Found at i:1377319 original size:24 final size:25
Alignment explanation
Indices: 1377210--1377307 Score: 67
Period size: 25 Copynumber: 3.9 Consensus size: 25
1377200 TATACTTATT
* * *
1377210 TTTTTAGTTTCTTTTATTTT-TATT
1 TTTTTATTTTATTTTATTTTATATG
*
1377234 TTATTTATTACTATTATTATTTTATAT-
1 TT-TTTATT-TTATT-TTATTTTATATG
** * *
1377261 ACTTCATTATTATTGTATTTTATATG
1 TTTTTATT-TTATTTTATTTTATATG
1377287 -TTTTATTTTATTTTATTTTAT
1 TTTTTATTTTATTTTATTTTAT
1377308 CTTTTATTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
24 15 0.26
25 20 0.34
26 13 0.22
27 7 0.12
28 3 0.05
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.70
Consensus pattern (25 bp):
TTTTTATTTTATTTTATTTTATATG
Found at i:1377403 original size:7 final size:6
Alignment explanation
Indices: 1377374--1377406 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1377364 TATTTGTTCC
1377374 TTTTA- TTTTAT TTTTAT TTTTAT TTATTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT-TTAT TTT
1377407 CTTTTACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:1377462 original size:9 final size:9
Alignment explanation
Indices: 1377448--1377587 Score: 83
Period size: 9 Copynumber: 15.1 Consensus size: 9
1377438 TCATTTTTGC
1377448 CTTTATTTT
1 CTTTATTTT
1377457 CTTTATTTT
1 CTTTATTTT
*
1377466 AGTTTATTTT
1 -CTTTATTTT
*
1377476 ATTTATTTT
1 CTTTATTTT
*
1377485 ATTTATTTTT
1 CTTTA-TTTT
1377495 CTTTA-TTT
1 CTTTATTTT
1377503 CTTTTATTTAT
1 C-TTTATTT-T
*
1377514 TTTTATTTATT
1 CTTTA-TT-TT
*
1377525 TTTTATTATT
1 CTTTATT-TT
1377535 -TTTATTTTT
1 CTTTA-TTTT
1377544 ACTTTATTTT
1 -CTTTATTTT
*
1377554 -TTT-TTAT
1 CTTTATTTT
*
1377561 -TTTATTCT
1 CTTTATTTT
1377569 CTTTATTTT
1 CTTTATTTT
* *
1377578 ATTCATTTT
1 CTTTATTTT
1377587 C
1 C
1377588 GTTCTTTTCC
Statistics
Matches: 109, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
7 6 0.06
8 10 0.09
9 46 0.42
10 33 0.30
11 13 0.12
12 1 0.01
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.76
Consensus pattern (9 bp):
CTTTATTTT
Found at i:1377471 original size:5 final size:5
Alignment explanation
Indices: 1377449--1377580 Score: 93
Period size: 5 Copynumber: 27.2 Consensus size: 5
1377439 CATTTTTGCC
* *
1377449 TTTAT TTT-C TTTAT TTTAG TTTAT TTTA- TTTAT TTTA- TTTAT TTT-T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
*
1377495 CTTTA- TTTCT TTTA- TTTAT TTT-T ATTTAT TTT-T TATTATT TTTATT
1 -TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT T-TTA-T TTTA-T
* * * *
1377541 TTTAC TTTAT TTTTT TTTAT TTTAT TCT-C TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
1377581 CATTTTCGTT
Statistics
Matches: 100, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
4 24 0.24
5 64 0.64
6 10 0.10
7 2 0.02
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:1377473 original size:19 final size:18
Alignment explanation
Indices: 1377449--1377587 Score: 108
Period size: 19 Copynumber: 7.5 Consensus size: 18
1377439 CATTTTTGCC
1377449 TTTATTTTCTTTATTTTA
1 TTTATTTTCTTTATTTTA
*
1377467 GTTTATTTTATTTATTTTA
1 -TTTATTTTCTTTATTTTA
1377486 TTTATTTTTCTTTATTTCT-
1 TTTA-TTTTCTTTATTT-TA
* *
1377505 TTTATTTATTTTTATTTATTT
1 TTTATTT-TCTTTA-TT-TTA
1377526 TTTATTATT-TTTATTTTTA
1 TTTATT-TTCTTTA-TTTTA
*
1377545 CTTTATTTT-TTT-TTAT-
1 -TTTATTTTCTTTATTTTA
*
1377561 TTTATTCTCTTTATTTTA
1 TTTATTTTCTTTATTTTA
*
1377579 TTCATTTTC
1 TTTATTTTC
1377588 GTTCTTTTCC
Statistics
Matches: 100, Mismatches: 9, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.07
16 3 0.03
17 6 0.06
18 14 0.14
19 44 0.44
20 17 0.17
21 8 0.08
22 1 0.01
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.77
Consensus pattern (18 bp):
TTTATTTTCTTTATTTTA
Found at i:1377480 original size:14 final size:13
Alignment explanation
Indices: 1377449--1377585 Score: 86
Period size: 14 Copynumber: 10.2 Consensus size: 13
1377439 CATTTTTGCC
*
1377449 TTTATTTTCTTTA
1 TTTATTTTATTTA
*
1377462 TTTTAGTTTATTTTA
1 -TTTATTTTA-TTTA
1377477 TTTATTTTATTTA
1 TTTATTTTATTTA
* *
1377490 TTTTTCTTTATTTCT
1 TTTAT-TTTATTT-A
*
1377505 TTTATTTATTTTTA
1 TTTATTT-TATTTA
*
1377519 TTTATTTTTTATTA
1 TTTATTTTAT-TTA
1377533 TTT-TTATT-TTTA
1 TTTATT-TTATTTA
1377545 CTTTA-TTT-TTT-
1 -TTTATTTTATTTA
*
1377556 TTTATTTTATTCTC
1 TTTATTTTATT-TA
*
1377570 TTTATTTTATTCA
1 TTTATTTTATTTA
1377583 TTT
1 TTT
1377586 TCGTTCTTTT
Statistics
Matches: 101, Mismatches: 10, Indels: 25
0.74 0.07 0.18
Matches are distributed among these distances:
10 4 0.04
11 3 0.03
12 10 0.10
13 22 0.22
14 50 0.50
15 12 0.12
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:1385032 original size:15 final size:15
Alignment explanation
Indices: 1385012--1385058 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
1385002 TCTGATGTCA
1385012 CTACAGAGCTATGTT
1 CTACAGAGCTATGTT
1385027 CTACAGAGCTATGTT
1 CTACAGAGCTATGTT
1385042 CTACAGAGCTATGTT
1 CTACAGAGCTATGTT
1385057 CT
1 CT
1385059 GGGAGTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (15 bp):
CTACAGAGCTATGTT
Found at i:1386450 original size:16 final size:16
Alignment explanation
Indices: 1386431--1386467 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1386421 TTGAAAGGGA
* *
1386431 GAGCAATTGATATAGG
1 GAGCAATTCATAGAGG
1386447 GAGCAATTCATAGAGG
1 GAGCAATTCATAGAGG
1386463 GAGCA
1 GAGCA
