Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 126 of 187
Found at i:38241190 original size:30 final size:30
Alignment explanation
Indices: 38241156--38241219 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
38241146 TTGTTTACTT
38241156 ACTTGCTTATTTAAATAACTCATGATTATA
1 ACTTGCTTATTTAAATAACTCATGATTATA
38241186 ACTTGCTTATTTAAATAACTCATGATTATA
1 ACTTGCTTATTTAAATAACTCATGATTATA
38241216 ACTT
1 ACTT
38241220 CTCCTCCCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (30 bp):
ACTTGCTTATTTAAATAACTCATGATTATA
Found at i:38241522 original size:50 final size:50
Alignment explanation
Indices: 38241447--38241639 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 50
38241437 TTTCTTGTAC
* * * **
38241447 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
38241497 TGCCTATGCCATGTCCAAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * **
38241547 TGCCAATGGCATGTCCCGGACATGGTGTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
38241603 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
38241640 TCTCATCCAC
Statistics
Matches: 115, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
50 79 0.69
53 2 0.02
56 34 0.30
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:38244139 original size:7 final size:7
Alignment explanation
Indices: 38244123--38244164 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
38244113 AAAATTCTTA
38244123 TTTTTAT
1 TTTTTAT
*
38244130 TTTTTGT
1 TTTTTAT
*
38244137 TTTTTCT
1 TTTTTAT
38244144 TCTTTTAT
1 T-TTTTAT
38244152 TTTTTAT
1 TTTTTAT
38244159 TTTTTA
1 TTTTTA
38244165 ATTATTAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.10, C:0.05, G:0.02, T:0.83
Consensus pattern (7 bp):
TTTTTAT
Found at i:38244149 original size:23 final size:22
Alignment explanation
Indices: 38244117--38244163 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
38244107 CTTAGGAAAA
*
38244117 TTCTTATTTTTATTTTTTGTTTT
1 TTCTTA-TTTTATTTTTTATTTT
*
38244140 TTCTTCTTTTATTTTTTATTTT
1 TTCTTATTTTATTTTTTATTTT
38244162 TT
1 TT
38244164 AATTATTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.09, C:0.06, G:0.02, T:0.83
Consensus pattern (22 bp):
TTCTTATTTTATTTTTTATTTT
Found at i:38246154 original size:18 final size:17
Alignment explanation
Indices: 38246110--38246157 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
38246100 GGTTTATTGA
*
38246110 TTTAGTTAATTTGTTTAT
1 TTTAGTT-ATTTATTTAT
**
38246128 TTTTCTTATTTATATTAT
1 TTTAGTTATTTAT-TTAT
38246146 TTTAGTTATTTA
1 TTTAGTTATTTA
38246158 GTTTTCTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTAGTTATTTATTTAT
Found at i:38246214 original size:3 final size:3
Alignment explanation
Indices: 38246206--38246233 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38246196 ATAGTGATTA
38246206 ACT ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT A
38246234 GTTAGACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:38247582 original size:45 final size:45
Alignment explanation
Indices: 38247533--38247751 Score: 269
Period size: 45 Copynumber: 4.9 Consensus size: 45
38247523 ATACCATAAA
*
38247533 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * * **
38247578 CGAGTAAGACCGTGACTGAAAGATGTTATGGAATCATAATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * *
38247623 CAAGTAAGAACATGACTGAAAGACGTTATGGCATCACGATCCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * *
38247668 CGAGTAAGACCAGGACTGAATGACCTTATGGCATCACGATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * ***
38247713 CGGGTAAGACCAT-AGCTTAAAGACACAATGGCATCACGA
1 CGAGTAAGACCATGA-CTGAAAGACGTTATGGCATCACGA
38247752 ATCAAAGGAA
Statistics
Matches: 147, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
44 1 0.01
45 146 0.99
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (45 bp):
CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
Found at i:38247789 original size:45 final size:46
Alignment explanation
Indices: 38247717--38247838 Score: 124
Period size: 47 Copynumber: 2.7 Consensus size: 46
38247707 TTCTATCGGG
* *
38247717 TAAGACCATAGCTTAAAGACACAATGGCA-TC-AC-GAATCAAAGGAA
1 TAAGACCATGGCTGAAAGACACAATGGCACTCGACAGAA--AAAGGAA
* * * *
38247762 TAAGACCATGGGTGAAATACACTATGGCAACTCGACAGAAAAATGAA
1 TAAGACCATGGCTGAAAGACACAATGGC-ACTCGACAGAAAAAGGAA
* *
38247809 TAAGACCATGGTTGAAAGACACCATGGCAC
1 TAAGACCATGGCTGAAAGACACAATGGCAC
38247839 ACTCCGACCA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 23 0.36
46 3 0.05
47 33 0.52
48 2 0.03
49 3 0.05
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.16
Consensus pattern (46 bp):
TAAGACCATGGCTGAAAGACACAATGGCACTCGACAGAAAAAGGAA
Found at i:38260685 original size:22 final size:22
Alignment explanation
Indices: 38260657--38260809 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
38260647 TGTTGATAGT
*
38260657 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
38260679 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
38260701 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
38260723 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
38260745 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
38260767 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
38260789 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
38260810 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:38267304 original size:34 final size:34
Alignment explanation
Indices: 38267261--38267329 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
38267251 CTAATGAATT
*
38267261 AATTATTAAATCGTATTGAAATTTTAATTAGTCG
1 AATTATTAAATCGTATTGAAATTGTAATTAGTCG
38267295 AATTATTAAATCGTATTGAAATTGTAATTAGTCG
1 AATTATTAAATCGTATTGAAATTGTAATTAGTCG
38267329 A
1 A
38267330 CACAATACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (34 bp):
AATTATTAAATCGTATTGAAATTGTAATTAGTCG
Found at i:38283042 original size:6 final size:6
Alignment explanation
Indices: 38283010--38283078 Score: 83
Period size: 6 Copynumber: 12.0 Consensus size: 6
38283000 GACCCCTTCT
* *
38283010 ATTAAA A-T-AA A-TAAA ACTAAT ATTAAA ATTAAA GATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA -ATTAAA ATTAAA
38283056 A-TAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA
38283079 GACAAAGACA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.07
5 9 0.16
6 37 0.66
7 6 0.11
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (6 bp):
ATTAAA
Found at i:38283071 original size:36 final size:34
Alignment explanation
Indices: 38283010--38283080 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 34
38283000 GACCCCTTCT
*
38283010 ATTAAAATAAATAAAACTAATATTAAAATTAAAG
1 ATTAAAATAAATAAAACTAAAATTAAAATTAAAG
*
38283044 ATTAAAATTAAAATAAAATTAAAATTAAAATTAAAG
1 ATTAAAA-T-AAATAAAACTAAAATTAAAATTAAAG
38283080 A
1 A
38283081 CAAAGACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 7 0.21
35 1 0.03
36 25 0.76
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (34 bp):
ATTAAAATAAATAAAACTAAAATTAAAATTAAAG
Found at i:38287288 original size:20 final size:21
Alignment explanation
Indices: 38287263--38287303 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
38287253 TTGGACTAAA
* *
38287263 TCAGAAAGTCA-GAGAATTTT
1 TCAGAAAATCATGAAAATTTT
38287283 TCAGAAAATCATGAAAATTTT
1 TCAGAAAATCATGAAAATTTT
38287304 CAACACTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.32
Consensus pattern (21 bp):
TCAGAAAATCATGAAAATTTT
Found at i:38292252 original size:340 final size:341
Alignment explanation
Indices: 38291622--38292252 Score: 887
Period size: 340 Copynumber: 1.9 Consensus size: 341
38291612 GGATGATTAG
** *
38291622 GTAACATTTAACGTCTTTAAGTCTATTTAATTTCTTGACAAAATGGATGATTGCTCTGCAGTGTC
1 GTAACATTTAACGTCTTTAAGTCTATGCAATTTCCTGACAAAATGGATGATTGCTCTGCAGTGTC
* * * *
38291687 CGATTTAGAGGATTTAATAGTGGAGAAGGAACTCAACTGTGTTGAGGACCCACTGGAAAGAATTT
66 CAATTTAGAGGAATTAATAGTGGAAAAGGAACTCAACTATGTTGAGGACCCACTGGAAAGAATTT
** * *
38291752 TGACATTGGATCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGCTAATCAA
131 TGACATCAGACCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGATAATCAA
* *
38291817 AGGGGATTTAATCCACAATCCTGTTTTGAATCTTTGGAGTTAGAAAAGAGGGACTATTCTCAACC
196 AGCGGATTTAATCCACAATCCTGTTTTGAATCTTTGGAGTTAGAAAAGAGGGACTATCCTCAACC
* * *
38291882 AAAAGCATCGATCGAGGAGCCACCTAAATTAGAACTCAAGGTATTACCTTCTCATTTAAAATGCG
261 AAAAGCATCAATCGAGGAGCAACATAAATTAGAACTCAAGGTATTACCTTCTCATTTAAAATGCG
38291947 TATTCAGGACGACCAA
326 TATTCAGGACGACCAA
* * * * * * * * *
38291963 GTAACATTTAATGTTTTTAAGTTTATGCGATTTCCTGACACAATTGATTATTGTTCTGTAGTGTC
1 GTAACATTTAACGTCTTTAAGTCTATGCAATTTCCTGACAAAATGGATGATTGCTCTGCAGTGTC
* * *
38292028 TAATTTAGAGGAATTAATCA-TGGAAAAGGAACTCAACTATGTTGAGGACTCA-TTGAACA-AAT
66 CAATTTAGAGGAATTAAT-AGTGGAAAAGGAACTCAACTATGTTGAGGACCCACTGGAA-AGAAT
38292090 TTTGACATCAGACCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGATAATC
129 TTTGACATCAGACCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGATAATC
** * *
38292155 AAAGCGGATTTAATTTACAATCCTGTTTTGAATCTTTGGAGTTA-AAGAATAGGGATTATGCCT-
194 AAAGCGGATTTAATCCACAATCCTGTTTTGAATCTTTGGAGTTAGAA-AAGAGGGACTAT-CCTC
38292218 AACCAAAAG-AGTCAATCGAGGAGCAACATAAATTA
257 AACCAAAAGCA-TCAATCGAGGAGCAACATAAATTA
38292253 CAATTGAAAG
Statistics
Matches: 253, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
339 3 0.01
340 149 0.59
341 100 0.40
342 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (341 bp):
