Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007801.1 Hibiscus syriacus cultivar Beakdansim tig00110118_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: 951604
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:853859 original size:19 final size:18
Alignment explanation
Indices: 853832--853879 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
853822 CCTATTTGAC
*
853832 AAATTATAAAACAACATAT
1 AAATAATAAAACAACA-AT
*
853851 AAATAATAACAACAATAAT
1 AAATAATAA-AACAACAAT
*
853870 AATTAATAAA
1 AAATAATAAA
853880 TAAATAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 18 0.72
20 6 0.24
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATAATAAAACAACAAT
Found at i:855309 original size:3 final size:3
Alignment explanation
Indices: 855301--855330 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
855291 ATATTAATTT
*
855301 TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
855331 AGCAGGCCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:856900 original size:3 final size:3
Alignment explanation
Indices: 856892--856950 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
856882 GGTTTAGTTT
856892 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA -GA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
856939 GGA GGA GGA GGA
1 GGA GGA GGA GGA
856951 TTGACGGGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:858465 original size:15 final size:15
Alignment explanation
Indices: 858437--858474 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
858427 TACACCAGGT
*
858437 TGGCACTCATTGCAA
1 TGGCACTAATTGCAA
*
858452 TGGTACTAATTGCAA
1 TGGCACTAATTGCAA
858467 TGGCACTA
1 TGGCACTA
858475 GTGTTATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (15 bp):
TGGCACTAATTGCAA
Found at i:859596 original size:13 final size:13
Alignment explanation
Indices: 859578--859602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
859568 ACCTGACCTG
859578 ACCCGACCCGTTC
1 ACCCGACCCGTTC
859591 ACCCGACCCGTT
1 ACCCGACCCGTT
859603 GACCGTTGAT
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:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTC
Found at i:870714 original size:21 final size:21
Alignment explanation
Indices: 870690--870731 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
870680 CAATTAAGAA
* *
870690 TCAAGGAGCTTTACTTTAAAG
1 TCAAGGAGCCTTACTTCAAAG
*
870711 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
870732 CCATAGCTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Found at i:875227 original size:21 final size:20
Alignment explanation
Indices: 875201--875246 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
875191 ATTTTTATTT
*
875201 TTTTTCTCTTTC-TTTATTAA
1 TTTTTCTATTTCATTT-TTAA
875221 CTTTTTCTATTTCATTTTTAA
1 -TTTTTCTATTTCATTTTTAA
875242 TTTTT
1 TTTTT
875247 ACATTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 15 0.65
22 3 0.13
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTCTATTTCATTTTTAA
Found at i:877239 original size:13 final size:13
Alignment explanation
Indices: 877221--877247 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
877211 TTGGAACTCT
877221 CTTTAATAAATGG
1 CTTTAATAAATGG
877234 CTTTAATAAATGG
1 CTTTAATAAATGG
877247 C
1 C
877248 AGCCTCGCGC
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:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (13 bp):
CTTTAATAAATGG
Found at i:882474 original size:11 final size:11
Alignment explanation
Indices: 882458--882482 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
882448 CTTTACAACG
882458 GATGATGAATT
1 GATGATGAATT
882469 GATGATGAATT
1 GATGATGAATT
882480 GAT
1 GAT
882483 CGTTTGTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (11 bp):
GATGATGAATT
Found at i:884100 original size:35 final size:35
Alignment explanation
Indices: 884061--884131 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
884051 GTCTAACTTA
884061 AGATTAATTTATGGTGGATGTTAACTTAAAACATT
1 AGATTAATTTATGGTGGATGTTAACTTAAAACATT
884096 AGATTAATTTATGGTGGATGTTAACTTAAAACATT
1 AGATTAATTTATGGTGGATGTTAACTTAAAACATT
884131 A
1 A
884132 AATCGTTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (35 bp):
AGATTAATTTATGGTGGATGTTAACTTAAAACATT
Found at i:888597 original size:28 final size:29
Alignment explanation
Indices: 888565--888635 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 29
888555 GACTTTCTCA
*
888565 GTCAAAGTCAACGTTCAAC-ATTAGAC-TG
1 GTCAAAGTCAACGGTCAACGATT-GACTTG
*
888593 GTCAAAGTCAATGGTCAACGTATTGACTTG
1 GTCAAAGTCAACGGTCAACG-ATTGACTTG
888623 GTCAAAGTCAACG
1 GTCAAAGTCAACG
888636 AGTTGACTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 17 0.46
29 3 0.08
30 17 0.46
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (29 bp):
GTCAAAGTCAACGGTCAACGATTGACTTG
Found at i:891265 original size:36 final size:37
Alignment explanation
Indices: 891225--891522 Score: 309
Period size: 36 Copynumber: 8.2 Consensus size: 37
891215 ATGTGTATGT
** **
891225 ATATATATATTATATAGTTTGCAAATGATTTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
