Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007936.1 Hibiscus syriacus cultivar Beakdansim tig00110346_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: 2869312
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1508138 original size:13 final size:13
Alignment explanation
Indices: 1508122--1508152 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1508112 ATAGTTTTAA
1508122 AAAATGGTTTTTG
1 AAAATGGTTTTTG
*
1508135 AAAACGGTTTTTG
1 AAAATGGTTTTTG
1508148 AAAAT
1 AAAAT
1508153 ATATTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (13 bp):
AAAATGGTTTTTG
Found at i:1508196 original size:29 final size:30
Alignment explanation
Indices: 1508141--1508205 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
1508131 TTTGAAAACG
*
1508141 GTTTTTGAAAATATATTAATATATTATATA
1 GTTTTTGAAAATATAATAATATATTATATA
* *
1508171 GTTTTTGGAAATATAAT-ATATGTTATATA
1 GTTTTTGAAAATATAATAATATATTATATA
*
1508200 GATTTT
1 GTTTTT
1508206 ATTATTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (30 bp):
GTTTTTGAAAATATAATAATATATTATATA
Found at i:1508216 original size:27 final size:28
Alignment explanation
Indices: 1508193--1508269 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
1508183 ATAATATATG
1508193 TTATATAG-ATTTTAT-TATTTATATTAT
1 TTAT-TAGTATTTTATATATTTATATTAT
**
1508220 TTATTAGTATTTTATATA-TTAGGTTAT
1 TTATTAGTATTTTATATATTTATATTAT
* *
1508247 ATTATTATTA-TTTATTTATTTAT
1 -TTATTAGTATTTTATATATTTAT
1508270 TAAATTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
26 3 0.07
27 25 0.61
28 13 0.32
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (28 bp):
TTATTAGTATTTTATATATTTATATTAT
Found at i:1508269 original size:15 final size:16
Alignment explanation
Indices: 1508203--1508271 Score: 72
Period size: 15 Copynumber: 4.4 Consensus size: 16
1508193 TTATATAGAT
1508203 TTTATTATTTATATTA
1 TTTATTATTTATATTA
* *
1508219 TTTATTA-GTATTTTA
1 TTTATTATTTATATTA
* *
1508234 TATATTAGGTTATATTA
1 TTTATTA-TTTATATTA
1508251 -TTATTATTTAT-TTA
1 TTTATTATTTATATTA
1508265 TTTATTA
1 TTTATTA
1508272 AATTTTAACA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
14 3 0.07
15 22 0.51
16 12 0.28
17 6 0.14
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTATTATTTATATTA
Found at i:1514614 original size:74 final size:74
Alignment explanation
Indices: 1514536--1514718 Score: 271
Period size: 74 Copynumber: 2.4 Consensus size: 74
1514526 AAATGACTAC
1514536 GGGTATCGATACCTCTAAGGGGGTATCGGTACCCATTGGGCATTATGTTTTTCTCGGAGCCAAAA
1 GGGTATCGATACCTCTAAGGGGGTATCGGTACCCATTGGGCATTATGTTTTTCTCGGAGCCAAAA
1514601 TTGGCATAG
66 TTGGCATAG
* * *
1514610 GGGTATCGATA-CTCTATAAGGGGTATCGGTACCCATTTGGCATTCTGTTTTTCTCGGAGCCAAA
1 GGGTATCGATACCTCTA-AGGGGGTATCGGTACCCATTGGGCATTATGTTTTTCTCGGAGCCAAA
*
1514674 ATTGTCATAG
65 ATTGGCATAG
*
1514684 GGGTATCGGTATACC-CTACGAGGGGTATCGGTACC
1 GGGTATC-G-ATACCTCTAAG-GGGGTATCGGTACC
1514719 TCCCTATTTA
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
73 5 0.05
74 71 0.72
75 1 0.01
76 20 0.20
77 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (74 bp):
GGGTATCGATACCTCTAAGGGGGTATCGGTACCCATTGGGCATTATGTTTTTCTCGGAGCCAAAA
TTGGCATAG
Found at i:1515029 original size:13 final size:13
Alignment explanation
Indices: 1515011--1515043 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1515001 TAAGATTTTC
*
1515011 TTTGAAAATCATT
1 TTTGAAAATCAAT
1515024 TTTG-AAATCAAT
1 TTTGAAAATCAAT
1515036 TTTGAAAA
1 TTTGAAAA
1515044 ATTACTCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:1517449 original size:13 final size:13
Alignment explanation
Indices: 1517431--1517504 Score: 103
Period size: 13 Copynumber: 5.3 Consensus size: 13
1517421 GTCACAACCC
1517431 GACCCGACCCGTT
1 GACCCGACCCGTT
1517444 GACCCGACCCGTT
1 GACCCGACCCGTT
1517457 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
1517475 GACCCGACCCGTT
1 GACCCGACCCGTT
1517488 GACCCGACCCGTT
1 GACCCGACCCGTT
1517501 GACC
1 GACC
1517505 GTTGACCCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
13 43 0.77
18 13 0.23
ACGTcount: A:0.16, C:0.47, G:0.23, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1517463 original size:31 final size:31
Alignment explanation
Indices: 1517427--1517498 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
1517417 ACCGGTCACA
1517427 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1517458 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1517489 ACCCGACCCG
1 ACCCGACCCG
1517499 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.17, C:0.50, G:0.22, T:0.11
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:1517498 original size:18 final size:18
Alignment explanation
Indices: 1517444--1517485 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1517434 CCGACCCGTT
1517444 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
1517462 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
1517480 GACCCG
1 GACCCG
1517486 TTGACCCGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.24, T:0.10
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:1517517 original size:15 final size:15
Alignment explanation
Indices: 1517493--1517526 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1517483 CCGTTGACCC
*
1517493 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
1517508 GACCCATTGACCGTT
1 GACCCATTGACCGTT
1517523 GACC
1 GACC
1517527 ACTGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:1518855 original size:18 final size:18
Alignment explanation
Indices: 1518829--1518864 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1518819 TCGAAAGGAC
*
1518829 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1518847 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1518865 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1520034 original size:23 final size:23
Alignment explanation
Indices: 1520008--1520090 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
1519998 TCCGACTTGA
* *
1520008 ATTCTGTTATGATCCTGACCTGG
1 ATTCTGATATGATCATGACCTGG
* *
1520031 ATTCTGATCTGAT-ATTGACATGG
1 ATTCTGATATGATCA-TGACCTGG
*
1520054 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGAT-CATGACCTGG
1520078 ATTCTGATATGAT
1 ATTCTGATATGAT
1520091 ACTTGACTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 31 0.61
24 19 0.37
25 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTCTGATATGATCATGACCTGG
Found at i:1520078 original size:24 final size:24
Alignment explanation
Indices: 1520023--1520097 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
1520013 GTTATGATCC
1520023 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
1520046 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
1520070 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
1520094 TGAC
1 TGAC
1520098 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:1522306 original size:13 final size:13
Alignment explanation
Indices: 1522288--1522361 Score: 94
Period size: 13 Copynumber: 5.3 Consensus size: 13
1522278 GTCACAACCC
1522288 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1522301 GACCCGACCCATT
1 GACCCGACCCGTT
1522314 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
1522332 GACCCGACCCGTT
1 GACCCGACCCGTT
1522345 GACCCGACCCGTT
1 GACCCGACCCGTT
1522358 GACC
1 GACC
1522362 GTTGACCCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
13 42 0.78
18 12 0.22
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1522319 original size:26 final size:26
Alignment explanation
Indices: 1522288--1522376 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 26
1522278 GTCACAACCC
1522288 GACCCGACCCGTTGACCCGACCCATT
1 GACCCGACCCGTTGACCCGACCCATT
*
1522314 GACCCGACCCGACCCGTTGACCCGACCCGTT
1 -----GACCCGACCCGTTGACCCGACCCATT
*
1522345 GACCCGACCCGTTGACCGTTGACCCATT
1 GACCCGACCCGTTGACC--CGACCCATT
1522373 GACC
1 GACC
1522377 GTTGACCACT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
26 17 0.32
28 11 0.21
31 25 0.47
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (26 bp):
GACCCGACCCGTTGACCCGACCCATT
Found at i:1522320 original size:31 final size:31
Alignment explanation
Indices: 1522284--1522355 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
1522274 ACCGGTCACA
1522284 ACCCGACCCGACCCGTTGACCCGACCCATTG
1 ACCCGACCCGACCCGTTGACCCGACCCATTG
*
1522315 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCATTG
1522346 ACCCGACCCG
1 ACCCGACCCG
1522356 TTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCGACCCATTG
Found at i:1522335 original size:8 final size:8
Alignment explanation
Indices: 1522324--1522393 Score: 57
Period size: 8 Copynumber: 9.5 Consensus size: 8
1522314 GACCCGACCC
1522324 GACCCGTT
1 GACCCGTT
1522332 GACCC---
1 GACCCGTT
1522337 GACCCGTT
1 GACCCGTT
1522345 GACCC---
1 GACCCGTT
1522350 GACCCGTT
1 GACCCGTT
1522358 GA-CCGTT
1 GACCCGTT
*
1522365 GACCCATT
1 GACCCGTT
1522373 GA-CCGTT
1 GACCCGTT
1522380 GACCACTGTT
1 GACC-C-GTT
1522390 GACC
1 GACC
1522394 AAAACTTTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
5 10 0.20
7 13 0.26
8 19 0.38
9 1 0.02
10 7 0.14
ACGTcount: A:0.17, C:0.39, G:0.23, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:1522355 original size:18 final size:18
Alignment explanation
Indices: 1522284--1522342 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
1522274 ACCGGTCACA
1522284 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1522302 ACCCGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
1522315 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1522333 ACCCGACCCG
1 ACCCGACCCG
1522343 TTGACCCGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
13 12 0.33
14 1 0.03
17 1 0.03
18 22 0.61
ACGTcount: A:0.19, C:0.51, G:0.20, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1522374 original size:15 final size:15
Alignment explanation