GTAACATTTAACGTCTTTAAGTCTATGCAATTTCCTGACAAAATGGATGATTGCTCTGCAGTGTC
CAATTTAGAGGAATTAATAGTGGAAAAGGAACTCAACTATGTTGAGGACCCACTGGAAAGAATTT
TGACATCAGACCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGATAATCAA
AGCGGATTTAATCCACAATCCTGTTTTGAATCTTTGGAGTTAGAAAAGAGGGACTATCCTCAACC
AAAAGCATCAATCGAGGAGCAACATAAATTAGAACTCAAGGTATTACCTTCTCATTTAAAATGCG
TATTCAGGACGACCAA
Found at i:38295593 original size:22 final size:22
Alignment explanation
Indices: 38295550--38295591 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38295540 TGATAATCAT
38295550 TAATATATAATTATATCTATTA
1 TAATATATAATTATATCTATTA
38295572 TAATATAT-ATTA-AT-TATTA
1 TAATATATAATTATATCTATTA
38295591 T
1 T
38295592 TAACTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATATAATTATATCTATTA
Found at i:38296332 original size:25 final size:25
Alignment explanation
Indices: 38296273--38296332 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
38296263 AATTTTAATT
*
38296273 TTATTTAATTATTTAAGTTTTAAAG
1 TTATTAAATTATTTAAGTTTTAAAG
* *
38296298 TTATTGAATTA-TTAATGTTTTATA-
1 TTATTAAATTATTTAA-GTTTTAAAG
38296322 TTAATTAAATT
1 TT-ATTAAATT
38296333 TTTGTGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 6 0.20
25 24 0.80
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (25 bp):
TTATTAAATTATTTAAGTTTTAAAG
Found at i:38297211 original size:3 final size:3
Alignment explanation
Indices: 38297203--38297233 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
38297193 GAGGATCCTA
*
38297203 AAG AAG AAG ATG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
38297234 TCCCACAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:38303010 original size:51 final size:52
Alignment explanation
Indices: 38302896--38303020 Score: 166
Period size: 51 Copynumber: 2.4 Consensus size: 52
38302886 TGACTCAAAT
*
38302896 GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCAAAAGT
1 GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCAAAAGG
* * * *
38302948 GTAGTGCTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGG-CTACAAGG
1 GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTC-AAAAGG
38302999 GTGGTACTATGTGCAA-GCCACT
1 GTGGTACTATGTG-AAGGCCACT
38303021 GGGTATCTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.02
51 33 0.52
52 30 0.47
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.28
Consensus pattern (52 bp):
GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCAAAAGG
Found at i:38305539 original size:30 final size:30
Alignment explanation
Indices: 38305503--38305578 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
38305493 TGGTTGACCC
* * ** *
38305503 ATCCCTTTTCGTAATTCGATAACTGAAGTT
1 ATCCCTTTTCATAATTCGACAACCAAAGCT
*
38305533 ATCCCTTTTCATAGTTCGACAACCAAAGCT
1 ATCCCTTTTCATAATTCGACAACCAAAGCT
38305563 ATCCCTTTTCATAATT
1 ATCCCTTTTCATAATT
38305579 TGATGGTGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGACAACCAAAGCT
Found at i:38305658 original size:60 final size:60
Alignment explanation
Indices: 38305563--38305752 Score: 195
Period size: 60 Copynumber: 3.2 Consensus size: 60
38305553 AACCAAAGCT
* ** * * * *
38305563 ATCCCTTTTCATAATTTGATGGTGGTCA-CCTTCCCTTTTCATTGTTCGATGGTTGTCACC
1 ATCCCTTTTCATAATTTGATAGCCG-AAGCCATCCCTTTTCATAGTTCGATGGTCGTCACC
* * * * * * * *
38305623 ATGCCTTTTCATAATTTGATAGCTGAAGCTATCCCTTTCCATAGTTCGATAGCCG-AAGCT
1 ATCCCTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATAGTTCGATGGTCGTCA-CC
* *
38305683 ATCCCTTTTCATAGTTTGATAGCCGGAGCCATCCCTTTTCATAGTTCGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATAGTTCGATGGTCGTCACC
38305743 ATCCCTTTTC
1 ATCCCTTTTC
38305753 TTTGTTGATG
Statistics
Matches: 103, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
59 2 0.02
60 100 0.97
61 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.38
Consensus pattern (60 bp):
ATCCCTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATAGTTCGATGGTCGTCACC
Found at i:38305719 original size:120 final size:119
Alignment explanation
Indices: 38305490--38305752 Score: 341
Period size: 120 Copynumber: 2.2 Consensus size: 119
38305480 GGTAATAATA
* * * *
38305490 CGATGGTTGAC-CCATCCCTTTTCGTAATTCGATAACTGAAGTTATCCCTTTTCATAGTTCGACA
1 CGATGGTTGTCACCATCCCTTTTCATAATTCGATAACTGAAGCTATCCCTTTCCATAGTTCGACA
** * *
38305554 ACCAAAGCTATCCCTTTTCATAATTTGATGGTGGTCACCTTCCCTTTTCATTGTT
66 ACCAAAGCTATCCCTTTTCATAATTTGATGCCGG-CACCATCCCTTTTCATAGTT
* * * *
38305609 CGATGGTTGTCACCATGCCTTTTCATAATTTGATAGCTGAAGCTATCCCTTTCCATAGTTCGATA
1 CGATGGTTGTCACCATCCCTTTTCATAATTCGATAACTGAAGCTATCCCTTTCCATAGTTCGACA
* * *
38305674 GCCGAAGCTATCCCTTTTCATAGTTTGATAGCCGG-AGCCATCCCTTTTCATAGTT
66 ACCAAAGCTATCCCTTTTCATAATTTGAT-GCCGGCA-CCATCCCTTTTCATAGTT
*
38305729 CGATGGTCGTCACCATCCCTTTTC
1 CGATGGTTGTCACCATCCCTTTTC
38305753 TTTGTTGATG
Statistics
Matches: 124, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
119 11 0.09
120 110 0.89
121 3 0.02
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (119 bp):
CGATGGTTGTCACCATCCCTTTTCATAATTCGATAACTGAAGCTATCCCTTTCCATAGTTCGACA
ACCAAAGCTATCCCTTTTCATAATTTGATGCCGGCACCATCCCTTTTCATAGTT
Found at i:38305770 original size:29 final size:30
Alignment explanation
Indices: 38305563--38305784 Score: 157
Period size: 30 Copynumber: 7.4 Consensus size: 30
38305553 AACCAAAGCT
* * *
38305563 ATCCCTTTTCATAATTTGATGGTGGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * *
38305593 TTCCCTTTTCATTGTTCGATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * * * * *
38305623 ATGCCTTTTCATAATTTGATAG-C-TGAAGCT
1 ATCCCTTTTCATAGTTCGATGGTCGT-CA-CC
* * * * *
38305653 ATCCCTTTCCATAGTTCGATAGCCG-AAGCT
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
* * * *
38305683 ATCCCTTTTCATAGTTTGATAGCCG-GAGCC
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
38305713 ATCCCTTTTCATAGTTCGATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* *
38305743 ATCCCTTTTCTTTGTT-GATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
*
38305772 ATCCCTTTGCATA
1 ATCCCTTTTCATA
38305785 ATCTATAGCC
Statistics
Matches: 156, Mismatches: 31, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
28 1 0.01
29 24 0.15
30 129 0.83
31 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATGGTCGTCACC
Found at i:38310392 original size:18 final size:18
Alignment explanation
Indices: 38310365--38310405 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
38310355 CTAATTGAAG
38310365 GTTC-TTATTCTATCGTT
1 GTTCTTTATTCTATCGTT
38310382 GTTCTTTATTCTATCGTT
1 GTTCTTTATTCTATCGTT
38310400 GTTCTT
1 GTTCTT
38310406 AATACTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.10, C:0.17, G:0.12, T:0.61
Consensus pattern (18 bp):
GTTCTTTATTCTATCGTT
Found at i:38311290 original size:14 final size:15
Alignment explanation
Indices: 38311273--38311301 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38311263 TAAAGTCTTT
38311273 TTCTTTA-TGTTATA
1 TTCTTTATTGTTATA
38311287 TTCTTTATTGTTATA
1 TTCTTTATTGTTATA
38311302 AAAATCCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (15 bp):
TTCTTTATTGTTATA
Found at i:38314186 original size:20 final size:20
Alignment explanation
Indices: 38314158--38314201 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
38314148 TTTAGCTCGG
* *
38314158 TTCATCTCACATGAGTTTAA
1 TTCAACTCACATGAGCTTAA
38314178 TTCAACTCACATGAGCTTAA
1 TTCAACTCACATGAGCTTAA
38314198 TTCA
1 TTCA
38314202 GCTTGTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (20 bp):
TTCAACTCACATGAGCTTAA
Found at i:38316469 original size:5 final size:6
Alignment explanation
Indices: 38316433--38316544 Score: 64
Period size: 6 Copynumber: 18.0 Consensus size: 6
38316423 ATCGAAAAAG
* * ** * *
38316433 AAGAAA AAGAAA AGGCAA GTGAAA AAGAAA AAGAAAA AAGAGA ATGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG-AAA AAGAAA AAGAAA
* * ** * *
38316482 ATGAGAA AAGAAA AAG-AG AAGTGA GAGAAA AAGAAA ACGAAA AAGAGAA
1 AAGA-AA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGA-AA
38316531 AATTGAAA AAGAAA
1 AA--GAAA AAGAAA
38316545 TTGAGATTGA
Statistics
Matches: 80, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
5 4 0.05
6 55 0.69
7 15 0.19
8 4 0.05
9 2 0.03
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:38316470 original size:25 final size:25
Alignment explanation
Indices: 38316433--38316544 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
38316423 ATCGAAAAAG
38316433 AAGAAAAAG-AAAAG-GCAAGTGAAA
1 AAGAAAAAGAAAAAGAG-AAGTGAAA
38316457 AAGAAAAAGAAAAAAGAGAA-TGAAA
1 AAGAAAAAG-AAAAAGAGAAGTGAAA
*
38316482 ATGAGAAAAGAAAAAGAGAAGTGAGAGAAA
1 AAGA-AAAAGAAAAAGAGAAGT----GAAA
* *
38316512 AAGAAAACGAAAAAGAGAAAATTGAAA
1 AAGAAAAAGAAAAAGAG--AAGTGAAA
38316539 AAGAAA
1 AAGAAA
38316545 TTGAGATTGA
Statistics
Matches: 73, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
24 9 0.12
25 18 0.25
26 13 0.18
27 11 0.15
29 12 0.16
30 7 0.10
31 3 0.04
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.05
Consensus pattern (25 bp):
AAGAAAAAGAAAAAGAGAAGTGAAA
Found at i:38316524 original size:42 final size:42
Alignment explanation
Indices: 38316452--38316599 Score: 108
Period size: 45 Copynumber: 3.5 Consensus size: 42
38316442 AAAAGGCAAG
* * * *
38316452 TGAAAAAGAAA--AAGA-AAAAAGAGAATGAAAATGAGAAAA
1 TGAAAAAGAAAGTGAGAGAAAAAGAAAACGAAAAAGAGAAAA
38316491 -GAAAAAGAGAAGTGAGAGAAAAAGAAAACGAAAAAGAGAAAA
