Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009581.1 Hibiscus syriacus cultivar Beakdansim tig00116958_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: 2551150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2431849 original size:23 final size:23
Alignment explanation
Indices: 2431820--2431874 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2431810 GATAATTTAA
*
2431820 AAATAATGTTATTT-AAAGTAAAT
1 AAATAATATTATTTCAAA-TAAAT
* *
2431843 AATTAATATTGTTTCAAATAAAT
1 AAATAATATTATTTCAAATAAAT
2431866 AAATAATAT
1 AAATAATAT
2431875 GGTTTTAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (23 bp):
AAATAATATTATTTCAAATAAAT
Found at i:2431919 original size:21 final size:21
Alignment explanation
Indices: 2431884--2431948 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
2431874 TGGTTTTAGA
*
2431884 AATTAAATAAATATTTTAAAAT
1 AATTTAAT-AATATTTTAAAAT
* *
2431906 AATTTTATAATATTATAAAAT
1 AATTTAATAATATTTTAAAAT
*
2431927 CATTTAATAAGT-TTTTAAAAT
1 AATTTAATAA-TATTTTAAAAT
2431948 A
1 A
2431949 CATAAATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
21 28 0.80
22 7 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTTAATAATATTTTAAAAT
Found at i:2434819 original size:3 final size:3
Alignment explanation
Indices: 2434811--2434840 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2434801 AACAAAAAAG
2434811 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2434841 CGCCTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2436099 original size:26 final size:24
Alignment explanation
Indices: 2436043--2436101 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
2436033 TATGAACAAA
*
2436043 TATTAAA-A-ATATATATTAATTT
1 TATTAAATATATATATATTAATAT
2436065 TAGTT-AATATATATATATATATATAT
1 TA-TTAAATATATATATAT-TA-ATAT
2436091 TATTAAATATA
1 TATTAAATATA
2436102 AAATGATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 8 0.27
25 4 0.13
26 11 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TATTAAATATATATATATTAATAT
Found at i:2436568 original size:19 final size:19
Alignment explanation
Indices: 2436544--2436583 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2436534 CATATATTTT
* *
2436544 TTAATTTTGATTTTTAGTC
1 TTAATTTCGATTTTCAGTC
*
2436563 TTAATTTCGGTTTTCAGTC
1 TTAATTTCGATTTTCAGTC
2436582 TT
1 TT
2436584 TTATTCATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.60
Consensus pattern (19 bp):
TTAATTTCGATTTTCAGTC
Found at i:2438335 original size:16 final size:16
Alignment explanation
Indices: 2438306--2438348 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2438296 AGGTTAGTAT
* *
2438306 ACATACATACATACAC
1 ACATATATATATACAC
* *
2438322 ACATATGTATATACAT
1 ACATATATATATACAC
2438338 ACATATATATA
1 ACATATATATA
2438349 ATTGGCAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (16 bp):
ACATATATATATACAC
Found at i:2441104 original size:44 final size:42
Alignment explanation
Indices: 2441055--2441258 Score: 113
Period size: 44 Copynumber: 5.2 Consensus size: 42
2441045 TTAAATATTA
2441055 TATTTTATTTTTGTTTTATGTATTTTAGTTTAAATAGATTTTAG
1 TATTTTATTTTTGTTTTA-GTATTTTAGTTTAAATAG-TTTTAG
* ** *
2441099 TATTTTAATTAAGTTTTAG---GTTA--TT--AT--TTTTA-
1 TATTTTATTTTTGTTTTAGTATTTTAGTTTAAATAGTTTTAG
*
2441131 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATTTTTGTTTTA-GTATTTTAGTTTAAATA-GTTTTAG
* ** * *
2441175 TATTTTAATTAAGTTTTAGGA---TA--TT--AT-TTTTTA-
1 TATTTTATTTTTGTTTTAGTATTTTAGTTTAAATAGTTTTAG
*
2441208 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAG
1 TATTTTATTTTTGTTTTA-GTATTTTAGTTTAAATAGTTTT-AG
*
2441252 TGTTTTA
1 TATTTTA
2441259 ATTAGGATTT
Statistics
Matches: 115, Mismatches: 22, Indels: 46
0.63 0.12 0.25
Matches are distributed among these distances:
32 14 0.12
33 20 0.17
34 7 0.06
36 7 0.06
37 2 0.02
38 6 0.05
39 2 0.02
40 7 0.06
41 2 0.02
42 4 0.03
43 9 0.08
44 35 0.30
ACGTcount: A:0.25, C:0.01, G:0.12, T:0.61
Consensus pattern (42 bp):
TATTTTATTTTTGTTTTAGTATTTTAGTTTAAATAGTTTTAG
Found at i:2441243 original size:77 final size:76
Alignment explanation
Indices: 2441052--2441262 Score: 352
Period size: 76 Copynumber: 2.8 Consensus size: 76
2441042 ATTTTAAATA
* * *
2441052 TTATATTTTATTTTTGTTTTATGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
*
2441117 GGTTATTATTT
66 GGATATTATTT
2441128 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
2441193 GGATATTATTTT
66 GGATATTA-TTT