Indices: 1522350--1522383 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1522340 CCGTTGACCC
*
1522350 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
1522365 GACCCATTGACCGTT
1 GACCCATTGACCGTT
1522380 GACC
1 GACC
1522384 ACTGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:1523713 original size:18 final size:18
Alignment explanation
Indices: 1523687--1523722 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1523677 TCGAAAGGAC
*
1523687 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1523705 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1523723 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1524893 original size:23 final size:23
Alignment explanation
Indices: 1524867--1524949 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
1524857 TCCGACTTGA
* *
1524867 ATTCTGTTATGATCCTGACCTGG
1 ATTCTGATATGATCATGACCTGG
* *
1524890 ATTCTGATCTGAT-ATTGACATGG
1 ATTCTGATATGATCA-TGACCTGG
*
1524913 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGAT-CATGACCTGG
1524937 ATTCTGATATGAT
1 ATTCTGATATGAT
1524950 ACTTGACTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 31 0.61
24 19 0.37
25 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTCTGATATGATCATGACCTGG
Found at i:1524937 original size:24 final size:24
Alignment explanation
Indices: 1524882--1524956 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
1524872 GTTATGATCC
1524882 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
1524905 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
1524929 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
1524953 TGAC
1 TGAC
1524957 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:1529074 original size:21 final size:20
Alignment explanation
Indices: 1529048--1529092 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1529038 GATCATTTTC
*
1529048 ATTTTTCAATTTTGAAATATA
1 ATTTTTCAATTTT-AAAAATA
**
1529069 ATTTTTGTATTTTAAAAATA
1 ATTTTTCAATTTTAAAAATA
1529089 ATTT
1 ATTT
1529093 CTCATAATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTTCAATTTTAAAAATA
Found at i:1529858 original size:117 final size:117
Alignment explanation
Indices: 1529652--1529888 Score: 456
Period size: 117 Copynumber: 2.0 Consensus size: 117
1529642 CGAGGGTTAA
*
1529652 AGATTTTATATTCTTAGCTCGATAATTGCAATCTTCTTTGATTGCCAAGCTTTTGGAATAGAGTA
1 AGATTTTATATTCTTAGCTCGATAATTGCAATCTTCTTTGATTGCCAAGCTTTTGGAAGAGAGTA
1529717 AACTAACTTTCTCACAAGCTTCTCATTTGCAATGATCTCTCCATATGATTTG
66 AACTAACTTTCTCACAAGCTTCTCATTTGCAATGATCTCTCCATATGATTTG
*
1529769 AGATTTTATATTCTTAGCTCGATAATTGCAATCTTCTTTGATTTCCAAGCTTTTGGAAGAGAGTA
1 AGATTTTATATTCTTAGCTCGATAATTGCAATCTTCTTTGATTGCCAAGCTTTTGGAAGAGAGTA
1529834 AACTAACTTTCTCACAAGCTTCTCATTTGCAATGATCTCTCCATATGATTTG
66 AACTAACTTTCTCACAAGCTTCTCATTTGCAATGATCTCTCCATATGATTTG
1529886 AGA
1 AGA
1529889 CCATTGACAA
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (117 bp):
AGATTTTATATTCTTAGCTCGATAATTGCAATCTTCTTTGATTGCCAAGCTTTTGGAAGAGAGTA
AACTAACTTTCTCACAAGCTTCTCATTTGCAATGATCTCTCCATATGATTTG
Found at i:1531198 original size:54 final size:54
Alignment explanation
Indices: 1531113--1531226 Score: 183
Period size: 54 Copynumber: 2.1 Consensus size: 54
1531103 AAATGACTAG
* *
1531113 GGGTATCGGTACCCATTGGGCATTATGTTTTTCTCGGAGCCAAAATTGGCATAA
1 GGGTATCGGTACCCATTGGGCATTATATTTTTCTCGGAGCCAAAATTAGCATAA
* * *
1531167 GGGTATCGGTACCCATTTGGCATTCTATTTTTCTCGGAGCCAAAATTAGCATAG
1 GGGTATCGGTACCCATTGGGCATTATATTTTTCTCGGAGCCAAAATTAGCATAA
1531221 GGGTAT
1 GGGTAT
1531227 TGGTTCCTGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (54 bp):
GGGTATCGGTACCCATTGGGCATTATATTTTTCTCGGAGCCAAAATTAGCATAA
Found at i:1535782 original size:4 final size:4
Alignment explanation
Indices: 1535769--1535895 Score: 91
Period size: 4 Copynumber: 32.2 Consensus size: 4
1535759 CCATTATACT
* * * * * *
1535769 TATA -ATA TATA TATA TGATG TATG TATA TACT- TATG TGTA TGTA TACA
1 TATA TATA TATA TATA T-ATA TATA TATA TA-TA TATA TATA TATA TATA
* * * * * *
1535817 TATA TATA TATA TGTA TGTA TGTA TATA TGTA TGTA TGTA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
1535865 TATA TATA TATA TATA TATG TA-A T-TA TATA T
1 TATA TATA TATA TATA TATA TATA TATA TATA T
1535896 GATCAATGGT
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
3 7 0.07
4 93 0.89
5 4 0.04
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:1536003 original size:10 final size:10
Alignment explanation
Indices: 1535988--1536080 Score: 61
Period size: 12 Copynumber: 9.1 Consensus size: 10
1535978 TGATATACAC
1535988 ATAAGTATAT
1 ATAAGTATAT
1535998 ATAAGTATAT
1 ATAAGTATAT
1536008 ACATAAGTATAT
1 --ATAAGTATAT
1536020 AT-A-TATA-
1 ATAAGTATAT
*
1536027 AGT-A-CATAT
1 A-TAAGTATAT
1536036 ATAAGTATATAT
1 ATAAG--TATAT
*
1536048 ATAAATATAT
1 ATAAGTATAT
1536058 AAATAAGTATAT
1 --ATAAGTATAT
*
1536070 GTAAGTATAT
1 ATAAGTATAT
1536080 A
1 A
1536081 ATTAAACATG
Statistics
Matches: 67, Mismatches: 6, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
7 1 0.01
8 10 0.15
9 3 0.04
10 26 0.39
12 27 0.40
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (10 bp):
ATAAGTATAT
Found at i:1536011 original size:22 final size:22
Alignment explanation
Indices: 1535969--1536080 Score: 98
Period size: 22 Copynumber: 4.8 Consensus size: 22
1535959 ATGTGTGTGT
* *
1535969 GTATATATATGATATACACATAA
1 GTATATATAAG-TATATACATAA
1535992 GTATATATAAGTATATACATAA
1 GTATATATAAGTATATACATAA
* *
1536014 GTATATATATATAAGTACATATATAA
1 G----TATATATAAGTATATACATAA
* *
1536040 GTATATATATAAATATATAAATAA
1 G--TATATATAAGTATATACATAA
*
1536064 GTATATGTAAGTATATA
1 GTATATATAAGTATATA
1536081 ATTAAACATG
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
22 25 0.33
23 10 0.13
24 21 0.28
26 20 0.26
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (22 bp):
GTATATATAAGTATATACATAA
Found at i:1536029 original size:26 final size:26
Alignment explanation
Indices: 1535993--1536069 Score: 113
Period size: 26 Copynumber: 3.0 Consensus size: 26
1535983 TACACATAAG
*
1535993 TATATATAAGTATATACATAAGTATA
1 TATATATAAGTATATAAATAAGTATA
* *
1536019 TATATATAAGTACATATATAAGTATA
1 TATATATAAGTATATAAATAAGTATA
1536045 TATATA-AA-TATATAAATAAGTATA
1 TATATATAAGTATATAAATAAGTATA
1536069 T
1 T
1536070 GTAAGTATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
24 15 0.32
25 2 0.04
26 30 0.64
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (26 bp):
TATATATAAGTATATAAATAAGTATA
Found at i:1536080 original size:12 final size:12
Alignment explanation
Indices: 1535993--1536069 Score: 100
Period size: 12 Copynumber: 6.2 Consensus size: 12
1535983 TACACATAAG
1535993 TATATATAAGTA
1 TATATATAAGTA
*
1536005 TATACATAAGTATA
1 TATATATAAG--TA
1536019 TATATATAAGTA
1 TATATATAAGTA
*
1536031 CATATATAAGTA
1 TATATATAAGTA
*
1536043 TATATATAAATA
1 TATATATAAGTA
*
1536055 TATAAATAAGTA
1 TATATATAAGTA
1536067 TAT
1 TAT
1536070 GTAAGTATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
12 45 0.80
14 11 0.20
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (12 bp):
TATATATAAGTA
Found at i:1536618 original size:2 final size:2
Alignment explanation
Indices: 1536611--1536646 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1536601 ACTCATTTGG
1536611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1536647 CAATCTCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1536717 original size:23 final size:23
Alignment explanation
Indices: 1536674--1536723 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 23
1536664 ATCTTATATG
1536674 TATATTTAAAAATTTTAAATTAAAT
1 TATATTT-AAAATTTTAAATT-AAT
1536699 TATATTT-AAATTATT-AATTAAT
1 TATATTTAAAATT-TTAAATTAAT
1536721 TAT
1 TAT
1536724 TACATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
23 9 0.38
24 2 0.08
25 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTTAAAATTTTAAATTAAT
Found at i:1536836 original size:13 final size:13
Alignment explanation
Indices: 1536820--1536863 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1536810 TGAAATTAAT
*
1536820 TTAATAATTATAA
1 TTAAGAATTATAA
*
1536833 TTAAGATTTATAA
1 TTAAGAATTATAA
*
1536846 TATAAGGATTATAA
1 T-TAAGAATTATAA
1536860 TTAA
1 TTAA
1536864 TATAGAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (13 bp):
TTAAGAATTATAA
Found at i:1537087 original size:16 final size:16
Alignment explanation
Indices: 1537068--1537116 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
1537058 GGTCAAGTTC
1537068 ATAACATGTCAGGTTG
1 ATAACATGTCAGGTTG
*
1537084 ATAACA----A-GTTC
1 ATAACATGTCAGGTTG
1537095 ATAACATGTCAGGTTG
1 ATAACATGTCAGGTTG
1537111 ATAACA
1 ATAACA
1537117 AGTCGGGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
11 9 0.35
12 1 0.04
15 1 0.04
16 15 0.58
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (16 bp):
ATAACATGTCAGGTTG
Found at i:1537091 original size:27 final size:27
Alignment explanation
Indices: 1537061--1537119 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
1537051 AATTATAGGT
1537061 CAAGTTCATAACATGTCAGGTTGATAA
1 CAAGTTCATAACATGTCAGGTTGATAA
1537088 CAAGTTCATAACATGTCAGGTTGATAA
1 CAAGTTCATAACATGTCAGGTTGATAA
1537115 CAAGT
1 CAAGT
1537120 CGGGTAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (27 bp):
CAAGTTCATAACATGTCAGGTTGATAA
Found at i:1538341 original size:23 final size:22
Alignment explanation
Indices: 1538288--1538328 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1538278 AAAAAGTGCA
* *
1538288 AAAGGCAAAAGAAAAGTGTTAT
1 AAAGGCAGATGAAAAGTGTTAT
1538310 AAAGGCAGATGAAAA-TGTT
1 AAAGGCAGATGAAAAGTGTT
1538329 TTATACAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (22 bp):
AAAGGCAGATGAAAAGTGTTAT
Found at i:1538626 original size:18 final size:17
Alignment explanation
Indices: 1538603--1538637 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1538593 ATAAATTTAA
1538603 TTTATAATAATAAATAAT
1 TTTATAA-AATAAATAAT
*
