Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 30
Found at i:2997533 original size:110 final size:110
Alignment explanation
Indices: 2997335--2997572 Score: 306
Period size: 110 Copynumber: 2.2 Consensus size: 110
2997325 GCTTCCCAGT
* * * *
2997335 TTCAGAGCCAATTTTAACTTCACAGCGATGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * *
2997400 CAACGAAGGGGCGACTGATTGTCAACAAATAACTTTCC-AGTTTCA
66 CAACGAAGGGACGACTGACTGTCAACAAACAA-TTTCCTAGTTTCA
**
2997445 TTCAGAGTTAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
** * *
2997510 CAGTGAAGGGACGGCTGGCTGTCAACAAACAATTTCCTAG-TTC-
66 CAACGAAGGGACGACTGACTGTCAACAAACAATTTCCTAGTTTCA
*
2997553 --CAGAGCAAATTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCA
2997573 CGACGGAGGA
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
106 18 0.16
109 8 0.07
110 86 0.77
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGACGACTGACTGTCAACAAACAATTTCCTAGTTTCA
Found at i:2997912 original size:83 final size:84
Alignment explanation
Indices: 2997772--2997954 Score: 221
Period size: 83 Copynumber: 2.2 Consensus size: 84
2997762 ATCCAACTCA
* * * *
2997772 AAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGGCACAT-AAT
1 AAGAAGGGTTATCTGTCAATAAAGACCTTCGAGCTCGACTACGATTAACTCCAAGGCAAATAAAT
*
2997836 TTGCAGCATAACTCAAGGC
66 TTACAGCATAACTCAAGGC
* *
2997855 AAGAAGGGTTATCTGTC-ATCAAATACCTTCGAGCTCGATTAC-ATTCAACT-CAGAGGCAAATC
1 AAGAAGGGTTATCTGTCAAT-AAAGACCTTCGAGCTCGACTACGATT-AACTCCA-AGGCAAAT-
*
2997917 AAATTTACAGCATAGCTCAAGGC
62 AAATTTACAGCATAACTCAAGGC
*
2997940 AAGAAGGGCTATCTG
1 AAGAAGGGTTATCTG
2997955 CCAACAAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
82 6 0.07
83 46 0.53
85 34 0.40
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (84 bp):
AAGAAGGGTTATCTGTCAATAAAGACCTTCGAGCTCGACTACGATTAACTCCAAGGCAAATAAAT
TTACAGCATAACTCAAGGC
Found at i:2999253 original size:30 final size:30
Alignment explanation
Indices: 2999219--2999276 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
2999209 TAACATTTTG
2999219 TTTATCTTATATCTATTTT-C-TTTATTTAAT
1 TTTATCTTATAT-T-TTTTGCATTTATTTAAT
*
2999249 TTTATTTTATATTTTTTGCATTTATTTA
1 TTTATCTTATATTTTTTGCATTTATTTA
2999277 TTTATTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 4 0.16
29 2 0.08
30 19 0.76
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (30 bp):
TTTATCTTATATTTTTTGCATTTATTTAAT
Found at i:3002700 original size:874 final size:876
Alignment explanation
Indices: 3001319--3003075 Score: 3374
Period size: 875 Copynumber: 2.0 Consensus size: 876
3001309 GCGCTTGTTT
* *
3001319 TGTTTGTGGAGAAATGGGTTACTATGCTCAGAATTATCCATAGAGGTTCGGGGATAGATCAGTAC
1 TGTTTCTGGACAAATGGGTTACTATGCTCAGAATTATCCATAGAGGTTCGGGGATAGATCAGTAC
3001384 AATCTGAGCGATCAATTGCAGCCCCTAGTAGAAGCAGAGGAAGATCAGGCAGTCAAAATGATGCT
66 AATCTGAGCGATCAATTGCAGCCCCTAGTAGAAGCAGAGGAAGATCAGGCAGTCAAAATGATGCT
3001449 AGCCAAAGACGAAAGACTCGGGGGGTAGCCCGAATTTTATAACATAAAGATGAGTAAAGATCGGG
131 AGCCAAAGACGAAAGACTCGGGGGGTAGCCCGAATTTTATAACATAAAGATGAGTAAAGATCGGG
3001514 ATGATCCAGAGATCATAACATGCACATTCCACCTTTTTGATGAGCCTGTTTTTGTTCTAGTTGAC
196 ATGATCCAGAGATCATAACATGCACATTCCACCTTTTTGATGAGCCTGTTTTTGTTCTAGTTGAC
*
3001579 CCTGGTTCTACACATTCATTTATTAGTACAAAGTTGGTTAGAACTAGAAGAATTCCTTTAGAACC
261 CCTGGTTCTACACATTCATTTATTAGTAAAAAGTTGGTTAGAACTAGAAGAATTCCTTTAGAACC
*
3001644 AATTTTTTGTGAAATGGTAGCAATAAACCCTATGGGTCATAGTGCAAGGGTAACACGGGTGTGTA
326 AATTTTTTGTGAAATGGTAGCAATAAACCATATGGGTCATAGTGCAAGGGTAACACGGGTGTGTA
*
3001709 GAAAATGTCTAATTAAGATTCAAGGGATTGTGTTTTCGGCCAACTTGATGGAGTTGCCTTTTTGC
391 GAAAATGTCTAATTAAGATTCAAGGGATTGTGTTTTCGACCAACTTGATGGAGTTGCCTTTTTGC
3001774 AAGTTTGAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATGGGTGGATTGTCGCAA
456 AAGTTTGAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATGGGTGGATTGTCGCAA
3001839 GAAGTGATTA-TTTTTAAGGATGCGGAAGGCTCCGAAATAGTAGTGATTGGCAAGAAGTGAAATC
521 GAAGTGATTATTTTTTAAGGATGCGGAAGGCTCCGAAATAGTAGTGATTGGCAAGAAGTGAAATC
3001903 TCACTCCAATGTGATATCAGTCATGACAGCAAGAAAAATGATATCGAAAGGATGTGTAGCTTTTC
586 TCACTCCAATGTGATATCAGTCATGACAGCAAGAAAAATGATATCGAAAGGATGTGTAGCTTTTC
3001968 TCGCTAATCTGATAGATACTCGAGTGTCGAAAGTGAGGTTACATGATATTCACATAGTTAAGGAG
651 TCGCTAATCTGATAGATACTCGAGTGTCGAAAGTGAGGTTACATGATATTCACATAGTTAAGGAG
*
3002033 TTTCAATATGTATTTTCGAAAGAGTTATCGGGTTTACCTCTAAATCGTGAAGTATAATTCAGGAT
716 TTTCAAGATGTATTTTCGAAAGAGTTATCGGGTTTACCTCTAAATCGTGAAGTATAATTCAGGAT
*
3002098 TGAGGTTTACCCGGGCACCAAACCTGTTTCAATGGATCCGGAGACATTAAAAGCATAGTTGCAAG
781 TGAGGTTTACCCGGGCACCAAACCTGTTTCAATGGATCCAGAGACATTAAAAGCATAGTTGCAAG
3002163 AGCTACTTGATAAAGGATTTATCACACCCAG
846 AGCTACTTGATAAAGGATTTATCACACCCAG
*
3002194 TGTTTCTGGACAAATGGGTTACTATGCTCAGAATTATCCGTAGAGGTTCGGGGATAGATCAGTAC
1 TGTTTCTGGACAAATGGGTTACTATGCTCAGAATTATCCATAGAGGTTCGGGGATAGATCAGTAC
3002259 AATCTGAGCGATCAATTGCAGCCCCTAGTAGAAGCAGAGGAAGATCAGGCAGTCAAAATGATGCT
66 AATCTGAGCGATCAATTGCAGCCCCTAGTAGAAGCAGAGGAAGATCAGGCAGTCAAAATGATGCT
3002324 AGCCAAAGACGAAAGACTCGGGGGGTAGCCCGAA-TTTATAACATAAAGATGAGTAAAGATCGGG
131 AGCCAAAGACGAAAGACTCGGGGGGTAGCCCGAATTTTATAACATAAAGATGAGTAAAGATCGGG
* *
3002388 ATGATCCAGAGATCATAACATGTACATTCCACCTTTTTGATGAGCCTGTTTTTGTTCTTGTTGAC
196 ATGATCCAGAGATCATAACATGCACATTCCACCTTTTTGATGAGCCTGTTTTTGTTCTAGTTGAC
3002453 CCTGGTTCTACACATTCATTTATTAGTAAAAAGTTGGTTAGAACTAGAAGAATTCCTTTAGAACC
261 CCTGGTTCTACACATTCATTTATTAGTAAAAAGTTGGTTAGAACTAGAAGAATTCCTTTAGAACC
3002518 AATTTTTTGTGAAATGGTAGCAATAAACCATATGGGTCATAGTGCAAGGGTAACACGGGTGTGTA
326 AATTTTTTGTGAAATGGTAGCAATAAACCATATGGGTCATAGTGCAAGGGTAACACGGGTGTGTA
3002583 GAAAATGTCTAATTAAGATTCAAGGGATTGTGTTTTCGACCAACTTGATGGAGTTGCCTTTTTGC
391 GAAAATGTCTAATTAAGATTCAAGGGATTGTGTTTTCGACCAACTTGATGGAGTTGCCTTTTTGC
3002648 AAGTTTGAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATGGGTGGATTGTCGCAA
456 AAGTTTGAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATGGGTGGATTGTCGCAA
*
3002713 GAAGTGATTATTTTTTAAGGATGCGGAAGGCTCCGAAATAGTAGTGATTGGCAAGAGGTGAAATC
521 GAAGTGATTATTTTTTAAGGATGCGGAAGGCTCCGAAATAGTAGTGATTGGCAAGAAGTGAAATC
3002778 TCACTCCAATGTGATATCAGTCATGACAGCAAGAAAAATGATATCGAAAGGATGTGTAGCTTTTC
586 TCACTCCAATGTGATATCAGTCATGACAGCAAGAAAAATGATATCGAAAGGATGTGTAGCTTTTC
3002843 TCGCTAATCTGATAGATACTCGAGTGTCGAAAGTGAGGTTACATGATATTCACATAGTTAAGGAG
651 TCGCTAATCTGATAGATACTCGAGTGTCGAAAGTGAGGTTACATGATATTCACATAGTTAAGGAG
* *
3002908 TTTCCAGATGTATTTTCGAAAGAGTTATCGGGTTTACCTCTAGATCGTGAAGTATAATTCAGGAT
716 TTTCAAGATGTATTTTCGAAAGAGTTATCGGGTTTACCTCTAAATCGTGAAGTATAATTCAGGAT
3002973 TGAGGTTTACCCGGGCACCAAACCTGTTTCAATGGATCCAGAGACATTAAAAGCATAGTTGCAAG
781 TGAGGTTTACCCGGGCACCAAACCTGTTTCAATGGATCCAGAGACATTAAAAGCATAGTTGCAAG
*
3003038 AGCTACTTGATAAAGGATTTATCAGACCCAG
846 AGCTACTTGATAAAGGATTTATCACACCCAG
3003069 TGTTTCT
1 TGTTTCT
3003076 CCTTGGGGAG
Statistics
Matches: 867, Mismatches: 14, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
874 360 0.42
875 507 0.58
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (876 bp):
TGTTTCTGGACAAATGGGTTACTATGCTCAGAATTATCCATAGAGGTTCGGGGATAGATCAGTAC
AATCTGAGCGATCAATTGCAGCCCCTAGTAGAAGCAGAGGAAGATCAGGCAGTCAAAATGATGCT
AGCCAAAGACGAAAGACTCGGGGGGTAGCCCGAATTTTATAACATAAAGATGAGTAAAGATCGGG
ATGATCCAGAGATCATAACATGCACATTCCACCTTTTTGATGAGCCTGTTTTTGTTCTAGTTGAC
CCTGGTTCTACACATTCATTTATTAGTAAAAAGTTGGTTAGAACTAGAAGAATTCCTTTAGAACC
AATTTTTTGTGAAATGGTAGCAATAAACCATATGGGTCATAGTGCAAGGGTAACACGGGTGTGTA
GAAAATGTCTAATTAAGATTCAAGGGATTGTGTTTTCGACCAACTTGATGGAGTTGCCTTTTTGC
AAGTTTGAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATGGGTGGATTGTCGCAA
GAAGTGATTATTTTTTAAGGATGCGGAAGGCTCCGAAATAGTAGTGATTGGCAAGAAGTGAAATC
TCACTCCAATGTGATATCAGTCATGACAGCAAGAAAAATGATATCGAAAGGATGTGTAGCTTTTC
TCGCTAATCTGATAGATACTCGAGTGTCGAAAGTGAGGTTACATGATATTCACATAGTTAAGGAG
TTTCAAGATGTATTTTCGAAAGAGTTATCGGGTTTACCTCTAAATCGTGAAGTATAATTCAGGAT
TGAGGTTTACCCGGGCACCAAACCTGTTTCAATGGATCCAGAGACATTAAAAGCATAGTTGCAAG
AGCTACTTGATAAAGGATTTATCACACCCAG
Found at i:3007105 original size:54 final size:54
Alignment explanation
Indices: 3007041--3007413 Score: 458
Period size: 54 Copynumber: 6.9 Consensus size: 54
3007031 CTATGTGTAC
* *
3007041 TACAGACACTATGTGTGCAATTCACAGAATTCATCATGAGTTGATGAACAACCG
1 TACAGGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCG
* * * *
3007095 TACAGGCACTATATGTGCAATTCACGGAATTCATCATGTGTAGATAAACAACCG
1 TACAGGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCG
* * ** * *
3007149 TACAGGCACTATGTGTGCAATTAATGGAATTCATCATGTTTTGTTGAACAACTG
1 TACAGGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCG
** * * *
3007203 TACATACACTATATGTGCAATTCACGAAATTCATCATGAGTTGATAAACAACCG
1 TACAGGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCG
* * * *
3007257 TACATGCACTATGTGTACAAATCACTGAATTCATCATGAGTTGATGAACAACCG
1 TACAGGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCG
** * * *
3007311 TACAGGCACTATGTGTATAATTCATGGAATTTATCATGAGTTGATGAACAATCG
1 TACAGGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCG
* * * ** *
3007365 TACATGTACTATGTGTGAAAACCACGAAATTCATCATGAGTTGATGAAC
1 TACAGGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAAC
3007414 TACCATATTG
Statistics
Matches: 271, Mismatches: 48, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 271 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (54 bp):
TACAGGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCG
Found at i:3008036 original size:19 final size:18
Alignment explanation
Indices: 3008008--3008043 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3007998 GAACGACTGC
*
3008008 AAAAAAAAAGGAAAAAAT
1 AAAAAAAAAGCAAAAAAT
3008026 AAAAAAGAAAGCAAAAAA
1 AAAAAA-AAAGCAAAAAA
3008044 ATCGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAGCAAAAAAT
Found at i:3008620 original size:21 final size:21
Alignment explanation
Indices: 3008579--3008617 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
3008569 ATTTGTTCAA
3008579 ATAATTAAATATAAAATAAAT
1 ATAATTAAATATAAAATAAAT
3008600 ATAA-TAAA-ATAAAATAAA
1 ATAATTAAATATAAAATAAA
3008618 AATTACCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 4 0.22
21 4 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAATTAAATATAAAATAAAT
Found at i:3008965 original size:16 final size:17
Alignment explanation
Indices: 3008929--3008966 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3008919 GTTGCATGTT
*
3008929 TTATATATATTGTAACA
1 TTATTTATATTGTAACA
3008946 -TATTTATATTGTAA-A
1 TTATTTATATTGTAACA
3008961 TTATTT
1 TTATTT
3008967 TATAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
TTATTTATATTGTAACA
Found at i:3011586 original size:99 final size:99
Alignment explanation
Indices: 3011357--3011939 Score: 470
Period size: 99 Copynumber: 5.9 Consensus size: 99
3011347 TGCAGATTCT
* * ** *
3011357 TGAGACTGACCATCTTTTT-TCGAGTAATATATCAGGGGGAATTGAGGACT-GTTTGGTCAAAAT
1 TGAGATTGGCCATCTTTTTCTCGAGTAATATATCAAAGGGAATTGAGGA-TGGTTTGGTCGAAAT
* * * * * * *
3011420 -TCTTCACAAAAGACTTACCATCTTCTACAGGCTCA
65 CT-TTGACAAAAGATTTATCATTTTCAACATGCTCC
* * * * * **
3011455 TGCGATTGACTATCCTTTT-TGGAGTAATATATCAAAGATAATTGAGGATGGTTTGGATCGAAAT
1 TGAGATTGGCCATCTTTTTCTCGAGTAATATATCAAAGGGAATTGAGGATGGTTTGG-TCGAAAT
*
3011519 CTTTGACAAATGATTTATCATTTTCAACATGCTCC
65 CTTTGACAAAAGATTTATCATTTTCAACATGCTCC
* * *
3011554 TGAGATTGGCCATCTTTATTCTC-A-TAATATATCAAGGGGAATTGAGGACGGTTTGTGTCTAAA
1 TGAGATTGGCCATCTTT-TTCTCGAGTAATATATCAAAGGGAATTGAGGATGGTTTG-GTCGAAA
* *
3011617 TCTTTGACAAATGATTTATCATTATCAACATGCTCC
64 TCTTTGACAAAAGATTTATCATTTTCAACATGCTCC
* * * * *
3011653 TGAGACTAGCCATCTTTAT-TCGCA-TAATATATCAAGGGGAACTGAGGATGGTTTGGGTCGAAA
1 TGAGATTGGCCATCTTTTTCTCG-AGTAATATATCAAAGGGAATTGAGGATGGTTT-GGTCGAAA
* * *** *
