Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 39
Found at i:3160121 original size:16 final size:15
Alignment explanation
Indices: 3160100--3160161 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
3160090 TTTGGCCTGT
3160100 AATAATAATAATAATA
1 AATAATAATAA-AATA
3160116 AATAATAATAAAATAA
1 AATAATAATAAAAT-A
*
3160132 AATAA-AATGGAAATA
1 AATAATAAT-AAAATA
*
3160147 TAT-A-AATAAAATA
1 AATAATAATAAAATA
3160160 AA
1 AA
3160162 AGATCCGAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 6 0.15
14 4 0.10
15 9 0.22
16 21 0.52
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AATAATAATAAAATA
Found at i:3160136 original size:13 final size:16
Alignment explanation
Indices: 3160100--3160132 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3160090 TTTGGCCTGT
3160100 AATAATAATAATAATA
1 AATAATAATAATAATA
3160116 AATAATAATAA-AATA
1 AATAATAATAATAATA
3160131 AA
1 AA
3160133 ATAAAATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:3160145 original size:11 final size:10
Alignment explanation
Indices: 3160100--3160162 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 10
3160090 TTTGGCCTGT
3160100 AATAATAATAA
1 AATAA-AATAA
3160111 TAAT-AAATAA
1 -AATAAAATAA
3160121 TAATAAAATAA
1 -AATAAAATAA
3160132 AATAAAATGGAA
1 AATAAAAT--AA
3160144 ATATATAAATAA
1 A-ATA-AAATAA
3160156 AATAAAA
1 AATAAAA
3160163 GATCCGAGCG
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
10 20 0.43
11 10 0.22
12 9 0.20
13 3 0.07
14 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (10 bp):
AATAAAATAA
Found at i:3168296 original size:22 final size:22
Alignment explanation
Indices: 3168270--3168329 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
3168260 TTAACAAATC
*
3168270 GTAAATCTAATAAATATGAAAAA
1 GTAAAT-TAATAAATATAAAAAA
3168293 -TAAAATATAA-AAA-ATAAAAAA
1 GT-AAAT-TAATAAATATAAAAAA
3168314 GTAAATT-ATAAATATA
1 GTAAATTAATAAATATA
3168330 TAAATTAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
19 1 0.03
20 4 0.13
21 14 0.45
22 5 0.16
23 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (22 bp):
GTAAATTAATAAATATAAAAAA
Found at i:3168300 original size:14 final size:14
Alignment explanation
Indices: 3168281--3168311 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3168271 TAAATCTAAT
*
3168281 AAATATGAAAAATA
1 AAATATAAAAAATA
3168295 AAATATAAAAAATA
1 AAATATAAAAAATA
3168309 AAA
1 AAA
3168312 AAGTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATATAAAAAATA
Found at i:3168469 original size:31 final size:31
Alignment explanation
Indices: 3168433--3168491 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3168423 ATAAAAATAT
3168433 ATATTTATAAATATAATAAT-ATATAAAACAC
1 ATATTTATAAAT-TAATAATAATATAAAACAC
*
3168464 ATATTTATATATTAATAATAATATAAAA
1 ATATTTATAAATTAATAATAATATAAAA
3168492 ATATATGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (31 bp):
ATATTTATAAATTAATAATAATATAAAACAC
Found at i:3168486 original size:33 final size:30
Alignment explanation
Indices: 3168423--3168492 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
3168413 AATTAAATTC
* *
3168423 ATAAAAATATATATTTATAAATATAATAAT
1 ATAAAAACACATATTTATAAATATAATAAT
*
3168453 ATATAAAACACATATTTATATATTAATAATAAT
1 ATA-AAAACACATATTTATA-AAT-ATAATAAT
3168486 ATAAAAA
1 ATAAAAA
3168493 TATATGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.09
31 14 0.41
32 6 0.18
33 11 0.32
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (30 bp):
ATAAAAACACATATTTATAAATATAATAAT
Found at i:3170274 original size:20 final size:20
Alignment explanation
Indices: 3170249--3170286 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3170239 TACATGTTAA
3170249 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
3170269 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
3170287 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:3171867 original size:23 final size:23
Alignment explanation
Indices: 3171823--3171867 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3171813 CATTTTATAT
*
3171823 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTATACGC
*
3171846 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
3171868 AACTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:3177139 original size:3 final size:3
Alignment explanation
Indices: 3177126--3177164 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
3177116 TATTTTTATT
*
3177126 ATA ATA CTA ATA ATA ATA ATA ATA ATA AT- ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
3177165 GTTGAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3178757 original size:254 final size:254
Alignment explanation
Indices: 3178307--3178803 Score: 730
Period size: 254 Copynumber: 2.0 Consensus size: 254
3178297 TGGTTACTTA
* * * * *
3178307 AAATTTTATAAATTTATCATCTAATATTAATTTTAAGGTAAACTTTGTATTGAGTATCTAAACTA
1 AAATTTTATAAATTTATCATCTAAAATTAAATTTAAGGTAAACTCTGCATTGAGTACCTAAACTA
* * * * * ** *
3178372 TCAGTTTTGGTTTGTTTTAGTACCTTAACTTTCAATTTTTTTTCGAAATCATATCTAAAGTTTAT
66 TCAGTTCTGATCTATTTTAGTACCTAAACTTTCAA-TTTTTTTAAAAATCATATCTAAAGTTTAG
**
3178437 TTTTTGTTTCATTTTAATACCCTGCCATTAAGTTTTGAAAAAACAATGAAAGTCTAGGTACCAAA
130 TTTTTGTTTCATTTTAATACCCCACCATTAAGTTTTGAAAAAACAATGAAAGTCTAGGTACCAAA
3178502 ACACGTTTAGTACCTAAATCATACTTAAGTTTTGATTTTTTTTAAAAAAAATTAGGTACT
195 ACACGTTTAGTACCTAAATCATACTTAAGTTTTGATTTTTTTTAAAAAAAATTAGGTACT
*
3178562 AAATTTTATAAATTTATCATCTAAAATTAAATTTAAGGGTAAACTCCT-CATTTAGTACCTAAAC
1 AAATTTTATAAATTTATCATCTAAAATTAAATTTAA-GGTAAACT-CTGCATTGAGTACCTAAAC
*
3178626 TATCAGTTCTGATCTATTTTAGTACCTAAACTTTTAA-TTTTTTAAAAATCATA-CATAAAGTTT
64 TATCAGTTCTGATCTATTTTAGTACCTAAACTTTCAATTTTTTTAAAAATCATATC-TAAAGTTT
* * * * *
3178689 AGTTTTTGTTTCTTTTTAGTACCCCACTATTAAGTTTTGAAAAAAGAATGAATGTCTAGGTACCA
128 AGTTTTTGTTTCATTTTAATACCCCACCATTAAGTTTTGAAAAAACAATGAAAGTCTAGGTACCA
*
3178754 AAACACGTTTAGTACCTAAATCATACTTAAGTTTTGATTTTTTTTGAAAA
193 AAACACGTTTAGTACCTAAATCATACTTAAGTTTTGATTTTTTTTAAAAA
3178804 TTCAAGTACT
Statistics
Matches: 216, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
253 1 0.00
254 128 0.59
255 34 0.16
256 52 0.24
257 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (254 bp):
AAATTTTATAAATTTATCATCTAAAATTAAATTTAAGGTAAACTCTGCATTGAGTACCTAAACTA
TCAGTTCTGATCTATTTTAGTACCTAAACTTTCAATTTTTTTAAAAATCATATCTAAAGTTTAGT
TTTTGTTTCATTTTAATACCCCACCATTAAGTTTTGAAAAAACAATGAAAGTCTAGGTACCAAAA
CACGTTTAGTACCTAAATCATACTTAAGTTTTGATTTTTTTTAAAAAAAATTAGGTACT
Found at i:3185398 original size:23 final size:23
Alignment explanation
Indices: 3185368--3185444 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
3185358 ATACACAGCA
3185368 GAATGCATCGATGCACATTCAAG
1 GAATGCATCGATGCACATTCAAG
*
3185391 GAATGCATCGATGCATC-TTC-AT
1 GAATGCATCGATGCA-CATTCAAG
* * *
3185413 G-ATGTATCAATGCACATTTAAG
1 GAATGCATCGATGCACATTCAAG
*
3185435 GCATGCATCG
1 GAATGCATCG
3185445 GTACACTGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 13 0.30
22 4 0.09
23 24 0.56
24 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (23 bp):
GAATGCATCGATGCACATTCAAG
Found at i:3189313 original size:22 final size:21
Alignment explanation
Indices: 3189271--3189310 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3189261 AATACTATTT
3189271 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
3189292 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
3189311 ATAAAGCCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:3189477 original size:15 final size:15
Alignment explanation
Indices: 3189454--3189492 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
3189444 TTCTTGTTCC
3189454 TCTTCATCGGAACCT
1 TCTTCATCGGAACCT
*
3189469 TCTTTATCGGAACCT
1 TCTTCATCGGAACCT
3189484 TCTTCATCG
1 TCTTCATCG
3189493 CTCCATGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.31, G:0.13, T:0.38
Consensus pattern (15 bp):
TCTTCATCGGAACCT
Found at i:3191389 original size:64 final size:65
Alignment explanation
Indices: 3191241--3191396 Score: 208
Period size: 64 Copynumber: 2.4 Consensus size: 65
3191231 ATAAGACTTA
* * *
3191241 GTGCATCGGTACACTAATTACATTCGATGTTTCAAACAAGCCTAAAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAACAACCCTAAAGTGCATCGATGCATGGTCT
* * * * *
3191306 ATGCATCGGTACACAAAATGCATTCGATGTTTCAATA-AACCCT-TAGTGCATCGGTGCATGGTG
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAA-ACAACCCTAAAGTGCATCGATGCATGGTC
3191369 T
65 T
*
3191370 GTGCAACGGTACACTAAATGCATTCGA
1 GTGCATCGGTACACTAAATGCATTCGA
3191397 AATGGGGTGT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 42 0.53
65 36 0.46
66 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACACTAAATGCATTCGATGTTTCAAACAACCCTAAAGTGCATCGATGCATGGTCT
Found at i:3192953 original size:2 final size:2
Alignment explanation
Indices: 3192946--3192970 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3192936 ATTTAAAAAT
3192946 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 T
3192971 GGATTGGAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3195134 original size:3 final size:3
Alignment explanation
Indices: 3195126--3195152 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3195116 TCTTAATTGT
3195126 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3195153 ATATCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3195854 original size:22 final size:23
Alignment explanation
Indices: 3195826--3195885 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
3195816 GAACACCAGA
3195826 AAAAAAAAGGAAAAAATGA-AAG
1 AAAAAAAAGGAAAAAATGAGAAG
* *
3195848 AAAAAAAA--AGAGAATGAGAAG
1 AAAAAAAAGGAAAAAATGAGAAG
3195869 AAAAATCAAAGGAAAAA
1 AAAAA--AAAGGAAAAA
3195886 CGAAAAGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 7 0.24
21 8 0.28
22 8 0.28
23 3 0.10
25 3 0.10
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (23 bp):
AAAAAAAAGGAAAAAATGAGAAG
Found at i:3197896 original size:2 final size:2
Alignment explanation
Indices: 3197889--3197926 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3197879 GTTTTAATTA
3197889 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
3197927 TTTTTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3204450 original size:99 final size:102
Alignment explanation
Indices: 3204320--3204557 Score: 279
Period size: 99 Copynumber: 2.3 Consensus size: 102
3204310 AACTTTCCAA
* *
3204320 AAATTTTGAAATT-TTTGCACTTGAAATAAAATTGATCTCACTTGAGT-TTGTTTTACT-AAAA-
1 AAATTTTGAAATTGTTT-CACTTGAAACAAAATTGATCTCACTTGA-TACTGTTTTACTAAAAAC
* * * *
3204381 AAATTT-GTCTCGCTTGAGACAGTTTTTCGTCGAAACAC
64 AAATTTCATCTCGCTTGAGACAATTTTCCCTCGAAACAC
*
3204419 AAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGATACTGTTTTCCTAAAAAAAA
1 AAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGATACTGTTTTACT---AAAAA
* * * *
3204484 CAAATTTCATCTTGCTTGAGATAATTTTCCCTTGAAACGC
63 CAAATTTCATCTCGCTTGAGACAATTTTCCCTCGAAACAC
*
3204524 AAATTTTGGAAATTGTTTCCCTTGAAACAAAATT
1 AAATTTT-GAAATTGTTTCACTTGAAACAAAATT
3204558 TTATATCACC
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
98 1 0.01
99 48 0.41
100 3 0.03
103 4 0.03
104 6 0.05
105 31 0.26
106 25 0.21
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (102 bp):
AAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGATACTGTTTTACTAAAAACAA
ATTTCATCTCGCTTGAGACAATTTTCCCTCGAAACAC
Found at i:3205229 original size:138 final size:139
Alignment explanation
Indices: 3204946--3205367 Score: 485
Period size: 138 Copynumber: 3.1 Consensus size: 139
3204936 ATCAAACCAT
* * * * * *
3204946 CAAAGTACGACTAGATGTCCTCAACACGAATGAACAATGTCATCCACCGACCAGATTTCCTCAAC
1 CAAA-TACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAAC
* * * * * * *
3205011 GTGAAGGAGCAGTGTCATCCTCATACAATTAGACTTACTTAACGTGAATGAACCGTTTTGTCTCC
65 GTGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTTCTCAACGCGAAAGAACCGTATTGTCTCC