*
891262 TATATATATAATATATAGTTTTTAAAACA-TTTTGAAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
891299 ATACATATATATTATATAG-TTTT------TTTTTGAAA
1 AT--ATATATATTATATAGTTTTTAAAACATTTTTGAAA
*
891331 ATATATATAATATATAGTTTTTAAAACATTTTTGAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTG-AAA
*
891369 CATATATATATTATATAGTTTTTAAAACA-TTTTAAAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
*
891406 ATATATATAATATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * *
891442 ACATATATATTATAAAGTTTTAAAAAAAACA-TTTTGAAA
1 ATATATATATTATATAGTTTT---TAAAACATTTTTGAAA
*
891481 ACATATA-A-TATATAG-TTTTAAAACATTTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
891515 ACTATATA
1 A-TATATA
891523 ATTTTGAAAA
Statistics
Matches: 225, Mismatches: 18, Indels: 37
0.80 0.06 0.13
Matches are distributed among these distances:
30 14 0.06
31 4 0.02
32 10 0.04
33 6 0.03
34 9 0.04
35 5 0.02
36 57 0.25
37 27 0.12
38 45 0.20
39 48 0.21
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
ATATATATATTATATAGTTTTTAAAACATTTTTGAAA
Found at i:891331 original size:32 final size:30
Alignment explanation
Indices: 891253--891352 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
891243 TTGCAAATGA
891253 TTTTTGAAATATATATATAATATATAGTTTT
1 TTTTTGAAA-ATATATATAATATATAGTTTT
*
891284 TAAAACATTTTGAAAATACATATATATTATATAGTTTT
1 T------TTTTGAAAAT--ATATATAATATATAGTTTT
891322 TTTTTGAAAATATATATAATATATAGTTTT
1 TTTTTGAAAATATATATAATATATAGTTTT
891352 T
1 T
891353 AAAACATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
30 19 0.32
31 1 0.02
32 10 0.17
36 2 0.03
37 8 0.14
38 19 0.32
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (30 bp):
TTTTTGAAAATATATATAATATATAGTTTT
Found at i:891538 original size:28 final size:29
Alignment explanation
Indices: 891467--891554 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 29
891457 AGTTTTAAAA
*
891467 AAAACATTTTGAAAACATATAATATATAGTTTT
1 AAAACATTTTGAAAAC-TAT-ATA-ATA-TTTG
891500 AAAACATTTTTGAAAACTATATAAT-TTTG
1 AAAACA-TTTTGAAAACTATATAATATTTG
* *
891529 AAAACATTTTAAAAAATATATAATAT
1 AAAACATTTTGAAAACTATATAATAT
891555 ATAATGTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
28 16 0.32
29 10 0.20
31 2 0.04
32 3 0.06
33 9 0.18
34 10 0.20
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.39
Consensus pattern (29 bp):
AAAACATTTTGAAAACTATATAATATTTG
Found at i:891634 original size:22 final size:20
Alignment explanation
Indices: 891606--891654 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
891596 TGGAAAATGT
891606 TTTTTATTATTATGGTTATTTA
1 TTTTTATTATTAT--TTATTTA
891628 TTTTTA-T-TTATTTATTTA
1 TTTTTATTATTATTTATTTA
*
891646 TTTGTATTA
1 TTTTTATTA
891655 ATTTTACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 12 0.50
19 1 0.04
20 4 0.17
21 1 0.04
22 6 0.25
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (20 bp):
TTTTTATTATTATTTATTTA
Found at i:891644 original size:18 final size:18
Alignment explanation
Indices: 891621--891658 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
891611 ATTATTATGG
* *
891621 TTATTTATTTTTATTTAT
1 TTATTTATTTGTATTAAT
891639 TTATTTATTTGTATTAAT
1 TTATTTATTTGTATTAAT
891657 TT
1 TT
891659 TACTTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTATTTATTTGTATTAAT
Found at i:892036 original size:15 final size:16
Alignment explanation
Indices: 892013--892042 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
892003 AACAAGATCA
892013 AAAACCACAACCAAAG
1 AAAACCACAACCAAAG
892029 AAAA-CACAACCAAA
1 AAAACCACAACCAAA
892043 ATCAACAAGA
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:0.67, C:0.30, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAACCACAACCAAAG
Found at i:892826 original size:18 final size:18
Alignment explanation
Indices: 892793--892828 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
892783 GACTATCGCA
*
892793 TTGCGATTTTCCAAATTC
1 TTGCGATTTTACAAATTC
*
892811 TTGCGATTTTAGAAATTC
1 TTGCGATTTTACAAATTC
892829 GCAATGCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (18 bp):
TTGCGATTTTACAAATTC
Found at i:892872 original size:20 final size:20
Alignment explanation
Indices: 892846--892934 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
892836 GAATATGTAA
892846 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
892866 ATTGCAA--CGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* *
892884 AATCACAACACGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
892905 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
892925 ATCGCAACGC
1 ATCGCAACGC
892935 TAAATTTCAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
17 2 0.04
18 6 0.11
19 5 0.09
20 34 0.62
21 6 0.11
22 2 0.04
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:893804 original size:24 final size:24
Alignment explanation
Indices: 893753--893806 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
893743 GTATTTGAAA
*
893753 TTTGATCTTGGTCAATACCCGTAC
1 TTTGATCTTGGTCAATACCCGAAC
* *
893777 TTTGATCTTGGTCAATACTCGAAT
