Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 29
Found at i:2563484 original size:24 final size:24
Alignment explanation
Indices: 2563452--2563532 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
2563442 GTTTGCAGTG
*
2563452 TTTTCTTACATTTTTATCATTAAT
1 TTTTATTACATTTTTATCATTAAT
*
2563476 TTTTATTACCTTTTTAGT-ATTAAT
1 TTTTATTACATTTTTA-TCATTAAT
** *
2563500 TTATT-TTTTATATTTTAACATTAAAT
1 TT-TTATTACAT-TTTTATCATT-AAT
2563526 TTTTATT
1 TTTTATT
2563533 TATAGTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
24 25 0.56
25 13 0.29
26 7 0.16
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.64
Consensus pattern (24 bp):
TTTTATTACATTTTTATCATTAAT
Found at i:2563611 original size:13 final size:13
Alignment explanation
Indices: 2563593--2563622 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2563583 CTCGGTCGAT
*
2563593 TTTTAAATTTTTA
1 TTTTAAATTTTAA
2563606 TTTTAAATTTTAA
1 TTTTAAATTTTAA
2563619 TTTT
1 TTTT
2563623 CGCGATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:2568349 original size:32 final size:33
Alignment explanation
Indices: 2568288--2568352 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2568278 TTCAAAATCA
*
2568288 TACCATTTTACTATGTATATTTTTATTAAGAAC
1 TACCATTTTACTATGCATATTTTTATTAAGAAC
2568321 TACCATTTTACTATGCATA-TTTTATTAAGAAC
1 TACCATTTTACTATGCATATTTTTATTAAGAAC
2568353 GATTAGTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (33 bp):
TACCATTTTACTATGCATATTTTTATTAAGAAC
Found at i:2569664 original size:51 final size:51
Alignment explanation
Indices: 2569557--2569657 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
2569547 AACACCCTTT
* * * *
2569557 GGCGCGCCCCCTGCATCGCGTTTTACGTTGATATGGCGCCACATGGGGTAA
1 GGCGCGCCCCCTGCAGCGCGCTTTAAGCTGATATGGCGCCACATGGGGTAA
* *
2569608 GGCGCGCCCCCTGCAGCGCGCTTTAAGCTGATCTGGCGCCACGTGGGGTA
1 GGCGCGCCCCCTGCAGCGCGCTTTAAGCTGATATGGCGCCACATGGGGTA
2569658 TAGCGCGAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.14, C:0.32, G:0.34, T:0.21
Consensus pattern (51 bp):
GGCGCGCCCCCTGCAGCGCGCTTTAAGCTGATATGGCGCCACATGGGGTAA
Found at i:2580168 original size:20 final size:20
Alignment explanation
Indices: 2580143--2580182 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2580133 AATGAGGAAA
2580143 ATGACTTTGATTAGTGAAGC
1 ATGACTTTGATTAGTGAAGC
2580163 ATGACTTTGATTAGTGAAGC
1 ATGACTTTGATTAGTGAAGC
2580183 TCTGGACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (20 bp):
ATGACTTTGATTAGTGAAGC
Found at i:2592380 original size:21 final size:21
Alignment explanation
Indices: 2592350--2592390 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2592340 TGACAAGGAA
*
2592350 TATCGATACTTCCTTAATAAG
1 TATCGATACTACCTTAATAAG
* *
2592371 TATCGGTACTACCTTTATAA
1 TATCGATACTACCTTAATAA
2592391 TTTTTAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (21 bp):
TATCGATACTACCTTAATAAG
Found at i:2593125 original size:10 final size:10
Alignment explanation
Indices: 2593110--2593135 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2593100 GACATATTAT
2593110 TATTATATAA
1 TATTATATAA
2593120 TATTATATAA
1 TATTATATAA
2593130 TATTAT
1 TATTAT
2593136 TATATTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATTATATAA
Found at i:2593125 original size:13 final size:14
Alignment explanation
Indices: 2593103--2593140 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
2593093 CTCGAGTGAC
2593103 ATATTATTAT-TAT
1 ATATTATTATATAT
*
2593116 ATAATATTATATA-
1 ATATTATTATATAT
2593129 ATATTATTATAT
1 ATATTATTATAT
2593141 TGTTTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTATTATATAT
Found at i:2595027 original size:11 final size:11
Alignment explanation
Indices: 2595011--2595044 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
2595001 AAATAATAAA
2595011 TTTGTTTTAAT
1 TTTGTTTTAAT
2595022 TTTGTTTTAAT
1 TTTGTTTTAAT
2595033 TTTGTTTTAAT
1 TTTGTTTTAAT
2595044 T
1 T
2595045 ATTTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (11 bp):
TTTGTTTTAAT
Found at i:2601520 original size:20 final size:20
Alignment explanation
Indices: 2601410--2601514 Score: 149
Period size: 20 Copynumber: 5.2 Consensus size: 20
2601400 TCTAGAAAAT
* *
2601410 TAAAGCCTTCCGGTAATTTG
1 TAAATCCTTCGGGTAATTTG
2601430 TAAAGT-CTTCGGGTAATTTG
1 TAAA-TCCTTCGGGTAATTTG
* *
2601450 TAAAGCCTTCGAGTAATTTG
1 TAAATCCTTCGGGTAATTTG
2601470 TAAATCCTTCGGGTAATTTG
1 TAAATCCTTCGGGTAATTTG
*
2601490 TAAATCCTTTGGGTAATTTG
1 TAAATCCTTCGGGTAATTTG
2601510 TAAAT
1 TAAAT
2601515 TCTTTGAGTC
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (20 bp):
TAAATCCTTCGGGTAATTTG
Found at i:2603508 original size:21 final size:22
Alignment explanation
Indices: 2603462--2603511 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2603452 ATTAGGATTA
* *
2603462 ATTAATT-TTAATATTTTATAT
1 ATTAATTATTAATATATTAAAT
*
2603483 TTTAATTATTAA-ATATTAAAT
1 ATTAATTATTAATATATTAAAT
2603504 ATTAATTA
1 ATTAATTA
2603512 CACTATTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTAATTATTAATATATTAAAT
Found at i:2604517 original size:6 final size:6
Alignment explanation
Indices: 2604506--2606391 Score: 3680
Period size: 6 Copynumber: 315.3 Consensus size: 6
2604496 GGTCTCTTAA
2604506 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2604554 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2604602 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2604650 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2604698 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
*
2604746 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TAGTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2604794 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2604842 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2604890 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2604938 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2604986 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605034 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605082 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605130 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605178 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605226 TATTAG TATTAG TATTAG --TTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605272 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605320 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG ---TAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605365 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605413 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605461 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605509 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605557 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605605 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605653 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605701 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605749 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605797 TATATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 --TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605847 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605895 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605943 TATTAG TATTAG TA-TAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2605990 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2606038 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2606086 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TA-TAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2606133 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2606181 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2606229 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TA-TAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2606276 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
*
2606324 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTTG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
2606372 TATTAG TATTAG TATTAG TA
1 TATTAG TATTAG TATTAG TA
2606392 CATTTTATTT
Statistics
Matches: 1866, Mismatches: 4, Indels: 20
0.99 0.00 0.01
Matches are distributed among these distances:
3 3 0.00
4 4 0.00
5 15 0.01
6 1838 0.98
8 6 0.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATTAG
Found at i:2613318 original size:18 final size:19
Alignment explanation
Indices: 2613276--2613324 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
2613266 CGATGAACAA
*
2613276 TATCGATACTGATGCAATTAG
1 TATCGATACTGATG--ATGAG
2613297 TATCGATACTGATG-TGAG
1 TATCGATACTGATGATGAG
2613315 TATCGATACT
1 TATCGATACT
