Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 35
Found at i:1775754 original size:16 final size:16
Alignment explanation
Indices: 1775728--1775761 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1775718 AGATCCAATC
1775728 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
1775743 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
1775760 AA
1 AA
1775762 AAAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:1775772 original size:16 final size:16
Alignment explanation
Indices: 1775753--1775812 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
1775743 AAGAAGCAAA
1775753 AAAGCAAAAAAAAAAC
1 AAAGCAAAAAAAAAAC
1775769 AAAG-AAAAAAGAGAAAC
1 AAAGCAAAAAA-A-AAAC
* *
1775786 AAGAACAAAAGGAAAAA-
1 AA-AGCAAAA-AAAAAAC
1775803 AAAGCAAAAA
1 AAAGCAAAAA
1775813 TCAAAAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
17 8 0.23
18 4 0.11
19 5 0.14
20 1 0.03
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAGCAAAAAAAAAAC
Found at i:1776487 original size:22 final size:22
Alignment explanation
Indices: 1776462--1776510 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1776452 CCATCAATCT
* *
1776462 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
1776484 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
1776506 TTTGA
1 TTTGA
1776511 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:1776944 original size:18 final size:18
Alignment explanation
Indices: 1776921--1776956 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1776911 TCAACATCAA
* *
1776921 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
1776939 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
1776957 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:1777451 original size:36 final size:36
Alignment explanation
Indices: 1777394--1777609 Score: 166
Period size: 36 Copynumber: 6.2 Consensus size: 36
1777384 GTTTTTCTTA
*
1777394 AAACAAGA-TTTGTCTCGCTTGAGACAGTTTCCCTTG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
1777430 AAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * *
1777466 AAACAAA------ATAT-TTGA-ATATGTTTTCTTTG
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCCCTTG
** * **
1777495 AAACAAATTCCGTCTC-CCTGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
1777530 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1777567 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTG
1777603 AAACAAA
1 AAACAAA
1777610 ACCTTTGAAT
Statistics
Matches: 140, Mismatches: 26, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
28 2 0.01
29 18 0.13
30 2 0.01
35 21 0.15
36 75 0.54
37 22 0.16
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1778449 original size:105 final size:105
Alignment explanation
Indices: 1778271--1779096 Score: 1266
Period size: 105 Copynumber: 7.9 Consensus size: 105
1778261 GAGGCAACAT
* * * *
1778271 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGTCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCAA
*
1778336 TTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGC
65 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* *
1778377 AAGTTCAACTTCACGACGAAGGGACCGCTACCTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
* *
1778442 TTCAACTTCACAATGAAGGATATTGGACTTCAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* *
1778482 AAGTTCAACTTCATGACGAAGGGACAGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
1778547 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
*
1778587 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCATAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
*
1778652 TTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* *
1778692 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
*
1778757 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* * *
1778797 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
1778862 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* * **
1778902 AAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAATAA-AA-TT-TC-A-TTCAGATTCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
* **
1778962 TTCAACTTCACAACGAAGGATATTGGACTCGAGACAACAT
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* * * * * ** * *
1779002 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAACCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCAA
* *
1779067 TTTCAACTTCACGACGGAGGATATTGGACT
65 TTTCAACTTCACAACGAAGGATATTGGACT
1779097 TGGAACAATG
Statistics
Matches: 666, Mismatches: 48, Indels: 12
0.92 0.07 0.02
Matches are distributed among these distances:
100 79 0.12
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 504 0.76
106 70 0.11
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
AAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAAT
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
Found at i:1779688 original size:34 final size:36
Alignment explanation
Indices: 1779644--1779745 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1779634 TTTCGTCCTA
1779644 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
1779679 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1779714 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1779746 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:1780343 original size:16 final size:18
Alignment explanation
Indices: 1780322--1780356 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1780312 TTTACTCATT
1780322 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
1780338 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
1780356 T
1 T
1780357 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:1781909 original size:22 final size:22
Alignment explanation
Indices: 1781881--1781925 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1781871 AAAATACGGT
*
1781881 ATGAACAGTACAATGAACAGTG
1 ATGAACAATACAATGAACAGTG
**
1781903 ATGAACAATACTGTGAACAGTG
1 ATGAACAATACAATGAACAGTG
1781925 A
1 A
1781926 AATATTTCGA
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:0.44, C:0.13, G:0.22, T:0.20
Consensus pattern (22 bp):
ATGAACAATACAATGAACAGTG
Found at i:1785455 original size:25 final size:25
Alignment explanation
Indices: 1785417--1785464 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1785407 AACAATAATA
1785417 AACAATAACATGCTACAGTACCGTG
1 AACAATAACATGCTACAGTACCGTG
* *
1785442 AACAGTAACCTGCTACAGTACCG
1 AACAATAACATGCTACAGTACCG
1785465 ATTACACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.19
Consensus pattern (25 bp):
AACAATAACATGCTACAGTACCGTG
Found at i:1785519 original size:22 final size:22
Alignment explanation
Indices: 1785494--1785537 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1785484 TTGCAAATAA
1785494 GGAACCGATTCCCCTGCTACAG
1 GGAACCGATTCCCCTGCTACAG
1785516 GGAACCGATTCCCCTGCTACAG
1 GGAACCGATTCCCCTGCTACAG
1785538 TACTTCGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.18
Consensus pattern (22 bp):
GGAACCGATTCCCCTGCTACAG
Found at i:1786123 original size:22 final size:22
Alignment explanation
Indices: 1786095--1786138 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1786085 ACTGAATATT
1786095 TATCCCGAAGGACCACTGTATA
1 TATCCCGAAGGACCACTGTATA
1786117 TATCCCGAAGGACCACTGTATA
1 TATCCCGAAGGACCACTGTATA
1786139 ACCCTCTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (22 bp):
TATCCCGAAGGACCACTGTATA
Found at i:1791907 original size:6 final size:6
Alignment explanation
Indices: 1790549--1791904 Score: 2554
Period size: 6 Copynumber: 225.7 Consensus size: 6
1790539 TAATAAAATG
* * * * * * *
1790549 CATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
* * * *
1790597 TATACA TATACA TATACA TATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1790645 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1790693 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1790741 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1790789 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1790837 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1790885 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1790933 CATACA CATACA CATACA CATACA CATACA CATACACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CAT--ACA CATACA CATACA
1790983 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791031 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791079 CATACA CATACA CATACA CATACA CATACA C--ACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791125 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791173 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CAT--ACA
1791223 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791271 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791319 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791367 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791415 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791463 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791511 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791559 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791607 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791655 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791703 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791751 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791799 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1791847 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
