Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 43
Found at i:944963 original size:57 final size:57
Alignment explanation
Indices: 944789--944964 Score: 170
Period size: 57 Copynumber: 3.1 Consensus size: 57
944779 AAATGATTTA
944789 ATAATGATTTAAATA-TTAATGATTTGATGATTTAGT-ATGATTTGATAATAATCATTAT
1 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGA-TTGATAATAATCA-T-T
* * * *
944847 AGTAATGATTTGATAAAATCATTTAAT-A----ATGATTTAGTAAT-AATCATTATAAATGATT
1 A-TAATGA-TT--T-AAAT-ATTTAATGATTTGATGATTTAGTAATGATTGATAAT-AATCATT
944905 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTGATAATAATCATT
1 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTGATAATAATCATT
944962 ATA
1 ATA
944965 GTAATGATTT
Statistics
Matches: 95, Mismatches: 8, Indels: 31
0.71 0.06 0.23
Matches are distributed among these distances:
52 7 0.07
53 5 0.05
54 1 0.01
56 2 0.02
57 28 0.29
58 9 0.09
59 12 0.13
60 17 0.18
61 2 0.02
62 1 0.01
63 4 0.04
64 2 0.02
65 5 0.05
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (57 bp):
ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTGATAATAATCATT
Found at i:944995 original size:143 final size:144
Alignment explanation
Indices: 944821--945170 Score: 501
Period size: 143 Copynumber: 2.5 Consensus size: 144
944811 TTTGATGATT
944821 TAGT-ATGATTTGATAATAATCATTATAGTAATGATTTGATAA-AATCATT-TAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGA-TTA
* *
944883 GTAATAATCAT-TATAAATGA-TT-ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAAT
65 GTAATAATCATATAAAAATGATTTAATAATGATTTAAATA-TTAATAATTTGATGATTTAGTAAT
944945 GA-TTGATAATAATCATTA
129 GATTTGATAAT-A--ATTA
*
944963 TAGTAATGATTTGATAATAATCATTATAGTAAT-AATTGATAATAATCATTATAATAATGATTAG
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTAG
945027 TAATAATCATATAAAAATGATTTAATAATGATTTAAATATTAATAATTTGATGATTTAGTAATGA
66 TAATAATCATATAAAAATGATTTAATAATGATTTAAATATTAATAATTTGATGATTTAGTAATGA
945092 TTTGATAATAATTA
131 TTTGATAATAATTA
* *
945106 TAGTAATGATTTG---ATAATCATTATAATAATGATTT-AGTAATAATC-TTATAAAAATGATTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATTA
*
945166 ATAAT
65 GTAAT
945171 GATTTAAATA
Statistics
Matches: 192, Mismatches: 7, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
140 35 0.18
141 11 0.06
142 12 0.06
143 66 0.34
144 17 0.09
145 28 0.15
146 23 0.12
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.43
Consensus pattern (144 bp):
TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTAG
TAATAATCATATAAAAATGATTTAATAATGATTTAAATATTAATAATTTGATGATTTAGTAATGA
TTTGATAATAATTA
Found at i:945132 original size:20 final size:23
Alignment explanation
Indices: 944821--945341 Score: 130
Period size: 25 Copynumber: 22.0 Consensus size: 23
944811 TTTGATGATT
944821 TAGT-ATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAAT-A--ATTA
*
944846 TAGTAATGATTTGATAA-AATCATT
1 TAGTAATGATTTGATAATAAT--TA
* *
944870 TAATAATGATTT-AGTAATAATCA
1 TAGTAATGATTTGA-TAATAATTA
*
944893 TTA-TAAATGA-TT-ATAATGATTTAAA
1 -TAGT-AATGATTTGATAAT-AATT--A
* *
944918 TATTTAATGATTTG---ATGATT-
1 TA-GTAATGATTTGATAATAATTA
944938 TAGTAATGA-TTGATAATAATCATTA
1 TAGTAATGATTTGATAAT-A--ATTA
944963 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAAT-A--ATTA
*
944989 TAGTAAT-AATTGATAATAATCATTA
1 TAGTAATGATTTGATAAT-A--ATTA
* *
945014 TAATAATGATTAG-TAATAATCATA
1 TAGTAATGATTTGATAATAAT--TA
** * *
945038 TAAAAATGATTTAATAATGATTTAAA
1 TAGTAATGATTTGATAAT-AATT--A
* * *
945064 TATTAATAATTTG---ATGATT-
1 TAGTAATGATTTGATAATAATTA
945083 TAGTAATGATTTGATAATAATTA
1 TAGTAATGATTTGATAATAATTA
*
945106 TAGTAATGATTTGATAATCATTA
1 TAGTAATGATTTGATAATAATTA
*
945129 TAATAATGATTT-AGTAATAATCTTA
1 TAGTAATGATTTGA-TAATAA--TTA
** * *
945154 TAAAAATGA-TTAATAATGATT-
1 TAGTAATGATTTGATAATAATTA
* *
945175 TA--AAT-ATTTAATGATTGATGATT-
1 TAGTAATGA-TT--TGA-TAATAATTA
945198 TAGT-ATGATTTGATAATATCATTA
1 TAGTAATGATTTGATAATA--ATTA
* *
945222 TAATAATGATTTAGTAATAATCATTA
1 TAGTAATGATTT-G--ATAATAATTA
** * *
945248 TAAAAATGATTTAATAATGATTTAAA
1 TAGTAATGATTTGATAAT-AATT--A
* *
945274 TATTTAATGATTTG---ATGATT-
1 TA-GTAATGATTTGATAATAATTA
*
945294 TAGTAATGATTTGATAATAATCA
1 TAGTAATGATTTGATAATAATTA
*
945317 TTAAATAATGATTT-ATAATAATTA
1 -T-AGTAATGATTTGATAATAATTA
945341 T
1 T
945342 TTAGTTATTA
Statistics
Matches: 382, Mismatches: 52, Indels: 126
0.68 0.09 0.22
Matches are distributed among these distances:
18 4 0.01
19 30 0.08
20 5 0.01
21 7 0.02
22 27 0.07
23 69 0.18
24 72 0.19
25 83 0.22
26 72 0.19
27 8 0.02
28 5 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.43
Consensus pattern (23 bp):
TAGTAATGATTTGATAATAATTA
Found at i:945156 original size:116 final size:116
Alignment explanation
Indices: 944963--945265 Score: 425
Period size: 115 Copynumber: 2.6 Consensus size: 116
944953 ATAATCATTA
* *
944963 TAGTAATGATTTGATAATAATCATTATAGTAATAATTGATAATAATCATTATAATAATGA-TTAG
1 TAGTAATGATTTGATAAT-A-CATTATAGTAATGATT--TGATAATCATTATAATAATGATTTAG
945027 TAATAATCATATAAAAATGATTTAATAATGATTTAAATA-TTAATAATTTGATGATT
62 TAATAATCATATAAAAATGA-TTAATAATGATTTAAATATTTAATAA-TTGATGATT
945083 TAGTAATGATTTGATAATA-ATTATAGTAATGATTTGATAATCATTATAATAATGATTTAGTAAT
1 TAGTAATGATTTGATAATACATTATAGTAATGATTTGATAATCATTATAATAATGATTTAGTAAT
* *
945147 AATCTTATAAAAATGATTAATAATGATTTAAATATTTAATGATTGATGATT
66 AATCATATAAAAATGATTAATAATGATTTAAATATTTAATAATTGATGATT
* * *
945198 TAGT-ATGATTTGATAATATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTAA
1 TAGTAATGATTTGATAATA-CATTATAGTAATGATTT-G--ATAATCATTATAATAATGATTTAG
945262 TAAT
62 TAAT
945266 GATTTAAATA
Statistics
Matches: 169, Mismatches: 7, Indels: 15
0.88 0.04 0.08
Matches are distributed among these distances:
114 14 0.08
115 51 0.30
116 44 0.26
117 15 0.09
119 27 0.16
120 18 0.11
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (116 bp):
TAGTAATGATTTGATAATACATTATAGTAATGATTTGATAATCATTATAATAATGATTTAGTAAT
AATCATATAAAAATGATTAATAATGATTTAAATATTTAATAATTGATGATT
Found at i:945239 original size:14 final size:13
Alignment explanation
Indices: 945202--945344 Score: 75
Period size: 13 Copynumber: 10.6 Consensus size: 13
945192 ATGATTTAGT
945202 ATGATTTGATAAT-
1 ATGATTT-ATAATA
*
945215 ATCA-TTATAATA
1 ATGATTTATAATA
945227 ATGATTTAGTAATA
1 ATGATTTA-TAATA
* *
945241 ATCA-TTATAAAA
1 ATGATTTATAATA
945253 ATGA-TT-TAATA
1 ATGATTTATAATA
*
945264 ATGATTTAAATATTTA
1 ATGATTT--ATA-ATA
945280 ATGATTTGATGATTTAGTA
1 ATGATTT-AT-A---A-TA
945299 ATGATTTGATAATA
1 ATGATTT-ATAATA
*
945313 ATCA-TTA-AATA
1 ATGATTTATAATA
945324 ATGATTTATAATA
1 ATGATTTATAATA
*
945337 ATTATTTA
1 ATGATTTA
945345 GTTATTATTT
Statistics
Matches: 104, Mismatches: 12, Indels: 28
0.72 0.08 0.19
Matches are distributed among these distances:
11 20 0.19
12 20 0.19
13 22 0.21
14 13 0.12
15 5 0.05
16 10 0.10
18 2 0.02
19 12 0.12
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (13 bp):
ATGATTTATAATA
Found at i:945375 original size:211 final size:208
Alignment explanation
Indices: 944998--945379 Score: 592
Period size: 211 Copynumber: 1.8 Consensus size: 208
944988 ATAGTAATAA
944998 TTGATAATAATCATTATAATAATGATTAGTAATAATCATATAAAAATGATTTAATAATGATTTAA
1 TTGATAATAATCATTATAATAATGATTAGTAATAATCATATAAAAATGATTTAATAATGATTTAA
* * *
945063 ATATTAATAATTTGATGATTTAGTAATGATTTGATAATAATTATAGTAATGATTTGATAATCATT
66 ATATTAATAATTTGATGATTTAGTAATGATTTGATAATAATCATAATAATGATTTGATAATAATT
945128 ATAATAATGATTTAGTAATAATCTTATAAAAATGATTAATAATGATTTAAATATTTAATGATTGA
131 ATAATAATGATTTAGTAAT-ATCTTATAAAAATGATTAATAATGATTTAAATATTTAATGATTGA
945193 TGATTTAGTATGAT
195 TGATTTAGTATGAT
945207 TTGATAAT-ATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTT
1 TTGATAATAATCATTATAATAATGA-TTAGTAATAATCA-TATAAAAATGATTTAATAATGATTT
*
945271 AAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTAAATAATGATTT-ATAA
64 AAATA-TTAATAATTTGATGATTTAGTAATGATTTGATAATAATCA-T-AATAATGATTTGATAA
* * * *
945335 TAATTATTTAGTTATTATTTAGTAAT-T-TTATAATAATGATTAATA
126 TAATTA--TAATAATGATTTAGTAATATCTTATAAAAATGATTAATA
945380 CTAATGATTT
Statistics
Matches: 158, Mismatches: 8, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
208 16 0.10
209 21 0.13
210 30 0.19
211 55 0.35
212 11 0.07
213 10 0.06
214 15 0.09
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (208 bp):
TTGATAATAATCATTATAATAATGATTAGTAATAATCATATAAAAATGATTTAATAATGATTTAA
ATATTAATAATTTGATGATTTAGTAATGATTTGATAATAATCATAATAATGATTTGATAATAATT
ATAATAATGATTTAGTAATATCTTATAAAAATGATTAATAATGATTTAAATATTTAATGATTGAT
GATTTAGTATGAT
Found at i:945390 original size:46 final size:47
Alignment explanation
Indices: 945320--945408 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 47
945310 ATAATCATTA
* * * * *
945320 AATAATGATTTATAATAATTATTTAGTTATTATT-TAGTAATTTTAT
1 AATAATGATTAATAATAATGATTTAATAATTATTCTACTAATTTTAT
*
945366 AATAATGATTAATACTAATGATTTAATAATTATTCTACTAATT
