Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008426.1 Hibiscus syriacus cultivar Beakdansim tig00111210_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: 4445546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:4260979 original size:110 final size:110
Alignment explanation
Indices: 4260783--4260991 Score: 332
Period size: 110 Copynumber: 1.9 Consensus size: 110
4260773 CCCTTTTTGG
* * *
4260783 ATTAATTCCTCCTCCAATTTCCCCAAATTGATTCCTACAATCCCTAACTCTTCCTCCGTTTTCCT
1 ATTAATTCCTCCTCCAATTTCCCCAAATTGATTCCTACAATCCCTAACCCTTCCTCCATTTTCCC
*
4260848 AATTCGCATTTCCTTGTGACCCTCTTCTTCTCCTCCAACTGTAAC
66 AATTCGCATTTCCTAGTGACCCTCTTCTTCTCCTCCAACTGTAAC
*
4260893 ATTAATTCCTTCC-CCAATTTCCTCAAATTGATTCCTACAATCCCTAACCCTTCCTCCATTTTCC
1 ATTAATTCC-TCCTCCAATTTCCCCAAATTGATTCCTACAATCCCTAACCCTTCCTCCATTTTCC
*
4260957 CAATTCGCGTTTCCTCAG-GACCCTCTTCTTCTCCT
65 CAATTCGCATTTCCT-AGTGACCCTCTTCTTCTCCT
4260992 TTATCCGTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
110 87 0.96
111 4 0.04
ACGTcount: A:0.20, C:0.37, G:0.05, T:0.38
Consensus pattern (110 bp):
ATTAATTCCTCCTCCAATTTCCCCAAATTGATTCCTACAATCCCTAACCCTTCCTCCATTTTCCC
AATTCGCATTTCCTAGTGACCCTCTTCTTCTCCTCCAACTGTAAC
Found at i:4266502 original size:14 final size:14
Alignment explanation
Indices: 4266483--4266516 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4266473 CTGTTGCATT
*
4266483 TGCATTCGCACCTA
1 TGCATTCACACCTA
*
4266497 TGCATTCACACCTT
1 TGCATTCACACCTA
4266511 TGCATT
1 TGCATT
4266517 TTTACGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (14 bp):
TGCATTCACACCTA
Found at i:4266538 original size:20 final size:19
Alignment explanation
Indices: 4266509--4266558 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
4266499 CATTCACACC
*
4266509 TTTGCATTTTTACGTTTGCA
1 TTTGCATTTTTACATTT-CA
*
4266529 TTTTCATTTTTTACATTTCA
1 TTTGCA-TTTTTACATTTCA
4266549 TTTGCATTTT
1 TTTGCATTTT
4266559 GTTTAAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 12 0.46
21 10 0.38
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTGCATTTTTACATTTCA
Found at i:4269073 original size:6 final size:6
Alignment explanation
Indices: 4269048--4269111 Score: 82
Period size: 6 Copynumber: 11.2 Consensus size: 6
4269038 TTTAAAGAAA
*
4269048 AAAAAG -AAAAG -AAAAG -AAAAG AAAAA- AGGAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG
4269093 AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG A
4269112 GAAGAAGAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
5 16 0.30
6 36 0.68
7 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:4269074 original size:12 final size:12
Alignment explanation
Indices: 4269047--4269120 Score: 75
Period size: 12 Copynumber: 6.2 Consensus size: 12
4269037 TTTTAAAGAA
4269047 AAAAAAGAAAAG
1 AAAAAAGAAAAG
4269059 --AAAAGAAAAG
1 AAAAAAGAAAAG
*
4269069 AAAAAAGGAAAG
1 AAAAAAGAAAAG
4269081 -AAAAAGAAAA-
1 AAAAAAGAAAAG
4269091 AGAAAAAGAAAAAG
1 A-AAAAAG-AAAAG
4269105 AAAAAGAGAAGAAG
1 AAAAA-AGAA-AAG
4269119 AA
1 AA
4269121 CGAGAAGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
10 10 0.19
11 9 0.17
12 15 0.29
13 10 0.19
14 8 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:4269079 original size:18 final size:18
Alignment explanation
Indices: 4269041--4269109 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
4269031 TAGCTCTTTT
* *
4269041 AAAGAAAAAAAAGAAAAGA
1 AAAGAAAAGAAA-AAAGGA
4269060 AAAGAAAAGAAAAAAGG-
1 AAAGAAAAGAAAAAAGGA
*
4269077 AAAGAAAA-AGAAAAAGAA
1 AAAGAAAAGA-AAAAAGGA
4269095 AAAGAAAAAGAAAAA
1 AAAG-AAAAGAAAAA
4269110 GAGAAGAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
16 1 0.02
17 14 0.33
18 8 0.19
19 19 0.44
20 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGAAAAAAGGA
Found at i:4271324 original size:139 final size:139
Alignment explanation
Indices: 4271068--4272108 Score: 1486
Period size: 139 Copynumber: 7.5 Consensus size: 139
4271058 ATTTCAATAT
* * * * * *
4271068 AGAGTTTATAATGAGAAGAACTCATCTGATAAGGAAGAAGAAGTTTATAATGAGAATAACTT-TT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
4271132 CCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACTCCTTACTCGAGGGATCAATA
66 -CAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACA
4271197 TTTCCAGTGG
130 TTTCCAGTGG
* *
4271207 AGAGTTCATAATGAGAAGAACTCATCCGGTGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
4271272 CAACCTTAGCTCGATTTATTGCAAATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACAT
66 CAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACAT
* *
4271337 CTACAGTGG
131 TTCCAGTGG
4271346 AGAGTTCATAATGAGAAGAACTCAT-CGATGAGGG-GAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
4271409 CAACCTTAGCTCGATTCATCACATATGGAGTTGAATC-GACGACCCCTAACTCGAGAGATCAATA
66 CAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAG-TGACCCCTCACTCGAGGGATCAACA
*
4271473 TTTCTAGTGG
130 TTTCCAGTGG
* * *
4271483 AGATTTTATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGAT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG-T
* *
4271548 T-AACCTTAGCTCGATTCATCGCATATCGAGTTGAATCAATGACCCCTCACTCGAGGGATCAACA
65 TCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACA
4271612 TTTCCAGTGG
130 TTTCCAGTGG
* *
4271622 ATAGTTCATAATGAGAAGAACTAATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
4271687 CAACCTTCGCTCGATTCATCGCATATGGAGTTGAATCAGTGACCCCTCACTCGAGTGATCAACAT
66 CAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACAT
4271752 TTCCTA-TGG
131 TTCC-AGTGG
* * * *
4271761 AGAGTTCATAATGATAATAACTCATCCGATGAGAGAGGAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
4271826 CAACCTTAGCTCGATTCATCGCATATGGAGTTAAATCAGTGACACTTTACTCAAGGGATCAACAT
66 CAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACAT
**
4271891 TTTTAGTGG
131 TTCCAGTGG
* * * *
4271900 AGATTTCAAAATGAGAAGAA-TCATCTGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
** * * *
4271964 CAACCTTAATTCGATTCATCGCATATGGAGTTGAATCAGCG-TCCTTCACTCGAGGGATCAACAT
66 CAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACAT
* *
4272028 TTTCAATGG
131 TTCCAGTGG
* *
4272037 AGAGTTCATAATGAGAATAACTCATTCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
