Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 462 of 770
Found at i:142567460 original size:96 final size:96
Alignment explanation
Indices: 142567296--142567567 Score: 361
Period size: 96 Copynumber: 2.8 Consensus size: 96
142567286 TGTGCCAGTA
* * *
142567296 TAAGACTATGTTTGGGATATGGCATCGGCCA-CGATATGAGAGC-CAGTGTAAGACCATGTTTGG
1 TAAGACTATGTTTGGGACATGGCATC-GACATCGATATGTGAGCTC-GTGTAAGACCATGTTTGG
142567359 AACATGGCATCGGCAATGTA-ATGAGAGCTAGTG
64 AACATGGCATCGGCAATG-AGATGAGAGCTAGTG
* * * **
142567392 TAAGACAATGTTTGGGACATGGCATCGACATTGATATGTGCGCTCGTGTAAGACTGTGTTTGGAA
1 TAAGACTATGTTTGGGACATGGCATCGACATCGATATGTGAGCTCGTGTAAGACCATGTTTGGAA
*
142567457 CATGGCATCGGCATTGAGATGAGAGCTAGTG
66 CATGGCATCGGCAATGAGATGAGAGCTAGTG
* * * * * *
142567488 TAAGACTATGTCTGGGACATGGCATCAACCTCAACATGTGAGCTAGTGTAAGACCATGTTTGGAA
1 TAAGACTATGTTTGGGACATGGCATCGACATCGATATGTGAGCTCGTGTAAGACCATGTTTGGAA
142567553 CATGGCATCGGCAAT
66 CATGGCATCGGCAAT
142567568 TCACCCCTTT
Statistics
Matches: 152, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
95 4 0.03
96 147 0.97
97 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (96 bp):
TAAGACTATGTTTGGGACATGGCATCGACATCGATATGTGAGCTCGTGTAAGACCATGTTTGGAA
CATGGCATCGGCAATGAGATGAGAGCTAGTG
Found at i:142567539 original size:144 final size:144
Alignment explanation
Indices: 142567279--142567562 Score: 349
Period size: 144 Copynumber: 2.0 Consensus size: 144
142567269 GACATTTGGG
* * * *
142567279 TGATATGTGTGCCAGTATAAGACTATGTTTGGGATATGGCATCGGCCACGATATGAGAGCCAGTG
1 TGATATGTGCGCCAGTATAAGACTATGTTTGGAACATGGCATCGGCCACGAGATGAGAGCCAGTG
* ** ** *
142567344 TAAGACCATGTTTGGAACATGGCATCGGCAATGTAATGAGAGCTAGTGTAAGACAATGTTTGGGA
66 TAAGACCATGTCTGGAACATGGCATCAACAATCAAATGAGAGCTAGTGTAAGACAATGTTTGGAA
142567409 CATGGCATCGACAT
131 CATGGCATCGACAT
* * * *
142567423 TGATATGTGCGCTC-GTGTAAGACTGTGTTTGGAACATGGCATCGG-CATTGAGATGAGAGCTAG
1 TGATATGTGCGC-CAGTATAAGACTATGTTTGGAACATGGCATCGGCCA-CGAGATGAGAGCCAG
* * * * *
142567486 TGTAAGACTATGTCTGGGACATGGCATCAAC-CTCAACATGTGAGCTAGTGTAAGACCATGTTTG
64 TGTAAGACCATGTCTGGAACATGGCATCAACAATCAA-ATGAGAGCTAGTGTAAGACAATGTTTG
142567550 GAACATGGCATCG
128 GAACATGGCATCG
142567563 GCAATTCACC
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
143 4 0.03
144 113 0.96
145 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (144 bp):
TGATATGTGCGCCAGTATAAGACTATGTTTGGAACATGGCATCGGCCACGAGATGAGAGCCAGTG
TAAGACCATGTCTGGAACATGGCATCAACAATCAAATGAGAGCTAGTGTAAGACAATGTTTGGAA
CATGGCATCGACAT
Found at i:142570561 original size:35 final size:35
Alignment explanation
Indices: 142570515--142570585 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
142570505 AGTACAAATA
*
142570515 TACTAGTGGAGTCTACTGAATTTTTGGTAAAAGTG
1 TACTAGTGGAGTCTACTGAATTTGTGGTAAAAGTG
142570550 TACTAGTGGAGTCTACTGAATTTGTGGTAAAAGTG
1 TACTAGTGGAGTCTACTGAATTTGTGGTAAAAGTG
142570585 T
1 T
142570586 CCAACTCGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (35 bp):
TACTAGTGGAGTCTACTGAATTTGTGGTAAAAGTG
Found at i:142572382 original size:66 final size:68
Alignment explanation
Indices: 142572306--142572492 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
142572296 TAGTACCACT
*
142572306 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
142572368 CACG
65 CACG
142572372 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
142572437 ATCACG
63 ATCACG
142572443 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
142572493 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:142572417 original size:71 final size:71
Alignment explanation
Indices: 142572329--142572492 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
142572319 CGATTTGTCT
142572329 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
142572394 CTTTCA
66 CTTTCA
142572400 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
142572465 CTTTCA
66 CTTTCA
142572471 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
142572493 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:142572530 original size:71 final size:70
Alignment explanation
Indices: 142572329--142572526 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
142572319 CGATTTGTCT
* * *
142572329 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
142572394 CTTTCA
65 CTTTCA
* * *
142572400 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
142572465 CTTTCA
65 CTTTCA
* *
142572471 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
142572527 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:142579976 original size:71 final size:71
Alignment explanation
Indices: 142579896--142580059 Score: 312
Period size: 71 Copynumber: 2.3 Consensus size: 71
142579886 CGATTTGTCT
142579896 CGTAGCTCTCTTGTCTACATGGTGT-CCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTA
1 CGTAGCTCTCTTGTCTACATGGTGTCCCTTCACTTGGAATCACGCATGCGA-CTAGCTACATTTA
142579960 TCTTTCA
65 TCTTTCA
142579967 CGTAGCTCTCTTGTCTACATGGTGTCCCTTCACTTGGAATCACGCATGCGACTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCCTTCACTTGGAATCACGCATGCGACTAGCTACATTTAT
142580032 CTTTCA
66 CTTTCA
142580038 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
142580060 GATACATCTC
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
71 67 0.73
72 25 0.27
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCCTTCACTTGGAATCACGCATGCGACTAGCTACATTTAT
CTTTCA
Found at i:142580097 original size:71 final size:71
Alignment explanation
Indices: 142579896--142580093 Score: 264
Period size: 71 Copynumber: 2.8 Consensus size: 71
142579886 CGATTTGTCT
* *
142579896 CGTAGCTCTCTTGTCTACATGGTGTC-CTTCACTTGGAATCACGCATGCGACCTAGCTACATTTA
1 CGTAGCTCTCTTGTCTACATGGTGTCACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTA
142579960 TCTTTCA
65 TCTTTCA
* * *
142579967 CGTAGCTCTCTTGTCTACATGGTGTCCCTTCACTTGGAATCACGCATGCGA-CTAGCTACATTTA
1 CGTAGCTCTCTTGTCTACATGGTGTCACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTA
142580031 TCTTTCA
65 TCTTTCA
* *
142580038 CGTAGCTCTCTTGTCTACATGG-GAT-ACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TCACATACTTCGAATCACGCATGCGACCTAGCTAC
142580094 TACAGGGTGT
Statistics
Matches: 119, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
67 14 0.12
68 9 0.08
70 3 0.03
71 69 0.58
72 24 0.20
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCACATACTTCGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:142581809 original size:37 final size:35
Alignment explanation
Indices: 142581755--142581871 Score: 119
Period size: 31 Copynumber: 3.5 Consensus size: 35
142581745 TCAATCATGC
142581755 ACTGGGCC-ATAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGA-AG-CCTTTTCATATTTCATATTT-AT--T
142581794 ACT-GGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
142581824 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
142581855 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
142581872 ACTGTAAACG
Statistics
Matches: 76, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
30 4 0.05
31 44 0.58
32 2 0.03
33 1 0.01
35 1 0.01
37 14 0.18
38 6 0.08
39 4 0.05
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:142581835 original size:31 final size:31
Alignment explanation
Indices: 142581778--142581871 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
142581768 CCTTTTCATA
*
142581778 TTTCATATTTCATAATACT-GGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
142581808 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
142581839 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
142581870 TT
1 TT
142581872 ACTGTAAACG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 18 0.29
31 44 0.71
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:142582144 original size:45 final size:47
Alignment explanation
Indices: 142582063--142582197 Score: 177
Period size: 45 Copynumber: 2.9 Consensus size: 47
142582053 GCTTTATCAT
* * *
142582063 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCTTTCA
* **
142582111 ATAACTGGGGCATAAGCCC-TTT-ATAACTAGGGCATAAGCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCTTTCA
142582156 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCC
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCC
142582198 CTTTTTCACT
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
45 38 0.49
46 6 0.08
47 22 0.28
48 12 0.15
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCTTTCA
Found at i:142582181 original size:24 final size:24
Alignment explanation
Indices: 142582063--142582202 Score: 173
Period size: 23 Copynumber: 6.0 Consensus size: 24
142582053 GCTTTATCAT
*
142582063 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
142582088 ATAACTGGGGCAAAAG-CCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
142582111 ATAACTGGGGCATAAGCCC-TTT-
1 ATAACTGGGGCATAAGCCCTTTTA
* *
142582133 ATAACTAGGGCATAAG-CCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
142582156 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
142582180 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
142582203 TCACTTCCTC
Statistics
Matches: 103, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.02
22 18 0.17
23 37 0.36
24 36 0.35
25 10 0.10
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:142582276 original size:20 final size:20
Alignment explanation
Indices: 142582251--142582310 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
142582241 TTTGATTACC
*
142582251 TCATGTGCCTATCATACATA
1 TCATGTGCATATCATACATA
*
142582271 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
142582291 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
142582311 CCATATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:142582381 original size:25 final size:25
Alignment explanation
Indices: 142582353--142582400 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
142582343 ATACATAAAC
* * *
142582353 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
142582378 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
142582401 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:142583649 original size:18 final size:19
Alignment explanation
Indices: 142583626--142583661 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
142583616 GATGACTAAT
142583626 TAAAGCATGCATG-CAAAA
1 TAAAGCATGCATGTCAAAA
*
142583644 TAAAGCTTGCATGTCAAA
1 TAAAGCATGCATGTCAAA
142583662 TTCCCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (19 bp):
TAAAGCATGCATGTCAAAA
Found at i:142585139 original size:40 final size:40
Alignment explanation
Indices: 142585073--142585239 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
142585063 AAATTGAATG
* * *
142585073 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
142585112 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
142585152 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
