Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008650.1 Hibiscus syriacus cultivar Beakdansim tig00111640_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: 1713193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:987532 original size:21 final size:21
Alignment explanation
Indices: 987506--987559 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
987496 GTTTCCAGAT
*
987506 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
987527 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
987548 TCGTAATGCGAA
1 TCGCAATGCGAA
987560 TATGTAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:987541 original size:121 final size:121
Alignment explanation
Indices: 987322--987579 Score: 435
Period size: 121 Copynumber: 2.1 Consensus size: 121
987312 AATGACCAAC
987322 TAAATCGCAATGCGATCGATAATTCGCAACGCGATCTCCGGTATAGCAAAGCAGTTTCCAGATTC
1 TAAATCGCAATGCGATCGATAATTCGCAACGCGATCTCCGGTATAGCAAAGCAGTTTCCAGATTC
* * *
987387 GCAACGTGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGTGAATATG
66 GCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATG
* * * * *
987443 TAAACCGCAATGCGATCGATAATTCGTAACGCGATCTCCGGTATCGTAAATCAGTTTCCAGATTC
1 TAAATCGCAATGCGATCGATAATTCGCAACGCGATCTCCGGTATAGCAAAGCAGTTTCCAGATTC
*
987508 GCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGTAATGCGAATATG
66 GCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATG
987564 TAAATCGCAATGCGAT
1 TAAATCGCAATGCGAT
987580 AGTCGAAGTT
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 127 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (121 bp):
TAAATCGCAATGCGATCGATAATTCGCAACGCGATCTCCGGTATAGCAAAGCAGTTTCCAGATTC
GCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATG
Found at i:987710 original size:6 final size:6
Alignment explanation
Indices: 987699--987736 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
987689 GACACGTATT
987699 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
987737 CGAGACGGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:988436 original size:32 final size:33
Alignment explanation
Indices: 988376--988438 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
988366 TCGCAACGCA
988376 AACTTCGACTATCGCAACGCGAACTTGGAATGCG
1 AACTTCGACTATCGCAAC-CGAACTTGGAATGCG
988410 AACTTCGACTATCGCAA-CGAACTTGGAAT
1 AACTTCGACTATCGCAACCGAACTTGGAAT
988439 AAATCGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 12 0.41
34 17 0.59
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (33 bp):
AACTTCGACTATCGCAACCGAACTTGGAATGCG
Found at i:988474 original size:21 final size:20
Alignment explanation
Indices: 988408--988474 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
988398 ACTTGGAATG
*
988408 CGAACTTCGACTATCGC-AA
1 CGAACTTGGACTATCGCAAA
* * *
988427 CGAACTTGGAATAAATCGTAACG
1 CGAACTTGGACT--ATCGCAA-A
988450 CGAACTTGGACTATCGCAATA
1 CGAACTTGGACTATCGCAA-A
988471 CGAA
1 CGAA
988475 TATGTAAATC
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 10 0.28
21 14 0.39
22 1 0.03
23 11 0.31
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
CGAACTTGGACTATCGCAAA
Found at i:991933 original size:4 final size:4
Alignment explanation
Indices: 991924--991948 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
991914 TATAGATTTT
991924 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
991949 ATTGATTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:995180 original size:103 final size:103
Alignment explanation
Indices: 995001--995207 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
994991 TGAGAAGGTA
995001 CTCTTCTTGTTTCCTGCATCCAATCTGCCTAACTTTGTTTCTTGACTACAAGAACTGCTTGTTGG
1 CTCTTCTTGTTTCCTGCATCCAATCTGCCTAACTTTGTTTCTTGACTACAAGAACTGCTTGTTGG
995066 AAGTTTAAGATGATTCCACTCGTTTTCCATTTATCTTT
66 AAGTTTAAGATGATTCCACTCGTTTTCCATTTATCTTT
995104 CTCTTCTTGTTTCCTGCATCCAATCTGCCTAACTTTGTTTCTTGACTACAAGAACTGCTTGTTGG
1 CTCTTCTTGTTTCCTGCATCCAATCTGCCTAACTTTGTTTCTTGACTACAAGAACTGCTTGTTGG
995169 AAGTTTAAGATGATTCCACTCGTTTTCCATTTATCTTT
66 AAGTTTAAGATGATTCCACTCGTTTTCCATTTATCTTT
995207 C
1 C
995208 CCCTTCTGCA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (103 bp):
CTCTTCTTGTTTCCTGCATCCAATCTGCCTAACTTTGTTTCTTGACTACAAGAACTGCTTGTTGG
AAGTTTAAGATGATTCCACTCGTTTTCCATTTATCTTT
Found at i:995325 original size:21 final size:21
Alignment explanation
Indices: 995299--995342 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
995289 TACGAAGAAA
995299 GCAAGTGTACAGAGATGCACT
1 GCAAGTGTACAGAGATGCACT
995320 GCAAGTGTACAGAGATGCACT
1 GCAAGTGTACAGAGATGCACT
995341 GC
1 GC
995343 GAAAGTGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (21 bp):
GCAAGTGTACAGAGATGCACT
Found at i:998219 original size:165 final size:164
Alignment explanation
Indices: 997983--998296 Score: 459
Period size: 165 Copynumber: 1.9 Consensus size: 164
997973 AAATGTTGGA
* * *
997983 TTCCAGTCGGTTTTACTCAGATACAACTGTGTTGGTTCCTATGACACATTGAAATAGATGTAGTC
1 TTCCAGTCAGTTTTAATCAGATACAACTGTGTTGGTTCCTATGACACATTGAAATACATGTAGTC
* * * *
998048 AAAGCAGTTTCAGGTTATGAGGGTGGGGGATTGATGTGATCTATGGAGCATTGAAATGAAGTAAT
66 AAAGCAGTTTCACGTTATGA-GGAGGGGAATTGATGTGATCTAAGGAGCATTGAAATGAAGTAAT
*
998113 GCGTGGTCAGCACATTCAAATAATGAATTCCAGAC
130 GCGCGGTCAGCACATTCAAATAATGAATTCCAGAC
* * *
998148 TTCCAGTCATTTTTAATCAGATACAATTGTGTTGGTTTCTATGACACATTGAAATACATGTAG-C
1 TTCCAGTCAGTTTTAATCAGATACAACTGTGTTGGTTCCTATGACACATTGAAATACATGTAGTC
* *
998212 AAAAGCAGTTTCACGTTATGAGGAGGGGAATTGATGTGATTTAAGGAGGATTGAAATGAAGTAAT
66 -AAAGCAGTTTCACGTTATGAGGAGGGGAATTGATGTGATCTAAGGAGCATTGAAATGAAGTAAT
* **
998277 GTGCGGTCAGTGCATTCAAA
130 GCGCGGTCAGCACATTCAAA
998297 CGTTTGGAAT
Statistics
Matches: 132, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
164 56 0.42
165 76 0.58
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (164 bp):
TTCCAGTCAGTTTTAATCAGATACAACTGTGTTGGTTCCTATGACACATTGAAATACATGTAGTC
AAAGCAGTTTCACGTTATGAGGAGGGGAATTGATGTGATCTAAGGAGCATTGAAATGAAGTAATG
CGCGGTCAGCACATTCAAATAATGAATTCCAGAC
Found at i:1015308 original size:3 final size:3
Alignment explanation
Indices: 1015300--1015354 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1015290 CACAAGATCA
1015300 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1015348 TAT TAT T
1 TAT TAT T
1015355 TCTTGTGATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1016241 original size:5 final size:5
Alignment explanation
Indices: 1016231--1016256 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1016221 TTTACCCTAA
1016231 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
1016257 ACATTGCATT
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:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1016283 original size:44 final size:42
Alignment explanation
Indices: 1016229--1016327 Score: 137
Period size: 44 Copynumber: 2.3 Consensus size: 42
1016219 TTTTTACCCT
1016229 AAACCCGACCCGACCCGACCCG-ACCCGAACATTGCATTTTAAAA
1 AAACCCGACCCGACCCGACCCGAACCCG-A-ATT-CATTTTAAAA
**
1016273 AAACCCGACCCGACCCGACCCGAACCCGAATTTTTTTTAAAA
1 AAACCCGACCCGACCCGACCCGAACCCGAATTCATTTTAAAA
*
1016315 AAATCCGACCCGA
1 AAACCCGACCCGA
1016328 TCGGGTCGTG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
42 20 0.39
43 3 0.06
44 23 0.45
45 5 0.10
ACGTcount: A:0.34, C:0.37, G:0.13, T:0.15
Consensus pattern (42 bp):
AAACCCGACCCGACCCGACCCGAACCCGAATTCATTTTAAAA
Found at i:1019115 original size:2 final size:2
Alignment explanation
Indices: 1019108--1019148 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1019098 AAGCTAAATA
1019108 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1019147 AT
1 AT
1019149 TAAATATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1022194 original size:214 final size:214
Alignment explanation
Indices: 1021799--1022234 Score: 818
Period size: 214 Copynumber: 2.0 Consensus size: 214
1021789 AGGATTGGTC
1021799 AAGACACAAGAGTTATACTCCCTCCATCTCCGTTCCATTCGTGTATGATATTGACTATATACATA
1 AAGACACAAGAGTTATACTCCCTCCATCTCCGTTCCATTCGTGTATGATATTGACTATATACATA
1021864 GTTTTAGGAGATATAGTTGACCAAGAGAAATGACAAAATTATCTTTAAAATATGATTGATAGATT
66 GTTTTAGGAGATATAGTTGACCAAGAGAAATGACAAAATTATCTTTAAAATATGATTGATAGATT
*
1021929 TAACATAATTGTTTTATATGTATAAAATAGTGAGATATAATGATAAAAAAAATATAAGTGTTGTT
131 TAACATAATTGTTTTATATGTATAAAATAGTGAGATATAAGGATAAAAAAAATATAAGTGTTGTT
1021994 ATTTGTTGATTTTTATAAT
196 ATTTGTTGATTTTTATAAT
1022013 AAGACACAAGAGTTATACTCCCTCCATCTCCGTTCCATTCGTGTATGATATTGACTATATACATA
1 AAGACACAAGAGTTATACTCCCTCCATCTCCGTTCCATTCGTGTATGATATTGACTATATACATA
*
1022078 GTTTTAGGAGATATAGTTGACCAAGAGAAATGATAAAATTATCTTTAAAATATGATTGATAGATT
66 GTTTTAGGAGATATAGTTGACCAAGAGAAATGACAAAATTATCTTTAAAATATGATTGATAGATT
* *
1022143 TGACATAATTATTTTTATATGTATAAAATAGTGAGATATAAGGATAAAAAAAATATAAGTGTTGT
131 TAACATAATT-GTTTTATATGTATAAAATAGTGAGATATAAGGATAAAAAAAATATAAGTGTTGT
*
1022208 TATTTGTTGATTTTTCTAAT
