Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 105 of 427
Found at i:27737108 original size:14 final size:14
Alignment explanation
Indices: 27737089--27737115 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27737079 ATACTTGATT
27737089 TGTTCTTAATTATG
1 TGTTCTTAATTATG
27737103 TGTTCTTAATTAT
1 TGTTCTTAATTAT
27737116 TGCTTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.59
Consensus pattern (14 bp):
TGTTCTTAATTATG
Found at i:27743435 original size:28 final size:28
Alignment explanation
Indices: 27743354--27743437 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 28
27743344 TGAAATAATC
* *
27743354 TAAAATAGAGAATATATAAAAAT-A-TTT
1 TAAAATAAATAATA-ATAAAAATGAGTTT
*
27743381 TAAAATAAATAAT-ATATGAAA-G-G-TT
1 TAAAATAAATAATAATA-AAAATGAGTTT
*
27743406 TAAAGTAAATAATAATAAAAATGAGTTT
1 TAAAATAAATAATAATAAAAATGAGTTT
27743434 TAAA
1 TAAA
27743438 CGATTAACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
25 20 0.44
26 7 0.16
27 12 0.27
28 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (28 bp):
TAAAATAAATAATAATAAAAATGAGTTT
Found at i:27743607 original size:20 final size:20
Alignment explanation
Indices: 27743577--27743624 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
27743567 CTAATATAGT
27743577 GATATATATAAACTTAAGATG
1 GATA-ATATAAACTTAAGATG
27743598 GATAATATAAACTTAAGATG
1 GATAATATAAACTTAAGATG
27743618 GATAATA
1 GATAATA
27743625 GTTTGAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (20 bp):
GATAATATAAACTTAAGATG
Found at i:27747919 original size:28 final size:23
Alignment explanation
Indices: 27747867--27747913 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
27747857 TTGGGCCAAT
27747867 AGAGATAGTGGGTGATTTAACCC
1 AGAGATAGTGGGTGATTTAACCC
27747890 AGAGATAGTGGGTGATTTAACCC
1 AGAGATAGTGGGTGATTTAACCC
27747913 A
1 A
27747914 ACCCAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.26
Consensus pattern (23 bp):
AGAGATAGTGGGTGATTTAACCC
Found at i:27748628 original size:12 final size:12
Alignment explanation
Indices: 27748611--27748641 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27748601 TTTGCTTTTG
27748611 AAAGAAAAAAAA
1 AAAGAAAAAAAA
*
27748623 AAAGAAAAAAAG
1 AAAGAAAAAAAA
27748635 AAAGAAA
1 AAAGAAA
27748642 GAGAGTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:27750604 original size:28 final size:29
Alignment explanation
Indices: 27750547--27750608 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
27750537 ATTAATTTAT
*
27750547 TTTTTAATTATGTTGTGAGGATTTAATTG
1 TTTTTAATTATGTTATGAGGATTTAATTG
*
27750576 TTTTTAATTATTTTATGAGG-TTCT-ATTG
1 TTTTTAATTATGTTATGAGGATT-TAATTG
27750604 TTTTT
1 TTTTT
27750609 TTAAACATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.21, C:0.02, G:0.16, T:0.61
Consensus pattern (29 bp):
TTTTTAATTATGTTATGAGGATTTAATTG
Found at i:27751113 original size:21 final size:21
Alignment explanation
Indices: 27751089--27751165 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
27751079 TAATAATTTT
27751089 TTATTAAAAATT-TTGAAAAAA
1 TTATTAAAAATTATT-AAAAAA
* *
27751110 TTATTAGAAATTATTAAAAAG
1 TTATTAAAAATTATTAAAAAA
27751131 TTA-TAAAAA--A-TAAAAAA
1 TTATTAAAAATTATTAAAAAA
*
27751148 TTA-TATAAATTATTAAAA
1 TTATTAAAAATTATTAAAA
27751166 TTTAAAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 14 0.30
18 1 0.02
19 1 0.02
20 10 0.21
21 19 0.40
22 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
TTATTAAAAATTATTAAAAAA
Found at i:27751165 original size:18 final size:18
Alignment explanation
Indices: 27751106--27751189 Score: 59
Period size: 17 Copynumber: 4.7 Consensus size: 18
27751096 AAATTTTGAA
*
27751106 AAAATTATTAGAAATTATT
1 AAAATTA-TAAAAATTATT
* *
27751125 AAAAAGTTATAAAAAATA-A
1 -AAAA-TTATAAAAATTATT
*
27751144 AAAATTATATAAATTATT
1 AAAATTATAAAAATTATT
* *
27751162 AAAATT-TAAAATTTA-A
1 AAAATTATAAAAATTATT
27751178 AAAATT-TAAAAA
1 AAAATTATAAAAA
27751190 ATACCACTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
16 11 0.21
17 17 0.33
18 10 0.19
20 11 0.21
21 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAATTATAAAAATTATT
Found at i:27751165 original size:19 final size:18
Alignment explanation
Indices: 27751105--27751188 Score: 70
Period size: 16 Copynumber: 4.7 Consensus size: 18
27751095 AAAATTTTGA
27751105 AAAAATTATTAGAAATTATT
1 AAAAATTA-TA-AAATTATT
* *
27751125 AAAAAGTTATAAAA-AATA
1 AAAAA-TTATAAAATTATT
27751143 AAAAATTATATAAATTATT
1 AAAAATTATA-AAATTATT
*
27751162 -AAAATT-TAAAATT-TA
1 AAAAATTATAAAATTATT
27751177 AAAAATT-TAAAA
1 AAAAATTATAAAA
27751189 AATACCACTT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
15 1 0.02
16 16 0.29
17 7 0.13
18 16 0.29
19 5 0.09
20 7 0.13
21 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAAATTATAAAATTATT
Found at i:27752917 original size:17 final size:18
Alignment explanation
Indices: 27752879--27752917 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
27752869 AAGTTTTGAG
*
27752879 AATTATACATTTAAGAAT
1 AATTATACATTTAAGAAA
*
27752897 AATTATA-ATTTAATAAA
1 AATTATACATTTAAGAAA
27752914 AATT
1 AATT
27752918 GTGATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
AATTATACATTTAAGAAA
Found at i:27757063 original size:23 final size:23
Alignment explanation
Indices: 27757019--27757063 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
27757009 AATTTGATGC
*
27757019 TTTTTTTCTAGTTTAGTATTTAA
1 TTTTTTTCTAGTTTAATATTTAA
*
27757042 TTTTTTT-TAGGTTTAATTTTTA
1 TTTTTTTCTA-GTTTAATATTTA
27757064 CCTAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (23 bp):
TTTTTTTCTAGTTTAATATTTAA
Found at i:27763236 original size:6 final size:6
Alignment explanation
Indices: 27763225--27763250 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27763215 TAATATTATA
27763225 CAAGCC CAAGCC CAAGCC CAAGCC CA
1 CAAGCC CAAGCC CAAGCC CAAGCC CA
27763251 TAATCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
CAAGCC
Found at i:27763873 original size:26 final size:24
Alignment explanation
Indices: 27763843--27763892 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
27763833 TAAATAAAAA
*
27763843 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
27763869 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
27763893 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:27766140 original size:27 final size:28
Alignment explanation
Indices: 27766110--27766162 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
27766100 AACCAACAAG
27766110 CATTAAACCAT-TCAT-AAAAAAAATCGA
1 CATTAAA-CATCTCATGAAAAAAAATCGA
* *
27766137 CATTTAACTTCTCATGAAAAAAAATC
1 CATTAAACATCTCATGAAAAAAAATC
27766163 AAACAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 2 0.09
27 10 0.45
28 10 0.45
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (28 bp):
CATTAAACATCTCATGAAAAAAAATCGA
Found at i:27768846 original size:40 final size:40
Alignment explanation
Indices: 27768802--27768994 Score: 271
Period size: 40 Copynumber: 4.8 Consensus size: 40
27768792 CGGGCTAATC
* *
27768802 CCCGAAGGCATTTATGCTAG-CGATTATATCCGGGTTAAGA
1 CCCGAAGGCATTTGTGCTAGTTG-TTATATCCGGGTTAAGA
* *
27768842 CCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGTTAAGA
1 CCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGTTAAGA
* *
27768882 CCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGA
1 CCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGTTAAGA
* *
27768922 CCCGAAGGCATTTGTGCTAGTTGCTATACCCGGGTTAAGA
1 CCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGTTAAGA
* * *
27768962 CCCGAAGGCAATTGTGCTTGTGGTTATATCCGG
1 CCCGAAGGCATTTGTGCTAGTTGTTATATCCGG
27768995 CTAAATTCCG
Statistics
Matches: 137, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 136 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
CCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGTTAAGA
Found at i:27770571 original size:22 final size:22
Alignment explanation
Indices: 27770542--27770609 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
27770532 TGCACAAACG
27770542 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
27770564 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
* *
27770586 AACAAAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
27770609 A
1 A
27770610 TAATAGAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:27770947 original size:3 final size:3
Alignment explanation
Indices: 27770939--27770975 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
27770929 TTCCATAATC
27770939 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
27770976 TATTTACTTA
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):
TAT
Found at i:27771805 original size:7 final size:7
Alignment explanation
Indices: 27771795--27771883 Score: 55
Period size: 7 Copynumber: 13.3 Consensus size: 7
27771785 TTCTTATGTT
27771795 TTATATA
1 TTATATA
27771802 -T-TATA
1 TTATATA
27771807 TTATATA
1 TTATATA
*
27771814 TAATATA
1 TTATATA
*
27771821 ATA-ATA
1 TTATATA
*
27771827 TAATATA
1 TTATATA
27771834 TTATATA
1 TTATATA
27771841 TTA-ATA