1 TGAAAAAGA-AAGTGAGAGAAAAAGAAAACGAAAAAGAGAAAA
* * * ** *
38316533 TTGAAAAAGAAATTGAGATTGACAAAGGAAGTGAAAAGGAGAAAA
1 -TGAAAAAGAAAGTGAGA--GAAAAAGAAAACGAAAAAGAGAAAA
*
38316578 TGGAAAAAAGAAATTGA-AGAAA
1 T-G-AAAAAGAAAGTGAGAGAAA
38316600 GAACAAAAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 16
0.77 0.10 0.14
Matches are distributed among these distances:
38 8 0.09
39 2 0.02
41 3 0.03
42 21 0.24
43 10 0.11
44 9 0.10
45 22 0.25
46 13 0.15
ACGTcount: A:0.65, C:0.01, G:0.24, T:0.09
Consensus pattern (42 bp):
TGAAAAAGAAAGTGAGAGAAAAAGAAAACGAAAAAGAGAAAA
Found at i:38321323 original size:14 final size:14
Alignment explanation
Indices: 38321304--38321334 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38321294 ATTAACATTA
*
38321304 TATTTTAATTTTTC
1 TATTTTAAATTTTC
38321318 TATTTTAAATTTTC
1 TATTTTAAATTTTC
38321332 TAT
1 TAT
38321335 GTAGGAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTAAATTTTC
Found at i:38327325 original size:17 final size:17
Alignment explanation
Indices: 38327303--38327336 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38327293 TATTCATATT
*
38327303 TTTTTCTTTTTTGTTTC
1 TTTTTCTTATTTGTTTC
38327320 TTTTTCTTATTTGTTTC
1 TTTTTCTTATTTGTTTC
38327337 AAATAAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTCTTATTTGTTTC
Found at i:38333206 original size:30 final size:30
Alignment explanation
Indices: 38333170--38333303 Score: 126
Period size: 30 Copynumber: 4.5 Consensus size: 30
38333160 ATGGTTGTCA
* *
38333170 CTATCCCTTATCATAGTTTGATAGCCGAAG
1 CTATCCCTTTTCATAATTTGATAGCCGAAG
**
38333200 CTATCCCTTTTCATAATTTGATAGTTGAAG
1 CTATCCCTTTTCATAATTTGATAGCCGAAG
* * ** *
38333230 TTATCCCTTTTCATAATTTGATGGTTGTCA-
1 CTATCCCTTTTCATAATTTGATAGCCG-AAG
* * * * *
38333260 CCATTCATTTTCATAATCTGATAGCTGAAG
1 CTATCCCTTTTCATAATTTGATAGCCGAAG
38333290 CTATCCCTTTTCAT
1 CTATCCCTTTTCAT
38333304 TGGTCGATGA
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
29 1 0.01
30 82 0.98
31 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.42
Consensus pattern (30 bp):
CTATCCCTTTTCATAATTTGATAGCCGAAG
Found at i:38339975 original size:8 final size:8
Alignment explanation
Indices: 38339962--38339990 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
38339952 TATATATATT
38339962 AAATAATA
1 AAATAATA
38339970 AAATAATA
1 AAATAATA
38339978 AAATAATA
1 AAATAATA
38339986 AAATA
1 AAATA
38339991 TCATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATAATA
Found at i:38343702 original size:54 final size:54
Alignment explanation
Indices: 38343617--38343851 Score: 301
Period size: 54 Copynumber: 4.4 Consensus size: 54
38343607 ATAATGGGCC
* * * * *
38343617 TAAAATTATCGAAATACCCTTAATGGCTAAAATTATCGAAATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCAATGGGTAAAATTACCGAAATACCCTCGAAGGG
* *
38343671 TAAAATTACCGAAATACCCTCAATGGGTAAAATTA-TGAAAATACCCTCGATGGG
1 TAAAATTACCGAAATACCCTCAATGGGTAAAATTACCG-AAATACCCTCGAAGGG
* * * *
38343725 TAAAATTACCAAAATACCCTCGATGGGTAAAATTACCAAAATACCCCCGAAGGG
1 TAAAATTACCGAAATACCCTCAATGGGTAAAATTACCGAAATACCCTCGAAGGG
* * * *
38343779 TAAAATGACTGAAATACCCTCGATAGGTAAAATTACCGAAATACCCTCGAAGGG
1 TAAAATTACCGAAATACCCTCAATGGGTAAAATTACCGAAATACCCTCGAAGGG
* *
38343833 TTAAATTATCGAAATACCC
1 TAAAATTACCGAAATACCC
38343852 CTAAAAGGTA
Statistics
Matches: 157, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 156 0.99
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTCAATGGGTAAAATTACCGAAATACCCTCGAAGGG
Found at i:38343753 original size:81 final size:80
Alignment explanation
Indices: 38343617--38343852 Score: 312
Period size: 81 Copynumber: 2.9 Consensus size: 80
38343607 ATAATGGGCC
** * * *
38343617 TAAAATTATCGAAATACCCTTAATGGCTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACCG
1 TAAAATTAT-GAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCG
*
38343682 AAATACCCTC-AATGGG
65 AAATACCCCCGAA-GGG
* * *
38343698 TAAAATTATGAAAATACCCTCGATGGGTAAAATTACCAAAATACCCTCGATGGGTAAAATTACCA
1 TAAAATTATG-AAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCG
38343763 AAATACCCCCGAAGGG
65 AAATACCCCCGAAGGG
* * * *
38343779 TAAAATGACTGAAATACCCTCGATAGGTAAAATTACCGAAATACCCTCGAAGGGTTAAATTATCG
1 TAAAATTA-TGAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCG
38343844 AAATACCCC
65 AAATACCCC
38343853 TAAAAGGTAA
Statistics
Matches: 136, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
80 1 0.01
81 131 0.96
82 4 0.03
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (80 bp):
TAAAATTATGAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCGA
AATACCCCCGAAGGG
Found at i:38343865 original size:27 final size:27
Alignment explanation
Indices: 38343617--38343851 Score: 271
Period size: 27 Copynumber: 8.7 Consensus size: 27
38343607 ATAATGGGCC
* * *
38343617 TAAAATTATCGAAATACCCT-TAATGGC
1 TAAAATTACCGAAATACCCTCGAA-GGG
* *
38343644 TAAAATTATCGAAATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
38343671 TAAAATTACCGAAATACCCTC-AATGGG
1 TAAAATTACCGAAATACCCTCGAA-GGG
* *
38343698 TAAAATTA-TGAAAATACCCTCGATGGG
1 TAAAATTACCG-AAATACCCTCGAAGGG
* *
38343725 TAAAATTACCAAAATACCCTCGATGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
* *
38343752 TAAAATTACCAAAATACCCCCGAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
* *
38343779 TAAAATGACTGAAATACCCTCGATA-GG
1 TAAAATTACCGAAATACCCTCGA-AGGG
38343806 TAAAATTACCGAAATACCCTCGAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
* *
38343833 TTAAATTATCGAAATACCC
1 TAAAATTACCGAAATACCC
38343852 CTAAAAGGTA
Statistics
Matches: 184, Mismatches: 17, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
26 4 0.02
27 176 0.96
28 4 0.02
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCGAAGGG
Found at i:38344071 original size:26 final size:26
Alignment explanation
Indices: 38344042--38344091 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
38344032 TTGCCACATA
38344042 TACTGTTACTAGCAGCCTTGCTGCGT
1 TACTGTTACTAGCAGCCTTGCTGCGT
* *
38344068 TACTGTTACTGGCAGCTTTGCTGC
1 TACTGTTACTAGCAGCCTTGCTGC
38344092 ATCATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.36
Consensus pattern (26 bp):
TACTGTTACTAGCAGCCTTGCTGCGT
Found at i:38346026 original size:22 final size:22
Alignment explanation
Indices: 38345982--38346026 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38345972 CTTAATAAAG
*
38345982 CTAGAAGCTTCCTTGAACTTTC
1 CTAGAAGCTTCCTTGAACGTTC
* *
38346004 CTAGCAGCTTCCTTGAAGGTTC
1 CTAGAAGCTTCCTTGAACGTTC
38346026 C
1 C
38346027 AAGGCCTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (22 bp):
CTAGAAGCTTCCTTGAACGTTC
Found at i:38351295 original size:16 final size:15
Alignment explanation
Indices: 38351268--38351301 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
38351258 ATAATTAGTA
*
38351268 TATAATTATATTTAT
1 TATAATTATATTAAT
38351283 TATAATATATATTAAT
1 TATAAT-TATATTAAT
38351299 TAT
1 TAT
38351302 TATGAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:38354699 original size:45 final size:45
Alignment explanation
Indices: 38354630--38354716 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
38354620 TATTTTTGTG
38354630 ATCACAAGAATAGTTGAGACTAATTTGAATGACATGTATACTGCT
1 ATCACAAGAATAGTTGAGACTAATTTGAATGACATGTATACTGCT
* *
38354675 ATCATAAGAATAGTTGAGACTAATTTGAATGATATGTATACT
1 ATCACAAGAATAGTTGAGACTAATTTGAATGACATGTATACT
38354717 TAAGTAGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.33
Consensus pattern (45 bp):
ATCACAAGAATAGTTGAGACTAATTTGAATGACATGTATACTGCT
Found at i:38356836 original size:12 final size:12
Alignment explanation
Indices: 38356819--38356845 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38356809 TATAGTATCA
38356819 AGTTCTAATATG
1 AGTTCTAATATG
38356831 AGTTCTAATATG
1 AGTTCTAATATG
38356843 AGT
1 AGT
38356846 CTTGAATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (12 bp):
AGTTCTAATATG
Found at i:38358103 original size:13 final size:13
Alignment explanation
Indices: 38358067--38358105 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
38358057 TTTAGTTTTG
*
38358067 TAATTTGAAAGCT
1 TAATTTGAAAACT
38358080 TAAGTTTTGAAAACT
1 TAA--TTTGAAAACT
38358095 TAATTTGAAAA
1 TAATTTGAAAA
38358106 TTTGAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 11 0.48
15 12 0.52
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:38358403 original size:35 final size:35
Alignment explanation
Indices: 38358359--38358500 Score: 169
Period size: 35 Copynumber: 4.1 Consensus size: 35
38358349 TTCACTTGTC
* * *
38358359 TTTTATTGCAGGGAATCTCTCCTGTTCACGTATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
* *
38358394 TTTTGTTGCAGGGAATCTCTCCTATTCACACATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
* * *
38358429 -TTTCTTGCAGGGAATCTCTCCTGTCCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
* * * *
38358463 TGTTGTTGCAGGGAATCTCTCCAGTTCATGTATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
38358498 TTT
1 TTT
38358501 CTTTTTGGAC
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
34 29 0.33
35 59 0.67
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATCA
Found at i:38358442 original size:34 final size:34
Alignment explanation
Indices: 38358364--38358490 Score: 173
Period size: 35 Copynumber: 3.7 Consensus size: 34
38358354 TTGTCTTTTA
*
38358364 TTGCAGGGAATCTCTCCTGTTCACGTATTATTTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTA-TTTG