3011716 TTTTTCACAAAAGATTTATCATTTTCTGTA-GACTCA
64 TCTTTGACAAAAGATTTATCATTTTCAACATG-CTCC
** * * * * * * * *
3011752 TGAGATTGATCATCTTTTTTTCTAGTAGTATATTAGAGGGAATTGAGGACGGGTTAGGTTGAAAT
1 TGAGATTGGCCATCTTTTTCTCGAGTAATATATCAAAGGGAATTGAGGA-TGGTTTGGTCGAAAT
* * * *
3011817 CTTTTACAAAAGATTTATCAGTTT-ATATAGGCTCC
65 CTTTGACAAAAGATTTATCATTTTCA-ACATGCTCC
* * * * *
3011852 TCAAATTGGCTATCTTTTT-TCGAGTAGTATAT-AAGAGGGAATTGAGGATGGTTTGGATCAAAA
1 TGAGATTGGCCATCTTTTTCTCGAGTAATATATCAA-AGGGAATTGAGGATGGTTTGG-TCGAAA
*
3011915 TCCTTGACAAAAGATTTATCATTTT
64 TCTTTGACAAAAGATTTATCATTTT
3011940 GGATAGATTT
Statistics
Matches: 391, Mismatches: 77, Indels: 33
0.78 0.15 0.07
Matches are distributed among these distances:
97 3 0.01
98 54 0.14
99 253 0.65
100 75 0.19
101 6 0.02
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (99 bp):
TGAGATTGGCCATCTTTTTCTCGAGTAATATATCAAAGGGAATTGAGGATGGTTTGGTCGAAATC
TTTGACAAAAGATTTATCATTTTCAACATGCTCC
Found at i:3013182 original size:20 final size:20
Alignment explanation
Indices: 3013145--3013182 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3013135 GAAAAGGTGG
*
3013145 GTATTGATACTCATGGGTTA
1 GTATTGATACTCAGGGGTTA
*
3013165 GTATTGATACTTAGGGGT
1 GTATTGATACTCAGGGGT
3013183 CAATATTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (20 bp):
GTATTGATACTCAGGGGTTA
Found at i:3013189 original size:20 final size:20
Alignment explanation
Indices: 3013146--3013191 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3013136 AAAAGGTGGG
* * *
3013146 TATTGATACTCATGGGTTAG
1 TATTGATACTCAGGGGTCAA
*
3013166 TATTGATACTTAGGGGTCAA
1 TATTGATACTCAGGGGTCAA
3013186 TATTGA
1 TATTGA
3013192 CACCAACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (20 bp):
TATTGATACTCAGGGGTCAA
Found at i:3019827 original size:20 final size:20
Alignment explanation
Indices: 3019802--3019852 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
3019792 CAAAAAGGTG
*
3019802 AGTATCGATACTCAGGGGTC-
1 AGTATCGATACT-AAGGGTCT
3019822 AGTATCGATACTAAGGGTCT
1 AGTATCGATACTAAGGGTCT
*
3019842 AGTATCAATAC
1 AGTATCGATAC
3019853 ATATGGACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (20 bp):
AGTATCGATACTAAGGGTCT
Found at i:3022945 original size:29 final size:28
Alignment explanation
Indices: 3022887--3022951 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
3022877 AAAATAAACT
* **
3022887 AACAAATAATAAAAATAAAAATAGTTAA
1 AACAAAGAATAAAAATAAAAATACATAA
3022915 AACAAAGAATAAAAATGAAATAA-ACATAA
1 AACAAAGAATAAAAAT-AAA-AATACATAA
3022944 AACAAAGA
1 AACAAAGA
3022952 CCTAATTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 15 0.47
29 15 0.47
30 2 0.06
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.15
Consensus pattern (28 bp):
AACAAAGAATAAAAATAAAAATACATAA
Found at i:3023928 original size:4 final size:4
Alignment explanation
Indices: 3023919--3023954 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
3023909 GAACGGCTGC
*
3023919 AAAG AAAG AAAG AAAAT AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAA
3023955 AATCGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:3027027 original size:8 final size:8
Alignment explanation
Indices: 3027014--3027039 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3027004 TATATAACAA
3027014 ACAATGGT
1 ACAATGGT
3027022 ACAATGGT
1 ACAATGGT
3027030 ACAATGGT
1 ACAATGGT
3027038 AC
1 AC
3027040 GATACTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (8 bp):
ACAATGGT
Found at i:3028446 original size:99 final size:99
Alignment explanation
Indices: 3028278--3028899 Score: 684
Period size: 99 Copynumber: 6.3 Consensus size: 99
3028268 AGAATCTTCA
* * * * * *
3028278 ACAAAAGATTTATCAGTTTT-TGC-GGATTCTTGAGACTGATCATCTTTTTTCGAGTAATATATC
1 ACAAAAGATTTATCA-TTTTCTACAGG-CTCCTGAGATTGACCATCCTTTTTCGAGTAATATATC
* * *
3028341 AGGGGGAATTGAGGACGGTTTGGGTCGAAATCCTTC
64 AAGGGGAATTGAGGACGGTTTGGGTCGAAATCTTTG
* * * * * *
3028377 ACAAAAGACTTACCATCTTCTACAGGCTCATGCGATTGACCATCCTTTTTGGAGTAATATATCAA
1 ACAAAAGATTTATCATTTTCTACAGGCTCCTGAGATTGACCATCCTTTTTCGAGTAATATATCAA
*
3028442 GGGGAATTGAGGACGGTTTGGATCGAAATCTTTG
66 GGGGAATTGAGGACGGTTTGGGTCGAAATCTTTG
* * * * *
3028476 ACAAATGATTTATCATTTTCAACATGCTCCTGAGATTGGCCGT-CTTTATTCGCA-TAATATATC
1 ACAAAAGATTTATCATTTTCTACAGGCTCCTGAGATTGACCATCCTTT-TTCG-AGTAATATATC
3028539 AAGGGGAATTGAGGACGGTTTGGGTCGAAATCTTTG
64 AAGGGGAATTGAGGACGGTTTGGGTCGAAATCTTTG
* * * *
3028575 ACAAATGATTTATCATTTTCAACATGCTCCTGAGACTGACCAT-CTTTATTCGCA-TAATATATC
1 ACAAAAGATTTATCATTTTCTACAGGCTCCTGAGATTGACCATCCTTT-TTCG-AGTAATATATC
* * * *
3028638 AAGGGGATTTGATGACGGTTTGGGTCGAAATTTTTC
64 AAGGGGAATTGAGGACGGTTTGGGTCGAAATCTTTG
** * * * * * *
3028674 ACAAAAGATTTATCATTTTCTGTAGACACCTGAGATTGATCATCTTTTTTCGAGTAGTATAT-TA
1 ACAAAAGATTTATCATTTTCTACAGGCTCCTGAGATTGACCATCCTTTTTCGAGTAATATATCAA
3028738 GAGGGAATTGAGGACGGTTTGGGTCGAAATCTTTG
66 G-GGGAATTGAGGACGGTTTGGGTCGAAATCTTTG
* * * * * * *
3028773 ACAAAAGATTTATCAGTTTCTATAGGCTCCTCAGATTGGCTATCTTTTTTCGAGTAGTATAT-AA
1 ACAAAAGATTTATCATTTTCTACAGGCTCCTGAGATTGACCATCCTTTTTCGAGTAATATATCAA
* *
3028837 GAGGGAATTGAGGACGGTTTGGATCGAAATCCTTG
66 G-GGGAATTGAGGACGGTTTGGGTCGAAATCTTTG
**
3028872 ACAAAAGATTTATCATTTTGGACAGGCT
1 ACAAAAGATTTATCATTTTCTACAGGCT
3028900 GTCGAGGCTT
Statistics
Matches: 451, Mismatches: 65, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
98 10 0.02
99 435 0.96
100 6 0.01
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.34
Consensus pattern (99 bp):
ACAAAAGATTTATCATTTTCTACAGGCTCCTGAGATTGACCATCCTTTTTCGAGTAATATATCAA
GGGGAATTGAGGACGGTTTGGGTCGAAATCTTTG
Found at i:3028845 original size:297 final size:297
Alignment explanation
Indices: 3028308--3028980 Score: 809
Period size: 297 Copynumber: 2.3 Consensus size: 297
3028298 TGCGGATTCT
* * *
3028308 TGAGACTGATCATCTTTTTTCGAGTAATATATCAGGGGGAATTGAGGACGGTTTGGGTCGAAATC
1 TGAGACTGACCATCTTTATTCGAGTAATATATCAAGGGGAATTGAGGACGGTTTGGGTCGAAATC
* * * *
3028373 CTTCACAAAAGACTTACCATCTTCTACAGGCTCATGCGATTGACCATCCTTTTTGGAGTAATATA
66 CTTCACAAAAGACTTACCATCTTCTACAGACACATGAGATTGACCATCCTTTTTCGAGTAATATA
* * *
3028438 TCAAGGGGAATTGAGGACGGTTTGGATCGAAATCTTTGACAAATGATTTATCATTTTCAACATGC
131 TCAAGGGGAATTGAGGACGGTTTGGATCGAAATCTTTGACAAAAGATTTATCAGTTTCAACAGGC
* * *
3028503 TCCTGAGATTGGCCGTCTTTATTCGCATAATATATCAAGGGGAATTGAGGACGGTTTGGGTCGAA
196 TCCTCAGATTGGCCATCTTTATTCGCATAATATATCAAGGGGAATTGAGGACGGTTTGGATCGAA
* *
3028568 ATCTTTGACAAATGATTTATCATTTTCAACATGCTCC
261 ATCCTTGACAAAAGATTTATCATTTTCAACATGCTCC
* *
3028605 TGAGACTGACCATCTTTATTCGCA-TAATATATCAAGGGGATTTGATGACGGTTTGGGTCGAAAT
1 TGAGACTGACCATCTTTATTCG-AGTAATATATCAAGGGGAATTGAGGACGGTTTGGGTCGAAAT
** * * * ** * * * *
3028669 TTTTCACAAAAGATTTATCATTTTCTGTAGACACCTGAGATTGATCATCTTTTTTCGAGTAGTAT
65 CCTTCACAAAAGACTTACCATCTTCTACAGACACATGAGATTGACCATCCTTTTTCGAGTAATAT
* * * *
3028734 AT-TAGAGGGAATTGAGGACGGTTTGGGTCGAAATCTTTGACAAAAGATTTATCAGTTTCTATAG
130 ATCAAG-GGGAATTGAGGACGGTTTGGATCGAAATCTTTGACAAAAGATTTATCAGTTTCAACAG
* * *
3028798 GCTCCTCAGATTGGCTATCTTTTTTCG-AGTAGTATAT-AAGAGGGAATTGAGGACGGTTTGGAT
194 GCTCCTCAGATTGGCCATCTTTATTCGCA-TAATATATCAAG-GGGAATTGAGGACGGTTTGGAT
** * *
3028861 CGAAATCCTTGACAAAAGATTTATCATTTTGGACAGGCT-G
257 CGAAATCCTTGACAAAAGATTTATCATTTTCAACATGCTCC
* * * * * * * * *
3028901 TCGAGGCTTACTATCTTTATTTGAGTAGTAAAT-TAGAGGAAATTGAGGACGGTTTGGATCGAAA
1 T-GAGACTGACCATCTTTATTCGAGTAATATATCAAG-GGGAATTGAGGACGGTTTGGGTCGAAA
*
3028965 TCCTTAACAAAAGACT
64 TCCTTCACAAAAGACT
3028981 CATGTTCTGT
Statistics
Matches: 315, Mismatches: 54, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
296 10 0.03
297 304 0.97
298 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (297 bp):
TGAGACTGACCATCTTTATTCGAGTAATATATCAAGGGGAATTGAGGACGGTTTGGGTCGAAATC
CTTCACAAAAGACTTACCATCTTCTACAGACACATGAGATTGACCATCCTTTTTCGAGTAATATA
TCAAGGGGAATTGAGGACGGTTTGGATCGAAATCTTTGACAAAAGATTTATCAGTTTCAACAGGC
TCCTCAGATTGGCCATCTTTATTCGCATAATATATCAAGGGGAATTGAGGACGGTTTGGATCGAA
ATCCTTGACAAAAGATTTATCATTTTCAACATGCTCC
Found at i:3028915 original size:99 final size:97
Alignment explanation
Indices: 3028309--3028978 Score: 623
Period size: 99 Copynumber: 6.8 Consensus size: 97
3028299 GCGGATTCTT
* * * *
3028309 GAGACTGATCATCTTTTTTCGAGTAATATATCAGGGGGAATTGAGGACGGTTTGGGTCGAAATCC
1 GAGATTGACCATCTTTTTTCGAGTAATATAT-AAGGGGAATTGAGGACGGTTTGGGTCGAAATCT
* * * * *
3028374 TTCACAAAAGACTTACCATCTTCTACAGGC-TC
65 TTGACAAAAGATTTATCATTTTCAACAGGCTTC
* * * *
3028406 ATGCGATTGACCATCCTTTTTGGAGTAATATATCAAGGGGAATTGAGGACGGTTTGGATCGAAAT
1 --GAGATTGACCATCTTTTTTCGAGTAATATAT-AAGGGGAATTGAGGACGGTTTGGGTCGAAAT
* * *
3028471 CTTTGACAAATGATTTATCATTTTCAACATGCTCC
63 CTTTGACAAAAGATTTATCATTTTCAACAGGCTTC
* * *
3028506 TGAGATTGGCCGTCTTTATTCGCA-TAATATATCAAGGGGAATTGAGGACGGTTTGGGTCGAAAT
1 -GAGATTGACCATCTTTTTTCG-AGTAATATAT-AAGGGGAATTGAGGACGGTTTGGGTCGAAAT
* * *
3028570 CTTTGACAAATGATTTATCATTTTCAACATGCTCC
63 CTTTGACAAAAGATTTATCATTTTCAACAGGCTTC
* * * *
3028605 TGAGACTGACCATCTTTATTCGCA-TAATATATCAAGGGGATTTGATGACGGTTTGGGTCGAAAT
1 -GAGATTGACCATCTTTTTTCG-AGTAATATAT-AAGGGGAATTGAGGACGGTTTGGGTCGAAAT
* * *** * **
3028669 TTTTCACAAAAGATTTATCATTTTCTGTAGACACC
63 CTTTGACAAAAGATTTATCATTTTCAACAGGCTTC
* * *
3028704 TGAGATTGATCATCTTTTTTCGAGTAGTATATTAGAGGGAATTGAGGACGGTTTGGGTCGAAATC
1 -GAGATTGACCATCTTTTTTCGAGTAATATATAAG-GGGAATTGAGGACGGTTTGGGTCGAAATC
* * *
3028769 TTTGACAAAAGATTTATCAGTTTCTATAGGCTCCTC
64 TTTGACAAAAGATTTATCATTTTCAACAGGCT--TC
* * * * *
3028805 -AGATTGGCTATCTTTTTTCGAGTAGTATATAAGAGGGAATTGAGGACGGTTTGGATCGAAATCC
1 GAGATTGACCATCTTTTTTCGAGTAATATATAAG-GGGAATTGAGGACGGTTTGGGTCGAAATCT
**
3028869 TTGACAAAAGATTTATCATTTTGGACAGGCTGTC
65 TTGACAAAAGATTTATCATTTTCAACAGGCT-TC
* * * * * * *
3028903 GAGGCTT-ACTATCTTTATTT-GAGTAGTAAATTAGAGGAAATTGAGGACGGTTTGGATCGAAAT
1 GA-GATTGACCATCTTT-TTTCGAGTAATATATAAG-GGGAATTGAGGACGGTTTGGGTCGAAAT
* *
3028966 CCTTAACAAAAGA
63 CTTTGACAAAAGA
3028979 CTCATGTTCT
Statistics
Matches: 494, Mismatches: 68, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
98 5 0.01
99 480 0.97
100 8 0.02
101 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (97 bp):
GAGATTGACCATCTTTTTTCGAGTAATATATAAGGGGAATTGAGGACGGTTTGGGTCGAAATCTT
TGACAAAAGATTTATCATTTTCAACAGGCTTC
Found at i:3028929 original size:198 final size:195
Alignment explanation
Indices: 3028319--3028978 Score: 692
Period size: 198 Copynumber: 3.3 Consensus size: 195
3028309 GAGACTGATC
* *
3028319 ATCTTTTTTCGAGTAATATATCAGGGGGAATTGAGGACGGTTTGGGTCGAAATCCTTCACAAAAG
1 ATCTTTTTTCGAGTAATATATCAGAGGGAATTGAGGACGGTTTGGGTCGAAATCCTTGACAAAAG
* * * * *
3028384 ACTTACCATCTTCTACAGGCTCATGC-GATTGACCATCCTTTTTGGAGTAATATATCAAGGGGAA
66 ATTTATCAT-TTCTACAGGCTCCT-CAGATTGACCATCTTTTTTCGAGTAATATATCAAGGGGAA
* ** *
3028448 TTGAGGACGGTTTGGATCGAAATCTTTGACAAATGATTTATCATTTTCAACATGCTCCTGAGATT
129 TTGAGGACGGTTTGGATCGAAATCTTTGACAAAAGATTTATCATTTTGGACA-GCTTC-GAGATT
* *
3028513 GGCC
192 GACT
* * *
3028517 GTCTTTATTCGCA-TAATATATCA-AGGGGAATTGAGGACGGTTTGGGTCGAAATCTTTGACAAA
1 ATCTTTTTTCG-AGTAATATATCAGA-GGGAATTGAGGACGGTTTGGGTCGAAATCCTTGACAAA
* * * * * *
3028580 TGATTTATCATTTTCAACATGCTCCTGAGACTGACCATCTTTATTCGCA-TAATATATCAAGGGG
64 AGATTTATCA-TTTCTACAGGCTCCTCAGATTGACCATCTTTTTTCG-AGTAATATATCAAGGGG
* * * * * *
3028644 ATTTGATGACGGTTTGGGTCGAAATTTTTCACAAAAGATTTATCATTTTCTGTAGACA-CCT-GA
127 AATTGAGGACGGTTTGGATCGAAATCTTTGACAAAAGATTTATCA-TTT-TG--GACAGCTTCGA
3028707 GATTGA-T
188 GATTGACT
* * *
3028714 CATCTTTTTTCGAGTAGTATATTAGAGGGAATTGAGGACGGTTTGGGTCGAAATCTTTGACAAAA
1 -ATCTTTTTTCGAGTAATATATCAGAGGGAATTGAGGACGGTTTGGGTCGAAATCCTTGACAAAA
* * * *
3028779 GATTTATCAGTTTCTATAGGCTCCTCAGATTGGCTATCTTTTTTCGAGTAGTATAT-AAGAGGGA
65 GATTTATCA-TTTCTACAGGCTCCTCAGATTGACCATCTTTTTTCGAGTAATATATCAAG-GGGA
