Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 15 of 39
Found at i:2169152 original size:20 final size:22
Alignment explanation
Indices: 2169121--2169164 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
2169111 GCTACATTTT
2169121 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
2169142 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
2169163 CA
1 CA
2169165 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:2177443 original size:20 final size:20
Alignment explanation
Indices: 2177400--2177445 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2177390 AAATCTTTTG
2177400 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2177421 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2177441 CAAAA
1 CAAAA
2177446 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2179893 original size:13 final size:13
Alignment explanation
Indices: 2179875--2179900 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2179865 TACACAAAGT
2179875 ATGTATCGATACA
1 ATGTATCGATACA
2179888 ATGTATCGATACA
1 ATGTATCGATACA
2179901 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2179898 original size:32 final size:33
Alignment explanation
Indices: 2179857--2179920 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2179847 TAGCCAAACT
*
2179857 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAT-TGTATCGATACAA
2179889 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
2179921 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 13 0.45
34 4 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:2179985 original size:20 final size:22
Alignment explanation
Indices: 2179954--2179997 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
2179944 GCTACATTTT
2179954 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
2179975 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
2179996 CA
1 CA
2179998 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:2183339 original size:81 final size:80
Alignment explanation
Indices: 2183223--2183877 Score: 552
Period size: 80 Copynumber: 8.1 Consensus size: 80
2183213 AAAATGAGGA
* * * * * *
2183223 TAGAGTATCCCTTTCAGAGATAGTGGGGTTGGAGTATCCTTGAAGATGAAAAATTAGATATTTTT
1 TAGAGTATCCC-CTCAGAAATGGTGGGGTTGGAGTATCCTCGAAAATGAAAAATTTGAT-TTTTT
* *
2183288 AGAAGTTAAAACCGGGT
64 AGAAGTAAAAACAGGGT
** * * *
2183305 TAGAGTATCTTCTCAAAAATGGTGGGGTTAGAGTAT-CTCCGAAAATGAAAAATCTGATCTTTTT
1 TAGAGTATCCCCTCAGAAATGGTGGGGTTGGAGTATCCT-CGAAAATGAAAAATTTGAT-TTTTT
* * *
2183369 AGAGGTAAAAACAAGTT
64 AGAAGTAAAAACAGGGT
* ** * ** * * * *
2183386 TAAAGTATCCTTTCAGAGATGACGAGGTTGGAATATCC-CTGAAGATGAAAAATTAGATTTTTTA
1 TAGAGTATCCCCTCAGAAATGGTGGGGTTGGAGTATCCTC-GAAAATGAAAAATTTGATTTTTTA
*
2183450 GAAGTAAAAACAAGGT
65 GAAGTAAAAACAGGGT
* * * * * * *
2183466 TGGAGTATCCCCTTAGAAATGGTTGGATTGGAGTATCCTTGAAAATGAAAATTTTGATTTTGTA-
1 TAGAGTATCCCCTCAGAAATGGTGGGGTTGGAGTATCCTCGAAAATGAAAAATTTGATTTTTTAG
*
2183530 AAGGTAAAAACGGGGT
66 AA-GTAAAAACAGGGT
* * * * * * *
2183546 TAGAGTATCCCCTCAAAAATGGCGAGGTTGGAGTATCCCCGAAGATGAAAAACTGGATATTTTTA
1 TAGAGTATCCCCTCAGAAATGGTGGGGTTGGAGTATCCTCGAAAATGAAAAATTTGAT-TTTTTA
* * *
2183611 AAAGTAAAAATAGAGT
65 GAAGTAAAAACAGGGT
* * * * *
2183627 TGGAGTATCTCCTCAGAAATGGTAGGGTTGGGGTATCC-CTAAAAAT-AAAAATTTTGATTTTTT
1 TAGAGTATCCCCTCAGAAATGGTGGGGTTGGAGTATCCTC-GAAAATGAAAAA-TTTGATTTTTT
2183690 AGAAGTAAAAACAGGGT
64 AGAAGTAAAAACAGGGT
* * *** * *
2183707 TGGAGTATCCCCTCAGAGATGGCAAGGTTGGAGTATCCTCGAAAAT-AGAAAATTGGATAGTTTT
1 TAGAGTATCCCCTCAGAAATGGTGGGGTTGGAGTATCCTCGAAAATGA-AAAATTTGAT-TTTTT
*
2183771 AGAAGTAAAAACGGGGT
64 AGAAGTAAAAACAGGGT
* ** * * * *
2183788 TGGAGTATCTTCTTA-AAAGTGGTGGGGTTGTAGTATCCTCGAAAATGAAAATTTTGTTTTTTTA
1 TAGAGTATCCCCTCAGAAA-TGGTGGGGTTGGAGTATCCTCGAAAATGAAAAATTTGATTTTTTA
2183852 -AAGGTAAAAACAGGGT
65 GAA-GTAAAAACAGGGT
2183868 TAGAGTATCC
1 TAGAGTATCC
2183878 TCTCGGAGAT
Statistics
Matches: 452, Mismatches: 106, Indels: 32
0.77 0.18 0.05
Matches are distributed among these distances:
79 4 0.01
80 221 0.49
81 214 0.47
82 13 0.03
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (80 bp):
TAGAGTATCCCCTCAGAAATGGTGGGGTTGGAGTATCCTCGAAAATGAAAAATTTGATTTTTTAG
AAGTAAAAACAGGGT
Found at i:2183461 original size:80 final size:81
Alignment explanation
Indices: 2183223--2183878 Score: 434
Period size: 81 Copynumber: 8.1 Consensus size: 81
2183213 AAAATGAGGA
* * * * * *
2183223 TAGAGTATCCCTTTCAGAGATAGTGGGGTTGGAGTATCCTTGAAGATGAAAAATTAGATATTTTT
1 TAGAGTAT-CCTTTCAGAAATGGCGAGGTTGGAGTATCCCTGAAAATGAAAAATTAGATATTTTT
* **
2183288 AGAAGTTAAAACCGGGT
65 AGAAGTAAAAACAAGGT
* * * * *
2183305 TAGAGTAT-CTTCTCAAAAATGGTGGGGTTAGAGTATCTCC-GAAAATGAAAAATCT-GATCTTT
1 TAGAGTATCCTT-TCAGAAATGGCGAGGTTGGAGTATC-CCTGAAAATGAAAAAT-TAGATATTT
* *
2183367 TTAGAGGTAAAAACAAGTT
63 TTAGAAGTAAAAACAAGGT
* * * * *
2183386 TAAAGTATCCTTTCAGAGATGACGAGGTTGGAATATCCCTGAAGATGAAAAATTAGAT-TTTTTA
1 TAGAGTATCCTTTCAGAAATGGCGAGGTTGGAGTATCCCTGAAAATGAAAAATTAGATATTTTTA
2183450 GAAGTAAAAACAAGGT
66 GAAGTAAAAACAAGGT
* * * * * * * *
2183466 TGGAGTATCCCCTT-AGAAATGGTTG-GATTGGAGTATCCTTGAAAATGAAAATTTTGAT-TTTG
1 TAGAGTAT-CCTTTCAGAAATGG-CGAGGTTGGAGTATCCCTGAAAATGAAAAATTAGATATTTT
**
2183528 TA-AAGGTAAAAACGGGGT
64 TAGAA-GTAAAAACAAGGT
** * * * * *
2183546 TAGAGTATCCCCTCAAAAATGGCGAGGTTGGAGTATCCCCGAAGATGAAAAACTGGATATTTTTA
1 TAGAGTATCCTTTCAGAAATGGCGAGGTTGGAGTATCCCTGAAAATGAAAAATTAGATATTTTTA
* *
2183611 AAAGTAAAAA-TAGAGT
66 GAAGTAAAAACAAG-GT
* * * * * *
2183627 TGGAGTAT-CTCCTCAGAAATGG-TAGGGTTGGGGTATCCCTAAAAAT-AAAAATTTTGAT-TTT
1 TAGAGTATCCT-TTCAGAAATGGCGA-GGTTGGAGTATCCCTGAAAATGAAAAA-TTAGATATTT
*
2183688 TTAGAAGTAAAAACAGGGT
63 TTAGAAGTAAAAACAAGGT
* ** * * * *
2183707 TGGAGTATCCCCTCAGAGATGGCAAGGTTGGAGTAT-CCTCGAAAAT-AGAAAATTGGATAGTTT
1 TAGAGTATCCTTTCAGAAATGGCGAGGTTGGAGTATCCCT-GAAAATGA-AAAATTAGATATTTT
**
2183770 TAGAAGTAAAAACGGGGT
64 TAGAAGTAAAAACAAGGT
* * * * * * * *
2183788 TGGAGTAT-CTTCTTA-AAAGTGGTGGGGTTGTAGTAT-CCTCGAAAATGAAAATTTTG-TTTTT
1 TAGAGTATCCTT-TCAGAAA-TGGCGAGGTTGGAGTATCCCT-GAAAATGAAAAATTAGATATTT
*
2183849 TTA-AAGGTAAAAACAGGGT
63 TTAGAA-GTAAAAACAAGGT
2183868 TAGAGTATCCT
1 TAGAGTATCCT
2183879 CTCGGAGATG
Statistics
Matches: 459, Mismatches: 87, Indels: 57
0.76 0.14 0.09
Matches are distributed among these distances:
79 12 0.03
80 213 0.46
81 218 0.47
82 16 0.03
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (81 bp):
TAGAGTATCCTTTCAGAAATGGCGAGGTTGGAGTATCCCTGAAAATGAAAAATTAGATATTTTTA
GAAGTAAAAACAAGGT
Found at i:2183889 original size:161 final size:161
Alignment explanation
Indices: 2183249--2183905 Score: 725
Period size: 161 Copynumber: 4.1 Consensus size: 161
2183239 GAGATAGTGG
* * * *
2183249 GGTTGGAGTATCCTTGAAGATGAAAAATTAGATATTTTTAGAAGTTAAAACCGGGTTAGAGTATC
1 GGTTGGAGTATCCTCGAAGATGAAAAATTAGATATTTTTAGAAGTAAAAACAGGGTTGGAGTATC
* * * * * *
2183314 TTCTCAAAAATGGTGGGGTTAGAGTAT-CTCCGAAAATGAAAAATCTGATCTTTTTAGAGGTAAA
66 TCCTCAGAAATGGTGGGGTTGGAGTATCCT-CGAAAATGAAAATTTTGAT-TTTTTAAAGGTAAA
* * * ** * *
2183378 AACAAGTTTAAAGTATCCTTTCAGAGATGACGA
129 AACAGGGTTAGAGTATCCCCTCAGAGATGGCAA
* *
2183411 GGTTGGAATATCC-CTGAAGATGAAAAATTAGAT-TTTTTAGAAGTAAAAACAAGGTTGGAGTAT
1 GGTTGGAGTATCCTC-GAAGATGAAAAATTAGATATTTTTAGAAGTAAAAACAGGGTTGGAGTAT
* * * * * *
2183474 CCCCTTAGAAATGGTTGGATTGGAGTATCCTTGAAAATGAAAATTTTGATTTTGTAAAGGTAAAA
65 CTCCTCAGAAATGGTGGGGTTGGAGTATCCTCGAAAATGAAAATTTTGATTTTTTAAAGGTAAAA
* * * *
2183539 ACGGGGTTAGAGTATCCCCTCAAAAATGGCGA
130 ACAGGGTTAGAGTATCCCCTCAGAGATGGCAA
* * * * * *
2183571 GGTTGGAGTATCCCCGAAGATGAAAAACTGGATATTTTTAAAAGTAAAAATAGAGTTGGAGTATC
1 GGTTGGAGTATCCTCGAAGATGAAAAATTAGATATTTTTAGAAGTAAAAACAGGGTTGGAGTATC
* * * *
2183636 TCCTCAGAAATGGTAGGGTTGGGGTATCC-CTAAAAATAAAAATTTTGATTTTTTAGAA-GTAAA
66 TCCTCAGAAATGGTGGGGTTGGAGTATCCTC-GAAAATGAAAATTTTGATTTTTTA-AAGGTAAA
*
2183699 AACAGGGTTGGAGTATCCCCTCAGAGATGGCAA
129 AACAGGGTTAGAGTATCCCCTCAGAGATGGCAA
* * * *
2183732 GGTTGGAGTATCCTCGAAAAT-AGAAAATTGGATAGTTTTAGAAGTAAAAACGGGGTTGGAGTAT
1 GGTTGGAGTATCCTCGAAGATGA-AAAATTAGATATTTTTAGAAGTAAAAACAGGGTTGGAGTAT
* * * *
2183796 CTTCTTA-AAAGTGGTGGGGTTGTAGTATCCTCGAAAATGAAAATTTTGTTTTTTTAAAGGTAAA
65 CTCCTCAGAAA-TGGTGGGGTTGGAGTATCCTCGAAAATGAAAATTTTGATTTTTTAAAGGTAAA
* * *
2183860 AACAGGGTTAGAGTATCCTCTCGGAGATGGCAG
129 AACAGGGTTAGAGTATCCCCTCAGAGATGGCAA
* *
2183893 GGCTGAAGTATCC
1 GGTTGGAGTATCC
2183906 CTATAAATAA
Statistics
Matches: 415, Mismatches: 70, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
160 70 0.17
161 310 0.75
162 35 0.08
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.30
Consensus pattern (161 bp):
GGTTGGAGTATCCTCGAAGATGAAAAATTAGATATTTTTAGAAGTAAAAACAGGGTTGGAGTATC
TCCTCAGAAATGGTGGGGTTGGAGTATCCTCGAAAATGAAAATTTTGATTTTTTAAAGGTAAAAA
CAGGGTTAGAGTATCCCCTCAGAGATGGCAA
Found at i:2183906 original size:241 final size:237
Alignment explanation
Indices: 2183249--2183915 Score: 709
Period size: 241 Copynumber: 2.8 Consensus size: 237