1538621 TTTATAACATAAATAAT
1 TTTATAAAATAAATAAT
1538638 AAATAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTATAAAATAAATAAT
Found at i:1540554 original size:78 final size:75
Alignment explanation
Indices: 1540425--1540579 Score: 249
Period size: 78 Copynumber: 2.0 Consensus size: 75
1540415 CTAGATGTGA
*
1540425 AACTAATGTACTCTGCTTAACGAGTTGGGGAAGGGCAGAGAAAATAGAGAGAAAGAACATTATTT
1 AACTAATGTACTCTGCTTAACGAGTTGGGGAAGGGCAGAGAAAATA-AGAG--AGAAAATTATTT
1540490 ATTCGGGTGGGGT
63 ATTCGGGTGGGGT
1540503 AACTAATGTACTCTGCTTAACGAGTTGGGGAAGGGCACAGAGAAAAT-AGAGAGAAAATTATTTA
1 AACTAATGTACTCTGCTTAACGAGTTGGGGAAGGG--CAGAGAAAATAAGAGAGAAAATTATTTA
1540567 TTCGGGTGGGGT
64 TTCGGGTGGGGT
1540579 A
1 A
1540580 GAACTCTAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
76 25 0.34
78 39 0.53
80 10 0.14
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (75 bp):
AACTAATGTACTCTGCTTAACGAGTTGGGGAAGGGCAGAGAAAATAAGAGAGAAAATTATTTATT
CGGGTGGGGT
Found at i:1545158 original size:57 final size:57
Alignment explanation
Indices: 1545091--1545209 Score: 202
Period size: 57 Copynumber: 2.1 Consensus size: 57
1545081 TATCCATTAT
*
1545091 TGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACACCCTATC
1 TGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACACCCTATC
* * *
1545148 TGAAATTCATACACTTAGTATTATTTCTTAACATTTTAGAGTACGAAACGCCCTATT
1 TGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACACCCTATC
1545205 TGAAA
1 TGAAA
1545210 GTAAAAAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (57 bp):
TGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGAGTACGAAACACCCTATC
Found at i:1545272 original size:79 final size:79
Alignment explanation
Indices: 1545141--1545288 Score: 269
Period size: 79 Copynumber: 1.9 Consensus size: 79
1545131 GTACGAAACA
* *
1545141 CCCTATCTGAAATTCATACACTTAGTATTATTTCTTAACATTTTAGAGTACGAAACGCCCTATTT
1 CCCTATCTGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGAGTACGAAACGCCCTATCT
1545206 GAAAGTAAAAAATG
66 GAAAGTAAAAAATG
*
1545220 CCCTATCTGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
1 CCCTATCTGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGAGTACGAAACGCCCTATCT
1545285 GAAA
66 GAAA
1545289 TTCATACACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (79 bp):
CCCTATCTGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGAGTACGAAACGCCCTATCT
GAAAGTAAAAAATG
Found at i:1545310 original size:57 final size:57
Alignment explanation
Indices: 1545219--1545655 Score: 703
Period size: 57 Copynumber: 7.7 Consensus size: 57
1545209 AGTAAAAAAT
*
1545219 GCCCTATCTGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTACGAAAC
1 GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
* *
1545276 GCCCTATCTGAAATTCATACACATAGTATGATTTCTTAACATTTTAGCTTACGAAAC
1 GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
* * * * *
1545333 ACTCTATTTGAAATTCATACACTTAGTATGGTTTCTTAATATTTTAGCGTACGAAAC
1 GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
** * *
1545390 ATCCTATTTGAAATTCATACACTTAGTATGATTTCTTAACGTTTTAGCGTACGAAAC
1 GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
* *
1545447 GACATATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
1 GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
* * * *
1545504 ACCCTATTTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAAT
1 GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
1545561 GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
1 GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
*
1545618 GCCCTATCTGAAATTCAAACACTTAGTATGATTTCTTA
1 GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTA
1545656 TATTTTGCAC
Statistics
Matches: 349, Mismatches: 31, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 349 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (57 bp):
GCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAAC
Found at i:1545320 original size:136 final size:136
Alignment explanation
Indices: 1545091--1545345 Score: 438
Period size: 136 Copynumber: 1.9 Consensus size: 136
1545081 TATCCATTAT
*
1545091 TGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTC
1 TGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTC
* * *
1545156 ATACACTTAGTATTATTTCTTAACATTTTAGAGTACGAAACGCCCTATTTGAAAGTAAAAAATGC
66 ATACACATAGTATGATTTCTTAACATTTTAGAGTACGAAACACCCTATTTGAAAGTAAAAAATGC
1545221 CCTATC
131 CCTATC
*
1545227 TGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTC
1 TGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTC
** *
1545292 ATACACATAGTATGATTTCTTAACATTTTAGCTTACGAAACACTCTATTTGAAA
66 ATACACATAGTATGATTTCTTAACATTTTAGAGTACGAAACACCCTATTTGAAA
1545346 TTCATACACT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
136 111 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (136 bp):
TGAAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTC
ATACACATAGTATGATTTCTTAACATTTTAGAGTACGAAACACCCTATTTGAAAGTAAAAAATGC
CCTATC
Found at i:1546004 original size:20 final size:20
Alignment explanation
Indices: 1545979--1546038 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 20
1545969 TCTGGTCCTT
1545979 TGGTATCGATACCCCTTTTA
1 TGGTATCGATACCCCTTTTA
* *
1545999 TGGTATCAATACTACCCTATTA
1 TGGTATCGATAC--CCCTTTTA
1546021 TGGTATCGATATCCCCTT
1 TGGTATCGATA-CCCCTT
1546039 AATGTATCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 11 0.33
21 4 0.12
22 17 0.52
23 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.38
Consensus pattern (20 bp):
TGGTATCGATACCCCTTTTA
Found at i:1546021 original size:22 final size:20
Alignment explanation
Indices: 1545979--1546051 Score: 62
Period size: 22 Copynumber: 3.6 Consensus size: 20
1545969 TCTGGTCCTT
*
1545979 TGGTATCGATAC-CCCTTTTA
1 TGGTATCAATACTCCC-TTTA
1545999 TGGTATCAATACTACCCTATTA
1 TGGTATCAATACT-CCCT-TTA
* *
1546021 TGGTATCGATA-TCCCCTTAA
1 TGGTATCAATACT-CCCTTTA
1546041 T-GTATCAATAC
1 TGGTATCAATAC
1546052 CGAAATTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 6 0.14
22 16 0.36
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (20 bp):
TGGTATCAATACTCCCTTTA
Found at i:1546144 original size:19 final size:21
Alignment explanation
Indices: 1546076--1546148 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
1546066 ATATAGCCTC
*
1546076 GTATCGATA-CCCTCA-CCATG
1 GTATCGATACCCCT-ATCTATG
1546096 GTATCGATACCCCTATGCTATG
1 GTATCGATACCCCTAT-CTATG
*
1546118 GTACCGATACACCCT-T-TA-G
1 GTATCGATAC-CCCTATCTATG
1546137 GTATCGATACCC
1 GTATCGATACCC
1546149 AATTTAGATT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.04
19 10 0.22
20 12 0.26
21 4 0.09
22 14 0.30
23 4 0.09
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (21 bp):
GTATCGATACCCCTATCTATG
Found at i:1548292 original size:2 final size:2
Alignment explanation
Indices: 1548285--1548319 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1548275 CCATAAAAGC
1548285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1548320 CTTTCTGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1550037 original size:2 final size:2
Alignment explanation
Indices: 1550030--1550069 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1550020 GATTATACAT
1550030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1550070 ATCCCTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1550690 original size:57 final size:57
Alignment explanation
Indices: 1550623--1550878 Score: 422
Period size: 57 Copynumber: 4.5 Consensus size: 57
1550613 TCCAATACAT
* * *
1550623 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCTTATGAAACGCCCTATTTA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATCTG
* * * *
1550680 AAATTCATACACTAAGTATGATTTCTTAACATATTAGCGTACGAAACGACCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATCTG
** *
1550737 AAATTCATACACTTAGTATGATTTCTTAACATTAGAGCGTATGAAATGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATCTG
1550794 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATCTG
1550851 AAATTCATACACTTAGTATGATTTCTTA
1 AAATTCATACACTTAGTATGATTTCTTA
1550879 TAATTTGCAC
Statistics
Matches: 182, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 182 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATCTG
Found at i:1551260 original size:22 final size:20
Alignment explanation
Indices: 1551218--1551273 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 20
1551208 CTGGTCCTTC
1551218 GGTATCGATACCCCTTCTAT
1 GGTATCGATACCCCTTCTAT
1551238 GGTATCGATACTACCCTAT-TAT
1 GGTATCGATAC--CCCT-TCTAT
1551260 GGTATCGATACCCC
1 GGTATCGATACCCC
1551274 CTTAATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 14 0.42
22 18 0.55
23 1 0.03
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (20 bp):
GGTATCGATACCCCTTCTAT
Found at i:1551413 original size:19 final size:18
Alignment explanation
Indices: 1551384--1551420 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
1551374 ATTCAATATT
1551384 TTTACTGGTATCGATACC
1 TTTACTGGTATCGATACC
1551402 TTTACATGGTATCGATACC
1 TTTAC-TGGTATCGATACC
1551421 CCATTGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTACTGGTATCGATACC
Found at i:1558502 original size:14 final size:14
Alignment explanation
Indices: 1558483--1558509 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1558473 GTGCAACAGT
1558483 GTATCGATACCTAG
1 GTATCGATACCTAG
1558497 GTATCGATACCTA
1 GTATCGATACCTA
1558510 CTCGCCATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (14 bp):
GTATCGATACCTAG
Found at i:1558540 original size:21 final size:20
Alignment explanation
Indices: 1558516--1558574 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 20
1558506 CCTACTCGCC
1558516 ATGTATCGATACACTATGAAT
1 ATGTATCGATACACT-TGAAT
*
1558537 ATGTACCGATACATTCCTTGAAT
1 ATGTATCGATACA---CTTGAAT
*
1558560 GTGTATCGATACACT
1 ATGTATCGATACACT
1558575 CAGGAGTGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 2 0.06
21 12 0.38