1 AATAATGATTAATAATAATGATTTAATAATTATTCTACTAATT
945409 ATAGAATACT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 29 0.81
47 7 0.19
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (47 bp):
AATAATGATTAATAATAATGATTTAATAATTATTCTACTAATTTTAT
Found at i:947831 original size:32 final size:32
Alignment explanation
Indices: 947752--947833 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
947742 ACTAAACCCT
* *
947752 TAAAC-AACTAATAAAATTTTTTTTATATAAC
1 TAAACTAACTAATAAACTTTTTTTCATATAAC
947783 TAAACTAACTAATAAACTATTTTTTCATTATAA-
1 TAAACTAACTAATAAACT-TTTTTTCA-TATAAC
*
947816 TATACT-ACTAATAAACTT
1 TAAACTAACTAATAAACTT
947834 ACTAACTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 6 0.13
32 22 0.49
33 12 0.27
34 5 0.11
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (32 bp):
TAAACTAACTAATAAACTTTTTTTCATATAAC
Found at i:948424 original size:29 final size:29
Alignment explanation
Indices: 948381--948501 Score: 201
Period size: 29 Copynumber: 4.2 Consensus size: 29
948371 CTCGTGAGGA
*
948381 GCGACCT--AAGGTCGCTGGGACTACATG
1 GCGACCTACAAGGTCGCCGGGACTACATG
948408 GCGACCTACAAGGTCGCCGGGACTACATG
1 GCGACCTACAAGGTCGCCGGGACTACATG
948437 GCGACCTACAAGGTCGCCGGGACTACATG
1 GCGACCTACAAGGTCGCCGGGACTACATG
**
948466 GCGACCTACAAGGTCGCCCAGACTACATG
1 GCGACCTACAAGGTCGCCGGGACTACATG
948495 GCGACCT
1 GCGACCT
948502 CTCGATTGGC
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
27 7 0.08
29 82 0.92
ACGTcount: A:0.24, C:0.31, G:0.30, T:0.15
Consensus pattern (29 bp):
GCGACCTACAAGGTCGCCGGGACTACATG
Found at i:948664 original size:29 final size:29
Alignment explanation
Indices: 948622--948681 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
948612 ACCCCGTATG
948622 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
*
948651 TCGCCTGGATTGCATGGCGTCCTACGAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
948680 TC
1 TC
948682 ACTGTAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCGTCCTACAAGA
Found at i:957249 original size:35 final size:35
Alignment explanation
Indices: 957176--957250 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
957166 CGTCACTAAC
**
957176 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
* *
957211 AGTAAGGCCCTGAGCACACAGCCGATGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
957246 AGTAA
1 AGTAA
957251 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:957388 original size:23 final size:23
Alignment explanation
Indices: 957328--957402 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
957318 CATAATTCAA
*
957328 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
957352 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
957376 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
957399 GTCA
1 GTCA
957403 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:957408 original size:23 final size:23
Alignment explanation
Indices: 957332--957417 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
957322 ATTCAAGTCA
*
957332 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
957355 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
957379 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* * *
957402 AGGATCATAACAGAAT
1 AGTATCAGATCAGAAT
957418 TCAAGTCGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 33 0.61
24 21 0.39
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:957435 original size:47 final size:47
Alignment explanation
Indices: 957311--957424 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
957301 TATATCAAAA
* * * * *
957311 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAGAACAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
957359 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
* *
957405 ATCATAACAGAATTCAAGTC
1 ATCAGAACAGAATCCAAGTC
957425 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 17 0.31
47 21 0.38
48 17 0.31
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:958583 original size:18 final size:18
Alignment explanation
Indices: 958562--958597 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
958552 CTTCCATCCG
*
958562 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
958580 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
958598 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:959896 original size:7 final size:7
Alignment explanation
Indices: 959884--959914 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
959874 GGTCAACGAG
959884 GGTCAAC
1 GGTCAAC
959891 GGTCAAC
1 GGTCAAC
959898 GGGTCAAC
1 -GGTCAAC
959906 GGTCAAC
1 GGTCAAC
959913 GG
1 GG
959915 GTCGGTCGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:959903 original size:15 final size:15
Alignment explanation
Indices: 959883--959917 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
959873 TGGTCAACGA
959883 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
959898 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
959913 GGGTC
1 GGGTC
959918 GGTCGGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:959904 original size:8 final size:8
Alignment explanation
Indices: 959883--959934 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
959873 TGGTCAACGA
959883 GGGTCAAC
1 GGGTCAAC
959891 -GGTCAAC
1 GGGTCAAC
959898 GGGTCAAC
1 GGGTCAAC
959906 -GGTCAAC
1 GGGTCAAC
**
959913 GGGTCGGTC
1 GGGTC-AAC
959922 GGGTCAAC
1 GGGTCAAC
959930 GGGTC
1 GGGTC
959935 GGTCGGGTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 14 0.38
8 17 0.46
9 6 0.16
ACGTcount: A:0.19, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGGTCAAC
Found at i:959928 original size:17 final size:17
Alignment explanation
Indices: 959906--959942 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
959896 ACGGGTCAAC
959906 GGTCAACGGGTCGGTCG
1 GGTCAACGGGTCGGTCG
959923 GGTCAACGGGTCGGTCG
1 GGTCAACGGGTCGGTCG
959940 GGT
1 GGT
959943 TGTGACCGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.19
Consensus pattern (17 bp):
GGTCAACGGGTCGGTCG
Found at i:962041 original size:35 final size:35
Alignment explanation
Indices: 961968--962042 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
961958 CGTCACTAAC
**
961968 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
* *
962003 AGTAAGGCCCTGAGCACACAGCCGATGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
962038 AGTAA
1 AGTAA
962043 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:962148 original size:24 final size:24
Alignment explanation
Indices: 962121--962195 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
962111 CATAATTCAA
*
962121 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
962145 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
962169 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
962192 GTCA
1 GTCA
962196 TGATCATAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:962191 original size:47 final size:46
Alignment explanation
Indices: 962104--962228 Score: 142
Period size: 47 Copynumber: 2.7 Consensus size: 46
962094 TATATCAAAA
* * * *
962104 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATG
1 ATCAGAACAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATG
* *
962151 TATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCATG
1 -ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATG
* * *
962198 ATCATAACAGAATTCAAGTCAGAAATCAGAT
1 ATCAGAACAGAATCCAAGTCA-ATATCAGAT
962229 AAAATATTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 17 0.26
47 31 0.48
48 17 0.26
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (46 bp):
ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATG
Found at i:962218 original size:23 final size:24
Alignment explanation
Indices: 962118--962218 Score: 107
Period size: 23 Copynumber: 4.3 Consensus size: 24
962108 AAACATAATT
* *
962118 CAAGTCAAGTATCATATCAGAATC
1 CAAGTCATGTATCAGATCAGAATC
*
962142 CAGGTCATGTATCAGATCAGAATC
1 CAAGTCATGTATCAGATCAGAATC
* *
962166 CATGTCA-ATATCAGATCAGAATC
1 CAAGTCATGTATCAGATCAGAATC
* * * *
962189 CAGGTCATG-ATCATAACAGAATT
1 CAAGTCATGTATCAGATCAGAATC
962212 CAAGTCA
1 CAAGTCA
962219 GAAATCAGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
23 38 0.58
24 27 0.42
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (24 bp):
CAAGTCATGTATCAGATCAGAATC
Found at i:963376 original size:18 final size:18
Alignment explanation
Indices: 963355--963390 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
963345 CTTCCATCCG
*
963355 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
963373 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
963391 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:964690 original size:8 final size:8
Alignment explanation
Indices: 964667--964748 Score: 73
Period size: 8 Copynumber: 10.4 Consensus size: 8
964657 TCAAAGTTTT
964667 GGTCAACAG
1 GGTCAAC-G
964676 TGGTCAACG
