Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008165.1 Hibiscus syriacus cultivar Beakdansim tig00110745_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: 2894944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1387207 original size:13 final size:13
Alignment explanation
Indices: 1387185--1387221 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1387175 TTACCATCAT
*
1387185 CGACCGCCACCGC
1 CGACCACCACCGC
*
1387198 TGACCACCACCGC
1 CGACCACCACCGC
1387211 CGACCACCACC
1 CGACCACCACC
1387222 CACGATGGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.22, C:0.59, G:0.16, T:0.03
Consensus pattern (13 bp):
CGACCACCACCGC
Found at i:1387857 original size:17 final size:17
Alignment explanation
Indices: 1387835--1387868 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1387825 CAAGTTTAGG
1387835 CCTGGAT-AAGGTCTGGA
1 CCTGGATCAA-GTCTGGA
1387852 CCTGGATCAAGTCTGGA
1 CCTGGATCAAGTCTGGA
1387869 TCGGGTCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (17 bp):
CCTGGATCAAGTCTGGA
Found at i:1388029 original size:3 final size:3
Alignment explanation
Indices: 1388023--1388096 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
1388013 TATTATTAGT
1388023 TAA TAA 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
1388071 TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1388097 AACGAGATAA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1391158 original size:27 final size:29
Alignment explanation
Indices: 1391109--1391165 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
1391099 TGATGATCTA
* *
1391109 TATTTTAATAATATATATTATGATATTAT
1 TATTTTAATAACATATATAATGATATTAT
1391138 TATTTTAATAACA-A-ATAATGATATTAT
1 TATTTTAATAACATATATAATGATATTAT
1391165 T
1 T
1391166 TACGTAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 13 0.50
28 1 0.04
29 12 0.46
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (29 bp):
TATTTTAATAACATATATAATGATATTAT
Found at i:1391267 original size:26 final size:25
Alignment explanation
Indices: 1391238--1391286 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1391228 TTTAATTATT
1391238 TTTCTTCAAAAATCAGTAAAATTTTG
1 TTTCTTCAAAAATCA-TAAAATTTTG
** *
1391264 TTTCTTTTAAAATCATCAAATTT
1 TTTCTTCAAAAATCATAAAATTT
1391287 AACATCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (25 bp):
TTTCTTCAAAAATCATAAAATTTTG
Found at i:1397536 original size:95 final size:95
Alignment explanation
Indices: 1397373--1397562 Score: 335
Period size: 95 Copynumber: 2.0 Consensus size: 95
1397363 ATAAAGACCA
* *
1397373 CATATCATTCCTTAAGAATCATATACATACACTAGGGATCAAGTATGTGTCTCACCAGACTTCAC
1 CATATCATTCCTTAAGAATCATATACATACACCAAGGATCAAGTATGTGTCTCACCAGACTTCAC
1397438 ACATGTTCCAAAGAATACATATATGTCCCG
66 ACATGTTCCAAAGAATACATATATGTCCCG
**
1397468 CATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCAC
1 CATATCATTCCTTAAGAATCATATACATACACCAAGGATCAAGTATGTGTCTCACCAGACTTCAC
*
1397533 ACATGTTCCAAAGAATATATATATGTCCCG
66 ACATGTTCCAAAGAATACATATATGTCCCG
1397563 AAGGACCACA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.29
Consensus pattern (95 bp):
CATATCATTCCTTAAGAATCATATACATACACCAAGGATCAAGTATGTGTCTCACCAGACTTCAC
ACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1403113 original size:23 final size:23
Alignment explanation
Indices: 1403087--1403164 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
1403077 CACCACAGCT
1403087 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
1403110 CATATAATTGCACCGGAGTGCCT
1 CATATAATTGCACCGAAGTGCCA
* * *
1403133 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
1403156 TATAATAAT
1 CAT-ATAAT
1403165 GTCCATAATG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1403343 original size:103 final size:103
Alignment explanation
Indices: 1403174--1403388 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
1403164 TGTCCATAAT
* * * *
1403174 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCCGAC
1 GACCACATATCATTCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
1403239 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
* *
1403277 GACCACATATCATTTATTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
1403342 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
1403380 GACCACATA
1 GACCACATA
1403389 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:1404323 original size:64 final size:64
Alignment explanation
Indices: 1404170--1404327 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
1404160 ATTCCCTACC
* * * * ** *
1404170 GATGAATCGATGCACTACTTGTGCATCGGTGCACAAAATACATTCGATGTTTGTTTATTACTGG
1 GATGCATCGATGCACTACCTGTGCATCGATGCACAAAATACATTCGATGTTTGTTGATTAAAGA
* * * * *
1404234 GATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTT-TTAGATTAAA-
1 GATGCATCGATGCACTACC-TGTGCATCGATGCACAAAATACATTCGATGTTTGTT-GATTAAAG
1404296 A
64 A
1404297 GAGTGCATCGATGCACTACCTGTGCATCGAT
1 GA-TGCATCGATGCACTACCTGTGCATCGAT
1404328 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
63 6 0.08
64 67 0.88
65 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (64 bp):
GATGCATCGATGCACTACCTGTGCATCGATGCACAAAATACATTCGATGTTTGTTGATTAAAGA
Found at i:1406286 original size:29 final size:29
Alignment explanation
Indices: 1406240--1406299 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
1406230 GTATGCAATA
* * *
1406240 TGCATTCGAAGGTTCCTCGTAGATAAATT
1 TGCACTCGAAAGTACCTCGTAGATAAATT
*
1406269 TGCACTCGAAAGTACCTCGTAGATAACTT
1 TGCACTCGAAAGTACCTCGTAGATAAATT
1406298 TG
1 TG
1406300 TACTATATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (29 bp):
TGCACTCGAAAGTACCTCGTAGATAAATT
Found at i:1407559 original size:17 final size:17
Alignment explanation
Indices: 1407537--1407569 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1407527 GCAATCTCAG
1407537 TCAATTCCATA-TCAATT
1 TCAATT-CATATTCAATT
1407554 TCAATTCATATTCAAT
1 TCAATTCATATTCAAT
1407570 CTTTACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
TCAATTCATATTCAATT
Found at i:1408504 original size:29 final size:30
Alignment explanation
Indices: 1408445--1408506 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1408435 TTTTCGGTCC
**
1408445 CTAAACTTTCACAAATTTATACTTTGGTCA
1 CTAAACTTTCACAAATTTATACTTTAATCA
*
1408475 CTAAACTTTCA-AAATTT-TCATTTTAATCA
1 CTAAACTTTCACAAATTTAT-ACTTTAATCA
1408504 CTA
1 CTA
1408507 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 16 0.57
30 11 0.39
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.42
Consensus pattern (30 bp):
CTAAACTTTCACAAATTTATACTTTAATCA
Found at i:1409820 original size:3 final size:3
Alignment explanation
Indices: 1409812--1409858 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1409802 TAAAAATGGG
1409812 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1409859 TATTATTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1409863 original size:3 final size:3
Alignment explanation
Indices: 1409857--1409891 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1409847 AATAATAATA
1409857 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1409892 ATTTCCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1417159 original size:26 final size:26
Alignment explanation
Indices: 1417071--1417159 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
1417061 AGTGAGAACA
*
1417071 AGTATTTAATTTAAACTAAACTACTT
1 AGTAGTTAATTTAAACTAAACTACTT
* * *
1417097 AGTAGTT-ATCCTT-ATCTATCTAACTTTCTA
1 AGTAGTTAAT--TTAAACTA---AAC-TACTT
1417127 AGT-GTTAATTTAAACTAAACTACTT
1 AGTAGTTAATTTAAACTAAACTACTT
1417152 AGTAGTTA
1 AGTAGTTA
1417160 TCTTTATCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 18
0.65 0.10 0.25
Matches are distributed among these distances:
25 8 0.17
26 17 0.36
27 2 0.04
28 2 0.04
29 10 0.21
30 8 0.17
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (26 bp):
AGTAGTTAATTTAAACTAAACTACTT
Found at i:1417160 original size:55 final size:55
Alignment explanation
Indices: 1417076--1417223 Score: 187
Period size: 55 Copynumber: 2.7 Consensus size: 55
1417066 GAACAAGTAT
*
1417076 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTATCTAACTTTCTAAGTG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTATCTAACTTTCTAAGAG
1417131 TTAATTTAAACTAAACTACTTAGTAGTTAT-C-T-T-TATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTATCTAACTTTCTAAGAG
* * * * * * *
1417182 TTAGTGTTATATTAAAATACTAATTAATTATCCTTATCTATC
1 TTAAT-TTAAACTAAACTACTTAGTAGTTATCCTTATCTATC
1417224 ACATAACCTA
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
51 21 0.26
52 20 0.25
53 2 0.03
54 2 0.03
55 31 0.39
56 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (55 bp):
TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTATCTAACTTTCTAAGAG
Found at i:1417170 original size:26 final size:26
Alignment explanation
Indices: 1417086--1417170 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
1417076 TTAATTTAAA
*
1417086 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTATCTTTAT
* * * *
1417112 CTATCTAACTTTCTAAGT-GTTAAT-TTAAA
1 CTA---AAC-TACTTAGTAGTT-ATCTTTAT
1417141 CTAAACTACTTAGTAGTTATCTTTAT
1 CTAAACTACTTAGTAGTTATCTTTAT
1417167 CTAA
1 CTAA
1417171 CTTTCTAAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
25 8 0.19
26 16 0.37
29 11 0.26
30 8 0.19
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (26 bp):
CTAAACTACTTAGTAGTTATCTTTAT
Found at i:1421128 original size:55 final size:51
Alignment explanation
Indices: 1421044--1421152 Score: 173
Period size: 55 Copynumber: 2.1 Consensus size: 51
1421034 GAACAAGTAT
1421044 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTAT-C-T-T-TATCTAACTTTCTAAGAG
*
1421099 TTAATTTAAACTAAACTACTTGGTAGTTATCTTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTAACTTTCTAAGAG
1421150 TTA
1 TTA
1421153 GTGTTATATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
51 21 0.40
52 1 0.02
53 1 0.02
54 1 0.02
55 29 0.55
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (51 bp):
TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTAACTTTCTAAGAG
Found at i:1428809 original size:30 final size:30
Alignment explanation
Indices: 1428773--1428832 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1428763 CAACCACCTT
* *
1428773 TTGTTTACTCTCTATGGTCAATCTTGATGG
1 TTGTTTACTCTCTATGCTCAAACTTGATGG
1428803 TTGTTTACTCTCTATGCTCAAACTTGATGG
1 TTGTTTACTCTCTATGCTCAAACTTGATGG
1428833 CTCTTCGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (30 bp):
TTGTTTACTCTCTATGCTCAAACTTGATGG
Found at i:1431263 original size:2 final size:2
Alignment explanation
Indices: 1431258--1431282 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1431248 AAAAAACCAA
1431258 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1431283 TGATGTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1432233 original size:108 final size:109
Alignment explanation
Indices: 1432106--1432326 Score: 435