*
2441205 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTA
2441263 GGATTTAAGA
Statistics
Matches: 128, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
76 74 0.58
77 54 0.42
ACGTcount: A:0.26, C:0.01, G:0.12, T:0.61
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
GGATATTATTT
Found at i:2442500 original size:5 final size:5
Alignment explanation
Indices: 2442492--2442597 Score: 61
Period size: 5 Copynumber: 20.8 Consensus size: 5
2442482 TCATTCTATT
* ** ****
2442492 TTTTA TTTTA TTTCA TTTTA TTTCG TTTTA TTTTTA TTTTA TTTTTA GCAAA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA -TTTTA TTTTA
* * * * * *
2442544 CTTTA TTTTCA TTCTA -TTTA TTTTA TTTTA TTTTA ATTAA TTTAA TTTAA
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
2442594 TTTT
1 TTTT
2442598 TCTCTGAATA
Statistics
Matches: 76, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
4 3 0.04
5 59 0.78
6 14 0.18
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (5 bp):
TTTTA
Found at i:2442532 original size:21 final size:20
Alignment explanation
Indices: 2442497--2442535 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2442487 CTATTTTTTA
2442497 TTTTATTTCATTTTATTTCG
1 TTTTATTTCATTTTATTTCG
*
2442517 TTTTATTTTTATTTTATTT
1 TTTTA-TTTCATTTTATTT
2442536 TTAGCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTATTTCATTTTATTTCG
Found at i:2446477 original size:41 final size:41
Alignment explanation
Indices: 2446420--2446533 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 41
2446410 GCCTAAAGGT
* *
2446420 CTTATAGATGAACCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTATCATCATGCTCGAAAGA
* *
2446461 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTT-ATCATCATGCTCGAAAGA
* *
2446503 CTTACT-GATGGCCCAAAGGACTTACTCATCA
1 CTTA-TAGATGACCCGAAGGACTTA-TCATCA
2446534 AGAAAACCTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
41 22 0.35
42 39 0.63
43 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (41 bp):
CTTATAGATGACCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:2447021 original size:41 final size:41
Alignment explanation
Indices: 2446975--2447088 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 41
2446965 TCCCGAAGGT
* *
2446975 CTTATAGATGTCCCGAAGGACTTATCATCTTGCTCAAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
*
2447016 CTTATAGATGGCCCGAAGGACTTATGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTAT-CATCATGCTCAAAAGA
* *
2447058 CTTACT-GAAGGCTCGAAGGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
2447089 AGAAAGCCTT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
41 24 0.37
42 39 0.60
43 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
Found at i:2447039 original size:20 final size:20
Alignment explanation
Indices: 2446966--2447040 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
2446956 AAATATCATT
* *
2446966 CCCGAAGGTCTTATAGATGT
1 CCCGAAGGACTTATAGATGG
** *
2446986 CCCGAAGGACTTATCATCTTG
1 CCCGAAGGACTTAT-AGATGG
* * *
2447007 CTCAAAAGACTTATAGATGG
1 CCCGAAGGACTTATAGATGG
2447027 CCCGAAGGACTTAT
1 CCCGAAGGACTTAT
2447041 GCATCATGCT
Statistics
Matches: 40, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 27 0.68
21 13 0.32
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (20 bp):
CCCGAAGGACTTATAGATGG
Found at i:2447048 original size:278 final size:276
Alignment explanation
Indices: 2446400--2447238 Score: 1141
Period size: 278 Copynumber: 3.0 Consensus size: 276
2446390 AGAGATGTTC
* ** * *
2446400 AAAACATCCTGCCTAAAGGTCTTATAGATGAACCGAAGGACTTATCATCTTGCTCGAAAGACTTA
1 AAAACATCATGCCCGAAGGTCTTATAGATGACCCGAAGGACTTATCATCTTGCTCAAAAGACTTA
* *
2446465 TAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTC
66 TAGATGACCCGAAGGATTTATGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTC
*
2446530 ATCAAGAAAACCTTGAAAATCAAGCTTAGTTTCTTAATTGTCATCAAGGAACCCTTAAAAATTTG
131 ATCAAGAAAACCTTGAAAATCAAGCTTAGTTTCTTAATTGTCATCAAGGAACCCTTAAAAATTAG
* * *
2446595 GCTTATCTTCCTTTACAAATTCTTTGGAGATAGTCATCGAGAAACCCCTGAAAATCAGGCTTAGT
196 GCTTAGCTTCATTTAAAAATTCTTTGGAGATAGTCATCGAGAAACCCCTGAAAATCAGGCTTAGT
2446660 TTCTAAAAGCTCATTTG
261 TTCTAAAA-CTCATTTG
* ** * * *
2446677 AAAACATCCTGCCCGAAGGTCTTACGGATGGCCCGAAGGACTTATCATCTTTCTCGAAAA-ATTT
1 AAAACATCATGCCCGAAGGTCTTATAGATGACCCGAAGGACTTATCATCTTGCTC-AAAAGACTT
* * * *
2446741 ATAAATGACCCGAATGATTTAAT-CATCATGCTCGAAAGACTTATTGATGTCCCGAAGGACTTAC