4272102 CAACCTT
66 CAACCTT
4272109 TTGCTCGACT
Statistics
Matches: 803, Mismatches: 89, Indels: 21
0.88 0.10 0.02
Matches are distributed among these distances:
136 1 0.00
137 155 0.19
138 144 0.18
139 498 0.62
140 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (139 bp):
AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACAT
TTCCAGTGG
Found at i:4272015 original size:415 final size:415
Alignment explanation
Indices: 4271077--4272108 Score: 1560
Period size: 415 Copynumber: 2.5 Consensus size: 415
4271067 TAGAGTTTAT
* *
4271077 AATGAGAAGAACTCATCTGAT-AAGGAAGAAGAAGTTTATAATGAGAATAACTT-TTCCAACCTT
1 AATGAGAAGAACTCATCTGATGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTT-CAACCTT
*
4271140 AGCTCGATTCATCGCATATGGAGTTGAATCAGCGACTCCTT-ACTCGAGGGATCAATATTTCCAG
64 AGCTCGATTCATCGCATATGGAGTTGAATCAGCGA-TCCTTCACTCGAGGGATCAACATTTCCAG
* *
4271204 TGGAGAGTTCATAATGAGAAGAACTCATCCGGTGAGGGAAAAGAAGTTCATAATGAGAAGAACTT
128 TGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
* *
4271269 GTTCAACCTTAGCTCGATTTATTGCAAATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAA
193 GTTCAACCTTAGCTCGATTCATCGCAAATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAA
4271334 CATCTACAGTGGAGAGTTCATAATGAGAAGAACTCATCGATGAGGGGAAGAAGTTCATAATGAGA
258 CATCTACAGTGGAGAGTTCATAATGAGAAGAACTCATCGATGAGGGGAAGAAGTTCATAATGAGA
* * *
4271399 AGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCGACGACCCCTAACTCGAG
323 AGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTAAATCGACGACACCTAACTCAAG
* * *
4271464 AGATCAATATTTCTAGTGGAGATTTTAT
388 AGATCAACATTTCTAGTGGAGATTTCAA
*
4271492 AATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGATT-AACCTTA
1 AATGAGAAGAACTCATCTGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTG-TTCAACCTTA
* ** * *
4271556 GCTCGATTCATCGCATATCGAGTTGAATCAATGACCCCTCACTCGAGGGATCAACATTTCCAGTG
65 GCTCGATTCATCGCATATGGAGTTGAATCAGCGATCCTTCACTCGAGGGATCAACATTTCCAGTG
* *
4271621 GATAGTTCATAATGAGAAGAACTAATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
130 GAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
4271686 TCAACCTTCGCTCGATTCATCGCATATGGAGTTGAATCAGTGACCCCTCACTCGAGTGATCAACA
195 TCAACCTTAGCTCGATTCATCGCAAATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACA
* * * *
4271751 TTTCCTA-TGGAGAGTTCATAATGATAATAACTCATCCGATGAGAGAGG-AGAAGTTCATAATGA
260 TCTAC-AGTGGAGAGTTCATAATGAGAAGAACTCAT-CGATGAG-G-GGAAGAAGTTCATAATGA
* * * *
4271814 GAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTAAATC-AGTGACACTTTACTC
321 GAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTAAATCGA-CGACACCTAACTC
* *
4271878 AAGGGATCAACATTTTTAGTGGAGATTTCAA
385 AAGAGATCAACATTTCTAGTGGAGATTTCAA
*
4271909 AATGAGAAGAA-TCATCTGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAA
1 AATGAGAAGAACTCATCTGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAG
* * *
4271973 TTCGATTCATCGCATATGGAGTTGAATCAGCG-TCCTTCACTCGAGGGATCAACATTTTCAATGG
66 CTCGATTCATCGCATATGGAGTTGAATCAGCGATCCTTCACTCGAGGGATCAACATTTCCAGTGG
* *
4272037 AGAGTTCATAATGAGAATAACTCATTCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
131 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
4272102 CAACCTT
196 CAACCTT
4272109 TTGCTCGACT
Statistics
Matches: 559, Mismatches: 48, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
414 3 0.01
415 356 0.64
416 88 0.16
417 110 0.20
418 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (415 bp):
AATGAGAAGAACTCATCTGATGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAG
CTCGATTCATCGCATATGGAGTTGAATCAGCGATCCTTCACTCGAGGGATCAACATTTCCAGTGG
AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTAGCTCGATTCATCGCAAATGGAGTTGAATCAGTGACCCCTCACTCGAGGGATCAACAT
CTACAGTGGAGAGTTCATAATGAGAAGAACTCATCGATGAGGGGAAGAAGTTCATAATGAGAAGA
ACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTAAATCGACGACACCTAACTCAAGAGA
TCAACATTTCTAGTGGAGATTTCAA
Found at i:4272181 original size:122 final size:117
Alignment explanation
Indices: 4272020--4272368 Score: 432
Period size: 122 Copynumber: 2.9 Consensus size: 117
4272010 CACTCGAGGG
* * * *
4272020 ATCAACATTTTCAATGGAGAGTTCATAATGAGAATAACTCATTCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAAT-GAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCAT
* *
4272085 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGACAA
65 AATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGAT-G---A
* *
4272142 GCATCAACATTTCCAAT-AGAGTTTATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAATTCA
1 --ATCAACATTTCCAATGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCA
* * * * *
4272206 TAATGAGAAGAACTTGATCAACC-TTAGTTTGATTCCATCACAGAATGAGATGA
64 TAATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATGA
* * * * * *
4272259 ATCAACATTTCTAATGGGGAGATCATAATGAGAAGAACTCATCCAAAGAAGAAGAAGAAGTTCAT
1 ATCAACATTTCCAAT-GAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCAT
*
4272324 AATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCATAGAA
65 AATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAA
4272369 AAAAATAGAT
Statistics
Matches: 196, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
115 14 0.07
117 63 0.32
118 18 0.09
120 1 0.01
121 22 0.11
122 64 0.33
124 14 0.07
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (117 bp):
ATCAACATTTCCAATGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATGA
Found at i:4272323 original size:117 final size:120
Alignment explanation
Indices: 4272020--4272347 Score: 407
Period size: 117 Copynumber: 2.7 Consensus size: 120
4272010 CACTCGAGGG
* * *
4272020 ATCAACATTT-TCAATGGAGAGTTCATAATGAGAATAACTCATTCGATGAGGGAGAAGAAGTTCA
1 ATCAACATTTCT-AATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCA
* *
4272084 TAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGACAAGC
65 TAATGAGAAGAACTTGTTCAACC-TTAGCTCGACTCCATCACAGAAGGAGATAG--AA-C
* * *
4272144 ATCAACATTTCCAAT--AGAGTTTATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAATTCAT
1 ATCAACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCAT
* * * * *
4272207 AATGAGAAGAACTTGATCAACCTTAGTTTGATTCCATCACAGAATGAGAT-G-A-