23 16 0.50
24 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACACTTGAAT
Found at i:1559096 original size:12 final size:12
Alignment explanation
Indices: 1559067--1559100 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1559057 GTATTATGAT
*
1559067 TTTTCAAACATTG
1 TTTTCAAA-ATAG
1559080 TTTTCAAAATAG
1 TTTTCAAAATAG
1559092 TTTTCAAAA
1 TTTTCAAAA
1559101 ATTGCCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (12 bp):
TTTTCAAAATAG
Found at i:1563220 original size:11 final size:11
Alignment explanation
Indices: 1563204--1563228 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1563194 TATGTTTTCA
1563204 TATATATAATT
1 TATATATAATT
1563215 TATATATAATT
1 TATATATAATT
1563226 TAT
1 TAT
1563229 TTAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATAATT
Found at i:1566759 original size:2 final size:2
Alignment explanation
Indices: 1566752--1566783 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1566742 GATGATCATG
1566752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1566784 GTATGTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1567193 original size:19 final size:19
Alignment explanation
Indices: 1567181--1567217 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1567171 AATCTGCAAT
1567181 TAAGTTATGAATCAGAAAG
1 TAAGTTATGAATCAGAAAG
*
1567200 TAAGTTCTGAATCAGAAA
1 TAAGTTATGAATCAGAAA
1567218 TGAATTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (19 bp):
TAAGTTATGAATCAGAAAG
Found at i:1568341 original size:34 final size:34
Alignment explanation
Indices: 1568293--1568368 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
1568283 TGTTTAAGGT
*
1568293 AAATAATAGAACAAGAGGTTCGAGAATAGGAAGA
1 AAATGATAGAACAAGAGGTTCGAGAATAGGAAGA
1568327 AAATGATAGAACAAGAGGTTCGAGAATAGGAAGA
1 AAATGATAGAACAAGAGGTTCGAGAATAGGAAGA
1568361 AAATGATA
1 AAATGATA
1568369 ATATTATAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.53, C:0.05, G:0.26, T:0.16
Consensus pattern (34 bp):
AAATGATAGAACAAGAGGTTCGAGAATAGGAAGA
Found at i:1570785 original size:20 final size:20
Alignment explanation
Indices: 1570756--1570793 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1570746 TAAGAGGTGA
1570756 CTTAGATAGCTAGCTAGGAG
1 CTTAGATAGCTAGCTAGGAG
*
1570776 CTTAGGTAGCTAGCTAGG
1 CTTAGATAGCTAGCTAGG
1570794 TAGTGTAGCT
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:0.16, G:0.32, T:0.26
Consensus pattern (20 bp):
CTTAGATAGCTAGCTAGGAG
Found at i:1571154 original size:30 final size:30
Alignment explanation
Indices: 1571120--1571221 Score: 177
Period size: 30 Copynumber: 3.4 Consensus size: 30
1571110 TGAGCTAAGT
*
1571120 ATAAGCTATAAAATGGCATGTATGCGTATG
1 ATAAGCTATGAAATGGCATGTATGCGTATG
*
1571150 ATAAGCTATGAAATGGCATGTATGTGTATG
1 ATAAGCTATGAAATGGCATGTATGCGTATG
*
1571180 ATGAGCTATGAAATGGCATGTATGCGTATG
1 ATAAGCTATGAAATGGCATGTATGCGTATG
1571210 ATAAGCTATGAA
1 ATAAGCTATGAA
1571222 TGGAGGTTTA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.30
Consensus pattern (30 bp):
ATAAGCTATGAAATGGCATGTATGCGTATG
Found at i:1574358 original size:15 final size:16
Alignment explanation
Indices: 1574318--1574359 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1574308 CTCGTTACTT
1574318 TCTTTCATTTTTCTTTA
1 TCTTTC-TTTTTCTTTA
*
1574335 T-TTTCTTTTTCTTTT
1 TCTTTCTTTTTCTTTA
1574350 TCTTT-TTTTT
1 TCTTTCTTTTT
1574360 TAAAAGGGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 15 0.65
16 7 0.30
17 1 0.04
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (16 bp):
TCTTTCTTTTTCTTTA
Found at i:1575634 original size:21 final size:21
Alignment explanation
Indices: 1575610--1575660 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 21
1575600 CTATGAACAA
1575610 TATCGATACTAATGCAATGAG
1 TATCGATACTAATGCAATGAG
*
1575631 TATCGATAC---TGCTATGAG
1 TATCGATACTAATGCAATGAG
1575649 TATCGATACTAA
1 TATCGATACTAA
1575661 GAGGAAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (21 bp):
TATCGATACTAATGCAATGAG
Found at i:1576260 original size:54 final size:53
Alignment explanation
Indices: 1576085--1576268 Score: 242
Period size: 54 Copynumber: 3.4 Consensus size: 53
1576075 TTGCATTTAC
*
1576085 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTT
1 CGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAA-TTT
* *
1576139 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTT
1 CGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTT
* * * * * *
1576192 CTGTATTGACACTATGTGTGCACCCCAAGTAATTCATAATGAGTTTGTGAATTA
1 C-GTATTGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTT
* *
1576246 CAGTATCGATACTATGTGTGCAA
1 C-GTATTGACACTATGTGTGCAA
1576269 AAACCACTGA
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 4 0.03
54 113 0.97
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Consensus pattern (53 bp):
CGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTT
Found at i:1577261 original size:17 final size:17
Alignment explanation
Indices: 1577235--1577268 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1577225 TAAAGGTAAC
*
1577235 TTAGTTAGCTAGCTAGG
1 TTAGTAAGCTAGCTAGG
1577252 TTAGTAAGCTAGCTAGG
1 TTAGTAAGCTAGCTAGG
1577269 AGCCTAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (17 bp):
TTAGTAAGCTAGCTAGG
Found at i:1578980 original size:20 final size:20
Alignment explanation
Indices: 1578955--1578992 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1578945 TTGGAGATTA
* *
1578955 ATGTTAGATTGTTAAATTTG
1 ATGTTAGAATGTGAAATTTG
1578975 ATGTTAGAATGTGAAATT
1 ATGTTAGAATGTGAAATT
1578993 ACACTATTTT
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:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (20 bp):
ATGTTAGAATGTGAAATTTG
Found at i:1580246 original size:2 final size:2
Alignment explanation
Indices: 1580239--1580268 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1580229 AAAGATCATG
1580239 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
1580269 GTTATGTGAT
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:1580707 original size:13 final size:13
Alignment explanation
Indices: 1580685--1580725 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1580675 CTTGTTATGT
1580685 AATG-AATATGAA
1 AATGAAATATGAA
*
1580697 AGTGAAATATGAA
1 AATGAAATATGAA
1580710 AATGAAATATGAA
1 AATGAAATATGAA
1580723 AAT
1 AAT
1580726 TCTGAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 3 0.12
13 23 0.88
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (13 bp):
AATGAAATATGAA
Found at i:1581675 original size:20 final size:20
Alignment explanation
Indices: 1581628--1581675 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1581618 AGTTTATAGT
1581628 AGGGATCGATCCTTTAGGGA
1 AGGGATCGATCCTTTAGGGA
***
1581648 ACAAATCGATCCTTTAGGGA
1 AGGGATCGATCCTTTAGGGA
1581668 AGGGATCG
1 AGGGATCG
1581676 TCAGAACGAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (20 bp):
AGGGATCGATCCTTTAGGGA
Found at i:1582946 original size:411 final size:411
Alignment explanation
Indices: 1582182--1582999 Score: 1546
Period size: 411 Copynumber: 2.0 Consensus size: 411
1582172 ACAAACATTT
1582182 TATCATAATTTTTTTTTATTAAAGATCCAATGTTGCCTCAAAATAAAACCAAAACTCAAGATGAC
1 TATCATAATTTTTTTTTATTAAAGATCCAATGTTGCCTCAAAATAAAACCAAAACTCAAGATGAC
*
1582247 TTTAGAACGCCTCCTTGCTTTCATCATCGCCTAGCGCATTGCTTCTCTAACTCCCAAATCAGCAA
66 TTTAGAACGCCTCCTTGCTTTCATCATCGCCTAACGCATTGCTTCTCTAACTCCCAAATCAGCAA
*
1582312 GTAACAATCTGAAAAAGCTTAAACAATGAGTGTGAGCGATAAAGCTTAGTGAATGACTAAACATT
131 GTAACAATCTGAAAAAGCTTAAACAACGAGTGTGAGCGATAAAGCTTAGTGAATGACTAAACATT
*
1582377 TAATTATGATGCACATATCAAGGCTAAAGGAAAGCATACCTAAATGCCATGCAAACATAACATGT
196 TAATTATGATGCACATATCAAGGCTAAAGGAAAGCATACCTAAATGCCATCCAAACATAACATGT
1582442 TCTTACCTCAATGATTATAAAAATATGTCATGCTATGATGTACACCTAATATATGCAAATGTACA
261 TCTTACCTCAATGATTATAAAAATATGTCATGCTATGATGTACACCTAATATATGCAAATGTACA
*
1582507 CAAACATCATATTATAAATATGCTTTAATTCAACATATTCACTATTTCAAATCACACGCACTCGT
326 CAAACATCATATTATAAATATGCTTTAATTCAACATATTCACTATTTCAAATCACACACACTCGT
1582572 GCACAAGTACTTTCATGTTAA
391 GCACAAGTACTTTCATGTTAA
1582593 TATCATAATTTTTTTTTATTAAAGATCCAATGTTGCCTCAAAATAAAACCAAAACTCAAGATGAC
1 TATCATAATTTTTTTTTATTAAAGATCCAATGTTGCCTCAAAATAAAACCAAAACTCAAGATGAC
*
1582658 TTTAGAACGCCTCCTTGCTTTGATCATCGCCTAACGCATTGCTTCTCTAACTCCCAAATCAGCAA
66 TTTAGAACGCCTCCTTGCTTTCATCATCGCCTAACGCATTGCTTCTCTAACTCCCAAATCAGCAA
1582723 GTAACAATCTGAAAAAGCTTAAACAACGAGTGTGAGCGATAAAGCTTAGTGAATGACTAAACATT
131 GTAACAATCTGAAAAAGCTTAAACAACGAGTGTGAGCGATAAAGCTTAGTGAATGACTAAACATT
* *
1582788 TATTTATGATGCACATATCAAGGCTAAAGGAAAGCATACTTAAATGCCATCCAAACATAACATGT
196 TAATTATGATGCACATATCAAGGCTAAAGGAAAGCATACCTAAATGCCATCCAAACATAACATGT
*
1582853 TCTTACCTCAATGATTATAAAAATATGTCATGCTATGATGTACACCTAATATATGCAAATGTGCA
261 TCTTACCTCAATGATTATAAAAATATGTCATGCTATGATGTACACCTAATATATGCAAATGTACA
*
1582918 CAAACATCATATTATAAATATTCTTTAATTCAACATATTCACTATTTCAAATCACACACACTCGT
326 CAAACATCATATTATAAATATGCTTTAATTCAACATATTCACTATTTCAAATCACACACACTCGT
*
1582983 GCATAAGTACTTTCATG
391 GCACAAGTACTTTCATG
1583000 CTAAGTTACA
Statistics
Matches: 397, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
411 397 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (411 bp):
TATCATAATTTTTTTTTATTAAAGATCCAATGTTGCCTCAAAATAAAACCAAAACTCAAGATGAC
TTTAGAACGCCTCCTTGCTTTCATCATCGCCTAACGCATTGCTTCTCTAACTCCCAAATCAGCAA
GTAACAATCTGAAAAAGCTTAAACAACGAGTGTGAGCGATAAAGCTTAGTGAATGACTAAACATT
TAATTATGATGCACATATCAAGGCTAAAGGAAAGCATACCTAAATGCCATCCAAACATAACATGT
TCTTACCTCAATGATTATAAAAATATGTCATGCTATGATGTACACCTAATATATGCAAATGTACA
CAAACATCATATTATAAATATGCTTTAATTCAACATATTCACTATTTCAAATCACACACACTCGT
GCACAAGTACTTTCATGTTAA
Found at i:1584421 original size:56 final size:56
Alignment explanation
Indices: 1584351--1584777 Score: 544
Period size: 56 Copynumber: 7.7 Consensus size: 56
1584341 ATATGTGTTC
* * *
1584351 AAAATTAAGAAATTCATAATGAGTTTCTGAATTTCTGTATGGGCAATTTGTGTGCA