65 ATAGATGACCCGAAGGATTT-ATGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
* * *
2446805 TCATCAAGAAACCCTTGAAAATCAAGCTTACTTTCTTAATTGTCATCAAGGAAACCTTAAAAAAT
129 TCATCAAGAAAACCTTGAAAATCAAGCTTAGTTTCTTAATTGTCATCAAGGAACCCTT-AAAAAT
* *
2446870 TAGGCTTAGCTTCATTTAAAAATTCTTTGGAGATAGTCATCGAGAACCCCCTGAAAATCAGGTTT
193 TAGGCTTAGCTTCATTTAAAAATTCTTTGGAGATAGTCATCGAGAAACCCCTGAAAATCAGGCTT
2446935 AGTTTCTGAAAACTCATTTG
258 AGTTTCT-AAAACTCATTTG
* * *
2446955 AAAATATCATTCCCGAAGGTCTTATAGATGTCCCGAAGGACTTATCATCTTGCTCAAAAGACTTA
1 AAAACATCATGCCCGAAGGTCTTATAGATGACCCGAAGGACTTATCATCTTGCTCAAAAGACTTA
* * * *
2447020 TAGATGGCCCGAAGGACTTATGCATCATGCTCGAAAGACTTACTGAAGGCTCGAAGGACTTACTC
66 TAGATGACCCGAAGGATTTATGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTC
* * * * * *
2447085 ATCAAGAAAGCCTTAAAAATCAAGTTTAGTTTATTAGTTG---TCAAGGAACCCCTAAAAATTAG
131 ATCAAGAAAACCTTGAAAATCAAGCTTAGTTTCTTAATTGTCATCAAGGAACCCTTAAAAATTAG
* * * * * * * *
2447147 GTTTAGTTTCCTTTTAAAAACTCATTGAAAATCA-TCATCAAGAAACCCCTGAAAATCAGGCTTA
196 GCTTAGCTT-CATTTAAAAATTCTTTGGAGAT-AGTCATCGAGAAACCCCTGAAAATCAGGCTTA
2447211 GTTTCTAAAAACTCATTTG
259 GTTTCT-AAAACTCATTTG
2447230 AAAACATCA
1 AAAACATCA
2447239 AGAAACACCT
Statistics
Matches: 494, Mismatches: 60, Indels: 18
0.86 0.10 0.03
Matches are distributed among these distances:
274 16 0.03
275 81 0.16
276 1 0.00
277 168 0.34
278 224 0.45
279 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (276 bp):
AAAACATCATGCCCGAAGGTCTTATAGATGACCCGAAGGACTTATCATCTTGCTCAAAAGACTTA
TAGATGACCCGAAGGATTTATGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTC
ATCAAGAAAACCTTGAAAATCAAGCTTAGTTTCTTAATTGTCATCAAGGAACCCTTAAAAATTAG
GCTTAGCTTCATTTAAAAATTCTTTGGAGATAGTCATCGAGAAACCCCTGAAAATCAGGCTTAGT
TTCTAAAACTCATTTG
Found at i:2447059 original size:22 final size:21
Alignment explanation
Indices: 2446988--2447061 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 21
2446978 ATAGATGTCC
*
2446988 CGAAGGACTTAT-CATCTTGCT
1 CGAAAGACTTATGCATC-TGCT
* * *
2447009 CAAAAGACTTATAG-AT-GGCC
1 CGAAAGACTTAT-GCATCTGCT
*
2447029 CGAAGGACTTATGCATCATGCT
1 CGAAAGACTTATGCATC-TGCT
2447051 CGAAAGACTTA
1 CGAAAGACTTA
2447062 CTGAAGGCTC
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 14 0.36
21 10 0.26
22 14 0.36
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (21 bp):
CGAAAGACTTATGCATCTGCT
Found at i:2447260 original size:52 final size:54
Alignment explanation
Indices: 2447125--2447268 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 54
2447115 TTATTAGTTG
* *
2447125 TCAAGGAACCCCTAAAAATTAGGTTTAGTTTCCTTTTAAAAACTCATTGAAAATCATCA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTT-C---TAAAAACTCATTGAAAA-CATCA
* *
2447184 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTG-AAA-A-CA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCA-TTGAAAACATCA
* *
2447236 TCAAGAAACACCTAAAAATTAGGCTTAGCTTCT
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCT
2447269 TTGTTTAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
52 31 0.41
53 1 0.01
55 13 0.17
56 3 0.04
58 1 0.01
59 27 0.36
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.28
Consensus pattern (54 bp):
TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTGAAAACATCA
Found at i:2451323 original size:21 final size:20
Alignment explanation
Indices: 2451279--2451326 Score: 80
Period size: 19 Copynumber: 2.4 Consensus size: 20
2451269 AAGGTGGGGA
2451279 CTAAGTTTAGCTCTCTCACG
1 CTAAGTTTAGCTCTCTCACG
2451299 -TAAGTTTAGCTCTCTCACG
1 CTAAGTTTAGCTCTCTCACG
2451318 TCTAAGTTT
1 -CTAAGTTT
2451327 TCACGGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 19 0.73
21 7 0.27
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (20 bp):
CTAAGTTTAGCTCTCTCACG
Found at i:2453370 original size:18 final size:20
Alignment explanation
Indices: 2453332--2453371 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2453322 AGGAAAAAAG
2453332 AAAACAAGTTAAGACGTATAA
1 AAAACAAGTTAAGA-GTATAA
2453353 AAAACAAG-TAAG-GTATAA
1 AAAACAAGTTAAGAGTATAA
2453371 A
1 A
2453372 GGTAAATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.60, C:0.07, G:0.15, T:0.17
Consensus pattern (20 bp):
AAAACAAGTTAAGAGTATAA
Found at i:2455114 original size:15 final size:15
Alignment explanation
Indices: 2455094--2455124 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2455084 AACCAGATGA
2455094 TTTTAATAAAACATT