*
3205076 AAATTATCTT
130 AAATTATCTC
* *
3205086 CAAATATGGCTAGACGTCCTCAACACAAAGGAA-AATGTCGTCCACTGACCAGATCTCCTCAACG
1 CAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACG
* * * * * * *
3205150 CGAATGAGTAGTTTCATCCTCAGACAATCATACTTTCTCAACGCGAAGGAACCGTATTGTCTCTA
66 TGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTTCTCAACGCGAAAGAACCGTATTGTCTCCA
3205215 AATTATCTC
131 AATTATCTC
* * * * *
3205224 CAAATACGGTTACACGTCCTCAACACGAAGGAACAATATCGTCCA-TAAACTAGATCTCCTCAAC
1 CAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACT-GACCAGATCTCCTCAAC
* * * * *
3205288 GTGAAGGAGCAATGTCATCCTCAGATAA-CTAGACTTTCTCAACACGAAAGAACTGTGTTGTCTC
65 GTGAAGGAGCAGTGTCATCCTCAGACAATC-AGACTTTCTCAACGCGAAAGAACCGTATTGTCTC
3205352 CAAATTA-C-C
129 CAAATTATCTC
3205361 CAAATAC
1 CAAATAC
3205368 TTCTAGAACA
Statistics
Matches: 238, Mismatches: 41, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
137 8 0.03
138 120 0.50
139 106 0.45
140 4 0.02
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (139 bp):
CAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACG
TGAAGGAGCAGTGTCATCCTCAGACAATCAGACTTTCTCAACGCGAAAGAACCGTATTGTCTCCA
AATTATCTC
Found at i:3205600 original size:122 final size:122
Alignment explanation
Indices: 3205378--3205600 Score: 311
Period size: 122 Copynumber: 1.8 Consensus size: 122
3205368 TTCTAGAACA
* *
3205378 TCTTCAACACCAAATTATCTCCGGAGTGACCCAATTTACTCAACGAGAAGGAACAACGTCATATT
1 TCTTCAACACCAAATTATCTCCAGAGTGACCCAACTTACTCAACGAGAAGGAACAACGTCATATT
* * *
3205443 TAGTAAACAATTTACCTAAAAGCGGCCAGAACTCTTCAAAATAGATGAGAAATGTCG
66 CAGTAAACAATTTAACTAAAAGCGACCAGAACTCTTCAAAATAGATGAGAAATGTCG
* * ** * * *
3205500 TCTTCAACACTAAATTATCTCCAGATTGACCTGACTTCCTCAACGAGAAGGAACAATGTCATCTT
1 TCTTCAACACCAAATTATCTCCAGAGTGACCCAACTTACTCAACGAGAAGGAACAACGTCATATT
* * *
3205565 CAGTAAACAATTTAACTGAAAGCGACTAGATCTCTT
66 CAGTAAACAATTTAACTAAAAGCGACCAGAACTCTT
3205601 TAACATGGAT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
122 86 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (122 bp):
TCTTCAACACCAAATTATCTCCAGAGTGACCCAACTTACTCAACGAGAAGGAACAACGTCATATT
CAGTAAACAATTTAACTAAAAGCGACCAGAACTCTTCAAAATAGATGAGAAATGTCG
Found at i:3205772 original size:3 final size:3
Alignment explanation
Indices: 3205764--3205828 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
3205754 CTTAATTATA
3205764 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
3205812 TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TA
3205829 TTATTTTTCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:3206512 original size:12 final size:12
Alignment explanation
Indices: 3206495--3206570 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 12
3206485 AGAAAAAAAG
3206495 GAAAAAATGAAA
1 GAAAAAATGAAA
*
3206507 G-AAAAACGAAA
1 GAAAAAATGAAA
*
3206518 -AGAAAATGAGAA
1 GAAAAAATGA-AA
*
3206530 G-AAAAATAAAA
1 GAAAAAATGAAA
*
3206541 GGAAAAACA-AAAA
1 -GAAAAA-ATGAAA
3206554 GAAGAAAATGAAA
1 GAA-AAAATGAAA
3206567 GAAA
1 GAAA
3206571 GATAGAGAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
11 17 0.34
12 15 0.30
13 17 0.34
14 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (12 bp):
GAAAAAATGAAA
Found at i:3211363 original size:19 final size:18
Alignment explanation
Indices: 3211339--3211395 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
3211329 ATAATTTTAA
3211339 AAATATTATTAAAATATTT
1 AAATATTATTAAAA-ATTT
*
3211358 AAATA-TAGATAAAAATTT
1 AAATATTA-TTAAAAATTT
3211376 -AA-ATTATTAAAAATTAT
1 AAATATTATTAAAAATT-T
3211393 AAA
1 AAA
3211396 ATGATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 8 0.25
19 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATATTATTAAAAATTT
Found at i:3211377 original size:18 final size:18
Alignment explanation
Indices: 3211348--3211403 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
3211338 AAAATATTAT
3211348 TAAAATATTTAAATATAGA
1 TAAAA-ATTTAAATATAGA
*
3211367 TAAAAATTTAAAT-TA-T
1 TAAAAATTTAAATATAGA
3211383 TAAAAATTATAAA-AT-GA
1 TAAAAATT-TAAATATAGA
3211400 TAAA
1 TAAA
3211404 TTATAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 8 0.25
17 11 0.34
18 8 0.25
19 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (18 bp):
TAAAAATTTAAATATAGA
Found at i:3225931 original size:13 final size:12
Alignment explanation
Indices: 3225899--3225929 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3225889 AAAAAAAAAA
3225899 GAAAAAATACTT
1 GAAAAAATACTT
3225911 GAAAAAATACTT
1 GAAAAAATACTT
3225923 GAAAAAA
1 GAAAAAA
3225930 ATGAAAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (12 bp):
GAAAAAATACTT
Found at i:3226750 original size:26 final size:26
Alignment explanation
Indices: 3226700--3226751 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3226690 TCTCACGTGG
*
3226700 CAGTTTCTAGAATGTCTAGTCAGCGC
1 CAGTTTCTAGAATGTCTACTCAGCGC
*
3226726 CAGTTTCTAGAA-GATCTACTTAGCGC
1 CAGTTTCTAGAATG-TCTACTCAGCGC
3226752 GCCTTCTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (26 bp):
CAGTTTCTAGAATGTCTACTCAGCGC
Found at i:3227183 original size:18 final size:19
Alignment explanation
Indices: 3227160--3227196 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
3227150 TTGCGCTTAT
3227160 TTTTCAAAATCAAA-ATAG
1 TTTTCAAAATCAAATATAG
3227178 TTTTCAAAATCAAATATAG
1 TTTTCAAAATCAAATATAG
3227197 ACTTTGGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (19 bp):
TTTTCAAAATCAAATATAG
Found at i:3231660 original size:23 final size:23
Alignment explanation
Indices: 3231634--3231691 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
3231624 AAATTAATAA
3231634 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
3231657 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
3231680 TATA--ATGTAAAA
1 TATATTATGTAAAA
3231692 ATTATAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:3231734 original size:13 final size:13
Alignment explanation
Indices: 3231705--3231739 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3231695 ATAACTAATA
*
3231705 ATATTAAAT-ATT
1 ATATTAAATAAAT
3231717 ATATTAAATAAAT
1 ATATTAAATAAAT
3231730 ATATTAAATA
1 ATATTAAATA
3231740 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:3235368 original size:33 final size:34
Alignment explanation
Indices: 3235307--3235406 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
3235297 AAATTTAATG
*
3235307 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
3235341 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
3235374 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
3235407 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:3236014 original size:21 final size:21
Alignment explanation
Indices: 3235926--3236019 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
3235916 TATGGTATAA
*
3235926 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
3235947 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
*
3235968 AA-CTTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
3235989 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
3236010 AACCCTGCGG
1 AACCCTGCGG
3236020 AGATGGCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 3 0.04
21 62 0.93
22 2 0.03
ACGTcount: A:0.20, C:0.26, G:0.35, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:3236049 original size:21 final size:21
Alignment explanation
Indices: 3236023--3236070 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3236013 CCTGCGGAGA
*
3236023 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
3236044 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
3236065 GGGCAT
1 TGGCAT
3236071 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:3239208 original size:21 final size:22
Alignment explanation
Indices: 3239175--3239216 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
3239165 AATCTTATAA
*
3239175 TTTAAAGTGTTAAATC-CTAAAT
1 TTTAAACTGTT-AATCTCTAAAT
3239197 TTTAAACT-TTAATCTCTAAA
1 TTTAAACTGTTAATCTCTAAA
3239217 CTCTAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTAAACTGTTAATCTCTAAAT
Found at i:3239230 original size:14 final size:14
Alignment explanation
Indices: 3239191--3239237 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3239181 GTGTTAAATC
*
3239191 CTAAATTTTAAACT
1 CTAAATCTTAAACT
*
3239205 -TTAATCTCTAAACT
1 CTAAATCT-TAAACT
*
3239219 CTAAATCTTAAAAT
1 CTAAATCTTAAACT
3239233 CTAAA
1 CTAAA
3239238 ATCATTAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 5 0.19
14 16 0.59
15 6 0.22
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (14 bp):
CTAAATCTTAAACT
Found at i:3239251 original size:28 final size:28
Alignment explanation
Indices: 3239213--3239292 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 28
3239203 CTTTAATCTC
*
3239213 TAAACTCTAAATCTTAAAATCTAAAATCA
1 TAAACT-TAAATCCTAAAATCTAAAATCA
* * *
3239242 TTAACTTAAACCCCAAAATCTAAAATCA
1 TAAACTTAAATCCTAAAATCTAAAATCA
3239270 TAAACTT-AATCCCTAAAATCTAA
1 TAAACTTAAAT-CCTAAAATCTAA
3239293 CCCAGAGACA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 2 0.05
28 36 0.84
29 5 0.12
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (28 bp):
TAAACTTAAATCCTAAAATCTAAAATCA
Found at i:3243020 original size:41 final size:41
Alignment explanation
Indices: 3242951--3243094 Score: 179
Period size: 41 Copynumber: 3.5 Consensus size: 41
3242941 GGTTAATCAA
*
3242951 TAGCGGCATTTATAG-TAAAAACGCCGTAATAGAGTAG-ACATT
1 TAGCGGCGTTTATAGCT-AAAACGCCGTAATAGAGT-GTA-ATT
3242993 TAGCGGCGTTT-TAGCTAAAACGCCGTAATAGAGTGTAATT
1 TAGCGGCGTTTATAGCTAAAACGCCGTAATAGAGTGTAATT
* *
3243033 TAGCGGCGTTTATA-CCATAAACGCCGTAATAGAGTGGTAAAT
1 TAGCGGCGTTTATAGCTA-AAACGCCGTAATAGAGT-GTAATT
*
3243075 TAGCGGCGTTTATACCTAAA
1 TAGCGGCGTTTATAGCTAAA
3243095 CTGCCATAAT
Statistics
Matches: 92, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
40 17 0.18
41 41 0.45
42 32 0.35
43 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (41 bp):
TAGCGGCGTTTATAGCTAAAACGCCGTAATAGAGTGTAATT
Found at i:3244616 original size:41 final size:41
Alignment explanation
Indices: 3244570--3244723 Score: 134
Period size: 41 Copynumber: 3.7 Consensus size: 41
3244560 AATAGTACTT
* *
3244570 TAGTGGCATTTTTATACAAACGCCGCAATTGGTATAATATA
1 TAGTGGCATTTTTAAACAAACGCCGCAATAGGTATAATATA
*** *
3244611 TAGTGGCATTTTTAAATGCAAACGCCGCAA-AAAAATTAGACAT-
1 TAGTGGCATTTTTAAA--CAAACGCCGCAATAGGTA-TA-ATATA
* * * *
3244654 TAGTGGCGTTTAT-AACAAACGCCGCAGTAGGTGTAATATA
1 TAGTGGCATTTTTAAACAAACGCCGCAATAGGTATAATATA
* * *
3244694 TAGTGGCGTTTTTCACCAAACGCCGCAATA
1 TAGTGGCATTTTTAAACAAACGCCGCAATA
3244724 TATTTGAACT
Statistics
Matches: 89, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
39 3 0.03
40 25 0.28
41 30 0.34
42 3 0.03
43 25 0.28
44 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
TAGTGGCATTTTTAAACAAACGCCGCAATAGGTATAATATA
Found at i:3244786 original size:43 final size:41
Alignment explanation
Indices: 3244650--3244788 Score: 111
Period size: 43 Copynumber: 3.4 Consensus size: 41
3244640 AAAAAATTAG
* * * ** *
3244650 ACATTAGTGGCGTTTAT-AACAAACGCCGCAGTAGGTGT-A
1 ACATTAGTGGCGTTTTTCACCAAACGCCGCAATATATATGA
* *
3244689 ATATATAGTGGCGTTTTTCACCAAACGCCGCAATATATTTGA
1 ACAT-TAGTGGCGTTTTTCACCAAACGCCGCAATATATATGA
* * * * * *
3244731 ACTTTTGCGGCGTTTTTAGACATAAACGCCGCAATATATATGG
1 ACATTAGTGGCGTTTTT-CAC-CAAACGCCGCAATATATATGA
3244774 ACATTAGTGGCGTTT
1 ACATTAGTGGCGTTT
3244789 ATTAAGAAAA
Statistics
Matches: 77, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
39 3 0.04
40 12 0.16
41 27 0.35
42 5 0.06
43 30 0.39
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (41 bp):
ACATTAGTGGCGTTTTTCACCAAACGCCGCAATATATATGA
Found at i:3247793 original size:21 final size:21
Alignment explanation
Indices: 3247767--3247890 Score: 158
Period size: 21 Copynumber: 5.9 Consensus size: 21
3247757 ATAAAGCAAG