2183239 GAGATAGTGG
* * *
2183249 GGTTGGAGTATCCTTGAAGATGAAAAATTAGATATTTTTAGAAGTTAAAACCGGGTTAGAGTATC
1 GGTTGGAGTATCCTTGAAAATG-AAAATTAGATA-TTTTAGAAGTAAAAACGGGGTTAGAGTATC
* * *
2183314 TTCTCAAAAATGGTGGGGTTAGAGTAT-CTCCGAAAATGAAAAATCTGATCTTTTTAGAGGTAAA
64 TTCTCAAAAATGGTGGGGTT-GAGTATCCT-CGAAAATGAAAAATTTGATATTTTTAAAGGTAAA
* * * * * * *
2183378 AACAAGTTTAAAGTATCCTTTCAGAGATGAC-GAGGTTGGAA-TATCCCTGAAGATGAAAAATTA
127 AACAGGGTTAGAGTATCCTCTCAGAGATGGCAG-GGTT-GAAGTATCCCTAAAAAT-AAAAATTA
* **
2183441 GATTTTTTAGAAGTAAAAACAAGGTTGGAGTATCCCCTTAGAAATGGTT
189 GATTTTTTAGAAGTAAAAACAAGGTTGGAGTATCCCCTCAGAAATGGAA
*
2183490 GGATTGGAGTATCCTTGAAAATGAAAATTTTGAT-TTTGTA-AAGGTAAAAACGGGGTTAGAGTA
1 GG-TTGGAGTATCCTTGAAAATGAAAA-TTAGATATTT-TAGAA-GTAAAAACGGGGTTAGAGTA
** * * * * * * *
2183553 TCCCCTCAAAAATGGCGAGGTTGGAGTATCCCCGAAGATGAAAAACTGGATATTTTTAAAAGTAA
62 TCTTCTCAAAAATGGTGGGGTT-GAGTATCCTCGAAAATGAAAAATTTGATATTTTTAAAGGTAA
* * * * * ** *
2183618 AAATAGAGTTGGAGTAT-CTCCTCAGAAATGGTAGGGTTGGGGTATCCCTAAAAATAAAAATTTT
126 AAACAGGGTTAGAGTATCCT-CTCAGAGATGGCAGGGTTGAAGTATCCCTAAAAATAAAAA-TTA
* *
2183682 GATTTTTTAGAAGTAAAAACAGGGTTGGAGTATCCCCTCAGAGATGGCAA
189 GATTTTTTAGAAGTAAAAACAAGGTTGGAGTATCCCCTCAGAAATGG-AA
* * *
2183732 GGTTGGAGTATCCTCGAAAATAGAAAATTGGATAGTTTTAGAAGTAAAAACGGGGTTGGAGTATC
1 GGTTGGAGTATCCTTGAAAAT-GAAAATTAGATA-TTTTAGAAGTAAAAACGGGGTTAGAGTATC
* * * *
2183797 TTCTTAAAAGTGGTGGGGTTGTAGTATCCTCGAAAATGAAAATTTTG-TTTTTTTAAAGGTAAAA
64 TTCTCAAAAATGGTGGGGTTG-AGTATCCTCGAAAATGAAAAATTTGATATTTTTAAAGGTAAAA
* * *
2183861 ACAGGGTTAGAGTATCCTCTCGGAGATGGCAGGGCTGAAGTATCCCTATAAATAA
128 ACAGGGTTAGAGTATCCTCTCAGAGATGGCAGGGTTGAAGTATCCCTAAAAATAA
2183916 TGATTTTGGT
Statistics
Matches: 347, Mismatches: 63, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
240 13 0.04
241 237 0.68
242 92 0.27
243 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (237 bp):
GGTTGGAGTATCCTTGAAAATGAAAATTAGATATTTTAGAAGTAAAAACGGGGTTAGAGTATCTT
CTCAAAAATGGTGGGGTTGAGTATCCTCGAAAATGAAAAATTTGATATTTTTAAAGGTAAAAACA
GGGTTAGAGTATCCTCTCAGAGATGGCAGGGTTGAAGTATCCCTAAAAATAAAAATTAGATTTTT
TAGAAGTAAAAACAAGGTTGGAGTATCCCCTCAGAAATGGAA
Found at i:2185271 original size:2 final size:2
Alignment explanation
Indices: 2185266--2185299 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2185256 TTCAAAAAAC
2185266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2185300 TAGTACACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2185546 original size:18 final size:17
Alignment explanation
Indices: 2185522--2185576 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
2185512 TTTCATTATC
2185522 TTTTTTCTCTTTTTTCT
1 TTTTTTCTCTTTTTTCT
* *
2185539 TGTTTTTCTTCTTCTTCCT
1 T-TTTTTC-TCTTTTTTCT
*
2185558 TTCTTTTTTCTTTTTTCT
1 TT-TTTTCTCTTTTTTCT
2185576 T
1 T
2185577 CTTCACCCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.03
18 16 0.53
19 13 0.43
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTTCTCTTTTTTCT
Found at i:2194534 original size:14 final size:14
Alignment explanation
Indices: 2194502--2194539 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
2194492 TTTAAATATA
2194502 AATTATATATTTTAT
1 AATTA-ATATTTTAT
2194517 -ATTAATATTTTAT
1 AATTAATATTTTAT
2194530 AATTAA-ATTT
1 AATTAATATTT
2194540 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTAATATTTTAT
Found at i:2194574 original size:45 final size:44
Alignment explanation
Indices: 2194465--2194578 Score: 110
Period size: 45 Copynumber: 2.6 Consensus size: 44
2194455 ATTTGTTTGA
* * * *
2194465 AAATTTTAT-TTTATTATTTA-AAATACATTTAAATATAAATTAT
1 AAATTTTATATTAATAATTTATAATTAAATTTAAATATAAA-TAT
* *
2194508 ATATTTTATATTAATATTTTATAATTAAATTTAAATA-AAA-AT
1 AAATTTTATATTAATAATTTATAATTAAATTTAAATATAAATAT
2194550 AAATTTTATTAATTAAATAATTTATAATT
1 AAATTTTA-T-ATT-AATAATTTATAATT
2194579 TATAACTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
42 9 0.16
43 9 0.16
44 14 0.24
45 26 0.45
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (44 bp):
AAATTTTATATTAATAATTTATAATTAAATTTAAATATAAATAT
Found at i:2195820 original size:14 final size:15
Alignment explanation
Indices: 2195793--2195827 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
2195783 ACAAAGCTTC
2195793 TTATTTATTTTATTT
1 TTATTTATTTTATTT
2195808 TTATTTA-TTTATTT
1 TTATTTATTTTATTT
2195822 TTATTT
1 TTATTT
2195828 TGCTGCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTATTTTATTT
Found at i:2196070 original size:16 final size:17
Alignment explanation
Indices: 2196044--2196076 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2196034 GATGATTTAG
2196044 TTTAGATTTAATATTAA
1 TTTAGATTTAATATTAA
*
2196061 TTTA-ATTTAATTTTAA
1 TTTAGATTTAATATTAA
2196077 ATATTGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTAGATTTAATATTAA
Found at i:2197928 original size:25 final size:25
Alignment explanation
Indices: 2197883--2197935 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2197873 TTATAAACAA
2197883 AATTAAAAAATTATTAAATTT-TTT
1 AATTAAAAAATTATTAAATTTGTTT
* **
2197907 AATTAAATAAGTTATTTTATTTGTTT
1 AATTAAA-AAATTATTAAATTTGTTT
2197933 AAT
1 AAT
2197936 ATATCTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 11 0.46
26 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
AATTAAAAAATTATTAAATTTGTTT
Found at i:2198517 original size:24 final size:24
Alignment explanation
Indices: 2198484--2198531 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2198474 CTAAAAAGAA
2198484 TTTATCAAATATAAAAAAATTAAT
1 TTTATCAAATATAAAAAAATTAAT
* * *
2198508 TTTATTAAATATAAGAAGATTAAT
1 TTTATCAAATATAAAAAAATTAAT
2198532 ATTAGTGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
TTTATCAAATATAAAAAAATTAAT
Found at i:2198650 original size:28 final size:29
Alignment explanation
Indices: 2198593--2198650 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 29
2198583 ATGATTATGA
2198593 TTAATATTTATCAAATTTATGGGTAATTATAT
1 TTAATATTTATCAAATTTA---GTAATTATAT
*
2198625 TTAATATTTATTAAATTTA-TAATTAT
1 TTAATATTTATCAAATTTAGTAATTAT
2198651 TATCAATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 7 0.28
32 18 0.72
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (29 bp):
TTAATATTTATCAAATTTAGTAATTATAT
Found at i:2199966 original size:27 final size:29
Alignment explanation
Indices: 2199922--2199976 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
2199912 AATTTGATCA
2199922 AATATTTTTATTTATAATATA-TATTTTT
1 AATATTTTTATTTATAATATATTATTTTT
*
2199950 AATA-TTTTA-TTATTAATTTATTATTTT
1 AATATTTTTATTTA-TAATATATTATTTT
2199977 GTCCTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.12
27 11 0.46
28 10 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
AATATTTTTATTTATAATATATTATTTTT
Found at i:2202735 original size:17 final size:17
Alignment explanation
Indices: 2202713--2202751 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2202703 CTTTATTTTT
2202713 TTTTTTTAA-TTTTATAA
1 TTTTTTTAATTTTTAT-A
*
2202730 TTTTTTTAGTTTTTATA
1 TTTTTTTAATTTTTATA
2202747 TTTTT
1 TTTTT
2202752 ACTAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTTTAATTTTTATA
Found at i:2204563 original size:3 final size:3
Alignment explanation
Indices: 2204545--2204592 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
2204535 GGTCTTAAAT
* *
2204545 ATA ATA ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2204593 TAAAAGGACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2208699 original size:14 final size:16
Alignment explanation
Indices: 2208673--2208706 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2208663 TTAAATTTAA
2208673 ATTTGATGTTTG-ATT
1 ATTTGATGTTTGAATT
2208688 ATTTGA-GTTTGAATT
1 ATTTGATGTTTGAATT
2208703 ATTT
1 ATTT
2208707 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (16 bp):
ATTTGATGTTTGAATT
Found at i:2209039 original size:8 final size:8
Alignment explanation
Indices: 2209026--2209055 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
2209016 TTTATGATAC
2209026 ATTTAAAA
1 ATTTAAAA
2209034 ATTTAAAA
1 ATTTAAAA
2209042 ATTTAAAA
1 ATTTAAAA
2209050 ATTTAA
1 ATTTAA
2209056 GTTATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATTTAAAA
Found at i:2210993 original size:2 final size:2
Alignment explanation
Indices: 2210986--2211021 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2210976 GAATTTCGAA
2210986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2211022 TTAAAGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2211384 original size:27 final size:27
Alignment explanation
Indices: 2211341--2211403 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
2211331 TTTTATCATG
*
2211341 AAATAT-TAATGTGTTAAA-ATATATAA
1 AAATATATAATATGTTAAATATA-ATAA
* *
2211367 AAATATATAATATTTTAAATATAATTA
1 AAATATATAATATGTTAAATATAATAA
*
2211394 TAATATATAA
1 AAATATATAA
2211404 AAATAACGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 6 0.19
27 22 0.71