2613325 AATAAGAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 13 0.48
21 14 0.52
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (19 bp):
TATCGATACTGATGATGAG
Found at i:2614180 original size:111 final size:111
Alignment explanation
Indices: 2613979--2614182 Score: 284
Period size: 111 Copynumber: 1.8 Consensus size: 111
2613969 GCCACTAATT
* * *
2613979 AAAGTTATCGATCAATTTTGTTAAATGCATAACGATGCATTTTCGGCATAGAAGGTGCCACCCAT
1 AAAGATATCGATCAATTTTGTTAAATGCATAACGATGCATTTTCGACATAAAAGGTGCCACCCAT
*
2614044 GGTATTCATAAAAGGTGAATTACCATTTCGACATACTTCGTGTATG
66 GGTATTCATAAAAGGTGAATGACCATTTCGACATACTTCGTGTATG
* * * * *
2614090 AAAGATATCGATCGATTTT-TTGTAATGTATAACGGTGCATTTTCGACATAAAAGGTGCCACTCA
1 AAAGATATCGATCAATTTTGTT-AAATGCATAACGATGCATTTTCGACATAAAAGGTGCCACCCA
* * *
2614154 TGGTATTCATAAACGTTGACTGACCATTT
65 TGGTATTCATAAAAGGTGAATGACCATTT
2614183 TGGCATTTTG
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
110 2 0.03
111 78 0.98
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (111 bp):
AAAGATATCGATCAATTTTGTTAAATGCATAACGATGCATTTTCGACATAAAAGGTGCCACCCAT
GGTATTCATAAAAGGTGAATGACCATTTCGACATACTTCGTGTATG
Found at i:2627701 original size:12 final size:11
Alignment explanation
Indices: 2627657--2627717 Score: 60
Period size: 12 Copynumber: 5.8 Consensus size: 11
2627647 AAAATAAAAA
2627657 AATAAA-AAAT
1 AATAAATAAAT
*
2627667 -ATTAAT-AAT
1 AATAAATAAAT
2627676 AAT-AAT-AAT
1 AATAAATAAAT
2627685 AATAAATAAAT
1 AATAAATAAAT
2627696 ACATAAATAAAT
1 A-ATAAATAAAT
2627708 AAATAAATAA
1 -AATAAATAA
2627718 TATATTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
9 16 0.36
10 5 0.11
11 4 0.09
12 18 0.41
13 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:2627715 original size:8 final size:8
Alignment explanation
Indices: 2627643--2627717 Score: 63
Period size: 8 Copynumber: 9.9 Consensus size: 8
2627633 TCATGGGGCC
*
2627643 TAAAAAAA
1 TAAATAAA
*
2627651 TAAAAAAA
1 TAAATAAA
2627659 TAAA-AAA
1 TAAATAAA
2627666 TATTAAT-AA
1 TA--AATAAA
2627675 T-AAT-AA
1 TAAATAAA
2627681 T-AAT-AA
1 TAAATAAA
2627687 TAAATAAA
1 TAAATAAA
*
2627695 TACATAAA
1 TAAATAAA
2627703 TAAATAAA
1 TAAATAAA
2627711 TAAATAA
1 TAAATAA
2627718 TATATTTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
6 12 0.20
7 8 0.13
8 35 0.58
9 5 0.08
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.25
Consensus pattern (8 bp):
TAAATAAA
Found at i:2629430 original size:121 final size:121
Alignment explanation
Indices: 2629046--2629708 Score: 771
Period size: 120 Copynumber: 5.5 Consensus size: 121
2629036 CGAAAGCTCA
* * *
2629046 TTCGCTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGG
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCC-A---AG-GG
* * * * * *
2629111 -TGGA-TACAGCTTGTGTGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCAC
61 TTGCATTGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* * * ** *
2629170 TTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCCAAGTATTGTA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCA
* * * * *
2629235 -TGTTGATGGTGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTCCCC
66 TTGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* * *
2629290 TTCGTCGTGAAGTCGAGCCTTAAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCA
* * * *
2629355 TTGCTTCTTGTGGGCATGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCT
66 TTGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* * * ** *
2629411 TTCGTTGTAAAGTTGAGCCTGGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAAGTATTGTA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCA
* * * * *
2629476 TAT--TGCTGGTGAACACGATATCATTCGTCATGAAGTTGAAATCCTGGATGGCCCC
66 T-TGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* * * *
2629531 TTCGTCGTAAAGTTGAGCCTT-AAATGAGATATCCTTCATCGTGAAGTTGAAATCCAAAGGTTGC
1 TTCGTTGTGAAGTTGAGCCTTGAATTG-GATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGC
* * * *
2629595 ATTGCTGCTTGTGGGCATGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGTCCC
65 ATTGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
* * **
2629652 TTTGTTGTGAAGTTGAGCCTGGAATTGGATATCCTTTTTCGTGAAGTTGAAATCCAA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAA
2629709 TCTCGAGTAA
Statistics
Matches: 455, Mismatches: 77, Indels: 17
0.83 0.14 0.03
Matches are distributed among these distances:
119 5 0.01
120 202 0.44
121 191 0.42
122 5 0.01
123 1 0.00
124 51 0.11
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (121 bp):
TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCA
TTGCTGCTTGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCC
Found at i:2629488 original size:241 final size:241
Alignment explanation
Indices: 2629052--2629708 Score: 948
Period size: 241 Copynumber: 2.7 Consensus size: 241
2629042 CTCATTCGCT
* * * *
2629052 GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGG-TGGA-
1 GTGAAGTTGAGCCTTAAATTGGATATCCTTCATCGTGAAGTTGAAATCC-A---AG-GGTTGCAT
* * * * * *
2629115 TACAGCTTGTGTGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCAC-TTCATTGTG
61 TGCTGCTTGTGGGCATGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCC-CTTTCGTTGTG
* * * * *
2629179 AAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCCAAGTATTGTATGTTGATGG
125 AAGTTGAGCCTGGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAAGTATTGTATATTGATGG
* * * *
2629244 TGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTCCCCTTCGTC
190 TGAACACGATATCATTCGTCATGAAGTTGAAATCCTGGATGGCCCCTTCGTC
* *
2629296 GTGAAGTCGAGCCTTAAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTT
1 GTGAAGTTGAGCCTTAAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTG
*
2629361 CTTGTGGGCATGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCTTTCGTTGTAAAGTTG
66 CTTGTGGGCATGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCTTTCGTTGTGAAGTTG
*
2629426 AGCCTGGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAAGTATTGTATATTGCTGGTGAACA
131 AGCCTGGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAAGTATTGTATATTGATGGTGAACA
2629491 CGATATCATTCGTCATGAAGTTGAAATCCTGGATGGCCCCTTCGTC
196 CGATATCATTCGTCATGAAGTTGAAATCCTGGATGGCCCCTTCGTC
* *
2629537 GTAAAGTTGAGCCTTAAA-TGAGATATCCTTCATCGTGAAGTTGAAATCCAAAGGTTGCATTGCT
1 GTGAAGTTGAGCCTTAAATTG-GATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCT
*
2629601 GCTTGTGGGCATGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGTCCCTTT-GTTGTGAAGT
65 GCTTGTGGGCATGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGG-CCCTTTCGTTGTGAAGT
*
2629665 TGAGCCTGGAATTGGATATCCTT-TTTCGTGAAGTTGAAATCCAA
129 TGAGCCTGGAATTGGATATCCTTCATT-GTGAAGTTGAAATCCAA
2629709 TCTCGAGTAA
Statistics
Matches: 377, Mismatches: 30, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
239 2 0.01
240 10 0.03
241 313 0.83
242 6 0.02
243 1 0.00
244 45 0.12
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (241 bp):
GTGAAGTTGAGCCTTAAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTG
CTTGTGGGCATGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCTTTCGTTGTGAAGTTG
AGCCTGGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAAGTATTGTATATTGATGGTGAACA
CGATATCATTCGTCATGAAGTTGAAATCCTGGATGGCCCCTTCGTC
Found at i:2632686 original size:36 final size:36
Alignment explanation
Indices: 2632616--2632717 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 36
2632606 GTCCTACCCC
* * * *
2632616 ACATGATATCTACCCCACATGCTTTAATTCCTACCCGA-
1 ACATGATCTCTATCCCGCATG--TTAATTTCTACCC-AT
2632654 ACATGATCTCTATCCCGCATGTTAATTTCTACCCAT
1 ACATGATCTCTATCCCGCATGTTAATTTCTACCCAT
* *
2632690 ACATGATCTTTATCCTGCATGTTAATTT
1 ACATGATCTCTATCCCGCATGTTAATTT
2632718 TTAACAAGTC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.02
36 38 0.67
38 18 0.32
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.36
Consensus pattern (36 bp):
ACATGATCTCTATCCCGCATGTTAATTTCTACCCAT
Found at i:2633567 original size:13 final size:13
Alignment explanation
Indices: 2633551--2633575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2633541 TTAACAGCAA
2633551 AAATTAAAATTTT
1 AAATTAAAATTTT
2633564 AAATTAAAATTT
1 AAATTAAAATTT
2633576 AAAAACCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTAAAATTTT
Found at i:2633702 original size:12 final size:12
Alignment explanation
Indices: 2633685--2633709 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2633675 AAGGGAAAAG
2633685 AAATAAAATAAA
1 AAATAAAATAAA
2633697 AAATAAAATAAA
1 AAATAAAATAAA
2633709 A
1 A
2633710 TATGAATAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:2634729 original size:3 final size:3
Alignment explanation
Indices: 2634723--2634762 Score: 62
Period size: 3 Copynumber: 12.7 Consensus size: 3
2634713 TAAAAGATAT