142585192 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
142585232 ATATCCGG
1 ATATCCGG
142585240 TTATTCCGAA
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:142593503 original size:40 final size:40
Alignment explanation
Indices: 142593458--142593608 Score: 218
Period size: 40 Copynumber: 3.8 Consensus size: 40
142593448 CTGGAAATTA
* * *
142593458 TATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGT--CATTC
*
142593499 -ATCCGGGCTAAGACCTGAAGGCATTCGTGCGAGTCATTC
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTC
142593538 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTC
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTC
142593578 TATCCGGGCTAAGACCCGAAGGCATTCGTGC
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGC
142593609 ACATGGTTAT
Statistics
Matches: 102, Mismatches: 5, Indels: 7
0.89 0.04 0.06
Matches are distributed among these distances:
38 1 0.01
39 5 0.05
40 96 0.94
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTC
Found at i:142599386 original size:31 final size:31
Alignment explanation
Indices: 142599215--142599385 Score: 270
Period size: 31 Copynumber: 5.5 Consensus size: 31
142599205 TTTAACGGTT
*
142599215 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
142599246 ACTGGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
* *
142599277 ACTGGACCGGAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
*
142599308 ACTGGGCCGAAGCCTTATCGTAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
* * *
142599339 ACTGTGCCGAAGCCTTTTCATAAAACATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
*
142599370 ACTGGGCAGAAGCCTT
1 ACTGGGCCGAAGCCTT
142599386 TACTGTAAAT
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 128 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTATCATAAATCATATC
Found at i:142599633 original size:25 final size:25
Alignment explanation
Indices: 142599605--142599674 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
142599595 CTCTTTTAAT
142599605 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
142599630 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
* *
142599655 AGCTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
142599675 AGCACTTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:142600513 original size:27 final size:26
Alignment explanation
Indices: 142600483--142600570 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
142600473 GGGCATATTC
142600483 GTCATTTTACCGTATAGGGGTATTACG
1 GTCATTTTACC-TATAGGGGTATTACG
* * *
142600510 GTCACTTTACCCTACAGGGGCT-GTACG
1 GTCATTTTA-CCTATAGGGG-TATTACG
* * *
142600537 GTCTTTTTACCTAATAGGGGTATTTCA
1 GTCATTTTACCT-ATAGGGGTATTACG
142600564 GTCATTT
1 GTCATTT
142600571 CACCCTACAA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
26 4 0.09
27 40 0.85
28 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (26 bp):
GTCATTTTACCTATAGGGGTATTACG
Found at i:142600631 original size:27 final size:27
Alignment explanation
Indices: 142600601--142600910 Score: 164
Period size: 27 Copynumber: 11.4 Consensus size: 27
142600591 GTAAATCTAC
142600601 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
*
142600628 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTT-TAGTAATTTTGT
*
142600654 AGAAAGTCAAGGGTATTTCTA-TAATTTTGT
1 --AAA-CCAAGGGTATTT-TAGTAATTTTGT
* * * **
142600684 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTTAGTAATTTTGT
**** ** **
142600711 AAGTTGAGGGTATTTCGGTAATTTTAC
1 AAACCAAGGGTATTTTAGTAATTTTGT
* **
142600738 AAACC-AGTGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTTAGTAATTTTGT
* * * **
142600765 AAACTAGGGGTATTTTAGCAATTTTAC
1 AAACCAAGGGTATTTTAGTAATTTTGT
* * *
142600792 AGACCAA-GGTATTTTGGTAATTTTACT
1 AAACCAAGGGTATTTTAGTAATTTT-GT
* * * *
142600819 -AATCGAGGGTATTTTGGTAATCTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
*
142600845 AAACCAAGGGTATTTTAGTACTTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
* * **** *
142600872 AAATCGAGGGTAAAACAGTAATTCTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
*
142600899 AAATCAAGGGTA
1 AAACCAAGGGTA
142600911 AAATAGTAAT
Statistics
Matches: 226, Mismatches: 46, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
26 23 0.10
27 173 0.77
28 9 0.04
29 20 0.09
30 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
AAACCAAGGGTATTTTAGTAATTTTGT
Found at i:142600880 original size:54 final size:54
Alignment explanation
Indices: 142600578--142600937 Score: 246
Period size: 54 Copynumber: 6.6 Consensus size: 54
142600568 TTTCACCCTA
* * * * * *
142600578 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTTAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTAGTAATTTTGTAAAC
* * * * *
142600632 CAATGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCTA-TAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAA-TTTTATAAA-TCGAGGGTATTT-TAGTAATTTTGTAAAC
* * * * ** **
142600688 CAGGGGTATTTTGGTAATTTTACAAGTTGAGGGTATTTCGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTAGTAATTTTGTAAAC
* * * ** *
142600742 C-AGTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTAGCAATTTTACAGAC
1 CAAG-GGTATTTTGGTAATTTTATAAATCGA-GGGTATTTTAGTAATTTTGTAAAC
* *
142600796 CAA-GGTATTTTGGTAATTTTACT-AATCGAGGGTATTTTGGTAATCTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTA-TAAATCGAGGGTATTTTAGTAATTTTGTAAAC
* * * **** * *
142600849 CAAGGGTATTTTAGTACTTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTAGTAATTTTGTAAAC
*** * *
142600903 CAAGGGTAAAATAGTAATTCTATAAATCGAGGGTA
1 CAAGGGTATTTTGGTAATTTTATAAATCGAGGGTA
142600938 AAACGGTAAT
Statistics
Matches: 240, Mismatches: 53, Indels: 26
0.75 0.17 0.08
Matches are distributed among these distances:
53 44 0.18
54 143 0.60
55 16 0.07
56 35 0.15
57 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTAGTAATTTTGTAAAC
Found at i:142600911 original size:27 final size:27
Alignment explanation
Indices: 142600869--142600964 Score: 129
Period size: 27 Copynumber: 3.6 Consensus size: 27
142600859 TTAGTACTTT
142600869 TGTAAATCGAGGGTAAAACAGTAATTC
1 TGTAAATCGAGGGTAAAACAGTAATTC
* *
142600896 TGTAAATCAAGGGTAAAATAGTAATTC
1 TGTAAATCGAGGGTAAAACAGTAATTC
* * *
142600923 TATAAATCGAGGGTAAAACGGTAATTA
1 TGTAAATCGAGGGTAAAACAGTAATTC
* *
142600950 TGCAAATCGGGGGTA
1 TGTAAATCGAGGGTA
142600965 CTTTGGTAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (27 bp):
TGTAAATCGAGGGTAAAACAGTAATTC
Found at i:142603747 original size:39 final size:39
Alignment explanation
Indices: 142603674--142603817 Score: 243
Period size: 39 Copynumber: 3.7 Consensus size: 39
142603664 CCGCACAAAG
*
142603674 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAATTTGCACAATT
* *
142603714 GCCTTCGGGCTTAGCCCGGATATCATAACTTGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
*
142603753 GCCTTCGGGCTTAGCCCGGGTATCACAATTTGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
142603792 GCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCAC
142603818 TCGAACATTC
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 88 0.91
40 9 0.09
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
Found at i:142610972 original size:40 final size:39
Alignment explanation
Indices: 142610936--142611049 Score: 129
Period size: 48 Copynumber: 2.7 Consensus size: 39
142610926 CCGCACAAAG
142610936 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAACCCGGATATCACAATTTGCACAATT
142610976 GCCTTCGGGCTTAGCCCGGGTAGCCCGGATATCACAATTTGCACAATT
1 GCCTTCGGGCTTA--------A-CCCGGATATCACAATTTGCACAATT
*
142611024 GCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAACCCGGATATCAC
142611050 TCGAACATTC
Statistics
Matches: 64, Mismatches: 1, Indels: 19
0.76 0.01 0.23
Matches are distributed among these distances:
39 16 0.25
40 9 0.14
47 1 0.02
48 38 0.59
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (39 bp):
GCCTTCGGGCTTAACCCGGATATCACAATTTGCACAATT
Found at i:142611022 original size:48 final size:48
Alignment explanation
Indices: 142610951--142611042 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
142610941 CGGGACTTAA
142610951 CCCGGATATCACAATTTGCACAATTGCCTTCGGGCTTAGCCCGGGTAG
1 CCCGGATATCACAATTTGCACAATTGCCTTCGGGCTTAGCCCGGGTAG
142610999 CCCGGATATCACAATTTGCACAATTGCCTTCGGGCTTAGCCCGG
1 CCCGGATATCACAATTTGCACAATTGCCTTCGGGCTTAGCCCGG
142611043 ATATCACTCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (48 bp):
CCCGGATATCACAATTTGCACAATTGCCTTCGGGCTTAGCCCGGGTAG
Found at i:142612666 original size:40 final size:40
Alignment explanation
Indices: 142612611--142612792 Score: 305
Period size: 40 Copynumber: 4.6 Consensus size: 40
142612601 TATTCGAATG
142612611 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
142612651 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
142612691 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
142612731 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
*
142612771 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
142612793 TACTTGGGTT
Statistics
Matches: 134, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 14 0.10
40 117 0.87
41 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:142616000 original size:47 final size:47
Alignment explanation
Indices: 142615930--142616366 Score: 696
Period size: 47 Copynumber: 9.3 Consensus size: 47
142615920 ATGATATACA
142615930 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* * *
142615977 TATATATGTGATAAGGCCTAATGGCCCATGTGATGAATGTGAAAGTG
1 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
142616024 CATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* * *
142616071 TATATATGTGATAAGGCCTAATGGCCCATGTGATGAATGTGAAAGTG
1 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
142616118 CATATGTGTGATAAGGCCGAATGGCCAATGTGAGGAATGTGAAAGTG
1 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
142616165 TATATATGTGATAAGGCCTAATGGCC-ATGTGATGAATGTGAAAGTG
1 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
142616211 CATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
142616258 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTG
1 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* * ** *
142616305 TATATATGTGATAAGGCCTAATGGCTGATATGATGAATGTGAAAGTG
1 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
142616352 CATATGTGTGATAAG
1 TATATGTGTGATAAG
142616367 TCCCGAAGGG
Statistics
Matches: 356, Mismatches: 33, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 42 0.12
47 314 0.88
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
Found at i:142616366 original size:234 final size:235
Alignment explanation
Indices: 142615930--142616366 Score: 768
Period size: 234 Copynumber: 1.9 Consensus size: 235
142615920 ATGATATACA
* *
142615930 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGCATATATGTGATAAGGCC
* *
142615995 TAATGGCCCATGTGATGAATGTGAAAGTGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGA
66 GAATGGCCAATGTGATGAATGTGAAAGTGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGA
*
142616060 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCCATGTGATGAATGTGAAAGTGCATATGT
131 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCCATATGATGAATGTGAAAGTGCATATGT
142616125 GTGATAAGGCCGAATGGCCAATGTGAGGAATGTGAAAGTG
196 GTGATAAGGCCGAATGGCCAATGTGAGGAATGTGAAAGTG
* *
142616165 TATATATGTGATAAGGCCTAATGGCC-ATGTGATGAATGTGAAAGTGCATATGTGTGATAAGGCC
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGCATATATGTGATAAGGCC
* *
142616229 GAATGGCCAATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGG
66 GAATGGCCAATGTGATGAATGTGAAAGTGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGA
**
142616294 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCTGATATGATGAATGTGAAAGTGCATATGT
131 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCCATATGATGAATGTGAAAGTGCATATGT
142616359 GTGATAAG
196 GTGATAAG
142616367 TCCCGAAGGG
Statistics
Matches: 191, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
234 167 0.87
235 24 0.13
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (235 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGCATATATGTGATAAGGCC
GAATGGCCAATGTGATGAATGTGAAAGTGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGA
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCCATATGATGAATGTGAAAGTGCATATGT
GTGATAAGGCCGAATGGCCAATGTGAGGAATGTGAAAGTG
Found at i:142622282 original size:41 final size:41
Alignment explanation
Indices: 142622148--142622407 Score: 380
Period size: 41 Copynumber: 6.3 Consensus size: 41
142622138 ACATAAAATT
* * *
142622148 TGCTAGGC-ATAAAGGCTGGTATAATACACCGGCACAGAGCC
1 TGCTAGGCAAT-AAGCCTGATATAATACACCGGCACAAAGCC
* * * *
142622189 TGCTA-GCAATGAGCCTGATATAATCCACCAGCATATAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGC--ACAAAGCC
142622231 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* *
142622272 TGCTATGCAATAAGCCTGATTTAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* *
142622313 TGCTAGGCAATAAGCCTGATTTAAAACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
142622354 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
142622395 TGCTAGGCAATAA
1 TGCTAGGCAATAA
142622408 AGCCCGAATA
Statistics
Matches: 198, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
40 19 0.10
41 144 0.73
42 11 0.06
43 24 0.12
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (41 bp):
TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
Found at i:142629227 original size:124 final size:124
Alignment explanation
Indices: 142629005--142629229 Score: 308
Period size: 124 Copynumber: 1.8 Consensus size: 124
142628995 GAATTATGTG
* * ** * * *
142629005 AAATGAAATATGGATGTATATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCGG
1 AAATGAAATATGAATGTATAATGATTATTGATGCATGTGTGCATGAGCAATTGAATGATACCCGG
* * **
142629070 GCTAAGTCCCGAAGGCGACTATGCTTGTGATTATATTTGCGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGACGACTATGCTGGAAATTATATTTGCGTTTGAGCCTTAGTAACGA
* *
142629129 AAATGAAATATGAATGTCTAATGATTATTGATGCATGTGTGCATGAGCAATTGAATGATATCCGG
1 AAATGAAATATGAATGTATAATGATTATTGATGCATGTGTGCATGAGCAATTGAATGATACCCGG
*
142629194 GCTAAGTCCCGAAGAC-AGTTATGCTGGAAATTATAT
66 GCTAAGTCCCGAAGACGA-CTATGCTGGAAATTATAT
142629230 CCGGGTTAAG
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
123 1 0.01
124 85 0.99
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (124 bp):
AAATGAAATATGAATGTATAATGATTATTGATGCATGTGTGCATGAGCAATTGAATGATACCCGG
GCTAAGTCCCGAAGACGACTATGCTGGAAATTATATTTGCGTTTGAGCCTTAGTAACGA
Found at i:142629351 original size:40 final size:40
Alignment explanation
Indices: 142629224--142629353 Score: 156
Period size: 40 Copynumber: 3.2 Consensus size: 40
142629214 ATGCTGGAAA
* *
142629224 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * * **
142629264 CTACATTCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
142629304 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
142629344 TTATATCCGG
1 TTATATCCGG
142629354 TTGTATTCCG
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
39 4 0.05
40 70 0.95
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:142637678 original size:42 final size:42
Alignment explanation
Indices: 142637615--142637769 Score: 199
Period size: 42 Copynumber: 3.7 Consensus size: 42
142637605 ACTAAGATTA
142637615 CGTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTT
1 CGTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTT
*
142637657 CGTATAAGACCATATCTGGGATATGGCATCGATATGAGACTT
1 CGTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTT
* * * * *
142637699 -GTGTAAGACCATAGT-TAGGCTATTAGCATTGATACT-AGATTT
1 CGTGTAAGACCATA-TCTGGGATA-TGGCATCGATA-TGAGACTT
*
142637741 CATGTAAGACCATATCTGGGATATGGCAT
1 CGTGTAAGACCATATCTGGGATATGGCAT
142637770 TGGTATGGTA
Statistics
Matches: 97, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
41 17 0.18
42 62 0.64
43 18 0.19
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATGGCATCGATATGAGACTT
Found at i:142640089 original size:40 final size:40
Alignment explanation
Indices: 142640017--142640228 Score: 212
Period size: 40 Copynumber: 5.3 Consensus size: 40
142640007 TCTTTGGGAT
** * *
142640017 TTAG-CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* * * * *
142640055 TTAGCCCGTATATGGTCGCTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* *
142640095 TTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGGTT
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* * * * * *
142640135 TTGGCCGGGATATAGTAACTCGCACAAATGCCTTTGGATC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* * * *
142640175 TTAGTCCGGATATAATCACTTAGCACAAAAGCCTTCGGGAC
1 TTAGCCCGGATATAGTCAC-TAGCACAAATGCCTTCGGGTC
142640216 TTAGCCCGGATAT
1 TTAGCCCGGATAT
142640229 CATTTGAATA
Statistics
Matches: 138, Mismatches: 33, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
38 4 0.03
39 13 0.09
40 93 0.67
41 28 0.20
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (40 bp):
TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
Found at i:142642896 original size:29 final size:29
Alignment explanation
Indices: 142642863--142642947 Score: 170
Period size: 29 Copynumber: 2.9 Consensus size: 29
142642853 GTGACGAGAT
142642863 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
142642892 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
142642921 TGGCACTAAGTGTGCGTGCTGGAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATA
142642948 ATTACGGGCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:142650594 original size:29 final size:29
Alignment explanation
Indices: 142650561--142650692 Score: 201
Period size: 29 Copynumber: 4.6 Consensus size: 29
142650551 GTGACGAGAT
142650561 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
142650590 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
142650619 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
** *
142650648 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
142650677 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
142650693 AGTTCGGAGG
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 94 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:142657790 original size:40 final size:40
Alignment explanation
Indices: 142657682--142657891 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
142657672 CGGGATTTAA
* * * * *
142657682 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
142657722 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
142657762 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
142657802 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
142657842 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
142657882 CCGGATATAT
1 CCGGATATAT
142657892 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:142663760 original size:40 final size:40
Alignment explanation
Indices: 142663703--142663900 Score: 310
Period size: 40 Copynumber: 5.0 Consensus size: 40
142663693 TCGAATGATG
* * * *
142663703 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
**
142663743 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
142663783 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
142663823 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
142663863 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
142663901 TAACCGTGTC
Statistics
Matches: 149, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
39 1 0.01
40 140 0.94
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:142686594 original size:24 final size:23
Alignment explanation
Indices: 142686563--142686607 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
142686553 TGATTTGGCC
*
142686563 ATATACATATATCCAT-TCATGGT
1 ATATACAT-TAACCATCTCATGGT
142686586 ATATCACATTAACCATCTCATG
1 ATAT-ACATTAACCATCTCATG
142686608 AACATTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (23 bp):
ATATACATTAACCATCTCATGGT
Found at i:142690301 original size:40 final size:40
Alignment explanation
Indices: 142690140--142690345 Score: 208
Period size: 40 Copynumber: 5.2 Consensus size: 40
142690130 TGAATGATAC
* *
142690140 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAAT-ATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-ATCATAT
* * *
142690180 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATCATAT
* *
142690220 CCGGGCTAAGA-CCGAAGGCATTCGTGCGAGTTG-TCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATCATAT
* * *
142690259 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATCATAT
* * * * *
142690299 CCGGGTTAAGA-CCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATCATAT
142690338 CC-GGCTAA
1 CCGGGCTAA
142690346 ATTCCGAAGA
Statistics
Matches: 142, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
38 6 0.04
39 55 0.39
40 81 0.57
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATCATAT
Found at i:142690338 original size:79 final size:79
Alignment explanation
Indices: 142690140--142690345 Score: 220
Period size: 79 Copynumber: 2.6 Consensus size: 79
142690130 TGAATGATAC
* * * ** *
142690140 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATATCCGGGCTAAGTCCCGAAGGCATTTA
1 CCGGGCTAAG-ACCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTTA
* ** *
142690205 TGCTAGTGATTATAT
65 TGCAAGTGACCAAAT
* * * *
142690220 CCGGGCTAAGACCGAAGGC-ATTCGTGCGAGTTGTCATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCGAAGGCAATT-GTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTTA
142690284 TGCAAGAT-ACCAAAT
65 TGCAAG-TGACCAAAT
* *
142690299 CCGGGTTAAGACCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAA
142690346 ATTCCGAAGA
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
78 8 0.08
79 82 0.79
80 14 0.13