1 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCA
* * *
1584407 AAAACTAAGAAATTCATAATGAG-TT-T--ATTTATGTATGAGCACTTTGTGTGAA
1 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCA
*
1584459 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
1 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCA
* * *
1584515 AAAAGTAAGAAATTCATAATGAGTTTATGAATTT-TCGAATGGCCACTTTGTGTGCA
1 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCT-GTATGGGCACTTTGTGTGCA
* * * * *
1584571 AAAACTAAGAATTTTAGAATGAGTTTATGAATTT-TCGTATGGGCATTTTGTGTACA
1 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCT-GTATGGGCACTTTGTGTGCA
* ** * *
1584627 AAAACCAATTAATTCATAATGAGTTTATGAATTTCCGTATGGACACTTTGTGTGCA
1 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCA
* *
1584683 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGCCACTTTGTGTGC-
1 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCA
* * * * *
1584738 AAAACTAAGAAGTTCATAATAAATATATGAATTTATGTAT
1 AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTAT
1584778 TGGTAGTGTG
Statistics
Matches: 324, Mismatches: 41, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
52 45 0.14
53 2 0.01
54 2 0.01
55 36 0.11
56 239 0.74
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (56 bp):
AAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCA
Found at i:1586527 original size:29 final size:30
Alignment explanation
Indices: 1586484--1586547 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1586474 ACAAGTCTTA
* * *
1586484 GAAAAATTGGGGATCATTTCGTAAGTTTT-
1 GAAAAATTGGAGATCAATTCGTAAATTTTG
*
1586513 GAAAAGTTGGAGATCAATTCGTAAATTTTG
1 GAAAAATTGGAGATCAATTCGTAAATTTTG
1586543 GAAAA
1 GAAAA
1586548 TGGAGGGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (30 bp):
GAAAAATTGGAGATCAATTCGTAAATTTTG
Found at i:1587285 original size:59 final size:59
Alignment explanation
Indices: 1587186--1587322 Score: 195
Period size: 59 Copynumber: 2.3 Consensus size: 59
1587176 CAGCAGGCTG
** *
1587186 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
* ** *
1587245 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
1587304 CATATTCGGG-ATAACACTA
1 CATATTCGGGAAT-ACACTA
1587323 CGGTGCTTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
58 1 0.02
59 65 0.98
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
Found at i:1591444 original size:56 final size:56
Alignment explanation
Indices: 1591371--1591802 Score: 620
Period size: 56 Copynumber: 7.8 Consensus size: 56
1591361 TGTCATTATA
* * *
1591371 TGTGTGC-AAAATTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGTACAT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* * * *
1591426 TGTGTGAAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGAATGTGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* *
1591482 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTGTAAGG-ACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT-GGGCACTT
* *
1591538 TGTGTGCAAAAACTAAGAAATTCATAATTAGTTTATGAATTTTCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* * *
1591594 TGTGTGCAAAAACTAAAAAATTCATAATGAGTTTATGAATTTCCTTATGAGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* *
1591650 TGTGTGTAAAAACTAAGAAATTCATAATGAGTTTATGAATATT-CGTATGGGTACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAAT-TTCCGTATGGGCACTT
* *
1591706 TGTGTGCAAAAACTAAAAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* * * *
1591762 TGTGTGC-AAAACTAAGAAGTTCATAATAACTATATGAATTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
1591803 ATGTATTGGT
Statistics
Matches: 337, Mismatches: 35, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
55 39 0.12
56 295 0.88
57 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (56 bp):
TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
Found at i:1593383 original size:19 final size:21
Alignment explanation
Indices: 1593359--1593429 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 21
1593349 TGCAGAAATG
*
1593359 GTATCGATATCATA-ATAG-A
1 GTATCGATACCATAGATAGTA
*
1593378 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
* **
1593400 GTATCGATACCAT-GGTAGGG
1 GTATCGATACCATAGATAGTA
1593420 GTATCGATAC
1 GTATCGATAC
1593430 TAGTGAGCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 12 0.28
20 13 0.30
21 5 0.12
22 13 0.30
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:1593841 original size:56 final size:56
Alignment explanation
Indices: 1593759--1594186 Score: 636
Period size: 56 Copynumber: 7.8 Consensus size: 56
1593749 TGGCATTATA
* *
1593759 TGTGTGC-AAAATTAATAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
*
1593814 TGTGTGCAAAAAGTAAGAAATTCATAATGAGTTTAT---TTAT--GTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT-TCCGTATGGGCACTT
**
1593866 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTTGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* *
1593922 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCATTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
1593978 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* * * *
1594034 TGTGTGCAGAAACTAAGAAATTCATAATGAGTTTATGAATTTTCATATGGGTACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* * * *
1594090 TGTGTGCAAAAACTAAGAAAGTCATGATGAGTTTATGAATTTTCGTATGAGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* * *
1594146 TGTGTGC-AAAACTAAGAAGTTCATAATAAGTATATGAATTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
1594187 ATGTATTGGT
Statistics
Matches: 344, Mismatches: 22, Indels: 14
0.91 0.06 0.04
Matches are distributed among these distances:
52 47 0.14
53 2 0.01
54 2 0.01
55 38 0.11
56 255 0.74
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (56 bp):
TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
Found at i:1596687 original size:38 final size:37
Alignment explanation
Indices: 1596645--1596765 Score: 122
Period size: 38 Copynumber: 3.3 Consensus size: 37
1596635 CCTAATTCTC
1596645 AAATTATTTCACCCTAACATTCTAAATTCTTATTTTTT
1 AAATTATTTCACCCTAACATTCTAAATT-TTATTTTTT
* * * *
1596683 AAATTATTTTACAC-AATATTCTAAATTATTAATTTCTT
1 AAATTATTTCACCCTAACATTCTAAATT-TT-ATTTTTT
** * *
1596721 AAATTATTTCACCCTATGAATCTAAA--TTATTTTTC
1 AAATTATTTCACCCTAACATTCTAAATTTTATTTTTT
1596756 AAATTATTTC
1 AAATTATTTC
1596766 TCTTAACTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
35 15 0.22
36 2 0.03
37 14 0.20
38 30 0.43
39 8 0.12
ACGTcount: A:0.36, C:0.15, G:0.01, T:0.49
Consensus pattern (37 bp):
AAATTATTTCACCCTAACATTCTAAATTTTATTTTTT
Found at i:1597016 original size:15 final size:16
Alignment explanation
Indices: 1596996--1597029 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1596986 TACCTAGGTT
*
1596996 TTATGAGTA-TCTGAC
1 TTATGAGTACTCAGAC
1597011 TTATGAGTACTCAGAC
1 TTATGAGTACTCAGAC
1597027 TTA
1 TTA
1597030 GCGGTCCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (16 bp):
TTATGAGTACTCAGAC
Found at i:1608036 original size:23 final size:23
Alignment explanation
Indices: 1607989--1608038 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1607979 AATAACATAT
**
1607989 TAGGTAACACTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
* *
1608012 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
1608035 TAGG
1 TAGG
1608039 CATTTAACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:1608099 original size:87 final size:87
Alignment explanation
Indices: 1607953--1608201 Score: 435
Period size: 87 Copynumber: 2.9 Consensus size: 87
1607943 ATGTTATATT
* * * *
1607953 ATTTAATCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
*
1608018 GCGCTTATATAATAAAATAGGC
66 GCGCTTATATAATAAAATAGAC
*
1608040 ATTTAACCGGAAATATTATCAAGTACAATAATATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1608105 GCGCTTATATAATAAAATAGAC
66 GCGCTTATATAATAAAATAGAC
*
1608127 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
1 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1608192 GCGCTTATAT
66 GCGCTTATAT
1608202 TGACATATTT
Statistics
Matches: 154, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 154 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.33
Consensus pattern (87 bp):
ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
GCGCTTATATAATAAAATAGAC
Found at i:1608102 original size:23 final size:23
Alignment explanation
Indices: 1608067--1608124 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1608057 ATCAAGTACA
*
1608067 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1608090 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1608113 ATAATAAAATAG
1 ATAATATAATAG
1608125 ACATTTAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:1608561 original size:200 final size:200
Alignment explanation
Indices: 1608242--1608720 Score: 533
Period size: 200 Copynumber: 2.4 Consensus size: 200
1608232 TATACCGGTA
* * * *
1608242 ACATTGCATATTTACCTATTATATTATAATTATCGGTTTTGATGTTTTTGGGATCGATA-TAATT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACT--TT
* * * ** *
1608306 T--TAAATGTATCGACACTTTATGCGTGTATCTCGTTGGGTATTCATTCTGGAAAAAA-GTATCG
64 TAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGACATTCATTCTAGAAAAAATGTATCG
* *
1608368 ACACAAACTTAAA-ACGTGTCGATACATTAGGTAGACCTATTTTCTCATAAAA-TCGGTATATTT
129 ACA-AAACTTAAATACGTGTCGATACATTAGGTAGACCTATTATATCATAAAACT-GGTATATTT
*
1608431 CTATGGGGGT
192 ATAT-GGGGT
* *
1608441 ACATTGTAAATTTATCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTA
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTA
* *
1608506 ATAAATATATCGACACTTTATGCGTGCACCTCATTTGACATTCATTCTAGAAAAAATGTATCGAC
66 ATAAATGTATCGACACTTTATGCGTGCACCTCATTGGACATTCATTCTAGAAAAAATGTATCGAC
**** ** * *
1608571 ATTTTTTAAATTTGTGTCGATACATTATGTTGACCTATTATATCATAAAACTGGTATATTTATAT
131 AAAACTTAAATACGTGTCGATACATTAGGTAGACCTATTATATCATAAAACTGGTATATTTATAT
* *
1608636 TGGTT
196 GGGGT