1 TTTGATCTTGGTCAATACCCGAAC
893801 TTTGAT
1 TTTGAT
893807 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGAAC
Found at i:894025 original size:14 final size:14
Alignment explanation
Indices: 894006--894032 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
893996 GAAAAAGAAA
894006 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
894020 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
894033 TGCCACGGGA
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:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:896087 original size:18 final size:18
Alignment explanation
Indices: 896064--896098 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
896054 AGAAAAAGGC
*
896064 AATCAAAATCTCAATCAA
1 AATCAAAATCCCAATCAA
896082 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
896099 CAACCTGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:896294 original size:20 final size:21
Alignment explanation
Indices: 896269--896344 Score: 106
Period size: 20 Copynumber: 3.8 Consensus size: 21
896259 TTACACATTC
896269 ATTTGAAC-ATCGCAACGCGA
1 ATTTGAACTATCGCAACGCGA
896289 ATTTG-ACTATCGCAACGCGA
1 ATTTGAACTATCGCAACGCGA
*
896309 ATTTG-ACTATCGCAACGCAA
1 ATTTGAACTATCGCAACGCGA
*
896329 ATTTG-ATTATCGCAAC
1 ATTTGAACTATCGCAAC
896345 TCAAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 2 0.04
20 51 0.96
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
ATTTGAACTATCGCAACGCGA
Found at i:896349 original size:20 final size:20
Alignment explanation
Indices: 896277--896513 Score: 255
Period size: 20 Copynumber: 12.4 Consensus size: 20
896267 TCATTTGAAC
896277 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
896297 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
896317 ATCGCAACGCAAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
896337 ATCGCAACTC-AA----A-A
1 ATCGCAACGCGAATTTGACT
896351 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
896371 ATCGCAACGCGAATTTAACT
1 ATCGCAACGCGAATTTGACT
** *
896391 ATCGCAACATGAATATGACT
1 ATCGCAACGCGAATTTGACT
* *
896411 ATCACAACGC-AA----A-A
1 ATCGCAACGCGAATTTGACT
*
896425 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
896445 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
896465 ATCGCAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
896485 ATCGCAACGGGAATTTAACT
1 ATCGCAACGCGAATTTGACT
896505 ATCGCAACG
1 ATCGCAACG
896514 AGAAAATCGC
Statistics
Matches: 182, Mismatches: 23, Indels: 24
0.79 0.10 0.10
Matches are distributed among these distances:
14 18 0.10
15 6 0.03
19 6 0.03
20 152 0.84
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:896398 original size:74 final size:74
Alignment explanation
Indices: 896277--896493 Score: 353
Period size: 74 Copynumber: 2.9 Consensus size: 74
896267 TCATTTGAAC
**
896277 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGC
*
896342 AACTCAAAA
66 AACGCAAAA
* * * * *
896351 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTAACTATCGCAACATGAATATGACTATCAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGC
896416 AACGCAAAA
66 AACGCAAAA
*
896425 ATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGC
896490 AACG
66 AACG
896494 GGAATTTAAC
Statistics
Matches: 129, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 129 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGC
AACGCAAAA
Found at i:896429 original size:54 final size:54
Alignment explanation
Indices: 896371--896473 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
896361 GAATTTGACT
*
896371 ATCGCAACGCGAATTTAACTATCGCAACATGAATATGACTATCACAACGCAAAA
1 ATCGCAACGCGAATTTAACTATCGCAACACGAATATGACTATCACAACGCAAAA
* * * * *
896425 ATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACG
1 ATCGCAACGCGAATTTAACTATCGCAACACGAATATGACTATCACAACG
896474 TGAATTTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (54 bp):
ATCGCAACGCGAATTTAACTATCGCAACACGAATATGACTATCACAACGCAAAA
Found at i:896449 original size:94 final size:94
Alignment explanation
Indices: 896351--896563 Score: 268
Period size: 94 Copynumber: 2.3 Consensus size: 94
896341 CAACTCAAAA
* *
896351 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTAACTATCGCAACATGAATATGACTATCAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTAACTATCGCAACAGGAATATAACTATCAC
* * *
896416 AACGCA-AAAATCGCAACGCGAATTTGATT
66 AACG-AGAAAATCGCAAAGCGAATTAGACT
* * * * * *
896445 ATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTAACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTAACTATCGCAACAGGAATATAACTATCAC
*
896510 AACGAGAAAATCGCAAAGCGTATTAGACT
66 AACGAGAAAATCGCAAAGCGAATTAGACT
* * *
896539 ATCACAATGCGAA-TTGACTTTCGCA
1 ATCGCAACGCGAATTTGACTATCGCA
896564 TTGCGATTTT
Statistics
Matches: 103, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
93 12 0.12
94 91 0.88
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTAACTATCGCAACAGGAATATAACTATCAC
AACGAGAAAATCGCAAAGCGAATTAGACT
Found at i:896773 original size:63 final size:65
Alignment explanation
Indices: 896661--896818 Score: 248