195 TATTTGTTGATTTTTATAAT
1022228 AAGACAC
1 AAGACAC
1022235 TTTGAACAAG
Statistics
Matches: 216, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
214 138 0.64
215 78 0.36
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (214 bp):
AAGACACAAGAGTTATACTCCCTCCATCTCCGTTCCATTCGTGTATGATATTGACTATATACATA
GTTTTAGGAGATATAGTTGACCAAGAGAAATGACAAAATTATCTTTAAAATATGATTGATAGATT
TAACATAATTGTTTTATATGTATAAAATAGTGAGATATAAGGATAAAAAAAATATAAGTGTTGTT
ATTTGTTGATTTTTATAAT
Found at i:1027580 original size:17 final size:17
Alignment explanation
Indices: 1027558--1027594 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1027548 TAAACTTGTG
1027558 TGTTGGTCTTATTCATA
1 TGTTGGTCTTATTCATA
1027575 TGTTGGTCTTATTCATA
1 TGTTGGTCTTATTCATA
1027592 TGT
1 TGT
1027595 GAGAATGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.54
Consensus pattern (17 bp):
TGTTGGTCTTATTCATA
Found at i:1030464 original size:326 final size:327
Alignment explanation
Indices: 1029868--1030526 Score: 1194
Period size: 326 Copynumber: 2.0 Consensus size: 327
1029858 TTTATTTGTT
*
1029868 GACTATTAATGGTTATAAAATAGTCATCTGATTATTCATTATGTTTCAAACTCGTTCTTTTTTCG
1 GACTATTAATGGTTATAAAATAATCATCTGATTATTCATTATGTTTCAAACTCGTTCTTTTTTCG
* * *
1029933 TTAAAATTTTGATTGTCATCTGAGCTGGATGTTAACATGATGACTGTGATATGATAGTCGTTTGA
66 TTAAAATTTTGATTATCATCTGAGCTGGATATTAACATGAT-A-TGGGATATGATAGTCGTTTGA
**
1029998 GATTCTTGGATTGAATTTTATCATATCACAGTCAACGAGTTAATGTACAACTCAGATTGCCATCA
129 GATTCTAAGATTGAATTTTATCATATCACAGTCAACGAGTTAATGTACAACTCAGATTGCCATCA
*
1030063 ATTTTTAAAGAAAAATGGCGAGTTTGAAAATAATAAATAGTTGTGTGACTATTTTGTAACTTTTA
194 ATTTTTAAAGAAAAATGGCGAGTTTGAAAATAATAAATAGTTGTGTGACTATTTTATAACTTTTA
*
1030128 ATAGTCGAAGGACTTAACAAAGTAACATTTTATAGTTAGAGAATCATTTTGTAACTTTTTTATAG
259 ATAGTCGAAGGACTTAACAAAGTAACATTTTATAGTTAGAAAATCATTTTGTAACTTTTTTATAG
1030193 TCGA
324 TCGA
1030197 GACTATTAATGGTTATAAAATAATCATCTGATTATTCATTATGTTTCAAACTCGTTCTTTTTTCG
1 GACTATTAATGGTTATAAAATAATCATCTGATTATTCATTATGTTTCAAACTCGTTCTTTTTTCG
* *
1030262 TTAAAATTTTGATTATCGTCTGAGTTGGATATTAACATGAT-TGGGATATGATAGTCGTTTGAGA
66 TTAAAATTTTGATTATCATCTGAGCTGGATATTAACATGATATGGGATATGATAGTCGTTTGAGA
1030326 TTCTAAGATTGAATTTTATCATATCACAGTCAACGAGTTAATGTACAACTCAGATTGCCATCAAT
131 TTCTAAGATTGAATTTTATCATATCACAGTCAACGAGTTAATGTACAACTCAGATTGCCATCAAT
*
1030391 TTTTAAAGGAAAATGGCGAGTTTGAAAATAATAAATAGTTGTGTGACTATTTTATAACTTTTAAT
196 TTTTAAAGAAAAATGGCGAGTTTGAAAATAATAAATAGTTGTGTGACTATTTTATAACTTTTAAT
1030456 AGTCGAAGGACTTAACAAAGTAACATTTTATAGTTAGAAAATCATTTTGTAACTTTTTTATAGTC
261 AGTCGAAGGACTTAACAAAGTAACATTTTATAGTTAGAAAATCATTTTGTAACTTTTTTATAGTC
1030521 GA
326 GA
1030523 GACT
1 GACT
1030527 CAACAAAACA
Statistics
Matches: 319, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
326 218 0.68
329 101 0.32
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.39
Consensus pattern (327 bp):
GACTATTAATGGTTATAAAATAATCATCTGATTATTCATTATGTTTCAAACTCGTTCTTTTTTCG
TTAAAATTTTGATTATCATCTGAGCTGGATATTAACATGATATGGGATATGATAGTCGTTTGAGA
TTCTAAGATTGAATTTTATCATATCACAGTCAACGAGTTAATGTACAACTCAGATTGCCATCAAT
TTTTAAAGAAAAATGGCGAGTTTGAAAATAATAAATAGTTGTGTGACTATTTTATAACTTTTAAT
AGTCGAAGGACTTAACAAAGTAACATTTTATAGTTAGAAAATCATTTTGTAACTTTTTTATAGTC
GA
Found at i:1033228 original size:23 final size:25
Alignment explanation
Indices: 1033186--1033234 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1033176 TATATAGTAT
1033186 TTTTAAAAAATGTTTCATTAA-AAA
1 TTTTAAAAAATGTTTCATTAATAAA
1033210 TTTTAAAAATAT-TTT-ATTAATAAA
1 TTTTAAAAA-ATGTTTCATTAATAAA
1033234 T
1 T
1033235 GAAAATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.22
24 16 0.70
25 2 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTTAAAAAATGTTTCATTAATAAA
Found at i:1049115 original size:37 final size:36
Alignment explanation
Indices: 1049040--1049115 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1049030 TTTTTATATT
*
1049040 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1049076 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1049113 TTT
1 TTT
1049116 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1050776 original size:2 final size:2
Alignment explanation
Indices: 1050769--1050798 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1050759 TGGACTGTCC
1050769 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
1050799 TGATAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1051536 original size:14 final size:15
Alignment explanation
Indices: 1051517--1051546 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1051507 GATTTGAAGA
1051517 TTTAATTT-TTTAAT
1 TTTAATTTATTTAAT
1051531 TTTAATTTATTTAAT
1 TTTAATTTATTTAAT
1051546 T
1 T
1051547 AAATGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATTTATTTAAT
Found at i:1052070 original size:15 final size:16
Alignment explanation
Indices: 1052036--1052075 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1052026 ATTAATTATT
* *
1052036 TTTAAATATAAATTAA
1 TTTAAAAATAAATCAA
1052052 TTTAAAAAT-AATCAA
1 TTTAAAAATAAATCAA
1052067 TTTAAAAAT
1 TTTAAAAAT
1052076 TATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTAAAAATAAATCAA
Found at i:1052416 original size:19 final size:18
Alignment explanation
Indices: 1052379--1052419 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1052369 ATTGGATAAA
**
1052379 AAATTAATTTAATTGAAT
1 AAATTAATTTAATAAAAT
1052397 AAATTAATATTAATAAAAT
1 AAATTAAT-TTAATAAAAT
1052416 AAAT
1 AAAT
1052420 CTTCAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATTAATTTAATAAAAT
Found at i:1055908 original size:3 final size:3
Alignment explanation
Indices: 1055900--1055925 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1055890 TTTCAACCCT
1055900 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1055926 TCCATGTTGA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1057047 original size:2 final size:2
Alignment explanation
Indices: 1057040--1057067 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1057030 AACACAGAAG
1057040 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
1057068 TAGTTTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1058459 original size:31 final size:30
Alignment explanation
Indices: 1058402--1058468 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
1058392 GTATGTTTTT
* *
1058402 AAAGTTTAGTGACCAAAGTATAAATTTAC-A
1 AAAGTTTAGGGACCAAAATATAAATTT-CTA
1058432 AAAGTTTAGGGGACCAAAA-ATATAATTTCTA
1 AAAGTTTA-GGGACCAAAATATA-AATTTCTA
1058463 AAAGTT
1 AAAGTT
1058469 ATATATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (30 bp):
AAAGTTTAGGGACCAAAATATAAATTTCTA
Found at i:1061015 original size:15 final size:15
Alignment explanation
Indices: 1060995--1061024 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1060985 TGAAAGCTAT
*
1060995 GAAAAGTATATGAAA
1 GAAAAGAATATGAAA
1061010 GAAAAGAATATGAAA
1 GAAAAGAATATGAAA
1061025 ATGAAAAATG
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:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (15 bp):
GAAAAGAATATGAAA
Found at i:1062367 original size:219 final size:218
Alignment explanation
Indices: 1061988--1062425 Score: 858
Period size: 219 Copynumber: 2.0 Consensus size: 218
1061978 TTAACCTTTC
1061988 TGATGTATGGTCTTTATATGATCTAAAGTGGTTAGTTTCAATGCTATAGAAAAATGTCCAAATTA
1 TGATGTATGGTCTTTATATGATCTAAAGTGGTTAGTTTCAATGCTATAGAAAAATGTCCAAATTA
1062053 TGTATTTAGTTTACAATGGTAGTTATAAATCTTATTTTAGTTTTGGATATTTTTCACTTTTTAAT
66 TGTATTTAGTTTACAATGGTAGTTATAAATCTTATTTTAGTTTTGGATATTTTTCACTTTTTAAT
1062118 AATACTAGCGCCTTTTATTCAAAAAAAAAACTTAAAATGAAATCAATACATATTACAATTAGAAA
131 AATACTAGCGCCTTTTATTCAAAAAAAAAACTTAAAATGAAATCAATACATATTACAATTAG-AA
1062183 AACATAAAATATTACAAACGGGGT
195 AACATAAAATATTACAAACGGGGT
1062207 TGATGTATGGTCTTTATATGATCTAAAGTGGTTAGTTTCAATGCTATAGAAAAATGTCCAAATTA
1 TGATGTATGGTCTTTATATGATCTAAAGTGGTTAGTTTCAATGCTATAGAAAAATGTCCAAATTA
1062272 TGTATTTAGTTTACAATGGTAGTTATAAATCTTATTTTAGTTTTGGATATTTTTCACTTTTTAAT
66 TGTATTTAGTTTACAATGGTAGTTATAAATCTTATTTTAGTTTTGGATATTTTTCACTTTTTAAT
*
1062337 AATACTAGCGGCTTTTATTCAAAAAAAAAACTTAAAATGAAATCAATACATATTACAATTAGAAA
131 AATACTAGCGCCTTTTATTCAAAAAAAAAACTTAAAATGAAATCAATACATATTACAATTAGAAA
1062402 ACATAAAATATTACAAACGGGGT
196 ACATAAAATATTACAAACGGGGT
1062425 T
1 T
1062426 TGTTCAAGTG
Statistics
Matches: 218, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
218 27 0.12
219 191 0.88
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (218 bp):
TGATGTATGGTCTTTATATGATCTAAAGTGGTTAGTTTCAATGCTATAGAAAAATGTCCAAATTA
TGTATTTAGTTTACAATGGTAGTTATAAATCTTATTTTAGTTTTGGATATTTTTCACTTTTTAAT
AATACTAGCGCCTTTTATTCAAAAAAAAAACTTAAAATGAAATCAATACATATTACAATTAGAAA
ACATAAAATATTACAAACGGGGT
Found at i:1065463 original size:23 final size:23
Alignment explanation
Indices: 1065412--1065464 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1065402 AAAAAATGTA