Period size: 108 Copynumber: 2.0 Consensus size: 109
1432096 TATGGCACCT
1432106 AAAAACCACACGTGTTGTCTCAGAGTGAAAATGAGCTTCAAACAAAAAGTCCTCATTCAAACCTC
1 AAAAACCACACGTGTTGTCTCAGAGTGAAAATGAGCTTCAAACAAAAAGTCCTCATTCAAACCTC
1432171 TTTCATGAATTTCATCCACTAGCAACTGACTTTCTTGAGAAAAA
66 TTTCATGAATTTCATCCACTAGCAACTGACTTTCTTGAGAAAAA
1432215 AAAAACCACACG-GTTGTCTCAGAGTGAAAATGAGCTTCAAACAAAAAGTCCTCATTCAAACCTC
1 AAAAACCACACGTGTTGTCTCAGAGTGAAAATGAGCTTCAAACAAAAAGTCCTCATTCAAACCTC
1432279 TTTCATGAATTTCATCCACTAGCAACTGACTTTCTTGAGAAAAA
66 TTTCATGAATTTCATCCACTAGCAACTGACTTTCTTGAGAAAAA
1432323 AAAA
1 AAAA
1432327 CTAGAACTCA
Statistics
Matches: 112, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 100 0.89
109 12 0.11
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (109 bp):
AAAAACCACACGTGTTGTCTCAGAGTGAAAATGAGCTTCAAACAAAAAGTCCTCATTCAAACCTC
TTTCATGAATTTCATCCACTAGCAACTGACTTTCTTGAGAAAAA
Found at i:1433704 original size:15 final size:15
Alignment explanation
Indices: 1433684--1433713 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1433674 CAAATTATGT
1433684 CTCTAAATTAGGAAA
1 CTCTAAATTAGGAAA
*
1433699 CTCTAACTTAGGAAA
1 CTCTAAATTAGGAAA
1433714 GATACTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (15 bp):
CTCTAAATTAGGAAA
Found at i:1442340 original size:21 final size:21
Alignment explanation
Indices: 1442312--1442362 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1442302 GCTTCCCTTG
1442312 TCTT-ATTCTCCATCATCTTT
1 TCTTCATTCTCCATCATCTTT
1442332 TCTTCATTCTCCATCATCTTT
1 TCTTCATTCTCCATCATCTTT
1442353 TCTTCATTCT
1 TCTTCATTCT
1442363 TTTCTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.55
Consensus pattern (21 bp):
TCTTCATTCTCCATCATCTTT
Found at i:1443627 original size:43 final size:43
Alignment explanation
Indices: 1443580--1443662 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
1443570 AATAGGTAAC
** *
1443580 GATATATAGTGGTGTTTGTTCA-ACAAACGCCGCAATAGGTGTT
1 GATATATAGTGACGTTTG-TAAGACAAACGCCGCAATAGGTGTT
* *
1443623 GATATTTAGTGACGTTTGTAAGACAAACGCCGTAATAGGT
1 GATATATAGTGACGTTTGTAAGACAAACGCCGCAATAGGT
1443663 TTAGATGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 32 0.94
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (43 bp):
GATATATAGTGACGTTTGTAAGACAAACGCCGCAATAGGTGTT
Found at i:1443729 original size:18 final size:18
Alignment explanation
Indices: 1443706--1443743 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1443696 GTAATAAGGG
1443706 TTGAGATTTAGCGGCGTT
1 TTGAGATTTAGCGGCGTT
1443724 TTGAGATTTAGCGGCGTT
1 TTGAGATTTAGCGGCGTT
1443742 TT
1 TT
1443744 TATCACAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.42
Consensus pattern (18 bp):
TTGAGATTTAGCGGCGTT
Found at i:1443819 original size:42 final size:42
Alignment explanation
Indices: 1443758--1443838 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
1443748 ACAAACGACA
1443758 AACGCCGCAATAAGCGTTGAGATTTAGCGACATTTTTCTCAC
1 AACGCCGCAATAAGCGTTGAGATTTAGCGACATTTTTCTCAC
* * *
1443800 AACGCCGCAATAAGTGTTGAGATTTCGCGACGTTTTTCT
1 AACGCCGCAATAAGCGTTGAGATTTAGCGACATTTTTCT
1443839 GATACAACGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
AACGCCGCAATAAGCGTTGAGATTTAGCGACATTTTTCTCAC
Found at i:1444329 original size:21 final size:21
Alignment explanation
Indices: 1444265--1444373 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
1444255 TGATATGCTA
* *
1444265 CTTCTCTCTGTGATGCCGCTG
1 CTTCTCTCTCTGATTCCGCTG
* *
1444286 CATCTCTCTGTG-TTACCGCTG
1 CTTCTCTCTCTGATT-CCGCTG
* *
1444307 CTTCTCTCTCTGCTTCCGTTG
1 CTTCTCTCTCTGATTCCGCTG
* ** *
1444328 CTGCTCTGGCTGCTTCCGCTG
1 CTTCTCTCTCTGATTCCGCTG
* *
1444349 CTACTCTCTTTGATTCC-CTTG
1 CTTCTCTCTCTGATTCCGC-TG
1444370 CTTC
1 CTTC
1444374 ATTTTCGCTT
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
20 2 0.03
21 66 0.94
22 2 0.03
ACGTcount: A:0.05, C:0.36, G:0.18, T:0.41
Consensus pattern (21 bp):
CTTCTCTCTCTGATTCCGCTG
Found at i:1450382 original size:83 final size:82
Alignment explanation
Indices: 1450179--1450389 Score: 246
Period size: 82 Copynumber: 2.6 Consensus size: 82
1450169 ACGTTTACTT
* * **
1450179 AACAAACACCACTATAGATTACACCTATTGC-AGCGTTTGTACAAAAATGCCACTAATGTATAAA
1 AACAAACGCCACTATAGATTACACCTATTGCGA-CGTTTGTACAAAAACGCCACTAAAATATAAA
* *
1450243 TATTTGCGGTGTTTGTTG
65 TATTTACGGCGTTTGTTG
* * * * *
1450261 AAAAAATGCCACTATAGATTAGACCTATTGTGACGTTTGTGCAAAAACGCCACTAAAATATAAAT
1 AACAAACGCCACTATAGATTACACCTATTGCGACGTTTGTACAAAAACGCCACTAAAATATAAAT
1450326 ATTTTACGGCGTTTGTT-
66 A-TTTACGGCGTTTGTTG
* * * *
1450343 ATTCAAACGCCACTATAGATTACACCTATTACGATGTTTGTATAAAA
1 A-ACAAACGCCACTATAGATTACACCTATTGCGACGTTTGTACAAAA
1450390 CGCAGGAAAA
Statistics
Matches: 106, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
82 56 0.53
83 50 0.47
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (82 bp):
AACAAACGCCACTATAGATTACACCTATTGCGACGTTTGTACAAAAACGCCACTAAAATATAAAT
ATTTACGGCGTTTGTTG
Found at i:1452136 original size:83 final size:82
Alignment explanation
Indices: 1451814--1452145 Score: 255
Period size: 83 Copynumber: 4.0 Consensus size: 82
1451804 GTACATGTTT
* * * * *
1451814 TTGTGACATTT-TT-ATAAAAACGCCACTATAAACAACATATTGC-AGCATTTGTGCTACAAACG
1 TTGTGACATTTATTGA-AAAAACGCCACTATAAACAACCTATTACGA-CGTTTGAGCTATAAACG
* * *
1451876 CCACTAAAATATTACTCTA
64 CCGCTAAATTACTACTCTA
* * * * * **
1451895 TTATGACATTTTTTGCATAAACGCCACTATAAACAACCCTATTACGATGTTTG-TTTGATAAACG
1 TTGTGACATTTATTGAAAAAACGCCACTATAAACAA-CCTATTACGACGTTTGAGCT-ATAAACG
* *
1451959 TCGCTAAATTACTTCTCTA
64 CCGCTAAATTACTACTCTA
* * * * * * * * *
1451978 TAGTGTCGTTTGTTGAACAAATGCCACTATAAAATAACCATATTACGATGTTTGTA-C-AAAAAC
1 TTGTGACATTTATTGAAAAAACGCCACTAT-AAACAACC-TATTACGACGTTTG-AGCTATAAAC
* *
1452041 ACCGCTACATTACTACTCTA
63 GCCGCTAAATTACTACTCTA
*
1452061 TTGTGGCATTTATTGAAAAAACGCCACTATAAACAACTCTATT-CTGACGTTTGAGCTATAAACG
1 TTGTGACATTTATTGAAAAAACGCCACTATAAACAAC-CTATTAC-GACGTTTGAGCTATAAACG
* *
1452125 CTGCTAAATTACCACTCTA
64 CCGCTAAATTACTACTCTA
1452144 TT
1 TT
1452146 AAGATGTTTG
Statistics
Matches: 195, Mismatches: 43, Indels: 24
0.74 0.16 0.09
Matches are distributed among these distances:
81 12 0.06
82 40 0.21
83 123 0.63
84 20 0.10
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (82 bp):
TTGTGACATTTATTGAAAAAACGCCACTATAAACAACCTATTACGACGTTTGAGCTATAAACGCC
GCTAAATTACTACTCTA
Found at i:1452769 original size:21 final size:20
Alignment explanation
Indices: 1452745--1452797 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1452735 ATAATACCTC
*
1452745 AGTATTAATACTGG-CCCTCTG
1 AGTATTGATACTGGACCC-C-G
*
1452766 AGTATCGATACTGGACCCCG
1 AGTATTGATACTGGACCCCG
1452786 AGTATTGATACT
1 AGTATTGATACT
1452798 CCTTGAAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.43
21 13 0.46
22 3 0.11
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (20 bp):
AGTATTGATACTGGACCCCG
Found at i:1452790 original size:20 final size:21
Alignment explanation
Indices: 1452752--1452797 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1452742 CTCAGTATTA
1452752 ATACTGGCCCTCTGAGTATCG
1 ATACTGGCCCTCTGAGTATCG
*
1452773 ATACTGGACCC-C-GAGTATTG
1 ATACTGG-CCCTCTGAGTATCG
1452793 ATACT
1 ATACT
1452798 CCTTGAAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
21 8 0.35
22 3 0.13
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (21 bp):
ATACTGGCCCTCTGAGTATCG
Found at i:1456993 original size:23 final size:22
Alignment explanation
Indices: 1456917--1457022 Score: 90
Period size: 23 Copynumber: 4.7 Consensus size: 22
1456907 ATAAATTGCA
1456917 CCGAAGTG-CCACATA-TTTGTC
1 CCGAAG-GACCACATAGTTTGTC
* * *
1456938 CCGACGGACCACATAAGATTATC
1 CCGAAGGACCACAT-AGTTTGTC
*
1456961 CCGAATGACCACATAGTTTTGTC
1 CCGAAGGACCACATAG-TTTGTC
* * *
1456984 CTGAAGGACCAAATAGCTTTTTC
1 CCGAAGGACCACATAG-TTTGTC
*
1457007 CTGAAGGACCACATAG
1 CCGAAGGACCACATAG
1457023 AACCCTCAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.01
21 11 0.16
22 3 0.04
23 53 0.78
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (22 bp):
CCGAAGGACCACATAGTTTGTC
Found at i:1460308 original size:23 final size:24
Alignment explanation
Indices: 1460282--1460336 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
1460272 TGTCCCAACA
1460282 GACCACATAAG-ATTGTCCCGAAG
1 GACCACATAAGTATTGTCCCGAAG
* *
1460305 GACCCCAT-AGTTTTGTCCCGAAG
1 GACCACATAAGTATTGTCCCGAAG
1460328 GACCACATA
1 GACCACATA
1460337 TAACCATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (24 bp):
GACCACATAAGTATTGTCCCGAAG
Found at i:1460940 original size:18 final size:17
Alignment explanation
Indices: 1460914--1460947 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1460904 ACTCTTTTAT
1460914 GGTACCGATACACATTTC
1 GGTACCGATAC-CATTTC
*
1460932 GGTATCGATACCATTT
1 GGTACCGATACCATTT
1460948 TGCCATTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (17 bp):
GGTACCGATACCATTTC
Found at i:1464827 original size:22 final size:22
Alignment explanation
Indices: 1464799--1464847 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1464789 GTGTTTTTTT
1464799 GCTTTCGAATACAAAAATAATA
1 GCTTTCGAATACAAAAATAATA
** *
1464821 GCTTTCGAATATGATAATAATA
1 GCTTTCGAATACAAAAATAATA
1464843 GCTTT
1 GCTTT
1464848 TCAAAACGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
GCTTTCGAATACAAAAATAATA
Found at i:1470853 original size:44 final size:44
Alignment explanation
Indices: 1470788--1471048 Score: 301
Period size: 44 Copynumber: 6.0 Consensus size: 44
1470778 TTTAACAAAC
* * *
1470788 GCCGCTATATAGCA-ACCTTTAGCAGCGTTTGTATTCTAAAAAT
1 GCCGCTATATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAAT
* *
1470831 GCCGCTATCTACCAGACCTTTAGCGACGTTTGTATCCTAAAAAT
1 GCCGCTATATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAAT
* * * * ** *
1470875 TCCGCTATATACCAGATCTTTAGTGGCATTTGTATTATAAAAAC
1 GCCGCTATATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAAT
* * * * * *
1470919 GCCGCTATAAACCAGACCTTTAGCGGTGTTTATATACTGAAAAC
1 GCCGCTATATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAAT
* *
1470963 GCCTCTATATACCAAACCTTTAGCGGCGTTTGTATCCTAAAAAT
1 GCCGCTATATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAAT
** *
1471007 GTTGTTATATACCAGACCTTTAGCGGCGTTTGTATCC-AAAAA
1 GCCGCTATATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAA
1471049 CACCGCTAAA
Statistics
Matches: 180, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
43 17 0.09
44 163 0.91
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (44 bp):
GCCGCTATATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAAT
Found at i:1470982 original size:132 final size:131
Alignment explanation
Indices: 1470784--1471041 Score: 338
Period size: 132 Copynumber: 2.0 Consensus size: 131
1470774 TTTTTTTAAC
* * * * * * *
1470784 AAACGCCGCTATATAGCAACCTTTAGCAGCGTTTGTATTCTAAAAATGCCGCTATCTACCAGACC
1 AAACGCCGCTATAAACCAACCTTTAGCAGCGTTTATATACTAAAAACGCCGCTATATACCAAACC
* *