2634723 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TA
2634763 TATTTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 29 0.81
4 7 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2635358 original size:21 final size:18
Alignment explanation
Indices: 2635334--2635382 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
2635324 CGATTAACAA
*
2635334 TATCGATACTGATGCAATTAG
1 TATCGATACTGAT---ATGAG
*
2635355 TATCGATATTGATATGAG
1 TATCGATACTGATATGAG
2635373 TATCGATACT
1 TATCGATACT
2635383 AATAGGAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 13 0.52
21 12 0.48
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (18 bp):
TATCGATACTGATATGAG
Found at i:2636363 original size:27 final size:27
Alignment explanation
Indices: 2636328--2636379 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
2636318 TAATATAATT
2636328 ATAACA-TTTTATAAATTATTTTGTAAA
1 ATAACATTTTTATAAA-TATTTTGTAAA
*
2636355 ATAATATTTTTATAAATATTTTGTA
1 ATAACATTTTTATAAATATTTTGTA
2636380 GTATTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (27 bp):
ATAACATTTTTATAAATATTTTGTAAA
Found at i:2636368 original size:38 final size:37
Alignment explanation
Indices: 2636286--2636369 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 37
2636276 AATTTTTTAT
* * * *
2636286 TTTTTTTAATATTTTATAATTTATATTATAATTAATA
1 TTTTTATAACATTTTATAAATTATATTATAAATAATA
** * *
2636323 TAATTATAACATTTTATAAATTATTTTGTAAAATAATA
1 TTTTTATAACATTTTATAAATTATATTAT-AAATAATA
2636361 TTTTTATAA
1 TTTTTATAA
2636370 ATATTTTGTA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
37 22 0.61
38 14 0.39
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (37 bp):
TTTTTATAACATTTTATAAATTATATTATAAATAATA
Found at i:2636556 original size:61 final size:61
Alignment explanation
Indices: 2636419--2636556 Score: 188
Period size: 61 Copynumber: 2.3 Consensus size: 61
2636409 ATACTAGAAT
* * * * *
2636419 TATAAATTCAATTCATGTTATATTCAGTGTTATAAAGTTTGTATTATTATTTTTAGTCGTA
1 TATAATTTCAATTCGTGTCATATTCAGTGTTATAAAGTTTGTATTATTATTGTTAGTCATA
* * *
2636480 TATAATTTTAGTTCGTGTCATAGTT-GGTGTTATAAAGTTTGTATTATTATTGTTAGTCATA
1 TATAATTTCAATTCGTGTCATA-TTCAGTGTTATAAAGTTTGTATTATTATTGTTAGTCATA
2636541 TATAATTTCAATTCGT
1 TATAATTTCAATTCGT
2636557 TTTATACTTG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
61 64 0.97
62 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.51
Consensus pattern (61 bp):
TATAATTTCAATTCGTGTCATATTCAGTGTTATAAAGTTTGTATTATTATTGTTAGTCATA
Found at i:2639252 original size:4 final size:4
Alignment explanation
Indices: 2639245--2639276 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
2639235 ATATATAATA
2639245 ATAG ATAG ATAG ATAG AT-- ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
2639277 TTGTCTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.08
4 24 0.92
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (4 bp):
ATAG
Found at i:2639268 original size:14 final size:14
Alignment explanation
Indices: 2639249--2639276 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2639239 ATAATAATAG
2639249 ATAGATAGATAGAT
1 ATAGATAGATAGAT
2639263 ATAGATAGATAGAT
1 ATAGATAGATAGAT
2639277 TTGTCTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
ATAGATAGATAGAT
Found at i:2650740 original size:13 final size:13
Alignment explanation
Indices: 2650722--2650748 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2650712 ACTCCGGTTG
2650722 CTTCCTTGGTCGT
1 CTTCCTTGGTCGT
2650735 CTTCCTTGGTCGT
1 CTTCCTTGGTCGT
2650748 C
1 C
2650749 GGAAAATCAG
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:0.00, C:0.33, G:0.22, T:0.44
Consensus pattern (13 bp):
CTTCCTTGGTCGT
Found at i:2657292 original size:15 final size:15
Alignment explanation
Indices: 2657272--2657311 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
2657262 CTCTCAATCA
2657272 AGATTTCCTTGCATC
1 AGATTTCCTTGCATC
2657287 AGATTTCCTTGCATC
1 AGATTTCCTTGCATC
*
2657302 GGATTTCCTT
1 AGATTTCCTT
2657312 TTCATTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.42
Consensus pattern (15 bp):
AGATTTCCTTGCATC
Found at i:2659017 original size:20 final size:21
Alignment explanation
Indices: 2658972--2659023 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
2658962 CTGTTGAAGA
*
2658972 GGTATCGATACTGTAAGGGGT
1 GGTATCGATACTGTAAGGGAT
2658993 GGTATCGATATCTG-AA-GGAT
1 GGTATCGATA-CTGTAAGGGAT
2659013 GGTATCGATAC
1 GGTATCGATAC
2659024 CCTTGAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 13 0.45
21 12 0.41
22 3 0.10
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.29
Consensus pattern (21 bp):
GGTATCGATACTGTAAGGGAT
Found at i:2659074 original size:54 final size:54
Alignment explanation
Indices: 2659008--2659137 Score: 178
Period size: 53 Copynumber: 2.4 Consensus size: 54
2658998 CGATATCTGA
2659008 AGGATGGTATCGATACCCTTGAAACATCGAATGAC-AGATT-GGTATCGGTACCT-TG
1 AGGA-GGTATCGATACCCTTGAAACATCGAATG-CTA-ATTCGGTATCGGTA-CTATG
* *
2659063 AGGAGGTATCGATACCCTTG-AACATCGAATGCTATTTCGGTATTGGTACTATG
1 AGGAGGTATCGATACCCTTGAAACATCGAATGCTAATTCGGTATCGGTACTATG
2659116 AGGAGGTATCGATACCCTTGAA
1 AGGAGGTATCGATACCCTTGAA
2659138 GGGAAGTATC
Statistics
Matches: 69, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
52 5 0.07
53 43 0.62
54 17 0.25
55 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (54 bp):
AGGAGGTATCGATACCCTTGAAACATCGAATGCTAATTCGGTATCGGTACTATG
Found at i:2659545 original size:21 final size:21
Alignment explanation
Indices: 2659521--2659581 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
2659511 TATGATCATA
*
2659521 TGAATATGGAAATGTGAACTT
1 TGAATAAGGAAATGTGAACTT
*
2659542 TGAATAAGTAAATGTGAACTT
1 TGAATAAGGAAATGTGAACTT
*
2659563 TGAATCAATG-AATGTGAAC
1 TGAAT-AAGGAAATGTGAAC
2659582 AGACTCTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (21 bp):
TGAATAAGGAAATGTGAACTT
Found at i:2659748 original size:21 final size:21
Alignment explanation
Indices: 2659715--2659794 Score: 67
Period size: 21 Copynumber: 3.7 Consensus size: 21
2659705 TCGAGGGTCT
2659715 TATGTGGTC-CTTCGGGATAAA
1 TATGTGG-CACTTCGGGATAAA
* *
2659736 TATGCGGCACTTCGGTGCA-AACC
1 TATGTGGCACTTCGG-G-ATAA-A
*
2659759 TATGTGGTC-CTTCGGGATAAT
1 TATGTGG-CACTTCGGGATAAA
2659780 TATGTGGCACTTCGG
1 TATGTGGCACTTCGG
2659795 TGCAAATTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
20 2 0.04
21 26 0.54
22 6 0.12
23 13 0.27
24 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (21 bp):
TATGTGGCACTTCGGGATAAA
Found at i:2659778 original size:44 final size:44
Alignment explanation
Indices: 2659715--2659800 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
2659705 TCGAGGGTCT
2659715 TATGTGGTCCTTCGGGATAAATATGCGGCACTTCGGTGCAAACC
1 TATGTGGTCCTTCGGGATAAATATGCGGCACTTCGGTGCAAACC
* *
2659759 TATGTGGTCCTTCGGGATAATTATGTGGCACTTCGGTGCAAA
1 TATGTGGTCCTTCGGGATAAATATGCGGCACTTCGGTGCAAA
2659801 TTACGAGCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (44 bp):
TATGTGGTCCTTCGGGATAAATATGCGGCACTTCGGTGCAAACC
Found at i:2666235 original size:21 final size:23
Alignment explanation
Indices: 2666210--2666258 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
2666200 CGTATGCTAA
*
2666210 AAAACCTATTCTA-A-TATTTTT
1 AAAACCTATACTATATTATTTTT
2666231 AAAA-CTATACTATATTATTTTT
1 AAAACCTATACTATATTATTTTT
2666253 AAAACC
1 AAAACC
2666259 AAAACTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 11 0.46
23 1 0.04
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAACCTATACTATATTATTTTT
Found at i:2666265 original size:23 final size:22
Alignment explanation
Indices: 2666224--2666279 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2666214 CCTATTCTAA
* * *
2666224 TATTTTTAAAACTATACTATAT
1 TATTTTTAAAACAAAACTACAT
2666246 TATTTTTAAAACCAAAACTACAT
1 TATTTTTAAAA-CAAAACTACAT
* *
2666269 TAGTATTAAAA
1 TATTTTTAAAA
2666280 AATTAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
TATTTTTAAAACAAAACTACAT
Found at i:2669577 original size:60 final size:58
Alignment explanation
Indices: 2669481--2669615 Score: 164
Period size: 59 Copynumber: 2.3 Consensus size: 58
2669471 AATTAAGGGT
* *
2669481 AAAG-TACACAAATGGTCCCCGACTATAGAATATTGTTTTGTTGAGTCCCCTGACAATTG
1 AAAGTTACA-AAATGGTCCCCGACTATAGAATATTGTTTTGTTGAGTCCCC-AACAATTA
* ** * *
2669540 AAAGTTACAAAATGGTCCATCGACTATAGGGTGTTGTTTTGTTGAGTCCCCAACTATTA
1 AAAGTTACAAAATGGTCC-CCGACTATAGAATATTGTTTTGTTGAGTCCCCAACAATTA
*
2669599 AAAATTACAAAATGGTC
1 AAAGTTACAAAATGGTC
2669616 ACTCAACTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 34 0.52
60 32 0.48
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (58 bp):
AAAGTTACAAAATGGTCCCCGACTATAGAATATTGTTTTGTTGAGTCCCCAACAATTA
Found at i:2669612 original size:59 final size:59
