Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 59 of 89
Found at i:13437323 original size:111 final size:111
Alignment explanation
Indices: 13437126--13437331 Score: 286
Period size: 111 Copynumber: 1.9 Consensus size: 111
13437116 ACCGAAGTAC
* * * * * *
13437126 CGAAATGGTCATTCACCTTTTATGAATACCATGGGTTACACCTTTTATGCTGATAATGCACCATT
1 CGAAATGGTAATTCACCTTTTATGAATACAATGGATGACACCTTTTATGCCGAAAATGCACCATT
* *
13437191 ATGCATTTAGCAAAATCGATCGTTAACTTTCATACACGAAGTCTAT
66 ATGCATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTCTAT
* * * *
13437237 CGAAATGGTAATTCACCTTTTATGAATATAATGGATGGCACCTTTTATGCCGAAAATGTACCGTT
1 CGAAATGGTAATTCACCTTTTATGAATACAATGGATGACACCTTTTATGCCGAAAATGCACCATT
* *
13437302 ATGCATTAATCAAAATGGATCGATAACTTT
66 ATGCATTAAGCAAAATCGATCGATAACTTT
13437332 TATTAGTGGT
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
111 81 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (111 bp):
CGAAATGGTAATTCACCTTTTATGAATACAATGGATGACACCTTTTATGCCGAAAATGCACCATT
ATGCATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTCTAT
Found at i:13437504 original size:12 final size:12
Alignment explanation
Indices: 13437487--13437511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13437477 AGAGAAAGGT
13437487 CATACTCTAAAA
1 CATACTCTAAAA
13437499 CATACTCTAAAA
1 CATACTCTAAAA
13437511 C
1 C
13437512 TTATTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (12 bp):
CATACTCTAAAA
Found at i:13439942 original size:21 final size:21
Alignment explanation
Indices: 13439913--13439969 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
13439903 TTCAAAAATA
13439913 CTCT-AGTATCGATACTA-ATC
1 CTCTAAGTATCGATACTAGA-C
*
13439933 CTCTAAGTATTGATACTAGAC
1 CTCTAAGTATCGATACTAGAC
*
13439954 C-CCAAGTATCGATACT
1 CTCTAAGTATCGATACT
13439970 TATTGAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.53
21 14 0.44
22 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (21 bp):
CTCTAAGTATCGATACTAGAC
Found at i:13448248 original size:20 final size:20
Alignment explanation
Indices: 13448220--13448268 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13448210 GACCCTCTAG
* *
13448220 GTATCGATATTGGACCTTGA
1 GTATCGATAATGAACCTTGA
*
13448240 GTATTGATAATGAACCTTGA
1 GTATCGATAATGAACCTTGA
*
13448260 ATATCGATA
1 GTATCGATA
13448269 CTCCTTGAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (20 bp):
GTATCGATAATGAACCTTGA
Found at i:13456023 original size:29 final size:29
Alignment explanation
Indices: 13455959--13456025 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
13455949 ATATACTTAA
* ** *
13455959 ATAATATATGTTTACAAAATATATTATAT
1 ATAATATATGTTTACAAAATAAAAGACAT
*
13455988 ACT-ATATATGTTTACAAAGTAAAAGACAT
1 A-TAATATATGTTTACAAAATAAAAGACAT
13456017 ATAATATAT
1 ATAATATAT
13456026 TATGGGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (29 bp):
ATAATATATGTTTACAAAATAAAAGACAT
Found at i:13457516 original size:3 final size:3
Alignment explanation
Indices: 13457504--13457548 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
13457494 TATTGACAAC
* *
13457504 AAT AAC AAT AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
13457549 TTAAAAGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:13457835 original size:111 final size:110
Alignment explanation
Indices: 13457641--13458014 Score: 504
Period size: 111 Copynumber: 3.4 Consensus size: 110
13457631 ACTGTCACTC
* * * *
13457641 AGGGAATATCAGATCT-GGAGATGTTGATTCATTGAATCAGAGTAGACTTGTTCCGCTGTTACTC
1 AGGGAATATCAGATCTGGGAGA-GTTGATCCATTGAATCAGGGTAGACTTGTTCCACTG-TACTT
13457705 AGGGAATATCAAATCTTGAAAGAGAGAGATCTGTTCCGCTTCCTCTG
64 AGGGAATATCAAATCTTGAAAGAGAGAGATCTGTTCCGCTTCCTCTG
* * * *
13457752 AGGGAATATCAGATATGGGAGAGTTGATCCATTGAATCGGGGCAGATTTGTTCCACTGTCACTTA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTGT-ACTTA
* *
13457817 GGGAATATCAAATCTTGAAAGAAAGAGATCTATTCCGCTTCCTCTG
65 GGGAATATCAAATCTTGAAAGAGAGAGATCTGTTCCGCTTCCTCTG
13457863 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACT-TACTCTG
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTGTACT-T-
* * *
13457927 AAGGGAATATCAAATCTTGGATA-AGAGAGACCTGTTCCGCTTACTCTG
64 -AGGGAATATCAAATCTT-GAAAGAGAGAGATCTGTTCCGCTTCCTCTG
* *
13457975 AAGGAAATATCAGATCTGGGGGA-TATGATCCATTGAATCA
1 -AGGGAATATCAGATCTGGGAGAGT-TGATCCATTGAATCA
13458015 AGATATACAA
Statistics
Matches: 234, Mismatches: 21, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
109 3 0.01
110 3 0.01
111 146 0.62
112 44 0.19
113 38 0.16
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (110 bp):
AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTGTACTTAG
GGAATATCAAATCTTGAAAGAGAGAGATCTGTTCCGCTTCCTCTG
Found at i:13472533 original size:2 final size:2
Alignment explanation
Indices: 13472526--13472621 Score: 69
Period size: 2 Copynumber: 50.0 Consensus size: 2
13472516 TATCAACTAA
*
13472526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AA AT -T GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* * * * * *
13472566 GT TT A- AT AA AA AT A- AT A- AT AT GT AT AA AT CAT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
13472606 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
13472622 GAGTAAATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
1 6 0.08
2 66 0.88
3 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13472830 original size:29 final size:29
Alignment explanation
Indices: 13472766--13472832 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
13472756 ATATACTTAA
* ** *
13472766 ATAATATATGTTTACAAAATATATTATAT
1 ATAATATATGTTTACAAAATAAAAGACAT
*
13472795 ACT-ATATATGTTTACAAAGTAAAAGACAT
1 A-TAATATATGTTTACAAAATAAAAGACAT
13472824 ATAATATAT
1 ATAATATAT
13472833 TATGGGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (29 bp):
ATAATATATGTTTACAAAATAAAAGACAT
Found at i:13474325 original size:3 final size:3
Alignment explanation
Indices: 13474319--13474353 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
13474309 TATTGACAAC
13474319 AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
13474354 TTAAAAGACG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:13474341 original size:14 final size:14
Alignment explanation
Indices: 13474322--13474353 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
13474312 TGACAACAAT
13474322 AATAATAATAATAA
1 AATAATAATAATAA
13474336 AATAATAATAATAA
1 AATAATAATAATAA
13474350 AATA
1 AATA
13474354 TTAAAAGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:13480664 original size:137 final size:137
Alignment explanation
Indices: 13480412--13481312 Score: 1327
Period size: 137 Copynumber: 6.6 Consensus size: 137
13480402 AGATCCAACT
* * * *
13480412 GGTGTATGACATTGTTCCTTCATGATGAGGACGTCTGACCATCTTTGAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
*** * * * * * * * *
13480477 AGGTTCCTTT-ATGATGAGGA-AGTCTGGTTATCTGAGGATCA-CTCGACTCCTACGTGATGAGC
66 CTATT-CTTTCATGATGAGGATA-TCTAGTTATCTAAGAATGATGTTG-CTCCTTCGTGATGAGG
*
13480539 AGTTTTGATC
128 AGTTCTGATC
* *
13480549 GGTGGATGACATTGTTCCTTCGTGATGAGGATGTCTGGCCATCTTTAAATATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
** * * * *
13480614 CGGTTCCTTCATGATGAGGACATC-ATGCTATCTAAGAATGATGTTGCTCCTTCGTAATGAGGAG
66 CTATTCTTTCATGATGAGGATATCTA-GTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAG
13480678 TTCTGATC
130 TTCTGATC
* *
13480686 GGTGGATGACATTGTTCCTTCGTGATGAGTACGTCTGGCCATCTTTAAAGATGTTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* * *
13480751 TTATTCTTTCATGATAAGGATATCTGGTTATCTAAGAATGATGTTGCTCCTTCGTGAT---GAGT
66 CTATTCTTTCATGATGAGGATATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
13480813 TCTGATC
131 TCTGATC
13480820 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
*
13480885 CTATTCTTTCATGATAAGGATATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
66 CTATTCTTTCATGATGAGGATATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
*
13480950 TCTGATT
131 TCTGATC
13480957 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
*
13481022 CTATTCTTTCATGATGATGATATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
66 CTATTCTTTCATGATGAGGATATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
13481087 TCTGATC
131 TCTGATC
*
13481094 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTAAAGATATTT-ATGATAAC
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGA-GATAAC
*
13481158 ATTATTCTTTCATGATGAGGATATCT-GATTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGA
65 ACTATTCTTTCATGATGAGGATATCTAG-TTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGA
13481222 GTTCTGATC
129 GTTCTGATC
* *
13481231 GGTGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTGAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
* *
13481296 -GAGTTCCTTCATGATGA
66 CTA-TTCTTTCATGATGA
13481313 AAACATCTGA
Statistics
Matches: 704, Mismatches: 48, Indels: 24