28 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
AAATATATAATATGTTAAATATAATAA
Found at i:2211804 original size:28 final size:29
Alignment explanation
Indices: 2211767--2211834 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
2211757 ATTTTTTATA
*
2211767 TTATAATTATATTTAAAT-TATT-ATACAT
1 TTATATTTATATTTAAATATATTAATA-AT
* *
2211795 TTATATTTATATTTTAATATGTTAATAAT
1 TTATATTTATATTTAAATATATTAATAAT
2211824 TTAT-TTTATAT
1 TTATATTTATAT
2211835 AAATTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 23 0.66
29 9 0.26
30 3 0.09
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (29 bp):
TTATATTTATATTTAAATATATTAATAAT
Found at i:2211855 original size:27 final size:26
Alignment explanation
Indices: 2211797--2211886 Score: 66
Period size: 26 Copynumber: 3.7 Consensus size: 26
2211787 TTATACATTT
*
2211797 ATATTTATATTTTA-AT--ATGTT-A
1 ATATTTATATTTTATATAAATTTTAA
*
2211819 ATAATT-TATTTTATATAAATTTTAAA
1 ATATTTATATTTTATATAAATTTT-AA
* *
2211845 ATATTTATATTATAT-TATATTTTAA
1 ATATTTATATTTTATATAAATTTTAA
* * *
2211870 TTATTTTTATATTATAT
1 ATATTTATATTTTATAT
2211887 TTTGTGATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
21 7 0.13
22 7 0.13
24 4 0.08
25 13 0.25
26 14 0.27
27 7 0.13
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (26 bp):
ATATTTATATTTTATATAAATTTTAA
Found at i:2211857 original size:25 final size:25
Alignment explanation
Indices: 2211796--2211886 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
2211786 ATTATACATT
*
2211796 TATATTTATATT-T-TAATATGTTAA
1 TATATTTATATTATATAA-ATTTTAA
*
2211820 TA-ATTTATTTTATATAAATTTTAA
1 TATATTTATATTATATAAATTTTAA
* *
2211844 AATATTTATATTATATTATATTTTAA
1 TATATTTATATTATA-TAAATTTTAA
*
2211870 TTATTTTTATATTATAT
1 -TATATTTATATTATAT
2211887 TTTGTGATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
23 8 0.15
24 10 0.18
25 14 0.25
26 10 0.18
27 13 0.24
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (25 bp):
TATATTTATATTATATAAATTTTAA
Found at i:2211887 original size:27 final size:26
Alignment explanation
Indices: 2211822--2211887 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
2211812 TATGTTAATA
*
2211822 ATTTATTTTATA-TAAATTTTAAAAT
1 ATTTATATTATATTAAATTTTAAAAT
* *
2211847 ATTTATATTATATTATATTTTAATTAT
1 ATTTATATTATATTAAATTTTAA-AAT
*
2211874 TTTTATATTATATT
1 ATTTATATTATATT
2211888 TTGTGATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 11 0.31
26 9 0.26
27 15 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTATATTATATTAAATTTTAAAAT
Found at i:2212130 original size:16 final size:17
Alignment explanation
Indices: 2212088--2212146 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 17
2212078 ATTTAAAAAG
*
2212088 TTTAAATAATTAATTTAA
1 TTTAAAAAATTAA-TTAA
2212106 TTTAATAAAAAATTAA-TAA
1 -TT--TAAAAAATTAATTAA
2212125 TTT-AAAAATTAATTAA
1 TTTAAAAAATTAATTAA
2212141 TTTAAA
1 TTTAAA
2212147 TTTTAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 9 0.26
16 7 0.20
17 2 0.06
18 2 0.06
19 5 0.14
21 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAAAATTAATTAA
Found at i:2212133 original size:15 final size:16
Alignment explanation
Indices: 2212113--2212146 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2212103 TAATTTAATA
2212113 AAAAATTAA-TAATTT
1 AAAAATTAATTAATTT
2212128 AAAAATTAATTAATTT
1 AAAAATTAATTAATTT
2212144 AAA
1 AAA
2212147 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATTAATTAATTT
Found at i:2212138 original size:19 final size:19
Alignment explanation
Indices: 2212088--2212141 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2212078 ATTTAAAAAG
2212088 TTTAAATAATTAATT--TAA
1 TTTAAA-AATTAATTAATAA
*
2212106 TTTAATAAA-AAATTAATAA
1 TTTAA-AAATTAATTAATAA
2212125 TTTAAAAATTAATTAAT
1 TTTAAAAATTAATTAAT
2212142 TTAAATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 4 0.13
18 10 0.33
19 16 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAAAAATTAATTAATAA
Found at i:2212141 original size:40 final size:38
Alignment explanation
Indices: 2212094--2212178 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 38
2212084 AAAGTTTAAA
2212094 TAATTAATTT-AATTTAATAAAAAATTAATAATTTAAAAAT
1 TAATTAATTTAAATTTAA-AAAAAATTAAT-ATTT-AAAAT
* *
2212134 TAATTAATTTAAATTTTAAAAAAATTCATATTTAAAAT
1 TAATTAATTTAAATTTAAAAAAAATTAATATTTAAAAT
*
2212172 GAATTAA
1 TAATTAA
2212179 ACCTAAAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
38 11 0.27
39 4 0.10
40 20 0.49
41 6 0.15
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (38 bp):
TAATTAATTTAAATTTAAAAAAAATTAATATTTAAAAT
Found at i:2212216 original size:16 final size:15
Alignment explanation
Indices: 2212165--2212217 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
2212155 AAATTCATAT
2212165 TTAAAATGAATTAAAC
1 TTAAAAT-AATTAAAC
* * *
2212181 CTAAAATCATCTAAAT
1 TTAAAATAAT-TAAAC
2212197 TTAAAATAATTAAAAC
1 TTAAAATAATT-AAAC
2212213 TTAAA
1 TTAAA
2212218 TTTACTCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 26 0.90
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (15 bp):
TTAAAATAATTAAAC
Found at i:2212340 original size:25 final size:25
Alignment explanation
Indices: 2212276--2212341 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
2212266 ATTAAATTTA
2212276 ATTAATTAATTTTATTATTTAAAAT
1 ATTAATTAATTTTATTATTTAAAAT
* * *
2212301 ATAAAAATATTTTTATTATTT-AAAT
1 AT-TAATTAATTTTATTATTTAAAAT
*
2212326 ATTAATTTAAATTTAT
1 ATTAA-TTAATTTTAT
2212342 CAAATTAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
24 2 0.06
25 15 0.47
26 15 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTAATTAATTTTATTATTTAAAAT
Found at i:2212369 original size:23 final size:25
Alignment explanation
Indices: 2212343--2212393 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
2212333 TAAATTTATC
2212343 AAATTAATT-ATTATA-TCAATTTA
1 AAATTAATTGATTATATTCAATTTA
* *
2212366 AAA-TATTTGTTTATATTCAATTTA
1 AAATTAATTGATTATATTCAATTTA
2212390 AAAT
1 AAAT
2212394 ATTTTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 11 0.48
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (25 bp):
AAATTAATTGATTATATTCAATTTA
Found at i:2212390 original size:24 final size:23
Alignment explanation
Indices: 2212353--2212397 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
2212343 AAATTAATTA
2212353 TTATATCAATTTAAAATATTTGT
1 TTATATCAATTTAAAATATTTGT
2212376 TTATATTCAATTTAAAATATTT
1 TTATA-TCAATTTAAAATATTT
2212398 TTATTATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATATCAATTTAAAATATTTGT
Found at i:2212724 original size:7 final size:7
Alignment explanation
Indices: 2212699--2212807 Score: 66
Period size: 7 Copynumber: 15.6 Consensus size: 7
2212689 AATATTATGG
2212699 TAAAATA
1 TAAAATA
*
2212706 T-AGATA
1 TAAAATA
2212712 TAAAATA
1 TAAAATA
*
2212719 TTAAATA
1 TAAAATA
2212726 TAAAA-A
1 TAAAATA
*
2212732 -ATAATA
1 TAAAATA
2212738 -AAAATA
1 TAAAATA
* *
2212744 TGATATA
1 TAAAATA
*
2212751 AAAAATA
1 TAAAATA
2212758 -ATAAATA
1 TA-AAATA
2212765 TAAAATA
1 TAAAATA
2212772 TAAAATTA
1 TAAAA-TA
*
2212780 TAATATA
1 TAAAATA
2212787 TTAAAATTTA
1 -TAAAA--TA
*
2212797 TATAATA
1 TAAAATA
2212804 TAAA
1 TAAA
2212808 TTATTAATTT
Statistics
Matches: 78, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
5 3 0.04
6 13 0.17
7 45 0.58
8 11 0.14
9 4 0.05
10 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (7 bp):
TAAAATA
Found at i:2212791 original size:23 final size:23
Alignment explanation
Indices: 2212714--2212793 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
2212704 TATAGATATA
*
2212714 AAATATTAAATATAAAAAATAAT
1 AAATATAAAATATAAAAAATAAT
* **
2212737 AAAAATATGATATAAAAAATAAT
1 AAATATAAAATATAAAAAATAAT
*
2212760 AAATATAAAATATAAAATTATAAT
1 AAATATAAAATATAAAA-AATAAT
*
2212784 ATAT-TAAAAT
1 AAATATAAAAT
2212794 TTATATAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 39 0.83
24 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (23 bp):
AAATATAAAATATAAAAAATAAT
Found at i:2212792 original size:39 final size:39
Alignment explanation
Indices: 2212700--2212774 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
2212690 ATATTATGGT
*
2212700 AAAATATAGATAT--AAAATATTAAATATAAAAAATAATA
1 AAAATAT-GATATAAAAAATAATAAATATAAAAAATAATA
*
2212738 AAAATATGATATAAAAAATAATAAATATAAAATATAA
1 AAAATATGATATAAAAAATAATAAATATAAAAAATAA
2212775 AATTATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 5 0.15
38 7 0.21
39 21 0.64
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (39 bp):
AAAATATGATATAAAAAATAATAAATATAAAAAATAATA
Found at i:2212821 original size:32 final size:32
Alignment explanation
Indices: 2212763--2212831 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
2212753 AAATAATAAA
*
2212763 TATAAAATATAAAATTATAATATATTAAAATT
1 TATAAAATATAAAATTATAATATATTAAAAAT
* *
2212795 TATATAATAT-AAATTATTAATTTATTAAAAAT
1 TATAAAATATAAAATTA-TAATATATTAAAAAT
2212827 TATAA
1 TATAA