Alignment explanation
Indices: 2669485--2669615 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 59
2669475 AAGGGTAAAG
* * *
2669485 TACACAAATGGTCCCCGACTATAGAATATTGTTTTGTTGAGTCCCCTGACAATTGAAAGT
1 TACA-AAATGGTCCCCGACTATAGAATATTGTTTTGTTGAGTCCCCTAACAATTAAAAAT
* ** * *
2669545 TACAAAATGGTCCATCGACTATAGGGTGTTGTTTTGTTGAGTCCCC-AACTATTAAAAAT
1 TACAAAATGGTCC-CCGACTATAGAATATTGTTTTGTTGAGTCCCCTAACAATTAAAAAT
2669604 TACAAAATGGTC
1 TACAAAATGGTC
2669616 ACTCAACTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 30 0.48
60 32 0.52
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (59 bp):
TACAAAATGGTCCCCGACTATAGAATATTGTTTTGTTGAGTCCCCTAACAATTAAAAAT
Found at i:2669881 original size:22 final size:22
Alignment explanation
Indices: 2669853--2669905 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
2669843 GGAATATATG
2669853 AATAGTCGGATGACCAACTTTT
1 AATAGTCGGATGACCAACTTTT
2669875 AATAGTCGGATGACCAACTTTT
1 AATAGTCGGATGACCAACTTTT
2669897 AATAGTCGG
1 AATAGTCGG
2669906 GAGACTCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (22 bp):
AATAGTCGGATGACCAACTTTT
Found at i:2676035 original size:15 final size:15
Alignment explanation
Indices: 2676009--2676060 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
2675999 TAGTAATTTA
*
2676009 ATTTTTAT-TTTAGT
1 ATTTTTATATTTAAT
2676023 ATTTTTATATTTAAT
1 ATTTTTATATTTAAT
2676038 -TTTTTAATATTTGAAT
1 ATTTTT-ATATTT-AAT
2676054 AATTTTT
1 -ATTTTT
2676061 TACTTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 13 0.41
15 11 0.34
16 3 0.09
18 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
ATTTTTATATTTAAT
Found at i:2676035 original size:20 final size:20
Alignment explanation
Indices: 2675990--2676040 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2675980 AATGTGTGCT
*
2675990 TATTTTTTTTAGTAATTTAA
1 TATTTATTTTAGTAATTTAA
* * *
2676010 TTTTTATTTTAGTATTTTTA
1 TATTTATTTTAGTAATTTAA
2676030 TATTTAATTTT
1 TATTT-ATTTT
2676041 TTAATATTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (20 bp):
TATTTATTTTAGTAATTTAA
Found at i:2680779 original size:2 final size:2
Alignment explanation
Indices: 2680772--2680806 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2680762 CTGTTGAATG
2680772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2680807 TGTGTATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2691171 original size:3 final size:3
Alignment explanation
Indices: 2691163--2691199 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2691153 TTCTCGGGAT
2691163 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2691200 AAATAATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2692319 original size:30 final size:31
Alignment explanation
Indices: 2692285--2692358 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
2692275 GGGGCCGTGA
*
2692285 GGCCTACCTAAGAA-CATCTTAGGGCCGCAG
1 GGCCTACCTAAGAATCATCTCAGGGCCGCAG
** *
2692315 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAATCATCTCAGGGCCGCAG
*
2692346 AGCCTACCTAAGA
1 GGCCTACCTAAGA
2692359 GTCACATTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (31 bp):
GGCCTACCTAAGAATCATCTCAGGGCCGCAG
Found at i:2692341 original size:61 final size:61
Alignment explanation
Indices: 2692235--2692358 Score: 155
Period size: 61 Copynumber: 2.0 Consensus size: 61
2692225 TACCCTAAGG
* * *
2692235 GAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAA
1 GAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAA
* *
2692296 GAACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAA
1 GAACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAA
2692357 GA
1 GA
2692359 GTCACATTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
60 2 0.04
61 51 0.93
62 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (61 bp):
GAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAA
Found at i:2693250 original size:13 final size:13
Alignment explanation
Indices: 2693232--2693257 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2693222 AAGAAAGTCA
2693232 ACGGTCAACGGTC
1 ACGGTCAACGGTC
2693245 ACGGTCAACGGTC
1 ACGGTCAACGGTC
2693258 GGGTCGGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:2693269 original size:17 final size:17
Alignment explanation
Indices: 2693247--2693304 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
2693237 CAACGGTCAC
2693247 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2693264 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
2693281 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2693298 GGTCAAC
1 GGTCAAC
2693305 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2693274 original size:7 final size:7
Alignment explanation
Indices: 2693228--2693257 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2693218 GTCAAAGAAA
2693228 GTCAACG
1 GTCAACG
2693235 GTCAACG
1 GTCAACG
2693242 GTC-ACG
1 GTCAACG
2693248 GTCAACG
1 GTCAACG
2693255 GTC
1 GTC
2693258 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:2693322 original size:19 final size:19
Alignment explanation
Indices: 2693298--2693387 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
2693288 AGTCGGGTCG
*
2693298 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
2693317 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
2693336 GGTCAAACCAGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
2693355 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
2693375 GGTCAAACCGGTT
1 GGTCAAACCGGTT
2693388 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 47 0.75
20 15 0.24
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:2693370 original size:10 final size:10
Alignment explanation
Indices: 2693300--2693387 Score: 85
Period size: 9 Copynumber: 9.1 Consensus size: 10
2693290 TCGGGTCGGG
*
2693300 TCAACCCGGT
1 TCAAACCGGT
*
2693310 TCAGACCGG-
1 TCAAACCGGT
2693319 TCAAACCGGT
1 TCAAACCGGT
*
2693329 TCAGACCGG-
1 TCAAACCGGT
*
2693338 TCAAACCAGT
1 TCAAACCGGT
*
2693348 TCGAACCGG-
1 TCAAACCGGT
2693357 TCAAACCGGT
1 TCAAACCGGT
*
2693367 TCAAAACTGG-
1 TC-AAACCGGT
2693377 TCAAACCGGT
1 TCAAACCGGT
2693387 T
1 T
2693388 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 29 0.47
10 27 0.44
11 6 0.10
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:2702397 original size:2 final size:2
Alignment explanation
Indices: 2702390--2702423 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2702380 TATATGTATA
2702390 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2702424 AATGTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2709932 original size:2 final size:2
Alignment explanation
Indices: 2709927--2709957 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2709917 TATAAAAATA
2709927 TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2709958 ATTGTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2712563 original size:67 final size:67
Alignment explanation
Indices: 2712424--2712573 Score: 160
Period size: 67 Copynumber: 2.2 Consensus size: 67
2712414 ACTATCTGTC
* ** ** *
2712424 GCCTTTGAAATTATTTCTCTTGAAGAAAAGTTTCATCTCCCTTAAGACATTTTCTCTTTAAATAT
1 GCCTTTGAAATTGTTTCTCTCCAAGAAAAGTTTCATCTCCCTTAAGACATACTCTCTTTAAACAT
2712489 AA
66 AA
* * * * *
2712491 ACCTTTAAAATTGTTTCTCTCCAA-ACAAAGTTTCGTCTCGCTTGAGACATACTCT-TTTAAAAC
1 GCCTTTGAAATTGTTTCTCTCCAAGA-AAAGTTTCATCTCCCTTAAGACATACTCTCTTT-AAAC
2712554 ATAA
64 ATAA
*
2712558 GCCTTTGAGATTGTTT
1 GCCTTTGAAATTGTTT
2712574 TCTTAAAAAC
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
66 4 0.06
67 63 0.94
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (67 bp):
GCCTTTGAAATTGTTTCTCTCCAAGAAAAGTTTCATCTCCCTTAAGACATACTCTCTTTAAACAT
AA
Found at i:2712756 original size:101 final size:101
Alignment explanation
Indices: 2712562--2712955 Score: 485
Period size: 101 Copynumber: 3.9 Consensus size: 101
2712552 ACATAAGCCT
* * * * * *
2712562 TTGAGATTGTTTTCTTAAAAACAAATTTTATTTTC-CTTGAGATAATTTTCCC-TCAGAACATAA
1 TTGAGATTGTTCTC-TCAAAACAAATTTCA-TCTCGCTTGAGATAATTTTCCCTTGA-AACACAA
* *
2712625 ATTTTTAAATTGTTTCACTTGAAACGAAATTGATCTCAC
63 ATTTTAAAATTGTTTCACTTGAAACAAAATTGATCTCAC
* *
2712664 TTGAGATTGTTCTCTCAAAACAAATTTCATCTCGCTTGAGAAAAGTTTCCCTTGAAACACAAATT
1 TTGAGATTGTTCTCTCAAAACAAATTTCATCTCGCTTGAGATAATTTTCCCTTGAAACACAAATT
* *
2712729 TTGAAATTGATTCACTTGAAACAAAATTGATCTCAC
66 TTAAAATTGTTTCACTTGAAACAAAATTGATCTCAC
*
2712765 TTGAGATTGTTCTCTCAAAACAAATTTCATCTTGCTTGAGATAATTTTCCCTTGAAACACAAATT
1 TTGAGATTGTTCTCTCAAAACAAATTTCATCTCGCTTGAGATAATTTTCCCTTGAAACACAAATT
* *
2712830 TTCAAATTGTTTCACTTGAAACAAAATTGATCTCAT
66 TTAAAATTGTTTCACTTGAAACAAAATTGATCTCAC
* * * * *** **
2712866 TTGTGATTGTTTTC-CTTAAA-AAA-TT-GTCTCGCTTGAGATAATTTTAATTTGAAATGCAAAT