1 -GGTCAACG
964685 GGTCAAC-
1 GGTCAACG
964692 GGTCAACG
1 GGTCAACG
*
964700 GGTCAACA
1 GGTCAACG
964708 GGTCAACG
1 GGTCAACG
** *
964716 GGTCGGTCA
1 GGTC-AACG
964725 GGTCAACG
1 GGTCAACG
964733 GGT---CG
1 GGTCAACG
964738 GGTCAACG
1 GGTCAACG
964746 GGT
1 GGT
964749 AGGGTCGGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 5 0.08
7 7 0.12
8 34 0.58
9 6 0.10
10 7 0.12
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:964697 original size:15 final size:16
Alignment explanation
Indices: 964667--964736 Score: 88
Period size: 15 Copynumber: 4.2 Consensus size: 16
964657 TCAAAGTTTT
964667 GGTCAACAGTGGTCAACG
1 GGTCAACA--GGTCAACG
964685 GGTCAAC-GGTCAACG
1 GGTCAACAGGTCAACG
964700 GGTCAACAGGTCAACG
1 GGTCAACAGGTCAACG
**
964716 GGTCGGTCAGGTCAACG
1 GGTC-AACAGGTCAACG
964733 GGTC
1 GGTC
964737 GGGTCAACGG
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
15 15 0.31
16 12 0.25
17 14 0.29
18 7 0.15
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (16 bp):
GGTCAACAGGTCAACG
Found at i:964706 original size:23 final size:25
Alignment explanation
Indices: 964667--964716 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
964657 TCAAAGTTTT
*
964667 GGTCAACAGTGGTCAACGGGTCAAC
1 GGTCAACAGTGGTCAACAGGTCAAC
964692 GGTCAAC-G-GGTCAACAGGTCAAC
1 GGTCAACAGTGGTCAACAGGTCAAC
964715 GG
1 GG
964717 GTCGGTCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.67
24 1 0.04
25 7 0.29
ACGTcount: A:0.28, C:0.24, G:0.34, T:0.14
Consensus pattern (25 bp):
GGTCAACAGTGGTCAACAGGTCAAC
Found at i:964728 original size:17 final size:17
Alignment explanation
Indices: 964677--964738 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
964667 GGTCAACAGT
*
964677 GGTCAACGGGTC-AAC-
1 GGTCAACGGGTCGGACA
*
964692 GGTCAACGGGTC-AACA
1 GGTCAACGGGTCGGACA
*
964708 GGTCAACGGGTCGGTCA
1 GGTCAACGGGTCGGACA
964725 GGTCAACGGGTCGG
1 GGTCAACGGGTCGG
964739 GTCAACGGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
15 15 0.35
16 12 0.28
17 16 0.37
ACGTcount: A:0.23, C:0.24, G:0.39, T:0.15
Consensus pattern (17 bp):
GGTCAACGGGTCGGACA
Found at i:964741 original size:13 final size:13
Alignment explanation
Indices: 964720--964754 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
964710 TCAACGGGTC
*
964720 GGTCAGGTCAACG
1 GGTCGGGTCAACG
964733 GGTCGGGTCAACG
1 GGTCGGGTCAACG
*
964746 GGTAGGGTC
1 GGTCGGGTC
964755 GGGTTGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.17
Consensus pattern (13 bp):
GGTCGGGTCAACG
Found at i:971140 original size:17 final size:17
Alignment explanation
Indices: 971113--971149 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
971103 ATATAATTTA
971113 ATTTGAATTTATTTATGT
1 ATTTGAATTTATTTAT-T
971131 ATTT-AATTTATTTATT
1 ATTTGAATTTATTTATT
971147 ATT
1 ATT
971150 AATAAAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 11 0.58
18 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
ATTTGAATTTATTTATT
Found at i:978771 original size:29 final size:29
Alignment explanation
Indices: 978723--978783 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
978713 GAGCTATATG
978723 AGAATAAGTAATATTCTTACATGATCACA
1 AGAATAAGTAATATTCTTACATGATCACA
* *
978752 AGAATAAGTAATGTTTTTACATGATCACA
1 AGAATAAGTAATATTCTTACATGATCACA
978781 AGA
1 AGA
978784 TATGCGACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (29 bp):
AGAATAAGTAATATTCTTACATGATCACA
Found at i:984378 original size:18 final size:18
Alignment explanation
Indices: 984355--984389 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
984345 AGACATATGG
*
984355 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCATTCGGGAC
984373 ATAGTGGTCATTCGGGA
1 ATAGTGGTCATTCGGGA
984390 AAAATTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
ATAGTGGTCATTCGGGAC
Found at i:984898 original size:13 final size:13
Alignment explanation
Indices: 984882--984907 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
984872 GAGAATAGAC
984882 GCTAAGAAGAGCA
1 GCTAAGAAGAGCA
984895 GCTAAGAAGAGCA
1 GCTAAGAAGAGCA
984908 AGACAGGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.31, T:0.08
Consensus pattern (13 bp):
GCTAAGAAGAGCA
Found at i:996125 original size:29 final size:29
Alignment explanation
Indices: 996061--996125 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
996051 TACATAGATG
*
996061 AATTGATAAAGTTTAGACACTTATTTGAA
1 AATTAATAAAGTTTAGACACTTATTTGAA
* * * * *
996090 AACTAATATAGTTTGGACACTTATTTTAT
1 AATTAATAAAGTTTAGACACTTATTTGAA
996119 AATTAAT
1 AATTAAT
996126 CTTTTTTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.42
Consensus pattern (29 bp):
AATTAATAAAGTTTAGACACTTATTTGAA
Found at i:998080 original size:21 final size:21
Alignment explanation
Indices: 998021--998066 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
998011 ATAACAATAT
*
998021 ATAAACATATAAATTAAAATAAA
1 ATAAACA-ATGAA-TAAAATAAA
*
998044 ATAAACAATGACTAAAATAAA
1 ATAAACAATGAATAAAATAAA
998065 AT
1 AT
998067 TAAAAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 3 0.14
23 7 0.33
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
ATAAACAATGAATAAAATAAA
Found at i:999553 original size:3 final size:3
Alignment explanation
Indices: 999547--999591 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
999537 AATTTTTTAT
* *
999547 TAA TAA TAA TAA TAA TTA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
999592 ATCAAATGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1000481 original size:113 final size:113
Alignment explanation
Indices: 1000157--1000484 Score: 466
Period size: 113 Copynumber: 2.9 Consensus size: 113
1000147 AGAGTCATGC
*
1000157 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * ** *
1000221 ATGAACTTTCTCTGGAAA-AGTTGATGCATCGAGTGATGAATTCGAGCA
66 ATGAACTCTATCTGGAAATA-TTGATCCATCGAGTGATGAATTAAAGAA
*
1000269 AAAGGCTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** *
1000334 ATGAACTCTACCT-GACAATGCTAATCCATCGAGTGATGAATTAAAGAA
66 ATGAACTCTATCTGGA-AATATTGATCCATCGAGTGATGAATTAAAGAA
* *
1000382 AAAGGTTAAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCCTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1000447 ATGAACTCT-TCTGGAAATATTGATCCATTTGAGTGATG
66 ATGAACTCTATCTGGAAATATTGATCCA-TCGAGTGATG
1000485 GATCCAAATC
Statistics
Matches: 191, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
112 52 0.27
113 139 0.73
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTATCTGGAAATATTGATCCATCGAGTGATGAATTAAAGAA
Found at i:1000881 original size:22 final size:22
Alignment explanation
Indices: 1000847--1000927 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 22
1000837 AAATCCAATA
* *
1000847 AATCTTTCCTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
*
1000869 AATCTATCATCTTCG--AAGAG
1 AATCTATCATCTTTGAAAAGAG
** *
1000889 AAAATATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
*
1000911 TATCTATCATCTTTGAA
1 AATCTATCATCTTTGAA
1000928 GAATTTAGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 17 0.36
22 30 0.64
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:1000889 original size:20 final size:20
Alignment explanation
Indices: 1000864--1000929 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
1000854 CCTCTTTGAA
*
1000864 AAGAGAATCTATCATCTTCG
1 AAGAGAATCTATCATCTTTG
**
1000884 AAGAGAAAATATCATCTTTG
1 AAGAGAATCTATCATCTTTG
1000904 AAGAGAGTATCTATCATCTTTG
1 AAGAGA--ATCTATCATCTTTG
1000926 AAGA
1 AAGA
1000930 ATTTAGATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 23 0.59
22 16 0.41
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (20 bp):
AAGAGAATCTATCATCTTTG
Found at i:1000928 original size:22 final size:21
Alignment explanation
Indices: 1000856--1000929 Score: 87
Period size: 22 Copynumber: 3.5 Consensus size: 21
1000846 AAATCTTTCC
*
1000856 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAGAGAG-ATCTATCA
* **
1000878 TCTTCGAAGAGA-AAATATCA
1 TCTTTGAAGAGAGATCTATCA
1000898 TCTTTGAAGAGAGTATCTATCA
1 TCTTTGAAGAGAG-ATCTATCA
1000920 TCTTTGAAGA
1 TCTTTGAAGA
1000930 ATTTAGATGT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 17 0.40
22 26 0.60
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (21 bp):
TCTTTGAAGAGAGATCTATCA
Found at i:1004056 original size:27 final size:29
Alignment explanation
Indices: 1003999--1004056 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
1003989 AGAGGTGTAC
* *
1003999 AAAAAATCCGAATATCCGATTTTGTGCAA
1 AAAAAATCCGAATATCCGATTTTGGGAAA
1004028 AAAAAATCCGAA-A-CCGGA-TTTGGGAAA
1 AAAAAATCCGAATATCC-GATTTTGGGAAA
1004055 AA
1 AA
1004057 CCGGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 11 0.42
28 3 0.12
29 12 0.46
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.21
Consensus pattern (29 bp):
AAAAAATCCGAATATCCGATTTTGGGAAA
Found at i:1004288 original size:15 final size:17
Alignment explanation