1386468 TTTGCTTACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.32, T:0.19
Consensus pattern (16 bp):
GAGCAATTCATAGAGG
Found at i:1388725 original size:18 final size:18
Alignment explanation
Indices: 1388702--1388736 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1388692 ACTGAATATT
1388702 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1388720 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1388737 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1389383 original size:20 final size:20
Alignment explanation
Indices: 1389333--1389383 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1389323 TAAGGGGGGT
*
1389333 TATCGATACCCCTTATAGGG
1 TATCGATACCCCCTATAGGG
* *
1389353 TATCAAAACCCCCTATAGGG
1 TATCGATACCCCCTATAGGG
1389373 TATCGATACCC
1 TATCGATACCC
1389384 TTATTGCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (20 bp):
TATCGATACCCCCTATAGGG
Found at i:1393221 original size:21 final size:20
Alignment explanation
Indices: 1393206--1393243 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1393196 GATCCCACTG
*
1393206 ATCGTGTTTGTCATCCCCTC
1 ATCGTATTTGTCATCCCCTC
1393226 ATCGTATTTG--ATCCCCTC
1 ATCGTATTTGTCATCCCCTC
1393244 GCAGAGGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.13, C:0.34, G:0.13, T:0.39
Consensus pattern (20 bp):
ATCGTATTTGTCATCCCCTC
Found at i:1394850 original size:18 final size:18
Alignment explanation
Indices: 1394820--1394870 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
1394810 TGAATATTTG
*
1394820 TCCCGAAGCACCACTATA
1 TCCCGAAGGACCACTATA
* *
1394838 TCCTGAAGGACCACTATG
1 TCCCGAAGGACCACTATA
1394856 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
1394871 GATAATCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:1408136 original size:21 final size:21
Alignment explanation
Indices: 1408110--1408150 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1408100 AAAAGGTAGC
1408110 AGATTGAAAGGGAGAGTGAGA
1 AGATTGAAAGGGAGAGTGAGA
1408131 AGATTGAAAGGGAGAGTGAG
1 AGATTGAAAGGGAGAGTGAG
1408151 CAAGTAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (21 bp):
AGATTGAAAGGGAGAGTGAGA
Found at i:1413239 original size:21 final size:21
Alignment explanation
Indices: 1413213--1413270 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1413203 GATTTATTAT
1413213 TATGGATTTCAAGTTTCTTGA
1 TATGGATTTCAAGTTTCTTGA
* *
1413234 TATGGATTTCAAGTTTGTTGT
1 TATGGATTTCAAGTTTCTTGA
*
1413255 TATGGATGTCAAGTTT
1 TATGGATTTCAAGTTT
1413271 ATTGGATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (21 bp):
TATGGATTTCAAGTTTCTTGA
Found at i:1420630 original size:118 final size:119
Alignment explanation
Indices: 1420459--1420672 Score: 265
Period size: 118 Copynumber: 1.8 Consensus size: 119
1420449 TACTATAATA
* ** *
1420459 GTAAATAATTCTAAAAATAATATTTAAAATTATTATTTTAAAAATAAAGGATTAAAATTGT-AAA
1 GTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAAATAAAGGATT-AAATTGTAAAA
*
1420523 ATATCA-AAATTAAAAATCTTAATTCTAAATATCATGAAATCTAGGTATTATTAGT
65 ATAT-ATAAATTAAAAATCTTAATTCAAAATATCATGAAATCTAGGTATTATTAGT
* ** *
1420578 GTAAATAATCCT-AAAATATTATTTAAAATTAAAATATTAAACCT-CAGTGATTAAATTGTAAAA
1 GTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAAATAAAG-GATTAAATTGTAAAA
***
1420641 ATATATAAATTAATGGTCTTAATTCAAAATAT
65 ATATATAAATTAAAAATCTTAATTCAAAATAT
1420673 TATAAAATAT
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
117 10 0.12
118 59 0.74
119 11 0.14
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (119 bp):
GTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAAATAAAGGATTAAATTGTAAAAA
TATATAAATTAAAAATCTTAATTCAAAATATCATGAAATCTAGGTATTATTAGT
Found at i:1420696 original size:118 final size:119
Alignment explanation
Indices: 1420446--1420699 Score: 257
Period size: 118 Copynumber: 2.1 Consensus size: 119
1420436 TTAATATGCA
* * ** *
1420446 AAGTACT-ATAATAGTAAATAATTCTAAAAATAATATTTAAAATTATTATTTTAAAAATAAAGGA
1 AAGTACTAATAGT-GTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAAATAAAGGA
* * *
1420510 TTAAAATTGTAAAATATCAAAATTAAAAATCTTAATTCTAAATATCATGAAATCT
65 TTAAAATTGTAAAATATCAAAATTAAAAATCTTAATTCAAAATATCATAAAATAT
* * * * ** *
1420565 AGGTATTATTAGTGTAAATAATCCT-AAAATATTATTTAAAATTAAAATATTAAACCT-CAGTGA
1 AAGTACTAATAGTGTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAAATAAAG-GA
*** *
1420628 TT-AAATTGTAAAAATAT-ATAAATTAATGGTCTTAATTCAAAATATTATAAAATAT
65 TTAAAATTGT-AAAATATCA-AAATTAAAAATCTTAATTCAAAATATCATAAAATAT
*
1420683 AATTACTAATAGTGTAA
1 AAGTACTAATAGTGTAA
1420700 TTTAACCCTA
Statistics
Matches: 108, Mismatches: 23, Indels: 9
0.77 0.16 0.06
Matches are distributed among these distances:
117 10 0.09
118 79 0.73
119 16 0.15
120 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (119 bp):
AAGTACTAATAGTGTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAAATAAAGGAT
TAAAATTGTAAAATATCAAAATTAAAAATCTTAATTCAAAATATCATAAAATAT
Found at i:1421676 original size:3 final size:3
Alignment explanation
Indices: 1421664--1421737 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
1421654 TATTATTTAT
*
1421664 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1421712 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1421738 TAAAAAGGAC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1422150 original size:137 final size:137