* * *
1065412 AAAAACATAAGAAAATATGTCAT
1 AAAAACATAAGAAAATATATAAC
*
1065435 AAAAACATATGAAAATATATAAC
1 AAAAACATAAGAAAATATATAAC
*
1065458 ACAAACA
1 AAAAACA
1065465 GATTTATTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.64, C:0.11, G:0.06, T:0.19
Consensus pattern (23 bp):
AAAAACATAAGAAAATATATAAC
Found at i:1072520 original size:31 final size:31
Alignment explanation
Indices: 1072485--1072548 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1072475 CAAAAGTGGC
1072485 CAAATCTAAATTAAAACAAAATGAAAATAAT
1 CAAATCTAAATTAAAACAAAATGAAAATAAT
* * *
1072516 CAAATCTTAATTAAAACGAAATGAAAATGAT
1 CAAATCTAAATTAAAACAAAATGAAAATAAT
1072547 CA
1 CA
1072549 TTTTTGTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.59, C:0.11, G:0.06, T:0.23
Consensus pattern (31 bp):
CAAATCTAAATTAAAACAAAATGAAAATAAT
Found at i:1072573 original size:2 final size:2
Alignment explanation
Indices: 1072566--1072602 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1072556 AGTTTCCCTA
1072566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1072603 GTATTGGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1077051 original size:42 final size:42
Alignment explanation
Indices: 1076964--1077058 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 42
1076954 ATTGAATTAA
**
1076964 ACGGGGACGGGAAAAAACCGTTTATGCTAAACGGGAAAGGAG
1 ACGGGGACGGGAAAAAACCGTTTATGCTAAACGCCAAAGGAG
* *
1077006 AC-GGGACGGGGAAAAACCGTTTATGCTAAACGCCAAACGGGG
1 ACGGGGACGGGAAAAAACCGTTTATGCTAAACGCCAAA-GGAG
1077048 ACGGGGACGGG
1 ACGGGGACGGG
1077059 TTTGATAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
41 32 0.68
42 7 0.15
43 8 0.17
ACGTcount: A:0.34, C:0.18, G:0.38, T:0.11
Consensus pattern (42 bp):
ACGGGGACGGGAAAAAACCGTTTATGCTAAACGCCAAAGGAG
Found at i:1077141 original size:2 final size:2
Alignment explanation
Indices: 1077134--1077189 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
1077124 ATTTAAATTA
* *
1077134 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT TT A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1077174 AA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1077190 CCGGCCCGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1081553 original size:11 final size:11
Alignment explanation
Indices: 1081535--1081568 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1081525 AATAAGTTTT
1081535 TTAAATTA-AA
1 TTAAATTATAA
1081545 TTGAAATTATAA
1 TT-AAATTATAA
1081557 TTAAATTATAA
1 TTAAATTATAA
1081568 T
1 T
1081569 CTTGGTGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 16 0.73
12 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
TTAAATTATAA
Found at i:1082691 original size:20 final size:20
Alignment explanation
Indices: 1082666--1082763 Score: 151
Period size: 20 Copynumber: 4.9 Consensus size: 20
1082656 TATAGATTCA
*
1082666 TTACGATTTTACTATTCATG
1 TTACGATTTTACTATTCACG
1082686 TTACGATTTTACTATTCACG
1 TTACGATTTTACTATTCACG
** *
1082706 TTGTGATTTTACTATTAACG
1 TTACGATTTTACTATTCACG
*
1082726 TTACGATTTTACTATTAACG
1 TTACGATTTTACTATTCACG
1082746 TTACGATTTTACTATTCA
1 TTACGATTTTACTATTCA
1082764 TGTTGCGAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (20 bp):
TTACGATTTTACTATTCACG
Found at i:1084503 original size:17 final size:16
Alignment explanation
Indices: 1084481--1084549 Score: 70
Period size: 15 Copynumber: 4.3 Consensus size: 16
1084471 CCGTGTCCCG
*
1084481 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
1084498 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
1084513 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
1084530 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
1084545 ACCCG
1 ACCCG
1084550 ATACCCGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:1084513 original size:15 final size:15
Alignment explanation
Indices: 1084493--1084549 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
1084483 CCGGATGTTA
1084493 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
1084508 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
1084524 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
1084540 CGGGTACCCG
1 CGGGTACCCG
1084550 ATACCCGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:1084517 original size:32 final size:32
Alignment explanation
Indices: 1084481--1084549 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
1084471 CCGTGTCCCG
1084481 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
* *
1084513 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
1084545 ACCCG
1 ACCCG
1084550 ATACCCGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGGGT
Found at i:1087148 original size:3 final size:3
Alignment explanation
Indices: 1087136--1087197 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
1087126 GATTTCTTCT
* * * *
1087136 TCC TCT TCC TCC TCC TCC TCC TCC TCC TCC TCT TCC TCT TCC TCC TCA
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
* *
1087184 TCA TCC TCG TCC TC
1 TCC TCC TCC TCC TC
1087198 GTCAATTTCA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.03, C:0.56, G:0.02, T:0.39
Consensus pattern (3 bp):
TCC
Found at i:1087182 original size:9 final size:9
Alignment explanation
Indices: 1087130--1087173 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
1087120 AGGCTTGATT
*
1087130 TCTTCTTCC
1 TCTTCCTCC
1087139 TCTTCCTCC
1 TCTTCCTCC
*
1087148 TCCTCCTCC
1 TCTTCCTCC
*
1087157 TCCTCCTCC
1 TCTTCCTCC
1087166 TCTTCCTC
1 TCTTCCTC
1087174 TTCCTCCTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (9 bp):
TCTTCCTCC
Found at i:1087468 original size:34 final size:34
Alignment explanation
Indices: 1087425--1087493 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1087415 CATGCACAGC
*
1087425 AGTTCAAACTGAAAACCAAGCATGTGACGAGAGT
1 AGTTCAAACTGAAAACCAAGCATATGACGAGAGT
1087459 AGTTCAAACTGAAAACCAAGCATATGACGAGAGT
1 AGTTCAAACTGAAAACCAAGCATATGACGAGAGT
1087493 A
1 A
1087494 CATGAAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (34 bp):
AGTTCAAACTGAAAACCAAGCATATGACGAGAGT
Found at i:1091564 original size:13 final size:13
Alignment explanation
Indices: 1091548--1091573 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1091538 TAAATGAATT
1091548 TAATTTTTTAAAG
1 TAATTTTTTAAAG
1091561 TAATTTTTTAAAG
1 TAATTTTTTAAAG
1091574 AGTTTGCATA
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:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TAATTTTTTAAAG
Found at i:1093467 original size:122 final size:122
Alignment explanation
Indices: 1093318--1093554 Score: 429
Period size: 122 Copynumber: 1.9 Consensus size: 122
1093308 ACATGACTCG
* *
1093318 GTATCTCTAATTTAGTGTTACGAATAAATAAATCTAATATATGATCATTCACCTAATTAAATAAA
1 GTATCTCTAATTTAGTGTAACGAATAAATAAATCTAATATACGATCATTCACCTAATTAAATAAA
*
1093383 ATAGTATACAAAATTAAAATATAAACTAATATTAAAAAATAAATGAACAATAAAATA
66 ATAGTATACAAAATTAAAATATAAACTAATACTAAAAAATAAATGAACAATAAAATA
* *
1093440 GTATCTCTAATTTAGTGTAACGAATAAATAAATCTAATATACGATCATTTATCTAATTAAATAAA
1 GTATCTCTAATTTAGTGTAACGAATAAATAAATCTAATATACGATCATTCACCTAATTAAATAAA
1093505 ATAGTATACAAAATTAAAATATAAACTAATACTAAAAAATAAATGAACAA
66 ATAGTATACAAAATTAAAATATAAACTAATACTAAAAAATAAATGAACAA
1093555 AACATTCATA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 110 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (122 bp):
GTATCTCTAATTTAGTGTAACGAATAAATAAATCTAATATACGATCATTCACCTAATTAAATAAA
ATAGTATACAAAATTAAAATATAAACTAATACTAAAAAATAAATGAACAATAAAATA
Found at i:1094941 original size:24 final size:25
Alignment explanation
Indices: 1094909--1094978 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
1094899 ACCTCACCCA
*
1094909 ATATATGTTTAATAATTAATATAAT
1 ATATTTGTTTAATAATTAATATAAT
*
1094934 A-ATTTGTTTAATAATATAA-ATTAT
1 ATATTTGTTTAATAAT-TAATATAAT
*
1094958 ATATTT-TTTAAAAAGTTAATA
1 ATATTTGTTTAATAA-TTAATA
1094979 ATTTGAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 28 0.74
25 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
ATATTTGTTTAATAATTAATATAAT
Found at i:1097926 original size:25 final size:25
Alignment explanation
Indices: 1097892--1097941 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1097882 TATAACTAAA
1097892 AAAAGTTATTAT-TTTATAATAATTT
1 AAAAGTTATTATGTTTATAA-AATTT
* *
1097917 AAAATTTATTTTGTTTATAAAATTT
1 AAAAGTTATTATGTTTATAAAATTT
1097942 TAATAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
AAAAGTTATTATGTTTATAAAATTT
Found at i:1099732 original size:11 final size:11
Alignment explanation
Indices: 1099711--1099740 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1099701 TTATTGATAA
1099711 ATTTAAATTATT
1 ATTT-AATTATT
1099723 ATTTAATTATT
1 ATTTAATTATT
1099734 ATTTAAT
1 ATTTAAT
1099741 AATACATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTAATTATT
Found at i:1099808 original size:66 final size:67