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGACTCCATCACAGAAGGAGATAGAAC
* * * * *
4272259 ATCAACATTTCTAATGGGGAGATCATAATGAGAAGAACTCATCCAAAGAAGAAGAAGAAGTTCAT
1 ATCAACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCAT
4272324 AATGAGAAGAACTTGTTCAACCTT
66 AATGAGAAGAACTTGTTCAACCTT
4272348 TTGCTTGATT
Statistics
Matches: 179, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
115 14 0.08
117 65 0.36
120 1 0.01
121 22 0.12
122 64 0.36
124 13 0.07
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (120 bp):
ATCAACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGACTCCATCACAGAAGGAGATAGAAC
Found at i:4272505 original size:43 final size:41
Alignment explanation
Indices: 4272396--4272534 Score: 125
Period size: 43 Copynumber: 3.2 Consensus size: 41
4272386 GACATTTTTC
* ** *
4272396 TTGATTCTTCACAGAATGAGTTAGATCAATATTTATCATTTTAC
1 TTGATTCTTCACAGAA-GAGTTGGATCAATA-AAATC-TTTTAT
* * *
4272440 TTGGTCCTTCACAGAAGGAGTTGGATCAATAACAATCTTTCAT
1 TTGATTCTTCACAGAA-GAGTTGGATCAATAA-AATCTTTTAT
* * *
4272483 TTGATTCTTCACAGAAGAAGTTGGATTAGTGAAAATCTTTTGT
1 TTGATTCTTCACAGAAG-AGTTGGATCAAT-AAAATCTTTTAT
4272526 TTGATTCTT
1 TTGATTCTT
4272535 TACACATGGA
Statistics
Matches: 78, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
42 1 0.01
43 45 0.58
44 32 0.41
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (41 bp):
TTGATTCTTCACAGAAGAGTTGGATCAATAAAATCTTTTAT
Found at i:4272548 original size:43 final size:43
Alignment explanation
Indices: 4272396--4272554 Score: 113
Period size: 43 Copynumber: 3.7 Consensus size: 43
4272386 GACATTTTTC
* * * *** * *
4272396 TTGATTCTTCACAGAATGAGTTAGATCAATATTTATCATTTTAC
1 TTGATTCTTCACACAAGGAGTTGGATCAATAACAATC-TTTCAT
* * *
4272440 TTGGTCCTTCACAGAAGGAGTTGGATCAATAACAATCTTTCAT
1 TTGATTCTTCACACAAGGAGTTGGATCAATAACAATCTTTCAT
* * * * **
4272483 TTGATTCTTCACAGAAGAAGTTGGATTAGTGAA-AATCTTTTGT
1 TTGATTCTTCACACAAGGAGTTGGATCAAT-AACAATCTTTCAT
* * *
4272526 TTGATTCTTTACACATGGAGTTGAATCAA
1 TTGATTCTTCACACAAGGAGTTGGATCAA
4272555 CGCCAATATG
Statistics
Matches: 91, Mismatches: 23, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
43 59 0.65
44 32 0.35
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (43 bp):
TTGATTCTTCACACAAGGAGTTGGATCAATAACAATCTTTCAT
Found at i:4275268 original size:81 final size:81
Alignment explanation
Indices: 4275105--4276406 Score: 1852
Period size: 81 Copynumber: 16.1 Consensus size: 81
4275095 ATTCCTTTAG
* * * * ** * *
4275105 TCTTTTACCCAAAGGCATTTAGCATTTCATCTAACTTACATGATTGA-ACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
4275169 ACAGCTAGGCTATTAA
66 ACAGCTAGGCCATTAA
* * * * * ** *
4275185 TCTTTTACTCAAATGCATTTAACCTATCATCTAACTAGCATAATTAACATTTTTCTGTCATATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* *
4275250 ACGGTTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
4275266 TCTTTTACTCAAAGGTATATAACCTTTCATCTAACTGGCATAATAGACATCTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* * *
4275331 AAAACTAGTCCATTAA
66 ACAGCTAGGCCATTAA
* * *
4275347 TCTTTTACTCATATGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
4275412 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * ** *
4275428 TCTTTTACTCAAAGGTATTTAACCTTTCATATAACTGACATAAGGGACACCTTTCAGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
4275493 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
**
4275509 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
4275574 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
4275590 TCTTTTACTCAAAGGTATTTAATCTTTCATCTAACTGGCATAATTGACAACTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* * *
4275655 ATAGTTAGGTCATTAA
66 ACAGCTAGGCCATTAA
* * * *
4275671 TCTTTTACTCAAAAGTATTTAACCTTTCATCTAAAC-AGCATGATTGACACATTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCT-AACTGGCATAATTGACACCTTTCTGTCAAATG
*
4275735 CACAGCTATGCCATTAA
65 CACAGCTAGGCCATTAA
* *
4275752 TCATTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
4275817 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
4275833 TCTTTTACTCAATGGTATTTAACCTTTCATCTAACTGACATAATTGGCAACTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
4275898 ACATCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
4275914 TCTTTTACTCAAAAGTATTTAACCTTTCATCTAACTGGCATAACTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* *
4275979 ACAACTAAGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
4275995 TATTTTACTCAAAGGTATTTAAACTTTCATCTAACTGGCATAATTGACACATTTTTGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* *
4276060 ACAGCTTGACCATTAA
66 ACAGCTAGGCCATTAA
* * * *
4276076 TCTTATACTTAGAGGTATTTAACCTTTTATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* *
4276141 ATAGTTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
4276157 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
4276222 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * **
4276238 TCTTTTACACAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTAACAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
4276303 ACAGCTAGGCCAATAA
66 ACAGCTAGGCCATTAA
* *
4276319 TCTTATACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
4276384 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
4276400 TCTTTTA
1 TCTTTTA
4276407 ACTTTAGAAT
Statistics
Matches: 1078, Mismatches: 141, Indels: 5
0.88 0.12 0.00
Matches are distributed among these distances:
80 41 0.04
81 1034 0.96
82 3 0.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCCATTAA
Found at i:4283530 original size:81 final size:81
Alignment explanation
Indices: 4283339--4283750 Score: 632
Period size: 81 Copynumber: 5.1 Consensus size: 81
4283329 ATTCCTTTAG
* * * * *
4283339 TCTTTTACGCAAAGGCATTTAGCCTTTCATCTAATTTACATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGC
4283404 A-AGCTA-GCCTATTAA
66 ACAGCTAGGCC-ATTAA
* * * *
4283419 TC-TTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGAAACATTTCTGTCAAATTC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGC
*
4283483 ACAGCTATGCCATTAA
66 ACAGCTAGGCCATTAA
*
4283499 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGC
4283564 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
4283580 TCTTTTACTCAACGGTATTTAACCTTTCATCTAACTTGCATAATTGACACTTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGC
*
4283645 ACAGTTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
4283661 TCTTTTACTCAAAGGTATTTAACCTTTCATTTAATTTGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGC
* *
4283726 AAAGCTAGGTCATTAA
66 ACAGCTAGGCCATTAA
4283742 TCTTTTACT
1 TCTTTTACT
4283751 TTAGAATAGT
Statistics
Matches: 306, Mismatches: 23, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
79 56 0.18
80 14 0.05
81 236 0.77
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGC
ACAGCTAGGCCATTAA
Found at i:4286825 original size:23 final size:24
Alignment explanation
Indices: 4286799--4286853 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
4286789 TTTCTATCTT
4286799 TATACCTAT-AGATACTTA-TTTCA
1 TATA-CTATAAGATACTTATTTTCA
* *
4286822 TATATTATAAGATAGTTATTTTCA
1 TATACTATAAGATACTTATTTTCA
4286846 TATA-TATA
1 TATACTATA
4286854 TATTATACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 16 0.57
24 9 0.32
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.47
Consensus pattern (24 bp):
TATACTATAAGATACTTATTTTCA
Found at i:4286849 original size:24 final size:24
Alignment explanation
Indices: 4286808--4286855 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4286798 TTATACCTAT
4286808 AGATACTTATTTCATATAT-TATA
1 AGATACTTATTTCATATATATATA
*
4286831 AGATAGTTATTTTCATATATATATA
1 AGATACTTA-TTTCATATATATATA
4286856 TTATACCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.36
24 10 0.45
25 4 0.18
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (24 bp):
AGATACTTATTTCATATATATATA
Found at i:4288493 original size:8 final size:8
Alignment explanation
Indices: 4288482--4288506 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4288472 GAGAAAAATC
4288482 AGAAAAGA
1 AGAAAAGA
4288490 AGAAAAGA
1 AGAAAAGA
4288498 AGAAAAGA
1 AGAAAAGA
4288506 A
1 A
4288507 AAGAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:4292264 original size:8 final size:8
Alignment explanation
Indices: 4292253--4292277 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4292243 GAGAAAAATC
4292253 AGAAAAGA
1 AGAAAAGA
4292261 AGAAAAGA
1 AGAAAAGA
4292269 AGAAAAGA
1 AGAAAAGA
4292277 A
1 A
4292278 AAGAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:4309778 original size:81 final size:80
Alignment explanation
Indices: 4309690--4310341 Score: 896
Period size: 81 Copynumber: 8.1 Consensus size: 80
4309680 ATTCCTTTAG
* * * * ** * * *
4309690 TCTTTTACCCAAAGGCATTTATCCTTTCATCTAATTTACATAATTAACACATTTATGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC-TTTCTGTCAAATGC
4309755 ACAGCTAGGCCATTAA
65 ACAGCTAGGCCATTAA
* * *
4309771 TCTTTTACTCAAAGGCATTTAACATTTCATCTAACTGGCATAATTGACACATTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC-TTTCTGTCAAATGC
*
4309836 ACAACTAGGCCATTAA
65 ACAGCTAGGCCATTAA
* * *
4309852 TCTTTTACGCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTCACATCTTTTTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAAATGC
*
4309917 ACATCTAGGCCATTAA
65 ACAGCTAGGCCATTAA
* * *
4309933 TCTTTTACTCAAAGGTATTTAACCATTCATCTAACTGGCATAATT-ATACCTTTCGGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAAATGC
*
4309997 ACAGATAGGCCATTAA
65 ACAGCTAGGCCATTAA
* * * * *
4310013 TCTTTTACTCAAAGGTATTTAACATTTCATCT-ACTAGCATTATTGACGCCTTTCAGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAC-ACTTTCTGTCAAATGC
*
4310077 ATAGCTAGGCCATTAA
65 ACAGCTAGGCCATTAA
* *
4310093 TCTTTTACTCAAATGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTTAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAAATGC
*
4310158 ACAACTAGGCCATTAA
65 ACAGCTAGGCCATTAA
*
4310174 TCTTTTACTCAAATGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAAATGC
*
4310239 ACAGCTAGGTCATTAA
65 ACAGCTAGGCCATTAA
*
4310255 TATTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GCATAATTGACATCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAAATGC
* *
4310319 ACAGCTTGGACATTAA
65 ACAGCTAGGCCATTAA
4310335 TCTTTTA
1 TCTTTTA
4310342 ACTTTAGAAT
Statistics
Matches: 513, Mismatches: 53, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
79 10 0.02
80 165 0.32
81 337 0.66
82 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (80 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACTTTCTGTCAAATGCA
CAGCTAGGCCATTAA
Found at i:4310335 original size:322 final size:322
Alignment explanation
Indices: 4309748--4310341 Score: 974
Period size: 322 Copynumber: 1.8 Consensus size: 322
4309738 ACATTTATGC
4309748 CAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGCATTTAACATTTCATCTAACTGGCATA
1 CAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGCATTTAACATTTCATCTAACTGGCATA
4309813 ATTGACACATTTCTATCAAATGCACAACTAGGCCATTAATCTTTTACGCAAAGGTATTTAACCTT
66 ATTGACACATTTCTATCAAATGCACAACTAGGCCATTAATCTTTTACGCAAAGGTATTTAACCTT
* * * *
4309878 TCATCTAACTGGCATAATTCACATCTTTTTGTCAAATGCACATCTAGGCCATTAATCTTTTACTC
131 TCATCTAACTGGCATAATTCACACCTTTCTGTCAAATGCACAGCTAGGCCATTAATATTTTACTC
* *
4309943 AAAGGTATTTAACCATTCATCTAACTGGCATAATTATACCTTTCGGTCAAATGCACAGATAGGCC
196 AAAGGTATTTAACCATTCATCTAACTGGCATAATTACACCTTTCGGTCAAATGCACAGATAGGAC
4310008 ATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTACTAGCATTATTGACGCCTTTCAGT
261 ATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTACTAGCATTATTGACGCCTTTCAGT
* * * *
4310070 CAAATGCATAGCTAGGCCATTAATCTTTTACTCAAATGTATTTAACCTTTCATCTAACTGGCATA
1 CAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGCATTTAACATTTCATCTAACTGGCATA
* * * * *
4310135 ATTGACACCTTTCTGTTAAATGCACAACTAGGCCATTAATCTTTTACTCAAATGTATTTAACCTT
66 ATTGACACATTTCTATCAAATGCACAACTAGGCCATTAATCTTTTACGCAAAGGTATTTAACCTT
* *
4310200 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGTCATTAATATTTTACTC
131 TCATCTAACTGGCATAATTCACACCTTTCTGTCAAATGCACAGCTAGGCCATTAATATTTTACTC
* * * * *
4310265 AAAGGTATTTAACCTTTCATCTAACT-GCATAATTGACATCTTTCTGTCAAATGCACAGCTTGGA
196 AAAGGTATTTAACCATTCATCTAACTGGCATAATT-ACACCTTTCGGTCAAATGCACAGATAGGA
4310329 CATTAATCTTTTA
260 CATTAATCTTTTA
4310342 ACTTTAGAAT
Statistics