1 TTATATA
*
27771847 CTTAAATA
1 -TTATATA
27771855 TTA-AGT-
1 TTATA-TA
*
27771861 TAATATA
1 TTATATA
*
27771868 ATATATA
1 TTATATA
*
27771875 ATATATA
1 TTATATA
27771882 TT
1 TT
27771884 TTTATATAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.06
6 13 0.20
7 44 0.69
8 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (7 bp):
TTATATA
Found at i:27772537 original size:22 final size:22
Alignment explanation
Indices: 27772494--27772537 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
27772484 TGAACTTAAT
*
27772494 ATTTTTTCTAGTTTAGTATTTA
1 ATTTTTTCTAGTTTAATATTTA
*
27772516 ATTTTTT-TAGGTTTAATTTTTA
1 ATTTTTTCTA-GTTTAATATTTA
27772538 CCTAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (22 bp):
ATTTTTTCTAGTTTAATATTTA
Found at i:27774462 original size:19 final size:19
Alignment explanation
Indices: 27774430--27774466 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27774420 TTTGAAGGTG
27774430 TATTTCTTTAATAATTTTA
1 TATTTCTTTAATAATTTTA
* *
27774449 TATTTTTTTTATAATTTT
1 TATTTCTTTAATAATTTT
27774467 TGAAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTCTTTAATAATTTTA
Found at i:27775583 original size:2 final size:2
Alignment explanation
Indices: 27775576--27775600 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27775566 ATGCAATCAA
27775576 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27775601 AATTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27779494 original size:7 final size:6
Alignment explanation
Indices: 27779453--27779493 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
27779443 ATAATTTAAT
*
27779453 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
27779494 ACATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:27779494 original size:20 final size:20
Alignment explanation
Indices: 27779456--27779495 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27779446 ATTTAATAAA
**
27779456 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
27779476 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
27779496 ATATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:27779553 original size:18 final size:18
Alignment explanation
Indices: 27779513--27779554 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
27779503 TTTATACAAA
*
27779513 TAATTCGGTTAATTCAGG
1 TAATTTGGTTAATTCAGG
*
27779531 AAATTTGGTTAATTC-GG
1 TAATTTGGTTAATTCAGG
27779548 TTAATTT
1 -TAATTT
27779555 TATACTGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (18 bp):
TAATTTGGTTAATTCAGG
Found at i:27781184 original size:3 final size:3
Alignment explanation
Indices: 27781168--27781242 Score: 109
Period size: 3 Copynumber: 25.3 Consensus size: 3
27781158 TGTATTTTTT
*
27781168 TTA TT- TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
27781215 TTA TTA TTA TTA TT- TATA TTA ATA TTA T
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
27781243 GATAATAGTC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 3 0.05
3 61 0.94
4 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:27790803 original size:15 final size:15
Alignment explanation
Indices: 27790779--27790810 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27790769 AAAGTTTGGG
27790779 CAGTTAGTTTTCCAA
1 CAGTTAGTTTTCCAA
*
27790794 CAGTTGGTTTTCCAA
1 CAGTTAGTTTTCCAA
27790809 CA
1 CA
27790811 AGGTTTGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (15 bp):
CAGTTAGTTTTCCAA
Found at i:27792042 original size:20 final size:19
Alignment explanation
Indices: 27791998--27792043 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
27791988 CATCCAAACA
27791998 CTAGAAAAGTAAATCATTT
1 CTAGAAAAGTAAATCATTT
*
27792017 CCAGAAAAGTAAATCATTTT
1 CTAGAAAAGTAAATCA-TTT
27792037 CTAGAAA
1 CTAGAAA
27792044 TCATTTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (19 bp):
CTAGAAAAGTAAATCATTT
Found at i:27795425 original size:21 final size:22
Alignment explanation
Indices: 27795399--27795445 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
27795389 TCAGTAACTC
27795399 TGATAGGGCATCAATACTTT-T
1 TGATAGGGCATCAATACTTTGT
* * *
27795420 TGATAGGGTATCGATAGTTTGT
1 TGATAGGGCATCAATACTTTGT
27795442 TGAT
1 TGAT
27795446 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (22 bp):
TGATAGGGCATCAATACTTTGT
Found at i:27799748 original size:32 final size:34
Alignment explanation
Indices: 27799712--27799776 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
27799702 TAACAGTGGT
*
27799712 ACTGGGCCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
**
27799744 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGGCCAGAGCCCCTTATTCAGATAACAATA
27799777 TGGCCCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.36
33 5 0.18
34 13 0.46
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (34 bp):
ACTGGGCCAGAGCCCCTTATTCAGATAACAATAA
Found at i:27801561 original size:26 final size:26
Alignment explanation
Indices: 27801525--27801632 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
27801515 TGAAATGCCC
* * *
27801525 ATCATGGAACATTTACCTAAACCTTT
1 ATCATGAAACATTTACCTAACCCATT
27801551 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
* * *
27801577 ATCATGGAATATTTACCTAATCCATT
1 ATCATGAAACATTTACCTAACCCATT
27801603 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
27801629 ATCA
1 ATCA
27801633 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGAAACATTTACCTAACCCATT
Found at i:27801591 original size:52 final size:52
Alignment explanation
Indices: 27801525--27801632 Score: 189
Period size: 52 Copynumber: 2.1 Consensus size: 52
27801515 TGAAATGCCC
*
27801525 ATCATGGAACATTTACCTAAACCTTTATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATT
* *
27801577 ATCATGGAATATTTACCTAATCCATTATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATT
27801629 ATCA
1 ATCA
27801633 ATTTGTACCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCTAACCCATT
Found at i:27802652 original size:88 final size:87
Alignment explanation
Indices: 27802534--27802749 Score: 256
Period size: 88 Copynumber: 2.5 Consensus size: 87
27802524 AAAGTGAATT
* * **
27802534 AAATCTATTTCAGGATTTATTCTCAACGTTCAACGGATTTTATTCCA-ATTTTGATTTTATTTC-
1 AAATCTACTTC-GGATTTATTCCCGCCGTTCAACGGATTTTATTCCATATTTTG-TTTTATTTCT
* * *
27802597 CAAAGCGAGTTTTAAAATTAAAATA
64 CAAA-CAAGTATTAAAACTAAAATA
* * * * * *
27802622 AAATTTATTTTGTGATTTGTTCCCGCCGTTCAACGGATTTTATTCCATTTTTTGTTTTATTTCTG
1 AAATCTACTTCG-GATTTATTCCCGCCGTTCAACGGATTTTATTCCATATTTTGTTTTATTTCTC
27802687 AAACAAGTATTAAAACTAAAATA
65 AAACAAGTATTAAAACTAAAATA
*
27802710 AAATCTACTTCGGATTTATTCCCGCCGTTCAATGGATTTT
1 AAATCTACTTCGGATTTATTCCCGCCGTTCAACGGATTTT
27802750 GAATTTATTT
Statistics
Matches: 109, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
87 27 0.25
88 74 0.68
89 8 0.07
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (87 bp):
AAATCTACTTCGGATTTATTCCCGCCGTTCAACGGATTTTATTCCATATTTTGTTTTATTTCTCA
AACAAGTATTAAAACTAAAATA
Found at i:27802892 original size:164 final size:160
Alignment explanation
Indices: 27802580--27803072 Score: 416
Period size: 164 Copynumber: 3.0 Consensus size: 160
27802570 ATTTTATTCC
* * * * * * * * *
27802580 AATTTTGATTTTATTTCCAAAGCGAGTTTTAAAATTAAAATAAAATTTATTTTGTGATTTGTTCC
1 AATTTTGAATTTATTTCCAAAACAAGTATTAAAATTAAAATAAAATATGTTTCGAGATTTATTCC
* * ** * * *
27802645 CGCCGTTCAACGGATTTTATTCCATTTTTTGTTTTATTTCTGAAACAAGTATTAAAACTAAAATA
66 CGCCGTTTAACGAATTTTATT-CAAATTTTGTTTTATTTC-CAAATAAGAATT-AAA-TAAAATA
**
27802710 AAATCTACTTCGGATTTATTCCCGCCGTTCAATG
127 AAATCTGTTTCGGATTTATTCCCGCCGTTCAATG
* * *
27802744 GATTTTGAATTTATTTCCAAAACTAGTATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCC
1 AATTTTGAATTTATTTCCAAAACAAGTATTAAAATTAAAATAAAATATGTTTCGAGATTTATTCC
* * * * *
27802809 CACCGTTTAACGAATTCTATTCAAATTCTGATTTTATTTCCAAATGAGAAATTAAAGTTAAATAA
66 CGCCGTTTAACGAATTTTATTCAAATTTTG-TTTTATTTCCAAATAAG-AATTAAA-TAAAATAA
* *
27802874 AATCTGTTTCGAGATTTATTCTCGCCATTCAATG
128 AATCTGTTTCG-GATTTATTCCCGCCGTTCAATG
* * **
27802908 AATTTATTACATTTTGATTTTGTTATCAAAACGAAAAATTAAAATT-AAATAAAATATGTTTC-A
1 AATTT-TGA-A-TTT-A---T-TT-CCAAAAC-AAGTATTAAAATTAAAATAAAATATGTTTCGA
* * * * * *
27802971 GGATTTATTCTCGCCCTTTAACAAGATTTTATT-TAATTTTGTTTTGTTTCCAAATTAGAATTAA
56 -GATTTATTCCCGCCGTTTAACGA-ATTTTATTCAAATTTTGTTTTATTTCCAAATAAGAATTAA
* *
27803035 ATGAAATAAAATATGTTTCGGGATTTATTCCCGCCGTT
119 ATAAAATAAAATCTGTTTC-GGATTTATTCCCGCCGTT
27803073 TAAGAAGATT
Statistics
Matches: 266, Mismatches: 47, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
163 30 0.11
164 108 0.41
165 2 0.01
166 1 0.00
167 3 0.01
168 1 0.00
170 31 0.12
171 9 0.03
172 18 0.07
173 46 0.17
174 17 0.06
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (160 bp):
AATTTTGAATTTATTTCCAAAACAAGTATTAAAATTAAAATAAAATATGTTTCGAGATTTATTCC
CGCCGTTTAACGAATTTTATTCAAATTTTGTTTTATTTCCAAATAAGAATTAAATAAAATAAAAT
CTGTTTCGGATTTATTCCCGCCGTTCAATG
Found at i:27802911 original size:87 final size:85
Alignment explanation
Indices: 27802775--27803192 Score: 393
Period size: 84 Copynumber: 4.9 Consensus size: 85