1 TTTTAATAAAACATT
*
2455109 TTTTAATAAAATATT
1 TTTTAATAAAACATT
2455124 T
1 T
2455125 AGTTTTAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTAATAAAACATT
Found at i:2456762 original size:29 final size:29
Alignment explanation
Indices: 2456726--2456793 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
2456716 CATACATATA
2456726 AAAAAGGGAATATATACATTAGCACCTAT
1 AAAAAGGGAATATATACATTAGCACCTAT
2456755 AAAAAGGGAATATATACATTAGCACCTAT
1 AAAAAGGGAATATATACATTAGCACCTAT
2456784 AAAAAGGGAA
1 AAAAAGGGAA
2456794 AATAACTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (29 bp):
AAAAAGGGAATATATACATTAGCACCTAT
Found at i:2458497 original size:44 final size:44
Alignment explanation
Indices: 2458447--2458573 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 44
2458437 TTAAATATTA
2458447 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
* **
2458491 AATTTTAAT-TAAGTTTTAGG-A---TA--TT--AT---TTTTA-
1 TATTTT-ATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
*
2458523 TATTTTATCTTTGTTTTATGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
2458567 TATTTTA
1 TATTTTA
2458574 ATTAAGTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 28
0.64 0.07 0.29
Matches are distributed among these distances:
31 2 0.03
32 13 0.21
33 6 0.10
36 4 0.06
38 4 0.06
40 4 0.06
43 6 0.10
44 21 0.34
45 2 0.03
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.60
Consensus pattern (44 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
Found at i:2458647 original size:74 final size:76
Alignment explanation
Indices: 2458444--2458651 Score: 350
Period size: 76 Copynumber: 2.8 Consensus size: 76
2458434 ATTTTAAATA
*
2458444 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGAATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
*
2458509 GGATATTATTT
66 GAATATTATTT
*
2458520 TTATATTTTATCTTTGTTTTATGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
2458585 GAATATTA-TT
66 GAATATTATTT
*
2458595 TT-TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTA
2458652 GGATTTAAGA
Statistics
Matches: 126, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
73 5 0.04
74 47 0.37
75 4 0.03
76 70 0.56
ACGTcount: A:0.27, C:0.01, G:0.12, T:0.60
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
GAATATTATTT
Found at i:2459367 original size:15 final size:15
Alignment explanation
Indices: 2459331--2459359 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2459321 TTTTAAAATC
2459331 ATTA-TTTATTATTT
1 ATTATTTTATTATTT
2459345 ATTATTTTATTATTT
1 ATTATTTTATTATTT
2459360 TCTCTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTATTTTATTATTT
Found at i:2461958 original size:21 final size:21
Alignment explanation
Indices: 2461934--2461978 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2461924 AAAATAAAAT
*
2461934 AAAACTAA-ACTTTAGATAGA
1 AAAAATAAGACTTTAGATAGA
* *
2461954 AAAAATAAGAGTTTAGATAGT
1 AAAAATAAGACTTTAGATAGA
2461975 AAAA
1 AAAA
2461979 CGAATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.24
Consensus pattern (21 bp):
AAAAATAAGACTTTAGATAGA
Found at i:2462349 original size:74 final size:74
Alignment explanation
Indices: 2462221--2462359 Score: 172
Period size: 74 Copynumber: 1.9 Consensus size: 74
2462211 CACGATTATT
* * * * * * *
2462221 TTCAAAATACTGTTTGGATTCTTGGAAATTTGGAAAATAAATTGTCTACAAACTTTTAAAAGCTT
1 TTCAAAATACTCTTCGGATTCTCGGAAATTTGGAAAAGAAACTATCAACAAACTTTTAAAAGCTT
2462286 TCACGAAAA
66 TCACGAAAA
* * *
2462295 TTCAAAATACTCTTCGGATTGTCGGAGATTTGGAAAAGAAACTATCAATC-AACTTTTGAAAGCT
1 TTCAAAATACTCTTCGGATTCTCGGAAATTTGGAAAAGAAACTATCAA-CAAACTTTTAAAAGCT
2462359 T
65 T
2462360 CGACTGATTC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 53 0.98
75 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (74 bp):
TTCAAAATACTCTTCGGATTCTCGGAAATTTGGAAAAGAAACTATCAACAAACTTTTAAAAGCTT
TCACGAAAA
Found at i:2479274 original size:58 final size:60
Alignment explanation
Indices: 2479197--2479358 Score: 188
Period size: 58 Copynumber: 2.8 Consensus size: 60
2479187 ACCCATATTT
* * *
2479197 TAAATT-GGTCCTTTAACTTTTGAATATTCTAATTTCATACCCAAGCTATGA-CTCATTC
1 TAAATTAGTTCCTTAAACTTTTGAATATTCTAATTTCATACCCAACCTATGACCTCATTC
* * * *
2479255 TAAATTA-TTCCTTAAACTTTTTAACATTCTAATTTCATCCCCAACCTATGACCCTCATTT
1 TAAATTAGTTCCTTAAACTTTTGAATATTCTAATTTCATACCCAACCTATGA-CCTCATTC
* * * *
2479315 TAAATTAGTTCC-CAAACTTTTGAATCTTTTAATTTCATTCCCAA