*
1791895 CATATA CATA
1 CATACA CATA
1791905 TACCATCATC
Statistics
Matches: 1341, Mismatches: 3, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.00
6 1325 0.99
8 12 0.01
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
CATACA
Found at i:1792285 original size:23 final size:23
Alignment explanation
Indices: 1792255--1792298 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1792245 AATACATATA
1792255 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
* *
1792278 TGTCCCGAATGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
1792299 CCCTCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:1793651 original size:21 final size:21
Alignment explanation
Indices: 1793627--1793666 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1793617 TTTTCAAAGG
1793627 CATGCACCGATGCATCAATAT
1 CATGCACCGATGCATCAATAT
* *
1793648 CATGCATCGATGCGTCAAT
1 CATGCACCGATGCATCAAT
1793667 GAATAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAT
Found at i:1793716 original size:19 final size:19
Alignment explanation
Indices: 1793692--1793730 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1793682 TCGAATGCAT
1793692 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1793711 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1793730 T
1 T
1793731 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1793754 original size:64 final size:65
Alignment explanation
Indices: 1793672--1793856 Score: 202
Period size: 64 Copynumber: 2.9 Consensus size: 65
1793662 TCAATGAATA
* * *
1793672 AATTGAAACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTC-TG-ATT
1 AATTAAAACATCGAATGCATT-CATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGCATT
1793735 T
65 T
* **
1793736 AATTAAAACATCGAATGCATTTGATGCATCGATGCACAATCCATGCATCGATGCAC-CAGGCTAT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGC-AT
1793800 TT
64 TT
* * *
1793802 --TTCAAACATCGAATGCACTTCATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCTCCA-TGCATCGATGCACT
1793857 AGGAGTCCAA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
63 2 0.02
64 94 0.92
65 2 0.02
66 4 0.04
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AATTAAAACATCGAATGCATTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGCATTT
Found at i:1793836 original size:17 final size:19
Alignment explanation
Indices: 1793808--1793856 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1793798 ATTTTTCAAA
1793808 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
1793826 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
1793845 CACCGATGCACT
1 CATCGATGCACT
1793857 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:1796038 original size:33 final size:38
Alignment explanation
Indices: 1795977--1796058 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 38
1795967 TATATAAATA
1795977 TTTTCATAAAAGCATATAATTGAAGAATTAT-A-T-AT
1 TTTTCATAAAAGCATATAATTGAAGAATTATAAGTGAT
* *
1796012 TTTTCATAAATG-ATA-ATTTGAAGAATTATGAAGTGAT
1 TTTTCATAAAAGCATATAATTGAAGAATTAT-AAGTGAT
1796049 TTTTCATAAA
1 TTTTCATAAA
1796059 GAATAACATG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 13 0.32
34 3 0.07
35 12 0.29
36 1 0.02
37 12 0.29
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (38 bp):
TTTTCATAAAAGCATATAATTGAAGAATTATAAGTGAT
Found at i:1801622 original size:18 final size:18
Alignment explanation
Indices: 1801599--1801633 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1801589 ACATGTTGAC
1801599 TGAGA-TATGATAGTCATT
1 TGAGATTATGATA-TCATT
1801617 TGAGATTATGATATCAT
1 TGAGATTATGATATCAT
1801634 ATTTTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (18 bp):
TGAGATTATGATATCATT
Found at i:1802067 original size:33 final size:33
Alignment explanation
Indices: 1802030--1802099 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
1802020 ATGTTCAACT
1802030 AAATATTTAATTACATGTCAATTGTACTCATTA
1 AAATATTTAATTACATGTCAATTGTACTCATTA
1802063 AAATATTTAATTACATGTCAATTGTACTCATTA
1 AAATATTTAATTACATGTCAATTGTACTCATTA
1802096 AAAT
1 AAAT
1802100 CAAATACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (33 bp):
AAATATTTAATTACATGTCAATTGTACTCATTA
Found at i:1802682 original size:21 final size:21
Alignment explanation
Indices: 1802641--1802700 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1802631 ATATAGAATT
* *
1802641 TGTCCCAAAAGACCA-TATATA
1 TGTCCCGAAGGACCACT-TATA
1802662 TGTCCCGAAGGACCACTTATA
1 TGTCCCGAAGGACCACTTATA
* *
1802683 CGTCTCGAAGGACCACTT
1 TGTCCCGAAGGACCACTT
1802701 CTTAAGGATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTTATA
Found at i:1802796 original size:21 final size:21
Alignment explanation
Indices: 1802704--1802797 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 21
1802694 ACCACTTCTT
*
1802704 AAGGATCACATATATATTCC-
1 AAGGATCACATATATATCCCG
* * * *
1802724 AATGGACCAAATATGTGTCCCG
1 AA-GGATCACATATATATCCCG
* * *
1802746 AAGAATCGCATATAT-T-CCA
1 AAGGATCACATATATATCCCG
*
1802765 AAGGATTACATATATATCCCG
1 AAGGATCACATATATATCCCG
*
1802786 AAGGACCACATA
1 AAGGATCACATA
1802798 GAACCCTCGA
Statistics
Matches: 53, Mismatches: 17, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
19 14 0.26
20 4 0.08
21 33 0.62
22 2 0.04
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.24
Consensus pattern (21 bp):
AAGGATCACATATATATCCCG
Found at i:1803577 original size:19 final size:20
Alignment explanation
Indices: 1803527--1803578 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
1803517 TCTTACTATA
*
1803527 GTACCGATACTGCCCTCTTATG
1 GTACCGATAC--CCCCCTTATG
* *
1803549 GTATCAATACCCCCCTTA-G
1 GTACCGATACCCCCCTTATG
1803568 GTACCGATACC
1 GTACCGATACC
1803579 ATTTTGACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 10 0.40
20 7 0.28
22 8 0.32
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (20 bp):
GTACCGATACCCCCCTTATG
Found at i:1808199 original size:60 final size:60
Alignment explanation
Indices: 1808103--1808262 Score: 173
Period size: 60 Copynumber: 2.7 Consensus size: 60
1808093 AGTATGATTG
* **
1808103 TCATTTT-AATTGGTCC-CTAAACTTTTAAATGTTTCAATTCCATCCCTAAACTATGAC-T
1 TCATTTTAAATTGGTCCTC-AAACTTTTGAACATTTCAATTCCATCCCTAAACTATGACAT
* ** * *
1808161 ATCATTTTAAATTAGTCCTCAAACTTTTGAACATTTCAATTTTATCCTTAAACTATGTCAT
1 -TCATTTTAAATTGGTCCTCAAACTTTTGAACATTTCAATTCCATCCCTAAACTATGACAT
* * *
1808222 TCATTCTAAATTGGTTCTCAAACTTTTTGAACATTCCAATT
1 TCATTTTAAATTGGTCCTCAAAC-TTTTGAACATTTCAATT
1808263 TAATCCCAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
59 7 0.08
60 60 0.71
61 18 0.21
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (60 bp):
TCATTTTAAATTGGTCCTCAAACTTTTGAACATTTCAATTCCATCCCTAAACTATGACAT
Found at i:1808520 original size:60 final size:60
Alignment explanation
Indices: 1808443--1808558 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
1808433 TTGGGACCAA
* * *
1808443 TTTAGAATGAGGATCATAGTTTAGGGA-TGAAAGTAGAATATTCAAAAGTTTAAGGATTAG
1 TTTAGAATGAGGATCATAATTCAGGGATTG-AAGTAAAATATTCAAAAGTTTAAGGATTAG
* * *
1808503 TTTAGAATTA-GAGTCATAATTCGGGGATTGAATTAAAATATTCAAAAGTTTAAGGA
1 TTTAGAATGAGGA-TCATAATTCAGGGATTGAAGTAAAATATTCAAAAGTTTAAGGA
1808559 CCGAAGCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 44 0.92
61 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (60 bp):
TTTAGAATGAGGATCATAATTCAGGGATTGAAGTAAAATATTCAAAAGTTTAAGGATTAG
Found at i:1809066 original size:18 final size:18
Alignment explanation
Indices: 1809045--1809086 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1809035 GTTTTTTTCC
*
1809045 TTTGTTATTTT-TTATTGT
1 TTTGTTATTTTATT-GTGT
1809063 TTTGTTATTTTATTGTGT
1 TTTGTTATTTTATTGTGT
1809081 TTTGTT
1 TTTGTT
1809087 CATAGTGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.10, C:0.00, G:0.14, T:0.76
Consensus pattern (18 bp):
TTTGTTATTTTATTGTGT
Found at i:1813088 original size:13 final size:14
Alignment explanation
Indices: 1813065--1813094 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1813055 TTCCCATTAC
1813065 AGACGTGCATATGA
1 AGACGTGCATATGA
1813079 AGAC-TGCATATGA
1 AGACGTGCATATGA
1813092 AGA
1 AGA
1813095 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:1831057 original size:2 final size:2
Alignment explanation
Indices: 1831050--1831079 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1831040 ATGAATGAAG
*
1831050 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1831080 GCCTAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1840628 original size:2 final size:2
Alignment explanation
Indices: 1840621--1840675 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1840611 GTCTTTTAAA
1840621 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1840663 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
1840676 TATATATATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1840893 original size:24 final size:24
Alignment explanation
Indices: 1840866--1840964 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
1840856 TATATCAACA
* * *
1840866 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* * *
1840890 ATCATATCAGAATCCATGCCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
*
1840914 ATCATATCAGAATCCAGGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* *
1840938 ATCAAATCAGAATCCATGTCAGGT
1 ATCAAATCAGAATCCAGGTCAAGT
1840962 ATC
1 ATC
1840965 GTAACCGAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (24 bp):
ATCAAATCAGAATCCAGGTCAAGT