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGACCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAGACCCGAAGGCATTTAT
GCAAGTGACCAAAT
Found at i:142697461 original size:37 final size:37
Alignment explanation
Indices: 142697408--142697498 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
142697398 TATAAAAGAA
142697408 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
142697445 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
142697482 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
142697499 TTCCAAGTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
37 46 0.92
38 4 0.08
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:142697649 original size:49 final size:49
Alignment explanation
Indices: 142697594--142697799 Score: 313
Period size: 49 Copynumber: 4.4 Consensus size: 49
142697584 TTTTACATTA
142697594 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
142697643 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
142697692 GCCATTAGG------C-C-T-TACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
142697732 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
142697781 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
142697800 CACATATGTA
Statistics
Matches: 144, Mismatches: 4, Indels: 18
0.87 0.02 0.11
Matches are distributed among these distances:
40 37 0.26
41 1 0.01
42 1 0.01
43 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 101 0.70
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:142697711 original size:89 final size:89
Alignment explanation
Indices: 142697615--142697794 Score: 324
Period size: 89 Copynumber: 2.0 Consensus size: 89
142697605 TTATCACATA
142697615 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACA
1 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACA
142697680 TTCACCACATCGGCCATTAGGCCT
66 TTCACCACATCGGCCATTAGGCCT
142697704 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACA
1 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACA
* * * *
142697769 TTCATCGCATTGGCCATTCGGCCT
66 TTCACCACATCGGCCATTAGGCCT
142697793 TA
1 TA
142697795 TCACACACAT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.29
Consensus pattern (89 bp):
TACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACA
TTCACCACATCGGCCATTAGGCCT
Found at i:142701226 original size:29 final size:29
Alignment explanation
Indices: 142701190--142701382 Score: 341
Period size: 29 Copynumber: 6.7 Consensus size: 29
142701180 TGTTGAAAAA
*
142701190 CTCGCACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
*
142701219 CTCGCACACGTAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
*
142701248 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
*
142701277 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
142701306 CTCGCACACATAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
*
142701335 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCAATTACTGAT
142701364 CTCGCACACATAGTGCCTC
1 CTCGCACACATAGTGCCTC
142701383 TATTCATTCG
Statistics
Matches: 158, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 158 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCAATTACTGAT
Found at i:142701639 original size:39 final size:39
Alignment explanation
Indices: 142701556--142701757 Score: 289
Period size: 40 Copynumber: 5.1 Consensus size: 39
142701546 CGAATACACG
* *
142701556 TCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
* *
142701596 TCACTAGCACGAATGCTCTTCGGACTTTGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
*
142701635 TCACTAGCACGAATGCTCTTCGGACTT-GCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
* *
142701673 TCACTAGCATGAATGCTCTTCGGAACTTAGTCCGGATATA
1 TCACTAGCATGAATGCTCTTCGG-ACTTAGCCCGGATACA
* *
142701713 TCACTAGCATGAATGCTCTTCGGAACTTAGTCCGGATATA
1 TCACTAGCATGAATGCTCTTCGG-ACTTAGCCCGGATACA
142701753 TCACT
1 TCACT
142701758 CTCAATTCTC
Statistics
Matches: 153, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
38 33 0.22
39 47 0.31
40 73 0.48
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (39 bp):
TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
Found at i:142703627 original size:37 final size:37
Alignment explanation
Indices: 142703574--142703664 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
142703564 TATAAAAGAA
142703574 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
142703611 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
142703648 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
142703665 TTCCAAGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
37 46 0.92
38 4 0.08
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:142703815 original size:49 final size:49
Alignment explanation
Indices: 142703760--142704005 Score: 330
Period size: 49 Copynumber: 5.4 Consensus size: 49
142703750 TTTTACATTA
142703760 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
142703809 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
142703858 GCCATTAGG------C-C-T-TACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
142703898 GCCATTAGG------C-C-T-TACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
142703938 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
142703987 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
142704006 CACATATGTA
Statistics
Matches: 184, Mismatches: 4, Indels: 18
0.89 0.02 0.09
Matches are distributed among these distances:
40 77 0.42
41 1 0.01
42 1 0.01
43 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 101 0.55
ACGTcount: A:0.28, C:0.33, G:0.10, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:142703874 original size:40 final size:40
Alignment explanation
Indices: 142703830--142703951 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
142703820 TTATCACATA
142703830 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCT
1 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCT
142703870 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCT
1 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCT
142703910 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCT
1 TACATACACTTTCACATTCACCACATCGGCCATTAGGCCT
142703950 TA
1 TA
142703952 TCACATATAC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.28, C:0.34, G:0.10, T:0.28
Consensus pattern (40 bp):
TACATACACTTTCACATTCACCACATCGGCCATTAGGCCT
Found at i:142707605 original size:45 final size:46
Alignment explanation
Indices: 142707542--142707710 Score: 274
Period size: 45 Copynumber: 3.8 Consensus size: 46
142707532 TATATATACA
142707542 CATCTCATACA--TTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
*
142707586 CATCTC-TACACGTTTCGCATTAGCCATTCGACTTTACCTCATATC
1 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
142707631 CATCTCATACACGTTTCGCATTAGCCATTC-GCTTTACCTCATATC
1 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
* * *
142707676 CATCTCTTACACATTTCACATTAGCCATTCGGCTT
1 CATCTCATACACGTTTCGCATTAGCCATTCGGCTT
142707711 CGCCACATAT
Statistics
Matches: 116, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
43 4 0.03
44 6 0.05
45 79 0.68
46 27 0.23
ACGTcount: A:0.22, C:0.33, G:0.09, T:0.36
Consensus pattern (46 bp):
CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
Found at i:142707698 original size:91 final size:89
Alignment explanation
Indices: 142707542--142707706 Score: 278
Period size: 91 Copynumber: 1.8 Consensus size: 89
142707532 TATATATACA
* *
142707542 CATCTCATACATTTCGCATTAGCCATTCGGCTTTACCTCATATCCATCTCTACACGTTTCGCATT
1 CATCTCATACATTTCGCATTAGCCATTCGGCTTTACCTCATATCCATCTCTACACATTTCACATT
142707607 AGCCATTCGACTTTACCTCATATC
66 AGCCATTCGACTTTACCTCATATC
142707631 CATCTCATACACGTTTCGCATTAGCCATTC-GCTTTACCTCATATCCATCTCTTACACATTTCAC
1 CATCTCATACA--TTTCGCATTAGCCATTCGGCTTTACCTCATATCCATCTC-TACACATTTCAC
142707695 ATTAGCCATTCG
63 ATTAGCCATTCG
142707707 GCTTCGCCAC
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
89 11 0.15
90 21 0.30
91 39 0.55
ACGTcount: A:0.23, C:0.33, G:0.08, T:0.36
Consensus pattern (89 bp):
CATCTCATACATTTCGCATTAGCCATTCGGCTTTACCTCATATCCATCTCTACACATTTCACATT
AGCCATTCGACTTTACCTCATATC
Found at i:142707751 original size:47 final size:47
Alignment explanation
Indices: 142707734--142708026 Score: 505
Period size: 47 Copynumber: 6.2 Consensus size: 47
142707724 CACTTCCACG
** *
142707734 TTCATCACATTGGCCATTCTACCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
* * *
142707781 TTCATCACGTTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
*
142707828 TTCATCACGTTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
142707875 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
142707922 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
*
142707969 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
*
142708016 TTCATTACATT
1 TTCATCACATT
142708027 AAATCCTAAA
Statistics
Matches: 237, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 237 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
Found at i:142707810 original size:22 final size:22
Alignment explanation
Indices: 142707784--142707857 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
142707774 GTTCACATTC
142707784 ATCACGTTGGCCATTCGGCCTT
1 ATCACGTTGGCCATTCGGCCTT
* * *
142707806 ATCACATATGTG-CATGTTC-ACATT
1 ATCACGT-TG-GCCA--TTCGGCCTT
142707830 CATCACGTTGGCCATTCGGCCTT
1 -ATCACGTTGGCCATTCGGCCTT
142707853 ATCAC
1 ATCAC
142707858 ACATATGCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 14 0.36
23 8 0.21
24 8 0.21
25 9 0.23
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (22 bp):
ATCACGTTGGCCATTCGGCCTT
Found at i:142707929 original size:25 final size:25
Alignment explanation
Indices: 142707853--142707977 Score: 76
Period size: 23 Copynumber: 5.2 Consensus size: 25
142707843 ATTCGGCCTT
142707853 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
* *
142707878 AT--CACAT-TGGCCA--TTCGGCCTT-
1 ATCACACATAT-G-CATGTTC-ACATTC
142707900 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
* *
142707925 AT--CACAT-TGGCCA--TTCGGCCTT-
1 ATCACACATAT-G-CATGTTC-ACATTC
142707947 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
142707972 ATCACA
1 ATCACA
142707978 TTGGCCATTC
Statistics
Matches: 74, Mismatches: 8, Indels: 36
0.63 0.07 0.31
Matches are distributed among these distances:
22 12 0.16
23 22 0.30
24 22 0.30
25 18 0.24
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.31
Consensus pattern (25 bp):
ATCACACATATGCATGTTCACATTC
Found at i:142708057 original size:94 final size:94
Alignment explanation
Indices: 142707691--142708026 Score: 514
Period size: 94 Copynumber: 3.6 Consensus size: 94
142707681 CTTACACATT
* ** * * * *
142707691 TCACATTAGCCATTCGG-CTTCGCCACATATATACACT-TCCACGTTCATCACATTGGCCATTCT
1 TCACATTGGCCATTCGGCCTT-ATCACATATATGCA-TGTTCACATTCATCACATTGGCCATTCG
* *
142707754 ACCTTATCACATATATGCATGTTCACATTCA