1470849 TTTAGCGACGTTTGTATCCTAAAAAT-TCCGCTATATACCAGATCTTTAGTGGCATTTGTATTAT
66 TTTAGCGACGTTTGTATCCTAAAAATGT-CGCTATATACCAGACCTTTAGCGGCATTTGTATTAT
1470913 AA
130 AA
* * * *
1470915 AAACGCCGCTATAAACCAGACCTTTAGCGGTGTTTATATACTGAAAACGCCTCTATATACCAAAC
1 AAACGCCGCTATAAACCA-ACCTTTAGCAGCGTTTATATACTAAAAACGCCGCTATATACCAAAC
* * * *
1470980 CTTTAGCGGCGTTTGTATCCTAAAAATGTTGTTATATACCAGACCTTTAGCGGCGTTTGTAT
65 CTTTAGCGACGTTTGTATCCTAAAAATGTCGCTATATACCAGACCTTTAGCGGCATTTGTAT
1471042 CCAAAAACAC
Statistics
Matches: 108, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
131 16 0.15
132 91 0.84
133 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (131 bp):
AAACGCCGCTATAAACCAACCTTTAGCAGCGTTTATATACTAAAAACGCCGCTATATACCAAACC
TTTAGCGACGTTTGTATCCTAAAAATGTCGCTATATACCAGACCTTTAGCGGCATTTGTATTATA
A
Found at i:1473701 original size:26 final size:26
Alignment explanation
Indices: 1473665--1473723 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
1473655 ATATACAATA
*
1473665 TTTGAACCTGAAACCTTAAGGGGTTT
1 TTTGAACCTGAAACCTTAAGGGGTTG
1473691 TTTGAACCTGAAACCTTAAGGGGTTG
1 TTTGAACCTGAAACCTTAAGGGGTTG
1473717 TTTGAAC
1 TTTGAAC
1473724 GATGGAGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (26 bp):
TTTGAACCTGAAACCTTAAGGGGTTG
Found at i:1477514 original size:21 final size:21
Alignment explanation
Indices: 1477487--1477559 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1477477 GTAGTGGGTC
1477487 GGTATCCATA-CTGGATAAACT
1 GGTATCCATATC-GGATAAACT
* * **
1477508 AGTATCCATATCGGGTAAGTT
1 GGTATCCATATCGGATAAACT
*
1477529 GGTATCCATATCGGATGAACT
1 GGTATCCATATCGGATAAACT
1477550 GGTATCCATA
1 GGTATCCATA
1477560 CCAAAGGTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (21 bp):
GGTATCCATATCGGATAAACT
Found at i:1498963 original size:18 final size:18
Alignment explanation
Indices: 1498940--1498982 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1498930 CCTGTTGTAT
1498940 GTGCATTGAGAGTCGTAG
1 GTGCATTGAGAGTCGTAG
1498958 GTGCATTGAGAGTCGTAG
1 GTGCATTGAGAGTCGTAG
1498976 GTGCATT
1 GTGCATT
1498983 TCGACATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.37, T:0.30
Consensus pattern (18 bp):
GTGCATTGAGAGTCGTAG
Found at i:1499074 original size:18 final size:18
Alignment explanation
Indices: 1499048--1499086 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1499038 CATTTTTGTA
* * *
1499048 TCAGTACTATGTGTACTT
1 TCAGCACTATATGTACAT
1499066 TCAGCACTATATGTACAT
1 TCAGCACTATATGTACAT
1499084 TCA
1 TCA
1499087 TGGTATTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (18 bp):
TCAGCACTATATGTACAT
Found at i:1508391 original size:53 final size:53
Alignment explanation
Indices: 1508230--1508391 Score: 279
Period size: 53 Copynumber: 3.1 Consensus size: 53
1508220 CTAAGTGTGT
* *
1508230 ATATGGTAACTCACAAACTCATTATGAATTCCATGGTTGCACACATAGTGTCG
1 ATATGGTAATTCACAAACTCATTATGAATTCCATGGTTACACACATAGTGTCG
*
1508283 AAATGGTAATTCACAAACTCATTATGAATTCCATGGTTACACACATAGTGTCG
1 ATATGGTAATTCACAAACTCATTATGAATTCCATGGTTACACACATAGTGTCG
* *
1508336 ATATGGTAATTCACAAGCTCATTATGAATTCCATGGTTACACACATAGTGCCG
1 ATATGGTAATTCACAAACTCATTATGAATTCCATGGTTACACACATAGTGTCG
1508389 ATA
1 ATA
1508392 GTACACATAG
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 103 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (53 bp):
ATATGGTAATTCACAAACTCATTATGAATTCCATGGTTACACACATAGTGTCG
Found at i:1514484 original size:40 final size:40
Alignment explanation
Indices: 1514440--1514549 Score: 184
Period size: 40 Copynumber: 2.8 Consensus size: 40
1514430 AGGACATTAA
*
1514440 GTGTACATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1514480 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* * *
1514520 ATGTATATTGTGGGCACGATCTTATGTGTA
1 GTGTATATGGTGGGCACGACCTTATGTGTA
1514550 GTACTACGGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:1514747 original size:47 final size:47
Alignment explanation
Indices: 1514654--1515000 Score: 567
Period size: 47 Copynumber: 7.5 Consensus size: 47
1514644 GTAAGTATGC
*
1514654 AAATAAGCTTACGAGCTTAT-GAA--T-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGATA
* *
1514697 AAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGCATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGATA
* *
1514744 AAATAAGCTTGCGAGCTTATGGAATTTAAATGGTAAGCATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGATA
1514791 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGATA
*
1514838 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATGTTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGATA
* *
1514885 AAATAAGCTTACGAGCTTCTGGAATTTAAATGGTAAGTATGTTGATA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGATA
* * *
1514932 AAATAACCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGATA
1514979 AAATAAGCTTACGAGCTTATGG
1 AAATAAGCTTACGAGCTTATGG
1515001 GATAAAAGGT
Statistics
Matches: 286, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
43 19 0.07
44 3 0.01
46 1 0.00
47 263 0.92
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGATA
Found at i:1516215 original size:21 final size:19
Alignment explanation
Indices: 1516187--1516232 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1516177 TCATTGAATC
1516187 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
1516207 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
1516226 ACTTAGT
1 A-TTAGT
1516233 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:1529945 original size:3 final size:3
Alignment explanation
Indices: 1529937--1529962 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1529927 TATATTTTAA
1529937 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1529963 CGTTCATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1530531 original size:53 final size:53
Alignment explanation
Indices: 1530462--1530736 Score: 462
Period size: 53 Copynumber: 5.2 Consensus size: 53
1530452 GTTGCACCTA
1530462 AGTGTCGATATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACAT
1 AGTGTCGATATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACAT
* *
1530515 AGTGTCGATATGGTAATTCATAAACTCATTATGAATTCCATGATTGCACACAT
1 AGTGTCGATATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACAT
* *
1530568 AGTGTCGACATGGTAATTCACAAACTCATTACGAATTCCATGGTTGCACACAT
1 AGTGTCGATATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACAT
*
1530621 AGTGTCGATATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACATAT
1 AGTGTCGATATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACAT
* * *
1530674 AATG-CTAAAATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACAT
1 AGTGTC-GATATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACAT
1530727 AGTGTCGATA
1 AGTGTCGATA
1530737 GTACACATAG
Statistics
Matches: 204, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
52 1 0.00
53 202 0.99
54 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (53 bp):
AGTGTCGATATGGTAATTCACAAACTCATTATGAATTCCATGGTTGCACACAT
Found at i:1539449 original size:13 final size:14
Alignment explanation
Indices: 1539422--1539453 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1539412 TTAGTTTGCA
1539422 TTTTTCTTTTCATT
1 TTTTTCTTTTCATT
1539436 TTTTTCTTTT-ATT
1 TTTTTCTTTTCATT
1539449 TTTTT
1 TTTTT
1539454 ATGTGCAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTCATT
Found at i:1539781 original size:16 final size:16
Alignment explanation
Indices: 1539757--1539788 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1539747 TTCATTCAAT
1539757 CTTTCCATGACATTTA
1 CTTTCCATGACATTTA
*
1539773 CTTTTCATGACATTTA
1 CTTTCCATGACATTTA
1539789 GATAGATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (16 bp):
CTTTCCATGACATTTA
Found at i:1542616 original size:20 final size:20
Alignment explanation
Indices: 1542585--1542640 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1542575 ACTGGAATCC
* *
1542585 AAGGGATTGATCCTTTTTC-
1 AAGGGATCGATCCTTTTGCT
1542604 AAGGGGATCGATCCTTTTGCT
1 AA-GGGATCGATCCTTTTGCT
1542625 AAGGGATCGATCCTTT
1 AAGGGATCGATCCTTT
1542641 GAACCAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
AAGGGATCGATCCTTTTGCT
Found at i:1549914 original size:21 final size:21
Alignment explanation
Indices: 1549881--1549954 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
1549871 ATGTTTGTTT
* *
1549881 AAGTTAGTAAATAATTTTTTG
1 AAGTTCGTGAATAATTTTTTG
* *
1549902 ACGTTCGTGAAT-ATTTTGTTT
1 AAGTTCGTGAATAATTTT-TTG
* *
1549923 AAGTTAGTAAATAATTTTTTG
1 AAGTTCGTGAATAATTTTTTG
1549944 AAGTTCGTGAA
1 AAGTTCGTGAA
1549955 CATGTTATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 5 0.12
21 31 0.76
22 5 0.12
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (21 bp):
AAGTTCGTGAATAATTTTTTG
Found at i:1549933 original size:42 final size:42
Alignment explanation
Indices: 1549874--1549954 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
1549864 TTAATTTATG
*
1549874 TTTGTTTAAGTTAGTAAATAATTTTTTGACGTTCGTGAATAT
1 TTTGTTTAAGTTAGTAAATAATTTTTTGAAGTTCGTGAATAT
1549916 TTTGTTTAAGTTAGTAAATAATTTTTTGAAGTTCGTGAA
1 TTTGTTTAAGTTAGTAAATAATTTTTTGAAGTTCGTGAA
1549955 CATGTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (42 bp):
TTTGTTTAAGTTAGTAAATAATTTTTTGAAGTTCGTGAATAT
Found at i:1551245 original size:2 final size:2
Alignment explanation
Indices: 1551238--1551292 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1551228 ATAGTGTTAG
1551238 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
1551280 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1551293 ACACTATGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1551515 original size:80 final size:80
Alignment explanation
Indices: 1551382--1551554 Score: 267
Period size: 80 Copynumber: 2.2 Consensus size: 80
1551372 AAACTATTGG
* * *
1551382 AAGTTCTTCTCATTAGGAACTTCTTCATTGGAAATGTTGATTCACCTCCTTCTGTGATGGAATC-
1 AAGTTCTTCTCATTAGGAACTTATTCATTGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCG
*
1551446 AAGTGAAATGTTGAAC
66 AA-CGAAATGTTGAAC
1551462 AAGTTCTTCTCATTAGGAACTTATTCATTGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCG
1 AAGTTCTTCTCATTAGGAACTTATTCATTGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCG
* **
1551527 AACGAAGTGTTGAGT
66 AACGAAATGTTGAAC
1551542 AAGTTCTTCTCAT
1 AAGTTCTTCTCAT
1551555 GTTTTTACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
80 83 0.98
81 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (80 bp):
AAGTTCTTCTCATTAGGAACTTATTCATTGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCG
AACGAAATGTTGAAC
Found at i:1553030 original size:108 final size:108
Alignment explanation
Indices: 1552865--1553575 Score: 872
Period size: 107 Copynumber: 6.6 Consensus size: 108
1552855 TCAAAAATTC
* * * * * * *
1552865 ATTTGTAAATATCAAGAGACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGTAAACG
1 ATTTGTAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAAACA
* * **
1552930 TCAAGAAACCCTTGAAAATCAGGTTTAGCTCTTTTAAAAAGT-T