Found at i:1844220 original size:23 final size:22
Alignment explanation
Indices: 1844176--1844220 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1844166 AATGTTAGGG
*
1844176 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
1844198 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1844221 AAGTTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1845803 original size:23 final size:23
Alignment explanation
Indices: 1845777--1845835 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1845767 TGGCACTACG
1845777 GTGCAATTCTACGCAGCACTCCA
1 GTGCAATTCTACGCAGCACTCCA
** * *
1845800 GTGCAATTCTACGTGGCACTTCG
1 GTGCAATTCTACGCAGCACTCCA
*
1845823 GTGCAATTATACG
1 GTGCAATTCTACG
1845836 AGCTGTGGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (23 bp):
GTGCAATTCTACGCAGCACTCCA
Found at i:1847315 original size:19 final size:19
Alignment explanation
Indices: 1847273--1847321 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1847263 TGTAAACTTT
1847273 GGTCAAAGTCAATAGGTAA
1 GGTCAAAGTCAATAGGTAA
* *
1847292 CGTCAAAGTCAAT-GGATCA
1 GGTCAAAGTCAATAGG-TAA
1847311 GGTCAAAGTCA
1 GGTCAAAGTCA
1847322 TGGGTCAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (19 bp):
GGTCAAAGTCAATAGGTAA
Found at i:1847374 original size:20 final size:20
Alignment explanation
Indices: 1847338--1847390 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1847328 AGACCGGTAA
* *
1847338 GGGTTGACTCAGATCGATTC
1 GGGTTGACTCGGATCGATCC
*
1847358 GGGTTGACTCGGTTCGATCC
1 GGGTTGACTCGGATCGATCC
**
1847378 AAGTTGACTCGGA
1 GGGTTGACTCGGA
1847391 CCGGTTCTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (20 bp):
GGGTTGACTCGGATCGATCC
Found at i:1847897 original size:19 final size:19
Alignment explanation
Indices: 1847855--1847903 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1847845 TGTAAACTTT
1847855 GGTCAAAGTCAATAGGTAA
1 GGTCAAAGTCAATAGGTAA
* *
1847874 TGTCAAAGTCAAT-GGATCA
1 GGTCAAAGTCAATAGG-TAA
1847893 GGTCAAAGTCA
1 GGTCAAAGTCA
1847904 TGGGTCAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (19 bp):
GGTCAAAGTCAATAGGTAA
Found at i:1848102 original size:582 final size:582
Alignment explanation
Indices: 1846998--1848165 Score: 2086
Period size: 582 Copynumber: 2.0 Consensus size: 582
1846988 GAACCGGGTC
1846998 AAGCAGACGAATAGTCAGAAGATCCACGAGTACCTGAAATATACAATAACTTTAATTAGTCATCG
1 AAGCAGACGAATAGTCAGAAGATCCACGAGTACCTGAAATATACAATAACTTTAATTAGTCATCG
1847063 ATCCTTCAGAAAAATTTGATGAATTGAAATAAATACTTAATTTAAAAATGCACATTCGGGTTTAA
66 ATCCTTCAGAAAAATTTGATGAATTGAAATAAATACTTAATTTAAAAATGCACATTCGGGTTTAA
** *
1847128 CGGTCAATTCGAAGGCTTTCGGGTTCGAATTTGGCAAAACGAACTTCAGATTCGGACTTAGGACG
131 CGGTCAATTCGAAGGCTTTCGGGTTCGAATTTGGCAAAACGAACTTCAGATTCAAACCTAGGACG
* *
1847193 TCAAAAAACATAAAATATGACTTTTCGAAAAATTTAACTTTTTGGGTCAAAGTCAATGATCAAAG
196 TCAAAAAACATAAAATATGACTTTTCGAAAAATTTAACTTTTTAGGTCAAAGTCAACGATCAAAG
1847258 TCAACTGTAAACTTTGGTCAAAGTCAATAGGTAACGTCAAAGTCAATGGATCAGGTCAAAGTCAT
261 TCAACTGTAAACTTTGGTCAAAGTCAATAGGTAACGTCAAAGTCAATGGATCAGGTCAAAGTCAT
1847323 GGGTCAGACCGGTAAGGGTTGACTCAGATCGATTCGGGTTGACTCGGTTCGATCCAAGTTGACTC
326 GGGTCAGACCGGTAAGGGTTGACTCAGATCGATTCGGGTTGACTCGGTTCGATCCAAGTTGACTC
*
1847388 GGACCGGTTCTAGAAGGCTCCAAAGCTATGGACGAGCCCCATACGCACTTGGAGACGATTGGTGG
391 AGACCGGTTCTAGAAGGCTCCAAAGCTATGGACGAGCCCCATACGCACTTGGAGACGATTGGTGG
1847453 CATATGAACGGGCAAAAAGGGGTTTAGTCGGCGACCGATTACTACCAAGCTCACCTAACAACACC
456 CATATGAACGGGCAAAAAGGGGTTTAGTCGGCGACCGATTACTACCAAGCTCACCTAACAACACC
*
1847518 AAATAATCCAATCCAATTCAAATCAAGCCAAAACCACGGTAAATTTAACCGTAAAACGTACG
521 AAATAATCCAATCCAATTCAAATCAAGCCAAAACCACGATAAATTTAACCGTAAAACGTACG
* *
1847580 AAGCAGACGAATAGTCAGGAGATCCACGAGTACCTGAAATATACAATAACTTTAATTAGTCATTG
1 AAGCAGACGAATAGTCAGAAGATCCACGAGTACCTGAAATATACAATAACTTTAATTAGTCATCG
1847645 ATCCTTCAGAAAAATTTGATGAATTGAAATAAATACTTAATTTAAAAATGCACATTCGGGTTTAA
66 ATCCTTCAGAAAAATTTGATGAATTGAAATAAATACTTAATTTAAAAATGCACATTCGGGTTTAA
* *
1847710 CGGTCAATTC-AGAGGCTTTCGGGTTCGAATTTGGCAAAATGAACTTCATATTCAAACCTAGGAC
131 CGGTCAATTCGA-AGGCTTTCGGGTTCGAATTTGGCAAAACGAACTTCAGATTCAAACCTAGGAC
* *
1847774 GTCGAAAAACATAAAATATGACTTTTCGAAAAATTTAACTTTTTATGTCAAAGTCAACGATCAAA
195 GTCAAAAAACATAAAATATGACTTTTCGAAAAATTTAACTTTTTAGGTCAAAGTCAACGATCAAA
*
1847839 GTCAACTGTAAACTTTGGTCAAAGTCAATAGGTAATGTCAAAGTCAATGGATCAGGTCAAAGTCA
260 GTCAACTGTAAACTTTGGTCAAAGTCAATAGGTAACGTCAAAGTCAATGGATCAGGTCAAAGTCA
* * *
1847904 TGGGTCAGACCGGTTAGGGTTGACTTAGATCGATTCGGGTTGACTCGGTTTGATCCAAGTTGACT
325 TGGGTCAGACCGGTAAGGGTTGACTCAGATCGATTCGGGTTGACTCGGTTCGATCCAAGTTGACT
* * *
1847969 CAGATCGGTTCTAGAAGGCTCCAAAGCTATGGACGAGCCCCATACGCACTTGGCGATGATTGGTG
390 CAGACCGGTTCTAGAAGGCTCCAAAGCTATGGACGAGCCCCATACGCACTTGGAGACGATTGGTG
* * * * * *
1848034 GCATGTGAATGGGTAAAAAGGGGTTTATTCGGTGACCTATTACTACCAAGCTCACCTAACAACAC
455 GCATATGAACGGGCAAAAAGGGGTTTAGTCGGCGACCGATTACTACCAAGCTCACCTAACAACAC
1848099 CAAATAATCCAATCCAATTCAAATCAAGCCAAAACCACGATAAATTTAACCGTAAAACGTACG
520 CAAATAATCCAATCCAATTCAAATCAAGCCAAAACCACGATAAATTTAACCGTAAAACGTACG
1848162 AAGC
1 AAGC
1848166 TTACCCTCAA
Statistics
Matches: 559, Mismatches: 26, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
581 1 0.00
582 558 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (582 bp):
AAGCAGACGAATAGTCAGAAGATCCACGAGTACCTGAAATATACAATAACTTTAATTAGTCATCG
ATCCTTCAGAAAAATTTGATGAATTGAAATAAATACTTAATTTAAAAATGCACATTCGGGTTTAA
CGGTCAATTCGAAGGCTTTCGGGTTCGAATTTGGCAAAACGAACTTCAGATTCAAACCTAGGACG
TCAAAAAACATAAAATATGACTTTTCGAAAAATTTAACTTTTTAGGTCAAAGTCAACGATCAAAG
TCAACTGTAAACTTTGGTCAAAGTCAATAGGTAACGTCAAAGTCAATGGATCAGGTCAAAGTCAT
GGGTCAGACCGGTAAGGGTTGACTCAGATCGATTCGGGTTGACTCGGTTCGATCCAAGTTGACTC
AGACCGGTTCTAGAAGGCTCCAAAGCTATGGACGAGCCCCATACGCACTTGGAGACGATTGGTGG
CATATGAACGGGCAAAAAGGGGTTTAGTCGGCGACCGATTACTACCAAGCTCACCTAACAACACC
AAATAATCCAATCCAATTCAAATCAAGCCAAAACCACGATAAATTTAACCGTAAAACGTACG
Found at i:1850310 original size:27 final size:27
Alignment explanation
Indices: 1850256--1850313 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1850246 TTTGGATGAT
* *
1850256 AAATTATGAGAATACTCTGATTTGGTA
1 AAATTATGAAAATACCCTGATTTGGTA
*
1850283 AAATTATGAAAATACCCTTATGTT-GTA
1 AAATTATGAAAATACCCTGAT-TTGGTA
1850310 AAAT
1 AAAT
1850314 GACAAGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (27 bp):
AAATTATGAAAATACCCTGATTTGGTA
Found at i:1852432 original size:31 final size:32
Alignment explanation
Indices: 1852388--1852460 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
1852378 TGTGACTCTT
* *
1852388 AGGTAGGCTCTGCGGCCCTGAGAT-CATTCTC
1 AGGTAGGCCCTGCGGCCCTAAGATGCATTCTC
* **
1852419 GGGTAGGCCCTGCGGCCCTAAGATGTGTTCTC
1 AGGTAGGCCCTGCGGCCCTAAGATGCATTCTC
1852451 AGGTAGGCCC
1 AGGTAGGCCC
1852461 CGTGGCCCCG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.15, C:0.29, G:0.33, T:0.23
Consensus pattern (32 bp):
AGGTAGGCCCTGCGGCCCTAAGATGCATTCTC
Found at i:1857071 original size:3 final size:3
Alignment explanation
Indices: 1857065--1857107 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
1857055 CTTTTTTTTA
*
1857065 TAT TAT T-T AAT T-T TAT TAAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA
1857108 AATTATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 29 0.83
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1857083 original size:9 final size:10
Alignment explanation
Indices: 1857065--1857119 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
1857055 CTTTTTTTTA
1857065 TATTATTTAAT
1 TATTA-TTAAT
1857076 T-TTATTAAT
1 TATTATTAAT
1857085 TATTATT-AT
1 TATTATTAAT
1857094 TATTATT-AT
1 TATTATTAAT
1857103 TATTA--AAT
1 TATTATTAAT
1857111 TATATATTA
1 TAT-TATTA
1857120 CAAATTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 5 0.13
9 24 0.62
10 8 0.21
11 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTAAT
Found at i:1857265 original size:25 final size:25
Alignment explanation
Indices: 1857236--1857360 Score: 216
Period size: 25 Copynumber: 5.0 Consensus size: 25
1857226 GAACCAACCC
1857236 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1857261 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1857286 ATCA-ATTTAGGGTTTCAAACCCTAA
1 ATCAGA-TTAGGGTTTCAAACCCTAA
*
1857311 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
1857336 ATCAGACTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1857361 TCCCCTAACT
Statistics
Matches: 95, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
24 1 0.01
25 94 0.99
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1871018 original size:24 final size:24
Alignment explanation
Indices: 1870993--1871044 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1870983 AAAAAAAAAA
*
1870993 AAAAAAG-GAAAATGAAAAA-ATG
1 AAAAAAGAAAAAATGAAAAAGATG
1871015 AAAAAATGAAAAAATGAAAAAGATG
1 AAAAAA-GAAAAAATGAAAAAGATG
1871040 AAAAA
1 AAAAA
1871045 TAAATAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 6 0.23
23 1 0.04
24 11 0.42
25 8 0.31
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (24 bp):
AAAAAAGAAAAAATGAAAAAGATG
Found at i:1871019 original size:9 final size:8
Alignment explanation
Indices: 1871001--1871044 Score: 79
Period size: 8 Copynumber: 5.4 Consensus size: 8
1870991 AAAAAAAAGG
1871001 AAAATGAA
1 AAAATGAA
1871009 AAAATGAA
1 AAAATGAA
1871017 AAAATGAA
1 AAAATGAA
1871025 AAAATGAA
1 AAAATGAA
1871033 AAAGATGAA
1 AAA-ATGAA
1871042 AAA
1 AAA
1871045 TAAATAAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 27 0.77