27802765 ACTAGTATTA
* * *
27802775 AAATTAAAATAAAATCTGTTTCGAGATTTATTCCCACCGTTTAACGA-ATTCTATTCAAATTCTG
1 AAATT-AAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTTAACGAGATTTTATT-AAATTTTG
*
27802839 ATTTTATTTCCAAATGAGAAATT
64 ATTTTGTTTCCAAATGAG-AATT
* * * * *
27802862 AAAGTTAAATAAAATCTGTTTCGAGATTTATTCTCGCCATTCAATGA-A-TTTATTACATTTTGA
1 AAA-TTAAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTTAACGAGATTTTATTAAATTTTGA
* * *
27802925 TTTTGTTATCAAAACGAAAAATT
65 TTTTGTT-TCCAAATG-AGAATT
* * * * *
27802948 AAAATTAAATAAAATATGTTTC-AGGATTTATTCTCGCCCTTTAACAAGATTTTATTTAATTTTG
1 -AAATTAAATAAAATCTGTTTCGA-GATTTATTCCCGCCGTTTAACGAGATTTTATTAAATTTTG
*
27803012 -TTTTGTTTCCAAATTAGAATT
64 ATTTTGTTTCCAAATGAGAATT
* * * **
27803033 AAATGAAATAAAATATGTTTCGGGATTTATTCCCGCCGTTTAA-GAAGATTTTATTTGATTTT-A
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTTAACG-AGATTTTATTAAATTTTGA
*
27803096 TTTTGTTTCCAAATTAGAATT
65 TTTTGTTTCCAAATGAGAATT
* * * * * * * ** *
27803117 AAATTAAATAAAATCTATTTCGGGATTTGTTTCCACTGTTTAACAAGATTTTATTCGATATTGA-
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTTAACGAGATTTTATTAAATTTTGAT
27803181 TTTGTTTCCAAA
66 TTTGTTTCCAAA
27803193 CAAAAACTTA
Statistics
Matches: 280, Mismatches: 39, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
84 138 0.49
85 20 0.07
86 56 0.20
87 52 0.19
88 14 0.05
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (85 bp):
AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTTAACGAGATTTTATTAAATTTTGAT
TTTGTTTCCAAATGAGAATT
Found at i:27803059 original size:84 final size:84
Alignment explanation
Indices: 27802775--27803254 Score: 386
Period size: 84 Copynumber: 5.7 Consensus size: 84
27802765 ACTAGTATTA
* * * * * * * *
27802775 AAATTAAAATAAAATCTGTTTCGAGATTTATTCCCACCGTTTAACGA-ATTCTATTCAAATTCTG
1 AAATT-AAATAAAATATGTTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATT-TAATTTTG
* *
27802839 ATTTTATTTCCAAATGAGAAATT
64 -TTTTGTTTCCAAATAAG-AATT
* * * *
27802862 AAAGTTAAATAAAATCTGTTTCGAGATTTATTCTCGCC-ATT--CAATGAATTTA-TTACATTTT
1 AAA-TTAAATAAAATATGTTTCGGGATTTATTCTCGCCGTTTAACAA-GATTTTATTTA-ATTTT
* * *
27802923 GATTTTGTTATCAAAACGAAAAATT
63 G-TTTTGTT-TCCAAA-TAAGAATT
* *
27802948 AAAATTAAATAAAATATGTTTCAGGATTTATTCTCGCCCTTTAACAAGATTTTATTTAATTTTGT
1 -AAATTAAATAAAATATGTTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATTTAATTTTGT
*
27803013 TTTGTTTCCAAATTAGAATT
65 TTTGTTTCCAAATAAGAATT
* * * * *
27803033 AAATGAAATAAAATATGTTTCGGGATTTATTCCCGCCGTTTAAGAAGATTTTATTTGATTTTATT
1 AAATTAAATAAAATATGTTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATTTAATTTTGTT
*
27803098 TTGTTTCCAAATTAGAATT
66 TTGTTTCCAAATAAGAATT
* * * ** *
27803117 AAATTAAATAAAATCTATTTCGGGATTTGTT-TC-CACTGTTTAACAAGATTTTATTCGATATTG
1 AAATTAAATAAAATATGTTTCGGGATTTATTCTCGC-C-GTTTAACAAGATTTTATTTAATTTTG
* * *
27803180 ATTTGTTTCCAAACAAAAACTT
64 TTTTGTTTCCAAATAAGAA-TT
* * * * ** *
27803202 -AATCAAAT-AATTATGTTTCGGGAATTATTCTTGTTGTTTAGC-AGATTTTATTT
1 AAATTAAATAAAATATGTTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATTT
27803255 TGATGTAATT
Statistics
Matches: 324, Mismatches: 53, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
82 11 0.03
83 24 0.07
84 152 0.47
85 20 0.06
86 51 0.16
87 46 0.14
88 14 0.04
89 6 0.02
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (84 bp):
AAATTAAATAAAATATGTTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATTTAATTTTGTT
TTGTTTCCAAATAAGAATT
Found at i:27803165 original size:168 final size:167
Alignment explanation
Indices: 27802745--27803231 Score: 439
Period size: 168 Copynumber: 2.9 Consensus size: 167
27802735 CGTTCAATGG
* * * * *
27802745 ATTTTGAATTTATTTCCAAAACTAGTATTAAAATTAAAATAAAATCTGTTTCGAGATTTATTCCC
1 ATTTTGATTTTGTTTCC-AAACTAGAATTAAAATT-AAATAAAATCTGTTTCGGGATTTATTTCC
* * * * * *
27802810 ACCGTTTAACGA-ATTCTATTCAAATTCTGATTTTATTTCCAAATGAGAAATTAAAGTTAAATAA
64 A-CGTTTAACAAGATTTTATT-AAATTTTG-TTTTGTTTCCAAATAAG-AATTAAA-TCAAATAA
* * *
27802874 AATCTGTTTCGAGATTTATTCTCGCCATTCAATGAATTTATTAC
124 AATATGTTTCGGGATTTATTCCCGCCATTCAATGAATTTATTAC
* * * * *
27802918 ATTTTGATTTTGTTATCAAAACGAAAAATTAAAATTAAATAAAATATGTTTCAGGATTTATTCTC
1 ATTTTGATTTTGTT-TCCAAAC-TAGAATTAAAATTAAATAAAATCTGTTTCGGGATTTATT-TC
* * * *
27802983 GC-CCTTTAACAAGATTTTATTTAATTTTGTTTTGTTTCCAAATTAGAATTAAATGAAATAAAAT
63 -CACGTTTAACAAGATTTTATTAAATTTTGTTTTGTTTCCAAATAAGAATTAAATCAAATAAAAT
* * **
27803047 ATGTTTCGGGATTTATTCCCGCCGTTTAA-GAAGATTTTATTTG
127 ATGTTTCGGGATTTATTCCCGCCATTCAATG-A-A-TTTATTAC
* * *
27803090 ATTTT-ATTTTGTTTCCAAATTAGAATT-AAATTAAATAAAATCTATTTCGGGATTTGTTTCCAC
1 ATTTTGATTTTGTTTCCAAACTAGAATTAAAATTAAATAAAATCTGTTTCGGGATTTATTTCCAC
** * * * * *
27803153 TGTTTAACAAGATTTTATTCGATATTGATTTGTTTCCAAACAAAAACTT-AATCAAAT-AATTAT
66 -GTTTAACAAGATTTTATTAAATTTTGTTTTGTTTCCAAATAAGAA-TTAAATCAAATAAAATAT
*
27803216 GTTTCGGGAATTATTC
129 GTTTCGGGATTTATTC
27803232 TTGTTGTTTA
Statistics
Matches: 259, Mismatches: 44, Indels: 28
0.78 0.13 0.08
Matches are distributed among these distances:
166 1 0.00
167 23 0.09
168 71 0.27
169 8 0.03
170 40 0.15
171 16 0.06
172 26 0.10
173 53 0.20
174 20 0.08
175 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (167 bp):
ATTTTGATTTTGTTTCCAAACTAGAATTAAAATTAAATAAAATCTGTTTCGGGATTTATTTCCAC
GTTTAACAAGATTTTATTAAATTTTGTTTTGTTTCCAAATAAGAATTAAATCAAATAAAATATGT
TTCGGGATTTATTCCCGCCATTCAATGAATTTATTAC
Found at i:27805779 original size:16 final size:16
Alignment explanation
Indices: 27805716--27805784 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 16
27805706 TAATTATTCA
27805716 AAGATATTTATTATTTAT
1 AAGATATTTA-TA-TTAT
*
27805734 AAAATATGTT-TATTAATT
1 AAGATAT-TTATATT-A-T
*
27805752 AA-ATAATTATATTAT
1 AAGATATTTATATTAT
*
27805767 AAGATATTTATATGAT
1 AAGATATTTATATTAT
27805783 AA
1 AA
27805785 ATAAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
15 3 0.07
16 18 0.43
17 10 0.24
18 9 0.21
19 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
AAGATATTTATATTAT
Found at i:27805850 original size:19 final size:19
Alignment explanation
Indices: 27805822--27805860 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27805812 TGATCTATGG
*
27805822 ATACATATGTA-ATAATAAT
1 ATACACATGTATA-AATAAT
27805841 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
27805860 A
1 A
27805861 AATAAGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:27806844 original size:22 final size:20
Alignment explanation
Indices: 27806817--27806856 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
27806807 ATTTGACTGT
27806817 TACTGAATAAATGAATGATTGA
1 TACTGAAT-AAT-AATGATTGA
27806839 TACTGAATAATAATGATT
1 TACTGAATAATAATGATT
27806857 AAATGATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (20 bp):
TACTGAATAATAATGATTGA
Found at i:27812270 original size:2 final size:2
Alignment explanation
Indices: 27812263--27812308 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
27812253 AATATAATGT
27812263 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
27812305 TA TA
1 TA TA
27812309 ACAAGTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27812378 original size:4 final size:4
Alignment explanation
Indices: 27812369--27812393 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27812359 AGAACAGGGG
27812369 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
27812394 AGGGAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:27813573 original size:22 final size:20
Alignment explanation
Indices: 27813546--27813585 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
27813536 ATTTGACTGT
27813546 TACTGAATAAATGAATGATTGA
1 TACTGAAT-AAT-AATGATTGA
27813568 TACTGAATAATAATGATT
1 TACTGAATAATAATGATT
27813586 AAATGACTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (20 bp):
TACTGAATAATAATGATTGA
Found at i:27813594 original size:22 final size:22
Alignment explanation
Indices: 27813546--27813587 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
27813536 ATTTGACTGT
*
27813546 TACTGAATAAATGAATGATTGA
1 TACTGAATAAATGAATGATTAA
27813568 TACTGAAT-AAT-AATGATTAA
1 TACTGAATAAATGAATGATTAA
27813588 ATGACTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (22 bp):
TACTGAATAAATGAATGATTAA
Found at i:27814687 original size:21 final size:21
Alignment explanation
Indices: 27814645--27814691 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
27814635 ACGGTGTGCC
* *
27814645 CACACGGGTGTGTTATGGAAA
1 CACACGGGTGTGTCATCGAAA
*
27814666 CACACGGGTGTGTCATCTAAA
1 CACACGGGTGTGTCATCGAAA
27814687 C-CACG
1 CACACG
27814692 CGGACGTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (21 bp):
CACACGGGTGTGTCATCGAAA
Found at i:27815973 original size:86 final size:85
Alignment explanation
Indices: 27815835--27815996 Score: 193
Period size: 86 Copynumber: 1.9 Consensus size: 85
27815825 ATAGGATCCG
* ** *
27815835 ATATGTGATTTCGTGTAAGACCACGTCTGGGACGTTAGCATCGACTTATGATTTACGTATAAGAC
1 ATATGTGATTTCGTGTAAGACCACGTCTAGGACAATAGCATCGACTTATGA-TTACATATAAGAC
*
27815900 CATGTCTGGGACATCGGCATC
65 CACGTCTGGGACATCGGCATC