3247767 GGAAGCAGAGAGAGTAGCAGC
1 GGAAGCAGAGAGAGTAGCAGC
*
3247788 GTAAGCAGAGAGAGTAGCAGC
1 GGAAGCAGAGAGAGTAGCAGC
** * *
3247809 ATAAGCAGAGAGAGCAGCAGT
1 GGAAGCAGAGAGAGTAGCAGC
3247830 GGAAGCAGAGAGAGTAGCAGC
1 GGAAGCAGAGAGAGTAGCAGC
* *
3247851 GGAAGCAGAGAAAGAAGCAGC
1 GGAAGCAGAGAGAGTAGCAGC
* * *
3247872 GGCAGCATAGAGAGAAGCA
1 GGAAGCAGAGAGAGTAGCA
3247891 ACATATCAGC
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 90 1.00
ACGTcount: A:0.41, C:0.15, G:0.39, T:0.06
Consensus pattern (21 bp):
GGAAGCAGAGAGAGTAGCAGC
Found at i:3247828 original size:42 final size:42
Alignment explanation
Indices: 3247769--3247905 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
3247759 AAAGCAAGGG
* *
3247769 AAGCAGAGAGAGTAGCAGCGTAAGCAGAGAGAGTAGCAGCAT
1 AAGCAGAGAGAGAAGCAGCGGAAGCAGAGAGAGTAGCAGCAT
* * **
3247811 AAGCAGAGAGAGCAGCAGTGGAAGCAGAGAGAGTAGCAGCGG
1 AAGCAGAGAGAGAAGCAGCGGAAGCAGAGAGAGTAGCAGCAT
* * * * *
3247853 AAGCAGAGAAAGAAGCAGCGGCAGCATAGAGAGAAGCAACAT
1 AAGCAGAGAGAGAAGCAGCGGAAGCAGAGAGAGTAGCAGCAT
3247895 ATCAGCAGAGA
1 A--AGCAGAGA
3247906 TGTGAAGAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 71 0.90
44 8 0.10
ACGTcount: A:0.42, C:0.15, G:0.36, T:0.07
Consensus pattern (42 bp):
AAGCAGAGAGAGAAGCAGCGGAAGCAGAGAGAGTAGCAGCAT
Found at i:3247884 original size:63 final size:63
Alignment explanation
Indices: 3247767--3247890 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 63
3247757 ATAAAGCAAG
* * * * *
3247767 GGAAGCAGAGAGAGTAGCAGCGTAAGCAGAGAGAGTAGCAGCATAAGCAGAGAGAGCAGCAGT
1 GGAAGCAGAGAGAGTAGCAGCGGAAGCAGAGAAAGAAGCAGCAGAAGCAGAGAGAGAAGCAGT
* * *
3247830 GGAAGCAGAGAGAGTAGCAGCGGAAGCAGAGAAAGAAGCAGCGGCAGCATAGAGAGAAGCA
1 GGAAGCAGAGAGAGTAGCAGCGGAAGCAGAGAAAGAAGCAGCAGAAGCAGAGAGAGAAGCA
3247891 ACATATCAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.41, C:0.15, G:0.39, T:0.06
Consensus pattern (63 bp):
GGAAGCAGAGAGAGTAGCAGCGGAAGCAGAGAAAGAAGCAGCAGAAGCAGAGAGAGAAGCAGT
Found at i:3248988 original size:64 final size:63
Alignment explanation
Indices: 3248872--3249034 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 63
3248862 TTCTGGGCAA
* * *
3248872 GGTGTATCGATGCATATTGAATGTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATT
1 GGTGTATCGATGCATA-AGAA-GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATT
* * * *
3248937 GGTGCATCGATGCATAAGAAATGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATT
1 GGTGTATCGATGCATAAGAAGTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAATT
* * *
3249001 TGTGTATCGATGCATGAGTAGTGCATCGATGCAC
1 GGTGTATCGATGCATAAGAAGTGCATCGATGCAC
3249035 ATGTTAAAGA
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 15 0.18
64 54 0.64
65 15 0.18
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (63 bp):
GGTGTATCGATGCATAAGAAGTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATT
Found at i:3249067 original size:20 final size:20
Alignment explanation
Indices: 3249022--3249099 Score: 120
Period size: 20 Copynumber: 3.7 Consensus size: 20
3249012 GCATGAGTAG
3249022 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
3249046 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
3249066 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
3249086 TGCATCGATGCACT
1 TGCATCGATGCACT
3249100 TCAAGGGGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
20 38 0.70
22 1 0.02
23 2 0.04
24 13 0.24
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:3249094 original size:40 final size:43
Alignment explanation
Indices: 3249006--3249099 Score: 126
Period size: 40 Copynumber: 2.3 Consensus size: 43
3248996 TAATTTGTGT
*
3249006 ATCGATGCA-TGAGTAGTGCATCGATGCACATGTTAAAGAATGC
1 ATCGATGCACTGAGTAATGCATCGATGCACATGTT-AAGAATGC
3249049 ATCGATGCACTGTAG-AATGCATCGATGCAC-TG-T-AGAATGC
1 ATCGATGCACTG-AGTAATGCATCGATGCACATGTTAAGAATGC
3249089 ATCGATGCACT
1 ATCGATGCACT
3249100 TCAAGGGGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
40 18 0.38
42 1 0.02
43 11 0.23
44 16 0.33
45 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (43 bp):
ATCGATGCACTGAGTAATGCATCGATGCACATGTTAAGAATGC
Found at i:3250321 original size:374 final size:373
Alignment explanation
Indices: 3249632--3250380 Score: 1401
Period size: 374 Copynumber: 2.0 Consensus size: 373
3249622 AAGTTATATG
* *
3249632 TAACAAATATATACATATATATGCCATTATCACTCATATCTCTTATCTCCTGTTCCTATGATCTT
1 TAACAAATACATACATATATATGCCATTATCACTCATATCTCTTATCTCATGTTCCTATGATCTT
3249697 TTATGTCCATATTATATATCTGATAGACTTGTTATTATATCATCATGTAAATCAATTATACTCAT
66 TTATGTCCATATTATATATCTGATAGACTTGTTATTATATCATCATGTAAATCAATTATACTCAT
3249762 TTACATATACCTTAACAAGTACTCACGTATACCATATAACATATATATATATCATGTCATGTAAA
131 TTACATATACCTTAACAAGTACTCACGTATACCATATAACA-ATATATATATCATGTCATGTAAA
3249827 ACATATATCCTATCGTAAATCAAACACACAAGCAACTATATCATCATCATCATTCTTATCACTAT
195 ACATATATCCTATCGTAAATCAAACACACAAGCAACTATATCATCATCATCATTCTTATCACTAT
3249892 CATTGATTCCTTTTATCATATAATCTTATAATTACAATTTGTACCATCATATATCACACATAACA
260 CATTGATTCCTTTTATCATATAATCTTATAATTACAATTTGTACCATCATATATCACACATAACA
3249957 TTTCATAAGGAAACAAACATATCATCATATCCATTTTATTAATATTATC
325 TTTCATAAGGAAACAAACATATCATCATATCCATTTTATTAATATTATC
* *
3250006 TAACAAATACATACATACATATATGCCATTATCATTCATATCTCTTATCTCATGTTCTTATGATC
1 TAACAAATACATACAT--ATATATGCCATTATCACTCATATCTCTTATCTCATGTTCCTATGATC
3250071 TTTTATGTCCATATTATATATCTGATAGACTTGTTATTATATCATCATGTAAATCAATTATACTC
64 TTTTATGTCCATATTATATATCTGATAGACTTGTTATTATATCATCATGTAAATCAATTATACTC
*
3250136 ATTTACATATACCTTAACAGGTACTCACGTATACCATATAAC-ATATATATATCATGTCATGTAA
129 ATTTACATATACCTTAACAAGTACTCACGTATACCATATAACAATATATATATCATGTCATGTAA
*
3250200 AACATATATCCTATCGTAAATCAAACACACAAGCAACTATATCATCATCCTCATTCTTATCACTA
194 AACATATATCCTATCGTAAATCAAACACACAAGCAACTATATCATCATCATCATTCTTATCACTA
*
3250265 TCATTGATTCCTTTTATCATATAATCTTATAATTACCATTTGTACCATCATATATCACACATAAC
259 TCATTGATTCCTTTTATCATATAATCTTATAATTACAATTTGTACCATCATATATCACACATAAC
3250330 ATTTCATAAGGAAACAAACATATCATCATATCCATTTTATTAATATTATC
324 ATTTCATAAGGAAACAAACATATCATCATATCCATTTTATTAATATTATC
3250380 T
1 T
3250381 CTTTATTAGC
Statistics
Matches: 366, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
374 216 0.59
376 150 0.41
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (373 bp):
TAACAAATACATACATATATATGCCATTATCACTCATATCTCTTATCTCATGTTCCTATGATCTT
TTATGTCCATATTATATATCTGATAGACTTGTTATTATATCATCATGTAAATCAATTATACTCAT
TTACATATACCTTAACAAGTACTCACGTATACCATATAACAATATATATATCATGTCATGTAAAA
CATATATCCTATCGTAAATCAAACACACAAGCAACTATATCATCATCATCATTCTTATCACTATC
ATTGATTCCTTTTATCATATAATCTTATAATTACAATTTGTACCATCATATATCACACATAACAT
TTCATAAGGAAACAAACATATCATCATATCCATTTTATTAATATTATC
Found at i:3250520 original size:30 final size:30
Alignment explanation
Indices: 3250486--3250618 Score: 230
Period size: 30 Copynumber: 4.4 Consensus size: 30
3250476 CCCGAAGGAC
* *
3250486 CTATCCAGAGGTCATAAAGATCATCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3250516 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3250546 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3250576 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3250606 CTATCCATAGGTC
1 CTATCCAGAGGTC
3250619 CCGAAGAACC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 99 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3250635 original size:60 final size:60
Alignment explanation
Indices: 3250486--3250635 Score: 194
Period size: 60 Copynumber: 2.5 Consensus size: 60
3250476 CCCGAAGGAC
* * * *
3250486 CTATCCAGAGGTCATAAAGATCATCA-GTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCT-AGGTAACTATCCAGAGGTCATAAAGATCCTCGATAA
* * *
3250546 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGATAA
* * *
3250606 CTATCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAA
3250636 ACTGTCCATA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGATAA
Found at i:3251576 original size:20 final size:22
Alignment explanation
Indices: 3251551--3251608 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
3251541 TTCCCCTCGA
3251551 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
3251571 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
3251594 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3251609 CTACTCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:3251683 original size:64 final size:63
Alignment explanation
Indices: 3251596--3251757 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
3251586 TCTTTAACAT
* * * * *
3251596 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCAATTCTTATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
3251659 GATGCATCGATGCATTTCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCAATTCTTATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
*
3251723 GTGCATCGATGCACATTCAATATGCATCGATACAC
1 GTGCATCGATGCA-ATTC-TTATGCATCGATACAC
3251758 CTTGCCCAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 18 0.22
64 51 0.61
65 14 0.17
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCAATTCTTATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:3261315 original size:2 final size:2
Alignment explanation
Indices: 3261308--3261369 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3261298 CTTAATCATT
3261308 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
3261350 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
3261370 CAATTTACTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3266033 original size:21 final size:21
Alignment explanation
Indices: 3266007--3266055 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
3265997 GCAAATTCTT
3266007 GGGGTATGCTGATGGTGTAAA
1 GGGGTATGCTGATGGTGTAAA
3266028 GGGGTATGCTGATGGTGTAAA
1 GGGGTATGCTGATGGTGTAAA
3266049 GGGGTAT
1 GGGGTAT
3266056 CGCTTGTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.04, G:0.45, T:0.29
Consensus pattern (21 bp):
GGGGTATGCTGATGGTGTAAA
Found at i:3272470 original size:19 final size:19
Alignment explanation
Indices: 3272448--3272514 Score: 77
Period size: 18 Copynumber: 3.6 Consensus size: 19
3272438 ATTTTCATTA
3272448 TTATTATATTTTTTC-CTCT
1 TTATT-TATTTTTTCTCTCT
*
3272467 TTATTTTTTTTTTCTCTCT
1 TTATTTATTTTTTCTCTCT
*
3272486 ATATTTATTTTTT-TCT-T
1 TTATTTATTTTTTCTCTCT
3272503 TATATTTATTTT
1 T-TATTTATTTT
3272515 CTTTTTTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 1 0.02
18 21 0.50
19 20 0.48
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
TTATTTATTTTTTCTCTCT
Found at i:3272493 original size:23 final size:21
Alignment explanation
Indices: 3272466--3272526 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 21
3272456 TTTTTTCCTC
3272466 TTTATTTTTTTTTTCTCTCTATA
1 TTTATTTTTTTTTTCT-T-TATA
3272489 TTTA---TTTTTTTCTTTATA
1 TTTATTTTTTTTTTCTTTATA
3272507 TTTATTTTCTTTTTTTCTTT
1 TTTA-TTT-TTTTTTTCTTT
3272527 TTTTATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
18 8 0.24
19 1 0.03
20 9 0.27
23 15 0.45
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTATTTTTTTTTTCTTTATA
Found at i:3272583 original size:37 final size:34
Alignment explanation
Indices: 3272501--3272696 Score: 104
Period size: 38 Copynumber: 5.6 Consensus size: 34
3272491 TATTTTTTTC
*
3272501 TTTATATTTATTT-TCTTTTTTTCTTT-T-TTTATGT
1 TTTAT-TTTATTTAT-TTATTTTCTTTATCTTTAT-T
*
3272535 ATTTA-TGTATTTATTTACTTTTCTTTATCTTTATT
1 -TTTATTTTATTTATTTA-TTTTCTTTATCTTTATT
* *
3272570 TAGTTATTTTATTTATTTATATCTTTTTTATTTTTATT
1 T--TTATTTTATTTATTTAT-T-TTCTTTATCTTTATT
*
3272608 TTTATTTTCATTTTCTTTATTTTTTCTTTATC-TTATT
1 TTTATTTT-A-TTTATTTA--TTTTCTTTATCTTTATT
* * * *
3272645 TTT-CTTTATTTCATTTGTTTT-TTT-GCTTT-GT
1 TTTATTTTATTT-ATTTATTTTCTTTATCTTTATT
*
3272676 TTTATTTTCTTTATCTTATTT
1 TTTATTTTATTTAT-TTATTT
3272697 ATTTTCATTA
Statistics
Matches: 128, Mismatches: 16, Indels: 37
0.71 0.09 0.20
Matches are distributed among these distances:
31 7 0.05
32 16 0.12
33 12 0.09
34 13 0.10
35 10 0.08
36 19 0.15
37 21 0.16
38 28 0.22
39 1 0.01
40 1 0.01
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (34 bp):
TTTATTTTATTTATTTATTTTCTTTATCTTTATT
Found at i:3272632 original size:17 final size:16
Alignment explanation
Indices: 3272624--3272653 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3272614 TTCATTTTCT
3272624 TTATTTTTTCTTTATC
1 TTATTTTTTCTTTATC
3272640 TTA-TTTTTCTTTAT
1 TTATTTTTTCTTTAT
3272654 TTCATTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 11 0.79
16 3 0.21
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTTTCTTTATC
Found at i:3272652 original size:26 final size:27
Alignment explanation
Indices: 3272596--3272655 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
3272586 TTATATCTTT
* *
3272596 TTTATTTTTATTTTTATTTTCATTTTC
1 TTTATTTTTATCTTTATCTTCATTTTC
3272623 TTTATTTTT-TCTTTATCTT-ATTTTTC
1 TTTATTTTTATCTTTATCTTCA-TTTTC
3272649 TTTATTT
1 TTTATTT
3272656 CATTTGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 1 0.03
26 20 0.67
27 9 0.30
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTATTTTTATCTTTATCTTCATTTTC
Found at i:3277576 original size:64 final size:64
Alignment explanation
Indices: 3277500--3277671 Score: 290
Period size: 64 Copynumber: 2.7 Consensus size: 64
3277490 TTTTGCAGCT
* *
3277500 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAATAACTTTCCAATTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAATTTCA
* *
3277564 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAATTTCA
* *
3277628 TTCAGAGTCAATTTCAACTTCACAACGAATGATATTGGACTCAA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
3277672 AGTGACACCA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 102 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.29
Consensus pattern (64 bp):
TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAATTTCA
Found at i:3277729 original size:59 final size:60
Alignment explanation
Indices: 3277638--3277795 Score: 167
Period size: 64 Copynumber: 2.6 Consensus size: 60
3277628 TTCAGAGTCA
*** * *
3277638 ATTTCAACTTCACAACGAATGATATTGGACTCAAAG-T-GACACCATTTACTCGAGATTGG
1 ATTTCAACTTCACAACGAATGATATCCAACTCAAAGATGGACA-CACTTACTCAAGATTGG
* ** *
3277697 ATTTTAACTTCACAACGAATGATATCCAACTCAAAGCAAATTGGTGAGACTTACTCAAGATTGG
1 ATTTCAACTTCACAACGAATGATATCCAACTCAAAG---A-TGGACACACTTACTCAAGATTGG
*
3277761 ATTTCAACTTCACGACGAATGATATCCAACTCAAA
1 ATTTCAACTTCACAACGAATGATATCCAACTCAAA
3277796 TCCAATTTTG
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
59 32 0.39
64 48 0.59
65 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (60 bp):
ATTTCAACTTCACAACGAATGATATCCAACTCAAAGATGGACACACTTACTCAAGATTGG
Found at i:3277949 original size:124 final size:124
Alignment explanation
Indices: 3277821--3278341 Score: 817
Period size: 124 Copynumber: 4.2 Consensus size: 124
3277811 CAATACTTGA
* * * *
3277821 ATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAAGAACCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCAC
* * *
3277886 GATTTCAACTTCACGACGAAGGATATTGTGTTCACCAGCAACATTCATCTTTAGATTGG
66 AATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATTGG
* * * *
3277945 ATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTAACAATGAATGGGCTATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCAC
* *
3278010 GATTTCAACTTCACGACAAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATTGG
66 AATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATTGG
* * *
3278069 ATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCAC
* * * *
3278134 AATTTTAACTTCACGACGAAGGATATCATGTCCACCAGCAACATTCATCTTTATATTGA
66 AATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATTGG
* * * *
3278193 ATTTCAACTTCACAACGAAGGAAATCCAATTCAAGGCTCAACTTCAGAACGAATGAGTCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCAC
*
3278258 AATTTCAACTTCACGACGAAGGATATCGTGTTCACCAGCAACATTCATCTTTAGATTGG
66 AATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATTGG
3278317 ATTTCAACTTCACGACGAAGGATAT
1 ATTTCAACTTCACGACGAAGGATAT
3278342 AGTGTCCATC
Statistics
Matches: 363, Mismatches: 34, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 363 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (124 bp):
ATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCAC
AATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATTGG
Found at i:3277956 original size:58 final size:58
Alignment explanation
Indices: 3277886--3278400 Score: 283
Period size: 58 Copynumber: 8.5 Consensus size: 58
3277876 AACCATCCAC
*
3277886 GATTTCAACTTCACGACGAAGGATATTGTGTTCACCAGCAACATTCATCTTTAGATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGTTCACCAGCAACATTCATCTTTAGATTG
*** * ** * **
3277944 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTAACAATGAATGGGCTATCCA
1 GATTTCAACTTCACGACGAAGGATATCGTGTTC-A--C-CAGC--AAC-ATTCAT---CTTTAGA
*
3278009 --C
56 TTG
* *
3278010 GATTTCAACTTCACGACAAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGTTCACCAGCAACATTCATCTTTAGATTG
*** ***
3278068 GATTTCAACTTCACGACGAAGGATATCCAATTCA--AGGCTCAAC-TTCA-CAACGAAGGGGTCA
1 GATTTCAACTTCACGACGAAGGATATCGTGTTCACCA-G--CAACATTCATC--TTTA---G--A
**
3278129 TCCAC
56 T--TG
* * * * *
3278134 AATTTTAACTTCACGACGAAGGATATCATGTCCACCAGCAACATTCATCTTTATATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGTTCACCAGCAACATTCATCTTTAGATTG
* * * *** * * *
3278192 AATTTCAACTTCACAACGAAGGAAATCCAATTCA--AGGCTCAAC-TTCAGAACGAATGAGTCAT
1 GATTTCAACTTCACGACGAAGGATATCGTGTTCACCA-G--CAACATTC--ATC--TTTAG--AT
**
3278254 CCAC
57 --TG
*
3278258 AATTTCAACTTCACGACGAAGGATATCGTGTTCACCAGCAACATTCATCTTTAGATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGTTCACCAGCAACATTCATCTTTAGATTG
* * * *
3278316 GATTTCAACTTCACGACGAAGGATATAGTGTCCATCATCAACATTCATCTTTAGATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGTTCACCAGCAACATTCATCTTTAGATTG
*
3278374 GATTTCAACTTCACAACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
3278401 CAATTCAAAG
Statistics
Matches: 340, Mismatches: 75, Indels: 84
0.68 0.15 0.17
Matches are distributed among these distances:
56 6 0.02
57 3 0.01
58 170 0.50
59 14 0.04
60 9 0.03
61 1 0.00
62 12 0.04
63 1 0.00
64 9 0.03
65 14 0.04
66 92 0.27
67 3 0.01
68 6 0.02
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (58 bp):
GATTTCAACTTCACGACGAAGGATATCGTGTTCACCAGCAACATTCATCTTTAGATTG
Found at i:3280049 original size:2 final size:2
Alignment explanation
Indices: 3280042--3280075 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3280032 AATATTATTA
3280042 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
3280076 TAGTAGGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3280370 original size:4 final size:4
Alignment explanation
Indices: 3280363--3280509 Score: 59
Period size: 4 Copynumber: 35.8 Consensus size: 4
3280353 TCTCTCTATC
* * * * *
3280363 TTTA TTTA TTTC TTTA TATTT TTTA TGTA TTTA TTTA TATA TTTA CTT-
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
** * * * * *
3280411 TTCG TTATC TTTA TTTA GTTA TTTTA TTTA TTTA TATC TTT- TTTA TTTC
1 TTTA TT-TA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
3280460 TTTCA TTTTC TTTA TTTTT TTTC TTTA TCTTA -TT- TTTA TTTA TTTCA
1 TTT-A -TTTA TTTA -TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTT-A
3280507 TTT
1 TTT
3280510 GTTATTTTCT
Statistics
Matches: 105, Mismatches: 26, Indels: 23
0.68 0.17 0.15
Matches are distributed among these distances:
3 8 0.08
4 76 0.72
5 18 0.17
6 3 0.03
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:3280379 original size:32 final size:31
Alignment explanation
Indices: 3280315--3280384 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
3280305 TTTATATATA
* * *
3280315 TATATATTC-CTCTTTATTTTATTATTTTTT
1 TATATTTTCTCTCTCTATTTTATTATTTCTT
3280345 TAT-TTTTCTCTCTCTATCTTTATTTATTTCTT
1 TATATTTTCTCTCTCTAT-TTTA-TTATTTCTT
3280377 TATATTTT
1 TATATTTT
3280385 TTATGTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 4 0.12
30 10 0.30
31 4 0.12
32 11 0.33
33 4 0.12
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (31 bp):
TATATTTTCTCTCTCTATTTTATTATTTCTT
Found at i:3280393 original size:21 final size:21
Alignment explanation
Indices: 3280363--3280402 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3280353 TCTCTCTATC
* *
3280363 TTTATTTATTTCTTTATATTT
1 TTTATGTATTTATTTATATTT
3280384 TTTATGTATTTATTTATAT
1 TTTATGTATTTATTTATAT
3280403 ATTTACTTTT
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:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTATGTATTTATTTATATTT
Found at i:3280441 original size:9 final size:9
Alignment explanation
Indices: 3280420--3280558 Score: 63
Period size: 9 Copynumber: 14.9 Consensus size: 9
3280410 TTTCGTTATC
3280420 TTTA-TTTA
1 TTTATTTTA
*
3280428 GTTATTTTA
1 TTTATTTTA
3280437 TTTATTTATA
1 TTTATTT-TA
3280447 TCTT-TTTTA
1 T-TTATTTTA
* *
3280456 TTTCTTTCA
1 TTTATTTTA
3280465 TTT-TCTTTA
1 TTTAT-TTTA
* *
3280474 TTTTTTTTC
1 TTTATTTTA
*
3280483 TTTATCTTA
1 TTTATTTTA
*
3280492 TTTTTATTTA
1 TTTAT-TTTA
3280502 TTTCATTTGTTA
1 TTT-A-TT-TTA
*
3280514 TTT-TCTTTGT
1 TTTAT-TTT-A
*
3280524 TTTATTTTC
1 TTTATTTTA
*
3280533 TTTATCTTA
1 TTTATTTTA
3280542 TTTATTTT-
1 TTTATTTTA
3280550 TATTATTTT
1 T-TTATTTT
3280559 TTTTCTCTAA
Statistics
Matches: 101, Mismatches: 16, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
8 7 0.07
9 63 0.62
10 20 0.20
11 4 0.04
12 7 0.07
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:3280487 original size:50 final size:50
Alignment explanation
Indices: 3280433--3280553 Score: 149
Period size: 50 Copynumber: 2.4 Consensus size: 50
3280423 ATTTAGTTAT
* *
3280433 TTTAT-TTATTTATATCTT-TTTTATTTCTTTCATTTTCTTTATTTT-TTTTC
1 TTTATCTTATTTATAT-TTATTTCATTT-GTT-ATTTTCTTTATTTTATTTTC
* *
3280483 TTTATCTTATTTTTATTTATTTCATTTGTTATTTTCTTTGTTTTATTTTC
1 TTTATCTTATTTATATTTATTTCATTTGTTATTTTCTTTATTTTATTTTC
*
3280533 TTTATCTTATTTATTTTTATT
1 TTTATCTTATTTATATTTATT
3280554 ATTTTTTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
49 13 0.21
50 33 0.53
51 16 0.26
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (50 bp):
TTTATCTTATTTATATTTATTTCATTTGTTATTTTCTTTATTTTATTTTC
Found at i:3286186 original size:27 final size:27
Alignment explanation
Indices: 3286151--3286226 Score: 143
Period size: 27 Copynumber: 2.8 Consensus size: 27
3286141 TTCGTGGTCG
3286151 TGAATGTTAAACAAATGAACATGTTCT
1 TGAATGTTAAACAAATGAACATGTTCT
3286178 TGAATGTTAAACAAATGAACATGTTCT
1 TGAATGTTAAACAAATGAACATGTTCT
*
3286205 TGAATGTTAAACAAACGAACAT
1 TGAATGTTAAACAAATGAACAT
3286227 AAACACCTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (27 bp):
TGAATGTTAAACAAATGAACATGTTCT
Found at i:3296434 original size:20 final size:20
Alignment explanation
Indices: 3296392--3296434 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3296382 TTGTTTTCAT
* *
3296392 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
3296412 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
3296432 TTT
1 TTT
3296435 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:3305206 original size:20 final size:20
Alignment explanation
Indices: 3305181--3305221 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3305171 AGTTTGAACA
3305181 AACTTTAAATCACAAACATC
1 AACTTTAAATCACAAACATC
3305201 AACTTTAAATCACAAACATC
1 AACTTTAAATCACAAACATC
3305221 A
1 A
3305222 CTATGTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (20 bp):
AACTTTAAATCACAAACATC
Found at i:3308267 original size:32 final size:33
Alignment explanation
Indices: 3308226--3308288 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
3308216 AAATTGTCAT
* *
3308226 TATTATATAT-TTGTTTTTTAACAAATTTAAAAA
1 TATTATATATATT-TTCTTTAAAAAATTTAAAAA
3308259 TATT-TATATATTTTCTTTAAAAAATTTAAA