Alignment explanation
Indices: 1421899--1422529 Score: 926
Period size: 137 Copynumber: 4.6 Consensus size: 137
1421889 AGATCCAACT
* * * * * *
1421899 GGTGTATGACATTGTTCTTTCATGATGAGGACGTTT-GACCATCTTTGAAGGTATTTGAGTTAAC
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAG-CCATCTTTAAAGATATTTGAGATAAC
* * * * * *
1421963 AAGGTTCCTTTGTGATGAGGACATCTGGTTATCTGAGGATGACTCG--GCTCCTGCGTGATGAGG
65 ACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGA-T-GTTGCTCCTTCGTGATGAGG
*
1422026 AGTTCTGGTC
128 AGTTCTGATC
* *
1422036 AGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAGCCATCTTTAAATATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAGCCATCTTTAAAGATATTTGAGATAACA
* *
1422101 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTTGTGATAAGGAGT
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
1422166 TCTGATC
131 TCTGATC
*
1422173 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAGCCATCTTTAAATATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAGCCATCTTTAAAGATATTTGAGATAACA
1422238 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
1422303 TCTGATC
131 TCTGATC
* *
1422310 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCATTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAGCCATCTTTAAAGATATTTGAGATAACA
* * * * * *
1422375 CTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCTCCTTCGTGATGGGGAGT
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
1422440 TCTGATC
131 TCTGATC
* *
1422447 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAGCCATCTTTAAAGATATTTGAGATAACA
** * *
1422512 ATGTTCTTTCATGATGAG
66 CGGTTCCTTCGTGATGAG
1422530 ATAACACTGT
Statistics
Matches: 459, Mismatches: 32, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
135 1 0.00
136 1 0.00
137 456 0.99
138 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (137 bp):
GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAGCCATCTTTAAAGATATTTGAGATAACA
CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
TCTGATC
Found at i:1422393 original size:274 final size:274
Alignment explanation
Indices: 1421899--1422855 Score: 1234
Period size: 274 Copynumber: 3.4 Consensus size: 274
1421889 AGATCCAACT
* * * * * * *
1421899 GGTGTATGACATTGTTCTTTCATGATGAGGACGTTTGACCATCTTTGAAGGTATTTGAGTTAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTAAAGATATTTGAGATAACA
* * * * * *
1421964 AGGTTCCTTTGTGATGAGGACATCTGGTTATCTGAGGATGACTCG--GCTCCTGCGTGATGAGGA
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGA-T-GTTGCTCCTTCGTGATGAGGA
* * * *
1422027 GTTCTGGTCAGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAGCCATCTTTAAATATATTT
129 GTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTAAAGATATTT
* * * * *
1422092 GAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTTGTG
194 GAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATGTTGCTCCTTCGTG
*
1422157 ATAAGGAGTTCTGATC
259 ATGAGGAGTTCTGATC
* *
1422173 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTAGCCATCTTTAAATATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTAAAGATATTTGAGATAACA
1422238 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
*
1422303 TCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCATTAAAGATATTTGA
131 TCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTAAAGATATTTGA
*
1422368 GATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCTCCTTCGTGAT
196 GATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATGTTGCTCCTTCGTGAT
*
1422433 GGGGAGTTCTGATC
261 GAGGAGTTCTGATC
*
1422447 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTAAAGATATTTGAGATAAC-
* * * *
1422512 ATGTTCTTTCATGATGAGATAACACTGTTCTTTCATGATGAGGATATCTGGTTATCTAAGAATGA
65 A--------C-------G--------GTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGA
*
1422577 TGTTGCTCCTTCGTGATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGT
107 TGTTGCTCCTTCGTGATGAGGAGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGT
* * *
1422642 CTGGCCATCTTTAAAGATATTTGAGATAACATTGTTCTTTCATGATGAGGATATCTGGTTATCTA
172 TTGGCCATCTTTAAAGATATTTGAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTA
*
1422707 ATAATGATGTTGCTCCTTCGTGATGAGGAGTTCTGATC
237 AGAATGATGTTGCTCCTTCGTGATGAGGAGTTCTGATC
* * * *
1422745 GATGGATGACATTGTTCCTTCGTGATGAGGACGTATGGCCATCTTTGAAGATACTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTAAAGATATTTGAGATAACA
* * * * * *
1422810 CAGTTCCTTCGTGATAAGGACGTTTGGCTTTCTAAGGATGATGTTG
66 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTG
1422856 ATGGACACGA
Statistics
Matches: 600, Mismatches: 57, Indels: 52
0.85 0.08 0.07
Matches are distributed among these distances:
272 1 0.00
273 1 0.00
274 338 0.56
275 1 0.00
283 1 0.00
289 1 0.00
290 1 0.00
297 1 0.00
298 255 0.43
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (274 bp):
GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTAAAGATATTTGAGATAACA
CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
TCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTAAAGATATTTGA
GATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATGTTGCTCCTTCGTGAT
GAGGAGTTCTGATC
Found at i:1422534 original size:24 final size:24
Alignment explanation
Indices: 1422502--1422553 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1422492 TAAAGATATT