66 TCAAGAAACCCCTAAAAATCAGGTTTAGCTCTTTTCCAAA-TCT
* * ** * *
1552973 ATTTGAAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCATTTCCAAATCCATTTGTAAACA
1 ATTTGTAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAAACA
* **
1553038 TTAAGAAACCCCTAAAAAAT-AGGTTTAGCT-TCTTTAAAAAT-T
66 TCAAGAAACCCCT-AAAAATCAGGTTTAGCTCT-TTTCCAAATCT
* **
1553080 CATTTGTAAACATCGAGAAACCTATGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAAAC
1 -ATTTGTAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAAAC
* * *
1553145 GTCAAGAAACCCCT-AAAATCAGGTTTAGCTCATTTCCAAATCC
65 ATCAAGAAACCCCTAAAAATCAGGTTTAGCTCTTTTCCAAATCT
** *
1553188 ATTTGTAAACATCAAGAAACCTATGAAAATCAGGCTTAACTCCTTTAAAAATTCATTTGAAAACA
1 ATTTGTAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAAACA
* *
1553253 TCAAGAAACCCCTAAAAATCAGG-CTAGCT-TCTTTCCAAATCC
66 TCAAGAAACCCCTAAAAATCAGGTTTAGCTCT-TTTCCAAATCT
*
1553295 ATTTGTAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCT-C-TTATAGAATTCATTTGAAAAC
1 ATTTGTAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTA-AAAATTCATTTGAAAAC
* * * * * *
1553358 ATCAAGAAACCCATGAAAATCAAGCTT-GACTCCTTTCCAAATCC
65 ATCAAGAAACCCCTAAAAATCAGGTTTAG-CTCTTTTCCAAATCT
* *
1553402 ATTTGTAAACATCAAGAAATCCTTG-AAATCA-GCTTAGCTCCTTTAAAAATTCATTTGAAAACA
1 ATTTGTAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAAACA
*
1553465 TCAAGAAACCCCTAAAAATCAGGCTTT-GCTCCTTTCCAAATCT
66 TCAAGAAACCCCTAAAAATCAGG-TTTAGCTCTTTTCCAAATCT
* *
1553508 ATTTGTAAACATCCAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGCAAACA
1 ATTTGTAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAAACA
1553573 TCA
66 TCA
1553576 TATTGTTTGG
Statistics
Matches: 531, Mismatches: 55, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
105 11 0.02
106 124 0.23
107 198 0.37
108 193 0.36
109 5 0.01
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (108 bp):
ATTTGTAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAAACA
TCAAGAAACCCCTAAAAATCAGGTTTAGCTCTTTTCCAAATCT
Found at i:1553191 original size:53 final size:54
Alignment explanation
Indices: 1552820--1553575 Score: 857
Period size: 54 Copynumber: 14.1 Consensus size: 54
1552810 AATGACTCAT
* ** ** * *
1552820 CATCGAGAAACCTTTGAAAATCAAACTTAGCTTCTTCAAAAATTCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
* * * * *
1552874 TATCAAGAGACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
* * * * *
1552928 CGTCAAGAAACCCTTGAAAATCAGGTTTAGCTCTTTTAAAAAGTT-ATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAA-TTCATTTGTAAA
* ** *
1552982 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCATTTCCAAATCCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
* * * *
1553036 CATTAAGAAACCCCTAAAAAAT-AGGTTTAGCTTCTTTAAAAATTCATTTGTAAA
1 CATCAAGAAACCCCT-GAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
* ** *
1553090 CATCGAGAAACCTATGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
* * * ** *
1553144 CGTCAAGAAACCCCT-AAAATCAGGTTTAGCTCATTTCCAAATCCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
** * *
1553197 CATCAAGAAACCTATGAAAATCAGGCTTAACTCCTTTAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
* * ** *
1553251 CATCAAGAAACCCCTAAAAATCAGGC-TAGCTTCTTTCCAAATCCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
* *
1553304 CATCAAGAAACCCCTGAAAATCAGGCTTAGCT-C-TTATAGAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTA-AAAATTCATTTGTAAA
* * ** *
1553357 CATCAAGAAACCCATGAAAATCAAGCTT-GACTCCTTTCCAAATCCATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAG-CTCCTTTAAAAATTCATTTGTAAA
* * *
1553411 CATCAAGAAATCCTTG-AAATCA-GCTTAGCTCCTTTAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
* * **
1553463 CATCAAGAAACCCCTAAAAATCAGGCTTTGCTCCTTTCCAAA-TCTATTTGTAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTC-ATTTGTAAA
* *
1553517 CATCCAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGCAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
1553571 CATCA
1 CATCA
1553576 TATTGTTTGG
Statistics
Matches: 581, Mismatches: 106, Indels: 30
0.81 0.15 0.04
Matches are distributed among these distances:
52 40 0.07
53 152 0.26
54 378 0.65
55 11 0.02
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (54 bp):
CATCAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGTAAA
Found at i:1555188 original size:43 final size:43
Alignment explanation
Indices: 1555140--1555226 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
1555130 ATGATTCCGC
1555140 TAAAGAACTTTTATTGACGTAATCTCCTCATTTCTCAGTTCTT
1 TAAAGAACTTTTATTGACGTAATCTCCTCATTTCTCAGTTCTT
*
1555183 TAAAGACCTTTTATTGACGTAATCTCCTCATTTCTCAGTTCTT
1 TAAAGAACTTTTATTGACGTAATCTCCTCATTTCTCAGTTCTT
1555226 T
1 T
1555227 GATTCCATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (43 bp):
TAAAGAACTTTTATTGACGTAATCTCCTCATTTCTCAGTTCTT
Found at i:1558519 original size:18 final size:18
Alignment explanation
Indices: 1558461--1558558 Score: 76
Period size: 18 Copynumber: 5.5 Consensus size: 18
1558451 ATTAATTTGT
1558461 ATCTGATAACTGTAAAAT-
1 ATCTGATAACTG-AAAATC
* ** * *
1558479 ATTTGATATTTG-TAATT
1 ATCTGATAACTGAAAATC
*
1558496 ATCTGATAACTGCAAATC
1 ATCTGATAACTGAAAATC
1558514 ATCTGATAACTGTAAAAT-
1 ATCTGATAACTG-AAAATC
* * *
1558532 TTCTTACAACTGAAAATC
1 ATCTGATAACTGAAAATC
1558550 ATCTGATAA
1 ATCTGATAA
1558559 TTGTAAACAT
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
16 3 0.05
17 14 0.23
18 39 0.65
19 4 0.07
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (18 bp):
ATCTGATAACTGAAAATC
Found at i:1558521 original size:35 final size:35
Alignment explanation
Indices: 1558460--1558564 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 35
1558450 TATTAATTTG
* *
1558460 TATCTGATAACTGTAAAAT-ATTTGATATTTGTAAT
1 TATCTGATAACTG-AAAATCATCTGATAATTGTAAT
* *
1558495 TATCTGATAACTGCAAATCATCTGATAACTGTAAAAT
1 TATCTGATAACTGAAAATCATCTGATAATTGT--AAT
* *
1558532 T-TCTTACAACTGAAAATCATCTGATAATTGTAA
1 TATCTGATAACTGAAAATCATCTGATAATTGTAA
1558565 ACATTTAGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
34 6 0.10
35 23 0.39
36 26 0.44
37 4 0.07
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38
Consensus pattern (35 bp):
TATCTGATAACTGAAAATCATCTGATAATTGTAAT
Found at i:1558777 original size:3 final size:3
Alignment explanation
Indices: 1558769--1558806 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1558759 AACACTTTAC
1558769 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1558807 AATCAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1563603 original size:19 final size:19
Alignment explanation
Indices: 1563581--1563625 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1563571 TAGTTAAATA
1563581 TTTATTATTTTGAATTCAG
1 TTTATTATTTTGAATTCAG
**
1563600 TTTATT-TTTTTTATTCAG
1 TTTATTATTTTGAATTCAG
1563618 TTTGATTA
1 TTT-ATTA
1563626 AAAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.22, C:0.04, G:0.09, T:0.64
Consensus pattern (19 bp):
TTTATTATTTTGAATTCAG
Found at i:1563629 original size:114 final size:114
Alignment explanation
Indices: 1563498--1563724 Score: 454
Period size: 114 Copynumber: 2.0 Consensus size: 114
1563488 GATATATTCG
1563498 ATTCAGTTTGATTAAAAAATATTTTTTTAATCTTTGGAAAAGTTTTAATTCACTAGTATGTACTT
1 ATTCAGTTTGATTAAAAAATATTTTTTTAATCTTTGGAAAAGTTTTAATTCACTAGTATGTACTT
1563563 TTGATATTTAGTTAAATATTTATTATTTTGAATTCAGTTTATTTTTTTT
66 TTGATATTTAGTTAAATATTTATTATTTTGAATTCAGTTTATTTTTTTT
1563612 ATTCAGTTTGATTAAAAAATATTTTTTTAATCTTTGGAAAAGTTTTAATTCACTAGTATGTACTT
1 ATTCAGTTTGATTAAAAAATATTTTTTTAATCTTTGGAAAAGTTTTAATTCACTAGTATGTACTT
1563677 TTGATATTTAGTTAAATATTTATTATTTTGAATTCAGTTTATTTTTTT
66 TTGATATTTAGTTAAATATTTATTATTTTGAATTCAGTTTATTTTTTT
1563725 GGTGAATTAC
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (114 bp):
ATTCAGTTTGATTAAAAAATATTTTTTTAATCTTTGGAAAAGTTTTAATTCACTAGTATGTACTT
TTGATATTTAGTTAAATATTTATTATTTTGAATTCAGTTTATTTTTTTT
Found at i:1573454 original size:72 final size:72
Alignment explanation
Indices: 1573334--1573474 Score: 237
Period size: 72 Copynumber: 2.0 Consensus size: 72
1573324 GATGATCACT
* * * * *
1573334 AAAAACTATGTTGTTATCGAGTCATATCGTACAGATGATTGCATATGCTTCTATTAGGTATACAT
1 AAAAACTATGTTGTTAACAAGTCATATCGTACAGATGAATGCACATGCTTCCATTAGGTATACAT
1573399 TCATTTA
66 TCATTTA
1573406 AAAAACTATGTTGTTAACAAGTCATATCGTACAGATGAATGCACATGCTTCCATTAGGTATACAT
1 AAAAACTATGTTGTTAACAAGTCATATCGTACAGATGAATGCACATGCTTCCATTAGGTATACAT
1573471 TCAT
66 TCAT
1573475 AAACCAACAT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (72 bp):
AAAAACTATGTTGTTAACAAGTCATATCGTACAGATGAATGCACATGCTTCCATTAGGTATACAT
TCATTTA
Found at i:1576014 original size:19 final size:19
Alignment explanation
Indices: 1575978--1576021 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1575968 ATATTTCAAT
1575978 TATTAAAAAAATCATTATA
1 TATTAAAAAAATCATTATA
1575997 -ATTATAAAAAAT-AGTTATA
1 TATTA-AAAAAATCA-TTATA
1576016 TATTAA
1 TATTAA
1576022 TTATTTACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.23
19 13 0.59
20 4 0.18
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TATTAAAAAAATCATTATA
Found at i:1576818 original size:16 final size:13
Alignment explanation
Indices: 1576788--1576813 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1576778 TTATAAGGTA
1576788 ATTTTTTTATAAT
1 ATTTTTTTATAAT
1576801 ATTTTTTTATAAT
1 ATTTTTTTATAAT
1576814 TATATATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTTTATAAT
Found at i:1582710 original size:28 final size:28
Alignment explanation
Indices: 1582666--1582746 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 28
1582656 TTATATCTGC
*
1582666 AAAAAAATTT-AA-TTAAATAAAATATT
1 AAAAAATTTTAAATTTAAATAAAATATT
* *
1582692 AAAAAATTTTAAATTTAAATAAATTACT
1 AAAAAATTTTAAATTTAAATAAAATATT
** *
1582720 AAGAAAATACTAAATAT-AATAAAATAT
1 AA-AAAATTTTAAATTTAAATAAAATAT
1582747 ACCTTAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
26 9 0.20
27 2 0.05
28 22 0.50
29 11 0.25
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (28 bp):
AAAAAATTTTAAATTTAAATAAAATATT
Found at i:1584699 original size:105 final size:104
Alignment explanation
Indices: 1584513--1584801 Score: 303
Period size: 104 Copynumber: 2.8 Consensus size: 104
1584503 AAGAGTGATG
* * * * * * *
1584513 TATGTGACAACATTAGGCGCAATGCCTTGATTTATCATTGTGTGAACAATA-CTTTTAGCTTCGT
1 TATGTGACAACATTAGGCTCAATGCCTTGCTTTATCATTGTGTTAACGATATC-TTCAGCTTTGC
* * * * * *
1584577 AAATCGAT-CCCTCCTTGCAATGGGCATCCACCAGTATGGTA
65 AAA-CCATCCCCTTCTTGCAAAGGGCAT-AAACAATATGGTA
* *
1584618 TATGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGTTAATGATATCTTCAGCTTTGCA
1 TATGTGACAACATTAGGCTCAATGCCTTGCTTTATCATTGTGTTAACGATATCTTCAGCTTTGCA
* *
1584683 AACCATCCCCTTCTTGCAAAGTGCATAAACAATATGTTA
66 AACCATCCCCTTCTTGCAAAGGGCATAAACAATATGGTA
*** * * * * * *
1584722 TACAAGACAACATCAGGCTTAATACCTTGCTTTATCATTGTGTTAACGATTTATTCAGCTTTGGA