1 TATTATATATATTTTCTTTAAAAAATTTAAA
3308289 TTCATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (33 bp):
TATTATATATATTTTCTTTAAAAAATTTAAAAA
Found at i:3308306 original size:2 final size:2
Alignment explanation
Indices: 3308299--3308333 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3308289 TTCATAAATT
3308299 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
3308334 TTACAAAATT
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:3309035 original size:18 final size:18
Alignment explanation
Indices: 3309012--3309054 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
3309002 TCCTTCTTAA
3309012 TTGTTTCTACCAACCTTC
1 TTGTTTCTACCAACCTTC
3309030 TTGTTTCTACCAACCTTC
1 TTGTTTCTACCAACCTTC
3309048 TTGTTTC
1 TTGTTTC
3309055 ATTGTGTTCA
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:0.14, C:0.30, G:0.07, T:0.49
Consensus pattern (18 bp):
TTGTTTCTACCAACCTTC
Found at i:3309279 original size:17 final size:17
Alignment explanation
Indices: 3309257--3309299 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3309247 ATCTAATACA
3309257 AATGTATTATGATAAAT
1 AATGTATTATGATAAAT
3309274 AATGTATTATGATAAAT
1 AATGTATTATGATAAAT
*
3309291 GATGTATTA
1 AATGTATTA
3309300 ACTAACTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (17 bp):
AATGTATTATGATAAAT
Found at i:3311989 original size:2 final size:2
Alignment explanation
Indices: 3311959--3312216 Score: 144
Period size: 2 Copynumber: 140.0 Consensus size: 2
3311949 GATCTTTTTT
3311959 TA TA T- TA TA GTA T- TA TA CTA TA T- TA TA TA TA T- TA T- TA T-
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* *
3311997 TT TA TA TA -A TA TA T- TA TA TA TA TA T- TA TGG TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
*
3312036 TA TA -A TA TT TA TA TA GTA TA T- 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
*
3312077 TA T- TA T- TT TA T- TA TA T- TA TA TA T- TA TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3312112 TG TA -A TA TA TGA TA TA TA T- TA TA GTA TT TA TA T- TA TA TA -A
1 TA TA TA TA TA T-A TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
3312152 TA TA CA -A TA TT TA TG TA CTC TA T- TA TA TA -A TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
3312193 TA T- TA TA -A TA T- TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3312217 ATTATTATGT
Statistics
Matches: 201, Mismatches: 17, Indels: 76
0.68 0.06 0.26
Matches are distributed among these distances:
1 30 0.15
2 157 0.78
3 14 0.07
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3312185 original size:111 final size:109
Alignment explanation
Indices: 3311959--3312233 Score: 274
Period size: 111 Copynumber: 2.5 Consensus size: 109
3311949 GATCTTTTTT
* * * * *
3311959 TATAT-TATAGTATTATACTATATTATATATATTATTATTTTATATAATATATTATATATATATT
1 TATATATATA-TATTTTATTATATTATATATATTATTATATTATGTAATATA-TAGATATATATT
* * *
3312023 ATGGTATATATATTATAATATTTATATAGTATATTATATATATATA
64 ATAGTATATATATTATAATATATAAATAGTATATTATATATATATA
3312069 TATATATATATTATTTTATTATATTATATAT-TATATTATATTATGTAATATAT-GATATATATT
1 TATATATATA-TATTTTATTATATTATATATAT-TATTATATTATGTAATATATAGATATATATT
* * *
3312132 ATAGTATTTATATTAT-ATAATATACAATA-TTTATGTACTCTAT-TATA
64 ATAGTATATATATTATAAT-ATATA-AATAGTATAT-TA-TATATATATA
* * * *
3312179 TAATATATACTATATATTATAATATTATATATATTATAATTATTATGTTATATAT
1 T-ATATATA-TATATTTTATTATATTATATATATTATTA-TATTATGTAATATAT
3312234 TATTATTTTT
Statistics
Matches: 139, Mismatches: 16, Indels: 18
0.80 0.09 0.10
Matches are distributed among these distances:
108 2 0.01
109 31 0.22
110 17 0.12
111 72 0.52
112 17 0.12
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (109 bp):
TATATATATATATTTTATTATATTATATATATTATTATATTATGTAATATATAGATATATATTAT
AGTATATATATTATAATATATAAATAGTATATTATATATATATA
Found at i:3316699 original size:24 final size:25
Alignment explanation
Indices: 3316667--3316717 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
3316657 GCATTGAAAG
3316667 TTTCATGCATCTTGCA-TT-TTTACA
1 TTTCATGCAT-TTGCATTTCTTTACA
* *
3316691 TTTCTTGCATTTTCATTTCTTTACA
1 TTTCATGCATTTGCATTTCTTTACA
3316716 TT
1 TT
3316718 CAAAATCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 11 0.48
25 8 0.35
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.57
Consensus pattern (25 bp):
TTTCATGCATTTGCATTTCTTTACA
Found at i:3316709 original size:15 final size:17
Alignment explanation
Indices: 3316676--3316711 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
3316666 GTTTCATGCA
3316676 TCTTGCATTTTTACATT
1 TCTTGCATTTTTACATT
3316693 TCTTGCA-TTTT-CATT
1 TCTTGCATTTTTACATT
3316708 TCTT
1 TCTT
3316712 TACATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 4 0.21
17 7 0.37
ACGTcount: A:0.14, C:0.19, G:0.06, T:0.61
Consensus pattern (17 bp):
TCTTGCATTTTTACATT
Found at i:3321900 original size:42 final size:42
Alignment explanation
Indices: 3321853--3321943 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
3321843 AAGAAGAACG
* *
3321853 AAACCATGCTCATCAAATCATCCAACT-TATCAACCAAAAACC
1 AAACCAAGCTCATCAAATCATCCAA-TATATCAACAAAAAACC
* ** *
3321895 AAACCAAGCTTATCAAATCATTGAATATATCCACAAAAAACC
1 AAACCAAGCTCATCAAATCATCCAATATATCAACAAAAAACC
3321937 AAACCAA
1 AAACCAA
3321944 ACTATTGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.49, C:0.29, G:0.03, T:0.19
Consensus pattern (42 bp):
AAACCAAGCTCATCAAATCATCCAATATATCAACAAAAAACC
Found at i:3324555 original size:23 final size:22
Alignment explanation
Indices: 3324529--3324579 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
3324519 TTAATGTTTT
* * *
3324529 AATTATAAATATAATATTTATTG
1 AATTATAAAAATAAT-TATATAG
*
3324552 AATTTTAAAAATAATTATATAG
1 AATTATAAAAATAATTATATAG
3324574 AATTAT
1 AATTAT
3324580 GTTTGAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (22 bp):
AATTATAAAAATAATTATATAG
Found at i:3324695 original size:20 final size:19
Alignment explanation
Indices: 3324670--3324717 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
3324660 TTTGTTTAAT
3324670 AATAAAGAATTCGATTCTTA
1 AATAAAGAATT-GATTCTTA
3324690 AATAAAG-A-TGATTCTTA
1 AATAAAGAATTGATTCTTA
*
3324707 ATTAAAGAATT
1 AATAAAGAATT
3324718 TATCACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.56
18 2 0.08
19 2 0.08
20 7 0.28
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (19 bp):
AATAAAGAATTGATTCTTA
Found at i:3326765 original size:119 final size:121
Alignment explanation
Indices: 3326592--3326832 Score: 387
Period size: 119 Copynumber: 2.0 Consensus size: 121
3326582 TAGATAGGTT
*
3326592 ATTTATATCTTCTCTAATAAATTACTATCTTATAGATTACTCACTTCAGATGCTACTAAATTCTT
1 ATTTATATCTTCTCTAAT-AA-TACTATCTTATAGATTACACACTTCAGATGCTACTAAATTCTT
* * *
3326657 TTTAATTCAAAAAGTAAAACAGATTGTTGAGATGAATGATACTTCAAGTGCTATTTTG
64 TTTAATTCAAAAAGTAAAACAGATTGTTAAGATAAATGATACCTCAAGTGCTATTTTG
3326715 ATTTATATCTTCTCTAAT-A-ACTATCTTATAGATTACACACTTCAGATGCTACTAAATTCTTTT
1 ATTTATATCTTCTCTAATAATACTATCTTATAGATTACACACTTCAGATGCTACTAAATTCTTTT
* * *
3326778 TCATTCAAAACGTAAAACAGATTGTTAAGATAAATGATACCTCAAGTTCTATTTT
66 TAATTCAAAAAGTAAAACAGATTGTTAAGATAAATGATACCTCAAGTGCTATTTT
3326833 AATCACCAAT
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
119 92 0.83
121 1 0.01
123 18 0.16
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (121 bp):
ATTTATATCTTCTCTAATAATACTATCTTATAGATTACACACTTCAGATGCTACTAAATTCTTTT
TAATTCAAAAAGTAAAACAGATTGTTAAGATAAATGATACCTCAAGTGCTATTTTG
Found at i:3338021 original size:14 final size:14
Alignment explanation
Indices: 3338004--3338039 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3337994 ACACCTATAT
*
3338004 GAATTCACCCTCTC
1 GAATCCACCCTCTC
3338018 GAATCCACCCTCTC
1 GAATCCACCCTCTC
3338032 GAATCCAC
1 GAATCCAC
3338040 TTCAACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.44, G:0.08, T:0.22
Consensus pattern (14 bp):
GAATCCACCCTCTC
Found at i:3343916 original size:2 final size:2
Alignment explanation
Indices: 3343909--3343954 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
3343899 CAATATCTCT
* * * *
3343909 TA TA TA TA TA TA TA TA TA TA TA TA AA TA AA TA AA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3343951 TA TA
1 TA TA
3343955 ATGATTTCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (2 bp):
TA
Found at i:3351940 original size:36 final size:36
Alignment explanation
Indices: 3351899--3352008 Score: 139
Period size: 36 Copynumber: 3.0 Consensus size: 36
3351889 AGCAAAGTCA
3351899 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
* * * *
3351935 ATCTTAAGCCTTCACTAAAAAGGAGGGAAGCAAATCA
1 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAA-CC
* * *
3351972 ATTTGTAAGCCTTCACCAAAGAGTAGTGAAACAAACC
1 ATCT-TAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
3352009 CATCAGTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
36 31 0.51
37 5 0.08
38 25 0.41
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
Found at i:3352389 original size:54 final size:54
Alignment explanation
Indices: 3352059--3352760 Score: 399
Period size: 54 Copynumber: 12.9 Consensus size: 54
3352049 AGTGAAGCAA
* **
3352059 AAGAAGATGTTTGAGTTCTATAC-TCCTTGAAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCTATACTTCC-TGAAGAAAGAGGGAGCGAACCCGTTTG
* *
3352113 AAGAAGATGTTCGAGTT-TCATACTTTCTGAAAAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCT-ATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
3352167 AAAAAGATG-CCTGAGTTTTATACTCCCT-AGAGAAAGAGGGAGCGAACCCATTTG
1 AAGAAGATGTTC-GAGTTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTG
* *
3352221 AAGAAGATGTCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCTAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* * * * **
3352275 AAGAAGATGTCCGAGTTTTATACTTCCTGAAGAAAAAAGGAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* *
3352329 AAGAAGATGTTCGAGTTCCATACTTCCT-AGAGAATGAGGGAGCGAACCCGTTT-
1 AAGAAGATGTTCGAGTTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTG
* * * * *
3352382 ATTGAAGATTGTTCGAG-TCTTATAC-TCTCTGAAGAAATAGGAAGC-AGACACGATTG
1 A-AGAAGA-TGTTCGAGTTC-TATACTTC-CTGAAGAAAGAGGGAGCGA-ACCCGTTTG
** * * * * * *
3352438 TTGAAGATTATTCGAG-TCTTATAC-TCTCTGAAGAAATAGAGAGCAAACACGATTG
1 AAGAAGA-TGTTCGAGTTC-TATACTTC-CTGAAGAAAGAGGGAGCGAACCCGTTTG
** * * * * *
3352493 TTGAAAATTGTCCGAG-TCTTATAC-TCTCTGAAGAAATAGAGAGC-AGACACGAATGTTG
1 AAGAAGA-TGTTCGAGTTC-TATACTTC-CTGAAGAAAGAGGGAGCGA-ACCCG--T-TTG
* * * * *
3352551 AA-AA-TTGTTCGA-ATCATATAC-TCTCTGAAGAAATAGGGAGC-ATACACATTTG
1 AAGAAGATGTTCGAGTTC-TATACTTC-CTGAAGAAAGAGGGAGCGA-ACCCGTTTG
** * * * * * * *
3352603 TTGAAGATTTGTTCAAGTCCTATGC-TCTCTGAAGGAATAGGGAGCGGACACGTTTG
1 AAGAAGA--TGTTCGAGTTCTATACTTC-CTGAAGAAAGAGGGAGCGAACCCGTTTG
** * * * *
3352659 TTGAAGA---TCTAGTTCTATACTCCCTGAAGAAAGAGGGAGTGAACCCGTTTTC
1 AAGAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCG-TTTG
* * * * *
3352711 AA-AAGATTTCTCGAGTTCTATACTCCCTTAAGCAATAGGGAGCGAACCCG
1 AAGAAGATGT-TCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCG
3352761 CTGGTCGAAT
Statistics
Matches: 535, Mismatches: 80, Indels: 65
0.79 0.12 0.10
Matches are distributed among these distances:
51 33 0.06
52 7 0.01
53 8 0.01
54 232 0.43
55 203 0.38
56 46 0.09
57 3 0.01
58 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (54 bp):
AAGAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG
Found at i:3352389 original size:108 final size:107
Alignment explanation
Indices: 3352059--3352418 Score: 440
Period size: 108 Copynumber: 3.3 Consensus size: 107
3352049 AGTGAAGCAA
** *
3352059 AAGAAGATGTTTGAGTTCTATACTCCTTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTT
1 AAGAAGATGTCCGAGTTTTATACTCC-TGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTT
* * *
3352124 CGAGTTTCATACTTTCTGAAAAAAGAGGGAGCGAACCCGTTTG