Period size: 63 Copynumber: 2.4 Consensus size: 65
896651 GATTGAAATC
*
896661 AACAAATCAACTTTTACATTTCAATCAATTAAATAAGAACAAATAAGAATTATTTACACATC-A-
1 AACAAATCAACTTTTACA----AATCAATTAAACAAGAACAAATAAGAATTATTTACACATCAAT
896724 ATTA
62 ATTA
*
896728 AACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAACAAATAAGAATTATTTACACATCAATATTA
896793 AACAAATCAACTTTTACAAATCAATT
1 AACAAATCAACTTTTACAAATCAATT
896819 TTTACAAATC
Statistics
Matches: 87, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
63 38 0.44
64 1 0.01
65 30 0.34
67 18 0.21
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGAACAAATAAGAATTATTTACACATCAATATTA
Found at i:896831 original size:14 final size:14
Alignment explanation
Indices: 896771--896832 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
896761 CACAAATAAG
*
896771 AATTATTTACACATC
1 AATT-TTTACAAATC
**
896786 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
896801 AACTTTTACAAATC
1 AATTTTTACAAATC
896815 AATTTTTACAAATC
1 AATTTTTACAAATC
896829 AATT
1 AATT
896833 AAACAAGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:898261 original size:42 final size:42
Alignment explanation
Indices: 898213--898306 Score: 129
Period size: 42 Copynumber: 2.2 Consensus size: 42
898203 ATGAATCGGG
*
898213 CTCTTGAATGGTGGGA-GGGACCTCTTCAA-CGATGAAAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTT-AAGCGATGAAAGGGGC
* *
898255 CTCTTGAACGGTGGGAGGGGACTCTTAAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTAAGCGATGAAAGGGGC
898297 CTCTTGAACG
1 CTCTTGAACG
898307 ATAGCAGAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 2 0.04
42 41 0.87
43 4 0.09
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTAAGCGATGAAAGGGGC
Found at i:898273 original size:21 final size:21
Alignment explanation
Indices: 898213--898306 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
898203 ATGAATCGGG
* * *
898213 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGAGAGGGGC
* * *
898234 CTCTTCAACGATGAAAGGGGC
1 CTCTTGAACGGTGAGAGGGGC
* *
898255 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGAGAGGGGC
* *
898276 CTCTT-AAGGGATGATAGGGGC
1 CTCTTGAACGG-TGAGAGGGGC
898297 CTCTTGAACG
1 CTCTTGAACG
898307 ATAGCAGAGG
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 4 0.07
21 48 0.87
22 3 0.05
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGGC
Found at i:898322 original size:42 final size:42
Alignment explanation
Indices: 898234--898335 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
898224 TGGGAGGGAC
* * * * * * *
898234 CTCTTCAACGATGAAAGGGGCCTCTTGAACGGTGGGAGGGGA
1 CTCTTAAAGGATGATAGGGGCCTCTTGAACGATAGCAGAGGA
* *
898276 CTCTTAAGGGATGATAGGGGCCTCTTGAACGATAGCAGAGGC
1 CTCTTAAAGGATGATAGGGGCCTCTTGAACGATAGCAGAGGA
*
898318 CTCTTAAATGATGATAGG
1 CTCTTAAAGGATGATAGG
898336 TGAGTCGGGC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (42 bp):
CTCTTAAAGGATGATAGGGGCCTCTTGAACGATAGCAGAGGA
Found at i:898841 original size:19 final size:20
Alignment explanation
Indices: 898809--898851 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
898799 AATAGTTTCT
898809 GAAACTTAAAATCGAAACAC
1 GAAACTTAAAATCGAAACAC
* *
898829 GAAACTT-AAATCGCAACGC
1 GAAACTTAAAATCGAAACAC
898848 GAAA
1 GAAA
898852 ATGACTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.51, C:0.21, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGAAACAC
Found at i:898863 original size:20 final size:20
Alignment explanation
Indices: 898838--898886 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
898828 CGAAACTTAA
898838 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
898858 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
898878 ATCGCAACG
1 ATCGCAACG
898887 GGATAATCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:900980 original size:20 final size:20
Alignment explanation
Indices: 900955--901000 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
900945 CTTAAAAACA
900955 CGCAACACACAAAATGA-AAT
1 CGCAACAC-CAAAATGACAAT
* *
900975 CGCAACACGAAAATGACTAT
1 CGCAACACCAAAATGACAAT
900995 CGCAAC
1 CGCAAC
901001 GCGAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.48, C:0.28, G:0.13, T:0.11
Consensus pattern (20 bp):
CGCAACACCAAAATGACAAT
Found at i:901416 original size:22 final size:22
Alignment explanation
Indices: 901378--901433 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
901368 GATGGAGATA
* *
901378 GACGGATTTTGCAGGAGATGTG
1 GACGGATTTCGCAGGAGATGGG
901400 GACGGATTTCGTC-GGAGATGGG
1 GACGGATTTCG-CAGGAGATGGG
* *
901422 GATGGATGTCGC
1 GACGGATTTCGC
901434 CGTAGAGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.20, C:0.12, G:0.43, T:0.25
Consensus pattern (22 bp):
GACGGATTTCGCAGGAGATGGG
Found at i:901795 original size:21 final size:21
Alignment explanation
Indices: 901726--901795 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
901716 TGGCGCTTTG
* *
901726 AAAATCGCATTGCGATTTTGT
1 AAAATCGCGTTGCGATTTTCT
** **
901747 ATTATCGCGTTGCGATAGTC-
1 AAAATCGCGTTGCGATTTTCT
*
901767 AGAATCGCGTTGCGATTTTCT
1 AAAATCGCGTTGCGATTTTCT
901788 AAAATCGC