2212832 TGTTTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
TATAAAATATAAAATTATAATATATTAAAAAT
Found at i:2214065 original size:24 final size:24
Alignment explanation
Indices: 2214019--2214066 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2214009 TTTTTTCAAA
*
2214019 AAAAAAAAGTTATAATCTGAAAAT
1 AAAAAAAAGTTATAATATGAAAAT
*
2214043 AAAAAAAA-TTATAAATATTAAAAT
1 AAAAAAAAGTTAT-AATATGAAAAT
2214067 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (24 bp):
AAAAAAAAGTTATAATATGAAAAT
Found at i:2214067 original size:15 final size:15
Alignment explanation
Indices: 2214047--2214092 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
2214037 GAAAATAAAA
2214047 AAAATTATAAATATT
1 AAAATTATAAATATT
2214062 AAAATT-TAAA-ATTT
1 AAAATTATAAATA-TT
2214076 AAAATTATAAAATATT
1 AAAATTAT-AAATATT
2214092 A
1 A
2214093 TTATAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 12 0.44
15 7 0.26
16 6 0.22
17 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:2214077 original size:14 final size:16
Alignment explanation
Indices: 2214047--2214107 Score: 74
Period size: 15 Copynumber: 3.8 Consensus size: 16
2214037 GAAAATAAAA
2214047 AAAATTAT-AAATATT
1 AAAATTATAAAATATT
2214062 AAAATT-TAAAAT-TT
1 AAAATTATAAAATATT
2214076 AAAATTATAAAATATT
1 AAAATTATAAAATATT
2214092 ATTATAATTATAAAAT
1 A--A-AATTATAAAAT
2214108 CAATTGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.22
15 16 0.40
16 3 0.08
18 1 0.03
19 11 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTATAAAATATT
Found at i:2214080 original size:22 final size:23
Alignment explanation
Indices: 2214046--2214088 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
2214036 TGAAAATAAA
2214046 AAAAATTATAAA-TATTAAAATTT
1 AAAAATTATAAATTA-TAAAATTT
*
2214069 AAAATTTA-AAATTATAAAAT
1 AAAAATTATAAATTATAAAAT
2214089 ATTATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAATTATAAATTATAAAATTT
Found at i:2214792 original size:16 final size:16
Alignment explanation
Indices: 2214751--2214797 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
2214741 TAAATTTATT
* * *
2214751 AAATATTTTATTTTAA
1 AAATAATTTATATAAA
2214767 AAATAA-TTATATAAA
1 AAATAATTTATATAAA
*
2214782 AAATAATTTATGTAAA
1 AAATAATTTATATAAA
2214798 CCCGGGTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AAATAATTTATATAAA
Found at i:2216036 original size:2 final size:2
Alignment explanation
Indices: 2216031--2216059 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2216021 GGGGGGACTC
2216031 TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2216060 GGGAAGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
TG
Found at i:2216757 original size:34 final size:34
Alignment explanation
Indices: 2216709--2216776 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2216699 TATTATAATA
*
2216709 TAAAAATAATTTTAAAT-TAATATTTATATATTTT
1 TAAAAATAAATTTAAATATAATATTTAT-TATTTT
*
2216743 TAAAATTAAATTTAAATAATAATATTTATTATTT
1 TAAAAATAAATTTAAAT-ATAATATTTATTATTT
2216777 AAATAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 15 0.50
35 5 0.17
36 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TAAAAATAAATTTAAATATAATATTTATTATTTT
Found at i:2216787 original size:34 final size:33
Alignment explanation
Indices: 2216709--2216795 Score: 88
Period size: 34 Copynumber: 2.6 Consensus size: 33
2216699 TATTATAATA
* *
2216709 TAAAAATAATTTTAAATTAATATTTATATATTTT
1 TAAAAGTAAATTTAAATTAATATTTATATA-TTT
*
2216743 TAAAATTAAATTTAAATAATAATATTTAT-TA-TT
1 TAAAAGTAAATTTAAAT--TAATATTTATATATTT
*
2216776 TAAATAGTAAATTCAAATTA
1 TAAA-AGTAAATTTAAATTA
2216796 GGGTGGATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
32 2 0.04
33 6 0.13
34 26 0.57
35 2 0.04
36 10 0.22
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (33 bp):
TAAAAGTAAATTTAAATTAATATTTATATATTT
Found at i:2216829 original size:3 final size:3
Alignment explanation
Indices: 2216821--2216852 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2216811 AATTATCAAA
2216821 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2216853 AGATATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2217649 original size:15 final size:16
Alignment explanation
Indices: 2217629--2217662 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2217619 ATTCATGGTT
2217629 TACATG-TAAATATGC
1 TACATGATAAATATGC
2217644 TACATGAATAAATATGC
1 TACATG-ATAAATATGC
2217661 TA
1 TA
2217663 TCTCACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
17 11 0.65
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (16 bp):
TACATGATAAATATGC
Found at i:2219112 original size:2 final size:2
Alignment explanation
Indices: 2219105--2219145 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2219095 TTCAAGTTAC
*
2219105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2219146 CACACACATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2222595 original size:18 final size:19
Alignment explanation
Indices: 2222573--2222621 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
2222563 AAAATATGAC
2222573 ATAAATATAAAATAAT-TA
1 ATAAATATAAAATAATATA
*
2222591 GTAAATATAAAAAATAATATA
1 ATAAATAT--AAAATAATATA
2222612 ATAAATATAA
1 ATAAATATAA
2222622 TATGATTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.27
19 2 0.08
20 8 0.31
21 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAATATAAAATAATATA
Found at i:2222609 original size:12 final size:14
Alignment explanation
Indices: 2222573--2222624 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
2222563 AAAATATGAC
*
2222573 ATAAATATAAAATA
1 ATAAATATAATATA
* *
2222587 ATTAGTA-AATATA
1 ATAAATATAATATA
2222600 A-AAA-ATAATATA
1 ATAAATATAATATA
2222612 ATAAATATAATAT
1 ATAAATATAATAT
2222625 GATTCGTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
11 1 0.03
12 8 0.27
13 9 0.30
14 12 0.40
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATAAATATAATATA
Found at i:2222696 original size:2 final size:2
Alignment explanation
Indices: 2222689--2222738 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2222679 TTACATGACT
2222689 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2222731 TA TA TA TA
1 TA TA TA TA
2222739 AAACAAAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2229522 original size:2 final size:2
Alignment explanation
Indices: 2229515--2229548 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2229505 GAGATCAAAG
2229515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2229549 GTAAACAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2229810 original size:147 final size:147
Alignment explanation
Indices: 2229577--2229883 Score: 359
Period size: 147 Copynumber: 2.1 Consensus size: 147
2229567 GGGCGACGAT
* *
2229577 CTAGTGGCACCTTTTATTTTAATCCTCAAAGAGTAAAACATTTTTCTTTTGTCTTTTTCAAAGCT
1 CTAGTGGCACCTTTTATTTTAATCCTCAAAGAGCAAAACATTTTTCTTTTGTCTTTTTCAAAGCC
* *
2229642 CACATAAATTGGTGATACCTTTATATCCTTTTAGTCCTCAAAAAGCAAGGCGTCTTTT-TTTTTT
66 CACATAAATTGGTGATACCTTT-TATCATTTTAGTCCTCAAAAAGCAAGACGTCTTTTCTTTTTT
2229706 TTTTAAAGCCCACACAAG
130 TTTTAAAGCCCACACAAG
* * * ** * *
2229724 CTAGTGGTACCTTTTATTTTAGTTCTCAAAGAGCATGACGTTTTTCTTTTTTCTTTTT-AAAGCC
1 CTAGTGGCACCTTTTATTTTAATCCTCAAAGAGCAAAACATTTTTCTTTTGTCTTTTTCAAAGCC
** * * * *
2229788 CTTATAAGTTGGTAGCA-CCCTTTTATCATTTTAGTCCTCAAAGAGTAAGACGTCTTTTCTTTTT
66 CACATAAATTGGT-G-ATACCTTTTATCATTTTAGTCCTCAAAAAGCAAGACGTCTTTTC-TTTT
* * *
2229852 TTTTTTAACGCCTACACAGG
128 TTTTTTAAAGCCCACACAAG
* *
2229872 TTGGTGGCACCT
1 CTAGTGGCACCT
2229884 ACTTTCTTGA
Statistics
Matches: 133, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
146 46 0.35
147 56 0.42
148 31 0.23
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (147 bp):
CTAGTGGCACCTTTTATTTTAATCCTCAAAGAGCAAAACATTTTTCTTTTGTCTTTTTCAAAGCC
CACATAAATTGGTGATACCTTTTATCATTTTAGTCCTCAAAAAGCAAGACGTCTTTTCTTTTTTT
TTTAAAGCCCACACAAG
Found at i:2229875 original size:76 final size:75
Alignment explanation
Indices: 2229659--2229922 Score: 223
Period size: 76 Copynumber: 3.6 Consensus size: 75
2229649 ATTGGTGATA
* * * *
2229659 CCTTTATATCCTTTTAGTCCTCAAAAAGCAAGGCGTC-TTT-TTTTTTTTTTTAAAGCCCACACA
1 CCTTT-TATCATTTTAGTCCTCAAAGAGCAAGACGTCTTTTCTTTTTTTTTTTAAAGCCTACAC-
* * *
2229722 AGCTAGTGGTA-
64 AGTTGGTGGCAC
* * *
2229733 CC-TTT-T-ATTTTAGTTCTCAAAGAGCATGACGT-TTTTCTTTTTTCTTTTTAAAGCCCTTATA
1 CCTTTTATCATTTTAGTCCTCAAAGAGCAAGACGTCTTTTCTTTTTT-TTTTTAAAG-CC-TACA
*
2229794 -AGTTGGTAGCAC
63 CAGTTGGTGGCAC
* *
2229806 CCTTTTATCATTTTAGTCCTCAAAGAGTAAGACGTCTTTTCTTTTTTTTTTTAACGCCTACACAG
1 CCTTTTATCATTTTAGTCCTCAAAGAGCAAGACGTCTTTTCTTTTTTTTTTTAAAGCCTACACA-
2229871 GTTGGTGGCA-
65 GTTGGTGGCAC
* * *
2229881 CCTACTT-TC--TTGAGTCCTCAAAGAGCAAGATGT-TTTT-TTTTT
1 CCT-TTTATCATTTTAGTCCTCAAAGAGCAAGACGTCTTTTCTTTTT
2229923 CAAAGCCCAC
Statistics
Matches: 156, Mismatches: 21, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
70 24 0.15
71 12 0.08
72 21 0.13
73 27 0.17