1 TATGTGACAACATTAGGCTCAATGCCTTGCTTTATCATTGTGTTAACGATATCTTCAGCTTTGCA
1584787 AACCATCCCCTTCTT
66 AACCATCCCCTTCTT
1584802 ACACATAGCA
Statistics
Matches: 154, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
104 81 0.53
105 72 0.47
106 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (104 bp):
TATGTGACAACATTAGGCTCAATGCCTTGCTTTATCATTGTGTTAACGATATCTTCAGCTTTGCA
AACCATCCCCTTCTTGCAAAGGGCATAAACAATATGGTA
Found at i:1588752 original size:5 final size:5
Alignment explanation
Indices: 1588742--1588767 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1588732 ACGAGGAATC
1588742 GAGAA GAGAA GAGAA GAGAA GAGAA G
1 GAGAA GAGAA GAGAA GAGAA GAGAA G
1588768 TGAGAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:1596677 original size:49 final size:49
Alignment explanation
Indices: 1596011--1596665 Score: 720
Period size: 49 Copynumber: 13.4 Consensus size: 49
1596001 ATTTTATTTC
** * *
1596011 AAAATGCACTGTTATACATTTAAC-TGTCATTAGTGACACCTTATATGCC-
1 AAAATGCACCATTATGCATTTAACTTG-CATTAGTGACACCTT-TCTGCCA
* * * * *
1596060 GAAATGCACCGTTATACATTTAAC-TGTTATTAGTGGCACCTTTCTGCC-
1 AAAATGCACCATTATGCATTTAACTTG-CATTAGTGACACCTTTCTGCCA
** *** * * * *
1596108 AAAATGCACCGA-TACACATTTAACTCAAATTAGTGGA-ACATTTTTTCAA
1 AAAATGCACC-ATTATGCATTTAACTTGCATTAGT-GACACCTTTCTGCCA
** * *
1596157 AAAATGCACCATTATGCATTTAACTTGCATTAGTGGTACTTTTTTGCCA
1 AAAATGCACCATTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
* * * * *
1596206 AAAATGAACCATTATGAATTTAACTTGCATTAGTGAAACATTTCTTCCA
1 AAAATGCACCATTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
*
1596255 AAAATGCACCATTATGCA-TTAACTTGCATTAGTGGCACCTTTCTGCCA
1 AAAATGCACCATTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
*
1596303 AAAATGCA-CATTTATGCATTTAACTTGCATTAGTGACACATTTCTGCCA
1 AAAATGCACCA-TTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
* * *
1596352 AAAATGCA-CATTTGTGCATTTAACTTGCATTAGTGACACCTTTTTTCCA
1 AAAATGCACCA-TTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
*
1596401 AAAATGCA-CATTTATGCATTTAACTTGCATTAGTGACACATTTCTGCCA
1 AAAATGCACCA-TTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
* * *
1596450 AAAATGCACCATTATGCATTTAAGTTGCATTGGTGACACCTTTTTGCCA
1 AAAATGCACCATTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
* *
1596499 AAAATGCACCATTATGTATTTAACTTTG-ATTAGTGGCACCTTTCTGCCA
1 AAAATGCACCATTATGCATTTAAC-TTGCATTAGTGACACCTTTCTGCCA
* * * *
1596548 AAATTGCACCATTATGCAATTAACTTGCATTAGTGGCACCTTTCTACCA
1 AAAATGCACCATTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
* * * *
1596597 AAACTGCACCATTTTGCATTTAACTTGCATTAGTGGCACCTTTCAGCCA
1 AAAATGCACCATTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
* *
1596646 AAAATACACCGTTATGCATT
1 AAAATGCACCATTATGCATT
1596666 GAACATTCAT
Statistics
Matches: 525, Mismatches: 70, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
47 2 0.00
48 84 0.16
49 434 0.83
50 5 0.01
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (49 bp):
AAAATGCACCATTATGCATTTAACTTGCATTAGTGACACCTTTCTGCCA
Found at i:1604523 original size:49 final size:49
Alignment explanation
Indices: 1604404--1604824 Score: 562
Period size: 49 Copynumber: 8.6 Consensus size: 49
1604394 TTTTATACCG
* * *
1604404 AAATGCA-CAGTTATACATTTAA-TTGTCGTTAGTGGCATCTTTCTGCC-A
1 AAATGCACCA-TTATGCATTTAACTTG-CATTAGTGGCACCTTTCTGCCAA
* * ** * *
1604452 AAATACACCGTTATGCATTTAACTCACATTAATGGCATCTTTCTGCCAA
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
*
1604501 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCAGCCAA
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
* *
1604550 AAATGCACTATTATGCATTTAACTTGCATTAGTGGCACCTTTCT-CCCA
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * *
1604598 AAATGCACCTTTATGCATTTAACTTGCATTAATGGCACCTTTCTACCAA
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
* *
1604647 AAATGCATCATTATGCATTTAACTTACATTAGTGGCACCTTTCTGCCAA
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * * *
1604696 AAATGCACCATTTTGCATTTAACTTGCATTAGTGACACATTTATGCCAA
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
* *
1604745 AAATGCACCATTTTGCATTTAACTTGCATTAGTGGCACCTTTCTGTCAA
1 AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
** *
1604794 AAATGCACTGTTATGCATTTAACTTTCATTA
1 AAATGCACCATTATGCATTTAACTTGCATTA
1604825 TAGATCGGTT
Statistics
Matches: 329, Mismatches: 40, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
48 80 0.24
49 249 0.76
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (49 bp):
AAATGCACCATTATGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAA
Found at i:1604649 original size:146 final size:145
Alignment explanation
Indices: 1604404--1604824 Score: 567
Period size: 146 Copynumber: 2.9 Consensus size: 145
1604394 TTTTATACCG
* * * * * *
1604404 AAATGCACAGTTATACATTTAA-TTGTCGTTAGTGGCATCTTTCTGCCAAAATACACCGTTATGC
1 AAATGCACA-TTATGCATTTAACTTG-CATTAGTGGCACCTTTCTCCCAAAATGCACCTTTATGC
** * *
1604468 ATTTAACTCACATTAATGGCATCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTGCATTAG
64 ATTTAACTTGCATTAATGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTACATTAG
1604533 TGGCACCTTTCAGCCAA
129 TGGCACCTTTCAGCCAA
1604550 AAATGCACTATTATGCATTTAACTTGCATTAGTGGCACCTTTCTCCCAAAATGCACCTTTATGCA
1 AAATGCAC-ATTATGCATTTAACTTGCATTAGTGGCACCTTTCTCCCAAAATGCACCTTTATGCA
* *
1604615 TTTAACTTGCATTAATGGCACCTTTCTACCAAAAATGCATCATTATGCATTTAACTTACATTAGT
65 TTTAACTTGCATTAATGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTACATTAGT
*
1604680 GGCACCTTTCTGCCAA
130 GGCACCTTTCAGCCAA
* * * * *
1604696 AAATGCACCATTTTGCATTTAACTTGCATTAGTGACACATTTATGCCAAAAATGCACCATTT-TG
1 AAATGCA-CATTATGCATTTAACTTGCATTAGTGGCACCTTTCT-CCCAAAATGCACC-TTTATG
* * ** *
1604760 CATTTAACTTGCATTAGTGGCACCTTTCTGTCAAAAATGCACTGTTATGCATTTAACTTTCATTA
63 CATTTAACTTGCATTAATGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTACATTA
1604825 TAGATCGGTT
Statistics
Matches: 245, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
146 165 0.67
147 77 0.31
148 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (145 bp):
AAATGCACATTATGCATTTAACTTGCATTAGTGGCACCTTTCTCCCAAAATGCACCTTTATGCAT
TTAACTTGCATTAATGGCACCTTTCTGCCAAAAATGCACCATTATGCATTTAACTTACATTAGTG
GCACCTTTCAGCCAA
Found at i:1617659 original size:20 final size:20
Alignment explanation
Indices: 1617621--1617659 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1617611 ATTAGGTTTG
* **
1617621 ATTTTTTTGATATTTTTTTT
1 ATTTTTCTGATATGATTTTT
1617641 ATTTTTCTGATATGATTTT
1 ATTTTTCTGATATGATTTT
1617660 GAAACAGGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.72
Consensus pattern (20 bp):
ATTTTTCTGATATGATTTTT
Found at i:1617925 original size:16 final size:16
Alignment explanation
Indices: 1617904--1617953 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1617894 TAAGCCCGAA
1617904 AAATAAATAGA-ATAAT
1 AAATAAATA-ATATAAT
*
1617920 AAATAATTAATATAAT
1 AAATAAATAATATAAT
1617936 AATATAAATAATA-AAT
1 AA-ATAAATAATATAAT
1617952 AA
1 AA
1617954 TTGAAACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 1 0.03
16 20 0.67
17 9 0.30
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AAATAAATAATATAAT
Found at i:1619416 original size:41 final size:41
Alignment explanation
Indices: 1619371--1619455 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
1619361 TTAATTAAAT
* *
1619371 TTTCTTTCAACGTTCTTGTATCATTTCTTCCTTTTCTTTGA
1 TTTCTTTCAACATTCTTGTATCATTTCTTACTTTTCTTTGA
* * *
1619412 TTTCTTTCAACATTTTTGTATCGTTTCTTATTTTTCTTTGA
1 TTTCTTTCAACATTCTTGTATCATTTCTTACTTTTCTTTGA
1619453 TTT
1 TTT
1619456 TTGTTTAGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.13, C:0.18, G:0.07, T:0.62
Consensus pattern (41 bp):
TTTCTTTCAACATTCTTGTATCATTTCTTACTTTTCTTTGA
Found at i:1623037 original size:34 final size:33
Alignment explanation
Indices: 1622981--1623044 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1622971 ATGCTGTTGG
* *
1622981 CCTTTTATGTTCTGTTTTTAATTCTTATTTTTGC
1 CCTTTTATCTTCTCTTTTTAATT-TTATTTTTGC
1623015 CCTTTT-TCTTCTCTTTTATAATTTTATTTT
1 CCTTTTATCTTCTCTTTT-TAATTTTATTTT
1623045 GTGAATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 16 0.59
34 11 0.41
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (33 bp):
CCTTTTATCTTCTCTTTTTAATTTTATTTTTGC
Found at i:1626561 original size:36 final size:36
Alignment explanation
Indices: 1626507--1626582 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
1626497 CCTATCTAAT
* *
1626507 TGAAATTCCATTCGAACAAGATATCATCTGATTTTG
1 TGAAATTCCATGCAAACAAGATATCATCTGATTTTG
*
1626543 TGAAATTCCATGCAAACAATATATCATCTGATTTTG
1 TGAAATTCCATGCAAACAAGATATCATCTGATTTTG
1626579 TGAA
1 TGAA
1626583 TTCATTCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (36 bp):
TGAAATTCCATGCAAACAAGATATCATCTGATTTTG
Found at i:1630671 original size:49 final size:49
Alignment explanation
Indices: 1630610--1630981 Score: 377
Period size: 49 Copynumber: 7.6 Consensus size: 49
1630600 TTATGACACA
** * * *
1630610 TTTCTACCAAAAATGCACTGTTAGGCATTTAACTTGCATTAATGGCACT
1 TTTCTACCAAAAATGCACCCTTAGGCATCTAACTTGCATTAGTGGCACC
* * * * *
1630659 TTTCTGCCAAAAATGCAGCATTTGTCATCTAACTTGCATTAGTGGCACC
1 TTTCTACCAAAAATGCACCCTTAGGCATCTAACTTGCATTAGTGGCACC
* * * **
1630708 TTTCTGCCAAAAATGCACCCTTTGGCATCAAACTTGCATTAGTTACACC
1 TTTCTACCAAAAATGCACCCTTAGGCATCTAACTTGCATTAGTGGCACC
* * * * *
1630757 TTTCTACCAGAAATGCACTAC-GAGGCATTTAACTTGCATTAGTGGCACAT
1 TTTCTACCAAAAATGCAC-CCTTAGGCATCTAACTTGCATTAGTGGCAC-C
* * * * *
1630807 TTTCTGCCAAAACTGCACCCTTTGTCATCTAACTTGCATTAGTGACACC
1 TTTCTACCAAAAATGCACCCTTAGGCATCTAACTTGCATTAGTGGCACC
* * *
1630856 TTTCTACCAAAAATGCACCGTTAGGCATTTAACTTGCATTTGTGGCACC
1 TTTCTACCAAAAATGCACCCTTAGGCATCTAACTTGCATTAGTGGCACC
* * * * * * * *
1630905 TTTATGCCAAAAATGTACCCTTTGTCATCTAAATTACATTAGTGACACC
1 TTTCTACCAAAAATGCACCCTTAGGCATCTAACTTGCATTAGTGGCACC
* *
1630954 TTTCTACAAAAAATGCACCGTTAGGCAT
1 TTTCTACCAAAAATGCACCCTTAGGCAT
1630982 TTAAATTTCG
Statistics
Matches: 259, Mismatches: 61, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
49 221 0.85
50 38 0.15
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (49 bp):
TTTCTACCAAAAATGCACCCTTAGGCATCTAACTTGCATTAGTGGCACC
Found at i:1630905 original size:148 final size:147
Alignment explanation
Indices: 1630603--1630919 Score: 445
Period size: 148 Copynumber: 2.1 Consensus size: 147
1630593 TTTTCATTTA
* ***
1630603 TGACACATTTCTACCAAAAATGCACTGTTAGGCATTTAACTTGCATTAATGGCACTTTTCTGCCA
1 TGACACCTTTCTACCAAAAATGCACTACGAGGCATTTAACTTGCATTAATGGCACTTTTCTGCCA
* * * *
1630668 AAAATGCAGCATTTGTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCCTTTGG
66 AAAATGCACCATTTGTCATCTAACTTGCATTAGTGACACCTTTCTACCAAAAATGCACCCTTAGG
1630733 CATCAAACTTGCATTAG
131 CATCAAACTTGCATTAG
* * *
1630750 TTACACCTTTCTACCAGAAATGCACTACGAGGCATTTAACTTGCATTAGTGGCACATTTTCTGCC
1 TGACACCTTTCTACCAAAAATGCACTACGAGGCATTTAACTTGCATTAATGGCAC-TTTTCTGCC
* * *
1630815 AAAACTGCACCCTTTGTCATCTAACTTGCATTAGTGACACCTTTCTACCAAAAATGCACCGTTAG