1 AAAATCGC
901796 AACGCGAATT
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (21 bp):
AAAATCGCGTTGCGATTTTCT
Found at i:901802 original size:21 final size:21
Alignment explanation
Indices: 901778--901818 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
901768 GAATCGCGTT
* *
901778 GCGATTTTCTAAAATCGCAAC
1 GCGAATTTCGAAAATCGCAAC
*
901799 GCGAATTTGGAAAATCGCAA
1 GCGAATTTCGAAAATCGCAA
901819 TGTGATAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
GCGAATTTCGAAAATCGCAAC
Found at i:901893 original size:19 final size:19
Alignment explanation
Indices: 901869--901905 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
901859 TGTCATATTG
*
901869 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
901888 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
901906 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:902039 original size:3 final size:3
Alignment explanation
Indices: 902031--902056 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
902021 GTTTTGACAT
902031 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
902057 TACTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:902106 original size:21 final size:19
Alignment explanation
Indices: 902082--902130 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
902072 TATTCTTTTA
902082 TTTTATTTTATCTTATATATT
1 TTTTATTTTAT-TTA-ATATT
**
902103 TTTTGGTTTATTTAATATT
1 TTTTATTTTATTTAATATT
902122 TTTTATTTT
1 TTTTATTTT
902131 CTCCCTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 12 0.50
20 3 0.12
21 9 0.38
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTATTTTATTTAATATT
Found at i:902153 original size:23 final size:23
Alignment explanation
Indices: 902120--902176 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
902110 TTATTTAATA
*
902120 TTTTTTA-TTTTCTCCCTTTGAT
1 TTTTTTATTTTTCTCCATTTGAT
*
902142 TTTTTTATTTTTTTCCATTTGAT
1 TTTTTTATTTTTCTCCATTTGAT
*
902165 TTATTTATTTTT
1 TTTTTTATTTTT
902177 ATTTTATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.12, C:0.11, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTTTTATTTTTCTCCATTTGAT
Found at i:902195 original size:24 final size:23
Alignment explanation
Indices: 902136--902205 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 23
902126 ATTTTCTCCC
**
902136 TTTGATTTTTTTATTTTT-TTCCA
1 TTTGA-TTTTTTATTTTTATTTTA
902159 TTTGATTTATTTATTTTTATTTTA
1 TTTGATTT-TTTATTTTTATTTTA
* * *
902183 TCTTTATTTTTTATATATATTTT
1 T-TTGATTTTTTATTTTTATTTT
902206 TTAAATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 3 0.08
23 14 0.36
24 16 0.41
25 6 0.15
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (23 bp):
TTTGATTTTTTATTTTTATTTTA
Found at i:903619 original size:23 final size:23
Alignment explanation
Indices: 903591--903634 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
903581 ATACCTAAAT
903591 TTTAAAAACAATAACAAAAAAAA
1 TTTAAAAACAATAACAAAAAAAA
903614 TTTAAAAACAATAACAAAAAA
1 TTTAAAAACAATAACAAAAAA
903635 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (23 bp):
TTTAAAAACAATAACAAAAAAAA
Found at i:904274 original size:19 final size:20
Alignment explanation
Indices: 904247--904284 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
904237 TTAACTTAAT
904247 ATATCAAAAATTA-TAAATA
1 ATATCAAAAATTATTAAATA
*
904266 ATATTAAAAATTATTAAAT
1 ATATCAAAAATTATTAAAT
904285 TCAAATAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATCAAAAATTATTAAATA
Found at i:907377 original size:63 final size:64
Alignment explanation
Indices: 907239--907400 Score: 204
Period size: 63 Copynumber: 2.5 Consensus size: 64
907229 ATTATTCAAG
* * * *
907239 GTGTATCGATGAACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTTAAAATAAAAACATCGAATGCCATCA
* ** *
907303 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTT-AAATATAAACATCGAATGGGATTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTTAAAATAAAAACATCGAATGCCA-TCA
*
907367 -TGTATCGATGCA-TAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
907401 GTCAAGGGAT
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
62 2 0.02
63 48 0.55
64 37 0.43
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTTAAAATAAAAACATCGAATGCCATCA
Found at i:908470 original size:15 final size:15
Alignment explanation
Indices: 908446--908493 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
908436 GAGAAATGAA
*
908446 ATAAGGTATGTGATT
1 ATAAGATATGTGATT
*
908461 ATAAGATATGTGATA
1 ATAAGATATGTGATT
* *
908476 ATAAGTTATATGATT
1 ATAAGATATGTGATT
908491 ATA
1 ATA
908494 TGATCATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (15 bp):
ATAAGATATGTGATT
Found at i:908955 original size:23 final size:23
Alignment explanation
Indices: 908928--908995 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
908918 CATTTTATAT
908928 GGCACTTCGGTGCAATTATACGC
1 GGCACTTCGGTGCAATTATACGC
* * *
908951 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCGGTGCAATTATACGC
*
908974 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