1 TAAATTAGTTCCTTAAACTTTTGAATATTCTAATTTCATACCCAA
2479359 ATTCGTCCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
58 44 0.51
60 39 0.45
61 4 0.05
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (60 bp):
TAAATTAGTTCCTTAAACTTTTGAATATTCTAATTTCATACCCAACCTATGACCTCATTC
Found at i:2479348 original size:60 final size:58
Alignment explanation
Indices: 2479211--2479358 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 58
2479201 TTGGTCCTTT
* * *
2479211 AACTTTTGAATATTCTAATTTCATACCCAAGCTATGACTCATTCTAAATTATTCCTTA
1 AACTTTTGAATCTTCTAATTTCATACCCAACCTATGACTCATTCTAAATTATTCCTCA
* * *
2479269 AACTTTTTAA-CATTCTAATTTCATCCCCAACCTATGACCCTCATTTTAAATTAGTTCC-CA
1 AACTTTTGAATC-TTCTAATTTCATACCCAACCTATGA--CTCATTCTAAATTA-TTCCTCA
* *
2479329 AACTTTTGAATCTTTTAATTTCATTCCCAA
1 AACTTTTGAATCTTCTAATTTCATACCCAA
2479359 ATTCGTCCAA
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
58 32 0.42
60 39 0.51
61 5 0.07
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (58 bp):
AACTTTTGAATCTTCTAATTTCATACCCAACCTATGACTCATTCTAAATTATTCCTCA
Found at i:2482724 original size:34 final size:34
Alignment explanation
Indices: 2482676--2482748 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
2482666 ATGCAGATTG
2482676 GGGTAGCAGCGTGGATGACAGAAGGTCCATATCA
1 GGGTAGCAGCGTGGATGACAGAAGGTCCATATCA
*
2482710 GGGTAGCAGTGTGGATGACAGAAGGTCCATATCA
1 GGGTAGCAGCGTGGATGACAGAAGGTCCATATCA
2482744 GGGTA
1 GGGTA
2482749 TCGTGAAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.29, C:0.15, G:0.37, T:0.19
Consensus pattern (34 bp):
GGGTAGCAGCGTGGATGACAGAAGGTCCATATCA
Found at i:2491364 original size:21 final size:23
Alignment explanation
Indices: 2491321--2491371 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
2491311 TAATCAATGA
2491321 TATTTTTAAATTTTGATATTATT
1 TATTTTTAAATTTTGATATTATT
*
2491344 TATTTTT-ATTTTTGATA-TATT
1 TATTTTTAAATTTTGATATTATT
2491365 TATTTTT
1 TATTTTT
2491372 TGAGTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 11 0.41
22 9 0.33
23 7 0.26
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (23 bp):
TATTTTTAAATTTTGATATTATT
Found at i:2491372 original size:22 final size:23
Alignment explanation
Indices: 2491321--2491372 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
2491311 TAATCAATGA
*
2491321 TATTTTTAAATTTTGATATTATT
1 TATTTTTTAATTTTGATATTATT
*
2491344 TA-TTTTTATTTTTGATA-TATT
1 TATTTTTTAATTTTGATATTATT
2491365 TATTTTTT
1 TATTTTTT
2491373 GAGTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 18 0.69
23 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (23 bp):
TATTTTTTAATTTTGATATTATT
Found at i:2493833 original size:81 final size:81
Alignment explanation
Indices: 2493742--2494041 Score: 363
Period size: 81 Copynumber: 3.7 Consensus size: 81
2493732 AGGCATCTAG
* ** * * * * *
2493742 AGATGATACTGATTTATGTCCTCTGCGAAAATGGAGGGTTCAGAATGACACACCATCACCTGAAC
1 AGATGATACTGATTTATCTCCTCCACGGAAACGGAGGGTTCGGAATGATACACCATCACCAGAAC
*
2493807 CTTTAGTAAACAGTGC
66 CTTTAGTAAACAGAGC
* *
2493823 AGATGGTACTGATTTATCTCCTCCACGGAAACGGAGGGTTCGGAATGATACACAATCACCAGAAC
1 AGATGATACTGATTTATCTCCTCCACGGAAACGGAGGGTTCGGAATGATACACCATCACCAGAAC
2493888 CTTTAGTAAACAGAGC
66 CTTTAGTAAACAGAGC
* * * * * *
2493904 AGATGTTAATGATTTATCTCCTCCACGGAAACGGAGGGCTCGGAATGGTACACCTTCACCAAAAC
1 AGATGATACTGATTTATCTCCTCCACGGAAACGGAGGGTTCGGAATGATACACCATCACCAGAAC
2493969 CTTTAGTAAACAGAGC
66 CTTTAGTAAACAGAGC
* * * ** * *
2493985 AGATG---CTGATTTATCACCACCTCGGAAACGGAGGGTGAGAAATGATACACCTTCACC
1 AGATGATACTGATTTATCTCCTCCACGGAAACGGAGGGTTCGGAATGATACACCATCACC
2494042 GAAACGGAGG
Statistics
Matches: 192, Mismatches: 27, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
78 43 0.22
81 149 0.78
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (81 bp):
AGATGATACTGATTTATCTCCTCCACGGAAACGGAGGGTTCGGAATGATACACCATCACCAGAAC
CTTTAGTAAACAGAGC
Found at i:2496015 original size:23 final size:23
Alignment explanation
Indices: 2495979--2496039 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
2495969 CTGAATGATT
* *
2495979 CAGTGCTGACTGATTCAACAAAA
1 CAGTGATGAATGATTCAACAAAA
2496002 CAGTGATGAATGATTCAACAAAA
1 CAGTGATGAATGATTCAACAAAA
*
2496025 CA-TTACTGAATGATT
1 CAGTGA-TGAATGATT
2496040 TAGCACAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 2 0.06
23 32 0.94
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (23 bp):
CAGTGATGAATGATTCAACAAAA
Found at i:2496142 original size:16 final size:16