* *
3028843 ATTGAGGACGGTTTGGATCGAAATCCTTGACAAAAGATTTATCATTTTGGACAGGCTGTCGAGGC
128 ATTGAGGACGGTTTGGATCGAAATCTTTGACAAAAGATTTATCATTTTGGACA-GCT-TCGA-GA
3028908 TT-ACT
190 TTGACT
* * * * * *
3028913 ATCTTTATTT-GAGTAGTAAATTAGAGGAAATTGAGGACGGTTTGGATCGAAATCCTTAACAAAA
1 ATCTTT-TTTCGAGTAATATATCAGAGGGAATTGAGGACGGTTTGGGTCGAAATCCTTGACAAAA
3028977 GA
65 GA
3028979 CTCATGTTCT
Statistics
Matches: 385, Mismatches: 56, Indels: 42
0.80 0.12 0.09
Matches are distributed among these distances:
194 4 0.01
196 3 0.01
197 9 0.02
198 350 0.91
199 14 0.04
200 2 0.01
202 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (195 bp):
ATCTTTTTTCGAGTAATATATCAGAGGGAATTGAGGACGGTTTGGGTCGAAATCCTTGACAAAAG
ATTTATCATTTCTACAGGCTCCTCAGATTGACCATCTTTTTTCGAGTAATATATCAAGGGGAATT
GAGGACGGTTTGGATCGAAATCTTTGACAAAAGATTTATCATTTTGGACAGCTTCGAGATTGACT
Found at i:3030016 original size:24 final size:25
Alignment explanation
Indices: 3029984--3030035 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
3029974 TAATACGTAG
*
3029984 TGACTATATTGTA-GTACGA-AAGTA
1 TGACAATA-TGTATGTACGATAAGTA
*
3030008 TGACAATATGTATGTCCGATAAGTA
1 TGACAATATGTATGTACGATAAGTA
3030033 TGA
1 TGA
3030036 TTTTTGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 12 0.50
25 8 0.33
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (25 bp):
TGACAATATGTATGTACGATAAGTA
Found at i:3040194 original size:21 final size:20
Alignment explanation
Indices: 3040170--3040210 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3040160 TGAATAGTGC
*
3040170 ATAACAATATATGTTGTTTTT
1 ATAA-AATATATCTTGTTTTT
*
3040191 ATAAAATGTATCTTGTTTTT
1 ATAAAATATATCTTGTTTTT
3040211 TGTATTCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.54
Consensus pattern (20 bp):
ATAAAATATATCTTGTTTTT
Found at i:3046125 original size:23 final size:23
Alignment explanation
Indices: 3046086--3046147 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
3046076 GCAGCCCTTC
* *
3046086 GGACATATTTATGTGGTCATTTG
1 GGACAAATCTATGTGGTCATTTG
* *
3046109 GGATAATTCTATGTGGTCATTTG
1 GGACAAATCTATGTGGTCATTTG
3046132 GGACAAATCTATGTGG
1 GGACAAATCTATGTGG
3046148 CACTTCGGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (23 bp):
GGACAAATCTATGTGGTCATTTG
Found at i:3046190 original size:24 final size:24
Alignment explanation
Indices: 3046145--3046191 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3046135 CAAATCTATG
*
3046145 TGGCACTTCGGTGCATAGTCTACA
1 TGGCACTTCGGTGCAAAGTCTACA
*
3046169 TGGCACTTCGGTGCAAATTCTAC
1 TGGCACTTCGGTGCAAAGTCTAC
3046192 GCGACAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAAGTCTACA
Found at i:3051096 original size:182 final size:182
Alignment explanation
Indices: 3050806--3051191 Score: 625
Period size: 182 Copynumber: 2.1 Consensus size: 182
3050796 AATTCTTACT
*
3050806 GGATATATT-AAACGTGTCGATACATTAATATAAGGATCGACACTTTGTGAATTTAAAAGAGAAG
1 GGATATATTGAAA-GTGACGATACATTAATATAAGGATCGACACTTTGTGAATTTAAAAGAGAAG
*
3050870 CAGTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAG
65 CAGTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACAATATAACAG
* *
3050935 GTAAAAATATTACAAAACCGGTATCGAAATGATAAAACCGGTAAAGAGCTACCA
130 GTAAAAATATGACAAAACCGGTATCAAAATGATAAAACCGGTAAAGAGCTA-CA
* *
3050989 -GATATATTTG-AAGTGACGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAG
1 GGATATA-TTGAAAGTGACGATACATTAATATAAGGATCGACACTTTGTGAATTTAAAAGAGAAG
*
3051052 CAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACAATATAACAG
65 CAGTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACAATATAACAG
* * *
3051117 GTAAAAATATGATAAAACCGGTATCAAAATGATAAAGCCGGTAAAGCGCTACA
130 GTAAAAATATGACAAAACCGGTATCAAAATGATAAAACCGGTAAAGAGCTACA
*
3051170 GGATATATTGAAAGTGTCGATA
1 GGATATATTGAAAGTGACGATA
3051192 TTTTCATAAG
Statistics
Matches: 188, Mismatches: 11, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
181 5 0.03
182 179 0.95
183 4 0.02
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (182 bp):
GGATATATTGAAAGTGACGATACATTAATATAAGGATCGACACTTTGTGAATTTAAAAGAGAAGC
AGTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACAATATAACAGG
TAAAAATATGACAAAACCGGTATCAAAATGATAAAACCGGTAAAGAGCTACA
Found at i:3053271 original size:15 final size:15
Alignment explanation
Indices: 3053251--3053283 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3053241 TGGTTGTATT
3053251 GGGGGATGACGGTGA
1 GGGGGATGACGGTGA
3053266 GGGGGATGACGGTGA
1 GGGGGATGACGGTGA
3053281 GGG
1 GGG
3053284 AAAATAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.64, T:0.12
Consensus pattern (15 bp):
GGGGGATGACGGTGA
Found at i:3053468 original size:33 final size:33
Alignment explanation
Indices: 3053431--3053494 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
3053421 AAATAGATGG
*
3053431 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
3053464 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGT
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGT
3053495 TATCTTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:3054693 original size:4 final size:4
Alignment explanation
Indices: 3054684--3054848 Score: 321
Period size: 4 Copynumber: 41.2 Consensus size: 4
3054674 TAAGAGATTG
3054684 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3054732 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3054780 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
3054828 ATAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT G
3054849 AAAGGACATT
Statistics
Matches: 159, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 159 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:3055451 original size:19 final size:19
Alignment explanation
Indices: 3055427--3055471 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
3055417 AATGTATGGT
*
3055427 TAATTTTTTATAAGATTTA
1 TAATTTTGTATAAGATTTA
3055446 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
3055465 TAATTTT
1 TAATTTT
3055472 ATATGTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3056098 original size:201 final size:201
Alignment explanation
Indices: 3055738--3056679 Score: 1326
Period size: 201 Copynumber: 4.7 Consensus size: 201
3055728 AGGTAAAATT
* * * * * * *
3055738 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAATTTTTCAATGTAACAGG
1 TATCGATCCCAAAAACATACGAACCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGG
*
3055803 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTGTATCGACACTTTTTTAATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGT
* *
3055868 GTCCATACTTTTGGTCCAGAA-AAGATGCCAAAAAGGGTG-AACGCATAAAGTGTCGATACATTT
131 GTCGATACTTTTGGTCCAGAATGA-ATGCCAAAAAGGGTGCAAC-CATAAAGTGTCGATACATTT
3055931 -TCAAAAAG
194 AT-AAAAAG
* * *
3055939 TGTTGATCCCAAAAACAT-CGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
1 TATCGATCCCAAAAACATACG-AACCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
3056003 GTATAAATATACCGGTTTTATGAGAGAATAAGTCTACAACATGTATCGACACTTTTTTCATTTTG
65 GTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTG
* * *
3056068 TGTCGATACTTTTGGTCCATAATGGATGCCAAAAAGGGTG-AACGCATAAAGTGTTGATACATTT
130 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAAC-CATAAAGTGTCGATACATTT
3056132 -TCAAAAAG
194 AT-AAAAAG
* * * * *
3056140 TGTCGATCACAAAAACAT-CGAACCCCATAATTATAATGTAATAGTTAAATTTACAATGTAACTG
1 TATCGATCCCAAAAACATACGAA-CCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
3056204 GTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTATTTTAATTTTG
65 GTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTG
3056269 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
130 TGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
3056334 TAAAAAG
195 TAAAAAG
* * * * * *
3056341 TATCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTGCAATATAACCGG
1 TATCGATCCCAAAAACATACGAACCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGG
* * *
3056406 TATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATAGACACGTTTTTAATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGT
* *
3056471 GCCGATAAC-TTTGGTCCATAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
131 GTCGAT-ACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTA
3056535 TAAAAAG
195 TAAAAAG
* * * * * * * * **
3056542 TATCGA-CCCAGAAACATATGCATCTACAAGTATAATGTAATATGTAAATTTTCAATGTAACCAA
1 TATCGATCCCAAAAACATACGAACCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGG
*
3056606 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACATTTTTAATTTTGT
66 TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGT
3056671 GTCGATACT
131 GTCGATACT
3056680 AATTTAAATA
Statistics
Matches: 677, Mismatches: 56, Indels: 17
0.90 0.07 0.02
Matches are distributed among these distances:
199 2 0.00
200 121 0.18
201 546 0.81
202 8 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (201 bp):
TATCGATCCCAAAAACATACGAACCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGG
TATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGT
GTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTAT
AAAAAG
Found at i:3060010 original size:200 final size:198
Alignment explanation
Indices: 3059666--3060231 Score: 821
Period size: 201 Copynumber: 2.8 Consensus size: 198
3059656 ATAGAGTGTC
* * *
3059666 GATCC-AAAAGGGTTGCACGCATAAAGTGACGATACATTTAT-TAAAAGTGTTGATCCCAAAAAC
1 GATCCAAAAAGGG-TGAACGCATAAAGTGTCGATACATTT-TCAAAAAGTGTTGATCCCAAAAAC
* * * * * *
3059729 ATCGAAATCCATAATTATAATGTAATAGGTAATTTTGTAATATAACTGGTATATATATACTGGTT
64 ATCGAAA-CCATAATTATAATGTAATAGGTAAATTTATAATGTAACCGGTATAAATATACCGGTT
* * *
3059794 TTATGAGAGAATAGGTCTATAATATGTATCGACACTTCTTAATATTGTGTTGATAATTTTTGTCC
128 TTATGAGAGAATAGGTCTATAACATGTATCGACACTTCTTAATATTGTGTCGATAATTTTGGTCC
*
3059859 TGAATG
193 AGAATG
* *
3059865 GAATCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCTCAAAAACA
1 G-ATCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTTGATCCCAAAAACA
3059930 TCGAAACCTATAATTATAATGTAATAGGTAAATTTATAATGTAACCGGTATAAATATACCGGTTT
65 TCGAAACC-ATAATTATAATGTAATAGGTAAATTTATAATGTAACCGGTATAAATATACCGGTTT
* * * *
3059995 TATGAGAGAATAGGTCTATAACATGTAGCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCC
129 TATGAGAGAATAGGTCTATAACATGTATCGACAC-TTCTTAATATTGTGTCGATAATTTTGGTCC
3060060 AGAATG
193 AGAATG
* *
3060066 GATGCCAAAAAGGGTAAACGCATAAAGTGTCAATACATTTTCAAAAAGTGTTGATCCCAAAAACA
1 GAT-CCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTTGATCCCAAAAACA
* *
3060131 TCGAAACCCATAATTATAATGTAATAGATAAATTTACAATGTAACCGGTATAAATATACCGGTTT
65 TCGAAA-CCATAATTATAATGTAATAGGTAAATTTATAATGTAACCGGTATAAATATACCGGTTT
* *
3060196 TATGAGAGAATATGTCTACAACATGTATCGACACTT
129 TATGAGAGAATAGGTCTATAACATGTATCGACACTT
3060232 TGTTGAAAAA
Statistics
Matches: 332, Mismatches: 28, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
199 4 0.01
200 140 0.42
201 186 0.56
202 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (198 bp):
GATCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTTGATCCCAAAAACAT
CGAAACCATAATTATAATGTAATAGGTAAATTTATAATGTAACCGGTATAAATATACCGGTTTTA
TGAGAGAATAGGTCTATAACATGTATCGACACTTCTTAATATTGTGTCGATAATTTTGGTCCAGA
ATG
Found at i:3063160 original size:200 final size:195
Alignment explanation
Indices: 3062753--3063468 Score: 741
Period size: 200 Copynumber: 3.6 Consensus size: 195
3062743 ACAATAACTA
* * * *
3062753 CATAAATGTGTCGATACATTT-TATACAAGTATTGA-CCCAAAAAACATCAAAACCAATAATTAT
1 CATAAA-GTGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTAT
* *
3062816 AATGTAATAGGTAAATTAACAATGTAATCGGTATAAATATACCGGTTAATTA-GAAAACA-T-GT
63 AATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTT--TTATGAAAA-ATTGGT