* * * * *
27815921 ATATTTGATTTCGTGTAAGACC-CTGTCTAGGACAATGGCATTGA-TATTTGATTACATGTAAGA
1 ATATGTGATTTCGTGTAAGACCAC-GTCTAGGACAATAGCATCGACT-TATGATTACATATAAGA
27815984 CCACGTCTGGGAC
64 CCACGTCTGGGAC
27815997 GTTGGCATTG
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
85 24 0.38
86 40 0.62
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (85 bp):
ATATGTGATTTCGTGTAAGACCACGTCTAGGACAATAGCATCGACTTATGATTACATATAAGACC
ACGTCTGGGACATCGGCATC
Found at i:27816003 original size:43 final size:43
Alignment explanation
Indices: 27815834--27816006 Score: 163
Period size: 43 Copynumber: 4.0 Consensus size: 43
27815824 CATAGGATCC
* * * * *
27815834 GATATGTGATTTCGTGTAAGACCACGTCTGGGACGTTAGCATC
1 GATATTTGATTACGTGTAAGACCACGTCTGGGACATTGGCATT
* * * *
27815877 GACT-TATGATTTACGTATAAGACCATGTCTGGGACATCGGCA-T
1 GA-TATTTGA-TTACGTGTAAGACCACGTCTGGGACATTGGCATT
* * * *
27815920 CATATTTGATTTCGTGTAAGACC-CTGTCTAGGACAATGGCATT
1 GATATTTGATTACGTGTAAGACCAC-GTCTGGGACATTGGCATT
* *
27815963 GATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCATT
1 GATATTTGATTACGTGTAAGACCACGTCTGGGACATTGGCATT
27816006 G
1 G
27816007 TATGAGTTTT
Statistics
Matches: 102, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
42 26 0.25
43 48 0.47
44 28 0.27
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
GATATTTGATTACGTGTAAGACCACGTCTGGGACATTGGCATT
Found at i:27816612 original size:18 final size:18
Alignment explanation
Indices: 27816589--27816648 Score: 102
Period size: 18 Copynumber: 3.3 Consensus size: 18
27816579 ATTTGCTTAT
*
27816589 GGCTTACTAAGCTTTTAA
1 GGCTTACTAAGCTTTCAA
27816607 GGCTTACTAAGCTTTCAA
1 GGCTTACTAAGCTTTCAA
27816625 GGCTTACTAAGCTTTCAA
1 GGCTTACTAAGCTTTCAA
*
27816643 AGCTTA
1 GGCTTA
27816649 TTCTGTGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (18 bp):
GGCTTACTAAGCTTTCAA
Found at i:27816638 original size:9 final size:9
Alignment explanation
Indices: 27816590--27816648 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
27816580 TTTGCTTATG
27816590 GCTTACTAA
1 GCTTACTAA
*
27816599 GCTT-TTAA
1 GCTTACTAA
27816607 GGCTTACTAA
1 -GCTTACTAA
*
27816617 GCTTTC-AA
1 GCTTACTAA
27816625 GGCTTACTAA
1 -GCTTACTAA
* *
27816635 GCTTTCAAA
1 GCTTACTAA
27816644 GCTTA
1 GCTTA
27816649 TTCTGTGTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
8 5 0.13
9 29 0.74
10 5 0.13
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (9 bp):
GCTTACTAA
Found at i:27819405 original size:42 final size:41
Alignment explanation
Indices: 27819346--27819463 Score: 137
Period size: 43 Copynumber: 2.8 Consensus size: 41
27819336 TAGGGTTATT
27819346 TGAGTTCTCATGTAAGACCATATCTGGGATATGACATCGATA
1 TGAGTTCTCATGTAAGACCATATCTGGGATATG-CATCGATA
* * * * *
27819388 TGAGTTTTCGTGTAAGACTATAGCTGAGATATTTGCATCGATA
1 TGAGTTCTCATGTAAGACCATATCTGGGATA--TGCATCGATA
* * *
27819431 TGAGATCCCATGTAAGACCATATCCGGGATATG
1 TGAGTTCTCATGTAAGACCATATCTGGGATATG
27819464 GCATTGGTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
41 2 0.03
42 26 0.43
43 31 0.51
44 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (41 bp):
TGAGTTCTCATGTAAGACCATATCTGGGATATGCATCGATA
Found at i:27822709 original size:20 final size:20
Alignment explanation
Indices: 27822684--27822736 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
27822674 GAACCCTTCT
*
27822684 ATTTACTTACTTTTCATAGC
1 ATTTACTTACTTTCCATAGC
*
27822704 ATTTACTTACTTTCCATTGC
1 ATTTACTTACTTTCCATAGC
*
27822724 GTTTACTTACTTT
1 ATTTACTTACTTT
27822737 ACCTTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (20 bp):
ATTTACTTACTTTCCATAGC
Found at i:27825070 original size:56 final size:56
Alignment explanation
Indices: 27825005--27825113 Score: 173
Period size: 56 Copynumber: 1.9 Consensus size: 56
27824995 AAAACCATAA
* * * *
27825005 TTGACTCATAAATATTCATAAATTATATTTATGAACTTGCTCATCGGATTTGTGGT
1 TTGACTCATAAATATTCATAAATAATATTTACGAACTTACTCATCAGATTTGTGGT
*
27825061 TTGACTCATAAATATTCATAAGTAATATTTACGAACTTACTCATCAGATTTGT
1 TTGACTCATAAATATTCATAAATAATATTTACGAACTTACTCATCAGATTTGT
27825114 TGCCTTGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (56 bp):
TTGACTCATAAATATTCATAAATAATATTTACGAACTTACTCATCAGATTTGTGGT
Found at i:27827342 original size:52 final size:50
Alignment explanation
Indices: 27827285--27827393 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 50
27827275 AATATTTATA
27827285 GTGCCGCCACATTATTTGAAGGAA-CTAAAATAAAATAAACAATTATTTTTTG
1 GTGCCGCCACATTATTTGAAGGAATC-AAAATAAAA-AAA-AATTATTTTTTG
* * * *
27827337 GTGCCGCCACATTATTTGGAGGCATCAAAATGAAAAAAAATTGTTTTTTG
1 GTGCCGCCACATTATTTGAAGGAATCAAAATAAAAAAAAATTATTTTTTG
27827387 GTGCCGC
1 GTGCCGC
27827394 TTTCTTTCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
50 18 0.35
51 3 0.06
52 30 0.58
53 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (50 bp):
GTGCCGCCACATTATTTGAAGGAATCAAAATAAAAAAAAATTATTTTTTG
Found at i:27827770 original size:25 final size:25
Alignment explanation
Indices: 27827734--27827788 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
27827724 CTAGAGTATA
*
27827734 TATAG-TTGGTGGTGTTGCCACCTT
1 TATAGTTTGGTGGTGTCGCCACCTT
27827758 TATAGTTTGGTGGTGTCGCCACCTT
1 TATAGTTTGGTGGTGTCGCCACCTT
27827783 TATAGT
1 TATAGT
27827789 AGGCAGTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.15, C:0.16, G:0.27, T:0.42
Consensus pattern (25 bp):
TATAGTTTGGTGGTGTCGCCACCTT
Found at i:27828464 original size:30 final size:31
Alignment explanation
Indices: 27828390--27828469 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
27828380 ATCTCAAAAC
*
27828390 TATACATG-AATTATGATTTAAAGTGCAATTG
1 TATACATGAAATTTTGATTT-AAGTGCAATTG
* *
27828421 TATACAT-AAATTTTGATTT-TGTGCAATTT
1 TATACATGAAATTTTGATTTAAGTGCAATTG
27828450 TATACATGAAATTTTGATTT
1 TATACATGAAATTTTGATTT
27828470 GATTCAATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
29 15 0.34
30 12 0.27
31 17 0.39
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46
Consensus pattern (31 bp):
TATACATGAAATTTTGATTTAAGTGCAATTG
Found at i:27828470 original size:29 final size:29
Alignment explanation
Indices: 27828390--27828484 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 29
27828380 ATCTCAAAAC
* *
27828390 TATACATG-AATTATGATTTAAAGTGCAATTG
1 TATACATGAAATTTTGATTT---GTGCAATTT
27828421 TATACAT-AAATTTTGATTTTGTGCAATTT
1 TATACATGAAATTTTGA-TTTGTGCAATTT
*
27828450 TATACATGAAATTTTGATTTGATTCAATTCT
1 TATACATGAAATTTTGATTTG-TGCAATT-T
27828481 TATA
1 TATA
27828485 AATTATTAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
29 19 0.34
30 15 0.27
31 19 0.34
32 3 0.05
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
TATACATGAAATTTTGATTTGTGCAATTT
Found at i:27828478 original size:30 final size:29
Alignment explanation
Indices: 27828412--27828469 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
27828402 ATGATTTAAA
*
27828412 GTGCAATTGTATACATAAATTTTGATTTT
1 GTGCAATTTTATACATAAATTTTGATTTT
27828441 GTGCAATTTTATACATGAAATTTTGATTT
1 GTGCAATTTTATACAT-AAATTTTGATTT
27828470 GATTCAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (29 bp):
GTGCAATTTTATACATAAATTTTGATTTT
Found at i:27836000 original size:2 final size:2
Alignment explanation
Indices: 27835993--27836034 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27835983 TAGAGGGCTA
27835993 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
27836035 TGTAATTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27836463 original size:7 final size:7
Alignment explanation
Indices: 27836451--27836504 Score: 58
Period size: 7 Copynumber: 7.6 Consensus size: 7
27836441 TGCCATAGCT
27836451 TTTTAAA
1 TTTTAAA
27836458 TTTTAAA
1 TTTTAAA
27836465 TTTTAAA
1 TTTTAAA
27836472 TTTT-AA
1 TTTTAAA
*
27836478 -TTTCAA
1 TTTTAAA
27836484 TTATTAATA
1 TT-TTAA-A
27836493 TTATTAAA
1 TT-TTAAA
27836501 TTTT
1 TTTT
27836505 GTTTGCTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 3 0.07
6 4 0.10
7 21 0.50
8 6 0.14
9 8 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:27836913 original size:25 final size:25
Alignment explanation
Indices: 27836879--27836939 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
27836869 TAGCCACACC
27836879 AGTTTTTAACAATAGAGAT-AATTGA
1 AGTTTTTAACAATAGAGATGAA-TGA
*
27836904 AGTTTTTAACAGTAGAGATGAATGA
1 AGTTTTTAACAATAGAGATGAATGA
*
27836929 AATTTTTAACA
1 AGTTTTTAACA
27836940 GAAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 31 0.94
26 2 0.06
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (25 bp):
AGTTTTTAACAATAGAGATGAATGA
Found at i:27841058 original size:47 final size:47
Alignment explanation
Indices: 27840989--27841082 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
27840979 AGAATATAAA
27840989 GGACAGAATTAAAAAGAAGATTAATGGCTGAAGCTTCAGGTTTTTAT
1 GGACAGAATTAAAAAGAAGATTAATGGCTGAAGCTTCAGGTTTTTAT
27841036 GGACAGAATTAAAAAGAAGATTAATGGCTGAAGCTTCAGGTTTTTAT
1 GGACAGAATTAAAAAGAAGATTAATGGCTGAAGCTTCAGGTTTTTAT
27841083 CACAGGGAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (47 bp):
GGACAGAATTAAAAAGAAGATTAATGGCTGAAGCTTCAGGTTTTTAT