9 8 0.23
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
AAAATGAA
Found at i:1872215 original size:141 final size:133
Alignment explanation
Indices: 1871995--1872295 Score: 343
Period size: 141 Copynumber: 2.2 Consensus size: 133
1871985 CAACATCAAC
* *
1871995 TGACCAGATCTCCTCATCACATAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
1 TGACCAGAT-TCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGACGTCCTCATCACGT
* * ** *
1872060 AGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCAT
65 AGGAACCGAATTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCA-
1872125 CTACCCT
129 -T-CCCT
* * * * **
1872132 TAGACGACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAATCGGATTTCCTCAT
1 T----GACCAGA-TTCCTCATCACGTAGGAG-AGTGTCAACATTAGGATAACCAGACGTCCTCAT
* * * *
1872196 CACGTAGGAACCGAATTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCGT
60 CACGTAGGAACCGAATTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCAT
1872261 GTCATCCCT
125 GTCATCCCT
1872270 TGACCAGATTTCCTCATCACGTAGGA
1 TGACCAGA-TTCCTCATCACGTAGGA
1872296 ACCGAGTTAT
Statistics
Matches: 140, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
134 24 0.17
137 1 0.01
138 5 0.04
139 1 0.01
141 97 0.69
142 12 0.09
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.26
Consensus pattern (133 bp):
TGACCAGATTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGACGTCCTCATCACGTA
GGAACCGAATTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
CCT
Found at i:1872287 original size:40 final size:40
Alignment explanation
Indices: 1872230--1872400 Score: 128
Period size: 40 Copynumber: 4.0 Consensus size: 40
1872220 TTCTTAAAGA
** * *
1872230 TGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATCCCT
1 TGACCAGATTTCTTCATCACGTAGGAGCCGTGTCATCCCT
* * * *
1872270 TGACCAGATTTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTT
1 TGACCAGATTTCTTCATCACGTAGGAGCC--G-TGTCATCC--C-T
** * *
1872316 AAAGATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATCCCT
1 -----TGACCAGATTTCTTCATCACGTAGGAGCCGTGTCATCCCT
1872361 TGACCAGATTTCTTCATCACGTAGGAGCCGTGTCA-CCCT
1 TGACCAGATTTCTTCATCACGTAGGAGCCGTGTCATCCCT
1872400 T
1 T
1872401 AGACGACCAG
Statistics
Matches: 100, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
39 5 0.05
40 54 0.54
42 1 0.01
43 6 0.06
45 2 0.02
46 2 0.02
48 6 0.06
49 1 0.01
51 23 0.23
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (40 bp):
TGACCAGATTTCTTCATCACGTAGGAGCCGTGTCATCCCT
Found at i:1872298 original size:91 final size:91
Alignment explanation
Indices: 1872185--1872386 Score: 386
Period size: 91 Copynumber: 2.2 Consensus size: 91
1872175 TAGATAATCG
1872185 GATTTCCTCATCACGTAGGAACCGAATTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGC
1 GATTTCCTCATCACGTAGGAACCGAATTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGC
1872250 GTATGAGCCGTGTCATCCCTTGACCA
66 GTATGAGCCGTGTCATCCCTTGACCA
*
1872276 GATTTCCTCATCACGTAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGC
1 GATTTCCTCATCACGTAGGAACCGAATTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGC
1872341 GTATGAGCCGTGTCATCCCTTGACCA
66 GTATGAGCCGTGTCATCCCTTGACCA
*
1872367 GATTTCTTCATCACGTAGGA
1 GATTTCCTCATCACGTAGGA
1872387 GCCGTGTCAC
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 109 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (91 bp):
GATTTCCTCATCACGTAGGAACCGAATTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGC
GTATGAGCCGTGTCATCCCTTGACCA
Found at i:1872437 original size:43 final size:39
Alignment explanation
Indices: 1872321--1872442 Score: 111
Period size: 40 Copynumber: 3.0 Consensus size: 39
1872311 TTCTTAAAGA
*
1872321 TGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATCCCT
1 TGACCAG-ACTTTTCATCGCGTATGAGCCGTGTCATCCCT
* * *
1872361 TGACCAGATTTCTTCATCACGTAGGAGCCGTGTCA-CCCT
1 TGACCAGACTT-TTCATCGCGTATGAGCCGTGTCATCCCT
* * *
1872400 TAGACGACCAGACCTTTTCATTGCGTATGAGCAGTGTCGTCCC
1 T----GACCAGA-CTTTTCATCGCGTATGAGCCGTGTCATCCC
1872443 CAACAACCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
39 7 0.11
40 28 0.43
43 25 0.38
44 5 0.08
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.28
Consensus pattern (39 bp):
TGACCAGACTTTTCATCGCGTATGAGCCGTGTCATCCCT
Found at i:1872602 original size:3 final size:3
Alignment explanation
Indices: 1872596--1872638 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
1872586 CTTTTTTTTA
*
1872596 TAT TAT T-T AAT T-T TAT TAAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA
1872639 AATTATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 29 0.83
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1872614 original size:9 final size:10
Alignment explanation
Indices: 1872596--1872650 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
1872586 CTTTTTTTTA
1872596 TATTATTTAAT
1 TATTA-TTAAT
1872607 T-TTATTAAT
1 TATTATTAAT
1872616 TATTATT-AT
1 TATTATTAAT
1872625 TATTATT-AT
1 TATTATTAAT
1872634 TATTA--AAT
1 TATTATTAAT
1872642 TATATATTA
1 TAT-TATTA
1872651 CAAATTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 5 0.13
9 24 0.62
10 8 0.21
11 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTAAT
Found at i:1872796 original size:25 final size:25
Alignment explanation
Indices: 1872767--1872891 Score: 223
Period size: 25 Copynumber: 5.0 Consensus size: 25
1872757 GAACCAACCC
1872767 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1872792 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
1872817 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
1872842 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
1872867 ATCAGACTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1872892 TCCCCTAACT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 97 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1881794 original size:16 final size:18
Alignment explanation
Indices: 1881773--1881805 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1881763 CAGTACAGGA
1881773 TCCGAA-CAAA-AAACTG
1 TCCGAATCAAACAAACTG
1881789 TCCGAATCAAACAAACT
1 TCCGAATCAAACAAACT
1881806 AATCAACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.48, C:0.27, G:0.09, T:0.15
Consensus pattern (18 bp):
TCCGAATCAAACAAACTG
Found at i:1886169 original size:22 final size:23
Alignment explanation
Indices: 1886136--1886184 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1886126 ATAAGGTAAT
* *
1886136 ATTT-TTTCAAAGACTTTCAATC
1 ATTTGTTTCAAAGACTCTCAACC
1886158 ATTTGTTT-AAAGACTCTCAACC
1 ATTTGTTTCAAAGACTCTCAACC
1886180 ATTTG
1 ATTTG
1886185 ACATTGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (23 bp):
ATTTGTTTCAAAGACTCTCAACC
Found at i:1891904 original size:136 final size:134
Alignment explanation
Indices: 1891673--1892047 Score: 439
Period size: 136 Copynumber: 2.8 Consensus size: 134
1891663 AGCGCTCCAG
* * *
1891673 CGTTAAGAGTTGGAAGGGGGACATAGTTCATGTCAAGCACTTCCAGTGGGGAGTAGGCAAGATGA
1 CGTTAAGAGTTGGAAGGGGGACAGAGTTCATGTCGAGCGCTTCCAGTGGGGAGTAGG-AAGATGA
* * * *
1891738 CCTGATCTTACGTCG-GGCGTTCTAACGTGTGGAGTAGGCAGGGTATTCCTATTTTTCACCGAGT
65 CATGATCTTACGTCGACGC-TT-TAACGTGTGGAGTAGGCAGGGTATTCCTATTTCTCACCGAGC
1891802 ACTTCAC
128 ACTTCAC
* *
1891809 CGTTAAGAGTTGGAAGGGGGACAGAGTTCATGTCGAGCGCTTCCCGTGGAGAGTAGGAATGATGA
1 CGTTAAGAGTTGGAAGGGGGACAGAGTTCATGTCGAGCGCTTCCAGTGGGGAGTAGGAA-GATGA
* * * ** *
1891874 CTTGATCTTACGCCAGACGCTTTAACGTGTGGAGTAGGCAGGGTATTTCTATTTCTCGTCGAGCG
65 CATGATCTTACGTC-GACGCTTTAACGTGTGGAGTAGGCAGGGTATTCCTATTTCTCACCGAGCA
*
1891939 CTTTAC
129 CTTCAC
* * * * ** * *
1891945 CGTTACGAGTTGGAATAGGGG-CAGGGTTTATACCGAGCGCTTCCAGTGGGGGAGTAGCAGGATG
1 CGTTAAGAGTTGGAA-GGGGGACAGAGTTCATGTCGAGCGCTTCCAGT-GGGGAGTAGGAAGATG
*
1892009 ACATGATCTTACGTCGAGCGCTCTAACGTGTGGAGTAGG
64 ACATGATCTTACGTCGA-CGCTTTAACGTGTGGAGTAGG
1892048 TCGGGTGAAA
Statistics
Matches: 205, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
135 4 0.02
136 183 0.89
137 16 0.08
138 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (134 bp):
CGTTAAGAGTTGGAAGGGGGACAGAGTTCATGTCGAGCGCTTCCAGTGGGGAGTAGGAAGATGAC
ATGATCTTACGTCGACGCTTTAACGTGTGGAGTAGGCAGGGTATTCCTATTTCTCACCGAGCACT
TCAC
Found at i:1892196 original size:149 final size:149
Alignment explanation
Indices: 1891996--1892506 Score: 588
Period size: 149 Copynumber: 3.4 Consensus size: 149
1891986 TCCAGTGGGG
* ** * *
1891996 GAGTA-GCAGGATGACATGATCTTACGTCGAGCGCTCTAACGTGTGGAGTAGGTCGGGTGAAATA
1 GAGTAGGCAGGATGACTTGATCTTACACCGAGCGCCCTAACGTGTGGAGTAGGCCGGGTGAAATA
* * * * * * * *
1892060 AGATGTACTTT-AATATCTCGCCGAGCGCTTAAACAT-TGAGAGTAGGCAGGGGAGACAGTGTAC
66 AGGTGTACTTTAAAT-TCACGCCGAGCACTTCAACGTATGAGGGTAGGCAGGGTAGACAGTGTTC
1892123 ATGCCGAGCGCTTCAAGAGA
130 ATGCCGAGCGCTTCAAGAGA
* *
1892143 TGAGTAGGCAGGATGACTTGATCTTACACCGGGCACCCTAACGTGTGGAGTAGGCCGGGTGAAAT
1 -GAGTAGGCAGGATGACTTGATCTTACACCGAGCGCCCTAACGTGTGGAGTAGGCCGGGTGAAAT
* * * * * *
1892208 GAGGTGTGCTTTAAATTCACGCCGAGCACTTCAACGTGTG-GGGTAGGTAGGATAAACAGAT-TT
65 AAGGTGTACTTTAAATTCACGCCGAGCACTTCAACGTATGAGGGTAGGCAGGGTAGACAG-TGTT
* *
1892271 CATGCCGAGCGCTCCAAGAAGG
129 CATGCCGAGCGCTTCAAG-AGA
* *
1892293 GAGTAGGCAGGATAACTTGATCTTACACCGAGCGCCCTAACGTGTGGAGTAGGCCGGGTGAAATG
1 GAGTAGGCAGGATGACTTGATCTTACACCGAGCGCCCTAACGTGTGGAGTAGGCCGGGTGAAATA
* * * *
1892358 AGGTGTACTTTAAATTCACGCCGAGCACTCCAACGTAT-AGGGTAGACAAGGTAGACAGAGTTCA
66 AGGTGTACTTTAAATTCACGCCGAGCACTTCAACGTATGAGGGTAGGCAGGGTAGACAGTGTTCA
* *
1892422 TGTCGAGCGCTTCCTATG-G-