** *
3062878 CAACATAATGTATCGACACTTGTGTAATTTGTGTCGATACTTATTGTCCAGGATGAATGCACAAA
125 C-ACATAATGTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCATAATGAATCCA-AAA
3062943 CGAGGTGC-AC
186 CG-GGTGCAAC
*
3062953 GCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATTGAAACCGATAATTATAA
1 -CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
* * *
3063018 TGTATTAGGTAAATTTACAATGTAACCGATATAAATATATCGGTTTTATGATAAAATTGGTCAGC
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGA-AAAATTGGTCA-C
* * *
3063083 ATCAA-GTATCGACACTTGCTAAATTTGTGTCGACACTTTTGGTCCATAATGAATACCAAAAAGG
128 AT-AATGTATCGACACTTG-TTAATTTGTGTCGATACTTTT-GTCCATAATGAAT-CCAAAACGG
3063147 GTGCAAC
189 GTGCAAC
* * * *
3063154 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAAT
1 CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * *
3063219 GTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAAA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGA-AAAATTGGTC-ACA
* * * * *
3063284 TAATGTATCGACACGTTATTAGTTTGTGTCGATACTTTTTTTCAAAATGAAATATGAATGCCCAA
129 TAATGTATCGACAC-TTGTTAATTTGTGTCGATAC-TTTTGTC--CAT---A-ATGAAT-CCAAA
* *
3063349 CCGGGTGCAAG
185 ACGGGTGCAAC
** * *
3063360 CATAAAGTGTCGATACATTTA--AAATTA-TATCGATCTAAAAAACATCGTAACCGATAATAATA
1 CATAAAGTGTCGATACATTTATTAAA--AGTATCGATCCCAAAAACATCGAAACCGATAATTATA
* * *
3063422 ATGTAATAGGTAAATTTGCAATGTTACCGGTATAAATATATCGGTTT
64 ATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTT
3063469 ACTTCGAAAA
Statistics
Matches: 441, Mismatches: 50, Indels: 44
0.82 0.09 0.08
Matches are distributed among these distances:
198 3 0.01
199 5 0.01
200 241 0.55
201 69 0.16
202 7 0.02
204 3 0.01
205 73 0.17
206 40 0.09
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (195 bp):
CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAAAAATTGGTCACATA
ATGTATCGACACTTGTTAATTTGTGTCGATACTTTTGTCCATAATGAATCCAAAACGGGTGCAAC
Found at i:3063593 original size:87 final size:87
Alignment explanation
Indices: 3063486--3063648 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
3063476 AAATAGGTCA
3063486 ATATAAGCACTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCACTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
*
3063551 CCGGTTAAATGCCTATTTTATT
66 CAGGTTAAATGCCTATTTTATT
* * *
3063573 ATATAAGCGCTATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCACTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
3063638 CAGGTTAAATG
66 CAGGTTAAATG
3063649 ATATAACATT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCACTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
CAGGTTAAATGCCTATTTTATT
Found at i:3063620 original size:23 final size:23
Alignment explanation
Indices: 3063570--3063614 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3063560 TGCCTATTTT
* *
3063570 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
3063593 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
3063615 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:3064943 original size:21 final size:21
Alignment explanation
Indices: 3064877--3064943 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3064867 TCAGTTAAAT
*
3064877 AAATGAGTTATGATCTACCAG
1 AAATGAGTTATGATCTACAAG
* * * *
3064898 AAAT-ATGTTAAG-TAATATAAT
1 AAATGA-GTTATGAT-CTACAAG
3064919 AAATGAGTTATGATCTACAAG
1 AAATGAGTTATGATCTACAAG
3064940 AAAT
1 AAAT
3064944 ATATTAATTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.31
Consensus pattern (21 bp):
AAATGAGTTATGATCTACAAG
Found at i:3067253 original size:2 final size:2
Alignment explanation
Indices: 3067246--3067273 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3067236 GGTGTTTTCT
3067246 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
3067274 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3068173 original size:14 final size:14
Alignment explanation
Indices: 3068156--3068193 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
3068146 TTTGTCTTTA
3068156 TATATGTAGT-TGTG
1 TATATGT-GTATGTG
3068170 TATATGTGTATGTG
1 TATATGTGTATGTG
3068184 TATATGTGTA
1 TATATGTGTA
3068194 AATAATAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (14 bp):
TATATGTGTATGTG
Found at i:3070819 original size:11 final size:12
Alignment explanation
Indices: 3070794--3070819 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3070784 GTAGAAATTA
3070794 TTTTAATGACTT
1 TTTTAATGACTT
3070806 TTTTAATGACTT
1 TTTTAATGACTT
3070818 TT
1 TT
3070820 AACAACTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTTAATGACTT
Found at i:3071809 original size:21 final size:21
Alignment explanation
Indices: 3071785--3071827 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3071775 TCCTCCCTAC
*
3071785 TCATGCCCATGCCCATCCCCA
1 TCATCCCCATGCCCATCCCCA
*
3071806 TCATCCCCATGCCCATTCCCA
1 TCATCCCCATGCCCATCCCCA
3071827 T
1 T
3071828 ACTCATGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.51, G:0.07, T:0.23
Consensus pattern (21 bp):
TCATCCCCATGCCCATCCCCA
Found at i:3073346 original size:21 final size:21
Alignment explanation
Indices: 3073322--3073363 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3073312 ACTTTTATCT
3073322 TTTAAAAAATA-TTATTTAATA
1 TTTAAAAAATATTTA-TTAATA
*
3073343 TTTAAAACATATTTATTAATA
1 TTTAAAAAATATTTATTAATA
3073364 ATGTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAAAAAATATTTATTAATA
Found at i:3075466 original size:11 final size:11
Alignment explanation
Indices: 3075450--3075476 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3075440 TTATTTTATA
3075450 TTTTACTATTT
1 TTTTACTATTT
3075461 TTTTACTATTT
1 TTTTACTATTT
3075472 TTTTA
1 TTTTA
3075477 AATTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTACTATTT
Found at i:3079299 original size:21 final size:21
Alignment explanation
Indices: 3079273--3079325 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
3079263 TACGTCAGAA
3079273 GTTTTGAAACCTTAGTGGGAG
1 GTTTTGAAACCTTAGTGGGAG
3079294 GTTTTGAAACCTTAGTGGGAG
1 GTTTTGAAACCTTAGTGGGAG
*
3079315 GTTTCGAAACC
1 GTTTTGAAACC
3079326 ATGCTCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (21 bp):
GTTTTGAAACCTTAGTGGGAG
Found at i:3084165 original size:42 final size:41
Alignment explanation
Indices: 3084084--3084184 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
3084074 AGGTTTTATG
* * * *
3084084 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCAAAAGACTTACA
* * *
3084125 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCAAAAGACTTACA
*
3084167 GATGGCCCGAAGAACTTA
1 GATGGCCCGAAGGACTTA
3084185 TAAATTGTGA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCAAAAGACTTACA
Found at i:3084391 original size:42 final size:41
Alignment explanation
Indices: 3084299--3084399 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
3084289 AGGTTTTATG
* * * * *
3084299 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAAGACTTAGCATCATGCTCGAAAGACTTACA
* * * *
3084340 GACGACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAAGACTT-AGCATCATGCTCGAAAGACTTACA
*
3084382 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAAGACTTA
3084400 TAAATTGTGA
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
41 14 0.30
42 32 0.70
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (41 bp):
GATGGCCCGAAAGACTTAGCATCATGCTCGAAAGACTTACA
Found at i:3084671 original size:214 final size:215
Alignment explanation
Indices: 3083915--3085039 Score: 1970
Period size: 215 Copynumber: 5.2 Consensus size: 215
3083905 CTTAAAAATT
*
3083915 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTA
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
* * *
3083980 AAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT-TCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTCTCATT
3084044 TTCAAATTC-TTGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCT
131 TTCAAATTCATT-TGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCT
*
3084108 TGCTCTAAAGGCTTACAGATG
195 TGCTCTAAAGGCTTACAGACG
* *
3084129 ACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGAACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
3084194 AAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTCTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTCTCATT
3084259 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
131 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
3084324 GCTCTAAAGGCTTACAGACG
196 GCTCTAAAGGCTTACAGACG
*
3084344 ACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
3084409 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATATTCTTGAAACGTCATTTTCTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTCTCATT
3084474 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
131 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
* *
3084539 GTTCTAAAGGCTTACACACG
196 GCTCTAAAGGCTTACAGACG
*
3084559 A-CCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
3084623 AAATTTTGAAAATCGTATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTCTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTCTCATT
* *
3084688 TTCAAATTCATTTGAAAACATCCTACTCGAAGGTTTTATGGATGGCCCGAAGAACTTATCATCTT
131 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
*
3084753 ACTCTAAAGGCTTACAGACG
196 GCTCTAAAGGCTTACAGACG
*
3084773 ACCCGAAGGATTTAAGCATTATGCTCGAAAGA-TTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
* * * *
3084837 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTTTCAT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCA-TTTTCTCAT
*
3084902 TTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCT
130 TTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCT
*
3084967 TGCTCTAAAGGCTTACAGATG
195 TGCTCTAAAGGCTTACAGACG
* *
3084988 ACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGA
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGA
3085040 TTTAAGCATC
Statistics
Matches: 869, Mismatches: 37, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
214 407 0.47
215 442 0.51
216 20 0.02
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (215 bp):
ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTCTCATT
TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
GCTCTAAAGGCTTACAGACG
Found at i:3084700 original size:429 final size:428
Alignment explanation
Indices: 3083915--3085039 Score: 1993
Period size: 429 Copynumber: 2.6 Consensus size: 428
3083905 CTTAAAAATT
*
3083915 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTA
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
3083980 AAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTT
3084045 TCAAATTC-TTGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
131 TCAAATTCATT-TGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
* *
3084109 GCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCC
195 GCTCTAAAGGCTTACAGATGA-CCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC
*
3084174 CGAAGAACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCT
259 CGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCT
3084239 TGAAACGTCATTTTCTCATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGG
324 TGAAACGTCATTTTCTCATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGG
* *
3084304 CCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGACG
389 CCCGAAGAACTTATCATCTTACTCTAAAGGCTTACAGACG
*
3084344 ACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
* * *
3084409 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATATTCTTGAAACGTCATTTTCTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT-TCATT
3084474 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
130 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
* * *