Found at i:27848381 original size:55 final size:55
Alignment explanation
Indices: 27848296--27848421 Score: 137
Period size: 55 Copynumber: 2.3 Consensus size: 55
27848286 ATAGATGTGT
* ** * * * *
27848296 ACGCCCGTGTTATTTTGACAGTTTCGACCACGGGTGGTGGGCACGGGCGTGTCGC
1 ACGCCCGTGTTATTTTGACAGTCTCGACCACGACTGCTAGGCACGAGCGTGTCAC
* * *
27848351 ACGCCCGTGTTAATTTT-TCAGTCTCTACCACGACTTCTAGGCACGAGCGTGTCAC
1 ACGCCCGTGTT-ATTTTGACAGTCTCGACCACGACTGCTAGGCACGAGCGTGTCAC
27848406 ACGCCCGTGTTGATTT
1 ACGCCCGTGTT-ATTT
27848422 AGTAGTTTCG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 54 0.92
56 5 0.08
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.29
Consensus pattern (55 bp):
ACGCCCGTGTTATTTTGACAGTCTCGACCACGACTGCTAGGCACGAGCGTGTCAC
Found at i:27852637 original size:62 final size:61
Alignment explanation
Indices: 27852564--27852685 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 61
27852554 TGCTTCAAAC
*
27852564 CGTGTTTGAGTCTGTTAAATAGACACGGGCGTGTGGTCTACCCATGTGA-GGAAGTCCAGGT
1 CGTGTTTGAGTCTGTTAAATAGACACGGGCGTGTGATCTACCCATGT-ACGGAAGTCCAGGT
* * *
27852625 CGTGTTTAGAGTCTGTTGAATAGGCACGGGCGTGTGATCTACCCGTGTACGGAAGTCCAGG
1 CGTGTTT-GAGTCTGTTAAATAGACACGGGCGTGTGATCTACCCATGTACGGAAGTCCAGG
27852686 CCATGTCGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 8 0.15
62 47 0.85
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.27
Consensus pattern (61 bp):
CGTGTTTGAGTCTGTTAAATAGACACGGGCGTGTGATCTACCCATGTACGGAAGTCCAGGT
Found at i:27853748 original size:51 final size:51
Alignment explanation
Indices: 27853693--27853794 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
27853683 TATAGGCTAG
* *
27853693 TCATATCCCATCATAGCACAATAATGCCTTCCATAACTTTACCACTAGTTT
1 TCATATCCCATCATAGCACAATAATACCCTCCATAACTTTACCACTAGTTT
* *
27853744 TCATATCCCATTATAGCACAATAATACCCTCCATAACTTTATCACTAGTTT
1 TCATATCCCATCATAGCACAATAATACCCTCCATAACTTTACCACTAGTTT
27853795 CACATGCTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (51 bp):
TCATATCCCATCATAGCACAATAATACCCTCCATAACTTTACCACTAGTTT
Found at i:27858838 original size:141 final size:137
Alignment explanation
Indices: 27858462--27858883 Score: 571
Period size: 136 Copynumber: 3.1 Consensus size: 137
27858452 TAGAAAAAGG
* * * ** * *
27858462 AATTATATTATTTCCAAAAGAATATTAATGTCCATGCCTTTTATATTTTAACTAAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACCAAAATTAATTAA
* *
27858527 TATAACTGTTTATATTAATAAATTCAGTAAAATAT-ACAATTAATATTTTGTATGAATAAAATTT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATAACAATTAATATTTTGTATGAATCAAATTA
27858591 ATATATT
131 ATATATT
* * * *
27858598 AATTATATTCTTTCTAAAATAATATTAATTTCCATATCTTTAATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACCAAAATTAATTAA
* * *
27858663 TGTAACAGTTTATATTAATAAATTCTGTAAAATATACACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATA-ACAATTAATATTTTGTATGAATCAAATT
27858728 AATATATT
130 AATATATT
* * *
27858736 GATTATATTCTTTCCAAAAAAAATATTAATTTTTCATTTCTTTTATATTTTTGACCAAAATTAAT
1 AATTATATTCTTTCC-AAAAAAATATTAA-TTTCCATATCTTTTATA-TTTTGACCAAAATTAAT
* * *
27858801 TAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATA--TTGTCTGAATCAA
63 TAATATAACTGTTTATATTAATAAATTCAGTAAAATATA-ACAATTAATATTTTGTATGAATCAA
*
27858864 ATTCATATATT
127 ATTAATATATT
27858875 AATTATATT
1 AATTATATT
27858884 TATGTTCTCT
Statistics
Matches: 251, Mismatches: 30, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
136 87 0.35
138 47 0.19
139 42 0.17
140 14 0.06
141 61 0.24
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACCAAAATTAATTAA
TATAACTGTTTATATTAATAAATTCAGTAAAATATAACAATTAATATTTTGTATGAATCAAATTA
ATATATT
Found at i:27863720 original size:33 final size:31
Alignment explanation
Indices: 27863683--27863761 Score: 113
Period size: 33 Copynumber: 2.5 Consensus size: 31
27863673 TCTTTCTGAT
27863683 TGGTATACACAAAGTACACCTTTCCTTTTCATA
1 TGGTATACACAAAGTACACC-TTCCTTTTCA-A
*
27863716 TGGTATACACAAAGTATACCTTCCTTTTCAA
1 TGGTATACACAAAGTACACCTTCCTTTTCAA
* *
27863747 TTGTACACACAAAGT
1 TGGTATACACAAAGT
27863762 GTACATAGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 14 0.33
32 10 0.23
33 19 0.44
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (31 bp):
TGGTATACACAAAGTACACCTTCCTTTTCAA
Found at i:27863745 original size:32 final size:33
Alignment explanation
Indices: 27863683--27863874 Score: 178
Period size: 32 Copynumber: 5.9 Consensus size: 33
27863673 TCTTTCTGAT
* * * **
27863683 TGGTATACACAAAGTACACCTTTCCTTTTCATA
1 TGGTACACACAAAGTATACATAACCTTTTCATA
* * *
27863716 TGGTATACACAAAGTATACCT-TCCTTTTCA-A
1 TGGTACACACAAAGTATACATAACCTTTTCATA
* * * *
27863747 TTGTACACACAAAGTGTACATAGCCTTTTCATG
1 TGGTACACACAAAGTATACATAACCTTTTCATA
*
27863780 T-GTACACACAAAGTGTACATAACCTTTTCA-A
1 TGGTACACACAAAGTATACATAACCTTTTCATA
* *
27863811 -GTGTACACACAAAGTGTACATAACCTTTTCATG
1 TG-GTACACACAAAGTATACATAACCTTTTCATA
* * *
27863844 TGGTATACACAAAGTATTCCTAACCTTTTCA
1 TGGTACACACAAAGTATACATAACCTTTTCA
27863875 CATTCGATAA
Statistics
Matches: 139, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
31 18 0.13
32 74 0.53
33 46 0.33
34 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (33 bp):
TGGTACACACAAAGTATACATAACCTTTTCATA
Found at i:27863774 original size:64 final size:65
Alignment explanation
Indices: 27863706--27863874 Score: 252
Period size: 64 Copynumber: 2.6 Consensus size: 65
27863696 GTACACCTTT
* * * *
27863706 CCTTTTCATATGGTATACACAAAGTATACCT-TCCTTTTCAATTGTACACACAAAGTGTACATAG
1 CCTTTTCATGTGGTATACACAAAGTATACCTAACCTTTTCAAGTGTACACACAAAGTGTACATAA
* * *
27863770 CCTTTTCATGT-GTACACACAAAGTGTACATAACCTTTTCAAGTGTACACACAAAGTGTACATAA
1 CCTTTTCATGTGGTATACACAAAGTATACCTAACCTTTTCAAGTGTACACACAAAGTGTACATAA
*
27863834 CCTTTTCATGTGGTATACACAAAGTATTCCTAACCTTTTCA
1 CCTTTTCATGTGGTATACACAAAGTATACCTAACCTTTTCA
27863875 CATTCGATAA
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
63 16 0.17
64 51 0.55
65 25 0.27
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (65 bp):
CCTTTTCATGTGGTATACACAAAGTATACCTAACCTTTTCAAGTGTACACACAAAGTGTACATAA
Found at i:27863909 original size:29 final size:29
Alignment explanation
Indices: 27863867--27863964 Score: 169
Period size: 29 Copynumber: 3.4 Consensus size: 29
27863857 GTATTCCTAA
* *
27863867 CCTTTTCACATTCGATAACTGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
27863896 CCTTTCCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
27863925 CCTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
27863954 CCTTTTCACAT
1 CCTTTTCACAT
27863965 GGTACACAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.33
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCGAAGCTATC
Found at i:27867539 original size:27 final size:26
Alignment explanation
Indices: 27867500--27867641 Score: 158
Period size: 27 Copynumber: 5.3 Consensus size: 26
27867490 AGCATGGCCG
* *
27867500 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
* *
27867526 ACAGATACAAATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
27867554 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
27867581 CCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
27867608 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
27867635 CCAGAAC
1 CCAGAAC
27867642 GCTTCCTCCA
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
26 4 0.04
27 83 0.81
28 16 0.16
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:27867600 original size:54 final size:55
Alignment explanation
Indices: 27867500--27867639 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 55
27867490 AGCATGGCCG
* * *
27867500 CCAGAACAGATA-ATGTGACAGAGTCAACAGATACAAATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAAATAATCGTGGCAGAGCCA
* * *
27867554 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAAATAATCGTGGCAGAGCCA
* * *
27867608 CCAGATCAGATATTTGTGGCATAGCCACCAGA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGA
27867640 ACGCTTCCTC
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
54 59 0.78
55 17 0.22
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (55 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATACAAATAATCGTGGCAGAGCCA
Found at i:27869362 original size:26 final size:26
Alignment explanation
Indices: 27869253--27869354 Score: 177
Period size: 26 Copynumber: 3.9 Consensus size: 26
27869243 CATGGTATTC
27869253 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
27869279 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
27869305 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
27869331 TTATCATGGAACATTTACCTAACC
1 TTATCATGAAACATTTACCTAACC
27869355 TTTTATCAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:27878776 original size:5 final size:5
Alignment explanation
Indices: 27878759--27878794 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
27878749 GTTCTTTATT
27878759 TTTTA TCTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA
27878795 CAAATTTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:27880003 original size:48 final size:48