65 AAAAATGCACCATTTGTCATCTAACTTGCATTAGTGACACCTTTCTACCAAAAATGCACCCTTAG
** *
1630880 GCATTTAACTTGCATTTG
130 GCATCAAACTTGCATTAG
* * *
1630898 TGGCACCTTTATGCCAAAAATG
1 TGACACCTTTCTACCAAAAATG
1630920 TACCCTTTGT
Statistics
Matches: 147, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
147 48 0.33
148 99 0.67
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (147 bp):
TGACACCTTTCTACCAAAAATGCACTACGAGGCATTTAACTTGCATTAATGGCACTTTTCTGCCA
AAAATGCACCATTTGTCATCTAACTTGCATTAGTGACACCTTTCTACCAAAAATGCACCCTTAGG
CATCAAACTTGCATTAG
Found at i:1630945 original size:148 final size:147
Alignment explanation
Indices: 1630603--1630972 Score: 391
Period size: 148 Copynumber: 2.5 Consensus size: 147
1630593 TTTTCATTTA
* * *** * * * *
1630603 TGACACATTTCTACCAAAAATGCACTGTTAGGCATTTAACTTGCATTAATGGCACTTTTCTGCCA
1 TGACACCTTTATACCAAAAATGCACTACGAGGCATCTAAATTACATTAGTGGCACTTTTCTGCCA
* * * *
1630668 AAAATGCAGCATTTGTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCCTTTGG
66 AAAATGCACCATTTGTCATCTAACTTGCATTAGTGACACCTTTCTACCAAAAATGCACCCTTAGG
1630733 CATCAAACTTGCATTAG
131 CATCAAACTTGCATTAG
* * * * * *
1630750 TTACACCTTTCTACCAGAAATGCACTACGAGGCATTTAACTTGCATTAGTGGCACATTTTCTGCC
1 TGACACCTTTATACCAAAAATGCACTACGAGGCATCTAAATTACATTAGTGGCAC-TTTTCTGCC
* * *
1630815 AAAACTGCACCCTTTGTCATCTAACTTGCATTAGTGACACCTTTCTACCAAAAATGCACCGTTAG
65 AAAAATGCACCATTTGTCATCTAACTTGCATTAGTGACACCTTTCTACCAAAAATGCACCCTTAG
** *
1630880 GCATTTAACTTGCATTTG
130 GCATCAAACTTGCATTAG
* * * * ** * * * * *
1630898 TGGCACCTTTATGCCAAAAATGTAC-CCTTTGTCATCTAAATTACATTAGTGACACCTTTCTACA
1 TGACACCTTTATACCAAAAATGCACTAC-GAGGCATCTAAATTACATTAGTGGCACTTTTCTGCC
1630962 AAAAATGCACC
65 AAAAATGCACC
1630973 GTTAGGCATT
Statistics
Matches: 186, Mismatches: 35, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
147 65 0.35
148 121 0.65
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (147 bp):
TGACACCTTTATACCAAAAATGCACTACGAGGCATCTAAATTACATTAGTGGCACTTTTCTGCCA
AAAATGCACCATTTGTCATCTAACTTGCATTAGTGACACCTTTCTACCAAAAATGCACCCTTAGG
CATCAAACTTGCATTAG
Found at i:1630972 original size:98 final size:98
Alignment explanation
Indices: 1630610--1630985 Score: 452
Period size: 98 Copynumber: 3.8 Consensus size: 98
1630600 TTATGACACA
* ** * * * * * * * *
1630610 TTTCTACCAAAAATGCACTGTTAGGCATTTAACTTGCATTAATGGCACTTTTCTGCCAAAAATGC
1 TTTCTGCCAAAAATGCACCCTTTGTCATCTAAATTGCATTAGTGACACCTTTCTACCAAAAATGC
* * * * *
1630675 AGCATTTGTCATCTAACTTGCATTAGTGGCACC
66 ACCGTTAGGCATTTAACTTGCATTAGTGGCACC
* * *
1630708 TTTCTGCCAAAAATGCACCCTTTGGCATC-AAACTTGCATTAGTTACACCTTTCTACCAGAAATG
1 TTTCTGCCAAAAATGCACCCTTTGTCATCTAAA-TTGCATTAGTGACACCTTTCTACCAAAAATG
*
1630772 CACTACG--AGGCATTTAACTTGCATTAGTGGCACAT
65 CAC--CGTTAGGCATTTAACTTGCATTAGTGGCAC-C
* *
1630807 TTTCTGCCAAAACTGCACCCTTTGTCATCTAACTTGCATTAGTGACACCTTTCTACCAAAAATGC
1 TTTCTGCCAAAAATGCACCCTTTGTCATCTAAATTGCATTAGTGACACCTTTCTACCAAAAATGC
*
1630872 ACCGTTAGGCATTTAACTTGCATTTGTGGCACC
66 ACCGTTAGGCATTTAACTTGCATTAGTGGCACC
* * * *
1630905 TTTATGCCAAAAATGTACCCTTTGTCATCTAAATTACATTAGTGACACCTTTCTACAAAAAATGC
1 TTTCTGCCAAAAATGCACCCTTTGTCATCTAAATTGCATTAGTGACACCTTTCTACCAAAAATGC
1630970 ACCGTTAGGCATTTAA
66 ACCGTTAGGCATTTAA
1630986 ATTTCGTTTT
Statistics
Matches: 240, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
97 4 0.02
98 149 0.62
99 84 0.35
100 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (98 bp):
TTTCTGCCAAAAATGCACCCTTTGTCATCTAAATTGCATTAGTGACACCTTTCTACCAAAAATGC
ACCGTTAGGCATTTAACTTGCATTAGTGGCACC
Found at i:1634725 original size:19 final size:18
Alignment explanation
Indices: 1634699--1634751 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
1634689 CGGTCAACTC
1634699 TGGTCAAAGTCAACAGGT
1 TGGTCAAAGTCAACAGGT
* *
1634717 TGCGTCAAAGTTAACGGGT
1 TG-GTCAAAGTCAACAGGT
1634736 TGGATCAAAGTCAACA
1 TGG-TCAAAGTCAACA
1634752 AGTCAGGTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 3 0.10
19 26 0.90
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (18 bp):
TGGTCAAAGTCAACAGGT
Found at i:1637864 original size:55 final size:55
Alignment explanation
Indices: 1637801--1638079 Score: 411
Period size: 55 Copynumber: 5.1 Consensus size: 55
1637791 AACATGTTCA
1637801 CTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
* * * *
1637856 CTCCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAATAATAGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
* ** *
1637911 CTCCCTATTCTTTCA-AGAGTATGA-ACTCGAACAATCTTC-ATAATTATGTTTG
1 CTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
*
1637963 TTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
* * * *
1638018 TTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTTTG
1 CTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
*
1638073 TTCCCTA
1 CTCCCTA
1638080 AGACTCGAAC
Statistics
Matches: 202, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
52 23 0.11
53 24 0.12
54 23 0.11
55 132 0.65
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (55 bp):
CTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
Found at i:1637981 original size:107 final size:110
Alignment explanation
Indices: 1637801--1638079 Score: 447
Period size: 107 Copynumber: 2.6 Consensus size: 110
1637791 AACATGTTCA
* * * * *
1637801 CTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATTT
1 CTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTTTGTTCCCTATTC
*
1637866 CTTTAGAGAGTATAAGACTCGAACAATCTTCAATAATAGTGTCTG
66 CTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATAGTGTCTG
*
1637911 CTCCCTATTCTTTCA-AGAGTATGA-ACTCGAACAATCTTC-ATAATTATGTTTGTTCCCTATTC
1 CTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTTTGTTCCCTATTC
* *
1637973 CTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
66 CTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATAGTGTCTG
*
1638018 TTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTTTGTTCCCTA
1 CTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTTTGTTCCCTA
1638080 AGACTCGAAC
Statistics
Matches: 155, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
107 74 0.48
108 24 0.15
109 24 0.15
110 33 0.21
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (110 bp):
CTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTTTGTTCCCTATTC
CTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATAGTGTCTG
Found at i:1638093 original size:38 final size:38
Alignment explanation
Indices: 1638042--1638117 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1638032 AGAGAGTATG
*
1638042 AGACTCGAACAATCTTCAATAATTGTGTTTGTTCCCTA
1 AGACTCGAACAATCTTCAATAATCGTGTTTGTTCCCTA
1638080 AGACTCGAACAATCTTCAATAATCGTGTTTGTTCCCTA
1 AGACTCGAACAATCTTCAATAATCGTGTTTGTTCCCTA
1638118 TTCTTTCAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (38 bp):
AGACTCGAACAATCTTCAATAATCGTGTTTGTTCCCTA
Found at i:1638170 original size:54 final size:53
Alignment explanation
Indices: 1638112--1638790 Score: 600
Period size: 54 Copynumber: 12.8 Consensus size: 53
1638102 TCGTGTTTGT
* **
1638112 TCCCTATTCTTTCAGAGAGTATGAG-ACTCGAACATCTTCTTCTTACGGGTTCGC
1 TCCCTCTT-TTTCAG-GAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * **
1638166 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCAAAAAATCGTCTTCTTACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTC-GAACATCTTCTTCAAACGGGTTCGC
* *
1638221 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGAACATCTTTTTCAAACGAGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * *
1638275 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGGATAGCTTCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
*
1638329 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
*
1638383 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
*
1638437 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * * *
1638491 TCCCTCTTTTTTCAGGAAGTAT-AGAACTCCAATAAC-T-TT-ATACGGGTTCAC
1 TCCCTC-TTTTTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
1638542 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGGACA---TCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * *
1638593 TCCCTCTTTCTCTAGG-GAATTTAGAACTCGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-AGGAGTA-TGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* ** *
1638647 TCCCTCTTTCTTCAGGAAGTAT-AGAACTC-CA-AT-AACTTCACACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
1638698 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGGACA---TCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
1638749 TCCCTCTTTCTCTAGGGAGTATG-GAAC-CTGAATATCTTCTTC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTC-GAACATCTTCTTC
1638791 CGCTTCACTA
Statistics
Matches: 544, Mismatches: 48, Indels: 66
0.83 0.07 0.10
Matches are distributed among these distances:
49 3 0.01
50 13 0.02
51 146 0.27
52 9 0.02
53 11 0.02
54 299 0.55
55 61 0.11
56 2 0.00
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (53 bp):
TCCCTCTTTTTCAGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
Found at i:1638361 original size:108 final size:108
Alignment explanation
Indices: 1638122--1638790 Score: 764
Period size: 108 Copynumber: 6.3 Consensus size: 108
1638112 TCCCTATTCT
* ** *
1638122 TTCAGAGAGTAT-GAGACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCT-TCAGGAAG
1 TTCAGGGAGTATAGA-ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAG
* * * **
1638185 TATAGAACTCAAAAAATCGTCTTCTTACGGGTTCGCTCCCTCTTTC
64 TATAGAACTC-GAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
* * *
1638231 TTCAGGAAGTATAGAACTCGAACATCTTTTTCAAACGAGTTCGCTCCCTCTTTCTCTAGGGAGTA
1 TTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTA
* * * *
1638296 TGGAACTCGGATAGCTTCTTCAAACGGGTTCGCTCCCTCTTTC
66 TAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
*
1638339 -TCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
1 TTC-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
*
1638403 ATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
65 ATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
* * * *
1638447 TTCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTT-TTTCAGGAAGT
1 TTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGT
* * * * *
1638511 ATAGAACTCCAATAAC-T-TT-ATACGGGTTCACTCCCTCTTTC
65 ATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
* * *
1638552 -TCTAGGGAGTATGGAACTCGGACA---TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAAT
1 TTC-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
* *
1638613 TTAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
65 ATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
* * ** *
1638657 TTCAGGAAGTATAGAACTC-CA-AT-AACTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTA
1 TTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTA
* *
1638719 TGGAACTCGGACA---TCTTCAAACGGGTTCGCTCCCTCTTTC
66 TAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