3084539 GTTCTAAAGGCTTACACACGACCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCC
195 GCTCTAAAGGCTTACAGATGACCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCC
**
3084604 GAAGGACTTATAAATTGTGAAATTTTGAAAATCGTATTCTTCGTTTTCAAAAATTCCATCTTCTT
260 GAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTT
*
3084669 GAAACGTCATTTTCTCATTTTCAAATTCATTTGAAAACATCCTACTCGAAGGTTTTATGGATGGC
325 GAAACGTCATTTTCTCATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGC
3084734 CCGAAGAACTTATCATCTTACTCTAAAGGCTTACAGACG
390 CCGAAGAACTTATCATCTTACTCTAAAGGCTTACAGACG
*
3084773 ACCCGAAGGATTTAAGCATTATGCTCGAAAGA-TTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
3084837 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTTTCAT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA--TTTTTCAT
*
3084902 TTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCT
129 TTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCT
*
3084967 TGCTCTAAAGGCTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGAC
194 TGCTCTAAAGGCTTACAGATGACCT-AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGC
3085032 CCGAAGGA
258 CCGAAGGA
3085040 TTTAAGCATC
Statistics
Matches: 663, Mismatches: 28, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
428 83 0.13
429 443 0.67
430 135 0.20
431 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (428 bp):
ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTT
TCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTG
CTCTAAAGGCTTACAGATGACCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCG
AAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTG
AAACGTCATTTTCTCATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCC
CGAAGAACTTATCATCTTACTCTAAAGGCTTACAGACG
Found at i:3085024 original size:42 final size:42
Alignment explanation
Indices: 3084943--3085071 Score: 179
Period size: 42 Copynumber: 3.1 Consensus size: 42
3084933 AGGTTTTATG
* * * * * * *
3084943 GATGGCCCGAAGGACTT-ATCATCTTGCTCTAAAGGCTTACA
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
*
3084984 GATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
3085026 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
3085068 GATG
1 GATG
3085072 GGTTTGCTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 14 0.18
42 64 0.82
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
Found at i:3085125 original size:34 final size:35
Alignment explanation
Indices: 3085075--3085250 Score: 119
Period size: 36 Copynumber: 4.9 Consensus size: 35
3085065 ACTGATGGGT
* * * *
3085075 TTGCTTTACTATTCTTCTATGAAGGCTTAAGGTGG
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
* *
3085110 -TGCTTCACTACTCTTCGGTGAAGGTTTAAGATGG
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
* *
3085144 TTTGCTTCACTCCTCTT-TGGTGAAGGCTTAAGATTGAT
1 -TTGCTTCACTACTCTTCT-GTGAAGGCTTAAGA-TG-G
* *
3085182 TTGCTTCA--AC-CTTATTGGTGAAGGCTTAAGATTGAT
1 TTGCTTCACTACTCTT-CT-GTGAAGGCTTAAGA-TG-G
* * * *
3085218 TTGCTTCATTCCTTTTCAGTGAAGGCTTAAGAT
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGAT
3085251 TGACTTTGCT
Statistics
Matches: 116, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
34 31 0.27
35 1 0.01
36 57 0.49
37 24 0.21
38 1 0.01
39 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (35 bp):
TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
Found at i:3085160 original size:36 final size:36
Alignment explanation
Indices: 3085094--3085260 Score: 162
Period size: 36 Copynumber: 4.6 Consensus size: 36
3085084 TATTCTTCTA
* * *
3085094 TGAAGGCTTAAGGTG--GTGCTTCACTACTCTTCGG
1 TGAAGGCTTAAGATGATTTGCTTCACTCCTCTTCGG
* * *
3085128 TGAAGGTTTAAGATGGTTTGCTTCACTCCTCTTTGG
1 TGAAGGCTTAAGATGATTTGCTTCACTCCTCTTCGG
* *
3085164 TGAAGGCTTAAGATTGATTTGCTTCA-ACCT-TATTGG
1 TGAAGGCTTAAGA-TGATTTGCTTCACTCCTCT-TCGG
* * *
3085200 TGAAGGCTTAAGATTGATTTGCTTCATTCCTTTTCAG
1 TGAAGGCTTAAGA-TGATTTGCTTCACTCCTCTTCGG
3085237 TGAAGGCTTAAGATTGACTTTGCT
1 TGAAGGCTTAAGA-TGA-TTTGCT
3085261 CTAATCTCAT
Statistics
Matches: 115, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
34 13 0.11
35 1 0.01
36 61 0.53
37 33 0.29
38 7 0.06
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (36 bp):
TGAAGGCTTAAGATGATTTGCTTCACTCCTCTTCGG
Found at i:3085249 original size:37 final size:35
Alignment explanation
Indices: 3085126--3085260 Score: 173
Period size: 36 Copynumber: 3.7 Consensus size: 35
3085116 ACTACTCTTC
* *
3085126 GGTGAAGGTTTAAGA-TGGTTTGCTTCACTCCTCTTT
1 GGTGAAGGCTTAAGATTGATTTGCTTCA-TCCT-TTT
*
3085162 GGTGAAGGCTTAAGATTGATTTGCTTCAACCTTATT
1 GGTGAAGGCTTAAGATTGATTTGCTTCATCCTT-TT
3085198 GGTGAAGGCTTAAGATTGATTTGCTTCATTCCTTTT
1 GGTGAAGGCTTAAGATTGATTTGCTTCA-TCCTTTT
*
3085234 CAGTGAAGGCTTAAGATTGACTTTGCT
1 -GGTGAAGGCTTAAGATTGA-TTTGCT
3085261 CTAATCTCAT
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
35 1 0.01
36 49 0.55
37 33 0.37
38 6 0.07
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (35 bp):
GGTGAAGGCTTAAGATTGATTTGCTTCATCCTTTT
Found at i:3086592 original size:125 final size:125
Alignment explanation
Indices: 3086370--3086620 Score: 296
Period size: 125 Copynumber: 2.0 Consensus size: 125
3086360 TACCACAATG
* * * *
3086370 TTATCTCATATTGGTACATGCCTTCAAAATGCCCCAACATCTCAGATTGTAAGGCTCACTCTCAA
1 TTATCTCATACTGGTACATGCCTTCAAAATGCCCCAACACCTCAAATCGTAAGGCTCACTCTCAA
*
3086435 TGTCTTCTTGGTCCGAATCTTGTCATCCCAACACGATGTGGGTTCAGTCATGTCCC-AACA
66 TGTCTTCTTGGTCCGAATCATGTCATCCCAACACGATGTGGGTTCAGTCATG-CCCTAACA
* * * **
3086495 TTATCTTATACTGGTACGA-GCCTTCGAAATGCCCCATCACCTCAAATCGTAAGGCTCGTTCTTC
1 TTATCTCATACTGGTAC-ATGCCTTCAAAATGCCCCAACACCTCAAATCGTAAGGCTCACTC-TC
* * * *
3086559 -ATGCCTCTT-TT-GTCTGAATCATGTCATCTCAACATGATGTGGGTTCCGTCATGCCCTAACA
64 AATG--TCTTCTTGGTCCGAATCATGTCATCCCAACACGATGTGGGTTCAGTCATGCCCTAACA
3086620 T
1 T
3086621 ATCACAACTT
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
124 3 0.03
125 95 0.89
126 5 0.05
127 4 0.04
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (125 bp):
TTATCTCATACTGGTACATGCCTTCAAAATGCCCCAACACCTCAAATCGTAAGGCTCACTCTCAA
TGTCTTCTTGGTCCGAATCATGTCATCCCAACACGATGTGGGTTCAGTCATGCCCTAACA
Found at i:3092013 original size:21 final size:21
Alignment explanation
Indices: 3091989--3092045 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
3091979 AATGCGAAGT
*
3091989 GGTCTTCATGTCTTTATAAAG
1 GGTCTTCATGTCTTTATAAAC
*
3092010 GGTCTTCATGTCTTTATGAAC
1 GGTCTTCATGTCTTTATAAAC
3092031 GGTCTTC-TCGTCTTT
1 GGTCTTCAT-GTCTTT
3092046 GGTATGACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.46
Consensus pattern (21 bp):
GGTCTTCATGTCTTTATAAAC
Found at i:3094290 original size:27 final size:27
Alignment explanation
Indices: 3094252--3094311 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
3094242 AAAGCAACAC
3094252 TAAAATAAATCTAACATAACATCAAAA
1 TAAAATAAATCTAACATAACATCAAAA
*
3094279 TAAAATAAATCTAACATAACATCAAAC
1 TAAAATAAATCTAACATAACATCAAAA
3094306 TAAAAT
1 TAAAAT
3094312 GAAACTCGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (27 bp):
TAAAATAAATCTAACATAACATCAAAA
Found at i:3097947 original size:27 final size:28
Alignment explanation
Indices: 3097917--3097973 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 28
3097907 ATTATATCAT
3097917 AAATCTTAATTTAAAATTTAAAAT-TTA
1 AAATCTTAATTTAAAATTTAAAATCTTA
3097944 AAATCTTAATTTAAAATTTAAAATCTTA
1 AAATCTTAATTTAAAATTTAAAATCTTA
3097972 AA
1 AA
3097974 TTGGATATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (28 bp):
AAATCTTAATTTAAAATTTAAAATCTTA
Found at i:3097954 original size:20 final size:20
Alignment explanation
Indices: 3097931--3097972 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3097921 CTTAATTTAA
3097931 AATTTAAAATTTAAAATCTT
1 AATTTAAAATTTAAAATCTT
3097951 AATTTAAAATTTAAAATCTT
1 AATTTAAAATTTAAAATCTT
3097971 AA
1 AA
3097973 ATTGGATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTTAAAATTTAAAATCTT
Found at i:3097974 original size:7 final size:7
Alignment explanation
Indices: 3097924--3097973 Score: 68
Period size: 7 Copynumber: 7.1 Consensus size: 7
3097914 CATAAATCTT
3097924 AATTTAA
1 AATTTAA
3097931 AATTTAA
1 AATTTAA
3097938 AATTTAA
1 AATTTAA
3097945 AATCTT--
1 AAT-TTAA
3097951 AATTTAA
1 AATTTAA
3097958 AATTTAA
1 AATTTAA
3097965 AATCTTAA
1 AAT-TTAA
3097973 A
1 A
3097974 TTGGATATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.05
6 3 0.08
7 27 0.69
8 7 0.18
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTTAA
Found at i:3098554 original size:33 final size:32
Alignment explanation
Indices: 3098515--3098597 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 32
3098505 CAACCCATTG
3098515 TCTGCGCCGCTCGTCCTCCTAAAAAAACACTTC
1 TCTGCGCCGCTC-TCCTCCTAAAAAAACACTTC
*
3098548 TCTGCGCCGCTTCTCCTCCTAAAAAAACCCTTC
1 TCTGCGCCGC-TCTCCTCCTAAAAAAACACTTC
*
3098581 TCTGTGCCGCTTCTCCT
1 TCTGCGCCGC-TCTCCT
3098598 TTCGTTGTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 45 0.96
34 2 0.04
ACGTcount: A:0.18, C:0.41, G:0.12, T:0.29
Consensus pattern (32 bp):
TCTGCGCCGCTCTCCTCCTAAAAAAACACTTC
Found at i:3098992 original size:16 final size:18
Alignment explanation
Indices: 3098957--3098995 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3098947 ACTAGGCTAT
*
3098957 TATATATATGCTGATTTA
1 TATATATATGCTGATGTA
3098975 TATATATATG-T-ATGTA
1 TATATATATGCTGATGTA
3098991 TATAT
1 TATAT
3098996 TGTATTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 10 0.50
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (18 bp):
TATATATATGCTGATGTA
Found at i:3099035 original size:32 final size:35
Alignment explanation
Indices: 3098965--3099041 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
3098955 ATTATATATA
*
3098965 TGCTGATTTATATATATATGTATGTATATATTGTATT
1 TGCTG-TTTATATATATATGTA-GTATATATTGAATT
*
3099002 TGTTGTTTATATATATATGTA-TAT-TA-TGAATT
1 TGCTGTTTATATATATATGTAGTATATATTGAATT
3099034 TGCTGTTT
1 TGCTGTTT
3099042 GTATGTTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 12 0.32
33 2 0.05
34 3 0.08
36 16 0.43
37 4 0.11
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (35 bp):
TGCTGTTTATATATATATGTAGTATATATTGAATT
Found at i:3099092 original size:21 final size:22
Alignment explanation
Indices: 3099019--3099104 Score: 138
Period size: 22 Copynumber: 4.0 Consensus size: 22
3099009 TATATATATA
*
3099019 TGTATATTATGAATTTGCTGTT
1 TGTATGTTATGAATTTGCTGTT
*
3099041 TGTATGTTATGAATTTGTTGTT
1 TGTATGTTATGAATTTGCTGTT
3099063 TGTATGTTATGAATTTGCTGTT
1 TGTATGTTATGAATTTGCTGTT
*
3099085 TG-ATGTTATGTATTTGCTGT
1 TGTATGTTATGAATTTGCTGT
3099105 GTATGATGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 17 0.28
22 43 0.72
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (22 bp):
TGTATGTTATGAATTTGCTGTT
Found at i:3100243 original size:57 final size:57
Alignment explanation
Indices: 3100155--3100312 Score: 262
Period size: 57 Copynumber: 2.8 Consensus size: 57
3100145 TGTAAGAAAT
* *
3100155 ATTATATGGTTTATGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTTAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
* * *
3100212 ATTATATGGTTTGTGGTTTATGTTAAAAATATTATATGGTTTTTCGATGTTCAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
*
3100269 ATTATATGGTTTGTGGTCCATGTTAGAAATATTATATGGTTTGT
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
3100313 ATTAAAGTTA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 92 1.00
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (57 bp):
ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
Found at i:3100311 original size:30 final size:30
Alignment explanation
Indices: 3100144--3100312 Score: 183
Period size: 30 Copynumber: 5.8 Consensus size: 30