Alignment explanation
Indices: 2496121--2496163 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
2496111 ACAGAGTCTC
2496121 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
2496137 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
2496153 TGAATCATTCA
1 TGAATCATTCA
2496164 ACGCTTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:2498844 original size:23 final size:23
Alignment explanation
Indices: 2498799--2498845 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2498789 CTGAGTCTAG
**
2498799 ATTAATGAAGGTGTTGCGTCCTT
1 ATTAATGAAGGTGTTGCCACCTT
*
2498822 ATTAATGAAGGTGTTTCCACCTT
1 ATTAATGAAGGTGTTGCCACCTT
2498845 A
1 A
2498846 ATCTTGACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (23 bp):
ATTAATGAAGGTGTTGCCACCTT
Found at i:2500985 original size:22 final size:22
Alignment explanation
Indices: 2500957--2501019 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
2500947 CTTTAATTCA
2500957 AAATTTATATACTCTAAACTTT
1 AAATTTATATACTCTAAACTTT
* *
2500979 AAATTTAAAT-CT-TAAACCGTT
1 AAATTTATATACTCTAAA-CTTT
2501000 AAATTTATA-ACTCTAAACTT
1 AAATTTATATACTCTAAACTT
2501020 CTAACCTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 4 0.12
21 17 0.50
22 13 0.38
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (22 bp):
AAATTTATATACTCTAAACTTT
Found at i:2507045 original size:2 final size:2
Alignment explanation
Indices: 2507038--2507063 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2507028 ACGCTACAAA
2507038 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
2507064 TCATAACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2510346 original size:2 final size:2
Alignment explanation
Indices: 2510339--2510368 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2510329 TGATTACCTC
2510339 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
2510369 TTACTATGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2510520 original size:222 final size:222
Alignment explanation
Indices: 2510134--2510562 Score: 786
Period size: 222 Copynumber: 1.9 Consensus size: 222
2510124 TAATCATGTC
2510134 TATATATATATATTTACTATGACCGGCACCAAGGTCCAGGTCAAGAGTAAACACTAAAGGGTTGT
1 TATATATATATATTTACTATGACCGGCACCAAGGTCCAGGTCAAGAGTAAACACTAAAGGGTTGT
*
2510199 TTGGTACAAGGTATATCTTATTACCGGGGGAATGAAATCCTCATTCTCACGTTTGGTTGGCCAAT
66 TTGGTACAAGGTATATCTTATTACCGGGGGAATGAAATCCTCATTCCCACGTTTGGTTGGCCAAT
* *
2510264 ATTCCTAGCCCTCAGTAATCTTTTGTTACCAACAGTGGATTTTTTGGGGTATATTACCTGGAATG
131 ATTCCTAGCCCACAGTAATCTTTTGTTACCAACAGTGGATTTTTTGGGGTATATTACCGGGAATG
*
2510329 TGATTACCTCATATATATATATATATA
196 TAATTACCTCATATATATATATATATA
*
2510356 TATATATATATATTTACTATGACCGGCACCAAGGTCCAGGTCAAGAGTAAACACTAAGGGGTTGT
1 TATATATATATATTTACTATGACCGGCACCAAGGTCCAGGTCAAGAGTAAACACTAAAGGGTTGT
*
2510421 TTGGTTCAAGGTATATCTTATTACCGGGGGAATGAAATCCTCATTCCCACGTTTGGTTGGCCAAT
66 TTGGTACAAGGTATATCTTATTACCGGGGGAATGAAATCCTCATTCCCACGTTTGGTTGGCCAAT
*
2510486 ATTCCTAGCCCACAGTAATCTTTTGTTACCAACAGTGGATTTTTTTGGGTATATTACCGGGAATG
131 ATTCCTAGCCCACAGTAATCTTTTGTTACCAACAGTGGATTTTTTGGGGTATATTACCGGGAATG
*
2510551 TAATTACGTCAT
196 TAATTACCTCAT
2510563 TCCCTTAGAT
Statistics
Matches: 199, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
222 199 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (222 bp):
TATATATATATATTTACTATGACCGGCACCAAGGTCCAGGTCAAGAGTAAACACTAAAGGGTTGT
TTGGTACAAGGTATATCTTATTACCGGGGGAATGAAATCCTCATTCCCACGTTTGGTTGGCCAAT
ATTCCTAGCCCACAGTAATCTTTTGTTACCAACAGTGGATTTTTTGGGGTATATTACCGGGAATG
TAATTACCTCATATATATATATATATA
Found at i:2524684 original size:31 final size:32
Alignment explanation
Indices: 2524649--2524730 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 32
2524639 TTCGAGGCCT
*
2524649 CGAGAT-ATTTCTTGGGTAGGCCCTGCGACCC
1 CGAGATAATTTCTTGGGTAGGCCCCGCGACCC
* * * *
2524680 CGAGATCA-TTCTAGGGTAGGCCCCGTGGCCC
1 CGAGATAATTTCTTGGGTAGGCCCCGCGACCC
2524711 CGAG-TAACTTTCTTGGGTAG
1 CGAGATAA-TTTCTTGGGTAG
2524731 ACTCTCGGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
30 2 0.05
31 29 0.69
32 11 0.26
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.26
Consensus pattern (32 bp):
CGAGATAATTTCTTGGGTAGGCCCCGCGACCC
Found at i:2527540 original size:3 final size:3
Alignment explanation
Indices: 2527532--2527582 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
2527522 CTCACTCTCG
* * * *