* * * *
38358399 TTGCAGGGAATCTCTCCTATTCACACATCATTTC
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
*
38358433 TTGCAGGGAATCTCTCCTGTCCACGCATTATGTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTAT-TTG
*
38358468 TTGCAGGGAATCTCTCCAGTTCA
1 TTGCAGGGAATCTCTCCTGTTCA
38358491 TGTATCATTT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 30 0.38
35 49 0.62
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (34 bp):
TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
Found at i:38361330 original size:21 final size:22
Alignment explanation
Indices: 38361300--38361344 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
38361290 GAACAAATTG
38361300 TTGATTCTATTTCTTTCTTG-AT
1 TTGATTCTA-TTCTTTCTTGTAT
*
38361322 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTCTTGTAT
38361343 TT
1 TT
38361345 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCTTTCTTGTAT
Found at i:38365878 original size:29 final size:29
Alignment explanation
Indices: 38365846--38366115 Score: 283
Period size: 29 Copynumber: 9.3 Consensus size: 29
38365836 TGGATAGTTT
*
38365846 CGACCATCGACTATGAAAAGGGATGGTAA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* *
38365875 CGACCATCAACAATGAAAAGGGATGGTGA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* *
38365904 TGACCATCAACTATGAAAAGGGATGGTGA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* * * **
38365933 CGACCATCAAATATGAAAAGGGATAGTTT
1 CGACCATCGACTATGAAAAGGGATGGTGA
* *
38365962 CGACTATCAACTATGAAAAGGGATGGTGA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* * **
38365991 CGATCATCGAATATGAAAAGGGA-GAGTTT
1 CGACCATCGACTATGAAAAGGGATG-GTGA
*
38366020 CGACTATCGACTATGAAAAGGGATGGTGA
1 CGACCATCGACTATGAAAAGGGATGGTGA
* * *
38366049 TGACCATTGATTATGAAAAGGGATGGTTG-
1 CGACCATCGACTATGAAAAGGGATGG-TGA
* * * *
38366078 TGACCATCGAATATTAAAAGGGATGGTTA
1 CGACCATCGACTATGAAAAGGGATGGTGA
*
38366107 TGACCATCG
1 CGACCATCG
38366116 TTTAGCACAC
Statistics
Matches: 203, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
28 2 0.01
29 198 0.98
30 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (29 bp):
CGACCATCGACTATGAAAAGGGATGGTGA
Found at i:38365978 original size:87 final size:87
Alignment explanation
Indices: 38365831--38366115 Score: 326
Period size: 87 Copynumber: 3.3 Consensus size: 87
38365821 ATTAATTAAA
* * * * *
38365831 GAAAATGGATAGTTTCGACCATCGACTATGAAAAGGGATGGTAACGACCATCAACAATGAAAAGG
1 GAAAAGGGATGGTTACGACCATCGACTATGAAAAGGGATGGTATCGACCATCAACTATGAAAAGG
38365896 GATGGTGATGACCATC-AACTAT
66 GATGGTGATGACCATCGAA-TAT
* * * * * *
38365918 GAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGG
1 GAAAAGGGATGGTTACGACCATCGACTATGAAAAGGGATGGTATCGACCATCAACTATGAAAAGG
* *
38365983 GATGGTGACGATCATCGAATAT
66 GATGGTGATGACCATCGAATAT
* * ** *
38366005 GAAAAGGGA-GAGTTTCGACTATCGACTATGAAAAGGGATGGTGAT-GACCATTGATTATGAAAA
1 GAAAAGGGATG-GTTACGACCATCGACTATGAAAAGGGATGGT-ATCGACCATCAACTATGAAAA
38366068 GGGATGGTTG-TGACCATCGAATAT
64 GGGATGG-TGATGACCATCGAATAT
* *
38366092 TAAAAGGGATGGTTATGACCATCG
1 GAAAAGGGATGGTTACGACCATCG
38366116 TTTAGCACAC
Statistics
Matches: 163, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
86 1 0.01
87 156 0.96
88 6 0.04
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (87 bp):
GAAAAGGGATGGTTACGACCATCGACTATGAAAAGGGATGGTATCGACCATCAACTATGAAAAGG
GATGGTGATGACCATCGAATAT
Found at i:38366254 original size:20 final size:20
Alignment explanation
Indices: 38366229--38366267 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
38366219 TTATGAAAGG
38366229 AACGATTTAAGTGATGTTAA
1 AACGATTTAAGTGATGTTAA
38366249 AACGATTTAAGTGATGTTA
1 AACGATTTAAGTGATGTTA
38366268 TGTTTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (20 bp):
AACGATTTAAGTGATGTTAA
Found at i:38369817 original size:20 final size:20
Alignment explanation
Indices: 38369792--38369838 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38369782 AGCTCGTTTC
*
38369792 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
38369812 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
38369832 CAGCTCA
1 CAGCTCA
38369839 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:38371374 original size:13 final size:14
Alignment explanation
Indices: 38371358--38371386 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38371348 AAAAAAAATC
38371358 AAAATTC-AAAAAA
1 AAAATTCGAAAAAA
38371371 AAAATTCGAAAAAA
1 AAAATTCGAAAAAA
38371385 AA
1 AA
38371387 GAAAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAATTCGAAAAAA
Found at i:38371420 original size:13 final size:13
Alignment explanation
Indices: 38371379--38371440 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 13
38371369 AAAAAATTCG
38371379 AAAAAA-AAGAAA
1 AAAAAAGAAGAAA
*
38371391 AAAAGAAGTGAGCAAA
1 AAAA-AAG-AAG-AAA
*
38371407 AAAAAAG-AGTAA
1 AAAAAAGAAGAAA
38371419 AAAAAAGAAG-AA
1 AAAAAAGAAGAAA
38371431 AAAAAAGAAG
1 AAAAAAGAAG
38371441 TGAAAAGTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
12 25 0.58
13 6 0.14
15 5 0.12
16 7 0.16
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (13 bp):
AAAAAAGAAGAAA
Found at i:38371433 original size:26 final size:26
Alignment explanation
Indices: 38371379--38371436 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
38371369 AAAAAATTCG
*
38371379 AAAAAAAAGAAAAAAAGAAGTGAGCAA
1 AAAAAAAAGAAAAAAAGAAGTAAG-AA
*
38371406 AAAAAAAGAGTAAAAAA-AAG-AAGAA
1 AAAAAAA-AGAAAAAAAGAAGTAAGAA
38371431 AAAAAA
1 AAAAAA
38371437 GAAGTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.29
26 2 0.07
27 10 0.36
28 8 0.29
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (26 bp):
AAAAAAAAGAAAAAAAGAAGTAAGAA
Found at i:38372508 original size:15 final size:15
Alignment explanation
Indices: 38372483--38372529 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
38372473 AGAAAAGAAT
38372483 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
38372499 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
38372514 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
38372529 A
1 A
38372530 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:38372563 original size:18 final size:18
Alignment explanation
Indices: 38372542--38372602 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 18
38372532 TTTCAAAAAT
38372542 AAAAGAGAGTGAAAAGAA
1 AAAAGAGAGTGAAAAGAA
* *
38372560 AAAAAAGATTGAAAAAGAA
1 AAAAGAGAGTG-AAAAGAA
38372579 ATTGAAAGAGAGCTTGAAAAGAA
1 A---AAAGAGAG--TGAAAAGAA
38372602 A
1 A
38372603 TCGAGTGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 9 0.27
19 8 0.24
22 6 0.18
23 8 0.24
24 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.23, T:0.11
Consensus pattern (18 bp):
AAAAGAGAGTGAAAAGAA
Found at i:38374489 original size:20 final size:20
Alignment explanation
Indices: 38374464--38374510 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38374454 AGCTTGTTTC
*
38374464 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
38374484 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
38374504 CAGCTCA
1 CAGCTCA
38374511 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:38375901 original size:30 final size:30
Alignment explanation
Indices: 38375862--38376036 Score: 124
Period size: 30 Copynumber: 5.9 Consensus size: 30
38375852 GGATCACATC
*
38375862 ACCATCCCTTTTCATAGTTCAATAGTCG-A
1 ACCATCCCTTTTCATAGTTCGATAGTCGTA
* * * * *
38375891 AGCTATCCCTTATCATAATTCGATGGTCGTC
1 A-CCATCCCTTTTCATAGTTCGATAGTCGTA
* * * *
38375922 ACCATCCCTTTTCATTGTT-TATGGTCGTC
1 ACCATCCCTTTTCATAGTTCGATAGTCGTA
* * * *
38375951 ACCATCCTTTTTCATTGTT-GATGGTCGTT
1 ACCATCCCTTTTCATAGTTCGATAGTCGTA
* * *
38375980 ACCATCCCTTTTCACAATTCGATAGCCG-A
1 ACCATCCCTTTTCATAGTTCGATAGTCGTA
* * *
38376009 AGCTATCCCTTTTCGTATTTCGATAGTC
1 A-CCATCCCTTTTCATAGTTCGATAGTC
38376037 AAAGCTATCC
Statistics
Matches: 116, Mismatches: 26, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
29 52 0.45
30 63 0.54
31 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.39
Consensus pattern (30 bp):
ACCATCCCTTTTCATAGTTCGATAGTCGTA
Found at i:38375948 original size:29 final size:29
Alignment explanation
Indices: 38375912--38375993 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
38375902 ATCATAATTC
38375912 GATGGTCGTCACCATCCCTTTTCATTGTT
1 GATGGTCGTCACCATCCCTTTTCATTGTT
* *
38375941 TATGGTCGTCACCATCCTTTTTCATTGTT
1 GATGGTCGTCACCATCCCTTTTCATTGTT
*
38375970 GATGGTCGTTACCATCCCTTTTCA
1 GATGGTCGTCACCATCCCTTTTCA
38375994 CAATTCGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.43
Consensus pattern (29 bp):
GATGGTCGTCACCATCCCTTTTCATTGTT
Found at i:38376042 original size:30 final size:30
Alignment explanation
Indices: 38375983--38376054 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
38375973 GGTCGTTACC
** *
38375983 ATCCCTTTTCACAATTCGATAGCCGAAGCT
1 ATCCCTTTTCGTAATTCGATAGCCAAAGCT
* *
38376013 ATCCCTTTTCGTATTTCGATAGTCAAAGCT
1 ATCCCTTTTCGTAATTCGATAGCCAAAGCT
38376043 ATCCCTTTTCGT
1 ATCCCTTTTCGT
38376055 TGGTCGACGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCGTAATTCGATAGCCAAAGCT
Found at i:38389979 original size:18 final size:18
Alignment explanation
Indices: 38389956--38389990 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38389946 CAAGAATAGT
38389956 AAGCATAAAAATAGTTTC
1 AAGCATAAAAATAGTTTC