3100134 CTTTTTGATT
* * *
3100144 ATGTAAGAAATATTATATGGTTTATGGTCT
1 ATGTTAGAAATATTATATGGTTTGTGGTCG
3100174 ATGTTAGAAATATTATATGG-TT-T-GTCG
1 ATGTTAGAAATATTATATGGTTTGTGGTCG
* **
3100201 ATGTTTA-AAACATTATATGGTTTGTGGTTT
1 ATG-TTAGAAATATTATATGGTTTGTGGTCG
*
3100231 ATGTTAAAAATATTATATGGTTT-T--TCG
1 ATGTTAGAAATATTATATGGTTTGTGGTCG
* *
3100258 ATGTTCA-AAACATTATATGGTTTGTGGTCC
1 ATGTT-AGAAATATTATATGGTTTGTGGTCG
3100288 ATGTTAGAAATATTATATGGTTTGT
1 ATGTTAGAAATATTATATGGTTTGT
3100313 ATTAAAGTTA
Statistics
Matches: 118, Mismatches: 11, Indels: 20
0.79 0.07 0.13
Matches are distributed among these distances:
27 39 0.33
28 8 0.07
29 8 0.07
30 63 0.53
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.46
Consensus pattern (30 bp):
ATGTTAGAAATATTATATGGTTTGTGGTCG
Found at i:3101671 original size:31 final size:31
Alignment explanation
Indices: 3101634--3101692 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
3101624 AGTTGTATGG
3101634 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGTAAAACTAAA
3101665 ATTATTTAAATTTCAGTATTGTAAAACT
1 ATTATTTAAATTTCAGTATTGTAAAACT
3101693 CTTTTCAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGTAAAACTAAA
Found at i:3102124 original size:25 final size:25
Alignment explanation
Indices: 3102096--3102164 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 25
3102086 TTATGAGTTT
3102096 TTTATTATTAAAAATTATAAAATTA
1 TTTATTATTAAAAATTATAAAATTA
*
3102121 TTTA-T-TT---AATTATATAAATTT
1 TTTATTATTAAAAATTATA-AAATTA
* *
3102142 TTTATTATTAAAAGTTACAAAAT
1 TTTATTATTAAAAATTATAAAAT
3102165 CGTCACTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
20 7 0.20
21 9 0.26
22 1 0.03
23 4 0.11
24 1 0.03
25 8 0.23
26 5 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
TTTATTATTAAAAATTATAAAATTA
Found at i:3103140 original size:18 final size:17
Alignment explanation
Indices: 3103100--3103140 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
3103090 ATAAATATAA
3103100 AAAAATCAGAAAAATAC
1 AAAAATCAGAAAAATAC
*
3103117 ATAAAATCTGAAAAATTAC
1 A-AAAATCAGAAAAA-TAC
3103136 AAAAA
1 AAAAA
3103141 AATTAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 16 0.76
19 4 0.19
ACGTcount: A:0.68, C:0.10, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAATCAGAAAAATAC
Found at i:3107940 original size:3 final size:3
Alignment explanation
Indices: 3107932--3108031 Score: 164
Period size: 3 Copynumber: 33.3 Consensus size: 3
3107922 GAATTGTCTG
* * * *
3107932 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AAT GAT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3107980 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3108028 AAT A
1 AAT A
3108032 CGGGTAAACT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3124636 original size:22 final size:22
Alignment explanation
Indices: 3124608--3124658 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3124598 TGGGTTCATG
* *
3124608 AGATAAGTACACCTTTTATCAA
1 AGATAAGTACACATTCTATCAA
3124630 AGATAAGTACACATTCTATCAA
1 AGATAAGTACACATTCTATCAA
3124652 AGATAAG
1 AGATAAG
3124659 ATTGATAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (22 bp):
AGATAAGTACACATTCTATCAA
Found at i:3126348 original size:17 final size:17
Alignment explanation
Indices: 3126328--3126385 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
3126318 GTTTTGAAAA
*
3126328 TATATATGTTTATATAG
1 TATATATGTTAATATAG
**
3126345 TATATTAT-AAAATATAG
1 TATA-TATGTTAATATAG
*
3126362 TATATATGTTAAAATAG
1 TATATATGTTAATATAG
3126379 TATATAT
1 TATATAT
3126386 ATATATATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 3 0.09
17 27 0.82
18 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (17 bp):
TATATATGTTAATATAG
Found at i:3136611 original size:9 final size:9
Alignment explanation
Indices: 3136578--3136612 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
3136568 AGAAAAACAA
3136578 AAAAAAGATC
1 AAAAAA-ATC
3136588 AAAAAAATC
1 AAAAAAATC
3136597 -AAAAAATC
1 AAAAAAATC
3136605 AAAAAAAT
1 AAAAAAAT
3136613 ATAAAAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 10 0.42
10 6 0.25
ACGTcount: A:0.77, C:0.09, G:0.03, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:3136618 original size:17 final size:18
Alignment explanation
Indices: 3136579--3136612 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3136569 GAAAAACAAA
3136579 AAAAAGATCAAAAAAATC
1 AAAAAGATCAAAAAAATC
3136597 AAAAA-ATCAAAAAAAT
1 AAAAAGATCAAAAAAAT
3136613 ATAAAAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAAAGATCAAAAAAATC
Found at i:3145968 original size:17 final size:17
Alignment explanation
Indices: 3145946--3146001 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
3145936 TAGTCCCTAA
3145946 ACTTTTACAAAGTTTAT
1 ACTTTTACAAAGTTTAT
3145963 ACTTTTACAAAGTTTAT
1 ACTTTTACAAAGTTTAT
3145980 ACTTTTACAAAGTTTAT
1 ACTTTTACAAAGTTTAT
3145997 ACTTT
1 ACTTT
3146002 AGCCACTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.48
Consensus pattern (17 bp):
ACTTTTACAAAGTTTAT
Found at i:3148427 original size:22 final size:22
Alignment explanation
Indices: 3148399--3148470 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
3148389 CAATTTTATA
3148399 AATTAACTTCATTTTAAGCTTC
1 AATTAACTTCATTTTAAGCTTC
* * *
3148421 AATTAACATAACCAATTT-A---TA
1 AATTAAC-T--TCATTTTAAGCTTC
3148442 AATTAACTTCATTTTAAGCTTC
1 AATTAACTTCATTTTAAGCTTC
3148464 AATTAAC
1 AATTAAC
3148471 ATAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
18 5 0.14
19 1 0.03
20 1 0.03
21 8 0.22
22 15 0.41
23 1 0.03
24 1 0.03
25 5 0.14
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (22 bp):
AATTAACTTCATTTTAAGCTTC
Found at i:3148441 original size:43 final size:43
Alignment explanation
Indices: 3148393--3148478 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
3148383 TCTTATCAAT
3148393 TTTATAAATTAACTTCATTTTAAGCTTCAATTAACATAACCAA
1 TTTATAAATTAACTTCATTTTAAGCTTCAATTAACATAACCAA
3148436 TTTATAAATTAACTTCATTTTAAGCTTCAATTAACATAACCAA
1 TTTATAAATTAACTTCATTTTAAGCTTCAATTAACATAACCAA
3148479 AATTTCCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (43 bp):
TTTATAAATTAACTTCATTTTAAGCTTCAATTAACATAACCAA
Found at i:3150550 original size:18 final size:18
Alignment explanation
Indices: 3150519--3150567 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
3150509 TAAGTAGCTG
*
3150519 AGTT-GAGGACTTATGGC
1 AGTTGGAGGAGTTATGGC
3150536 AGTTGGAGGAGTTATGGC
1 AGTTGGAGGAGTTATGGC
3150554 AGTTGGAGGCAGTT
1 AGTTGGAGG-AGTT
3150568 GGAGTGACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 4 0.14
18 21 0.72
19 4 0.14
ACGTcount: A:0.22, C:0.08, G:0.41, T:0.29
Consensus pattern (18 bp):
AGTTGGAGGAGTTATGGC
Found at i:3150602 original size:12 final size:11
Alignment explanation
Indices: 3150583--3150640 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 11
3150573 GACACTACTA
3150583 TACTACCTAGC
1 TACTACCTAGC
3150594 TAGCTACCTAAGC
1 TA-CTACCT-AGC
*
3150607 TACTAGCTAGC
1 TACTACCTAGC
*
3150618 TTACTAACATAGC
1 -TACT-ACCTAGC
3150631 TAGCTACCTA
1 TA-CTACCTA
3150641 TGTCACTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 5 0.13
12 21 0.55
13 12 0.32
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (11 bp):
TACTACCTAGC
Found at i:3150612 original size:20 final size:18
Alignment explanation
Indices: 3150589--3150640 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
3150579 ACTATACTAC
3150589 CTAGCTAGCTACCTAAGCTA
1 CTAGCTAGCTACCTAA-C-A
3150609 CTAGCTAGCTTA-CTAACA
1 CTAGCTAGC-TACCTAACA
3150627 -TAGCTAGCTACCTA
1 CTAGCTAGCTACCTA
3150641 TGTCACTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.07
17 11 0.37
18 1 0.03
19 1 0.03
20 13 0.43
21 2 0.07
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (18 bp):
CTAGCTAGCTACCTAACA
Found at i:3153303 original size:21 final size:20
Alignment explanation
Indices: 3153279--3153334 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
3153269 TTTAATCACT
3153279 TTTAATAT-AATAATATAATAA
1 TTTAATATCAA-AATATAAT-A
*
3153300 TTTAATATCAAAATATTATA
1 TTTAATATCAAAATATAATA
*
3153320 TTTAAACATCAAAAT
1 TTT-AATATCAAAAT
3153335 CGATATCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 4 0.13
21 25 0.81
22 2 0.06
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAATATCAAAATATAATA
Found at i:3155581 original size:20 final size:21
Alignment explanation
Indices: 3155541--3155590 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3155531 AGCTTAATCC
3155541 AAAAATCAATCATGTAGGCTT
1 AAAAATCAATCATGTAGGCTT
3155562 AAAAATCAATCATGTA-GCTT
1 AAAAATCAATCATGTAGGCTT
3155582 AAAAATCAA
1 AAAAATCAA
3155591 AATGAAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (21 bp):
AAAAATCAATCATGTAGGCTT
Found at i:3157380 original size:15 final size:15
Alignment explanation
Indices: 3157349--3157377 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3157339 TGATGTGATC
3157349 CTACTTTTACATCTT
1 CTACTTTTACATCTT
3157364 CTACTTTT-CATCTT
1 CTACTTTTACATCTT
3157378 TCTTTCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (15 bp):
CTACTTTTACATCTT
Found at i:3159956 original size:138 final size:138
Alignment explanation
Indices: 3159708--3159983 Score: 543
Period size: 138 Copynumber: 2.0 Consensus size: 138
3159698 AAATAAATGT
3159708 GAAAATACATGTTTATTTGATTTGTTGAAAGTAAATCTTTCATTGAATATTATGATTTGGCATAA
1 GAAAATACATGTTTATTTGATTTGTTGAAAGTAAATCTTTCATTGAATATTATGATTTGGCATAA
3159773 AATTCCATATATCTGAACTGTTTATTTTGATATGTGGATTCTGAAATGTTGATTTTTAGATTTCA
66 AATTCCATATATCTGAACTGTTTATTTTGATATGTGGATTCTGAAATGTTGATTTTTAGATTTCA
3159838 GTTCAAAG
131 GTTCAAAG
*
3159846 GAAAATACATGTTTTTTTGATTTGTTGAAAGTAAATCTTTCATTGAATATTATGATTTGGCATAA
1 GAAAATACATGTTTATTTGATTTGTTGAAAGTAAATCTTTCATTGAATATTATGATTTGGCATAA
3159911 AATTCCATATATCTGAACTGTTTATTTTGATATGTGGATTCTGAAATGTTGATTTTTAGATTTCA
66 AATTCCATATATCTGAACTGTTTATTTTGATATGTGGATTCTGAAATGTTGATTTTTAGATTTCA
3159976 GTTCAAAG
131 GTTCAAAG
3159984 AAAGGTTTGA
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 137 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (138 bp):
GAAAATACATGTTTATTTGATTTGTTGAAAGTAAATCTTTCATTGAATATTATGATTTGGCATAA
AATTCCATATATCTGAACTGTTTATTTTGATATGTGGATTCTGAAATGTTGATTTTTAGATTTCA
GTTCAAAG
Found at i:3160383 original size:14 final size:14
Alignment explanation
Indices: 3160333--3160383 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3160323 TTTTATTATT
*
3160333 ATAATATT-CTTATA
1 ATAATATTATTTA-A
*
3160347 ATATATATTATTTAT
1 ATA-ATATTATTTAA
*
3160362 ATATTATTATTTAA
1 ATAATATTATTTAA
3160376 ATAATATT
1 ATAATATT
3160384 TAAATTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 19 0.63
15 8 0.27
16 3 0.10
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
ATAATATTATTTAA
Found at i:3164190 original size:32 final size:32
Alignment explanation
Indices: 3164149--3164212 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
3164139 AAAGATTGAG
*
3164149 ATAGTTGGAAAGATACTTGGCATCTCATCTAC
1 ATAGTTGGAAAGACACTTGGCATCTCATCTAC
3164181 ATAGTTGGAAAGACACTTGGCATCTCATCTAC
1 ATAGTTGGAAAGACACTTGGCATCTCATCTAC
3164213 GATGTCAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (32 bp):
ATAGTTGGAAAGACACTTGGCATCTCATCTAC
Found at i:3166505 original size:24 final size:24
Alignment explanation
Indices: 3166470--3166547 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
3166460 TTAGAATCAT
*
3166470 GAGTGCACGAATACACTGATTCAA
1 GAGTGCACGAATACACTGATACAA
* * *
3166494 GAGTGCATGAATGCACTGATACAG
1 GAGTGCACGAATACACTGATACAA
* * * *
3166518 GAGTGCAAGGAT-CACTAATACAG
1 GAGTGCACGAATACACTGATACAA
3166541 GAGTGCA
1 GAGTGCA
3166548 ACAAATGAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 17 0.36