131 TGCCGAGCGCTT-C-AAGAGA
* ** * *
1892441 GAGTAGGCAGGATGACCTGATCTTACGTCGAGCGCCCTAACATGGGGAGTAGGCCGGGTGAAATA
1 GAGTAGGCAGGATGACTTGATCTTACACCGAGCGCCCTAACGTGTGGAGTAGGCCGGGTGAAATA
1892506 A
66 A
1892507 AATGGTCTAG
Statistics
Matches: 310, Mismatches: 44, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
148 64 0.21
149 235 0.76
150 9 0.03
151 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (149 bp):
GAGTAGGCAGGATGACTTGATCTTACACCGAGCGCCCTAACGTGTGGAGTAGGCCGGGTGAAATA
AGGTGTACTTTAAATTCACGCCGAGCACTTCAACGTATGAGGGTAGGCAGGGTAGACAGTGTTCA
TGCCGAGCGCTTCAAGAGA
Found at i:1899737 original size:30 final size:30
Alignment explanation
Indices: 1899701--1899787 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 30
1899691 AGAGAGGGTG
* *
1899701 AAGCTTAGCAAAGCTTAGGAATAT-TATTGA
1 AAGCTTAGCAAAGCTTAGGAATATCGAGT-A
*
1899731 AAGCTTAGAAAAGC-TAGAGAGA-ATCGAGTA
1 AAGCTTAGCAAAGCTTAG-GA-ATATCGAGTA
*
1899761 AAGCTTAGCAAAGCTTA-GAATAGCGAG
1 AAGCTTAGCAAAGCTTAGGAATATCGAG
1899788 GTTGTGTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
28 1 0.02
29 10 0.21
30 31 0.66
31 5 0.11
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (30 bp):
AAGCTTAGCAAAGCTTAGGAATATCGAGTA
Found at i:1900861 original size:20 final size:20
Alignment explanation
Indices: 1900836--1900880 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1900826 TTGCTTCAAT
1900836 AAAATTAATTAATTAGAAAA
1 AAAATTAATTAATTAGAAAA
* *
1900856 AAAATTCATTAATTTGAAAA
1 AAAATTAATTAATTAGAAAA
*
1900876 GAAAT
1 AAAAT
1900881 CTCGCATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAATTAATTAATTAGAAAA
Found at i:1901784 original size:19 final size:19
Alignment explanation
Indices: 1901756--1901882 Score: 236
Period size: 19 Copynumber: 6.7 Consensus size: 19
1901746 AATGTAATTT
*
1901756 GTGCACCGATGCATAGGTA
1 GTGCATCGATGCATAGGTA
*
1901775 GTGCATCGATGCATATGTA
1 GTGCATCGATGCATAGGTA
1901794 GTGCATCGATGCATAGGTA
1 GTGCATCGATGCATAGGTA
1901813 GTGCATCGATGCATAGGTA
1 GTGCATCGATGCATAGGTA
1901832 GTGCATCGATGCATAGGTA
1 GTGCATCGATGCATAGGTA
1901851 GTGCATCGATGCATAGGTA
1 GTGCATCGATGCATAGGTA
1901870 GTGCATCGATGCA
1 GTGCATCGATGCA
1901883 CACGTTAAGG
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 105 1.00
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (19 bp):
GTGCATCGATGCATAGGTA
Found at i:1901922 original size:20 final size:20
Alignment explanation
Indices: 1901897--1901946 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1901887 TTAAGGAATT
1901897 CATCGATACACTGTAGAGTG
1 CATCGATACACTGTAGAGTG
1901917 CATCGATACACTGTAGAGTG
1 CATCGATACACTGTAGAGTG
1901937 CATCGATACA
1 CATCGATACA
1901947 TACCTTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (20 bp):
CATCGATACACTGTAGAGTG
Found at i:1902760 original size:19 final size:19
Alignment explanation
Indices: 1902736--1902781 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1902726 GAGAAAGAAC
1902736 AAGTGATATGAAATGTTAT
1 AAGTGATATGAAATGTTAT
1902755 AAGTGATATGAAATGTTAT
1 AAGTGATATGAAATGTTAT
*
1902774 AAATGATA
1 AAGTGATA
1902782 ATACTCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.35
Consensus pattern (19 bp):
AAGTGATATGAAATGTTAT
Found at i:1902960 original size:31 final size:31
Alignment explanation
Indices: 1902840--1902961 Score: 113
Period size: 31 Copynumber: 3.9 Consensus size: 31
1902830 TAGTCGAGGG
* *
1902840 TTTACCTATGTTCTACGGAACATATAGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACA-A
*
1902872 TTTACCTATG-TCTTTC-GAGACATATGGACAA
1 TTTACCTATGTTC-TACGGA-ACATATGGACAA
* * *
1902903 TATACCTATGTTCTAAGGAATATATGGACAA
1 TTTACCTATGTTCTACGGAACATATGGACAA
* * * *
1902934 TTTACCTAGGTTCTTCGGGACCTATGGA
1 TTTACCTATGTTCTACGGAACATATGGA
1902962 TAGTTGTCGA
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
31 46 0.64
32 26 0.36
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (31 bp):
TTTACCTATGTTCTACGGAACATATGGACAA
Found at i:1903748 original size:22 final size:22
Alignment explanation
Indices: 1903699--1903748 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1903689 TTTGCACGAA
* *
1903699 ATAATATAATAAATTTTTTAAG
1 ATAATATAATAAAATATTTAAG
* *
1903721 AAAATATAATAAAATATTTATG
1 ATAATATAATAAAATATTTAAG
1903743 ATAATA
1 ATAATA
1903749 ATATTTTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
ATAATATAATAAAATATTTAAG
Found at i:1905689 original size:3 final size:3
Alignment explanation
Indices: 1905683--1905754 Score: 64
Period size: 3 Copynumber: 24.7 Consensus size: 3
1905673 ATAATTTTAT
* *
1905683 TAA TAA TAAA TAA -AA TAA -ATA TAA TAA TAA TGA TATT TAA -AA TAA
1 TAA TAA T-AA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA
1905728 TAA TAA TAA TAA TAA TAA -AA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1905755 TATATATATA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
2 9 0.16
3 42 0.74
4 6 0.11
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1905759 original size:2 final size:2
Alignment explanation
Indices: 1905747--1905781 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1905737 TAATAATAAA
1905747 AT AT A- 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
1905782 TTTTAAGTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1905922 original size:14 final size:14
Alignment explanation
Indices: 1905905--1905931 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1905895 CTTATAATTT
1905905 AGGATTTAGGGTTA
1 AGGATTTAGGGTTA
1905919 AGGATTTAGGGTT
1 AGGATTTAGGGTT
1905932 TGAGGTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
AGGATTTAGGGTTA
Found at i:1910939 original size:37 final size:36
Alignment explanation
Indices: 1910864--1910939 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1910854 TTTTTATATT
*
1910864 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1910900 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1910937 TTT
1 TTT
1910940 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1911435 original size:23 final size:23
Alignment explanation
Indices: 1911405--1911461 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1911395 ACTTTAATGC
1911405 TGAATCATTCAGCAGTGTTTTGT
1 TGAATCATTCAGCAGTGTTTTGT
*
1911428 TGAATCATTCAGTAGTGTTTTGT
1 TGAATCATTCAGCAGTGTTTTGT
**
1911451 TGTTTCATTCA
1 TGAATCATTCA
1911462 ACATAGTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (23 bp):
TGAATCATTCAGCAGTGTTTTGT
Found at i:1911977 original size:21 final size:21
Alignment explanation
Indices: 1911951--1911996 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1911941 TTATCTTTTC
1911951 AATTTTGTAAA-AAAATATATA
1 AATTTT-TAAATAAAATATATA
1911972 AATTTTTAAATAAAATATATA
1 AATTTTTAAATAAAATATATA
1911993 AATT
1 AATT
1911997 AATTATAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTTTTAAATAAAATATATA
Found at i:1920631 original size:19 final size:20
Alignment explanation
Indices: 1920607--1920657 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1920597 AAATGACCAA
*
1920607 CAAATTCGCAACGCGATCT-
1 CAAATTCGCAACGCGAACTC
* *
1920626 CAAATTCGTAATGCGAACTC
1 CAAATTCGCAACGCGAACTC
*
1920646 CAATTTCGCAAC
1 CAAATTCGCAAC
1920658 CCAGTTTCCA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACGCGAACTC
Found at i:1920731 original size:20 final size:20
Alignment explanation
Indices: 1920706--1920783 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
1920696 ACACAGAATT
** *
1920706 CAAATTCGCAACGTGATAGC
1 CAAATTCGCAACACGAAAGC
* *
1920726 CAAATTCACAACACGAAAGT
1 CAAATTCGCAACACGAAAGC
* *
1920746 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACGAAAGC
*
1920766 CAAATTCGCAACGCGAAA
1 CAAATTCGCAACACGAAA
1920784 CACAATATTA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.45, C:0.26, G:0.14, T:0.15
Consensus pattern (20 bp):
CAAATTCGCAACACGAAAGC
Found at i:1920923 original size:22 final size:22
Alignment explanation
Indices: 1920893--1920943 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1920883 CTACGGCAAC
* *
1920893 ATCCATCCCCATCTTTGACGAA
1 ATCCATCCCCATCTTCGACAAA
*
1920915 ATCCGTCCCCATCTTCGACAAA
1 ATCCATCCCCATCTTCGACAAA
1920937 ATCCATC
1 ATCCATC
1920944 TATCTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.39, G:0.08, T:0.25
Consensus pattern (22 bp):
ATCCATCCCCATCTTCGACAAA
Found at i:1921308 original size:20 final size:20
Alignment explanation
Indices: 1921285--1921335 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1921275 TTTGAAACTT
* *
1921285 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACCAAAATA
1921305 AAAATCGCAACACCAAAATA
1 AAAATCGCAACACCAAAATA
1921325 AAAATCGCAAC
1 AAAATCGCAAC
1921336 GTGATTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.57, C:0.24, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACACCAAAATA
Found at i:1921389 original size:20 final size:19
Alignment explanation
Indices: 1921338--1921389 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1921328 ATCGCAACGT
* *
1921338 GATTTTAGTTTCGCGTTGC
1 GATTTAAGTTTCGCGTTAC
* *
1921357 GATTTTCATTTTCGCGTTAC
1 GA-TTTAAGTTTCGCGTTAC
1921377 GGATTTAAGTTTC
1 -GATTTAAGTTTC
1921390 AGAAACTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (19 bp):
GATTTAAGTTTCGCGTTAC
Found at i:1923352 original size:4 final size:4
Alignment explanation
Indices: 1923343--1923388 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
1923333 TTTTTCGGTA
* *
1923343 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1923389 TCAACGGCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:1923579 original size:21 final size:20