74 10 0.06
75 9 0.06
76 42 0.27
77 11 0.07
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (75 bp):
CCTTTTATCATTTTAGTCCTCAAAGAGCAAGACGTCTTTTCTTTTTTTTTTTAAAGCCTACACAG
TTGGTGGCAC
Found at i:2230331 original size:2 final size:2
Alignment explanation
Indices: 2230324--2230368 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2230314 ATGAGATCAA
2230324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2230366 AT A
1 AT A
2230369 AACAAATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2232420 original size:51 final size:51
Alignment explanation
Indices: 2232344--2232449 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
2232334 CATCCCCAAC
2232344 TAGTTTGGGATTGTGGAATGAACTTGTGATACGCATGTCAGCCCCTTCTCT
1 TAGTTTGGGATTGTGGAATGAACTTGTGATACGCATGTCAGCCCCTTCTCT
2232395 TAGTTTGGGATTGTGGAATGAACTTGTGATACGCATGTCAGCCCCTTCTCT
1 TAGTTTGGGATTGTGGAATGAACTTGTGATACGCATGTCAGCCCCTTCTCT
2232446 TAGT
1 TAGT
2232450 CATGAACGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (51 bp):
TAGTTTGGGATTGTGGAATGAACTTGTGATACGCATGTCAGCCCCTTCTCT
Found at i:2233520 original size:52 final size:52
Alignment explanation
Indices: 2233458--2233577 Score: 131
Period size: 52 Copynumber: 2.3 Consensus size: 52
2233448 CAACATCAAG
* * *
2233458 AGGGGTACTCCAACCCT-GTTTTTACTTCTAAAACAT-C-AAACTTTTCATCTCC
1 AGGGATACTCCAACCCTCGTTTCTACTTC-AAAA-ATGCAAAAATTTTCATCT-C
*
2233510 AGGGATACTCCAA-CCTCGTTTCTACTTCCAAAATGCAAAAATTTTCATCTC
1 AGGGATACTCCAACCCTCGTTTCTACTTCAAAAATGCAAAAATTTTCATCTC
*
2233561 TGGGAATACTCCAACCC
1 AGGG-ATACTCCAACCC
2233578 CAACATCAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
50 2 0.03
51 11 0.19
52 43 0.74
53 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (52 bp):
AGGGATACTCCAACCCTCGTTTCTACTTCAAAAATGCAAAAATTTTCATCTC
Found at i:2238748 original size:13 final size:13
Alignment explanation
Indices: 2238707--2238754 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
2238697 CCGTTACAAG
*
2238707 CAATGTATTGATA
1 CAATGTATCGATA
2238720 CAAT-T-TC-AT-
1 CAATGTATCGATA
2238729 C-ATGTATCGATA
1 CAATGTATCGATA
2238741 CAATGTATCGATA
1 CAATGTATCGATA
2238754 C
1 C
2238755 GTTGTCTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 4 0.14
11 3 0.10
12 2 0.07
13 16 0.55
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2238830 original size:20 final size:20
Alignment explanation
Indices: 2238805--2238861 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
2238795 CTGCCAATCT
2238805 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
**
2238825 CATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGTC
2238844 CATGTATCGATAC-ATTGT
1 CATGTATCGATACAATTGT
2238862 ATCAATACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 17 0.52
20 15 0.45
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:2241432 original size:13 final size:13
Alignment explanation
Indices: 2241414--2241441 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2241404 AATAGTACCT
2241414 AATGTATCGATAC
1 AATGTATCGATAC
2241427 AATGTATCGATAC
1 AATGTATCGATAC
2241440 AA
1 AA
2241442 GGAATACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2243667 original size:15 final size:15
Alignment explanation
Indices: 2243647--2243677 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2243637 CGGAGGAGTT
2243647 AGAATCATCAAAAAC
1 AGAATCATCAAAAAC
2243662 AGAATCATCAAAAAC
1 AGAATCATCAAAAAC
2243677 A
1 A
2243678 ATATAGATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.19, G:0.06, T:0.13
Consensus pattern (15 bp):
AGAATCATCAAAAAC
Found at i:2247655 original size:13 final size:13
Alignment explanation
Indices: 2247613--2247708 Score: 79
Period size: 13 Copynumber: 8.2 Consensus size: 13
2247603 GCCGTTACAA
2247613 ACAATGTATCGAT
1 ACAATGTATCGAT
2247626 ACAAT-T-TC-AT
1 ACAATGTATCGAT
2247636 -C-ATGTATCGAT
1 ACAATGTATCGAT
2247647 ACAATGTATCGAT
1 ACAATGTATCGAT
* *
2247660 ATAATTTATCGAT
1 ACAATGTATCGAT
2247673 AC-A--T-T-G-T
1 ACAATGTATCGAT
* *
2247680 CCCATGTATCGAT
1 ACAATGTATCGAT
2247693 ACAATGTATCGAT
1 ACAATGTATCGAT
2247706 ACA
1 ACA
2247709 CAGTGGTAGG
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 3 0.05
10 6 0.09
11 5 0.08
12 4 0.06
13 42 0.64
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:2247780 original size:19 final size:20
Alignment explanation
Indices: 2247736--2247788 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2247726 CTGTCAATCT
*
2247736 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATC
* *
2247756 CATGTATCGATATAATGA-G
1 CATGTATCGATACAATGATC
2247775 CATGTATCGATACA
1 CATGTATCGATACA
2247789 TTGTATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATGATC
Found at i:2250947 original size:34 final size:33
Alignment explanation
Indices: 2250904--2251084 Score: 221
Period size: 34 Copynumber: 5.4 Consensus size: 33
2250894 TTAATTTCTT
2250904 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGATGT-TTTGGTGAGAA
2250938 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGATGT-TTTGGTGAGAA
*
2250972 TGTTAGGTGTGTTAGGTG-TG-TTAGGTGATG--
1 TGTTAGGTGTGTTAGGTGATGTTTTGGTGA-GAA
* *
2251002 TGTTTGGTGAGAATGTTAGGTG-TG-TTAGGTGAGAA
1 TGTTAGGT--G--TGTTAGGTGATGTTTTGGTGAGAA
2251037 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGATGT-TTTGGTGAGAA
2251071 TGTTAGGTGTGTTA
1 TGTTAGGTGTGTTA
2251085 ACATGTATAT
Statistics
Matches: 132, Mismatches: 5, Indels: 20
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.05
31 16 0.12
32 4 0.03
33 4 0.03
34 94 0.71
35 7 0.05
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.41
Consensus pattern (33 bp):
TGTTAGGTGTGTTAGGTGATGTTTTGGTGAGAA
Found at i:2250985 original size:43 final size:43
Alignment explanation
Indices: 2250938--2251032 Score: 190
Period size: 43 Copynumber: 2.2 Consensus size: 43
2250928 TTGGTGAGAA
2250938 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTG
1 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTG
2250981 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTG
1 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTG
2251024 TGTTAGGTG
1 TGTTAGGTG
2251033 AGAATGTTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (43 bp):
TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTG
Found at i:2250986 original size:9 final size:9
Alignment explanation
Indices: 2250972--2251054 Score: 58
Period size: 9 Copynumber: 8.0 Consensus size: 9
2250962 TTGGTGAGAA
2250972 TGTTAGGTG
1 TGTTAGGTG
2250981 TGTTAGGTG
1 TGTTAGGTG
2250990 TGTTAGGTGATG
1 TGTTA-G-G-TG
*
2251002 TGTTTGGTGAG
1 TGTTAGGT--G
2251013 AATGTTAGGTG
1 --TGTTAGGTG
2251024 TGTTAGGTGAG
1 TGTTAGGT--G
2251035 AATGTTAGGTG
1 --TGTTAGGTG
2251046 TGTTAGGTG
1 TGTTAGGTG
2251055 ATGTATTTGG
Statistics
Matches: 61, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
9 32 0.52
10 2 0.03
11 6 0.10
12 6 0.10
13 15 0.25
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.41
Consensus pattern (9 bp):
TGTTAGGTG
Found at i:2250989 original size:22 final size:22
Alignment explanation
Indices: 2250957--2251055 Score: 125
Period size: 22 Copynumber: 4.5 Consensus size: 22
2250947 TGTTAGGTGA
*
2250957 TGTGTTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2250979 TGTGTTAGGT--G--TGTTAGGTG
1 TGTGTTAGGTGAGAATGTTA-G-G
*
2250999 ATGTGTTTGGTGAGAATGTTAGG
1 -TGTGTTAGGTGAGAATGTTAGG
2251022 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2251044 TGTGTTAGGTGA
1 TGTGTTAGGTGA
2251056 TGTATTTGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
18 5 0.07
19 1 0.01
20 2 0.03
21 9 0.13
22 42 0.63
23 2 0.03
24 1 0.01
25 5 0.07
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.40
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAGG
Found at i:2255799 original size:34 final size:34
Alignment explanation
Indices: 2255756--2255876 Score: 233
Period size: 34 Copynumber: 3.6 Consensus size: 34
2255746 TTAATTTCTT
*
2255756 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAA
2255790 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAA
2255824 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAA
2255858 TGTTAGGTGTGTTAGGTGA
1 TGTTAGGTGTGTTAGGTGA
2255877 GAATGTTAGG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 86 1.00
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.41
Consensus pattern (34 bp):
TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAA
Found at i:2255875 original size:22 final size:22
Alignment explanation
Indices: 2255843--2255898 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
2255833 TGTTAGGTGA
*
2255843 TGTGTTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2255865 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
2255887 TGTGTTAGGTGA
1 TGTGTTAGGTGA
2255899 TGTATTTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAGG
Found at i:2255910 original size:68 final size:66
Alignment explanation