24 30 0.64
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (24 bp):
GAGTGCACGAATACACTGATACAA
Found at i:3166613 original size:14 final size:14
Alignment explanation
Indices: 3166594--3166620 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3166584 TATATCAATT
3166594 TTCATAGAAAAATG
1 TTCATAGAAAAATG
3166608 TTCATAGAAAAAT
1 TTCATAGAAAAAT
3166621 TATCATATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (14 bp):
TTCATAGAAAAATG
Found at i:3166626 original size:14 final size:13
Alignment explanation
Indices: 3166593--3166627 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
3166583 TTATATCAAT
3166593 TTTCATAGAAAAA
1 TTTCATAGAAAAA
3166606 TGTTCATAGAAAAA
1 T-TTCATAGAAAAA
3166620 TTATCATA
1 TT-TCATA
3166628 TTCATATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (13 bp):
TTTCATAGAAAAA
Found at i:3176816 original size:356 final size:352
Alignment explanation
Indices: 3176166--3176873 Score: 1348
Period size: 356 Copynumber: 2.0 Consensus size: 352
3176156 CTTTGTCAAG
3176166 CATTGTATATATAGGAACAGGGACGGAGCCATGATCAAATATTGGGAGGAGCAAGGTACTTAAGT
1 CATTGTATATATAGGAACAGGGACGGAGCCATGATCAAATATTGGGAGGAGCAAGGTACTTAAGT
3176231 TCAAAATAAGGACTTATTATGTATTAATATAAAAATTTAGGGGAGCAAAAGTCCAATTACTTAAA
66 TCAAAATAAGGACTTATTATGTATTAATATAAAAATTTAGGGGAGCAAAAGTCCAATTACTTAAA
3176296 TTTAAATTGATAAAAGACCTAAACATGCTATTAAACCAAAATATTGGGAGGGACAAGAGCATTGA
131 TTTAAATTGATAAAAGACCTAAACATGCTATTAAACCAAAATATTGGGAGGGACAAGAGCATTGA
3176361 TTGTCATATGATTGAAAGTTTTGAAGAGATACTACATTGTAGAAAAGATTGATAAAAATAGTCCA
196 TTGTCATATGATTGAAAGTTTTGAAGAGATACTACATTGTAGAAAAGATTGATAAAAATAGTCCA
3176426 TAATTAAGGGTTTATTTGTGTATTTTATCCAATATATATATCAGTTC-TTTAAGTACATCAGACA
261 TAATTAAGGGTTTATTTGTGTATTTTATCCAATATATATATCAGTTCATTTAAGTACATCAGACA
3176490 TTTCTCGTCCAATACGATCAGATGCTCGA
326 -TT-TCGTCCAATACGATCAGATGCTCGA
3176519 CATTGTATATATAGGAACAGGGACGGAGCCATGATCAAATATTGGGAGGAGCAAGGTACTTAAGT
1 CATTGTATATATAGGAACAGGGACGGAGCCATGATCAAATATTGGGAGGAGCAAGGTACTTAAGT
3176584 TCAAAATAAGGACTTATTATGTATTTAATATAAAAATTTAGGGGAGCAAAAGTCCAATTTTACTT
66 TCAAAATAAGGACTTATTATGTA-TTAATATAAAAATTTAGGGGAGCAAAAGTCCAA--TTACTT
3176649 AAATTTAAATTGATAAAAGACCTAAA-ATGCTATTAAACCAAAAATATTGGGAGGGACAAGAGCA
128 AAATTTAAATTGATAAAAGACCTAAACATGCTATTAAACC-AAAATATTGGGAGGGACAAGAGCA
3176713 TTGATTGTCATATGATTGAAAGTTTTGAAGAGATACTACATTGTAGAAAAGATTGATAAAAATAG
192 TTGATTGTCATATGATTGAAAGTTTTGAAGAGATACTACATTGTAGAAAAGATTGATAAAAATAG
3176778 TCCATAATTAAGGGTTTATTTGTGTATTTTATCCAATATATATATCAGTTCATTTAAGTACATCA
257 TCCATAATTAAGGGTTTATTTGTGTATTTTATCCAATATATATATCAGTTCATTTAAGTACATCA
3176843 GACATTTCGTCCAATACGATCAGATGCTCGA
322 GACATTTCGTCCAATACGATCAGATGCTCGA
3176874 ATTTGAACTC
Statistics
Matches: 350, Mismatches: 0, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
353 88 0.25
354 33 0.09
355 38 0.11
356 174 0.50
357 17 0.05
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (352 bp):
CATTGTATATATAGGAACAGGGACGGAGCCATGATCAAATATTGGGAGGAGCAAGGTACTTAAGT
TCAAAATAAGGACTTATTATGTATTAATATAAAAATTTAGGGGAGCAAAAGTCCAATTACTTAAA
TTTAAATTGATAAAAGACCTAAACATGCTATTAAACCAAAATATTGGGAGGGACAAGAGCATTGA
TTGTCATATGATTGAAAGTTTTGAAGAGATACTACATTGTAGAAAAGATTGATAAAAATAGTCCA
TAATTAAGGGTTTATTTGTGTATTTTATCCAATATATATATCAGTTCATTTAAGTACATCAGACA
TTTCGTCCAATACGATCAGATGCTCGA
Found at i:3181274 original size:2 final size:2
Alignment explanation
Indices: 3181267--3181306 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3181257 ACTGATCAGG
3181267 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3181307 AATTGGTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3183353 original size:21 final size:21
Alignment explanation
Indices: 3183327--3183367 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3183317 ACAAAAAAAG
3183327 ACATTGAATTTAATAATAGTA
1 ACATTGAATTTAATAATAGTA
* **
3183348 ACATTGTATTTTTTAATAGT
1 ACATTGAATTTAATAATAGT
3183368 CTAAAATGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (21 bp):
ACATTGAATTTAATAATAGTA
Found at i:3184397 original size:30 final size:29
Alignment explanation
Indices: 3184342--3184399 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
3184332 ACACTGCCCA
* *
3184342 ATTTTTTTAAAAAAAAGTTTTTAAATAAT
1 ATTTTTTTAAAAAAAAGTATATAAATAAT
3184371 ATTTTATTTAAAAAAATA-TATATAAATAA
1 ATTTT-TTTAAAAAAA-AGTATATAAATAA
3184400 ACAAGTGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 19 0.76
31 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
ATTTTTTTAAAAAAAAGTATATAAATAAT
Found at i:3193658 original size:22 final size:22
Alignment explanation
Indices: 3193633--3193701 Score: 57
Period size: 24 Copynumber: 3.0 Consensus size: 22
3193623 TATTTTCGTG
3193633 ATTTTGTTTTAATTATTCAACT
1 ATTTTGTTTTAATTATTCAACT
* * * * *
3193655 ATTTTCTTTGAAATCATATCTATT
1 ATTTTGTTT-TAATTAT-TCAACT
*
3193679 ATTATGGTTTTAATTATTCAACT
1 ATT-TTGTTTTAATTATTCAACT
3193702 TTTGATCCTC
Statistics
Matches: 33, Mismatches: 11, Indels: 5
0.67 0.22 0.10
Matches are distributed among these distances:
22 8 0.24
23 9 0.27
24 12 0.36
25 4 0.12
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (22 bp):
ATTTTGTTTTAATTATTCAACT
Found at i:3200324 original size:47 final size:47
Alignment explanation
Indices: 3200255--3200348 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
3200245 GTTGTCTAAG
*
3200255 ATTTGTTTGAATGTGTATGATTTGATTTCAACGTT-ATCTTGAGGATA
1 ATTTGTTTGAATGTGTATGATTTAATTTCAACGTTAAT-TTGAGGATA
* * * *
3200302 ATTTGTTTGGATTTGTATGATTTAATTTCGATGTTAATTTGAGGATA
1 ATTTGTTTGAATGTGTATGATTTAATTTCAACGTTAATTTGAGGATA
3200349 TTTCTTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 39 0.95
48 2 0.05
ACGTcount: A:0.26, C:0.04, G:0.21, T:0.49
Consensus pattern (47 bp):
ATTTGTTTGAATGTGTATGATTTAATTTCAACGTTAATTTGAGGATA
Found at i:3207487 original size:12 final size:11
Alignment explanation
Indices: 3207472--3207510 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
3207462 TGAAAAAGTG
*
3207472 AAAAAAAAGGA
1 AAAAAAAAGAA
3207483 AAAAAAAAGAA
1 AAAAAAAAGAA
3207494 AAGAAAAAAGAA
1 AA-AAAAAAGAA
3207506 AAAAA
1 AAAAA
3207511 TGTGTACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:3210854 original size:14 final size:15
Alignment explanation
Indices: 3210828--3210913 Score: 65
Period size: 15 Copynumber: 5.7 Consensus size: 15
3210818 ATATTATGCT
3210828 AATAAGAAAAAGAAA
1 AATAAGAAAAAGAAA
3210843 AATAAG-AAAAGAAA
1 AATAAGAAAAAGAAA
3210857 AA-AATGAAAAATGAGAA
1 AATAA-GAAAAA-GA-AA
*
3210874 AA-ATGAAAAA-AGAA
1 AATAAGAAAAAGA-AA
*
3210888 AA-AAGAAAAAAGAGA
1 AATAAG-AAAAAGAAA
*
3210903 AATGAGAAAAA
1 AATAAGAAAAA
3210914 AAGGAAAAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
13 2 0.03
14 19 0.32
15 23 0.38
16 11 0.18
17 5 0.08
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (15 bp):
AATAAGAAAAAGAAA
Found at i:3210859 original size:7 final size:7
Alignment explanation
Indices: 3210834--3210929 Score: 77
Period size: 7 Copynumber: 12.7 Consensus size: 7
3210824 TGCTAATAAG
3210834 AAAAAGAA
1 AAAAAG-A
3210842 AAATAAGA
1 AAA-AAGA
3210850 AAAGAA-A
1 AAA-AAGA
*
3210857 AAAATGA
1 AAAAAGA
3210864 AAAATGAGA
1 AAAA--AGA
*
3210873 AAAATGA
1 AAAAAGA
3210880 AAAAAGA
1 AAAAAGA
3210887 AAAAAGA
1 AAAAAGA
3210894 AAAAAGA
1 AAAAAGA
*
3210901 GAAATGAGAA
1 -AAA-AAG-A
*
3210911 AAAAAGG
1 AAAAAGA
3210918 AAAAAGA
1 AAAAAGA
3210925 AAAAA
1 AAAAA
3210930 TAAGGAAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
6 1 0.01
7 42 0.58
8 14 0.19
9 14 0.19
10 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (7 bp):
AAAAAGA
Found at i:3210865 original size:23 final size:21
Alignment explanation
Indices: 3210834--3210929 Score: 72
Period size: 23 Copynumber: 4.2 Consensus size: 21
3210824 TGCTAATAAG
3210834 AAAAAGAAAAATAAGAAAAGAA
1 AAAAAGAAAAATAAGAAAA-AA
*
3210856 AAAAATGAAAAATGAGAAAAATGA
1 AAAAA-GAAAAATAAGAAAAA--A
3210880 AAAAAG-AAAA-AAGAAAAAA
1 AAAAAGAAAAATAAGAAAAAA
3210899 GAGAAATGAGAAAAA-AAGGAAAAAGA
1 -A-AAA--AGAAAAATAA-GAAAAA-A
3210925 AAAAA
1 AAAAA
3210930 TAAGGAAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 10 0.16
22 11 0.18
23 16 0.26
24 15 0.24
25 7 0.11
26 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (21 bp):
AAAAAGAAAAATAAGAAAAAA
Found at i:3210898 original size:16 final size:16
Alignment explanation
Indices: 3210849--3210929 Score: 80
Period size: 15 Copynumber: 5.2 Consensus size: 16
3210839 GAAAAATAAG
3210849 AAAAGA-AAAAAATGAA
1 AAAAGAGAAAAAA-GAA
* *
3210865 AAATGAGAAAAATG-A
1 AAAAGAGAAAAAAGAA
3210880 AAAA-AGAAAAAAGAA
1 AAAAGAGAAAAAAGAA
**
3210895 AAAAGAGAAATGAGAA
1 AAAAGAGAAAAAAGAA
*
3210911 AAAA-AGGAAAAAGAA
1 AAAAGAGAAAAAAGAA
3210926 AAAA
1 AAAA
3210930 TAAGGAAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.15
15 21 0.40
16 19 0.36
17 5 0.09
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (16 bp):
AAAAGAGAAAAAAGAA
Found at i:3210915 original size:17 final size:15
Alignment explanation
Indices: 3210879--3210940 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 15
3210869 GAGAAAAATG
*
3210879 AAAAAAGAAAAAAG-
1 AAAAAAGGAAAAAGA
*
3210893 AAAAAAGAGAAATGAGA
1 AAAAAAG-GAAA-AAGA
3210910 AAAAAAGGAAAAAGAA
1 AAAAAAGGAAAAAG-A
3210926 AAAATAAGGAAAAAG
1 AAAA-AAGGAAAAAG
3210941 GTGAAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 7 0.17
15 5 0.12
16 11 0.28
17 17 0.43
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAAAAGGAAAAAGA
Found at i:3210947 original size:18 final size:17
Alignment explanation
Indices: 3210885--3210950 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
3210875 AATGAAAAAA
3210885 GAAAAA-AGAAAA-AA-
1 GAAAAAGAGAAAATAAG
* *
3210899 GAGAAATGAGAAAAAAAG
1 GA-AAAAGAGAAAATAAG
*
3210917 GAAAAAGAAAAAATAAG
1 GAAAAAGAGAAAATAAG
*
3210934 GAAAAAGGTGAAAATAA
1 GAAAAA-GAGAAAATAA
3210951 AAAGGAGGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
14 2 0.05
15 3 0.07
16 6 0.15
17 20 0.49
18 10 0.24
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (17 bp):
GAAAAAGAGAAAATAAG
Found at i:3212292 original size:23 final size:22
Alignment explanation
Indices: 3212266--3212326 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 22
3212256 TGTCTCATCA
3212266 ATCACATAAGGAGTTGGA-TCAGC
1 ATCACATAAGGAGTTGGATTC--C
* *
3212289 ATCAACATTATGA-TT-GATTCC
1 ATC-ACATAAGGAGTTGGATTCC
3212310 ATCACATAAGGAGTTGG
1 ATCACATAAGGAGTTGG
3212327 GTCAACATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 3 0.10
23 7 0.23
24 7 0.23
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (22 bp):
ATCACATAAGGAGTTGGATTCC
Found at i:3213948 original size:23 final size:22
Alignment explanation
Indices: 3213892--3213964 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 22
3213882 TCCTTATGTT
** *
3213892 TTTAATTAACCTTTTATTTTAT
1 TTTAATTAATTTTTTATTTTAA
* *
3213914 TTTATTTTATTTTTTAATTTTAA
1 TTTAATTAATTTTTT-ATTTTAA
*
3213937 TTTAATTAATTTGTT-TTTT-A
1 TTTAATTAATTTTTTATTTTAA
3213957 TTTGAATT
1 TTT-AATT
3213965 TGCAAGACTA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.10
21 8 0.20
22 11 0.27
23 18 0.44
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTAATTAATTTTTTATTTTAA
Found at i:3214735 original size:11 final size:11
Alignment explanation
Indices: 3214706--3214737 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3214696 ATAGAGAAAG
*
3214706 CCTTAATCTAC
1 CCTTAATTTAC
3214717 CCTTAATTTAC
1 CCTTAATTTAC
3214728 CCTTAATTTA
1 CCTTAATTTA
3214738 ATTAGGGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (11 bp):
CCTTAATTTAC
Found at i:3218819 original size:225 final size:225
Alignment explanation
Indices: 3218428--3218872 Score: 827
Period size: 225 Copynumber: 2.0 Consensus size: 225