64 GCCTTATCACACATATGCATGTTCACATTCA
* * *
142707785 TCACGTTGGCCATTCGGCCTTATCACATATGTGCATGTTCACATTCATCACGTTGGCCATTCGGC
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
142707850 CTTATCACACATATGCATGTTCACATTCA
66 CTTATCACACATATGCATGTTCACATTCA
*
142707879 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
142707944 CTTATCACACATATGCATGTTCACATTCA
66 CTTATCACACATATGCATGTTCACATTCA
*
142707973 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATTACATT
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATT
142708027 AAATCCTAAA
Statistics
Matches: 222, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
93 1 0.00
94 218 0.98
95 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (94 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
CTTATCACACATATGCATGTTCACATTCA
Found at i:142709828 original size:2 final size:2
Alignment explanation
Indices: 142709821--142709852 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
142709811 ACATTCGGCA
142709821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
142709853 GACTAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142711289 original size:25 final size:25
Alignment explanation
Indices: 142711256--142711308 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
142711246 CGGTTAAAGA
142711256 ATTCGCACACACAGTGCCTCA-ATTC
1 ATTCGCACACACAGTGCCT-ATATTC
*
142711281 ATTCGCACACATAGTGCCTATATTC
1 ATTCGCACACACAGTGCCTATATTC
142711306 ATT
1 ATT
142711309 TGTTATTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (25 bp):
ATTCGCACACACAGTGCCTATATTC
Found at i:142711565 original size:40 final size:40
Alignment explanation
Indices: 142711469--142711866 Score: 595
Period size: 40 Copynumber: 10.0 Consensus size: 40
142711459 GCCTGATTAC
* **
142711469 ACATCACTGGCACGAATGC-CTTTAGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
** * * * *
142711508 GTAACACCAGCACGAATGCTCTTCGAGACTTAGCCTGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
*
142711548 ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
142711588 ATAACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
142711628 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
142711668 ATAACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
142711708 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
*
142711748 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCAGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
142711788 ATAACACCAGCACGAATGCTCTTC-GGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
142711827 ACATCACTAGCACGAATGCTCTTC-GGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
142711866 A
1 A
142711867 TATATAACTC
Statistics
Matches: 321, Mismatches: 37, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 65 0.20
40 256 0.80
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
Found at i:142713531 original size:46 final size:46
Alignment explanation
Indices: 142713349--142713521 Score: 301
Period size: 46 Copynumber: 3.8 Consensus size: 46
142713339 TATATATACA
* *
142713349 CATCTCATACGCGTTCCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
142713395 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
*
142713441 CATCTCATACACGTTTCGCATTAGCCATTCGACTTTACCTCATATC
1 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
* *
142713487 CATCTCATACACATTTCGTATTAGCCATTCGGCTT
1 CATCTCATACACGTTTCGCATTAGCCATTCGGCTT
142713522 CGCCACATAT
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 121 1.00
ACGTcount: A:0.22, C:0.32, G:0.11, T:0.35
Consensus pattern (46 bp):
CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
Found at i:142713574 original size:22 final size:22
Alignment explanation
Indices: 142713548--142713810 Score: 82
Period size: 22 Copynumber: 11.3 Consensus size: 22
142713538 TTCCACGTTC
*
142713548 ATCACATTGGCCATTCTACCTT
1 ATCACATTGGCCATTCGACCTT
* *
142713570 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGACCTT
* *
142713594 CATCACGTTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
* *
142713617 ATCACATATGTGCATATTC-ACATT
1 ATCACAT-TG-GC-CATTCGACCTT
*
142713641 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
*
142713664 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGACCTT
*
142713688 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
*
142713711 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGACCTT
142713735 CATCACATTGGCCATTCG-CCTT
1 -ATCACATTGGCCATTCGACCTT
* *
142713757 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGACCTT
*
142713781 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
142713804 ATCACAT
1 ATCACAT
142713811 ATATGCATGT
Statistics
Matches: 178, Mismatches: 25, Indels: 76
0.64 0.09 0.27
Matches are distributed among these distances:
21 7 0.04
22 48 0.27
23 38 0.21
24 46 0.26
25 39 0.22
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGACCTT
Found at i:142713576 original size:47 final size:47
Alignment explanation
Indices: 142713545--142713836 Score: 505
Period size: 47 Copynumber: 6.2 Consensus size: 47
142713535 CACTTCCACG
**
142713545 TTCATCACATTGGCCATTCTACCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * *
142713592 TTCATCACGTTGGCCATTCGGCCTTATCACATATGTGCATATTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
142713639 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
142713686 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
142713733 TTCATCACATTGGCCATTC-GCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
142713779 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
142713826 TTCATTACATT
1 TTCATCACATT
142713837 AAATCCTAAA
Statistics
Matches: 233, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
46 45 0.19
47 188 0.81
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:142713867 original size:140 final size:140
Alignment explanation
Indices: 142713568--142713849 Score: 415
Period size: 140 Copynumber: 2.0 Consensus size: 140
142713558 CCATTCTACC
* * *
142713568 TTATCACATATATGCATGTTCACATTCATCACGTTGGCCATTCGGCCTTATCACATATGTGCATA
1 TTATCACAAATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATA
142713633 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
66 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATT-
** * ***
142713698 GCCATTCGGCC
130 GAAATCCGAAA
* *
142713709 TTATCACACATATGCATGTTCACATTCATCACATTGGCCATTC-GCCTTATCACATATATGCATG
1 TTATCACAAATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATA
* *
142713773 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATTACATT-
66 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
*
142713837 AAATCCTAAA
131 AAATCCGAAA
142713847 TTA
1 TTA
142713850 AAATATAAAT
Statistics
Matches: 128, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
138 6 0.05
140 81 0.63
141 41 0.32
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.34
Consensus pattern (140 bp):
TTATCACAAATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATA
TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTG
AAATCCGAAA
Found at i:142717804 original size:18 final size:18
Alignment explanation
Indices: 142717781--142717827 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
142717771 TGGCCCATTG
142717781 CAGTAACAATAGA-CAGTA
1 CAGTAACAATA-ATCAGTA
* *
142717799 CAGTAACAGTAATCAGTG
1 CAGTAACAATAATCAGTA
142717817 CAGTAACAATA
1 CAGTAACAATA
142717828 TACAAGTCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (18 bp):
CAGTAACAATAATCAGTA
Found at i:142718355 original size:27 final size:27
Alignment explanation
Indices: 142718153--142718340 Score: 268
Period size: 27 Copynumber: 7.0 Consensus size: 27
142718143 ACACAGGGGA
* * *
142718153 AAAATAGTCATCTTACCATATAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
* *
142718180 AAAATAGTCATTTTACCACATAAGGGA
1 AAAACAGTCATTTTACCACATAAGGGC
*
142718207 AAAATAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
*
142718234 AAAACAGTCATTTTACCATATAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
* *
142718261 AAAACAGTCATTTTACAACATAAGAGC
1 AAAACAGTCATTTTACCACATAAGGGC
* *
142718288 AAAACAATCATTTTACCACATAAGGGA
1 AAAACAGTCATTTTACCACATAAGGGC
*
142718315 AAAACAGTCATTTTACCACATCAGGG
1 AAAACAGTCATTTTACCACATAAGGG
142718341 TAAGATAGTT
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 146 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (27 bp):
AAAACAGTCATTTTACCACATAAGGGC
Found at i:142722281 original size:51 final size:51
Alignment explanation
Indices: 142722224--142722616 Score: 667
Period size: 51 Copynumber: 7.9 Consensus size: 51
142722214 GTATGAGATA
*
142722224 TATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
*
142722275 TATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
142722326 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
142722377 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
*
142722428 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
* *
142722479 TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGT-AAA-AG--TG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
* *
142722526 TATATATGTGATGAGGCCTAAGGGCCGATGTGATGAATGTGAAA--G--TG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
142722573 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
142722617 TATATGTGCG
Statistics
Matches: 333, Mismatches: 8, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
47 85 0.26
48 3 0.01
49 1 0.00
50 3 0.01
51 241 0.72
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.31
Consensus pattern (51 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATG
Found at i:142722806 original size:37 final size:36
Alignment explanation
Indices: 142722751--142722837 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 36
142722741 AACTTGGAAA
142722751 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGT-AGACCCGATGACTACGTGTGGAGAT
142722789 TATGTCCGGGTACGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTA-GACCCGATGACTACGTGTGGAGAT
*
142722826 TATGTCTGGGTA
1 TATGTCCGGGTA
142722838 AGACTTCGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.89
38 4 0.09
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (36 bp):
TATGTCCGGGTAGACCCGATGACTACGTGTGGAGAT
Found at i:142731244 original size:12 final size:12
Alignment explanation
Indices: 142731227--142731251 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
142731217 TTTTGGATGA
142731227 ATTTGATTGAAT
1 ATTTGATTGAAT
142731239 ATTTGATTGAAT
1 ATTTGATTGAAT
142731251 A
1 A
142731252 AGTTTAATTT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
ATTTGATTGAAT
Found at i:142731704 original size:41 final size:41
Alignment explanation
Indices: 142731598--142731708 Score: 120
Period size: 40 Copynumber: 2.7 Consensus size: 41
142731588 GATATTCGGG
* * * *
142731598 CTTTGAGCCTAGTAAGCCTTGTGCTGGTGAATTAAATCAGG