65 CGAGTTCCATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* * **
3352167 AAAAAGATG-CCTGAGTTTTATACTCCCT-AGAGAAAGAGGGAGCGAACCCATTTGAAGAAGATG
1 AAGAAGATGTCC-GAGTTTTATACT-CCTGA-AGAAAGAGGGAGCGAACCCGTAAGAAGAAGATG
* * *
3352230 TCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCTAACCCGTTTG
63 TTCGAGTTCCATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG
* *
3352275 AAGAAGATGTCCGAGTTTTATACTTCCTGAAGAAAAAAGGAGCGAACCCGTAAGAAGAAGATGTT
1 AAGAAGATGTCCGAGTTTTATAC-TCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTT
*
3352340 CGAGTTCCATACTTCCT-AGAGAATGAGGGAGCGAACCCGTTT-
65 CGAGTTCCATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTG
* * *
3352382 ATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAA
1 A-AGAAGA-TGTCCGAGTTTTATACTC-CTGAAGAAA
3352419 TAGGAAGCAG
Statistics
Matches: 216, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
107 3 0.01
108 184 0.85
109 29 0.13
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (107 bp):
AAGAAGATGTCCGAGTTTTATACTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC
GAGTTCCATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG
Found at i:3352442 original size:55 final size:55
Alignment explanation
Indices: 3352383--3352666 Score: 358
Period size: 55 Copynumber: 5.1 Consensus size: 55
3352373 AACCCGTTTA
3352383 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGAAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGAAGCAGACACGATTG
* *
3352438 TTGAAGATTATTCGAGTCTTATACTCTCTGAAGAAATA-GAGAGCAAACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGA-AGCAGACACGATTG
* * *
3352493 TTGAAAATTGTCCGAGTCTTATACTCTCTGAAGAAATA-GAGAGCAGACACGAATG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGA-AGCAGACACGATTG
* * * * *
3352548 TTGAAAATTGTTCGAATCATATACTCTCTGAAGAAATAGGGAGCATACAC-ATTTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGAAGCAGACACGA-TTG
* * * * * * *
3352603 TTGAAGATTTGTTCAAGTCCTATGCTCTCTGAAGGAATAGGGAGCGGACACGTTTG
1 TTGAAGA-TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGAAGCAGACACGATTG
3352659 TTGAAGAT
1 TTGAAGAT
3352667 CTAGTTCTAT
Statistics
Matches: 202, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
54 3 0.01
55 152 0.75
56 47 0.23
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGAAGCAGACACGATTG
Found at i:3352956 original size:3 final size:3
Alignment explanation
Indices: 3352938--3352988 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
3352928 TAAAAATATA
*
3352938 TAT TA- TAT TGAT TAT TAT TAT TAT TA- TAT TAA TA- TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3352981 TAA TAT TA
1 TAT TAT TA
3352989 CTAATAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3353001 original size:28 final size:25
Alignment explanation
Indices: 3352948--3353005 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
3352938 TATTATATTG
* *
3352948 ATTATTATTATTATTATATTAATAT
1 ATTATTATTAATATTATAATAATAT
*
3352973 ATTATTATTAATATTACTAATAATTT
1 ATTATTATTAATATTA-TAATAATAT
*
3352999 ATAATTA
1 ATTATTA
3353006 CATATTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTATTATTAATATTATAATAATAT
Found at i:3360849 original size:22 final size:22
Alignment explanation
Indices: 3360824--3360876 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
3360814 GAACTCGGTC
3360824 GGTGGCGACGGGAATCAGATCT
1 GGTGGCGACGGGAATCAGATCT
*
3360846 GGTGGCGACGGGAATTAGATCT
1 GGTGGCGACGGGAATCAGATCT
*
3360868 GGCGGCGAC
1 GGTGGCGAC
3360877 TACTGCTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.43, T:0.17
Consensus pattern (22 bp):
GGTGGCGACGGGAATCAGATCT
Found at i:3361551 original size:32 final size:32
Alignment explanation
Indices: 3361510--3361575 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
3361500 TTCTCTCTTG
*
3361510 TTGGATGAGTTTTTCTCATTACGAACCCTTCA
1 TTGGATGAGTTCTTCTCATTACGAACCCTTCA
* *
3361542 TTGGATGAGTTCTTCTCATTATGAACTCTTCA
1 TTGGATGAGTTCTTCTCATTACGAACCCTTCA
3361574 TT
1 TT
3361576 TATCCACCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (32 bp):
TTGGATGAGTTCTTCTCATTACGAACCCTTCA
Found at i:3362487 original size:111 final size:112
Alignment explanation
Indices: 3362287--3362504 Score: 334
Period size: 111 Copynumber: 2.0 Consensus size: 112
3362277 TGAGAACTCC
* * *
3362287 GAAATTCATTAAAAATTTGGGAGTTTTACAAAATTATGGAAATCACATAAGACAAAAAGTAAAAC
1 GAAATTCATTAAAAATTTGAGAGTTTTACAAAATCATGGAAATCACACAAGACAAAAAGTAAAAC
*
3362352 CCTAAGAGTAAGGATCTACTCCCCAAGGATCCCTAGCAAGAGTGTTT
66 CCTAAGAGTAAGGATCTACACCCCAAGGATCCCTAGCAAGAGTGTTT
*
3362399 GAAATTCATTAAAAATTTGAGAG-TTTACAAAATCAT-GACAATCACACAAGACGAAAAGTAAAA
1 GAAATTCATTAAAAATTTGAGAGTTTTACAAAATCATGGA-AATCACACAAGACAAAAAGTAAAA
* *
3362462 CCCTAATAGTAAGGAT-TGACACCCCAAGGATCCCTCGCAAGAG
65 CCCTAAGAGTAAGGATCT-ACACCCCAAGGATCCCTAGCAAGAG
3362505 CATTTTTGAG
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
110 3 0.03
111 72 0.74
112 22 0.23
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (112 bp):
GAAATTCATTAAAAATTTGAGAGTTTTACAAAATCATGGAAATCACACAAGACAAAAAGTAAAAC
CCTAAGAGTAAGGATCTACACCCCAAGGATCCCTAGCAAGAGTGTTT
Found at i:3364923 original size:469 final size:469
Alignment explanation
Indices: 3364045--3364977 Score: 1686
Period size: 469 Copynumber: 2.0 Consensus size: 469
3364035 ATATTTCTGC
3364045 ATCTTAATCAACATCATATATGCCTTCATACTTGCTTTAAACATAGAAGCTAGTGTAGCTAGAGT
1 ATCTTAATCAACATCATATATGCCTTCATACTTGCTTTAAACATAGAAGCTAGTGTAGCTAGAGT
*
3364110 ATCGACCATTTGGTTATCTTTATGAGGAAGGTAGTTGAATGTCACCTCTTCAAACTCCTTTATTA
66 ATCGACCATTTGGTTATCTTTATGAGGAAGGTAGTTGAATGTCACCTCTTCAAACCCCTTTATTA
3364175 ATTCGAGGACCAAATTTCGACACTCAACCAATTTTGGTCTTTAATTTCCCATTCTCCTTGGAGTT
131 ATTCGAGGACCAAATTTCGACACTCAACCAATTTTGGTCTTTAATTTCCCATTCTCCTTGGAGTT
3364240 GGTTCACGACTAGAGAGAAATCTCCATATACTTTAAGCACTTTGACATTTCTTTCTATAGCTGCC
196 GGTTCACGACTAGAGAGAAATCTCCATATACTTTAAGCACTTTGACATTTCTTTCTATAGCTGCC
* *
3364305 CTTAATCCCATGGCACATGCCTCATATTCTTCCATATTATTGGTATAAAATAACTTGAGACTACT
261 CTTAATCCCATGGCACATGCCTCATATTCTTCCATATTATTGGTACAAAAGAACTTGAGACTACT
* *
3364370 CGTGAAAGGGTAACAAAAATCTTTCGGGGAAATCAAAACTGCCCCAATTCCCCGTCCCAGAGCAT
326 CATGAAAGGGTAACAAAAATCTTTCAGGGAAATCAAAACTGCCCCAATTCCCCGTCCCAGAGCAT
3364435 TAGAGGCTCCATCAAAGTAAAGCTTACAAGATTCATCATTTGAGAAGTCATTCTCTTCAACCGAG
391 TAGAGGCTCCATCAAAGTAAAGCTTACAAGATTCATCATTTGAGAAGTCATTCTCTTCAACCGAG
3364500 ATACTCATTTGGTT
456 ATACTCATTTGGTT
* *
3364514 ATCTTAATCGACATCATATATGCCTTCATACTTGCTTTAAACATATAAGCTAGTGTAGCTAGAGT
1 ATCTTAATCAACATCATATATGCCTTCATACTTGCTTTAAACATAGAAGCTAGTGTAGCTAGAGT
*
3364579 ATCGACCATTTGGTTATCTTTGTGAGGAAGGTAGTTGAATGTCACCTCTTCAAACCCCTTTATTA
66 ATCGACCATTTGGTTATCTTTATGAGGAAGGTAGTTGAATGTCACCTCTTCAAACCCCTTTATTA
* *
3364644 ATTCGAGGACCAAATTTTGACACTCAACCAATTTTGGTCTTTAATTTCCCATTCTTCTTGGAGTT
131 ATTCGAGGACCAAATTTCGACACTCAACCAATTTTGGTCTTTAATTTCCCATTCTCCTTGGAGTT
* * * *
3364709 GGTTCACGACTAGAGGGGAATCTCTATATACTTTAAGCACTTTGACCTTTCTTTCTATAGCTGCC
196 GGTTCACGACTAGAGAGAAATCTCCATATACTTTAAGCACTTTGACATTTCTTTCTATAGCTGCC
* * *
3364774 CTTAATCCCATGGCACATGCCTCGTATTTTTCCATATTATTGGTACAGAAGAACTTGAGACTACT
261 CTTAATCCCATGGCACATGCCTCATATTCTTCCATATTATTGGTACAAAAGAACTTGAGACTACT
* *
3364839 CATGAAAGGGTAACAGAAATCTTTCAGGGAAATCAACACTGCCCCAATTCCCCGTCCCAGAGCAT
326 CATGAAAGGGTAACAAAAATCTTTCAGGGAAATCAAAACTGCCCCAATTCCCCGTCCCAGAGCAT
*
3364904 TAGAGGCTCCATCAAAGTAAAGCTTACAAGATTCATCATTTGAGAAGTCCTTCTCTTCAACCGAG
391 TAGAGGCTCCATCAAAGTAAAGCTTACAAGATTCATCATTTGAGAAGTCATTCTCTTCAACCGAG
3364969 ATACTCATT
456 ATACTCATT
3364978 AAGTCTTCAT
Statistics
Matches: 444, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
469 444 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (469 bp):
ATCTTAATCAACATCATATATGCCTTCATACTTGCTTTAAACATAGAAGCTAGTGTAGCTAGAGT
ATCGACCATTTGGTTATCTTTATGAGGAAGGTAGTTGAATGTCACCTCTTCAAACCCCTTTATTA
ATTCGAGGACCAAATTTCGACACTCAACCAATTTTGGTCTTTAATTTCCCATTCTCCTTGGAGTT
GGTTCACGACTAGAGAGAAATCTCCATATACTTTAAGCACTTTGACATTTCTTTCTATAGCTGCC
CTTAATCCCATGGCACATGCCTCATATTCTTCCATATTATTGGTACAAAAGAACTTGAGACTACT
CATGAAAGGGTAACAAAAATCTTTCAGGGAAATCAAAACTGCCCCAATTCCCCGTCCCAGAGCAT
TAGAGGCTCCATCAAAGTAAAGCTTACAAGATTCATCATTTGAGAAGTCATTCTCTTCAACCGAG
ATACTCATTTGGTT
Found at i:3369157 original size:20 final size:20
Alignment explanation
Indices: 3369132--3369183 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
3369122 TACTGCTGTG
3369132 GGTATCGATACTGTGAGAAA
1 GGTATCGATACTGTGAGAAA
3369152 GGTATCGATACTGTGAGAAA
1 GGTATCGATACTGTGAGAAA
3369172 GGTATCGATACT
1 GGTATCGATACT
3369184 ATGGAGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (20 bp):
GGTATCGATACTGTGAGAAA
Found at i:3369723 original size:49 final size:49
Alignment explanation
Indices: 3369649--3369919 Score: 452
Period size: 49 Copynumber: 5.5 Consensus size: 49
3369639 AATGCTCAAA
* *
3369649 AATGAAAGTTAAAAGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* * *
3369698 AATGAAAGTTAAATGCATAATGGTGCTTTTCGGCATAAAAGGTGCCACA
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
3369747 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* * * * *
3369796 AATAAAAGTTAAATGCATAACGGTGCATTACAGAATAAAAGGTGACACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
3369845 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
3369894 AATGAAAGTTAAATGCATAACGGTGC
1 AATGAAAGTTAAATGCATAACGGTGC
3369920 CACTAATGAA
Statistics
Matches: 204, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 204 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (49 bp):
AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
Found at i:3369920 original size:30 final size:30
Alignment explanation
Indices: 3369885--3369949 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
3369875 CGGCATAAAA
3369885 GGTGCCACTAATGAAAGTTAAATGCATAAC
1 GGTGCCACTAATGAAAGTTAAATGCATAAC
3369915 GGTGCCACTAATGAAAGTTAAATGCATAAC
1 GGTGCCACTAATGAAAGTTAAATGCATAAC
3369945 GGTGC
1 GGTGC
3369950 ATTTCTGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (30 bp):
GGTGCCACTAATGAAAGTTAAATGCATAAC
Found at i:3369929 original size:79 final size:79
Alignment explanation
Indices: 3369836--3369998 Score: 272
Period size: 79 Copynumber: 2.1 Consensus size: 79
3369826 CAGAATAAAA
* * *
3369836 GGTGACACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAA
1 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAAGTGCCACTAATAAAA
*
3369901 GTTAAATGCATAAC
66 GTAAAATGCATAAC
* *
3369915 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCTGCATAAAAAGTGTCACTAATAAAA
1 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAAGTGCCACTAATAAAA
3369980 GTAAAATGCATAAC
66 GTAAAATGCATAAC
3369994 GGTGC
1 GGTGC
3369999 ATTTCGACGT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (79 bp):
GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAAGTGCCACTAATAAAA
GTAAAATGCATAAC
Found at i:3369935 original size:128 final size:128
Alignment explanation
Indices: 3369787--3370047 Score: 414
Period size: 128 Copynumber: 2.0 Consensus size: 128
3369777 CGGCATAAAA
* *
3369787 GGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTACAGAATAAAAGGTGACACTAATGAAA
1 GGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTACAGAATAAAAAGTGACACTAATAAAA
* * *
3369852 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
66 GTAAAATGCATAACGGTGCATTTCGACATAAAAGATGCCACTAATGAAAGTTAAATGCATAAC
* * * * *
3369915 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCTGCATAAAAAGTGTCACTAATAAAA
1 GGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTACAGAATAAAAAGTGACACTAATAAAA
* *
3369980 GTAAAATGCATAACGGTGCATTTCGACGTAAACGATGCCACTAATGAAAGTTAAATGCATAAC
66 GTAAAATGCATAACGGTGCATTTCGACATAAAAGATGCCACTAATGAAAGTTAAATGCATAAC
3370043 GGTGC
1 GGTGC
3370048 ATTTCGACAT
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
128 121 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (128 bp):
GGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTACAGAATAAAAAGTGACACTAATAAAA
GTAAAATGCATAACGGTGCATTTCGACATAAAAGATGCCACTAATGAAAGTTAAATGCATAAC
Found at i:3369981 original size:49 final size:49
Alignment explanation
Indices: 3369915--3370168 Score: 357
Period size: 49 Copynumber: 5.2 Consensus size: 49
3369905 AATGCATAAC
3369915 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCTG-CATAAAA
1 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTC-GACATAAAA
* * * * * *
3369964 AGTGTCACTAATAAAAGTAAAATGCATAACGGTGCATTTCGACGTAAAC
1 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAA
*
3370013 GATGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAA
1 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAA
* * *
3370062 GGTGTCACAAATGAAAGTTCAATGCATAACGGTGCATTTCGACATAAAA
1 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAA
* * **
3370111 GGTGCCATTAATGAAAGTTAAATGCAGAACGGTGCATTTTAACATAAAA
1 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAA
*
3370160 GATGCCACT
1 GGTGCCACT
3370169 CATGTTATTA
Statistics
Matches: 178, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
48 1 0.01
49 177 0.99
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (49 bp):
GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAA
Found at i:3370034 original size:177 final size:177
Alignment explanation
Indices: 3369738--3370096 Score: 576
Period size: 177 Copynumber: 2.0 Consensus size: 177
3369728 CGGCATAAAA
*
3369738 GGTGCCACAAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
1 GGTGCCACAAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAAGTGCCACTAATAAAA
* *
3369803 GTTAAATGCATAACGGTGCATTACAGAATAAAAGGTGACACTAATGAAAGTTAAATGCATAACGG
66 GTAAAATGCATAACGGTGCATTACAGAATAAAAGATGACACTAATGAAAGTTAAATGCATAACGG
* *
3369868 TGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAC
131 TGCATTTCGACATAAAAGGTGCCACAAATGAAAGTTAAATGCATAAC
* * *
3369915 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCTGCATAAAAAGTGTCACTAATAAAA
1 GGTGCCACAAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAAGTGCCACTAATAAAA
* * * *
3369980 GTAAAATGCATAACGGTGCATTTC-GACGTAAACGATGCCACTAATGAAAGTTAAATGCATAACG
66 GTAAAATGCATAACGGTGCATTACAGA-ATAAAAGATGACACTAATGAAAGTTAAATGCATAACG
* *
3370044 GTGCATTTCGACATAAAAGGTGTCACAAATGAAAGTTCAATGCATAAC
130 GTGCATTTCGACATAAAAGGTGCCACAAATGAAAGTTAAATGCATAAC
3370092 GGTGC
1 GGTGC
3370097 ATTTCGACAT
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 2 0.01
177 165 0.99
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (177 bp):
GGTGCCACAAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAAGTGCCACTAATAAAA
GTAAAATGCATAACGGTGCATTACAGAATAAAAGATGACACTAATGAAAGTTAAATGCATAACGG
TGCATTTCGACATAAAAGGTGCCACAAATGAAAGTTAAATGCATAAC
Found at i:3370088 original size:226 final size:226
Alignment explanation
Indices: 3369689--3370145 Score: 718
Period size: 226 Copynumber: 2.0 Consensus size: 226
3369679 CAGCATAAAA
* * * *
3369689 GGTGCCACTAATGAAAGTTAAATGCATAATGGTGCTTTTCGGCATAAAAGGTGCCACAAATGAAA
1 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAAGTGCCACAAATAAAA
* * *
3369754 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGG
66 GTAAAATGCATAACGGTGCATTTCGACATAAAAGATGCCACTAATAAAAGTTAAATGCATAACGG
* *
3369819 TGCATTACAGAATAAAAGGTGACACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAA
131 TGCATTACAGAATAAAAGGTGACACAAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAA
*
3369884 AGGTGCCACTAATGAAAGTTAAATGCATAAC
196 AGGTGCCACTAATGAAAGTTAAATGCAGAAC
* * *
3369915 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCTGCATAAAAAGTGTCACTAATAAAA
1 GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAAGTGCCACAAATAAAA
* * *
3369980 GTAAAATGCATAACGGTGCATTTCGACGTAAACGATGCCACTAATGAAAGTTAAATGCATAACGG
66 GTAAAATGCATAACGGTGCATTTCGACATAAAAGATGCCACTAATAAAAGTTAAATGCATAACGG
* * *
3370045 TGCATTTC-GACATAAAAGGTGTCACAAATGAAAGTTCAATGCATAACGGTGCATTTCGACATAA
131 TGCATTACAGA-ATAAAAGGTGACACAAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAA
*
3370109 AAGGTGCCATTAATGAAAGTTAAATGCAGAAC
195 AAGGTGCCACTAATGAAAGTTAAATGCAGAAC
3370141 GGTGC
1 GGTGC
3370146 ATTTTAACAT
Statistics
Matches: 210, Mismatches: 20, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
225 2 0.01
226 208 0.99
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (226 bp):
GGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAAGTGCCACAAATAAAA
GTAAAATGCATAACGGTGCATTTCGACATAAAAGATGCCACTAATAAAAGTTAAATGCATAACGG
TGCATTACAGAATAAAAGGTGACACAAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAA
AGGTGCCACTAATGAAAGTTAAATGCAGAAC
Found at i:3370144 original size:275 final size:275
Alignment explanation
Indices: 3369649--3370168 Score: 790
Period size: 275 Copynumber: 1.9 Consensus size: 275
3369639 AATGCTCAAA
* * *
3369649 AATGAAAGTTAAAAGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTAATGAAAGTTAAATGC
1 AATGAAAGTTAAAAGCATAACGGTGCATTTCAGCATAAAAAGTGCCACTAATAAAAGTAAAATGC
* * * *
3369714 ATAATGGTGCTTTTCGGCATAAAAGGTGCCACAAATGAAAGTTAAATGCATAACGGTGCATTTCG
66 ATAACGGTGCATTTCGACATAAAAGATGCCACAAATGAAAGTTAAATGCATAACGGTGCATTTCG
* *
3369779 GCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTACAGAATAAAAGGTGACAC
131 ACATAAAAGGTGCCACAAATAAAAGTTAAATGCATAACGGTGCATTACAGAATAAAAGGTGACAC
* ** *
3369844 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATG
196 TAATGAAAGTTAAATGCAGAACGGTGCATTTCAACATAAAAGATGCCACTAATGAAAGTTAAATG
3369909 CATAACGGTGCCACT
261 CATAACGGTGCCACT
* * *
3369924 AATGAAAGTTAAATGCATAACGGTGCATTTCTGCATAAAAAGTGTCACTAATAAAAGTAAAATGC
1 AATGAAAGTTAAAAGCATAACGGTGCATTTCAGCATAAAAAGTGCCACTAATAAAAGTAAAATGC
* * *
3369989 ATAACGGTGCATTTCGACGTAAACGATGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
66 ATAACGGTGCATTTCGACATAAAAGATGCCACAAATGAAAGTTAAATGCATAACGGTGCATTTCG
* * * * *
3370054 ACATAAAAGGTGTCACAAATGAAAGTTCAATGCATAACGGTGCATTTC-GACATAAAAGGTGCCA
131 ACATAAAAGGTGCCACAAATAAAAGTTAAATGCATAACGGTGCATTACAGA-ATAAAAGGTGACA
* *
3370118 TTAATGAAAGTTAAATGCAGAACGGTGCATTTTAACATAAAAGATGCCACT
195 CTAATGAAAGTTAAATGCAGAACGGTGCATTTCAACATAAAAGATGCCACT
3370169 CATGTTATTA
Statistics
Matches: 218, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
274 2 0.01
275 216 0.99
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (275 bp):
AATGAAAGTTAAAAGCATAACGGTGCATTTCAGCATAAAAAGTGCCACTAATAAAAGTAAAATGC
ATAACGGTGCATTTCGACATAAAAGATGCCACAAATGAAAGTTAAATGCATAACGGTGCATTTCG
ACATAAAAGGTGCCACAAATAAAAGTTAAATGCATAACGGTGCATTACAGAATAAAAGGTGACAC
TAATGAAAGTTAAATGCAGAACGGTGCATTTCAACATAAAAGATGCCACTAATGAAAGTTAAATG
CATAACGGTGCCACT
Found at i:3376507 original size:19 final size:19
Alignment explanation
Indices: 3376483--3376519 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3376473 TGATAAAATA
3376483 TTATTTAAAATATTAATTG
1 TTATTTAAAATATTAATTG
3376502 TTATTTAAAATATTAATT
1 TTATTTAAAATATTAATT
3376520 TCATTACCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTATTTAAAATATTAATTG
Found at i:3376685 original size:76 final size:77
Alignment explanation
Indices: 3376533--3376706 Score: 234
Period size: 76 Copynumber: 2.3 Consensus size: 77
3376523 TTACCTAATT
*
3376533 TTTTA-TAAAAA-A-TAATATTTTAAATAACAACTAATATTAATATTTCTGATAAAAAAATAATA
1 TTTTACTAAAAATATTAAAATTTTAAATAACAACTAATATTAATATTTCTGATAAAAAAATAATA
**
3376595 TTTTATGTAACA
66 TTTTAAATAACA
* * *
3376607 TTTTA-TAAAAAATATTAAACATTTTAAATAACATCTAATATTAATATTTCT-A-ATAAAAATAT
1 TTTTACT-AAAAATATTAAA-ATTTTAAATAACAACTAATATTAATATTTCTGATAAAAAAATAA
3376669 TATTTTAAATAACA
64 TATTTTAAATAACA
3376683 TTTTACTAAAAATATTAAAATTTT
1 TTTTACTAAAAATATTAAAATTTT
3376707 CGACATCACA
Statistics
Matches: 89, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
74 6 0.07
75 10 0.11
76 38 0.43
77 5 0.06
78 30 0.34
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.43
Consensus pattern (77 bp):
TTTTACTAAAAATATTAAAATTTTAAATAACAACTAATATTAATATTTCTGATAAAAAAATAATA
TTTTAAATAACA
Found at i:3376820 original size:46 final size:45
Alignment explanation
Indices: 3376746--3376842 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 45
3376736 GGCTGCCGCT
*
3376746 GTGTAAGAAAAAAACTAAAAAGTCAAAAAGCTCGATGAAAGCAAA
1 GTGTAAGAAAAAAACAAAAAAGTCAAAAAGCTCGATGAAAGCAAA
* *
3376791 GTGTAAGAAAGAAAGAAAACAAGTCAAAAAGCTCGATGAAAGCAAA
1 GTGTAAGAAAAAAACAAAA-AAGTCAAAAAGCTCGATGAAAGCAAA
3376837 GTGTAA
1 GTGTAA
3376843 TTCCCAATCT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 16 0.33
46 32 0.67
ACGTcount: A:0.56, C:0.10, G:0.21, T:0.13
Consensus pattern (45 bp):
GTGTAAGAAAAAAACAAAAAAGTCAAAAAGCTCGATGAAAGCAAA
Found at i:3380574 original size:30 final size:30
Alignment explanation
Indices: 3380538--3380599 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
3380528 AAGATATACC
3380538 CATGATCTGTAATGCTTGAATACTCCTAAG
1 CATGATCTGTAATGCTTGAATACTCCTAAG
*
3380568 CATGATCTGTAATGCTTGAATATTCCTAAG
1 CATGATCTGTAATGCTTGAATACTCCTAAG
3380598 CA
1 CA
3380600 GACCCAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (30 bp):
CATGATCTGTAATGCTTGAATACTCCTAAG
Found at i:3392275 original size:126 final size:127
Alignment explanation
Indices: 3392101--3392441 Score: 388
Period size: 126 Copynumber: 2.7 Consensus size: 127
3392091 GCAATGAAGC
* * * * *
3392101 ATATCCCTTTTTCTAGATTTGATATTTTTTAAAAAGCAGTGAAACAAATCAACCTCAATTCAATA
1 ATATCCCTTTTTCCAGATTTGATATTCTATAAAAAGCAGTGAAGCAAATCAACCTCAATTCAATC
* * *
3392166 TTCCCTGAAGAACAAATGAATCAATGTTTCTAGATCTGATCTACCCTGAA-AAGTAG-GG-GA
66 TTCCCTGAAGAACAAATGAATCAACGTTTCTAGATCTAATCTACCCTGAAGAA-CAGCGGAGA
* * * *
3392226 ATCGATCCC-TTTTCCATATTTGATATTCTATGAAGAGCAGTGAAGCAAATCAACCTCGATTCAA
1 AT--ATCCCTTTTTCCAGATTTGATATTCTATAAAAAGCAGTGAAGCAAATCAACCTCAATTCAA
*
3392290 TCTTCCCTGAAGAGCAGTAAAGTGAATCAACGTTTCTAGATCTAATCTACCCTGAAGAACAGCGG
64 TCTTCCCTGAAGA--A-CAAA-TGAATCAACGTTTCTAGATCTAATCTACCCTGAAGAACAGCGG
*
3392355 AGC
125 AGA
* ** *
3392358 ATATCCCTTTTTCCAGATTTGATCTTCCCTAAAAAGCAGTGAAGCAAATCATCC-CAGATTCAAT
1 ATATCCCTTTTTCCAGATTTGATATTCTATAAAAAGCAGTGAAGCAAATCAACCTCA-ATTCAAT
* *
3392422 CTTTCCTGAAGAGC-AATGAA
65 CTTCCCTGAAGAACAAATGAA
3392442 GTGAATCAAC
Statistics
Matches: 180, Mismatches: 25, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
125 2 0.01
126 63 0.35
127 7 0.04
128 1 0.01
129 3 0.02
130 40 0.22
131 61 0.34
132 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (127 bp):
ATATCCCTTTTTCCAGATTTGATATTCTATAAAAAGCAGTGAAGCAAATCAACCTCAATTCAATC
TTCCCTGAAGAACAAATGAATCAACGTTTCTAGATCTAATCTACCCTGAAGAACAGCGGAGA
Found at i:3392418 original size:131 final size:130
Alignment explanation
Indices: 3392080--3392456 Score: 421
Period size: 131 Copynumber: 2.9 Consensus size: 130
3392070 AGATTGGATT
* * * * * * *
3392080 TACCCTGAAGAGCAATGAAGCATATCCCTTTTTCTAGATTTGATATTTTTTAAAAAGCAGTGAAA
1 TACCCTGAAGAAC-AGGGAGCATATCCCTTTTTCCAGATTTGATATTCTATAAAAAGCAGTGAAG
* * * *
3392145 CAAATCAACCTCA-ATTCAATATTCCCTGAAGA--ACAAA-TGAATCAATGTTTCTAGATCTGAT
65 CAAATCAACCTCAGATTCAATCTTCCCTGAAGAGCATAAAGTGAATCAACGTTTCTAGATCTAAT
3392206 C
130 C
* * * * *
3392207 TACCCTGAA-AAGTAGGG-GAATCGATCCC-TTTTCCATATTTGATATTCTATGAAGAGCAGTGA
1 TACCCTGAAGAA-CAGGGAGCAT--ATCCCTTTTTCCAGATTTGATATTCTATAAAAAGCAGTGA
3392269 AGCAAATCAACCTC-GATTCAATCTTCCCTGAAGAGCAGTAAAGTGAATCAACGTTTCTAGATCT
63 AGCAAATCAACCTCAGATTCAATCTTCCCTGAAGAGCA-TAAAGTGAATCAACGTTTCTAGATCT
3392333 AATC
127 AATC
* **
3392337 TACCCTGAAGAACAGCGGAGCATATCCCTTTTTCCAGATTTGATCTTCCCTAAAAAGCAGTGAAG
1 TACCCTGAAGAACAG-GGAGCATATCCCTTTTTCCAGATTTGATATTCTATAAAAAGCAGTGAAG
* * * *
3392402 CAAATCATCC-CAGATTCAATCTTTCCTGAAGAGCAATGAAGTGAATCAACCTTTC
65 CAAATCAACCTCAGATTCAATCTTCCCTGAAGAGC-ATAAAGTGAATCAACGTTTC
3392457 CAAATTTGTT
Statistics
Matches: 208, Mismatches: 28, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
125 3 0.01
126 62 0.30
127 14 0.07