0.91 0.06 0.03
Matches are distributed among these distances:
134 130 0.18
136 6 0.01
137 564 0.80
138 4 0.01
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (137 bp):
GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
CTATTCTTTCATGATGAGGATATCTAGTTATCTAAGAATGATGTTGCTCCTTCGTGATGAGGAGT
TCTGATC
Found at i:13481172 original size:408 final size:409
Alignment explanation
Indices: 13480412--13481310 Score: 1371
Period size: 408 Copynumber: 2.2 Consensus size: 409
13480402 AGATCCAACT
* * *
13480412 GGTGTATGACATTGTTCCTTCATGATGAGGACGTCTGACCATCTTTGAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTGAAGATATTTGAGATAACA
* * * * *
13480477 AGGTTCCTTTATGATGAGGAAGTCTGGTTATCTGAGGATCACTCGACTCCTACGTGATGAGCAGT
66 AGATTCCTTTATGATAAGGAAGTCTAGTTATCTAAGAATCACTCGACTCCTACGTGATGAGCAGT
* * *
13480542 TTTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGATGTCTGGCCATCTTTAAATATATTTGA
131 TCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGA
*
13480607 GATAACACGGTTCCTTCATGATGAGGACATCATGCTATCTAAGAATGATGTTGCTCCTTCGTAAT
196 GATAACACGATTCCTTCATGATGAGGACATCATGCTATCTAAGAATGATGTTGCTCCTTCGTAAT
*
13480672 GAGGAGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGTACGTCTGGCCATCTTTAAAGA
261 GAGGAGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGA
* *
13480737 TGTTTGAGATAACATTATTCTTTCATGATAAGGATATCTGGTTATCTAAGAATGATGTTGCTCCT
326 TATTTGAGATAACATTATTCTTTCATGATAAGGATATCTGATTATCTAAGAATGATGTTGCTCCT
13480802 TCGTGAT-GAGTTCTGATC
391 TCGTGATGGAGTTCTGATC
*
13480820 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTGAAGATATTTGAGATAACA
** * * * * *
13480885 CTATT-CTTTCATGATAAGGATA-TCTAGTTATCTAAGAATGATGTTG-CTCCTTCGTGATGAGG
66 AGATTCCTTT-ATGATAAGGA-AGTCTAGTTATCTAAGAATCA-CTCGACTCCTACGTGATGAGC
*
13480947 AGTTCTGATTGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATT
128 AGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATT
* * * * *
13481012 TGAGATAACACTATTCTTTCATGATGATGATATC-TAGTTATCTAAGAATGATGTTGCTCCTTCG
193 TGAGATAACACGATTCCTTCATGATGAGGACATCAT-GCTATCTAAGAATGATGTTGCTCCTTCG
* *
13481076 TGATGAGGAGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTTTGGCCATCTTTA
257 TAATGAGGAGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTA
*
13481141 AAGATATTT-ATGATAACATTATTCTTTCATGATGAGGATATCTGATTATCTAAGAATGATGTTG
322 AAGATATTTGA-GATAACATTATTCTTTCATGATAAGGATATCTGATTATCTAAGAATGATGTTG
13481205 CTCCTTCGTGATGAGGAGTTCTGATC
386 CTCCTTCGTGAT--GGAGTTCTGATC
*
13481231 GGTGGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTGAAGATATTTGAGATAAC-
1 GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTGAAGATATTTGAGATAACA
*
13481295 AGAGTTCCTTCATGAT
66 AGA-TTCCTTTATGAT
13481311 GAAAACATCT
Statistics
Matches: 444, Mismatches: 37, Indels: 17
0.89 0.07 0.03
Matches are distributed among these distances:
407 6 0.01
408 351 0.79
409 3 0.01
410 1 0.00
411 80 0.18
412 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (409 bp):
GGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTGAAGATATTTGAGATAACA
AGATTCCTTTATGATAAGGAAGTCTAGTTATCTAAGAATCACTCGACTCCTACGTGATGAGCAGT
TCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGA
GATAACACGATTCCTTCATGATGAGGACATCATGCTATCTAAGAATGATGTTGCTCCTTCGTAAT
GAGGAGTTCTGATCGGTGGATGACATTGTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGA
TATTTGAGATAACATTATTCTTTCATGATAAGGATATCTGATTATCTAAGAATGATGTTGCTCCT
TCGTGATGGAGTTCTGATC
Found at i:13483082 original size:41 final size:41
Alignment explanation
Indices: 13483034--13483111 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
13483024 CCCTTATGGA
13483034 TCATTTCT-GTCAGAAATGTG-CCTTCAAAATGTACCAAATTT
1 TCATTTCTGGTCA-AAATG-GACCTTCAAAATGTACCAAATTT
*
13483075 TCATTTCTGGTCAAAATGGACCTTCAAAATGTCCCAA
1 TCATTTCTGGTCAAAATGGACCTTCAAAATGTACCAA
13483112 CATGATGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
40 1 0.03
41 29 0.85
42 4 0.12
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (41 bp):
TCATTTCTGGTCAAAATGGACCTTCAAAATGTACCAAATTT
Found at i:13490307 original size:3 final size:3
Alignment explanation
Indices: 13490301--13490332 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
13490291 TATTATTTAT
*
13490301 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
13490333 TAAAAAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:13496501 original size:29 final size:28
Alignment explanation
Indices: 13496464--13496518 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
13496454 TAATCTTTTC
13496464 CAAAGTTTATACTTTGGCCACTTAACTTT
1 CAAAGTTTATACTTTGGCCAC-TAACTTT
* * *
13496493 CAAATTTTATATTTTGGTCACTAACT
1 CAAAGTTTATACTTTGGCCACTAACT
13496519 AAAATTTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (28 bp):
CAAAGTTTATACTTTGGCCACTAACTTT
Found at i:13498998 original size:13 final size:13
Alignment explanation
Indices: 13498982--13499012 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13498972 TTTTTGGAAT
*
13498982 ATCTTCCTCGTTA
1 ATCTTCCTCATTA
13498995 ATCTTCCTCATTA
1 ATCTTCCTCATTA
13499008 ATCTT
1 ATCTT
13499013 TAGATGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.29, G:0.03, T:0.48
Consensus pattern (13 bp):
ATCTTCCTCATTA
Found at i:13504435 original size:226 final size:224
Alignment explanation
Indices: 13504109--13504640 Score: 627
Period size: 226 Copynumber: 2.4 Consensus size: 224
13504099 TTGAAAAGAT
* * * * * * * * *
13504109 TTGACTGAAAGATGGCTCCTCGCCGTTGAGTTAAGCCAAAATACAGTCGGTTCTAGTTGCATTTT
1 TTGACTGAAAGATGGCTCTTAGCCATTGAGTTAAGCTAAAATGCAGTTGGTTCTGGATGC-TTTC
* * * *
13504174 TGGGTCAAGAATCCTTCTTTGTGAAGTTGAGACTTGGATTAAAAACTTTGACTTGAA-ACTAACT
65 TGGGTCAAGAATCCTCCATCGTGAAGTTGAGACTTGGACTAAAAACTTTGAC-TGAATACTAACT
* * *
13504238 CATCATCACTGAGTTAAGCTAGACTGCAGTCGATTCGGAATTGGTTTTCAAACCAAATATCCTCC
129 CATCATCACTGAGTTAAGCTAGACTGCAATCAATTCGAAATTGGTTTTCAAACCAAATATCCTCC
*
13504303 GTCATGGAATTGAGATTAACTTCAAAAAAAAA
194 GTCATGGAATTGAGATTAAATTC-AAAAAAAA
* *
13504335 TTGACTCAAAGATGGCTCTTAGCCAATGAGTTAAGCTAAAATGCAGTTGGTTCTGGATGCGTTTC
1 TTGACTGAAAGATGGCTCTTAGCCATTGAGTTAAGCTAAAATGCAGTTGGTTCTGGATGC-TTTC
* *
13504400 TGGGTCAAGAATCCTCCATCGTGAAGTTGAGACTTGGCCTAAAAACTTTGACTGAATACTAGCTC
65 TGGGTCAAGAATCCTCCATCGTGAAGTTGAGACTTGGACTAAAAACTTTGACTGAATACTAACTC
* * ** * * ** * *
13504465 CTCGTCTTTGAGTTAAGCTAGACTGTAATCAATTCTAAATTGGTTTTTGAACCCAATATCCTCTG
130 ATCATCACTGAGTTAAGCTAGACTGCAATCAATTCGAAATTGGTTTTCAAACCAAATATCCTCCG
* * * * *
13504530 TCGTGGAGTTGATATTAAATTCAAAAACAT
195 TCATGGAATTGAGATTAAATTCAAAAAAAA
* ** *
13504560 TTAACTGAAAGATGGCTCTTTTCCATTGAGTTAAG-TCAAAATGCAGCTGGTTCTGGATGCTTTA
1 TTGACTGAAAGATGGCTCTTAGCCATTGAGTTAAGCT-AAAATGCAGTTGGTTCTGGATGCTTT-
*
13504624 CTAGGTCAAGAATCCTC
64 CTGGGTCAAGAATCCTC
13504641 ATATGTGATG
Statistics
Matches: 259, Mismatches: 44, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
224 4 0.02
225 78 0.30
226 177 0.68
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (224 bp):
TTGACTGAAAGATGGCTCTTAGCCATTGAGTTAAGCTAAAATGCAGTTGGTTCTGGATGCTTTCT
GGGTCAAGAATCCTCCATCGTGAAGTTGAGACTTGGACTAAAAACTTTGACTGAATACTAACTCA
TCATCACTGAGTTAAGCTAGACTGCAATCAATTCGAAATTGGTTTTCAAACCAAATATCCTCCGT
CATGGAATTGAGATTAAATTCAAAAAAAA
Found at i:13504921 original size:72 final size:71
Alignment explanation
Indices: 13504780--13504957 Score: 184
Period size: 72 Copynumber: 2.5 Consensus size: 71
13504770 ATGCAGTCGA
* * * ***
13504780 TTTTGGAT-ACTCCCATTCATGAGAAAGTCAAGTGAGATGACTCCCTTTCATGGTTTAAGTTGGT
1 TTTTGGATGACTCCCATTCATGAGAAAGTCAAGTGAGATGACTCCCCTTCACGGCTTAAGTCAAT
*
13504844 CTTGAT
66 ATTGAT
* * *
13504850 GTTTTGGATGACTTCCATTCATGGGAAAG-CTATGTGAGATGACTCCCCTTCACGGCTTAAGTCA
1 -TTTTGGATGACTCCCATTCATGAGAAAGTC-AAGTGAGATGACTCCCCTTCACGGCTTAAGTCA
13504914 ATATTGAT
64 ATATTGAT
*
13504922 TCCTTGGATGACTCCCATT-A-GCAGGAAAGTCAAGTG
1 T-TTTGGATGACTCCCATTCATG-A-GAAAGTCAAGTG
13504958 GGAATTTCTT
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
70 1 0.01
71 11 0.13
72 74 0.85
73 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (71 bp):
TTTTGGATGACTCCCATTCATGAGAAAGTCAAGTGAGATGACTCCCCTTCACGGCTTAAGTCAAT
ATTGAT
Found at i:13507963 original size:11 final size:11
Alignment explanation
Indices: 13507947--13507975 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
13507937 CTATCTTCTC
13507947 TTGTTTCATGG
1 TTGTTTCATGG
13507958 TTGTTTCATGG
1 TTGTTTCATGG
13507969 TTGTTTC
1 TTGTTTC
13507976 TACCATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.24, T:0.59
Consensus pattern (11 bp):
TTGTTTCATGG
Found at i:13511873 original size:26 final size:27
Alignment explanation
Indices: 13511819--13511889 Score: 90
Period size: 26 Copynumber: 2.6 Consensus size: 27
13511809 TATATAAGCT
*
13511819 TTTTCAAAACTATATCATATATTATATATG
1 TTTTCAAAAC--TAT-ATATATTACATATG
*
13511849 TTTT-AAAATTATATATATTACATATG
1 TTTTCAAAACTATATATATTACATATG