1 CTTTGAGCCTAGTAAGCCTTGTGCCGGTGTATAAAATCAGA
*
142731639 C-TT-ATGCCTAGTAAG-CTTATTGCCGGTGTATAAAATCAGA
1 CTTTGA-GCCTAGTAAGCCTT-GTGCCGGTGTATAAAATCAGA
* *
142731679 CTTTGAGTCTAGTAGGCCTTGTGCCGGTGT
1 CTTTGAGCCTAGTAAGCCTTGTGCCGGTGT
142731709 GAGATACAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
39 4 0.07
40 29 0.51
41 20 0.35
42 4 0.07
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (41 bp):
CTTTGAGCCTAGTAAGCCTTGTGCCGGTGTATAAAATCAGA
Found at i:142747696 original size:46 final size:46
Alignment explanation
Indices: 142747625--142747797 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
142747615 TGTAACCCGC
* **
142747625 CCATAAGCGAACTCGGACTCTACTCAACGAACTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
142747671 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
142747721 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
142747764 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC
142747798 AGATGCTCAA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 58 0.55
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:142747745 original size:93 final size:93
Alignment explanation
Indices: 142747632--142747803 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
142747622 CGCCCATAAG
* * *
142747632 CGAACTCGGACTCTACTCAACGAACTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
142747697 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCAGATGCCTAGTTACATCTCA
**
142747725 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
142747790 ACGAGTTCAGATGC
66 ACGAGTTCAGATGC
142747804 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCAGATGCCTAGTTACATCTCA
Found at i:142747819 original size:46 final size:44
Alignment explanation
Indices: 142747676--142747819 Score: 123
Period size: 46 Copynumber: 3.1 Consensus size: 44
142747666 CGCATCCATA
*
142747676 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCC-A---ACCATCT
* * * * *
142747723 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTC--AGATGC-CAACCATCT
142747769 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGC-CAACCAT-CT
142747815 AGTGA
1 AGTGA
142747820 CATGTCACTT
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
44 10 0.13
45 1 0.01
46 31 0.40
47 29 0.38
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCAACCATCT
Found at i:142757165 original size:28 final size:28
Alignment explanation
Indices: 142757100--142757200 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
142757090 ATAGTGAATC
*
142757100 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
142757129 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
142757157 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
142757187 CGCACACTTAGTGC
1 CGCACACTTAGTGC
142757201 CATACCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:142757249 original size:29 final size:29
Alignment explanation
Indices: 142757217--142757289 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
142757207 CTTCGAGCTC
*
142757217 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
142757246 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
142757275 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
142757290 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:142759524 original size:20 final size:20
Alignment explanation
Indices: 142759499--142759557 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
142759489 TAAATATGGT
142759499 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
142759519 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
142759539 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
142759558 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:142759635 original size:24 final size:24
Alignment explanation
Indices: 142759608--142759750 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
142759598 GAGGAAGTGA
*
142759608 AAAAGGGCTTATGCCCTAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
142759632 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
142759656 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
142759679 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
142759703 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
142759727 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
142759751 ATGATAAAGC
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:142759700 original size:47 final size:47
Alignment explanation
Indices: 142759608--142759750 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
142759598 GAGGAAGTGA
*
142759608 AAAAGGGCTTATGCCCTAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
142759656 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
142759703 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
142759751 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
47 43 0.49
48 33 0.38
49 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:142759724 original size:71 final size:72
Alignment explanation
Indices: 142759608--142759751 Score: 211
Period size: 71 Copynumber: 2.0 Consensus size: 72
142759598 GAGGAAGTGA
* *
142759608 AAAAGGGCTTATGCCCTAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
142759671 CCAGTTAT
65 CCAGTTAT
** * *
142759679 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
142759744 CAGTTAT
66 CAGTTAT
142759751 A
1 A
142759752 TGATAAAGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 53 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:142759977 original size:31 final size:31
Alignment explanation
Indices: 142759942--142760036 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
142759932 CGTTTACAGT
142759942 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
142759973 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
142760004 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
142760035 AA
1 AA
142760037 TATGAAAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:142765854 original size:24 final size:24
Alignment explanation
Indices: 142765826--142765881 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
142765816 TCCTAAAATC
*
142765826 CCTCCATAATCCTCTCCTTGATTT
1 CCTCCACAATCCTCTCCTTGATTT
* * * *
142765850 TCTCCCCCATCCTTTCCTTGATTT
1 CCTCCACAATCCTCTCCTTGATTT
142765874 CCTCCACA
1 CCTCCACA
142765882 TAACACTCCC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.43, G:0.04, T:0.39
Consensus pattern (24 bp):
CCTCCACAATCCTCTCCTTGATTT
Found at i:142767427 original size:45 final size:45
Alignment explanation
Indices: 142767359--142767477 Score: 195
Period size: 45 Copynumber: 2.7 Consensus size: 45
142767349 CAGCACTAAA
142767359 CAGT-ATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
1 CAGTGATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
* *
142767403 CAGTGATTTGCAGTAGAGTTGCCAGTATAATAGGCTTAGAGCCAT
1 CAGTGATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
* *
142767448 CAGTGATTTGTAGCAGAGCTGCTAGTATAA
1 CAGTGATTTGCAGCAGAGCTGCCAGTATAA
142767478 AACACTTCCT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 4 0.06
45 64 0.94
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (45 bp):
CAGTGATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
Found at i:142767753 original size:54 final size:54
Alignment explanation
Indices: 142767636--142767794 Score: 201
Period size: 54 Copynumber: 2.9 Consensus size: 54
142767626 TCACATAGGA
* * * *
142767636 CAAAACAGTAATCTTACCATATAAGGGCAAAACAATCATTTCACCACATAAAGG
1 CAAAACAGTCATTTTACCATATAAGGGTAAAACAGTCATTTCACCACATAAAGG
* *
142767690 CAAAACAGTCATTTTACCATATAAGGGTAAAACAGTCATTTGACCATATAAAGG
1 CAAAACAGTCATTTTACCATATAAGGGTAAAACAGTCATTTCACCACATAAAGG
* * * * * * *
142767744 CAAAACAGTCATTTTTCAACATAAGGGTAATATAGTCATTTTATCACATAA
1 CAAAACAGTCATTTTACCATATAAGGGTAAAACAGTCATTTCACCACATAA
142767795 GGGCTCTAGG
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.26
Consensus pattern (54 bp):
CAAAACAGTCATTTTACCATATAAGGGTAAAACAGTCATTTCACCACATAAAGG
Found at i:142767767 original size:27 final size:27
Alignment explanation
Indices: 142767627--142767798 Score: 175
Period size: 27 Copynumber: 6.4 Consensus size: 27
142767617 ATATTTACAT
* * *
142767627 CACAT-AGGACAAAACAGTAATCTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
142767653 CATATAAGGGCAAAACAATCATTTCAC
1 CACATAAGGGCAAAACAGTCATTTTAC
*
142767680 CACATAAAGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
142767707 CATATAAGGGTAAAACAGTCATTTGAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
142767734 CATATAAAGGCAAAACAGTCATTTTTC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * * * *
142767761 AACATAAGGGTAATATAGTCATTTTAT
1 CACATAAGGGCAAAACAGTCATTTTAC
142767788 CACATAAGGGC
1 CACATAAGGGC
142767799 TCTAGGTAAA
Statistics
Matches: 117, Mismatches: 28, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
26 4 0.03
27 113 0.97
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:142767781 original size:81 final size:81
Alignment explanation
Indices: 142767637--142767797 Score: 198
Period size: 81 Copynumber: 2.0 Consensus size: 81
142767627 CACATAGGAC
* *
142767637 AAAACAGTAATCTTACCATATAAGGGCAAAACAATCATTTCACCACATAAAGGCAAAACAGTCAT
1 AAAACAGTAATCTTACCATATAAAGGCAAAACAATCATTTCACAACATAAAGGCAAAACAGTCAT
*
142767702 TTTACCATATAAGGGT
66 TTTACCACATAAGGGT
* * ** * * * *
142767718 AAAACAGTCAT-TTGACCATATAAAGGCAAAACAGTCATTTTTCAACATAAGGGTAATATAGTCA
1 AAAACAGTAATCTT-ACCATATAAAGGCAAAACAATCATTTCACAACATAAAGGCAAAACAGTCA
*
142767782 TTTTATCACATAAGGG
65 TTTTACCACATAAGGG
142767798 CTCTAGGTAA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 2 0.03
81 65 0.97
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (81 bp):
AAAACAGTAATCTTACCATATAAAGGCAAAACAATCATTTCACAACATAAAGGCAAAACAGTCAT
TTTACCACATAAGGGT
Found at i:142768186 original size:18 final size:18
Alignment explanation
Indices: 142768163--142768198 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
142768153 ACACCTGCTA
142768163 GGATACTAGGTACGCAAC
1 GGATACTAGGTACGCAAC
142768181 GGATACTAGGTACGCAAC
1 GGATACTAGGTACGCAAC
142768199 TCTTTCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (18 bp):
GGATACTAGGTACGCAAC
Found at i:142773627 original size:26 final size:25
Alignment explanation
Indices: 142773519--142773626 Score: 141
Period size: 25 Copynumber: 4.4 Consensus size: 25
142773509 CTGGAGGCTT
*
142773519 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTGATAAACTGGGGCAAA
142773543 AGCCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
*
142773568 AGCCCTTTTAATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
* *
142773593 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTT-GATAAACTGGGGCAAA
142773619 A-CCCTTTT
1 AGCCCTTTT
142773627 TGCACTTCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.09
24 13 0.17
25 42 0.55
26 14 0.18