*
38389974 AAGCATGAAAATAGTTT
1 AAGCATAAAAATAGTTT
38389991 GGCACATCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (18 bp):
AAGCATAAAAATAGTTTC
Found at i:38404861 original size:63 final size:63
Alignment explanation
Indices: 38404740--38404897 Score: 226
Period size: 63 Copynumber: 2.5 Consensus size: 63
38404730 TGTCTCTGTG
* * ** *
38404740 GATGCCATGGAGTCTTTCATCAATGGTCTTACAATGATCTGCCACCTTAGCGTACTATCATAT
1 GATGCCATGGAGTCTTTCATCCATGGTCTTACAATAATCCACCACCTTAGCGTACTATCATAC
* * * * *
38404803 GATGTCATGCAGTCTTTCATCCATGGTCTTACAATAATCCACCATCTTGGCGTGCTATCATAC
1 GATGCCATGGAGTCTTTCATCCATGGTCTTACAATAATCCACCACCTTAGCGTACTATCATAC
38404866 GATGCCATGGAGTCTTTCATCCATGGTCTTAC
1 GATGCCATGGAGTCTTTCATCCATGGTCTTAC
38404898 TCATTATACC
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 83 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (63 bp):
GATGCCATGGAGTCTTTCATCCATGGTCTTACAATAATCCACCACCTTAGCGTACTATCATAC
Found at i:38407516 original size:27 final size:27
Alignment explanation
Indices: 38407486--38407601 Score: 121
Period size: 26 Copynumber: 4.4 Consensus size: 27
38407476 GTGGATGATT
38407486 GAAATACCCCCGAAGGGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGACC
** *
38407513 GAAATA-CCCTAAAGGGTAAAATAACC
1 GAAATACCCCCGAAGGGTAAAATGACC
* *
38407539 AAAATACCCTCGAAGGGTAAAATGACC
1 GAAATACCCCCGAAGGGTAAAATGACC
* * *
38407566 AAAATACCCTCGTAA-GG-AAAATGACT
1 GAAATACCCCCG-AAGGGTAAAATGACC
*
38407592 GATATACCCC
1 GAAATACCCC
38407602 TAGGAGTCGG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
26 37 0.49
27 36 0.48
28 2 0.03
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (27 bp):
GAAATACCCCCGAAGGGTAAAATGACC
Found at i:38407599 original size:53 final size:53
Alignment explanation
Indices: 38407480--38407601 Score: 140
Period size: 53 Copynumber: 2.3 Consensus size: 53
38407470 TTGTGGGTGG
* *
38407480 ATGATTGAAATACCCCCGAAGGGTAAAATGACCGAAATACCCTAAAGGGTAAA
1 ATGACTGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCTAAAGGGTAAA
* ** * *
38407533 ATAACCAAAATACCCTCGAAGGGTAAAATGACCAAAATACCCTCGTAA-GG-AAA
1 ATGACTGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCT--AAAGGGTAAA
*
38407586 ATGACTGATATACCCC
1 ATGACTGAAATACCCC
38407602 TAGGAGTCGG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
53 51 0.93
54 2 0.04
55 2 0.04
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.17
Consensus pattern (53 bp):
ATGACTGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCTAAAGGGTAAA
Found at i:38407600 original size:26 final size:27
Alignment explanation
Indices: 38407487--38407590 Score: 142
Period size: 27 Copynumber: 3.9 Consensus size: 27
38407477 TGGATGATTG
* *
38407487 AAATACCCCCGAAGGGTAAAATGACCG
1 AAATACCCTCGAAGGGTAAAATGACCA
* *
38407514 AAATACCCT-AAAGGGTAAAATAACCA
1 AAATACCCTCGAAGGGTAAAATGACCA
38407540 AAATACCCTCGAAGGGTAAAATGACCA
1 AAATACCCTCGAAGGGTAAAATGACCA
38407567 AAATACCCTCGTAA-GG-AAAATGAC
1 AAATACCCTCG-AAGGGTAAAATGAC
38407591 TGATATACCC
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 31 0.45
27 36 0.52
28 2 0.03
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.14
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATGACCA
Found at i:38408743 original size:17 final size:18
Alignment explanation
Indices: 38408716--38408756 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38408706 AACTCTTAAA
*
38408716 GTAGAGAAAACT-GATACT
1 GTAG-GAAAACTAGAAACT
38408734 GTAGGAAAACTAGAAACT
1 GTAGGAAAACTAGAAACT
38408752 GTAGG
1 GTAGG
38408757 GAGACTCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.20
Consensus pattern (18 bp):
GTAGGAAAACTAGAAACT
Found at i:38416023 original size:18 final size:18
Alignment explanation
Indices: 38416000--38416039 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
38415990 AAAGGTAGAT
38416000 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
38416018 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
38416036 AGAA
1 AGAA
38416040 CAAAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:38417831 original size:33 final size:34
Alignment explanation
Indices: 38417794--38417865 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
38417784 GAGTTAGTTT
*
38417794 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
* * *
38417827 ATTAATTTTAGTTCAACTTAAATAAGTGTTGGTA
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
38417861 ATTAA
1 ATTAA
38417866 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
Found at i:38418971 original size:12 final size:12
Alignment explanation
Indices: 38418954--38418978 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38418944 CCTTATACAC
38418954 ATTACACATTGA
1 ATTACACATTGA
38418966 ATTACACATTGA
1 ATTACACATTGA
38418978 A
1 A
38418979 ATCAGATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:38421115 original size:27 final size:27
Alignment explanation
Indices: 38420978--38421131 Score: 150
Period size: 27 Copynumber: 5.7 Consensus size: 27
38420968 TCGTGGGCGG
*
38420978 ATGACTGAAATACCCTCGAAA-GGTAAA
1 ATGACTGAAATACCC-CTAAAGGGTAAA
* ** * * *
38421005 ATAACCAAAATACCCTTGAAGCGTAAA
1 ATGACTGAAATACCCCTAAAGGGTAAA
* *
38421032 ATAACTAAAATACCCCTAAAGGGTAAA
1 ATGACTGAAATACCCCTAAAGGGTAAA
*
38421059 ATGACTTAAATACCCCTAAAGGGTAAA
1 ATGACTGAAATACCCCTAAAGGGTAAA
**
38421086 ATGA-TCGAAATACCCCTGTAGGGTAAA
1 ATGACT-GAAATACCCCTAAAGGGTAAA
* *
38421113 ATGACTGATATACACCTAA
1 ATGACTGAAATACCCCTAA
38421132 GAGTCGGAAT
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
26 3 0.03
27 100 0.96
28 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (27 bp):
ATGACTGAAATACCCCTAAAGGGTAAA
Found at i:38421131 original size:81 final size:81
Alignment explanation
Indices: 38420978--38421131 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 81
38420968 TCGTGGGCGG
*
38420978 ATGACTGAAATACCCTCGAAAGGTAAAATAACCAAAATACCCTTGAAGCGTAAAATAACTAAAAT
1 ATGACTGAAATACCCTCGAAAGGTAAAATAACCAAAATACCCCTGAAGCGTAAAATAACTAAAAT
*
38421043 ACCCCTAAAGGGTAAA
66 ACACCTAAAGGGTAAA
* * * * * * * * * *
38421059 ATGACTTAAATACCC-CTAAAGGGTAAAATGATCGAAATACCCCTGTAGGGTAAAATGACTGATA
1 ATGACTGAAATACCCTCGAAA-GGTAAAATAACCAAAATACCCCTGAAGCGTAAAATAACTAAAA
38421123 TACACCTAA
65 TACACCTAA
38421132 GAGTCGGAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
80 4 0.07
81 56 0.93
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (81 bp):
ATGACTGAAATACCCTCGAAAGGTAAAATAACCAAAATACCCCTGAAGCGTAAAATAACTAAAAT
ACACCTAAAGGGTAAA
Found at i:38424357 original size:27 final size:27
Alignment explanation
Indices: 38424126--38424378 Score: 273
Period size: 27 Copynumber: 9.4 Consensus size: 27
38424116 CTAATAGATG
* *
38424126 AAAATGACTGAAATACACCTATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
38424153 AAAATGACTGAAATACCCCTATAAGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
38424180 AAAATGACT-AAAGTACCCTCATAGGGT
1 AAAATGACTGAAA-TACCCCCATAGGGT
**
38424207 AAAATGACTGAAATACCCAAATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
38424234 AAAATAACTGAAATACCCTCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
38424261 AAAATGATTGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * *
38424288 AACATGA-TCGAAATACCCCCATAAGAT
1 AAAATGACT-GAAATACCCCCATAGGGT
*
38424315 AAAATGA-TCAAAATACCCCCATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
* **
38424342 AAAATGATTGTTATA-CCCC-TAGGAGAT
1 AAAATGACTGAAATACCCCCATAGG-G-T
38424369 AAAATGACTG
1 AAAATGACTG
38424379 TTATGGCCTT
Statistics
Matches: 196, Mismatches: 24, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
25 4 0.02
26 9 0.05
27 179 0.91
28 4 0.02
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (27 bp):
AAAATGACTGAAATACCCCCATAGGGT
Found at i:38424619 original size:26 final size:26
Alignment explanation
Indices: 38424583--38424663 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
38424573 TTTGCCACAT
*
38424583 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* *
38424609 ATACTGATACTGACAGCTCTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
38424635 ATGCT-ATTACTGGCAGCTTTGCTGCG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
38424661 ATA
1 ATA
38424664 TTGGTGTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 46 0.98
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:38424814 original size:28 final size:28
Alignment explanation
Indices: 38424765--38424915 Score: 182
Period size: 28 Copynumber: 5.4 Consensus size: 28
38424755 TATTGCACTG
*
38424765 CACTGTTATTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* * *
38424793 CAGTGATT-CTGTATTGGACTAAGCCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
** * *
38424821 TGCTGTTACTGTATTAGACTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
38424849 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
*
38424877 CACTGTTACTGTATTGGGCTAAGGACCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
38424905 CACTG-TACTGT
1 CACTGTTACTGT
38424916 CACTGAATAG
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.10
28 91 0.87
29 4 0.04
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:38424856 original size:56 final size:56
Alignment explanation
Indices: 38424765--38424909 Score: 209
Period size: 56 Copynumber: 2.6 Consensus size: 56
38424755 TATTGCACTG
* *
38424765 CACTGTTATTGTATTGGGCTAAGGCCCACAGTGATTCTGTATTGGACTAAGCCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGACTAAGCCCCA
** * * * *
38424821 TGCTGTTACTGTATTAGACTAAGGCCCACACTGATTCTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGACTAAGCCCCA
*
38424877 CACTGTTACTGTATTGGGCTAAGGACCACACTG
1 CACTGTTACTGTATTGGGCTAAGGCCCACACTG
38424910 TACTGTCACT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 76 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (56 bp):
CACTGTTACTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGACTAAGCCCCA
Found at i:38424947 original size:61 final size:56
Alignment explanation
Indices: 38424765--38424947 Score: 150
Period size: 56 Copynumber: 3.2 Consensus size: 56
38424755 TATTGCACTG
* * * * * * * * *
38424765 CACTGTTATTGTATTGGGCTAAGGCCCACAGTGATTCTGTATTGGACTAAGCCCCA
1 CACTGTTACTGTATTAGACTAAGGACCACACTGATTCTGAATAGGGCTAAGGCCCA
** * * *
38424821 TGCTGTTACTGTATTAGACTAAGGCCCACACTGATTCTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTAGACTAAGGACCACACTGATTCTGAATAGGGCTAAGGCCCA
* * *
38424877 CACTGTTACTGTATTGGGCTAAGGACCACACTGTACTGTCACTGAATAGGGCTTAGGCCCA
1 CACTGTTACTGTATTAGACTAAGGACCACACTG-A-T-T--CTGAATAGGGCTAAGGCCCA
**
38424938 GTCTGTTACT
1 CACTGTTACT
38424948 ACATGTTGTT
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
56 76 0.73
57 1 0.01
58 1 0.01
59 1 0.01
61 25 0.24
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (56 bp):
CACTGTTACTGTATTAGACTAAGGACCACACTGATTCTGAATAGGGCTAAGGCCCA
Found at i:38431576 original size:16 final size:16
Alignment explanation
Indices: 38431555--38431611 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
38431545 TCCTATAGTA
38431555 TCACAATTTATAGTTT
1 TCACAATTTATAGTTT
*
38431571 TCACAATTCTATTG-TT
1 TCACAATT-TATAGTTT
*
38431587 TCA-AAGTCTATAGTTT
1 TCACAA-TTTATAGTTT
38431603 TCAC-ATTTA
1 TCACAATTTA
38431612 AACAACACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
15 9 0.27
16 20 0.61
17 4 0.12
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (16 bp):
TCACAATTTATAGTTT
Found at i:38431602 original size:15 final size:16
Alignment explanation
Indices: 38431547--38431607 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
38431537 CTATAGTCTC
*
38431547 CTATAGTATCACAA-T
1 CTATAGTTTCACAAGT
* *
38431562 TTATAGTTTTCACAATT
1 CTATAG-TTTCACAAGT
*
38431579 CTATTGTTTCA-AAGT
1 CTATAGTTTCACAAGT
38431594 CTATAGTTTTCACA
1 CTATAG-TTTCACA
38431608 TTTAAACAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
15 13 0.36
16 17 0.47
17 6 0.17
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.44
Consensus pattern (16 bp):
CTATAGTTTCACAAGT
Found at i:38433073 original size:20 final size:20
Alignment explanation
Indices: 38433050--38433091 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
38433040 CATAAATTAA
* *
38433050 TTAATTAAATAAAATTTTAT
1 TTAAGTAAATAAAATTATAT
38433070 TTAAGTAAATAAAATTATAT
1 TTAAGTAAATAAAATTATAT
38433090 TT
1 TT
38433092 CACTTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAGTAAATAAAATTATAT
Found at i:38441340 original size:17 final size:16
Alignment explanation
Indices: 38441314--38441345 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
38441304 TGATAGATCT
38441314 CCGACGAGCTTCCAAA
1 CCGACGAGCTTCCAAA
38441330 CCGATCGAGCTTCCAA
1 CCGA-CGAGCTTCCAA
38441346 TAATCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.38, G:0.19, T:0.16
Consensus pattern (16 bp):
CCGACGAGCTTCCAAA
Found at i:38449358 original size:43 final size:43
Alignment explanation
Indices: 38449308--38449394 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
38449298 CCATAAGTTA
*
38449308 ACCTATACATGTCATTATAACCTTGATTACGACATCAAAATCT
1 ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
38449351 ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
1 ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
38449394 A
1 A
38449395 AAAATATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (43 bp):
ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
Found at i:38450742 original size:138 final size:138
Alignment explanation
Indices: 38450491--38450749 Score: 335
Period size: 138 Copynumber: 1.9 Consensus size: 138
38450481 AGGCCTACTC
* *
38450491 ACACAAGCTGACGGTTAAAATGTAAGCTACATGATGCTGCTCACACAAGCTGATAAATATCTGTG
1 ACACAAGCTGACGGTTAAAATGAAAGCTACATGATGCTGCTCACACAAGCTGATAAATATCTGTA
** * **
38450556 ACTAAAGCCGAACTGCAGCCATCAGTAGGACATTCAGGACCAGTACCCGAAACATGGTAACTTGG
66 ACTAAAGAAGAACTGCAGCCATCAGTAGAACATTCAGGACCAAAACCCGAAACATGGTAACTTGG
38450621 GTCTGCTT
131 GTCTGCTT
* * * * *
38450629 ACACAAGCTGACGGTTAGAATGAAAGTTACATGATGCTGCTCATACAAGCTGATGAGTAT-TCGT
1 ACACAAGCTGACGGTTAAAATGAAAGCTACATGATGCTGCTCACACAAGCTGATAAATATCT-GT
* * *
38450693 AAC-AAATGTAAGACCT-CAGCCATCGGTAGAACATTCAGGACCAAAACCCGCAACATG
65 AACTAAA-G-AAGAACTGCAGCCATCAGTAGAACATTCAGGACCAAAACCCGAAACATG
38450750 AAAGCCCTAA
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
137 4 0.04
138 95 0.92
139 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (138 bp):
ACACAAGCTGACGGTTAAAATGAAAGCTACATGATGCTGCTCACACAAGCTGATAAATATCTGTA
ACTAAAGAAGAACTGCAGCCATCAGTAGAACATTCAGGACCAAAACCCGAAACATGGTAACTTGG
GTCTGCTT
Found at i:38451969 original size:20 final size:20
Alignment explanation
Indices: 38451944--38451988 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
38451934 TAAATACACA
38451944 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
38451964 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
38451984 TAATT
1 TAATT
38451989 CGGTTAGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:38451994 original size:20 final size:19
Alignment explanation
Indices: 38451954--38451998 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
38451944 TAATTAAAAC
38451954 TAGACACAATTAATTAAGT
1 TAGACACAATTAATTAAGT
**
38451973 TAAGACACAATTAATTCGGT
1 T-AGACACAATTAATTAAGT
38451993 TAGACA
1 TAGACA
38451999 AGACATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (19 bp):
TAGACACAATTAATTAAGT
Found at i:38456433 original size:19 final size:19
Alignment explanation
Indices: 38456411--38456513 Score: 75
Period size: 19 Copynumber: 5.3 Consensus size: 19
38456401 CACTTACATG
*
38456411 CCCCTGTCGTACTTCGGTA
1 CCCCTGTCGTACTTCAGTA
* * *
38456430 CCCCTGATTGCACTT-ACGTG
1 CCCCTG-TCGTACTTCA-GTA
* *
38456450 CTCCTATCGTACTTCAGTA
1 CCCCTGTCGTACTTCAGTA
*
38456469 CCCCTGATCGTACTT-ACGTG
1 CCCCTG-TCGTACTTCA-GTA
* *
38456489 TCCCTGTCGTACTTTAGTA
1 CCCCTGTCGTACTTCAGTA
38456508 CCCCTG
1 CCCCTG
38456514 GTTGCGCTTA
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
19 34 0.54
20 29 0.46
ACGTcount: A:0.15, C:0.35, G:0.17, T:0.33
Consensus pattern (19 bp):
CCCCTGTCGTACTTCAGTA
Found at i:38456460 original size:39 final size:39
Alignment explanation
Indices: 38456393--38456528 Score: 166
Period size: 39 Copynumber: 3.5 Consensus size: 39
38456383 TAATTATACT
* * *
38456393 CCTGATCGCACTTACATGCCCCTGTCGTACTTCGGTACC
1 CCTGATCGCACTTACGTGCTCCTGTCGTACTTCAGTACC
* *
38456432 CCTGATTGCACTTACGTGCTCCTATCGTACTTCAGTACC
1 CCTGATCGCACTTACGTGCTCCTGTCGTACTTCAGTACC
* *
38456471 CCTGATCGTACTTACGTG-TCCCTGTCGTACTTTAGTACC
1 CCTGATCGCACTTACGTGCT-CCTGTCGTACTTCAGTACC
* * *
38456510 CCTGGTTGCGCTTACGTGC
1 CCTGATCGCACTTACGTGC
38456529 CCCAGTTGTA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
38 1 0.01
39 81 0.99
ACGTcount: A:0.15, C:0.34, G:0.19, T:0.32
Consensus pattern (39 bp):
CCTGATCGCACTTACGTGCTCCTGTCGTACTTCAGTACC
Found at i:38460465 original size:20 final size:20
Alignment explanation
Indices: 38460422--38460478 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
38460412 GATGCATAAC
*
38460422 AGGGGCACCAAAGTGCAAAC
1 AGGGGCACCAAAGTGCAAAA
** *
38460442 AGGGGCACTGAAGTTCAAAA
1 AGGGGCACCAAAGTGCAAAA
*
38460462 AGGGTCA-CAAACGTGCA
1 AGGGGCACCAAA-GTGCA
38460479 TTCAAGGGTA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.39, C:0.21, G:0.30, T:0.11
Consensus pattern (20 bp):
AGGGGCACCAAAGTGCAAAA
Found at i:38468103 original size:14 final size:14
Alignment explanation
Indices: 38468084--38468130 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
38468074 AAATGCAAAG
38468084 TATGAAGTGAAATA
1 TATGAAGTGAAATA
* * *
38468098 TATGAAATG-AGTT
1 TATGAAGTGAAATA
*
38468111 TATGAAGTGAAATG
1 TATGAAGTGAAATA
38468125 TATGAA
1 TATGAA
38468131 ATGAGTTTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (14 bp):
TATGAAGTGAAATA
Found at i:38468115 original size:27 final size:27
Alignment explanation
Indices: 38468084--38468139 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
38468074 AAATGCAAAG
38468084 TATGAAGTGAAATATATGAAATGAGTT
1 TATGAAGTGAAATATATGAAATGAGTT
*
38468111 TATGAAGTGAAATGTATGAAATGAGTT
1 TATGAAGTGAAATATATGAAATGAGTT
38468138 TA
1 TA
38468140 GCAACAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (27 bp):
TATGAAGTGAAATATATGAAATGAGTT
Found at i:38469646 original size:20 final size:20
Alignment explanation
Indices: 38469621--38469672 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
38469611 AATCAAGTGC
*
38469621 AAATGATTTTAACCATGTCA
1 AAATGATTTTAACCAAGTCA
* *
38469641 AAATGATTTCAATCAAGTCA
1 AAATGATTTTAACCAAGTCA
*
38469661 AAATCATTTTAA
1 AAATGATTTTAA
38469673 AATAATTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (20 bp):
AAATGATTTTAACCAAGTCA
Found at i:38472731 original size:54 final size:53
Alignment explanation
Indices: 38472649--38472788 Score: 156