* * *** ** *
1608641 ACATTATAAATTTACCTATTACATTATAAATATTAATTTCGATAATTTT-AGATCGATACTTTTA
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTA
1608705 GA-AAATGTATCGACAC
66 -ATAAATGTATCGACAC
1608721 ATATATTTAC
Statistics
Matches: 235, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
198 3 0.01
199 80 0.34
200 97 0.41
201 54 0.23
202 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (200 bp):
ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTA
ATAAATGTATCGACACTTTATGCGTGCACCTCATTGGACATTCATTCTAGAAAAAATGTATCGAC
AAAACTTAAATACGTGTCGATACATTAGGTAGACCTATTATATCATAAAACTGGTATATTTATAT
GGGGT
Found at i:1614679 original size:24 final size:24
Alignment explanation
Indices: 1614633--1614682 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1614623 CAACTCGTAT
*
1614633 AAATTGCACCAAAGTGCCGCATAG
1 AAATTGCACCAAAGTGCCACATAG
* **
1614657 AAATTGCACCGAAGTTTCACATAG
1 AAATTGCACCAAAGTGCCACATAG
1614681 AA
1 AA
1614683 TGTCTCGAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (24 bp):
AAATTGCACCAAAGTGCCACATAG
Found at i:1614719 original size:23 final size:23
Alignment explanation
Indices: 1614674--1614773 Score: 114
Period size: 23 Copynumber: 4.4 Consensus size: 23
1614664 ACCGAAGTTT
1614674 CACATAGAA-TG-TCTCGAAGGAC
1 CACATAGAATTGTTC-CGAAGGAC
* *
1614696 CACATAGAATTATTCTGAAGGAC
1 CACATAGAATTGTTCCGAAGGAC
* * *
1614719 CATATAGAATTGTCCCAAAGGAC
1 CACATAGAATTGTTCCGAAGGAC
*
1614742 CACGTAGAATTGTTCCGAAGGAC
1 CACATAGAATTGTTCCGAAGGAC
*
1614765 CACTTAGAA
1 CACATAGAA
1614774 CCCTCGACTC
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.14
23 53 0.83
24 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (23 bp):
CACATAGAATTGTTCCGAAGGAC
Found at i:1614740 original size:46 final size:45
Alignment explanation
Indices: 1614677--1614766 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
1614667 GAAGTTTCAC
* * *
1614677 ATAGAATGTCTCGAAGGACCACATAGAATTATTCTGAAGGACCAT
1 ATAGAATGTCCCAAAGGACCACATAGAATTATTCCGAAGGACCAT
* *
1614722 ATAGAATTGTCCCAAAGGACCACGTAGAATTGTTCCGAAGGACCA
1 ATAGAA-TGTCCCAAAGGACCACATAGAATTATTCCGAAGGACCA
1614767 CTTAGAACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 6 0.15
46 33 0.85
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (45 bp):
ATAGAATGTCCCAAAGGACCACATAGAATTATTCCGAAGGACCAT
Found at i:1620222 original size:23 final size:23
Alignment explanation
Indices: 1620189--1620261 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1620179 TGTCTTGAAT
*
1620189 GACCACATAGAATTGTCCCGAAG
1 GACCACGTAGAATTGTCCCGAAG
**
1620212 GACTGCGTAGAATTGTCCCGAAG
1 GACCACGTAGAATTGTCCCGAAG
1620235 GACCACGTAGAATTGTCCCGAAG
1 GACCACGTAGAATTGTCCCGAAG
1620258 GACC
1 GACC
1620262 TCATAGAACC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
GACCACGTAGAATTGTCCCGAAG
Found at i:1623633 original size:44 final size:44
Alignment explanation
Indices: 1623511--1623633 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 44
1623501 AACATCATCA
*
1623511 TTTCGCTCGA-TTCTATCACATAAGGAGTTTA-ATCATCATTACAC
1 TTTCACTCGATTTC-ATCACATAAGGAG-TTAGATCATCATTACAC
* *
1623555 TTTCACTCGATTTCATCGCATAAGGAGTTGGATCATCATTAC-C
1 TTTCACTCGATTTCATCACATAAGGAGTTAGATCATCATTACAC
*** *
1623598 TTTTTGTTTGATTTCATCACATAAGGAGTTAGATCA
1 -TTTCACTCGATTTCATCACATAAGGAGTTAGATCA
1623634 CCATCATCGC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 3 0.04
44 61 0.91
45 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (44 bp):
TTTCACTCGATTTCATCACATAAGGAGTTAGATCATCATTACAC
Found at i:1623739 original size:36 final size:36
Alignment explanation
Indices: 1623695--1624209 Score: 549
Period size: 36 Copynumber: 14.4 Consensus size: 36
1623685 CACTAAAGAA
* * * *
1623695 TTTATCTCACTTGAGATGGTTTTTCTCAAAACAAAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
* * * *
1623731 TTTATCTCACTCGAGATTGTTCTTCTTCAAACAGAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
*
1623767 TTTATCTCACTTAAGATTGTTTTTCTTAAAATAGAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
* * * *
1623803 TTTATCTTATTTGAGATTGTTCTTATTAAAATAGAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
** * *
1623839 TTTATCTCACTTGAGATTGTTCCTCTTAAAACATAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
** *
1623875 TTTATCTCACTTGAGATTAATTCTCTTAAAATAGAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
** **
1623911 TTTATCTCACTTGAGATTAATCCTCTTAAAATAGAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
* *
1623947 TTTATCTCGCTTGAGATAAT-TTTTTCTAAAAATAGAT
1 TTTATCTCACTTGAGAT--TGTTTTTCTTAAAATAGAT
*
1623984 TTTATTTCACTTGAGATTGTTTTTCTTAAAATAGAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
* * *
1624020 CTTATCTCACTTTAGATTGTTTTTCTTAAAACATG-T
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATA-GAT
* *
1624056 TTTATTTCACTTGAGATTGTCTTTCTTAAAATAGAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
* * *
1624092 TTTATCTCATTTTAGATTATTTTTC-T----TAGAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
* * * *
1624123 TTTATCTCACTTTAGATTGTTTTTTCTGAAAACAAAT
1 TTTATCTCACTTGAGATTG-TTTTTCTTAAAATAGAT
* * * * *
1624160 TTTATCTCATTTCAGATTGTTTTCCTTAAAACAAAT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
1624196 TTTATCTCACTTGA
1 TTTATCTCACTTGA
1624210 AAGTGTTTCT
Statistics
Matches: 407, Mismatches: 61, Indels: 22
0.83 0.12 0.04
Matches are distributed among these distances:
31 22 0.05
32 6 0.01
35 3 0.01
36 326 0.80
37 49 0.12
38 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (36 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAATAGAT
Found at i:1624109 original size:17 final size:17
Alignment explanation
Indices: 1624087--1624140 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1624077 TTTCTTAAAA
1624087 TAGATTTTATCTCATTT
1 TAGATTTTATCTCATTT
*
1624104 TAGATTATT-T-T--TCT
1 TAGATT-TTATCTCATTT
*
1624118 TAGATTTTATCTCACTT
1 TAGATTTTATCTCATTT
1624135 TAGATT
1 TAGATT
1624141 GTTTTTTCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
13 2 0.07
14 9 0.31
15 1 0.03
16 1 0.03
17 14 0.48
18 2 0.07
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.57
Consensus pattern (17 bp):
TAGATTTTATCTCATTT
Found at i:1624125 original size:31 final size:31
Alignment explanation
Indices: 1624087--1624146 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1624077 TTTCTTAAAA
*
1624087 TAGATTTTATCTCATTTTAGATTATTTTTCT
1 TAGATTTTATCTCACTTTAGATTATTTTTCT
*
1624118 TAGATTTTATCTCACTTTAGATTGTTTTT
1 TAGATTTTATCTCACTTTAGATTATTTTT
1624147 TCTGAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.60
Consensus pattern (31 bp):
TAGATTTTATCTCACTTTAGATTATTTTTCT
Found at i:1624673 original size:32 final size:32
Alignment explanation
Indices: 1624632--1624697 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
1624622 CGGATAATTC
1624632 AAATTGGATTGAAGACGATCAAAGATCAGTTT
1 AAATTGGATTGAAGACGATCAAAGATCAGTTT
* *
1624664 AAATTGGATTGAAGATGATCAAATATCAGTTT
1 AAATTGGATTGAAGACGATCAAAGATCAGTTT
1624696 AA
1 AA
1624698 GGTGGTTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (32 bp):
AAATTGGATTGAAGACGATCAAAGATCAGTTT
Found at i:1625322 original size:2 final size:2
Alignment explanation
Indices: 1625315--1625346 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1625305 AGCGAAAATA
1625315 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1625347 GTTTAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1625508 original size:20 final size:20
Alignment explanation
Indices: 1625480--1625525 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1625470 GTTTACATTC
*
1625480 TAAACTAAGGGATTAAATTA
1 TAAATTAAGGGATTAAATTA
1625500 TAAATTAAGGGATTAAATTA
1 TAAATTAAGGGATTAAATTA
1625520 TAAATT
1 TAAATT
1625526 TTAAGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (20 bp):
TAAATTAAGGGATTAAATTA
Found at i:1627150 original size:16 final size:16
Alignment explanation
Indices: 1627129--1627173 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1627119 GGTTAAACGC
1627129 TGAATGATTCAAATAT
1 TGAATGATTCAAATAT
*
1627145 TGAATGATTCAAATGT
1 TGAATGATTCAAATAT
*
1627161 TGAATTATTCAAA
1 TGAATGATTCAAA
1627174 GGCTCTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (16 bp):
TGAATGATTCAAATAT
Found at i:1628263 original size:20 final size:20
Alignment explanation
Indices: 1628221--1628264 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1628211 TATTAGAACT
* *
1628221 TTTAGATTTTAGATTTGATC
1 TTTAAATTTTAGATTTCATC
1628241 TTTAAATTTTAG-TTTCATAC
1 TTTAAATTTTAGATTTCAT-C
1628261 TTTA
1 TTTA
1628265 GTCCCTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTAAATTTTAGATTTCATC
Found at i:1637225 original size:6 final size:6
Alignment explanation
Indices: 1637216--1637328 Score: 217
Period size: 6 Copynumber: 18.8 Consensus size: 6
1637206 AAATACTACT
1637216 TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC
1 TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC
1637264 TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC
1 TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC TCTATC
*
1637312 TCTATA TCTATC TCTAT
1 TCTATC TCTATC TCTAT
1637329 TTTAGTTGAA
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 105 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTATC
Found at i:1640471 original size:44 final size:45
Alignment explanation
Indices: 1640410--1640578 Score: 245
Period size: 44 Copynumber: 3.8 Consensus size: 45
1640400 CATAAAATCT
*
1640410 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTT-CCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
1640454 CTTACCATTTATTCCATAAACTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1640499 CTT-GCAATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1640543 CTTTCCA-TTATTCCATAAGCTCATAAGCTTAGTTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTA-TTTT
1640579 CATGTTTACC
Statistics