1422502 TGAGATAACAATGTTCTTTCATGA
1 TGAGATAACAATGTTCTTTCATGA
*
1422526 TGAGATAACACTGTTCTTTCATGA
1 TGAGATAACAATGTTCTTTCATGA
1422550 TGAG
1 TGAG
1422554 GATATCTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (24 bp):
TGAGATAACAATGTTCTTTCATGA
Found at i:1422630 original size:161 final size:161
Alignment explanation
Indices: 1422365--1422690 Score: 607
Period size: 161 Copynumber: 2.0 Consensus size: 161
1422355 TAAAGATATT
1422365 TGAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCTCCTTCGT
1 TGAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCTCCTTCGT
* *
1422430 GATGGGGAGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAA
66 GATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAA
1422495 AGATATTTGAGATAACAATGTTCTTTCATGA
131 AGATATTTGAGATAACAATGTTCTTTCATGA
* *
1422526 TGAGATAACACTGTTCTTTCATGATGAGGATATCTGGTTATCTAAGAATGATGTTGCTCCTTCGT
1 TGAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCTCCTTCGT
1422591 GATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAA
66 GATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAA
*
1422656 AGATATTTGAGATAACATTGTTCTTTCATGA
131 AGATATTTGAGATAACAATGTTCTTTCATGA
1422687 TGAG
1 TGAG
1422691 GATATCTGGT
Statistics
Matches: 160, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
161 160 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (161 bp):
TGAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCTCCTTCGT
GATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAA
AGATATTTGAGATAACAATGTTCTTTCATGA
Found at i:1422764 original size:298 final size:298
Alignment explanation
Indices: 1422228--1422809 Score: 1011
Period size: 298 Copynumber: 2.0 Consensus size: 298
1422218 TAAATATATT
*
1422228 TGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGT
1 TGAGATAACACGGTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGT
* *
1422293 GATGAGGAGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCATTAA
66 GATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCATTAA
1422358 AGATATTTGAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCT
131 AGATATTTGAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCT
* * *
1422423 CCTTCGTGATGGGGAGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCA
196 CCTTCGTGATGAGGAGTTCTGATCGATGGATGACATTGTTCCTTCGTGATGAGGACGTATGGCCA
*
1422488 TCTTTAAAGATATTTGAGATAACAATGTTCTTTCATGA
261 TCTTTAAAGATACTTGAGATAACAATGTTCTTTCATGA
* * * *
1422526 TGAGATAACACTGTTCTTTCATGATGAGGATATCTGGTTATCTAAGAATGATGTTGCTCCTTCGT
1 TGAGATAACACGGTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGT
*
1422591 GATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAA
66 GATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCATTAA
* * * *
1422656 AGATATTTGAGATAACATTGTTCTTTCATGATGAGGATATCTGGTTATCTAATAATGATGTTGCT
131 AGATATTTGAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCT
1422721 CCTTCGTGATGAGGAGTTCTGATCGATGGATGACATTGTTCCTTCGTGATGAGGACGTATGGCCA
196 CCTTCGTGATGAGGAGTTCTGATCGATGGATGACATTGTTCCTTCGTGATGAGGACGTATGGCCA
*
1422786 TCTTTGAAGATACTTGAGATAACA
261 TCTTTAAAGATACTTGAGATAACA
1422810 CAGTTCCTTC
Statistics
Matches: 267, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
298 267 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (298 bp):
TGAGATAACACGGTTCCTTCATGATGAGGACATCTGGCTATCTAAGAATGATGTTGCTCCTTCGT
GATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCATTAA
AGATATTTGAGATAACACTGTTCTTTCATGATGAGGACATCTGGTTATCTAAGAATGATATTGCT
CCTTCGTGATGAGGAGTTCTGATCGATGGATGACATTGTTCCTTCGTGATGAGGACGTATGGCCA
TCTTTAAAGATACTTGAGATAACAATGTTCTTTCATGA
Found at i:1422772 original size:137 final size:137
Alignment explanation
Indices: 1422526--1422855 Score: 509
Period size: 137 Copynumber: 2.4 Consensus size: 137
1422516 TCTTTCATGA
1422526 TGAGATAACACTGTTCTTTCATGATGAGGATATCTGGTTATCTAAGAATGATGTTGCTCCTTCGT
1 TGAGATAACACTGTTCTTTCATGATGAGGATATCTGGTTATCTAAGAATGATGTTGCTCCTTCGT
* *
1422591 GATGAGGAGTTCTAATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAA
66 GATGAGGAGTTCTAATCGATGGATGACATTGTTCCTTCGTGATGAGGACGTATGGCCATCTTTAA
*
1422656 AGATATT
131 AGATACT
* *
1422663 TGAGATAACATTGTTCTTTCATGATGAGGATATCTGGTTATCTAATAATGATGTTGCTCCTTCGT
1 TGAGATAACACTGTTCTTTCATGATGAGGATATCTGGTTATCTAAGAATGATGTTGCTCCTTCGT
* *
1422728 GATGAGGAGTTCTGATCGATGGATGACATTGTTCCTTCGTGATGAGGACGTATGGCCATCTTTGA
66 GATGAGGAGTTCTAATCGATGGATGACATTGTTCCTTCGTGATGAGGACGTATGGCCATCTTTAA
1422793 AGATACT
131 AGATACT
* * * * ** * *
1422800 TGAGATAACACAGTTCCTTCGTGATAAGGACGTTTGGCTT-TCTAAGGATGATGTTG
1 TGAGATAACACTGTTCTTTCATGATGAGGATATCTGG-TTATCTAAGAATGATGTTG
1422856 ATGGACACGA
Statistics
Matches: 175, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
137 173 0.99
138 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (137 bp):
TGAGATAACACTGTTCTTTCATGATGAGGATATCTGGTTATCTAAGAATGATGTTGCTCCTTCGT
GATGAGGAGTTCTAATCGATGGATGACATTGTTCCTTCGTGATGAGGACGTATGGCCATCTTTAA
AGATACT
Found at i:1428998 original size:43 final size:42
Alignment explanation
Indices: 1428937--1429021 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
1428927 TTAGTTTTGT
* * * * *
1428937 CATTTGCTCTTTTGAATCATCTTGGAATTTTTTTTGCTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAA-CTTTTTTACTTGATC
*