13511875 TTTTCAAAACTATAT
1 TTTTCAAAACTATAT
13511890 TGCGTATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 17 0.46
27 12 0.32
29 4 0.11
30 4 0.11
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (27 bp):
TTTTCAAAACTATATATATTACATATG
Found at i:13512976 original size:12 final size:12
Alignment explanation
Indices: 13512959--13512989 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13512949 CTAATTCTTG
*
13512959 AAAATAATAATA
1 AAAATAACAATA
13512971 AAAATAACAATA
1 AAAATAACAATA
13512983 AAAATAA
1 AAAATAA
13512990 AATCTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAATAACAATA
Found at i:13513769 original size:16 final size:16
Alignment explanation
Indices: 13513744--13513798 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
13513734 AGTATTACCC
*
13513744 GACCTATTTTCAACCT
1 GACCTGTTTTCAACCT
13513760 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
** *
13513776 GATATGTTTTTAACCT
1 GACCTGTTTTCAACCT
13513792 GACCTGT
1 GACCTGT
13513799 AAATGATCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:13514315 original size:18 final size:18
Alignment explanation
Indices: 13514279--13514316 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13514269 AATAATATAA
*
13514279 ATATAAACTATATCGTTT
1 ATATAAACTATATAGTTT
*
13514297 ATATAAACTATATATTTT
1 ATATAAACTATATAGTTT
13514315 AT
1 AT
13514317 TACTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATAAACTATATAGTTT
Found at i:13514713 original size:2 final size:2
Alignment explanation
Indices: 13514706--13514732 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13514696 TATGTTTAAT
13514706 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 T
13514733 TACTCAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13515105 original size:7 final size:7
Alignment explanation
Indices: 13515094--13515189 Score: 104
Period size: 7 Copynumber: 13.7 Consensus size: 7
13515084 TATAGTTTAT
13515094 ATAAACC
1 ATAAACC
*
13515101 CTAAACC
1 ATAAACC
* *
13515108 CTAAACT
1 ATAAACC
13515115 ATAAACC
1 ATAAACC
*
13515122 ATAAATC
1 ATAAACC
*
13515129 ATAAACG
1 ATAAACC
13515136 ATAAACC
1 ATAAACC
* *
13515143 CTAAATC
1 ATAAACC
13515150 ATAAA-C
1 ATAAACC
13515156 ACTAAACC
1 A-TAAACC
13515164 ATAAACC
1 ATAAACC
13515171 ATAAACC
1 ATAAACC
13515178 ATAAACC
1 ATAAACC
*
13515185 CTAAA
1 ATAAA
13515190 ATATGTATAA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
6 2 0.03
7 71 0.95
8 2 0.03
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.18
Consensus pattern (7 bp):
ATAAACC
Found at i:13515119 original size:21 final size:21
Alignment explanation
Indices: 13515093--13515189 Score: 115
Period size: 21 Copynumber: 4.6 Consensus size: 21
13515083 ATATAGTTTA
*
13515093 TATAAACCCTAAACCCTAAAC
1 TATAAACCCTAAACCATAAAC
* *
13515114 TATAAACCATAAATCATAAAC
1 TATAAACCCTAAACCATAAAC
* *
13515135 GATAAACCCTAAATCATAAAC
1 TATAAACCCTAAACCATAAAC
*
13515156 -ACTAAACCATAAACCATAAAC
1 TA-TAAACCCTAAACCATAAAC
*
13515177 CATAAACCCTAAA
1 TATAAACCCTAAA
13515190 ATATGTATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.19
Consensus pattern (21 bp):
TATAAACCCTAAACCATAAAC
Found at i:13515245 original size:2 final size:2
Alignment explanation
Indices: 13515206--13515236 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
13515196 ATAAACCATG
13515206 TA TA GTA 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
13515237 AACTATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13515382 original size:68 final size:68
Alignment explanation
Indices: 13515303--13515449 Score: 204
Period size: 68 Copynumber: 2.1 Consensus size: 68
13515293 TAATGCATAC
* * * *
13515303 ATATATATACTATATTAATATAGATTATAACATATAAACTATATAGTTTATATAGTTTATATATA
1 ATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTATATAGTTTATACATA
13515368 TAT
66 TAT
*** *
13515371 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTATATAGTTTATACATA
13515436 TAT
66 TAT
*
13515439 AGTTTATATAC
1 A-TATATATAC
13515450 ATAGTTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
68 61 0.88
69 8 0.12
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (68 bp):
ATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTATATAGTTTATACATA
TAT
Found at i:13515453 original size:13 final size:13
Alignment explanation
Indices: 13515421--13515598 Score: 108
Period size: 13 Copynumber: 12.8 Consensus size: 13
13515411 ATATACTTTT
13515421 TATAGTTTATACATA
1 TATAGTTTAT--ATA
13515436 TATAGTTTATATA
1 TATAGTTTATATA
*
13515449 CATAGTTTATATA
1 TATAGTTTATATA
* *
13515462 TATAGTTCACATAAA
1 TATAGTT--TATATA
* *
13515477 CATAATTTATATA
1 TATAGTTTATATA
13515490 TATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
13515508 TATAGTTTATA-A
1 TATAGTTTATATA
** *
13515520 TATA-AATATAGTT
1 TATAGTTTATA-TA
*
13515533 TATTATTTTATATA
1 TA-TAGTTTATATA
*
13515547 CATAGTTTATATA
1 TATAGTTTATATA
* *
13515560 TATAGTTCACATTAA
1 TATAGTTTATA-T-A
*
13515575 TATAATTTATATA
1 TATAGTTTATATA
13515588 TATAGTTTATA
1 TATAGTTTATA
13515599 ATAATTATAT
Statistics
Matches: 125, Mismatches: 25, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
11 4 0.03
12 5 0.04
13 59 0.47
14 9 0.07
15 35 0.28
16 3 0.02
17 3 0.02
18 7 0.06
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:13515476 original size:68 final size:68
Alignment explanation
Indices: 13515303--13515489 Score: 195
Period size: 68 Copynumber: 2.8 Consensus size: 68
13515293 TAATGCATAC
* * * * * *
13515303 ATATATATACTATATTAATATAGATTATAACATATAAACTATATAGTTTATATAGTTTATATATA
1 ATATATATACTATATTAATATAAATAATATCACATAAACTATATACTTTATATAGTTTATACATA
13515368 TAT
66 TAT
*** *
13515371 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATATCACATAAACTATATACTTTATATAGTTTATACATA
13515436 TAT
66 TAT
* * * *
13515439 AGTTTATATAC-ATAGTTTATATATATAGT-TCACATAAAC-ATA-A-TTTATATA
1 A-TATATATACTATA-TTAATATAAATAATATCACATAAACTATATACTTTATATA
13515490 TATAGCTTAT
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
65 7 0.07
66 1 0.01
67 3 0.03
68 71 0.70
69 19 0.19
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (68 bp):
ATATATATACTATATTAATATAAATAATATCACATAAACTATATACTTTATATAGTTTATACATA
TAT
Found at i:13515479 original size:28 final size:26
Alignment explanation
Indices: 13515422--13515599 Score: 90
Period size: 28 Copynumber: 6.9 Consensus size: 26
13515412 TATACTTTTT
* *
13515422 ATAGTTTATACATATATAGTTTATATAC
1 ATAGTTTAT--ATATATAGTTCATAAAC
13515450 ATAGTTTATATATATAGTTCACATAAAC
1 ATAGTTTATATATATAGTT--CATAAAC
*
13515478 ATAATTTATATATATAGCTT-ATAATA-
1 ATAGTTTATATATATAG-TTCATAA-AC
* * * *
13515504 AT--TATATAGTTTATA-AT-ATAAAT
1 ATAGTTTATA-TATATAGTTCATAAAC
*
13515527 ATAGTTTAT-TAT-T--TT-ATATAC
1 ATAGTTTATATATATAGTTCATAAAC
* *
13515548 ATAGTTTATATATATAGTTCACATTAAT
1 ATAGTTTATATATATAGTT--CATAAAC
* *
13515576 ATAATTTATATATATAGTTTATAA
1 ATAGTTTATATATATAGTTCATAA
13515600 TAATTATATA
Statistics
Matches: 118, Mismatches: 17, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
21 14 0.12
22 5 0.04
23 10 0.08
24 5 0.04
25 11 0.09
26 19 0.16
27 1 0.01
28 51 0.43
29 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (26 bp):
ATAGTTTATATATATAGTTCATAAAC
Found at i:13515528 original size:18 final size:18
Alignment explanation
Indices: 13515484--13515638 Score: 104
Period size: 18 Copynumber: 8.2 Consensus size: 18
13515474 AAACATAATT
*
13515484 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
13515502 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
* *
13515520 TATAAATATAGTTTATTATTT
1 TATATATATAGTTTA-TA--A
*
13515541 TATATACATAGTTTAT-A
1 TATATATATAGTTTATAA
*
13515558 TATATAGT-TCACATTAATATAA
1 TATATA-TAT-A-GTT--TATAA
13515580 TTTATATATATAGTTTATAA
1 --TATATATATAGTTTATAA
13515600 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
* *
13515618 TAAAAATATAGTTTAT-A
1 TATATATATAGTTTATAA
13515635 TATA
1 TATA
13515639 ATTTTATATT
Statistics
Matches: 110, Mismatches: 11, Indels: 33
0.71 0.07 0.21
Matches are distributed among these distances:
17 13 0.12
18 57 0.52
19 6 0.05
20 6 0.05
21 16 0.15
22 3 0.03
23 2 0.02
24 7 0.06
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:13515557 original size:98 final size:98
Alignment explanation
Indices: 13515441--13515633 Score: 350
Period size: 98 Copynumber: 2.0 Consensus size: 98
13515431 ACATATATAG
13515441 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
*
13515506 TATATAGTTTATAATATAAATATAGTTTATTAT
66 TATATAGTTTATAATAAAAATATAGTTTATTAT
* * *
13515539 TTTATATACATAGTTTATATATATAGTTCACATTAATATAATTTATATATATAGTTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
13515604 TATATAGTTTATAATAAAAATATAGTTTAT
66 TATATAGTTTATAATAAAAATATAGTTTAT
13515634 ATATAATTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (98 bp):
TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