* *
1638759 -TCTAGGGAGTATGGAAC-CTGAATATCTTCTTC
1 TTC-AGGGAGTATAGAACTC-GAACATCTTCTTC
1638791 CGCTTCACTA
Statistics
Matches: 484, Mismatches: 58, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
101 3 0.01
102 81 0.17
103 5 0.01
104 7 0.01
105 123 0.25
106 4 0.01
107 5 0.01
108 191 0.39
109 62 0.13
110 3 0.01
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (108 bp):
TTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTA
TAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
Found at i:1638790 original size:156 final size:156
Alignment explanation
Indices: 1638128--1638775 Score: 863
Period size: 156 Copynumber: 4.1 Consensus size: 156
1638118 TTCTTTCAGA
* **
1638128 GAGTAT-GAGACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAA
1 GAGTATAGA-ACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAA
* * * *
1638192 CTCAAAAAATCGTCTTCTTACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCGAACAT
65 CTCAAATAA----CTTCATACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACAT
*
1638256 CTTTTTCAAACGAGTTCGCTCCCTCTTTCTCTAGG
125 C---TTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * * * *
1638291 GAGTATGGAACTCGGATAGCTTCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAA
1 GAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAA
** *
1638355 CTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCT
65 CTC-AA-AT-AACTTCATACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACA---
1638420 TCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGG
124 TCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* *
1638453 AAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTTTTCAGGAAGTATAGAAC
1 GAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
* * * *
1638518 TCCAATAACTTTATACGGGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCAA
66 TCAAATAACTTCATACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAA
1638583 ACGGGTTCGCTCCCTCTTTCTCTAGG
131 ACGGGTTCGCTCCCTCTTTCTCTAGG
* *
1638609 GAATTTAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
1 GAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
* * *
1638674 TCCAATAACTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTCAA
66 TCAAATAACTTCATACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAA
1638739 ACGGGTTCGCTCCCTCTTTCTCTAGG
131 ACGGGTTCGCTCCCTCTTTCTCTAGG
*
1638765 GAGTATGGAAC
1 GAGTATAGAAC
1638776 CTGAATATCT
Statistics
Matches: 434, Mismatches: 39, Indels: 31
0.86 0.08 0.06
Matches are distributed among these distances:
156 188 0.43
157 1 0.00
159 46 0.11
160 2 0.00
161 2 0.00
162 131 0.30
163 57 0.13
164 4 0.01
165 3 0.01
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (156 bp):
GAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
TCAAATAACTTCATACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAA
ACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:1640092 original size:11 final size:11
Alignment explanation
Indices: 1640078--1640116 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
1640068 ATTTTCTTTC
1640078 TTTTTTGTTCT
1 TTTTTTGTTCT
1640089 TTTTTTGTTCCT
1 TTTTTTGTT-CT
1640101 TTTTTT-TTCT
1 TTTTTTGTTCT
1640111 TTTTTT
1 TTTTTT
1640117 CTTTTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 8 0.30
11 11 0.41
12 8 0.30
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (11 bp):
TTTTTTGTTCT
Found at i:1640094 original size:22 final size:22
Alignment explanation
Indices: 1640069--1640120 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1640059 TGAACCCTCA
1640069 TTTTCTTTCTTTTTTGTTCTTT
1 TTTTCTTTCTTTTTTGTTCTTT
* * *
1640091 TTTTGTTCCTTTTTTTTTCTTT
1 TTTTCTTTCTTTTTTGTTCTTT
1640113 TTTTCTTT
1 TTTTCTTT
1640121 TTCATTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (22 bp):
TTTTCTTTCTTTTTTGTTCTTT
Found at i:1640116 original size:10 final size:10
Alignment explanation
Indices: 1640069--1640116 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
1640059 TGAACCCTCA
*
1640069 TTTTCTTTCT
1 TTTTTTTTCT
*
1640079 TTTTTGTTCT
1 TTTTTTTTCT
1640089 TTTTTTGTTCCT
1 TTTTTT-TT-CT
1640101 TTTTTTTTCT
1 TTTTTTTTCT
1640111 TTTTTT
1 TTTTTT
1640117 CTTTTTCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 21 0.64
11 4 0.12
12 8 0.24
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.83
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:1654617 original size:19 final size:19
Alignment explanation
Indices: 1654568--1654628 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1654558 GATCAACTTT
* *
1654568 GGTCAAAGTCAACTAGTCG
1 GGTCAAAGTCAACGAGTCA
*
1654587 GGTCATAA-TCAACGGGTCA
1 GGTCA-AAGTCAACGAGTCA
* *
1654606 GGTCAAAGTCAATGAGTTA
1 GGTCAAAGTCAACGAGTCA
1654625 GGTC
1 GGTC
1654629 GGGTTGACCC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 2 0.06
19 30 0.88
20 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (19 bp):
GGTCAAAGTCAACGAGTCA
Found at i:1656372 original size:12 final size:11
Alignment explanation
Indices: 1656349--1656380 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
1656339 AATAAATAAT
1656349 TGAATGCAATG
1 TGAATGCAATG
1656360 TGAATGTCAATG
1 TGAATG-CAATG
1656372 TGAATGCAA
1 TGAATGCAA
1656381 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (11 bp):
TGAATGCAATG
Found at i:1657387 original size:20 final size:22
Alignment explanation
Indices: 1657351--1657402 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
1657341 CAACCCCATT
1657351 ATATAATATGTTATTTTATATA
1 ATATAATATGTTATTTTATATA
*
1657373 ATATAA-ATG-TATTTTTTATA
1 ATATAATATGTTATTTTATATA
*
1657393 ACATACATAT
1 ATATA-ATAT
1657403 TACGTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 14 0.54
21 4 0.15
22 8 0.31
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (22 bp):
ATATAATATGTTATTTTATATA
Found at i:1658450 original size:16 final size:17
Alignment explanation
Indices: 1658422--1658464 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1658412 TTTATCTTTC
*
1658422 TTTTAATTT-AGTC-CT
1 TTTTAATTTAAGTCACA
*
1658437 TTTTTATTTAAGTCACA
1 TTTTAATTTAAGTCACA
1658454 TTTTAATTTAA
1 TTTTAATTTAA
1658465 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 4 0.17
17 11 0.48
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTTAATTTAAGTCACA
Found at i:1663054 original size:99 final size:99
Alignment explanation
Indices: 1662944--1663129 Score: 302
Period size: 99 Copynumber: 1.9 Consensus size: 99
1662934 AATCATATAT
*
1662944 ATATACAATAAAGCTTGAACTATCACTCTAGAGCAATTGATTAAACGCCCCGA-CTTTATGGATA
1 ATATACAATAAAACTTGAACTATCACTCTAGAGCAATTGATTAAACGCCCC-ATCTTTATGGATA
1663008 AGATTAAGCTAGCCTGATAAAGGTGATTATAATAC
65 AGATTAAGCTAGCCTGATAAAGGTGATTATAATAC
* * * *
1663043 ATATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCATCTTTATGGATAA
1 ATATACAATAAAACTTGAACTATCACTCTAGAGCAATTGATTAAACGCCCCATCTTTATGGATAA
*
1663108 GATTCAGCTAGCCTGATAAAGG
66 GATTAAGCTAGCCTGATAAAGG
1663130 AAAATTAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
98 1 0.01
99 79 0.99
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (99 bp):
ATATACAATAAAACTTGAACTATCACTCTAGAGCAATTGATTAAACGCCCCATCTTTATGGATAA
GATTAAGCTAGCCTGATAAAGGTGATTATAATAC
Found at i:1667851 original size:12 final size:12
Alignment explanation
Indices: 1667834--1667858 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1667824 TTGTAAATAC
1667834 ACATGACGTTGG
1 ACATGACGTTGG
1667846 ACATGACGTTGG
1 ACATGACGTTGG
1667858 A
1 A
1667859 GAACCATCAT
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:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (12 bp):
ACATGACGTTGG
Found at i:1669905 original size:21 final size:22
Alignment explanation
Indices: 1669876--1669923 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
1669866 CCCCCTGTTA
*
1669876 TGTATCGATACA-CCTTGAATG
1 TGTACCGATACATCCTTGAATG
1669897 TGTACCGATACATTCCTTGAATG
1 TGTACCGATACA-TCCTTGAATG
1669920 TGTA
1 TGTA
1669924 TCGGTACCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.46
23 13 0.54
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (22 bp):
TGTACCGATACATCCTTGAATG
Found at i:1670358 original size:19 final size:20
Alignment explanation
Indices: 1670336--1670377 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1670326 AAAAAAAATG
*
1670336 TTTTGTTTTAAAT-TGTTGT
1 TTTTGATTTAAATATGTTGT
*
1670355 TTTTGATTTAATTATGTTGT
1 TTTTGATTTAAATATGTTGT
1670375 TTT
1 TTT
1670378 GAAAACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (20 bp):
TTTTGATTTAAATATGTTGT
Found at i:1672219 original size:13 final size:13
Alignment explanation
Indices: 1672197--1672232 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
1672187 AGGGGGAGTA
1672197 ATTTTCAAAAATG
1 ATTTTCAAAAATG
1672210 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1672222 ATTTTCAAAAA
1 ATTTTCAAAAA
1672233 GAAAATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1673545 original size:16 final size:16
Alignment explanation
Indices: 1673504--1673548 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1673494 CATCACATTT
*
1673504 ATAATTTTTCGCATAC
1 ATAATTTTTTGCATAC
1673520 ATAATTTTTTGCATAC
1 ATAATTTTTTGCATAC
1673536 ATAATTTTTTGCA
1 ATAATTTTTTGCA
1673549 GTTTTAGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (16 bp):
ATAATTTTTTGCATAC
Found at i:1674142 original size:85 final size:85
Alignment explanation
Indices: 1673996--1674839 Score: 1167
Period size: 85 Copynumber: 9.9 Consensus size: 85
1673986 AACTTTTCGA
* * * * *
1673996 AGCATATCTCAAGGAGATAAGGTCTATCTGTCAACAAAAACCTTCGAGTTCGATTAGATTCAGCT
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
1674061 CAAGGGCATATCAAATTTAC
66 CAAGGGCATATCAAATTTAC
1674081 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
*
1674146 CAA-GTCATATCAAATTT-C
66 CAAGGGCATATCAAATTTAC
* * ** * *
1674164 TAGCATAGCTCAATGAGAGAAGGGCTATCTGTCAATGAAAACCATCGAGTTCAATTACATTCAGC
1 -AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* * *
1674229 TGAAAGGCATATCAAATTTAT
65 TCAAGGGCATATCAAATTTAC
* * * *
1674250 AACATAGCTCAAGGCGAGAAGGGTTATCTGTCAGCATAAAACCTTCAAGTTCGATTACATTCAGC
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACA-AAAACCTTCGAGTTCGATTACATTCAGC
*
1674315 TCAAGAGCATATCAAATTTAC
65 TCAAGGGCATATCAAATTTAC
* * * * *
1674336 AGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACGAAAACCTTCAAGTTCGATTGCATTTAGCT
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
* *
1674401 CAA-GTCATATCAAGTTTAC
66 CAAGGGCATATCAAATTTAC
* * * * *
1674420 AGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACGAAAACCTTCAAGTTCGATTGCATTTAGCT
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
* * *
1674485 CAA-GTCATATCAAGTTTAT
66 CAAGGGCATATCAAATTTAC
** * *
1674504 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAATGAAAACCTTCAAGTTCGATTACATTCAACT
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
1674569 CAAGGGCATATCAAATTTAC