1428980 CATTTGTTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
1429022 AATCATCCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 13 0.36
43 23 0.64
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (42 bp):
CATTTGCTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
Found at i:1430255 original size:45 final size:46
Alignment explanation
Indices: 1430161--1430256 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 46
1430151 GAAAATATAA
* * *
1430161 AAAGAAATAAATAATATACAACACACAAAATATAATCTTTAAATCT
1 AAAGAAACAAATAATATACAACACAAAAAATATAATCTTTAAATAT
* * * *
1430207 AAAGAAACAAATAATGTACAACA-AAAAAATTTATTCTTTCAATAT
1 AAAGAAACAAATAATATACAACACAAAAAATATAATCTTTAAATAT
1430252 AAAGA
1 AAAGA
1430257 CATATAATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.26
Consensus pattern (46 bp):
AAAGAAACAAATAATATACAACACAAAAAATATAATCTTTAAATAT
Found at i:1432217 original size:18 final size:21
Alignment explanation
Indices: 1432185--1432237 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1432175 TGTAAATATC
*
1432185 TATTGTAATAA-AATT-T-AT
1 TATTATAATAATAATTATAAT
*
1432203 TATT-TATTAATAATTATAAT
1 TATTATAATAATAATTATAAT
1432223 TATTATAATAATAAT
1 TATTATAATAATAAT
1432238 AATATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 5 0.17
18 8 0.28
19 1 0.03
20 6 0.21
21 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTATAATAATAATTATAAT
Found at i:1436345 original size:21 final size:21
Alignment explanation
Indices: 1436312--1436354 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1436302 AAATTACATA
1436312 TTTAATATCTAAA-TTATCAAT
1 TTTAATATCTAAACTT-TCAAT
* *
1436333 TTTAGTATTTAAACTTTCAAT
1 TTTAATATCTAAACTTTCAAT
1436354 T
1 T
1436355 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTAATATCTAAACTTTCAAT
Found at i:1438951 original size:24 final size:22
Alignment explanation
Indices: 1438912--1438968 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
1438902 CTGTAATTTG
* * *
1438912 ATTGTTGTTATAACAGTTTGTTT
1 ATTGTTGTGATTACAG-CTGTTT
1438935 ATTAGTTGTGATTACAGCTGTTT
1 ATT-GTTGTGATTACAGCTGTTT
1438958 ATTGTTG-GATT
1 ATTGTTGTGATT
1438969 TTAGGCATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 4 0.13
23 11 0.37
24 11 0.37
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (22 bp):
ATTGTTGTGATTACAGCTGTTT
Found at i:1443380 original size:28 final size:28
Alignment explanation
Indices: 1443346--1443471 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
1443336 TTTCATTTTA
*
1443346 ATACCTAAAGTATTTT-TGGTGAAAATAG
1 ATACCTAAAGTATTTTAT-GTCAAAATAG
*
1443374 ATGCCTAAAGTATTTTATGTCAAAATAG
1 ATACCTAAAGTATTTTATGTCAAAATAG
* *
1443402 ATGCCTAAAGTATTTTATATCAAAATAG
1 ATACCTAAAGTATTTTATGTCAAAATAG
*
1443430 ATACCTAAAGTATTTTATGTCAACATAG
1 ATACCTAAAGTATTTTATGTCAAAATAG
*
1443458 GTACCTAAAGTATT
1 ATACCTAAAGTATT
1443472 CAAACTTTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
28 89 0.99
29 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (28 bp):
ATACCTAAAGTATTTTATGTCAAAATAG
Found at i:1447267 original size:23 final size:23
Alignment explanation
Indices: 1447237--1447315 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
1447227 AATTTATCTT
1447237 GAAGGACCTCATGTATATGTCCC
1 GAAGGACCTCATGTATATGTCCC
1447260 GAAGGACCTCATGTATATGTCCC
1 GAAGGACCTCATGTATATGTCCC
*
1447283 GAAGGACCTGA--TATATGTCCC
1 GAAGGACCTCATGTATATGTCCC
*
1447304 GAATGACCTCAT
1 GAAGGACCTCAT
1447316 ATAACCCTCG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
21 19 0.37
23 33 0.63
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (23 bp):
GAAGGACCTCATGTATATGTCCC
Found at i:1450506 original size:3 final size:3
Alignment explanation
Indices: 1450498--1450545 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
1450488 TTTTTCACTA
*
1450498 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
1450544 TA
1 TA
1450546 AATTAAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1451862 original size:15 final size:17
Alignment explanation
Indices: 1451842--1451879 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1451832 TTGTTTAATC
*
1451842 ATATTTTA-C-TTTTAT
1 ATATTTTATCGTTATAT
1451857 ATATTTTATCGTTATAT
1 ATATTTTATCGTTATAT
1451874 ATATTT
1 ATATTT
1451880 AATTATCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 1 0.05
17 11 0.55
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (17 bp):
ATATTTTATCGTTATAT
Found at i:1452288 original size:11 final size:13
Alignment explanation
Indices: 1452251--1452290 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
1452241 TGTTTAATAA
1452251 AATATA-TATATT
1 AATATATTATATT
*
1452263 AATATATTATCTT
1 AATATATTATATT
1452276 AA-A-ATTATATT
1 AATATATTATATT
1452287 AATA
1 AATA
1452291 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:1455348 original size:15 final size:14
Alignment explanation
Indices: 1455306--1455347 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
1455296 AAATAATTTA
1455306 CATTTACATTTTTG
1 CATTTACATTTTTG
1455320 CATTTATGCA-TTTTG
1 CATTTA--CATTTTTG
1455335 CATTTACATTTTT
1 CATTTACATTTTT
1455348 TATTTGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
15 11 0.44
16 2 0.08
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
CATTTACATTTTTG
Found at i:1461847 original size:22 final size:22
Alignment explanation
