Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004846.1 Hibiscus syriacus cultivar Beakdansim tig00010927_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: 1467214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1125535 original size:12 final size:10
Alignment explanation
Indices: 1125509--1125533 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1125499 ACTTATACTT
1125509 TATATTGTTA
1 TATATTGTTA
1125519 TATATTGTTA
1 TATATTGTTA
1125529 TATAT
1 TATAT
1125534 ATATATATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (10 bp):
TATATTGTTA
Found at i:1126199 original size:55 final size:55
Alignment explanation
Indices: 1126086--1126503 Score: 619
Period size: 55 Copynumber: 7.6 Consensus size: 55
1126076 ATCAAAACAT
* * * * * * *
1126086 AAATTTATACACTTAGTATAAATTT-TCT-AGTTTGCACCTAAAGTGTCCATAC-A
1 AAATTCATCCACTTAGTATGAATTTCT-TAAGTTTACACATATAGTGCCCATACGA
*
1126139 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTTCCCATACGA
1 -AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGA
*
1126195 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGA
* **
1126250 AAATTCATCCACTTAGTATGTATTTCTTAAGTTTACACATATAGTGCCCATATAA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGA
1126305 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGA
** * *
1126360 AAATTCATATACTTAGTTTGAATTTATTAAGTTTACACATATAGTGCCCATACGA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGA
* *
1126415 AAATTCAAT-CACTTAGTATGAATTTCTTAAGTTTACACATATAGTGGCCATACGG
1 AAATTC-ATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGA
1126470 AAATTCATCCACTTAGTATGAATTTCTTAAGTTT
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTT
1126504 TTTCACACTT
Statistics
Matches: 333, Mismatches: 26, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
54 25 0.08
55 305 0.92
56 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (55 bp):
AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGA
Found at i:1126886 original size:22 final size:20
Alignment explanation
Indices: 1126842--1126893 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
1126832 GGCTCCTCAA
*
1126842 TATCGATACCCCTACCATGG
1 TATCGATACCCATACCATGG
*
1126862 TATCGATACTACCATACTATGG
1 TATCGATAC--CCATACCATGG
*
1126884 TATAGATACC
1 TATCGATACC
1126894 TTGTTATGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (20 bp):
TATCGATACCCATACCATGG
Found at i:1127006 original size:20 final size:20
Alignment explanation
Indices: 1126936--1127005 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1126926 GTTTTGAATG
1126936 GTATCGATACCTTCCCTTCA
1 GTATCGATACCTTCCCTTCA
*
1126956 GTATCGATACCTTCCCTTCG
1 GTATCGATACCTTCCCTTCA
*
1126976 GTAACGATA-CTTCCCCTTCA
1 GTATCGATACCTT-CCCTTCA
*
1126996 GTATTGATAC
1 GTATCGATAC
1127006 TGATTCAATC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.07
20 40 0.93
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.34
Consensus pattern (20 bp):
GTATCGATACCTTCCCTTCA
Found at i:1133182 original size:55 final size:55
Alignment explanation
Indices: 1133117--1133561 Score: 729
Period size: 55 Copynumber: 8.1 Consensus size: 55
1133107 AATTTATACT
* * *
1133117 AGTTTGCACATAAAGTGCCCATACATAAATTCATCCACTTAGTATGAATTTCTTA
1 AGTTTACACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTA
*
1133172 AGTTTACACATATAGTGCCCATACGGAAATTCATCCACTTAGTATGAATTTCTTA
1 AGTTTACACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTA
1133227 AGTTTACACATATAGTGCCCATAC-GAAAATTCATCCACTTAGTATGAATTTCTTA
1 AGTTTACACATATAGTGCCCATACAG-AAATTCATCCACTTAGTATGAATTTCTTA
1133282 AGTTTACACATAT-GATGCCCATAC-GAAAATTCATCCACTTAGTATGAATTTCTTA
1 AGTTTACACATATAG-TGCCCATACAG-AAATTCATCCACTTAGTATGAATTTCTTA
1133337 AGTTTACACATATAGTGCGCC-TAC-GAAAATTCATCCACTTAGTATGAATTTCTTA
1 AGTTTACACATATAGTGC-CCATACAG-AAATTCATCCACTTAGTATGAATTTCTTA
*
1133392 AGTTTACACATATAGTGCCCATATAGAAATTCATCCACTTAGTATGAATTTCTTA
1 AGTTTACACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTA
* *
1133447 AGTTTACACATATAGTGCCCATACGGAAATTCATCCACTTACTATGAATTTCTTA