TATATAGTTTATAATAAAAATATAGTTTATTAT
Found at i:13515603 original size:28 final size:28
Alignment explanation
Indices: 13515552--13515657 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 28
13515542 ATATACATAG
* * *
13515552 TTTATATATATAGTTCACATTAATATAA
1 TTTATATATATAGTTTATAATAATATAA
13515580 TTTATATATATAGTTTATAATAATTATATA
1 TTTATATATATAGTTTATAATAA-TATA-A
* *
13515610 GTTTATAATAAAAATATAGTTTATATATAATTTTA
1 -TTTAT-AT----ATATAGTTTATA-ATAATATAA
13515645 TATTATATATATA
1 T-TTATATATATA
13515658 TTATATTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
28 20 0.32
29 4 0.06
30 6 0.10
31 5 0.08
32 2 0.03
34 3 0.05
35 5 0.08
36 14 0.22
37 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (28 bp):
TTTATATATATAGTTTATAATAATATAA
Found at i:13518284 original size:19 final size:20
Alignment explanation
Indices: 13518242--13518285 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
13518232 CATTAGGTAT
*
13518242 CAATACCACTAGTGTAGTAC
1 CAATACCACTAGTGTAGTAA
13518262 CAATACC-CTA-TGTCAGTAA
1 CAATACCACTAGTGT-AGTAA
13518281 CAATA
1 CAATA
13518286 TCCATAGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.55
20 7 0.32
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (20 bp):
CAATACCACTAGTGTAGTAA
Found at i:13521528 original size:4 final size:4
Alignment explanation
Indices: 13521519--13521546 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
13521509 GTTTAAGTGG
13521519 AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT
13521547 GTTGAGGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:13527522 original size:44 final size:44
Alignment explanation
Indices: 13527423--13527547 Score: 135
Period size: 44 Copynumber: 2.9 Consensus size: 44
13527413 GTCACATTTT
* * *
13527423 TAGCAGCGTTTGTATCAT-AAAATGCCGCTATATACCAGGAATA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGGAATA
* * * ***
13527466 TAGTGGCATTTGTATCCTAAAAACGCCGTTATATACCAGTCCTA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGGAATA
* * *
13527510 TCGCGGCGTTTGTATCCTAAAAACGCAGCTAAATACCA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCA
13527548 TACCTATTGC
Statistics
Matches: 66, Mismatches: 15, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
43 14 0.21
44 52 0.79
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (44 bp):
TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGGAATA
Found at i:13527554 original size:44 final size:44
Alignment explanation
Indices: 13527474--13527560 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
13527464 TATAGTGGCA
* * *
13527474 TTTGTATCCTAAAAACGCCGTTATATACCAGTCCTATCGCGGCG
1 TTTGTATCCTAAAAACGCAGCTAAATACCAGTCCTATCGCGGCG
*
13527518 TTTGTATCCTAAAAACGCAGCTAAATACCA-TACCTATTGCGGC
1 TTTGTATCCTAAAAACGCAGCTAAATACCAGT-CCTATCGCGGC
13527561 ATTTTCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 1 0.03
44 37 0.97
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (44 bp):
TTTGTATCCTAAAAACGCAGCTAAATACCAGTCCTATCGCGGCG
Found at i:13528052 original size:2 final size:2
Alignment explanation
Indices: 13528045--13528074 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13528035 AATATCATAA
13528045 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
13528075 TATTTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13529370 original size:14 final size:14
Alignment explanation
Indices: 13529351--13529381 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13529341 AGGCGAGATC
13529351 TTTTAAAAATCAAA
1 TTTTAAAAATCAAA
*
13529365 TTTTAAAAATTAAA
1 TTTTAAAAATCAAA
13529379 TTT
1 TTT
13529382 GCTGTTTAAA
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTTAAAAATCAAA
Found at i:13530251 original size:27 final size:27
Alignment explanation
Indices: 13530214--13530285 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
13530204 ATGGGGGTAG
*
13530214 AAAA-CATGTCTAGGTAGAACCGTTGT
1 AAAAGCATGTCTGGGTAGAACCGTTGT
13530240 AAAAGCATGTCTGGGTAGAACCGTTGT
1 AAAAGCATGTCTGGGTAGAACCGTTGT
*
13530267 AAAAGAATGTCTGGGTAGA
1 AAAAGCATGTCTGGGTAGA
13530286 TACCATGTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
26 4 0.09
27 39 0.91
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (27 bp):
AAAAGCATGTCTGGGTAGAACCGTTGT
Found at i:13534373 original size:16 final size:16
Alignment explanation
Indices: 13534339--13534372 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
13534329 TTCAACTTTA
13534339 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTTCT
13534355 TTTCTTTTTC-TTTCT
1 TTTCTTTTTCTTTTCT
13534370 TTT
1 TTT
13534373 TGAGTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTCTTTTCT
Found at i:13534401 original size:23 final size:24
Alignment explanation
Indices: 13534361--13534414 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
13534351 TTCTTTTCTT
13534361 TTTCTTTCTTTTTGAGTGCTTTCAA
1 TTTC-TTCTTTTTGAGTGCTTTCAA
* *
13534386 TTTCTTCTTTTT-AGTGCTTTGAT
1 TTTCTTCTTTTTGAGTGCTTTCAA
13534409 TTTCTT
1 TTTCTT
13534415 TGCTGGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 15 0.56
24 8 0.30
25 4 0.15
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTGCTTTCAA
Found at i:13534988 original size:25 final size:25
Alignment explanation
Indices: 13534960--13535011 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
13534950 CAAGCTTGCT
13534960 TGAGTGTGTAGCTAGCTAGCAAGCA
1 TGAGTGTGTAGCTAGCTAGCAAGCA
13534985 TGAGTGTGTAGCTAGCTAGCAAGCA
1 TGAGTGTGTAGCTAGCTAGCAAGCA
13535010 TG
1 TG
13535012 GGATGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (25 bp):
TGAGTGTGTAGCTAGCTAGCAAGCA
Found at i:13541441 original size:15 final size:14
Alignment explanation
Indices: 13541412--13541450 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
13541402 AGTGCTTCAA
*
13541412 CTTTTTTTTCTTTT
1 CTTTTTTTGCTTTT
13541426 CTTTTCTTTGCTTTT
1 CTTTT-TTTGCTTTT
13541441 CTTCTTTTTG
1 CTT-TTTTTG
13541451 AGTGCTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 15 0.68
16 2 0.09
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (14 bp):
CTTTTTTTGCTTTT
Found at i:13546280 original size:20 final size:20
Alignment explanation
Indices: 13546255--13546295 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13546245 TAAGAGCCCC
*
13546255 TTTAGGATCATATAGATGCA
1 TTTAGGAGCATATAGATGCA
*
13546275 TTTAGGAGCATATAGTTGCA
1 TTTAGGAGCATATAGATGCA
13546295 T
1 T
13546296 GTGGTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (20 bp):
TTTAGGAGCATATAGATGCA
Found at i:13551141 original size:20 final size:20
Alignment explanation
Indices: 13551116--13551155 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
13551106 TTTTGGTGCA
*
13551116 GAGGGAATCGATCCCCCCTT
1 GAGGGAAGCGATCCCCCCTT
*
13551136 GAGGGAAGCGATTCCCCCTT
1 GAGGGAAGCGATCCCCCCTT
13551156 TGAAGGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.20
Consensus pattern (20 bp):
GAGGGAAGCGATCCCCCCTT
Found at i:13551170 original size:23 final size:21
Alignment explanation
Indices: 13551116--13551177 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
13551106 TTTTGGTGCA
*
13551116 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
* *
13551136 GAGGGAAGCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
13551157 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
13551178 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 15 0.43
ACGTcount: A:0.21, C:0.34, G:0.27, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:13551203 original size:20 final size:20
Alignment explanation
Indices: 13551118--13551203 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
13551108 TTGGTGCAGA
*
13551118 GGGAATCGA-TCCCCCCTTG
1 GGGAATCGATTCCCCCCTAG
* *
13551137 AGGGAAGCGATTCCCCCTTTGAAG
1 -GGGAATCGATTCCCCC-CT--AG
* *
13551161 GGGAACCGATTCCCCCCACAG
1 GGGAATCGATTCCCCCC-TAG
*
13551182 GGGAATCGATACCCCCCTAG
1 GGGAATCGATTCCCCCCTAG
13551202 GG
1 GG
13551204 TTCTGGTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
20 12 0.23
21 23 0.44
22 1 0.02
23 15 0.29
24 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.28, T:0.16
Consensus pattern (20 bp):
GGGAATCGATTCCCCCCTAG
Found at i:13560554 original size:33 final size:33
Alignment explanation
Indices: 13560512--13560580 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
13560502 GTTGATGAAT
*
13560512 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
13560545 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
13560578 GAA
1 GAA
13560581 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:13562277 original size:32 final size:32
Alignment explanation
Indices: 13562233--13562296 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
13562223 CCATAAGAAG
*
13562233 AAGGTACCCGAGGAACAATTTGATTAGATATT
1 AAGGTACCCGAGGAACAATTTGATGAGATATT
*
13562265 AAGGTACTCGAGGAACAATTTGATGAGATATT
1 AAGGTACCCGAGGAACAATTTGATGAGATATT