Alignment explanation
Indices: 27879932--27880029 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
27879922 TTCGACGCGA
27879932 ACATAGCTTGCTACTCGTGAACCCATGATAGTATGAAGGTCACTAATT
1 ACATAGCTTGCTACTCGTGAACCCATGATAGTATGAAGGTCACTAATT
27879980 ACATAGCTTGCTACTCGTGAACCCATGATAGTATGAAGGTCACTAATT
1 ACATAGCTTGCTACTCGTGAACCCATGATAGTATGAAGGTCACTAATT
27880028 AC
1 AC
27880030 TCTTCCAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (48 bp):
ACATAGCTTGCTACTCGTGAACCCATGATAGTATGAAGGTCACTAATT
Found at i:27881963 original size:16 final size:16
Alignment explanation
Indices: 27881942--27881975 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27881932 TTATTTACAG
*
27881942 TTTTTTATCATTTACT
1 TTTTTTAACATTTACT
*
27881958 TTTTTTAACTTTTACT
1 TTTTTTAACATTTACT
27881974 TT
1 TT
27881976 AATTTATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTAACATTTACT
Found at i:27882247 original size:38 final size:38
Alignment explanation
Indices: 27882205--27882278 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
27882195 GGTGTTGGTA
27882205 AATAAAATAAAAAAATTTCTTTACTTATAAGTTTTGTG
1 AATAAAATAAAAAAATTTCTTTACTTATAAGTTTTGTG
27882243 AATAAAATAAAAAAATTTCTTTACTTATAAGTTTTG
1 AATAAAATAAAAAAATTTCTTTACTTATAAGTTTTG
27882279 AAAATAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (38 bp):
AATAAAATAAAAAAATTTCTTTACTTATAAGTTTTGTG
Found at i:27886618 original size:2 final size:2
Alignment explanation
Indices: 27886613--27886654 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27886603 GTGTATCATC
27886613 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
27886655 TATCTCAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27891708 original size:59 final size:59
Alignment explanation
Indices: 27891627--27891769 Score: 259
Period size: 59 Copynumber: 2.4 Consensus size: 59
27891617 TCTAATTGAC
*
27891627 AGGATTTAGCCTGGACTTGTAATCCAAAATGAACTCTATAGGGAATTCTTTGTCATACA
1 AGGATTTAGCCTGGACTGGTAATCCAAAATGAACTCTATAGGGAATTCTTTGTCATACA
*
27891686 AGGATTTAGCCTGGACTGGTAATCCAGAATGAACTCTATAGGGAATTCTTTGTCATACA
1 AGGATTTAGCCTGGACTGGTAATCCAAAATGAACTCTATAGGGAATTCTTTGTCATACA
*
27891745 AGGATTTAGCCTAGACTGGTAATCC
1 AGGATTTAGCCTGGACTGGTAATCC
27891770 GACAAAGCCC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 81 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (59 bp):
AGGATTTAGCCTGGACTGGTAATCCAAAATGAACTCTATAGGGAATTCTTTGTCATACA
Found at i:27892618 original size:42 final size:42
Alignment explanation
Indices: 27892564--27892655 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
27892554 ACAGCCAGAG
*
27892564 ACACGGGTGTGTGTCTCAGCCATGTGGATGACACAGCCTTAA
1 ACACGGGCGTGTGTCTCAGCCATGTGGATGACACAGCCTTAA
* * *
27892606 ACATGGGCGTGTGTCTCAGCCGTGTGGATGACACAGCCTTAG
1 ACACGGGCGTGTGTCTCAGCCATGTGGATGACACAGCCTTAA
27892648 ACACGGGC
1 ACACGGGC
27892656 ATGCAATACG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.25, G:0.32, T:0.22
Consensus pattern (42 bp):
ACACGGGCGTGTGTCTCAGCCATGTGGATGACACAGCCTTAA
Found at i:27895943 original size:2 final size:2
Alignment explanation
Indices: 27895938--27895968 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27895928 ATTTTTTTAA
27895938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27895969 AAAGGTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27896135 original size:21 final size:19
Alignment explanation
Indices: 27896104--27896143 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
27896094 AAAATAGATT
27896104 AAAAAAAAAGAAAACAATA
1 AAAAAAAAAGAAAACAATA
*
27896123 AAAAAAAGTAAGAAAATAATA
1 AAAAAAA--AAGAAAACAATA
27896144 TTTTTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAAAAAGAAAACAATA
Found at i:27901060 original size:14 final size:14
Alignment explanation
Indices: 27901037--27901075 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
27901027 TTTGGGGTTT
*
27901037 AATT-AAATTATAA
1 AATTGAAATTAAAA
27901050 AATTGAAATTAAAA
1 AATTGAAATTAAAA
*
27901064 AAATGAAATTAA
1 AATTGAAATTAA
27901076 CCCTTATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (14 bp):
AATTGAAATTAAAA
Found at i:27902623 original size:107 final size:108
Alignment explanation
Indices: 27902496--27902711 Score: 398
Period size: 107 Copynumber: 2.0 Consensus size: 108
27902486 AAAAAACATG
*
27902496 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
1 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAAGTTTGTTAGAAATTTTATTATTT
*
27902561 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA
66 AAAACTTATTCCAACTTAACATATCATTATTTTGTTAAACTAA
27902604 TCAAAAATTTTAT-AGAGTAATTAACAAAAATTTTAATACAAGTTTGTTAGAAATTTTATTATTT
1 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAAGTTTGTTAGAAATTTTATTATTT
*
27902668 AAAACTTATTCTAACTTAACATATCATTATTTTGTTAAACTAA
66 AAAACTTATTCCAACTTAACATATCATTATTTTGTTAAACTAA
27902711 T
1 T
27902712 TTTTTGTTTA
Statistics
Matches: 105, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 92 0.88
108 13 0.12
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (108 bp):
TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAAGTTTGTTAGAAATTTTATTATTT
AAAACTTATTCCAACTTAACATATCATTATTTTGTTAAACTAA
Found at i:27912171 original size:2 final size:2
Alignment explanation
Indices: 27912164--27912192 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27912154 GATGTCCTTG
27912164 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27912193 GTTAGTGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27913755 original size:3 final size:3
Alignment explanation
Indices: 27913749--27913807 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
27913739 GATTTAAAAA
* * * * *
27913749 AAT AAT ATT AAT AAT AAT GAT AGT AAT ATT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27913797 ACA- AAT AAT AA
1 A-AT AAT AAT AA
27913808 ATATTCTAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 1 0.02
3 42 0.95
4 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27913796 original size:21 final size:21
Alignment explanation
Indices: 27913749--27913807 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
27913739 GATTTAAAAA
* *
27913749 AATAATATTAATAATAATGAT
1 AATAATATTAATAATAATAAC
*
27913770 AGTAATATTAATAATAATAAC
1 AATAATATTAATAATAATAAC
**
27913791 AATAATACAAATAATAA
1 AATAATATTAATAATAA
27913808 ATATTCTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
AATAATATTAATAATAATAAC
Found at i:27913989 original size:3 final size:3
Alignment explanation
Indices: 27913974--27914108 Score: 119
Period size: 3 Copynumber: 45.3 Consensus size: 3
27913964 AAAAGAAAAT
* * * * *
27913974 ATA ATA ATG ATA ATA ATA ATA GTA AT- ACA ATA GTA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
27914021 ACA AAA ATA GTA ATA ATA ATA GTA ATA AAA ATA ATA GTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
27914069 ATC ATA ATA ACA AAA ATA GTA ATA ATA GTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
27914109 AATTAATTAA
Statistics
Matches: 101, Mismatches: 30, Indels: 2
0.76 0.23 0.02
Matches are distributed among these distances:
2 1 0.01
3 100 0.99
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:27925643 original size:35 final size:35
Alignment explanation
Indices: 27925616--27925781 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
27925606 CATGGCAAAG
*
27925616 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
27925651 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
27925686 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
27925726 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
27925761 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
27925782 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:27925735 original size:75 final size:75
Alignment explanation
Indices: 27925616--27925786 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
27925606 CATGGCAAAG
** *
27925616 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
27925675 CCATACTGAGC
65 CCATACCGAGC
27925686 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
27925751 CATACCGAGT
66 CATACCGAGC
**
27925761 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
27925787 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:27933134 original size:35 final size:35
Alignment explanation
Indices: 27933107--27933272 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
27933097 CATGGCAAAG
*
27933107 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
27933142 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
27933177 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
27933217 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
27933252 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
27933273 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:27933226 original size:75 final size:75
Alignment explanation
Indices: 27933107--27933277 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
27933097 CATGGCAAAG
** *
27933107 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