Indices: 2255756--2255927 Score: 238
Period size: 56 Copynumber: 2.7 Consensus size: 66
2255746 TTAATTTCTT
*
2255756 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTAGGT-A
2255821 GAA
65 G-A
*
2255824 TGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA---G--GTG--A-G-A-
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTAGGTAG
2255879 A
66 A
2255880 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
2255928 ACATGTATAT
Statistics
Matches: 101, Mismatches: 3, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
56 48 0.48
58 1 0.01
60 1 0.01
63 3 0.03
65 1 0.01
68 47 0.47
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.41
Consensus pattern (66 bp):
TGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTAGGTAG
A
Found at i:2256888 original size:20 final size:19
Alignment explanation
Indices: 2256864--2256911 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2256854 ATTATTTATT
2256864 ATATTTATTTATTATTAAAA
1 ATATTT-TTTATTATTAAAA
* * *
2256884 TTATTTTTAAATATTAAAA
1 ATATTTTTTATTATTAAAA
2256903 ATATTTTTT
1 ATATTTTTT
2256912 TATCAAACTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTTTTTATTATTAAAA
Found at i:2257314 original size:19 final size:18
Alignment explanation
Indices: 2257262--2257316 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
2257252 GCATGAATCA
*
2257262 TTATATATATTTAA-TAT
1 TTATATTTATTTAATTAT
2257279 TTAAATATTTA-TTAATTAT
1 TT--ATATTTATTTAATTAT
2257298 TTATATTTATTTAAATTAT
1 TTATATTTATTT-AATTAT
2257317 ATAAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 9 0.28
18 6 0.19
19 17 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTTATTTAATTAT
Found at i:2259325 original size:9 final size:10
Alignment explanation
Indices: 2259290--2259322 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2259280 TTTTATTTGT
*
2259290 ATATTATTAT
1 ATATTATTAC
2259300 ATATTATTAC
1 ATATTATTAC
2259310 -TATTATTAC
1 ATATTATTAC
2259319 ATAT
1 ATAT
2259323 ATTTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATTATTAC
Found at i:2262211 original size:2 final size:2
Alignment explanation
Indices: 2262204--2262247 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
2262194 AGTATGAGCA
*
2262204 AT AT AT AT AT AT A- AT -T AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2262244 AT AT
1 AT AT
2262248 TGTTTATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2262770 original size:26 final size:27
Alignment explanation
Indices: 2262706--2262774 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
2262696 ATAATGCAAT
* *
2262706 ATATTT-TATTAATATAAATATTTAAA
1 ATATTTATATTATTAAAAATATTTAAA
* *
2262732 A-AATAATATTTATTAAAAATA-TTAAA
1 ATATTTATA-TTATTAAAAATATTTAAA
2262758 ATATTTATATTATTAAA
1 ATATTTATATTATTAAA
2262775 GCAATAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 2 0.06
26 17 0.50
27 15 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATTTATATTATTAAAAATATTTAAA
Found at i:2263464 original size:31 final size:31
Alignment explanation
Indices: 2263429--2263492 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2263419 TTGATAATTC
2263429 TTGTTATTCTTCAGCTGTTAGAAACTCATAT
1 TTGTTATTCTTCAGCTGTTAGAAACTCATAT
2263460 TTGTTATTCTTCAGCTGTTAGAAACTCATAT
1 TTGTTATTCTTCAGCTGTTAGAAACTCATAT
2263491 TT
1 TT
2263493 ATAGACTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (31 bp):
TTGTTATTCTTCAGCTGTTAGAAACTCATAT
Found at i:2264656 original size:16 final size:17
Alignment explanation
Indices: 2264622--2264666 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
2264612 AGATTAGATC
*
2264622 AAAATTTAAAATATTAA
1 AAAATTTAAAATATAAA
*
2264639 AAAATATAAAA-ATAAA
1 AAAATTTAAAATATAAA
2264655 AAAATTTAAAAT
1 AAAATTTAAAAT
2264667 TATATAGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTTAAAATATAAA
Found at i:2265847 original size:14 final size:13
Alignment explanation
Indices: 2265845--2265895 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
2265835 TATTTAATAA
*
2265845 AATATAATATATTT
1 AATAAAATATA-TT
2265859 AATAAAATATATT
1 AATAAAATATATT
*
2265872 --TAAAATACATT
1 AATAAAATATATT
2265883 AATAAAATATATT
1 AATAAAATATATT
2265896 TAAAATCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
11 10 0.31
13 12 0.38
14 10 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
AATAAAATATATT
Found at i:2265853 original size:19 final size:19
Alignment explanation
Indices: 2265831--2265869 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2265821 AAATATTTAA
2265831 AATATATTTAATAAAATAT
1 AATATATTTAATAAAATAT
2265850 AATATATTTAATAAAATAT
1 AATATATTTAATAAAATAT
2265869 A
1 A
2265870 TTTAAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATATTTAATAAAATAT
Found at i:2273557 original size:49 final size:49
Alignment explanation
Indices: 2273499--2273596 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
2273489 AATTGAATTG
2273499 GTAATGGTTATTATTTAGATTGATAAAATTTGGCTGTTTTTAAATTAGA
1 GTAATGGTTATTATTTAGATTGATAAAATTTGGCTGTTTTTAAATTAGA
2273548 GTAATGGTTATTATTTAGATTGATAAAATTTGGCTGTTTTTAAATTAGA
1 GTAATGGTTATTATTTAGATTGATAAAATTTGGCTGTTTTTAAATTAGA
2273597 TTTATTTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (49 bp):
GTAATGGTTATTATTTAGATTGATAAAATTTGGCTGTTTTTAAATTAGA
Found at i:2273973 original size:20 final size:19
Alignment explanation
Indices: 2273949--2273996 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
2273939 CATATTAATT
2273949 ATATTTATTTAATATTAAAA
1 ATATTT-TTTAATATTAAAA
* *
2273969 TTATTTTTAAATATTAAAA
1 ATATTTTTTAATATTAAAA
2273988 ATATTTTTT
1 ATATTTTTT
2273997 TATCAAATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTTTTAATATTAAAA
Found at i:2274093 original size:21 final size:20
Alignment explanation
Indices: 2274064--2274105 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2274054 TGATCCTTTC
*
2274064 AAATTTAAATAAAAAGTAAAA
1 AAATATAAATAAAAA-TAAAA
*
2274085 AAATATAAATATAAATAAAA
1 AAATATAAATAAAAATAAAA
2274105 A
1 A
2274106 TAAAAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
AAATATAAATAAAAATAAAA
Found at i:2275777 original size:5 final size:5
Alignment explanation
Indices: 2275769--2275793 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2275759 ATCAAATTAA
2275769 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
2275794 TAAATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:2275814 original size:21 final size:22
Alignment explanation
Indices: 2275784--2275827 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2275774 ATTTTATTTT
*
2275784 ATTTTATTTTTAAATTAATATA
1 ATTTTATTTTTAAAATAATATA
*
2275806 ATTTT-TTTTTAAAATACTATA
1 ATTTTATTTTTAAAATAATATA
2275827 A
1 A
2275828 AAAGTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTATTTTTAAAATAATATA
Found at i:2275874 original size:20 final size:20
Alignment explanation
Indices: 2275851--2275890 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2275841 TAAAATTTTA
* *
2275851 AAAAATTGATTTAAATTGAT
1 AAAAATTAATTCAAATTGAT
*
2275871 AAAATTTAATTCAAATTGAT
1 AAAAATTAATTCAAATTGAT
2275891 TTATATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (20 bp):
AAAAATTAATTCAAATTGAT
Found at i:2276724 original size:19 final size:20
Alignment explanation
Indices: 2276700--2276737 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2276690 TTTTATTTGT
*
2276700 ATATTATTTTATAT-TATTA
1 ATATTATTATATATATATTA
2276719 ATATTATTATATATATATT
1 ATATTATTATATATATATT
2276738 TAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTATTATATATATATTA
Found at i:2276871 original size:22 final size:21
Alignment explanation
Indices: 2276829--2276872 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2276819 ATTATTTTTA
* *
2276829 TTTATTATAACAAATAGATTT
1 TTTAATATAACAAATAAATTT
*
2276850 TTTAATATGAACATATAAATTT
1 TTTAATAT-AACAAATAAATTT
2276872 T
1 T
2276873 AGATATACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTAATATAACAAATAAATTT
Found at i:2282911 original size:22 final size:21
Alignment explanation
Indices: 2282894--2282951 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
2282884 TTAAAAGTTG
2282894 CATTCTTTTATCCAAAAAATA
1 CATTCTTTTATCCAAAAAATA
* ** *
2282915 CATTCTTTTGTCCAACCATTA
1 CATTCTTTTATCCAAAAAATA
2282936 CA-TCATTTTATCCAAA
1 CATTC-TTTTATCCAAA
2282952 TATACCTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (21 bp):
CATTCTTTTATCCAAAAAATA
Found at i:2288128 original size:2 final size:2
Alignment explanation
Indices: 2288121--2288156 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2288111 AAGTCATTTG
*
2288121 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2288157 TGCAAATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2290839 original size:2 final size:2
Alignment explanation
Indices: 2290832--2290899 Score: 111
Period size: 2 Copynumber: 34.0 Consensus size: 2
2290822 TTATACAGCA
*