1 AGTTTACACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTA
* *
1133502 AGTTTACACATATAGTGCCCGTATAGAAATTCATCCACTTAGTATGAATTTCTTA
1 AGTTTACACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTA
1133557 AGTTT
1 AGTTT
1133562 TTTCACACTT
Statistics
Matches: 372, Mismatches: 12, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
54 4 0.01
55 364 0.98
56 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (55 bp):
AGTTTACACATATAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTA
Found at i:1134847 original size:39 final size:38
Alignment explanation
Indices: 1134787--1134860 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 38
1134777 AGGAAAATTA
**
1134787 TTTTTCAAAATCATAATATATATGTTTTCAACAAAAATG
1 TTTTTCAAAATCATAATATATACATTTTCAA-AAAAATG
1134826 TTTTTCAAAAGT-AT-ATAATATACATTTTCAAAAAA
1 TTTTTCAAAA-TCATAAT-ATATACATTTTCAAAAAA
1134861 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 6 0.19
39 24 0.77
40 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (38 bp):
TTTTTCAAAATCATAATATATACATTTTCAAAAAAATG
Found at i:1134878 original size:36 final size:36
Alignment explanation
Indices: 1134838--1134931 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 36
1134828 TTTCAAAAGT
*
1134838 ATATAATATACATTTTCAAAAAATATTTTAAAAACC
1 ATATAATATACATTTTTAAAAAATATTTTAAAAACC
** ** *
1134874 ATAT-ATCATATGTTTTTTTAAAATGTTTTAAAAACC
1 ATATAAT-ATACATTTTTAAAAAATATTTTAAAAACC
* * *
1134910 ATGTATTATACTTTTTTAAAAA
1 ATATAATATACATTTTTAAAAA
1134932 TGTGTTCAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
35 2 0.05
36 41 0.93
37 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (36 bp):
ATATAATATACATTTTTAAAAAATATTTTAAAAACC
Found at i:1134943 original size:36 final size:36
Alignment explanation
Indices: 1134856--1134943 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
1134846 TACATTTTCA
* * *
1134856 AAAAATATTTTAAAAACCATATATCATATGTTTTTT
1 AAAAATGTTTCAAAAACCATATATCATATCTTTTTT
* * * *
1134892 TAAAATGTTTTAAAAACCATGTATTATA-CTTTTTT
1 AAAAATGTTTCAAAAACCATATATCATATCTTTTTT
1134927 AAAAATGTGTTCAAAAA
1 AAAAATGT-TTCAAAAA
1134944 TGTTTTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 13 0.30
36 31 0.70
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (36 bp):
AAAAATGTTTCAAAAACCATATATCATATCTTTTTT
Found at i:1134944 original size:12 final size:12
Alignment explanation
Indices: 1134927--1134956 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1134917 ATACTTTTTT
1134927 AAAAATGTGTTC
1 AAAAATGTGTTC
*
1134939 AAAAATGTTTTC
1 AAAAATGTGTTC
1134951 AAAAAT
1 AAAAAT
1134957 TATATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (12 bp):
AAAAATGTGTTC
Found at i:1135111 original size:36 final size:35
Alignment explanation
Indices: 1134931--1135153 Score: 188
Period size: 35 Copynumber: 6.3 Consensus size: 35
1134921 TTTTTTAAAA
* * * * *
1134931 ATGTGTTCAAAAATGTTTTCAAAAATTATATATTAT
1 ATGTTTTCAAAATTATTTT-AAAAACTATATACTAT
* *
1134967 -TCG-TTTCAAAATTATTTTAAAACCCATAT--TAT
1 AT-GTTTTCAAAATTATTTTAAAAACTATATACTAT
** *
1134999 CCGTTTTCAAAATTATTATTTTAAAAACTATATACAAT
1 ATGTTTTC-AAA--ATTATTTTAAAAACTATATACTAT
* *
1135037 ATGTTTTCAAAATTATTTT-AAAACCATATACTAC
1 ATGTTTTCAAAATTATTTTAAAAACTATATACTAT
* * *
1135071 ATGTTTTTCAAAACTGTTTTAAAAACTATATATTAT
1 ATG-TTTTCAAAATTATTTTAAAAACTATATACTAT
* *
1135107 ATGTTTTCAAAATTACTTTGAAAACTATATACTAT
1 ATGTTTTCAAAATTATTTTAAAAACTATATACTAT
1135142 ATAG-TTTCAAAA
1 AT-GTTTTCAAAA
1135154 CCTATATTTG
Statistics
Matches: 151, Mismatches: 25, Indels: 23
0.76 0.13 0.12
Matches are distributed among these distances:
32 4 0.03
33 4 0.03
34 26 0.17
35 72 0.48
36 34 0.23
37 3 0.02
38 8 0.05
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (35 bp):
ATGTTTTCAAAATTATTTTAAAAACTATATACTAT
Found at i:1150527 original size:16 final size:17
Alignment explanation
Indices: 1150508--1150543 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1150498 TTAATGTAAT
1150508 TTTAAAATTAAATT-AA
1 TTTAAAATTAAATTGAA
*
1150524 TTTAAATTTAAATTGAA
1 TTTAAAATTAAATTGAA
1150541 TTT
1 TTT