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:142773697 original size:20 final size:20
Alignment explanation
Indices: 142773674--142773720 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
142773664 TTATGAATAC
*
142773674 ATCATGTGCATATCATA-CA
1 ATCATGTGCACATCATATCA
142773693 TATCATGTGCACATCATATCA
1 -ATCATGTGCACATCATATCA
142773714 ATCATGT
1 ATCATGT
142773721 ATATTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCACATCATATCA
Found at i:142781797 original size:20 final size:20
Alignment explanation
Indices: 142781768--142781812 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
142781758 ATCACATGTA
* *
142781768 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
142781788 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
142781808 TTCAT
1 TTCAT
142781813 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:142785054 original size:13 final size:13
Alignment explanation
Indices: 142785036--142785087 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
142785026 AGTTTGGAAA
142785036 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
142785049 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
142785062 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
142785075 T-CTTTTGAAAAG
1 TGCTTTTGAAAAG
142785087 T
1 T
142785088 TTAGTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:142787915 original size:29 final size:29
Alignment explanation
Indices: 142787882--142787983 Score: 177
Period size: 29 Copynumber: 3.5 Consensus size: 29
142787872 GTGACGAGAT
142787882 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
142787911 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* *
142787940 TGGCACTGATTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
142787969 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
142787984 GAGCTCGAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:142788000 original size:58 final size:59
Alignment explanation
Indices: 142787882--142788043 Score: 188
Period size: 58 Copynumber: 2.8 Consensus size: 59
142787872 GTGACGAGAT
* * *
142787882 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTGGAAAAATA
1 TGGCACTGATTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAAATA
***
142787940 TGGCACTGATTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTGATTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAAATA
* * **
142787998 TGGCACTG-TGTGTGCTTGCT-TAAATCGCATGGCACTAAGTGTGCGA
1 TGGCACTGAT-TGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
142788044 AATCGAGTAT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
57 5 0.05
58 85 0.93
59 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (59 bp):
TGGCACTGATTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAAATA
Found at i:142794794 original size:80 final size:80
Alignment explanation
Indices: 142794710--142794858 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
142794700 TATGGTAACC
* * * *
142794710 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
142794774 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
142794790 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
142794855 CCGG
66 CCGG
142794859 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:142794800 original size:40 final size:38
Alignment explanation
Indices: 142794751--142794858 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
142794741 ATCACGATTT
*
142794751 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
142794791 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
142794831 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
142794859 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:142802902 original size:80 final size:80
Alignment explanation
Indices: 142802818--142802966 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
142802808 TATGGTAACC
* * * *
142802818 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
142802882 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
142802898 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
142802963 CCGG
66 CCGG
142802967 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:142802908 original size:40 final size:38
Alignment explanation
Indices: 142802859--142802966 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
142802849 ATCACGATTT
*
142802859 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
142802899 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
142802939 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
142802967 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:142805350 original size:46 final size:46
Alignment explanation
Indices: 142805300--142805472 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
142805290 TGGTTGAGCA
*
142805300 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
142805346 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
142805393 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
142805439 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
142805473 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:142805456 original size:93 final size:93
Alignment explanation
Indices: 142805297--142805467 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
142805287 GGATGGTTGA
* *
142805297 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
142805362 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
142805390 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
142805455 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
142805468 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:142812925 original size:46 final size:46
Alignment explanation
Indices: 142812872--142813044 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
142812862 TGGTTGAGCA
*
142812872 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
142812918 TCCGAACTCGTTGAGTTGAGTCCAAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
142812965 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGAGGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
142813011 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
142813045 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 59 0.57
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:142821944 original size:68 final size:68
Alignment explanation
Indices: 142821795--142821952 Score: 153
Period size: 68 Copynumber: 2.3 Consensus size: 68
142821785 CTAGCCGATT
* * * *
142821795 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACTCATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
*
142821860 TTTA
65 TATA
* * *
142821864 TCTCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
142821926 CTATATA
63 C-ATATA
142821933 GTATCTCGTAGC-CTTCTTGT
1 -TATCTCGTAGCTC-TCTTGT
142821953 ACACATGATG
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.45
69 8 0.11
70 6 0.08
71 26 0.35
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAT
ATA
Found at i:142823909 original size:13 final size:13
Alignment explanation
Indices: 142823891--142823915 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
142823881 CCAAGCACAC
142823891 GCCCGTGTCCTTA
1 GCCCGTGTCCTTA
142823904 GCCCGTGTCCTT
1 GCCCGTGTCCTT
142823916 CATATGGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.40, G:0.24, T:0.32
Consensus pattern (13 bp):
GCCCGTGTCCTTA
Found at i:142831179 original size:23 final size:23
Alignment explanation
Indices: 142831151--142831195 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
142831141 GTGTGCAAGA
*
142831151 TAGTTCATCGAATACTCGGATAT
1 TAGTTCATCGAATACTCAGATAT
142831174 TAGTTCATCGAATACTCAGATA
1 TAGTTCATCGAATACTCAGATA
142831196 GTATTGTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (23 bp):
TAGTTCATCGAATACTCAGATAT
Found at i:142833185 original size:40 final size:40
Alignment explanation
Indices: 142833102--142833254 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 40
142833092 TCGAATGATG
* *
142833102 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAA
* **
142833142 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAA
* **
142833182 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCT-ATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACCA-AA
* * *
142833223 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
142833255 CGCTATATCC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 81 0.86
41 11 0.12
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:142841222 original size:40 final size:40
Alignment explanation
Indices: 142841139--142841291 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 40
142841129 TCGAATGATG
* *
142841139 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAA
* **
142841179 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAA
* **
142841219 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCT-ATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACCA-AA
* * *
142841260 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
142841292 CGCTATATCC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 81 0.86
41 11 0.12
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:142843665 original size:39 final size:39
Alignment explanation
Indices: 142843570--142843765 Score: 193
Period size: 39 Copynumber: 5.0 Consensus size: 39
142843560 ACTTGAAACC
** **
142843570 AATTACCAGCACA-AGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACATAGCCTGC-GGACCTTAAGTCCGGATAT
* * * * *
142843609 AATACCAGCTAGA-AGCCTGCTGGA-CTTTAGCCCGGACAT
1 AATTCCAGC-ACATAGCCTGC-GGACCTTAAGTCCGGATAT
* *
142843648 ATTTCCAGCACATAGCCTACGGACCTTAAGTCCGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
* *
142843687 AATTCCAGCACATAGCCTGTGGACCCTAAGTCCGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
* *
142843726 AATTCCAGCACATAGCCTGCGGACCCTAAGTCTGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
142843765 A
1 A
142843766 CATCACTGAA
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
38 18 0.14
39 115 0.86
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (39 bp):
AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
Found at i:142846470 original size:2 final size:2
Alignment explanation
Indices: 142846463--142846496 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
142846453 TTGGTTGTCT
142846463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
142846497 CCTTCGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:142847277 original size:49 final size:49
Alignment explanation
Indices: 142847150--142847366 Score: 352
Period size: 49 Copynumber: 4.5 Consensus size: 49
142847140 CCCTTCGGGA
* *
142847150 CTTATCACAT-T-TATACACTTTCACATTCATCACATTGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
142847197 CTTATCAC--ATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