Matches: 249, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
321 8 0.03
322 241 0.97
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (322 bp):
CAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGCATTTAACATTTCATCTAACTGGCATA
ATTGACACATTTCTATCAAATGCACAACTAGGCCATTAATCTTTTACGCAAAGGTATTTAACCTT
TCATCTAACTGGCATAATTCACACCTTTCTGTCAAATGCACAGCTAGGCCATTAATATTTTACTC
AAAGGTATTTAACCATTCATCTAACTGGCATAATTACACCTTTCGGTCAAATGCACAGATAGGAC
ATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTACTAGCATTATTGACGCCTTTCAGT
Found at i:4310664 original size:55 final size:55
Alignment explanation
Indices: 4310489--4310708 Score: 268
Period size: 55 Copynumber: 4.0 Consensus size: 55
4310479 CCCAACACCA
* * * * * * *
4310489 ATACGGAAATTCA-CCAACTTATTATGAACTTCTTA-TATTTGTACATATATTTCCC
1 ATACGGAAATTCATAC-ACTTAGTATGAATTTCTTAGT-TTTGCACACATAGTGCCC
*
4310544 ATACGGAAATTCATACACTTAGTATGAATTTCTTAG-TTTGCACACCTAGTGCCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
* **
4310598 ATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCTT
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
4310653 ATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTTGCACAC-TCAGTGCC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAG--TTTTGCACACAT-AGTGCC
4310709 ATTTGGTAAT
Statistics
Matches: 145, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
54 48 0.33
55 80 0.55
56 2 0.01
57 15 0.10
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (55 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
Found at i:4319098 original size:124 final size:124
Alignment explanation
Indices: 4318877--4319130 Score: 483
Period size: 124 Copynumber: 2.0 Consensus size: 124
4318867 AAATAAACAG
4318877 TGACCTTCAATTGAGTTTGACCAACAATATCATAATTATTTTTTCGTCATTCTTAAAAATAAAAT
1 TGACCTTCAATTGAGTTTGACCAACAATATCATAATTATTTTTTCGTCATTCTTAAAAATAAAAT
4318942 TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGATAAAAATACATAAGATGTTT
66 TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGAT-AAAATACATAAGATGTTT
4319002 TGACCTTCAATTGAGTTTGACCAACAATATCATAATTA-TTTTTCGTCATTCTTAAAAATAAAAT
1 TGACCTTCAATTGAGTTTGACCAACAATATCATAATTATTTTTTCGTCATTCTTAAAAATAAAAT
*
4319066 TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGATAAAATCCATAAGATGTTT
66 TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGATAAAATACATAAGATGTTT
4319125 TGACCT
1 TGACCT
4319131 ACAACAAGTC
Statistics
Matches: 128, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
123 23 0.18
124 67 0.52
125 38 0.30
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (124 bp):
TGACCTTCAATTGAGTTTGACCAACAATATCATAATTATTTTTTCGTCATTCTTAAAAATAAAAT
TTATCTCCATTATTTTTCTTTCTTATTTAATAATTATTGATAAAATACATAAGATGTTT
Found at i:4322184 original size:20 final size:20
Alignment explanation
Indices: 4322161--4322202 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4322151 CTAAGTATAA
*
4322161 TTTCAATATTTATTTTTTGT
1 TTTCAATATTTATTTATTGT
*
4322181 TTTCAATTTTTATTTATTGT
1 TTTCAATATTTATTTATTGT
4322201 TT
1 TT
4322203 GCTATGACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTCAATATTTATTTATTGT
Found at i:4322290 original size:21 final size:21
Alignment explanation
Indices: 4322266--4322330 Score: 58
Period size: 25 Copynumber: 2.9 Consensus size: 21
4322256 AATATTACCA
*
4322266 ATGTTTGCTGTGTATTCAAGT
1 ATGTTTGATGTGTATTCAAGT
*
4322287 ATGTTTGATGTGAAAAATTTCAAGT
1 ATGTTTGATGTG---TA-TTCAAGT
**
4322312 ATGTTTTTTGTGTATTCAA
1 ATGTTTGATGTGTATTCAA
4322331 TATTTGATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
21 16 0.46
22 1 0.03
24 1 0.03
25 17 0.49
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.48
Consensus pattern (21 bp):
ATGTTTGATGTGTATTCAAGT
Found at i:4322358 original size:43 final size:45
Alignment explanation
Indices: 4322274--4322360 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 45
4322264 CAATGTTTGC
* * *
4322274 TGTGTATTCAAGTATGTTTGATGTGAAAAATTTCAAGTATGTTTTT
1 TGTGTATTCAAGTA-GTTTGATCTGAAAAATCTCAAATATGTTTTT
*
4322320 TGTGTATTCAA-TA-TTTGATCTGACAAATCTCAAATATGTTT
1 TGTGTATTCAAGTAGTTTGATCTGAAAAATCTCAAATATGTTT
4322361 GTTGCGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 24 0.65
45 2 0.05
46 11 0.30
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (45 bp):
TGTGTATTCAAGTAGTTTGATCTGAAAAATCTCAAATATGTTTTT
Found at i:4324511 original size:27 final size:27
Alignment explanation
Indices: 4324481--4324548 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
4324471 TAAAATTATA
*
4324481 AAAATATCTCTAAAGGGTAAAATGACC-
1 AAAATACCTCTAAAGGGT-AAATGACCT
* * * *
4324508 AAAATGCCCCTAAAGTGTAAATGGCCT
1 AAAATACCTCTAAAGGGTAAATGACCT
4324535 AAAATACCTCTAAA
1 AAAATACCTCTAAA
4324549 CCCTGGAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
26 7 0.21
27 26 0.79
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (27 bp):
AAAATACCTCTAAAGGGTAAATGACCT
Found at i:4327109 original size:33 final size:33
Alignment explanation
Indices: 4327072--4327176 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 33
4327062 TTCAACTTCA
* *
4327072 GCACCTTAAAGGATTCAATCATATTCAATTGGT
1 GCACCTTAAGGGTTTCAATCATATTCAATTGGT
* **
4327105 GCACCTCT-AGGGTTTCAATCATCTTCAATTGAC
1 GCACCT-TAAGGGTTTCAATCATATTCAATTGGT
*
4327138 GCA-C-TACTAGGGTTTCAATCATATTCAACTGGT
1 GCACCTTA--AGGGTTTCAATCATATTCAATTGGT
4327171 GCACCT
1 GCACCT
4327177 CCAACTACTC
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
30 1 0.02
32 1 0.02
33 53 0.93
34 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (33 bp):
GCACCTTAAGGGTTTCAATCATATTCAATTGGT
Found at i:4329376 original size:12 final size:13
Alignment explanation
Indices: 4329361--4329393 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4329351 TTTATTTTAG
4329361 TTTTTAAAATA-A
1 TTTTTAAAATATA
4329373 TTTTTAAAATATA
1 TTTTTAAAATATA
*
4329386 ATTTTAAA
1 TTTTTAAA
4329394 GGATGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:4330852 original size:13 final size:13
Alignment explanation
Indices: 4330834--4330858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4330824 TACTATCTAC
4330834 GAATGCAAATTGT
1 GAATGCAAATTGT