1150544 TTCTCATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAATTAAATTGAA
Found at i:1151701 original size:24 final size:24
Alignment explanation
Indices: 1151669--1151725 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1151659 GATGACGACG
* * *
1151669 ATGATGGTGGTGGTTGTGGTGATC
1 ATGACGGTGGTGGTTGTGATGACC
1151693 ATGACGGTGGTGGTTGTGATGACC
1 ATGACGGTGGTGGTTGTGATGACC
1151717 ATGACGGTG
1 ATGACGGTG
1151726 ATAGATGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.09, G:0.44, T:0.32
Consensus pattern (24 bp):
ATGACGGTGGTGGTTGTGATGACC
Found at i:1152450 original size:20 final size:20
Alignment explanation
Indices: 1152407--1152450 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1152397 TGTTTTTAAT
*
1152407 AAATTTTTATCTATAAAATT
1 AAATTTTTATCTATAAAATA
*
1152427 AAATTTTTAT-TTTCAAAATA
1 AAATTTTTATCTAT-AAAATA
1152447 AAAT
1 AAAT
1152451 ATTAAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATTTTTATCTATAAAATA
Found at i:1158741 original size:16 final size:16
Alignment explanation
Indices: 1158720--1158757 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1158710 AAAAATAATT
1158720 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
1158736 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
1158752 T-ATAAA
1 TAATAAA
1158758 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:1158984 original size:27 final size:25
Alignment explanation
Indices: 1158930--1158984 Score: 58
Period size: 27 Copynumber: 2.1 Consensus size: 25
1158920 GTTAATAGTA
*
1158930 AAATAATAATAAATATAATAGTTAT
1 AAATAATAATAAATATAATACTTAT
*
1158955 AAATATATATATATATATAATAACTT-T
1 AAATA-ATA-ATAAATATAAT-ACTTAT
1158982 AAA
1 AAA
1158985 AAACATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 5 0.20
26 3 0.12
27 14 0.56
28 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
AAATAATAATAAATATAATACTTAT
Found at i:1159022 original size:2 final size:2
Alignment explanation
Indices: 1159015--1159043 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1159005 AATAAAAATA
1159015 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
1159044 ATTAATAATA
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:1159480 original size:37 final size:37
Alignment explanation
Indices: 1159430--1159521 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 37
1159420 GTGCTTGTGG
*
1159430 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAAACATAGCAAAATTCT
* * * *
1159467 ATCCTATTTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAGGAGTTTAAAACATAGCAAAATTCT
*
1159503 ATCCT-TTTTTTGAGAGTTT
1 ATCCTATTTTTAG-GAGTTT
1159522 GAATCCTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 6 0.13
36 24 0.51
37 17 0.36
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAAACATAGCAAAATTCT
Found at i:1159502 original size:36 final size:37
Alignment explanation
Indices: 1159430--1159530 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
1159420 GTGCTTGTGG
* * * *
1159430 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
1159467 ATCCTATTTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
1159503 ATCCT-TTTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTTAG-GAGTTTGAATCCTAG
1159531 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 6 0.11
36 24 0.43
37 26 0.46
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:1203450 original size:25 final size:24
Alignment explanation
Indices: 1203399--1203450 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1203389 TTTGTTATTT
* * *
1203399 TATTTTGAAGGAATTTTTTATTAA
1 TATTTTGAAGGAAATTTTAAATAA
1203423 TATTTTGAAGGAAATTTTAAATATA
1 TATTTTGAAGGAAATTTTAAATA-A
1203448 TAT
1 TAT
1203451 AATTTGGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
TATTTTGAAGGAAATTTTAAATAA
Found at i:1211243 original size:20 final size:21
Alignment explanation
Indices: 1211204--1211252 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
1211194 GTACTAGTGT
1211204 TTATTTTATTTCGTTTTTATTG
1 TTATTTTATTTC-TTTTTATTG
1211226 TT-TTTTATTT-TTTATTATTG
1 TTATTTTATTTCTTT-TTATTG