66 CAAGGGCATATCAAATTTAC
* *
1674589 AGCATAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAAAAACCTTCGAGTTCGATTACATTCAG
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC--AAAAACCTTCGAGTTCGATTACATTCAG
*
1674654 CTCAAGGGTATATCAAATTTAC
64 CTCAAGGGCATATCAAATTTAC
*
1674676 AGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
1 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
*
1674741 CAAGGGCTTATCAAATTTAC
66 CAAGGGCATATCAAATTTAC
* * *
1674761 AGCATAGCTCAAGG-GAAGAAGGGCTATCTGTCAACAAACACCTTCGAGTTCGATTCCATTTAGC
1 AGCATAGCTCAAGGCG-AGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* *
1674825 TCGAGGGCCTATCAA
65 TCAAGGGCATATCAA
1674840 CCACATGGTA
Statistics
Matches: 685, Mismatches: 66, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
83 1 0.00
84 233 0.34
85 300 0.44
86 73 0.11
87 78 0.11
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (85 bp):
AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCT
CAAGGGCATATCAAATTTAC
Found at i:1675263 original size:21 final size:22
Alignment explanation
Indices: 1675226--1675278 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1675216 CGACCCCATT
1675226 ATATAATATGTAATTTTATATA
1 ATATAATATGTAATTTTATATA
* *
1675248 ATATAA-ATGTATTTTTTTATA
1 ATATAATATGTAATTTTATATA
*
1675269 ACATACATAT
1 ATATA-ATAT
1675279 TACATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 17 0.65
22 7 0.27
23 2 0.08
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
ATATAATATGTAATTTTATATA
Found at i:1675342 original size:3 final size:3
Alignment explanation
Indices: 1675334--1675363 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1675324 CTATACTATA
1675334 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1675364 AATGTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1676465 original size:2 final size:2
Alignment explanation
Indices: 1676458--1676492 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1676448 AACTTTTGTT
1676458 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
1676493 TCTTTTTTAT
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:1678822 original size:21 final size:21
Alignment explanation
Indices: 1678796--1678835 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1678786 CAGAACCCCA
*
1678796 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1678817 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1678836 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1682660 original size:22 final size:21
Alignment explanation
Indices: 1682618--1682657 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1682608 GAGTTTATTT
*
1682618 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1682639 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1682658 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:1685957 original size:2 final size:2
Alignment explanation
Indices: 1685950--1685996 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1685940 GTTTAAACGT
1685950 TA 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 TA
1685992 TA TA T
1 TA TA T
1685997 TTGAGCCTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1686596 original size:38 final size:38
Alignment explanation
Indices: 1686543--1686730 Score: 244
Period size: 38 Copynumber: 5.1 Consensus size: 38
1686533 TTTTTGAAAG
* *
1686543 TATATCATATAGTTTTGAAAATTATTTTTGAAAATACA
1 TATATTATATAGTTTTGAAAATTATTTTTGAAAATATA
* *
1686581 TATATTATATGGTTTTGAAAATGATTTTTGAAAATATA
1 TATATTATATAGTTTTGAAAATTATTTTTGAAAATATA
1686619 TATA-T-TATAGTTTTGAAAATTATTTTTGAAAATATA
1 TATATTATATAGTTTTGAAAATTATTTTTGAAAATATA
* **
1686655 TA-A-TATAT-GTTTTTGAAAA-CATTTTAAAAACATATA
1 TATATTATATAG-TTTTGAAAATTATTTTTGAAA-ATATA
*
1686691 TATAATATATAGTTTTGAAAATTATTTTTGAAAATATA
1 TATATTATATAGTTTTGAAAATTATTTTTGAAAATATA
1686729 TA
1 TA
1686731 GTTTTTGAAA
Statistics
Matches: 131, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
35 11 0.08
36 50 0.38
37 2 0.02
38 59 0.45
39 9 0.07
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (38 bp):
TATATTATATAGTTTTGAAAATTATTTTTGAAAATATA
Found at i:1686632 original size:74 final size:72
Alignment explanation
Indices: 1686533--1686730 Score: 260
Period size: 74 Copynumber: 2.7 Consensus size: 72
1686523 ATAGTTTTTG
* * *
1686533 TTTTTGAAAGTATAT-CA-TATAGTTTTGAAAATTATTTTTGAAAATACATATATTATATGGTTT
1 TTTTTGAAAATATATATATTATAGTTTTGAAAATTATTTTTGAAAATA-ATATAATATATGGTTT
*
1686596 TGAAAATGA
65 TGAAAA-CA
*
1686605 TTTTTGAAAATATATATATTATAGTTTTGAAAATTATTTTTGAAAAT-ATATAATATATGTTTTT
1 TTTTTGAAAATATATATATTATAGTTTTGAAAATTATTTTTGAAAATAATATAATATATGGTTTT
1686669 GAAAACA
66 GAAAACA
**
1686676 TTTTAAAAACATATATATAATATATAGTTTTGAAAATTATTTTTGAAAAT-ATATA
1 TTTTTGAAA-ATATATAT-AT-TATAGTTTTGAAAATTATTTTTGAAAATAATATA
1686731 GTTTTTGAAA
Statistics
Matches: 114, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
71 8 0.07
72 42 0.37
73 3 0.03
74 61 0.54
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.46
Consensus pattern (72 bp):
TTTTTGAAAATATATATATTATAGTTTTGAAAATTATTTTTGAAAATAATATAATATATGGTTTT
GAAAACA
Found at i:1686733 original size:29 final size:28
Alignment explanation
Indices: 1686694--1686758 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
1686684 ACATATATAT
* *
1686694 AATATATAG-TTTTGAAAATTATTTTTGAA
1 AATATATAGTTTTTGAAAA-CA-TTCTGAA
1686723 AATATATAGTTTTTGAAAACATTCTGAA
1 AATATATAGTTTTTGAAAACATTCTGAA
1686751 AATATATA
1 AATATATA
1686759 ATATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 14 0.42
29 10 0.30
30 9 0.27
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (28 bp):
AATATATAGTTTTTGAAAACATTCTGAA
Found at i:1686737 original size:17 final size:17
Alignment explanation
Indices: 1686694--1686741 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1686684 ACATATATAT
1686694 AATATATAG-TTTTG-A
1 AATATATAGTTTTTGAA
1686709 AA-AT-TA-TTTTTGAA
1 AATATATAGTTTTTGAA
1686723 AATATATAGTTTTTGAA
1 AATATATAGTTTTTGAA
1686740 AA
1 AA
1686742 CATTCTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 4 0.14
16 2 0.07
17 10 0.36
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (17 bp):
AATATATAGTTTTTGAA
Found at i:1686834 original size:3 final size:3
Alignment explanation
Indices: 1686821--1686867 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
1686811 ATTTAAGTAA
* *
1686821 TAT TAT T-T TAT TAT TTT TAT TTT TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
1686866 TA
1 TA
1686868 ATTCTTATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:1686852 original size:22 final size:23
Alignment explanation
Indices: 1686821--1686863 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1686811 ATTTAAGTAA
*
1686821 TATTATTTTATTATTTTTATTTT
1 TATTATTTTATTATTATTATTTT
1686844 TATTA-TTTATTATTATTATT
1 TATTATTTTATTATTATTATT
1686864 ATTAATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TATTATTTTATTATTATTATTTT
Found at i:1686859 original size:19 final size:19
Alignment explanation
Indices: 1686830--1686881 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1686820 ATATTATTTT
*
1686830 ATTATTTTTATTTTTATTA
1 ATTATTATTATTTTTATTA
* *
1686849 TTTATTATTATTATTATTA
1 ATTATTATTATTTTTATTA
*
1686868 ATTCTTATTCATTT
1 ATTATTATT-ATTT
1686882 AATTTTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTATTATTATTTTTATTA
Found at i:1687185 original size:16 final size:16
Alignment explanation
Indices: 1687159--1687218 Score: 84
Period size: 16 Copynumber: 3.7 Consensus size: 16
1687149 TCGGAGAACA
*
1687159 AACCACAACAACATCG
1 AACCACAACAACATTG
* *
1687175 AACCCCGACAACATTG
1 AACCACAACAACATTG
1687191 AAACCACAACAACATTG
1 -AACCACAACAACATTG
1687208 AACCACAACAA
1 AACCACAACAA
1687219 GCACAAAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
16 24 0.63
17 14 0.37
ACGTcount: A:0.50, C:0.35, G:0.07, T:0.08
Consensus pattern (16 bp):
AACCACAACAACATTG
Found at i:1687338 original size:18 final size:18
Alignment explanation
Indices: 1687312--1687346 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1687302 TCGTTCAACC
*
1687312 GAAGAAGTCTTCGGAGAA
1 GAAGAAGTCGTCGGAGAA
*
1687330 GAAGGAGTCGTCGGAGA
1 GAAGAAGTCGTCGGAGA
1687347 GTCGGACAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.11, G:0.40, T:0.14
Consensus pattern (18 bp):
GAAGAAGTCGTCGGAGAA
Found at i:1687910 original size:28 final size:27
Alignment explanation
Indices: 1687879--1687988 Score: 91
Period size: 28 Copynumber: 4.0 Consensus size: 27
1687869 AATTTAACCT
1687879 TTTTTATTTTTTATTTTATTTTATTTCA
1 TTTTTATTTTTTATTTTATTTTATTT-A
* *
1687907 TTTTTGTTTTTTATTTT-CTTTATTT-
1 TTTTTATTTTTTATTTTATTTTATTTA
* *
1687932 TTATTATTTTTCTATTACTCAATTTTATTTA
1 TTTTTATTTTT-TATT--T-TATTTTATTTA
* *
1687963 TCTTTATTTATCTATTTTA-TTTATTT
1 TTTTTATTT-TTTATTTTATTTTATTT
1687989 TAATATTATT
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
25 9 0.14
26 4 0.06
27 14 0.22
28 18 0.28
29 1 0.02
30 7 0.11
31 11 0.17
32 1 0.02
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (27 bp):
TTTTTATTTTTTATTTTATTTTATTTA
Found at i:1687918 original size:23 final size:21
Alignment explanation
Indices: 1687881--1687933 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
1687871 TTTAACCTTT
1687881 TTTATTTTTTATTTTATTTTA
1 TTTATTTTTTATTTTATTTTA
* *
1687902 TTTCATTTTTGTTTTTTATTTTC
1 TTT-ATTTTT-TATTTTATTTTA
1687925 TTTATTTTT
1 TTTATTTTT
1687934 ATTATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 12 0.43
23 13 0.46
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTATTTTTTATTTTATTTTA
Found at i:1687930 original size:9 final size:8
Alignment explanation
Indices: 1687878--1687947 Score: 54
Period size: 9 Copynumber: 8.1 Consensus size: 8
1687868 AAATTTAACC
1687878 TTTTTTA-
1 TTTTTTAT
1687885 TTTTTTATT
1 TTTTTTA-T
1687894 TTATTTTAT
1 TT-TTTTAT
1687903 TTCATTTT-T
1 TT--TTTTAT
1687912 GTTTTTTAT
1 -TTTTTTAT
1687921 TTTCTTTAT
1 TTT-TTTAT
1687930 TTTTATTAT
1 TTTT-TTAT
*
1687939 TTTTCTAT
1 TTTTTTAT
1687947 T
1 T
1687948 ACTCAATTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
7 7 0.13
8 12 0.22
9 23 0.43
10 12 0.22
ACGTcount: A:0.14, C:0.04, G:0.01, T:0.80
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1687957 original size:57 final size:58
Alignment explanation
Indices: 1687896--1688007 Score: 138
Period size: 57 Copynumber: 1.9 Consensus size: 58
1687886 TTTTTATTTT
* * * * * *
1687896 ATTTTATTTCATTTTTGTTT-TTTATTTTCTTTATTTT-TATTATTTTTCTATTACTCA
1 ATTTTATTT-ATCTTTATTTATCTATTTTATTTATTTTATATTATTATTATATTACTCA
1687953 ATTTTATTTATCTTTATTTATCTATTTTATTTATTTTAATATTATTATTATATTA
1 ATTTTATTTATCTTTATTTATCTATTTTATTTATTTT-ATATTATTATTATATTA
1688008 ATATTTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 8 0.17
57 24 0.52
59 14 0.30
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (58 bp):
ATTTTATTTATCTTTATTTATCTATTTTATTTATTTTATATTATTATTATATTACTCA
Done.