Alignment explanation
Indices: 1099671--1099809 Score: 201
Period size: 67 Copynumber: 2.1 Consensus size: 67
1099661 AGATCAAATA
* * *
1099671 AATAATACATTTTCTTAATATGCCAAGTGGTTATTGATAAATTTAAATTATTATTTAATTATTAT
1 AATAATACATCTTCTTAATATGCAAAGTGGTTATGGATAAATTTAAATTATTATTTAATTATTAT
1099736 TT
66 TT
* * *
1099738 AATAATACATCTTCTTAATATGTAAAGTGG-TGTGGAT-AATTTTAATTATTATATTAATTATTA
1 AATAATACATCTTCTTAATATGCAAAGTGGTTATGGATAAATTTAAATTATTAT-TTAATTATTA
1099801 TTT
65 TTT
1099804 AATAAT
1 AATAAT
1099810 CTAAAAATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 14 0.22
66 24 0.37
67 27 0.42
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (67 bp):
AATAATACATCTTCTTAATATGCAAAGTGGTTATGGATAAATTTAAATTATTATTTAATTATTAT
TT
Found at i:1100811 original size:10 final size:10
Alignment explanation
Indices: 1100798--1100839 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1100788 GGCCATCCGA
1100798 CCGAGGCCAT
1 CCGAGGCCAT
*
1100808 CCGAAAG-CAT
1 CCG-AGGCCAT
*
1100818 TCGAGGCCAT
1 CCGAGGCCAT
1100828 CCGAGGCCAT
1 CCGAGGCCAT
1100838 CC
1 CC
1100840 AAACGAGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.24, C:0.38, G:0.26, T:0.12
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:1100855 original size:23 final size:23
Alignment explanation
Indices: 1100829--1100879 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1100819 CGAGGCCATC
*
1100829 CGAGGCCATCCAAACGAGCTATG
1 CGAGGCCAACCAAACGAGCTATG
* * *
1100852 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGCCAACCAAACGAGCTATG
1100875 CGAGG
1 CGAGG
1100880 GAATCCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.35, T:0.10
Consensus pattern (23 bp):
CGAGGCCAACCAAACGAGCTATG
Found at i:1100880 original size:23 final size:23
Alignment explanation
Indices: 1100843--1100888 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1100833 GCCATCCAAA
1100843 CGAGCTATGCGAGGGCAA-CCGAG
1 CGAGCTATGCGAGGG-AATCCGAG
1100866 CGAGCTATGCGAGGGAATCCGAG
1 CGAGCTATGCGAGGGAATCCGAG
1100889 GGCAACCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.26, C:0.24, G:0.39, T:0.11
Consensus pattern (23 bp):
CGAGCTATGCGAGGGAATCCGAG
Found at i:1101007 original size:23 final size:23
Alignment explanation
Indices: 1100949--1101008 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1100939 CTCGGTTGCC
*
1100949 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
1100972 CTCGGTTGCCCTCGCATAGCTTG
1 CTCGGATGCCCTCGCATAGCTCG
* *
1100995 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
1101009 GTCGGATGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.28
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:1101015 original size:14 final size:14
Alignment explanation
Indices: 1100996--1101023 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1100986 CATAGCTTGT
1100996 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1101010 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1101024 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:1102054 original size:12 final size:12
Alignment explanation
Indices: 1102039--1102093 Score: 83
Period size: 12 Copynumber: 4.6 Consensus size: 12
1102029 GTTATTTAAA
1102039 CGGGTATTGGGC
1 CGGGTATTGGGC
*
1102051 CGGGTATTGGGT
1 CGGGTATTGGGC
1102063 CGGGTATTGGGC
1 CGGGTATTGGGC
* *
1102075 CGGGAATCGGGC
1 CGGGTATTGGGC
1102087 CGGGTAT
1 CGGGTAT
1102094 ATATATATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.11, C:0.16, G:0.49, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:1102180 original size:13 final size:12
Alignment explanation
Indices: 1102149--1102185 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1102139 TTTTAATATT
*
1102149 TATCGGGTCGGG
1 TATCGGGGCGGG
1102161 TATCGGGGCGGG
1 TATCGGGGCGGG
1102173 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
1102186 GATTATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:1104091 original size:60 final size:60
Alignment explanation
Indices: 1103945--1104076 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 60
1103935 AACATAATAA
* *
1103945 ATAGTCGAGTGATCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACTAT
1 ATAGTCGGGTGATCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAACACTAT
* * * * * * *
1104005 GTAGTCGGATGATCATTTTATAACTTTTAATAGTCAATGGACTTAATAAAGTAATA-TCAT
1 ATAGTCGGGTGATCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAACACT-AT
1104065 ATAGTCGGGTGA
1 ATAGTCGGGTGA
1104077 CTATTTGTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 59 0.98
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (60 bp):
ATAGTCGGGTGATCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAACACTAT
Found at i:1119147 original size:21 final size:21
Alignment explanation
Indices: 1119123--1119162 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1119113 CCAGAAATGT
*
1119123 TAGAAACATTAATGTTTTATG
1 TAGAAACAATAATGTTTTATG
*
1119144 TAGAAATAATAATGTTTTA
1 TAGAAACAATAATGTTTTA
1119163 AGTAATTTTT
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:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (21 bp):
TAGAAACAATAATGTTTTATG
Found at i:1119767 original size:30 final size:30
Alignment explanation
Indices: 1119731--1119794 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
1119721 TCGTTTAAAA
1119731 TTTAAACGAAATGACCGATGTGGAATTACT
1 TTTAAACGAAATGACCGATGTGGAATTACT
1119761 TTTAAACGAAATGACCGATGTGGAATTACT
1 TTTAAACGAAATGACCGATGTGGAATTACT
1119791 TTTA
1 TTTA
1119795 TGTTTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (30 bp):
TTTAAACGAAATGACCGATGTGGAATTACT
Found at i:1121167 original size:25 final size:25
Alignment explanation
Indices: 1121130--1121207 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
1121120 TATTTTTATA
*
1121130 TAATTTTCTATATATACTCATTAA-AT
1 TAATTTT-AATATATA-TCATTAATAT
* *
1121156 TATTTTTAATATA-ATTATTAATTAT
1 TAATTTTAATATATATCATTAA-TAT
1121181 TAATTTTAATATATAT-A-T-ATAT
1 TAATTTTAATATATATCATTAATAT
1121203 TAATT
1 TAATT
1121208 AGGTTAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 8 0.18
23 7 0.16
24 2 0.04
25 20 0.44
26 8 0.18
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TAATTTTAATATATATCATTAATAT
Found at i:1121312 original size:19 final size:19
Alignment explanation
Indices: 1121284--1121351 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
1121274 GTTTCGATAA
* * *
1121284 AAATTAATTTTTAATTTTT
1 AAATTTATTTTTAAATATT
*
1121303 AAATTTATTTTAAAATATT
1 AAATTTATTTTTAAATATT
1121322 AAATTTATTTTAATAAATATT
1 AAATTTATTTT--TAAATATT
1121343 AAATTTATT
1 AAATTTATT
1121352 ATTATTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 26 0.62
21 16 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTTATTTTTAAATATT
Found at i:1121353 original size:24 final size:20
Alignment explanation
Indices: 1121301--1121356 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
1121291 TTTTTAATTT
1121301 TTAAATTTATTTTA-AAATA
1 TTAAATTTATTTTATAAATA
1121320 TTAAATTTATTTTAATAAATA
1 TTAAATTTATTTT-ATAAATA
1121341 TTAAATTTATTATTAT
1 TTAAATTTATT-TTAT
1121357 TTTAAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.38
20 1 0.03
21 18 0.53
22 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATTTATTTTATAAATA
Found at i:1121378 original size:17 final size:17
Alignment explanation
Indices: 1121338--1121384 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1121328 ATTTTAATAA
*
1121338 ATATTAAATTTATTATT
1 ATATTAAATTTATTAGT
*
1121355 ATTTTAAATATTA-TAGT
1 ATATTAAAT-TTATTAGT
1121372 ATATT-AATTTATT
1 ATATTAAATTTATT
1121385 TTAAATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.12
16 4 0.16
17 15 0.60
18 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATATTAAATTTATTAGT
Found at i:1127665 original size:231 final size:231
Alignment explanation
Indices: 1127259--1127722 Score: 865
Period size: 231 Copynumber: 2.0 Consensus size: 231
1127249 CCTCCGCATA
*
1127259 CTTGGACTAACCATTTCCACAATAACCTCGCTGCACCAGCTCTCCGGCATTAGAAGTTTAATCAG
1 CTTGGACTAACCATTTCCACAATAACCTCGCTGCACAAGCTCTCCGGCATTAGAAGTTTAATCAG
1127324 ATGCATACAGTATTTATTCATAAAAGAATGAGAAGGTCTGCATCAACTAGAATTATCACCAACTT
66 ATGCATACAGTATTTATTCATAAAAGAATGAGAAGGTCTGCATCAACTAGAATTATCACCAACTT
1127389 TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAAGACTGCAATGACTTAAATTGCTTGGTA
131 TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAAGACTGCAATGACTTAAATTGCTTGGTA
*
1127454 GTGGATGCCGAGGATGGAGAGAATTGGTTACCTAAT
196 GTGGATGCCGAGGATGGAGAGAACTGGTTACCTAAT
*
1127490 CTTGGACTAACCATTTCCACAATAACCTCGCTGCACAAGCTCTCCGGCATTAGAAGTTTAATTAG
1 CTTGGACTAACCATTTCCACAATAACCTCGCTGCACAAGCTCTCCGGCATTAGAAGTTTAATCAG
* *
1127555 ATGCATACAGTATTTATTCATAAAAGAATGTGAAGGTCTGCATCAATTAGAATTATCACCAACTT
66 ATGCATACAGTATTTATTCATAAAAGAATGAGAAGGTCTGCATCAACTAGAATTATCACCAACTT