908996 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:909337 original size:13 final size:13
Alignment explanation
Indices: 909319--909356 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
909309 GATATAAGAG
*
909319 GATATAATTATAA
1 GATATAATGATAA
909332 GATATAAATGATAA
1 GATAT-AATGATAA
909346 GA-ATAATGATA
1 GATATAATGATA
909357 GTGAACTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 7 0.30
14 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (13 bp):
GATATAATGATAA
Found at i:914541 original size:14 final size:14
Alignment explanation
Indices: 914508--914535 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
914498 CTCTACCACC
914508 ACGCGTATCCGCGT
1 ACGCGTATCCGCGT
914522 ACGCGTATCCGCGT
1 ACGCGTATCCGCGT
914536 GTGCGTGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.29, T:0.21
Consensus pattern (14 bp):
ACGCGTATCCGCGT
Found at i:914677 original size:14 final size:14
Alignment explanation
Indices: 914660--914722 Score: 81
Period size: 14 Copynumber: 4.5 Consensus size: 14
914650 AACTCATTCG
*
914660 AGTCAACTTGTCTA
1 AGTCAACTCGTCTA
914674 AGTCAACTCGTCTA
1 AGTCAACTCGTCTA
*
914688 AGTCAACCCGTCTA
1 AGTCAACTCGTCTA
* * *
914702 AATTAACTCGTCTG
1 AGTCAACTCGTCTA
914716 AGTCAAC
1 AGTCAAC
914723 CCATTGACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (14 bp):
AGTCAACTCGTCTA
Found at i:918111 original size:28 final size:28
Alignment explanation
Indices: 918079--918146 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
918069 GACATGATCG
* * *
918079 AGTCAACTCGTTTGTGTTAACTCATCCT
1 AGTCAACTCGTTTGAGTCAACTCATCCA
* *
918107 AGTCAACTCATTTGAGTCAACTCGTCCA
1 AGTCAACTCGTTTGAGTCAACTCATCCA
*
918135 AGTCAACCCGTT
1 AGTCAACTCGTT
918147 GACTTTGACC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (28 bp):
AGTCAACTCGTTTGAGTCAACTCATCCA
Found at i:927802 original size:2 final size:2
Alignment explanation
Indices: 927795--927831 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
927785 TAAGCACGTA
927795 AT AT AT 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 AT AT AT A
927832 CATAAAGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:929194 original size:13 final size:13
Alignment explanation
Indices: 929176--929205 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
929166 AAGTCTATAT
929176 TGGGTCAGGTTAC
1 TGGGTCAGGTTAC
*
929189 TGGGTCAGGTTGC
1 TGGGTCAGGTTAC
929202 TGGG
1 TGGG
929206 ACTGGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.47, T:0.30
Consensus pattern (13 bp):
TGGGTCAGGTTAC
Found at i:929912 original size:40 final size:40
Alignment explanation
Indices: 929826--929917 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 40
929816 ACACGTTTCC
* *
929826 TACGTGATGAGGACGACTGGTTATCTGGGGTGACACGGATCT
1 TACGTGATGAGGACGACTGG-T-TCGGGGGTGACACGGATCA
* *
929868 TACGTGATGAGGACGGCTGG-TCGGGGGATGACACGGCTCA
1 TACGTGATGAGGACGACTGGTTCGGGGG-TGACACGGATCA
929908 TACGTGATGA
1 TACGTGATGA
929918 AGAGTTCTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 6 0.13
40 20 0.44
42 19 0.42
ACGTcount: A:0.22, C:0.17, G:0.38, T:0.23
Consensus pattern (40 bp):
TACGTGATGAGGACGACTGGTTCGGGGGTGACACGGATCA
Found at i:930251 original size:59 final size:59
Alignment explanation
Indices: 930159--930272 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
930149 CAATGGAATG
* * *
930159 ACAAACTCAAAGATTTAATTTGTTTCAATGGAAACGATCTCAAAGATGTTTGTTTAGAA
1 ACAAACTCAAAGATTTAATTCGTTTCAAGGGAAACGATCTCAAAGATGATTGTTTAGAA
* * *
930218 ACAAACTCAAATATTTAATTCGTTTCAAGGGAAATGATTTCAAAGATGATTGTTT
1 ACAAACTCAAAGATTTAATTCGTTTCAAGGGAAACGATCTCAAAGATGATTGTTT
930273 TACAAGAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (59 bp):
ACAAACTCAAAGATTTAATTCGTTTCAAGGGAAACGATCTCAAAGATGATTGTTTAGAA
Found at i:930906 original size:23 final size:24
Alignment explanation
Indices: 930845--930906 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
930835 TTCTTCTTTT
* *
930845 ATTTTCAAAATA-TTAATTAGAAG
1 ATTTTGAAAATATTTAATCAGAAG
930868 AGTTTTGAAAAATATTTAATCA-AAG
1 A-TTTTG-AAAATATTTAATCAGAAG
930893 ATTTTGAAAATATT
1 ATTTTGAAAATATT
930907 GTCCATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 9 0.26
24 9 0.26
25 10 0.29
26 6 0.18
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (24 bp):
ATTTTGAAAATATTTAATCAGAAG
Found at i:931647 original size:23 final size:24
Alignment explanation
Indices: 931586--931647 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
931576 TTCTTCTTTT
* *
931586 ATTTTCAAAATA-TTAATTAGAAG
1 ATTTTGAAAATATTTAATCAGAAG
931609 AGTTTTGAAAAATATTTAATCA-AAG
1 A-TTTTG-AAAATATTTAATCAGAAG
931634 ATTTTGAAAATATT
1 ATTTTGAAAATATT
931648 GTCCATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 9 0.26
24 9 0.26
25 10 0.29
26 6 0.18
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (24 bp):
ATTTTGAAAATATTTAATCAGAAG
Found at i:931845 original size:741 final size:741
Alignment explanation
Indices: 930423--931890 Score: 2783
Period size: 741 Copynumber: 2.0 Consensus size: 741
930413 TAAGAAGCTA
930423 TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