Alignment explanation
Indices: 1923532--1923630 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 20
1923522 GATGCACCTA
*
1923532 TCATCATTCAAAAGGCGCCTC
1 TCATCATTCAAGAGGC-CCTC
1923553 -CTATCATTCAAGAGGCCCATC
1 TC-ATCATTCAAGAGGCCC-TC
*
1923574 TCATCA-TCGAAGAAGCCCCTC
1 TCATCATTC-AAG-AGGCCCTC
* * * *
1923595 CCACCGTTCAAGAGGCCCTTG
1 TCATCATTCAAGAGGCCC-TC
*
1923616 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
1923631 TCCCGTCCGC
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
20 10 0.16
21 44 0.71
22 8 0.13
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.22
Consensus pattern (20 bp):
TCATCATTCAAGAGGCCCTC
Found at i:1925084 original size:14 final size:14
Alignment explanation
Indices: 1925065--1925101 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1925055 GCTTGTTTAA
1925065 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1925079 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
1925093 TTTATTTGT
1 TTGATTTGT
1925102 TTAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1925157 original size:81 final size:78
Alignment explanation
Indices: 1925011--1925166 Score: 249
Period size: 81 Copynumber: 2.0 Consensus size: 78
1925001 TTTTACATTG
1925011 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTAA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTAA
1925076 AAGTTGATTTGTA
66 AAGTTGATTTGTA
* * * *
1925089 AAAGTTTATTTGTTTAATTTGATGTGTAAATAAGAATTGTTTTTTATGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT-ATTTTT-TGCTTGTTTAATTGATTTG
1925154 TAAAAGTTGATTT
63 TAAAAGTTGATTT
1925167 TTTGTTTTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
78 16 0.23
79 18 0.25
80 5 0.07
81 32 0.45
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (78 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTAA
AAGTTGATTTGTA
Found at i:1925283 original size:13 final size:14
Alignment explanation
Indices: 1925247--1925285 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1925237 GAAAGTCAAA
1925247 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
1925261 TTCG-GTTTGCGA-T
1 TTCGCG-TTGCGATT
1925274 TTCGCGTTGCGA
1 TTCGCGTTGCGA
1925286 ATTTGACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.08, C:0.21, G:0.31, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:1925289 original size:14 final size:14
Alignment explanation
Indices: 1925247--1925289 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1925237 GAAAGTCAAA
*
1925247 TTCGCGTTGCGATT
1 TTCGCGTTGCGAAT
1925261 TTCG-GTTTGCG-AT
1 TTCGCG-TTGCGAAT
1925274 TTCGCGTTGCGAAT
1 TTCGCGTTGCGAAT
1925288 TT
1 TT
1925290 GACTATCGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (14 bp):
TTCGCGTTGCGAAT
Found at i:1926070 original size:20 final size:20
Alignment explanation
Indices: 1926047--1926178 Score: 128
Period size: 20 Copynumber: 6.6 Consensus size: 20
1926037 TAAAGCATCA
*
1926047 GTTGTGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* * *
1926067 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
1926087 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
1926107 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
*
1926127 GTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
* *
1926147 GTTGCGAAATTGGAGT-TCGC
1 GTTGCG-AATTTGACTATCGC
1926167 GTTGCGAATTTG
1 GTTGCGAATTTG
1926179 TTGGTCATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.02
19 11 0.12
20 72 0.79
21 2 0.02
22 3 0.03
23 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:1926107 original size:40 final size:40
Alignment explanation
Indices: 1926047--1926178 Score: 162
Period size: 40 Copynumber: 3.3 Consensus size: 40
1926037 TAAAGCATCA
* *
1926047 GTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1926087 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
* * * *
1926127 GTTGCG-ATTT-ACAAATTCGCGTTGCGAAATTGGAGTTC-GC
1 GTTGCGAATTTGAC-TA-TCGCGTTGCG-AATTTGACTTCTGT
1926167 GTTGCGAATTTG
1 GTTGCGAATTTG
1926179 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
38 2 0.02
39 5 0.06
40 61 0.75
41 13 0.16
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.39
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
Found at i:1926633 original size:30 final size:31
Alignment explanation
Indices: 1926591--1926655 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
1926581 TTTAATTAAG
* *
1926591 TTTAGATGTTAAATTAATATTTTATCTAAAA
1 TTTAGATGTTAAAATAATATTTTATATAAAA
1926622 TTTAGA-GTTAAAATAATATTTTATATAAAA
1 TTTAGATGTTAAAATAATATTTTATATAAAA
1926652 TTTA
1 TTTA
1926656 AAATTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.48
Consensus pattern (31 bp):
TTTAGATGTTAAAATAATATTTTATATAAAA
Found at i:1926657 original size:7 final size:7
Alignment explanation
Indices: 1926647--1926673 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1926637 ATATTTTATA
1926647 TAAAATT
1 TAAAATT
1926654 TAAAATT
1 TAAAATT
1926661 TAAAATT
1 TAAAATT
1926668 TAAAAT
1 TAAAAT
1926674 AATTGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAAAATT
Found at i:1934746 original size:42 final size:42
Alignment explanation
Indices: 1934682--1934761 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1934672 TTCATAAGCA
*
1934682 TATAGAATGTATCATTGTATACAGATAACAAAATGAACTACT
1 TATAGAATGTATCATTGCATACAGATAACAAAATGAACTACT
* *
1934724 TATAGAATGTATCATTGCATACATATAACAAACTGAAC
1 TATAGAATGTATCATTGCATACAGATAACAAAATGAAC
1934762 ATAATTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (42 bp):
TATAGAATGTATCATTGCATACAGATAACAAAATGAACTACT
Found at i:1936510 original size:22 final size:22
Alignment explanation
Indices: 1936485--1936529 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1936475 CGGATCTAAC
*
1936485 AAATTTTTA-AATATTTTCTATA
1 AAATTTTTATAA-ATTTTATATA
1936507 AAATTTTTATAAATTTTATATA
1 AAATTTTTATAAATTTTATATA
1936529 A
1 A
1936530 GTTTACTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATTTTTATAAATTTTATATA
Found at i:1937173 original size:21 final size:22
Alignment explanation
Indices: 1937147--1937188 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1937137 CCAACACCCT
1937147 CAAGACGCCGA-AAATCCCAAA
1 CAAGACGCCGAGAAATCCCAAA
*
1937168 CAAGACGCCGAGAGATCCCAA
1 CAAGACGCCGAGAAATCCCAA
1937189 GCAATACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.43, C:0.33, G:0.19, T:0.05
Consensus pattern (22 bp):
CAAGACGCCGAGAAATCCCAAA
Found at i:1937849 original size:12 final size:10
Alignment explanation
Indices: 1937807--1937847 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1937797 TTTATCACAC
1937807 CAAATTCTCT
1 CAAATTCTCT
1937817 CAAATTCTCT
1 CAAATTCTCT
1937827 -AAATTTCTCT
1 CAAA-TTCTCT
*
1937837 CAAATACTCT
1 CAAATTCTCT
1937847 C
1 C
1937848 TCTTTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1938192 original size:111 final size:111
Alignment explanation
Indices: 1937973--1938297 Score: 522
Period size: 111 Copynumber: 3.0 Consensus size: 111
1937963 TGGAAATCAT
* *
1937973 ATATCTCTACACTTTGCTGATACGATAACATTTTAACATTTTAATTTAATTTAAATTATTAGT-A
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
* *
1938037 T--TTAGTTGA-TTATTTAATCCATG---ATT-GATTCAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1938076 ATATCTCGACATTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1938141 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
1938187 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
*
1938252 TAATTAGTTGATTTATTTAATGCGTGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1938298 TTTTTGTAAT
Statistics
Matches: 205, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
103 60 0.29
104 2 0.01
106 8 0.04
107 13 0.06
110 3 0.01
111 119 0.58
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1940248 original size:21 final size:21
Alignment explanation
Indices: 1940188--1940240 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1940178 TCAGGACGAC
1940188 GACGACGACGATGACGATGGT
1 GACGACGACGATGACGATGGT
*
1940209 GACGACGACGATGATGATGGT
1 GACGACGACGATGACGATGGT
1940230 GACGACGACGA
1 GACGACGACGA
1940241 CGCCGATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.38, T:0.13
Consensus pattern (21 bp):
GACGACGACGATGACGATGGT
Found at i:1940509 original size:35 final size:33
Alignment explanation
Indices: 1940470--1940554 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
1940460 ATATTTCAGT
1940470 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
* *
1940505 TAATTTGGTTATCATTTACTATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
1940540 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1940555 TAAATACCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:1943337 original size:26 final size:26
Alignment explanation
Indices: 1943288--1943337 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1943278 ACTTTAATAT
* *
1943288 AAAAATTATATACATATTTTATAACC
1 AAAAATTACATACATATTTCATAACC
1943314 AAAAATTACATAC-TATGTTCATAA
1 AAAAATTACATACATAT-TTCATAA
1943338 TAATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAAATTACATACATATTTCATAACC
Found at i:1947311 original size:51 final size:52
Alignment explanation
Indices: 1947208--1947323 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 52
1947198 CCCCTACGTG
* * *
1947208 GCGTATAGCGCGG-AGAAGGGGGTGCGCTATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGTAGAAGGGGGCGCGCTATACCCCACGTGTAACCAAATCA