13562297 GCCTGGCCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (32 bp):
AAGGTACCCGAGGAACAATTTGATGAGATATT
Found at i:13567400 original size:45 final size:45
Alignment explanation
Indices: 13567344--13567576 Score: 358
Period size: 45 Copynumber: 5.2 Consensus size: 45
13567334 ATAAAATTTC
* * *
13567344 TTACCATTATACTTACTATTTAACCCATAAGCTTGTAAGCTTATT
1 TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
**
13567389 TTACCAATATACTTAGTATTTAACCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
* *
13567434 TTACCAATATATTTACCATTTAACACATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
**
13567479 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
* **
13567524 TTACGAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
13567569 TTACCAAT
1 TTACCAAT
13567577 TTATCATTTA
Statistics
Matches: 175, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 175 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
Found at i:13571189 original size:15 final size:14
Alignment explanation
Indices: 13571169--13571249 Score: 56
Period size: 15 Copynumber: 5.4 Consensus size: 14
13571159 GCATCAATCA
*
13571169 TTTTTCCTTCTTTTC
1 TTTTT-CTTATTTTC
13571184 TTTTTCTATATTTTC
1 TTTTTCT-TATTTTC
* *
13571199 TTCTTCTTTTTCTTTTTC
1 -T-TT-TTCTT-ATTTTC
13571217 TTTTTCTT-TTTTC
1 TTTTTCTTATTTTC
*
13571230 TCTTTTTTTATTTTC
1 T-TTTTCTTATTTTC
13571245 TTTTT
1 TTTTT
13571250 ATGTTTTATG
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 6 0.11
14 12 0.22
15 21 0.39
16 3 0.06
17 4 0.07
18 8 0.15
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCTTATTTTC
Found at i:13571233 original size:21 final size:20
Alignment explanation
Indices: 13571179--13571277 Score: 71
Period size: 21 Copynumber: 4.8 Consensus size: 20
13571169 TTTTTCCTTC
*
13571179 TTTTCTTTTTCTATATTTTCT
1 TTTTCTTTTTCT-TTTTTTCT
*
13571200 TCTTCTTTTTC--TTTTTCT
1 TTTTCTTTTTCTTTTTTTCT
13571218 TTTTCTTTTTTCTCTTTTTT-T
1 TTTTC-TTTTTCT-TTTTTTCT
* * *
13571239 ATTTTCTTTTTATGTTTTATGT
1 -TTTTCTTTTTCT-TTTTTTCT
13571261 TTTT-TGTTTTCTTTTTT
1 TTTTCT-TTTTCTTTTTT
13571278 AGCTCTTATG
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
18 10 0.16
19 6 0.10
20 5 0.08
21 31 0.49
22 11 0.17
ACGTcount: A:0.05, C:0.12, G:0.03, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTTCTTTTTTTCT
Found at i:13571233 original size:27 final size:27
Alignment explanation
Indices: 13571179--13571277 Score: 78
Period size: 27 Copynumber: 3.7 Consensus size: 27
13571169 TTTTTCCTTC
* * *
13571179 TTTTCT-TTTTCTATATTTTCTTCTTCT
1 TTTTCTATTTTCTTTTTTTTTTTC-TCT
13571206 TTTTCT-TTTTCTTTTTCTTTTTTCTCT
1 TTTTCTATTTTCTTTTT-TTTTTTCTCT
* * * *
13571233 TTTTTTATTTTCTTTTTATGTTTTATGT
1 TTTTCTATTTTCTTTTT-TTTTTTCTCT
*
13571261 TTTT-TGTTTTCTTTTTT
1 TTTTCTATTTTCTTTTTT
13571278 AGCTCTTATG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 1 0.02
27 33 0.54
28 27 0.44
ACGTcount: A:0.05, C:0.12, G:0.03, T:0.80
Consensus pattern (27 bp):
TTTTCTATTTTCTTTTTTTTTTTCTCT
Found at i:13571276 original size:6 final size:6
Alignment explanation
Indices: 13571179--13571227 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
13571169 TTTTTCCTTC
*
13571179 TTTTCT TTTTCTAT ATTTTCT TCTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTC--T -TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
13571228 TCTCTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 31 0.82
7 1 0.03
8 1 0.03
9 5 0.13
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:13573639 original size:22 final size:22
Alignment explanation
Indices: 13573594--13573642 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
13573584 GAATAGACCA
*
13573594 TGAACAGTAATGAACTATATCG
1 TGAACAGTAATGAACTATACCG
*
13573616 TGAATAGTAATGAAC-AGTACCG
1 TGAACAGTAATGAACTA-TACCG
13573638 TGAAC
1 TGAAC
13573643 TGTGAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (22 bp):
TGAACAGTAATGAACTATACCG
Found at i:13573672 original size:21 final size:21
Alignment explanation
Indices: 13573648--13573694 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
13573638 TGAACTGTGA
*
13573648 ACAATGTATCGATGCACTGCT
1 ACAATGCATCGATGCACTGCT
13573669 ACAATGCATCGATGCACTGCT
1 ACAATGCATCGATGCACTGCT
13573690 ACAAT
1 ACAAT
13573695 AATTTCAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (21 bp):
ACAATGCATCGATGCACTGCT
Found at i:13574137 original size:45 final size:45
Alignment explanation
Indices: 13574081--13574268 Score: 322
Period size: 45 Copynumber: 4.2 Consensus size: 45
13574071 ATAAAATTTC
* *
13574081 TTACCATTATACTTACTATTTAACCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
*
13574126 TTACCAATATACTTACTATTTAACCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
*
13574171 TTACCAATATACTTGCCATTTAACCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
**
13574216 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
13574261 TTACCAAT
1 TTACCAAT
13574269 TTATCATTTA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 137 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTAACCCATAAGCTCGTAAGCTTATT
Found at i:13575256 original size:31 final size:32
Alignment explanation
Indices: 13575198--13575257 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
13575188 AACCATTTAC
* * **
13575198 AACTTTTCCAAAATTGTCAAATTGGTCCCCCA
1 AACTTTTCAAAAATTGACAAAACGGTCCCCCA
13575230 AACTTTTCAAAAATT-ACAAAACGGTCCC
1 AACTTTTCAAAAATTGACAAAACGGTCCC
13575258 TAAATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.42
32 14 0.58
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.28
Consensus pattern (32 bp):
AACTTTTCAAAAATTGACAAAACGGTCCCCCA
Found at i:13576270 original size:20 final size:20
Alignment explanation
Indices: 13576240--13576285 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
13576230 CTAATCTATT
* *
13576240 GAAAGTTTATACTTTGGTCAC
1 GAAA-TTTATAATATGGTCAC
13576261 GAAATTTATAATATGGTCAC
1 GAAATTTATAATATGGTCAC
*
13576281 TAAAT
1 GAAAT
13576286 AAATCCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (20 bp):
GAAATTTATAATATGGTCAC
Found at i:13587942 original size:24 final size:24
Alignment explanation
Indices: 13587887--13587942 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
13587877 GTGGATCACA
* *
13587887 AAAAGTCACACCTATTGGTTCTTC
1 AAAAGTCACACCTATTAGTCCTTC
* * * *
13587911 AAAGGTCACATCTTTTAGTCCTTT
1 AAAAGTCACACCTATTAGTCCTTC
13587935 AAAAGTCA
1 AAAAGTCA
13587943 TGATTCTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (24 bp):
AAAAGTCACACCTATTAGTCCTTC
Found at i:13593877 original size:18 final size:17
Alignment explanation
Indices: 13593841--13593891 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
13593831 TTTGGTTCGT
13593841 AAGAAA-AAAAGAAAAAGA
1 AAGAAAGAAAAG--AAAGA
13593859 AATG-AAGAAAATGAAAGA
1 AA-GAAAGAAAA-GAAAGA
13593877 AAGAAAGAAAAGAAA
1 AAGAAAGAAAAGAAA
13593892 TGGTGACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 5 0.17
18 18 0.62
19 5 0.17
20 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (17 bp):
AAGAAAGAAAAGAAAGA
Found at i:13595948 original size:13 final size:12
Alignment explanation
Indices: 13595930--13595960 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
13595920 AATTTGGAGT
13595930 AAAAAAAGAAAGA
1 AAAAAAAGAAA-A
13595943 AAAAAAAGAAAA
1 AAAAAAAGAAAA
13595955 AAAAAA
1 AAAAAA
13595961 GTCTAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:13597726 original size:24 final size:24
Alignment explanation
Indices: 13597699--13597798 Score: 67
Period size: 24 Copynumber: 4.2 Consensus size: 24
13597689 GATATCATAA
*
13597699 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * * *
13597723 ATCAGAACAAAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* * * *
13597747 ATCAGAACAGATTTTATATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
13597771 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
13597795 ATCA
1 ATCA
13597799 GATAAAATAT
Statistics
Matches: 55, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:13602442 original size:19 final size:20
Alignment explanation
Indices: 13602418--13602468 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
13602408 CGGCCAAGAG
* **
13602418 CATGTATCTTCATTTAAA-T
1 CATGTATTTTCATAAAAACT
13602437 CATGTATTTTCATAAAAACT
1 CATGTATTTTCATAAAAACT
13602457 CATGTATTTTCA
1 CATGTATTTTCA
13602469 AAGAGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATAAAAACT
Found at i:13606457 original size:19 final size:20
Alignment explanation
Indices: 13606433--13606481 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 20
13606423 CAAGAGCATT
13606433 TATTTTCATTT-AAATCATG
1 TATTTTCATTTAAAATCATG
13606452 TATTTTCATTTAAAAAATCATG
1 TATTTTCATTT--AAAATCATG
13606474 TATTTTCA
1 TATTTTCA
13606482 AAAGGGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.41
22 16 0.59