Indices: 1461822--1461898 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
1461812 ATCTACACTT
1461822 TTCAAAGATGATAGACTCTTTC
1 TTCAAAGATGATAGACTCTTTC
* * *
1461844 TTCAAAGATGATAGCCTATCTC
1 TTCAAAGATGATAGACTCTTTC
* * *
1461866 TTTAAAGATGATATATTCTCTT-
1 TTCAAAGATGATAGACTCT-TTC
1461888 TTCAAAGATGA
1 TTCAAAGATGA
1461899 AAGCTTTATT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
22 43 0.98
23 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGACTCTTTC
Found at i:1462703 original size:45 final size:45
Alignment explanation
Indices: 1462560--1463466 Score: 1442
Period size: 45 Copynumber: 20.0 Consensus size: 45
1462550 CTATTTCCAA
*
1462560 CATCTGTAAGTCCTTCAGTGCATGATGTTTTTCAAAACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTTCAAAACCTTCGGGT
*
1462606 CATCTGTAA-TCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGT-CCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1462652 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1462697 CATCTGTAAG-CCTTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCC-TTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1462743 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1462789 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1462834 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
1462879 CATCTATAAGCCCTTCATTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1462924 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1462969 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1463015 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
1463061 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * **
1463106 CATCTGTAAGTCCTTCAGTGCATAATGTTTTCAAAAACTTTAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1463151 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC-TCTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC-GGGT
* * *
1463196 CATTTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
1463242 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1463288 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1463333 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1463378 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1463423 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAACCTTCGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1463467 AGCTTTTTGA
Statistics
Matches: 808, Mismatches: 43, Indels: 21
0.93 0.05 0.02
Matches are distributed among these distances:
44 3 0.00
45 476 0.59
46 324 0.40
47 5 0.01
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1462950 original size:272 final size:271
Alignment explanation
Indices: 1462560--1463466 Score: 1539
Period size: 272 Copynumber: 3.3 Consensus size: 271
1462550 CTATTTCCAA
* *
1462560 CATCTGTAAGTCCTTCAGTGCATGATGTTTTTCAAAACCTCCGGGTCATCTGTAATCCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
1462625 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
65 GCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
1462690 TCCGGGTCATCTGTAAGCCTTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTC
129 TCCGGGTCATCTGTAAGCC-TTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTC
1462755 CTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
193 CTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
*
1462820 CAAAACCTTTGGGT
258 CAAAACCTTCGGGT
* *
1462834 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCATTG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1462899 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTC
66 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTC
1462964 CGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCT
131 CGGGTCATCTGTAAG-CCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCT
1463029 TCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCA
195 TCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCA
*
1463094 AAACCTTCGAGT
260 AAACCTTCGGGT
* * ** *
1463106 CATCTGTAAGTCCTTCAGTGCATAATGTTTTCAAAAACTTTAGGTCATCTGTAAGTCCTTCAGTG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* * *
1463171 CATGATGTTTTCAAAACC-TCTGGGTCATTTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACC
66 CATGATGTTTTCAAAACCTTC-GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACC
* *
1463235 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTCCGGGTCATCTGTAAGTC
129 TCCGGGTCATCTGTAAG-CCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTC
* *
1463300 CTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
193 CTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
1463364 CAAAACCTTCGGGT
258 CAAAACCTTCGGGT
* *
1463378 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
*
1463443 CATGATGTTTTTAAAACCTTCGGG
66 CATGATGTTTTCAAAACCTTCGGG
1463467 AGCTTTTTGA
Statistics
Matches: 598, Mismatches: 31, Indels: 10
0.94 0.05 0.02
Matches are distributed among these distances:
271 2 0.00
272 433 0.72
273 136 0.23
274 27 0.05
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (271 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTC
CGGGTCATCTGTAAGCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTT
CAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAA
AACCTTCGGGT
Found at i:1463054 original size:227 final size:226