4330847 GAATGCAAATTG
1 GAATGCAAATTG
4330859 CGTATCAAAA
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:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (13 bp):
GAATGCAAATTGT
Found at i:4333151 original size:75 final size:76
Alignment explanation
Indices: 4333000--4333312 Score: 350
Period size: 75 Copynumber: 4.2 Consensus size: 76
4332990 CTTAATCGGT
* * * * *
4333000 TAAAATAAAAT-AGTCGCTACCTATTAAGTAAAAACTA-CTTACCGATTTGTTTGAAGGTTGCTA
1 TAAAATAAAATAAGACGCTACCTATTAAGTTAAAA-TATC-TACCGGTTTGTTTAAAGGTTACTA
4333063 ATAATGTAAACGG
64 ATAATGTAAACGG
* * * *
4333076 TAAAATAAAATAAG-CGCTATCTATTACGTTAAAATATCTACGGGTTTGTTTAAAGATTACTAAT
1 TAAAATAAAATAAGACGCTACCTATTAAGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAAT
*
4333140 AATGTGAACGG
66 AATGTAAACGG
** *
4333151 TAAAATAAAAT-AGACAATACCTATTAAGTTAAAATATCTACCGGTTAT-TTTAAATGTTACTAA
1 TAAAATAAAATAAGACGCTACCTATTAAGTTAAAATATCTACCGGTT-TGTTTAAAGGTTACTAA
*
4333214 TAATGTAAACGA
65 TAATGTAAACGG
* * ** * * * * *
4333226 TAAAATAAAATAAG-TGTTGTCTATTACGTTAAACTAGCTACTGGTTTGTTTAAAGGTTAATAAT
1 TAAAATAAAATAAGACGCTACCTATTAAGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAAT
4333290 AATGTAAACGG
66 AATGTAAACGG
4333301 TAAAATAAAATA
1 TAAAATAAAATA
4333313 GGCGTACATA
Statistics
Matches: 201, Mismatches: 30, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
74 3 0.01
75 164 0.82
76 32 0.16
77 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (76 bp):
TAAAATAAAATAAGACGCTACCTATTAAGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAAT
AATGTAAACGG
Found at i:4333272 original size:150 final size:151
Alignment explanation
Indices: 4333000--4333313 Score: 427
Period size: 150 Copynumber: 2.1 Consensus size: 151
4332990 CTTAATCGGT
* ** * *
4333000 TAAAATAAAATAGTCGCTACCTATTAAGTAAAAACTACTTACCGATTTGTTTGAAGGTTGCTAAT
1 TAAAATAAAATAGACAATACCTATTAAGTAAAAACTACTTACCGATTTGTTTAAAGGTTACTAAT
* *
4333065 AATGTAAACGGTAAAATAAAATAAGCGCTATCTATTACGTTAAAATATCTACGGGTTTGTTTAAA
66 AATGTAAACGATAAAATAAAATAAGCGCTATCTATTACGTTAAAATAGCTACGGGTTTGTTTAAA
* *
4333130 GATTACTAATAATGTGAACGG
131 GATTAATAATAATGTAAACGG
* * *
4333151 TAAAATAAAATAGACAATACCTATTAAGTTAAAA-TA-TCTACCGGTTAT-TTTAAATGTTACTA
1 TAAAATAAAATAGACAATACCTATTAAGTAAAAACTACT-TACCGATT-TGTTTAAAGGTTACTA
* * * * *
4333213 ATAATGTAAACGATAAAATAAAATAAGTGTTGTCTATTACGTTAAACTAGCTACTGGTTTGTTTA
64 ATAATGTAAACGATAAAATAAAATAAGCGCTATCTATTACGTTAAAATAGCTACGGGTTTGTTTA
*
4333278 AAGGTTAATAATAATGTAAACGG
129 AAGATTAATAATAATGTAAACGG
4333301 TAAAATAAAATAG
1 TAAAATAAAATAG
4333314 GCGTACATAT
Statistics
Matches: 143, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
149 1 0.01
150 111 0.78
151 31 0.22
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (151 bp):
TAAAATAAAATAGACAATACCTATTAAGTAAAAACTACTTACCGATTTGTTTAAAGGTTACTAAT
AATGTAAACGATAAAATAAAATAAGCGCTATCTATTACGTTAAAATAGCTACGGGTTTGTTTAAA
GATTAATAATAATGTAAACGG
Found at i:4333333 original size:22 final size:23
Alignment explanation
Indices: 4333308--4333378 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
4333298 CGGTAAAATA
4333308 AAATAGGCG-TACATATTATGTT
1 AAATAGGCGCTACATATTATGTT
* *
4333330 AAATAGGTGCTACCA-ATTACGTT
1 AAATAGGCGCTA-CATATTATGTT
*
4333353 AAATAAGCGCTACATATTATGTT
1 AAATAGGCGCTACATATTATGTT
4333376 AAA
1 AAA
4333379 CTAGCTATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 10 0.24
23 29 0.71
24 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (23 bp):
AAATAGGCGCTACATATTATGTT
Found at i:4333490 original size:21 final size:20
Alignment explanation
Indices: 4333462--4333502 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
4333452 ATTTTTTAAA
*
4333462 ATTCAAAAGTATAGATACTT
1 ATTCAAAAGTATAAATACTT
4333482 ATTCTAAAAGTATAAATACTT
1 ATTC-AAAAGTATAAATACTT
4333503 TAAAGGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (20 bp):
ATTCAAAAGTATAAATACTT
Found at i:4333624 original size:23 final size:23
Alignment explanation
Indices: 4333595--4333666 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
4333585 CCTGAAAATA
* * *
4333595 AAATAGGTGATATCTATTATGTT
1 AAATAGGCGATACCTATTACGTT
*
4333618 AAATAGGCGTTACCTATTACGTT
1 AAATAGGCGATACCTATTACGTT
*
4333641 AAATAAGC-ACTACCTATTACGTT
1 AAATAGGCGA-TACCTATTACGTT
4333664 AAA
1 AAA
4333667 CTAGCTACTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (23 bp):
AAATAGGCGATACCTATTACGTT
Found at i:4338036 original size:34 final size:33
Alignment explanation
Indices: 4337998--4338064 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
4337988 GTAATAAACA
4337998 AAATTAAGCAAAATAAATTAACAA-AAAGTCCAAC
1 AAATTAAGCAAAATAAATTAA-AATAAA-TCCAAC
* *
4338032 AAATTTATCAAAATAAATTAAAATAAATCCAAC
1 AAATTAAGCAAAATAAATTAAAATAAATCCAAC
4338065 CATATTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.22
Consensus pattern (33 bp):
AAATTAAGCAAAATAAATTAAAATAAATCCAAC
Found at i:4340399 original size:9 final size:9
Alignment explanation
Indices: 4340369--4340414 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
4340359 ATCTACAAAA
*
4340369 AAATTAATT
1 AAATTAAAT
4340378 AAA-TAAA-
1 AAATTAAAT
*
4340385 ATATTAAAT
1 AAATTAAAT
4340394 AAATTAAAT
1 AAATTAAAT
4340403 AAATTAAAT
1 AAATTAAAT
4340412 AAA
1 AAA
4340415 AATATTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 2 0.06
8 7 0.22
9 23 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:4345895 original size:19 final size:20
Alignment explanation
Indices: 4345848--4345898 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4345838 GAAACCCTTT
**
4345848 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
4345868 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
4345887 TGAAGATACATG
1 TGAAAATACATG
4345899 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:4349994 original size:27 final size:27
Alignment explanation
Indices: 4349952--4350019 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
4349942 TTGTAGGAAT
4349952 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
4349977 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
4350004 TATAGAGATATGATTT
1 TATAGAGATATGATTT