2527532 TCA TCA TCA CCA CCA TCA TCA TCA CCA TCA CCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
2527580 TCA
1 TCA
2527583 GGAGCATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.25
Consensus pattern (3 bp):
TCA
Found at i:2530144 original size:18 final size:18
Alignment explanation
Indices: 2530121--2530161 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2530111 AGGCATTTGA
* *
2530121 TCCTCTAGTTGTGCTTGT
1 TCCTCTACTCGTGCTTGT
2530139 TCCTCTACTCGTGCTTGT
1 TCCTCTACTCGTGCTTGT
2530157 TCCTC
1 TCCTC
2530162 GTGTTATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.32, G:0.17, T:0.46
Consensus pattern (18 bp):
TCCTCTACTCGTGCTTGT
Found at i:2538574 original size:30 final size:30
Alignment explanation
Indices: 2538538--2538609 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
2538528 CCCGCAGGAC
2538538 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
2538568 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
2538598 CTGTCCATAGGT
1 CTATCCAGAGGT
2538610 TCCGAAGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:2538650 original size:31 final size:30
Alignment explanation
Indices: 2538593--2538783 Score: 183
Period size: 31 Copynumber: 6.1 Consensus size: 30
2538583 AAAGATCCTC
* *
2538593 GGTAACTGTCCATAGGTTCCGAAGAACCTA
1 GGTAACTGTCCATATGTTCCGAAGAACATA
**
2538623 GGTGAACTGTCCATATGTTCCTTAGAACATA
1 GGT-AACTGTCCATATGTTCCGAAGAACATA
* *
2538654 GGTATATTGTCCATATG-TCTCGAA-AGATATA
1 GGTA-ACTGTCCATATGTTC-CGAAGA-ACATA
*
2538685 GGTAATTCTGTCCATATGTTCCGTAGAACATA
1 GGTAA--CTGTCCATATGTTCCGAAGAACATA
2538717 GGTATACTGTCCATATG-TCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTTC-CGAAGA-ACATA
*
2538748 GGTAATTCTGTCCATATGTTCCGTAGAACATA
1 GGTAA--CTGTCCATATGTTCCGAAGAACATA
2538780 GGTA
1 GGTA
2538784 CCCTCGACTC
Statistics
Matches: 133, Mismatches: 13, Indels: 28
0.76 0.07 0.16
Matches are distributed among these distances:
30 12 0.09
31 70 0.53
32 44 0.33
33 7 0.05
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCGAAGAACATA
Found at i:2538702 original size:32 final size:32
Alignment explanation
Indices: 2538649--2538766 Score: 147
Period size: 32 Copynumber: 3.8 Consensus size: 32
2538639 GTTCCTTAGA
2538649 ACATAGGT-ATAT-TGTCCATATGTCTCGAAAG
1 ACATAGGTAAT-TCTGTCCATATGTCTCGAAAG
* *
2538680 ATATAGGTAATTCTGTCCATATGT-TCCG-TAG
1 ACATAGGTAATTCTGTCCATATGTCT-CGAAAG
*
2538711 AACATAGGT-ATACTGTCCATATGTCTCGAAAG
1 -ACATAGGTAATTCTGTCCATATGTCTCGAAAG
2538743 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGTAATTCTGTCCATATGT
2538767 TCCGTAGAAC
Statistics
Matches: 74, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
31 35 0.47
32 39 0.53
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCTCGAAAG
Found at i:2538704 original size:63 final size:63
Alignment explanation
Indices: 2538629--2538783 Score: 283
Period size: 63 Copynumber: 2.5 Consensus size: 63
2538619 CCTAGGTGAA
* * *
2538629 CTGTCCATATGTTCCTTAGAACATAGGTATATTGTCCATATGTCTCGAAAGATATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
2538692 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
2538755 CTGTCCATATGTTCCGTAGAACATAGGTA
1 CTGTCCATATGTTCCGTAGAACATAGGTA
2538784 CCCTCGACTC
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 89 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (63 bp):
CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
Found at i:2539584 original size:64 final size:64
Alignment explanation
Indices: 2539433--2539589 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
2539423 TAATGAAGGT
** * ** *
2539433 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACCAATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTAAAGAG
* * *
2539497 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTATT-TATT-TTAAA
1 ATGCATCGATGCACTACC-AATGCATCGATGCA-TAAAATGCATTCGATGT-TTGT-TTATTAAA
2539558 -AG
62 GAG
2539560 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACCAATGCATCGAT
2539590 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
63 4 0.05
64 65 0.84
65 8 0.10
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACCAATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTAAAGAG
Found at i:2543638 original size:30 final size:30
Alignment explanation
Indices: 2543602--2543673 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
2543592 CCCGCAGGAC
*
2543602 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