Alignment explanation
Indices: 1462560--1463466 Score: 1496
Period size: 227 Copynumber: 4.0 Consensus size: 226
1462550 CTATTTCCAA
*
1462560 CATCTGTAAGTCCTTCAGTGCATGATGTTTTTCAAAACCTCCGGGTCATCTGTAA-TCCCTTCAG
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTATCAAAACCTCCGGGTCATCTGTAAGT-CCTTCAG
* *
1462624 TGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAC
64 TGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAC
* * *
1462689 CTCCGGGTCATCTGTAAG-CCTTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAG
128 CTTCGGGTCATCTGTAAGTCC-TTCAGTGCATGATGTTTTC-AAAACCTCCGGGTCATCTGTAAG
*
1462753 TCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
191 CCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* **
1462789 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGTCCTTCAGTG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAACCTCCGGGTCATCTGTAAGTCCTTCAGTG
* *
1462854 CATGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCATTGCATGATGTTTTCAAAACCTT
66 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
1462919 CGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCTT
131 CGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCTT
1462984 CAGTGCATGATGTTATCAAAAACCTTCGGGT
196 CAGTGCATGATGTTATCAAAAACCTTCGGGT
*
1463015 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATC-AAAACCTCCGGGTCATCTGTAAGTCCTTCAGT
* * * *
1463080 GCATGATGTTTTCAAAACCTTCGAGTCATCTGTAAGTCCTTCAGTGCATAATGTTTTCAAAAACT
65 GCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
** * *
1463145 TTAGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCTGGGTCATTTGTAAGCCCT
130 TCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCT
1463210 TCAGTGCATGATGTTATCAAAAACCTTCGGGT
195 TCAGTGCATGATGTTATCAAAAACCTTCGGGT
1463242 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTCCGGGTCATCTGTAAGTCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATC-AAAACCTCCGGGTCATCTGTAAGTCCTTCAGT
1463307 GCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
65 GCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
* * *
1463372 TCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCT
130 TCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCT
**
1463437 TCAGTGCATGATGTT-TTTAAAACCTTCGGG
195 TCAGTGCATGATGTTATCAAAAACCTTCGGG
1463467 AGCTTTTTGA
Statistics
Matches: 639, Mismatches: 36, Indels: 9
0.93 0.05 0.01
Matches are distributed among these distances:
226 101 0.16
227 463 0.72
228 47 0.07
229 28 0.04
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (226 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAACCTCCGGGTCATCTGTAAGTCCTTCAGTG
CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
CGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCTT
CAGTGCATGATGTTATCAAAAACCTTCGGGT
Found at i:1463709 original size:24 final size:24
Alignment explanation
Indices: 1463676--1463726 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1463666 TTTTTCACTA
* *
1463676 TATTATTATTATTATAA-TATATAT
1 TATTAATATTATTA-AATTAAATAT
1463700 TATTAATATTATTAAATTAAATAT
1 TATTAATATTATTAAATTAAATAT
1463724 TAT
1 TAT
1463727 AAAACCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTAATATTATTAAATTAAATAT
Found at i:1465435 original size:11 final size:13
Alignment explanation
Indices: 1465398--1465437 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
1465388 TGTTTAATAA
1465398 AATATA-TATATT
1 AATATATTATATT
*
1465410 AATATATTATCTT
1 AATATATTATATT
1465423 AA-A-ATTATATT
1 AATATATTATATT
1465434 AATA
1 AATA
1465438 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:1472134 original size:27 final size:27
Alignment explanation
Indices: 1472104--1472155 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1472094 ACTACTTGGG
1472104 AAAGAGAGGAGAACATGAGGAAGCAGT
1 AAAGAGAGGAGAACATGAGGAAGCAGT
*
1472131 AAAGATAGGAGAACATGAGGAAGCA
1 AAAGAGAGGAGAACATGAGGAAGCA
1472156 ATTTACATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.35, T:0.08
Consensus pattern (27 bp):
AAAGAGAGGAGAACATGAGGAAGCAGT
Found at i:1475809 original size:18 final size:18
Alignment explanation
Indices: 1475786--1475891 Score: 167
Period size: 18 Copynumber: 5.9 Consensus size: 18
1475776 GTGTAGAATT
*
1475786 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1475804 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
1475822 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1475840 TGTCCCGAGGGACCATTA
1 TGTCCCGAAGGACCACTA
*
1475858 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
1475876 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
1475892 ATAGACCCTC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 79 1.00
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1476684 original size:20 final size:22
Alignment explanation
Indices: 1476659--1476716 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1476649 TTCCCCTTGA
1476659 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1476679 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1476702 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1476717 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1476794 original size:64 final size:63
Alignment explanation
Indices: 1476704--1476844 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