Matches: 114, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
44 97 0.85
45 17 0.15
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1640486 original size:21 final size:21
Alignment explanation
Indices: 1640462--1640531 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1640452 TACTTACCAT
1640462 TTATTCCATAAACTCGTAAGC
1 TTATTCCATAAACTCGTAAGC
* * *
1640483 TTATTTTACCAAAATACTTGCAA--
1 TTA--TT-CCATAA-ACTCGTAAGC
*
1640506 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAACTCGTAAGC
1640527 TTATT
1 TTATT
1640532 TTACCAATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
19 5 0.14
20 5 0.14
21 10 0.28
23 5 0.14
24 5 0.14
25 6 0.17
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (21 bp):
TTATTCCATAAACTCGTAAGC
Found at i:1641235 original size:12 final size:12
Alignment explanation
Indices: 1641218--1641242 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1641208 TTATTGTTCA
1641218 TGCTACAGTAAC
1 TGCTACAGTAAC
1641230 TGCTACAGTAAC
1 TGCTACAGTAAC
1641242 T
1 T
1641243 TCCGAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (12 bp):
TGCTACAGTAAC
Found at i:1641847 original size:40 final size:40
Alignment explanation
Indices: 1641803--1641884 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
1641793 ACCGTAGTGC
*
1641803 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGAGTAT
*
1641843 TACACATAAGGTTGTGCCCACCATATACACCGAAGAGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGAGTAT
1641883 TA
1 TA
1641885 TAAACCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGAGTAT
Found at i:1648966 original size:47 final size:45
Alignment explanation
Indices: 1648896--1649021 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
1648886 TATAAAATCT
*
1648896 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1648941 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* ** *
1648988 CTTGCCA-TTATTCTGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1649022 GCATGGTCGC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 38 0.53
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1649170 original size:40 final size:40
Alignment explanation
Indices: 1649126--1649207 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1649116 ACCGTAATGC
1649126 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1649166 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1649206 TA
1 TA
1649208 TAAACCTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1661068 original size:24 final size:22
Alignment explanation
Indices: 1661041--1661085 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1661031 TATCAAAATC
1661041 ATGATCCA-GTAGTATATTATAAAA
1 ATGAT-CATGTAGT-TATT-TAAAA
1661065 ATGATCATGTAGTTATTTAAA
1 ATGATCATGTAGTTATTTAAA
1661086 TCACATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (22 bp):
ATGATCATGTAGTTATTTAAAA
Found at i:1664130 original size:2 final size:2
Alignment explanation
Indices: 1664123--1664186 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1664113 TATGTCGTAA
1664123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1664165 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1664187 TGTAGATTGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1670442 original size:6 final size:6
Alignment explanation
Indices: 1670433--1670473 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
1670423 TCCAACACGT
1670433 CTATCC CTATCC CTATCC CTATCC CTATCC CTATCC CTATC
1 CTATCC CTATCC CTATCC CTATCC CTATCC CTATCC CTATC
1670474 TGACCTATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.49, G:0.00, T:0.34
Consensus pattern (6 bp):
CTATCC
Found at i:1671127 original size:31 final size:31
Alignment explanation
Indices: 1671092--1671190 Score: 162
Period size: 31 Copynumber: 3.2 Consensus size: 31
1671082 TGGCAATCCA
*
1671092 GTCCCCTAATATTTAGTCTGTTTGCAAAATG
1 GTCCCCTAACATTTAGTCTGTTTGCAAAATG
* *
1671123 GTCCCTTAACATTTAGTCTATTTGCAAAATG
1 GTCCCCTAACATTTAGTCTGTTTGCAAAATG
*
1671154 GTCCCCTAACATTTAGTCTGTTTGCAATATG
1 GTCCCCTAACATTTAGTCTGTTTGCAAAATG
1671185 GTCCCC
1 GTCCCC
1671191 GACCGTTTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (31 bp):
GTCCCCTAACATTTAGTCTGTTTGCAAAATG
Found at i:1673844 original size:26 final size:26
Alignment explanation
Indices: 1673808--1673862 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
1673798 TTGTGGTAAC
1673808 TACAAATGTATTAAACTACTCAGTCA
1 TACAAATGTATTAAACTACTCAGTCA
*
1673834 TACAGATGTATTAAACTACTCAGTCA
1 TACAAATGTATTAAACTACTCAGTCA
1673860 TAC
1 TAC
1673863 CATAAAGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (26 bp):
TACAAATGTATTAAACTACTCAGTCA
Found at i:1676353 original size:30 final size:30
Alignment explanation
Indices: 1676317--1676379 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1676307 AACGGTCGGA
* *
1676317 GACCATATTACAAACAG-ACTAAATGTTGGG
1 GACCATATTACAAAC-GTACTAAATATTGAG
*
1676347 GACCATATTGCAAACGTACTAAATATTGAG
1 GACCATATTACAAACGTACTAAATATTGAG
1676377 GAC
1 GAC
1676380 TGTATTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (30 bp):
GACCATATTACAAACGTACTAAATATTGAG
Found at i:1676895 original size:22 final size:22
Alignment explanation
Indices: 1676869--1676913 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1676859 TGGTGATTTG
* *
1676869 AAAAAAAAATCAACTAAGTTTAT
1 AAAATAAAAT-AAATAAGTTTAT
*
1676892 AAAATGAAATAAATAAGTTTAT
1 AAAATAAAATAAATAAGTTTAT
1676914 TTGTATACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (22 bp):
AAAATAAAATAAATAAGTTTAT
Found at i:1680212 original size:31 final size:31
Alignment explanation
Indices: 1680177--1680244 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1680167 TTGCAATACA
1680177 GTCCCCCAACATTTAGTCTGTGTGCAAAATG
1 GTCCCCCAACATTTAGTCTGTGTGCAAAATG
* * * *
1680208 GTCCCCTAACATTTAGTTTGTTTGCAATATG
1 GTCCCCCAACATTTAGTCTGTGTGCAAAATG
1680239 GTCCCC
1 GTCCCC
1680245 GACCGTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCTGTGTGCAAAATG
Found at i:1682220 original size:31 final size:31
Alignment explanation
Indices: 1682185--1682261 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
1682175 TCAAATGGTC
*
1682185 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATATTG
** *
1682216 GGGGACCATATTATAAACGGACTAAATATTG
1 GGGGACCATATTGCAAACAGACTAAATATTG
**
1682247 GGGGACTGTATTGCA
1 GGGGACCATATTGCA
1682262 TGTTTTAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATATTG
Found at i:1688386 original size:20 final size:21
Alignment explanation
Indices: 1688348--1688392 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1688338 TAAATAAAAC
*
1688348 AAAATGAAAATAAAGATTA-A
1 AAAATGAAAATAAACATTATA
1688368 AAAAT-AAAATAAAACATTATA
1 AAAATGAAAAT-AAACATTATA
1688389 AAAA
1 AAAA
1688393 ATACCATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 12 0.55
21 5 0.23
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAATGAAAATAAACATTATA
Found at i:1691031 original size:139 final size:139
Alignment explanation
Indices: 1690799--1691374 Score: 695
Period size: 139 Copynumber: 4.2 Consensus size: 139
1690789 TACTCCTTCA
* * ** * *
1690799 CGTTGAGAAGATCTGGTCAGTGGATGACATTGTTCTTACGTGATGAGGATGTCTAGCCATCTTTA
1 CGTTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTA
** * * * * *
1690864 GGGATGGTTTGGAGAAAACAAGGTTCCTACGTGATGAGGAAGTCTGGTAATCTAAGGATGACGTT
66 GGGATAATTTGGAGACAACATGATTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGTT
1690929 GCTCCTACG
131 GCTCCTACG
* * * * * * *
1690938 CGTTGAGGAGATCTGGTCGATGAACAATATTTTTCCTACGTGATAAGGATGTCTAGCCATATTTA
1 CGTTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTA
* * * * **
1691003 GGGATACTTTGGAGACAACACGATTCCTATGTGATGAGGAAGTCTGGTTATATGA-GATGACACT
66 GGGATAATTTGGAGACAACATGATTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGTT
* *
1691067 ACTTCTACG
131 GCTCCTACG
* * * * *
1691076 CGTTGAGGAGATTTGATCGGTGGACAACATTGTTCTTACGTGATGAGGACATCTAGCCGTCTTTA
1 CGTTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTA
* * *
1691141 GGGATAATTTGGAGACAACATGGTTCATACGTGATGAGGAAGTTTGGTTATCTGAGGATGACGTT
66 GGGATAATTTGGAGACAACATGATTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGTT
1691206 GCTCCTACG
131 GCTCCTACG
* * * * ***
1691215 CATTGAGGATATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGAACGTCTAGTTGTCTTTA
1 CGTTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTA
* * * *
1691280 GGGATAATTTGGAGACAACATTATTCCTACGTGATGAGGAAGTTTGATTGTCTGAGGATGACGTT
66 GGGATAATTTGGAGACAACATGATTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGTT
*
1691345 GCTCATACG
131 GCTCCTACG
* *
1691354 TGTTGAGGAGATCTTGTCGGT
1 CGTTGAGGAGATCTGGTCGGT
1691375 TGCCAATGAT
Statistics
Matches: 369, Mismatches: 67, Indels: 2
0.84 0.15 0.00
Matches are distributed among these distances:
138 115 0.31
139 254 0.69
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (139 bp):
CGTTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTA
GGGATAATTTGGAGACAACATGATTCCTACGTGATGAGGAAGTCTGGTTATCTGAGGATGACGTT
GCTCCTACG
Found at i:1691282 original size:277 final size:277
Alignment explanation
Indices: 1690781--1691322 Score: 742
Period size: 277 Copynumber: 2.0 Consensus size: 277
1690771 GTTGTCTGAT
* * **
1690781 GATGACACTACTCCTTCACGTTGAGAAGATCTGGTCAGTGGATGACATTGTTCTTACGTGATGAG
1 GATGACACTACTCCTACACGTTGAGAAGATCTGATCAGTGGACAACATTGTTCTTACGTGATGAG
** ** *
1690846 GATGTCTAGCCATCTTTAGGGATGGTTTGGAGAAAACAAGGTTCCTACGTGATGAGGAAGTCTGG
66 GACATCTAGCCATCTTTAGGGATAATTTGGAGAAAACAAGGTTCATACGTGATGAGGAAGTCTGG
* * *
1690911 TAATCTAAGGATGACGTTGCTCCTACGCGTTGAGGAGATCTGGTCGATGAACAATATTTTTCCTA
131 TAATCTAAGGATGACGTTGCTCCTACGCATTGAGGAGATCTGGTCGATGAACAACATTGTTCCTA
* * * *
1690976 CGTGATAAGGATGTCTAGCCATATTTAGGGATACTTTGGAGACAACACGATTCCTATGTGATGAG
196 CGTGATAAGAACGTCTAGCCATATTTAGGGATAATTTGGAGACAACACGATTCCTACGTGATGAG
1691041 GAAGTCTGGTTATATGA
261 GAAGTCTGGTTATATGA
* * * * *