2290832 AT AT AT AT CCT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2290874 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2290900 GACAATAAAC
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.02
2 60 0.97
3 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2291412 original size:19 final size:19
Alignment explanation
Indices: 2291388--2291425 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2291378 TTGGTTATTA
2291388 TTATATTAA-TATAATAATT
1 TTATATTAATTATAA-AATT
2291407 TTATATTAATTATAAAATT
1 TTATATTAATTATAAAATT
2291426 AAATATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATATTAATTATAAAATT
Found at i:2291431 original size:19 final size:19
Alignment explanation
Indices: 2291390--2291431 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2291380 GGTTATTATT
**
2291390 ATATTAATATAATAATTTT
1 ATATTAATATAATAATTAA
2291409 ATATTAATTATAA-AATTAA
1 ATATTAA-TATAATAATTAA
2291428 ATAT
1 ATAT
2291432 ACAAGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTAATATAATAATTAA
Found at i:2291874 original size:19 final size:20
Alignment explanation
Indices: 2291850--2291892 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2291840 TGAAATTATT
*
2291850 TGATAATGTTAGTTA-AATA
1 TGATAATGTTAGATACAATA
*
2291869 TGATAATTTTAGATACAATA
1 TGATAATGTTAGATACAATA
2291889 TGAT
1 TGAT
2291893 TGTATAGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (20 bp):
TGATAATGTTAGATACAATA
Found at i:2292210 original size:27 final size:28
Alignment explanation
Indices: 2292153--2292218 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
2292143 TATATATATG
*
2292153 ATATGAATATAATATAAAAAAAATTAAA
1 ATATGAATATAATATAAAAAAAATCAAA
* *
2292181 ATATG-ATATGATATAAAAAAAATCATA
1 ATATGAATATAATATAAAAAAAATCAAA
*
2292208 ATATAAATATA
1 ATATGAATATA
2292219 CAAATATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 23 0.72
28 9 0.28
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (28 bp):
ATATGAATATAATATAAAAAAAATCAAA
Found at i:2292437 original size:18 final size:17
Alignment explanation
Indices: 2292404--2292441 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2292394 ACGAAAAATT
*
2292404 TATTAAATATAATATAA
1 TATTAAACATAATATAA
2292421 TATTAAACATGAATATAA
1 TATTAAACAT-AATATAA
2292439 TAT
1 TAT
2292442 GTGTATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
TATTAAACATAATATAA
Found at i:2297912 original size:23 final size:24
Alignment explanation
Indices: 2297862--2297913 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2297852 ATATTTTTTT
* *
2297862 ATTTTTTTAAAACAAATAAAGATC
1 ATTTTTTTAAAACAAATAAACATA
2297886 ATTTTTTTAAAA-AAA-AAACATA
1 ATTTTTTTAAAACAAATAAACATA
*
2297908 AATTTT
1 ATTTTT
2297914 GAACTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.40
23 3 0.12
24 12 0.48
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTTTTTTAAAACAAATAAACATA
Found at i:2298456 original size:17 final size:17
Alignment explanation
Indices: 2298434--2298469 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2298424 CATTTCATAT
* *
2298434 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
2298451 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
2298468 TT
1 TT
2298470 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:2299636 original size:49 final size:45
Alignment explanation
Indices: 2299583--2299687 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 45
2299573 CAAGGTCAAT
*
2299583 GACATCGGACTAAGGGAAAAGTGGACCAATGTGCTGACTCAAGGCCAGC
1 GACATCGGACTAA--GAAAAGT-G-CCAATATGCTGACTCAAGGCCAGC
* * * * *
2299632 GACATTGGGCTTAGAAAGGTGCCAATATGCTGATTCAAGGCCAGC
1 GACATCGGACTAAGAAAAGTGCCAATATGCTGACTCAAGGCCAGC
*
2299677 GATATCGGACT
1 GACATCGGACT
2299688 TTAAGATGAC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
45 30 0.64
46 1 0.02
47 6 0.13
49 10 0.21
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (45 bp):
GACATCGGACTAAGAAAAGTGCCAATATGCTGACTCAAGGCCAGC
Found at i:2299758 original size:32 final size:32
Alignment explanation
Indices: 2299709--2300055 Score: 552
Period size: 32 Copynumber: 10.8 Consensus size: 32
2299699 AAAATGGTGA
* * *
2299709 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
2299741 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
2299773 TTTTAAATGGGTTGCCACCAACTTGTGGGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
2299805 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2299837 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2299869 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
2299901 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2299933 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2299965 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2299997 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
2300029 TTTGGAATGGGTTGCCACCGATTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
2300056 AATTTAAAAG
Statistics
Matches: 296, Mismatches: 17, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
31 1 0.00
32 294 0.99
33 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:2300107 original size:27 final size:27
Alignment explanation
Indices: 2300041--2300832 Score: 1154
Period size: 27 Copynumber: 28.9 Consensus size: 27
2300031 TGGAATGGGT
* * * *
2300041 TGCCACCGATTTGTGAATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
2300068 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
*
2300096 TGCCACGGAGTTGTGGACTTAAGAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
2300123 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
2300151 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
* *
2300179 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
2300206 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
2300234 TGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
* *
2300262 TGCCACAGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
2300289 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
2300316 TGCTACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
2300343 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
2300370 ATGCCATGGAGTTATGGACTTAAAAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
2300398 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
2300425 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
2300452 TGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
2300480 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
2300507 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
2300534 TGCCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-G
** *
2300562 TGCCATAGAGTTGTGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
2300589 TGCCACGGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
2300616 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
2300643 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
2300670 TGCCACAGAGTTGTGGACTAAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
2300697 TACCACGGAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
*
2300725 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
2300752 TACCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
2300780 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
2300807 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
2300833 AAAATGCCAC
Statistics
Matches: 695, Mismatches: 58, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
27 444 0.64
28 251 0.36
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:2300110 original size:55 final size:54
Alignment explanation
Indices: 2300041--2300832 Score: 1154
Period size: 55 Copynumber: 14.5 Consensus size: 54
2300031 TGGAATGGGT
* * * *
2300041 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
*
2300096 TGCCACGGAGTTGTGGACTTAAGAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
* *
2300151 ATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
2300206 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGG
* *
2300262 TGCCACAGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
2300316 TGCTACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
2300370 ATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
2300425 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
2300480 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* ** *
2300534 TGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACGGAGTTGTGGACTTAAAAGGG
*
2300589 TGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
2300643 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
2300697 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
2300752 TACCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
2300807 TGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
2300833 AAAATGCCAC
Statistics
Matches: 672, Mismatches: 55, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
54 235 0.35
55 390 0.58
56 47 0.07