1 TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
*
930488 TAAAATTTGTTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTATTTCGAGAGAAACAACAT
66 TAAAATTTATTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTATTTCGAGAGAAACAACAT
930553 TAAATGATACTGATATTCTGCTTGTTCCCACTGGTGGAGGAAATGCCTTCAGAAGATCTAATAAT
131 TAAATGATACTGATATTCTGCTTGTTCCCACTGGTGGAGGAAATGCCTTCAGAAGATCTAATAAT
930618 TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATGCCC
196 TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATGCCC
* *
930683 CAACATTTACAATTGAATCTTTAAATATGCCCCAATTATTCCTCCTTGCTTGCTTCAGCGTTGAT
261 CAACATTTACAATTGAATCTTTAAAGATGCCCCAATTATTCCTCCTTGCTTGCTTCAGCGCTGAT
930748 TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTACTCTAGAGAGATTG
326 TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTACTCTAGAGAGATTG
930813 TCTTGTTTGAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
391 TCTTGTTTGAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
930878 AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATAGGTTTTACAATTGACAAATCATAAA
456 AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATAGGTTTTACAATTGACAAATCATAAA
*
930943 ACAAGAGTTAATTGGATATCAAAGAATTAATTACACTGTTAATCCTTTAATAAATTATAGCTATT
521 ACAAGAGTTAATTGGATATCAAAGAATTAATTACACTGTTAATCCTTCAATAAATTATAGCTATT
931008 TGACAAGTGTCAAGATCAAAGCTATCTTTGGGAAATGGGTAGGTGAGAAAATGGTAAAATGTCTC
586 TGACAAGTGTCAAGATCAAAGCTATCTTTGGGAAATGGGTAGGTGAGAAAATGGTAAAATGTCTC
*
931073 AGGTTGTTATTTTTTGTCAATGGTTTGGCCTTCTTGTTTCTTTGATGTTCACTGATTTAATGGGG
651 AAGTTGTTATTTTTTGTCAATGGTTTGGCCTTCTTGTTTCTTTGATGTTCACTGATTTAATGGGG
931138 TAGCTTGTATGCCCCAACATTTTGTT
716 TAGCTTGTATGCCCCAACATTTTGTT
931164 TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
1 TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
*
931229 TAAAATTTATTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTGTTTCGAGAGAAACAACAT
66 TAAAATTTATTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTATTTCGAGAGAAACAACAT
* *
931294 TAAATGATATTGATATTCTGCTTGTTCCCATTGGTGGAGGAAATGCCTTCAGAAGATCTAATAAT
131 TAAATGATACTGATATTCTGCTTGTTCCCACTGGTGGAGGAAATGCCTTCAGAAGATCTAATAAT
931359 TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATGCCC
196 TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATGCCC
* * *
931424 CAACATTTACTATTGAATCTTTAAAGATGCCCTAATTGTTCCTCCTTGCTTGCTTCAGCGCTGAT
261 CAACATTTACAATTGAATCTTTAAAGATGCCCCAATTATTCCTCCTTGCTTGCTTCAGCGCTGAT
931489 TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTACTCTAGAGAGATTG
326 TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTACTCTAGAGAGATTG
*
931554 TCTTGTTTGAAAATTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
391 TCTTGTTTGAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
*
931619 AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATATGTTTTACAATTGACAAATCATAAA
456 AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATAGGTTTTACAATTGACAAATCATAAA
*
931684 ACAAGAGTTAATTGGATATCAAATAATTAATTACACTGTTAATCCTTCAATAAATTATAGCTATT
521 ACAAGAGTTAATTGGATATCAAAGAATTAATTACACTGTTAATCCTTCAATAAATTATAGCTATT
* *
931749 TGACAAGTGTCAAGATCAAAGTTATCTTTGGGAAATGGGTAGGTGAGGAAATGGTAAAATGTCTC
586 TGACAAGTGTCAAGATCAAAGCTATCTTTGGGAAATGGGTAGGTGAGAAAATGGTAAAATGTCTC
*
931814 AAGTTGTTATTTTTTGTCAATGGTTTGGCCTTCTTGTTTCTTTGATGTTCACTGATTTGATGGGG
651 AAGTTGTTATTTTTTGTCAATGGTTTGGCCTTCTTGTTTCTTTGATGTTCACTGATTTAATGGGG
931879 TAGCTTGTATGC
716 TAGCTTGTATGC
931891 TCTTCTACTG
Statistics
Matches: 710, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
741 710 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (741 bp):
TCTTGAGAGACAAAATTTTGTTTTAAGAGAAACAAACTCAAAGATTATTTATGCCTCAAATTAGA
TAAAATTTATTTTGAAAGAAAATTGTCTCAAGAGAGACAACATTTTATTTCGAGAGAAACAACAT
TAAATGATACTGATATTCTGCTTGTTCCCACTGGTGGAGGAAATGCCTTCAGAAGATCTAATAAT
TTGCATCAGGATATTAAATCCACAAAGATGTCCCAATATTCGATGTTAAATCTCCAAATATGCCC
CAACATTTACAATTGAATCTTTAAAGATGCCCCAATTATTCCTCCTTGCTTGCTTCAGCGCTGAT
TTTGAGCATGAGCTTTGTGTCTGAGAGCTACATGTCATTTATCAAGATCTACTCTAGAGAGATTG
TCTTGTTTGAAAAGTGTTTTTCTTCTTCTTTTATTTTCAAAATATTAATTAGAAGAGTTTTGAAA
AATATTTAATCAAAGATTTTGAAAATATTGTCCATTTATAGGTTTTACAATTGACAAATCATAAA
ACAAGAGTTAATTGGATATCAAAGAATTAATTACACTGTTAATCCTTCAATAAATTATAGCTATT
TGACAAGTGTCAAGATCAAAGCTATCTTTGGGAAATGGGTAGGTGAGAAAATGGTAAAATGTCTC
AAGTTGTTATTTTTTGTCAATGGTTTGGCCTTCTTGTTTCTTTGATGTTCACTGATTTAATGGGG
TAGCTTGTATGCCCCAACATTTTGTT
Found at i:935859 original size:15 final size:13
Alignment explanation
Indices: 935835--935877 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
935825 CTTAAAAATG
935835 AAATGCAGATGCA
1 AAATGCAGATGCA
935848 AAATGCAAAGATGC-
1 AAATGC--AGATGCA
935862 AAATGCAGATGCA
1 AAATGCAGATGCA
935875 AAA
1 AAA
935878 AATGTTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.22
13 9 0.33
14 6 0.22
15 6 0.22
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (13 bp):
AAATGCAGATGCA
Found at i:935861 original size:21 final size:20
Alignment explanation
Indices: 935837--935876 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
935827 TAAAAATGAA