142847244 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTTGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
142847293 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
142847342 CTTATCACATATATATACACTTTCA
1 CTTATCACATATATATACACTTTCA
142847367 TGTACAGACT
Statistics
Matches: 156, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
46 1 0.01
47 49 0.31
49 106 0.68
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:142848667 original size:2 final size:2
Alignment explanation
Indices: 142848626--142848658 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
142848616 TAAGGCATAC
142848626 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
142848659 CCTATATATG
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:142850703 original size:28 final size:28
Alignment explanation
Indices: 142850672--142850808 Score: 114
Period size: 29 Copynumber: 4.8 Consensus size: 28
142850662 ACTGACCGAT
**
142850672 CTCGCACACATAGTGCTCGGTTGGAGAA
1 CTCGCACACATAGTGCTCGGTTACAGAA
* ** * *
142850700 CTCGCACACACAGTGCCTCATTTACCGAT
1 CTCGCACACATAGTG-CTCGGTTACAGAA
*
142850729 CTCGCTCACATAGTGCTCGGTTA-AGGAA
1 CTCGCACACATAGTGCTCGGTTACA-GAA
* * ** * *
142850757 TTCGCACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTG-CTCGGTTACAGAA
142850786 CTCGCACACATAGTGCTCGGTTA
1 CTCGCACACATAGTGCTCGGTTA
142850809 AAGGAATTCA
Statistics
Matches: 81, Mismatches: 24, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
28 40 0.49
29 41 0.51
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (28 bp):
CTCGCACACATAGTGCTCGGTTACAGAA
Found at i:142850739 original size:57 final size:57
Alignment explanation
Indices: 142850666--142850814 Score: 228
Period size: 57 Copynumber: 2.6 Consensus size: 57
142850656 GTGCCCACTG
* *
142850666 ACCGATCTCGCACACATAGTGCTCGGTT-GGAGAACTCGCACACACAGTGCCTCATTT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAG-GAACTCGCACACACAGTGCCTCAATT
* *
142850723 ACCGATCTCGCTCACATAGTGCTCGGTTAAGGAATTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAGGAACTCGCACACACAGTGCCTCAATT
*
142850780 ACTGATCTCGCACACATAGTGCTCGGTTAAAGGAA
1 ACCGATCTCGCACACATAGTGCTCGGTT-AAGGAA
142850815 TTCATACGGT
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
57 77 0.92
58 7 0.08
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (57 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAGGAACTCGCACACACAGTGCCTCAATT
Found at i:142850944 original size:43 final size:43
Alignment explanation
Indices: 142850861--142851068 Score: 382
Period size: 43 Copynumber: 4.9 Consensus size: 43
142850851 CATCGGCATT
*
142850861 AAGCCTGCTAGGCACGAAGACCC-AATACATATCACCGGCACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
*
142850903 AAGCCTGCTAGGCTCGAAGGCCCGAATACATATCACCGGCACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
*
142850946 AAGCCTGCTAGGCTCGAAGGCCCGAATACATATCACCGGCACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
142850989 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
142851032 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACC
1 AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACC
142851069 AGCATAACTG
Statistics
Matches: 162, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
42 21 0.13
43 141 0.87
ACGTcount: A:0.32, C:0.33, G:0.22, T:0.13
Consensus pattern (43 bp):
AAGCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACA
Found at i:142851158 original size:40 final size:42
Alignment explanation
Indices: 142851051--142851224 Score: 142
Period size: 40 Copynumber: 4.2 Consensus size: 42
142851041 AGGCACGAAG
* * * * *
142851051 GCCCGAATACATATCACCAGCA-TAACTGCTCTTCGGGACCTG
1 GCCCGGATATATATCACCAGCACGAA-TGCTCTTCGGGACTTA
* * * * * *
142851093 GTCCGG--ATACATCACTAGCATGAATGCTCTTCGAGATTTA
1 GCCCGGATATATATCACCAGCACGAATGCTCTTCGGGACTTA
* *
142851133 GCCCGGATGTA-A-CACCAGCACGAATGCTCTACGGGACTTA
1 GCCCGGATATATATCACCAGCACGAATGCTCTTCGGGACTTA
* * *
142851173 ACCTGGATATATATATCGCCAGCACGAATGCTCTTCGGGACTTA
1 GCCCGG--ATATATATCACCAGCACGAATGCTCTTCGGGACTTA
142851217 GCCCGGAT
1 GCCCGGAT
142851225 CATCGTCGAG
Statistics
Matches: 101, Mismatches: 24, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
40 55 0.54
41 3 0.03
42 12 0.12
43 1 0.01
44 30 0.30
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (42 bp):
GCCCGGATATATATCACCAGCACGAATGCTCTTCGGGACTTA
Found at i:142852408 original size:2 final size:2
Alignment explanation
Indices: 142852401--142852434 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
142852391 TTGGCTGTCT
142852401 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
142852435 CCTTCGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:142853216 original size:49 final size:49
Alignment explanation
Indices: 142853089--142853305 Score: 361
Period size: 49 Copynumber: 4.5 Consensus size: 49
142853079 CCCTTCGGGA
* *
142853089 CTTATCACAT-T-TATACACTTTCACATTCATCACATTGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
142853136 CTTATCAC--ATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
142853183 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
142853232 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
142853281 CTTATCACATATATATACACTTTCA
1 CTTATCACATATATATACACTTTCA
142853306 TGTACAGACT
Statistics
Matches: 158, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.01
47 49 0.31
49 108 0.68
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:142854602 original size:2 final size:2
Alignment explanation
Indices: 142854563--142854593 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
142854553 TAAGGCATAC
142854563 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 A
142854594 CCTATATATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:142865064 original size:30 final size:30
Alignment explanation
Indices: 142865009--142865168 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
142864999 ATAGTGAATC
142865009 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
142865038 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
142865068 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
142865097 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
142865125 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
142865155 CGCACACTTAGTGC
1 CGCACACTTAGTGC
142865169 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:142865101 original size:59 final size:57
Alignment explanation
Indices: 142865009--142865168 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
142864999 ATAGTGAATC
*
142865009 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
142865068 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
142865125 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
142865169 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:142866951 original size:40 final size:39
Alignment explanation
Indices: 142866906--142867156 Score: 286
Period size: 40 Copynumber: 6.3 Consensus size: 39
142866896 CGTTTTTCTT
* * * * *
142866906 TTTTTTAAAAACTCCGTTATAGATCGAGAATTAGTGGCG
1 TTTTTTAAAAACACCGCTATAGATCGAGCATTAGCGGCA
* * * *
142866945 TGTTTTTAAAAACGCCGTTATAGATCGAGAATTAGCGGCGC
1 T-TTTTTAAAAACACCGCTATAGATCGAGCATTAGCGGC-A
* * *
142866986 TTTTTTAAAAGCGCCACTATAGATCGAGCATTAGCGGCA
1 TTTTTTAAAAACACCGCTATAGATCGAGCATTAGCGGCA
* * *
142867025 TTTTTGAAAAAGAACCGCTATAGATCGAGCATTAGCGGCT
1 TTTTTTAAAAA-CACCGCTATAGATCGAGCATTAGCGGCA
142867065 TTTTTTAAAAAGCACCGCTATAGATCGAGCATTAGCGGCA
1 TTTTTTAAAAA-CACCGCTATAGATCGAGCATTAGCGGCA
* ** *
142867105 TTTTTAAAAAAGTGCCGCTATAGATTGAGCATTAGCGGCA
1 TTTTTTAAAAA-CACCGCTATAGATCGAGCATTAGCGGCA
142867145 TTTTTTAAAAAC
1 TTTTTTAAAAAC
142867157 GTTGCAAAAA
Statistics
Matches: 186, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
39 10 0.05
40 175 0.94
41 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (39 bp):
TTTTTTAAAAACACCGCTATAGATCGAGCATTAGCGGCA
Found at i:142867052 original size:120 final size:120
Alignment explanation
Indices: 142866923--142867155 Score: 326
Period size: 120 Copynumber: 1.9 Consensus size: 120
142866913 AAAACTCCGT
* * * *
142866923 TATAGATCGAGAATTAGTGGCGTGTTTTTAAAAA-CGCCGTTATAGATCGAGAATTAGCGGCGCT
1 TATAGATCGAGAATTAGCGGC-TGTTTTTAAAAAGCACCGCTATAGATCGAGAATTAGCGGC-AT
*
142866987 TTTT-TAAAAGCGCCACTATAGATCGAGCATTAGCGGCATTTTTGAAAAAGAACCGC
64 TTTTAAAAAAGCGCCACTATAGATCGAGCATTAGCGGCATTTTTGAAAAAGAACCGC
* * *
142867043 TATAGATCGAGCATTAGCGGCTTTTTTTAAAAAGCACCGCTATAGATCGAGCATTAGCGGCATTT
1 TATAGATCGAGAATTAGCGGCTGTTTTTAAAAAGCACCGCTATAGATCGAGAATTAGCGGCATTT
* * * *
142867108 TTAAAAAAGTGCCGCTATAGATTGAGCATTAGCGGCATTTTTTAAAAA
66 TTAAAAAAGCGCCACTATAGATCGAGCATTAGCGGCATTTTTGAAAAA
142867156 CGTTGCAAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
119 16 0.16
120 83 0.84
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (120 bp):
TATAGATCGAGAATTAGCGGCTGTTTTTAAAAAGCACCGCTATAGATCGAGAATTAGCGGCATTT
TTAAAAAAGCGCCACTATAGATCGAGCATTAGCGGCATTTTTGAAAAAGAACCGC
Found at i:142867539 original size:28 final size:29
Alignment explanation
Indices: 142867478--142867546 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
142867468 AGGGTATATG
** *
142867478 GTTTAGGGTTTATTATTTATGAGTTTATA
1 GTTTAGGGTTTAGGATTTATGAGTTTAGA
* *
142867507 TTTTAAGGTTTAGGATTTA-GAGTTTAGA
1 GTTTAGGGTTTAGGATTTATGAGTTTAGA
142867535 GTTTAGGGTTTA
1 GTTTAGGGTTTA
142867547 AGGGTTAGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
28 18 0.55
29 15 0.45
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (29 bp):
GTTTAGGGTTTAGGATTTATGAGTTTAGA
Found at i:142867554 original size:21 final size:21
Alignment explanation
Indices: 142867530--142867596 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
142867520 GATTTAGAGT
* *
142867530 TTAGAGTTTAGGGTTTAAGGG
1 TTAGAGGTTAGGGGTTAAGGG
*
142867551 TTAGTGGTTAGGGGTTAAGGG
1 TTAGAGGTTAGGGGTTAAGGG
* *
142867572 TTA-AGGGAATAGGGGTTAGGGG
1 TTAGA-GG-TTAGGGGTTAAGGG
142867594 TTA
1 TTA
142867597 AGGGATAGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.61
22 15 0.39
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (21 bp):
TTAGAGGTTAGGGGTTAAGGG
Found at i:142867559 original size:7 final size:7
Alignment explanation
Indices: 142867537--142867613 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
142867527 AGTTTAGAGT
*
142867537 TTAGGGT
1 TTAGGGG
*
142867544 TTAAGGG
1 TTAGGGG
*
142867551 TTAGTGG
1 TTAGGGG
142867558 TTAGGGG
1 TTAGGGG
*
142867565 TTAAGGG
1 TTAGGGG
*
142867572 TTAAGGGA
1 TT-AGGGG
*
142867580 ATAGGGG
1 TTAGGGG
142867587 TTAGGGG
1 TTAGGGG
*
142867594 TTAAGGG
1 TTAGGGG
* *
142867601 ATAGAGG
1 TTAGGGG
142867608 TTAGGG
1 TTAGGG
142867614 ATTTATAGTT
Statistics
Matches: 52, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
7 48 0.92
8 4 0.08
ACGTcount: A:0.25, C:0.00, G:0.47, T:0.29
Consensus pattern (7 bp):
TTAGGGG
Done.