1 TTGAGATTGTTCTCTC-AAAACAAATTTCATCTCGCTTGAGATAATTTTCCCTTGAAACACAAAT
*
2712927 TTTAAAATTGTTTCACTCGAAACAAAATT
65 TTTAAAATTGTTTCACTTGAAACAAAATT
2712956 TTATCTCATC
Statistics
Matches: 260, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
98 56 0.22
99 2 0.01
100 7 0.03
101 180 0.69
102 15 0.06
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (101 bp):
TTGAGATTGTTCTCTCAAAACAAATTTCATCTCGCTTGAGATAATTTTCCCTTGAAACACAAATT
TTAAAATTGTTTCACTTGAAACAAAATTGATCTCAC
Found at i:2713433 original size:45 final size:45
Alignment explanation
Indices: 2713383--2713497 Score: 194
Period size: 45 Copynumber: 2.6 Consensus size: 45
2713373 AATAACCAGG
*
2713383 CTTTCTCAACATGAAGGAACAATGTTATCTCCAAATATTGTTAGA
1 CTTTCTCAACATGAAGGAACAATGTTATCTCCAAATACTGTTAGA
*
2713428 CTTTCTCAACATGAAGGAACAATATTATCTCCAAATACTGTTAGA
1 CTTTCTCAACATGAAGGAACAATGTTATCTCCAAATACTGTTAGA
* *
2713473 CTTCCTCAACACGAAGGAACAATGT
1 CTTTCTCAACATGAAGGAACAATGT
2713498 CGTCCACCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (45 bp):
CTTTCTCAACATGAAGGAACAATGTTATCTCCAAATACTGTTAGA
Found at i:2715441 original size:21 final size:23
Alignment explanation
Indices: 2715417--2715464 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
2715407 TTATTAAAAC
2715417 ATTAAAT-AAATAAA-TTAAGTT
1 ATTAAATAAAATAAATTTAAGTT
*
2715438 ATT-AATAAAATAAATTTGAGTT
1 ATTAAATAAAATAAATTTAAGTT
2715460 ATTAA
1 ATTAA
2715465 TAGATGGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
22 9 0.39
23 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (23 bp):
ATTAAATAAAATAAATTTAAGTT
Found at i:2715462 original size:22 final size:21
Alignment explanation
Indices: 2715424--2715466 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
2715414 AACATTAAAT
2715424 AAATAAATTAAGTTATTAATA
1 AAATAAATTAAGTTATTAATA
*
2715445 AAATAAATTTGAGTTATTAATA
1 AAATAAA-TTAAGTTATTAATA
2715467 GATGGCATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATAAATTAAGTTATTAATA
Found at i:2717728 original size:96 final size:95
Alignment explanation
Indices: 2717552--2717734 Score: 249
Period size: 96 Copynumber: 1.9 Consensus size: 95
2717542 AGTAGTAACC
* * ** * *
2717552 AGTAGATTTCATGATCTATAAATCAGGAATGATCATATTTTCTAGTGAAAATAAGAAACTAGATA
1 AGTAGATTCCATGATCCATAAATCAGGAATGATCATATTTTAAAGTGAAAATAAGAAACCAGAGA
* *
2717617 ACACATTTTAGGTAACCATAGTTCGTAAACT
66 ACACATTTCAAGTAACC-TAGTTCGTAAACT
* * *
2717648 AGTAGATTCCATGATCCATAAATCAGGAATGATCATATTTTAAATTGAAAATAGGTAACCAGAGA
1 AGTAGATTCCATGATCCATAAATCAGGAATGATCATATTTTAAAGTGAAAATAAGAAACCAGAGA
*
2717713 ACATATTTCAAGTAACCTAGTT
66 ACACATTTCAAGTAACCTAGTT
2717735 TATAAACCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
95 5 0.07
96 70 0.93
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (95 bp):
AGTAGATTCCATGATCCATAAATCAGGAATGATCATATTTTAAAGTGAAAATAAGAAACCAGAGA
ACACATTTCAAGTAACCTAGTTCGTAAACT
Found at i:2722652 original size:96 final size:96
Alignment explanation
Indices: 2722479--2722678 Score: 283
Period size: 96 Copynumber: 2.1 Consensus size: 96
2722469 TTTAAGTAGT
* * *
2722479 AACCAGTAGATTTCATGATCCATAAATCAGGAATGATCATATTTTCCAGTGAAAACAAGAAACCA
1 AACCAGTAGATTCCATGATCCATAAATCAGGAACGATCATATTTTACAGTGAAAACAAGAAACCA
* * *
2722544 GATAACACATTTCAGGTAACCATAGTTCATA
66 AAGAACACATTTCAAGTAACCATAGTTCATA
** ** *
2722575 AACCAGTAGATTCCATGATCCATAAATCTTGAACGATCATATTTTACAGTGAAAACTGGTAACCA
1 AACCAGTAGATTCCATGATCCATAAATCAGGAACGATCATATTTTACAGTGAAAACAAGAAACCA
* *
2722640 AAGAACATATTTCAAGTAACTATAGTTCATA
66 AAGAACACATTTCAAGTAACCATAGTTCATA
2722671 AACCAGTA
1 AACCAGTA
2722679 AATCAGTGAT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (96 bp):
AACCAGTAGATTCCATGATCCATAAATCAGGAACGATCATATTTTACAGTGAAAACAAGAAACCA
AAGAACACATTTCAAGTAACCATAGTTCATA
Found at i:2729932 original size:20 final size:20
Alignment explanation
Indices: 2729909--2729950 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2729899 TTTATTTTAA
2729909 TTCTATTCAATTTAGTCGTG
1 TTCTATTCAATTTAGTCGTG
*
2729929 TTCTATTCAATTTAGTTGTG
1 TTCTATTCAATTTAGTCGTG
2729949 TT
1 TT
2729951 GTGGTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.55
Consensus pattern (20 bp):
TTCTATTCAATTTAGTCGTG
Found at i:2733472 original size:19 final size:18
Alignment explanation
Indices: 2733448--2733501 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
2733438 AGAGTCAGAT
2733448 ATCAGATTAGAAATCAAAG
1 ATCAGA-TAGAAATCAAAG
* *
2733467 ATCAGAATAGATATCCAAG
1 ATCAG-ATAGAAATCAAAG
*
2733486 TTCAGGATAGAAATCA
1 ATCA-GATAGAAATCA
2733502 GAGGTTAGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (18 bp):
ATCAGATAGAAATCAAAG
Found at i:2735144 original size:22 final size:23
Alignment explanation
Indices: 2735119--2735162 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2735109 CTTATCAAAG
*
2735119 GTCAGACCGGTCAAA-GTCAACA
1 GTCAGACCGATCAAAGGTCAACA
2735141 GTCAGACCGATCAAAGGTCAAC
1 GTCAGACCGATCAAAGGTCAAC
2735163 GGGTTAGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (23 bp):
GTCAGACCGATCAAAGGTCAACA
Found at i:2735192 original size:17 final size:17
Alignment explanation
Indices: 2735156--2735188 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2735146 ACCGATCAAA
*
2735156 GGTCAACGGGTTAGATC
1 GGTCAACGAGTTAGATC
2735173 GGTCAACGAGTT-GATC
1 GGTCAACGAGTTAGATC
2735189 CGGTTCGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (17 bp):
GGTCAACGAGTTAGATC
Found at i:2737584 original size:19 final size:19
Alignment explanation
Indices: 2737543--2737587 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2737533 AAGAATAAAG
* *
2737543 ATCATAGATCATAATAGAA
1 ATCAAAGATCATAACAGAA
2737562 ATCAAAGATCATAACA-AA
1 ATCAAAGATCATAACAGAA
2737580 TATCAAAG
1 -ATCAAAG
2737588 TTTAGGACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.56, C:0.13, G:0.09, T:0.22
Consensus pattern (19 bp):
ATCAAAGATCATAACAGAA
Found at i:2739278 original size:17 final size:17
Alignment explanation
Indices: 2739256--2739301 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
2739246 ACCGGTCAAA
2739256 GGTTAACAGGTCAGACC
1 GGTTAACAGGTCAGACC
2739273 GGTTAACAGGTCAGACC
1 GGTTAACAGGTCAGACC
*
2739290 GGTCAAC-GGTCA
1 GGTTAACAGGTCA
2739302 ACGAGTTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 5 0.18
17 23 0.82
ACGTcount: A:0.28, C:0.24, G:0.30, T:0.17
Consensus pattern (17 bp):
GGTTAACAGGTCAGACC
Found at i:2740098 original size:22 final size:23
Alignment explanation
Indices: 2740070--2740133 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
2740060 TATCTCCAGC
2740070 AGTGCTAAGGCACTTTAGTA-TA
1 AGTGCTAAGGCACTTTAGTATTA
**
2740092 AGTGCTAATACACTTCTA-TATTA
1 AGTGCTAAGGCACTT-TAGTATTA
2740115 A-TGCTAAGGCACTTTAGTA
1 AGTGCTAAGGCACTTTAGTA
2740134 ACAGTGTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.06
22 28 0.80
23 5 0.14
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (23 bp):
AGTGCTAAGGCACTTTAGTATTA
Found at i:2740780 original size:29 final size:28
Alignment explanation
Indices: 2740748--2740822 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 28
2740738 AAACATGAAG
2740748 GGGAATTAATCAT-ATGCAAAA-ATAGGATA
1 GGGAATTAATC-TCATGCAAAATA-AGGA-A
*
2740777 GGGAATTAATCTCATGCAAAATAAGGAC
1 GGGAATTAATCTCATGCAAAATAAGGAA
*
2740805 GGGAATTAATCCCATGCA
1 GGGAATTAATCTCATGCA
2740823 GAATCTGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 18 0.43
29 23 0.55
30 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (28 bp):
GGGAATTAATCTCATGCAAAATAAGGAA
Found at i:2740808 original size:28 final size:29
Alignment explanation
Indices: 2740748--2740822 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 29
2740738 AAACATGAAG
2740748 GGGAATTAATCAT-ATGCAAAAATAGGATA
1 GGGAATTAATC-TCATGCAAAAATAGGATA
*
2740777 GGGAATTAATCTCATGC-AAAATAAGGA-C
1 GGGAATTAATCTCATGCAAAAAT-AGGATA
*
2740805 GGGAATTAATCCCATGCA
1 GGGAATTAATCTCATGCA
2740823 GAATCTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 22 0.54
29 19 0.46
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (29 bp):
GGGAATTAATCTCATGCAAAAATAGGATA
Found at i:2740869 original size:29 final size:27
Alignment explanation
Indices: 2740806--2740873 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
2740796 AATAAGGACG
* *
2740806 GGAATTAATCCCATGCAGAATCTGAAT
1 GGAATTAATCCCACGCAGAATCAGAAT
2740833 GAGAAATTAATCCCACGCAGAATCAGAACAT
1 G-G-AATTAATCCCACGCAGAATCAG-A-AT
2740864 GGAATTAATC
1 GGAATTAATC
2740874 ACATTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 28 0.80
30 2 0.06
31 3 0.09
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (27 bp):
GGAATTAATCCCACGCAGAATCAGAAT
Found at i:2745538 original size:20 final size:21
Alignment explanation
Indices: 2745484--2745546 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