4350020 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:4363317 original size:321 final size:321
Alignment explanation
Indices: 4362735--4363376 Score: 1203
Period size: 321 Copynumber: 2.0 Consensus size: 321
4362725 GCATTAATGT
4362735 TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCCTTTATATCCTGCTTT
1 TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCCTTTATATCCTGCTTT
* *
4362800 CACATTGATAGTTACTGAACTAGATTGCTCAACAATCAGGGATAGTGATTAAAAATTTAACAAAT
66 CACATTGATAGTTACTGAACTAGATTGCTCAACAATCAGGAATACTGATTAAAAATTTAACAAAT
* *
4362865 GCTAGACTATCATCAGTTTAATTTTATAGATATGAAAATCTGGAAATATGTACCTCAGTGTAGGC
131 GCTAGACCATCATCAGTTTAATTTTATAGATATGAAAATCTGGAAATATGTACCTCAGTATAGGC
*
4362930 TTGCATCGAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAA
196 TTGCATCCAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAA
4362995 ATGCATGATCATCATTTTGCAGGAATGGACTCAAGGGCGTACCGGTTAAGCTGCTTGAAAG
261 ATGCATGATCATCATTTTGCAGGAATGGACTCAAGGGCGTACCGGTTAAGCTGCTTGAAAG
4363056 TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCCTTTATATCCTGCTTT
1 TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCCTTTATATCCTGCTTT
* **
4363121 CACATTGATATTTACTTTACTAGATTGCTCAACAATCAGGAATACTGATTAAAAATTTAACAAAT
66 CACATTGATAGTTACTGAACTAGATTGCTCAACAATCAGGAATACTGATTAAAAATTTAACAAAT
4363186 GCTAGACCATCATCAGTTTAATTTTATAGATATGAAAATCTGGAAATATGTACCTCAGTATAGGC
131 GCTAGACCATCATCAGTTTAATTTTATAGATATGAAAATCTGGAAATATGTACCTCAGTATAGGC
4363251 TTGCATCCAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAA
196 TTGCATCCAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAA
*
4363316 ATGCATGATCATCATTTTGCAGGAATGGACTTAAGGGCGTACCGGTTAAGCTGCTTGAAAG
261 ATGCATGATCATCATTTTGCAGGAATGGACTCAAGGGCGTACCGGTTAAGCTGCTTGAAAG
4363377 AAAGTGATGT
Statistics
Matches: 312, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
321 312 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (321 bp):
TAGAAGCAATGAAGATATGCATAGCCTTGCTTTTAGAAGGCACTGATCCCTTTATATCCTGCTTT
CACATTGATAGTTACTGAACTAGATTGCTCAACAATCAGGAATACTGATTAAAAATTTAACAAAT
GCTAGACCATCATCAGTTTAATTTTATAGATATGAAAATCTGGAAATATGTACCTCAGTATAGGC
TTGCATCCAGAGCAGATAAATTCTTCACCGATTCCGAAGAACAGCGGTCATATTTCAAAATAAAA
ATGCATGATCATCATTTTGCAGGAATGGACTCAAGGGCGTACCGGTTAAGCTGCTTGAAAG
Found at i:4364729 original size:13 final size:13
Alignment explanation
Indices: 4364711--4364746 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
4364701 TACTTGAAAA
4364711 AATTGAATTTTAT
1 AATTGAATTTTAT
4364724 AATTGAATTTTAT
1 AATTGAATTTTAT
* *
4364737 GATTCAATTT
1 AATTGAATTT
4364747 GATGTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (13 bp):
AATTGAATTTTAT
Found at i:4365296 original size:23 final size:23
Alignment explanation
Indices: 4365244--4365300 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
4365234 TTGTAACATG
*
4365244 TTATCTGTCTTTATGACACGTTT
1 TTATCTATCTTTATGACACGTTT
* * * *
4365267 ATCTCTATCTTTGTGGCACGTTT
1 TTATCTATCTTTATGACACGTTT
4365290 TTATCTA-CTTT
1 TTATCTATCTTT
4365301 TTGGTAGCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.16, C:0.19, G:0.12, T:0.53
Consensus pattern (23 bp):
TTATCTATCTTTATGACACGTTT
Found at i:4375515 original size:2 final size:2
Alignment explanation
Indices: 4375508--4375574 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
4375498 CCTTGGTTAT
4375508 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
4375550 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 T
4375575 TAAGTAAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4383683 original size:13 final size:13
Alignment explanation
Indices: 4383665--4383690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4383655 TTACCTAGCC
4383665 TTAAGCTCCTCTA
1 TTAAGCTCCTCTA
4383678 TTAAGCTCCTCTA
1 TTAAGCTCCTCTA
4383691 GCTGAATCGA
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:0.08, T:0.38
Consensus pattern (13 bp):
TTAAGCTCCTCTA
Found at i:4392681 original size:35 final size:36
Alignment explanation
Indices: 4392594--4392681 Score: 142
Period size: 35 Copynumber: 2.5 Consensus size: 36
4392584 TACAATCTGT
*
4392594 TCATCACCATCTTCCATCACCATTATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
4392630 TCATCACCATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
4392665 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
4392682 TTCCATTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 28 0.58
36 20 0.42
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.28
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:4393164 original size:17 final size:17
Alignment explanation
Indices: 4393134--4393170 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4393124 AGTACAAAAG
4393134 AAATAAAAGAAAAAGAA
1 AAATAAAAGAAAAAGAA
4393151 AAATCAAAAG-AAAAGAA
1 AAAT-AAAAGAAAAAGAA
4393168 AAA
1 AAA
4393171 GTGAAGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.81, C:0.03, G:0.11, T:0.05
Consensus pattern (17 bp):
AAATAAAAGAAAAAGAA
Found at i:4397193 original size:35 final size:36
Alignment explanation
Indices: 4397106--4397193 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 36
4397096 TACAATCTGT
* *
4397106 TCATCACCATCTTCTATCACCATTATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
4397142 TCATCACCATAGTCCATCACCA-TATCACGCCTATA
1 TCATCACCATATTCCATCACCATTATCACGCCTATA
*
4397177 TCATCACCAAATTCCAT
1 TCATCACCATATTCCAT
4397194 TTCCATTTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 28 0.60
36 19 0.40
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (36 bp):
TCATCACCATATTCCATCACCATTATCACGCCTATA
Found at i:4406253 original size:24 final size:25
Alignment explanation
Indices: 4406216--4406262 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
4406206 ATTTTGCAAC
4406216 TTTTTCTCTCTTTTTCTTTGCTTTGA
1 TTTTTCTCTCTTTTTCTTT-CTTTGA
4406242 TTTTTCT-T-TTTTTCTTTCTTT
1 TTTTTCTCTCTTTTTCTTTCTTT
4406263 TTTTTGCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 9 0.43
25 1 0.05
26 7 0.33
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTTTCTCTCTTTTTCTTTCTTTGA
Found at i:4406520 original size:12 final size:12
Alignment explanation