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (54 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:2300313 original size:82 final size:81
Alignment explanation
Indices: 2300041--2300832 Score: 1172
Period size: 82 Copynumber: 9.6 Consensus size: 81
2300031 TGGAATGGGT
* * * * *
2300041 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
2300106 TTGTGGACTTAAGAGGG
65 TTGTGGACTTAAAAGGG
* *
2300123 ATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGA
1 -TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
*
2300188 GTTGTGGACTAAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * *
2300206 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGATGCCACAGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTT-AAAAGGGTGCCACGGA
*
2300271 GTTATGGACTTAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * *
2300289 TGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
2300354 TGTGGACTTAAAAGGG
66 TGTGGACTTAAAAGGG
* * * *
2300370 ATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
2300435 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
*
2300452 TGCCACGGAGTTGTGGTA-TTAAAAGGAATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
2300516 GTTGTGGACTTAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * *
2300534 TGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAAGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
2300599 TTGTGGGCTTAAAAGGG
65 TTGTGGACTTAAAAGGG
*
2300616 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
* *
2300681 TGTGGACTAAAAAAGG
66 TGTGGACTTAAAAGGG
* * *
2300697 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGGAG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
2300762 TTGTGGACTTTAAAAGGG
65 TTGTGGAC-TTAAAAGGG
* *
2300780 TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAG
2300833 AAAATGCCAC
Statistics
Matches: 651, Mismatches: 49, Indels: 18
0.91 0.07 0.03
Matches are distributed among these distances:
81 116 0.18
82 374 0.57
83 161 0.25
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.23
Consensus pattern (81 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
TGTGGACTTAAAAGGG
Found at i:2311897 original size:25 final size:25
Alignment explanation
Indices: 2311841--2311897 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
2311831 GAAGGAAGAG
* *
2311841 ATATTTTTTGTTTTAATAGCTGTAT
1 ATATTTTTTGTTTTAATAGCTATAA
*
2311866 ATTTTTTTTGTTTTAATAGCTATAA
1 ATATTTTTTGTTTTAATAGCTATAA
2311891 ATATTTT
1 ATATTTT
2311898 GTGACTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (25 bp):
ATATTTTTTGTTTTAATAGCTATAA
Found at i:2312457 original size:3 final size:3
Alignment explanation
Indices: 2312449--2312496 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2312439 TTCTAAACAT
2312449 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2312497 AAACAACCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2319591 original size:15 final size:15
Alignment explanation
Indices: 2319571--2319630 Score: 70
Period size: 15 Copynumber: 3.9 Consensus size: 15
2319561 TATAAAGTGT
2319571 TGTATCGATACATTA
1 TGTATCGATACATTA
2319586 TGTATCGATACATAAGTA
1 TGTATCGATACAT---TA
2319604 TTGTATCGATACA--A
1 -TGTATCGATACATTA
2319618 TGTATCGATACAT
1 TGTATCGATACAT
2319631 AAGCTTTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 12 0.30
14 1 0.03
15 13 0.32
18 2 0.05
19 12 0.30
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (15 bp):
TGTATCGATACATTA
Found at i:2319610 original size:19 final size:19
Alignment explanation
Indices: 2319550--2319648 Score: 85
Period size: 19 Copynumber: 5.7 Consensus size: 19
2319540 TTTCAACGAT
* *
2319550 TTGTATCGATATATAAAGTG
1 TTGTATCGATACAT-AAGTA
2319570 TTGTATCGATACAT---TA
1 TTGTATCGATACATAAGTA
2319586 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
2319604 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
2319618 -TGTATCGATACATAAGCT-
1 TTGTATCGATACATAAG-TA
2319636 TTGTATCGATACA
1 TTGTATCGATACA
2319649 ATGTATCGCT
Statistics
Matches: 66, Mismatches: 2, Indels: 23
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.17
14 1 0.02
15 13 0.20
16 3 0.05
18 2 0.03
19 23 0.35
20 13 0.20
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:2319623 original size:13 final size:13
Alignment explanation
Indices: 2319605--2319629 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2319595 ACATAAGTAT
2319605 TGTATCGATACAA
1 TGTATCGATACAA
2319618 TGTATCGATACA
1 TGTATCGATACA
2319630 TAAGCTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2319626 original size:32 final size:31
Alignment explanation
Indices: 2319551--2319656 Score: 149
Period size: 32 Copynumber: 3.2 Consensus size: 31
2319541 TTCAACGATT
*
2319551 TGTATCGATATATAAAGTGTTGTATCGATACATTA
1 TGTATCGATACAT-AAGT-TTGTATCGATACA--A
2319586 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGT-TTGTATCGATACAA
2319618 TGTATCGATACATAAGCTTTGTATCGATACAA
1 TGTATCGATACATAAG-TTTGTATCGATACAA
2319650 TGTATCG
1 TGTATCG
2319657 CTACGAAGCT
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
32 38 0.56
33 1 0.01
34 17 0.25
35 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (31 bp):
TGTATCGATACATAAGTTTGTATCGATACAA
Found at i:2319739 original size:52 final size:52
Alignment explanation
Indices: 2319700--2319828 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2319690 CACTGATCTT
*
2319700 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
2319752 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2319804 TGTATCGACACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2319829 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2324467 original size:13 final size:13
Alignment explanation
Indices: 2324449--2324523 Score: 91
Period size: 13 Copynumber: 5.9 Consensus size: 13
2324439 TTAGTTCGTA
*
2324449 GTATCGATACGTT
1 GTATCGATACATT
*
2324462 GTATCGATATATT
1 GTATCGATACATT
*
2324475 -TATCGATACACT
1 GTATCGATACATT
*
2324487 GTATCGATATATT
1 GTATCGATACATT
*
2324500 -TATCGATACACT
1 GTATCGATACATT
2324512 GTATCGATACAT
1 GTATCGATACAT
2324524 GGGCACTATT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
12 20 0.39
13 31 0.61
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2324480 original size:12 final size:12
Alignment explanation
Indices: 2324463--2324507 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
2324453 CGATACGTTG
2324463 TATCGATATATT
1 TATCGATATATT
* *
2324475 TATCGATACACTG
1 TATCGATATA-TT
2324488 TATCGATATATT
1 TATCGATATATT
2324500 TATCGATA
1 TATCGATA
2324508 CACTGTATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (12 bp):
TATCGATATATT
Found at i:2324489 original size:25 final size:25
Alignment explanation
Indices: 2324450--2324520 Score: 124
Period size: 25 Copynumber: 2.8 Consensus size: 25
2324440 TAGTTCGTAG
**
2324450 TATCGATACGTTGTATCGATATATT
1 TATCGATACACTGTATCGATATATT
2324475 TATCGATACACTGTATCGATATATT
1 TATCGATACACTGTATCGATATATT
2324500 TATCGATACACTGTATCGATA
1 TATCGATACACTGTATCGATA
2324521 CATGGGCACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (25 bp):
TATCGATACACTGTATCGATATATT
Found at i:2326394 original size:13 final size:13
Alignment explanation
Indices: 2326375--2326406 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2326365 GATATTTTGA
2326375 AATAAATTTGTTT
1 AATAAATTTGTTT
*
2326388 TATAAATTTGTTT
1 AATAAATTTGTTT
2326401 AATAAA
1 AATAAA
2326407 GGGGGATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
AATAAATTTGTTT
Found at i:2327192 original size:15 final size:15
Alignment explanation
Indices: 2327169--2327198 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2327159 GTCAAAACCG
2327169 TAGAAAGTATCGATA
1 TAGAAAGTATCGATA
*
2327184 TAGATAGTATCGATA
1 TAGAAAGTATCGATA
2327199 CACACCCAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (15 bp):
TAGAAAGTATCGATA
Found at i:2327262 original size:33 final size:32
Alignment explanation
Indices: 2327213--2327287 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
2327203 CCCAGATGTA
* * *
2327213 TAGTATGGATATATTGTATCGATACATATTGCT
1 TAGTATCGATACATTGTATCAATACATATT-CT
*
2327246 TAGTATCGATACATTGTATCAATACATGTTCT
1 TAGTATCGATACATTGTATCAATACATATTCT
*
2327278 TGGTATCGAT
1 TAGTATCGAT
2327288 TCACACTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 11 0.30
33 26 0.70
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (32 bp):
TAGTATCGATACATTGTATCAATACATATTCT
Found at i:2327358 original size:13 final size:13
Alignment explanation
Indices: 2327338--2327379 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
2327328 AAACTTACTC
2327338 AGTATCGATACAGT
1 AGTATCGATACA-T
2327352 A-TATCGATACAT
1 AGTATCGATACAT
2327364 AGTATCGATACAT
1 AGTATCGATACAT
2327377 AGT
1 AGT
2327380 GAAATGTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.07
13 24 0.89
14 1 0.04
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
AGTATCGATACAT
Done.