* * * *
1947259 GCGTATAGCGCGGTA-CAGGGGGCGCGCTATACTCTACGTG-ATGCCAAATCA
1 GCGTATAGCGCGGTAGAAGGGGGCGCGCTATACCCCACGTGTA-ACCAAATCA
* *
1947310 GCATATAGTGCGGT
1 GCGTATAGCGCGGT
1947324 TTACTACTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
50 1 0.02
51 52 0.96
52 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (52 bp):
GCGTATAGCGCGGTAGAAGGGGGCGCGCTATACCCCACGTGTAACCAAATCA
Found at i:1947397 original size:23 final size:23
Alignment explanation
Indices: 1947364--1947417 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1947354 GTGTTATACC
*
1947364 GATCACTGGTGATTTTTGGGGAA
1 GATCACCGGTGATTTTTGGGGAA
1947387 GATCACCGGTGATTTTTGGGGAA
1 GATCACCGGTGATTTTTGGGGAA
*
1947410 AATCACCG
1 GATCACCG
1947418 TGGGTATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (23 bp):
GATCACCGGTGATTTTTGGGGAA
Found at i:1948080 original size:19 final size:20
Alignment explanation
Indices: 1948056--1948101 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1948046 TTTTAATATT
* *
1948056 TAAAAATCTAA-ATAAATTA
1 TAAAAATCAAACAAAAATTA
1948075 TAAAAAATCAAACAAAAATTA
1 T-AAAAATCAAACAAAAATTA
1948096 TAAAAA
1 TAAAAA
1948102 AATAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 14 0.61
21 8 0.35
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAATCAAACAAAAATTA
Found at i:1948112 original size:21 final size:21
Alignment explanation
Indices: 1948069--1948112 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1948059 AAATCTAAAT
*
1948069 AAATTATAAAAAATCAAACAA
1 AAATTATAAAAAATCAAAAAA
1948090 AAATTATAAAAAAAT-AAAAAA
1 AAATTAT-AAAAAATCAAAAAA
1948111 AA
1 AA
1948113 TAGTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (21 bp):
AAATTATAAAAAATCAAAAAA
Found at i:1949635 original size:18 final size:20
Alignment explanation
Indices: 1949612--1949648 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1949602 TACTCTACTT
1949612 TTATA-TTTT-ATAAAATTA
1 TTATATTTTTAATAAAATTA
1949630 TTATATTTTTAATAAAATT
1 TTATATTTTTAATAAAATT
1949649 TAGTTGAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATTTTTAATAAAATTA
Found at i:1953596 original size:43 final size:43
Alignment explanation
Indices: 1953515--1953600 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
1953505 GCGTTTGCAG
* *
1953515 AATATGTCTTGATATTTAGCGGCATTTTCGTCGAAAACGCCGC
1 AATATGTCTTGAGATTTAGCGGCATTTTCATCGAAAACGCCGC
* * *
1953558 AATATGTCTTGAGATTTCGCGGCGTTTTTATC-ACAAACGCCGC
1 AATATGTCTTGAGATTTAGCGGCATTTTCATCGA-AAACGCCGC
1953601 TAAATGTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (43 bp):
AATATGTCTTGAGATTTAGCGGCATTTTCATCGAAAACGCCGC
Found at i:1954033 original size:21 final size:21
Alignment explanation
Indices: 1953978--1954027 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1953968 TGTACTGCCA
1953978 CTGCTTCCGCTGCTGCTCTAG
1 CTGCTTCCGCTGCTGCTCTAG
**
1953999 CTGCTTCCGCTGCTGCTCTCT
1 CTGCTTCCGCTGCTGCTCTAG
1954020 CTGCTTCC
1 CTGCTTCC
1954028 CTTGCTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.42, G:0.20, T:0.36
Consensus pattern (21 bp):
CTGCTTCCGCTGCTGCTCTAG
Found at i:1956284 original size:22 final size:22
Alignment explanation
Indices: 1956256--1956299 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1956246 CTTCTTCACT
1956256 AACTTCTCTCCCACTCCAAACC
1 AACTTCTCTCCCACTCCAAACC
1956278 AACTTCTCTCCCACTCCAAACC
1 AACTTCTCTCCCACTCCAAACC
1956300 TATTACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.50, G:0.00, T:0.23
Consensus pattern (22 bp):
AACTTCTCTCCCACTCCAAACC
Found at i:1962936 original size:81 final size:80
Alignment explanation
Indices: 1962844--1963109 Score: 365
Period size: 81 Copynumber: 3.3 Consensus size: 80
1962834 GTTAAAATTA
* * *
1962844 ATTGCGGCGTTTACAGAAAAACACCACTAATGTACGACCCATATGCGGCGTTTCTTGTAAAACGT
1 ATTGCGGCGTTTATATAAAAACACCACTAATGTACGACCCATATGCGGCGTTT-TTGTAAAACGC
1962909 CACTATAAACAACTCT
65 CACTATAAACAACTCT
* *
1962925 ATTGCGGCGTTTATATAAAAACACCACTAATGTACGACCCATTTGCAGCGTTTTTTGTAAAACGC
1 ATTGCGGCGTTTATATAAAAACACCACTAATGTACGACCCATATGCGGCG-TTTTTGTAAAACGC
1962990 CACTATAAACAACTCT
65 CACTATAAACAACTCT
* * * * * *
1963006 ATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TACTACTC-TATTGCGGTGTTTTTTTAGAAAA
1 ATTGCGGCGTTTATATAAAAACACCACT-AATGTACGACCCATA-TGCGGCGTTTTTGT--AAAA
1963069 CGCCACTATAAACAACTCT
62 CGCCACTATAAACAACTCT
1963088 ATTGCGGCGTTTATATAAAAAC
1 ATTGCGGCGTTTATATAAAAAC
1963110 GCCGCTAAAT
Statistics
Matches: 167, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
80 7 0.04
81 109 0.65
82 51 0.31
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (80 bp):
ATTGCGGCGTTTATATAAAAACACCACTAATGTACGACCCATATGCGGCGTTTTTGTAAAACGCC
ACTATAAACAACTCT
Found at i:1963087 original size:41 final size:40
Alignment explanation
Indices: 1962902--1963112 Score: 221
Period size: 41 Copynumber: 5.2 Consensus size: 40
1962892 CGTTTCTTGT
*
1962902 AAAACGTCACTATAAACAACTCTATTGCGGCGTTTATATA
1 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
* ** * * * * *
1962942 AAAACACCACTAATGTACGAC-CCATTTGCAGCGTTT-TTTGT
1 AAAACGCCACT-ATAAACAACTCTA-TTGCGGCGTTTATAT-A
1962983 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
1 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
* * * * *
1963023 AAAACGCCGCTA-AATTACTACTCTATTGCGGTGTTTTTTTA
1 AAAACGCCACTATAA--ACAACTCTATTGCGGCGTTTATATA
1963064 GAAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
1 -AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
1963105 AAAACGCC
1 AAAACGCC
1963113 GCTAAATTAC
Statistics
Matches: 135, Mismatches: 27, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.01
40 48 0.36
41 72 0.53
42 11 0.08
43 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (40 bp):
AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
Found at i:1963103 original size:82 final size:80
Alignment explanation
Indices: 1962844--1963154 Score: 342
Period size: 81 Copynumber: 3.8 Consensus size: 80
1962834 GTTAAAATTA
* * * * * * * *
1962844 ATTGCGGCGTTTACAGAAAAACACCACT-AATGTACGACCCATATGCGGCGTTTCTTGTAAAACG
1 ATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TACCACCTAT-TGCAGCGTTTTTTGTAAAACG
*
1962908 TCACTATAAACAACTCT
64 CCACTATAAACAACTCT
* * * *
1962925 ATTGCGGCGTTTATATAAAAACACCACT-AATGTACGACCCATTTGCAGCGTTTTTTGTAAAACG
1 ATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TACCACCTA-TTGCAGCGTTTTTTGTAAAACG
1962989 CCACTATAAACAACTCT
64 CCACTATAAACAACTCT
* * *
1963006 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACTACTCTATTGCGGTGTTTTTT-TAGAAAAC
1 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCAC-CTATTGCAGCGTTTTTTGT--AAAAC
1963070 GCCACTATAAACAACTCT
63 GCCACTATAAACAACTCT
* *
1963088 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCACCCTATTG-AGGCGTTTGTTGAAAAAAC
1 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCA-CCTATTGCA-GCGTTTTTTG-TAAAAC
1963152 GCC
63 GCC
1963155 GCTAAAGTTT
Statistics
Matches: 205, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
80 1 0.00
81 117 0.57
82 86 0.42
83 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (80 bp):
ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCACCTATTGCAGCGTTTTTTGTAAAACGCC
ACTATAAACAACTCT
Found at i:1963131 original size:41 final size:41
Alignment explanation
Indices: 1962844--1963140 Score: 213
Period size: 41 Copynumber: 7.3 Consensus size: 41
1962834 GTTAAAATTA
* * * * *
1962844 ATTGCGGCGTTTACAGAAAAACACCACT-AATGTACGAC-CC
1 ATTGCGGCGTTTATATAAAAACGCCACTAAAT-TACAACTCT
* * *
1962884 ATATGCGGCGTTTCT-TGTAAAACGTCACTATAA--ACAACTCT
1 AT-TGCGGCGTTTATAT-AAAAACGCCACTA-AATTACAACTCT
* * *
1962925 ATTGCGGCGTTTATATAAAAACACCACT-AATGTACGAC-CC
1 ATTGCGGCGTTTATATAAAAACGCCACTAAAT-TACAACTCT
* * *
1962965 ATTTGCAGCGTTT-TTTGTAAAACGCCACTATAA--ACAACTCT
1 A-TTGCGGCGTTTATAT-AAAAACGCCACTA-AATTACAACTCT
* *
1963006 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACTACTCT
1 ATTGCGGCGTTTATATAAAAACGCCACTAAATTACAACTCT
* * *
1963047 ATTGCGGTGTTTTTTTAGAAAACGCCACTATAA--ACAACTCT
1 ATTGCGGCGTTTATATA-AAAACGCCACTA-AATTACAACTCT
* * *
1963088 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCACCCT
1 ATTGCGGCGTTTATATAAAAACGCCACTAAATTACAACTCT
*
1963129 ATTGAGGCGTTT
1 ATTGCGGCGTTT
1963141 GTTGAAAAAA
Statistics
Matches: 199, Mismatches: 37, Indels: 41
0.72 0.13 0.15
Matches are distributed among these distances:
38 2 0.01
39 4 0.02
40 66 0.33
41 110 0.55
42 11 0.06
43 6 0.03
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (41 bp):
ATTGCGGCGTTTATATAAAAACGCCACTAAATTACAACTCT
Found at i:1964889 original size:13 final size:13
Alignment explanation
Indices: 1964871--1964916 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1964861 TTTAGTTGTA
1964871 ATTTTATAATTTT
1 ATTTTATAATTTT
**
1964884 ATTTTATTTTTTGT
1 ATTTTATAATTT-T
1964898 ATTTTATAATTTT
1 ATTTTATAATTTT
1964911 ATTTTA
1 ATTTTA
1964917 GATTATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
ATTTTATAATTTT
Found at i:1965894 original size:42 final size:42
Alignment explanation
Indices: 1965832--1965951 Score: 195
Period size: 42 Copynumber: 2.9 Consensus size: 42
1965822 TTTCCCCGAA
*
1965832 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
* * * *
1965874 TTTCCGTGTTTGTTTTACGTAACTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
1965916 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1965952 TGTAATTCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