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (20 bp):
TATTTTCATTTAAAATCATG
Found at i:13617993 original size:16 final size:17
Alignment explanation
Indices: 13617968--13618005 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
13617958 CTTATTGGAA
*
13617968 ATTTTGTTCTTTTTG-G
1 ATTTTATTCTTTTTGTG
13617984 ATTTTATTCTTTTTGTG
1 ATTTTATTCTTTTTGTG
13618001 ATTTT
1 ATTTT
13618006 CTCATTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.11, C:0.05, G:0.13, T:0.71
Consensus pattern (17 bp):
ATTTTATTCTTTTTGTG
Found at i:13627857 original size:19 final size:17
Alignment explanation
Indices: 13627833--13627875 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
13627823 ATTTATTTTC
*
13627833 TTTTCTTCTTTTCTGATTT
1 TTTTCTTCTTTT-T-ATCT
13627852 TTTTCTTCTTTTTATCT
1 TTTTCTTCTTTTTATCT
13627869 TTTTCTT
1 TTTTCTT
13627876 TTCTTTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.43
18 1 0.04
19 12 0.52
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTCTTCTTTTTATCT
Found at i:13627879 original size:19 final size:19
Alignment explanation
Indices: 13627826--13627883 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
13627816 CTTTTGAATT
13627826 TATTTTCTTTTCTTCTTTTC
1 TATTTTCTTTTCTT-TTTTC
*
13627846 TGATTTTTTTCTTCTTTTTATC
1 T-ATTTTCTT-TTCTTTTT-TC
13627868 T-TTTTCTTTTCTTTTT
1 TATTTTCTTTTCTTTTT
13627884 GCACTCCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 8 0.24
20 7 0.21
21 10 0.30
22 8 0.24
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.78
Consensus pattern (19 bp):
TATTTTCTTTTCTTTTTTC
Found at i:13628231 original size:13 final size:13
Alignment explanation
Indices: 13628213--13628246 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
13628203 TATGATGGTC
13628213 TTGATGAAGGATG
1 TTGATGAAGGATG
*
13628226 TTGATGATGGATG
1 TTGATGAAGGATG
*
13628239 ATGATGAA
1 TTGATGAA
13628247 ATGGCAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:13629012 original size:35 final size:36
Alignment explanation
Indices: 13628965--13629032 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
13628955 ATTTATAAGT
13628965 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
13629000 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
13629033 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:13629418 original size:19 final size:20
Alignment explanation
Indices: 13629371--13629421 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
13629361 GAAACCCCTT
**
13629371 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
13629391 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
13629410 TGAAGATACATG
1 TGAAAATACATG
13629422 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:13630985 original size:15 final size:16
Alignment explanation
Indices: 13630945--13630985 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
13630935 AATATTTTAA
13630945 TATAGTTATTTTCATC
1 TATAGTTATTTTCATC
*
13630961 TACA-TATATTTT-ATC
1 TATAGT-TATTTTCATC
13630976 TATAGTTATT
1 TATAGTTATT
13630986 ATGATGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (16 bp):
TATAGTTATTTTCATC
Found at i:13632761 original size:24 final size:24
Alignment explanation
Indices: 13632732--13632777 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
13632722 AACAAAGTGA
13632732 AGCACTCAAAAGAAAGAA-AAAATC
1 AGCACTCAAAA-AAAGAAGAAAATC
13632756 AGCACTCAAAAAAAGAAGAAAA
1 AGCACTCAAAAAAAGAAGAAAA
13632778 GCAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.65, C:0.15, G:0.13, T:0.07
Consensus pattern (24 bp):
AGCACTCAAAAAAAGAAGAAAATC
Found at i:13634352 original size:9 final size:9
Alignment explanation
Indices: 13634320--13634350 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
13634310 GAAACAGTGC
13634320 AAAACGAAG
1 AAAACGAAG
13634329 AAAACGAAG
1 AAAACGAAG
*
13634338 AAAATGAAG
1 AAAACGAAG
13634347 AAAA
1 AAAA
13634351 TGTAGATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.71, C:0.06, G:0.19, T:0.03
Consensus pattern (9 bp):
AAAACGAAG
Found at i:13641105 original size:24 final size:21
Alignment explanation
Indices: 13641071--13641113 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
13641061 TGCACAAGAT
*
13641071 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
13641093 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
13641114 AGAATGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:13642859 original size:13 final size:11
Alignment explanation
Indices: 13642817--13642901 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
13642807 ACAATCTGTC
13642817 CATCACCATTAT
1 CATCACCA-TAT
*
13642829 CA-CGCCTATAT
1 CATCACC-ATAT
*
13642840 TATCACCATAGT
1 CATCACCATA-T
13642852 CCATCACCATTAT
1 -CATCACCA-TAT
*
13642865 CA-CGCCTATAT
1 CATCACC-ATAT
13642876 CATCACCATATT
1 CATCACCATA-T
13642888 CCATCACCATAT
1 -CATCACCATAT
13642900 CA
1 CA
13642902 CGCCTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 23 0.40
12 15 0.26
13 18 0.31
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:13642861 original size:36 final size:36
Alignment explanation
Indices: 13642814--13642918 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
13642804 GATACAATCT
13642814 GTCCATCACCATTATCACGCCTATATTATCACCATA
1 GTCCATCACCATTATCACGCCTATATTATCACCATA
*
13642850 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATTATCACCATA
*
13642886 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATTATCACCA
13642919 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATTATCACCATA
Found at i:13643562 original size:16 final size:16
Alignment explanation
Indices: 13643541--13643593 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
13643531 GTAAGTTATC
*
13643541 TTCATTTTTTTTTCAT
1 TTCATTTTTTATTCAT
13643557 TTCATTTCTTTATTC-T
1 TTCATTT-TTTATTCAT
* *
13643573 TTCATCTTTTCTT-AT
1 TTCATTTTTTATTCAT
13643588 TTCATT
1 TTCATT
13643594 ACCATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 11 0.35
16 14 0.45
17 6 0.19
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCATTTTTTATTCAT
Found at i:13646522 original size:13 final size:11
Alignment explanation
Indices: 13646481--13646565 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
13646471 ACAATCTGTC
13646481 CATCACCATTAT
1 CATCACCA-TAT
*
13646493 CA-CGCCTATAT
1 CATCACC-ATAT
13646504 CATCACCATAGT
1 CATCACCATA-T
13646516 CCATCACCATTAT
1 -CATCACCA-TAT
*
13646529 CA-CGCCTATAT
1 CATCACC-ATAT
13646540 CATCACCATATT
1 CATCACCATA-T
13646552 CCATCACCATAT
1 -CATCACCATAT
13646564 CA
1 CA
13646566 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:13646525 original size:36 final size:36
Alignment explanation
Indices: 13646478--13646582 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
13646468 GATACAATCT
13646478 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
13646514 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
13646550 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
13646583 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:13655936 original size:21 final size:19
Alignment explanation
Indices: 13655912--13655951 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
13655902 TCCACCATGG
13655912 TTTATTAATTCTATTCATTTT
1 TTTATTAATT-T-TTCATTTT
*
13655933 TTTATTAGTTTTTCATTTT
1 TTTATTAATTTTTCATTTT
13655952 ATAACTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTATTAATTTTTCATTTT
Found at i:13658474 original size:21 final size:20
Alignment explanation
Indices: 13658444--13658482 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
13658434 CATCTCCATT
*
13658444 TCATCATCAATACCATCATC
1 TCATCATCAAGACCATCATC
13658464 TCATCCATCAAGACCATCA
1 TCAT-CATCAAGACCATCA
13658483 ATTCCACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.36, G:0.03, T:0.26
Consensus pattern (20 bp):
TCATCATCAAGACCATCATC
Found at i:13660430 original size:13 final size:11
Alignment explanation
Indices: 13660389--13660473 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
13660379 ACAATCTGTC
13660389 CATCACCATTAT
1 CATCACCA-TAT
*
13660401 CA-CGCCTATAT
1 CATCACC-ATAT
13660412 CATCACCATAGT
1 CATCACCATA-T
13660424 CCATCACCATTAT
1 -CATCACCA-TAT
*
13660437 CA-CGCCTATAT
1 CATCACC-ATAT
13660448 CATCACCATATT
1 CATCACCATA-T
13660460 CCATCACCATAT
1 -CATCACCATAT
13660472 CA
1 CA
13660474 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:13660433 original size:36 final size:36
Alignment explanation
Indices: 13660386--13660490 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
13660376 GATACAATCT
13660386 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
13660422 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
13660458 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
13660491 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:13660886 original size:14 final size:12