1691058 GATGACACTACTTCTACGCGTTGAGGAGATTTGATCGGTGGACAACATTGTTCTTACGTGATGAG
1 GATGACACTACTCCTACACGTTGAGAAGATCTGATCAGTGGACAACATTGTTCTTACGTGATGAG
* * * *
1691123 GACATCTAGCCGTCTTTAGGGATAATTTGGAGACAACATGGTTCATACGTGATGAGGAAGTTTGG
66 GACATCTAGCCATCTTTAGGGATAATTTGGAGAAAACAAGGTTCATACGTGATGAGGAAGTCTGG
* * * * * *
1691188 TTATCTGAGGATGACGTTGCTCCTACGCATTGAGGATATCTGGTCGGTGGACGACATTGTTCCTA
131 TAATCTAAGGATGACGTTGCTCCTACGCATTGAGGAGATCTGGTCGATGAACAACATTGTTCCTA
* *** * **
1691253 CGTGATGAGAACGTCTAGTTGTCTTTAGGGATAATTTGGAGACAACATTATTCCTACGTGATGAG
196 CGTGATAAGAACGTCTAGCCATATTTAGGGATAATTTGGAGACAACACGATTCCTACGTGATGAG
1691318 GAAGT
261 GAAGT
1691323 TTGATTGTCT
Statistics
Matches: 227, Mismatches: 38, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
277 227 1.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (277 bp):
GATGACACTACTCCTACACGTTGAGAAGATCTGATCAGTGGACAACATTGTTCTTACGTGATGAG
GACATCTAGCCATCTTTAGGGATAATTTGGAGAAAACAAGGTTCATACGTGATGAGGAAGTCTGG
TAATCTAAGGATGACGTTGCTCCTACGCATTGAGGAGATCTGGTCGATGAACAACATTGTTCCTA
CGTGATAAGAACGTCTAGCCATATTTAGGGATAATTTGGAGACAACACGATTCCTACGTGATGAG
GAAGTCTGGTTATATGA
Found at i:1691621 original size:67 final size:67
Alignment explanation
Indices: 1691556--1691768 Score: 202
Period size: 67 Copynumber: 3.2 Consensus size: 67
1691546 CGTTTCAAAA
*
1691556 TTTATGTTTCAAG-GAAAATATGACTCAAGCT-AGACGAAAA-TTTGTTTCGAAAGAAACAATGT
1 TTTATGTTTCAAGAG-AAAT-TGACTCAAG-TGAGA-GAAAACTTTGTTTCGAAAGAAACAATCT
1691618 CAAAGG
62 CAAAGG
* * * **
1691624 TTTTTGTTTCAAGAGAAATTGTCTCAAGTGAGATAAAACTTTGTTTCGAGCGAAACAATCTCAAA
1 TTTATGTTTCAAGAGAAATTGACTCAAGTGAGAGAAAACTTTGTTTCGAAAGAAACAATCTCAAA
1691689 GG
66 GG
* * * * * * * * *
1691691 TTTATGTTTTAAAAGAAATTGTCTCAA-TCA-AGATGAATTTTTTTTGGAGAGAAACAATCTCAA
1 TTTATGTTTCAAGAGAAATTGACTCAAGTGAGAGA-AAACTTTGTTTCGAAAGAAACAATCTCAA
1691754 AGG
65 AGG
*
1691757 TATATGTTTCAA
1 TTTATGTTTCAA
1691769 AATAAACTGT
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
65 2 0.02
66 44 0.36
67 60 0.49
68 16 0.13
69 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (67 bp):
TTTATGTTTCAAGAGAAATTGACTCAAGTGAGAGAAAACTTTGTTTCGAAAGAAACAATCTCAAA
GG
Found at i:1691744 original size:133 final size:132
Alignment explanation
Indices: 1691492--1691801 Score: 313
Period size: 133 Copynumber: 2.3 Consensus size: 132
1691482 GTGGAAGGAA
* * * * * * *
1691492 ATTTGTTTCAAGAGAAGCTATCTCAGGTGAGATAAAATTTTGTTTTGAGTGAAACGTTTCAAAAT
1 ATTTGTTTCAAGAGAAACTGTCTCAAGTGAGATAAAA-TTTGTTTCGAGCGAAACATCTCAAAAT
* * * *
1691557 TTATGTTTCAAGGAAAATATGACTCAAGCTAGACGAAAATTTGTTTCGAAAGAAACAATGTCAAA
65 TTATGTTTAAAAGAAAATATGACTCAAGCAAGACGAAAATTTGTTTCGAAAGAAACAATCTCAAA
1691622 GGT
130 GGT
* *
1691625 TTTTGTTTCAAGAGAAATTGTCTCAAGTGAGATAAAACTTTGTTTCGAGCGAAACAATCTCAAAG
1 ATTTGTTTCAAGAGAAACTGTCTCAAGTGAGATAAAA-TTTGTTTCGAGCGAAAC-ATCTCAAA-
* * * * * * * *
1691690 GTTTATGTTTTAAAAG-AAAT-TGTCTCAATCAAGATG-AATTTTTTTTGGAGAGAAACAATCTC
63 ATTTATG-TTTAAAAGAAAATATGACTCAAGCAAGACGAAAATTTGTTTCGAAAGAAACAATCTC
1691752 AAAGGT
127 AAAGGT
* * * *
1691758 ATATGTTTCAAAATAAACTGTCTCAA-TCGAGACAAAATTTGTTT
1 ATTTGTTTCAAGAGAAACTGTCTCAAGT-GAGATAAAATTTGTTT
1691802 TTAGGAAAAT
Statistics
Matches: 145, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
132 8 0.06
133 103 0.71
134 18 0.12
135 10 0.07
136 6 0.04
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (132 bp):
ATTTGTTTCAAGAGAAACTGTCTCAAGTGAGATAAAATTTGTTTCGAGCGAAACATCTCAAAATT
TATGTTTAAAAGAAAATATGACTCAAGCAAGACGAAAATTTGTTTCGAAAGAAACAATCTCAAAG
GT
Found at i:1691763 original size:66 final size:67
Alignment explanation
Indices: 1691592--1691801 Score: 239
Period size: 66 Copynumber: 3.2 Consensus size: 67
1691582 AAGCTAGACG
* * * * *
1691592 AAAA-TTTGTTTCGAAAGAAACAATGTCAAAGGTTTTTGTTTCAAGAGAAATTGTCTCAAGT-GA
1 AAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAATTGTCTCAA-TCAA
1691655 GAT
65 GAT
* *
1691658 AAAACTTTGTTTCGAGCGAAACAATCTCAAAGGTTTATGTTTTAAAAGAAATTGTCTCAATCAAG
1 AAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAATTGTCTCAATCAAG
1691723 AT
66 AT
* * * * * * * *
1691725 -GAATTTTTTTTGGAGAGAAACAATCTCAAAGGTATATGTTTCAAAATAAACTGTCTCAATCGAG
1 AAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAATTGTCTCAATCAAG
*
1691789 AC
66 AT
1691791 AAAA-TTTGTTT
1 AAAACTTTGTTT
1691802 TTAGGAAAAT
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
66 66 0.55
67 55 0.45
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (67 bp):
AAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAATTGTCTCAATCAAG
AT
Found at i:1692211 original size:67 final size:67
Alignment explanation
Indices: 1692085--1692312 Score: 243
Period size: 67 Copynumber: 3.4 Consensus size: 67
1692075 CTTAAGGAAG
* * ** * * *
1692085 ACTGTCTCAAGTGAGACAAAATTTGTTTTCAA-A-AAATAAATCTCAAAGGCTTATATTTCAAAA
1 ACTGTCTCAACTGAGATAAAATTTG-TTTCAAGAGAAACGATTCTCAAAGGTTTATATTTCAAGA
1692148 GAA
65 GAA
* * ** *
1692151 AATGTCTCAACTGAGATGAAATTTTGTTTGGAGAGAAAC-ATTCTCAAAGGTTTATGTTTCAAGA
1 ACTGTCTCAACTGAGAT-AAAATTTGTTTCAAGAGAAACGATTCTCAAAGGTTTATATTTCAAGA
1692215 GAA
65 GAA
* *
1692218 ACTGTCTCAAGC-GAGACAAAACTTTGTTTCAAGATAAACGATT-TCAAAGGTTTATATTTCAAG
1 ACTGTCTCAA-CTGAGATAAAA-TTTGTTTCAAGAGAAACGATTCTCAAAGGTTTATATTTCAAG
1692281 AGAA
64 AGAA
1692285 ACTGTCTCAA-TCGAGATAAAATTTGTTT
1 ACTGTCTCAACT-GAGATAAAATTTGTTT
1692313 TTAGGAAAAC
Statistics
Matches: 135, Mismatches: 19, Indels: 16
0.79 0.11 0.09
Matches are distributed among these distances:
66 28 0.21
67 100 0.74
68 7 0.05
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (67 bp):
ACTGTCTCAACTGAGATAAAATTTGTTTCAAGAGAAACGATTCTCAAAGGTTTATATTTCAAGAG
AA
Found at i:1692460 original size:167 final size:167
Alignment explanation
Indices: 1692216--1692517 Score: 441
Period size: 167 Copynumber: 1.8 Consensus size: 167
1692206 GTTTCAAGAG
* * * * *
1692216 AAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGATAAACGATTTCAAAGGTTTATATTTCAAG
1 AAACTGTCTCAAGCAAGACAAAACTATGTTTCAAGAGAAACGATCTCAAAGGTTTATATTTCAAA
*
1692281 AGAAACTGTCTC-AATCGAGATAAAATTTGTTTTTAGGAAAACT-ATCTCAAGTGAGATCAATTT
66 AGAAACTGTCTCAAAT-GAGACAAAA-TT-TTTTTAGGAAAA-TAATCTCAAGTGAGATCAATTT
1692344 TGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTTGAGGGA
127 TGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTTGAGGGA
* * *
1692385 AAACTGTCTCAAGCAAGACGAAACTAT-TTT-GAGAGAAACGATCTCAAAGGTTTATGTTTCAAA
1 AAACTGTCTCAAGCAAGACAAAACTATGTTTCAAGAGAAACGATCTCAAAGGTTTATATTTCAAA
* *
1692448 AGAAATTGTCTCAAATGAGACAAAATTTTTTTAGGAAAATAATCTCAAGTTAGATCAATTTTGTT
66 AGAAACTGTCTCAAATGAGACAAAATTTTTTTAGGAAAATAATCTCAAGTGAGATCAATTTTGTT
1692513 TCAAG
131 TCAAG
1692518 AAAAACTGTC
Statistics
Matches: 120, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
164 1 0.01
165 40 0.33
166 2 0.02
167 47 0.39
168 6 0.05
169 24 0.20
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (167 bp):
AAACTGTCTCAAGCAAGACAAAACTATGTTTCAAGAGAAACGATCTCAAAGGTTTATATTTCAAA
AGAAACTGTCTCAAATGAGACAAAATTTTTTTAGGAAAATAATCTCAAGTGAGATCAATTTTGTT
TCAAGTGAAACAATTTCAAAATTTGTGTTTTGAGGGA
Found at i:1696590 original size:29 final size:30
Alignment explanation
Indices: 1696532--1696590 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 30
1696522 GACTATATTT
1696532 AATTTGTTATTGTAACGAAATAAATTTATTAC
1 AATTTGTTATTGT-A-GAAATAAATTTATTAC
*
1696564 AATTTGTTATTGT-GAAATAATTTTATT
1 AATTTGTTATTGTAGAAATAAATTTATT
1696591 TCTAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.50
32 13 0.50
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.49
Consensus pattern (30 bp):
AATTTGTTATTGTAGAAATAAATTTATTAC
Found at i:1696760 original size:194 final size:198
Alignment explanation
Indices: 1696346--1696804 Score: 529
Period size: 194 Copynumber: 2.3 Consensus size: 198
1696336 TTTTTTTATG
* * * * * *
1696346 ACTAAATAATTTTGTTACAATTTGTTATTCTGAAAGAATAATACTTGTCACATTTTTTATATTGA
1 ACTAAATAAATTTGTTACAATTTGTTATTCTGAAA-AATATTATTTGTCATAATTTTTATATTAA
* * * * * ** *
1696411 GAAATTAATATTTTTTTATAAATTGTTATTTTGATTAAATAAATTTATCACAATTTTTTTTATTT
65 GAAATTAATATTATGTTATAAATTGTTATTATGACTAAACAAATTTATCACAATAGTTGTTATTT
* * * * *
1696476 TGACAGAATATTGTGACGAAATAAATTTGACATAACATTTTGTTTTGACTATATTTAATTTGTTA
130 TGA-AGAATAATATGAAGAAATAAATTTGACATAACATTTTATTTTGACTAAATTTAATTTGTTA
1696541 TTGTA
194 TTGTA
* * * * * *
1696546 ACGAAATAAATTTATTACAATTTGTTATTGTGAAATAATTTTATTTCTAATAATTTTTATATTAA
1 ACTAAATAAATTTGTTACAATTTGTTATTCTGAAA-AATATTATTTGTCATAATTTTTATATTAA
*
1696611 GAAATTAATA-TATGTTATAAATTGTTATTATGACTAAACAAATTTGTCA-AA-AGTTGTTATTT
65 GAAATTAATATTATGTTATAAATTGTTATTATGACTAAACAAATTTATCACAATAGTTGTTATTT
*
1696673 TG-AGAA-AATATGAAGAAATAAATTTGACATAA-ATTTTTATTTTGATTAAATTT-A-TTGTAT
130 TGAAGAATAATATGAAGAAATAAATTTGACATAACA-TTTTATTTTGACTAAATTTAATTTGT-T
1696733 GATTGTA
193 -ATTGTA
* *
1696740 ACTAAATAAATTTGTTACAATTTGTTATTTTGAACAAATATTATTTGTCGTAATTTTTTATATTA
1 ACTAAATAAATTTGTTACAATTTGTTATTCTGAA-AAATATTATTTGTCATAA-TTTTTATATTA
1696805 TTTGTCTTAA
Statistics
Matches: 219, Mismatches: 35, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
192 4 0.02
193 3 0.01
194 89 0.41
195 16 0.07
197 10 0.05
198 2 0.01
199 33 0.15
200 62 0.28
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (198 bp):
ACTAAATAAATTTGTTACAATTTGTTATTCTGAAAAATATTATTTGTCATAATTTTTATATTAAG
AAATTAATATTATGTTATAAATTGTTATTATGACTAAACAAATTTATCACAATAGTTGTTATTTT
GAAGAATAATATGAAGAAATAAATTTGACATAACATTTTATTTTGACTAAATTTAATTTGTTATT
GTA
Found at i:1696804 original size:22 final size:22
Alignment explanation
Indices: 1696777--1696825 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1696767 TTTTGAACAA
1696777 ATATTATTTGTCGTAATTTTTT
1 ATATTATTTGTCGTAATTTTTT
*
1696799 ATATTATTTGTCTTAATTTTTT
1 ATATTATTTGTCGTAATTTTTT
1696821 ATATT
1 ATATT
1696826 GAGAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.65
Consensus pattern (22 bp):
ATATTATTTGTCGTAATTTTTT
Done.