27933166 CCATACTGAGC
65 CCATACCGAGC
27933177 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
27933242 CATACCGAGT
66 CATACCGAGC
**
27933252 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
27933278 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:27937904 original size:17 final size:17
Alignment explanation
Indices: 27937870--27937904 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27937860 AATAATGAAA
**
27937870 TTGTAATATTTTTTTAT
1 TTGTAATATTTTAATAT
27937887 TTGTAATATTTTAATAT
1 TTGTAATATTTTAATAT
27937904 T
1 T
27937905 AATTGTATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TTGTAATATTTTAATAT
Found at i:27939168 original size:23 final size:21
Alignment explanation
Indices: 27939142--27939191 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
27939132 AAATGTTTGA
27939142 ATTTTGAGTTTG-ATTTCTTTTCT
1 ATTTTGA-TTTGTATTT-TTTT-T
27939165 ATTTAT-ATTTGTATTTTTTTT
1 ATTT-TGATTTGTATTTTTTTT
27939186 ATTTTG
1 ATTTTG
27939192 TTTTAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
20 1 0.04
21 5 0.21
22 8 0.33
23 9 0.38
24 1 0.04
ACGTcount: A:0.16, C:0.04, G:0.10, T:0.70
Consensus pattern (21 bp):
ATTTTGATTTGTATTTTTTTT
Found at i:27941231 original size:18 final size:19
Alignment explanation
Indices: 27941188--27941231 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
27941178 ATTTGGCTTG
**
27941188 GATGTTTCTAATTGGATTT
1 GATGTTTCTAATTGGAGGT
27941207 GATGTTTCTAATTGGAGGT
1 GATGTTTCTAATTGGAGGT
27941226 -ATGTTT
1 GATGTTT
27941232 GATTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.50
Consensus pattern (19 bp):
GATGTTTCTAATTGGAGGT
Found at i:27942961 original size:39 final size:39
Alignment explanation
Indices: 27942907--27943073 Score: 262
Period size: 39 Copynumber: 4.3 Consensus size: 39
27942897 TTCAGTGATG
* *
27942907 ATTATATCCGGACTTAGGGTCCGCAGGCTATATGCTGGA
1 ATTATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGA
*
27942946 ATTATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGA
1 ATTATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGA
27942985 ATTATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGA
1 ATTATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGA
* * *
27943024 ATTATAACTGGACTTAAGGTCCGCAGGCTACGTGCTGGA
1 ATTATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGA
* *
27943063 AATATGTCCGG
1 ATTATATCCGG
27943074 GCTAAAATCC
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 119 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (39 bp):
ATTATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGA
Found at i:27943100 original size:78 final size:78
Alignment explanation
Indices: 27942909--27943111 Score: 225
Period size: 78 Copynumber: 2.6 Consensus size: 78
27942899 CAGTGATGAT
*** * *
27942909 TATATCCGGACTTAGGGTCCGCAGGCTAT-ATGCTGGAATTATATCCGGACTTAGGGTCCGCAGG
1 TATATCCGGACTTAAAATCCGCAGGCTATGA-GCTGGAATTATAACCGGACTTAAGGTCCGCAGG
* *
27942973 CTATGTGCTGGAAT
65 CTACGTGCTGGAAA
** * *
27942987 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTATAACTGGACTTAAGGTCCGCAGGC
1 TATATCCGGACTTAAAATCCGCAGGCTATGAGCTGGAATTATAACCGGACTTAAGGTCCGCAGGC
27943052 TACGTGCTGGAAA
66 TACGTGCTGGAAA
* * *
27943065 TATGTCCGGGC-TAAAATCCCGCAGGCT-TCGAGCTGGTATTAT-ACCGG
1 TATATCCGGACTTAAAAT-CCGCAGGCTAT-GAGCTGGAATTATAACCGG
27943112 GTTTAAATTT
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
77 9 0.08
78 99 0.92
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (78 bp):
TATATCCGGACTTAAAATCCGCAGGCTATGAGCTGGAATTATAACCGGACTTAAGGTCCGCAGGC
TACGTGCTGGAAA
Found at i:27946273 original size:29 final size:29
Alignment explanation
Indices: 27946231--27946318 Score: 176
Period size: 29 Copynumber: 3.0 Consensus size: 29
27946221 GGGATGCACA
27946231 TGTTCTTTCGGTCCTTTAAAAGGCAAGTT
1 TGTTCTTTCGGTCCTTTAAAAGGCAAGTT
27946260 TGTTCTTTCGGTCCTTTAAAAGGCAAGTT
1 TGTTCTTTCGGTCCTTTAAAAGGCAAGTT
27946289 TGTTCTTTCGGTCCTTTAAAAGGCAAGTT
1 TGTTCTTTCGGTCCTTTAAAAGGCAAGTT
27946318 T
1 T
27946319 CTAGCATATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (29 bp):
TGTTCTTTCGGTCCTTTAAAAGGCAAGTT
Found at i:27948406 original size:9 final size:9
Alignment explanation
Indices: 27948392--27948416 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
27948382 GAAACTGGGA
27948392 AAAAAAATG
1 AAAAAAATG
27948401 AAAAAAATG
1 AAAAAAATG
27948410 AAAAAAA
1 AAAAAAA
27948417 AATGGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (9 bp):
AAAAAAATG
Found at i:27953097 original size:15 final size:16
Alignment explanation
Indices: 27953072--27953101 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27953062 TTATGCATGA
27953072 AATTACTGTATCTGTT
1 AATTACTGTATCTGTT
27953088 AATT-CTGTATCTGT
1 AATTACTGTATCTGT
27953102 GACTAGGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (16 bp):
AATTACTGTATCTGTT
Found at i:27955679 original size:111 final size:113
Alignment explanation
Indices: 27955542--27955770 Score: 311
Period size: 111 Copynumber: 2.0 Consensus size: 113
27955532 TTTTCGAAGG
* * *
27955542 AGTTTTTCATGTAAAATTTGTGTGTTCGATCTTCTTTACTTTTCTTGTTCGTTATTTA-TACGA-
1 AGTTTTTCACGTAAAATTTATGTGTTCAATCTTCTTTACTTTTCTTGTTCGTTATTTATTA-GAG
* ** *
27955605 GTTGATCCCCGACAATT-AAAAATGCTTTTAAAGGTTAAATGACATGGC
65 GTTGATCCCCAACAATTAAAAAATAATTTTAAAAGTTAAATGACATGGC
* * * * *
27955653 TGTTTTTTACGTAAAATTTATGTGTTCAATCTTCTTTGCTTTTCTTGTTCGTTGTTTATTATAGG
1 AGTTTTTCACGTAAAATTTATGTGTTCAATCTTCTTTACTTTTCTTGTTCGTTATTTATTAGAGG
*
27955718 TTTATCCCCAACAATTAAAAAATAATTTTAAAAGTTAAATGACATGGC
66 TTGATCCCCAACAATTAAAAAATAATTTTAAAAGTTAAATGACATGGC
27955766 AGTTT
1 AGTTT
27955771 ATTTTTGGCA
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
111 52 0.51
112 17 0.17
113 32 0.32
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (113 bp):
AGTTTTTCACGTAAAATTTATGTGTTCAATCTTCTTTACTTTTCTTGTTCGTTATTTATTAGAGG
TTGATCCCCAACAATTAAAAAATAATTTTAAAAGTTAAATGACATGGC
Found at i:27964944 original size:17 final size:17
Alignment explanation
Indices: 27964924--27964957 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27964914 TGTCTCAGGC
*
27964924 ACATACCTATATTTGAG
1 ACATACCTAAATTTGAG
*
27964941 ACATATCTAAATTTGAG
1 ACATACCTAAATTTGAG
27964958 TAACTTAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (17 bp):
ACATACCTAAATTTGAG
Found at i:27968209 original size:11 final size:11
Alignment explanation
Indices: 27968193--27968226 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
27968183 TTTTGTCTCA
27968193 CGCTACAGTAT
1 CGCTACAGTAT
27968204 CGCTACAGTAT
1 CGCTACAGTAT
27968215 CGCTACAGTAT
1 CGCTACAGTAT
27968226 C
1 C
27968227 TAATCTCACC
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:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (11 bp):
CGCTACAGTAT
Found at i:27969562 original size:9 final size:9
Alignment explanation
Indices: 27969543--27969598 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
27969533 AGAGCCATGC
27969543 GAAACAGAAA
1 GAAA-AGAAA
27969553 GAAAAGAAA
1 GAAAAGAAA
27969562 GAAAA-AAA
1 GAAAAGAAA
*
27969570 AAAAAGAAA
1 GAAAAGAAA
27969579 -AAGAAGAAA
1 GAA-AAGAAA
*
27969588 G-AGAGAAA
1 GAAAAGAAA
27969596 GAA
1 GAA
27969599 GGTTCAACCC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 15 0.38
9 21 0.52
10 4 0.10
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (9 bp):
GAAAAGAAA
Found at i:27969570 original size:13 final size:13
Alignment explanation
Indices: 27969548--27969589 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
27969538 CATGCGAAAC
*
27969548 AGAAAGAAAAGAA
1 AGAAAAAAAAGAA
*
27969561 AGAAAAAAAAAAA
1 AGAAAAAAAAGAA
*
27969574 AGAAAAAGAAGAA
1 AGAAAAAAAAGAA
27969587 AGA
1 AGA
27969590 GAGAAAGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:27970870 original size:16 final size:15
Alignment explanation
Indices: 27970849--27970879 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
27970839 TTGAGTATGG
27970849 CATGAAATAATGTATT
1 CATGAAATAA-GTATT
27970865 CATGAAATAAGTATT
1 CATGAAATAAGTATT
27970880 GAATGGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (15 bp):
CATGAAATAAGTATT
Found at i:27973550 original size:24 final size:24
Alignment explanation
Indices: 27973500--27973599 Score: 118
Period size: 24 Copynumber: 4.2 Consensus size: 24
27973490 CATGGTTGGC
27973500 AAGCTCCT-CTGAGCTGATAAACAGT
1 AAGCT-CTACTGAGCTGA-AAACAGT
*
27973525 AAGCTCTACTGAGCTGAAAACGGT
1 AAGCTCTACTGAGCTGAAAACAGT
*
27973549 AAGCTCTATTGAGCTGAAAAC-GAT
1 AAGCTCTACTGAGCTGAAAACAG-T
*
27973573 AAGCTCTATTGAGCT--AAACAGT
1 AAGCTCTACTGAGCTGAAAACAGT
27973595 AAGCT
1 AAGCT
27973600 ATTTCGAGCT
Statistics
Matches: 70, Mismatches: 2, Indels: 9
0.86 0.02 0.11
Matches are distributed among these distances:
22 10 0.14
23 2 0.03
24 44 0.63
25 14 0.20
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (24 bp):
AAGCTCTACTGAGCTGAAAACAGT
Found at i:27973597 original size:22 final size:22
Alignment explanation
Indices: 27973517--27973622 Score: 99
Period size: 24 Copynumber: 4.6 Consensus size: 22