Indices: 1004247--1004281 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1004237 TTTTACCGGA
1004247 TTAAAAACCGGTTTTTT
1 TTAAAAACCGGTTTTTT
1004264 TTAAAAACCGGTTTTTT
1 TTAAAAACCGGTTTTTT
1004281 T
1 T
1004282 CAAACCGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TTAAAAACCGGTTTTTT
Found at i:1005602 original size:15 final size:14
Alignment explanation
Indices: 1005572--1005598 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1005562 TTTTTCCTTT
1005572 TTTCCCTTTTTTTC
1 TTTCCCTTTTTTTC
1005586 TTTCCCTTTTTTT
1 TTTCCCTTTTTTT
1005599 TCTTCAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCCCTTTTTTTC
Found at i:1008363 original size:20 final size:20
Alignment explanation
Indices: 1008335--1008373 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1008325 GCAAAGATGC
* *
1008335 AAATGCAAAAATGAAAATGT
1 AAATACAAAAATAAAAATGT
*
1008355 AAATACAAACATAAAAATG
1 AAATACAAAAATAAAAATG
1008374 CAAAAATGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (20 bp):
AAATACAAAAATAAAAATGT
Found at i:1008623 original size:43 final size:44
Alignment explanation
Indices: 1008561--1008649 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 44
1008551 TGCATCAAAC
* *
1008561 AAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTCAAT
1 AAAACTTTTACATATAGGGGACAAATTTCAGTCCTAACTTCAAT
* ** *
1008605 AAAAC-TTTACATATAGGGGATAAATTTCCTTCCTAACTTCTAT
1 AAAACTTTTACATATAGGGGACAAATTTCAGTCCTAACTTCAAT
1008648 AA
1 AA
1008650 GTTAGTTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 34 0.87
44 5 0.13
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (44 bp):
AAAACTTTTACATATAGGGGACAAATTTCAGTCCTAACTTCAAT
Found at i:1009533 original size:46 final size:49
Alignment explanation
Indices: 1009466--1009556 Score: 125
Period size: 46 Copynumber: 1.9 Consensus size: 49
1009456 TATAATATAT
* * * *
1009466 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTT-GGAAAAATTAA
1 CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAATTAA
1009512 CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAA
1 CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAA
1009557 ATGAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 20 0.53
47 5 0.13
48 6 0.16
49 7 0.18
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (49 bp):
CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAATTAA
Found at i:1010042 original size:24 final size:25
Alignment explanation
Indices: 1010015--1010061 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1010005 TGAAAATAAA
1010015 ATAAAAAAATTA-AAAAATAATATT
1 ATAAAAAAATTATAAAAATAATATT
* *
1010039 ATAAAAATATTATGAAAATAATA
1 ATAAAAAAATTATAAAAATAATA
1010062 AGTATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (25 bp):
ATAAAAAAATTATAAAAATAATATT
Found at i:1010082 original size:28 final size:27
Alignment explanation
Indices: 1010026--1010084 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 27
1010016 TAAAAAAATT
1010026 AAAAAATAATATTATAAAAATATTATG
1 AAAAAATAATATTATAAAAATATTATG
1010053 AAAATAATAAGTATATATAAAAAT-TT-TG
1 AAAA-AATAA-TAT-TATAAAAATATTATG
1010081 AAAA
1 AAAA
1010085 GAAAGAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 4 0.14
28 11 0.38
29 5 0.17
30 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
AAAAAATAATATTATAAAAATATTATG
Found at i:1010732 original size:2 final size:2
Alignment explanation
Indices: 1010725--1010757 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1010715 AACAATTAAA
1010725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1010758 ATTTATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1012876 original size:23 final size:23
Alignment explanation
Indices: 1012850--1012910 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1012840 CTCATATAAA
1012850 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
1012873 TGCACC-ATAGTGCCGCGTAGAAT
1 TGCACCGA-AGTGCCACATAGAAT
*
1012896 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1012911 TATAATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:1013097 original size:103 final size:103
Alignment explanation
Indices: 1012926--1013143 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1012916 TAATGTCCAT
* *
1012926 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1012991 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1013029 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1013094 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1013132 AAGGACCACATA
1 AAGGACCACATA
1013144 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1017878 original size:23 final size:23
Alignment explanation
Indices: 1017852--1017912 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1017842 CTCATATAAA
*
1017852 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* * *
1017875 TGCACTGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
1017898 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1017913 TATAATAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:1018095 original size:99 final size:99
Alignment explanation
Indices: 1017920--1018141 Score: 347
Period size: 99 Copynumber: 2.2 Consensus size: 99
1017910 CCATATAATA
* *
1017920 ATGT-CCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCA----TTAAGAATCATATACATATACCAAGGATCAAGTATGT
1017984 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
61 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
* *
1018023 ATGTCCCAAATGACCACATATCATTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTC
1 ATGTCCCAAAGGACCACATATCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTC
1018088 ACCAGACTTCACACATGTTCCAAAGAATACATAT
66 ACCAGACTTCACACATGTTCCAAAGAATACATAT
*
1018122 ATGTCCCGAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
1018142 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
99 91 0.81
103 18 0.16
104 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (99 bp):
ATGTCCCAAAGGACCACATATCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTC
ACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:1019008 original size:2 final size:2
Alignment explanation
Indices: 1019003--1019051 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1018993 TATATGTGTG
* *
1019003 TA TA TA TA TA TA TA TA TG TG 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
1019045 TA TA TA T
1 TA TA TA T
1019052 CAAAGATCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1019016 original size:20 final size:20
Alignment explanation
Indices: 1018991--1019051 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
1018981 ATATTTCATT
*
1018991 TATATATGTGTGTATATATA
1 TATATATATGTGTATATATA
1019011 TATATATATGTGTATATATA
1 TATATATATGTGTATATATA
* *
1019031 TATATATATATATATATATA
1 TATATATATGTGTATATATA
1019051 T
1 T
1019052 CAAAGATCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TATATATATGTGTATATATA
Found at i:1019019 original size:22 final size:22
Alignment explanation
Indices: 1018991--1019051 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
1018981 ATATTTCATT
*
1018991 TATATATGTGTGTATATATATA
1 TATATATGTGTATATATATATA
1019013 TATATATGTGTATATATATATA
1 TATATATGTGTATATATATATA
* *
1019035 TATATATATATATATAT
1 TATATATGTGTATATAT
1019052 CAAAGATCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (22 bp):
TATATATGTGTATATATATATA
Found at i:1020624 original size:3 final size:3
Alignment explanation
Indices: 1020618--1020675 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
1020608 AATTTTTTAT
* * *
1020618 TAA TAA TAA TAA GT-A TTA TAA TGA TAA TGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1020663 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
1020676 GAATCAAATG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 1 0.02
3 46 0.96
4 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1023658 original size:23 final size:22
Alignment explanation
Indices: 1023627--1023671 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1023617 ATATTCTTAG
*
1023627 ACTTAGCTCGATTGAAGCTCAA
1 ACTTAGCTCGATTCAAGCTCAA
*
1023649 ACTTGAGCTCGGTTCAAGCTCAA
1 ACTT-AGCTCGATTCAAGCTCAA
1023672 TCTCGAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (22 bp):
ACTTAGCTCGATTCAAGCTCAA
Found at i:1026663 original size:54 final size:53
Alignment explanation
Indices: 1026554--1026674 Score: 163
Period size: 54 Copynumber: 2.2 Consensus size: 53
1026544 TACGAAGGGA
* * *
1026554 TGTACCGATACACCCCCACTTCGAATATAATTTGGGAATCGATACACTCCTGTG
1 TGTACCGATACACCCCCACATAGAATATAATTTGGGAACCGATACAC-CCTGTG
* *
1026608 TGTACCGATACACCCCCTACATAGAATGTATTTTGGGAACCGATACA-CCTAGTG
1 TGTACCGATACACCCCC-ACATAGAATATAATTTGGGAACCGATACACCCT-GTG
1026662 TGTACCGATACAC
1 TGTACCGATACAC
1026675 TCGGTCATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
53 3 0.05
54 33 0.55
55 24 0.40