128 1 0.00
129 3 0.01
130 40 0.19
131 81 0.39
132 4 0.02
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29
Consensus pattern (130 bp):
TACCCTGAAGAACAGGGAGCATATCCCTTTTTCCAGATTTGATATTCTATAAAAAGCAGTGAAGC
AAATCAACCTCAGATTCAATCTTCCCTGAAGAGCATAAAGTGAATCAACGTTTCTAGATCTAATC
Found at i:3392546 original size:131 final size:129
Alignment explanation
Indices: 3392426--3393126 Score: 560
Period size: 131 Copynumber: 5.3 Consensus size: 129
3392416 TTCAATCTTT
* * * * * *
3392426 CCTGAAGAGCAATGAAG-TGAATCAACCTTTCCAAATTTGTTCTTCTCTGAAAAGAAATGAAGCA
1 CCTGAAGAGCAACGAAGCAG-ATC-ACCTTTCCAGATTTGATCTTCTCTGAAGAGCAATGAAGCA
* * * * *
3392490 AATCAACCTTGATTCAATCTTCCCTGAAGAGCAATGTAGTGAATAAATGTTTCCAGATATGATCT
64 AATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAGAT-TGATCT
3392555 AA
128 AA
* * * ** *
3392557 ACTGAAAAGCAACGGAGCAGATC-CCTTTTTCCAGATTTGATCTTCTCTGAAGAGCGGTGAAGTA
1 CCTGAAGAGCAACGAAGCAGATCACC--TTTCCAGATTTGATCTTCTCTGAAGAGCAATGAAGCA
* *
3392621 AATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAAATTTGATAT
64 AATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAGA-TTGATCT
*
3392686 AC
128 AA
* * * * ** *
3392688 CCTAAAGAGCAGCGAAACATATCCATTTTTCCAGATTTGATCTTCTATGAAGAGCAATGAAGCAA
1 CCTGAAGAGCAACGAAGCAGAT-CACCTTTCCAGATTTGATCTTCTCTGAAGAGCAATGAAGCAA
3392753 ATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAGATCTGATCT-
65 ATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAGAT-TGATCTA
3392817 A
129 A
* * * * * * * * * * * *
3392818 CCTTGAAGAGCAGCGGAGGAGATC-CTTTTTTTTCATATTTGGTCTTCCCTAAAGAGCAGTAAAA
1 CC-TGAAGAGCAACGAAGCAGATCAC---CTTTCCAGATTTGATCTTCTCTGAAGAGCAATGAAG
* * * *
3392882 CAAATCAACC-CAGATTCAATCTTTCCTGAATAGTAGTGAAGTGAATCAACCTTTCCAGATATGA
62 CAAATCAACCTC-GATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAGAT-TGA
*
3392946 TCT-T
125 TCTAA
* * * * * * * *
3392950 CCTTGAAGCA-TAAAGAAGCAGATACCATCTTTATCATATTTGATCTTC-CTTGAATAACAGTGA
1 CC-TGAAG-AGCAACGAAGCAGAT--CACCTTT-CCAGATTTGATCTTCTC-TGAAGAGCAATGA
* * * *
3393013 AGTAAATCAACCCCGATTCAATCTTCTCTGAAGAGCAGTGAAGTGAATCAAAGTTTCCAGATTTG
60 AGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAGA-TTG
*
3393078 ATAT-A
124 ATCTAA
* * * * *
3393083 CTCT-AGAGAGCAACGGAGTAGATC-TCTTTTCAGATTCGATCTTC
1 C-CTGA-AGAGCAACGAAGCAGATCACCTTTCCAGATTTGATCTTC
3393127 AAAAATCTCT
Statistics
Matches: 462, Mismatches: 85, Indels: 48
0.78 0.14 0.08
Matches are distributed among these distances:
129 15 0.03
130 9 0.02
131 229 0.50
132 112 0.24
133 93 0.20
134 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (129 bp):
CCTGAAGAGCAACGAAGCAGATCACCTTTCCAGATTTGATCTTCTCTGAAGAGCAATGAAGCAAA
TCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAGATTGATCTAA
Found at i:3392641 original size:217 final size:217
Alignment explanation
Indices: 3392266--3392681 Score: 602
Period size: 217 Copynumber: 1.9 Consensus size: 217
3392256 TGAAGAGCAG
* * *
3392266 TGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTAAAGTGAATCAACGTTTCTAGAT
1 TGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAATAAAGTGAATAAACGTTTCCAGAT
* ** * *
3392331 CTAATCTACCCTGAAGAACAGCGGAGCATATCCCTTTTTCCAGATTTGATCTTCCCTAAAAAGCA
66 ATAATCTAAACTGAAGAACAACGGAGCAGATCCCTTTTTCCAGATTTGATCTTCCCTAAAAAGCA
* *
3392396 GTGAAGCAAATCATCCCAGATTCAATCTTTCCTGAAGAGCAATGAAGTGAATCAACCTTTCCAAA
131 GTGAAGCAAATCAACCCAGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAACCTTTCCAAA
3392461 TTTGTTCTTCTCTGAAAAGAAA
196 TTTGTTCTTCTCTGAAAAGAAA
* ** *
3392483 TGAAGCAAATCAACCTTGATTCAATCTTCCCTGAAGAGCAATGTAGTGAATAAATGTTTCCAGAT
1 TGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAATAAAGTGAATAAACGTTTCCAGAT
* * * *
3392548 ATGATCTAAACTGAA-AAGCAACGGAGCAGATCCCTTTTTCCAGATTTGATCTTCTCTGAAGAGC
66 ATAATCTAAACTGAAGAA-CAACGGAGCAGATCCCTTTTTCCAGATTTGATCTTCCCTAAAAAGC
* * * *
3392612 GGTGAAGTAAATCAACCTC-GATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCA
130 AGTGAAGCAAATCAACC-CAGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAACCTTTCCA
3392676 AATTTG
194 AATTTG
3392682 ATATACCCTA
Statistics
Matches: 175, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
216 2 0.01
217 172 0.98
218 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (217 bp):
TGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAATAAAGTGAATAAACGTTTCCAGAT
ATAATCTAAACTGAAGAACAACGGAGCAGATCCCTTTTTCCAGATTTGATCTTCCCTAAAAAGCA
GTGAAGCAAATCAACCCAGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAACCTTTCCAAA
TTTGTTCTTCTCTGAAAAGAAA
Found at i:3392719 original size:348 final size:343
Alignment explanation
Indices: 3392140--3392806 Score: 906
Period size: 348 Copynumber: 1.9 Consensus size: 343
3392130 TAAAAAGCAG
* * *
3392140 TGAAACAAATCAACCTCAATTCAATATTCCCTGAAGAACAAATGAATCAATGTTTCTAGATCTGA
1 TGAAACAAATCAACCTCAATTCAATATTCCCTGAAGAACAAATGAATAAATGTTTCCAGATATGA
** * ** * *
3392205 TCTACCCTGAAAAGTAGGGGAATCGATCCCTTTTCCATATTTGATATTCTATGAAGAGCAGTGAA
66 TCTAAACTGAAAAGCAACGGAAGCGATCCCTTTTCCAGATTTGATATTCTATGAAGAGCAGTGAA
* *
3392270 GCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTAAAGTGAATCAACGTTTCTAGATCTAA
131 GCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTAAAGTGAATCAACGTTTCCAAATCTAA
* * * * * * *
3392335 TCTACCCTGAAGAACAGCGGAGCATATCCCTTTTTCCAGATTTGATCTTCCCTAAAAAGCAGTGA
196 TATACCCTAAAGAACAGCGAAACATATCCATTTTTCCAGATTTGATCTTCCATAAAAAGCAATGA
* *
3392400 AGCAAATCATCC-CAGATTCAATCTTTCCTGAAGAGCAATGAAGTGAATCAACCTTTCCAAATTT
261 AGCAAATCAACCTC-GATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAACCTTTCCAAATTT
3392464 GTTCTTCTCTGAAAAGAAA
325 GTTCTTCTCTGAAAAGAAA
* ** * *
3392483 TGAAGCAAATCAACCTTGATTCAATCTTCCCTGAAGAGCAATGTAGTGAATAAATGTTTCCAGAT
1 TGAAACAAATCAACCTCAATTCAATATTCCCTGAAGAACAA---A-TGAATAAATGTTTCCAGAT
* *
3392548 ATGATCTAAACTGAAAAGCAACGG-AGCAGATCCCTTTTTCCAGATTTGATCTTCTCTGAAGAGC
62 ATGATCTAAACTGAAAAGCAACGGAAGC-GATCCC-TTTTCCAGATTTGATATTCTATGAAGAGC
* * *
3392612 GGTGAAGTAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAA
125 AGTGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTAAAGTGAATCAACGTTTCCAA
* * * * * *
3392677 ATTTGATATACCCTAAAGAGCAGCGAAACATATCCATTTTTCCAGATTTGATCTTCTATGAAGAG
190 ATCTAATATACCCTAAAGAACAGCGAAACATATCCATTTTTCCAGATTTGATCTTCCATAAAAAG
* *
3392742 CAATGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCA
255 CAATGAAGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAACCTTTCCA
3392807 GATCTGATCT
Statistics
Matches: 278, Mismatches: 39, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
343 36 0.13
346 3 0.01
347 41 0.15
348 197 0.71
349 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (343 bp):
TGAAACAAATCAACCTCAATTCAATATTCCCTGAAGAACAAATGAATAAATGTTTCCAGATATGA
TCTAAACTGAAAAGCAACGGAAGCGATCCCTTTTCCAGATTTGATATTCTATGAAGAGCAGTGAA
GCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAGTAAAGTGAATCAACGTTTCCAAATCTAA
TATACCCTAAAGAACAGCGAAACATATCCATTTTTCCAGATTTGATCTTCCATAAAAAGCAATGA
AGCAAATCAACCTCGATTCAATCTTCCCTGAAGAGCAATGAAGTGAATCAACCTTTCCAAATTTG
TTCTTCTCTGAAAAGAAA
Found at i:3392825 original size:86 final size:86
Alignment explanation
Indices: 3392367--3392829 Score: 246
Period size: 86 Copynumber: 5.3 Consensus size: 86
3392357 CATATCCCTT
* * * * *
3392367 TTTCCAGATTTGATCTTCCCTAAAAAGCAGTGAAGCAAATCATCC-CAGATTCAATCTTTCCTGA
1 TTTCCAGATTTGATC-TCCTTGAAAAGCAATGAAGCAAATCAACCTCAGATTCAATCTTCCCTGA
* *
3392431 AGAGCAATGAAGTGAATCAACC
65 AGAGCAGTGAAGTGAATCAACG
* * * * *
3392453 TTTCCAAATTTGTTCTTCTCTGAAAAGAAATGAAGCAAATCAACCT-TGATTCAATCTTCCCTGA
1 TTTCCAGATTTGATCTCCT-TGAAAAGCAATGAAGCAAATCAACCTCAGATTCAATCTTCCCTGA
* * * *
3392517 AGAGCAATGTAGTGAATAAATG
65 AGAGCAGTGAAGTGAATCAACG
* * * * * **
3392539 TTTCCAGATATGATCTAAAC-TGAAAAGCAACGGAGCAGATC--CCTTTTTCCAGATTTGATCTT
1 TTTCCAGATTTGATCT--CCTTGAAAAGCAATGAAGCAAATCAACC----T-CAGATTCAATCTT
* * *
3392601 CTCTGAAGAGCGGTGAAGTAAATCAAC-
59 CCCTGAAGAGCAGTGAAGTGAATCAACG
* ** * * * ** * * ** * *
3392628 -CT-C-GATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCAACGTTTCCAAATTTGATATACCC
1 TTTCCAGATTTGATC-TCCTTGAAAAGCAATGAAGCAAATCAAC--CT-CAGATTCAATCTTCCC
* * ** * **
3392690 TAAAGAGCAGCGAA-ACATATCCATT
62 TGAAGAGCAGTGAAGTGA-ATCAACG
* *
3392715 TTTCCAGATTTGATCTTCTATGAAGAGCAATGAAGCAAATCAACCTC-GATTCAATCTTCCCTGA
1 TTTCCAGATTTGATCTCCT-TGAAAAGCAATGAAGCAAATCAACCTCAGATTCAATCTTCCCTGA
3392779 AGAGCAGTGAAGTGAATCAACG
65 AGAGCAGTGAAGTGAATCAACG
* *
3392801 TTTCCAGATCTGATCTACCTTGAAGAGCA
1 TTTCCAGATTTGATCT-CCTTGAAAAGCA
3392830 GCGGAGGAGA
Statistics
Matches: 274, Mismatches: 79, Indels: 48
0.68 0.20 0.12
Matches are distributed among these distances:
84 2 0.01
85 4 0.01
86 196 0.72
87 6 0.02
88 6 0.02
89 3 0.01
90 57 0.21
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (86 bp):
TTTCCAGATTTGATCTCCTTGAAAAGCAATGAAGCAAATCAACCTCAGATTCAATCTTCCCTGAA
GAGCAGTGAAGTGAATCAACG
Found at i:3393980 original size:10 final size:10
Alignment explanation
Indices: 3393961--3394021 Score: 70
Period size: 10 Copynumber: 5.9 Consensus size: 10
3393951 TTGAAATAAT
3393961 AAAAAA-AGG
1 AAAAAAGAGG
3393970 AAAAAAGAGG
1 AAAAAAGAGG
*
3393980 AAAAAAGAGA
1 AAAAAAGAGG
*
3393990 AAAAAAGAAAGA
1 AAAAAAG--AGG
3394002 AAAAAAGAGG
1 AAAAAAGAGG
3394012 AAAACAAGAG
1 AAAA-AAGAG
3394022 AGGAAAAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 6 0.13
10 25 0.54
11 5 0.11
12 10 0.22
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (10 bp):
AAAAAAGAGG
Found at i:3394011 original size:32 final size:33
Alignment explanation
Indices: 3393961--3394036 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 33
3393951 TTGAAATAAT
*
3393961 AAAA-AAAGGAAAAAAGAGGAAAA-AAGAGAAA
1 AAAAGAAAGAAAAAAAGAGGAAAACAAGAGAAA
**
3393992 AAAAGAAAGAAAAAAAGAGGAAAACAAGAGAGG
1 AAAAGAAAGAAAAAAAGAGGAAAACAAGAGAAA
3394025 AAAAGAAGAGAA
1 AAAAGAA-AGAA
3394037 GTTCTCACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 4 0.10
32 18 0.46
33 13 0.33
34 4 0.10
ACGTcount: A:0.74, C:0.01, G:0.25, T:0.00
Consensus pattern (33 bp):
AAAAGAAAGAAAAAAAGAGGAAAACAAGAGAAA
Found at i:3394023 original size:13 final size:12
Alignment explanation
Indices: 3393970--3394035 Score: 70
Period size: 11 Copynumber: 5.8 Consensus size: 12
3393960 TAAAAAAAGG
3393970 AAAAA-AGAGGA
1 AAAAAGAGAGGA
3393981 AAAAAGAGA--A
1 AAAAAGAGAGGA
*
3393991 AAAAAGA-AAGA
1 AAAAAGAGAGGA
3394002 AAAAA-AGAGGA
1 AAAAAGAGAGGA
3394013 AAACAAGAGAGGA
1 AAA-AAGAGAGGA
3394026 AAAGAAGAGA
1 AAA-AAGAGA
3394036 AGTTCTCACC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
9 1 0.02
10 9 0.19
11 17 0.36
12 5 0.11
13 15 0.32
ACGTcount: A:0.73, C:0.02, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAGGA
Found at i:3397603 original size:22 final size:22
Alignment explanation
Indices: 3397577--3397619 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3397567 CAATCACATA
*
3397577 TTATTATTATTATTATTATATT
1 TTATTATTATTATTATAATATT
* *
3397599 TTATTTTTATTTTTATAATAT
1 TTATTATTATTATTATAATAT
3397620 ATCCTTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTATTATTATTATAATATT
Found at i:3399884 original size:5 final size:5
Alignment explanation
Indices: 3399874--3399902 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3399864 GTGAAAAACT
3399874 CCGAC CCGAC CCGAC CCGAC CCGAC CCGA
1 CCGAC CCGAC CCGAC CCGAC CCGAC CCGA
3399903 GGGCAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.59, G:0.21, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:3401328 original size:18 final size:19
Alignment explanation
Indices: 3401305--3401342 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3401295 CCAAAAACAT
*
3401305 ATTTTTCATTTTAA-TAAA
1 ATTTTTAATTTTAATTAAA
3401323 ATTTTTAATTTTAATTAAA
1 ATTTTTAATTTTAATTAAA
3401342 A
1 A
3401343 CAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTAATTTTAATTAAA
Done.