Indices: 4406503--4406527 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4406493 AGAGATGGAT
4406503 TAATGAAAGAAA
1 TAATGAAAGAAA
4406515 TAATGAAAGAAA
1 TAATGAAAGAAA
4406527 T
1 T
4406528 GAATAGATTA
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:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (12 bp):
TAATGAAAGAAA
Found at i:4407044 original size:21 final size:21
Alignment explanation
Indices: 4407018--4407072 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
4407008 GAAACCCCTT
**
4407018 TGAAAATACATGCTTTTTTAA
1 TGAAAATACATGAGTTTTTAA
*
4407039 TGAAAATATATGAGTTTTTAA
1 TGAAAATACATGAGTTTTTAA
*
4407060 TGAAAATAAATGA
1 TGAAAATACATGA
4407073 TTATAATGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (21 bp):
TGAAAATACATGAGTTTTTAA
Found at i:4407081 original size:19 final size:20
Alignment explanation
Indices: 4407036--4407081 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
4407026 CATGCTTTTT
* *
4407036 TAATGAAAATATATGAGTTTT
1 TAATGAAAATAAATGAG-TTA
4407057 TAATGAAAATAAATGA-TTA
1 TAATGAAAATAAATGAGTTA
4407076 TAATGA
1 TAATGA
4407082 GGATACATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
21 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
TAATGAAAATAAATGAGTTA
Found at i:4409272 original size:36 final size:36
Alignment explanation
Indices: 4409226--4409297 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
4409216 CAACTTCAAA
*
4409226 AAGCTTTTCTTCATTTGAATTTTCCTCTAAACGTTC
1 AAGCTTTTCTTCATTTGAAGTTTCCTCTAAACGTTC
* *
4409262 AAGCTTTTCTTTATTTGAAGTTTCCTCTAAATGTTC
1 AAGCTTTTCTTCATTTGAAGTTTCCTCTAAACGTTC
4409298 TCCTTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.49
Consensus pattern (36 bp):
AAGCTTTTCTTCATTTGAAGTTTCCTCTAAACGTTC
Found at i:4410618 original size:12 final size:12
Alignment explanation
Indices: 4410601--4410625 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4410591 AAAGATGTAT
4410601 TAATGAAAGAAA
1 TAATGAAAGAAA
4410613 TAATGAAAGAAA
1 TAATGAAAGAAA
4410625 T
1 T
4410626 GAAATGATAA
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:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (12 bp):
TAATGAAAGAAA
Found at i:4411216 original size:19 final size:20
Alignment explanation
Indices: 4411167--4411208 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
4411157 GAAACCCCTT
4411167 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
4411187 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
4411206 TGA
1 TGA
4411209 GGAAACATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4418202 original size:23 final size:22
Alignment explanation
Indices: 4418169--4418229 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 22
4418159 TATTTTTTTC
4418169 AAAAAAA-CAAAAAAAAAAACA
1 AAAAAAAGCAAAAAAAAAAACA
4418190 AAAAAAATGCAAAAAAAAAAACAA
1 AAAAAAA-GCAAAAAAAAAAAC-A
*
4418214 AAAAAAAGCCAAAAAA
1 AAAAAAAGCAAAAAAA
4418230 GCCAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 7 0.19
23 21 0.58
24 8 0.22
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (22 bp):
AAAAAAAGCAAAAAAAAAAACA
Found at i:4418229 original size:1 final size:1
Alignment explanation
Indices: 4418169--4418220 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
4418159 TATTTTTTTC
* * *** *
4418169 AAAAAAACAAAAAAAAAAACAAAAAAAATGCAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4418221 GCCAAAAAAG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:4418229 original size:12 final size:12
Alignment explanation
Indices: 4418169--4418220 Score: 79
Period size: 12 Copynumber: 4.4 Consensus size: 12
4418159 TATTTTTTTC
4418169 AAAAAAACAAAA
1 AAAAAAACAAAA
4418181 AAAAAAAC-AAA
1 AAAAAAACAAAA
**
4418192 AAAAATGCAAAA
1 AAAAAAACAAAA
4418204 AAAAAAACAAAA
1 AAAAAAACAAAA
4418216 AAAAA
1 AAAAA
4418221 GCCAAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 9 0.26
12 26 0.74
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:4425526 original size:25 final size:25
Alignment explanation
Indices: 4425492--4425551 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
4425482 TAATAAAATA
4425492 TGGAAGAACTCCCTTAGAATCATCT
1 TGGAAGAACTCCCTTAGAATCATCT
* *
4425517 TGGAAAAACTCCCTTAGAATTATCT
1 TGGAAGAACTCCCTTAGAATCATCT
4425542 TGGAAGAACT
1 TGGAAGAACT
4425552 TCAAAGTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (25 bp):
TGGAAGAACTCCCTTAGAATCATCT
Found at i:4426653 original size:14 final size:14
Alignment explanation
Indices: 4426634--4426663 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4426624 GCTATAAGCT
4426634 CACTGGTCTCCGGA
1 CACTGGTCTCCGGA
4426648 CACTGGTCTCCGGA
1 CACTGGTCTCCGGA
4426662 CA
1 CA
4426664 ACTTTTCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.17, C:0.37, G:0.27, T:0.20
Consensus pattern (14 bp):
CACTGGTCTCCGGA
Found at i:4440705 original size:16 final size:17
Alignment explanation
Indices: 4440684--4440716 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4440674 AACAAATTAG
4440684 AATACAAAAGAA-AAAA
1 AATACAAAAGAAGAAAA
4440700 AATACAAAAGAAGAAAA
1 AATACAAAAGAAGAAAA
4440717 TTCAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (17 bp):
AATACAAAAGAAGAAAA
Found at i:4440726 original size:18 final size:18
Alignment explanation
Indices: 4440705--4440747 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
4440695 AAAAAAATAC
* *
4440705 AAAAGAAGAAAATTCAGA
1 AAAAGAAGAAAAGTCAAA
4440723 AAAAGAAGAAAAGTCAAA
1 AAAAGAAGAAAAGTCAAA
4440741 AAAAGAA
1 AAAAGAA
4440748 AGCAAGCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.05, G:0.16, T:0.07
Consensus pattern (18 bp):
AAAAGAAGAAAAGTCAAA
Found at i:4440741 original size:15 final size:15
Alignment explanation
Indices: 4440688--4440748 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 15
4440678 AATTAGAATA
*
4440688 CAAAAGAAAAAAAAT
1 CAAAAGAAGAAAAAT
*
4440703 ACAAAAGAAGAAAATT
1 -CAAAAGAAGAAAAAT
*
4440719 CAGAAAAAGAAGAAAAGT
1 C---AAAAGAAGAAAAAT
*
4440737 CAAAAAAAGAAA
1 CAAAAGAAGAAA
4440749 GCAAGCCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 11 0.29
16 13 0.34
18 14 0.37
ACGTcount: A:0.74, C:0.07, G:0.13, T:0.07
Consensus pattern (15 bp):
CAAAAGAAGAAAAAT
Done.