* *
1127620 TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAATACTGCAATGACTTCAATTGCTTGGTA
131 TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAAGACTGCAATGACTTAAATTGCTTGGTA
1127685 GTGGATGCCGAGGATGGAGAGAACTGGTTACCTAAT
196 GTGGATGCCGAGGATGGAGAGAACTGGTTACCTAAT
1127721 CT
1 CT
1127723 GGAAGTTTTA
Statistics
Matches: 226, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
231 226 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (231 bp):
CTTGGACTAACCATTTCCACAATAACCTCGCTGCACAAGCTCTCCGGCATTAGAAGTTTAATCAG
ATGCATACAGTATTTATTCATAAAAGAATGAGAAGGTCTGCATCAACTAGAATTATCACCAACTT
TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAAGACTGCAATGACTTAAATTGCTTGGTA
GTGGATGCCGAGGATGGAGAGAACTGGTTACCTAAT
Found at i:1127969 original size:36 final size:37
Alignment explanation
Indices: 1127921--1127995 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
1127911 ATAGCAAAAG
*
1127921 AAATCGTCTTTATTCGAA-TTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
1127957 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
1127994 AA
1 AA
1127996 TCCCGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (37 bp):
AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
Found at i:1132486 original size:15 final size:15
Alignment explanation
Indices: 1132468--1132497 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1132458 CCACGGTGCT
1132468 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
1132483 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
1132498 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:1132968 original size:36 final size:37
Alignment explanation
Indices: 1132920--1132994 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
1132910 ATAGCAAAAG
*
1132920 AAATCGTCTTTATTCGAA-TTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
1132956 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
1132993 AA
1 AA
1132995 TCCCGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (37 bp):
AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
Found at i:1134106 original size:34 final size:34
Alignment explanation
Indices: 1134063--1134130 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1134053 TCAAACCAAG
1134063 GACAAAACTTAACTACATTCAATCTCTCTAGAGC
1 GACAAAACTTAACTACATTCAATCTCTCTAGAGC
1134097 GACAAAACTTAACTACATTCAATCTCTCTAGAGC
1 GACAAAACTTAACTACATTCAATCTCTCTAGAGC
1134131 AAAGGACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.26
Consensus pattern (34 bp):
GACAAAACTTAACTACATTCAATCTCTCTAGAGC
Found at i:1135059 original size:16 final size:15
Alignment explanation
Indices: 1135040--1135073 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1135030 AAACACGAAT
1135040 AAAATAAAAATTATGA
1 AAAATAAAAATTAT-A
*
1135056 AAAATAATAATTATA
1 AAAATAAAAATTATA
1135071 AAA
1 AAA
1135074 CTAGAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAATAAAAATTATA
Found at i:1136183 original size:20 final size:20
Alignment explanation
Indices: 1136089--1136457 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
1136079 GATTTTCCAT
* ** *
1136089 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1136109 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1136129 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1136149 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1136169 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1136189 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1136209 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1136229 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1136249 AA-CAGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
1136269 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1136289 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1136309 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1136329 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1136349 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1136369 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1136389 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1136409 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1136429 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1136449 AATCACAAC
1 AATCGCAAC
1136458 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1137169 original size:24 final size:24
Alignment explanation
Indices: 1137130--1137176 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1137120 AAATTTGGTC
1137130 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1137154 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1137177 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1137368 original size:12 final size:12
Alignment explanation
Indices: 1137351--1137375 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1137341 ATATAATCCT
1137351 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1137363 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1137375 G
1 G
1137376 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1139696 original size:19 final size:19
Alignment explanation
Indices: 1139674--1139981 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
1139664 CGGAAAATAC
*
1139674 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1139693 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1139707 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1139727 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1139741 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1139760 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1139779 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1139793 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1139812 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
1139831 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
1139845 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1139864 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
1139883 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1139902 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1139921 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1139935 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1139955 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1139974 AATCGCAA
1 AATCGCAA
1139982 CGAGATAATC
Statistics
Matches: 249, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 12 0.05
17 18 0.07
18 6 0.02
19 140 0.56
20 24 0.10
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1139761 original size:33 final size:34
Alignment explanation
Indices: 1139674--1140003 Score: 276
Period size: 33 Copynumber: 9.5 Consensus size: 34
1139664 CGGAAAATAC
* *
1139674 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1139707 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
1139741 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1139779 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
1139812 AATCGCAATGCGAAATGAAAATCG-AACCGA-CAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CGATGAA
*
1139845 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--ATGAA
1139883 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
1139921 AATCGCAA--CGAAA-G--AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C-G--ATGAA
*
1139955 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
1139988 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1140004 TATAAACGCA
Statistics
Matches: 257, Mismatches: 14, Indels: 52
0.80 0.04 0.16
Matches are distributed among these distances:
33 108 0.42
34 48 0.19
35 9 0.04
36 17 0.07
37 8 0.03
38 59 0.23
39 8 0.03
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:1139789 original size:52 final size:53
Alignment explanation
Indices: 1139702--1139981 Score: 351
Period size: 52 Copynumber: 5.2 Consensus size: 53
1139692 AAATCCCAAC
*
1139702 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
1139755 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
1139807 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
1139859 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
1139916 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-G--A-GAAAATCGCAATGCGAA
1139969 ATGAAAATCGCAA
1 ATGAAAATCGCAA
1139982 CGAGATAATC
Statistics
Matches: 212, Mismatches: 8, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
51 2 0.01
52 121 0.57
53 53 0.25
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:1139825 original size:71 final size:71
Alignment explanation
Indices: 1139741--1139981 Score: 348
Period size: 71 Copynumber: 3.4 Consensus size: 71
1139731 GCAACGAGAG
*
1139741 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1139806 AATGAA
66 AATGAA
* * *