2745474 GATTCCCCTG
2745484 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
2745508 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
2745528 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
2745547 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:2751086 original size:13 final size:13
Alignment explanation
Indices: 2751064--2751143 Score: 70
Period size: 10 Copynumber: 6.8 Consensus size: 13
2751054 TACACATCTA
2751064 AAAATAATTTTAC
1 AAAATAATTTTAC
*
2751077 AAAATTA-TTT--
1 AAAATAATTTTAC
2751087 AAAATAATTTTAC
1 AAAATAATTTTAC
*
2751100 AAAATTA-TTT--
1 AAAATAATTTTAC
2751110 AAAATAATTTTAC
1 AAAATAATTTTAC
*
2751123 AAAATTA-TTT--
1 AAAATAATTTTAC
2751133 AAAATAATTTT
1 AAAATAATTTT
2751144 TCATAAATGT
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
10 18 0.33
11 9 0.17
12 9 0.17
13 18 0.33
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATAATTTTAC
Found at i:2751090 original size:23 final size:23
Alignment explanation
Indices: 2751064--2751143 Score: 160
Period size: 23 Copynumber: 3.5 Consensus size: 23
2751054 TACACATCTA
2751064 AAAATAATTTTACAAAATTATTT
1 AAAATAATTTTACAAAATTATTT
2751087 AAAATAATTTTACAAAATTATTT
1 AAAATAATTTTACAAAATTATTT
2751110 AAAATAATTTTACAAAATTATTT
1 AAAATAATTTTACAAAATTATTT
2751133 AAAATAATTTT
1 AAAATAATTTT
2751144 TCATAAATGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATAATTTTACAAAATTATTT
Found at i:2751775 original size:29 final size:27
Alignment explanation
Indices: 2751741--2751907 Score: 140
Period size: 29 Copynumber: 5.9 Consensus size: 27
2751731 AATAGAACAA
* * *
2751741 GGAATTAATCCAATGTAGAGTTAGAATG
1 GGAATTAATCC-ATGTAGAATCAGAACG
*
2751769 GGTAATTAATTCCATGCAGAATCAGAACGG
1 GG-AATTAA-TCCATGTAGAATCAGAAC-G
*
2751799 GGAATTAAACCCATGTAGAATCAGAACG
1 GGAATT-AATCCATGTAGAATCAGAACG
*
2751827 GGAATTAATCACATGCAGAA-CAGAACGG
1 GGAATTAATC-CATGTAGAATCAGAAC-G
* *
2751855 GGAATTAATCCCATGAAGAA-CTAGAATG
1 GGAATTAAT-CCATGTAGAATC-AGAACG
*
2751883 AGGAATTAATCCCATGCAGAATCAG
1 -GGAATTAAT-CCATGTAGAATCAG
2751908 GAATGCATCA
Statistics
Matches: 118, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
27 9 0.08
28 37 0.31
29 63 0.53
30 9 0.08
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.21
Consensus pattern (27 bp):
GGAATTAATCCATGTAGAATCAGAACG
Found at i:2752523 original size:26 final size:26
Alignment explanation
Indices: 2752493--2752546 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2752483 TAAAAGGGTT
2752493 AAAGTCAAAGTT-AACGATCAAAAGTC
1 AAAGTCAAA-TTCAACGATCAAAAGTC
* *
2752519 AAAGTCAAATTCAACGATTAGAAGTC
1 AAAGTCAAATTCAACGATCAAAAGTC
2752545 AA
1 AA
2752547 CATTCGACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (26 bp):
AAAGTCAAATTCAACGATCAAAAGTC
Found at i:2756214 original size:19 final size:19
Alignment explanation
Indices: 2756190--2756227 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2756180 AACTCAAACT
2756190 TTTGGTAATGAGTTAACAG
1 TTTGGTAATGAGTTAACAG
2756209 TTTGGTAATGAGTTAACAG
1 TTTGGTAATGAGTTAACAG
2756228 AAATTAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (19 bp):
TTTGGTAATGAGTTAACAG
Found at i:2760756 original size:16 final size:16
Alignment explanation
Indices: 2760735--2760766 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2760725 ATATGTATAT
2760735 TATATATAATTATAGA
1 TATATATAATTATAGA
2760751 TATATATAATTATAGA
1 TATATATAATTATAGA
2760767 AAATCATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TATATATAATTATAGA
Found at i:2761657 original size:20 final size:20
Alignment explanation
Indices: 2761634--2761671 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2761624 CGATTGAGCT
*
2761634 AAAAACCTAAAGGTTGACTC
1 AAAAACCTAAAGGCTGACTC
*
2761654 AAAAATCTAAAGGCTGAC
1 AAAAACCTAAAGGCTGAC
2761672 CCGAATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAACCTAAAGGCTGACTC
Found at i:2763375 original size:21 final size:21
Alignment explanation
Indices: 2763350--2763404 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
2763340 AACCATCGTA
2763350 GATTGTCACGTCAACACTATG
1 GATTGTCACGTCAACACTATG
* * * *
2763371 GATTGTCGCATCAGCATTATG
1 GATTGTCACGTCAACACTATG
* *
2763392 AACTGTCACGTCA
1 GATTGTCACGTCA
2763405 GTACCGTAAC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
GATTGTCACGTCAACACTATG
Found at i:2763559 original size:3 final size:3
Alignment explanation
Indices: 2763551--2763575 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2763541 GTTAATATCA
2763551 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2763576 GTAGACACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2763655 original size:23 final size:23
Alignment explanation
Indices: 2763613--2763672 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
2763603 CAAAAATATT
*
2763613 TTTATTA-TATTATATTTATTTA
1 TTTATTATTATTATATATATTTA
*
2763635 TTTATTATTATTA-ATAATATTTT
1 TTTATTATTATTATAT-ATATTTA
*
2763658 TTTATTATTTTTATA
1 TTTATTATTATTATA
2763673 GGATCCACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 9 0.28
23 22 0.69
24 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTATTATTATTATATATATTTA
Found at i:2763757 original size:33 final size:33
Alignment explanation
Indices: 2763720--2763800 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
2763710 AAAAATAAAT
*
2763720 TAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 TAACGTATTTGAGTCATATTAAAACACTAAAAC
*
2763753 TAACGTATTTGAGTCATATTGAAACACTAAAAC
1 TAACGTATTTGAGTCATATTAAAACACTAAAAC
2763786 TGAA-GTATTTGAGTC
1 T-AACGTATTTGAGTC
2763801 TAAGTAGGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.32
Consensus pattern (33 bp):
TAACGTATTTGAGTCATATTAAAACACTAAAAC
Found at i:2764207 original size:27 final size:27
Alignment explanation
Indices: 2764186--2764237 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2764176 TTTATTTATT
2764186 TATTTTTTATTAATATTATTATATTAA
1 TATTTTTTATTAATATTATTATATTAA
*
2764213 TATTTTTTATTAATATT-TTTTATTA
1 TATTTTTTATTAATATTATTATATTA
2764238 TTCTTTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TATTTTTTATTAATATTATTATATTAA
Found at i:2764244 original size:13 final size:13
Alignment explanation
Indices: 2764173--2764237 Score: 89
Period size: 13 Copynumber: 5.0 Consensus size: 13
2764163 ATATATATAT
2764173 ATATTTATTTATT-
1 ATATTT-TTTATTA
2764186 -TATTTTTTATTA
1 ATATTTTTTATTA
*
2764198 ATATTATTATATTA
1 ATATT-TTTTATTA
2764212 ATATTTTTTATTA
1 ATATTTTTTATTA
2764225 ATATTTTTTATTA
1 ATATTTTTTATTA
2764238 TTCTTTTCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
11 6 0.13
12 5 0.11
13 24 0.51
14 12 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATATTTTTTATTA
Found at i:2768259 original size:110 final size:110
Alignment explanation
Indices: 2768063--2768388 Score: 454
Period size: 110 Copynumber: 3.0 Consensus size: 110
2768053 GTGGTTGTTA
* * * *
2768063 AACTTCACAGCGAAGAGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTAGTCAGAGCCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
* * * * *
2768128 TCAACTTCATAGCGAAGGATATTGGACTTGAGATAACACAAGCTC
66 TCAACTTCACAACGAAAGATATTGGACTCGAGACAACACAAGCTC
* *
2768173 AACTTCACAGCGAAGGGGGGACTGACTGTCAACAAACAACTTTTTAGTTTCATTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
*
2768238 TCAACTTCACAATGAAAGATATTGGACTCGAGACAACACAAGCTC
66 TCAACTTCACAACGAAAGATATTGGACTCGAGACAACACAAGCTC
* * * *
2768283 AACTTCACAACTAAGGGGCGACTGATTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
* * * * * *
2768348 TCAACTTCTCAGCGAAGGAGATTGGACTCAAAACAACACAA
66 TCAACTTCACAACGAAAGATATTGGACTCGAGACAACACAA
2768389 TTTGCTCGAG
Statistics
Matches: 191, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 191 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (110 bp):
AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
TCAACTTCACAACGAAAGATATTGGACTCGAGACAACACAAGCTC
Found at i:2769521 original size:3 final size:3
Alignment explanation
Indices: 2769497--2769553 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
2769487 CAAAAACATT
2769497 TTA TTA -TA TTA -TA TTTA TTTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2769541 TTA TTA TTT TTA T
1 TTA TTA TTA TTA T
2769554 AGGCCCCACA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 6 0.12
3 36 0.75
4 6 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2769639 original size:33 final size:33
Alignment explanation
Indices: 2769602--2769683 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
2769592 AAAAATAAAT
2769602 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
* *
2769635 CAACGTATTTAAGTCATATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
*
2769668 CGAA-GCATTTGAGTCC
1 C-AACGTATTTGAGTCC