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TGTACCGATACACCCCCACATAGAATATAATTTGGGAACCGATACACCCTGTG
Found at i:1027986 original size:18 final size:18
Alignment explanation
Indices: 1027953--1028010 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
1027943 ACTTTTTTTT
1027953 TTCTTCTTCT--CA-TTC
1 TTCTTCTTCTAACACTTC
1027968 TTCTTCTTCTAACACTTC
1 TTCTTCTTCTAACACTTC
* *
1027986 TTCTTCTTCAAACACTTA
1 TTCTTCTTCTAACACTTC
1028004 TTCTTCT
1 TTCTTCT
1028011 CCTCCTCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 10 0.26
17 2 0.05
18 26 0.68
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (18 bp):
TTCTTCTTCTAACACTTC
Found at i:1041452 original size:19 final size:19
Alignment explanation
Indices: 1041420--1041457 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1041410 AATGATATAA
*
1041420 AATATTAAATTTCTTAAAT
1 AATATTAAATTTCTAAAAT
1041439 AATATATAAA-TTCTAAAAT
1 AATAT-TAAATTTCTAAAAT
1041458 TATTGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATTAAATTTCTAAAAT
Found at i:1041494 original size:13 final size:13
Alignment explanation
Indices: 1041452--1041499 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1041442 ATATAAATTC
1041452 TAAAATTATTGATT
1 TAAAATTATTGA-T
** * *
1041466 TAATTTTTTTGGT
1 TAAAATTATTGAT
1041479 TAAAATTATTGAT
1 TAAAATTATTGAT
1041492 TAAAATTA
1 TAAAATTA
1041500 AATTAAAACA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TAAAATTATTGAT
Found at i:1042860 original size:19 final size:20
Alignment explanation
Indices: 1042833--1042878 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1042823 TACAAATATA
1042833 AAAAAAAT-CAAAAAAATAC
1 AAAAAAATCCAAAAAAATAC
* * *
1042852 AAAACAATCCGAAAAATTAC
1 AAAAAAATCCAAAAAAATAC
1042872 AAAAAAA
1 AAAAAAA
1042879 AATTAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.74, C:0.13, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAAAATCCAAAAAAATAC
Found at i:1043992 original size:24 final size:24
Alignment explanation
Indices: 1043965--1044016 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1043955 CGTTCATTTA
*
1043965 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
1043989 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
1044013 CGTT
1 CGTT
1044017 TATGTTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.15, G:0.27, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:1044003 original size:14 final size:14
Alignment explanation
Indices: 1043975--1044016 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1043965 CGTTCGTGAA
1043975 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1043989 CG-T---TTATGTT
1 CGTTCGGTTATGTT
1043999 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1044013 CGTT
1 CGTT
1044017 TATGTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1044017 original size:24 final size:24
Alignment explanation
Indices: 1043975--1044023 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1043965 CGTTCGTGAA
1043975 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
1043999 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
1044023 C
1 C
1044024 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:1044033 original size:24 final size:24
Alignment explanation
Indices: 1043981--1044036 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1043971 TGAACGTTCG
* *
1043981 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
1044005 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
1044029 TTTATGTT
1 GTTATGTT
1044037 TAACCCAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:1045144 original size:16 final size:16
Alignment explanation
Indices: 1045111--1045182 Score: 96
Period size: 16 Copynumber: 4.7 Consensus size: 16
1045101 CCAACGTTTA
* *
1045111 TGTTCGTTT-TGTTTG
1 TGTTCATTTATGTTCG
1045126 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
1045142 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
1045158 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
1045174 T-TT-ATTTAT
1 TGTTCATTTAT
1045183 TAAATTATTC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
14 5 0.10
15 10 0.19
16 37 0.71
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:1049377 original size:14 final size:12
Alignment explanation
Indices: 1049345--1049375 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1049335 TTGAATGAAA
1049345 TGAGAGAAAATG
1 TGAGAGAAAATG
1049357 TGAGAGAAAATG
1 TGAGAGAAAATG
1049369 TGAGAGA
1 TGAGAGA
1049376 GATGTAAGTT
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:0.48, C:0.00, G:0.35, T:0.16
Consensus pattern (12 bp):
TGAGAGAAAATG
Found at i:1050811 original size:28 final size:29
Alignment explanation
Indices: 1050766--1050857 Score: 132
Period size: 28 Copynumber: 3.1 Consensus size: 29
1050756 TCTCTCTCCC
1050766 TCCCGAGAAGCATTACTTACAAATATCAG
1 TCCCGAGAAGCATTACTTACAAATATCAG
* **
1050795 TTCC-AGAAGCATTACTTACAAATCAGTCCC
1 TCCCGAGAAGCATTACTTACAAAT-A-TCAG
1050825 TCCCGAGAAGCATTACTTACAAATATCAG
1 TCCCGAGAAGCATTACTTACAAATATCAG
1050854 TCCC
1 TCCC
1050858 ATCTCTCTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 19 0.35
29 10 0.19
30 6 0.11
31 19 0.35
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (29 bp):
TCCCGAGAAGCATTACTTACAAATATCAG
Found at i:1056538 original size:2 final size:2
Alignment explanation
Indices: 1056531--1056561 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1056521 TGCAAATTAT
1056531 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 T
1056562 GATAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1064332 original size:18 final size:18
Alignment explanation
Indices: 1064309--1064346 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1064299 AAAAAACCTC
1064309 TGGAAACTCCTTAACTGT
1 TGGAAACTCCTTAACTGT
1064327 TGGAAACTCCTTAACTGT
1 TGGAAACTCCTTAACTGT
1064345 TG
1 TG
1064347 AGGTGGCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (18 bp):
TGGAAACTCCTTAACTGT
Found at i:1065774 original size:240 final size:240
Alignment explanation
Indices: 1065338--1065820 Score: 835
Period size: 240 Copynumber: 2.0 Consensus size: 240
1065328 TGCAGGAGTA
* *
1065338 TTTCAACAATCGCAAAGTGTAGTAAAGGCGTAACGACACACACAACTCTGATCCTTCAAAAACTC
1 TTTCAACAATCGCAAAGTGTAGTAAAGGCATAACGACACACACAACTCTGATCCTTCAAAAAATC
1065403 TCGGTGGTAGTAACCGAAAGATCTCATCGTCATAATACGACATCCAAGAAAACTATAAATATTAA
66 TCGGTGGTAGTAACCGAAAGATCTCATCGTCATAATACGACATCCAAGAAAACTATAAATATTAA
* *
1065468 TAATAAAAGTTAGTATAAATAAAGTCAAAAAATATAATTAAATTTTAATAATTAAAAACTTTAAT
131 TAATAAAAGTTAGTATAAATAAAGTCAAAAAATATAATTAAATTTTAATAATCAAAAACATTAAT
*
1065533 ATTTACCGCATGTTAACCGACGATATCGATTCTCATTTGTATATC
196 ATCTACCGCATGTTAACCGACGATATCGATTCTCATTTGTATATC
* *
1065578 TTTCAACAATCGCAAAGTGTAGTAAAGGCATAACGACACCCACAACTCTTATCCTTCAAAAAATC
1 TTTCAACAATCGCAAAGTGTAGTAAAGGCATAACGACACACACAACTCTGATCCTTCAAAAAATC
*
1065643 TCGGTGGTAGTAACCGGAAGATCTCATCGTCATAATAC-ATCATCCAAGAAAACTATAAATATTA
66 TCGGTGGTAGTAACCGAAAGATCTCATCGTCATAATACGA-CATCCAAGAAAACTATAAATATTA
* *
1065707 ATAGTAAAAGTTAGTATAAATAAAGTGAAAAAATATAATTAAATTTTAATAATCAAAATA-ATTA
130 ATAATAAAAGTTAGTATAAATAAAGTCAAAAAATATAATTAAATTTTAATAATCAAAA-ACATTA
*
1065771 ATATCTACCGCATGTTAACCGATGATATCGATTCTCATTTGTATATC
194 ATATCTACCGCATGTTAACCGACGATATCGATTCTCATTTGTATATC
1065818 TTT
1 TTT
1065821 TTTAGTTGTC
Statistics
Matches: 230, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
239 1 0.00
240 228 0.99
241 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.30
Consensus pattern (240 bp):
TTTCAACAATCGCAAAGTGTAGTAAAGGCATAACGACACACACAACTCTGATCCTTCAAAAAATC
TCGGTGGTAGTAACCGAAAGATCTCATCGTCATAATACGACATCCAAGAAAACTATAAATATTAA
TAATAAAAGTTAGTATAAATAAAGTCAAAAAATATAATTAAATTTTAATAATCAAAAACATTAAT
ATCTACCGCATGTTAACCGACGATATCGATTCTCATTTGTATATC
Found at i:1065925 original size:24 final size:24
Alignment explanation
Indices: 1065898--1065944 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1065888 AAAGCATTCC
*
1065898 AAAAAATAAAT-TTAAAAATTTACT
1 AAAAAAT-AATGTTAAAAAATTACT
1065922 AAAAAATAATGTTAAAAAATTAC
1 AAAAAATAATGTTAAAAAATTAC
1065945 CTTGCAGCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAAAATAATGTTAAAAAATTACT
Found at i:1068261 original size:44 final size:43
Alignment explanation
Indices: 1068133--1068292 Score: 198
Period size: 44 Copynumber: 3.7 Consensus size: 43
1068123 TCTTACCGAA
* * *
1068133 ATAAATGAAAATGCATAA-AGGTGCATTATTGGAAGAAAGGTACC
1 ATAAATGAAAATGCATAACA-GTGCATTATT-GCAGAAATGTGCC
*
1068177 ATAAATGAAAATGCATAACGGTGCATTATTGACAGAAATGTGCC
1 ATAAATGAAAATGCATAACAGTGCATTATTG-CAGAAATGTGCC
*
1068221 ATAAATGAAAATGCATAACAGTGCATTATTAGCATG-AATGTGTC
1 ATAAATGAAAATGCATAACAGTGCATTATT-GCA-GAAATGTGCC
* *
1068265 ATAAATGAAAATGAATAACAATGCATTA
1 ATAAATGAAAATGCATAACAGTGCATTA
1068293 CTGGGAGAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
43 1 0.01
44 101 0.97