1476694 TCTTTAACAT
* * * *
1476704 GTGCATCGATGCACTACCCATGCATCGATATACAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
1476767 GATGCATCGATGCACT-CCTTATTCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
1476831 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1476845 ATTGCACATT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 21 0.32
64 44 0.68
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:1480032 original size:2 final size:2
Alignment explanation
Indices: 1479993--1480022 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1479983 ATATTCATTC
1479993 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
1480023 TAACATATAT
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:1480303 original size:18 final size:18
Alignment explanation
Indices: 1480282--1480403 Score: 163
Period size: 18 Copynumber: 6.8 Consensus size: 18
1480272 TTAGAATTTA
* *
1480282 TCCCGTAGGACCACTATA
1 TCCCGAAGGACCACTATG
* * *
1480300 TCCCGAAAGACTACTGTG
1 TCCCGAAGGACCACTATG
1480318 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
1480336 TCCCGAAGGACCATTATG
1 TCCCGAAGGACCACTATG
*
1480354 TCCCGAATGACCACTATG
1 TCCCGAAGGACCACTATG
* *
1480372 TCCCAAATGACCACTATG
1 TCCCGAAGGACCACTATG
1480390 TCCCGAAGGACCAC
1 TCCCGAAGGACCAC
1480404 ATAGATCCTC
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 90 1.00
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:1481196 original size:20 final size:20
Alignment explanation
Indices: 1481171--1481208 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1481161 TTCCCCTTAA
1481171 AGTGCATCGATGAATTCTAT
1 AGTGCATCGATGAATTCTAT
*
1481191 AGTGCATCGATGCATTCT
1 AGTGCATCGATGAATTCT
1481209 TTAACATGTG
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:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGAATTCTAT
Found at i:1490307 original size:17 final size:18
Alignment explanation
Indices: 1490274--1490307 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1490264 ATTTAAATTG
1490274 CGGTTGCTGTAGCATTTT
1 CGGTTGCTGTAGCATTTT
*
1490292 CGGTTG-TGTTGCATTT
1 CGGTTGCTGTAGCATTT
1490308 ATGGCGATTG
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:0.09, C:0.15, G:0.29, T:0.47
Consensus pattern (18 bp):
CGGTTGCTGTAGCATTTT
Found at i:1495249 original size:14 final size:14
Alignment explanation
Indices: 1495230--1495267 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1495220 ACGCCCCAAA
1495230 TCTCGGGTTGGTAG
1 TCTCGGGTTGGTAG
1495244 TCTCGGGTTGGTAG
1 TCTCGGGTTGGTAG
*
1495258 TTTCGGGTTG
1 TCTCGGGTTG
1495268 ACTCGAGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.05, C:0.13, G:0.42, T:0.39
Consensus pattern (14 bp):
TCTCGGGTTGGTAG
Found at i:1499337 original size:19 final size:19
Alignment explanation
Indices: 1499276--1499339 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
1499266 TTAGTCAGTC
* *
1499276 AGTATCGATACCAAGAGGT
1 AGTATCGATACAAAGAGCT
* *
1499295 AGGTATCGATACTTAAGGGCT
1 A-GTATCGATAC-AAAGAGCT
1499316 AGTATCGATACAAAGAGCT
1 AGTATCGATACAAAGAGCT
1499335 AGTAT
1 AGTAT
1499340 TTAGTATCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 12 0.32
20 20 0.53
21 6 0.16
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (19 bp):
AGTATCGATACAAAGAGCT
Found at i:1505138 original size:36 final size:36
Alignment explanation
Indices: 1505098--1505172 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
1505088 ATAATAGAAG
*
1505098 TATTTTTTTATTTGGGTTAAAATTTTGGTTAAAAAA
1 TATTTTTTTATTTAGGTTAAAATTTTGGTTAAAAAA
1505134 TATTTTTTTATTTAGGTTAAAATTTTGGTTAAAAAA
1 TATTTTTTTATTTAGGTTAAAATTTTGGTTAAAAAA
1505170 TAT
1 TAT
1505173 GAGTCTTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (36 bp):
TATTTTTTTATTTAGGTTAAAATTTTGGTTAAAAAA
Found at i:1512474 original size:17 final size:18
Alignment explanation
Indices: 1512452--1512486 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1512442 AATTTTATGA
*
1512452 GGTG-AAAATATTGTTAT
1 GGTGAAAAATATAGTTAT
1512469 GGTGAAAAATATAGTTAT
1 GGTGAAAAATATAGTTAT
1512487 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (18 bp):
GGTGAAAAATATAGTTAT
Found at i:1512746 original size:21 final size:22
Alignment explanation
Indices: 1512705--1512744 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1512695 TTTCTTATAA
*
1512705 AATTTTATATTTAAATGTTTAT
1 AATTTAATATTTAAATGTTTAT
1512727 AATTTAATA-TTAAA-GTTT
1 AATTTAATATTTAAATGTTT
1512745 TACTTGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTTAATATTTAAATGTTTAT
Found at i:1514153 original size:17 final size:17
Alignment explanation
Indices: 1514131--1514163 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1514121 TACCCATGTA
1514131 CACAATTAATTGACGCG
1 CACAATTAATTGACGCG
1514148 CACAATTAATTGACGC
1 CACAATTAATTGACGC
1514164 TTATCATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAATTAATTGACGCG
Found at i:1516423 original size:18 final size:18
Alignment explanation
Indices: 1516400--1516442 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1516390 GTTACCTTCT
*
1516400 GGTAATCTTATTCCCGAA
1 GGTAATCTTATTCCCAAA
*
1516418 GGTAATCTTATTCTCAAA
1 GGTAATCTTATTCCCAAA
1516436 GGTAATC
1 GGTAATC
1516443 ATACATTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (18 bp):
GGTAATCTTATTCCCAAA
Done.