1139812 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
1139872 TACGAAATGAA
61 TGCGAAATGAA
1139883 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC-G
1139948 AAATGAA
65 AAATGAA
1139955 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1139982 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 21
0.83 0.05 0.12
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 78 0.52
72 37 0.25
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:1140119 original size:19 final size:19
Alignment explanation
Indices: 1140010--1140111 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1140000 AAATTATAAA
1140010 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1140029 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1140049 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1140065 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1140082 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1140101 CGCATTGCGAT
1 CGCATTGCGAT
1140112 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1140237 original size:14 final size:14
Alignment explanation
Indices: 1140218--1140254 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1140208 CATCAATTAC
1140218 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1140232 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1140246 ACAAATCAA
1 ACAAATCAA
1140255 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1140266 original size:12 final size:12
Alignment explanation
Indices: 1140249--1140321 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
1140239 ATCTTTTACA
1140249 AATCAATTAAAC
1 AATCAATTAAAC
*
1140261 AATCAA--AAATTG
1 AATCAATTAAA--C
**
1140273 AATCAACTTTTAC
1 AATCAA-TTAAAC
1140286 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
1140299 AATCAA-AAAAC
1 AATCAATTAAAC
1140310 AATCAATTAAAC
1 AATCAATTAAAC
1140322 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:1140283 original size:38 final size:38
Alignment explanation
Indices: 1140235--1140307 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1140225 AACTTTTACA
*
1140235 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
1140273 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1140308 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:1142195 original size:14 final size:14
Alignment explanation
Indices: 1142176--1142232 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1142166 GCGAAATGAA
*
1142176 AATCGCAACGACAG
1 AATCGCAACGAAAG
1142190 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1142207 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1142223 AATCGCAACG
1 AATCGCAACG
1142233 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1142203 original size:33 final size:33
Alignment explanation
Indices: 1142157--1142249 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1142147 GCGAAACCAA
*
1142157 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1142190 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1142223 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1142250 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1142214 original size:19 final size:19
Alignment explanation
Indices: 1142120--1142254 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1142110 TAGTTTACTT
* *
1142120 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1142140 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1142159 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1142178 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1142192 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1142211 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1142225 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1142244 TCGCAATGCGA
1 TCGCAACGCGA
1142255 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1142317 original size:18 final size:19
Alignment explanation
Indices: 1142250--1142363 Score: 132
Period size: 19 Copynumber: 6.3 Consensus size: 19
1142240 AAAATCGCAA
1142250 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1142269 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1142283 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
**
1142302 TGCGA-TTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1142320 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1142339 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1142359 TGCGA
1 TGCGA
1142364 AAGTAAACTA
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
14 11 0.14
15 1 0.01
16 1 0.01
17 1 0.01
18 17 0.21
19 36 0.45
20 13 0.16
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1142330 original size:37 final size:35
Alignment explanation
Indices: 1142250--1142346 Score: 146
Period size: 37 Copynumber: 2.8 Consensus size: 35
1142240 AAAATCGCAA
1142250 TGCGATTTTGGTTTCGCGTTGCGA--TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTCTTGTCGT
1142283 TGCGATTTTGGTTTCGCGTTGCGATTTCATT-TCGCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTC-TTGT--CGT
1142320 TGCGATTTTGGTTTCGCGTTGCGATTT
1 TGCGATTTTGGTTTCGCGTTGCGATTT
1142347 TAAGTTTCGT
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 24 0.41
35 3 0.05
36 2 0.03
37 30 0.51
ACGTcount: A:0.07, C:0.18, G:0.29, T:0.46
Consensus pattern (35 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTCTTGTCGT
Found at i:1142564 original size:92 final size:93
Alignment explanation
Indices: 1142407--1142783 Score: 733
Period size: 93 Copynumber: 4.1 Consensus size: 93
1142397 TTGAATGGAT
1142407 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1142472 GTTTAGCAGAATTGGCAGCAACCGAAC-
66 GTTTAGCAGAATTGGCAGCAACCGAACA
1142499 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1142564 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
1142592 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1142655 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
1142683 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1142748 GTTTAGCAGAATTGGCAGCAACCGAACA
66 GTTTAGCAGAATTGGCAGCAACCGAACA
1142776 AATTTACT
1 AATTTACT
1142784 AAGCAATCTA
Statistics
Matches: 282, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
91 89 0.32
92 96 0.34
93 97 0.34
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACA
Found at i:1142734 original size:184 final size:185
Alignment explanation
Indices: 1142407--1142783 Score: 731
Period size: 184 Copynumber: 2.0 Consensus size: 185
1142397 TTGAATGGAT
1142407 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1142472 GTTTAGCAGAATTGGCAGCAACCGAACAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
66 GTTTAGCAGAATTGGCAGCAACCGAACAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
1142537 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
131 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
1142592 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACACA
1 AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1142655 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAAC-AATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
1142720 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
130 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
1142776 AATTTACT
1 AATTTACT
1142784 AAGCAATCTA
Statistics
Matches: 191, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
183 50 0.26
184 103 0.54
185 38 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACA
Found at i:1144502 original size:14 final size:14
Alignment explanation
Indices: 1144483--1144572 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1144473 TTGAAATGAA
1144483 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1144497 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1144514 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1144530 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1144549 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1144563 AATCGCAACG
1 AATCGCAACG
1144573 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1144520 original size:33 final size:33
Alignment explanation
Indices: 1144475--1144589 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1144465 TCTTTTGGTT
1144475 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1144508 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1144541 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1144574 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1144590 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1144521 original size:19 final size:18
Alignment explanation
Indices: 1144482--1144594 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1144472 GTTGAAATGA