Period size: 54 Copynumber: 2.6 Consensus size: 53
38472639 AAATATTGTT
* * * **
38472649 AAATGACTGAATTACCCCCAGAGGGTAAAATGATCGAATTACCCCCGA-AGGGTA
1 AAATGACCGAAATA-CCCCAAAGGGTAAAATGATAAAATT-CCCCCGATAGGGTA
* *
38472703 AAATGACCGAAATACCCCTAAAGGGTAAAATGATAAAATTGCCCCTATAGGGTA
1 AAATGACCGAAATACCCC-AAAGGGTAAAATGATAAAATTCCCCCGATAGGGTA
* *
38472757 AAATGACCGTAATAACCCCATAGGGTAAAATG
1 AAATGACCGAAAT-ACCCCAAAGGGTAAAATG
38472789 TCTGAAATAC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
53 9 0.12
54 60 0.81
55 5 0.07
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (53 bp):
AAATGACCGAAATACCCCAAAGGGTAAAATGATAAAATTCCCCCGATAGGGTA
Found at i:38472797 original size:27 final size:28
Alignment explanation
Indices: 38472649--38472797 Score: 121
Period size: 27 Copynumber: 5.5 Consensus size: 28
38472639 AAATATTGTT
* * *
38472649 AAATGACTG-AATTACCCCCAGAGGGTA
1 AAATGACTGAAATAACCCCTATAGGGTA
* * *
38472676 AAATGA-TCGAATTACCCCCGA-AGGGTA
1 AAATGACT-GAAATAACCCCTATAGGGTA
* *
38472703 AAATGACCGAAAT-ACCCCTAAAGGGTA
1 AAATGACTGAAATAACCCCTATAGGGTA
* **
38472730 AAATGA-TAAAATTGCCCCTATAGGGTA
1 AAATGACTGAAATAACCCCTATAGGGTA
* *
38472757 AAATGACCGTAATAACCCC-ATAGGGTA
1 AAATGACTGAAATAACCCCTATAGGGTA
*
38472784 AAATGTCTGAAATA
1 AAATGACTGAAATA
38472798 CATGTGTAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
26 10 0.10
27 72 0.75
28 14 0.15
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (28 bp):
AAATGACTGAAATAACCCCTATAGGGTA
Found at i:38472871 original size:24 final size:23
Alignment explanation
Indices: 38472838--38472920 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 23
38472828 CTCGTGGGTA
* * *
38472838 AATGATTGATTTGTCCGTGATGT
1 AATGACTGATTTGTCTGTGATTT
*
38472861 ATATGACTGATTTGTCTTTGATTT
1 A-ATGACTGATTTGTCTGTGATTT
38472885 AAATGACTGATTTGTCTGTGATTT
1 -AATGACTGATTTGTCTGTGATTT
38472909 GAATGACTGATT
1 -AATGACTGATT
38472921 CTGAGCATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.02
24 50 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (23 bp):
AATGACTGATTTGTCTGTGATTT
Found at i:38473106 original size:32 final size:32
Alignment explanation
Indices: 38473065--38473267 Score: 291
Period size: 32 Copynumber: 6.4 Consensus size: 32
38473055 CCTTCGATGC
38473065 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
38473097 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
38473129 TACTGATGGCTTTGTGCCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* **
38473161 TATTGATGGCTTTGTGCAAATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * *
38473193 TACTGATGGCTGTGTACCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
38473225 TACTGATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
38473256 TACTTATGGCTT
1 TACTGATGGCTT
38473268 GTAGCCATTC
Statistics
Matches: 153, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
31 11 0.07
32 142 0.93
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:38473313 original size:29 final size:29
Alignment explanation
Indices: 38473258--38473313 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
38473248 TATTACTGTA
* * *
38473258 CTTATGGCTTGTAGCCATTCTGCTTATAG
1 CTTATAGCTTATAGCCATCCTGCTTATAG
* *
38473287 CTTATAGCTTATAGCTATCCTGTTTAT
1 CTTATAGCTTATAGCCATCCTGCTTAT
38473314 GGCTCTTAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.45
Consensus pattern (29 bp):
CTTATAGCTTATAGCCATCCTGCTTATAG
Found at i:38473980 original size:16 final size:17
Alignment explanation
Indices: 38473948--38473980 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
38473938 TTTCAAGAAG
38473948 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
38473966 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
38473981 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:38477842 original size:25 final size:27
Alignment explanation
Indices: 38477814--38477893 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
38477804 ACAATCATAC
*
38477814 ATAACATA-GAGCAT-GCAGTCATTTT
1 ATAACATAGGAGCATAACAGTCATTTT
*
38477839 ATAACATAGGGGCATAACAGTCATTTT
1 ATAACATAGGAGCATAACAGTCATTTT
*
38477866 ACT-ACGTGAGG-GCATAACAGTCATTTT
1 A-TAACAT-AGGAGCATAACAGTCATTTT
38477893 A
1 A
38477894 CATCAGTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.17
26 5 0.10
27 31 0.65
28 4 0.08
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (27 bp):
ATAACATAGGAGCATAACAGTCATTTT
Found at i:38477864 original size:27 final size:27
Alignment explanation
Indices: 38477829--38477894 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
38477819 ATAGAGCATG
38477829 CAGTCATTTTA-TAACAT-AGGGGCATAA
1 CAGTCATTTTACT-ACATGA-GGGCATAA
*
38477856 CAGTCATTTTACTACGTGAGGGCATAA
1 CAGTCATTTTACTACATGAGGGCATAA
38477883 CAGTCATTTTAC
1 CAGTCATTTTAC
38477895 ATCAGTTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 34 0.94
28 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (27 bp):
CAGTCATTTTACTACATGAGGGCATAA
Found at i:38481594 original size:20 final size:19
Alignment explanation
Indices: 38481566--38481616 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
38481556 AATCAAGTGC
*
38481566 AAATGATTTTAACCATGTCA
1 AAATAATTTTAACCA-GTCA
* *
38481586 AAATAATTTCAATCAGTCA
1 AAATAATTTTAACCAGTCA
*
38481605 AAATCATTTTAA
1 AAATAATTTTAA
38481617 AATGATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (19 bp):
AAATAATTTTAACCAGTCA
Found at i:38482926 original size:14 final size:15
Alignment explanation
Indices: 38482890--38482928 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
38482880 TCAATCTTTG
*
38482890 CACATAATCATGCAT
1 CACAAAATCATGCAT
38482905 CAACAAAATCATGC-T
1 C-ACAAAATCATGCAT
38482920 CACAAAATC
1 CACAAAATC
38482929 TTTTTATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 3 0.14
16 11 0.50
ACGTcount: A:0.46, C:0.28, G:0.05, T:0.21
Consensus pattern (15 bp):
CACAAAATCATGCAT
Found at i:38487828 original size:42 final size:42
Alignment explanation
Indices: 38487760--38487872 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
38487750 ACAGCCGTGG
* * * *
38487760 CACACGCCCGTGTGCCAGGCCGTGTAACTCTCGAAA-CTGGCC
1 CACACGCCCGTGTGCTAGGCCATGTAACTCTCAAAATC-AGCC
*
38487802 CACATGCCCGTGTGCTAGGCCATGTAACTCTCAAAATCAGCC
1 CACACGCCCGTGTGCTAGGCCATGTAACTCTCAAAATCAGCC
*
38487844 CACACGCCCGTGTGCTAGGCTATGTAACT
1 CACACGCCCGTGTGCTAGGCCATGTAACT
38487873 AACTGACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 62 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.20
Consensus pattern (42 bp):
CACACGCCCGTGTGCTAGGCCATGTAACTCTCAAAATCAGCC
Found at i:38490418 original size:24 final size:25
Alignment explanation
Indices: 38490376--38490422 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
38490366 CAAAATTTCT
38490376 TAACGAAACTTTAATACAACCTTAC
1 TAACGAAACTTTAATACAACCTTAC
38490401 TAACGAAAC-TTAATACAACCTT
1 TAACGAAACTTTAATACAACCTT
38490423 CATAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.28
Consensus pattern (25 bp):
TAACGAAACTTTAATACAACCTTAC
Found at i:38499315 original size:61 final size:61
Alignment explanation
Indices: 38499227--38499344 Score: 218
Period size: 61 Copynumber: 1.9 Consensus size: 61
38499217 ACATACGGCC
* *
38499227 TGGCGACATAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGTGTTACGGGT
1 TGGCGACACAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGAGTTACGGGT
38499288 TGGCGACACAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGAGTTAC
1 TGGCGACACAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGAGTTAC
38499345 ATGTCCCTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (61 bp):
TGGCGACACAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGAGTTACGGGT
Found at i:38507563 original size:24 final size:24
Alignment explanation
Indices: 38507531--38507578 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
38507521 CTAGATGATT
38507531 TGTTTGACCAATTGAAGGGAACCA
1 TGTTTGACCAATTGAAGGGAACCA
38507555 TGTTTGACCAATTGAAGGGAACCA
1 TGTTTGACCAATTGAAGGGAACCA
38507579 CTGTGTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (24 bp):
TGTTTGACCAATTGAAGGGAACCA
Found at i:38509506 original size:41 final size:42
Alignment explanation
Indices: 38509485--38509622 Score: 156
Period size: 41 Copynumber: 3.2 Consensus size: 42
38509475 ATCCAATATA
38509485 CATTT-CAATACCACAATAATTC-ATTTAATTCAAATCATAG
1 CATTTGCAATACCACAATAATTCAATTTAATTCAAATCATAG
*
38509525 CATTTGCAATACCACAATAATTCATTTAATTCATTTAATTCAAATCATAT
1 CATTTGCAATACCACAATAATTC-----A---ATTTAATTCAAATCATAG
* *
38509575 CTTTTGCAATACCACAATAATTC-ATTTAATTCAAATCATAT
1 CATTTGCAATACCACAATAATTCAATTTAATTCAAATCATAG
38509616 CATTTGC
1 CATTTGC
38509623 TAATTCACGT
Statistics
Matches: 85, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
40 5 0.06
41 41 0.48
50 39 0.46
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (42 bp):
CATTTGCAATACCACAATAATTCAATTTAATTCAAATCATAG
Found at i:38509510 original size:21 final size:21
Alignment explanation
Indices: 38509485--38509551 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
38509475 ATCCAATATA
38509485 CATTTCAATACCACAATAATT
1 CATTTCAATACCACAATAATT
* * *
38509506 CATTT-AAT-TCA-AATCATAG
1 CATTTCAATACCACAATAAT-T
38509525 CATTTGCAATACCACAATAATT
1 CATTT-CAATACCACAATAATT
38509547 CATTT
1 CATTT
38509552 AATTCATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
18 5 0.14
19 7 0.20
20 3 0.09