1211246 TTATTTT
1 TTATTTT
1211253 TTAATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 3 0.12
20 8 0.32
21 12 0.48
22 2 0.08
ACGTcount: A:0.14, C:0.02, G:0.06, T:0.78
Consensus pattern (21 bp):
TTATTTTATTTCTTTTTATTG
Found at i:1225906 original size:32 final size:32
Alignment explanation
Indices: 1225865--1225928 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1225855 CCTTTACTAT
1225865 TGTATCATCATTTGTTTCAATATCTCCATCTC
1 TGTATCATCATTTGTTTCAATATCTCCATCTC
1225897 TGTATCATCATTTGTTTCAATATCTCCATCTC
1 TGTATCATCATTTGTTTCAATATCTCCATCTC
1225929 CTACCGATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.06, T:0.47
Consensus pattern (32 bp):
TGTATCATCATTTGTTTCAATATCTCCATCTC
Found at i:1232749 original size:22 final size:22
Alignment explanation
Indices: 1232721--1232762 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1232711 ATGTGAAATC
* *
1232721 TATGTCCTGAATGACCTATGCA
1 TATGTCCTAAAGGACCTATGCA
1232743 TATGTCCTAAAGGACCTATG
1 TATGTCCTAAAGGACCTATG
1232763 TAACCCTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (22 bp):
TATGTCCTAAAGGACCTATGCA
Found at i:1236176 original size:25 final size:24
Alignment explanation
Indices: 1236125--1236176 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1236115 TTTGTTATTT
* * *
1236125 TATTTTGAAGGAATTTTTTATTAA
1 TATTTTGAAGGAAATTTTAAATAA
1236149 TATTTTGAAGGAAATTTTAAATATA
1 TATTTTGAAGGAAATTTTAAATA-A
1236174 TAT
1 TAT
1236177 AATTTGGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
TATTTTGAAGGAAATTTTAAATAA
Found at i:1242929 original size:27 final size:27
Alignment explanation
Indices: 1242864--1242930 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
1242854 ATAAATCTCC
*
1242864 TATTTGAATTTTTATTAAATTTAATGT
1 TATTTGAATTTTTATTAAAATTAATGT
*
1242891 TATTTGAA-TTTTATTAATAATTCAT-T
1 TATTTGAATTTTTATTAA-AATTAATGT
1242917 ATATTT-AATTTTTA
1 -TATTTGAATTTTTA
1242931 AATTTATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (27 bp):
TATTTGAATTTTTATTAAAATTAATGT
Found at i:1256895 original size:19 final size:17
Alignment explanation
Indices: 1256871--1256909 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
1256861 TTATTATAAA
1256871 TATATTATTATAATTTTAT
1 TATATTATTAT--TTTTAT
1256890 TATATTATTATTTTTAT
1 TATATTATTATTTTTAT
1256907 TAT
1 TAT
1256910 TTTGGTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTATTATTTTTAT
Found at i:1256897 original size:16 final size:17
Alignment explanation
Indices: 1256876--1256909 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1256866 ATAAATATAT
1256876 TATTA-TAATTTTATTA
1 TATTATTAATTTTATTA
*
1256892 TATTATTATTTTTATTA
1 TATTATTAATTTTATTA
1256909 T
1 T
1256910 TTTGGTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATTAATTTTATTA
Found at i:1269237 original size:35 final size:35
Alignment explanation
Indices: 1269191--1269328 Score: 231
Period size: 35 Copynumber: 3.9 Consensus size: 35
1269181 AAGTCATTTG
1269191 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
* *
1269226 AATCAATCCTTCACAAAAGAGTAGTGAAGCAATGC
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
* *
1269261 AATCAAACCTTTACAAAAGAGTAGTGAAGCAATGT
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
1269296 AATCAAGCCTTCACAAAAAGAGTAGTGAAGCAA
1 AATCAAGCCTTCAC-AAAAGAGTAGTGAAGCAA
1269329 GATTAGATCA
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 77 0.81
36 18 0.19
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.20
Consensus pattern (35 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
Found at i:1269539 original size:17 final size:18
Alignment explanation
Indices: 1269494--1269547 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1269484 TTCGTCCGAG
* *
1269494 TTATATTATAAATATATTA
1 TTATATT-TTAATATTTTA
1269513 TTATAATTTTAATATTTTA
1 TTAT-ATTTTAATATTTTA
*
1269532 TTAT-TTTTATTATTTT
1 TTATATTTTAATATTTT
1269548 GGTTACAGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 11 0.35
19 17 0.55
20 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATATTTTAATATTTTA
Found at i:1291677 original size:2 final size:2
Alignment explanation
Indices: 1291672--1291707 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1291662 TTATTCTTAT
1291672 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
1291708 ATTATCTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1291829 original size:16 final size:15
Alignment explanation
Indices: 1291792--1291865 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 15
1291782 ATTCTTTTTC
*
1291792 ATATATCATTATTATTT
1 ATATAT-ATTTTTA-TT
1291809 ATATATATTTTTATT
1 ATATATATTTTTATT
* *
1291824 ACTATA-ATTATATGTT
1 A-TATATATT-TTTATT
1291840 ATATATATTTATTATT
1 ATATATATTT-TTATT
*
1291856 TTATATATTT
1 ATATATATTT
1291866 CATTTTATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
15 11 0.23
16 30 0.64
17 6 0.13
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (15 bp):
ATATATATTTTTATT
Found at i:1291969 original size:33 final size:33
Alignment explanation
Indices: 1291897--1291969 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
1291887 TTATCTTCTA
* *
1291897 TTTTTATTTTTTGTATTGTTATTGTTATTATCT
1 TTTTTATTTTATGTATTGTTATTGTTATTATAT
*
1291930 TCTTTATTTTATGTATT-TTATT-TATATATATAT
1 TTTTTATTTTATGTATTGTTATTGT-TAT-TATAT
1291963 TTTTTAT
1 TTTTTAT
1291970 ATTTGTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 1 0.03
32 8 0.24
33 25 0.74
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (33 bp):
TTTTTATTTTATGTATTGTTATTGTTATTATAT
Found at i:1301907 original size:27 final size:27
Alignment explanation
Indices: 1301877--1302016 Score: 96
Period size: 26 Copynumber: 5.3 Consensus size: 27
1301867 TTACTATAAT
*
1301877 TATATTTTATATATATTTATTATTTTA
1 TATATTTTATTTATATTTATTATTTTA
* *
1301904 TATATTTCATTTCAT-TTTA-TCTTTTA
1 TATATTTTATTT-ATATTTATTATTTTA
* * *
1301930 TTTTTTTTATCTTCTATTT-TTATTTT-
1 TATATTTTAT-TTATATTTATTATTTTA
* *
1301956 TGTATTGTTA-TTATCTTCT-TTATTTTA
1 TATATT-TTATTTATATT-TATTATTTTA
* * *
1301983 TGTATTTTATTTATATATA-TATTTTT
1 TATATTTTATTTATATTTATTATTTTA
1302009 TATATTTT
1 TATATTTT
1302017 TTTTGTGCCT
Statistics
Matches: 88, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
25 5 0.06
26 43 0.49
27 38 0.43
28 2 0.02
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (27 bp):
TATATTTTATTTATATTTATTATTTTA
Found at i:1301939 original size:16 final size:16
Alignment explanation
Indices: 1301918--1301950 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1301908 TTTCATTTCA
*
1301918 TTTTATCTTTTATTTT
1 TTTTATCTTCTATTTT
1301934 TTTTATCTTCTATTTT
1 TTTTATCTTCTATTTT
1301950 T
1 T
1301951 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATCTTCTATTTT
Found at i:1301972 original size:30 final size:30
Alignment explanation
Indices: 1301917--1301983 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1301907 ATTTCATTTC
* *
1301917 ATTTTATCTTTTATTTTTTTTATCTTCTAT
1 ATTTTATCTTTTATTGTTATTATCTTCTAT
* *
1301947 -TTTTATTTTTGTATTGTTATTATCTTCTTT
1 ATTTTATCTTT-TATTGTTATTATCTTCTAT
1301977 ATTTTAT
1 ATTTTAT
1301984 GTATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 9 0.29
30 16 0.52
31 6 0.19
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.73
Consensus pattern (30 bp):
ATTTTATCTTTTATTGTTATTATCTTCTAT
Found at i:1302129 original size:29 final size:29
Alignment explanation
Indices: 1302070--1302132 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
1302060 TCTTTATCTG
* * *
1302070 TTTTATTTTATCTACTTTATTGCATTTAT
1 TTTTATTTCACCTACTTTATTGCATTCAT
* **
1302099 TTTTATTTCACCTTCTTTATTTTATTCAT
1 TTTTATTTCACCTACTTTATTGCATTCAT
1302128 TTTTA
1 TTTTA
1302133 CTACATTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.13, G:0.02, T:0.67
Consensus pattern (29 bp):
TTTTATTTCACCTACTTTATTGCATTCAT
Found at i:1303539 original size:21 final size:23
Alignment explanation
Indices: 1303504--1303551 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
1303494 CTATATATAA
*
1303504 GGAATATTCAATTTTA-TTAGAG
1 GGAATATTAAATTTTATTTAGAG
*
1303526 GGAATA-TAAATTTTATTTGGAG
1 GGAATATTAAATTTTATTTAGAG
1303548 GGAA