1144482 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1144497 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1144514 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1144530 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1144547 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1144563 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1144580 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1144595 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1144625 original size:14 final size:14
Alignment explanation
Indices: 1144606--1144660 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1144596 TTTGGTTTCG
1144606 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1144620 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
1144639 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1144653 CGTTGCGA
1 CGTTGCGA
1144661 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1144823 original size:33 final size:33
Alignment explanation
Indices: 1144781--1144851 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1144771 AATACTAACT
*
1144781 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1144814 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1144847 TGAAA
1 TGAAA
1144852 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1145083 original size:22 final size:21
Alignment explanation
Indices: 1145032--1145085 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1145022 TGGTTGTGAG
**
1145032 GGATTTCGCCGGAGATGGGAC
1 GGATTTCTTCGGAGATGGGAC
**
1145053 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGAT-GGGAC
1145075 GGATTTCTTCG
1 GGATTTCTTCG
1145086 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (21 bp):
GGATTTCTTCGGAGATGGGAC
Found at i:1145255 original size:20 final size:20
Alignment explanation
Indices: 1145230--1145422 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1145220 CTTTAAATAT
1145230 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1145250 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1145272 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1145291 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1145311 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1145331 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1145351 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1145371 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1145391 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1145411 CGCGTTGCGATT
1 CGCGTTGCGATT
1145423 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1145417 original size:60 final size:60
Alignment explanation
Indices: 1145230--1145422 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1145220 CTTTAAATAT
**
1145230 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1145291 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1145351 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1145411 CGCGTTGCGATT
1 CGCGTTGCGATT
1145423 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1145503 original size:20 final size:20
Alignment explanation
Indices: 1145478--1145529 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1145468 AAGAATCGCG
*
1145478 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1145498 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1145518 TTGCGATTCTGG
1 TTGCGATTCTGG
1145530 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1147155 original size:15 final size:14
Alignment explanation
Indices: 1147137--1147194 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
1147127 TTATAATATT
1147137 TATGTTTTTTAATCA
1 TATGTTTTTTAAT-A
* *
1147152 TATGTATCTTAATA
1 TATGTTTTTTAATA
*
1147166 TATTTTTGTTTAATA
1 TATGTTT-TTTAATA
*
1147181 TTTGTATTTTTAAT
1 TATGT-TTTTTAAT
1147195 TTTAGTTGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
14 6 0.18
15 26 0.76
16 2 0.06
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (14 bp):
TATGTTTTTTAATA
Found at i:1156817 original size:20 final size:20
Alignment explanation
Indices: 1156789--1156918 Score: 135
Period size: 20 Copynumber: 6.5 Consensus size: 20
1156779 GCGAATATGT
1156789 AAATT-GCAACACATAAGTC
1 AAATTCGCAACACATAAGTC
*
1156808 AAATTCGCAACACAAAAGTC
1 AAATTCGCAACACATAAGTC
1156828 AAATTCGCAACACGATAA-TC
1 AAATTCGCAACAC-ATAAGTC
*
1156848 AAATTCGCAACTCA-ATAGTC
1 AAATTCGCAACACATA-AGTC
* **
1156868 AAATTCGCAACGCGAATTTGT-
1 AAATTCGCAACAC--ATAAGTC
*
1156889 AAA-TCGTAACACATAAGTC
1 AAATTCGCAACACATAAGTC
1156908 AAATTCGCAAC
1 AAATTCGCAAC
1156919 GAGAACTCCA
Statistics
Matches: 91, Mismatches: 11, Indels: 17
0.76 0.09 0.14
Matches are distributed among these distances:
18 5 0.05
19 10 0.11
20 67 0.74
21 6 0.07
22 3 0.03
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.22
Consensus pattern (20 bp):
AAATTCGCAACACATAAGTC
Found at i:1156838 original size:40 final size:41
Alignment explanation
Indices: 1156789--1156918 Score: 153
Period size: 40 Copynumber: 3.3 Consensus size: 41
1156779 GCGAATATGT
1156789 AAATT-GCAACAC-ATAAGTCAAATTCGCAACACAAAAGTC
1 AAATTCGCAACACGATAAGTCAAATTCGCAACACAAAAGTC
* *
1156828 AAATTCGCAACACGATAA-TCAAATTCGCAACTCAATAGTC
1 AAATTCGCAACACGATAAGTCAAATTCGCAACACAAAAGTC
* ** * *
1156868 AAATTCGCAACGCGAATTTGT-AAA-TCGTAACACATAAGTC
1 AAATTCGCAACACG-ATAAGTCAAATTCGCAACACAAAAGTC
1156908 AAATTCGCAAC
1 AAATTCGCAAC
1156919 GAGAACTCCA
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
39 5 0.06
40 63 0.81
41 9 0.12
42 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.22
Consensus pattern (41 bp):
AAATTCGCAACACGATAAGTCAAATTCGCAACACAAAAGTC
Found at i:1156935 original size:80 final size:80
Alignment explanation
Indices: 1156816--1156964 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
1156806 TCAAATTCGC
*
1156816 AACACAAAAGTCAAATTCGCAACACGATAATCAAATTCGCAAC-TCAATAGTCAAATTCGCAACG
1 AACACAAAAGTCAAATTCGCAACACGATAATCAAATTCGCAACGTCAATAGT-AAAATCGCAACG
1156880 CGAATTTGTAAATCGT
65 CGAATTTGTAAATCGT
* * * *
1156896 AACACATAAGTCAAATTCGCAACGA-GA-ACTCCAATTTCGCAACGTGAATAGTAAAATCGCAAC
1 AACACAAAAGTCAAATTCGCAAC-ACGATAAT-CAAATTCGCAACGTCAATAGTAAAATCGCAAC
*
1156959 GTGAAT
64 GCGAAT
1156965 AGTAAAAATC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
79 2 0.03
80 50 0.83
81 8 0.13
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.21
Consensus pattern (80 bp):
AACACAAAAGTCAAATTCGCAACACGATAATCAAATTCGCAACGTCAATAGTAAAATCGCAACGC
GAATTTGTAAATCGT
Found at i:1156974 original size:21 final size:20
Alignment explanation
Indices: 1156932--1157000 Score: 129
Period size: 20 Copynumber: 3.4 Consensus size: 20
1156922 AACTCCAATT
1156932 TCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
1156952 TCGCAACGTGAATAGTAAAAA
1 TCGCAACGTGAATAGT-AAAA
1156973 TCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
1156993 TCGCAACG
1 TCGCAACG
1157001 AATCTATATG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 28 0.58
21 20 0.42
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.19
Consensus pattern (20 bp):
TCGCAACGTGAATAGTAAAA
Found at i:1157384 original size:20 final size:20
Alignment explanation
Indices: 1157356--1157474 Score: 148
Period size: 20 Copynumber: 5.9 Consensus size: 20
1157346 GATTTTCTAA
* *
1157356 ATTCGCGTTGCAATTTTACT
1 ATTCACGTTGCGATTTTACT
1157376 ATTCACGTTGCGATTTTACT
1 ATTCACGTTGCGATTTTACT
*
1157396 ATTCACATTGCGATTTTACT
1 ATTCACGTTGCGATTTTACT
* * *
1157416 ATTTATGTTACGATTTTACT
1 ATTCACGTTGCGATTTTACT
* *
1157436 ATTCACATTACGATTTTTACT
1 ATTCACGTTGCGA-TTTTACT
*
1157457 ATTCACGCTGCGATTTTA
1 ATTCACGTTGCGATTTTA
1157475 GAAAATGAGT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 68 0.80
21 17 0.20
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTCACGTTGCGATTTTACT
Found at i:1165627 original size:15 final size:16
Alignment explanation
Indices: 1165607--1165637 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1165597 ATAATCATTA
1165607 AATAAT-TTTTAATGT
1 AATAATCTTTTAATGT
1165622 AATAATCTTTTAATGT
1 AATAATCTTTTAATGT
1165638 TTTGTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
AATAATCTTTTAATGT
Found at i:1166569 original size:21 final size:22
Alignment explanation
Indices: 1166543--1166583 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1166533 TACTGAGTTT
*
1166543 GTATATAA-ATAATTTTTTTGA
1 GTATATAACAAAATTTTTTTGA
1166564 GTATATAACAAAATTTTTTT
1 GTATATAACAAAATTTTTTT
1166584 ACACTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (22 bp):
GTATATAACAAAATTTTTTTGA
Found at i:1174038 original size:16 final size:18
Alignment explanation
Indices: 1174001--1174038 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1173991 TTATGAGGTG
1174001 AAAATGTTATTATTGTACA
1 AAAATGTTATTATTGTA-A
1174020 AAAATGTTATTATT-TAA
1 AAAATGTTATTATTGTAA
1174037 AA
1 AA
1174039 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 2 0.11
19 14 0.74