21 8 0.23
22 7 0.20
23 5 0.14
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (21 bp):
CATTTCAATACCACAATAATT
Found at i:38509555 original size:50 final size:50
Alignment explanation
Indices: 38509501--38509607 Score: 196
Period size: 50 Copynumber: 2.1 Consensus size: 50
38509491 AATACCACAA
38509501 TAATTCATTTAATTCAAATCATAGCATTTGCAATACCACAATAATTCATT
1 TAATTCATTTAATTCAAATCATAGCATTTGCAATACCACAATAATTCATT
* *
38509551 TAATTCATTTAATTCAAATCATATCTTTTGCAATACCACAATAATTCATT
1 TAATTCATTTAATTCAAATCATAGCATTTGCAATACCACAATAATTCATT
38509601 TAATTCA
1 TAATTCA
38509608 AATCATATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (50 bp):
TAATTCATTTAATTCAAATCATAGCATTTGCAATACCACAATAATTCATT
Found at i:38509556 original size:9 final size:9
Alignment explanation
Indices: 38509542--38509566 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
38509532 AATACCACAA
38509542 TAATTCATT
1 TAATTCATT
38509551 TAATTCATT
1 TAATTCATT
38509560 TAATTCA
1 TAATTCA
38509567 AATCATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (9 bp):
TAATTCATT
Found at i:38509628 original size:22 final size:22
Alignment explanation
Indices: 38509560--38509629 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
38509550 TTAATTCATT
*
38509560 TAATTCAAATCATATCTTTTGC
1 TAATTCAAATCATATCATTTGC
* *
38509582 -AATACCACAATAAT-TCA-TT--
1 TAAT-TCA-AATCATATCATTTGC
38509601 TAATTCAAATCATATCATTTGC
1 TAATTCAAATCATATCATTTGC
38509623 TAATTCA
1 TAATTCA
38509630 CGTACAATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
18 5 0.14
19 5 0.14
20 5 0.14
21 5 0.14
22 11 0.31
23 5 0.14
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.40
Consensus pattern (22 bp):
TAATTCAAATCATATCATTTGC
Found at i:38511180 original size:45 final size:45
Alignment explanation
Indices: 38511116--38511204 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
38511106 AACAGATACT
* * *
38511116 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
* *
38511161 CGGTGGAATCAACACATAGCAACCACTTTGCTAATCAATGATGT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
38511205 TCAGTTCACA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:38511322 original size:51 final size:50
Alignment explanation
Indices: 38511211--38511402 Score: 233
Period size: 51 Copynumber: 3.8 Consensus size: 50
38511201 ATGTTCAGTT
* * * **
38511211 CACATAGTAGCCTGCACATAGGTTCTACACATGTGACCATTACCATTCAATA
1 CACATAGTAGCCTGCACATA-GTACTACACATGTGACCA-TACTATCCGGTA
* * *
38511263 CACGTAGTAGCCTGCACATAGTACTACACATGTGATCGAAACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATACTATCCGGTA
* * *
38511314 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATA-TTTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACC-ATACTATCCGGTA
*
38511364 CACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
38511403 CACTTTCACT
Statistics
Matches: 121, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
49 2 0.02
50 43 0.36
51 55 0.45
52 21 0.17
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATACTATCCGGTA
Found at i:38511380 original size:101 final size:102
Alignment explanation
Indices: 38511213--38511398 Score: 279
Period size: 101 Copynumber: 1.8 Consensus size: 102
38511203 GTTCAGTTCA
* *
38511213 CATAGTAGCCTGCACATAGGTTCTACACATGTGACCATTACCATTCAATACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGGTACTACACATGCGACCATTA-CATTCAATACACGTAGTAGCCTGC
38511278 ACATAGTACTACACATGTGATCGAAACTATCCGGTACG
65 ACATAGTACTACACATGTGATCGAAACTATCCGGTACG
* **
38511316 CATAGTAGCCTGCACATA-GTACTACACATGCGACC-TATA-TTTCCGGTACACGTAGTAGCCTG
1 CATAGTAGCCTGCACATAGGTACTACACATGCGACCAT-TACATT-CAATACACGTAGTAGCCTG
38511378 CACATAGTACTACACATGTGA
64 CACATAGTACTACACATGTGA
38511399 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
100 2 0.03
101 39 0.51
102 17 0.22
103 18 0.24
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGGTACTACACATGCGACCATTACATTCAATACACGTAGTAGCCTGCA
CATAGTACTACACATGTGATCGAAACTATCCGGTACG
Found at i:38513044 original size:18 final size:17
Alignment explanation
Indices: 38513018--38513052 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38513008 TTGAAAATCA
38513018 GGCCAAATTTGTCAAAGT
1 GGCCAAATTTGT-AAAGT
*
38513036 GGCCCAATTTGTAAAGT
1 GGCCAAATTTGTAAAGT
38513053 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (17 bp):
GGCCAAATTTGTAAAGT
Found at i:38515330 original size:50 final size:50
Alignment explanation
Indices: 38515223--38515376 Score: 191
Period size: 50 Copynumber: 3.0 Consensus size: 50
38515213 GGGGACGAGA
* **
38515223 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGATGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGG---TACCGA-G--ATGAGAGG
38515279 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
* * * *
38515329 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGA
38515377 ACTCCCATGT
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
50 52 0.57
52 1 0.01
53 4 0.04
56 34 0.37
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
Found at i:38515400 original size:50 final size:50
Alignment explanation
Indices: 38515279--38515407 Score: 141
Period size: 50 Copynumber: 2.6 Consensus size: 50
38515269 TTATGAGAGG
* * * * **
38515279 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
1 TCCCACGTAAGAACATATCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * * *
38515329 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTAAGAACATATCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * *
38515379 TCCCATGTACGAACATATCTGGGATATGG
1 TCCCACGTAAGAACATATCTGGGACATGG
38515408 TATTTGCAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
TCCCACGTAAGAACATATCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:38515690 original size:20 final size:20
Alignment explanation
Indices: 38515665--38515703 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
38515655 TGAGTTATTT
38515665 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
38515685 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
38515704 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:38518972 original size:18 final size:18
Alignment explanation
Indices: 38518949--38518988 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
38518939 AAAGGAAGAC
38518949 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
38518967 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
38518985 AGAA
1 AGAA
38518989 CAAAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:38520792 original size:33 final size:34
Alignment explanation
Indices: 38520755--38520826 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
38520745 GAGTTAGTTT
*
38520755 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTCAGTA
* *
38520788 ATTAATTTTAGTTCAGCTTAAATAAGTGTCAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTCAGTA
38520822 ATTAA
1 ATTAA
38520827 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTCAGTA
Found at i:38535225 original size:18 final size:18
Alignment explanation
Indices: 38535198--38535249 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 18
38535188 CTATCGAATC
38535198 AAAA-TTGTAATTACAAA
1 AAAACTTGTAATTACAAA
38535215 AAAACTTGTAATTAATACAAA
1 AAAACTTGTAA-T--TACAAA
*
38535236 GAAACTTGTAATTA
1 AAAACTTGTAATTA
38535250 ATATATATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.13
18 8 0.27
19 1 0.03
20 1 0.03
21 16 0.53
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (18 bp):
AAAACTTGTAATTACAAA
Found at i:38535235 original size:21 final size:21
Alignment explanation
Indices: 38535209--38535252 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
38535199 AAATTGTAAT
38535209 TACAAAAAAACTTGTAATTAA
1 TACAAAAAAACTTGTAATTAA
*
38535230 TACAAAGAAACTTGTAATTAA
1 TACAAAAAAACTTGTAATTAA
38535251 TA
1 TA
38535253 TATATTCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.30
Consensus pattern (21 bp):
TACAAAAAAACTTGTAATTAA
Found at i:38535558 original size:13 final size:13
Alignment explanation
Indices: 38535540--38535566 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38535530 CATAAAAAGT
38535540 AAACTTTTACAAA
1 AAACTTTTACAAA
38535553 AAACTTTTACAAA
1 AAACTTTTACAAA
38535566 A
1 A
38535567 GTTTTTCAGA
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:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
AAACTTTTACAAA
Found at i:38536836 original size:28 final size:28
Alignment explanation
Indices: 38536775--38536841 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
38536765 CCTATTCCGT
*
38536775 AACAGT-ACAGTGTGGGCCTTAGCCCAA
1 AACAGTAACAATGTGGGCCTTAGCCCAA
*
38536802 TACAGTAACAATGTGGGCCTTAGCCCAA
1 AACAGTAACAATGTGGGCCTTAGCCCAA
* *
38536830 AATAGTATCAAT
1 AACAGTAACAAT
38536842 ATCGTGCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (28 bp):
AACAGTAACAATGTGGGCCTTAGCCCAA
Found at i:38536966 original size:23 final size:24
Alignment explanation
Indices: 38536940--38536990 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
38536930 GCCAACACAC
38536940 AATATCGTAGCAAAGCTGCCAGTA
1 AATATCGTAGCAAAGCTGCCAGTA
*
38536964 ATAGTATTGTAGCAAAGCTGCCAGTA
1 A-A-TATCGTAGCAAAGCTGCCAGTA
38536990 A
1 A
38536991 TAGTAAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 1 0.04
25 1 0.04
26 22 0.92
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (24 bp):
AATATCGTAGCAAAGCTGCCAGTA
Done.