27973507 TCTGAGCTGA
*
27973517 TAAACAGTAAGCTCTACTGAGC
1 TAAACAGTAAGCTCTATTGAGC
*
27973539 TGAAAACGGTAAGCTCTATTGAGC
1 T--AAACAGTAAGCTCTATTGAGC
27973563 TGAAA-ACGATAAGCTCTATTGAGC
1 T-AAACA-G-TAAGCTCTATTGAGC
*
27973587 TAAACAGTAAGCTAT-TTCGAGC
1 TAAACAGTAAGCTCTATT-GAGC
*
27973609 TAAATCGGTAAGCT
1 TAAA-CAGTAAGCT
27973623 TCAATGAGCT
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.03
22 16 0.23
23 16 0.23
24 37 0.52
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (22 bp):
TAAACAGTAAGCTCTATTGAGC
Found at i:27973638 original size:46 final size:47
Alignment explanation
Indices: 27973509--27973638 Score: 126
Period size: 46 Copynumber: 2.8 Consensus size: 47
27973499 CAAGCTCCTC
* * *
27973509 TGAGCTGATAAAC-AGTAAGCTCTACTGAGCTGAAAACGGTAAGCTCTAT
1 TGAGCTGA-AAACGA-TAAGCTCTAATGAGCTG-AAACAGTAAGCTATAT
*
27973558 TGAGCTGAAAACGATAAGCTCTATTGAGCT-AAACAGTAAGCTAT-T
1 TGAGCTGAAAACGATAAGCTCTAATGAGCTGAAACAGTAAGCTATAT
* *
27973603 TCGAGCT-AAATCGGTAAGCT-TCAATGAGCTGAAACA
1 T-GAGCTGAAAACGATAAGCTCT-AATGAGCTGAAACA
27973639 ATAAACTCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
44 1 0.01
45 20 0.28
46 22 0.31
48 19 0.27
49 9 0.13
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (47 bp):
TGAGCTGAAAACGATAAGCTCTAATGAGCTGAAACAGTAAGCTATAT
Found at i:27975887 original size:45 final size:45
Alignment explanation
Indices: 27975836--27975926 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
27975826 AATTAAATTA
* *
27975836 ACCATTATTAGCAGGTTTAGA-TTCATTTAAGTCATGCATATATAT
1 ACCATTATTAGCAGGTTTA-ACTTCATTTAAATCAAGCATATATAT
*
27975881 ACCATTATTAGTAGGTTTAACTTCATTTAAATCAAGCATATATAT
1 ACCATTATTAGCAGGTTTAACTTCATTTAAATCAAGCATATATAT
27975926 A
1 A
27975927 TATATATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (45 bp):
ACCATTATTAGCAGGTTTAACTTCATTTAAATCAAGCATATATAT
Found at i:27982380 original size:85 final size:81
Alignment explanation
Indices: 27982141--27982412 Score: 312
Period size: 77 Copynumber: 3.4 Consensus size: 81
27982131 TTAGTGCGTG
* * * *
27982141 TTTTTTAATATGCATGC-A--A-T-TTTTTTAATCTGTCTATGTATAATTGTTGGTGGGGTTAGT
1 TTTTTTAATATGCATGCAATGACTATTTTTTAATTTGTCTATGTATGATTGTTGGTGGGGATGGT
*
27982201 TACATGCTGTTGACTA
66 CACATGCTGTTGACTA
* *
27982217 TTTTTTAATATTCATGC-A--A-TATTTTTTAATTTGTCTATGTATGATTGTTGGTGGGGATGAT
1 TTTTTTAATATGCATGCAATGACTATTTTTTAATTTGTCTATGTATGATTGTTGGTGGGGATGGT
* *
27982278 CATATACTGTTGACTA
66 CACATGCTGTTGACTA
* * *
27982294 TTTTTTAATATGCATGCAATGACTATTTTTTAGGTGTGTGTGTGTGTGTATGATTGTTGGT-GGG
1 TTTTTTAATATGCATGCAATGACTATTTTTTA---AT-T-TGTCTATGTATGATTGTTGGTGGGG
27982358 ATGGTCACATGCTGTTGACTA
61 ATGGTCACATGCTGTTGACTA
*
27982379 TTTTTTAATATGCATGCAGTGACTATTTTTTAAT
1 TTTTTTAATATGCATGCAATGACTATTTTTTAAT
27982413 AATATGCAAG
Statistics
Matches: 168, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
76 19 0.11
77 64 0.38
78 1 0.01
80 1 0.01
81 9 0.05
82 1 0.01
84 1 0.01
85 53 0.32
86 19 0.11
ACGTcount: A:0.22, C:0.08, G:0.21, T:0.48
Consensus pattern (81 bp):
TTTTTTAATATGCATGCAATGACTATTTTTTAATTTGTCTATGTATGATTGTTGGTGGGGATGGT
CACATGCTGTTGACTA
Found at i:27982427 original size:28 final size:27
Alignment explanation
Indices: 27982373--27982438 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 27
27982363 CACATGCTGT
*
27982373 TGACTA-TTTTT-TAATATGCATGCAG
1 TGACTATTTTTTATAATATGCAAGCAG
*
27982398 TGACTATTTTTTAATAATATGCAAGTAG
1 TGACTATTTTTT-ATAATATGCAAGCAG
*
27982426 TGACTGTTTTTTA
1 TGACTATTTTTTA
27982439 GGTATGTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.17
26 5 0.14
27 1 0.03
28 23 0.66
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (27 bp):
TGACTATTTTTTATAATATGCAAGCAG
Found at i:27994644 original size:6 final size:6
Alignment explanation
Indices: 27994633--27994658 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27994623 GGTTAATAAT
27994633 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
27994659 TATCATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:28000595 original size:126 final size:127
Alignment explanation
Indices: 28000427--28000744 Score: 413
Period size: 127 Copynumber: 2.5 Consensus size: 127
28000417 AATGAAAAAA
* * * ** *
28000427 CGAAATCCAACACAATAGGGCATAATTCCTCAAATTTGCAAACATTG-ACATTGCCTTGTTTTAG
1 CGAAACCCAGCACGATAGGGCACGATTCCTCAAATTTCCAAACATTGAACATTGCCTTGTTTTAG
* * *
28000491 AATTTATAAAATACGAGTGAAATACTAAAGGAACATTCAATTATTTGGAATAAACCAGAAAT
66 AATTTAGAAAACACGAGTGAAATACTAAAGGAACATTCAATTATTTGGAACAAACCAGAAAT
* *
28000553 CGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACCTTGAACATTGCCTTGTTTTAG
1 CGAAACCCAGCACGATAGGGCACGATTCCTCAAATTTCCAAACATTGAACATTGCCTTGTTTTAG
* * * * * **
28000618 AATTTGGAAAACACGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAAT
66 AATTTAGAAAACACGAGTGAAATACTAAAGGAACATTCAATTATTTGGAACAAACCAGAAAT
* * ** *
28000680 CGAAACCCAGCACGGTAGGGCACGATTTCTCAAATTTCCAAACATCAAACATTGTCTTCGTTTTA
1 CGAAACCCAGCACGATAGGGCACGATTCCTCAAATTTCCAAACATTGAACATTGCCTT-GTTTTA
28000745 AGGAATTTTC
Statistics
Matches: 165, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
126 39 0.24
127 120 0.73
128 6 0.04
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (127 bp):
CGAAACCCAGCACGATAGGGCACGATTCCTCAAATTTCCAAACATTGAACATTGCCTTGTTTTAG
AATTTAGAAAACACGAGTGAAATACTAAAGGAACATTCAATTATTTGGAACAAACCAGAAAT
Found at i:28001242 original size:23 final size:22
Alignment explanation
Indices: 28001212--28001262 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
28001202 TTAAAATAAC
28001212 ATATAAAAGGTCTAAAATAAATA
1 ATATAAAAGGT-TAAAATAAATA
* *
28001235 ATATAAAAATGTTAAAGTAAATA
1 ATAT-AAAAGGTTAAAATAAATA
28001258 ATATA
1 ATATA
28001263 CATAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 18 0.72
24 6 0.24
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (22 bp):
ATATAAAAGGTTAAAATAAATA
Found at i:28002745 original size:14 final size:14
Alignment explanation
Indices: 28002714--28002744 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28002704 TTTGTAGTAG
28002714 AAAATAAAAAATAT
1 AAAATAAAAAATAT
28002728 AAAATAAAAAA-AT
1 AAAATAAAAAATAT
28002741 AAAA
1 AAAA
28002745 AAACGAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAATAAAAAATAT
Found at i:28005575 original size:13 final size:13
Alignment explanation
Indices: 28005557--28005583 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28005547 GAACTTGCTC
28005557 CATTTATATATGT
1 CATTTATATATGT
28005570 CATTTATATATGT
1 CATTTATATATGT
28005583 C
1 C
28005584 GAGACCACAT
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:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (13 bp):
CATTTATATATGT
Found at i:28005800 original size:28 final size:28
Alignment explanation
Indices: 28005760--28005819 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
28005750 TTAACCCTTA
*
28005760 ACCTAAGCCCCTTTACAACCTTATAAAG
1 ACCTAAGCCCCTTTACAACATTATAAAG
*
28005788 ACCTAAGGCCCTTTACAACATTATAAAG
1 ACCTAAGCCCCTTTACAACATTATAAAG
28005816 ACCT
1 ACCT
28005820 CTTGTAGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.30, G:0.08, T:0.25
Consensus pattern (28 bp):
ACCTAAGCCCCTTTACAACATTATAAAG
Found at i:28006999 original size:27 final size:28
Alignment explanation
Indices: 28006969--28007038 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
28006959 ATAGTGAGTC
28006969 CGCACACTTAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
28006996 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
28007024 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28007039 GTACAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28010366 original size:30 final size:30
Alignment explanation
Indices: 28010332--28010389 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28010322 ACTTAACAAG
28010332 AAAATGCATCTAAAATAATAACAAAATTAA
1 AAAATGCATCTAAAATAATAACAAAATTAA
* * *
28010362 AAAATGCCTTTACAATAATAACAAAATT
1 AAAATGCATCTAAAATAATAACAAAATT
28010390 GACAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (30 bp):
AAAATGCATCTAAAATAATAACAAAATTAA
Found at i:28013756 original size:15 final size:15
Alignment explanation
Indices: 28013736--28013766 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28013726 ACCAAAATAA
28013736 AAGTGGATAAAGACC
1 AAGTGGATAAAGACC
28013751 AAGTGGATAAAGACC
1 AAGTGGATAAAGACC
28013766 A
1 A
28013767 TAGTCTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.26, T:0.13
Consensus pattern (15 bp):
AAGTGGATAAAGACC
Found at i:28032094 original size:34 final size:35
Alignment explanation
Indices: 28032040--28032115 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 35
28032030 TGCACAGTCA
* *
28032040 AACAGTCTTAGGCCTAAGCCCCTTTCAGTATCAGT
1 AACAGTCTTAGGCCTAAGCCCATCTCAGTATCAGT
* *
28032075 AACAGT-TTGGGCCTTAGCCCATCTCAGTATCAGT
1 AACAGTCTTAGGCCTAAGCCCATCTCAGTATCAGT
*
28032109 ATCAGTC
1 AACAGTC
28032116 ATGCAGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 29 0.83
35 6 0.17
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (35 bp):
AACAGTCTTAGGCCTAAGCCCATCTCAGTATCAGT
Done.