*
935837 ATGCAGATGCAAAATGCAAAG
1 ATGCAAATGC-AAATGCAAAG
*
935858 ATGCAAATGCAGATGCAAA
1 ATGCAAATGCAAATGCAAA
935877 AAATGTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (20 bp):
ATGCAAATGCAAATGCAAAG
Found at i:935873 original size:12 final size:12
Alignment explanation
Indices: 935835--935876 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 12
935825 CTTAAAAATG
935835 AAATGCAGATGC
1 AAATGCAGATGC
935847 AAAATGCAAAGATGC
1 -AAATGC--AGATGC
935862 AAATGCAGATGC
1 AAATGCAGATGC
935874 AAA
1 AAA
935877 AAATGTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
14 6 0.22
15 6 0.22
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (12 bp):
AAATGCAGATGC
Found at i:936631 original size:32 final size:32
Alignment explanation
Indices: 936595--936656 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
936585 ATGAAAAATG
936595 ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
*
936627 ACACAAACAAAAGAAAAGAAATTAGTTAGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGT
936657 ACATGAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
Found at i:938379 original size:2 final size:2
Alignment explanation
Indices: 938372--938406 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
938362 TAAGCACGTA
938372 AT AT 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 AT AT A
938407 CATAAAGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:939315 original size:8 final size:8
Alignment explanation
Indices: 939283--939314 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
939273 TCTCTCATTA
939283 TTCT-TTT
1 TTCTATTT
939290 TTCTATTT
1 TTCTATTT
939298 TTCTATTT
1 TTCTATTT
939306 TTCT-TTT
1 TTCTATTT
939313 TT
1 TT
939315 TTCCTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 9 0.38
8 15 0.62
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (8 bp):
TTCTATTT
Found at i:940427 original size:50 final size:50
Alignment explanation
Indices: 940361--940527 Score: 167
Period size: 50 Copynumber: 3.3 Consensus size: 50
940351 CTTAATATAT
* * * * *
940361 TTACATCGGTGCAAGTGAATAAAATAAACAAGTATATCACTTAATACATA
1 TTACACCGGTGTAAGTGAATAAAATAAAAAAGTATAACACTTAACACATA
* * * *
940411 TTATACCGGTGTAAGTGAA-AAAATAAAAAAACTGTAACACTTAACATATA
1 TTACACCGGTGTAAGTGAATAAAAT-AAAAAAGTATAACACTTAACACATA
** *
940461 CTTACACCAATGTAAGTAAATAAAA-AAAAAAGTATAACACTTAACACATA
1 -TTACACCGGTGTAAGTGAATAAAATAAAAAAGTATAACACTTAACACATA
**
940511 CTTACACTTGTGTAAGT
1 -TTACACCGGTGTAAGT
940528 ATGTACATCT
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
49 5 0.05
50 71 0.75
51 15 0.16
52 4 0.04
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (50 bp):
TTACACCGGTGTAAGTGAATAAAATAAAAAAGTATAACACTTAACACATA
Found at i:940524 original size:101 final size:99
Alignment explanation
Indices: 940338--940527 Score: 229
Period size: 101 Copynumber: 1.9 Consensus size: 99
940328 TTCATACTAC
* * * ** * * *
940338 AAAAACTGTAGCACTTAATATATTTACATCGGTGCAAGTGAATAAAATAAACAAGTATATCACTT
1 AAAAACTGTAACACTTAATATACTTACACCAATGCAAGTAAATAAAATAAAAAAGTATAACACTT
* *
940403 AATACATATTATACCGGTGTAAGTGAAAAAATAA
66 AACACATATTACACCGGTGTAAGTGAAAAAATAA
*
940437 AAAAACTGTAACACTTAACATATACTTACACCAATGTAAGTAAATAAAA-AAAAAAGTATAACAC
1 AAAAACTGTAACACTT-A-ATATACTTACACCAATGCAAGTAAATAAAATAAAAAAGTATAACAC
**
940501 TTAACACATACTTACACTTGTGTAAGT
64 TTAACACATA-TTACACCGGTGTAAGT
940528 ATGTACATCT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
99 15 0.20
100 23 0.31
101 37 0.49
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (99 bp):
AAAAACTGTAACACTTAATATACTTACACCAATGCAAGTAAATAAAATAAAAAAGTATAACACTT
AACACATATTACACCGGTGTAAGTGAAAAAATAA
Found at i:946095 original size:81 final size:81
Alignment explanation
Indices: 945960--946310 Score: 492
Period size: 81 Copynumber: 4.3 Consensus size: 81
945950 TGTTTTAAAA
* *
945960 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCGATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTTCCAATATTGCAAGTTAGATGAAAG
946025 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * *
946041 TAAAATATTAATTGCCTAGCTGTGCATTTGGCATAAA-GTTACTAATATTGCAAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTT-CCAATATTGCAAGTTAGATGAAA
*
946105 GACTAAATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* * *
946122 TAAAAGATTAATTTCCTAGCTGTGCATTTGGCAGAAATGTTCCAATATTGCAAGTTAGATGAATG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTTCCAATATTGCAAGTTAGATGAAAG
946187 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * * *
946203 T-AAAGATTAAATGCCTAACTGTGCATTTAGAAGAAAGGTTCCAATAATGTC-AGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTTCCAATATTG-CAAGTTAGATGAAA
*
946266 GGTTAAATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* * *
946283 ATAAAAGACTAATTGTCTATCTGTGCAT
1 -TAAAAGATTAATTGCCTAGCTGTGCAT
946311 AGCTGGCATG
Statistics
Matches: 240, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
80 70 0.29
81 146 0.61
82 24 0.10
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTTCCAATATTGCAAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Done.