2769684 AAGTAGGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 41 0.95
34 2 0.05
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAAAC
Found at i:2770143 original size:33 final size:33
Alignment explanation
Indices: 2770106--2770191 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
2770096 AGTCCTACTT
* *
2770106 GGACTCAAATGC-TTCGGTTTTAGTGTTTTAATA
1 GGACTCAAATACGTT-GATTTTAGTGTTTTAATA
2770139 GGACTCAAATACGTTGATTTTAGTGTTTTAATA
1 GGACTCAAATACGTTGATTTTAGTGTTTTAATA
2770172 GGACTCAAATACGTTGATTT
1 GGACTCAAATACGTTGATTT
2770192 ATTTTCTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 48 0.96
34 2 0.04
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.41
Consensus pattern (33 bp):
GGACTCAAATACGTTGATTTTAGTGTTTTAATA
Found at i:2770249 original size:3 final size:3
Alignment explanation
Indices: 2770241--2770297 Score: 50
Period size: 3 Copynumber: 19.3 Consensus size: 3
2770231 GGCCTACAAA
*
2770241 AAT AAT AAT AA- AAT ATT AAT AAT AAT AAT AAAT AAAT AA- ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT A-AT AAT
2770287 -AT AAT AA- AAT A
1 AAT AAT AAT AAT A
2770298 TTTTTATAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
2 7 0.15
3 31 0.67
4 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2770271 original size:23 final size:22
Alignment explanation
Indices: 2770241--2770299 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
2770231 GGCCTACAAA
2770241 AATAATAATAAAATATTAATAAT
1 AATAATAATAAAATATTAAT-AT
2770264 AATAATAA-ATAAATA--AATAT
1 AATAATAATA-AAATATTAATAT
2770284 AAT-ATAATAAAATATT
1 AATAATAATAAAATATT
2770300 TTTATAGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
19 9 0.28
20 6 0.19
21 3 0.09
22 1 0.03
23 13 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATAATAATAAAATATTAATAT
Found at i:2770278 original size:17 final size:17
Alignment explanation
Indices: 2770240--2770294 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
2770230 AGGCCTACAA
2770240 AAATAATAATAA-AATAT
1 AAATAATAATAATAA-AT
*
2770257 TAATAATAATAATAAAT
1 AAATAATAATAATAAAT
2770274 AAATAA-ATATAATATAAT
1 AAATAATA-ATAATA-AAT
2770292 AAA
1 AAA
2770295 ATATTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 1 0.03
17 24 0.73
18 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAATAATAATAAAT
Found at i:2770431 original size:13 final size:13
Alignment explanation
Indices: 2770401--2770432 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
2770391 AAATCAGAAA
2770401 TAAAATATAATTT
1 TAAAATATAATTT
2770414 T-AAATATAATTT
1 TAAAATATAATTT
2770426 TAAAATA
1 TAAAATA
2770433 AATGATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAATATAATTT
Found at i:2770464 original size:12 final size:12
Alignment explanation
Indices: 2770407--2770465 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
2770397 GAAATAAAAT
2770407 ATAATT-TTAAA
1 ATAATTATTAAA
2770418 TATAATT-TTAAA
1 -ATAATTATTAAA
* *
2770430 ATAAATGATCAAA
1 AT-AATTATTAAA
*
2770443 ACAA-TATTAAA
1 ATAATTATTAAA
2770454 ATAATTATTAAA
1 ATAATTATTAAA
2770466 TAGTTAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 10 0.26
12 23 0.61
13 5 0.13
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (12 bp):
ATAATTATTAAA
Found at i:2770766 original size:6 final size:6
Alignment explanation
Indices: 2770755--2770786 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2770745 TTTTATCCTG
2770755 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TC
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TC
2770787 TTCCTTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCCTC
Found at i:2782353 original size:20 final size:20
Alignment explanation
Indices: 2782327--2782378 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2782317 TGATTCAATC
*
2782327 GGTATCGATACCGAAGGGGTA
1 GGTATCGATACCGAA-GGGAA
2782348 -GTATCGATACCGAAGGGAA
1 GGTATCGATACCGAAGGGAA
2782367 GGTATCGATACC
1 GGTATCGATACC
2782379 ATTTCAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.31, C:0.17, G:0.33, T:0.19
Consensus pattern (20 bp):
GGTATCGATACCGAAGGGAA
Found at i:2782452 original size:22 final size:19
Alignment explanation
Indices: 2782404--2782456 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
2782394 GCAAAAATGA
*
2782404 TATCGATACCATAGTAGAG
1 TATCAATACCATAGTAGAG
*
2782423 CATCAATACCATAGTATAGTAG
1 TATCAATACCATAG--TAG-AG
2782445 TATCAATACCAT
1 TATCAATACCAT
2782457 GGAAGGGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.43
21 3 0.11
22 13 0.46
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (19 bp):
TATCAATACCATAGTAGAG
Found at i:2783013 original size:20 final size:20
Alignment explanation
Indices: 2782988--2783114 Score: 110
Period size: 20 Copynumber: 5.8 Consensus size: 20
2782978 GTGCATTATT
2782988 GGCATGAAAGGATGCATTAA
1 GGCATGAAAGGATGCATTAA
2783008 GGCATGAAAGGATGCCATAAATAAAA
1 GGCATGAAAGGATG-CAT---T--AA
* *
2783034 TGCATGAAAGGATCCATTAA
1 GGCATGAAAGGATGCATTAA
2783054 GGCATGAAAGGATGCCATAAATAAAA
1 GGCATGAAAGGATG-CAT---T--AA
* *
2783080 TGCATAAAAGGATGCATTAA
1 GGCATGAAAGGATGCATTAA
2783100 GGCATGAAAGGATGC
1 GGCATGAAAGGATGC
2783115 CATAAATAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
20 43 0.49
21 6 0.07
22 2 0.02
24 2 0.02
25 6 0.07
26 28 0.32
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (20 bp):
GGCATGAAAGGATGCATTAA
Found at i:2783038 original size:26 final size:26
Alignment explanation
Indices: 2783009--2783166 Score: 178
Period size: 26 Copynumber: 6.5 Consensus size: 26
2782999 ATGCATTAAG
2783009 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
*
2783035 GCATGAAAGGAT-CCAT---T--AAG
1 GCATGAAAGGATGCCATAAATAAAAT
2783055 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
* *
2783081 GCATAAAAGGATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAAATAAAAT
2783101 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
* *
2783127 GAATGAAAGGATACCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
*
2783153 GCATGAAATGATGC
1 GCATGAAAGGATGC
2783167 ATTAAGGAAT
Statistics
Matches: 109, Mismatches: 11, Indels: 24
0.76 0.08 0.17
Matches are distributed among these distances:
20 28 0.26
21 7 0.06
22 2 0.02
24 2 0.02
25 7 0.06
26 63 0.58
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAAATAAAAT
Found at i:2783056 original size:46 final size:46
Alignment explanation
Indices: 2782989--2783143 Score: 265
Period size: 46 Copynumber: 3.3 Consensus size: 46
2782979 TGCATTATTG
*
2782989 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATCCATTAAGGCATGAAAGGATGCCATAAATAAAAT
2783035 GCATGAAAGGATCCATTAAGGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATCCATTAAGGCATGAAAGGATGCCATAAATAAAAT
* *
2783081 GCATAAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATCCATTAAGGCATGAAAGGATGCCATAAATAAAAT
*
2783127 GAATGAAAGGATACCAT
1 GCATGAAAGGAT-CCAT
2783144 AAATAAAATG
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
46 99 0.97
47 3 0.03
ACGTcount: A:0.46, C:0.12, G:0.23, T:0.19
Consensus pattern (46 bp):
GCATGAAAGGATCCATTAAGGCATGAAAGGATGCCATAAATAAAAT
Found at i:2783134 original size:72 final size:72
Alignment explanation
Indices: 2783057--2783201 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 72
2783047 CCATTAAGGC
* * *
2783057 ATGAAAGGATGCCATAAATAAAATGCATAAAAGGATGCATTAAGGCATGAAAGGATGCCATAAAT
1 ATGAAAGGATACCATAAATAAAATGCATAAAAGGATGCATTAAGGAATGAAAGGACGCCATAAAT
2783122 AAAATGA
66 AAAATGA
* *
2783129 ATGAAAGGATACCATAAATAAAATGCATGAAATGATGCATTAAGGAATGAAAGGACGCCATAAAT
1 ATGAAAGGATACCATAAATAAAATGCATAAAAGGATGCATTAAGGAATGAAAGGACGCCATAAAT
2783194 AAAATGA
66 AAAATGA
2783201 A
1 A
2783202 ATTTAACAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.19
Consensus pattern (72 bp):
ATGAAAGGATACCATAAATAAAATGCATAAAAGGATGCATTAAGGAATGAAAGGACGCCATAAAT
AAAATGA
Found at i:2786350 original size:16 final size:17
Alignment explanation
Indices: 2786325--2786359 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2786315 TAAGGAAAAT
*
2786325 AAGAACAAGAGAAACTA
1 AAGAACAAGAAAAACTA
2786342 AAGAA-AAGAAAAACTA
1 AAGAACAAGAAAAACTA
2786358 AA
1 AA
2786360 CAAGAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.71, C:0.09, G:0.14, T:0.06
Consensus pattern (17 bp):
AAGAACAAGAAAAACTA
Found at i:2788079 original size:33 final size:33
Alignment explanation
Indices: 2788031--2788113 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
2788021 AACTTTAAAG
*
2788031 TTTTTTTTTT-TAAAAAAAACTTTAAATTAAGC
1 TTTTTTTTTTAAAAAAAAAACTTTAAATTAAGC
2788063 TTTTTTTTTTAAAAAAAAAACTTTAAATTAAGC
1 TTTTTTTTTTAAAAAAAAAACTTTAAATTAAGC
2788096 --TTTTTTTTAAAAAAAAAA
1 TTTTTTTTTTAAAAAAAAAA
2788114 TTGTAGGTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