Found at i:1966187 original size:22 final size:23
Alignment explanation
Indices: 1966140--1966200 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
1966130 TAATTATTAA
* *
1966140 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
1966161 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
1966184 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
1966201 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:1966263 original size:54 final size:52
Alignment explanation
Indices: 1966166--1966268 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 52
1966156 TTATTAATAT
*
1966166 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
*
1966218 TTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAATT
1966269 TTTTTTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
52 16 0.36
53 7 0.16
54 22 0.49
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (52 bp):
TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
Found at i:1966281 original size:23 final size:26
Alignment explanation
Indices: 1966163--1966288 Score: 68
Period size: 29 Copynumber: 4.8 Consensus size: 26
1966153 TATTTATTAA
* *
1966163 TATTTATAATAATATAATATTATATTTT
1 TATTT-TAATAATAT-ATAATAAATTTT
* * *
1966191 TAATATTATATAA-A-ATAATCAA-TTA
1 T-ATTTTA-ATAATATATAATAAATTTT
*
1966216 TATTATAATAATATA-AGATATTATATTTT
1 TATTTTAATAATATATA-ATA--A-ATTTT
1966245 TATTTTAATAATATATAATAAATTTT
1 TATTTTAATAATATATAATAAATTTT
*
1966271 T-TTTT-AT-ATATTTAATAA
1 TATTTTAATAATATATAATAA
1966289 TGAATAATAT
Statistics
Matches: 77, Mismatches: 11, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
23 14 0.18
24 8 0.10
25 10 0.13
26 11 0.14
27 2 0.03
28 5 0.06
29 26 0.34
30 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TATTTTAATAATATATAATAAATTTT
Found at i:1966514 original size:20 final size:20
Alignment explanation
Indices: 1966486--1966535 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1966476 TTTCCAGATG
*
1966486 TTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCA
1966506 TTTTACAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCA
*
1966526 TTTTTCAGAA
1 TTTTACAGAA
1966536 TTCAAATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTTACAGAAATGTAATTCA
Found at i:1966539 original size:14 final size:15
Alignment explanation
Indices: 1966518--1966604 Score: 88
Period size: 15 Copynumber: 5.9 Consensus size: 15
1966508 TTACAGAAAT
*
1966518 GTAATTCATTTTTCA
1 GTAATTCATTTTCCA
**
1966533 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
1966547 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
*
1966562 GTAATTCAAATTT-CA
1 GTAATTC-ATTTTCCA
* **
1966577 GTAATTTAAATTCCA
1 GTAATTCATTTTCCA
1966592 GTAATTCATTTTC
1 GTAATTCATTTTC
1966605 TGGAAAACCA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
14 15 0.26
15 39 0.67
16 4 0.07
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:1966543 original size:20 final size:20
Alignment explanation
Indices: 1966486--1966544 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
1966476 TTTCCAGATG
* **
1966486 TTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATCAAATTCA
**
1966506 TTTTACAGAAATGTAATTCA
1 TTTTACAGAAATCAAATTCA
* *
1966526 TTTTTCAGAATTCAAATTC
1 TTTTACAGAAATCAAATTC
1966545 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (20 bp):
TTTTACAGAAATCAAATTCA
Found at i:1966554 original size:15 final size:15
Alignment explanation
Indices: 1966534--1966599 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
1966524 CATTTTTCAG
1966534 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
**
1966549 AATTCATTTTCCAGT
1 AATTCAAATTCCAGT
*
1966564 AATTCAAATTTCAGT
1 AATTCAAATTCCAGT
*
1966579 AATTTAAATTCCAGT
1 AATTCAAATTCCAGT
1966594 AATTCA
1 AATTCA
1966600 TTTTCTGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:1966570 original size:30 final size:30
Alignment explanation
Indices: 1966518--1966599 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 30
1966508 TTACAGAAAT
*
1966518 GTAATTCATTTTTCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
1966547 GTAATTCATTTTCCAGTAATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* **
1966577 GTAATTTAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1966600 TTTTCTGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 15 0.32
30 32 0.68
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1966597 original size:45 final size:44
Alignment explanation
Indices: 1966518--1966604 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
1966508 TTACAGAAAT
**
1966518 GTAATTCATTTTTCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTTCAGAATTCAAATTCCAGTAATTCATTTTCCA
*
1966562 GTAATTCAAATTTCAGTAATTTAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTTCAG-AATTCAAATTCCAGTAATTCATTTTC
1966605 TGGAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (44 bp):
GTAATTCAAATTTCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:1975354 original size:28 final size:28
Alignment explanation
Indices: 1975301--1975361 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1975291 AATCTTCGTT
* *
1975301 TATTATGTCGTCAAGTTAATTCTTGAAA
1 TATTATGTCATCAAGTCAATTCTTGAAA
*
1975329 TATTATGTCATCAAGTCGATGT-TTGAAA
1 TATTATGTCATCAAGTCAAT-TCTTGAAA
1975357 -ATTAT
1 TATTAT
1975362 ATCGGTGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 23 0.79
29 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (28 bp):
TATTATGTCATCAAGTCAATTCTTGAAA
Found at i:1976456 original size:2 final size:2
Alignment explanation
Indices: 1976451--1976541 Score: 173
Period size: 2 Copynumber: 45.0 Consensus size: 2
1976441 TTATTTTTAT
1976451 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
1976493 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
1976535 TA GTA TA
1 TA -TA TA
1976542 ATTTTTGAAC
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 86 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1976641 original size:75 final size:73
Alignment explanation
Indices: 1976555--1976851 Score: 306
Period size: 76 Copynumber: 4.0 Consensus size: 73
1976545 TTTGAACTTT
* * * *
1976555 TTTTTAGAAAACTTTTTTTGAAA-ACATATA-ATATACTTTTTAAAAATCGGTTTTCGAAAATAT
1 TTTTT-GAAAACATATTTTGAAATATATATATATATA-TTTTTAAAAA-C-ATTTT-GAAAATAT
1976618 ATATAATATATAG
61 ATATAATATATAG
* *
1976631 TTTTTGAAAAC--ATTTCGAATATATATATATTATATAGTTTTAAAAACATTTTGAAAACT-TAT
1 TTTTTGAAAACATATTTTGAA-ATATATATA-TATATATTTTTAAAAACATTTTGAAAA-TATAT
*
1976693 ATAATATATGG
63 ATAATATATAG
* *
1976704 TTTTTTAAAAAATATTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAATATAT
1 TTTTTGAAAACATATTTTG-AAATATATAT-ATATATA-TTTTTAAAAACATTTTGAAAATATAT
1976769 ATAATATATAG
63 ATAATATATAG
*
1976780 TTTTT-AAAA-ACATTTTGAAAATATATATAATATATAGTTTTT-AAAACATTTT-AAAATATAT
1 TTTTTGAAAACATATTTTG-AAATATATAT-ATATATA-TTTTTAAAAACATTTTGAAAATATAT
1976841 ATATATATATA
63 ATA-ATATATA
1976852 TATATATAGT
Statistics
Matches: 197, Mismatches: 12, Indels: 27
0.83 0.05 0.11
Matches are distributed among these distances:
72 12 0.06
73 50 0.25
74 38 0.19
75 37 0.19
76 55 0.28
77 5 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (73 bp):
TTTTTGAAAACATATTTTGAAATATATATATATATATTTTTAAAAACATTTTGAAAATATATATA
ATATATAG
Found at i:1976726 original size:39 final size:37
Alignment explanation
Indices: 1976585--1976900 Score: 377
Period size: 37 Copynumber: 8.3 Consensus size: 37
1976575 AAAACATATA
* *
1976585 ATATACTTTTTAAAAATCGGTTTTCGAAAATATATATAAT
1 ATATAGTTTTTAAAAA-C-ATTTT-GAAAATATATATAAT
* * * *
1976625 ATATAGTTTTTGAAAACATTTCGAATATATATATATT
1 ATATAGTTTTTAAAAACATTTTGAAAATATATATAAT
1976662 ATATAG-TTTTAAAAACATTTTGAAAACT-TATATAAT
1 ATATAGTTTTTAAAAACATTTTGAAAA-TATATATAAT
* *
1976698 ATATGGTTTTTTAAAAAATATTTTGAAAATATATATAAT
1 ATATAG-TTTTT-AAAAACATTTTGAAAATATATATAAT
1976737 ATATAGTTTTTAAAAACATTTTGAAAATATATATAAT
1 ATATAGTTTTTAAAAACATTTTGAAAATATATATAAT
1976774 ATATAGTTTTTAAAAACATTTTGAAAATATATATAAT
1 ATATAGTTTTTAAAAACATTTTGAAAATATATATAAT
*
1976811 ATATAGTTTTT-AAAACATTTTAAAATATATATATATAT
1 ATATAGTTTTTAAAAACATTTTGAAA-ATATATATA-AT
* * * *
1976849 ATATATATATAGTTTTAAAATATTTTTGAAAATATATATATT
1 ATATA-GT-T--TTTAAAAACA-TTTTGAAAATATATATAAT
1976891 ATATAGTTTT
1 ATATAGTTTT
1976901 GGGAAATATT
Statistics
Matches: 243, Mismatches: 20, Indels: 28
0.84 0.07 0.10
Matches are distributed among these distances:
36 42 0.17
37 102 0.42
38 22 0.09
39 30 0.12
40 16 0.07
41 1 0.00
42 9 0.04
43 14 0.06
44 7 0.03
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (37 bp):
ATATAGTTTTTAAAAACATTTTGAAAATATATATAAT
Found at i:1976842 original size:2 final size:2
Alignment explanation
Indices: 1976835--1976859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1976825 ACATTTTAAA
1976835 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1976860 GTTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1976865 original size:33 final size:35
Alignment explanation
Indices: 1976828--1976900 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 35
1976818 TTTTAAAACA
*
1976828 TTTTAAAATATATAT-ATATATATATA-TATATAG
1 TTTTAAAATATATATAAAATATATATATTATATAG
* *
1976861 TTTTAAAATATTTTTGAAAATATATATATTATATAG
1 TTTTAAAATATATAT-AAAATATATATATTATATAG
1976897 TTTT
1 TTTT
1976901 GGGAAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 13 0.38
35 10 0.29
36 11 0.32
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (35 bp):
TTTTAAAATATATATAAAATATATATATTATATAG
Done.