1 GGAA
1303552 GTTGAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (23 bp):
GGAATATTAAATTTTATTTAGAG
Found at i:1303937 original size:16 final size:16
Alignment explanation
Indices: 1303916--1303962 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
1303906 AACCGTATTA
1303916 ATTATATTTATTTTTT
1 ATTATATTTATTTTTT
1303932 ATTATA-TTA-TTTTT
1 ATTATATTTATTTTTT
1303946 A-TA-ATTTAATTTTTT
1 ATTATATTT-ATTTTTT
1303961 AT
1 AT
1303963 GACACTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 4 0.15
14 7 0.26
15 9 0.33
16 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTATATTTATTTTTT
Found at i:1303953 original size:21 final size:20
Alignment explanation
Indices: 1303911--1303953 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1303901 TAAATAACCG
**
1303911 TATTAATTATATTTATTTTT
1 TATTAATTATATTTATAATT
*
1303931 TATTATATTATTTTTATAATT
1 TATTA-ATTATATTTATAATT
1303952 TA
1 TA
1303954 ATTTTTTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTAATTATATTTATAATT
Found at i:1317765 original size:25 final size:24
Alignment explanation
Indices: 1317714--1317765 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1317704 TTTGTTATTT
* * *
1317714 TATTTTGAAGGAATTTTTTATTAA
1 TATTTTGAAGGAAATTTTAAATAA
1317738 TATTTTGAAGGAAATTTTAAATATA
1 TATTTTGAAGGAAATTTTAAATA-A
1317763 TAT
1 TAT
1317766 AATTTGGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
TATTTTGAAGGAAATTTTAAATAA
Found at i:1325221 original size:31 final size:32
Alignment explanation
Indices: 1325179--1325245 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
1325169 CCGTCGCACA
1325179 GTGGCCAGAAGGCGGCTGGAGCTTGCT-AGGG
1 GTGGCCAGAAGGCGGCTGGAGCTTGCTAAGGG
* *
1325210 GTGGCCGGAAGGCGGTTGGAGCTTGCTAAGGG
1 GTGGCCAGAAGGCGGCTGGAGCTTGCTAAGGG
1325242 GTGG
1 GTGG
1325246 TCGGCCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.15, C:0.16, G:0.51, T:0.18
Consensus pattern (32 bp):
GTGGCCAGAAGGCGGCTGGAGCTTGCTAAGGG
Found at i:1325961 original size:17 final size:16
Alignment explanation
Indices: 1325905--1325957 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
1325895 TGTACTAGTG
* **
1325905 TTTATTTTATTTCGTT
1 TTTATTTTTTTTATTT
1325921 TTTATTGTTTTTTATTT
1 TTTATT-TTTTTTATTT
1325938 TTTATTTTTTTTATTT
1 TTTATTTTTTTTATTT
1325954 TTTA
1 TTTA
1325958 ATTTAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 20 0.61
17 13 0.39
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (16 bp):
TTTATTTTTTTTATTT
Found at i:1328620 original size:16 final size:17
Alignment explanation
Indices: 1328599--1328634 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1328589 TGAAACAGTA
*
1328599 AAAGCGAAAAGT-AAAG
1 AAAGCGAAAAATGAAAG
1328615 AAAGCGAAAAATGAAAG
1 AAAGCGAAAAATGAAAG
1328632 AAA
1 AAA
1328635 AAGAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.67, C:0.06, G:0.22, T:0.06
Consensus pattern (17 bp):
AAAGCGAAAAATGAAAG
Found at i:1333679 original size:8 final size:8
Alignment explanation
Indices: 1333666--1333700 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1333656 TATAAATATA
1333666 TTATTATT
1 TTATTATT
*
1333674 TTATTATA
1 TTATTATT
1333682 TTATTATTT
1 TTATTA-TT
1333691 TTATTATT
1 TTATTATT
1333699 TT
1 TT
1333701 GGTTACAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTATT
Found at i:1333683 original size:16 final size:17
Alignment explanation
Indices: 1333662--1333697 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1333652 TTATTATAAA
1333662 TATATTATTA-TTTTAT
1 TATATTATTATTTTTAT
1333678 TATATTATTATTTTTAT
1 TATATTATTATTTTTAT
1333695 TAT
1 TAT
1333698 TTTGGTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTATTATTTTTAT
Found at i:1340082 original size:27 final size:27
Alignment explanation
Indices: 1340018--1340083 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
1340008 TAAATTTCCA
1340018 ATTTGAATTTTTATTATATTCAATGTT
1 ATTTGAATTTTTATTATATTCAATGTT
1340045 ATTTGAA-TTTTATTAATAATTC-AT-TAT
1 ATTTGAATTTTTATT-AT-ATTCAATGT-T
1340072 ATTT-AATTTTTA
1 ATTTGAATTTTTA