31 18 0.37
32 10 0.20
33 21 0.43
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (33 bp):
TTTTTTTTTTAAAAAAAAAACTTTAAATTAAGC
Found at i:2788589 original size:2 final size:2
Alignment explanation
Indices: 2788584--2788615 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2788574 AATAAATTAA
2788584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2788616 TATGCATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2789403 original size:16 final size:16
Alignment explanation
Indices: 2789382--2789436 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
2789372 TACATATAAA
2789382 TAATTTTTT-AATAATT
1 TAATTTTTTGAAT-ATT
2789398 TAATTTTTTGAATATT
1 TAATTTTTTGAATATT
* *
2789414 TAAATATTTGAA-ATT
1 TAATTTTTTGAATATT
2789429 TAAATTTT
1 T-AATTTT
2789437 AAACTAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.12
16 26 0.79
17 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
TAATTTTTTGAATATT
Found at i:2790719 original size:15 final size:15
Alignment explanation
Indices: 2790699--2790781 Score: 85
Period size: 15 Copynumber: 5.5 Consensus size: 15
2790689 GCTCGATCCG
*
2790699 ATCCGAGTAACACAT
1 ATCCGAATAACACAT
2790714 ATCCGAATAACACAT
1 ATCCGAATAACACAT
* *
2790729 ATCCAAATAACATAT
1 ATCCGAATAACACAT
** *
2790744 ATCTAAATAACATAT
1 ATCCGAATAACACAT
**
2790759 ATATGAATAACACAT
1 ATCCGAATAACACAT
*
2790774 ATCTGAAT
1 ATCCGAAT
2790782 TATGATATGA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 60 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.27
Consensus pattern (15 bp):
ATCCGAATAACACAT
Found at i:2794058 original size:23 final size:23
Alignment explanation
Indices: 2794016--2794078 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
2794006 TAAGATTAAG
2794016 AATTAATTTAATAAATAAAATAT
1 AATTAATTTAATAAATAAAATAT
2794039 AATT-ATTTAA-AATATAAAA-AT
1 AATTAATTTAATAA-ATAAAATAT
*
2794060 -ATTAAATTAAATTAAATAA
1 AATT-AATTTAA-TAAATAA
2794079 TTTCTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 3 0.09
21 4 0.12
22 17 0.50
23 8 0.24
24 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTAATTTAATAAATAAAATAT
Found at i:2796419 original size:42 final size:43
Alignment explanation
Indices: 2796350--2796471 Score: 138
Period size: 43 Copynumber: 2.9 Consensus size: 43
2796340 TGTGAAGAGA
* * * *
2796350 AAACACCGTAAAAGGTCAAGTTATATAGCGATGTTTTT-TCAC
1 AAACACCGAAAAAGGTCGAGCTATATAGCGGTGTTTTTCTCAC
* * *
2796392 AAACACCAAAAAAGGTCGAGCTCTATAGCGGTGTTTTTCTTAC
1 AAACACCGAAAAAGGTCGAGCTATATAGCGGTGTTTTTCTCAC
* * * *
2796435 AAACGCTGAAAAAGGTCGAGCTTTATAGTGGTGTTTT
1 AAACACCGAAAAAGGTCGAGCTATATAGCGGTGTTTT
2796472 AATATTTTGT
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 32 0.48
43 35 0.52
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (43 bp):
AAACACCGAAAAAGGTCGAGCTATATAGCGGTGTTTTTCTCAC
Found at i:2801785 original size:7 final size:7
Alignment explanation
Indices: 2801773--2801809 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2801763 GTCAAAGAAA
2801773 GTCAACG
1 GTCAACG
2801780 GTCAACG
1 GTCAACG
2801787 GTC-ACG
1 GTCAACG
2801793 GTCAACG
1 GTCAACG
2801800 GTCAACG
1 GTCAACG
2801807 GTC
1 GTC
2801810 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2801795 original size:13 final size:14
Alignment explanation
Indices: 2801773--2801809 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
2801763 GTCAAAGAAA
2801773 GTCAACGGTCAACG
1 GTCAACGGTCAACG
2801787 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
2801800 GTCAACGGTC
1 GTCAACGGTC
2801810 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:2801821 original size:17 final size:17
Alignment explanation
Indices: 2801799--2801839 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2801789 CACGGTCAAC
* *
2801799 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGAGTCG
2801816 GGTCAACAGTCGAGTCG
1 GGTCAACAGTCGAGTCG
2801833 GGTCAAC
1 GGTCAAC
2801840 CCGGTTCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.39, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGAGTCG
Found at i:2801857 original size:19 final size:20
Alignment explanation
Indices: 2801833--2801884 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2801823 AGTCGAGTCG
* *
2801833 GGTCAACCCGGTTC-AGACC
1 GGTCAAACCGGTTCGAAACC
*
2801852 GGTCAAACCGGTTCGAAACT
1 GGTCAAACCGGTTCGAAACC
2801872 GGTCAAACCGGTT
1 GGTCAAACCGGTT
2801885 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (20 bp):
GGTCAAACCGGTTCGAAACC
Found at i:2809025 original size:13 final size:14
Alignment explanation
Indices: 2809007--2809036 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2808997 GTCAAAGAAA
2809007 GTCAACGGTC-ACG
1 GTCAACGGTCAACG
2809020 GTCAACGGTCAACG
1 GTCAACGGTCAACG
2809034 GTC
1 GTC
2809037 GGGTCAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:2809027 original size:7 final size:7
Alignment explanation
Indices: 2809007--2809036 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2808997 GTCAAAGAAA
2809007 GTCAACG
1 GTCAACG
2809014 GTC-ACG
1 GTCAACG
2809020 GTCAACG
1 GTCAACG
2809027 GTCAACG
1 GTCAACG
2809034 GTC
1 GTC
2809037 GGGTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:2809086 original size:9 final size:9
Alignment explanation
Indices: 2809072--2809135 Score: 65
Period size: 10 Copynumber: 6.7 Consensus size: 9
2809062 CCCGGTTCAG
2809072 ACCGGTCAA
1 ACCGGTCAA
*
2809081 ACCGGTTCAG
1 ACCGG-TCAA
2809091 ACCGGTCAA
1 ACCGGTCAA
*
2809100 ACCGGTTCGA
1 ACCGG-TCAA
2809110 ACCGGTTCAAA
1 ACCGG-TC-AA
*
2809121 ACTGGTCAA
1 ACCGGTCAA
2809130 ACCGGT
1 ACCGGT
2809136 TTTCCAGCAG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
9 20 0.43
10 21 0.46
11 5 0.11
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:2809087 original size:19 final size:19
Alignment explanation
Indices: 2809063--2809120 Score: 91
Period size: 19 Copynumber: 3.0 Consensus size: 19
2809053 CGGGTCAACC
2809063 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGGTCAAA
2809082 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGGTCAAA
2809101 CCGGTTC-GAACCGGTTCAAA
1 CCGGTTCAG-ACCGG-TCAAA
2809121 ACTGGTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
18 1 0.03
19 31 0.84
20 5 0.14
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (19 bp):
CCGGTTCAGACCGGTCAAA
Found at i:2809094 original size:10 final size:10
Alignment explanation
Indices: 2809063--2809118 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
2809053 CGGGTCAACC
2809063 CCGGTTCAGA
1 CCGGTTCAGA
*
2809073 CCGG-TCAAA
1 CCGGTTCAGA
2809082 CCGGTTCAGA
1 CCGGTTCAGA
*
2809092 CCGG-TCAAA
1 CCGGTTCAGA
2809101 CCGGTTC-GAA
1 CCGGTTCAG-A
2809111 CCGGTTCA
1 CCGGTTCA
2809119 AAACTGGTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 16 0.42
10 22 0.58
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (10 bp):
CCGGTTCAGA
Found at i:2811876 original size:14 final size:14
Alignment explanation
Indices: 2811859--2811888 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2811849 ATCTACATGT
*
2811859 AATAAAATAATAAA
1 AATAAAAAAATAAA
2811873 AATAAAAAAATAAA
1 AATAAAAAAATAAA
2811887 AA
1 AA
2811889 AAATGCTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AATAAAAAAATAAA
Found at i:2813571 original size:89 final size:89
Alignment explanation
Indices: 2813456--2813631 Score: 291
Period size: 89 Copynumber: 2.0 Consensus size: 89
2813446 TAATCCCAAA
* * *
2813456 TATTTAATTTTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATTCCTAATATGAT
1 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGAT
2813521 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
*
2813546 TATTAAATTCTAATT-ATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
*
2813610 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
2813632 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 33 0.41
89 35 0.43
90 13 0.16
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (89 bp):
TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:2824498 original size:2 final size:2
Alignment explanation
Indices: 2824491--2824538 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2824481 ACACATTAAG
2824491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2824533 AT AT AT
1 AT AT AT
2824539 GAAAAAATCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2824599 original size:17 final size:18
Alignment explanation
Indices: 2824579--2824612 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2824569 TCACAAATTG
2824579 ATTAAATAA-TAATATTT
1 ATTAAATAATTAATATTT
*
2824596 ATTAATTAATTAATATT
1 ATTAAATAATTAATATT
2824613 AAGAAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAAATAATTAATATTT
Done.