45 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.26
Consensus pattern (43 bp):
ATAAATGAAAATGCATAACAGTGCATTATTGCAGAAATGTGCC
Found at i:1072664 original size:3 final size:3
Alignment explanation
Indices: 1072656--1072770 Score: 137
Period size: 3 Copynumber: 38.0 Consensus size: 3
1072646 TCGTCTGATC
1072656 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * *
1072705 TAA TTA -TA TATA TTA -TA CTA CTA TTA TTA TATA TGA -TA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
1072749 TATA TTA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA
1072771 AATAATATTA
Statistics
Matches: 100, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
2 5 0.05
3 83 0.83
4 12 0.12
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1075208 original size:15 final size:15
Alignment explanation
Indices: 1075188--1075221 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1075178 ATTTTCAAAC
1075188 AAAGCATGAAACTAG
1 AAAGCATGAAACTAG
*
1075203 AAAGCATGGAACTAG
1 AAAGCATGAAACTAG
1075218 AAAG
1 AAAG
1075222 AATGGGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.24, T:0.12
Consensus pattern (15 bp):
AAAGCATGAAACTAG
Found at i:1075226 original size:15 final size:15
Alignment explanation
Indices: 1075197--1075226 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1075187 CAAAGCATGA
*
1075197 AACTAGAAAGCATGG
1 AACTAGAAAGAATGG
1075212 AACTAGAAAGAATGG
1 AACTAGAAAGAATGG
1075227 GGATAGGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.10, G:0.27, T:0.13
Consensus pattern (15 bp):
AACTAGAAAGAATGG
Found at i:1081450 original size:119 final size:119
Alignment explanation
Indices: 1081239--1081526 Score: 479
Period size: 119 Copynumber: 2.4 Consensus size: 119
1081229 TATTTCCACG
1081239 GATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGA-AGTTTTCGCATGAAAATAAG
1 GATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATA-TTTTCGCATGAAAATAAG
* * *
1081303 AAATCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGT
65 AAAGCAAGTTTCAAAGTTTCTCATTTAATGTTATAGAAAATTAAATCCTCCGGGT
* * * *
1081358 GATTTGTAAAACCTCTGGGACATCTGTAAAACCTCAGGGTATGATATTTTCGCATGAAAATGAGA
1 GATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATATTTTCGCATGAAAATAAGA
*
1081423 AAGCGAGTTTCAAAGTTTCTCATTTAATGTTATAGAAAATTAAATCCTCCGGGT
66 AAGCAAGTTTCAAAGTTTCTCATTTAATGTTATAGAAAATTAAATCCTCCGGGT
*
1081477 GATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATTTTTT
1 GATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATATTTT
1081527 TTATTTTTGA
Statistics
Matches: 156, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
119 155 0.99
120 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (119 bp):
GATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATATTTTCGCATGAAAATAAGA
AAGCAAGTTTCAAAGTTTCTCATTTAATGTTATAGAAAATTAAATCCTCCGGGT
Found at i:1081491 original size:20 final size:20
Alignment explanation
Indices: 1081463--1081516 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1081453 TATAGAAAAT
* * *
1081463 TAAATCCTCCGGGTGATTTG
1 TAAAACCTCCGGGTCATCTG
1081483 TAAAACCTCCGGGTCATCTG
1 TAAAACCTCCGGGTCATCTG
*
1081503 TAAAACCTCAGGGT
1 TAAAACCTCCGGGT
1081517 AGGATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (20 bp):
TAAAACCTCCGGGTCATCTG
Found at i:1081665 original size:3 final size:3
Alignment explanation
Indices: 1081657--1081741 Score: 68
Period size: 3 Copynumber: 28.0 Consensus size: 3
1081647 TCGTTCGGTC
* * *
1081657 TTA TTA TTA TTA TATA TAA TTA -TA TATA TTA -TA CTA CTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* *
1081702 -TA TATA ATA TTA TTA TATA TTA TTA TTA TTA ATA TTA TTA
1 TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
1081742 AATAATATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
2 6 0.09
3 51 0.75
4 11 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:1081699 original size:11 final size:9
Alignment explanation
Indices: 1081664--1081751 Score: 69
Period size: 9 Copynumber: 9.6 Consensus size: 9
1081654 GTCTTATTAT
1081664 TATTATATA
1 TATTATATA
1081673 TAATTATATA
1 T-ATTATATA
1081683 TATTATACTA
1 TATTATA-TA
1081693 CTATTAT-TA
1 -TATTATATA
1081702 TA-TATA-A
1 TATTATATA
1081709 TATTATTATA
1 TATTA-TATA
1081719 TATTAT-TA
1 TATTATATA
1081727 TTATTA-ATA
1 -TATTATATA
*
1081736 TTATTAAATAA
1 -TATTATAT-A
1081747 TATTA
1 TATTA
1081752 CAAAGCCCAA
Statistics
Matches: 68, Mismatches: 0, Indels: 21
0.76 0.00 0.24
Matches are distributed among these distances:
7 6 0.09
8 6 0.09
9 25 0.37
10 24 0.35
11 7 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (9 bp):
TATTATATA
Found at i:1081705 original size:25 final size:25
Alignment explanation
Indices: 1081661--1081751 Score: 98
Period size: 25 Copynumber: 3.7 Consensus size: 25
1081651 TCGGTCTTAT
* *
1081661 TATTATTATATATAATTATATATAT
1 TATTATTATATATTATTATATATAA
* *
1081686 TA-TACTA-CTATTATTATATATAA
1 TATTATTATATATTATTATATATAA
1081709 TATTATTATATATTATTAT-TATTAA
1 TATTATTATATATTATTATATA-TAA
* *
1081734 TATTATTAAATAATATTA
1 TATTATTATATATTATTA
1081752 CAAAGCCCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
23 15 0.27
24 10 0.18
25 30 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTATTATATATTATTATATATAA
Found at i:1083070 original size:22 final size:20
Alignment explanation
Indices: 1083035--1083084 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1083025 ATATATTAAG
* *
1083035 ATAATTTTACAATATAATTGTA
1 ATAATATTACAATAGAA-T-TA
*
1083057 ATAATATTATAATAGAATTA
1 ATAATATTACAATAGAATTA
1083077 ATAATATT
1 ATAATATT
1083085 TATATTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.40
21 1 0.04
22 14 0.56
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
ATAATATTACAATAGAATTA
Found at i:1083144 original size:161 final size:159
Alignment explanation
Indices: 1082963--1083288 Score: 611
Period size: 161 Copynumber: 2.0 Consensus size: 159
1082953 ATATTATTTC
1082963 AAATT-AGGATTAATTAATTTTACTAATATATATTTTAGTCACTATTTATTATCATAATATTAAT
1 AAATTAAGGATTAATTAATTTTACTAATATATATTTTAGTCACTATTTATTATCATAATATTAAT
1083027 ATATTAAGATAATTTTACAATATAATTGTAATAATATTATAATAGAATTAATAATATTTATATTT
66 ATATTAAGATAATTTTACAATATAATTGTAATAATATTAT-ATAGAATTAATAATA-TT-TATTT
1083092 AGTAATTATTTA-TTTAAGTTATTTGTAATTA
128 AGTAATTATTTATTTTAAGTTATTTGTAATTA
1083123 AAATTAAGGATTAATTAATTTTACTAATATATATTTTAGTCACTATTTATTATCATAATATTAAT
1 AAATTAAGGATTAATTAATTTTACTAATATATATTTTAGTCACTATTTATTATCATAATATTAAT
1083188 ATATTAAGATAATTTTACAATATAATTGTAATAATATTATATAGAATTAATAATATTTATTTAGT
66 ATATTAAGATAATTTTACAATATAATTGTAATAATATTATATAGAATTAATAATATTTATTTAGT
1083253 AATTATTTATTTTAAGTTATTTGTAATTA
131 AATTATTTATTTTAAGTTATTTGTAATTA
1083282 AAATTAA
1 AAATTAA
1083289 ATACAGATTT
Statistics
Matches: 164, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
158 17 0.10
159 28 0.17
160 20 0.12
161 99 0.60
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (159 bp):
AAATTAAGGATTAATTAATTTTACTAATATATATTTTAGTCACTATTTATTATCATAATATTAAT
ATATTAAGATAATTTTACAATATAATTGTAATAATATTATATAGAATTAATAATATTTATTTAGT
AATTATTTATTTTAAGTTATTTGTAATTA
Found at i:1087614 original size:68 final size:68
Alignment explanation
Indices: 1087536--1087669 Score: 268
Period size: 68 Copynumber: 2.0 Consensus size: 68
1087526 ATTACGGACA
1087536 TAAAACACACAAAAGAAAATTAAAATCCTAACCTCATGCATTCTAATTCTCTTAGGTTATCTACA
1 TAAAACACACAAAAGAAAATTAAAATCCTAACCTCATGCATTCTAATTCTCTTAGGTTATCTACA
1087601 TCC
66 TCC
1087604 TAAAACACACAAAAGAAAATTAAAATCCTAACCTCATGCATTCTAATTCTCTTAGGTTATCTACA
1 TAAAACACACAAAAGAAAATTAAAATCCTAACCTCATGCATTCTAATTCTCTTAGGTTATCTACA
1087669 T
66 T
1087670 GGCTCTAGCG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (68 bp):
TAAAACACACAAAAGAAAATTAAAATCCTAACCTCATGCATTCTAATTCTCTTAGGTTATCTACA
TCC
Found at i:1101049 original size:172 final size:168
Alignment explanation
Indices: 1100716--1101057 Score: 598
Period size: 168 Copynumber: 2.0 Consensus size: 168
1100706 CCCTGAGCAT
1100716 ACTTACGGAAGATATCTATGACCCAATAAGTGAACATTGCCTTAGGTTTTAAAAATAAGAGCAAT
1 ACTTACGGAAGATATCTAT-ACCCAATAAGTGAACATTGCCTTAGGTTTTAAAAATAAGAGCAAT
*
1100781 CAAACAATTTTTATTATAGTAATTAAACTAAAGGTAGATTAAGGTTTTCTATCTTAAAGTGTCAA
65 CAAACAATTATTATTATAGTAATTAAACTAAAGGTAGATTAAGGTTTTCTATCTTAAAGTGTCAA
1100846 ATTATGAAAATTAAAGAACCTAGAGGCATAAAACTAAAA
130 ATTATGAAAATTAAAGAACCTAGAGGCATAAAACTAAAA
1100885 ACTTACGGAAGATA-CTACT-CCCTAATAAGTGAACATTGCCTTAGGTTTTAAAAATAAGAGCAA
1 ACTTACGGAAGATATCTA-TACCC-AATAAGTGAACATTGCCTTAGGTTTTAAAAATAAGAGCAA
1100948 TCAAACAATTATTATTAATAGTAATTAAAACTAAAGGTAGATTAAGGTTTTCTCTATCTTAAAGT
64 TCAAACAATTATTATT-ATAGTAATT-AAACTAAAGGTAGATTAAGG-TTT-TCTATCTTAAAGT
1101013 GTCAAATTATGAAAATTAAAGAACCTAGAGGCATAAAACTAAAA
125 GTCAAATTATGAAAATTAAAGAACCTAGAGGCATAAAACTAAAA
1101057 A
1 A
1101058 TGTAGGCTCT
Statistics
Matches: 166, Mismatches: 1, Indels: 9
0.94 0.01 0.05
Matches are distributed among these distances:
167 3 0.02
168 58 0.35
169 24 0.14
170 20 0.12
171 3 0.02
172 58 0.35
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (168 bp):
ACTTACGGAAGATATCTATACCCAATAAGTGAACATTGCCTTAGGTTTTAAAAATAAGAGCAATC
AAACAATTATTATTATAGTAATTAAACTAAAGGTAGATTAAGGTTTTCTATCTTAAAGTGTCAAA
TTATGAAAATTAAAGAACCTAGAGGCATAAAACTAAAA
Found at i:1102939 original size:24 final size:24
Alignment explanation
Indices: 1102910--1102961 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1102900 ATTAGGTTAG
1102910 GGTTTTAATTTGGGCCCGGATTTA
1 GGTTTTAATTTGGGCCCGGATTTA
*
1102934 GGTTTTAATTTGGGCCCGGGTTTA
1 GGTTTTAATTTGGGCCCGGATTTA
1102958 GGTT
1 GGTT
1102962 GATTTGGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.13, C:0.12, G:0.33, T:0.42
Consensus pattern (24 bp):
GGTTTTAATTTGGGCCCGGATTTA
Found at i:1103611 original size:56 final size:57
Alignment explanation
Indices: 1103543--1103656 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 57
1103533 TTTATTAACA
1103543 TAAAATTTATATT-CTC-TTATATACGATTCCACCTGCGCGGCGCTTACTACGACGG
1 TAAAATTTATATTCCTCTTTATATACGATTCCACCTGCGCGGCGCTTACTACGACGG
1103598 TAAAATTTTATATTCCTCTTTATATACGATTCCACCTGCGCGGCGCTTACTACGACGG
1 TAAAA-TTTATATTCCTCTTTATATACGATTCCACCTGCGCGGCGCTTACTACGACGG
1103656 T
1 T
1103657 GGATCAGCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
55 5 0.09
56 8 0.14
57 3 0.05
58 40 0.71
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (57 bp):
TAAAATTTATATTCCTCTTTATATACGATTCCACCTGCGCGGCGCTTACTACGACGG
Found at i:1104373 original size:32 final size:32
Alignment explanation
Indices: 1104337--1104433 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
1104327 TTTGATAATC
*
1104337 TTAAAAACCATTTTATAATAGTTCGATAAGTT
1 TTAAAAACCATTTTATAATAGTTCAATAAGTT
* * * * **
1104369 TTAAAGACTATTTTATACTAGTTAAATAAACT
1 TTAAAAACCATTTTATAATAGTTCAATAAGTT
*
1104401 TTAACAACCATTTT-TCAATAGTTCAATAAGTT
1 TTAAAAACCATTTTAT-AATAGTTCAATAAGTT
1104433 T
1 T
1104434 AATGAACATT
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
31 1 0.02
32 49 0.98
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (32 bp):
TTAAAAACCATTTTATAATAGTTCAATAAGTT
Found at i:1105623 original size:19 final size:21
Alignment explanation
Indices: 1105599--1105668 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 21
1105589 TGCAAAAATG
*
1105599 GTATCGATACCGTA-ATAG-A
1 GTATCGATACCATAGATAGTA
*
1105618 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
* *
1105640 GTATCGATACCAT-GGTAG-G
1 GTATCGATACCATAGATAGTA
1105659 GTATCGATAC
1 GTATCGATAC
1105669 TATGGAGCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 22 0.51
20 3 0.07
21 5 0.12
22 13 0.30
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:1109773 original size:24 final size:23
Alignment explanation
Indices: 1109721--1109774 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1109711 TACTTTTAAA
1109721 TTATA-TATAAAAATAGATATCT
1 TTATATTATAAAAATAGATATCT
* * *
1109743 TTGTATTATAAAAATAAGTTATTT
1 TTATATTATAAAAAT-AGATATCT
1109767 TTATATTA
1 TTATATTA
1109775 AATTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 9 0.35
24 13 0.50
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (23 bp):
TTATATTATAAAAATAGATATCT
Found at i:1109776 original size:22 final size:23
Alignment explanation
Indices: 1109721--1109776 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1109711 TACTTTTAAA
1109721 TTATATATAAAAATAGATATCTT
1 TTATATATAAAAATAGATATCTT
*
1109744 TGTAT-TATAAAAATAAGTTAT-TT
1 T-TATATATAAAAAT-AGATATCTT
1109767 TTATAT-TAAA
1 TTATATATAAA
1109777 TTTAAATAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 7 0.24
23 14 0.48
24 8 0.28
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (23 bp):
TTATATATAAAAATAGATATCTT
Found at i:1110335 original size:24 final size:24
Alignment explanation
Indices: 1110290--1110336 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
1110280 AATTTAAATA
1110290 TTTAAGTAAATAAAAATAATTAAAG
1 TTTAAGTAAAT-AAAATAATTAAAG
1110315 TTTAAGTCAAAT-AAATAATTAA
1 TTTAAGT-AAATAAAATAATTAA
1110337 TATATATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 7 0.33
26 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (24 bp):
TTTAAGTAAATAAAATAATTAAAG
Found at i:1110510 original size:16 final size:16
Alignment explanation
Indices: 1110491--1110545 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
1110481 TTAAATTCAC
1110491 GTTACTTTCGATTCGG
1 GTTACTTTCGATTCGG
*
1110507 GTTATTTTCGATTC-G
1 GTTACTTTCGATTCGG
* * * *
1110522 ATAACTTTCGGTTCGA
1 GTTACTTTCGATTCGG
1110538 GTTACTTT
1 GTTACTTT
1110546 TGGTTGGCTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.47
Consensus pattern (16 bp):
GTTACTTTCGATTCGG
Found at i:1111546 original size:68 final size:68
Alignment explanation
Indices: 1111420--1111548 Score: 170
Period size: 68 Copynumber: 1.9 Consensus size: 68
1111410 TGCTAAAAAA
* * * * * *
1111420 AATCTTAACCAACAATTAGTTGGTTTAATGAGATGAGATACTATATTTTTTAGACAAGAATATTT
1 AATCTTAACCAACAATCAGTTGGTGTAATGAGATGAAATACTAGATTCTTAAGACAAGAATATTT
1111485 AAG
66 AAG
* *
1111488 AATCTTAATCAATAATCAGTTGGTGTAATGAGATGAAATACTAGATTGCTTAAG-CAAGAAT
1 AATCTTAACCAACAATCAGTTGGTGTAATGAGATGAAATACTAGATT-CTTAAGACAAGAAT
1111549 CAGGGGTTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 48 0.92
69 4 0.08
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (68 bp):
AATCTTAACCAACAATCAGTTGGTGTAATGAGATGAAATACTAGATTCTTAAGACAAGAATATTT
AAG
Found at i:1112056 original size:2 final size:2
Alignment explanation
Indices: 1112049--1112073 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1112039 AGAATTTAAT
1112049 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
1112074 CTTAAATCAT
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:1115541 original size:102 final size:102
Alignment explanation
Indices: 1115362--1115613 Score: 232
Period size: 102 Copynumber: 2.5 Consensus size: 102
1115352 CATCGCTTCC
* * * *
1115362 AGTTCAAGGGGAAGACATTCATCTGCCAATTTCTTTGACCTGAATATGAAGATGTTCTCGACACA
1 AGTTCAAGGGGAAGACATTCAACTGACAATTTCTTAGACCTGAATATGAAGATGTCCTCGACACA
*
1115427 ACAATCTATTCAATACCCATTTGACACGATGCTTATA
66 ACAATCTATTCAAAACCCATTTGACACGATGCTTATA
* * *
1115464 AGTTCTAGGGGGAGACATTCAACT-ACAAGTTTCTTAGACCAT-AATATGGAGATG-CCTGCGAC
1 AGTTCAAGGGGAAGACATTCAACTGACAA-TTTCTTAGACC-TGAATATGAAGATGTCCT-CGAC
* ** * *
1115526 ACAACACTC-AGTTCAAAACCCATACGACAGGATACCTTCAT-
63 ACAACAATCTA-TTCAAAACCCATTTGACACGAT-GCTT-ATA
* * *
1115567 -GTTCAAGGGGAATG-CATTCAACT-ACTAATTTATTCGACCTAAATATG
1 AGTTCAAGGGGAA-GACATTCAACTGAC-AATTTCTTAGACCTGAATATG
1115614 GACCTTCAAA
Statistics
Matches: 124, Mismatches: 17, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
101 7 0.06
102 108 0.87
103 7 0.06
104 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (102 bp):
AGTTCAAGGGGAAGACATTCAACTGACAATTTCTTAGACCTGAATATGAAGATGTCCTCGACACA
ACAATCTATTCAAAACCCATTTGACACGATGCTTATA
Found at i:1116342 original size:20 final size:21
Alignment explanation
Indices: 1116317--1116368 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1116307 TTTGCCCAAT
*
1116317 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1116337 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1116358 TCGCAATGCGA
1 TCGCAATGCGA
1116369 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1116382 original size:20 final size:20
Alignment explanation
Indices: 1116357--1116491 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1116347 AATTGGGAAA
1116357 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1116377 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1116397 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1116418 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1116438 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1116458 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1116478 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1116492 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1116401 original size:61 final size:61
Alignment explanation
Indices: 1116354--1116485 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
1116344 GCGAATTGGG
* * * * *
1116354 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1116415 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
1116476 ATAATCGCAA
1 AAAATCGCAA
1116486 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1116687 original size:22 final size:22
Alignment explanation
Indices: 1116659--1116702 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1116649 CACTCTCTCA
1116659 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
1116681 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1116703 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1116796 original size:16 final size:15
Alignment explanation