1340084 AATTTATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
26 10 0.29
27 21 0.60
28 4 0.11
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (27 bp):
ATTTGAATTTTTATTATATTCAATGTT
Found at i:1361056 original size:22 final size:22
Alignment explanation
Indices: 1361028--1361069 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1361018 ATGTGAAATC
* *
1361028 TATGTCCCGAATGACCTATGCA
1 TATGTCCCAAAGGACCTATGCA
1361050 TATGTCCCAAAGGACCTATG
1 TATGTCCCAAAGGACCTATG
1361070 TAACCCTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (22 bp):
TATGTCCCAAAGGACCTATGCA
Found at i:1364083 original size:23 final size:23
Alignment explanation
Indices: 1364035--1364085 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
1364025 TTTGTTATTT
* *
1364035 TATTTTGAAGGAATTTTTATTAA
1 TATTTTGAAGGAATTTTAAATAA
1364058 TATTTTGAAGGAAATTTTAAATATA
1 TATTTTGAAGG-AATTTTAAATA-A
1364083 TAT
1 TAT
1364086 AATTTGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.46
24 9 0.38
25 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (23 bp):
TATTTTGAAGGAATTTTAAATAA
Found at i:1371724 original size:22 final size:22
Alignment explanation
Indices: 1371692--1371746 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
1371682 CTTGTACTAG
1371692 TGTTTATTTTATTTCGTTTTTAT
1 TGTTT-TTTTATTTCGTTTTTAT
**
1371715 TGTTTTTTTATTTTTTTTTTAT
1 TGTTTTTTTATTTCGTTTTTAT
1371737 TGTTATTTTT
1 TGTT-TTTTT
1371747 TAATTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (22 bp):
TGTTTTTTTATTTCGTTTTTAT
Found at i:1371734 original size:11 final size:11
Alignment explanation
Indices: 1371698--1371748 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1371688 CTAGTGTTTA
**
1371698 TTTTATTTCGT
1 TTTTATTTTTT
*
1371709 TTTTATTGTTT
1 TTTTATTTTTT
1371720 TTTTATTTTTT
1 TTTTATTTTTT
1371731 TTTTATTGTTATT
1 TTTTATT-TT-TT
1371744 TTTTA
1 TTTTA
1371749 ATTTAATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 25 0.74
12 2 0.06
13 7 0.21
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:1379479 original size:19 final size:17
Alignment explanation
Indices: 1379455--1379493 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
1379445 TTATTATAAA
1379455 TATATTATTATAATTTTAT
1 TATATTATTAT--TTTTAT
1379474 TATATTATTATTTTTAT
1 TATATTATTATTTTTAT
1379491 TAT
1 TAT
1379494 TTTGGTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTATTATTTTTAT
Found at i:1379481 original size:16 final size:17
Alignment explanation
Indices: 1379460--1379493 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1379450 ATAAATATAT
1379460 TATTA-TAATTTTATTA
1 TATTATTAATTTTATTA
*
1379476 TATTATTATTTTTATTA
1 TATTATTAATTTTATTA
1379493 T
1 T
1379494 TTTGGTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATTAATTTTATTA
Found at i:1391833 original size:35 final size:35
Alignment explanation
Indices: 1391787--1391924 Score: 204
Period size: 35 Copynumber: 3.9 Consensus size: 35
1391777 AAGCCATTTG
*
1391787 AATCAAGCCTTCACAAAAGAGTAGTGAAACAATGT
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
* * *
1391822 AATCAATCCTTCAGAAAAGAGTAGTGAAGCAATGC
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
* * *
1391857 AATCAAACCTTTACAAAAGAGTAGTGAAGTAATGT
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
1391892 AATCAAGCCTTCACAAAAAGAGTAGTGAAGCAA
1 AATCAAGCCTTCAC-AAAAGAGTAGTGAAGCAA
1391925 GATTAGATCA
Statistics
Matches: 90, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 73 0.81
36 17 0.19
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (35 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
Found at i:1392137 original size:17 final size:18
Alignment explanation
Indices: 1392102--1392145 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1392092 TTTTATTATA
*
1392102 AATATATTATTATAATTTT
1 AATATTTTATTAT-ATTTT
1392121 AATATTTTATTAT-TTTT
1 AATATTTTATTATATTTT
*
1392138 ATTATTTT
1 AATATTTT
1392146 GGTTACAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 11 0.48
19 12 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATATTTTATTATATTTT
Found at i:1393388 original size:2 final size:2
Alignment explanation
Indices: 1393381--1393429 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
1393371 GTTACTACTG
*
1393381 TA TA TA TA CTG 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
1393424 TA TA TA
1 TA TA TA
1393430 CTTTAGGGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 43 0.98
3 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1393652 original size:22 final size:23
Alignment explanation
Indices: 1393587--1393652 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
1393577 AATTATTACT
* * *
1393587 TATTATTATAAGATTAATTATAA
1 TATTAGTATAATATTAAATATAA
* * *
1393610 TATTAGTATATTTTTATATATAA
1 TATTAGTATAATATTAAATATAA
*
1393633 TA-TAGTTTAATATTAAATAT
1 TATTAGTATAATATTAAATAT
1393653 TATAATAGGA
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
TATTAGTATAATATTAAATATAA
Found at i:1421524 original size:88 final size:88
Alignment explanation
Indices: 1421409--1421588 Score: 351
Period size: 88 Copynumber: 2.0 Consensus size: 88
1421399 AAGAAACCAG
*
1421409 TTAGCTACAAATGGTTTTTTACCGTGATATACAATGAAGATGACAGTGTTGAGTGGTATAAGGCT
1 TTAGCTACAAATGGTTTTTTACCGTGATATACAAGGAAGATGACAGTGTTGAGTGGTATAAGGCT
1421474 AGACTTGTGGGAAAGGGGTTTAC
66 AGACTTGTGGGAAAGGGGTTTAC
1421497 TTAGCTACAAATGGTTTTTTACCGTGATATACAAGGAAGATGACAGTGTTGAGTGGTATAAGGCT
1 TTAGCTACAAATGGTTTTTTACCGTGATATACAAGGAAGATGACAGTGTTGAGTGGTATAAGGCT
1421562 AGACTTGTGGGAAAGGGGTTTAC
66 AGACTTGTGGGAAAGGGGTTTAC
1421585 TTAG
1 TTAG
1421589 TCTCATGGAG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (88 bp):
TTAGCTACAAATGGTTTTTTACCGTGATATACAAGGAAGATGACAGTGTTGAGTGGTATAAGGCT
AGACTTGTGGGAAAGGGGTTTAC
Found at i:1431959 original size:25 final size:24
Alignment explanation
Indices: 1431908--1431959 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1431898 TTTGTTATTT
* * *
1431908 TATTTTGAAGGAATTTTTTATTAA
1 TATTTTGAAGGAAATTTTAAATAA
1431932 TATTTTGAAGGAAATTTTAAATATA
1 TATTTTGAAGGAAATTTTAAATA-A
1431957 TAT
1 TAT
1431960 AATTTGGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
TATTTTGAAGGAAATTTTAAATAA
Found at i:1447634 original size:16 final size:17
Alignment explanation
Indices: 1447613--1447648 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1447603 TGAAACAATA
*
1447613 AAAGCGAAAAGT-AAAG
1 AAAGCGAAAAATGAAAG
1447629 AAAGCGAAAAATGAAAG
1 AAAGCGAAAAATGAAAG
1447646 AAA
1 AAA
1447649 AATAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.67, C:0.06, G:0.22, T:0.06
Consensus pattern (17 bp):
AAAGCGAAAAATGAAAG
Found at i:1452653 original size:19 final size:17
Alignment explanation
Indices: 1452629--1452667 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
1452619 TTATTATAAA
1452629 TATATTATTATAATTTTAT
1 TATATTATTAT--TTTTAT
1452648 TATATTATTATTTTTAT
1 TATATTATTATTTTTAT
1452665 TAT
1 TAT
1452668 TTTGGTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTATTATTTTTAT
Found at i:1452655 original size:16 final size:17
Alignment explanation
Indices: 1452634--1452667 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1452624 ATAAATATAT
1452634 TATTA-TAATTTTATTA
1 TATTATTAATTTTATTA
*
1452650 TATTATTATTTTTATTA
1 TATTATTAATTTTATTA
1452667 T
1 T
1452668 TTTGGTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATTAATTTTATTA
Found at i:1464894 original size:35 final size:35
Alignment explanation
Indices: 1464848--1464981 Score: 196
Period size: 35 Copynumber: 3.8 Consensus size: 35
1464838 AAGTCATTTG
1464848 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
* ** **
1464883 AATCAATCCTTCACAAAAGAGTAGTGAATAAATAC
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
* * *
1464918 AATCAAACGTTTACAAAAGAGTAGTGAAGCAATGT
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
1464953 AATCAAGCCTTCACAAAAGAGTAGTGAAG
1 AATCAAGCCTTCACAAAAGAGTAGTGAAG
1464982 AAGATTAGAT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 84 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.21
Consensus pattern (35 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGT
Done.