Alignment explanation
Indices: 13660871--13660916 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
13660861 GTGCTACAAC
13660871 AAGAAAAAAGCAA
1 AAGAAAAAAG-AA
*
13660884 CAAGAAAGAAGAA
1 -AAGAAAAAAGAA
*
13660897 AAGAAAATAGAA
1 AAGAAAAAAGAA
13660909 AAGAAAAA
1 AAGAAAAA
13660917 GACTCCTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.61
13 2 0.07
14 9 0.32
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.02
Consensus pattern (12 bp):
AAGAAAAAAGAA
Found at i:13660900 original size:26 final size:23
Alignment explanation
Indices: 13660871--13660918 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
13660861 GTGCTACAAC
13660871 AAGAAAAAAGCAACAAGAAAGAAGAA
1 AAGAAAAAAG-AA-AAGAAA-AAGAA
*
13660897 AAGAAAATAGAAAAGAAAAAGA
1 AAGAAAAAAGAAAAGAAAAAGA
13660919 CTCCTACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 2 0.10
26 9 0.43
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (23 bp):
AAGAAAAAAGAAAAGAAAAAGAA
Found at i:13660974 original size:14 final size:15
Alignment explanation
Indices: 13660940--13660986 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
13660930 AATTTGGAGT
13660940 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
13660955 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
13660969 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
13660986 G
1 G
13660987 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:13664931 original size:23 final size:23
Alignment explanation
Indices: 13664903--13665076 Score: 89
Period size: 23 Copynumber: 7.3 Consensus size: 23
13664893 ACAATCTGTC
*
13664903 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
13664926 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
13664949 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCACCATA-T
*
13664974 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
13664998 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
13665021 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
13665046 CCATCACCA-TATCA-CGCCCATAT
1 -CATCACCATTATCATC-ACCATAT
*
13665069 TATCACCA
1 CATCACCA
13665077 ACTTATAAAT
Statistics
Matches: 120, Mismatches: 9, Indels: 45
0.69 0.05 0.26
Matches are distributed among these distances:
22 21 0.17
23 42 0.35
24 24 0.20
25 20 0.17
26 3 0.03
27 10 0.08
ACGTcount: A:0.31, C:0.37, G:0.05, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:13664944 original size:13 final size:11
Alignment explanation
Indices: 13664903--13665059 Score: 106
Period size: 11 Copynumber: 13.2 Consensus size: 11
13664893 ACAATCTGTC
13664903 CATCACCATTAT
1 CATCACCA-TAT
*
13664915 CA-CGCCTATAT
1 CATCACC-ATAT
13664926 CATCACCATAGT
1 CATCACCATA-T
13664938 CCATCACCATTAT
1 -CATCACCA-TAT
*
13664951 CA-CGCCTATAT
1 CATCACC-ATAT
13664962 CATCACCATAGT
1 CATCACCATA-T
13664974 CCATCACCATTAT
1 -CATCACCA-TAT
*
13664987 CA-CGCCTATAT
1 CATCACC-ATAT
13664998 CATCACCATAGT
1 CATCACCATA-T
13665010 CCATCACCATTAT
1 -CATCACCA-TAT
*
13665023 CA-CGCCTATAT
1 CATCACC-ATAT
13665034 CATCACCATATT
1 CATCACCATA-T
13665046 CCATCACCATAT
1 -CATCACCATAT
13665058 CA
1 CA
13665060 CGCCCATATT
Statistics
Matches: 118, Mismatches: 8, Indels: 39
0.72 0.05 0.24
Matches are distributed among these distances:
11 46 0.39
12 29 0.25
13 37 0.31
14 6 0.05
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:13664947 original size:36 final size:36
Alignment explanation
Indices: 13664900--13665076 Score: 320
Period size: 36 Copynumber: 4.9 Consensus size: 36
13664890 GATACAATCT
13664900 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
13664936 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
13664972 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
13665008 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
13665044 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
13665077 ACTTATAAAT
Statistics
Matches: 138, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
35 20 0.14
36 118 0.86
ACGTcount: A:0.31, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:13665571 original size:22 final size:24
Alignment explanation
Indices: 13665533--13665577 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
13665523 TGTGTGTATC
*
13665533 ATATTAAGCTATGAATG-CATTAT
1 ATATTAAGCTATAAATGCCATTAT
13665556 ATATTAA-CTATAAATGCCATTA
1 ATATTAAGCTATAAATGCCATTA
13665578 AACAACACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (24 bp):
ATATTAAGCTATAAATGCCATTAT
Found at i:13665729 original size:50 final size:50
Alignment explanation
Indices: 13665659--13665823 Score: 303
Period size: 50 Copynumber: 3.3 Consensus size: 50
13665649 GTATGCTGCC
* *
13665659 ATGAATGTGAATGCACGTGAATTAACAAAATAAATGATAAACATGCTGTT
1 ATGAATGTGAATGCATGTGAATTAACAAAATAAATGATAAACATGTTGTT
13665709 ATGAATGTGAATGCATGTGAATTAACAAAATAAATGATAAACATGTTGTT
1 ATGAATGTGAATGCATGTGAATTAACAAAATAAATGATAAACATGTTGTT
*
13665759 ATGAATGTGAATGCATGTTAATTAACAAAATAAATGATAAACATGTTGTT
1 ATGAATGTGAATGCATGTGAATTAACAAAATAAATGATAAACATGTTGTT
13665809 ATGAATGTGAATGCA
1 ATGAATGTGAATGCA
13665824 AAACTAATAT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 112 1.00
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (50 bp):
ATGAATGTGAATGCATGTGAATTAACAAAATAAATGATAAACATGTTGTT
Found at i:13668493 original size:6 final size:6
Alignment explanation
Indices: 13668482--13668526 Score: 56
Period size: 7 Copynumber: 7.2 Consensus size: 6
13668472 GATGTAGGAG
13668482 TCTTTT TC-TTT TCTTTT TCTTTTT TCTTATT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TC-TTTT TCTT-TT TCTTTT TCT-TTT T
13668527 TGTTGCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.14
6 14 0.40
7 16 0.46
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:13673817 original size:19 final size:17
Alignment explanation
Indices: 13673795--13673851 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
13673785 AAATTTTGGC
13673795 TTTTTTGGCTCTTTTTTT
1 TTTTTTGGC-CTTTTTTT
*
13673813 GTTTTTTTGCC--TTTTT
1 -TTTTTTGGCCTTTTTTT
13673829 TTTTTT-GCCTTTTTTGT
1 TTTTTTGGCCTTTTTT-T
13673846 TTTTTT
1 TTTTTT
13673852 TTGTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 3 0.09
15 6 0.18
16 9 0.26
17 7 0.21
18 1 0.03
19 8 0.24
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (17 bp):
TTTTTTGGCCTTTTTTT
Found at i:13673831 original size:14 final size:14
Alignment explanation
Indices: 13673809--13673849 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
13673799 TTGGCTCTTT
13673809 TTTTGTTTTTTTGCC
1 TTTT-TTTTTTTGCC
13673824 TTTTTTTTTTTGCC
1 TTTTTTTTTTTGCC
13673838 TTTTTTGTTTTT
1 TTTTTT-TTTTT
13673850 TTTTGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTTTGCC
Found at i:13673841 original size:23 final size:20
Alignment explanation
Indices: 13673806--13673853 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
13673796 TTTTTGGCTC
*
13673806 TTTTTTTGTTTTTTTGCCTTTT
1 TTTTTTTGCTTTTTTG--TTTT
13673828 TTTTTTTGCCTTTTTTGTTTT
1 TTTTTTTG-CTTTTTTGTTTT
13673849 TTTTT
1 TTTTT
13673854 GTTTTTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 8 0.33
23 7 0.29
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (20 bp):
TTTTTTTGCTTTTTTGTTTT
Found at i:13680077 original size:30 final size:31
Alignment explanation
Indices: 13680041--13680100 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
13680031 CTTAGCTTTA
13680041 TATTATGTTTACATATGT-TTTAGAT-TCATT
1 TATTATGTTTACATAT-TATTTAGATATCATT
*
13680071 TATTATGTTTGCATATTATTTAGATATCAT
1 TATTATGTTTACATATTATTTAGATATCAT
13680101 GGCAGCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
30 22 0.81
31 4 0.15
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATTATTTAGATATCATT
Found at i:13681041 original size:19 final size:20
Alignment explanation
Indices: 13681017--13681059 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
13681007 AGCATTTATC
*
13681017 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
13681036 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
13681056 TTCA
1 TTCA
13681060 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:13681713 original size:21 final size:20
Alignment explanation
Indices: 13681668--13681713 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
13681658 CTTACATCAT
* *
13681668 ATTTTCATTAAAGTCTTGTT
1 ATTTTCATTAAAGTCATGTC
*
13681688 TTTTTCATTAAAAGTCATGTC
1 ATTTTCATT-AAAGTCATGTC
13681709 ATTTT
1 ATTTT
13681714 AGGAAGGTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (20 bp):
ATTTTCATTAAAGTCATGTC
Found at i:13685224 original size:21 final size:21
Alignment explanation
Indices: 13685198--13685250 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
13685188 AAGGAAGATT
*
13685198 AAATGAAATGATAAATATAAG
1 AAATGAAATGATAAAGATAAG
13685219 AAATGAAATGATAAAGATAAG
1 AAATGAAATGATAAAGATAAG