2543632 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
2543662 CTGTCCATAGGT
1 CTATCCAGAGGT
2543674 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:2543765 original size:32 final size:31
Alignment explanation
Indices: 2543661--2543846 Score: 193
Period size: 31 Copynumber: 5.9 Consensus size: 31
2543651 ATCCTCGGCA
* * *
2543661 ACTGTCCATAGGTTCCGAAGAACCTAGGTGA-
1 ACTGTCCATATGTT-CGAAGAACATAGGTAAT
**
2543692 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTT-CGAAGAACATAGGTAAT
2543723 ACTGTCCATATGTCTCGAA-AGACATAGGTAAT
1 ACTGTCCATATGT-TCGAAGA-ACATAGGTAAT
* *
2543755 TCTGTCCATATGTTCCGTAGAACATAGGT-AT
1 ACTGTCCATATGTT-CGAAGAACATAGGTAAT
2543786 ACTGTCCATATGTCTCGAA-AGACATAGGTAAT
1 ACTGTCCATATGT-TCGAAGA-ACATAGGTAAT
* *
2543818 TCTGTCCATATGTTCGTAGAACATAGGTA
1 ACTGTCCATATGTTCGAAGAACATAGGTA
2543847 CCTCGACTCT
Statistics
Matches: 133, Mismatches: 12, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
30 3 0.02
31 87 0.65
32 42 0.32
33 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
ACTGTCCATATGTTCGAAGAACATAGGTAAT
Found at i:2543770 original size:63 final size:63
Alignment explanation
Indices: 2543693--2543846 Score: 292
Period size: 63 Copynumber: 2.5 Consensus size: 63
2543683 CCTAGGTGAA
*
2543693 CTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
2543756 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
2543819 CTGTCCATATGTT-CGTAGAACATAGGTA
1 CTGTCCATATGTTCCGTAGAACATAGGTA
2543847 CCTCGACTCT
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
62 15 0.17
63 75 0.83
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (63 bp):
CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
Found at i:2543842 original size:94 final size:94
Alignment explanation
Indices: 2543662--2543846 Score: 234
Period size: 94 Copynumber: 2.0 Consensus size: 94
2543652 TCCTCGGCAA
* **
2543662 CTGTCCATAGGTTCCGAAGAACCTAGGTGAACTGTCCATATGTTCCTTAGAACATAGGTATACTG
1 CTGTCCATAGGTTCCGAAGAACATAGGTGAACTGTCCATATGTTCCAAAGAACATAGGTATACTG
2543727 TCCATATGTCTCGAAAGACATAGGTAATT
66 TCCATATGTCTCGAAAGACATAGGTAATT
* * * *
2543756 CTGTCCATATGTTCCGTAGAACATAGGT-ATACTGTCCATATGTCTCGAAAG-ACATAGGTAATT
1 CTGTCCATAGGTTCCGAAGAACATAGGTGA-ACTGTCCATATGT-TCCAAAGAACATAGGT-ATA
*
2543819 CTGTCCATATGT-TCG-TAGAACATAGGTA
63 CTGTCCATATGTCTCGAAAG-ACATAGGTA
2543847 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
93 3 0.04
94 58 0.73
95 18 0.23
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (94 bp):
CTGTCCATAGGTTCCGAAGAACATAGGTGAACTGTCCATATGTTCCAAAGAACATAGGTATACTG
TCCATATGTCTCGAAAGACATAGGTAATT
Found at i:2544638 original size:64 final size:64
Alignment explanation
Indices: 2544487--2544643 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
2544477 TAATGAAGGT
** * ** *
2544487 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACCAATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTAAAGAG
* * *
2544551 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTATT-TATT-TTAAA
1 ATGCATCGATGCACTACC-AATGCATCGATGCA-TAAAATGCATTCGATGT-TTGT-TTATTAAA
2544612 -AG
62 GAG
2544614 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACCAATGCATCGAT
2544644 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
63 4 0.05
64 65 0.84
65 8 0.10
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACCAATGCATCGATGCATAAAATGCATTCGATGTTTGTTTATTAAAGAG
Found at i:2546779 original size:29 final size:28
Alignment explanation
Indices: 2546747--2546805 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
2546737 ATAATTAGTA
2546747 TAATTTAATT-TAATAAAATACTAAAATAT
1 TAATTT-ATTATAATAAAATA-TAAAATAT
*
2546776 TAATTTATTATAATAAAATATAATATAT
1 TAATTTATTATAATAAAATATAAAATAT
2546804 TA
1 TA
2546806 CATTCTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATTTATTATAATAAAATATAAAATAT
Found at i:2549554 original size:2 final size:2
Alignment explanation
Indices: 2549547--2549578 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2549537 TTGGTTATTA
2549547 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
2549579 TCCATTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2550168 original size:2 final size:2
Alignment explanation
Indices: 2550161--2550199 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2550151 TTAATGTCAA
2550161 AT 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 AT A
2550200 CTTCTCTCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.