Indices: 1116775--1116804 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1116765 GAGGGTTAGT
1116775 TTTTTTAATTATTTTC
1 TTTTTTAATT-TTTTC
1116791 TTTTTTAATTTTTT
1 TTTTTTAATTTTTT
1116805 GCATTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTAATTTTTTC
Found at i:1116975 original size:20 final size:20
Alignment explanation
Indices: 1116946--1116989 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1116936 GCGATTTTAG
1116946 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
1116966 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
1116986 TTTC
1 TTTC
1116990 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:1117180 original size:25 final size:24
Alignment explanation
Indices: 1117126--1117180 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1117116 TGTTTATTAT
* *
1117126 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1117150 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1117176 TGTTT
1 TGTTT
1117181 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1118330 original size:18 final size:18
Alignment explanation
Indices: 1118309--1118353 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1118299 TCCACTTCGG
*
1118309 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1118327 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1118345 GAGCCATCA
1 GAGCCATCA
1118354 TCTATCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1118359 original size:25 final size:25
Alignment explanation
Indices: 1118330--1118381 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1118320 TCGCCCAGAG
1118330 CTATCACCTCACCCAGAGCCATCAT
1 CTATCACCTCACCCAGAGCCATCAT
1118355 CTATCACCTCACCCAGAGCCATCAT
1 CTATCACCTCACCCAGAGCCATCAT
1118380 CT
1 CT
1118382 GATCGACCCG
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:0.44, G:0.08, T:0.21
Consensus pattern (25 bp):
CTATCACCTCACCCAGAGCCATCAT
Found at i:1118914 original size:19 final size:20
Alignment explanation
Indices: 1118860--1118926 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1118850 TAGTTTACTT
* *
1118860 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1118880 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1118900 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1118919 TCGCAACG
1 TCGCAACG
1118927 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1118934 original size:14 final size:14
Alignment explanation
Indices: 1118915--1118973 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1118905 ATGCGAAATG
1118915 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1118929 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1118948 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1118962 AAAATCGCAACG
1 AAAATCGCAACG
1118974 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1118941 original size:33 final size:33
Alignment explanation
Indices: 1118899--1118990 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
1118889 GGAAATGGCT
1118899 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1118932 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1118965 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1118991 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1118953 original size:19 final size:19
Alignment explanation
Indices: 1118899--1118995 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
1118889 GGAAATGGCT
1118899 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1118918 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1118932 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1118951 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1118965 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1118984 ATCGCAATGCGA
1 ATCGCAATGCGA
1118996 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1119026 original size:14 final size:14
Alignment explanation
Indices: 1119007--1119096 Score: 63
Period size: 14 Copynumber: 5.8 Consensus size: 14
1118997 TTGTGTTTCG
1119007 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1119021 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1119037 CGTATTGCGATTTTGT
1 CG--TTGCGATTTTGT
* *
1119053 CGTTGTGATTGTCATTT
1 CGTTGCGATT-T--TGT
1119070 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1119086 CATTGCGATTT
1 CGTTGCGATTT
1119097 ACATTTCGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
14 27 0.45
15 1 0.02
16 11 0.18
17 4 0.07
18 10 0.17
19 7 0.12
ACGTcount: A:0.12, C:0.16, G:0.23, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1119077 original size:33 final size:32
Alignment explanation
Indices: 1119002--1119113 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 32
1118992 GCGATTTGTG
*
1119002 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
* *
1119034 TTTCGTATTGCGATTTTGTCGTTGTGATTGTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATT-TCA
*
1119067 TTTCGCATTGCGATTTTGTCATTGCGATTTACA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTT-CA
1119100 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1119114 AGCCATTTCC
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
32 27 0.38
33 45 0.62
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.47
Consensus pattern (32 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
Found at i:1119135 original size:20 final size:20
Alignment explanation
Indices: 1119110--1119153 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1119100 TTTCGCATTG
1119110 CGATAGCCATTTCCGCGTTA
1 CGATAGCCATTTCCGCGTTA
* * *
1119130 CGATAGTCATTTTCGCGTTG
1 CGATAGCCATTTCCGCGTTA
1119150 CGAT
1 CGAT
1119154 TTTAAGTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (20 bp):
CGATAGCCATTTCCGCGTTA
Found at i:1119615 original size:41 final size:42
Alignment explanation
Indices: 1119519--1119606 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
1119509 GACTCACCTG
* *
1119519 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
1119561 TCCTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
1119602 TCATC
1 TCATC
1119607 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:1121051 original size:14 final size:14
Alignment explanation
Indices: 1121017--1121055 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1121007 TTGATTGTTT
1121017 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1121031 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1121045 TGTTGATTTGT
1 AATTGATTTGT
1121056 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1121214 original size:19 final size:19
Alignment explanation
Indices: 1121192--1121242 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
1121182 ATCGCAACGA
*
1121192 GAAAATCGTAATGCAAAAT
1 GAAAATCGCAATGCAAAAT
*
1121211 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCAAAAT
1121230 GAAAATCGCAATG
1 GAAAATCGCAATG
1121243 AGAAAATCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.18
Consensus pattern (19 bp):
GAAAATCGCAATGCAAAAT
Found at i:1121291 original size:20 final size:20
Alignment explanation
Indices: 1121266--1121359 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
1121256 GCGATTTTCA
*
1121266 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
***
1121286 TTTCGCGTTGCGATTTTTCA-
1 TTTCGCGTTGCGA-TAGCCAT
**
1121306 TTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
1121326 TTTCGCGTTACGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
1121346 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1121360 TTCCCCGTTG
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
19 3 0.05
20 53 0.90
21 3 0.05
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:1121309 original size:40 final size:40
Alignment explanation
Indices: 1121255--1121339 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
1121245 AAAATCGCAA
*
1121255 TGCGA-TTTTCATTTCGCATTGCGATAGCCATTTTCGCGT
1 TGCGATTTTTCATTTCGAATTGCGATAGCCATTTTCGCGT
1121294 TGCGATTTTTCATTTCGAATTGCGATAGCCATTTTCGCGT
1 TGCGATTTTTCATTTCGAATTGCGATAGCCATTTTCGCGT
*
1121334 TACGAT
1 TGCGAT
1121340 AGCCATTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
39 5 0.12
40 38 0.88
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (40 bp):
TGCGATTTTTCATTTCGAATTGCGATAGCCATTTTCGCGT
Found at i:1121350 original size:40 final size:40
Alignment explanation
Indices: 1121264--1121359 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
1121254 ATGCGATTTT
* ***
1121264 CATTTCGCATTGCGATAGCCATTTTCGCGTTGCGATTTTT
1 CATTTCGCATTGCGATAGCCATTTTCGCGTTACGATTAGC
*
1121304 CATTTCGAATTGCGATAGCCATTTTCGCGTTACGA-TAGC
1 CATTTCGCATTGCGATAGCCATTTTCGCGTTACGATTAGC
*
1121343 CATTTTCGCGTTGCGAT
1 CA-TTTCGCATTGCGAT
1121360 TTCCCCGTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.06
40 45 0.94
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.39
Consensus pattern (40 bp):
CATTTCGCATTGCGATAGCCATTTTCGCGTTACGATTAGC
Done.