13685240 AAATGAAATGA
1 AAATGAAATGA
13685251 AATAAGGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (21 bp):
AAATGAAATGATAAAGATAAG
Found at i:13685309 original size:22 final size:21
Alignment explanation
Indices: 13685283--13685323 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
13685273 TTGCGGAAAT
13685283 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
13685305 TGATGGTTTTGATGATGAA
1 TGATGGTCTTGATGATGAA
13685324 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.34, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:13689769 original size:33 final size:33
Alignment explanation
Indices: 13689725--13689793 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
13689715 CATCACCATA
*
13689725 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
13689758 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
13689791 TTC
1 TTC
13689794 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:13695442 original size:33 final size:33
Alignment explanation
Indices: 13695398--13695466 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
13695388 CATCACCATA
*
13695398 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
13695431 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
13695464 TTC
1 TTC
13695467 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:13701097 original size:33 final size:33
Alignment explanation
Indices: 13701053--13701121 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
13701043 CATCACCATA
*
13701053 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
13701086 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
13701119 TTC
1 TTC
13701122 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:13702692 original size:20 final size:22
Alignment explanation
Indices: 13702663--13702702 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
13702653 GGGAGAGCTT
13702663 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
13702683 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
13702703 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:13706403 original size:20 final size:22
Alignment explanation
Indices: 13706374--13706413 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
13706364 GGGAGAGCTT
13706374 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
13706394 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
13706414 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:13711897 original size:11 final size:10
Alignment explanation
Indices: 13711868--13711896 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
13711858 TTTTCACCTC
13711868 TTTTTTTTTG
1 TTTTTTTTTG
13711878 TTTTTTTTTG
1 TTTTTTTTTG
13711888 TTTTTTTTT
1 TTTTTTTTT
13711897 TTAAAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:13716396 original size:13 final size:12
Alignment explanation
Indices: 13716378--13716438 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 12
13716368 GTGCAAAAAG
13716378 AAAGAAAAGACAA
1 AAAGAAAAGA-AA
*
13716391 AAAGAAGAGAAAAA
1 AAAGAA-A-AGAAA
13716405 AATCAGAAAAGAAGA
1 AA--AGAAAAGAA-A
13716420 AAAGAAAAGAAA
1 AAAGAAAAGAAA
13716432 AAGAGAA
1 AA-AGAA
13716439 GTTCAAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
12 3 0.08
13 19 0.47
14 8 0.20
15 6 0.15
16 4 0.10
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:13717901 original size:13 final size:11
Alignment explanation
Indices: 13717860--13717944 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
13717850 ACAATTTGTC
13717860 CATCACCATTAT
1 CATCACCA-TAT
*
13717872 CA-CGCCTATAT
1 CATCACC-ATAT
13717883 CATCACCATAGT
1 CATCACCATA-T
13717895 CCATCACCATTAT
1 -CATCACCA-TAT
*
13717908 CA-CGCCTATAT
1 CATCACC-ATAT
13717919 CATCACCATATT
1 CATCACCATA-T
13717931 CCATCACCATAT
1 -CATCACCATAT
13717943 CA
1 CA
13717945 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:13717904 original size:36 final size:36
Alignment explanation
Indices: 13717857--13717961 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
13717847 GATACAATTT
13717857 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
13717893 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
13717929 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
13717962 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:13733447 original size:36 final size:36
Alignment explanation
Indices: 13733407--13733583 Score: 291
Period size: 36 Copynumber: 4.9 Consensus size: 36
13733397 AATACCATCT
13733407 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
13733443 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * *
13733479 TCCATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * *
13733515 TCCATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
*
13733551 TCCATCTCCATTATCACGCCTATATTATCACCA
1 TCCATCTCCATTATCACGCCTATATCATCACCA
13733584 ACTTATAAAT
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 134 1.00
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.32
Consensus pattern (36 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAG
Found at i:13733996 original size:24 final size:24
Alignment explanation
Indices: 13733956--13734002 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
13733946 AAAGTGCTAC
13733956 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
13733981 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
13734003 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:13739807 original size:20 final size:22
Alignment explanation
Indices: 13739778--13739817 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
13739768 GGGAGAGCTT
13739778 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
13739798 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
13739818 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:13741072 original size:36 final size:36
Alignment explanation
Indices: 13741032--13741208 Score: 291
Period size: 36 Copynumber: 4.9 Consensus size: 36
13741022 AATACCATCT
13741032 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
13741068 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * *
13741104 TCCATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * *
13741140 TCCATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
*
13741176 TCCATCTCCATTATCACGCCTATATTATCACCA
1 TCCATCTCCATTATCACGCCTATATCATCACCA
13741209 ACTTATAAAT
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 134 1.00
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.32
Consensus pattern (36 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAG
Found at i:13742566 original size:90 final size:91
Alignment explanation
Indices: 13742436--13742617 Score: 269
Period size: 90 Copynumber: 2.0 Consensus size: 91
13742426 CCTAGAACAC
* *
13742436 CCATGTGCCTTGCATATGACCAGACCCCATGTGTCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGACCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
13742501 AAGAG-TTCTCTCCCTATTCGGCCAAG
66 AAGAGATT-TCTCCCTATTCGGCCAAG
** * * * *
13742527 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGACCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
13742591 AAGAGATTTCTCCCTATTCGGCCAAG
66 AAGAGATTTCTCCCTATTCGGCCAAG
13742617 C
1 C
13742618 ATCATTTCCC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 61 0.74
91 21 0.26
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGACCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGATTTCTCCCTATTCGGCCAAG
Found at i:13752230 original size:17 final size:17
Alignment explanation
Indices: 13752208--13752251 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
13752198 ACTTTTGCAC
13752208 TTCTTTTTGTATTTTTT
1 TTCTTTTTGTATTTTTT
13752225 TTCTTTTTGTATTTTTT
1 TTCTTTTTGTATTTTTT
13752242 TTCTTTTTGT
1 TTCTTTTTGT
13752252 TGTTGTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.05, C:0.07, G:0.07, T:0.82
Consensus pattern (17 bp):
TTCTTTTTGTATTTTTT
Found at i:13772318 original size:82 final size:79
Alignment explanation
Indices: 13772151--13772318 Score: 174
Period size: 79 Copynumber: 2.1 Consensus size: 79
13772141 ATCATCATGT
* * *
13772151 AGCACGTCATGCACTCATATTAAACAAAACATCATGTTTATCCTTTATTTTAATTAACTCATGTG
1 AGCACGTCATGCACTCATATTAAACAAAACAACATGTTTATCATTTATTATAATTAACTCATGTG
* * *
13772216 TATTCCCATTGTTA
66 CATTCACATTGATA
* * * * ** * *
13772230 AACACGTCTTGCACTCTTATTCAACATGACAACATGTTTTTCATTTAATTATAATTACCATTCAT
1 AGCACGTCATGCACTCATATTAAACAAAACAACATGTTTATCATTT-ATTATAATTA--ACTCAT
*
13772295 GTGCATTCATATTGATA
63 GTGCATTCACATTGATA
13772312 AGCACGT
1 AGCACGT
13772319 TTTTTGCATT
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
79 37 0.53
80 9 0.13
82 24 0.34
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (79 bp):
AGCACGTCATGCACTCATATTAAACAAAACAACATGTTTATCATTTATTATAATTAACTCATGTG
CATTCACATTGATA
Done.