3218418 TGTGGAACCT
3218428 TATCACTTCCCACAACATTTTTCGCTATAGGTATGAGACATGTATCCTCTACTTACAGTCGACGT
1 TATCACTTCCCACAACATTTTTCGCTATAGGTATGAGACATGTATCCTCTACTTACAGTCGACGT
*
3218493 TATTTTATTAATACATCTGACAAATATATTTTTTGGTCATACTCCACAACTGTGAATTCCGTATA
66 TATTTTATTAATACATCTGACAAATATATTTTCTGGTCATACTCCACAACTGTGAATTCCGTATA
* *
3218558 AGCTTTAATACAAAACTCCTTCACAGCTAGTTGCACATCCTTTTTGCTCGCAAACTGTGACCCAA
131 AGCTTTAATACAAAACTCCTTCACAGCTAGTTGCACATCCTTCTTGCTCGCAAACTGTAACCCAA
3218623 CTCCAAACTCCACCGATACGTCATCTAAGG
196 CTCCAAACTCCACCGATACGTCATCTAAGG
3218653 TATCACTTCCCACAACATTTTTCGCTATAGGTATGAGACATGTATCCTCTACTTACAGTCGACGT
1 TATCACTTCCCACAACATTTTTCGCTATAGGTATGAGACATGTATCCTCTACTTACAGTCGACGT
*
3218718 TATTTTATTAATACATCTGACAAATATATTTTCTGGTCATACTCCACAACTGTGAATTCCGTATG
66 TATTTTATTAATACATCTGACAAATATATTTTCTGGTCATACTCCACAACTGTGAATTCCGTATA
* *
3218783 AGCTTTAATACAAAACTCCTTCACAGCTAGTTGCACATCCTTCTTGCTTGTAAACTGTAACCCAA
131 AGCTTTAATACAAAACTCCTTCACAGCTAGTTGCACATCCTTCTTGCTCGCAAACTGTAACCCAA
*
3218848 CTCCAAACTCCACCGATATGTCATC
196 CTCCAAACTCCACCGATACGTCATC
3218873 AGAGGTCCCC
Statistics
Matches: 213, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
225 213 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (225 bp):
TATCACTTCCCACAACATTTTTCGCTATAGGTATGAGACATGTATCCTCTACTTACAGTCGACGT
TATTTTATTAATACATCTGACAAATATATTTTCTGGTCATACTCCACAACTGTGAATTCCGTATA
AGCTTTAATACAAAACTCCTTCACAGCTAGTTGCACATCCTTCTTGCTCGCAAACTGTAACCCAA
CTCCAAACTCCACCGATACGTCATCTAAGG
Found at i:3223003 original size:24 final size:25
Alignment explanation
Indices: 3222957--3223011 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
3222947 ACAATTATGC
*
3222957 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTACAAAAAGATGTGAT
* * *
3222981 CACTTGAAGTACCACAAGTTGTGAT
1 CACTTGAAGTACAAAAAGATGTGAT
3223006 CA-TTGA
1 CACTTGA
3223012 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTACAAAAAGATGTGAT
Found at i:3232717 original size:10 final size:10
Alignment explanation
Indices: 3232693--3232728 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
3232683 TGAACCTTCT
*
3232693 CCATGC-ACG
1 CCATGCAACA
3232702 CCATGCAACA
1 CCATGCAACA
3232712 CCATGCAACA
1 CCATGCAACA
3232722 CCATGCA
1 CCATGCA
3232729 CACGTTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 6 0.24
10 19 0.76
ACGTcount: A:0.33, C:0.42, G:0.14, T:0.11
Consensus pattern (10 bp):
CCATGCAACA
Found at i:3237295 original size:10 final size:10
Alignment explanation
Indices: 3237271--3237306 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
3237261 TGAACCTTCT
*
3237271 CCATGC-ACG
1 CCATGCAACA
3237280 CCATGCAACA
1 CCATGCAACA
3237290 CCATGCAACA
1 CCATGCAACA
3237300 CCATGCA
1 CCATGCA
3237307 CACGTTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 6 0.24
10 19 0.76
ACGTcount: A:0.33, C:0.42, G:0.14, T:0.11
Consensus pattern (10 bp):
CCATGCAACA
Found at i:3239655 original size:12 final size:11
Alignment explanation
Indices: 3239653--3239754 Score: 69
Period size: 12 Copynumber: 8.2 Consensus size: 11
3239643 AAGATAAAGA
3239653 AAAATAAAAAGAT
1 AAAA-AAAAA-AT
*
3239666 AAAAAAGTAAAT
1 AAAAAA-AAAAT
3239678 AAGATAAATAAAAT
1 AA-A-AAA-AAAAT
*
3239692 AAAGATAAAAAT
1 AAA-AAAAAAAT
3239704 AAAAATAAAAAT
1 AAAAA-AAAAAT
3239716 AAAAATAAAAAT
1 AAAAA-AAAAAT
*
3239728 AAAGATAAAAAT
1 AAA-AAAAAAAT
3239740 AAATAAAGAAAAT
1 AAA-AAA-AAAAT
3239753 AA
1 AA
3239755 TAGTAATATA
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
11 1 0.01
12 46 0.62
13 18 0.24
14 9 0.12
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:3239705 original size:6 final size:6
Alignment explanation
Indices: 3239683--3239742 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
3239673 TAAATAAGAT
*
3239683 AAAT-A AAATAA AGATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
*
3239730 AGATAA AAATAA A
1 AAATAA AAATAA A
3239743 TAAAGAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
5 4 0.08
6 46 0.92
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:3239788 original size:12 final size:12
Alignment explanation
Indices: 3239654--3239797 Score: 68
Period size: 12 Copynumber: 11.5 Consensus size: 12
3239644 AGATAAAGAA
3239654 AAATAAA-AAGAT
1 AAATAAATAA-AT
3239666 AAA-AAAGTAAAT
1 AAATAAA-TAAAT
3239678 AAGATAAATAAAAT
1 AA-ATAAAT-AAAT
*
3239692 AAAGATAA-AAAT
1 AAATA-AATAAAT
*
3239704 AAA-AATAAAAAT
1 AAATAA-ATAAAT
*
3239716 AAA-AATAAAAAT
1 AAATAA-ATAAAT
*
3239728 AAAGATAA-AAAT
1 AAATA-AATAAAT
*
3239740 AAATAAAGAAA-
1 AAATAAATAAAT
3239751 ATAATAGTAATATAAT
1 A-AATA--AATA-AAT
*
3239767 ATATATAATAAAT
1 AAATA-AATAAAT
3239780 AAATAAATAAAT
1 AAATAAATAAAT
3239792 AAATAA
1 AAATAA
3239798 GTGCAAGAAG
Statistics
Matches: 111, Mismatches: 5, Indels: 32
0.75 0.03 0.22
Matches are distributed among these distances:
10 1 0.01
11 8 0.07
12 61 0.55
13 15 0.14
14 20 0.18
15 5 0.05
16 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.22
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:3239871 original size:20 final size:20
Alignment explanation
Indices: 3239848--3239899 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3239838 AAAGGATATA
*
3239848 AAAATAAAGTAAAG-ATAAAG
1 AAAATAAAG-AAAGAAAAAAG
3239868 AAAATTAAA-AAAGAAAAAAG
1 AAAA-TAAAGAAAGAAAAAAG
3239888 AAAATAAAGAAA
1 AAAATAAAGAAA
3239900 AAAGAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.29
20 16 0.57
21 4 0.14
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAATAAAGAAAGAAAAAAG
Found at i:3239884 original size:7 final size:7
Alignment explanation
Indices: 3239874--3239915 Score: 57
Period size: 7 Copynumber: 5.6 Consensus size: 7
3239864 AAAGAAAATT
3239874 AAAAAAG
1 AAAAAAG
3239881 AAAAAAG
1 AAAAAAG
3239888 AAAATAAAG
1 -AAA-AAAG
3239897 AAAAAAG
1 AAAAAAG
3239904 AAAAAAAG
1 -AAAAAAG
3239912 AAAA
1 AAAA
3239916 TGATAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 15 0.47
8 13 0.41
9 4 0.12
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:3239915 original size:29 final size:30
Alignment explanation
Indices: 3239847--3239915 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
3239837 TAAAGGATAT
*
3239847 AAAAATAAAGTAAAGATAAAGAAAATTAAAA
1 AAAAAAAAAGTAAAGATAAAGAAAA-TAAAA
*
3239878 AAGAAAAAAG-AAA-ATAAAGAAAA-AAGAA
1 AAAAAAAAAGTAAAGATAAAGAAAATAA-AA
3239906 AAAAAGAAAA
1 AAAAA-AAAA
3239916 TGATAGTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
28 6 0.18
29 14 0.42
30 3 0.09
31 8 0.24
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.09
Consensus pattern (30 bp):
AAAAAAAAAGTAAAGATAAAGAAAATAAAA
Found at i:3241087 original size:13 final size:13
Alignment explanation
Indices: 3241069--3241095 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3241059 TAAGACAAGT
3241069 ATAATAAAAATTA
1 ATAATAAAAATTA
3241082 ATAATAAAAATTA
1 ATAATAAAAATTA
3241095 A
1 A
3241096 ATAAACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATAAAAATTA
Found at i:3242811 original size:12 final size:12
Alignment explanation
Indices: 3242794--3242838 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
3242784 ACCCACCTTA
3242794 TTTCTTTTTCAT
1 TTTCTTTTTCAT
*
3242806 TTTCTTATTTCTT
1 TTTCTT-TTTCAT
*
3242819 TTCTCTTTTTCCT
1 TT-TCTTTTTCAT
3242832 TTTCTTT
1 TTTCTTT
3242839 GTTATTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
13 14 0.48
14 4 0.14
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTTTTTCAT
Found at i:3242814 original size:19 final size:20
Alignment explanation
Indices: 3242790--3242838 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3242780 TTGAACCCAC
3242790 CTTATTTCTTTT-TCATTTT
1 CTTATTTCTTTTCTCATTTT
*
3242809 CTTATTTCTTTTCTCTTTTT
1 CTTATTTCTTTTCTCATTTT
*
3242829 CCT-TTTCTTT
1 CTTATTTCTTT
3242839 GTTATTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.73
Consensus pattern (20 bp):
CTTATTTCTTTTCTCATTTT
Found at i:3242816 original size:7 final size:6
Alignment explanation
Indices: 3242794--3242848 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
3242784 ACCCACCTTA
* * *
3242794 TTTCTT TTTCAT TTTCTT ATTTCTT TTCTCTT TTTCCT TTTCTT TGTTATT
1 TTTCTT TTTCTT TTTCTT -TTTCTT TT-TCTT TTTCTT TTTCTT T-TTCTT
3242845 TTTC
1 TTTC
3242849 CTCTCTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
6 23 0.57
7 17 0.43
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:3242846 original size:26 final size:26
Alignment explanation
Indices: 3242796--3242846 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3242786 CCACCTTATT
*
3242796 TCTTTTTCATTTTCTTATTTCTTTTC
1 TCTTTTTCATTTTCTTATTTATTTTC
*
3242822 TCTTTTTCCTTTTCTT-TGTTATTTT
1 TCTTTTTCATTTTCTTAT-TTATTTT
3242847 TCCTCTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.75
Consensus pattern (26 bp):
TCTTTTTCATTTTCTTATTTATTTTC
Found at i:3242913 original size:6 final size:6
Alignment explanation
Indices: 3242897--3242959 Score: 94
Period size: 6 Copynumber: 10.7 Consensus size: 6
3242887 ATCCTAAAGG
*
3242897 TTTTCT CTTTCT TTTTCT TTTTCT TTTT-T TATTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT
3242945 TTTT-T TTTTCT TTTT
1 TTTTCT TTTTCT TTTT
3242960 TTGACTTAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
5 7 0.13
6 43 0.83
7 2 0.04
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:3242960 original size:24 final size:24
Alignment explanation
Indices: 3242904--3242959 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
3242894 AGGTTTTCTC
3242904 TTTCTTTTTCTTTTTCTTTTTTTA
1 TTTCTTTTTCTTTTTCTTTTTTTA
3242928 TTTCTTTTTCTTTTTCTTTTTTT-
1 TTTCTTTTTCTTTTTCTTTTTTTA
3242951 TTTCTTTTT
1 TTTCTTTTT
3242960 TTGACTTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (24 bp):
TTTCTTTTTCTTTTTCTTTTTTTA
Found at i:3250333 original size:24 final size:24
Alignment explanation
Indices: 3250300--3250346 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3250290 TGTTTAAAGA
*
3250300 AGATACAATAAGTA-AAGATCAAGG
1 AGATAAAAT-AGTATAAGATCAAGG
*
3250324 AGATAAAATATTATAAGATCAAG
1 AGATAAAATAGTATAAGATCAAG
3250347 TCTGATAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.21
Consensus pattern (24 bp):
AGATAAAATAGTATAAGATCAAGG
Found at i:3253641 original size:10 final size:10
Alignment explanation
Indices: 3253592--3253664 Score: 59
Period size: 10 Copynumber: 7.8 Consensus size: 10
3253582 TAAAGAAGAT
*
3253592 AAGATAAAGA
1 AAGATAAAAA
3253602 AAG-TAAAAA
1 AAGATAAAAA
*
3253611 AAGATAGAGAA
1 AAGATA-AAAA
3253622 AA-AT--AAA
1 AAGATAAAAA
3253629 AAGATAAAAA
1 AAGATAAAAA
*
3253639 AAG-T-AAAT
1 AAGATAAAAA
*
3253647 AAGATAAATA
1 AAGATAAAAA
3253657 AAGATAAA
1 AAGATAAA
3253665 GAAATAAAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
7 4 0.08
8 8 0.16
9 10 0.20
10 23 0.46
11 5 0.10
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (10 bp):
AAGATAAAAA
Found at i:3253672 original size:18 final size:19
Alignment explanation
Indices: 3253539--3253664 Score: 73
Period size: 18 Copynumber: 6.5 Consensus size: 19
3253529 AAAAAGGGGG
*
3253539 GAAAGGTAATAAAA-ATAAA
1 GAAA-GTAAAAAAAGATAAA
* * *
3253558 GAAAATAAAAAAAAACAAA
1 GAAAGTAAAAAAAGATAAA
3253577 TGAAA-TAAAGAAGATAAGATAAA
1 -GAAAGT-AA-AA-A-AAGATAAA
*
3253600 GAAAGTAAAAAAAGATAGA
1 GAAAGTAAAAAAAGATAAA
3253619 GAAA--AATAAAAAGATAAA
1 GAAAGTAA-AAAAAGATAAA
* *
3253637 AAAAGT-AAATAAGATAAA
1 GAAAGTAAAAAAAGATAAA
*
3253655 TAAAGATAAA
1 GAAAG-TAAA
3253665 GAAATAAAGA
Statistics
Matches: 85, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
17 2 0.02
18 34 0.40
19 22 0.26
20 9 0.11
21 4 0.05
22 7 0.08
23 7 0.08
ACGTcount: A:0.72, C:0.01, G:0.13, T:0.13
Consensus pattern (19 bp):
GAAAGTAAAAAAAGATAAA
Done.