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (18 bp):
AAAATGTTATTATTGTAA
Found at i:1176132 original size:29 final size:29
Alignment explanation
Indices: 1176070--1176125 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1176060 ACACCCAACA
1176070 TAGGTCGCCATGCACTCCCAGCGACCTAC
1 TAGGTCGCCATGCACTCCCAGCGACCTAC
* *
1176099 AAGGTCGTCATGCACTCCCAGCGACCT
1 TAGGTCGCCATGCACTCCCAGCGACCT
1176126 TGTAGGTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.39, G:0.21, T:0.18
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCTAC
Found at i:1193830 original size:2 final size:2
Alignment explanation
Indices: 1193823--1193848 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1193813 TACCCATACC
1193823 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1193849 TCTGTTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1195309 original size:20 final size:20
Alignment explanation
Indices: 1195260--1195312 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 20
1195250 TGAATTATAT
* **
1195260 TTAAATAATTATTTATTTTC
1 TTAAATAATTATTAAACTTC
1195280 -TAAA-AA-TATTAAACTTC
1 TTAAATAATTATTAAACTTC
1195297 TTAAATAATTATTAAA
1 TTAAATAATTATTAAA
1195313 AACATCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 8 0.30
18 6 0.22
19 6 0.22
20 7 0.26
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAATAATTATTAAACTTC
Found at i:1202155 original size:31 final size:31
Alignment explanation
Indices: 1202120--1202180 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1202110 TAAAAATATA
*
1202120 AGATAT-AGTCACTTTCGTTTTTATTTAATTT
1 AGATATGA-TCACTCTCGTTTTTATTTAATTT
1202151 AGATATGATCACTCTCGTTTTTATTTAATT
1 AGATATGATCACTCTCGTTTTTATTTAATT
1202181 AAGACGTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.52
Consensus pattern (31 bp):
AGATATGATCACTCTCGTTTTTATTTAATTT
Found at i:1202408 original size:21 final size:22
Alignment explanation
Indices: 1202356--1202414 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
1202346 TATTTTTAAA
*
1202356 TTAAGTTAGTAATAAAATATATT
1 TTAAGTTAAT-ATAAAATATATT
1202379 TAATAAGTTAATATAAAATAT-TT
1 T--TAAGTTAATATAAAATATATT
1202402 TTAAGTTAATATA
1 TTAAGTTAATATA
1202415 TATAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.36
23 4 0.12
24 9 0.27
25 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TTAAGTTAATATAAAATATATT
Found at i:1202423 original size:25 final size:24
Alignment explanation
Indices: 1202340--1202425 Score: 95
Period size: 25 Copynumber: 3.4 Consensus size: 24
1202330 TTAAATGAAA
1202340 ATAAAATATTTTTAAATTAAGTTAGT
1 ATAAAATATTTTT-AATTAAGTTA-T
*
1202366 AATAAAATATATTTAA-TAAGTTAAT
1 -ATAAAATATTTTTAATTAAGTT-AT
1202391 ATAAAATATTTTTAAGTTAA-TATAT
1 ATAAAATATTTTTAA-TTAAGT-TAT
1202416 ATAAAATATT
1 ATAAAATATT
1202426 ATGAATTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
24 14 0.26
25 20 0.38
26 7 0.13
27 12 0.23
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (24 bp):
ATAAAATATTTTTAATTAAGTTAT
Found at i:1213759 original size:99 final size:99
Alignment explanation
Indices: 1213588--1213786 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
1213578 TCGGCTGAAA
1213588 CCCGACCCATGCGCATCCCTAGATGTATCTCTGGATTTATGAACTATTGGCGGAGCAGAGGCACA
1 CCCGACCCATGCGCATCCCTAGATGTATCTCTGGATTTATGAACTATTGGCGGAGCAGAGGCACA
1213653 TGGACAATGGCCGATTGTATATAAAAAGTAGGGC
66 TGGACAATGGCCGATTGTATATAAAAAGTAGGGC
1213687 CCCGACCCATGCGCATCCCTAGATGTATCTCTGGATTTATGAACTATTGGCGGAGCAGAGGCACA
1 CCCGACCCATGCGCATCCCTAGATGTATCTCTGGATTTATGAACTATTGGCGGAGCAGAGGCACA
1213752 TGGACAATGGCCGATTGTATATAAAAAGTAGGGC
66 TGGACAATGGCCGATTGTATATAAAAAGTAGGGC
1213786 C
1 C
1213787 TGGCCACCTC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (99 bp):
CCCGACCCATGCGCATCCCTAGATGTATCTCTGGATTTATGAACTATTGGCGGAGCAGAGGCACA
TGGACAATGGCCGATTGTATATAAAAAGTAGGGC
Found at i:1215327 original size:32 final size:32
Alignment explanation
Indices: 1215290--1215355 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
1215280 TAGAAGTAAT
* *
1215290 AAAATAGTCATTAAATTTTATCAAACTATTAC
1 AAAATAATCATTAAAATTTATCAAACTATTAC
* *
1215322 AAAATAATCATTAAAATTTATTAAACTTTTAC
1 AAAATAATCATTAAAATTTATCAAACTATTAC
1215354 AA
1 AA
1215356 TTATCATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.38
Consensus pattern (32 bp):
AAAATAATCATTAAAATTTATCAAACTATTAC
Found at i:1215933 original size:2 final size:2
Alignment explanation
Indices: 1215922--1215961 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1215912 GCATAAGCTG
1215922 TA TA -A TA TA TA T- TA TA TA TA TA TA TA -A 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
1215961 T
1 T
1215962 TCCTCCAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1215944 original size:13 final size:13
Alignment explanation
Indices: 1215922--1215959 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1215912 GCATAAGCTG
1215922 TATA-ATATATAT
1 TATATATATATAT
1215934 TATATATATATAT
1 TATATATATATAT
*
1215947 AATATATATATAT
1 TATATATATATAT
1215960 ATTCCTCCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATATATATAT
Found at i:1215946 original size:15 final size:15
Alignment explanation
Indices: 1215922--1215961 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1215912 GCATAAGCTG
*
1215922 TATA-ATATATATTA
1 TATATATATATAATA
1215936 TATATATATATAATA
1 TATATATATATAATA
1215951 TATATATATAT
1 TATATATATAT
1215962 TCCTCCAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATATATAATA
Found at i:1215960 original size:13 final size:13
Alignment explanation
Indices: 1215926--1215960 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1215916 AAGCTGTATA
*
1215926 ATATATATTATAT
1 ATATATATAATAT
1215939 ATATATATAATAT
1 ATATATATAATAT
1215952 ATATATATA
1 ATATATATA
1215961 TTCCTCCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATATAATAT
Found at i:1218268 original size:16 final size:17
Alignment explanation
Indices: 1218247--1218278 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1218237 TATTGTTCAT
1218247 GTGAATAGT-AAATTTC
1 GTGAATAGTGAAATTTC
1218263 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
1218279 TGTCGGCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (17 bp):
GTGAATAGTGAAATTTC
Found at i:1226316 original size:27 final size:26
Alignment explanation
Indices: 1226270--1226322 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1226260 CCTAACATTT
1226270 AAATATTACTTATCAGGCATATTTTTC
1 AAATATTACTTATCAGGCAT-TTTTTC
1226297 AAATATTA-TTAATCTA-GCATTTTTTC
1 AAATATTACTT-ATC-AGGCATTTTTTC
1226323 TGACAAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 8 0.33
27 15 0.62
28 1 0.04
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (26 bp):
AAATATTACTTATCAGGCATTTTTTC
Found at i:1226460 original size:60 final size:60
Alignment explanation
Indices: 1226348--1226460 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
1226338 CATGAGACGT
* * * * *
1226348 GCCTTCGCAAGGTTCTGTCTAAGCTGGCGTCACGGTGAAAAAGCGTGGATCATAATCTAC
1 GCCTTAGCAAAGTTCTATCTAAGCTGGCGTCACGGTGAAAAAGCGCGAATCATAATCTAC
* * **
1226408 GCCTTAGCAAAGTTCTATCTTAGTTGGCGTCACGGTGGTAAAGCGCGAATCAT
1 GCCTTAGCAAAGTTCTATCTAAGCTGGCGTCACGGTGAAAAAGCGCGAATCAT
1226461 GAAACTCGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (60 bp):
GCCTTAGCAAAGTTCTATCTAAGCTGGCGTCACGGTGAAAAAGCGCGAATCATAATCTAC
Found at i:1227251 original size:47 final size:48
Alignment explanation
Indices: 1227179--1227278 Score: 143
Period size: 47 Copynumber: 2.1 Consensus size: 48
1227169 TTAGGGCTTT
*
1227179 TAAAATTTGGTACAAAATTAAATATAATACAAA-ATAAT-TAGTATAA
1 TAAAATTTGGTACAAAATTAAATATAATACAAATATAATATAATATAA
*
1227225 TAAAATTTGGT-CAAATAATTAAATATAATATAAATATAATATAATATAA
1 TAAAATTTGGTAC-AA-AATTAAATATAATACAAATATAATATAATATAA
1227274 TAAAA
1 TAAAA
1227279 AATAATTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
45 1 0.02
46 13 0.27
47 17 0.35
48 5 0.10
49 12 0.25
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (48 bp):
TAAAATTTGGTACAAAATTAAATATAATACAAATATAATATAATATAA
Found at i:1227252 original size:10 final size:10
Alignment explanation
Indices: 1227239--1227285 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
1227229 ATTTGGTCAA
1227239 ATAATTAAAT
1 ATAATTAAAT
1227249 ATAATATAAAT
1 ATAAT-TAAAT
1227260 ATAA-TATAAT
1 ATAATTA-AAT
* *
1227270 ATAATAAAAA
1 ATAATTAAAT
1227280 ATAATT
1 ATAATT
1227286 TTACCTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.06
10 19 0.61
11 10 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAATTAAAT
Found at i:1227256 original size:5 final size:5
Alignment explanation
Indices: 1227246--1227275 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1227236 CAAATAATTA
1227246 AATAT AATAT AAATAT AATAT AATAT AATA
1 AATAT AATAT -AATAT AATAT AATAT AATA
1227276 AAAAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Done.